From 2f73194d4f3fd99b3932b2457d8d28c161fb1b68 Mon Sep 17 00:00:00 2001 From: Lang Date: Thu, 14 May 2020 08:34:54 +0200 Subject: [PATCH 001/105] import_dat_general: test file format with endswith --- input/helpers/data_import.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/input/helpers/data_import.py b/input/helpers/data_import.py index c2dc9d4c..c5d563ca 100755 --- a/input/helpers/data_import.py +++ b/input/helpers/data_import.py @@ -73,9 +73,9 @@ def import_dat_general(in_file): header = [] c = 0 # ceck format of file - if "txt" in in_file: + if in_file.endswith(".txt"): file_format = "txt" - elif "csv" in in_file: + elif in_file.endswith(".csv"): file_format = "csv" else: logger.warn("Table should be in csv or txt format!!") From 369ce39bc0384ea4e5c3a0320b13f60635cd7f5c Mon Sep 17 00:00:00 2001 From: Pablo Riesgo Ferreiro Date: Sun, 17 May 2020 23:31:49 +0200 Subject: [PATCH 002/105] first iteration neoepitope model --- model/neoepitope.avdl | 83 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 83 insertions(+) create mode 100755 model/neoepitope.avdl diff --git a/model/neoepitope.avdl b/model/neoepitope.avdl new file mode 100755 index 00000000..c6e3f784 --- /dev/null +++ b/model/neoepitope.avdl @@ -0,0 +1,83 @@ +/** + * An example protocol in Avro IDL for defining neoepitopes + */ +@namespace("tron.neoepitope") +protocol Neoepitope { + + record Gene { + /** + The genome assembly to which the gene definition refers to (e.g.: GRCh37, GRCh38) + */ + string assembly = "GRCh37"; + /** + The gene symbol or gene identifier, optional as the transcript unequivocally identifies a gene + */ + union {string, null} gene; + /** + The transcript identifier to which this neoepitope definition refers (e.g.: Ensembl transcript id) + */ + string transcriptIdentifier; + } + + record Mutation { + /** + The aminoacid position within the protein. 1-based, starting in the N-terminus + */ + int position; + /** + IUPAC code for the wild type aminoacid in this position + */ + string wildTypeAminoacid; + /** + IUPAC code for the mutated aminoacid in this position + */ + string mutatedAminoacid; + + /** + The left flanking region of variable size in IUPAC codes + */ + string leftFlankingRegion; + /** + The size of the left flanking region + */ + union {string, null} sizeLeftFlankingRegion; + /** + The right flanking region of variable size in IUPAC codes + */ + string rightFlankingRegion; + /** + The size of the right flanking region + */ + union {string, null} sizeRightlankingRegion; + } + + /** + A neoepitope minimal definition + */ + record Neoepitope { + + /** + The gene where the neoepitope corresponds + */ + Gene gene; + + /** + The mutation + */ + Mutation mutation; + + // OPTIONAL + /** + Expression value of the transcript (any more definition on type of expression? ie: digital from RNAseq, from microarrays, etc.) + */ + union {float, null} expressionValue; + /** + Clonality estimation (any more definition on the method?) + */ + union {float, null} clonalityEstimation; + /** + Variant allele frequency in the range [0.0, 1.0] + */ + union {float, null} variantAlleleFrequency; + } +} From 14771ccbd671d98bc6cc2930e00a2ee96f6ec3ce Mon Sep 17 00:00:00 2001 From: Lang Date: Mon, 18 May 2020 09:49:38 +0200 Subject: [PATCH 003/105] change version --- input/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/input/__init__.py b/input/__init__.py index f82ff31d..ec04556c 100755 --- a/input/__init__.py +++ b/input/__init__.py @@ -1,4 +1,4 @@ -VERSION = '0.2.0' +VERSION = '0.2.1' REFERENCE_FOLDER_ENV = 'INPUT_REFERENCE_FOLDER' INPUT_BLASTP_ENV = 'INPUT_BLASTP' INPUT_MIXMHC2PRED_ENV = 'INPUT_MIXMHC2PRED' From ca4f78cb1f318c58467f16bab84d6129ab00e0eb Mon Sep 17 00:00:00 2001 From: Lang Date: Tue, 19 May 2020 11:16:31 +0200 Subject: [PATCH 004/105] adjust priority score if mutation_in_proteomt = T/F --- input/FeatureLiterature.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/input/FeatureLiterature.py b/input/FeatureLiterature.py index 2e1c7afe..c62bd8bc 100755 --- a/input/FeatureLiterature.py +++ b/input/FeatureLiterature.py @@ -221,6 +221,8 @@ def calc_priority_score(props, multiple_binding=False): score_mut = props["best%Rank_netmhcpan4"] score_wt = props["best%Rank_netmhcpan4_WT"] mut_in_prot = props["mutation_found_in_proteome"] + if mut_in_prot == "False" : mut_in_prot = "1" + if mut_in_prot == "True" : mut_in_prot = "0" L_mut = calc_logistic_function(score_mut) L_wt = calc_logistic_function(score_wt) priority_score = 0.0 From 04a7ac00716a88d775d0cb5cc8b105b7ec45484f Mon Sep 17 00:00:00 2001 From: Lang Date: Tue, 19 May 2020 11:16:43 +0200 Subject: [PATCH 005/105] version 0.2.2 --- input/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/input/__init__.py b/input/__init__.py index ec04556c..d62467c4 100755 --- a/input/__init__.py +++ b/input/__init__.py @@ -1,4 +1,4 @@ -VERSION = '0.2.1' +VERSION = '0.2.2' REFERENCE_FOLDER_ENV = 'INPUT_REFERENCE_FOLDER' INPUT_BLASTP_ENV = 'INPUT_BLASTP' INPUT_MIXMHC2PRED_ENV = 'INPUT_MIXMHC2PRED' From 61ccf4bdc62c4b870048772b85e9f41300d6e8c0 Mon Sep 17 00:00:00 2001 From: Lang Date: Tue, 19 May 2020 20:34:16 +0200 Subject: [PATCH 006/105] iedb.fasta from reactive T cell csv file --- input/references/build_IEDB_db.R | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 input/references/build_IEDB_db.R diff --git a/input/references/build_IEDB_db.R b/input/references/build_IEDB_db.R new file mode 100644 index 00000000..7bdae82b --- /dev/null +++ b/input/references/build_IEDB_db.R @@ -0,0 +1,27 @@ + +library(seqinr) +library(tidyverse) + +args <- commandArgs(trailingOnly = TRUE) +path_to_file <- args[1] +path_to_file <- "/home/franlang/refs_test/iedb" + +d2 <- read_csv(paste0(path_to_file, "/tcell_full_v3.csv"), skip = 1) + +# grep human MHC class I epitopes that were positive in context of infectious disease +d2.human <- d2 %>% + filter(Name == "Homo sapiens", + `Object Type` == "Linear peptide", + `Process Type` == "Occurrence of infectious disease", + `Qualitative Measure`== "Positive", + Class == "I") %>% + distinct(Description, .keep_all = T) %>% + mutate(epitope_id = gsub("http://www.iedb.org/epitope/", "", `Epitope IRI`), + #fasta_header = substr(paste(epitope_id, `Antigen Name`, `Parent Species`, sep = "_"), 1,50), + fasta_header = epitope_id, + seq = str_split_fixed(Description, " ", 2)[,1]) + +# write fasta file for DB +path_to_fasta = paste(path_to_file, "IEDB.fasta", sep = "/") +write.fasta(sequences = as.list(d2.human$seq), names = d2.human$fasta_header, file.out = path_to_fasta) + From db7fc89372674eec531a2bfb9b45c5fabc01a1d5 Mon Sep 17 00:00:00 2001 From: Lang Date: Tue, 19 May 2020 20:34:36 +0200 Subject: [PATCH 007/105] script to build references --- input/references/build_references.sh | 39 ++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100755 input/references/build_references.sh diff --git a/input/references/build_references.sh b/input/references/build_references.sh new file mode 100755 index 00000000..8cd05f83 --- /dev/null +++ b/input/references/build_references.sh @@ -0,0 +1,39 @@ +#!/bin/bash + +# remove and adjust +module load anaconda/3/2019 +INPUT_MIXMHC2PRED=/code/net/MixMHC2pred/1.1/MixMHC2pred +INPUT_MAKEBLASTDB=/code/ncbi-blast/2.8.1+/bin/makeblastdb +INPUT_RSCRIPT=/code/R/3.6.0/bin/Rscript +path_to_references="/home/franlang/refs_test/" + + +path_to_mixMHC2pred=`echo $INPUT_MIXMHC2PRED |sed 's/\(.*\)MixMHC2pred/\1/'` +echo $path_to_mixMHC2pred + +# available MHC alleles netMHCpan +/code/net/MHCpan/4.0/netMHCpan -listMHC | grep "HLA-" > "$path_to_references"/MHC_available.csv + + +# available MHCII alleles netMHCIIpan +/code/net/MHCIIpan/3.2/netMHCIIpan -list > "$path_to_references"/avail_mhcII.txt + + +# available MHCII alleles for MixMHC2pred +cp "$path_to_mixMHC2pred"/Alleles_list.txt $path_to_references + +# build IEDB blast database +mkdir "$path_to_references"/iedb +wget "http://www.iedb.org/downloader.php?file_name=doc/tcell_full_v3.zip" -O "$path_to_references"/iedb/Iedb.zip +unzip "$path_to_references"/iedb/Iedb.zip -d "$path_to_references"/iedb/ +$INPUT_RSCRIPT "$path_to_references"/build_IEDB_db.R "$path_to_references"/iedb/ +$INPUT_MAKEBLASTDB -in "$path_to_references"/iedb/IEDB.fasta -dbtype prot -parse_seqids -out "$path_to_references"/iedb/iedb + +# human proteome database +mkdir "$path_to_references"/proteom_db +wget ftp://ftp.ensembl.org/pub/release-100/fasta/homo_sapiens/pep/Homo_sapiens.GRCh38.pep.all.fa.gz -O "$path_to_references"/proteom_db/Homo_sapiens.fa.gz +gunzip "$path_to_references"/proteom_db/Homo_sapiens.fa.gz +$INPUT_MAKEBLASTDB -in "$path_to_references"/proteom_db/Homo_sapiens.fa -dbtype prot -parse_seqids -out "$path_to_references"/proteom_db/homo_sapiens + +# use Homo_sapiens.fa as uniprot_human_with_isoforms.fasta to be consistent with human proteome database +# provide BLOSUM62-2.matrix.txt as file and refer to "https://arxiv.org/abs/1205.6031" From 84d69fdf2c680f14bcec2e4a17751f5b29e6e7e8 Mon Sep 17 00:00:00 2001 From: Lang Date: Tue, 19 May 2020 20:44:21 +0200 Subject: [PATCH 008/105] generate reference files --- input/references/build_references.sh | 31 +++++++++++----------------- 1 file changed, 12 insertions(+), 19 deletions(-) diff --git a/input/references/build_references.sh b/input/references/build_references.sh index 8cd05f83..044ad2c1 100755 --- a/input/references/build_references.sh +++ b/input/references/build_references.sh @@ -1,39 +1,32 @@ #!/bin/bash -# remove and adjust -module load anaconda/3/2019 -INPUT_MIXMHC2PRED=/code/net/MixMHC2pred/1.1/MixMHC2pred -INPUT_MAKEBLASTDB=/code/ncbi-blast/2.8.1+/bin/makeblastdb -INPUT_RSCRIPT=/code/R/3.6.0/bin/Rscript -path_to_references="/home/franlang/refs_test/" - path_to_mixMHC2pred=`echo $INPUT_MIXMHC2PRED |sed 's/\(.*\)MixMHC2pred/\1/'` echo $path_to_mixMHC2pred # available MHC alleles netMHCpan -/code/net/MHCpan/4.0/netMHCpan -listMHC | grep "HLA-" > "$path_to_references"/MHC_available.csv +/code/net/MHCpan/4.0/netMHCpan -listMHC | grep "HLA-" > "$INPUT_REFERENCE_FOLDER"/MHC_available.csv # available MHCII alleles netMHCIIpan -/code/net/MHCIIpan/3.2/netMHCIIpan -list > "$path_to_references"/avail_mhcII.txt +/code/net/MHCIIpan/3.2/netMHCIIpan -list > "$INPUT_REFERENCE_FOLDER"/avail_mhcII.txt # available MHCII alleles for MixMHC2pred -cp "$path_to_mixMHC2pred"/Alleles_list.txt $path_to_references +cp "$path_to_mixMHC2pred"/Alleles_list.txt $INPUT_REFERENCE_FOLDER # build IEDB blast database -mkdir "$path_to_references"/iedb -wget "http://www.iedb.org/downloader.php?file_name=doc/tcell_full_v3.zip" -O "$path_to_references"/iedb/Iedb.zip -unzip "$path_to_references"/iedb/Iedb.zip -d "$path_to_references"/iedb/ -$INPUT_RSCRIPT "$path_to_references"/build_IEDB_db.R "$path_to_references"/iedb/ -$INPUT_MAKEBLASTDB -in "$path_to_references"/iedb/IEDB.fasta -dbtype prot -parse_seqids -out "$path_to_references"/iedb/iedb +mkdir "$INPUT_REFERENCE_FOLDER"/iedb +wget "http://www.iedb.org/downloader.php?file_name=doc/tcell_full_v3.zip" -O "$INPUT_REFERENCE_FOLDER"/iedb/Iedb.zip +unzip "$INPUT_REFERENCE_FOLDER"/iedb/Iedb.zip -d "$INPUT_REFERENCE_FOLDER"/iedb/ +$INPUT_RSCRIPT "$INPUT_REFERENCE_FOLDER"/build_IEDB_db.R "$INPUT_REFERENCE_FOLDER"/iedb/ +$INPUT_MAKEBLASTDB -in "$INPUT_REFERENCE_FOLDER"/iedb/IEDB.fasta -dbtype prot -parse_seqids -out "$INPUT_REFERENCE_FOLDER"/iedb/iedb # human proteome database -mkdir "$path_to_references"/proteom_db -wget ftp://ftp.ensembl.org/pub/release-100/fasta/homo_sapiens/pep/Homo_sapiens.GRCh38.pep.all.fa.gz -O "$path_to_references"/proteom_db/Homo_sapiens.fa.gz -gunzip "$path_to_references"/proteom_db/Homo_sapiens.fa.gz -$INPUT_MAKEBLASTDB -in "$path_to_references"/proteom_db/Homo_sapiens.fa -dbtype prot -parse_seqids -out "$path_to_references"/proteom_db/homo_sapiens +mkdir "$INPUT_REFERENCE_FOLDER"/proteom_db +wget ftp://ftp.ensembl.org/pub/release-100/fasta/homo_sapiens/pep/Homo_sapiens.GRCh38.pep.all.fa.gz -O "$INPUT_REFERENCE_FOLDER"/proteom_db/Homo_sapiens.fa.gz +gunzip "$INPUT_REFERENCE_FOLDER"/proteom_db/Homo_sapiens.fa.gz +$INPUT_MAKEBLASTDB -in "$INPUT_REFERENCE_FOLDER"/proteom_db/Homo_sapiens.fa -dbtype prot -parse_seqids -out "$INPUT_REFERENCE_FOLDER"/proteom_db/homo_sapiens # use Homo_sapiens.fa as uniprot_human_with_isoforms.fasta to be consistent with human proteome database # provide BLOSUM62-2.matrix.txt as file and refer to "https://arxiv.org/abs/1205.6031" From 53bb20e1d398660ce6571a4cafd30d2acbee374d Mon Sep 17 00:00:00 2001 From: Lang Date: Wed, 20 May 2020 08:48:45 +0200 Subject: [PATCH 009/105] absolute paths to environmental variables --- input/references/build_references.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/input/references/build_references.sh b/input/references/build_references.sh index 044ad2c1..a8f91724 100755 --- a/input/references/build_references.sh +++ b/input/references/build_references.sh @@ -5,11 +5,11 @@ path_to_mixMHC2pred=`echo $INPUT_MIXMHC2PRED |sed 's/\(.*\)MixMHC2pred/\1/'` echo $path_to_mixMHC2pred # available MHC alleles netMHCpan -/code/net/MHCpan/4.0/netMHCpan -listMHC | grep "HLA-" > "$INPUT_REFERENCE_FOLDER"/MHC_available.csv +$INPUT_NETMHCPAN -listMHC | grep "HLA-" > "$INPUT_REFERENCE_FOLDER"/MHC_available.csv # available MHCII alleles netMHCIIpan -/code/net/MHCIIpan/3.2/netMHCIIpan -list > "$INPUT_REFERENCE_FOLDER"/avail_mhcII.txt +$INPUT_NETMHC2PAN -list > "$INPUT_REFERENCE_FOLDER"/avail_mhcII.txt # available MHCII alleles for MixMHC2pred From 4edd3310ed576a135391d95a10f307861f91d9f0 Mon Sep 17 00:00:00 2001 From: Lang Date: Wed, 20 May 2020 08:49:50 +0200 Subject: [PATCH 010/105] change version from 0.2.2 to 0.2.1 --- input/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/input/__init__.py b/input/__init__.py index d62467c4..ec04556c 100755 --- a/input/__init__.py +++ b/input/__init__.py @@ -1,4 +1,4 @@ -VERSION = '0.2.2' +VERSION = '0.2.1' REFERENCE_FOLDER_ENV = 'INPUT_REFERENCE_FOLDER' INPUT_BLASTP_ENV = 'INPUT_BLASTP' INPUT_MIXMHC2PRED_ENV = 'INPUT_MIXMHC2PRED' From 6f1bf889c66ac6b592e11444f6d745f668af31a4 Mon Sep 17 00:00:00 2001 From: Pablo Riesgo Ferreiro Date: Wed, 20 May 2020 23:14:35 +0200 Subject: [PATCH 011/105] embed BLOSUM62 matrix in the binary + refactor self similarity --- MANIFEST.in | 3 +- input/epitope.py | 30 +++-- input/helpers/properties_manager.py | 24 ++++ input/references.py | 3 +- .../compute_self_similarity.py | 84 ------------- .../self_similarity/{ => docs}/1205.6031.pdf | Bin input/self_similarity/{ => docs}/Q.matrix.txt | 0 input/self_similarity/{ => docs}/README | 0 .../{ => docs}/fimmu-08-01566.pdf | Bin input/self_similarity/self_similarity.py | 110 ++++++++++++------ input/self_similarity/self_similiarity_nonsnv | 74 ------------ .../integration_tests/test_self_similarity.py | 38 ------ .../tests/unit_tests/test_self_similarity.py | 45 +++++++ 13 files changed, 165 insertions(+), 246 deletions(-) create mode 100755 input/helpers/properties_manager.py delete mode 100755 input/self_similarity/compute_self_similarity.py rename input/self_similarity/{ => docs}/1205.6031.pdf (100%) rename input/self_similarity/{ => docs}/Q.matrix.txt (100%) rename input/self_similarity/{ => docs}/README (100%) rename input/self_similarity/{ => docs}/fimmu-08-01566.pdf (100%) delete mode 100755 input/self_similarity/self_similiarity_nonsnv delete mode 100755 input/tests/integration_tests/test_self_similarity.py create mode 100755 input/tests/unit_tests/test_self_similarity.py diff --git a/MANIFEST.in b/MANIFEST.in index 859f6593..111d4f87 100755 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -1,2 +1,3 @@ include input/neoag/neoag-master/* -include input/Tcell_predictor/Classifier.pickle \ No newline at end of file +include input/Tcell_predictor/Classifier.pickle +include input/self_similarity/BLOSUM62-2.matrix.txt \ No newline at end of file diff --git a/input/epitope.py b/input/epitope.py index 75194a67..5043bef1 100755 --- a/input/epitope.py +++ b/input/epitope.py @@ -10,6 +10,7 @@ from input.MixMHCpred.mixmhc2pred import MixMhc2Pred from input.Tcell_predictor.tcellpredictor_wrapper import Tcellprediction from input.dissimilarity_garnish.dissimilaritycalculator import DissimilarityCalculator +from input.helpers import properties_manager from input.neoag.neoag_gbm_model import NeoagCalculator from input.neoantigen_fitness.neoantigen_fitness import NeoantigenFitnessCalculator from input.netmhcIIpan.combine_netmhcIIpan_pred_multiple_binders import BestAndMultipleBinderMhcII @@ -63,8 +64,15 @@ def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aa self.init_properties(col_nam, prop_list) logger.info(self.properties["X..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."]) - self.add_features(self_similarity.position_of_mutation_epitope(self.properties, MHC_I), "pos_MUT_MHCI") - self.add_features(self_similarity.position_of_mutation_epitope(self.properties, MHC_II), "pos_MUT_MHCII") + wild_type_mhci, mutation_mhci = properties_manager.get_wild_type_and_mutations( + properties=self.properties, mhc=MHC_I) + wild_type_mhcii, mutation_mhcii = properties_manager.get_wild_type_and_mutations( + properties=self.properties, mhc=MHC_II) + + self.add_features(self_similarity.position_of_mutation_epitope( + wild_type=wild_type_mhci, mutation=mutation_mhci), "pos_MUT_MHCI") + self.add_features(self_similarity.position_of_mutation_epitope( + wild_type=wild_type_mhcii, mutation=mutation_mhcii), "pos_MUT_MHCII") self.add_features(self_similarity.position_in_anchor_position(self.properties), "Mutation_in_anchor") # differential agretopicity index @@ -205,22 +213,26 @@ def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aa self.properties, MHC_I, multiple_binding=True), "Amplitude_mhcI_MB") # position of mutation - self.add_features(self_similarity.position_of_mutation_epitope_affinity(self.properties), - "pos_MUT_MHCI_affinity_epi") + wild_type_netmhcpan4, mutation_netmhcpan4 = properties_manager.get_wild_type_and_mutation_from_netmhcpan4( + properties=self.properties) + self.add_features(self_similarity.position_of_mutation_epitope( + wild_type=wild_type_netmhcpan4, mutation=mutation_netmhcpan4), "pos_MUT_MHCI_affinity_epi") # position of mutation - self.add_features(self_similarity.position_of_mutation_epitope_affinity(self.properties, nine_mer=True), - "pos_MUT_MHCI_affinity_epi_9mer") + wild_type_netmhcpan4_9mer, mutation_netmhcpan4_9mer = properties_manager.get_wild_type_and_mutation_from_netmhcpan4( + properties=self.properties, nine_mer=True) + self.add_features(self_similarity.position_of_mutation_epitope( + wild_type=wild_type_netmhcpan4_9mer, mutation=mutation_netmhcpan4_9mer),"pos_MUT_MHCI_affinity_epi_9mer") self.add_features(self_similarity.position_in_anchor_position(self.properties, netMHCpan=True), "Mutation_in_anchor_netmhcpan") self.add_features(self_similarity.position_in_anchor_position(self.properties, nine_mer=True), "Mutation_in_anchor_netmhcpan_9mer") # selfsimilarity + self.add_features(self_similarity.get_self_similarity(mutation=mutation_mhci, wild_type=wild_type_mhci), + "Selfsimilarity_mhcI") self.add_features(self_similarity.get_self_similarity( - props=self.properties, mhc=MHC_I, references=self.references), "Selfsimilarity_mhcI") - self.add_features(self_similarity.get_self_similarity( - props=self.properties, mhc=MHC_II, references=self.references), "Selfsimilarity_mhcII") + wild_type=wild_type_mhcii, mutation=mutation_mhcii), "Selfsimilarity_mhcII") self.add_features(self_similarity.is_improved_binder(self.properties, MHC_I), "ImprovedBinding_mhcI") self.add_features(self_similarity.is_improved_binder(self.properties, MHC_II), "ImprovedBinding_mhcII") self.add_features(self_similarity.selfsimilarity_of_conserved_binder_only(self.properties), diff --git a/input/helpers/properties_manager.py b/input/helpers/properties_manager.py new file mode 100755 index 00000000..90f06486 --- /dev/null +++ b/input/helpers/properties_manager.py @@ -0,0 +1,24 @@ +from input import MHC_I, MHC_II +from input.exceptions import INPuTInputParametersException + + +def get_wild_type_and_mutations(properties, mhc): + if mhc == MHC_I: + mutation = properties["MHC_I_epitope_.best_prediction."] + wild_type = properties["MHC_I_epitope_.WT."] + elif mhc == MHC_II: + mutation = properties["MHC_II_epitope_.best_prediction."] + wild_type = properties["MHC_II_epitope_.WT."] + else: + raise INPuTInputParametersException("Bad MHC value: {}".format(mhc)) + return wild_type, mutation + + +def get_wild_type_and_mutation_from_netmhcpan4(properties, nine_mer=False): + if nine_mer: + mutation = properties["best_affinity_epitope_netmhcpan4_9mer"] + wild_type = properties["best_epitope_netmhcpan4_9mer_WT"] + else: + mutation = properties["best_affinity_epitope_netmhcpan4"] + wild_type = properties["best_affinity_epitope_netmhcpan4_WT"] + return wild_type, mutation \ No newline at end of file diff --git a/input/references.py b/input/references.py index e1ad9fb8..2dbf4e77 100755 --- a/input/references.py +++ b/input/references.py @@ -44,7 +44,6 @@ def __init__(self): self.prov_scores_mapped3 = self._get_reference_file_name('PROV_scores_mapped3.csv') self.iedb = self._get_reference_file_name('iedb') self.proteome_db = self._get_reference_file_name('proteome_db') - self.blosum62 = self._get_reference_file_name('BLOSUM62-2.matrix.txt') self.tcell_predictor_sir_data = self._get_reference_file_name('SIRdata.mat') self.tcell_predictor_gene_expression = self._get_reference_file_name('genes-expression.pickle') self.tcell_predictor_aa_features = self._get_reference_file_name('amino-acids-features.pickle') @@ -54,7 +53,7 @@ def __init__(self): # TODO: add this files self.alleles_list_pred, self.avail_mhc_ii self.resources = [self.alleles_list_pred, self.available_mhc_ii, self.available_mhc_i, self.aa_freq_prot, self.four_mer_freq, self.aaindex1, self.aaindex2, self.prov_scores_mapped3, self.iedb, - self.proteome_db, self.blosum62, self.tcell_predictor_aa_features, + self.proteome_db, self.tcell_predictor_aa_features, self.tcell_predictor_gene_expression, self.tcell_predictor_sir_data, self.uniprot, self.gtex] self._check_resources(self.resources) diff --git a/input/self_similarity/compute_self_similarity.py b/input/self_similarity/compute_self_similarity.py deleted file mode 100755 index d09205c7..00000000 --- a/input/self_similarity/compute_self_similarity.py +++ /dev/null @@ -1,84 +0,0 @@ -import math - - -def read_K1(mfile="BLOSUM62-2.matrix.txt"): - bd = {} - colid = [] - rowid = [] - - c = 0 - with open(mfile) as f: - for line in f: - c += 1 - if c == 1: - colid = line.strip("\n").split(" ") - continue - w = line.strip("\n").split(" ") - id = w[0] - v = [float(x) for x in w[1:]] - rowid.append(id) - x = bd.get(id, {}) - for i, vi in enumerate(v): - x[colid[i]] = vi - bd[id] = x - - # print bd["A"]["Y"] - # print bd["Y"]["A"] - # print bd["C"]["A"], bd["A"]["C"] - # print bd["Y"]["C"], bd["C"]["Y"] - - BLOSUM62_2 = bd - K1 = {} - beta = 0.11387 - for i in list(BLOSUM62_2.keys()): - x = K1.get(i, {}) - for j in list(BLOSUM62_2[i].keys()): - x[j] = math.pow(BLOSUM62_2[i][j], beta) - K1[i] = x - return K1 - - -def compute_K2k(u, v, K1): - if len(u) != len(v): - return None - k = len(u) - p = K1[u[0]][v[0]] - for i in range(1, k): - p = p * K1[u[i]][v[i]] - return p - - -def compute_K3(f, g, K1): - max_k = min(len(f), len(g)) - s = 0 - for k in range(1, max_k + 1): - for i in range(len(f) - (k - 1)): - u = f[i:i + k] - for j in range(len(g) - (k - 1)): - v = g[j:j + k] - s += compute_K2k(u, v, K1) - return s - - -def compute_K_hat_3(x, y, K1): - return compute_K3(x, y, K1) / math.sqrt(compute_K3(x, x, K1) * compute_K3(y, y, K1)) - - -class selfsim(): - def __init__(self, mfile): - self.K1 = read_K1(mfile) - - def compute_K_hat_3(self, x, y): # K^3 - return compute_K_hat_3(x, y, self.K1) - - -if __name__ == "__main__": - K1 = read_K1() - print(compute_K_hat_3("AAAAA", "AAAAA", K1)) - for i in range(5): - print(i, compute_K_hat_3("AAAAA", "WWWWW" * (i + 1), K1)) - for i in list(K1.keys()): - print(i, compute_K_hat_3("AAAAA", "AA" + i + "AA", K1)) - print() - s = selfsim("BLOSUM62-2.matrix.txt") - print(s.compute_K_hat_3("AAAAA", "AAAAA")) diff --git a/input/self_similarity/1205.6031.pdf b/input/self_similarity/docs/1205.6031.pdf similarity index 100% rename from input/self_similarity/1205.6031.pdf rename to input/self_similarity/docs/1205.6031.pdf diff --git a/input/self_similarity/Q.matrix.txt b/input/self_similarity/docs/Q.matrix.txt similarity index 100% rename from input/self_similarity/Q.matrix.txt rename to input/self_similarity/docs/Q.matrix.txt diff --git a/input/self_similarity/README b/input/self_similarity/docs/README similarity index 100% rename from input/self_similarity/README rename to input/self_similarity/docs/README diff --git a/input/self_similarity/fimmu-08-01566.pdf b/input/self_similarity/docs/fimmu-08-01566.pdf similarity index 100% rename from input/self_similarity/fimmu-08-01566.pdf rename to input/self_similarity/docs/fimmu-08-01566.pdf diff --git a/input/self_similarity/self_similarity.py b/input/self_similarity/self_similarity.py index 78d5a607..aa59d32d 100755 --- a/input/self_similarity/self_similarity.py +++ b/input/self_similarity/self_similarity.py @@ -1,22 +1,82 @@ #!/usr/bin/env python -import input.self_similarity.compute_self_similarity as compute_self_similarity from input import MHC_I, MHC_II +import math +import os -def get_self_similarity(props, mhc, references): +BETA = 0.11387 +BLOSUM62_FILE_NAME = 'BLOSUM62-2.matrix.txt' + + +class SelfSimilarityCalculator(): + + def __init__(self): + blosum_file = os.path.join(os.path.abspath(os.path.dirname(__file__)), BLOSUM62_FILE_NAME) + blosum_dict = self._load_blosum(blosum_file) + self.k1 = self._compute_k1(blosum_dict) + + def _compute_k1(self, blosum_dict): + K1 = {} + for i in list(blosum_dict.keys()): + x = K1.get(i, {}) + for j in list(blosum_dict[i].keys()): + x[j] = math.pow(blosum_dict[i][j], BETA) + K1[i] = x + return K1 + + def _load_blosum(self, blosum): + blosum_dict = {} + colid = [] + rowid = [] + c = 0 + with open(blosum) as f: + for line in f: + c += 1 + if c == 1: + colid = line.strip("\n").split(" ") + continue + w = line.strip("\n").split(" ") + id = w[0] + v = [float(x) for x in w[1:]] + rowid.append(id) + x = blosum_dict.get(id, {}) + for i, vi in enumerate(v): + x[colid[i]] = vi + blosum_dict[id] = x + return blosum_dict + + def compute_k_hat_3(self, x, y): # K^3 + return self._compute_k3(x, y) / math.sqrt(self._compute_k3(x, x) * self._compute_k3(y, y)) + + def _compute_k3(self, f, g): + max_k = min(len(f), len(g)) + s = 0 + for k in range(1, max_k + 1): + for i in range(len(f) - (k - 1)): + u = f[i:i + k] + for j in range(len(g) - (k - 1)): + v = g[j:j + k] + s += self._compute_k2k(u, v, self.k1) + return s + + def _compute_k2k(self, u, v, K1): + if len(u) != len(v): + return None + k = len(u) + p = K1[u[0]][v[0]] + for i in range(1, k): + p = p * K1[u[i]][v[i]] + return p + + +def get_self_similarity(mutation, wild_type): """Returns self-similiarity between mutated and wt epitope according to Bjerregard et al., Argument mhc indicates if determination for MHC I or MHC II epitopes """ - if mhc == MHC_I: - mhcI_mut = props["MHC_I_epitope_.best_prediction."] - mhcI_wt = props["MHC_I_epitope_.WT."] - elif mhc == MHC_II: - mhcI_mut = props["MHC_II_epitope_.best_prediction."] - mhcI_wt = props["MHC_II_epitope_.WT."] self_similarity = 'NA' try: - self_similarity = str(compute_self_similarity.selfsim(references.blosum62).compute_K_hat_3(mhcI_mut, mhcI_wt)) + self_similarity = str(SelfSimilarityCalculator().compute_k_hat_3(mutation, wild_type)) except ZeroDivisionError: pass return self_similarity @@ -54,40 +114,14 @@ def selfsimilarity_of_conserved_binder_only(props): return "NA" -def position_of_mutation_epitope(props, mhc): - ''' - This function determines the position of the mutation within the epitope sequence. - ''' - if mhc == MHC_I: - mhc_mut = props["MHC_I_epitope_.best_prediction."] - mhc_wt = props["MHC_I_epitope_.WT."] - elif mhc == MHC_II: - mhc_mut = props["MHC_II_epitope_.best_prediction."] - mhc_wt = props["MHC_II_epitope_.WT."] - p1 = -1 - try: - for i, aa in enumerate(mhc_mut): - if aa != mhc_wt[i]: - p1 = i + 1 - return str(p1) - except: - return "NA" - - -def position_of_mutation_epitope_affinity(props, nine_mer=False): +def position_of_mutation_epitope(wild_type, mutation): ''' This function determines the position of the mutation within the epitope sequence. ''' - if nine_mer: - mhc_mut = props["best_affinity_epitope_netmhcpan4_9mer"] - mhc_wt = props["best_epitope_netmhcpan4_9mer_WT"] - else: - mhc_mut = props["best_affinity_epitope_netmhcpan4"] - mhc_wt = props["best_affinity_epitope_netmhcpan4_WT"] p1 = -1 try: - for i, aa in enumerate(mhc_mut): - if aa != mhc_wt[i]: + for i, aa in enumerate(mutation): + if aa != wild_type[i]: p1 = i + 1 return str(p1) except: diff --git a/input/self_similarity/self_similiarity_nonsnv b/input/self_similarity/self_similiarity_nonsnv deleted file mode 100755 index 558f4ab2..00000000 --- a/input/self_similarity/self_similiarity_nonsnv +++ /dev/null @@ -1,74 +0,0 @@ -#!/usr/bin/env python - -import sys -import os.path -import input.self_similarity.compute_self_similarity as compute_self_similarity -import input.self_similarity.self_similarity as self_similarity -from input import MHC_I, MHC_II - -my_path = os.path.abspath(os.path.dirname(__file__)) - -def selfsimilarity(props, mhc, db): - """Returns self-similiarity between mutated and wt epitope according to Bjerregard et al., - Argument mhc indicates if determination for MHC I or MHC II epitopes - """ - if mhc == MHC_I: - mhcI_mut = props["MHC_I_epitope_.best_prediction."] - mhcI_wt = props["WT_epitope_" + db] - elif mhc == MHC_II: - mhcI_mut = props["MHC_II_epitope_.best_prediction."] - mhcI_wt = props["WT_epitope_" + db] - selfsim = compute_self_similarity.selfsim(os.path.join(my_path, "./BLOSUM62-2.matrix.txt")) - try: - return str(selfsim.compute_K_hat_3(mhcI_mut, mhcI_wt)) - except ZeroDivisionError: - return "NA" - - -def improved_binder(props, mhc): - ''' - This function checks if mutated epitope is improved binder according to Bjerregard et al. - ''' - if mhc == MHC_I: - sc_mut = props["MHC_I_score_.best_prediction."].replace(",",".") - sc_wt = props["WT_best_MHC_score_"].replace(",",".") - elif mhc == MHC_II: - sc_mut = props["MHC_II_score_.best_prediction."].replace(",",".") - sc_wt = props["MHC_II_score_.WT."].replace(",",".") - imp_binder = 0 - try: - imp_binder = float(sc_wt)/float(sc_mut) >= 1.2 - return str(1) if imp_binder else str(0) - except (ZeroDivisionError, ValueError) as e: - return "NA" - - -def wrapper_selfsim_dbs(props, mhc): - ''' selfsimilarity and test if improved binding for all potential WT epitopes from different databases - ''' - list_dbs = ["ligandome", "proteome", "protein"] - for db in list_dbs: - selfsim = selfsimilarity(props, mhc, db) - bdg = improved_binder(props, mhc) - props["selfsimilarity_" + db] = selfsim - props["improved_binder_" + db] = selfsim - return props - - -if __name__ == '__main__': - import sys - basedir = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/INPuT2" - sys.path.append(basedir) - import data_import - - file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/INPuT2/nonprogramm_files/20170713_IS_IM_data.complete.update_Dv10.csv" - indel = False - dat = data_import.import_dat_icam(file, indel) - - properties = {} - for nam,char in zip(dat[0], dat[1][1]): - properties[nam] = char - - - print(selfsimilarity(properties, MHC_I)) - print(self_similarity.position_of_mutation_epitope(properties, MHC_I)) diff --git a/input/tests/integration_tests/test_self_similarity.py b/input/tests/integration_tests/test_self_similarity.py deleted file mode 100755 index dd62ec22..00000000 --- a/input/tests/integration_tests/test_self_similarity.py +++ /dev/null @@ -1,38 +0,0 @@ -from unittest import TestCase - -import input.self_similarity.self_similarity as self_similarity -import input.tests.integration_tests.integration_test_tools as integration_test_tools -from input import MHC_I, MHC_II - - -class TestSelfSimilarity(TestCase): - - def setUp(self): - self.references, self.configuration = integration_test_tools.load_references() - self.fastafile = integration_test_tools.create_temp_aminoacid_fasta_file() - - def test_get_self_similarity_mhci(self): - result = self_similarity.get_self_similarity( - props={'MHC_I_epitope_.best_prediction.': 'DDD', 'MHC_I_epitope_.WT.': 'DDD'}, - mhc=MHC_I, - references=self.references) - self.assertEqual('1.0', result) - - def test_get_self_similarity_mhcii(self): - result = self_similarity.get_self_similarity( - props={'MHC_II_epitope_.best_prediction.': 'DDD', 'MHC_II_epitope_.WT.': 'DDD'}, - mhc=MHC_II, - references=self.references) - self.assertEqual('1.0', result) - - def test_is_improved_binder_mhci(self): - result = self_similarity.is_improved_binder( - props={'best%Rank_netmhcpan4': '1.0', 'best%Rank_netmhcpan4_WT': '1.3'}, - mhc=MHC_I) - self.assertEqual('1', result) - - def test_is_improved_binder_mhcii(self): - result = self_similarity.is_improved_binder( - props={'MHC_II_score_.best_prediction.': '1,0', 'MHC_II_score_.WT.': '1,3'}, - mhc=MHC_II) - self.assertEqual('1', result) diff --git a/input/tests/unit_tests/test_self_similarity.py b/input/tests/unit_tests/test_self_similarity.py new file mode 100755 index 00000000..96d8782e --- /dev/null +++ b/input/tests/unit_tests/test_self_similarity.py @@ -0,0 +1,45 @@ +from unittest import TestCase + +import input.self_similarity.self_similarity as self_similarity +from input import MHC_I, MHC_II + + +class TestSelfSimilarity(TestCase): + + def test_get_self_similarity(self): + result = self_similarity.get_self_similarity(wild_type="DDD", mutation="DDD") + self.assertEqual('1.0', result) + + def test_is_improved_binder_mhci(self): + result = self_similarity.is_improved_binder( + props={'best%Rank_netmhcpan4': '1.0', 'best%Rank_netmhcpan4_WT': '1.3'}, + mhc=MHC_I) + self.assertEqual('1', result) + + def test_is_improved_binder_mhcii(self): + result = self_similarity.is_improved_binder( + props={'MHC_II_score_.best_prediction.': '1,0', 'MHC_II_score_.WT.': '1,3'}, + mhc=MHC_II) + self.assertEqual('1', result) + + def test_position_mutation(self): + position = self_similarity.position_of_mutation_epitope(wild_type="AAAAAA", mutation="AAANAA") + self.assertEqual(position, "4") + position = self_similarity.position_of_mutation_epitope(wild_type="AAAAAA", mutation="AAAAAA") + self.assertEqual(position, "-1") + position = self_similarity.position_of_mutation_epitope(wild_type="AAAAAA", mutation="AANNNN") + self.assertEqual(position, "6") + + def test_compute_self_similarity_calculator(self): + + s = self_similarity.SelfSimilarityCalculator() + self.assertEqual(s.compute_k_hat_3("AAAAA", "AAAAA"), 1.0) + for i in range(5): + self.assertTrue(s.compute_k_hat_3("AAAAA", "WWWWW" * (i + 1)) < 1.0) + for i in list(s.k1.keys()): + if i == "A": + self.assertTrue(s.compute_k_hat_3("AAAAA", "AA" + i + "AA") == 1.0) + else: + self.assertTrue(s.compute_k_hat_3("AAAAA", "AA" + i + "AA") < 1.0) + + From 59db628b2b517a6866390f58f31ab436da893e0a Mon Sep 17 00:00:00 2001 From: Pablo Riesgo Ferreiro Date: Wed, 20 May 2020 23:47:05 +0200 Subject: [PATCH 012/105] remove Alleles_list from the references folder, it is found through the configuration environment variable --- input/MixMHCpred/mixmhc2pred.py | 41 ++++++++++++++++++++-------- input/epitope.py | 5 ++-- input/predict_all_epitopes.py | 22 +-------------- input/references.py | 4 +-- input/references/build_references.sh | 8 ------ 5 files changed, 35 insertions(+), 45 deletions(-) diff --git a/input/MixMHCpred/mixmhc2pred.py b/input/MixMHCpred/mixmhc2pred.py index f46de2b3..0e73fef3 100755 --- a/input/MixMHCpred/mixmhc2pred.py +++ b/input/MixMHCpred/mixmhc2pred.py @@ -12,6 +12,7 @@ def __init__(self, runner, configuration): """ self.runner = runner self.configuration = configuration + self.available_alleles = self.load_available_allelles() self.all_peptides = "NA" self.all_ranks = "NA" self.all_alleles = "NA" @@ -23,6 +24,24 @@ def __init__(self, runner, configuration): self.best_rank_wt = "NA" self.difference_score_mut_wt = "NA" + def load_available_allelles(self): + """ + loads file with available hla alllels for MixMHC2pred prediction, returns set + :return: + """ + path_to_HLAII_file = self.configuration.mix_mhc2_pred_alleles_list + avail_alleles = [] + with open(path_to_HLAII_file) as f: + for line in f: + line = line.rstrip().lstrip() + if line: + if line.startswith(("L", "A")): + continue + line1 = line.split()[0] + if line1 is not None: + avail_alleles.append(line1) + return avail_alleles + def mut_position_xmer_seq(self, props): '''returns position of mutation in xmer sequence ''' @@ -89,17 +108,17 @@ def get_hla_allels(self, props, hla_patient_dict): patientid = props["patient.x"] return hla_patient_dict[patientid] - def prepare_dq_dp(self, list_alleles, avail_hlaII): + def prepare_dq_dp(self, list_alleles): ''' returns patient DQ/DP alleles that are relevant for prediction ''' list_alleles_pairs = ["__".join([p1, p2]) for p1 in list_alleles for p2 in list_alleles if p1 != p2] list_alleles_triplets = ["__".join([p1, p2, p3]) for p1 in list_alleles for p2 in list_alleles for p3 in list_alleles if p1 != p2 and p1 != p3 and p2 != p3] list_alleles_all = list_alleles_pairs + list_alleles_triplets - alleles4pred = [allele for allele in list_alleles_all if allele in avail_hlaII] + alleles4pred = [allele for allele in list_alleles_all if allele in self.available_alleles] return (alleles4pred) - def hlaIIallels2prediction(self, hla_alleles, avail_hlaII): + def hlaIIallels2prediction(self, hla_alleles): ''' prepares list of hla alleles for prediction ''' allels_for_prediction = [] @@ -110,24 +129,24 @@ def hlaIIallels2prediction(self, hla_alleles, avail_hlaII): # print allele allele = allele.replace("*", "_").replace(":", "_").replace("HLA-", "") if allele.startswith("DR"): - if allele in avail_hlaII: + if allele in self.available_alleles: allels_for_prediction.append(allele) elif allele.startswith("DP"): alleles_dp.append(allele) elif allele.startswith("DQ"): alleles_dq.append(allele) - alleles_dp4pred = self.prepare_dq_dp(alleles_dp, avail_hlaII) - alleles_dq4pred = self.prepare_dq_dp(alleles_dq, avail_hlaII) + alleles_dp4pred = self.prepare_dq_dp(alleles_dp) + alleles_dq4pred = self.prepare_dq_dp(alleles_dq) allels_for_prediction = allels_for_prediction + alleles_dq4pred + alleles_dp4pred hla_allele = " ".join(allels_for_prediction) # print hla_allele return hla_allele - def mixmhc2prediction(self, hla_alleles, tmpfasta, outtmp, avail_hlaII, wt=False): + def mixmhc2prediction(self, hla_alleles, tmpfasta, outtmp, wt=False): ''' Performs MixMHC2pred prediction for desired hla allele and writes result to temporary file. ''' if not wt: - hla_allele = self.hlaIIallels2prediction(hla_alleles, avail_hlaII) + hla_allele = self.hlaIIallels2prediction(hla_alleles) elif wt: # use best allele from mutated seq prediction hla_allele = hla_alleles[0] @@ -257,7 +276,7 @@ def import_available_HLAII_alleles(self, path_to_HLAII_file): avail_alleles.append(line1) return avail_alleles - def main(self, props_dict, dict_patient_hlaII, list_avail_hlaII): + def main(self, props_dict, dict_patient_hlaII): '''Wrapper for MHC binding prediction, extraction of best epitope and check if mutation is directed to TCR ''' tmp_fasta_file = tempfile.NamedTemporaryFile(prefix="tmp_sequence_", suffix=".fasta", delete=False) @@ -270,7 +289,7 @@ def main(self, props_dict, dict_patient_hlaII, list_avail_hlaII): alleles = self.get_hla_allels(props_dict, dict_patient_hlaII) # try except statement to prevent stop of input for mps shorter < 13aa try: - self.mixmhc2prediction(alleles, tmp_fasta, tmp_prediction, list_avail_hlaII) + self.mixmhc2prediction(alleles, tmp_fasta, tmp_prediction) except: pass try: @@ -297,7 +316,7 @@ def main(self, props_dict, dict_patient_hlaII, list_avail_hlaII): tmp_prediction_file = tempfile.NamedTemporaryFile(prefix="mixmhc2pred_wt_", suffix=".txt", delete=False) tmp_prediction = tmp_prediction_file.name self.generate_fasta(wt_list, tmp_fasta) - self.mixmhc2prediction([self.best_allele], tmp_fasta, tmp_prediction, list_avail_hlaII, wt=True) + self.mixmhc2prediction([self.best_allele], tmp_fasta, tmp_prediction, wt=True) pred_wt = self.read_mixmhcpred(tmp_prediction) self.best_peptide_wt = self.extract_WT_info(pred_wt, "Peptide") self.best_rank_wt = self.extract_WT_info(pred_wt, "%Rank") diff --git a/input/epitope.py b/input/epitope.py index 5043bef1..a4148c3e 100755 --- a/input/epitope.py +++ b/input/epitope.py @@ -57,8 +57,7 @@ def write_to_file(self): print(";".join([self.properties[key] for key in self.properties])) def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aaindex1_dict, aaindex2_dict, - set_available_mhc, set_available_mhcII, patient_hlaI, patient_hlaII, tumour_content, - list_HLAII_MixMHC2pred, rna_avail): + set_available_mhc, set_available_mhcII, patient_hlaI, patient_hlaII, tumour_content, rna_avail): """ Calculate new epitope features and add to dictonary that stores all properties """ self.init_properties(col_nam, prop_list) @@ -439,7 +438,7 @@ def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aa self.add_features(self.predpresentation.difference_score_mut_wt, "MixMHCpred_difference_score_mut_wt") # MixMHC2pred - self.predpresentation2.main(self.properties, patient_hlaII, list_HLAII_MixMHC2pred) + self.predpresentation2.main(self.properties, patient_hlaII) self.add_features(self.predpresentation2.all_peptides, "MixMHC2pred_all_peptides") self.add_features(self.predpresentation2.all_ranks, "MixMHC2pred_all_ranks") self.add_features(self.predpresentation2.all_alleles, "MixMHC2pred_all_alleles") diff --git a/input/predict_all_epitopes.py b/input/predict_all_epitopes.py index b15d6071..d78daea5 100755 --- a/input/predict_all_epitopes.py +++ b/input/predict_all_epitopes.py @@ -32,7 +32,6 @@ def __init__(self): self.patient_hla_I_alleles = {} self.patient_hla_II_alleles = {} self.tumour_content = {} - self.hlaII_available_MixMHC2pred = [] self.rna_avail = {} @staticmethod @@ -93,24 +92,6 @@ def load_available_hla_alleles(self, mhc=MHC_I): set_available_mhc.add(line.strip()) return set_available_mhc - def load_available_allelles_mixMHC2pred(self): - """ - loads file with available hla alllels for MixMHC2pred prediction, returns set - :return: - """ - path_to_HLAII_file = self.references.alleles_list_pred - avail_alleles = [] - with open(path_to_HLAII_file) as f: - for line in f: - line = line.rstrip().lstrip() - if line: - if line.startswith(("L", "A")): - continue - line1 = line.split()[0] - if line1 is not None: - avail_alleles.append(line1) - return avail_alleles - @staticmethod def load_patient_hla_I_allels(path_to_hla_file): """ @@ -213,7 +194,6 @@ def initialise_properties(self, data, path_to_hla_file, tissue, tumour_content_f prov_file = self.references.prov_scores_mapped3 self.hla_available_alleles = self.load_available_hla_alleles() self.hlaII_available_alleles = self.load_available_hla_alleles(mhc=MHC_II) - self.hlaII_available_MixMHC2pred = self.load_available_allelles_mixMHC2pred() self.patient_hla_I_allels = self.load_patient_hla_I_allels(path_to_hla_file) self.patient_hla_II_allels = self.load_patient_hla_II_allels(path_to_hla_file) # tumour content @@ -256,7 +236,7 @@ def wrapper_table_add_feature_annotation(self, file, indel, path_to_hla_file, ti dat[0], dat[1][ii], self.proteome_dictionary, self.rna_reference, self.aa_frequency, self.fourmer_frequency, self.aa_index1_dict, self.aa_index2_dict, self.hla_available_alleles, self.hlaII_available_alleles, self.patient_hla_I_allels, - self.patient_hla_II_allels, self.tumour_content, self.hlaII_available_MixMHC2pred, self.rna_avail) + self.patient_hla_II_allels, self.tumour_content, self.rna_avail) for key in z: if key not in self.Allepit: # keys are are feautres; values: list of feature values associated with mutated peptide sequence diff --git a/input/references.py b/input/references.py index 2dbf4e77..ab7fffbe 100755 --- a/input/references.py +++ b/input/references.py @@ -11,6 +11,7 @@ class DependenciesConfiguration(object): def __init__(self): self.blastp = self._check_and_load_binary(input.INPUT_BLASTP_ENV) self.mix_mhc2_pred = self._check_and_load_binary(input.INPUT_MIXMHC2PRED_ENV) + self.mix_mhc2_pred_alleles_list = os.path.join(os.path.dirname(self.mix_mhc2_pred), 'Alleles_list.txt') self.mix_mhc_pred = self._check_and_load_binary(input.INPUT_MIXMHCPRED_ENV) self.rscript = self._check_and_load_binary(input.INPUT_RSCRIPT_ENV) self.net_mhc2_pan = self._check_and_load_binary(input.INPUT_NETMHC2PAN_ENV) @@ -34,7 +35,6 @@ class ReferenceFolder(object): def __init__(self): self.reference_genome_folder = self._check_reference_genome_folder() # sets the right file names for the resources - self.alleles_list_pred = self._get_reference_file_name('Alleles_list_pred2.txt') self.available_mhc_ii = self._get_reference_file_name('avail_mhcII.txt') self.available_mhc_i = self._get_reference_file_name('MHC_available.csv') self.aa_freq_prot = self._get_reference_file_name('20181108_AA_freq_prot.csv') @@ -51,7 +51,7 @@ def __init__(self): self.gtex = self._get_reference_file_name('gtex_combined.csv') # TODO: add this files self.alleles_list_pred, self.avail_mhc_ii - self.resources = [self.alleles_list_pred, self.available_mhc_ii, self.available_mhc_i, self.aa_freq_prot, + self.resources = [self.available_mhc_ii, self.available_mhc_i, self.aa_freq_prot, self.four_mer_freq, self.aaindex1, self.aaindex2, self.prov_scores_mapped3, self.iedb, self.proteome_db, self.tcell_predictor_aa_features, self.tcell_predictor_gene_expression, self.tcell_predictor_sir_data, diff --git a/input/references/build_references.sh b/input/references/build_references.sh index a8f91724..02cf3d02 100755 --- a/input/references/build_references.sh +++ b/input/references/build_references.sh @@ -1,9 +1,6 @@ #!/bin/bash -path_to_mixMHC2pred=`echo $INPUT_MIXMHC2PRED |sed 's/\(.*\)MixMHC2pred/\1/'` -echo $path_to_mixMHC2pred - # available MHC alleles netMHCpan $INPUT_NETMHCPAN -listMHC | grep "HLA-" > "$INPUT_REFERENCE_FOLDER"/MHC_available.csv @@ -11,10 +8,6 @@ $INPUT_NETMHCPAN -listMHC | grep "HLA-" > "$INPUT_REFERENCE_FOLDER"/MHC_availabl # available MHCII alleles netMHCIIpan $INPUT_NETMHC2PAN -list > "$INPUT_REFERENCE_FOLDER"/avail_mhcII.txt - -# available MHCII alleles for MixMHC2pred -cp "$path_to_mixMHC2pred"/Alleles_list.txt $INPUT_REFERENCE_FOLDER - # build IEDB blast database mkdir "$INPUT_REFERENCE_FOLDER"/iedb wget "http://www.iedb.org/downloader.php?file_name=doc/tcell_full_v3.zip" -O "$INPUT_REFERENCE_FOLDER"/iedb/Iedb.zip @@ -29,4 +22,3 @@ gunzip "$INPUT_REFERENCE_FOLDER"/proteom_db/Homo_sapiens.fa.gz $INPUT_MAKEBLASTDB -in "$INPUT_REFERENCE_FOLDER"/proteom_db/Homo_sapiens.fa -dbtype prot -parse_seqids -out "$INPUT_REFERENCE_FOLDER"/proteom_db/homo_sapiens # use Homo_sapiens.fa as uniprot_human_with_isoforms.fasta to be consistent with human proteome database -# provide BLOSUM62-2.matrix.txt as file and refer to "https://arxiv.org/abs/1205.6031" From 12f704f5f407720c7dd8f85dd117e4f80a1ee6e6 Mon Sep 17 00:00:00 2001 From: Pablo Riesgo Ferreiro Date: Wed, 20 May 2020 23:55:26 +0200 Subject: [PATCH 013/105] fix typo in folder for proteome_db --- input/references/build_references.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/input/references/build_references.sh b/input/references/build_references.sh index 02cf3d02..9a4e4ef2 100755 --- a/input/references/build_references.sh +++ b/input/references/build_references.sh @@ -17,8 +17,8 @@ $INPUT_MAKEBLASTDB -in "$INPUT_REFERENCE_FOLDER"/iedb/IEDB.fasta -dbtype prot -p # human proteome database mkdir "$INPUT_REFERENCE_FOLDER"/proteom_db -wget ftp://ftp.ensembl.org/pub/release-100/fasta/homo_sapiens/pep/Homo_sapiens.GRCh38.pep.all.fa.gz -O "$INPUT_REFERENCE_FOLDER"/proteom_db/Homo_sapiens.fa.gz +wget ftp://ftp.ensembl.org/pub/release-100/fasta/homo_sapiens/pep/Homo_sapiens.GRCh38.pep.all.fa.gz -O "$INPUT_REFERENCE_FOLDER"/proteome_db/Homo_sapiens.fa.gz gunzip "$INPUT_REFERENCE_FOLDER"/proteom_db/Homo_sapiens.fa.gz -$INPUT_MAKEBLASTDB -in "$INPUT_REFERENCE_FOLDER"/proteom_db/Homo_sapiens.fa -dbtype prot -parse_seqids -out "$INPUT_REFERENCE_FOLDER"/proteom_db/homo_sapiens +$INPUT_MAKEBLASTDB -in "$INPUT_REFERENCE_FOLDER"/proteom_db/Homo_sapiens.fa -dbtype prot -parse_seqids -out "$INPUT_REFERENCE_FOLDER"/proteome_db/homo_sapiens # use Homo_sapiens.fa as uniprot_human_with_isoforms.fasta to be consistent with human proteome database From 7242c8e2e8affecbed89a98cdf565b8a6e5c707e Mon Sep 17 00:00:00 2001 From: Pablo Riesgo Ferreiro Date: Thu, 21 May 2020 05:48:13 +0200 Subject: [PATCH 014/105] refactor out get_hla_allele and get_patient_id --- input/FeatureLiterature.py | 15 ++++------- input/MixMHCpred/mixmhc2pred.py | 16 +++--------- input/MixMHCpred/mixmhcpred.py | 16 +++--------- input/helpers/properties_manager.py | 25 ++++++++++++++++++- ...mbine_netmhcIIpan_pred_multiple_binders.py | 3 ++- input/netmhcIIpan/netmhcIIpan_prediction.py | 15 ++--------- ...combine_netmhcpan_pred_multiple_binders.py | 3 ++- input/netmhcpan4/netmhcpan_prediction.py | 16 ++---------- 8 files changed, 43 insertions(+), 66 deletions(-) diff --git a/input/FeatureLiterature.py b/input/FeatureLiterature.py index c62bd8bc..e7d55a52 100755 --- a/input/FeatureLiterature.py +++ b/input/FeatureLiterature.py @@ -12,6 +12,7 @@ from input import MHC_I, MHC_II from input.IEDB_Immunogenicity import predict_immunogenicity_simple +from input.helpers import properties_manager def calc_IEDB_immunogenicity(props, mhc, affin_filtering=False): @@ -121,12 +122,9 @@ def rna_expression_mutation(props, rna_avail): to reflect the expression of the mutated transcript ''' transcript_expression = props["transcript_expression"] - if "patient.id" in props: - patid = props["patient.id"] - else: - patid = props["patient"] + patient_id = properties_manager.get_hla_allele(props) try: - rna_avail = rna_avail[patid] + rna_avail = rna_avail[patient_id] except (KeyError, ValueError) as e: rna_avail = "NA" logger.info("rna_avail: ".format(rna_avail)) @@ -147,12 +145,9 @@ def expression_mutation_tc(props, tumour_content): '''calculated expression of mutation corrected by tumour content ''' transcript_expression = props["Expression_Mutated_Transcript"] - if "patient.id" in props: - patid = props["patient.id"] - else: - patid = props["patient"] + patient_id = properties_manager.get_patient_id(props) try: - tumour_content = float(tumour_content[patid]) / 100 + tumour_content = float(tumour_content[patient_id]) / 100 except (KeyError, ValueError) as e: tumour_content = "NA" try: diff --git a/input/MixMHCpred/mixmhc2pred.py b/input/MixMHCpred/mixmhc2pred.py index 0e73fef3..dffcce66 100755 --- a/input/MixMHCpred/mixmhc2pred.py +++ b/input/MixMHCpred/mixmhc2pred.py @@ -2,6 +2,8 @@ import tempfile +from input.helpers import properties_manager + class MixMhc2Pred: @@ -96,18 +98,6 @@ def generate_fasta(self, seqs, tmpfile): f.write(seq + "\n") counter += 1 - def get_hla_allels(self, props, hla_patient_dict): - ''' returns hla allele of patients given in hla_file - ''' - if "patient.id" in props: - patientid = props["patient.id"] - else: - try: - patientid = props["patient"] - except KeyError: - patientid = props["patient.x"] - return hla_patient_dict[patientid] - def prepare_dq_dp(self, list_alleles): ''' returns patient DQ/DP alleles that are relevant for prediction ''' @@ -286,7 +276,7 @@ def main(self, props_dict, dict_patient_hlaII): # prediction for peptides of length 13 to 18 based on Suppl Fig. 6 a in Racle, J., et al. Robust prediction of HLA class II epitopes by deep motif deconvolution of immunopeptidomes. Nat. Biotech. (2019). seqs = self.generate_nmers(props_dict, [13, 14, 15, 16, 17, 18]) self.generate_fasta(seqs, tmp_fasta) - alleles = self.get_hla_allels(props_dict, dict_patient_hlaII) + alleles = properties_manager.get_hla_allele(props_dict, dict_patient_hlaII) # try except statement to prevent stop of input for mps shorter < 13aa try: self.mixmhc2prediction(alleles, tmp_fasta, tmp_prediction) diff --git a/input/MixMHCpred/mixmhcpred.py b/input/MixMHCpred/mixmhcpred.py index 4354ce23..ac22df39 100755 --- a/input/MixMHCpred/mixmhcpred.py +++ b/input/MixMHCpred/mixmhcpred.py @@ -4,6 +4,8 @@ from logzero import logger +from input.helpers import properties_manager + class MixMHCpred: @@ -77,18 +79,6 @@ def generate_fasta(self, seqs, tmpfile): f.write(seq + "\n") counter += 1 - def get_hla_allels(self, props, hla_patient_dict): - ''' returns hla allele of patients given in hla_file - ''' - if "patient.id" in props: - patientid = props["patient.id"] - else: - try: - patientid = props["patient"] - except KeyError: - patientid = props["patient.x"] - return hla_patient_dict[patientid] - def mixmhcprediction(self, hla_alleles, tmpfasta, outtmp): ''' Performs MixMHCpred prediction for desired hla allele and writes result to temporary file. ''' @@ -220,7 +210,7 @@ def main(self, props_dict, dict_patient_hla): tmp_prediction = tmp_prediction_file.name seqs = self.generate_nmers(props_dict, [8, 9, 10, 11]) self.generate_fasta(seqs, tmp_fasta) - alleles = self.get_hla_allels(props_dict, dict_patient_hla) + alleles = properties_manager.get_hla_allele(props_dict, dict_patient_hla) self.mixmhcprediction(alleles, tmp_fasta, tmp_prediction) pred = self.read_mixmhcpred(tmp_prediction) try: diff --git a/input/helpers/properties_manager.py b/input/helpers/properties_manager.py index 90f06486..62d31cbb 100755 --- a/input/helpers/properties_manager.py +++ b/input/helpers/properties_manager.py @@ -1,6 +1,12 @@ from input import MHC_I, MHC_II from input.exceptions import INPuTInputParametersException +PATIENT_ID3 = "patient.x" + +PATIENT_ID2 = "patient" + +PATIENT_ID = "patient.id" + def get_wild_type_and_mutations(properties, mhc): if mhc == MHC_I: @@ -21,4 +27,21 @@ def get_wild_type_and_mutation_from_netmhcpan4(properties, nine_mer=False): else: mutation = properties["best_affinity_epitope_netmhcpan4"] wild_type = properties["best_affinity_epitope_netmhcpan4_WT"] - return wild_type, mutation \ No newline at end of file + return wild_type, mutation + + +def get_hla_allele(props, hla_patient_dict): + ''' returns hla allele of patients given in hla_file + ''' + patient_id = get_patient_id(props) + return hla_patient_dict[patient_id] + + +def get_patient_id(props): + if PATIENT_ID in props: + patient_id = props[PATIENT_ID] + elif PATIENT_ID2 in props: + patient_id = props[PATIENT_ID2] + else: + patient_id = props[PATIENT_ID3] + return patient_id \ No newline at end of file diff --git a/input/netmhcIIpan/combine_netmhcIIpan_pred_multiple_binders.py b/input/netmhcIIpan/combine_netmhcIIpan_pred_multiple_binders.py index 1afd3b4b..45ed035a 100755 --- a/input/netmhcIIpan/combine_netmhcIIpan_pred_multiple_binders.py +++ b/input/netmhcIIpan/combine_netmhcIIpan_pred_multiple_binders.py @@ -6,6 +6,7 @@ import input.netmhcIIpan.netmhcIIpan_prediction as netmhcIIpan_prediction from input import MHC_II +from input.helpers import properties_manager from input.netmhcpan4 import multiple_binders @@ -84,7 +85,7 @@ def main(self, epi_dict, patient_hlaII, set_available_mhc): np = netmhcIIpan_prediction.NetMhcIIPanBestPrediction(runner=self.runner, configuration=self.configuration) mb = multiple_binders.MultipleBinding(runner=self.runner, configuration=self.configuration) np.generate_fasta(epi_dict, tmp_fasta, mut=True) - alleles = np.get_hla_alleles(epi_dict, patient_hlaII) + alleles = properties_manager.get_hla_allele(epi_dict, patient_hlaII) alleles_formated = np.generate_mhcII_alelles_combination_list(alleles, set_available_mhc) logger.debug(alleles_formated) np.mhcII_prediction(alleles, set_available_mhc, tmp_fasta, tmp_prediction) diff --git a/input/netmhcIIpan/netmhcIIpan_prediction.py b/input/netmhcIIpan/netmhcIIpan_prediction.py index a13ff957..fef6d115 100755 --- a/input/netmhcIIpan/netmhcIIpan_prediction.py +++ b/input/netmhcIIpan/netmhcIIpan_prediction.py @@ -4,7 +4,7 @@ from logzero import logger -from input.helpers import data_import +from input.helpers import data_import, properties_manager class NetMhcIIPanBestPrediction: @@ -40,17 +40,6 @@ def generate_fasta(self, props, tmpfile, mut=True): f.write(id + "\n") f.write(seq + "\n") - def get_hla_alleles(self, props, hla_patient_dict): - ''' returns hla allele of patients given in hla_file - ''' - if "patient.id" in props: - patient_id = props["patient.id"] - elif "patient" in props: - patient_id = props["patient"] - else: - patient_id = props["patient.x"] - return hla_patient_dict[patient_id] - def generate_mhcII_alelles_combination_list(self, hla_alleles, set_available_mhc): ''' given list of HLA II alleles, returns list of HLA-DRB1 (2x), all possible HLA-DPA1/HLA-DPB1 (4x) and HLA-DQA1/HLA-DPQ1 (4x) ''' @@ -247,7 +236,7 @@ def main(self, props_dict, set_available_mhc, dict_patient_hla): tmp_prediction_file = tempfile.NamedTemporaryFile(prefix="netmhcpanpred_", suffix=".csv", delete=False) tmp_prediction = tmp_prediction_file.name self.generate_fasta(props_dict, tmp_fasta) - alleles = self.get_hla_alleles(props_dict, dict_patient_hla) + alleles = properties_manager.get_hla_allele(props_dict, dict_patient_hla) self.mhcII_prediction(alleles, set_available_mhc, tmp_fasta, tmp_prediction) props_dict["Position_Xmer_Seq"] = self.mut_position_xmer_seq(props_dict) preds = self.filter_binding_predictions(props_dict, tmp_prediction) diff --git a/input/netmhcpan4/combine_netmhcpan_pred_multiple_binders.py b/input/netmhcpan4/combine_netmhcpan_pred_multiple_binders.py index a8b603d5..37f25875 100755 --- a/input/netmhcpan4/combine_netmhcpan_pred_multiple_binders.py +++ b/input/netmhcpan4/combine_netmhcpan_pred_multiple_binders.py @@ -6,6 +6,7 @@ import input.netmhcpan4.multiple_binders as multiple_binders import input.netmhcpan4.netmhcpan_prediction as netmhcpan_prediction +from input.helpers import properties_manager class BestAndMultipleBinder: @@ -91,7 +92,7 @@ def main(self, epi_dict, patient_hlaI, set_available_mhc): np = netmhcpan_prediction.NetMhcPanBestPrediction(runner=self.runner, configuration=self.configuration) mb = multiple_binders.MultipleBinding(runner=self.runner, configuration=self.configuration) np.generate_fasta(epi_dict, tmp_fasta, mut=True) - alleles = np.get_hla_allels(epi_dict, patient_hlaI) + alleles = properties_manager.get_hla_allele(epi_dict, patient_hlaI) # print alleles np.mhc_prediction(alleles, set_available_mhc, tmp_fasta, tmp_prediction) epi_dict["Position_Xmer_Seq"] = np.mut_position_xmer_seq(epi_dict) diff --git a/input/netmhcpan4/netmhcpan_prediction.py b/input/netmhcpan4/netmhcpan_prediction.py index 66e58147..3f82208c 100755 --- a/input/netmhcpan4/netmhcpan_prediction.py +++ b/input/netmhcpan4/netmhcpan_prediction.py @@ -2,7 +2,7 @@ import tempfile -from input.helpers import data_import +from input.helpers import data_import, properties_manager class NetMhcPanBestPrediction: @@ -46,18 +46,6 @@ def generate_fasta(self, props, tmpfile, mut=True): f.write(id + "\n") f.write(seq + "\n") - def get_hla_allels(self, props, hla_patient_dict): - ''' returns hla allele of patients given in hla_file - ''' - if "patient.id" in props: - patientid = props["patient.id"] - else: - try: - patientid = props["patient"] - except KeyError: - patientid = props["patient.x"] - return hla_patient_dict[patientid] - def mhc_prediction(self, hla_alleles, set_available_mhc, tmpfasta, tmppred): ''' Performs netmhcpan4 prediction for desired hla allele and writes result to temporary file. ''' @@ -258,7 +246,7 @@ def main(self, props_dict, set_available_mhc, dict_patient_hla): tmp_prediction = tmp_prediction_file.name print(tmp_prediction) self.generate_fasta(props_dict, tmp_fasta) - alleles = self.get_hla_allels(props_dict, dict_patient_hla) + alleles = properties_manager.get_hla_allele(props_dict, dict_patient_hla) self.mhc_prediction(alleles, set_available_mhc, tmp_fasta, tmp_prediction) props_dict["Position_Xmer_Seq"] = self.mut_position_xmer_seq(props_dict) preds = self.filter_binding_predictions(props_dict, tmp_prediction) From 7e1d25e10fb89d85cd84bafe25df58212c43a202 Mon Sep 17 00:00:00 2001 From: Pablo Riesgo Ferreiro Date: Thu, 21 May 2020 06:50:48 +0200 Subject: [PATCH 015/105] refactor some more properties to remove duplicated code --- .../Tcell_predictor/tcellpredictor_wrapper.py | 69 ++++++------------- input/epitope.py | 42 +++++++---- input/helpers/properties_manager.py | 14 ++++ .../neoantigen_fitness/neoantigen_fitness.py | 15 +--- .../amino_acid_frequency_scores.py | 46 ++----------- input/new_features/differential_expression.py | 33 ++++----- .../test_neoantigen_fitness.py | 13 +--- .../integration_tests/test_tcell_predictor.py | 9 ++- 8 files changed, 91 insertions(+), 150 deletions(-) diff --git a/input/Tcell_predictor/tcellpredictor_wrapper.py b/input/Tcell_predictor/tcellpredictor_wrapper.py index ddb16a41..75887ef6 100755 --- a/input/Tcell_predictor/tcellpredictor_wrapper.py +++ b/input/Tcell_predictor/tcellpredictor_wrapper.py @@ -7,50 +7,30 @@ import input.Tcell_predictor.prediction as prediction -class Tcellprediction: +class TcellPrediction: def __init__(self, references): - self.TcellPrdictionScore = "NA" - self.TcellPrdictionScore_9merPred = "NA" + self.tcell_prediction_score = "NA" + self.tcell_prediction_score_9mer = "NA" self.references = references - def _triple_gen_seq_subst_for_prediction(self, props, all=True, affinity=False): + def _triple_gen_seq_subst_for_prediction(self, gene, substitution, epitope, score, threshold, all=True): """ extracts gene id, epitope sequence and substitution from epitope dictionary Tcell predictor works with 9mers only! --> extract for 9mers only """ - if "gene.x" in props: - gene = props["gene.x"] - else: - gene = props["gene"] - subst = props["substitution"] - if affinity: - epi = props["best_affinity_epitope_netmhcpan4_9mer"] - score = props["best_affinity_netmhcpan4_9mer"] - else: - epi = props["MHC_I_epitope_.best_prediction."] - score = props["MHC_I_score_.best_prediction."] - logger.debug("{} {} {} {} {}".format(gene, epi, subst, score, str(len(epi)))) - if str(len(epi)) == str(9): - z = [gene.replace(" ", ""), epi, subst] + logger.debug("{} {} {} {} {}".format(gene, epitope, substitution, score, str(len(epitope)))) + result = (["NA", "NA", "NA"]) + if str(len(epitope)) == str(9): + z = [gene.replace(" ", ""), epitope, substitution] if all: - z = [gene.replace(" ", ""), epi, subst] - return (z) + z = [gene.replace(" ", ""), epitope, substitution] + result = (z) else: - if (affinity): - if float(score) < 500: - z = [gene.replace(" ", ""), epi, subst] - return (z) - else: - return (["NA", "NA", "NA"]) - else: - if float(score) < 2: - z = [gene.replace(" ", ""), epi, subst] - return (z) - else: - return (["NA", "NA", "NA"]) - else: - return (["NA", "NA", "NA"]) + if float(score) < threshold: + z = [gene.replace(" ", ""), epitope, substitution] + result = (z) + return result def _write_triple_to_file(self, triple, tmpfile_in): """ @@ -78,11 +58,12 @@ def _prediction_single_mps(self, tmpfile_in, tmpfile_out): return score - def _wrapper_tcellpredictor(self, props, tmpfile_in, tmpfile_out, all=True, affinity=False): + def _wrapper_tcellpredictor(self, gene, substitution, epitope, score, threshold, tmpfile_in, tmpfile_out, all=True): """ wrapper function to determine """ - trp = self._triple_gen_seq_subst_for_prediction(props, all, affinity) + trp = self._triple_gen_seq_subst_for_prediction( + gene=gene, substitution=substitution, epitope=epitope, score=score, threshold=threshold, all=all) logger.debug(trp) pred_out = "NA" if "NA" not in trp: @@ -90,19 +71,13 @@ def _wrapper_tcellpredictor(self, props, tmpfile_in, tmpfile_out, all=True, affi pred_out = self._prediction_single_mps(tmpfile_in, tmpfile_out) return pred_out - def main(self, props): + def calculate_tcell_predictor_score(self, gene, substitution, epitope, score, threshold): ''' returns Tcell_predictor score given mps in dictionary format - ''' + ''' tmp_tcellPredIN_file = tempfile.NamedTemporaryFile(prefix="tmp_TcellPredicIN_", suffix=".txt", delete=False) tmp_tcellPredIN = tmp_tcellPredIN_file.name tmp_tcellPredOUT_file = tempfile.NamedTemporaryFile(prefix="tmp_TcellPredicOUT_", suffix=".txt", delete=False) tmp_tcellPredOUT = tmp_tcellPredOUT_file.name - # returns score for all epitopes --> no filtering based on mhc affinity here! - self.TcellPrdictionScore = self._wrapper_tcellpredictor(props, tmp_tcellPredIN, tmp_tcellPredOUT) - tmp_tcellPredIN_file = tempfile.NamedTemporaryFile(prefix="tmp_TcellPredicIN_", suffix=".txt", delete=False) - tmp_tcellPredIN = tmp_tcellPredIN_file.name - tmp_tcellPredOUT_file = tempfile.NamedTemporaryFile(prefix="tmp_TcellPredicOUT_", suffix=".txt", delete=False) - tmp_tcellPredOUT = tmp_tcellPredOUT_file.name - # returns score for all epitopes --> do filtering based on mhc affinity here (threshold 500 nM)! - self.TcellPrdictionScore_9merPred = self._wrapper_tcellpredictor( - props, tmp_tcellPredIN, tmp_tcellPredOUT, all=False, affinity=True) + return self._wrapper_tcellpredictor( + gene=gene, substitution=substitution, epitope=epitope, score=score, threshold=threshold, + tmpfile_in=tmp_tcellPredIN, tmpfile_out=tmp_tcellPredOUT) diff --git a/input/epitope.py b/input/epitope.py index a4148c3e..702ea4f5 100755 --- a/input/epitope.py +++ b/input/epitope.py @@ -8,7 +8,7 @@ from input import MHC_I, MHC_II from input.MixMHCpred.mixmhcpred import MixMHCpred from input.MixMHCpred.mixmhc2pred import MixMhc2Pred -from input.Tcell_predictor.tcellpredictor_wrapper import Tcellprediction +from input.Tcell_predictor.tcellpredictor_wrapper import TcellPrediction from input.dissimilarity_garnish.dissimilaritycalculator import DissimilarityCalculator from input.helpers import properties_manager from input.neoag.neoag_gbm_model import NeoagCalculator @@ -40,7 +40,7 @@ def __init__(self, runner, references, configuration, provean_annotator): self.predpresentation2 = MixMhc2Pred(runner=runner, configuration=configuration) self.pred = BestAndMultipleBinder(runner=runner, configuration=configuration) self.predpresentation = MixMHCpred(runner=runner, configuration=configuration) - self.tcellpredict = Tcellprediction(references=self.references) + self.tcell_predictor = TcellPrediction(references=self.references) def init_properties(self, col_nam, prop_list): """Initiates epitope property storage in a dictionary @@ -67,6 +67,8 @@ def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aa properties=self.properties, mhc=MHC_I) wild_type_mhcii, mutation_mhcii = properties_manager.get_wild_type_and_mutations( properties=self.properties, mhc=MHC_II) + mutated_aminoacid = properties_manager.get_mutation_aminoacid() + gene = properties_manager.get_gene(properties=self.properties) self.add_features(self_similarity.position_of_mutation_epitope( wild_type=wild_type_mhci, mutation=mutation_mhci), "pos_MUT_MHCI") @@ -84,18 +86,18 @@ def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aa "Expression_Mutated_Transcript_tumor_content") # differential expression - self.add_features(differential_expression.add_rna_reference(self.properties, ref_dat, 0), "mean_ref_expression") - self.add_features(differential_expression.add_rna_reference(self.properties, ref_dat, 1), "sd_ref_expression") - self.add_features(differential_expression.add_rna_reference(self.properties, ref_dat, 2), "sum_ref_expression") + self.add_features(differential_expression.add_rna_reference(gene, ref_dat, 0), "mean_ref_expression") + self.add_features(differential_expression.add_rna_reference(gene, ref_dat, 1), "sd_ref_expression") + self.add_features(differential_expression.add_rna_reference(gene, ref_dat, 2), "sum_ref_expression") self.add_features(differential_expression.fold_change(self.properties), "log2_fc_tumour_ref") self.add_features(differential_expression.percentile_calc(self.properties), "percentile_tumour_ref") self.add_features(differential_expression.pepper_calc(self.properties), "DE_pepper") # amino acid frequency self.add_features(FeatureLiterature.wt_mut_aa(self.properties, "mut"), "MUT_AA") self.add_features(FeatureLiterature.wt_mut_aa(self.properties, "wt"), "WT_AA") - self.add_features(freq_score.freq_aa(self.properties, aa_freq_dict), "Frequency_mutated_AA") - self.add_features(freq_score.freq_prod_4mer(self.properties, aa_freq_dict), "Product_Frequency_4mer") - self.add_features(freq_score.freq_4mer(self.properties, nmer_freq_dict), "Frequency_of_4mer") + self.add_features(freq_score.freq_aa(mutated_aminoacid=mutated_aminoacid, dict_freq=aa_freq_dict), "Frequency_mutated_AA") + self.add_features(freq_score.freq_prod_4mer(mutation=mutation_mhci, dict_freq=aa_freq_dict), "Product_Frequency_4mer") + self.add_features(freq_score.freq_4mer(mutation=mutation_mhci, dict_freq=nmer_freq_dict), "Frequency_of_4mer") # amino acid index for k in aaindex1_dict: z = FeatureLiterature.add_aa_index1(self.properties, "wt", k, aaindex1_dict[k]) @@ -240,13 +242,14 @@ def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aa # neoantigen fitness tmp_fasta_file = tempfile.NamedTemporaryFile(prefix="tmpseq", suffix=".fasta", delete=False) tmp_fasta = tmp_fasta_file.name + self.add_features( self.neoantigen_fitness_calculator.wrap_pathogensimilarity( - props=self.properties, mhc=MHC_I, fastafile=tmp_fasta, iedb=self.references.iedb), + mutation=mutation_mhci, fastafile=tmp_fasta, iedb=self.references.iedb), "Pathogensimiliarity_mhcI") self.add_features( self.neoantigen_fitness_calculator.wrap_pathogensimilarity( - props=self.properties, mhc=MHC_II, fastafile=tmp_fasta, iedb=self.references.iedb), + mutation=mutation_mhcii, fastafile=tmp_fasta, iedb=self.references.iedb), "Pathogensimiliarity_mhcII") self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( self.properties, MHC_I), "Amplitude_mhcI") @@ -258,9 +261,18 @@ def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aa self.properties, MHC_II), "Recognition_Potential_mhcII") # T cell predictor - self.tcellpredict.main(self.properties) - self.add_features(self.tcellpredict.TcellPrdictionScore, "Tcell_predictor_score") - self.add_features(self.tcellpredict.TcellPrdictionScore_9merPred, "Tcell_predictor_score_9mersPredict") + substitution = properties_manager.get_substitution(properties=self.properties) + epitope = self.properties["MHC_I_epitope_.best_prediction."] + score = self.properties["MHC_I_score_.best_prediction."] + self.add_features(self.tcell_predictor.calculate_tcell_predictor_score( + gene=gene, substitution=substitution, epitope=epitope, score=score, threshold=2), + "Tcell_predictor_score") + + epitope = self.properties["best_affinity_epitope_netmhcpan4_9mer"] + score = self.properties["best_affinity_netmhcpan4_9mer"] + self.add_features(self.tcell_predictor.calculate_tcell_predictor_score( + gene=gene, substitution=substitution, epitope=epitope, score=score, threshold=500), + "Tcell_predictor_score_9mersPredict") # DAI with affinity values self.add_features(FeatureLiterature.dai(self.properties, MHC_I, multiple_binding=False, affinity=True), @@ -286,11 +298,11 @@ def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aa "Amplitude_mhcI_affinity_9mer_netmhcpan4") self.add_features( self.neoantigen_fitness_calculator.wrap_pathogensimilarity( - props=self.properties, mhc=MHC_I, fastafile=tmp_fasta, iedb=self.references.iedb, nine_mer=True), + mutation=mutation_netmhcpan4_9mer, fastafile=tmp_fasta, iedb=self.references.iedb), "Pathogensimiliarity_mhcI_9mer") self.add_features( self.neoantigen_fitness_calculator.wrap_pathogensimilarity( - props=self.properties, mhc=MHC_I, fastafile=tmp_fasta, iedb=self.references.iedb, affinity=True), + mutation=mutation_netmhcpan4, fastafile=tmp_fasta, iedb=self.references.iedb), "Pathogensimiliarity_mhcI_affinity_nmers") # recogntion potential with amplitude by affinity and netmhcpan4 score diff --git a/input/helpers/properties_manager.py b/input/helpers/properties_manager.py index 62d31cbb..c34c0c9f 100755 --- a/input/helpers/properties_manager.py +++ b/input/helpers/properties_manager.py @@ -8,6 +8,20 @@ PATIENT_ID = "patient.id" +def get_gene(properties): + if "gene.x" in properties: + gene = properties["gene.x"] + else: + gene = properties["gene"] + return gene + +def get_substitution(properties): + return properties["substitution"] + +def get_mutation_aminoacid(properties): + return properties["MUT_AA"] + + def get_wild_type_and_mutations(properties, mhc): if mhc == MHC_I: mutation = properties["MHC_I_epitope_.best_prediction."] diff --git a/input/neoantigen_fitness/neoantigen_fitness.py b/input/neoantigen_fitness/neoantigen_fitness.py index aa13ea85..a986b289 100755 --- a/input/neoantigen_fitness/neoantigen_fitness.py +++ b/input/neoantigen_fitness/neoantigen_fitness.py @@ -42,28 +42,17 @@ def _calc_pathogensimilarity(self, fasta_file, n, iedb): os.remove(outfile) return x if x is not None else "NA" - - def wrap_pathogensimilarity(self, props, mhc, fastafile, iedb, affinity=False, nine_mer=False): - if mhc == MHC_I: - if nine_mer: - mhc_mut = props["best_affinity_epitope_netmhcpan4_9mer"] - elif affinity: - mhc_mut = props["best_affinity_epitope_netmhcpan4"] - else: - mhc_mut = props["MHC_I_epitope_.best_prediction."] - elif mhc == MHC_II: - mhc_mut = props["MHC_II_epitope_.best_prediction."] + def wrap_pathogensimilarity(self, mutation, fastafile, iedb): with open(fastafile, "w") as f: id = ">M_1" f.write(id + "\n") - f.write(mhc_mut + "\n") + f.write(mutation + "\n") try: pathsim = self._calc_pathogensimilarity(fastafile, id, iedb) except: pathsim = "NA" return str(pathsim) if pathsim != "NA" else "0" - def calculate_amplitude_mhc(self, props, mhc, multiple_binding=False, affinity=False, netmhcscore=False, nine_mer=False): ''' This function calculates the amplitude between mutated and wt epitope according to Balachandran et al. diff --git a/input/new_features/amino_acid_frequency_scores.py b/input/new_features/amino_acid_frequency_scores.py index 3606852d..35acda62 100755 --- a/input/new_features/amino_acid_frequency_scores.py +++ b/input/new_features/amino_acid_frequency_scores.py @@ -3,25 +3,22 @@ # !/usr/bin/env python -def freq_aa(props, dict_freq): +def freq_aa(mutated_aminoacid, dict_freq): ''' This function annotates data frame with frequency of mutated AA in the human proteome ''' - mut_aa = props["MUT_AA"] try: - return str(dict_freq[mut_aa]) + return str(dict_freq[mutated_aminoacid]) except KeyError: return "NA" -def freq_prod_4mer(props, dict_freq): +def freq_prod_4mer(mutation, dict_freq): ''' This function extracts 4 aa that are directed to TCR (pos 4 to pos 7 within epitope) and calculates the product of aa frequencies ''' - mut_aa = props["MUT_AA"] - epitope = props["MHC_I_epitope_.best_prediction."] try: - epi_4mer = list(epitope[3:7]) + epi_4mer = list(mutation[3:7]) epi_freqs = [float(dict_freq[aa]) for aa in epi_4mer] freq_prod = reduce(lambda x, y: x * y, epi_freqs) return str(freq_prod) @@ -29,12 +26,11 @@ def freq_prod_4mer(props, dict_freq): return "NA" -def freq_4mer(props, dict_freq): +def freq_4mer(mutation, dict_freq): '''Returns the frequency of 4mer directed to TCR ''' - epitope = props["MHC_I_epitope_.best_prediction."] try: - epi_4mer = epitope[3:7] + epi_4mer = mutation[3:7] return str(dict_freq[epi_4mer]) except KeyError: return "NA" @@ -54,33 +50,3 @@ def build_frequency_dict(frequency_file, freq_dict): else: freq_dict[w[0]] = w[1] return freq_dict - - -if __name__ == '__main__': - import sys - - basedir = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/INPuT2" - sys.path.append(basedir) - import data_import - from input import FeatureLiterature - - file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/INPuT2/nonprogramm_files/20170713_IS_IM_data.complete.update_Dv10.csv" - indel = False - dat = data_import.import_dat_icam(file, indel) - - properties = {} - for nam, char in zip(dat[0], dat[1][1]): - properties[nam] = char - # add MUT AA - properties["MUT_AA"] = FeatureLiterature.wt_mut_aa(properties, "mut") - - freq_file1 = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/INPuT2/new_features/20181108_AA_freq_prot.csv" - freq_file2 = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/INPuT2/new_features/20181108_4mer_freq.csv" - freq_dict = {} - freq_dict_4mer = {} - freq_dict = build_frequency_dict(freq_file1, freq_dict) - freq_dict_4mer = build_frequency_dict(freq_file2, freq_dict_4mer) - - print(freq_aa(properties, freq_dict)) - print(freq_prod_4mer(properties, freq_dict)) - print(freq_4mer(properties, freq_dict_4mer)) diff --git a/input/new_features/differential_expression.py b/input/new_features/differential_expression.py index b35da255..6c0c7d21 100755 --- a/input/new_features/differential_expression.py +++ b/input/new_features/differential_expression.py @@ -20,16 +20,11 @@ def sd_of_list(list_numbs): return (sd_list) -def add_rna_reference(props, reference_dat, i): +def add_rna_reference(gene, reference_dat, i): ''' This function takes the output of load_rna_expression_reference function and appends the values to the epitope data i = (0,1,2) --> ("mean_ref_expression","sd_ref_expression", "sum_ref_expression") ''' - if "gene" in props: - gene = props["gene"] - else: - gene = props["gene.x"] - if gene in reference_dat: return str(reference_dat[gene][i]) else: @@ -76,16 +71,16 @@ def pepper_calc(props): return "NA" -if __name__ == '__main__': - import sys - import data_import - - ref_file = sys.argv[1] - # "/projects/CM27_IND_patients/GTEX_normal_tissue_data/Skin .csv" - ref_list = load_rna_expression_reference(ref_file) - f = sys.argv[2] - data = data_import.import_dat_icam(f) - dat_merged = merge_data_reference(data, ref_list) - print(wrapper_diff_expr(dat_merged)[0]) - - # write_ouptut_to_file(dat_epi,header) +# if __name__ == '__main__': +# import sys +# import data_import +# +# ref_file = sys.argv[1] +# # "/projects/CM27_IND_patients/GTEX_normal_tissue_data/Skin .csv" +# ref_list = load_rna_expression_reference(ref_file) +# f = sys.argv[2] +# data = data_import.import_dat_icam(f) +# dat_merged = merge_data_reference(data, ref_list) +# print(wrapper_diff_expr(dat_merged)[0]) +# +# # write_ouptut_to_file(dat_epi,header) diff --git a/input/tests/integration_tests/test_neoantigen_fitness.py b/input/tests/integration_tests/test_neoantigen_fitness.py index 50ddbd60..89a469e0 100755 --- a/input/tests/integration_tests/test_neoantigen_fitness.py +++ b/input/tests/integration_tests/test_neoantigen_fitness.py @@ -19,18 +19,9 @@ def _load_references(self): fastafile = integration_test_tools.create_temp_aminoacid_fasta_file() return references, configuration, fastafile - def test_pathogen_similarity_mhcI(self): + def test_pathogen_similarity(self): result = self.neoantigen_fitness_calculator.wrap_pathogensimilarity( - props={"MHC_I_epitope_.best_prediction.": "hey"}, - mhc=MHC_I, - fastafile=self.fastafile.name, - iedb=self.references.iedb) - self.assertEqual('0', result) - - def test_pathogen_similarity_mhcII(self): - result = self.neoantigen_fitness_calculator.wrap_pathogensimilarity( - props={"MHC_II_epitope_.best_prediction.": "hey"}, - mhc=MHC_II, + mutation='hey', fastafile=self.fastafile.name, iedb=self.references.iedb) self.assertEqual('0', result) diff --git a/input/tests/integration_tests/test_tcell_predictor.py b/input/tests/integration_tests/test_tcell_predictor.py index bce62d29..065cd18b 100755 --- a/input/tests/integration_tests/test_tcell_predictor.py +++ b/input/tests/integration_tests/test_tcell_predictor.py @@ -2,7 +2,7 @@ from unittest import TestCase import input.tests.integration_tests.integration_test_tools as integration_test_tools -from input.Tcell_predictor.tcellpredictor_wrapper import Tcellprediction +from input.Tcell_predictor.tcellpredictor_wrapper import TcellPrediction class TestTCellPredictor(TestCase): @@ -12,10 +12,9 @@ def setUp(self): self.fastafile = integration_test_tools.create_temp_aminoacid_fasta_file() def test_tcell_predictor(self): - tcell_predictor = Tcellprediction(references=self.references) - tcell_predictor.main(props=defaultdict(lambda: "blah")) - self.assertEqual("NA", tcell_predictor.TcellPrdictionScore) - self.assertEqual("NA", tcell_predictor.TcellPrdictionScore_9merPred) + tcell_predictor = TcellPrediction(references=self.references) + result = tcell_predictor.calculate_tcell_predictor_score(gene="BLAH", substitution='blaaaah', epitope="BLAHBLAH", score=5, threshold=10) + self.assertEqual("NA", result) """ From 9dd4c6829d56d7d2a0520b3f63f6f79759964092 Mon Sep 17 00:00:00 2001 From: Pablo Riesgo Ferreiro Date: Thu, 21 May 2020 09:54:10 +0200 Subject: [PATCH 016/105] refactor properties from FeatureLiterature.dai --- input/FeatureLiterature.py | 39 +++++----------------- input/epitope.py | 52 ++++++++++++++++++++--------- input/helpers/properties_manager.py | 44 +++++++++++++++++++++--- 3 files changed, 85 insertions(+), 50 deletions(-) diff --git a/input/FeatureLiterature.py b/input/FeatureLiterature.py index e7d55a52..b506d651 100755 --- a/input/FeatureLiterature.py +++ b/input/FeatureLiterature.py @@ -44,42 +44,19 @@ def calc_IEDB_immunogenicity(props, mhc, affin_filtering=False): return "NA" -def dai(props, mhc, multiple_binding=False, affinity=False, netmhcscore=False, affin_filtering=False): - '''Calculates DAI: Returns difference between wt and mut MHC binding score. If multiple_binding= true, harmonic means of MHC scores of top10 epitope candidates related to a mps is used ''' - if mhc == MHC_I: - if multiple_binding: - sc_mut = props["MB_score_top10_harmonic"] - sc_wt = props["MB_score_WT_top10_harmonic"] - elif affinity: - sc_mut = props["best_affinity_netmhcpan4"] - sc_wt = props["best_affinity_netmhcpan4_WT"] - elif netmhcscore: - sc_mut = props["best%Rank_netmhcpan4"] - sc_wt = props["best%Rank_netmhcpan4_WT"] - else: - sc_mut = props["MHC_I_score_.best_prediction."] - sc_wt = props["MHC_I_score_.WT."] - elif mhc == MHC_II: - if multiple_binding: - sc_mut = props["MB_score_MHCII_top10_harmonic"] - sc_wt = props["MB_score_MHCII_top10_WT_harmonic"] - elif affinity: - sc_mut = props["best_affinity_netmhcIIpan"] - sc_wt = props["best_affinity_netmhcIIpan_WT"] - elif netmhcscore: - sc_mut = props["best%Rank_netmhcIIpan"] - sc_wt = props["best%Rank_netmhcIIpan_WT"] - else: - sc_mut = props["MHC_II_score_.best_prediction."] - sc_wt = props["MHC_II_score_.WT."] +def dai(score_mutation, score_wild_type, affin_filtering=False): + """ + Calculates DAI: Returns difference between wt and mut MHC binding score. + """ + # TODO: these conversions to float need to go away from here try: if affin_filtering: - if float(sc_mut) < 500: - return str(float(sc_wt) - float(sc_mut)) + if float(score_mutation) < 500: + return str(float(score_wild_type) - float(score_mutation)) else: return "NA" else: - return str(float(sc_wt) - float(sc_mut)) + return str(float(score_wild_type) - float(score_mutation)) except ValueError: return "NA" diff --git a/input/epitope.py b/input/epitope.py index 702ea4f5..1ffde5ff 100755 --- a/input/epitope.py +++ b/input/epitope.py @@ -45,8 +45,10 @@ def __init__(self, runner, references, configuration, provean_annotator): def init_properties(self, col_nam, prop_list): """Initiates epitope property storage in a dictionary """ + properties = {} for nam, char in zip(col_nam, prop_list): - self.properties[nam] = char + properties[nam] = char + return properties def add_features(self, new_feature, new_feature_nam): """Adds new features to already present epitope properties, stored in form of a dictioninary @@ -60,12 +62,12 @@ def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aa set_available_mhc, set_available_mhcII, patient_hlaI, patient_hlaII, tumour_content, rna_avail): """ Calculate new epitope features and add to dictonary that stores all properties """ - self.init_properties(col_nam, prop_list) + self.properties = self.init_properties(col_nam, prop_list) logger.info(self.properties["X..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."]) - wild_type_mhci, mutation_mhci = properties_manager.get_wild_type_and_mutations( + wild_type_mhci, mutation_mhci = properties_manager.get_epitopes( properties=self.properties, mhc=MHC_I) - wild_type_mhcii, mutation_mhcii = properties_manager.get_wild_type_and_mutations( + wild_type_mhcii, mutation_mhcii = properties_manager.get_epitopes( properties=self.properties, mhc=MHC_II) mutated_aminoacid = properties_manager.get_mutation_aminoacid() gene = properties_manager.get_gene(properties=self.properties) @@ -77,8 +79,10 @@ def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aa self.add_features(self_similarity.position_in_anchor_position(self.properties), "Mutation_in_anchor") # differential agretopicity index - self.add_features(FeatureLiterature.dai(self.properties, MHC_I), "DAI_mhcI") - self.add_features(FeatureLiterature.dai(self.properties, MHC_II), "DAI_mhcII") + self.add_features( + FeatureLiterature.dai(score_mutation=mutation_mhci, score_wild_type=wild_type_mhci), "DAI_mhcI") + self.add_features( + FeatureLiterature.dai(score_mutation=mutation_mhcii, score_wild_type=wild_type_mhcii), "DAI_mhcII") # expression self.add_features(FeatureLiterature.rna_expression_mutation(self.properties, rna_avail=rna_avail), "Expression_Mutated_Transcript") @@ -179,7 +183,11 @@ def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aa # generator rate self.add_features(self.pred.epitope_affinities_WT, "MB_affinities_WT") self.add_features(self.pred.generator_rate_WT, "Generator_rate_WT") - self.add_features(FeatureLiterature.dai(self.properties, MHC_I, multiple_binding=True), "DAI_mhcI_MB") + wild_type_multiple_binding, mutation_multiple_binding = properties_manager.\ + get_scores_multiple_binding(self.properties, mhc=MHC_I) + self.add_features( + FeatureLiterature.dai(score_mutation=mutation_multiple_binding, score_wild_type=wild_type_multiple_binding), + "DAI_mhcI_MB") # netmhcpan4 wt affinity self.add_features(self.pred.best4_affinity_WT, "best_affinity_netmhcpan4_WT") @@ -275,12 +283,17 @@ def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aa "Tcell_predictor_score_9mersPredict") # DAI with affinity values - self.add_features(FeatureLiterature.dai(self.properties, MHC_I, multiple_binding=False, affinity=True), - "DAI_affinity") + wild_type_netmhcpan4, mutation_netmhcpan4 = properties_manager.get_scores_netmhcpan4_affinity( + properties=self.properties, mhc=MHC_I) + self.add_features( + FeatureLiterature.dai(score_mutation=mutation_netmhcpan4, score_wild_type=wild_type_netmhcpan4), + "DAI_affinity") # DAI wiht rank scores by netmhcpan4 + wild_type_netmhcpan4_rank, mutation_netmhcpan4_rank = properties_manager\ + .get_scores_netmhcpan4_ranks(properties=self.properties, mhc=MHC_I) self.add_features( - FeatureLiterature.dai(self.properties, MHC_I, multiple_binding=False, affinity=False, netmhcscore=True), + FeatureLiterature.dai(score_mutation=mutation_netmhcpan4_rank, score_wild_type=wild_type_netmhcpan4_rank), "DAI_rank_netmhcpan4") # Amplitude with affinity values @@ -376,18 +389,27 @@ def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aa self.add_features(self.predII.MHCII_number_weak_binders_WT, "MB_number_pep_MHCIIscore<10_WT") # dai mhc II affinity - self.add_features(FeatureLiterature.dai(self.properties, MHC_II, multiple_binding=False, affinity=True), - "DAI_mhcII_affinity") + wild_type_netmhciipan4, mutation_netmhciipan4 = properties_manager.get_scores_netmhcpan4_affinity( + properties=self.properties, mhc=MHC_II) self.add_features( - FeatureLiterature.dai(self.properties, MHC_II, multiple_binding=False, affinity=True, affin_filtering=True), + FeatureLiterature.dai(score_mutation=mutation_netmhciipan4, score_wild_type=wild_type_netmhciipan4), + "DAI_mhcII_affinity") + self.add_features( + FeatureLiterature.dai(score_mutation=mutation_netmhciipan4, score_wild_type=wild_type_netmhciipan4, + affin_filtering=True), "DAI_mhcII_affinity_aff_filtered") # dai mhc II netMHCIIpan score - self.add_features(FeatureLiterature.dai(self.properties, MHC_II, multiple_binding=False, affinity=False), + self.add_features(FeatureLiterature.dai(score_mutation=mutation_mhcii, score_wild_type=wild_type_mhcii), "DAI_mhcII_netmhcIIpan") # dai multiple binding mhc II - self.add_features(FeatureLiterature.dai(self.properties, MHC_II, multiple_binding=True), "DAI_mhcII_MB") + wild_type_multiple_binding_ii, mutation_multiple_binding_ii = properties_manager. \ + get_scores_multiple_binding(self.properties, mhc=MHC_II) + self.add_features( + FeatureLiterature.dai(score_mutation=mutation_multiple_binding_ii, + score_wild_type=wild_type_multiple_binding_ii), + "DAI_mhcII_MB") # difference number of binders self.add_features(FeatureLiterature.diff_number_binders(self.properties, mhc=MHC_II, threshold="2"), diff --git a/input/helpers/properties_manager.py b/input/helpers/properties_manager.py index c34c0c9f..01139811 100755 --- a/input/helpers/properties_manager.py +++ b/input/helpers/properties_manager.py @@ -2,9 +2,7 @@ from input.exceptions import INPuTInputParametersException PATIENT_ID3 = "patient.x" - PATIENT_ID2 = "patient" - PATIENT_ID = "patient.id" @@ -15,14 +13,16 @@ def get_gene(properties): gene = properties["gene"] return gene + def get_substitution(properties): return properties["substitution"] + def get_mutation_aminoacid(properties): return properties["MUT_AA"] -def get_wild_type_and_mutations(properties, mhc): +def get_epitopes(properties, mhc): if mhc == MHC_I: mutation = properties["MHC_I_epitope_.best_prediction."] wild_type = properties["MHC_I_epitope_.WT."] @@ -34,7 +34,43 @@ def get_wild_type_and_mutations(properties, mhc): return wild_type, mutation -def get_wild_type_and_mutation_from_netmhcpan4(properties, nine_mer=False): +def get_scores_multiple_binding(properties, mhc): + if mhc == MHC_I: + mutation = properties["MB_score_top10_harmonic"] + wild_type = properties["MB_score_WT_top10_harmonic"] + elif mhc == MHC_II: + mutation = properties["MB_score_MHCII_top10_harmonic"] + wild_type = properties["MB_score_MHCII_top10_WT_harmonic"] + else: + raise INPuTInputParametersException("Bad MHC value: {}".format(mhc)) + return wild_type, mutation + + +def get_scores_netmhcpan4_affinity(properties, mhc): + if mhc == MHC_I: + mutation = properties["best_affinity_netmhcpan4"] + wild_type = properties["best_affinity_netmhcpan4_WT"] + elif mhc == MHC_II: + mutation = properties["best_affinity_netmhcIIpan"] + wild_type = properties["best_affinity_netmhcIIpan_WT"] + else: + raise INPuTInputParametersException("Bad MHC value: {}".format(mhc)) + return wild_type, mutation + + +def get_scores_netmhcpan4_ranks(properties, mhc): + if mhc == MHC_I: + mutation = properties["best%Rank_netmhcpan4"] + wild_type = properties["best%Rank_netmhcpan4_WT"] + elif mhc == MHC_II: + mutation = properties["best%Rank_netmhcIIpan"] + wild_type = properties["best%Rank_netmhcIIpan_WT"] + else: + raise INPuTInputParametersException("Bad MHC value: {}".format(mhc)) + return wild_type, mutation + + +def get_netmhcpan4_epitopes(properties, nine_mer=False): if nine_mer: mutation = properties["best_affinity_epitope_netmhcpan4_9mer"] wild_type = properties["best_epitope_netmhcpan4_9mer_WT"] From 85d2de5b82180a7365826d3916fa57d2994bd90f Mon Sep 17 00:00:00 2001 From: Pablo Riesgo Ferreiro Date: Thu, 21 May 2020 10:15:26 +0200 Subject: [PATCH 017/105] refactor differential expression + refactor partially epitope.py --- input/epitope.py | 386 ++++++++++-------- input/new_features/differential_expression.py | 31 +- 2 files changed, 230 insertions(+), 187 deletions(-) diff --git a/input/epitope.py b/input/epitope.py index 1ffde5ff..96ceb765 100755 --- a/input/epitope.py +++ b/input/epitope.py @@ -78,116 +78,22 @@ def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aa wild_type=wild_type_mhcii, mutation=mutation_mhcii), "pos_MUT_MHCII") self.add_features(self_similarity.position_in_anchor_position(self.properties), "Mutation_in_anchor") - # differential agretopicity index - self.add_features( - FeatureLiterature.dai(score_mutation=mutation_mhci, score_wild_type=wild_type_mhci), "DAI_mhcI") - self.add_features( - FeatureLiterature.dai(score_mutation=mutation_mhcii, score_wild_type=wild_type_mhcii), "DAI_mhcII") - # expression - self.add_features(FeatureLiterature.rna_expression_mutation(self.properties, rna_avail=rna_avail), - "Expression_Mutated_Transcript") - self.add_features(FeatureLiterature.expression_mutation_tc(self.properties, tumour_content=tumour_content), - "Expression_Mutated_Transcript_tumor_content") + self.add_differential_agretopicity_index_features(mutation_mhci, mutation_mhcii, wild_type_mhci, + wild_type_mhcii) - # differential expression - self.add_features(differential_expression.add_rna_reference(gene, ref_dat, 0), "mean_ref_expression") - self.add_features(differential_expression.add_rna_reference(gene, ref_dat, 1), "sd_ref_expression") - self.add_features(differential_expression.add_rna_reference(gene, ref_dat, 2), "sum_ref_expression") - self.add_features(differential_expression.fold_change(self.properties), "log2_fc_tumour_ref") - self.add_features(differential_expression.percentile_calc(self.properties), "percentile_tumour_ref") - self.add_features(differential_expression.pepper_calc(self.properties), "DE_pepper") - # amino acid frequency - self.add_features(FeatureLiterature.wt_mut_aa(self.properties, "mut"), "MUT_AA") - self.add_features(FeatureLiterature.wt_mut_aa(self.properties, "wt"), "WT_AA") - self.add_features(freq_score.freq_aa(mutated_aminoacid=mutated_aminoacid, dict_freq=aa_freq_dict), "Frequency_mutated_AA") - self.add_features(freq_score.freq_prod_4mer(mutation=mutation_mhci, dict_freq=aa_freq_dict), "Product_Frequency_4mer") - self.add_features(freq_score.freq_4mer(mutation=mutation_mhci, dict_freq=nmer_freq_dict), "Frequency_of_4mer") - # amino acid index - for k in aaindex1_dict: - z = FeatureLiterature.add_aa_index1(self.properties, "wt", k, aaindex1_dict[k]) - self.add_features(z[1], z[0]) - z = FeatureLiterature.add_aa_index1(self.properties, "mut", k, aaindex1_dict[k]) - self.add_features(z[1], z[0]) - for k in aaindex2_dict: - try: - z = FeatureLiterature.add_aa_index2(self.properties, k, aaindex2_dict[k]) - self.add_features(z[1], z[0]) - except: - print(aaindex2_dict[k], wt, mut) + self.add_expression_features(rna_avail, tumour_content) - # PROVEAN score - ucsc_id = self.provean_annotator.build_ucsc_id_plus_position( - substitution=self.properties["substitution"], ucsc_id=self.properties["UCSC_transcript"]) - self.add_features(ucsc_id, "UCSC_ID_position") - self.add_features(self.provean_annotator.get_provean_annotation( - mutated_aminoacid=self.properties['MUT_AA'], ucsc_id_position=ucsc_id), - "PROVEAN_score") - self.pred.main(self.properties, patient_hlaI, set_available_mhc) + self.add_differential_expression_features(gene, ref_dat) - # netmhcpan4 MUT rank score - self.add_features(self.pred.best4_mhc_score, "best%Rank_netmhcpan4") - self.add_features(self.pred.best4_mhc_epitope, "best_epitope_netmhcpan4") - self.add_features(self.pred.best4_mhc_allele, "bestHLA_allele_netmhcpan4") - self.add_features(self.pred.directed_to_TCR, "directed_to_TCR") + self.add_aminoacid_frequency_features(aa_freq_dict, mutated_aminoacid, mutation_mhci, nmer_freq_dict) - # netmhcpan4 mut affinity - self.add_features(self.pred.best4_affinity, "best_affinity_netmhcpan4") - self.add_features(self.pred.best4_affinity_epitope, "best_affinity_epitope_netmhcpan4") - self.add_features(self.pred.best4_affinity_allele, "bestHLA_allele_affinity_netmhcpan4") - self.add_features(self.pred.best4_affinity_directed_to_TCR, "affinity_directed_to_TCR") + self.add_aminoacid_index_features(aaindex1_dict, aaindex2_dict) - # netMHCpan MUT best 9mer score - self.add_features(self.pred.mhcI_score_9mer, "best%Rank_netmhcpan4_9mer") - self.add_features(self.pred.mhcI_score_epitope_9mer, "best_epitope_netmhcpan4_9mer") - self.add_features(self.pred.mhcI_score_allele_9mer, "bestHLA_allele_netmhcpan4_9mer") + self.add_provean_score_features(patient_hlaI, set_available_mhc) - # netmhcpan4 mut best 9mer affinity - self.add_features(self.pred.mhcI_affinity_9mer, "best_affinity_netmhcpan4_9mer") - self.add_features(self.pred.mhcI_affinity_allele_9mer, "bestHLA_allele_affinity_netmhcpan4_9mer") - self.add_features(self.pred.mhcI_affinity_epitope_9mer, "best_affinity_epitope_netmhcpan4_9mer") - - # multiplexed representation MUT - for sc, mn in zip(self.pred.MHC_score_all_epitopes, self.pred.mean_type): - self.add_features(sc, "MB_score_all_epitopes_" + mn) - for sc, mn in zip(self.pred.MHC_score_top10, self.pred.mean_type): - self.add_features(sc, "MB_score_top10_" + mn) - for sc, mn in zip(self.pred.MHC_score_best_per_alelle, self.pred.mean_type): - self.add_features(sc, "MB_score_best_per_alelle_" + mn) - - # rename MB_score_best_per_alelle_harmonic to PHBR (described in Marty et al) - self.properties["PHBR-I"] = self.properties.pop("MB_score_best_per_alelle_harmonic") - self.add_features(self.pred.MHC_epitope_scores, "MB_epitope_scores") - self.add_features(self.pred.MHC_epitope_seqs, "MB_epitope_sequences") - self.add_features(self.pred.MHC_epitope_alleles, "MB_alleles") - self.add_features(self.pred.MHC_number_strong_binders, "MB_number_pep_MHCscore<1") - self.add_features(self.pred.MHC_number_weak_binders, "MB_number_pep_MHCscore<2") - - # generator rate - self.add_features(self.pred.epitope_affinities, "MB_affinities") - self.add_features(self.pred.generator_rate, "Generator_rate") - - # multiplexed representation WT - self.add_features(self.pred.MHC_epitope_scores_WT, "MB_epitope_WT_scores") - self.add_features(self.pred.MHC_epitope_seqs_WT, "MB_epitope_WT_sequences") - self.add_features(self.pred.MHC_epitope_alleles_WT, "MB_alleles_WT") - for sc, mn in zip(self.pred.MHC_score_top10_WT, self.pred.mean_type): - self.add_features(sc, "MB_score_WT_top10_" + mn) - for sc, mn in zip(self.pred.MHC_score_all_epitopes_WT, self.pred.mean_type): - self.add_features(sc, "MB_score_WT_all_epitopes_" + mn) - for sc, mn in zip(self.pred.MHC_score_best_per_alelle_WT, self.pred.mean_type): - self.add_features(sc, "MB_score_WT_best_per_alelle_" + mn) - self.properties["PHBR-I_WT"] = self.properties.pop("MB_score_WT_best_per_alelle_harmonic") - self.add_features(self.pred.MHC_number_strong_binders_WT, "MB_number_pep_WT_MHCscore<1") - self.add_features(self.pred.MHC_number_weak_binders_WT, "MB_number_pep_WT_MHCscore<2") + self.add_netmhcpan4_features() - # generator rate - self.add_features(self.pred.epitope_affinities_WT, "MB_affinities_WT") - self.add_features(self.pred.generator_rate_WT, "Generator_rate_WT") - wild_type_multiple_binding, mutation_multiple_binding = properties_manager.\ - get_scores_multiple_binding(self.properties, mhc=MHC_I) - self.add_features( - FeatureLiterature.dai(score_mutation=mutation_multiple_binding, score_wild_type=wild_type_multiple_binding), - "DAI_mhcI_MB") + self.add_multiple_binding_features() # netmhcpan4 wt affinity self.add_features(self.pred.best4_affinity_WT, "best_affinity_netmhcpan4_WT") @@ -237,50 +143,11 @@ def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aa self.add_features(self_similarity.position_in_anchor_position(self.properties, nine_mer=True), "Mutation_in_anchor_netmhcpan_9mer") - # selfsimilarity - self.add_features(self_similarity.get_self_similarity(mutation=mutation_mhci, wild_type=wild_type_mhci), - "Selfsimilarity_mhcI") - self.add_features(self_similarity.get_self_similarity( - wild_type=wild_type_mhcii, mutation=mutation_mhcii), "Selfsimilarity_mhcII") - self.add_features(self_similarity.is_improved_binder(self.properties, MHC_I), "ImprovedBinding_mhcI") - self.add_features(self_similarity.is_improved_binder(self.properties, MHC_II), "ImprovedBinding_mhcII") - self.add_features(self_similarity.selfsimilarity_of_conserved_binder_only(self.properties), - "Selfsimilarity_mhcI_conserved_binder") + self.add_self_similarity_features(mutation_mhci, mutation_mhcii, wild_type_mhci, wild_type_mhcii) - # neoantigen fitness - tmp_fasta_file = tempfile.NamedTemporaryFile(prefix="tmpseq", suffix=".fasta", delete=False) - tmp_fasta = tmp_fasta_file.name + tmp_fasta = self.add_neoantigen_fitness_features(mutation_mhci, mutation_mhcii) - self.add_features( - self.neoantigen_fitness_calculator.wrap_pathogensimilarity( - mutation=mutation_mhci, fastafile=tmp_fasta, iedb=self.references.iedb), - "Pathogensimiliarity_mhcI") - self.add_features( - self.neoantigen_fitness_calculator.wrap_pathogensimilarity( - mutation=mutation_mhcii, fastafile=tmp_fasta, iedb=self.references.iedb), - "Pathogensimiliarity_mhcII") - self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( - self.properties, MHC_I), "Amplitude_mhcI") - self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( - self.properties, MHC_II), "Amplitude_mhcII") - self.add_features(self.neoantigen_fitness_calculator.calculate_recognition_potential( - self.properties, MHC_I), "Recognition_Potential_mhcI") - self.add_features(self.neoantigen_fitness_calculator.calculate_recognition_potential( - self.properties, MHC_II), "Recognition_Potential_mhcII") - - # T cell predictor - substitution = properties_manager.get_substitution(properties=self.properties) - epitope = self.properties["MHC_I_epitope_.best_prediction."] - score = self.properties["MHC_I_score_.best_prediction."] - self.add_features(self.tcell_predictor.calculate_tcell_predictor_score( - gene=gene, substitution=substitution, epitope=epitope, score=score, threshold=2), - "Tcell_predictor_score") - - epitope = self.properties["best_affinity_epitope_netmhcpan4_9mer"] - score = self.properties["best_affinity_netmhcpan4_9mer"] - self.add_features(self.tcell_predictor.calculate_tcell_predictor_score( - gene=gene, substitution=substitution, epitope=epitope, score=score, threshold=500), - "Tcell_predictor_score_9mersPredict") + self.add_tcell_predictor_features(gene) # DAI with affinity values wild_type_netmhcpan4, mutation_netmhcpan4 = properties_manager.get_scores_netmhcpan4_affinity( @@ -456,6 +323,45 @@ def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aa self.add_features(FeatureLiterature.calc_IEDB_immunogenicity(self.properties, MHC_I, affin_filtering=True), "IEDB_Immunogenicity_mhcI_affinity_filtered") + self.add_mix_mhc_pred_features(patient_hlaI) + + self.add_mix_mhc2_pred_features(patient_hlaII) + + # dissimilarity to self-proteome + + # neoantigen fitness + tmp_fasta_file = tempfile.NamedTemporaryFile(prefix="tmpseq", suffix=".fasta", delete=False) + tmp_fasta = tmp_fasta_file.name + self.add_features(self.dissimilarity_calculator.calculate_dissimilarity( + self.properties, tmp_fasta, self.references), "dissimilarity") + self.add_features(self.dissimilarity_calculator.calculate_dissimilarity( + self.properties, tmp_fasta, self.references, filter_binder=True), "dissimilarity_filter500") + + self.add_vax_rank_features() + + return self.properties + + def add_vax_rank_features(self): + # vaxrank + vaxrankscore = vaxrank.VaxRank() + vaxrankscore.main(self.properties) + self.add_features(vaxrankscore.total_binding_score, "vaxrank_binding_score") + self.add_features(vaxrankscore.ranking_score, "vaxrank_total_score") + + def add_mix_mhc2_pred_features(self, patient_hlaII): + # MixMHC2pred + self.predpresentation2.main(self.properties, patient_hlaII) + self.add_features(self.predpresentation2.all_peptides, "MixMHC2pred_all_peptides") + self.add_features(self.predpresentation2.all_ranks, "MixMHC2pred_all_ranks") + self.add_features(self.predpresentation2.all_alleles, "MixMHC2pred_all_alleles") + self.add_features(self.predpresentation2.best_peptide, "MixMHC2pred_best_peptide") + self.add_features(self.predpresentation2.best_rank, "MixMHC2pred_best_rank") + self.add_features(self.predpresentation2.best_allele, "MixMHC2pred_best_allele") + self.add_features(self.predpresentation2.best_peptide_wt, "MixMHC2pred_best_peptide_wt") + self.add_features(self.predpresentation2.best_rank_wt, "MixMHC2pred_best_rank_wt") + self.add_features(self.predpresentation2.difference_score_mut_wt, "MixMHC2pred_difference_rank_mut_wt") + + def add_mix_mhc_pred_features(self, patient_hlaI): # MixMHCpred self.predpresentation.main(self.properties, patient_hlaI) self.add_features(self.predpresentation.all_peptides, "MixMHCpred_all_peptides") @@ -471,32 +377,176 @@ def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aa self.add_features(self.predpresentation.best_rank_wt, "MixMHCpred_best_rank_wt") self.add_features(self.predpresentation.difference_score_mut_wt, "MixMHCpred_difference_score_mut_wt") - # MixMHC2pred - self.predpresentation2.main(self.properties, patient_hlaII) - self.add_features(self.predpresentation2.all_peptides, "MixMHC2pred_all_peptides") - self.add_features(self.predpresentation2.all_ranks, "MixMHC2pred_all_ranks") - self.add_features(self.predpresentation2.all_alleles, "MixMHC2pred_all_alleles") - self.add_features(self.predpresentation2.best_peptide, "MixMHC2pred_best_peptide") - self.add_features(self.predpresentation2.best_rank, "MixMHC2pred_best_rank") - self.add_features(self.predpresentation2.best_allele, "MixMHC2pred_best_allele") - self.add_features(self.predpresentation2.best_peptide_wt, "MixMHC2pred_best_peptide_wt") - self.add_features(self.predpresentation2.best_rank_wt, "MixMHC2pred_best_rank_wt") - self.add_features(self.predpresentation2.difference_score_mut_wt, "MixMHC2pred_difference_rank_mut_wt") - - # dissimilarity to self-proteome + def add_tcell_predictor_features(self, gene): + # T cell predictor + substitution = properties_manager.get_substitution(properties=self.properties) + epitope = self.properties["MHC_I_epitope_.best_prediction."] + score = self.properties["MHC_I_score_.best_prediction."] + self.add_features(self.tcell_predictor.calculate_tcell_predictor_score( + gene=gene, substitution=substitution, epitope=epitope, score=score, threshold=2), + "Tcell_predictor_score") + epitope = self.properties["best_affinity_epitope_netmhcpan4_9mer"] + score = self.properties["best_affinity_netmhcpan4_9mer"] + self.add_features(self.tcell_predictor.calculate_tcell_predictor_score( + gene=gene, substitution=substitution, epitope=epitope, score=score, threshold=500), + "Tcell_predictor_score_9mersPredict") + def add_neoantigen_fitness_features(self, mutation_mhci, mutation_mhcii): # neoantigen fitness tmp_fasta_file = tempfile.NamedTemporaryFile(prefix="tmpseq", suffix=".fasta", delete=False) tmp_fasta = tmp_fasta_file.name - self.add_features(self.dissimilarity_calculator.calculate_dissimilarity( - self.properties, tmp_fasta, self.references), "dissimilarity") - self.add_features(self.dissimilarity_calculator.calculate_dissimilarity( - self.properties, tmp_fasta, self.references, filter_binder=True), "dissimilarity_filter500") + self.add_features( + self.neoantigen_fitness_calculator.wrap_pathogensimilarity( + mutation=mutation_mhci, fastafile=tmp_fasta, iedb=self.references.iedb), + "Pathogensimiliarity_mhcI") + self.add_features( + self.neoantigen_fitness_calculator.wrap_pathogensimilarity( + mutation=mutation_mhcii, fastafile=tmp_fasta, iedb=self.references.iedb), + "Pathogensimiliarity_mhcII") + self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( + self.properties, MHC_I), "Amplitude_mhcI") + self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( + self.properties, MHC_II), "Amplitude_mhcII") + self.add_features(self.neoantigen_fitness_calculator.calculate_recognition_potential( + self.properties, MHC_I), "Recognition_Potential_mhcI") + self.add_features(self.neoantigen_fitness_calculator.calculate_recognition_potential( + self.properties, MHC_II), "Recognition_Potential_mhcII") + return tmp_fasta - # vaxrank - vaxrankscore = vaxrank.VaxRank() - vaxrankscore.main(self.properties) - self.add_features(vaxrankscore.total_binding_score, "vaxrank_binding_score") - self.add_features(vaxrankscore.ranking_score, "vaxrank_total_score") + def add_self_similarity_features(self, mutation_mhci, mutation_mhcii, wild_type_mhci, wild_type_mhcii): + # selfsimilarity + self.add_features(self_similarity.get_self_similarity(mutation=mutation_mhci, wild_type=wild_type_mhci), + "Selfsimilarity_mhcI") + self.add_features(self_similarity.get_self_similarity( + wild_type=wild_type_mhcii, mutation=mutation_mhcii), "Selfsimilarity_mhcII") + self.add_features(self_similarity.is_improved_binder(self.properties, MHC_I), "ImprovedBinding_mhcI") + self.add_features(self_similarity.is_improved_binder(self.properties, MHC_II), "ImprovedBinding_mhcII") + self.add_features(self_similarity.selfsimilarity_of_conserved_binder_only(self.properties), + "Selfsimilarity_mhcI_conserved_binder") - return self.properties + def add_multiple_binding_features(self): + # multiplexed representation MUT + for sc, mn in zip(self.pred.MHC_score_all_epitopes, self.pred.mean_type): + self.add_features(sc, "MB_score_all_epitopes_" + mn) + for sc, mn in zip(self.pred.MHC_score_top10, self.pred.mean_type): + self.add_features(sc, "MB_score_top10_" + mn) + for sc, mn in zip(self.pred.MHC_score_best_per_alelle, self.pred.mean_type): + self.add_features(sc, "MB_score_best_per_alelle_" + mn) + # rename MB_score_best_per_alelle_harmonic to PHBR (described in Marty et al) + self.properties["PHBR-I"] = self.properties.pop("MB_score_best_per_alelle_harmonic") + self.add_features(self.pred.MHC_epitope_scores, "MB_epitope_scores") + self.add_features(self.pred.MHC_epitope_seqs, "MB_epitope_sequences") + self.add_features(self.pred.MHC_epitope_alleles, "MB_alleles") + self.add_features(self.pred.MHC_number_strong_binders, "MB_number_pep_MHCscore<1") + self.add_features(self.pred.MHC_number_weak_binders, "MB_number_pep_MHCscore<2") + # generator rate + self.add_features(self.pred.epitope_affinities, "MB_affinities") + self.add_features(self.pred.generator_rate, "Generator_rate") + # multiplexed representation WT + self.add_features(self.pred.MHC_epitope_scores_WT, "MB_epitope_WT_scores") + self.add_features(self.pred.MHC_epitope_seqs_WT, "MB_epitope_WT_sequences") + self.add_features(self.pred.MHC_epitope_alleles_WT, "MB_alleles_WT") + for sc, mn in zip(self.pred.MHC_score_top10_WT, self.pred.mean_type): + self.add_features(sc, "MB_score_WT_top10_" + mn) + for sc, mn in zip(self.pred.MHC_score_all_epitopes_WT, self.pred.mean_type): + self.add_features(sc, "MB_score_WT_all_epitopes_" + mn) + for sc, mn in zip(self.pred.MHC_score_best_per_alelle_WT, self.pred.mean_type): + self.add_features(sc, "MB_score_WT_best_per_alelle_" + mn) + self.properties["PHBR-I_WT"] = self.properties.pop("MB_score_WT_best_per_alelle_harmonic") + self.add_features(self.pred.MHC_number_strong_binders_WT, "MB_number_pep_WT_MHCscore<1") + self.add_features(self.pred.MHC_number_weak_binders_WT, "MB_number_pep_WT_MHCscore<2") + # generator rate + self.add_features(self.pred.epitope_affinities_WT, "MB_affinities_WT") + self.add_features(self.pred.generator_rate_WT, "Generator_rate_WT") + wild_type_multiple_binding, mutation_multiple_binding = properties_manager. \ + get_scores_multiple_binding(self.properties, mhc=MHC_I) + self.add_features( + FeatureLiterature.dai(score_mutation=mutation_multiple_binding, score_wild_type=wild_type_multiple_binding), + "DAI_mhcI_MB") + + def add_netmhcpan4_features(self): + # netmhcpan4 MUT rank score + self.add_features(self.pred.best4_mhc_score, "best%Rank_netmhcpan4") + self.add_features(self.pred.best4_mhc_epitope, "best_epitope_netmhcpan4") + self.add_features(self.pred.best4_mhc_allele, "bestHLA_allele_netmhcpan4") + self.add_features(self.pred.directed_to_TCR, "directed_to_TCR") + # netmhcpan4 mut affinity + self.add_features(self.pred.best4_affinity, "best_affinity_netmhcpan4") + self.add_features(self.pred.best4_affinity_epitope, "best_affinity_epitope_netmhcpan4") + self.add_features(self.pred.best4_affinity_allele, "bestHLA_allele_affinity_netmhcpan4") + self.add_features(self.pred.best4_affinity_directed_to_TCR, "affinity_directed_to_TCR") + # netMHCpan MUT best 9mer score + self.add_features(self.pred.mhcI_score_9mer, "best%Rank_netmhcpan4_9mer") + self.add_features(self.pred.mhcI_score_epitope_9mer, "best_epitope_netmhcpan4_9mer") + self.add_features(self.pred.mhcI_score_allele_9mer, "bestHLA_allele_netmhcpan4_9mer") + # netmhcpan4 mut best 9mer affinity + self.add_features(self.pred.mhcI_affinity_9mer, "best_affinity_netmhcpan4_9mer") + self.add_features(self.pred.mhcI_affinity_allele_9mer, "bestHLA_allele_affinity_netmhcpan4_9mer") + self.add_features(self.pred.mhcI_affinity_epitope_9mer, "best_affinity_epitope_netmhcpan4_9mer") + + def add_provean_score_features(self, patient_hlaI, set_available_mhc): + # PROVEAN score + ucsc_id = self.provean_annotator.build_ucsc_id_plus_position( + substitution=self.properties["substitution"], ucsc_id=self.properties["UCSC_transcript"]) + self.add_features(ucsc_id, "UCSC_ID_position") + self.add_features(self.provean_annotator.get_provean_annotation( + mutated_aminoacid=self.properties['MUT_AA'], ucsc_id_position=ucsc_id), + "PROVEAN_score") + self.pred.main(self.properties, patient_hlaI, set_available_mhc) + + def add_aminoacid_index_features(self, aaindex1_dict, aaindex2_dict): + # amino acid index + for k in aaindex1_dict: + z = FeatureLiterature.add_aa_index1(self.properties, "wt", k, aaindex1_dict[k]) + self.add_features(z[1], z[0]) + z = FeatureLiterature.add_aa_index1(self.properties, "mut", k, aaindex1_dict[k]) + self.add_features(z[1], z[0]) + for k in aaindex2_dict: + try: + z = FeatureLiterature.add_aa_index2(self.properties, k, aaindex2_dict[k]) + self.add_features(z[1], z[0]) + except: + print(aaindex2_dict[k], wt, mut) + + def add_aminoacid_frequency_features(self, aa_freq_dict, mutated_aminoacid, mutation_mhci, nmer_freq_dict): + # amino acid frequency + self.add_features(FeatureLiterature.wt_mut_aa(self.properties, "mut"), "MUT_AA") + self.add_features(FeatureLiterature.wt_mut_aa(self.properties, "wt"), "WT_AA") + self.add_features(freq_score.freq_aa(mutated_aminoacid=mutated_aminoacid, dict_freq=aa_freq_dict), + "Frequency_mutated_AA") + self.add_features(freq_score.freq_prod_4mer(mutation=mutation_mhci, dict_freq=aa_freq_dict), + "Product_Frequency_4mer") + self.add_features(freq_score.freq_4mer(mutation=mutation_mhci, dict_freq=nmer_freq_dict), "Frequency_of_4mer") + + def add_expression_features(self, rna_avail, tumour_content): + # expression + self.add_features(FeatureLiterature.rna_expression_mutation(self.properties, rna_avail=rna_avail), + "Expression_Mutated_Transcript") + self.add_features(FeatureLiterature.expression_mutation_tc(self.properties, tumour_content=tumour_content), + "Expression_Mutated_Transcript_tumor_content") + + def add_differential_agretopicity_index_features(self, mutation_mhci, mutation_mhcii, wild_type_mhci, + wild_type_mhcii): + # differential agretopicity index + self.add_features( + FeatureLiterature.dai(score_mutation=mutation_mhci, score_wild_type=wild_type_mhci), "DAI_mhcI") + self.add_features( + FeatureLiterature.dai(score_mutation=mutation_mhcii, score_wild_type=wild_type_mhcii), "DAI_mhcII") + + def add_differential_expression_features(self, gene, ref_dat): + # differential expression + expression_tumor = self.properties["transcript_expression"] + expression_reference = self.properties["mean_ref_expression"] + expression_reference_sum = self.properties["sum_ref_expression"] + expression_reference_sd = self.properties["sd_ref_expression"] + self.add_features(differential_expression.add_rna_reference(gene, ref_dat, 0), "mean_ref_expression") + self.add_features(differential_expression.add_rna_reference(gene, ref_dat, 1), "sd_ref_expression") + self.add_features(differential_expression.add_rna_reference(gene, ref_dat, 2), "sum_ref_expression") + self.add_features(differential_expression.fold_change( + expression_tumor=expression_tumor, expression_reference=expression_reference), "log2_fc_tumour_ref") + self.add_features(differential_expression.percentile_calc( + expression_tumor=expression_tumor, expression_reference_sum=expression_reference_sum), + "percentile_tumour_ref") + self.add_features(differential_expression.pepper_calc( + expression_tumor=expression_tumor, expression_reference=expression_reference, + expression_reference_sd=expression_reference_sd), "DE_pepper") diff --git a/input/new_features/differential_expression.py b/input/new_features/differential_expression.py index 6c0c7d21..a531800f 100755 --- a/input/new_features/differential_expression.py +++ b/input/new_features/differential_expression.py @@ -31,42 +31,35 @@ def add_rna_reference(gene, reference_dat, i): return "NA" -def fold_change(props): - ''' +def fold_change(expression_tumor, expression_reference): + """ This function determines the classical fold change between tumour and reference transcript expression. Log2(expr in tumor / expr in reference) - ''' - expr_tumour = props["transcript_expression"] - expr_reference = props["mean_ref_expression"] + """ try: - return str(math.log(float(expr_tumour) / float(expr_reference), 2)) + return str(math.log(float(expression_tumor) / float(expression_reference), 2)) except (ValueError, ZeroDivisionError) as e: return "NA" -def percentile_calc(props): - ''' +def percentile_calc(expression_tumor, expression_reference_sum): + """ This function calculates the expression difference between tumour and reference data in form of a percentile value. expr in tumor * 100 / (sum of expr in ref tissue + 1) - ''' - expr_tumour = props["transcript_expression"] - expr_reference = props["sum_ref_expression"] + """ try: - return str((float(expr_tumour) * 100) / (float(expr_reference) + 1)) + return str((float(expression_tumor) * 100) / (float(expression_reference_sum) + 1)) except (ValueError, ZeroDivisionError) as e: return "NA" -def pepper_calc(props): - ''' +def pepper_calc(expression_tumor, expression_reference, expression_reference_sd): + """ This function calculates the expression difference between tumour and reference data based on Pepper publication, in a z-score similar manner. expr in tumour - mean epxr in reference tissue / standard deviation of expression in refernce - ''' - expr_tumour = props["transcript_expression"] - expr_reference = props["mean_ref_expression"] - expr_reference_sd = props["sd_ref_expression"] + """ try: - return str((float(expr_tumour) - float(expr_reference)) / float(expr_reference_sd)) + return str((float(expression_tumor) - float(expression_reference)) / float(expression_reference_sd)) except (ValueError, ZeroDivisionError) as e: return "NA" From e4e0a44a224823a902930d463624482cea0838d5 Mon Sep 17 00:00:00 2001 From: Pablo Riesgo Ferreiro Date: Thu, 21 May 2020 16:53:05 +0200 Subject: [PATCH 018/105] moe refactor of FeatureLiterature --- input/FeatureLiterature.py | 134 +++++----------- input/epitope.py | 146 ++++++++++++------ input/self_similarity/self_similarity.py | 62 +++----- .../tests/unit_tests/test_self_similarity.py | 11 +- 4 files changed, 160 insertions(+), 193 deletions(-) diff --git a/input/FeatureLiterature.py b/input/FeatureLiterature.py index b506d651..5567a3a9 100755 --- a/input/FeatureLiterature.py +++ b/input/FeatureLiterature.py @@ -15,30 +15,21 @@ from input.helpers import properties_manager -def calc_IEDB_immunogenicity(props, mhc, affin_filtering=False): +def calc_IEDB_immunogenicity(epitope, mhc_allele, mhc_score, affin_filtering=False): ''' This function determines the IEDB immunogenicity score ''' - if mhc == MHC_I: - # mhc_mut = props["MHC_I_epitope_.best_prediction."] - # mhc_allele = props["MHC_I_allele_.best_prediction."] - mhc_mut = props["best_affinity_epitope_netmhcpan4"] - mhc_allele = props["bestHLA_allele_affinity_netmhcpan4"] - mhc_score = props["best_affinity_netmhcpan4"] - elif mhc == MHC_II: - mhc_mut = props["MHC_II_epitope_.best_prediction."] - mhc_allele = props["MHC_II_allele_.best_prediction."] try: if affin_filtering: if float(mhc_score) < 500: - return str(predict_immunogenicity_simple.predict_immunogenicity(mhc_mut, - mhc_allele.replace("*", "").replace(":", + return str(predict_immunogenicity_simple.predict_immunogenicity( + epitope, mhc_allele.replace("*", "").replace(":", ""))) else: return "NA" else: - return str(predict_immunogenicity_simple.predict_immunogenicity(mhc_mut, - mhc_allele.replace("*", "").replace(":", + return str(predict_immunogenicity_simple.predict_immunogenicity( + epitope, mhc_allele.replace("*", "").replace(":", ""))) except ValueError: return "NA" @@ -61,34 +52,25 @@ def dai(score_mutation, score_wild_type, affin_filtering=False): return "NA" -def diff_number_binders(props, mhc=MHC_I, threshold=1): - ''' returns absolute difference of potential candidate epitopes between mutated and wt epitope - ''' - if mhc == MHC_II: - num_mut = props["MB_number_pep_MHCIIscore<" + str(threshold)] - num_wt = props["MB_number_pep_MHCIIscore<" + str(threshold) + "_WT"] - else: - num_mut = props["MB_number_pep_MHCscore<" + str(threshold)] - num_wt = props["MB_number_pep_WT_MHCscore<" + str(threshold)] +def diff_number_binders(num_mutation, num_wild_type): + """ + returns absolute difference of potential candidate epitopes between mutated and wt epitope + """ + # TODO: this is not the absolute difference, just the difference :S try: - return str(float(num_mut) - float(num_wt)) + return str(float(num_mutation) - float(num_wild_type)) except ValueError: return "NA" -def ratio_number_binders(props, mhc=MHC_I, threshold=1): - ''' returns ratio of number of potential candidate epitopes between mutated and wt epitope. if no WT candidate epitopes, returns number of mutated candidate epitopes per mps - ''' - if mhc == MHC_II: - num_mut = props["MB_number_pep_MHCIIscore<" + str(threshold)] - num_wt = props["MB_number_pep_MHCIIscore<" + str(threshold) + "_WT"] - else: - num_mut = props["MB_number_pep_MHCscore<" + str(threshold)] - num_wt = props["MB_number_pep_WT_MHCscore<" + str(threshold)] +def ratio_number_binders(num_mutation, num_wild_type): + """ + returns ratio of number of potential candidate epitopes between mutated and wt epitope. if no WT candidate epitopes, returns number of mutated candidate epitopes per mps + """ try: - return str(float(num_mut) / float(num_wt)) + return str(float(num_mutation) / float(num_wild_type)) except ZeroDivisionError: - return str(num_mut) + return str(num_wild_type) except ValueError: return "NA" @@ -133,34 +115,27 @@ def expression_mutation_tc(props, tumour_content): return "NA" -def number_of_mismatches(props, mhc): - ''' +def number_of_mismatches(epitope_wild_type, epitope_mutation): + """ This function calculates the number of mismatches between the wt and the mutated epitope - ''' - if mhc == MHC_I: - mhc_epitope_mut = props["best_epitope_netmhcpan4"] - mhc_epitope_wt = props["best_epitope_netmhcpan4_WT"] - elif mhc == MHC_II: - mhc_epitope_mut = props["best_epitope_netmhcIIpan"] - mhc_epitope_wt = props["best_epitope_netmhcIIpan_WT"] + """ p1 = 0 try: - for i, aa in enumerate(mhc_epitope_mut): - if aa != mhc_epitope_wt[i]: + for i, aa in enumerate(epitope_mutation): + if aa != epitope_wild_type[i]: p1 += 1 return str(p1) except IndexError: return "NA" -def match_in_proteome(props, db): - ''' +def match_in_proteome(sequence, db): + """ This function checks if the mutated epitope has an exact match in a protein database (uniprot) Returns 0 if mutation is present in proteome and 1 if it not present - ''' - seq = props["X..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."] + """ try: - seq_in_db = [seq in entry for entry in db] + seq_in_db = [sequence in entry for entry in db] return "0" if any(seq_in_db) else "1" except: return "NA" @@ -193,6 +168,7 @@ def calc_priority_score(props, multiple_binding=False): score_mut = props["best%Rank_netmhcpan4"] score_wt = props["best%Rank_netmhcpan4_WT"] mut_in_prot = props["mutation_found_in_proteome"] + # TODO: is this a bug? if mut_in_prot == "False" : mut_in_prot = "1" if mut_in_prot == "True" : mut_in_prot = "0" L_mut = calc_logistic_function(score_mut) @@ -210,10 +186,9 @@ def calc_priority_score(props, multiple_binding=False): return "NA" -def wt_mut_aa(props, mut): +def wt_mut_aa(substitution, mut): '''Returns wt and mut aa. ''' - substitution = props["substitution"] try: if mut == "mut": return substitution[-1] @@ -223,32 +198,6 @@ def wt_mut_aa(props, mut): return "NA" -def add_aa_index1(props, mut, key, val): - """Adds amino acido index to dictioniary. output from aa index 1 append function = tuple of feature name and feature value (nam_wt, nam_mut, val_wt, val_mut) - mut indicates if mutated or wt aa - """ - if mut == "mut": - aa = props["MUT_AA"] - elif mut == "wt": - aa = props["WT_AA"] - try: - return "_".join([key, mut]), str(val[aa]) - except KeyError: - return "_".join([key, mut]), "NA" - - -def add_aa_index2(props, key, val): - """Adds amino acido index to dictioniary. output from aa index 1 append function = tuple of feature name and feature value (nam_wt, nam_mut, val_wt, val_mut) - mut indicates if mutated or wt aa - """ - mut_aa = props["MUT_AA"] - wt_aa = props["WT_AA"] - try: - return key, str(val[wt_aa][mut_aa]) - except KeyError: - return key, "NA" - - def write_ouptut_to_file(epitope_data): ''' This function prints output, semilicon separated --> csv file @@ -260,33 +209,22 @@ def write_ouptut_to_file(epitope_data): print(";".join(i)) -def classify_adn_cdn(props, mhc, category): - '''returns if an epitope belongs to classically and alternatively defined neoepitopes (CDN vs ADN) (indicate which category to examine by category)--> Rech et al, 2018 +def classify_adn_cdn(score_mutation, amplitude, bdg_cutoff_classical, bdg_cutoff_alternative, amplitude_cutoff, category): + """ + returns if an epitope belongs to classically and alternatively defined neoepitopes (CDN vs ADN) (indicate which category to examine by category)--> Rech et al, 2018 grouping is based on affinity and affinitiy foldchange between wt and mut - ''' + """ group = "NA" - if mhc == MHC_I: - score_mut = props["best_affinity_netmhcpan4"] - amplitude = props["Amplitude_mhcI_affinity"] - bdg_cutoff_classical = 50 - bdg_cutoff_alternative = 5000 - amplitude_cutoff = 10 - elif mhc == MHC_II: - score_mut = props["MHC_II_score_.best_prediction."] - amplitude = props["Amplitude_mhcII"] - bdg_cutoff_classical = 1 - bdg_cutoff_alternative = 4 - amplitude_cutoff = 4 try: if category == "CDN": - if float(score_mut) < float(bdg_cutoff_classical): + if float(score_mutation) < float(bdg_cutoff_classical): group = "True" - elif float(score_mut) > float(bdg_cutoff_classical): + elif float(score_mutation) > float(bdg_cutoff_classical): group = "False" elif category == "ADN": - if float(score_mut) < float(bdg_cutoff_alternative) and float(amplitude) > float(amplitude_cutoff): + if float(score_mutation) < float(bdg_cutoff_alternative) and float(amplitude) > float(amplitude_cutoff): group = "True" - elif float(score_mut) > float(bdg_cutoff_alternative) or float(amplitude) < float(amplitude_cutoff): + elif float(score_mutation) > float(bdg_cutoff_alternative) or float(amplitude) < float(amplitude_cutoff): group = "False" except ValueError: group = "NA" diff --git a/input/epitope.py b/input/epitope.py index 96ceb765..a9fba36a 100755 --- a/input/epitope.py +++ b/input/epitope.py @@ -76,7 +76,10 @@ def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aa wild_type=wild_type_mhci, mutation=mutation_mhci), "pos_MUT_MHCI") self.add_features(self_similarity.position_of_mutation_epitope( wild_type=wild_type_mhcii, mutation=mutation_mhcii), "pos_MUT_MHCII") - self.add_features(self_similarity.position_in_anchor_position(self.properties), "Mutation_in_anchor") + self.add_features(self_similarity.position_in_anchor_position( + position_mhci=self.properties["pos_MUT_MHCI"], + peptide_length=self.properties["MHC_I_peptide_length_.best_prediction."] + ), "Mutation_in_anchor") self.add_differential_agretopicity_index_features(mutation_mhci, mutation_mhcii, wild_type_mhci, wild_type_mhcii) @@ -116,14 +119,14 @@ def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aa self.add_features(self.pred.mhcI_affinity_epitope_9mer_WT, "best_affinity_epitope_netmhcpan4_9mer_WT") # multiplex representation - self.add_features(FeatureLiterature.diff_number_binders(self.properties, mhc=MHC_I, threshold="1"), - "Diff_numb_epis_<1") - self.add_features(FeatureLiterature.diff_number_binders(self.properties, mhc=MHC_I, threshold="2"), - "Diff_numb_epis_<2") - self.add_features(FeatureLiterature.ratio_number_binders(self.properties, mhc=MHC_I, threshold="1"), - "Ratio_numb_epis_<1") - self.add_features(FeatureLiterature.ratio_number_binders(self.properties, mhc=MHC_I, threshold="2"), - "Ratio_numb_epis_<2") + for threshold in [1, 2]: + num_mutation = self.properties["MB_number_pep_MHCscore<{}".format(threshold)] + num_wild_type = self.properties["MB_number_pep_WT_MHCscore<{}".format(threshold)] + self.add_features(FeatureLiterature.diff_number_binders( + num_mutation=num_mutation,num_wild_type=num_wild_type), "Diff_numb_epis_<{}".format(threshold)) + self.add_features(FeatureLiterature.ratio_number_binders( + num_mutation=num_mutation, num_wild_type=num_wild_type), "Ratio_numb_epis_<{}".format(threshold)) + self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( self.properties, MHC_I, multiple_binding=True), "Amplitude_mhcI_MB") @@ -138,10 +141,14 @@ def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aa properties=self.properties, nine_mer=True) self.add_features(self_similarity.position_of_mutation_epitope( wild_type=wild_type_netmhcpan4_9mer, mutation=mutation_netmhcpan4_9mer),"pos_MUT_MHCI_affinity_epi_9mer") - self.add_features(self_similarity.position_in_anchor_position(self.properties, netMHCpan=True), - "Mutation_in_anchor_netmhcpan") - self.add_features(self_similarity.position_in_anchor_position(self.properties, nine_mer=True), - "Mutation_in_anchor_netmhcpan_9mer") + self.add_features(self_similarity.position_in_anchor_position( + position_mhci=self.properties["pos_MUT_MHCI_affinity_epi"], + peptide_length=self.properties["best_epitope_netmhcpan4"]), + "Mutation_in_anchor_netmhcpan") + self.add_features(self_similarity.position_in_anchor_position( + position_mhci=self.properties["pos_MUT_MHCI_affinity_epi_9mer"], + peptide_length=9), + "Mutation_in_anchor_netmhcpan_9mer") self.add_self_similarity_features(mutation_mhci, mutation_mhcii, wild_type_mhci, wild_type_mhcii) @@ -194,10 +201,36 @@ def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aa # recogntion potential with amplitude by affinity and only 9mers considered --> value as published!! self.add_features(self.neoantigen_fitness_calculator.calculate_recognition_potential( self.properties, MHC_I, nine_mer=True), "Recognition_Potential_mhcI_9mer_affinity") - self.add_features(FeatureLiterature.classify_adn_cdn(self.properties, mhc=MHC_I, category="CDN"), "CDN_mhcI") - self.add_features(FeatureLiterature.classify_adn_cdn(self.properties, mhc=MHC_II, category="CDN"), "CDN_mhcII") - self.add_features(FeatureLiterature.classify_adn_cdn(self.properties, mhc=MHC_I, category="ADN"), "ADN_mhcI") - self.add_features(FeatureLiterature.classify_adn_cdn(self.properties, mhc=MHC_II, category="ADN"), "ADN_mhcII") + + score_mutation_mhci = self.properties["best_affinity_netmhcpan4"] + amplitude_mhci = self.properties["Amplitude_mhcI_affinity"] + bdg_cutoff_classical_mhci = 50 + bdg_cutoff_alternative_mhci = 5000 + amplitude_cutoff_mhci = 10 + self.add_features(FeatureLiterature.classify_adn_cdn( + score_mutation=score_mutation_mhci, amplitude=amplitude_mhci, + bdg_cutoff_classical=bdg_cutoff_classical_mhci, bdg_cutoff_alternative=bdg_cutoff_alternative_mhci, + amplitude_cutoff=amplitude_cutoff_mhci, category="CDN"), "CDN_mhcI") + + score_mutation_mhcii = self.properties["MHC_II_score_.best_prediction."] + amplitude_mhcii = self.properties["Amplitude_mhcII"] + bdg_cutoff_classical_mhcii = 1 + bdg_cutoff_alternative_mhcii = 4 + amplitude_cutoff_mhcii = 4 + self.add_features(FeatureLiterature.classify_adn_cdn( + score_mutation=score_mutation_mhcii, amplitude=amplitude_mhcii, + bdg_cutoff_classical=bdg_cutoff_classical_mhcii, bdg_cutoff_alternative=bdg_cutoff_alternative_mhcii, + amplitude_cutoff=amplitude_cutoff_mhcii, category="CDN"), "CDN_mhcII") + + self.add_features(FeatureLiterature.classify_adn_cdn( + score_mutation=score_mutation_mhci, amplitude=amplitude_mhci, + bdg_cutoff_classical=bdg_cutoff_classical_mhci, bdg_cutoff_alternative=bdg_cutoff_alternative_mhci, + amplitude_cutoff=amplitude_cutoff_mhci, + category="ADN"), "ADN_mhcI") + self.add_features(FeatureLiterature.classify_adn_cdn( + score_mutation=score_mutation_mhcii, amplitude=amplitude_mhcii, + bdg_cutoff_classical=bdg_cutoff_classical_mhcii, bdg_cutoff_alternative=bdg_cutoff_alternative_mhcii, + amplitude_cutoff=amplitude_cutoff_mhcii, category="ADN"), "ADN_mhcII") # netMHCIIpan predictions self.predII.main(self.properties, patient_hlaII, set_available_mhcII) @@ -279,14 +312,13 @@ def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aa "DAI_mhcII_MB") # difference number of binders - self.add_features(FeatureLiterature.diff_number_binders(self.properties, mhc=MHC_II, threshold="2"), - "Diff_numb_epis_mhcII<2") - self.add_features(FeatureLiterature.diff_number_binders(self.properties, mhc=MHC_II, threshold="10"), - "Diff_numb_epis_mhcII<10") - self.add_features(FeatureLiterature.ratio_number_binders(self.properties, mhc=MHC_II, threshold="2"), - "Ratio_numb_epis_mhcII<2") - self.add_features(FeatureLiterature.ratio_number_binders(self.properties, mhc=MHC_II, threshold="10"), - "Ratio_numb_epis_mhcII<10") + for threshold in [2, 10]: + num_mutation = self.properties["MB_number_pep_MHCIIscore<{}".format(threshold)] + num_wild_type = self.properties["MB_number_pep_MHCIIscore<{}_WT".format(threshold)] + self.add_features(FeatureLiterature.diff_number_binders( + num_mutation=num_mutation,num_wild_type=num_wild_type), "Diff_numb_epis_mhcII<{}".format(threshold)) + self.add_features(FeatureLiterature.ratio_number_binders( + num_mutation=num_mutation,num_wild_type=num_wild_type), "Ratio_numb_epis_mhcII<{}".format(threshold)) # amplitude affinity mhc II self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( @@ -303,10 +335,16 @@ def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aa logger.info("Amplitude mhc II: {}".format(self.properties["Amplitude_mhcII_rank_netmhcpan4"])) # priority score - self.add_features(FeatureLiterature.number_of_mismatches(self.properties, MHC_I), "Number_of_mismatches_mhcI") - self.add_features(FeatureLiterature.number_of_mismatches(self.properties, MHC_II), "Number_of_mismatches_mhcII") + self.add_features(FeatureLiterature.number_of_mismatches( + epitope_wild_type=self.properties["best_epitope_netmhcpan4_WT"], + epitope_mutation=self.properties["best_epitope_netmhcpan4"]), "Number_of_mismatches_mhcI") + self.add_features(FeatureLiterature.number_of_mismatches( + epitope_wild_type=self.properties["best_epitope_netmhcIIpan_WT"], + epitope_mutation=self.properties["best_epitope_netmhcIIpan"]), "Number_of_mismatches_mhcII") if "mutation_found_in_proteome" not in self.properties: - self.add_features(FeatureLiterature.match_in_proteome(self.properties, db), "mutation_found_in_proteome") + self.add_features(FeatureLiterature.match_in_proteome( + sequence=self.properties["X..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."], db=db), + "mutation_found_in_proteome") self.add_features(FeatureLiterature.calc_priority_score(self.properties), "Priority_score") # priority score using multiplexed representation score @@ -316,11 +354,17 @@ def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aa self.add_features(self.neoag_calculator.wrapper_neoag(self.properties), "neoag_immunogencity") # IEDB immunogenicity only for epitopes with affinity < 500 nM (predicted with netMHCpan) --> in publications - self.add_features(FeatureLiterature.calc_IEDB_immunogenicity(self.properties, MHC_I), - "IEDB_Immunogenicity_mhcI") - self.add_features(FeatureLiterature.calc_IEDB_immunogenicity(self.properties, MHC_II), - "IEDB_Immunogenicity_mhcII") - self.add_features(FeatureLiterature.calc_IEDB_immunogenicity(self.properties, MHC_I, affin_filtering=True), + mhci_epitope = self.properties["best_affinity_epitope_netmhcpan4"] + mhci_allele = self.properties["bestHLA_allele_affinity_netmhcpan4"] + mhci_score = self.properties["best_affinity_netmhcpan4"] + mhcii_epitope = self.properties["MHC_II_epitope_.best_prediction."] + mhcii_allele = self.properties["MHC_II_allele_.best_prediction."] + self.add_features(FeatureLiterature.calc_IEDB_immunogenicity( + epitope=mhci_epitope, mhc_allele=mhci_allele, mhc_score=mhci_score), "IEDB_Immunogenicity_mhcI") + self.add_features(FeatureLiterature.calc_IEDB_immunogenicity( + epitope=mhcii_epitope, mhc_allele=mhcii_allele, mhc_score=None), "IEDB_Immunogenicity_mhcII") + self.add_features(FeatureLiterature.calc_IEDB_immunogenicity( + epitope=mhci_epitope, mhc_allele=mhci_allele, mhc_score=mhci_score, affin_filtering=True), "IEDB_Immunogenicity_mhcI_affinity_filtered") self.add_mix_mhc_pred_features(patient_hlaI) @@ -419,10 +463,19 @@ def add_self_similarity_features(self, mutation_mhci, mutation_mhcii, wild_type_ "Selfsimilarity_mhcI") self.add_features(self_similarity.get_self_similarity( wild_type=wild_type_mhcii, mutation=mutation_mhcii), "Selfsimilarity_mhcII") - self.add_features(self_similarity.is_improved_binder(self.properties, MHC_I), "ImprovedBinding_mhcI") - self.add_features(self_similarity.is_improved_binder(self.properties, MHC_II), "ImprovedBinding_mhcII") - self.add_features(self_similarity.selfsimilarity_of_conserved_binder_only(self.properties), - "Selfsimilarity_mhcI_conserved_binder") + self.add_features(self_similarity.is_improved_binder( + score_mutation=self.properties["best%Rank_netmhcpan4"], + score_wild_type=self.properties["best%Rank_netmhcpan4_WT"] + ), "ImprovedBinding_mhcI") + self.add_features(self_similarity.is_improved_binder( + # TODO: conversion from float representation needs to be changed + score_mutation=self.properties["MHC_II_score_.best_prediction."].replace(",", "."), + score_wild_type=self.properties["MHC_II_score_.WT."].replace(",", ".") + ), "ImprovedBinding_mhcII") + self.add_features(self_similarity.self_similarity_of_conserved_binder_only( + has_conserved_binder=self.properties["ImprovedBinding_mhcI"], + similarity=self.properties["Selfsimilarity_mhcI"]), + "Selfsimilarity_mhcI_conserved_binder") def add_multiple_binding_features(self): # multiplexed representation MUT @@ -496,22 +549,19 @@ def add_provean_score_features(self, patient_hlaI, set_available_mhc): def add_aminoacid_index_features(self, aaindex1_dict, aaindex2_dict): # amino acid index + mutation_aminoacid = self.properties["MUT_AA"] + wild_type_aminoacid = self.properties["WT_AA"] for k in aaindex1_dict: - z = FeatureLiterature.add_aa_index1(self.properties, "wt", k, aaindex1_dict[k]) - self.add_features(z[1], z[0]) - z = FeatureLiterature.add_aa_index1(self.properties, "mut", k, aaindex1_dict[k]) - self.add_features(z[1], z[0]) + self.add_features(aaindex1_dict[k].get(wild_type_aminoacid, "NA"), "{}_{}".format(k, "wt")) + self.add_features(aaindex1_dict[k].get(mutation_aminoacid, "NA"), "{}_{}".format(k, "mut")) for k in aaindex2_dict: - try: - z = FeatureLiterature.add_aa_index2(self.properties, k, aaindex2_dict[k]) - self.add_features(z[1], z[0]) - except: - print(aaindex2_dict[k], wt, mut) + self.add_features(aaindex2_dict[k].get(wild_type_aminoacid, {}).get(mutation_aminoacid, "NA"), k) def add_aminoacid_frequency_features(self, aa_freq_dict, mutated_aminoacid, mutation_mhci, nmer_freq_dict): # amino acid frequency - self.add_features(FeatureLiterature.wt_mut_aa(self.properties, "mut"), "MUT_AA") - self.add_features(FeatureLiterature.wt_mut_aa(self.properties, "wt"), "WT_AA") + substitution = self.properties["substitution"] + self.add_features(FeatureLiterature.wt_mut_aa(substitution=substitution, mut="mut"), "MUT_AA") + self.add_features(FeatureLiterature.wt_mut_aa(substitution=substitution, mut="wt"), "WT_AA") self.add_features(freq_score.freq_aa(mutated_aminoacid=mutated_aminoacid, dict_freq=aa_freq_dict), "Frequency_mutated_AA") self.add_features(freq_score.freq_prod_4mer(mutation=mutation_mhci, dict_freq=aa_freq_dict), diff --git a/input/self_similarity/self_similarity.py b/input/self_similarity/self_similarity.py index aa59d32d..7285b0c8 100755 --- a/input/self_similarity/self_similarity.py +++ b/input/self_similarity/self_similarity.py @@ -71,7 +71,8 @@ def _compute_k2k(self, u, v, K1): def get_self_similarity(mutation, wild_type): - """Returns self-similiarity between mutated and wt epitope according to Bjerregard et al., + """ + Returns self-similiarity between mutated and wt epitope according to Bjerregard et al., Argument mhc indicates if determination for MHC I or MHC II epitopes """ self_similarity = 'NA' @@ -82,32 +83,25 @@ def get_self_similarity(mutation, wild_type): return self_similarity -def is_improved_binder(props, mhc): - ''' +def is_improved_binder(score_mutation, score_wild_type): + """ This function checks if mutated epitope is improved binder according to Bjerregard et al. - ''' - if mhc == MHC_I: - sc_mut = props["best%Rank_netmhcpan4"] - sc_wt = props["best%Rank_netmhcpan4_WT"] - elif mhc == MHC_II: - sc_mut = props["MHC_II_score_.best_prediction."].replace(",", ".") - sc_wt = props["MHC_II_score_.WT."].replace(",", ".") - + """ try: - improved_binder = float(sc_wt) / float(sc_mut) >= 1.2 + improved_binder = float(score_wild_type) / float(score_mutation) >= 1.2 except (ZeroDivisionError, ValueError) as e: return "NA" + # TODO: boolean in a string needs to go away return "1" if improved_binder else "0" -def selfsimilarity_of_conserved_binder_only(props): - '''this function returns selfsimilarity for conserved binder but not for improved binder - ''' - conserved_binder = props["ImprovedBinding_mhcI"] - similiarity = props["Selfsimilarity_mhcI"] +def self_similarity_of_conserved_binder_only(has_conserved_binder, similarity): + """ + this function returns selfsimilarity for conserved binder but not for improved binder + """ try: - if conserved_binder == str(0): - return similiarity + if has_conserved_binder == str(0): + return similarity else: return "NA" except (ZeroDivisionError, ValueError) as e: @@ -115,9 +109,9 @@ def selfsimilarity_of_conserved_binder_only(props): def position_of_mutation_epitope(wild_type, mutation): - ''' + """ This function determines the position of the mutation within the epitope sequence. - ''' + """ p1 = -1 try: for i, aa in enumerate(mutation): @@ -128,24 +122,16 @@ def position_of_mutation_epitope(wild_type, mutation): return "NA" -def position_in_anchor_position(props, netMHCpan=False, nine_mer=False): - ''' +def position_in_anchor_position(position_mhci, peptide_length): + """ This function determines if the mutation is located within an anchor position in mhc I. As an approximation, we assume that the second and the last position are anchor positions for all alleles. - ''' - if netMHCpan: - pos_mhcI = props["pos_MUT_MHCI_affinity_epi"] - pep_len = len(props["best_epitope_netmhcpan4"]) - elif nine_mer: - pos_mhcI = props["pos_MUT_MHCI_affinity_epi_9mer"] - pep_len = 9 - else: - pos_mhcI = props["pos_MUT_MHCI"] - pep_len = props["MHC_I_peptide_length_.best_prediction."] - - anchor = 0 + """ + anchor = "NA" try: - anchor = int(pos_mhcI) == int(pep_len) or int(pos_mhcI) == 2 - return str(1) if anchor else str(0) + anchor = int(position_mhci) == int(peptide_length) or int(position_mhci) == 2 + # TODO this conversion of a boolean to a numeric boolean in a string needs to go away + anchor = str(1) if anchor else str(0) except: - return "NA" + pass + return anchor diff --git a/input/tests/unit_tests/test_self_similarity.py b/input/tests/unit_tests/test_self_similarity.py index 96d8782e..021829f5 100755 --- a/input/tests/unit_tests/test_self_similarity.py +++ b/input/tests/unit_tests/test_self_similarity.py @@ -10,16 +10,9 @@ def test_get_self_similarity(self): result = self_similarity.get_self_similarity(wild_type="DDD", mutation="DDD") self.assertEqual('1.0', result) - def test_is_improved_binder_mhci(self): + def test_is_improved_binder(self): result = self_similarity.is_improved_binder( - props={'best%Rank_netmhcpan4': '1.0', 'best%Rank_netmhcpan4_WT': '1.3'}, - mhc=MHC_I) - self.assertEqual('1', result) - - def test_is_improved_binder_mhcii(self): - result = self_similarity.is_improved_binder( - props={'MHC_II_score_.best_prediction.': '1,0', 'MHC_II_score_.WT.': '1,3'}, - mhc=MHC_II) + score_mutation='1.0', score_wild_type='1.3') self.assertEqual('1', result) def test_position_mutation(self): From b565d763f000758b928b21f5ce0d6dc86d89adf6 Mon Sep 17 00:00:00 2001 From: Pablo Riesgo Ferreiro Date: Thu, 21 May 2020 18:47:37 +0200 Subject: [PATCH 019/105] refactor properties in neoantigen fitness --- input/epitope.py | 65 +++++++++++++---- .../neoantigen_fitness/neoantigen_fitness.py | 71 +++---------------- 2 files changed, 59 insertions(+), 77 deletions(-) diff --git a/input/epitope.py b/input/epitope.py index a9fba36a..1f4d93d4 100755 --- a/input/epitope.py +++ b/input/epitope.py @@ -128,7 +128,8 @@ def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aa num_mutation=num_mutation, num_wild_type=num_wild_type), "Ratio_numb_epis_<{}".format(threshold)) self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( - self.properties, MHC_I, multiple_binding=True), "Amplitude_mhcI_MB") + score_mutation=self.properties["MB_score_top10_harmonic"].replace(",", "."), + score_wild_type=self.properties["MB_score_WT_top10_harmonic"].replace(",", ".")), "Amplitude_mhcI_MB") # position of mutation wild_type_netmhcpan4, mutation_netmhcpan4 = properties_manager.get_wild_type_and_mutation_from_netmhcpan4( @@ -172,17 +173,22 @@ def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aa # Amplitude with affinity values self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( - self.properties, MHC_I, False, True), "Amplitude_mhcI_affinity") + score_mutation=self.properties["best_affinity_netmhcpan4"].replace(",", "."), + score_wild_type=self.properties["best_affinity_netmhcpan4_WT"].replace(",", "."), + apply_correction=True), "Amplitude_mhcI_affinity") # Amplitude with rank by netmhcpan4 self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( - self.properties, mhc=MHC_I, multiple_binding=False, affinity=False, netmhcscore=True), + score_mutation=self.properties["best%Rank_netmhcpan4"].replace(",", "."), + score_wild_type=self.properties["best%Rank_netmhcpan4_WT"].replace(",", ".")), "Amplitude_mhcI_rank_netmhcpan4") # Amplitude based on best affinity prediction restricted to 9mers self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( - self.properties, mhc=MHC_I, multiple_binding=False, nine_mer=True), - "Amplitude_mhcI_affinity_9mer_netmhcpan4") + score_mutation=self.properties["best_affinity_netmhcpan4_9mer"].replace(",", "."), + score_wild_type = self.properties["best_affinity_netmhcpan4_9mer_WT"].replace(",", "."), + apply_correction=True), "Amplitude_mhcI_affinity_9mer_netmhcpan4") + self.add_features( self.neoantigen_fitness_calculator.wrap_pathogensimilarity( mutation=mutation_netmhcpan4_9mer, fastafile=tmp_fasta, iedb=self.references.iedb), @@ -194,13 +200,23 @@ def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aa # recogntion potential with amplitude by affinity and netmhcpan4 score self.add_features(self.neoantigen_fitness_calculator.calculate_recognition_potential( - self.properties, MHC_I, affinity=True), "Recognition_Potential_mhcI_affinity") + amplitude=self.properties["Amplitude_mhcI_affinity"], + pathogen_similarity=self.properties["Pathogensimiliarity_mhcI_affinity_nmers"], + mutation_in_anchor=self.properties["Mutation_in_anchor_netmhcpan"]), + "Recognition_Potential_mhcI_affinity") self.add_features(self.neoantigen_fitness_calculator.calculate_recognition_potential( - self.properties, MHC_I, affinity=False, netmhcscore=True), "Recognition_Potential_mhcI_rank_netmhcpan4") + amplitude=self.properties["Amplitude_mhcI_rank_netmhcpan4"], + pathogen_similarity=self.properties["Pathogensimiliarity_mhcI"], + mutation_in_anchor=self.properties["Mutation_in_anchor_netmhcpan"]), + "Recognition_Potential_mhcI_rank_netmhcpan4") # recogntion potential with amplitude by affinity and only 9mers considered --> value as published!! self.add_features(self.neoantigen_fitness_calculator.calculate_recognition_potential( - self.properties, MHC_I, nine_mer=True), "Recognition_Potential_mhcI_9mer_affinity") + amplitude=self.properties["Amplitude_mhcI_affinity_9mer_netmhcpan4"], + pathogen_similarity=self.properties["Pathogensimiliarity_mhcI_9mer"], + mutation_in_anchor=self.properties["Mutation_in_anchor_netmhcpan_9mer"], + mhc_affinity_mut=float(self.properties["best_affinity_netmhcpan4_9mer"])), + "Recognition_Potential_mhcI_9mer_affinity") score_mutation_mhci = self.properties["best_affinity_netmhcpan4"] amplitude_mhci = self.properties["Amplitude_mhcI_affinity"] @@ -322,15 +338,20 @@ def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aa # amplitude affinity mhc II self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( - self.properties, MHC_II, False, True), "Amplitude_mhcII_affinity") + score_mutation=self.properties["best_affinity_netmhcIIpan"].replace(",", "."), + score_wild_type = self.properties["best_affinity_netmhcIIpan_WT"].replace(",", "."), + apply_correction=True), "Amplitude_mhcII_affinity") # amplitude multiple binding mhc II self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( - self.properties, MHC_II, True, False), "Amplitude_mhcII_mb") + score_mutation=self.properties["MB_score_MHCII_top10_harmonic"].replace(",", "."), + score_wild_type = self.properties["MB_score_MHCII_top10_WT_harmonic"].replace(",", ".")), + "Amplitude_mhcII_mb") # amplitude rank score mhc II self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( - self.properties, mhc=MHC_II, multiple_binding=False, affinity=False, netmhcscore=True), + score_mutation=self.properties["best%Rank_netmhcIIpan"].replace(",", "."), + score_wild_type = self.properties["best%Rank_netmhcIIpan_WT"].replace(",", ".")), "Amplitude_mhcII_rank_netmhcpan4") logger.info("Amplitude mhc II: {}".format(self.properties["Amplitude_mhcII_rank_netmhcpan4"])) @@ -447,14 +468,28 @@ def add_neoantigen_fitness_features(self, mutation_mhci, mutation_mhcii): self.neoantigen_fitness_calculator.wrap_pathogensimilarity( mutation=mutation_mhcii, fastafile=tmp_fasta, iedb=self.references.iedb), "Pathogensimiliarity_mhcII") + + score_mutation_mhci = self.properties["MHC_I_score_.best_prediction."].replace(",", ".") + score_wild_type_mhci = self.properties["MHC_I_score_.WT."].replace(",", ".") self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( - self.properties, MHC_I), "Amplitude_mhcI") + score_mutation=score_mutation_mhci, score_wild_type=score_wild_type_mhci), "Amplitude_mhcI") + score_mutation_mhcii = self.properties["MHC_II_score_.best_prediction."].replace(",", ".") + score_wild_type_mhcii = self.properties["MHC_II_score_.WT."].replace(",", ".") self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( - self.properties, MHC_II), "Amplitude_mhcII") + score_mutation=score_mutation_mhcii, score_wild_type=score_wild_type_mhcii), "Amplitude_mhcII") + + # TODO: Franziska, please, review that this is the right value for mutation_in_anchor, + # it is possible that there was a bug here and that it should use "Mutation_in_anchor" self.add_features(self.neoantigen_fitness_calculator.calculate_recognition_potential( - self.properties, MHC_I), "Recognition_Potential_mhcI") + amplitude=self.properties["Amplitude_mhcI"], + pathogen_similarity=self.properties["Pathogensimiliarity_mhcI"], + mutation_in_anchor=self.properties["Mutation_in_anchor_netmhcpan"]), + "Recognition_Potential_mhcI") self.add_features(self.neoantigen_fitness_calculator.calculate_recognition_potential( - self.properties, MHC_II), "Recognition_Potential_mhcII") + amplitude=self.properties["Amplitude_mhcII"], + pathogen_similarity=self.properties["Pathogensimiliarity_mhcII"], + mutation_in_anchor=self.properties["Mutation_in_anchor_netmhcpan"]), + "Recognition_Potential_mhcII") return tmp_fasta def add_self_similarity_features(self, mutation_mhci, mutation_mhcii, wild_type_mhci, wild_type_mhcii): diff --git a/input/neoantigen_fitness/neoantigen_fitness.py b/input/neoantigen_fitness/neoantigen_fitness.py index a986b289..2e2452b6 100755 --- a/input/neoantigen_fitness/neoantigen_fitness.py +++ b/input/neoantigen_fitness/neoantigen_fitness.py @@ -4,7 +4,6 @@ import os.path import tempfile -from input import MHC_I, MHC_II from input.neoantigen_fitness.Aligner_modified import Aligner @@ -53,45 +52,15 @@ def wrap_pathogensimilarity(self, mutation, fastafile, iedb): pathsim = "NA" return str(pathsim) if pathsim != "NA" else "0" - def calculate_amplitude_mhc(self, props, mhc, multiple_binding=False, affinity=False, netmhcscore=False, nine_mer=False): - ''' + def calculate_amplitude_mhc(self, score_mutation, score_wild_type, apply_correction=False): + """ This function calculates the amplitude between mutated and wt epitope according to Balachandran et al. when affinity is used, use correction from Luksza et al. *1/(1+0.0003*aff_wt) - ''' - if mhc == MHC_I: - if multiple_binding: - score_mutation = props["MB_score_top10_harmonic"].replace(",", ".") - score_wild_type = props["MB_score_WT_top10_harmonic"].replace(",", ".") - elif affinity: - score_mutation = props["best_affinity_netmhcpan4"].replace(",", ".") - score_wild_type = props["best_affinity_netmhcpan4_WT"].replace(",", ".") - elif netmhcscore: - score_mutation = props["best%Rank_netmhcpan4"].replace(",", ".") - score_wild_type = props["best%Rank_netmhcpan4_WT"].replace(",", ".") - elif nine_mer: - score_mutation = props["best_affinity_netmhcpan4_9mer"].replace(",", ".") - score_wild_type = props["best_affinity_netmhcpan4_9mer_WT"].replace(",", ".") - else: - score_mutation = props["MHC_I_score_.best_prediction."].replace(",", ".") - score_wild_type = props["MHC_I_score_.WT."].replace(",", ".") - elif mhc == MHC_II: - if multiple_binding: - score_mutation = props["MB_score_MHCII_top10_harmonic"].replace(",", ".") - score_wild_type = props["MB_score_MHCII_top10_WT_harmonic"].replace(",", ".") - elif affinity: - score_mutation = props["best_affinity_netmhcIIpan"].replace(",", ".") - score_wild_type = props["best_affinity_netmhcIIpan_WT"].replace(",", ".") - elif netmhcscore: - score_mutation = props["best%Rank_netmhcIIpan"].replace(",", ".") - score_wild_type = props["best%Rank_netmhcIIpan_WT"].replace(",", ".") - else: - score_mutation = props["MHC_II_score_.best_prediction."].replace(",", ".") - score_wild_type = props["MHC_II_score_.WT."].replace(",", ".") - + """ amplitude_mhc = "NA" try: candidate_amplitude_mhc = float(score_wild_type) / float(score_mutation) - if nine_mer or affinity: + if apply_correction: #nine_mer or affinity: amplitude_mhc = str(candidate_amplitude_mhc * (self._calculate_correction(score_wild_type))) else: amplitude_mhc = str(candidate_amplitude_mhc) @@ -99,46 +68,24 @@ def calculate_amplitude_mhc(self, props, mhc, multiple_binding=False, affinity=F pass return amplitude_mhc - def _calculate_correction(self, score_wild_type): return 1 / (1 + 0.0003 * float(score_wild_type)) - - def calculate_recognition_potential(self, props, mhc, affinity=False, netmhcscore=False, nine_mer=False): - ''' + def calculate_recognition_potential( + self, amplitude, pathogen_similarity, mutation_in_anchor, mhc_affinity_mut=None): + """ This function calculates the recognition potential, defined by the product of amplitude and pathogensimiliarity of an epitope according to Balachandran et al. F_alpha = - max (A_i x R_i) Returns (A_i x R_i) value only for nonanchor mutation and epitopes of length 9; only considered by Balachandran - ''' - if mhc == MHC_I: - if affinity: - amplitude = props["Amplitude_mhcI_affinity"] - pathogen_similarity = props["Pathogensimiliarity_mhcI_affinity_nmers"] - elif netmhcscore: - amplitude = props["Amplitude_mhcI_rank_netmhcpan4"] - pathogen_similarity = props["Pathogensimiliarity_mhcI"] - elif nine_mer: - amplitude = props["Amplitude_mhcI_affinity_9mer_netmhcpan4"] - pathogen_similarity = props["Pathogensimiliarity_mhcI_9mer"] - else: - amplitude = props["Amplitude_mhcI"] - pathogen_similarity = props["Pathogensimiliarity_mhcI"] - elif mhc == MHC_II: - amplitude = props["Amplitude_mhcII"] - pathogen_similarity = props["Pathogensimiliarity_mhcII"] - + """ recognition_potential = "NA" try: - # mutation_in_anchor = props["Mutation_in_anchor"] candidate_recognition_potential = str(float(amplitude) * float(pathogen_similarity)) - if nine_mer: - mutation_in_anchor = props["Mutation_in_anchor_netmhcpan_9mer"] - mhc_affinity_mut = float(props["best_affinity_netmhcpan4_9mer"]) + if mhc_affinity_mut: if mutation_in_anchor == "0" and mhc_affinity_mut < 500: recognition_potential = candidate_recognition_potential else: - mutation_in_anchor = props["Mutation_in_anchor_netmhcpan"] if mutation_in_anchor == "0": recognition_potential = candidate_recognition_potential except ValueError: From edaa17f4435f97f93244cb5512db812d48a260a5 Mon Sep 17 00:00:00 2001 From: Pablo Riesgo Ferreiro Date: Thu, 21 May 2020 22:15:46 +0200 Subject: [PATCH 020/105] refactor creation of intermediate files --- .../predict_immunogenicity.py | 11 ++--- input/MixMHCpred/mixmhc2pred.py | 33 ++++--------- input/MixMHCpred/mixmhcpred.py | 29 ++---------- .../Tcell_predictor/tcellpredictor_wrapper.py | 9 ++-- .../dissimilaritycalculator.py | 5 +- input/epitope.py | 14 +++--- input/helpers/intermediate_files.py | 21 +++++++++ .../neoantigen_fitness/neoantigen_fitness.py | 5 +- ...mbine_netmhcIIpan_pred_multiple_binders.py | 31 ++++--------- input/netmhcIIpan/netmhcIIpan_prediction.py | 46 +++++++------------ ...combine_netmhcpan_pred_multiple_binders.py | 20 +++----- input/netmhcpan4/multiple_binders.py | 29 ------------ input/netmhcpan4/netmhcpan_prediction.py | 25 ++-------- 13 files changed, 91 insertions(+), 187 deletions(-) create mode 100755 input/helpers/intermediate_files.py diff --git a/input/IEDB_Immunogenicity/predict_immunogenicity.py b/input/IEDB_Immunogenicity/predict_immunogenicity.py index 08334af2..be91a146 100755 --- a/input/IEDB_Immunogenicity/predict_immunogenicity.py +++ b/input/IEDB_Immunogenicity/predict_immunogenicity.py @@ -11,6 +11,8 @@ from logzero import logger +from input.helpers import intermediate_files + class Prediction(): @@ -160,21 +162,18 @@ def predict(self, cleaned_data): def create_csv(self, mask_choice, mask_out, data): import csv - import tempfile tmpdir = './output' # Create a temporary file inside the tmp/ directory - tmpfile = tempfile.NamedTemporaryFile(prefix="immunogenicity_", suffix=".csv", dir=tmpdir, delete=False) - - with open(tmpfile.name, 'wb') as result: + tmpfile = intermediate_files.create_temp_file(prefix="immunogenicity_", suffix=".csv", dir=tmpdir) + with open(tmpfile, 'wb') as result: writer = csv.writer(result, delimiter=',') data.insert(0, ['masking: ', '{0}'.format(mask_choice)]) data.insert(1, ['masked variables: ', '{0}'.format(mask_out)]) for score in data: writer.writerow(score) - tmpfile.close() - return tmpfile.name + return tmpfile def commandline_help(self): print(""" diff --git a/input/MixMHCpred/mixmhc2pred.py b/input/MixMHCpred/mixmhc2pred.py index dffcce66..6f2b2fad 100755 --- a/input/MixMHCpred/mixmhc2pred.py +++ b/input/MixMHCpred/mixmhc2pred.py @@ -1,8 +1,6 @@ #!/usr/bin/env python -import tempfile - -from input.helpers import properties_manager +from input.helpers import properties_manager, intermediate_files class MixMhc2Pred: @@ -87,17 +85,6 @@ def generate_nmers(self, props, list_lengths, mut=True): [list_peptides_fil.append(x) for x in list_peptides if not x == ""] return list_peptides_fil - def generate_fasta(self, seqs, tmpfile): - ''' Writes seqs given in seqs list into fasta file - ''' - counter = 0 - with open(tmpfile, "w") as f: - for seq in seqs: - id = "".join([">seq", str(counter)]) - f.write(id + "\n") - f.write(seq + "\n") - counter += 1 - def prepare_dq_dp(self, list_alleles): ''' returns patient DQ/DP alleles that are relevant for prediction ''' @@ -269,13 +256,12 @@ def import_available_HLAII_alleles(self, path_to_HLAII_file): def main(self, props_dict, dict_patient_hlaII): '''Wrapper for MHC binding prediction, extraction of best epitope and check if mutation is directed to TCR ''' - tmp_fasta_file = tempfile.NamedTemporaryFile(prefix="tmp_sequence_", suffix=".fasta", delete=False) - tmp_fasta = tmp_fasta_file.name - tmp_prediction_file = tempfile.NamedTemporaryFile(prefix="mixmhc2pred", suffix=".txt", delete=False) - tmp_prediction = tmp_prediction_file.name - # prediction for peptides of length 13 to 18 based on Suppl Fig. 6 a in Racle, J., et al. Robust prediction of HLA class II epitopes by deep motif deconvolution of immunopeptidomes. Nat. Biotech. (2019). + tmp_prediction = intermediate_files.create_temp_file(prefix="mixmhc2pred", suffix=".txt") + # prediction for peptides of length 13 to 18 based on Suppl Fig. 6 a in Racle, J., et al. + # Robust prediction of HLA class II epitopes by deep motif deconvolution of immunopeptidomes. + # Nat. Biotech. (2019). seqs = self.generate_nmers(props_dict, [13, 14, 15, 16, 17, 18]) - self.generate_fasta(seqs, tmp_fasta) + tmp_fasta = intermediate_files.generate_fasta(seqs, prefix="tmp_sequence_") alleles = properties_manager.get_hla_allele(props_dict, dict_patient_hlaII) # try except statement to prevent stop of input for mps shorter < 13aa try: @@ -301,11 +287,8 @@ def main(self, props_dict, dict_patient_hlaII): # prediction of for wt epitope that correspond to best epitope wt = self.extract_WT_for_best(props_dict, self.best_peptide) wt_list = [wt] - tmp_fasta_file = tempfile.NamedTemporaryFile(prefix="tmp_sequence_wt_", suffix=".fasta", delete=False) - tmp_fasta = tmp_fasta_file.name - tmp_prediction_file = tempfile.NamedTemporaryFile(prefix="mixmhc2pred_wt_", suffix=".txt", delete=False) - tmp_prediction = tmp_prediction_file.name - self.generate_fasta(wt_list, tmp_fasta) + tmp_prediction = intermediate_files.create_temp_file(prefix="mixmhc2pred_wt_", suffix=".txt") + tmp_fasta = intermediate_files.generate_fasta(wt_list, prefix="tmp_sequence_wt_") self.mixmhc2prediction([self.best_allele], tmp_fasta, tmp_prediction, wt=True) pred_wt = self.read_mixmhcpred(tmp_prediction) self.best_peptide_wt = self.extract_WT_info(pred_wt, "Peptide") diff --git a/input/MixMHCpred/mixmhcpred.py b/input/MixMHCpred/mixmhcpred.py index ac22df39..23555305 100755 --- a/input/MixMHCpred/mixmhcpred.py +++ b/input/MixMHCpred/mixmhcpred.py @@ -1,10 +1,8 @@ #!/usr/bin/env python -import tempfile - from logzero import logger -from input.helpers import properties_manager +from input.helpers import properties_manager, intermediate_files class MixMHCpred: @@ -68,17 +66,6 @@ def generate_nmers(self, props, list_lengths, mut=True): list_peptides.append(long_seq[s:e]) return list_peptides - def generate_fasta(self, seqs, tmpfile): - ''' Writes seqs given in seqs list into fasta file - ''' - counter = 0 - with open(tmpfile, "w") as f: - for seq in seqs: - id = "".join([">seq", str(counter)]) - f.write(id + "\n") - f.write(seq + "\n") - counter += 1 - def mixmhcprediction(self, hla_alleles, tmpfasta, outtmp): ''' Performs MixMHCpred prediction for desired hla allele and writes result to temporary file. ''' @@ -204,12 +191,9 @@ def difference_score(self, mut_score, wt_score): def main(self, props_dict, dict_patient_hla): '''Wrapper for MHC binding prediction, extraction of best epitope and check if mutation is directed to TCR ''' - tmp_fasta_file = tempfile.NamedTemporaryFile(prefix="tmp_sequence_", suffix=".fasta", delete=False) - tmp_fasta = tmp_fasta_file.name - tmp_prediction_file = tempfile.NamedTemporaryFile(prefix="mixmhcpred", suffix=".txt", delete=False) - tmp_prediction = tmp_prediction_file.name + tmp_prediction = intermediate_files.create_temp_file(prefix="mixmhcpred", suffix=".txt") seqs = self.generate_nmers(props_dict, [8, 9, 10, 11]) - self.generate_fasta(seqs, tmp_fasta) + tmp_fasta = intermediate_files.generate_fasta(seqs, prefix="tmp_sequence_") alleles = properties_manager.get_hla_allele(props_dict, dict_patient_hla) self.mixmhcprediction(alleles, tmp_fasta, tmp_prediction) pred = self.read_mixmhcpred(tmp_prediction) @@ -231,11 +215,8 @@ def main(self, props_dict, dict_patient_hla): # prediction of for wt epitope that correspond to best epitope wt = self.extract_WT_for_best(props_dict, self.best_peptide) wt_list = [wt] - tmp_fasta_file = tempfile.NamedTemporaryFile(prefix="tmp_sequence_wt_", suffix=".fasta", delete=False) - tmp_fasta = tmp_fasta_file.name - tmp_prediction_file = tempfile.NamedTemporaryFile(prefix="mixmhcpred_wt_", suffix=".txt", delete=False) - tmp_prediction = tmp_prediction_file.name - self.generate_fasta(wt_list, tmp_fasta) + tmp_prediction = intermediate_files.create_temp_file(prefix="mixmhcpred_wt_", suffix=".txt") + tmp_fasta = intermediate_files.generate_fasta(wt_list, prefix="tmp_sequence_wt_") self.mixmhcprediction(alleles, tmp_fasta, tmp_prediction) pred_wt = self.read_mixmhcpred(tmp_prediction) logger.debug(pred_wt) diff --git a/input/Tcell_predictor/tcellpredictor_wrapper.py b/input/Tcell_predictor/tcellpredictor_wrapper.py index 75887ef6..01c15aab 100755 --- a/input/Tcell_predictor/tcellpredictor_wrapper.py +++ b/input/Tcell_predictor/tcellpredictor_wrapper.py @@ -1,10 +1,9 @@ #!/usr/bin/env python -import tempfile - from logzero import logger import input.Tcell_predictor.prediction as prediction +from input.helpers import intermediate_files class TcellPrediction: @@ -74,10 +73,8 @@ def _wrapper_tcellpredictor(self, gene, substitution, epitope, score, threshold, def calculate_tcell_predictor_score(self, gene, substitution, epitope, score, threshold): ''' returns Tcell_predictor score given mps in dictionary format ''' - tmp_tcellPredIN_file = tempfile.NamedTemporaryFile(prefix="tmp_TcellPredicIN_", suffix=".txt", delete=False) - tmp_tcellPredIN = tmp_tcellPredIN_file.name - tmp_tcellPredOUT_file = tempfile.NamedTemporaryFile(prefix="tmp_TcellPredicOUT_", suffix=".txt", delete=False) - tmp_tcellPredOUT = tmp_tcellPredOUT_file.name + tmp_tcellPredIN = intermediate_files.create_temp_file(prefix="tmp_TcellPredicIN_", suffix=".txt") + tmp_tcellPredOUT = intermediate_files.create_temp_file(prefix="tmp_TcellPredicOUT_", suffix=".txt") return self._wrapper_tcellpredictor( gene=gene, substitution=substitution, epitope=epitope, score=score, threshold=threshold, tmpfile_in=tmp_tcellPredIN, tmpfile_out=tmp_tcellPredOUT) diff --git a/input/dissimilarity_garnish/dissimilaritycalculator.py b/input/dissimilarity_garnish/dissimilaritycalculator.py index c0c03c58..28887c13 100755 --- a/input/dissimilarity_garnish/dissimilaritycalculator.py +++ b/input/dissimilarity_garnish/dissimilaritycalculator.py @@ -2,8 +2,8 @@ import os import os.path -import tempfile +from input.helpers import intermediate_files from input.neoantigen_fitness.Aligner_modified import Aligner @@ -21,8 +21,7 @@ def _calc_dissimilarity(self, fasta_file, n, references): ''' This function determines the dissimilarity to self-proteome of epitopes as described in Richman et al ''' - outfile_file = tempfile.NamedTemporaryFile(prefix="tmp_prot_", suffix=".xml", delete=False) - outfile = outfile_file.name + outfile = intermediate_files.create_temp_file(prefix="tmp_prot_", suffix=".xml") self.runner.run_command(cmd=[ self.configuration.blastp, "-gapopen", "11", diff --git a/input/epitope.py b/input/epitope.py index 1f4d93d4..cf371119 100755 --- a/input/epitope.py +++ b/input/epitope.py @@ -10,7 +10,7 @@ from input.MixMHCpred.mixmhc2pred import MixMhc2Pred from input.Tcell_predictor.tcellpredictor_wrapper import TcellPrediction from input.dissimilarity_garnish.dissimilaritycalculator import DissimilarityCalculator -from input.helpers import properties_manager +from input.helpers import properties_manager, intermediate_files from input.neoag.neoag_gbm_model import NeoagCalculator from input.neoantigen_fitness.neoantigen_fitness import NeoantigenFitnessCalculator from input.netmhcIIpan.combine_netmhcIIpan_pred_multiple_binders import BestAndMultipleBinderMhcII @@ -249,7 +249,11 @@ def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aa amplitude_cutoff=amplitude_cutoff_mhcii, category="ADN"), "ADN_mhcII") # netMHCIIpan predictions - self.predII.main(self.properties, patient_hlaII, set_available_mhcII) + sequence = self.properties["X..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."] + sequence_reference = self.properties["X.WT._..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."] + alleles = properties_manager.get_hla_allele(self.properties, patient_hlaII) + self.predII.main(sequence=sequence, sequence_reference=sequence_reference, alleles=alleles, + set_available_mhc=set_available_mhcII) # netmhcpan4 MUT scores self.add_features(self.predII.best_mhcII_pan_score, "best%Rank_netmhcIIpan") @@ -395,8 +399,7 @@ def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aa # dissimilarity to self-proteome # neoantigen fitness - tmp_fasta_file = tempfile.NamedTemporaryFile(prefix="tmpseq", suffix=".fasta", delete=False) - tmp_fasta = tmp_fasta_file.name + tmp_fasta = intermediate_files.create_temp_file(prefix="tmpseq", suffix=".fasta") self.add_features(self.dissimilarity_calculator.calculate_dissimilarity( self.properties, tmp_fasta, self.references), "dissimilarity") self.add_features(self.dissimilarity_calculator.calculate_dissimilarity( @@ -458,8 +461,7 @@ def add_tcell_predictor_features(self, gene): def add_neoantigen_fitness_features(self, mutation_mhci, mutation_mhcii): # neoantigen fitness - tmp_fasta_file = tempfile.NamedTemporaryFile(prefix="tmpseq", suffix=".fasta", delete=False) - tmp_fasta = tmp_fasta_file.name + tmp_fasta = intermediate_files.create_temp_file(prefix="tmpseq", suffix=".fasta") self.add_features( self.neoantigen_fitness_calculator.wrap_pathogensimilarity( mutation=mutation_mhci, fastafile=tmp_fasta, iedb=self.references.iedb), diff --git a/input/helpers/intermediate_files.py b/input/helpers/intermediate_files.py new file mode 100755 index 00000000..3e64f995 --- /dev/null +++ b/input/helpers/intermediate_files.py @@ -0,0 +1,21 @@ +import tempfile + + +def create_temp_file(prefix=None, suffix=None, dir=None): + temp_file = tempfile.NamedTemporaryFile(prefix=prefix, suffix=suffix, dir=dir, delete=False) + return temp_file.name + + +def generate_fasta(sequences, prefix=None): + """ + Writes seqs given in seqs list into fasta file + """ + fasta_temp_file = create_temp_file(prefix=prefix, suffix='.fasta') + counter = 1 + with open(fasta_temp_file, "w") as f: + for seq in sequences: + _id = ">seq{}".format(counter) + f.write(_id + "\n") + f.write(seq + "\n") + counter += 1 + return fasta_temp_file diff --git a/input/neoantigen_fitness/neoantigen_fitness.py b/input/neoantigen_fitness/neoantigen_fitness.py index 2e2452b6..452ab5b0 100755 --- a/input/neoantigen_fitness/neoantigen_fitness.py +++ b/input/neoantigen_fitness/neoantigen_fitness.py @@ -2,8 +2,8 @@ import os import os.path -import tempfile +from input.helpers import intermediate_files from input.neoantigen_fitness.Aligner_modified import Aligner @@ -21,8 +21,7 @@ def _calc_pathogensimilarity(self, fasta_file, n, iedb): ''' This function determines the PATHOGENSIMILARITY of epitopes according to Balachandran et al. using a blast search against the IEDB pathogenepitope database ''' - outfile_file = tempfile.NamedTemporaryFile(prefix="tmp_iedb_", suffix=".xml", delete=False) - outfile = outfile_file.name + outfile = intermediate_files.create_temp_file(prefix="tmp_iedb_", suffix=".xml") self.runner.run_command(cmd=[ self.configuration.blastp, "-gapopen", "11", diff --git a/input/netmhcIIpan/combine_netmhcIIpan_pred_multiple_binders.py b/input/netmhcIIpan/combine_netmhcIIpan_pred_multiple_binders.py index 45ed035a..ed801b20 100755 --- a/input/netmhcIIpan/combine_netmhcIIpan_pred_multiple_binders.py +++ b/input/netmhcIIpan/combine_netmhcIIpan_pred_multiple_binders.py @@ -1,12 +1,10 @@ #!/usr/bin/env python -import tempfile - from logzero import logger import input.netmhcIIpan.netmhcIIpan_prediction as netmhcIIpan_prediction from input import MHC_II -from input.helpers import properties_manager +from input.helpers import properties_manager, intermediate_files from input.netmhcpan4 import multiple_binders @@ -71,27 +69,22 @@ def MHCII_MB_score_best_per_allele(self, tuple_best_per_allele): else: return ["NA", "NA", "NA"] - def main(self, epi_dict, patient_hlaII, set_available_mhc): + def main(self, sequence, sequence_reference, alleles, set_available_mhc): '''predicts MHC epitopes; returns on one hand best binder and on the other hand multiple binder analysis is performed ''' ### PREDICTION FOR MUTATED SEQUENCE - xmer_mut = epi_dict["X..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."] - logger.info("MUT seq MHC II: {}".format(xmer_mut)) - tmp_fasta_file = tempfile.NamedTemporaryFile(prefix="tmp_singleseq_", suffix=".fasta", delete=False) - tmp_fasta = tmp_fasta_file.name - tmp_prediction_file = tempfile.NamedTemporaryFile(prefix="netmhcpanpred_", suffix=".csv", delete=False) - tmp_prediction = tmp_prediction_file.name + logger.info("MUT seq MHC II: {}".format(sequence)) + tmp_prediction = intermediate_files.create_temp_file(prefix="netmhcpanpred_", suffix=".csv") logger.debug(tmp_prediction) np = netmhcIIpan_prediction.NetMhcIIPanBestPrediction(runner=self.runner, configuration=self.configuration) mb = multiple_binders.MultipleBinding(runner=self.runner, configuration=self.configuration) - np.generate_fasta(epi_dict, tmp_fasta, mut=True) - alleles = properties_manager.get_hla_allele(epi_dict, patient_hlaII) + tmp_fasta = intermediate_files.generate_fasta([sequence], prefix="tmp_singleseq_") alleles_formated = np.generate_mhcII_alelles_combination_list(alleles, set_available_mhc) logger.debug(alleles_formated) np.mhcII_prediction(alleles, set_available_mhc, tmp_fasta, tmp_prediction) - epi_dict["Position_Xmer_Seq"] = np.mut_position_xmer_seq(epi_dict) + position_xmer_sequence = np.mut_position_xmer_seq(xmer_wt=sequence_reference, xmer_mut=sequence) try: - preds = np.filter_binding_predictions(epi_dict, tmp_prediction) + preds = np.filter_binding_predictions(position_xmer_sequence, tmp_prediction) # multiple binding list_tups = mb.generate_epi_tuple(preds, mhc=MHC_II) self.MHCII_epitope_scores = "/".join([tup[0] for tup in list_tups]) @@ -122,18 +115,14 @@ def main(self, epi_dict, patient_hlaII, set_available_mhc): pass ### PREDICTION FOR WT SEQUENCE - xmer_wt = epi_dict["X.WT._..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."] - tmp_fasta_file = tempfile.NamedTemporaryFile(prefix="tmp_singleseq_", suffix=".fasta", delete=False) - tmp_fasta = tmp_fasta_file.name - tmp_prediction_file = tempfile.NamedTemporaryFile(prefix="netmhcpanpred_", suffix=".csv", delete=False) - tmp_prediction = tmp_prediction_file.name + tmp_prediction = intermediate_files.create_temp_file(prefix="netmhcpanpred_", suffix=".csv") logger.debug(tmp_prediction) np = netmhcIIpan_prediction.NetMhcIIPanBestPrediction(runner=self.runner, configuration=self.configuration) mb = multiple_binders.MultipleBinding(runner=self.runner, configuration=self.configuration) - np.generate_fasta(epi_dict, tmp_fasta, mut=False) + tmp_fasta = intermediate_files.generate_fasta([sequence_reference], prefix="tmp_singleseq_") np.mhcII_prediction(alleles, set_available_mhc, tmp_fasta, tmp_prediction) try: - preds = np.filter_binding_predictions(epi_dict, tmp_prediction) + preds = np.filter_binding_predictions(position_xmer_sequence, tmp_prediction) # multiple binding list_tups = mb.generate_epi_tuple(preds, mhc=MHC_II) self.MHCII_epitope_scores_WT = "/".join([tup[0] for tup in list_tups]) diff --git a/input/netmhcIIpan/netmhcIIpan_prediction.py b/input/netmhcIIpan/netmhcIIpan_prediction.py index fef6d115..5bc6f9e9 100755 --- a/input/netmhcIIpan/netmhcIIpan_prediction.py +++ b/input/netmhcIIpan/netmhcIIpan_prediction.py @@ -4,7 +4,7 @@ from logzero import logger -from input.helpers import data_import, properties_manager +from input.helpers import data_import, properties_manager, intermediate_files class NetMhcIIPanBestPrediction: @@ -28,18 +28,6 @@ def mhc_allele_in_netmhcpan_available(self, allele, set_available_mhc): ''' return allele in set_available_mhc - def generate_fasta(self, props, tmpfile, mut=True): - ''' Writes 27mer to fasta file. - ''' - if mut == True: - seq = props["X..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."] - elif mut == False: - seq = props["X.WT._..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."] - id = ">seq1" - with open(tmpfile, "w") as f: - f.write(id + "\n") - f.write(seq + "\n") - def generate_mhcII_alelles_combination_list(self, hla_alleles, set_available_mhc): ''' given list of HLA II alleles, returns list of HLA-DRB1 (2x), all possible HLA-DPA1/HLA-DPB1 (4x) and HLA-DQA1/HLA-DPQ1 (4x) ''' @@ -104,11 +92,10 @@ def mhcII_prediction(self, hla_alleles, set_available_mhc, tmpfasta, tmppred): line = line[0:-2] if len(line) > 11 else line f.write(";".join(line) + "\n") - def mut_position_xmer_seq(self, props): - '''returns position of mutation in xmer sequence - ''' - xmer_wt = props["X.WT._..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."] - xmer_mut = props["X..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."] + def mut_position_xmer_seq(self, xmer_wt, xmer_mut): + """ + returns position of mutation in xmer sequence + """ if len(xmer_wt) == len(xmer_mut): p1 = -1 for i, aa in enumerate(xmer_mut): @@ -133,17 +120,17 @@ def epitope_covers_mutation(self, position_mutation, position_epitope, length_ep cover = True return cover - def filter_binding_predictions(self, props, tmppred): - '''filters prediction file for predicted epitopes that cover mutations - ''' - pos_xmer = props["Position_Xmer_Seq"] + def filter_binding_predictions(self, position_xmer_sequence, tmppred): + """ + filters prediction file for predicted epitopes that cover mutations + """ header, data = data_import.import_dat_general(tmppred) dat_fil = [] logger.debug(header) pos_epi = header.index("Seq") epi = header.index("Peptide") for ii, i in enumerate(data): - if self.epitope_covers_mutation(pos_xmer, i[pos_epi], len(i[epi])): + if self.epitope_covers_mutation(position_xmer_sequence, i[pos_epi], len(i[epi])): dat_fil.append(data[ii]) return header, dat_fil @@ -231,15 +218,14 @@ def filter_for_WT_epitope(self, prediction_tuple, mut_seq): def main(self, props_dict, set_available_mhc, dict_patient_hla): '''Wrapper for MHC binding prediction, extraction of best epitope and check if mutation is directed to TCR ''' - tmp_fasta_file = tempfile.NamedTemporaryFile(prefix="tmp_singleseq_", suffix=".fasta", delete=False) - tmp_fasta = tmp_fasta_file.name - tmp_prediction_file = tempfile.NamedTemporaryFile(prefix="netmhcpanpred_", suffix=".csv", delete=False) - tmp_prediction = tmp_prediction_file.name - self.generate_fasta(props_dict, tmp_fasta) + tmp_prediction = intermediate_files.create_temp_file(prefix="netmhcpanpred_", suffix=".csv") + sequence = props_dict["X..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."] + tmp_fasta = intermediate_files.generate_fasta([sequence], prefix="tmp_singleseq_") alleles = properties_manager.get_hla_allele(props_dict, dict_patient_hla) self.mhcII_prediction(alleles, set_available_mhc, tmp_fasta, tmp_prediction) - props_dict["Position_Xmer_Seq"] = self.mut_position_xmer_seq(props_dict) - preds = self.filter_binding_predictions(props_dict, tmp_prediction) + sequence_reference = props_dict["X.WT._..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."] + position_xmer_sequence = self.mut_position_xmer_seq(xmer_wt=sequence_reference, xmer_mut=sequence) + preds = self.filter_binding_predictions(position_xmer_sequence, tmp_prediction) best_epi = self.minimal_binding_score(preds) best_epi_affinity = self.minimal_binding_score(preds, rank=False) diff --git a/input/netmhcpan4/combine_netmhcpan_pred_multiple_binders.py b/input/netmhcpan4/combine_netmhcpan_pred_multiple_binders.py index 37f25875..64d34dde 100755 --- a/input/netmhcpan4/combine_netmhcpan_pred_multiple_binders.py +++ b/input/netmhcpan4/combine_netmhcpan_pred_multiple_binders.py @@ -1,12 +1,10 @@ #!/usr/bin/env python -import tempfile - from logzero import logger import input.netmhcpan4.multiple_binders as multiple_binders import input.netmhcpan4.netmhcpan_prediction as netmhcpan_prediction -from input.helpers import properties_manager +from input.helpers import properties_manager, intermediate_files class BestAndMultipleBinder: @@ -84,14 +82,12 @@ def main(self, epi_dict, patient_hlaI, set_available_mhc): ### PREDICTION FOR MUTATED SEQUENCE xmer_mut = epi_dict["X..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."] logger.info("MUT seq: {}".format(xmer_mut)) - tmp_fasta_file = tempfile.NamedTemporaryFile(prefix="tmp_singleseq_", suffix=".fasta", delete=False) - tmp_fasta = tmp_fasta_file.name - tmp_prediction_file = tempfile.NamedTemporaryFile(prefix="netmhcpanpred_", suffix=".csv", delete=False) - tmp_prediction = tmp_prediction_file.name + tmp_prediction = intermediate_files.create_temp_file(prefix="netmhcpanpred_", suffix=".csv") logger.debug(tmp_prediction) np = netmhcpan_prediction.NetMhcPanBestPrediction(runner=self.runner, configuration=self.configuration) mb = multiple_binders.MultipleBinding(runner=self.runner, configuration=self.configuration) - np.generate_fasta(epi_dict, tmp_fasta, mut=True) + tmp_fasta = intermediate_files.generate_fasta(sequences=[epi_dict["X..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."]], + prefix="tmp_singleseq_") alleles = properties_manager.get_hla_allele(epi_dict, patient_hlaI) # print alleles np.mhc_prediction(alleles, set_available_mhc, tmp_fasta, tmp_prediction) @@ -142,14 +138,12 @@ def main(self, epi_dict, patient_hlaI, set_available_mhc): self.mhcI_affinity_epitope_9mer = np.add_best_epitope_info(best_9mer_affinity, "Peptide") ### PREDICTION FOR WT SEQUENCE - tmp_fasta_file = tempfile.NamedTemporaryFile(prefix="tmp_singleseq_", suffix=".fasta", delete=False) - tmp_fasta = tmp_fasta_file.name - tmp_prediction_file = tempfile.NamedTemporaryFile(prefix="netmhcpanpred_", suffix=".csv", delete=False) - tmp_prediction = tmp_prediction_file.name + tmp_prediction = intermediate_files.create_temp_file(prefix="netmhcpanpred_", suffix=".csv") logger.debug(tmp_prediction) np = netmhcpan_prediction.NetMhcPanBestPrediction(runner=self.runner, configuration=self.configuration) mb = multiple_binders.MultipleBinding(runner=self.runner, configuration=self.configuration) - np.generate_fasta(epi_dict, tmp_fasta, mut=False) + tmp_fasta = intermediate_files.generate_fasta(sequences=[epi_dict["X.WT._..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."]], + prefix="tmp_singleseq_") np.mhc_prediction(alleles, set_available_mhc, tmp_fasta, tmp_prediction) preds = np.filter_binding_predictions(epi_dict, tmp_prediction) # multiple binding diff --git a/input/netmhcpan4/multiple_binders.py b/input/netmhcpan4/multiple_binders.py index 17361bf1..c695afe2 100755 --- a/input/netmhcpan4/multiple_binders.py +++ b/input/netmhcpan4/multiple_binders.py @@ -166,35 +166,6 @@ def determine_number_of_binders(self, list_scores, threshold=2): number_binders += 1 return str(number_binders) - def main(self, epi_dict, alleles, set_available_mhc): - '''takes epitope dictionary as input and returns several scores that describe multiple binding. - ''' - # TODO: check if all of this object creation can be avoided - NetMhcPanBestPrediction(runner=self.runner, configuration=self.configuration).generate_fasta(epi_dict) - alleles = NetMhcPanBestPrediction(runner=self.runner, configuration=self.configuration).get_hla_alleles(epi_dict, patient_hlaI) - NetMhcPanBestPrediction( - runner=self.runner, configuration=self.configuration).mhc_prediction(alleles, set_available_mhc) - epi_dict["Position_Xmer_Seq"] = NetMhcPanBestPrediction(runner=self.runner, configuration=self.configuration).mut_position_xmer_seq(epi_dict) - preds = NetMhcIIPanBestPrediction( - runner=self.runner, configuration=self.configuration).filter_binding_predictions(epi_dict) - list_tups = self.generate_epi_tuple(preds) - self.epitope_scores = "/".join([tup[0] for tup in list_tups]) - self.epitope_affinities = "/".join([tup[1] for tup in list_tups]) - self.epitope_seqs = "/".join([tup[2] for tup in list_tups]) - self.epitope_alleles = "/".join([tup[3] for tup in list_tups]) - top10 = self.extract_top10_epis(list_tups) - best_per_alelle = self.extract_best_epi_per_alelle(list_tups, alleles) - all = self.scores_to_list(list_tups) - all_affinities = self.affinities_to_list(list_tups) - top10 = self.scores_to_list(top10) - self.score_top10 = self.wrapper_mean_calculation(top10) - best_per_alelle = self.scores_to_list(best_per_alelle) - self.score_all_epitopes = self.wrapper_mean_calculation(all) - self.score_best_per_alelle = self.wrapper_mean_calculation(best_per_alelle) - self.number_strong_binders = self.determine_number_of_binders(all, 0.5) - self.number_weak_binders = self.determine_number_of_binders(all, 2) - self.generator_rate = self.determine_number_of_binders(list_scores=all_affinities, threshold=50) - # if __name__ == '__main__': # diff --git a/input/netmhcpan4/netmhcpan_prediction.py b/input/netmhcpan4/netmhcpan_prediction.py index 3f82208c..b45e0b3b 100755 --- a/input/netmhcpan4/netmhcpan_prediction.py +++ b/input/netmhcpan4/netmhcpan_prediction.py @@ -1,8 +1,6 @@ #!/usr/bin/env python -import tempfile - -from input.helpers import data_import, properties_manager +from input.helpers import data_import, properties_manager, intermediate_files class NetMhcPanBestPrediction: @@ -34,18 +32,6 @@ def mhc_allele_in_netmhcpan_available(self, allele, set_available_mhc): ''' return allele in set_available_mhc - def generate_fasta(self, props, tmpfile, mut=True): - ''' Writes 27mer to fasta file. - ''' - if mut: - seq = props["X..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."] - elif not mut: - seq = props["X.WT._..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."] - id = ">seq1" - with open(tmpfile, "w") as f: - f.write(id + "\n") - f.write(seq + "\n") - def mhc_prediction(self, hla_alleles, set_available_mhc, tmpfasta, tmppred): ''' Performs netmhcpan4 prediction for desired hla allele and writes result to temporary file. ''' @@ -239,13 +225,10 @@ def filter_for_WT_epitope(self, prediction_tuple, mut_seq, mut_allele): def main(self, props_dict, set_available_mhc, dict_patient_hla): '''Wrapper for MHC binding prediction, extraction of best epitope and check if mutation is directed to TCR ''' - tmp_fasta_file = tempfile.NamedTemporaryFile(prefix="tmp_singleseq_", suffix=".fasta", delete=False) - tmp_fasta = tmp_fasta_file.name - print(tmp_fasta) - tmp_prediction_file = tempfile.NamedTemporaryFile(prefix="netmhcpanpred_", suffix=".csv", delete=False) - tmp_prediction = tmp_prediction_file.name + tmp_prediction = intermediate_files.create_temp_file(prefix="netmhcpanpred_", suffix=".csv") print(tmp_prediction) - self.generate_fasta(props_dict, tmp_fasta) + tmp_fasta = intermediate_files.generate_fasta(sequences=[props_dict["X..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."]], + prefix="tmp_singleseq_") alleles = properties_manager.get_hla_allele(props_dict, dict_patient_hla) self.mhc_prediction(alleles, set_available_mhc, tmp_fasta, tmp_prediction) props_dict["Position_Xmer_Seq"] = self.mut_position_xmer_seq(props_dict) From 726c1f2a73834346e4e5bfc18b2f17eb7a722779 Mon Sep 17 00:00:00 2001 From: Pablo Riesgo Ferreiro Date: Thu, 21 May 2020 23:35:20 +0200 Subject: [PATCH 021/105] finished properties refactoring --- input/FeatureLiterature.py | 51 +++-------- input/MixMHCpred/mixmhc2pred.py | 33 +++---- input/MixMHCpred/mixmhcpred.py | 28 ++---- .../dissimilaritycalculator.py | 8 +- input/epitope.py | 91 ++++++++++++++----- input/helpers/intermediate_files.py | 2 +- ...mbine_netmhcIIpan_pred_multiple_binders.py | 4 +- input/netmhcIIpan/netmhcIIpan_prediction.py | 2 +- ...combine_netmhcpan_pred_multiple_binders.py | 28 +++--- input/netmhcpan4/netmhcpan_prediction.py | 71 ++------------- .../integration_tests/test_dissimilarity.py | 2 +- input/vaxrank/vaxrank.py | 35 ++++--- 12 files changed, 147 insertions(+), 208 deletions(-) diff --git a/input/FeatureLiterature.py b/input/FeatureLiterature.py index 5567a3a9..50b9177a 100755 --- a/input/FeatureLiterature.py +++ b/input/FeatureLiterature.py @@ -75,36 +75,21 @@ def ratio_number_binders(num_mutation, num_wild_type): return "NA" -def rna_expression_mutation(props, rna_avail): - ''' +def rna_expression_mutation(transcript_expression, vaf_rna): + """ This function calculates the product of VAF in RNA and transcript expression to reflect the expression of the mutated transcript - ''' - transcript_expression = props["transcript_expression"] - patient_id = properties_manager.get_hla_allele(props) - try: - rna_avail = rna_avail[patient_id] - except (KeyError, ValueError) as e: - rna_avail = "NA" - logger.info("rna_avail: ".format(rna_avail)) - if rna_avail == "False": - vaf_rna = props["VAF_in_tumor"] - else: - try: - vaf_rna = props["VAF_in_RNA"] - except KeyError: - vaf_rna = props["VAF_in_tumor"] + """ try: return str(float(transcript_expression) * float(vaf_rna)) if float(vaf_rna) > 0 else "NA" except ValueError: return "NA" -def expression_mutation_tc(props, tumour_content): - '''calculated expression of mutation corrected by tumour content - ''' - transcript_expression = props["Expression_Mutated_Transcript"] - patient_id = properties_manager.get_patient_id(props) +def expression_mutation_tc(transcript_expression, patient_id, tumour_content): + """ + calculated expression of mutation corrected by tumour content + """ try: tumour_content = float(tumour_content[patient_id]) / 100 except (KeyError, ValueError) as e: @@ -150,25 +135,11 @@ def calc_logistic_function(mhc_score): return "NA" -def calc_priority_score(props, multiple_binding=False): - ''' +def calc_priority_score(vaf_tumor, vaf_rna, transcript_expr, no_mismatch, score_mut, score_wt, mut_in_prot): + """ This function calculates the Priority Score using parameters for mhc I. - ''' - vaf_tumor = props["VAF_in_tumor"] - try: - vaf_rna = props["VAF_in_RNA"] - except KeyError: - vaf_tumor = props["VAF_in_tumor"] - transcript_expr = props["transcript_expression"] - no_mismatch = props["Number_of_mismatches_mhcI"] - if multiple_binding: - score_mut = props["MB_score_top10_harmonic"] - score_wt = props["MB_score_WT_top10_harmonic"] - else: - score_mut = props["best%Rank_netmhcpan4"] - score_wt = props["best%Rank_netmhcpan4_WT"] - mut_in_prot = props["mutation_found_in_proteome"] - # TODO: is this a bug? + """ + # TODO: Franziska is this a bug? It is reversing its value if mut_in_prot == "False" : mut_in_prot = "1" if mut_in_prot == "True" : mut_in_prot = "0" L_mut = calc_logistic_function(score_mut) diff --git a/input/MixMHCpred/mixmhc2pred.py b/input/MixMHCpred/mixmhc2pred.py index 6f2b2fad..12cd19a7 100755 --- a/input/MixMHCpred/mixmhc2pred.py +++ b/input/MixMHCpred/mixmhc2pred.py @@ -42,11 +42,10 @@ def load_available_allelles(self): avail_alleles.append(line1) return avail_alleles - def mut_position_xmer_seq(self, props): - '''returns position of mutation in xmer sequence - ''' - xmer_wt = props["X.WT._..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."] - xmer_mut = props["X..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."] + def mut_position_xmer_seq(self, xmer_wt, xmer_mut): + """ + returns position of mutation in xmer sequence + """ p1 = -1 if len(xmer_wt) == len(xmer_mut): p1 = -1 @@ -61,15 +60,12 @@ def mut_position_xmer_seq(self, props): p1 += 1 return str(p1) - def generate_nmers(self, props, list_lengths, mut=True): + def generate_nmers(self, xmer_wt, xmer_mut, list_lengths): ''' generates peptides covering mutation of all lengths that are provided. Returns peptides as list ''' - xmer_wt = props["X.WT._..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."] - xmer_mut = props["X..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."] length_mut = len(xmer_mut) list_peptides = [] - pos_mut = int(self.mut_position_xmer_seq(props)) - long_seq = xmer_mut if mut else xmer_wt + pos_mut = int(self.mut_position_xmer_seq(xmer_mut=xmer_mut, xmer_wt=xmer_wt)) for l in list_lengths: l = int(l) if l <= length_mut: @@ -80,7 +76,7 @@ def generate_nmers(self, props, list_lengths, mut=True): ends = [] [ends.append(int(s + (l))) for s in starts] for s, e in zip(starts, ends): - list_peptides.append(long_seq[s:e]) + list_peptides.append(xmer_mut[s:e]) list_peptides_fil = [] [list_peptides_fil.append(x) for x in list_peptides if not x == ""] return list_peptides_fil @@ -209,11 +205,9 @@ def add_best_epitope_info(self, epitope_tuple, column_name): except IndexError: return "NA" - def extract_WT_for_best(self, props, best_mut_seq): + def extract_WT_for_best(self, xmer_wt, xmer_mut, best_mut_seq): '''extracts the corresponding WT epitope for best predicted mutated epitope ''' - xmer_wt = props["X.WT._..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."] - xmer_mut = props["X..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."] start = xmer_mut.find(best_mut_seq) l = len(best_mut_seq) wt_epi = xmer_wt[start:(start + l)] @@ -253,16 +247,15 @@ def import_available_HLAII_alleles(self, path_to_HLAII_file): avail_alleles.append(line1) return avail_alleles - def main(self, props_dict, dict_patient_hlaII): + def main(self, alleles, xmer_wt, xmer_mut): '''Wrapper for MHC binding prediction, extraction of best epitope and check if mutation is directed to TCR ''' tmp_prediction = intermediate_files.create_temp_file(prefix="mixmhc2pred", suffix=".txt") # prediction for peptides of length 13 to 18 based on Suppl Fig. 6 a in Racle, J., et al. # Robust prediction of HLA class II epitopes by deep motif deconvolution of immunopeptidomes. # Nat. Biotech. (2019). - seqs = self.generate_nmers(props_dict, [13, 14, 15, 16, 17, 18]) - tmp_fasta = intermediate_files.generate_fasta(seqs, prefix="tmp_sequence_") - alleles = properties_manager.get_hla_allele(props_dict, dict_patient_hlaII) + seqs = self.generate_nmers(xmer_wt=xmer_wt, xmer_mut=xmer_mut, list_lengths=list[13, 14, 15, 16, 17, 18]) + tmp_fasta = intermediate_files.create_temp_fasta(seqs, prefix="tmp_sequence_") # try except statement to prevent stop of input for mps shorter < 13aa try: self.mixmhc2prediction(alleles, tmp_fasta, tmp_prediction) @@ -285,10 +278,10 @@ def main(self, props_dict, dict_patient_hlaII): self.all_ranks = "|".join(pred_all["%Rank"]) self.all_alleles = "|".join(pred_all["BestAllele"]) # prediction of for wt epitope that correspond to best epitope - wt = self.extract_WT_for_best(props_dict, self.best_peptide) + wt = self.extract_WT_for_best(xmer_wt=xmer_wt, xmer_mut=xmer_mut, best_mut_seq=self.best_peptide) wt_list = [wt] tmp_prediction = intermediate_files.create_temp_file(prefix="mixmhc2pred_wt_", suffix=".txt") - tmp_fasta = intermediate_files.generate_fasta(wt_list, prefix="tmp_sequence_wt_") + tmp_fasta = intermediate_files.create_temp_fasta(wt_list, prefix="tmp_sequence_wt_") self.mixmhc2prediction([self.best_allele], tmp_fasta, tmp_prediction, wt=True) pred_wt = self.read_mixmhcpred(tmp_prediction) self.best_peptide_wt = self.extract_WT_info(pred_wt, "Peptide") diff --git a/input/MixMHCpred/mixmhcpred.py b/input/MixMHCpred/mixmhcpred.py index 23555305..89ec156e 100755 --- a/input/MixMHCpred/mixmhcpred.py +++ b/input/MixMHCpred/mixmhcpred.py @@ -27,11 +27,9 @@ def __init__(self, runner, configuration): self.best_rank_wt = "NA" self.difference_score_mut_wt = "NA" - def mut_position_xmer_seq(self, props): + def mut_position_xmer_seq(self, xmer_wt, xmer_mut): '''returns position of mutation in xmer sequence ''' - xmer_wt = props["X.WT._..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."] - xmer_mut = props["X..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."] p1 = -1 if len(xmer_wt) == len(xmer_mut): p1 = -1 @@ -46,14 +44,11 @@ def mut_position_xmer_seq(self, props): p1 += 1 return str(p1) - def generate_nmers(self, props, list_lengths, mut=True): + def generate_nmers(self, xmer_wt, xmer_mut, list_lengths): ''' generates peptides covering mutation of all lengts that are provided. Returns peptides as list ''' - xmer_wt = props["X.WT._..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."] - xmer_mut = props["X..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."] list_peptides = [] - pos_mut = int(self.mut_position_xmer_seq(props)) - long_seq = xmer_mut if mut else xmer_wt + pos_mut = int(self.mut_position_xmer_seq(xmer_wt=xmer_wt, xmer_mut=xmer_mut)) for l in list_lengths: l = int(l) start_first = pos_mut - (l) @@ -63,7 +58,7 @@ def generate_nmers(self, props, list_lengths, mut=True): ends = [] [ends.append(int(s + (l))) for s in starts] for s, e in zip(starts, ends): - list_peptides.append(long_seq[s:e]) + list_peptides.append(xmer_mut[s:e]) return list_peptides def mixmhcprediction(self, hla_alleles, tmpfasta, outtmp): @@ -159,11 +154,9 @@ def add_best_epitope_info(self, epitope_tuple, column_name): except IndexError: return "NA" - def extract_WT_for_best(self, props, best_mut_seq): + def extract_WT_for_best(self, xmer_wt, xmer_mut, best_mut_seq): '''extracts the corresponding WT epitope for best predicted mutated epitope ''' - xmer_wt = props["X.WT._..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."] - xmer_mut = props["X..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."] start = xmer_mut.find(best_mut_seq) l = len(best_mut_seq) wt_epi = xmer_wt[start:(start + l)] @@ -188,13 +181,12 @@ def difference_score(self, mut_score, wt_score): except ValueError: return "NA" - def main(self, props_dict, dict_patient_hla): + def main(self, xmer_wt, xmer_mut, alleles): '''Wrapper for MHC binding prediction, extraction of best epitope and check if mutation is directed to TCR ''' tmp_prediction = intermediate_files.create_temp_file(prefix="mixmhcpred", suffix=".txt") - seqs = self.generate_nmers(props_dict, [8, 9, 10, 11]) - tmp_fasta = intermediate_files.generate_fasta(seqs, prefix="tmp_sequence_") - alleles = properties_manager.get_hla_allele(props_dict, dict_patient_hla) + seqs = self.generate_nmers(xmer_wt=xmer_wt, xmer_mut=xmer_mut, list_lengths=[8, 9, 10, 11]) + tmp_fasta = intermediate_files.create_temp_fasta(seqs, prefix="tmp_sequence_") self.mixmhcprediction(alleles, tmp_fasta, tmp_prediction) pred = self.read_mixmhcpred(tmp_prediction) try: @@ -213,10 +205,10 @@ def main(self, props_dict, dict_patient_hla): self.all_ranks = "|".join(pred_all["%Rank_bestAllele"]) self.all_alleles = "|".join(pred_all["BestAllele"]) # prediction of for wt epitope that correspond to best epitope - wt = self.extract_WT_for_best(props_dict, self.best_peptide) + wt = self.extract_WT_for_best(xmer_wt=xmer_wt, xmer_mut=xmer_mut, best_mut_seq=self.best_peptide) wt_list = [wt] tmp_prediction = intermediate_files.create_temp_file(prefix="mixmhcpred_wt_", suffix=".txt") - tmp_fasta = intermediate_files.generate_fasta(wt_list, prefix="tmp_sequence_wt_") + tmp_fasta = intermediate_files.create_temp_fasta(wt_list, prefix="tmp_sequence_wt_") self.mixmhcprediction(alleles, tmp_fasta, tmp_prediction) pred_wt = self.read_mixmhcpred(tmp_prediction) logger.debug(pred_wt) diff --git a/input/dissimilarity_garnish/dissimilaritycalculator.py b/input/dissimilarity_garnish/dissimilaritycalculator.py index 28887c13..ecb88555 100755 --- a/input/dissimilarity_garnish/dissimilaritycalculator.py +++ b/input/dissimilarity_garnish/dissimilaritycalculator.py @@ -44,18 +44,16 @@ def _calc_dissimilarity(self, fasta_file, n, references): os.remove(outfile) return x_dis - def calculate_dissimilarity(self, props, fastafile, references, filter_binder=False): + def calculate_dissimilarity(self, mhc_mutation, mhc_affinity, fastafile, references, filter_binder=False): '''wrapper for dissimilarity calculation ''' - mhc_mut = props["best_affinity_epitope_netmhcpan4"] - mhc_aff = props["best_affinity_netmhcpan4"] with open(fastafile, "w") as f: id = ">M_1" f.write(id + "\n") - f.write(mhc_mut + "\n") + f.write(mhc_mutation + "\n") dissim = self._calc_dissimilarity(fastafile, id, references) if filter_binder: - if float(mhc_aff) < 500: + if float(mhc_affinity) < 500: sc = str(dissim) if dissim != "NA" else "0" else: sc = "NA" diff --git a/input/epitope.py b/input/epitope.py index cf371119..72e3df98 100755 --- a/input/epitope.py +++ b/input/epitope.py @@ -63,7 +63,10 @@ def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aa """ Calculate new epitope features and add to dictonary that stores all properties """ self.properties = self.init_properties(col_nam, prop_list) - logger.info(self.properties["X..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."]) + xmer_wt = self.properties["X.WT._..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."] + xmer_mut = self.properties["X..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."] + alleles = properties_manager.get_hla_allele(self.properties, patient_hlaI) + logger.info(xmer_mut) wild_type_mhci, mutation_mhci = properties_manager.get_epitopes( properties=self.properties, mhc=MHC_I) @@ -92,7 +95,9 @@ def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aa self.add_aminoacid_index_features(aaindex1_dict, aaindex2_dict) - self.add_provean_score_features(patient_hlaI, set_available_mhc) + alleles = properties_manager.get_hla_allele(self.properties, patient_hlaI) + self.add_provean_score_features( + xmer_wt=xmer_wt, xmer_mut=xmer_mut, alleles=alleles, set_available_mhc=set_available_mhc) self.add_netmhcpan4_features() @@ -132,13 +137,13 @@ def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aa score_wild_type=self.properties["MB_score_WT_top10_harmonic"].replace(",", ".")), "Amplitude_mhcI_MB") # position of mutation - wild_type_netmhcpan4, mutation_netmhcpan4 = properties_manager.get_wild_type_and_mutation_from_netmhcpan4( + wild_type_netmhcpan4, mutation_netmhcpan4 = properties_manager.get_netmhcpan4_epitopes( properties=self.properties) self.add_features(self_similarity.position_of_mutation_epitope( wild_type=wild_type_netmhcpan4, mutation=mutation_netmhcpan4), "pos_MUT_MHCI_affinity_epi") # position of mutation - wild_type_netmhcpan4_9mer, mutation_netmhcpan4_9mer = properties_manager.get_wild_type_and_mutation_from_netmhcpan4( + wild_type_netmhcpan4_9mer, mutation_netmhcpan4_9mer = properties_manager.get_netmhcpan4_epitopes( properties=self.properties, nine_mer=True) self.add_features(self_similarity.position_of_mutation_epitope( wild_type=wild_type_netmhcpan4_9mer, mutation=mutation_netmhcpan4_9mer),"pos_MUT_MHCI_affinity_epi_9mer") @@ -249,10 +254,8 @@ def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aa amplitude_cutoff=amplitude_cutoff_mhcii, category="ADN"), "ADN_mhcII") # netMHCIIpan predictions - sequence = self.properties["X..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."] - sequence_reference = self.properties["X.WT._..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."] - alleles = properties_manager.get_hla_allele(self.properties, patient_hlaII) - self.predII.main(sequence=sequence, sequence_reference=sequence_reference, alleles=alleles, + alleles_hlaII = properties_manager.get_hla_allele(self.properties, patient_hlaII) + self.predII.main(sequence=xmer_mut, sequence_reference=xmer_wt, alleles=alleles_hlaII, set_available_mhc=set_available_mhcII) # netmhcpan4 MUT scores @@ -370,13 +373,35 @@ def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aa self.add_features(FeatureLiterature.match_in_proteome( sequence=self.properties["X..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."], db=db), "mutation_found_in_proteome") - self.add_features(FeatureLiterature.calc_priority_score(self.properties), "Priority_score") + + vaf_tumor = self.properties["VAF_in_tumor"] + vaf_rna = self.properties.get("VAF_in_RNA") # TODO: Franziska what do we want to do when there is no value? + transcript_expr = self.properties["transcript_expression"] + no_mismatch = self.properties["Number_of_mismatches_mhcI"] + score_mut = self.properties["best%Rank_netmhcpan4"] + score_wt = self.properties["best%Rank_netmhcpan4_WT"] + mut_in_prot = self.properties["mutation_found_in_proteome"] + + self.add_features(FeatureLiterature.calc_priority_score( + vaf_tumor=vaf_tumor, vaf_rna=vaf_rna, transcript_expr=transcript_expr, no_mismatch=no_mismatch, + score_mut=score_mut, score_wt=score_wt, mut_in_prot=mut_in_prot), "Priority_score") # priority score using multiplexed representation score - self.add_features(FeatureLiterature.calc_priority_score(self.properties, True), "Priority_score_MB") + score_mut = self.properties["MB_score_top10_harmonic"] + score_wt = self.properties["MB_score_WT_top10_harmonic"] + self.add_features(FeatureLiterature.calc_priority_score( + vaf_tumor=vaf_tumor, vaf_rna=vaf_rna, transcript_expr=transcript_expr, no_mismatch=no_mismatch, + score_mut=score_mut, score_wt=score_wt, mut_in_prot=mut_in_prot), "Priority_score_MB") # neoag immunogenicity model - self.add_features(self.neoag_calculator.wrapper_neoag(self.properties), "neoag_immunogencity") + sample_id = properties_manager.get_patient_id(self.properties) + mut_peptide = self.properties["best_affinity_epitope_netmhcpan4"] + score_mut = self.properties["best_affinity_netmhcpan4"] + ref_peptide = self.properties["best_affinity_epitope_netmhcpan4_WT"] + peptide_variant_position = self.properties["pos_MUT_MHCI_affinity_epi"] + self.add_features(self.neoag_calculator.wrapper_neoag( + sample_id=sample_id, mut_peptide=mut_peptide, score_mut=score_mut, ref_peptide=ref_peptide, + peptide_variant_position=peptide_variant_position), "neoag_immunogencity") # IEDB immunogenicity only for epitopes with affinity < 500 nM (predicted with netMHCpan) --> in publications mhci_epitope = self.properties["best_affinity_epitope_netmhcpan4"] @@ -392,18 +417,22 @@ def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aa epitope=mhci_epitope, mhc_allele=mhci_allele, mhc_score=mhci_score, affin_filtering=True), "IEDB_Immunogenicity_mhcI_affinity_filtered") - self.add_mix_mhc_pred_features(patient_hlaI) + self.add_mix_mhc_pred_features(xmer_wt=xmer_wt, xmer_mut=xmer_mut, patient_hlaI=patient_hlaI) - self.add_mix_mhc2_pred_features(patient_hlaII) + self.add_mix_mhc2_pred_features(xmer_mut=xmer_mut, xmer_wt=xmer_wt, patient_hlaII=patient_hlaII) # dissimilarity to self-proteome # neoantigen fitness tmp_fasta = intermediate_files.create_temp_file(prefix="tmpseq", suffix=".fasta") + mhc_mutation = self.properties["best_affinity_epitope_netmhcpan4"] + mhc_affinity = self.properties["best_affinity_netmhcpan4"] self.add_features(self.dissimilarity_calculator.calculate_dissimilarity( - self.properties, tmp_fasta, self.references), "dissimilarity") + mhc_mutation=mhc_mutation, mhc_affinity=mhc_affinity, fastafile=tmp_fasta, references=self.references), + "dissimilarity") self.add_features(self.dissimilarity_calculator.calculate_dissimilarity( - self.properties, tmp_fasta, self.references, filter_binder=True), "dissimilarity_filter500") + mhc_mutation=mhc_mutation, mhc_affinity=mhc_affinity, fastafile=tmp_fasta, references=self.references, + filter_binder=True), "dissimilarity_filter500") self.add_vax_rank_features() @@ -412,13 +441,15 @@ def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aa def add_vax_rank_features(self): # vaxrank vaxrankscore = vaxrank.VaxRank() - vaxrankscore.main(self.properties) + vaxrankscore.main(mutation_scores=self.properties["MB_affinities"], + expression_score=self.properties["Expression_Mutated_Transcript"]) self.add_features(vaxrankscore.total_binding_score, "vaxrank_binding_score") self.add_features(vaxrankscore.ranking_score, "vaxrank_total_score") - def add_mix_mhc2_pred_features(self, patient_hlaII): + def add_mix_mhc2_pred_features(self, xmer_wt, xmer_mut, patient_hlaII): # MixMHC2pred - self.predpresentation2.main(self.properties, patient_hlaII) + alleles = properties_manager.get_hla_allele(self.properties, patient_hlaII) + self.predpresentation2.main(alleles=alleles, xmer_wt=xmer_wt, xmer_mut=xmer_mut) self.add_features(self.predpresentation2.all_peptides, "MixMHC2pred_all_peptides") self.add_features(self.predpresentation2.all_ranks, "MixMHC2pred_all_ranks") self.add_features(self.predpresentation2.all_alleles, "MixMHC2pred_all_alleles") @@ -429,9 +460,10 @@ def add_mix_mhc2_pred_features(self, patient_hlaII): self.add_features(self.predpresentation2.best_rank_wt, "MixMHC2pred_best_rank_wt") self.add_features(self.predpresentation2.difference_score_mut_wt, "MixMHC2pred_difference_rank_mut_wt") - def add_mix_mhc_pred_features(self, patient_hlaI): + def add_mix_mhc_pred_features(self, xmer_wt, xmer_mut, patient_hlaI): # MixMHCpred - self.predpresentation.main(self.properties, patient_hlaI) + alleles = properties_manager.get_hla_allele(self.properties, patient_hlaI) + self.predpresentation.main(xmer_wt=xmer_wt, xmer_mut=xmer_mut, alleles=alleles) self.add_features(self.predpresentation.all_peptides, "MixMHCpred_all_peptides") self.add_features(self.predpresentation.all_scores, "MixMHCpred_all_scores") self.add_features(self.predpresentation.all_ranks, "MixMHCpred_all_ranks") @@ -574,7 +606,7 @@ def add_netmhcpan4_features(self): self.add_features(self.pred.mhcI_affinity_allele_9mer, "bestHLA_allele_affinity_netmhcpan4_9mer") self.add_features(self.pred.mhcI_affinity_epitope_9mer, "best_affinity_epitope_netmhcpan4_9mer") - def add_provean_score_features(self, patient_hlaI, set_available_mhc): + def add_provean_score_features(self, xmer_mut, xmer_wt, alleles, set_available_mhc): # PROVEAN score ucsc_id = self.provean_annotator.build_ucsc_id_plus_position( substitution=self.properties["substitution"], ucsc_id=self.properties["UCSC_transcript"]) @@ -582,7 +614,7 @@ def add_provean_score_features(self, patient_hlaI, set_available_mhc): self.add_features(self.provean_annotator.get_provean_annotation( mutated_aminoacid=self.properties['MUT_AA'], ucsc_id_position=ucsc_id), "PROVEAN_score") - self.pred.main(self.properties, patient_hlaI, set_available_mhc) + self.pred.main(xmer_mut=xmer_mut, xmer_wt=xmer_wt, alleles=alleles, set_available_mhc=set_available_mhc) def add_aminoacid_index_features(self, aaindex1_dict, aaindex2_dict): # amino acid index @@ -607,9 +639,18 @@ def add_aminoacid_frequency_features(self, aa_freq_dict, mutated_aminoacid, muta def add_expression_features(self, rna_avail, tumour_content): # expression - self.add_features(FeatureLiterature.rna_expression_mutation(self.properties, rna_avail=rna_avail), - "Expression_Mutated_Transcript") - self.add_features(FeatureLiterature.expression_mutation_tc(self.properties, tumour_content=tumour_content), + transcript_expression = self.properties["Expression_Mutated_Transcript"] + patient_id = properties_manager.get_patient_id(self.properties) + vaf_tumor = self.properties["VAF_in_tumor"] + # TODO: Franziska please, review this. I think this is what was meant, but it was not what the code was doing + vaf_rna = vaf_tumor if rna_avail.get(patient_id, "False") == "False" else \ + self.properties.get("VAF_in_RNA", vaf_tumor) + + self.add_features(FeatureLiterature.rna_expression_mutation( + transcript_expression=transcript_expression, vaf_rna=vaf_rna), "Expression_Mutated_Transcript") + + self.add_features(FeatureLiterature.expression_mutation_tc( + transcript_expression=transcript_expression, patient_id=patient_id, tumour_content=tumour_content), "Expression_Mutated_Transcript_tumor_content") def add_differential_agretopicity_index_features(self, mutation_mhci, mutation_mhcii, wild_type_mhci, diff --git a/input/helpers/intermediate_files.py b/input/helpers/intermediate_files.py index 3e64f995..c5377e03 100755 --- a/input/helpers/intermediate_files.py +++ b/input/helpers/intermediate_files.py @@ -6,7 +6,7 @@ def create_temp_file(prefix=None, suffix=None, dir=None): return temp_file.name -def generate_fasta(sequences, prefix=None): +def create_temp_fasta(sequences, prefix=None): """ Writes seqs given in seqs list into fasta file """ diff --git a/input/netmhcIIpan/combine_netmhcIIpan_pred_multiple_binders.py b/input/netmhcIIpan/combine_netmhcIIpan_pred_multiple_binders.py index ed801b20..acd5fccb 100755 --- a/input/netmhcIIpan/combine_netmhcIIpan_pred_multiple_binders.py +++ b/input/netmhcIIpan/combine_netmhcIIpan_pred_multiple_binders.py @@ -78,7 +78,7 @@ def main(self, sequence, sequence_reference, alleles, set_available_mhc): logger.debug(tmp_prediction) np = netmhcIIpan_prediction.NetMhcIIPanBestPrediction(runner=self.runner, configuration=self.configuration) mb = multiple_binders.MultipleBinding(runner=self.runner, configuration=self.configuration) - tmp_fasta = intermediate_files.generate_fasta([sequence], prefix="tmp_singleseq_") + tmp_fasta = intermediate_files.create_temp_fasta([sequence], prefix="tmp_singleseq_") alleles_formated = np.generate_mhcII_alelles_combination_list(alleles, set_available_mhc) logger.debug(alleles_formated) np.mhcII_prediction(alleles, set_available_mhc, tmp_fasta, tmp_prediction) @@ -119,7 +119,7 @@ def main(self, sequence, sequence_reference, alleles, set_available_mhc): logger.debug(tmp_prediction) np = netmhcIIpan_prediction.NetMhcIIPanBestPrediction(runner=self.runner, configuration=self.configuration) mb = multiple_binders.MultipleBinding(runner=self.runner, configuration=self.configuration) - tmp_fasta = intermediate_files.generate_fasta([sequence_reference], prefix="tmp_singleseq_") + tmp_fasta = intermediate_files.create_temp_fasta([sequence_reference], prefix="tmp_singleseq_") np.mhcII_prediction(alleles, set_available_mhc, tmp_fasta, tmp_prediction) try: preds = np.filter_binding_predictions(position_xmer_sequence, tmp_prediction) diff --git a/input/netmhcIIpan/netmhcIIpan_prediction.py b/input/netmhcIIpan/netmhcIIpan_prediction.py index 5bc6f9e9..eebe0f3c 100755 --- a/input/netmhcIIpan/netmhcIIpan_prediction.py +++ b/input/netmhcIIpan/netmhcIIpan_prediction.py @@ -220,7 +220,7 @@ def main(self, props_dict, set_available_mhc, dict_patient_hla): ''' tmp_prediction = intermediate_files.create_temp_file(prefix="netmhcpanpred_", suffix=".csv") sequence = props_dict["X..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."] - tmp_fasta = intermediate_files.generate_fasta([sequence], prefix="tmp_singleseq_") + tmp_fasta = intermediate_files.create_temp_fasta([sequence], prefix="tmp_singleseq_") alleles = properties_manager.get_hla_allele(props_dict, dict_patient_hla) self.mhcII_prediction(alleles, set_available_mhc, tmp_fasta, tmp_prediction) sequence_reference = props_dict["X.WT._..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."] diff --git a/input/netmhcpan4/combine_netmhcpan_pred_multiple_binders.py b/input/netmhcpan4/combine_netmhcpan_pred_multiple_binders.py index 64d34dde..465f66e7 100755 --- a/input/netmhcpan4/combine_netmhcpan_pred_multiple_binders.py +++ b/input/netmhcpan4/combine_netmhcpan_pred_multiple_binders.py @@ -76,23 +76,22 @@ def MHC_MB_score_best_per_allele(self, tuple_best_per_allele): else: return ["NA", "NA", "NA"] - def main(self, epi_dict, patient_hlaI, set_available_mhc): - '''predicts MHC epitopes; returns on one hand best binder and on the other hand multiple binder analysis is performed - ''' + def main(self, xmer_wt, xmer_mut, alleles, set_available_mhc): + """ + predicts MHC epitopes; returns on one hand best binder and on the other hand multiple binder analysis is performed + """ ### PREDICTION FOR MUTATED SEQUENCE - xmer_mut = epi_dict["X..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."] logger.info("MUT seq: {}".format(xmer_mut)) tmp_prediction = intermediate_files.create_temp_file(prefix="netmhcpanpred_", suffix=".csv") logger.debug(tmp_prediction) np = netmhcpan_prediction.NetMhcPanBestPrediction(runner=self.runner, configuration=self.configuration) mb = multiple_binders.MultipleBinding(runner=self.runner, configuration=self.configuration) - tmp_fasta = intermediate_files.generate_fasta(sequences=[epi_dict["X..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."]], - prefix="tmp_singleseq_") - alleles = properties_manager.get_hla_allele(epi_dict, patient_hlaI) + tmp_fasta = intermediate_files.create_temp_fasta(sequences=[xmer_mut], prefix="tmp_singleseq_") # print alleles np.mhc_prediction(alleles, set_available_mhc, tmp_fasta, tmp_prediction) - epi_dict["Position_Xmer_Seq"] = np.mut_position_xmer_seq(epi_dict) - preds = np.filter_binding_predictions(epi_dict, tmp_prediction) + + position_xmer = np.mut_position_xmer_seq(xmer_mut=xmer_mut, xmer_wt=xmer_wt) + preds = np.filter_binding_predictions(position_xmer=position_xmer, tmppred=tmp_prediction) # multiple binding list_tups = mb.generate_epi_tuple(preds) @@ -118,12 +117,13 @@ def main(self, epi_dict, patient_hlaI, set_available_mhc): self.best4_mhc_score = np.add_best_epitope_info(best_epi, "%Rank") self.best4_mhc_epitope = np.add_best_epitope_info(best_epi, "Peptide") self.best4_mhc_allele = np.add_best_epitope_info(best_epi, "HLA") - self.directed_to_TCR = np.mutation_in_loop(epi_dict, best_epi) + self.directed_to_TCR = np.mutation_in_loop(position_xmer=position_xmer, epitope_tuple=best_epi) best_epi_affinity = np.minimal_binding_score(preds, rank=False) self.best4_affinity = np.add_best_epitope_info(best_epi_affinity, "Aff(nM)") self.best4_affinity_epitope = np.add_best_epitope_info(best_epi_affinity, "Peptide") self.best4_affinity_allele = np.add_best_epitope_info(best_epi_affinity, "HLA") - self.best4_affinity_directed_to_TCR = np.mutation_in_loop(epi_dict, best_epi_affinity) + self.best4_affinity_directed_to_TCR = np.mutation_in_loop( + position_xmer=position_xmer, epitope_tuple=best_epi_affinity) # multiple binding based on affinity self.generator_rate = mb.determine_number_of_binders(list_scores=all_affinities, threshold=50) # best predicted epitope of length 9 @@ -142,10 +142,10 @@ def main(self, epi_dict, patient_hlaI, set_available_mhc): logger.debug(tmp_prediction) np = netmhcpan_prediction.NetMhcPanBestPrediction(runner=self.runner, configuration=self.configuration) mb = multiple_binders.MultipleBinding(runner=self.runner, configuration=self.configuration) - tmp_fasta = intermediate_files.generate_fasta(sequences=[epi_dict["X.WT._..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."]], - prefix="tmp_singleseq_") + tmp_fasta = intermediate_files.create_temp_fasta(sequences=[xmer_wt], + prefix="tmp_singleseq_") np.mhc_prediction(alleles, set_available_mhc, tmp_fasta, tmp_prediction) - preds = np.filter_binding_predictions(epi_dict, tmp_prediction) + preds = np.filter_binding_predictions(position_xmer=position_xmer, tmppred=tmp_prediction) # multiple binding list_tups = mb.generate_epi_tuple(preds) self.MHC_epitope_scores_WT = "/".join([tup[0] for tup in list_tups]) diff --git a/input/netmhcpan4/netmhcpan_prediction.py b/input/netmhcpan4/netmhcpan_prediction.py index b45e0b3b..9aa584a5 100755 --- a/input/netmhcpan4/netmhcpan_prediction.py +++ b/input/netmhcpan4/netmhcpan_prediction.py @@ -67,11 +67,9 @@ def mhc_prediction(self, hla_alleles, set_available_mhc, tmpfasta, tmppred): line = ";".join(line) f.write(line + "\n") - def mut_position_xmer_seq(self, props): + def mut_position_xmer_seq(self, xmer_wt, xmer_mut): '''returns position of mutation in xmer sequence ''' - xmer_wt = props["X.WT._..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."] - xmer_mut = props["X..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."] if len(xmer_wt) == len(xmer_mut): p1 = -1 for i, aa in enumerate(xmer_mut): @@ -96,10 +94,9 @@ def epitope_covers_mutation(self, position_mutation, position_epitope, length_ep cover = True return cover - def filter_binding_predictions(self, props, tmppred): + def filter_binding_predictions(self, position_xmer, tmppred): '''filters prediction file for predicted epitopes that cover mutations ''' - pos_xmer = props["Position_Xmer_Seq"] dat_prediction = data_import.import_dat_general(tmppred) dat = dat_prediction[1] dat_head = dat_prediction[0] @@ -107,7 +104,7 @@ def filter_binding_predictions(self, props, tmppred): pos_epi = dat_head.index("Pos") epi = dat_head.index("Peptide") for ii, i in enumerate(dat): - if self.epitope_covers_mutation(pos_xmer, i[pos_epi], len(i[epi])): + if self.epitope_covers_mutation(position_xmer, i[pos_epi], len(i[epi])): dat_fil.append(dat[ii]) return dat_head, dat_fil @@ -141,10 +138,10 @@ def add_best_epitope_info(self, epitope_tuple, column_name): except IndexError: return "NA" - def mutation_in_loop(self, props, epitope_tuple): - '''returns if mutation is directed to TCR (yes or no) - ''' - pos_xmer = props["Position_Xmer_Seq"] + def mutation_in_loop(self, position_xmer, epitope_tuple): + """ + returns if mutation is directed to TCR (yes or no) + """ dat_head = epitope_tuple[0] dat_epi = epitope_tuple[1] pos_epi = dat_head.index("Pos") @@ -156,7 +153,7 @@ def mutation_in_loop(self, props, epitope_tuple): pos = int(dat_epi[pos_epi]) start = pos + int(dat_epi[del_pos]) - 1 end = start + int(dat_epi[del_len]) - if start < int(pos_xmer) <= end: + if start < int(position_xmer) <= end: directed_to_TCR = "yes" return directed_to_TCR except IndexError: @@ -186,23 +183,6 @@ def Hamming_check_0_or_1(self, seq1, seq2): return errors return errors - def filter_for_WT_epitope_same_allele(self, prediction_tuple, mut_seq, mut_allele): - '''returns wt epitope info for given mutated sequence. here best wt for same allele as mutated sequences - ''' - dat_head = prediction_tuple[0] - dat = prediction_tuple[1] - seq_col = dat_head.index("Peptide") - allele_col = dat_head.index("HLA") - wt_epi = "NA" - for ii, i in enumerate(dat): - wt_seq = i[seq_col] - wt_allele = i[allele_col] - if (len(wt_seq) == len(mut_seq)) and wt_allele == mut_allele: - numb_mismatch = self.Hamming_check_0_or_1(mut_seq, wt_seq) - if numb_mismatch == 1: - wt_epi = i - return dat_head, wt_epi - def filter_for_WT_epitope(self, prediction_tuple, mut_seq, mut_allele): '''returns wt epitope info for given mutated sequence. best wt that is allowed to bind to any allele of patient ''' @@ -222,41 +202,6 @@ def filter_for_WT_epitope(self, prediction_tuple, mut_seq, mut_allele): min = self.minimal_binding_score(dt) return (min) - def main(self, props_dict, set_available_mhc, dict_patient_hla): - '''Wrapper for MHC binding prediction, extraction of best epitope and check if mutation is directed to TCR - ''' - tmp_prediction = intermediate_files.create_temp_file(prefix="netmhcpanpred_", suffix=".csv") - print(tmp_prediction) - tmp_fasta = intermediate_files.generate_fasta(sequences=[props_dict["X..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."]], - prefix="tmp_singleseq_") - alleles = properties_manager.get_hla_allele(props_dict, dict_patient_hla) - self.mhc_prediction(alleles, set_available_mhc, tmp_fasta, tmp_prediction) - props_dict["Position_Xmer_Seq"] = self.mut_position_xmer_seq(props_dict) - preds = self.filter_binding_predictions(props_dict, tmp_prediction) - # print preds - best_epi = self.minimal_binding_score(preds) - best_epi_affinity = self.minimal_binding_score(preds, rank=False) - preds_9mer = self.filter_for_9mers(preds) - best_9mer = self.minimal_binding_score(preds_9mer) - best_9mer_affinity = self.minimal_binding_score(preds_9mer, rank=False) - self.mhc_score = self.add_best_epitope_info(best_epi, "%Rank") - self.epitope = self.add_best_epitope_info(best_epi, "Peptide") - self.allele = self.add_best_epitope_info(best_epi, "HLA") - self.directed_to_TCR = self.mutation_in_loop(props_dict, best_epi) - self.affinity = self.add_best_epitope_info(best_epi_affinity, "Aff(nM)") - self.affinity_epitope = self.add_best_epitope_info(best_epi_affinity, "Peptide") - self.affinity_allele = self.add_best_epitope_info(best_epi_affinity, "HLA") - self.affinity_directed_to_TCR = self.mutation_in_loop(props_dict, best_epi_affinity) - self.mhcI_score_9mer = self.add_best_epitope_info(best_9mer, "%Rank") - self.mhcI_score_allele_9mer = self.add_best_epitope_info(best_9mer, "HLA") - self.mhcI_score_epitope_9mer = self.add_best_epitope_info(best_9mer, "Peptide") - self.mhcI_affinity_9mer = self.add_best_epitope_info(best_9mer_affinity, "Aff(nM)") - self.mhcI_affinity_allele_9mer = self.add_best_epitope_info(best_9mer_affinity, "HLA") - self.mhcI_affinity_epitope_9mer = self.add_best_epitope_info(best_9mer_affinity, "Peptide") - print("mismatch") - print(self.Hamming_check_0_or_1("lsdcd", "lddcd")) - print(self.Hamming_check_0_or_1("lddcd", "lddcd")) - # if __name__ == '__main__': # diff --git a/input/tests/integration_tests/test_dissimilarity.py b/input/tests/integration_tests/test_dissimilarity.py index 603e614e..ce8431b1 100755 --- a/input/tests/integration_tests/test_dissimilarity.py +++ b/input/tests/integration_tests/test_dissimilarity.py @@ -14,7 +14,7 @@ def setUp(self): def test_dissimilarity(self): result = DissimilarityCalculator(runner=self.runner, configuration=self.configuration).calculate_dissimilarity( - props={'best_affinity_epitope_netmhcpan4': 'hey', 'best_affinity_netmhcpan4': 'ho'}, + mhc_mutation='hey', mhc_affinity='ho', fastafile=self.fastafile.name, references=self.references) self.assertEqual('0', result) diff --git a/input/vaxrank/vaxrank.py b/input/vaxrank/vaxrank.py index 1aa47178..de0b5547 100755 --- a/input/vaxrank/vaxrank.py +++ b/input/vaxrank/vaxrank.py @@ -70,24 +70,23 @@ def combined_score(self): except ValueError: return "NA" - def main(self, epi_dict): - mut_scores = epi_dict["MB_affinities"] - self.expression_score = epi_dict["Expression_Mutated_Transcript"] - self.total_binding_score = self.total_binding(mut_scores) + def main(self, mutation_scores, expression_score): + self.expression_score = expression_score + self.total_binding_score = self.total_binding(mutation_scores) self.ranking_score = self.combined_score() -if __name__ == '__main__': - # import epitope - # import predict_all_epitopes - # from helpers import data_import - - epi_dict = { - "MB_affinities": "2568.0/6085.8/582.9/18868.9/26941.9/3681.9/29802.4/38322.6/26393.7/527.4/15690.1/189.1/15413.3/834.6/18125.5/22573.8/11247.4/36754.7/21621.7/7136.1/20981.4/2814.9/38172.8/1398.2/20769.8/35079.3/29867.9/21218.6/19437.3/35460.1/28858.4/31746.6/7889.4/40069.6/43955.6/7185.5/19266.3/41141.1/2568.0/6085.8/582.9/18868.9/26941.9/3681.9/29802.4/38322.6/26393.7/527.4/15690.1/189.1/15413.3/834.6/18125.5/22573.8/11247.4/36754.7/21621.7/7136.1/20981.4/2814.9/38172.8/1398.2/20769.8/35079.3/29867.9/21218.6/19437.3/35460.1/28858.4/31746.6/7889.4/40069.6/43955.6/7185.5/19266.3/41141.1/13582.6/33153.6/30396.7/44630.4/41746.0/38070.1/40505.1/45367.0/43947.6/39591.2/2692.9/10750.1/17879.5/39429.2/45230.3/33230.2/29433.2/44502.6/37430.5/42170.9/39078.0/2488.5/34630.5/43600.9/40167.3/28268.1/43753.0/32705.8/36653.8/44132.0/26697.3/44069.0/42608.9/43093.9/45060.8/35449.8/42832.2/45441.2/13582.6/33153.6/30396.7/44630.4/41746.0/38070.1/40505.1/45367.0/43947.6/39591.2/2692.9/10750.1/17879.5/39429.2/45230.3/33230.2/29433.2/44502.6/37430.5/42170.9/39078.0/2488.5/34630.5/43600.9/40167.3/28268.1/43753.0/32705.8/36653.8/44132.0/26697.3/44069.0/42608.9/43093.9/45060.8/35449.8/42832.2/45441.2/13477.5/34902.1/35727.0/44343.5/34096.2/20217.5/42885.5/44374.7/43128.4/35133.2/23984.1/14154.1/20684.8/34442.9/43631.5/9376.9/21796.7/45814.9/30521.6/39908.7/32105.2/4218.7/18279.2/37758.8/20711.9/11696.2/45202.4/27644.4/27896.2/39722.5/23205.3/41291.8/27966.3/42898.0/42222.0/19525.7/40617.0/43220.4/13477.5/34902.1/35727.0/44343.5/34096.2/20217.5/42885.5/44374.7/43128.4/35133.2/23984.1/14154.1/20684.8/34442.9/43631.5/9376.9/21796.7/45814.9/30521.6/39908.7/32105.2/4218.7/18279.2/37758.8/20711.9/11696.2/45202.4/27644.4/27896.2/39722.5/23205.3/41291.8/27966.3/42898.0/42222.0/19525.7/40617.0/43220.4", - "Expression_Mutated_Transcript": "3.20194922282"} - - p = VaxRank() - p.main(epi_dict) - print("expression: " + p.expression_score) - print("binding score: " + p.total_binding_score) - print("total score: " + p.ranking_score) +# if __name__ == '__main__': +# # import epitope +# # import predict_all_epitopes +# # from helpers import data_import +# +# epi_dict = { +# "MB_affinities": "2568.0/6085.8/582.9/18868.9/26941.9/3681.9/29802.4/38322.6/26393.7/527.4/15690.1/189.1/15413.3/834.6/18125.5/22573.8/11247.4/36754.7/21621.7/7136.1/20981.4/2814.9/38172.8/1398.2/20769.8/35079.3/29867.9/21218.6/19437.3/35460.1/28858.4/31746.6/7889.4/40069.6/43955.6/7185.5/19266.3/41141.1/2568.0/6085.8/582.9/18868.9/26941.9/3681.9/29802.4/38322.6/26393.7/527.4/15690.1/189.1/15413.3/834.6/18125.5/22573.8/11247.4/36754.7/21621.7/7136.1/20981.4/2814.9/38172.8/1398.2/20769.8/35079.3/29867.9/21218.6/19437.3/35460.1/28858.4/31746.6/7889.4/40069.6/43955.6/7185.5/19266.3/41141.1/13582.6/33153.6/30396.7/44630.4/41746.0/38070.1/40505.1/45367.0/43947.6/39591.2/2692.9/10750.1/17879.5/39429.2/45230.3/33230.2/29433.2/44502.6/37430.5/42170.9/39078.0/2488.5/34630.5/43600.9/40167.3/28268.1/43753.0/32705.8/36653.8/44132.0/26697.3/44069.0/42608.9/43093.9/45060.8/35449.8/42832.2/45441.2/13582.6/33153.6/30396.7/44630.4/41746.0/38070.1/40505.1/45367.0/43947.6/39591.2/2692.9/10750.1/17879.5/39429.2/45230.3/33230.2/29433.2/44502.6/37430.5/42170.9/39078.0/2488.5/34630.5/43600.9/40167.3/28268.1/43753.0/32705.8/36653.8/44132.0/26697.3/44069.0/42608.9/43093.9/45060.8/35449.8/42832.2/45441.2/13477.5/34902.1/35727.0/44343.5/34096.2/20217.5/42885.5/44374.7/43128.4/35133.2/23984.1/14154.1/20684.8/34442.9/43631.5/9376.9/21796.7/45814.9/30521.6/39908.7/32105.2/4218.7/18279.2/37758.8/20711.9/11696.2/45202.4/27644.4/27896.2/39722.5/23205.3/41291.8/27966.3/42898.0/42222.0/19525.7/40617.0/43220.4/13477.5/34902.1/35727.0/44343.5/34096.2/20217.5/42885.5/44374.7/43128.4/35133.2/23984.1/14154.1/20684.8/34442.9/43631.5/9376.9/21796.7/45814.9/30521.6/39908.7/32105.2/4218.7/18279.2/37758.8/20711.9/11696.2/45202.4/27644.4/27896.2/39722.5/23205.3/41291.8/27966.3/42898.0/42222.0/19525.7/40617.0/43220.4", +# "Expression_Mutated_Transcript": "3.20194922282"} +# +# p = VaxRank() +# p.main(epi_dict) +# print("expression: " + p.expression_score) +# print("binding score: " + p.total_binding_score) +# print("total score: " + p.ranking_score) From 251ab522fff117c3ba5d94193948958b034054e7 Mon Sep 17 00:00:00 2001 From: Pablo Riesgo Ferreiro Date: Fri, 22 May 2020 00:35:19 +0200 Subject: [PATCH 022/105] make tests pass --- input/MixMHCpred/mixmhc2pred.py | 2 +- input/epitope.py | 22 ++++++------ input/predict_all_epitopes.py | 2 +- input/tests/integration_tests/test_neoag.py | 10 +++--- .../test_neoantigen_fitness.py | 35 +++---------------- 5 files changed, 23 insertions(+), 48 deletions(-) diff --git a/input/MixMHCpred/mixmhc2pred.py b/input/MixMHCpred/mixmhc2pred.py index 12cd19a7..5fab203f 100755 --- a/input/MixMHCpred/mixmhc2pred.py +++ b/input/MixMHCpred/mixmhc2pred.py @@ -254,7 +254,7 @@ def main(self, alleles, xmer_wt, xmer_mut): # prediction for peptides of length 13 to 18 based on Suppl Fig. 6 a in Racle, J., et al. # Robust prediction of HLA class II epitopes by deep motif deconvolution of immunopeptidomes. # Nat. Biotech. (2019). - seqs = self.generate_nmers(xmer_wt=xmer_wt, xmer_mut=xmer_mut, list_lengths=list[13, 14, 15, 16, 17, 18]) + seqs = self.generate_nmers(xmer_wt=xmer_wt, xmer_mut=xmer_mut, list_lengths=[13, 14, 15, 16, 17, 18]) tmp_fasta = intermediate_files.create_temp_fasta(seqs, prefix="tmp_sequence_") # try except statement to prevent stop of input for mps shorter < 13aa try: diff --git a/input/epitope.py b/input/epitope.py index 72e3df98..684a8dd0 100755 --- a/input/epitope.py +++ b/input/epitope.py @@ -72,7 +72,6 @@ def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aa properties=self.properties, mhc=MHC_I) wild_type_mhcii, mutation_mhcii = properties_manager.get_epitopes( properties=self.properties, mhc=MHC_II) - mutated_aminoacid = properties_manager.get_mutation_aminoacid() gene = properties_manager.get_gene(properties=self.properties) self.add_features(self_similarity.position_of_mutation_epitope( @@ -91,7 +90,7 @@ def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aa self.add_differential_expression_features(gene, ref_dat) - self.add_aminoacid_frequency_features(aa_freq_dict, mutated_aminoacid, mutation_mhci, nmer_freq_dict) + self.add_aminoacid_frequency_features(aa_freq_dict, mutation_mhci, nmer_freq_dict) self.add_aminoacid_index_features(aaindex1_dict, aaindex2_dict) @@ -626,10 +625,11 @@ def add_aminoacid_index_features(self, aaindex1_dict, aaindex2_dict): for k in aaindex2_dict: self.add_features(aaindex2_dict[k].get(wild_type_aminoacid, {}).get(mutation_aminoacid, "NA"), k) - def add_aminoacid_frequency_features(self, aa_freq_dict, mutated_aminoacid, mutation_mhci, nmer_freq_dict): + def add_aminoacid_frequency_features(self, aa_freq_dict, mutation_mhci, nmer_freq_dict): # amino acid frequency substitution = self.properties["substitution"] - self.add_features(FeatureLiterature.wt_mut_aa(substitution=substitution, mut="mut"), "MUT_AA") + mutated_aminoacid = FeatureLiterature.wt_mut_aa(substitution=substitution, mut="mut") + self.add_features(mutated_aminoacid, "MUT_AA") self.add_features(FeatureLiterature.wt_mut_aa(substitution=substitution, mut="wt"), "WT_AA") self.add_features(freq_score.freq_aa(mutated_aminoacid=mutated_aminoacid, dict_freq=aa_freq_dict), "Frequency_mutated_AA") @@ -639,7 +639,7 @@ def add_aminoacid_frequency_features(self, aa_freq_dict, mutated_aminoacid, muta def add_expression_features(self, rna_avail, tumour_content): # expression - transcript_expression = self.properties["Expression_Mutated_Transcript"] + transcript_expression = self.properties["transcript_expression"] patient_id = properties_manager.get_patient_id(self.properties) vaf_tumor = self.properties["VAF_in_tumor"] # TODO: Franziska please, review this. I think this is what was meant, but it was not what the code was doing @@ -664,12 +664,12 @@ def add_differential_agretopicity_index_features(self, mutation_mhci, mutation_m def add_differential_expression_features(self, gene, ref_dat): # differential expression expression_tumor = self.properties["transcript_expression"] - expression_reference = self.properties["mean_ref_expression"] - expression_reference_sum = self.properties["sum_ref_expression"] - expression_reference_sd = self.properties["sd_ref_expression"] - self.add_features(differential_expression.add_rna_reference(gene, ref_dat, 0), "mean_ref_expression") - self.add_features(differential_expression.add_rna_reference(gene, ref_dat, 1), "sd_ref_expression") - self.add_features(differential_expression.add_rna_reference(gene, ref_dat, 2), "sum_ref_expression") + expression_reference = differential_expression.add_rna_reference(gene, ref_dat, 0) + expression_reference_sum = differential_expression.add_rna_reference(gene, ref_dat, 2) + expression_reference_sd = differential_expression.add_rna_reference(gene, ref_dat, 1) + self.add_features(expression_reference, "mean_ref_expression") + self.add_features(expression_reference_sd, "sd_ref_expression") + self.add_features(expression_reference_sum, "sum_ref_expression") self.add_features(differential_expression.fold_change( expression_tumor=expression_tumor, expression_reference=expression_reference), "log2_fc_tumour_ref") self.add_features(differential_expression.percentile_calc( diff --git a/input/predict_all_epitopes.py b/input/predict_all_epitopes.py index d78daea5..602d9b3a 100755 --- a/input/predict_all_epitopes.py +++ b/input/predict_all_epitopes.py @@ -178,7 +178,7 @@ def write_to_file_sorted(self, d, header): header.extend(features_names) print("\t".join(header)) for i in range(len(d["mutation"])): - z = [d[col][i] for col in header] + z = [str(d[col][i]) for col in header] print("\t".join(z)) def initialise_properties(self, data, path_to_hla_file, tissue, tumour_content_file): diff --git a/input/tests/integration_tests/test_neoag.py b/input/tests/integration_tests/test_neoag.py index cbb392e2..614d078f 100755 --- a/input/tests/integration_tests/test_neoag.py +++ b/input/tests/integration_tests/test_neoag.py @@ -14,11 +14,11 @@ def setUp(self): def test_neoag(self): result = NeoagCalculator(runner=self.runner, configuration=self.configuration).wrapper_neoag( - props={'patient': "John Doe", - 'best_affinity_epitope_netmhcpan4': 'DDDDDDD', - 'best_affinity_netmhcpan4': 0, - 'best_affinity_epitope_netmhcpan4_WT': 'DDDDDDV', - 'pos_MUT_MHCI_affinity_epi': '12345'}) + sample_id="12345", + mut_peptide="DDDDDV", + score_mut="0", + ref_peptide="DDDDDD", + peptide_variant_position="123") self.assertTrue(isinstance(result, str)) self.assertTrue(float(result) > 0) diff --git a/input/tests/integration_tests/test_neoantigen_fitness.py b/input/tests/integration_tests/test_neoantigen_fitness.py index 89a469e0..60a592a4 100755 --- a/input/tests/integration_tests/test_neoantigen_fitness.py +++ b/input/tests/integration_tests/test_neoantigen_fitness.py @@ -27,39 +27,14 @@ def test_pathogen_similarity(self): self.assertEqual('0', result) def test_amplitude_mhc(self): - props = defaultdict(lambda: "1,0") - self.assertEqual('1.0', self.neoantigen_fitness_calculator.calculate_amplitude_mhc(props=props, mhc=MHC_I)) - self.assertEqual('1.0', self.neoantigen_fitness_calculator.calculate_amplitude_mhc(props=props, mhc=MHC_II)) - self.assertEqual('1.0', - self.neoantigen_fitness_calculator.calculate_amplitude_mhc(props=props, mhc=MHC_I, multiple_binding=True)) - self.assertEqual('1.0', - self.neoantigen_fitness_calculator.calculate_amplitude_mhc(props=props, mhc=MHC_II, multiple_binding=True)) - self.assertEqual('0.9997000899730081', - self.neoantigen_fitness_calculator.calculate_amplitude_mhc(props=props, mhc=MHC_I, affinity=True)) - self.assertEqual('0.9997000899730081', - self.neoantigen_fitness_calculator.calculate_amplitude_mhc(props=props, mhc=MHC_II, affinity=True)) - self.assertEqual('1.0', self.neoantigen_fitness_calculator.calculate_amplitude_mhc(props=props, mhc=MHC_I, netmhcscore=True)) - self.assertEqual('1.0', self.neoantigen_fitness_calculator.calculate_amplitude_mhc(props=props, mhc=MHC_II, netmhcscore=True)) - self.assertEqual('0.9997000899730081', - self.neoantigen_fitness_calculator.calculate_amplitude_mhc(props=props, mhc=MHC_I, nine_mer=True)) - self.assertEqual('0.9997000899730081', - self.neoantigen_fitness_calculator.calculate_amplitude_mhc(props=props, mhc=MHC_II, nine_mer=True)) + self.assertEqual('1.0', self.neoantigen_fitness_calculator.calculate_amplitude_mhc( + score_mutation="1.0", score_wild_type="1.0")) + self.assertEqual('0.9997000899730081', self.neoantigen_fitness_calculator.calculate_amplitude_mhc( + score_mutation="1.0", score_wild_type="1.0", apply_correction=True)) def test_recognition_potential(self): props = defaultdict(lambda: "1.0") props['Mutation_in_anchor_netmhcpan'] = '0' props['Mutation_in_anchor_netmhcpan_9mer'] = '0' - self.assertEqual('1.0', self.neoantigen_fitness_calculator.calculate_recognition_potential(props=props, mhc=MHC_I)) - self.assertEqual('1.0', self.neoantigen_fitness_calculator.calculate_recognition_potential(props=props, mhc=MHC_II)) - self.assertEqual('1.0', - self.neoantigen_fitness_calculator.calculate_recognition_potential(props=props, mhc=MHC_I, affinity=True)) - self.assertEqual('1.0', - self.neoantigen_fitness_calculator.calculate_recognition_potential(props=props, mhc=MHC_II, affinity=True)) - self.assertEqual('1.0', - self.neoantigen_fitness_calculator.calculate_recognition_potential(props=props, mhc=MHC_I, netmhcscore=True)) - self.assertEqual('1.0', - self.neoantigen_fitness_calculator.calculate_recognition_potential(props=props, mhc=MHC_II, netmhcscore=True)) self.assertEqual('1.0', self.neoantigen_fitness_calculator.calculate_recognition_potential( - props=props, mhc=MHC_I, nine_mer=True)) - self.assertEqual('1.0', self.neoantigen_fitness_calculator.calculate_recognition_potential( - props=props, mhc=MHC_II, nine_mer=True)) + amplitude="1.0", pathogen_similarity="1.0", mutation_in_anchor="0")) From 255c6deb069a3d6471bbfa11f1e89b89f716e5f1 Mon Sep 17 00:00:00 2001 From: Pablo Riesgo Ferreiro Date: Mon, 25 May 2020 16:43:35 +0200 Subject: [PATCH 023/105] correct wrong normalised expression value --- input/epitope.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/input/epitope.py b/input/epitope.py index 684a8dd0..d67e154e 100755 --- a/input/epitope.py +++ b/input/epitope.py @@ -649,8 +649,9 @@ def add_expression_features(self, rna_avail, tumour_content): self.add_features(FeatureLiterature.rna_expression_mutation( transcript_expression=transcript_expression, vaf_rna=vaf_rna), "Expression_Mutated_Transcript") + expression_mutated_transcript = self.properties.get("Expression_Mutated_Transcript") self.add_features(FeatureLiterature.expression_mutation_tc( - transcript_expression=transcript_expression, patient_id=patient_id, tumour_content=tumour_content), + transcript_expression=expression_mutated_transcript, patient_id=patient_id, tumour_content=tumour_content), "Expression_Mutated_Transcript_tumor_content") def add_differential_agretopicity_index_features(self, mutation_mhci, mutation_mhcii, wild_type_mhci, From 252898ce459977cbb1bd7709e137e49138c1533a Mon Sep 17 00:00:00 2001 From: Pablo Riesgo Ferreiro Date: Mon, 25 May 2020 16:46:41 +0200 Subject: [PATCH 024/105] remove TODO message that was done --- input/epitope.py | 1 - 1 file changed, 1 deletion(-) diff --git a/input/epitope.py b/input/epitope.py index d67e154e..e727a0d1 100755 --- a/input/epitope.py +++ b/input/epitope.py @@ -642,7 +642,6 @@ def add_expression_features(self, rna_avail, tumour_content): transcript_expression = self.properties["transcript_expression"] patient_id = properties_manager.get_patient_id(self.properties) vaf_tumor = self.properties["VAF_in_tumor"] - # TODO: Franziska please, review this. I think this is what was meant, but it was not what the code was doing vaf_rna = vaf_tumor if rna_avail.get(patient_id, "False") == "False" else \ self.properties.get("VAF_in_RNA", vaf_tumor) From 1d5e8743a2e2d8c5415256e18a2198407f49b049 Mon Sep 17 00:00:00 2001 From: Pablo Riesgo Ferreiro Date: Mon, 25 May 2020 16:56:33 +0200 Subject: [PATCH 025/105] improve handling of missing values --- input/FeatureLiterature.py | 8 ++++---- input/epitope.py | 4 ++-- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/input/FeatureLiterature.py b/input/FeatureLiterature.py index 50b9177a..d133f521 100755 --- a/input/FeatureLiterature.py +++ b/input/FeatureLiterature.py @@ -144,17 +144,17 @@ def calc_priority_score(vaf_tumor, vaf_rna, transcript_expr, no_mismatch, score_ if mut_in_prot == "True" : mut_in_prot = "0" L_mut = calc_logistic_function(score_mut) L_wt = calc_logistic_function(score_wt) - priority_score = 0.0 + priority_score = "NA" try: - if vaf_tumor != "-1": + if vaf_tumor not in ["-1", "NA"]: priority_score = (L_mut * float(vaf_tumor) * math.tanh(float(transcript_expr))) * ( float(mut_in_prot) * (1 - 2 ** (-float(no_mismatch)) * L_wt)) else: priority_score = (L_mut * float(vaf_rna) * math.tanh(float(transcript_expr))) * ( float(mut_in_prot) * (1 - 2 ** (-float(no_mismatch)) * L_wt)) - return str(priority_score) except (TypeError, ValueError) as e: - return "NA" + pass + return str(priority_score) def wt_mut_aa(substitution, mut): diff --git a/input/epitope.py b/input/epitope.py index e727a0d1..37af7277 100755 --- a/input/epitope.py +++ b/input/epitope.py @@ -373,8 +373,8 @@ def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aa sequence=self.properties["X..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."], db=db), "mutation_found_in_proteome") - vaf_tumor = self.properties["VAF_in_tumor"] - vaf_rna = self.properties.get("VAF_in_RNA") # TODO: Franziska what do we want to do when there is no value? + vaf_tumor = self.properties.get("VAF_in_tumor", "NA") + vaf_rna = self.properties.get("VAF_in_RNA", "NA") transcript_expr = self.properties["transcript_expression"] no_mismatch = self.properties["Number_of_mismatches_mhcI"] score_mut = self.properties["best%Rank_netmhcpan4"] From bd15f66c9e65c6b0e323ba934bde9ff504b71c0c Mon Sep 17 00:00:00 2001 From: Pablo Riesgo Ferreiro Date: Mon, 25 May 2020 17:07:59 +0200 Subject: [PATCH 026/105] fixing changed behaviour with filtering --- input/Tcell_predictor/tcellpredictor_wrapper.py | 10 +++++----- input/epitope.py | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/input/Tcell_predictor/tcellpredictor_wrapper.py b/input/Tcell_predictor/tcellpredictor_wrapper.py index 01c15aab..2a26b834 100755 --- a/input/Tcell_predictor/tcellpredictor_wrapper.py +++ b/input/Tcell_predictor/tcellpredictor_wrapper.py @@ -13,7 +13,7 @@ def __init__(self, references): self.tcell_prediction_score_9mer = "NA" self.references = references - def _triple_gen_seq_subst_for_prediction(self, gene, substitution, epitope, score, threshold, all=True): + def _triple_gen_seq_subst_for_prediction(self, gene, substitution, epitope, score, threshold): """ extracts gene id, epitope sequence and substitution from epitope dictionary Tcell predictor works with 9mers only! --> extract for 9mers only @@ -22,7 +22,7 @@ def _triple_gen_seq_subst_for_prediction(self, gene, substitution, epitope, scor result = (["NA", "NA", "NA"]) if str(len(epitope)) == str(9): z = [gene.replace(" ", ""), epitope, substitution] - if all: + if threshold is None: z = [gene.replace(" ", ""), epitope, substitution] result = (z) else: @@ -57,12 +57,12 @@ def _prediction_single_mps(self, tmpfile_in, tmpfile_out): return score - def _wrapper_tcellpredictor(self, gene, substitution, epitope, score, threshold, tmpfile_in, tmpfile_out, all=True): + def _wrapper_tcellpredictor(self, gene, substitution, epitope, score, threshold, tmpfile_in, tmpfile_out): """ wrapper function to determine """ trp = self._triple_gen_seq_subst_for_prediction( - gene=gene, substitution=substitution, epitope=epitope, score=score, threshold=threshold, all=all) + gene=gene, substitution=substitution, epitope=epitope, score=score, threshold=threshold) logger.debug(trp) pred_out = "NA" if "NA" not in trp: @@ -70,7 +70,7 @@ def _wrapper_tcellpredictor(self, gene, substitution, epitope, score, threshold, pred_out = self._prediction_single_mps(tmpfile_in, tmpfile_out) return pred_out - def calculate_tcell_predictor_score(self, gene, substitution, epitope, score, threshold): + def calculate_tcell_predictor_score(self, gene, substitution, epitope, score, threshold=None): ''' returns Tcell_predictor score given mps in dictionary format ''' tmp_tcellPredIN = intermediate_files.create_temp_file(prefix="tmp_TcellPredicIN_", suffix=".txt") diff --git a/input/epitope.py b/input/epitope.py index 37af7277..659f1f8a 100755 --- a/input/epitope.py +++ b/input/epitope.py @@ -482,7 +482,7 @@ def add_tcell_predictor_features(self, gene): epitope = self.properties["MHC_I_epitope_.best_prediction."] score = self.properties["MHC_I_score_.best_prediction."] self.add_features(self.tcell_predictor.calculate_tcell_predictor_score( - gene=gene, substitution=substitution, epitope=epitope, score=score, threshold=2), + gene=gene, substitution=substitution, epitope=epitope, score=score), "Tcell_predictor_score") epitope = self.properties["best_affinity_epitope_netmhcpan4_9mer"] score = self.properties["best_affinity_netmhcpan4_9mer"] From 1c2230f0e8a0c9440f33033d8ea48c0153cf512f Mon Sep 17 00:00:00 2001 From: Pablo Riesgo Ferreiro Date: Mon, 25 May 2020 17:40:54 +0200 Subject: [PATCH 027/105] fix strange reuse of temp files --- input/epitope.py | 12 +++++------- input/neoantigen_fitness/neoantigen_fitness.py | 7 ++----- 2 files changed, 7 insertions(+), 12 deletions(-) diff --git a/input/epitope.py b/input/epitope.py index 659f1f8a..2db5e1b0 100755 --- a/input/epitope.py +++ b/input/epitope.py @@ -157,7 +157,7 @@ def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aa self.add_self_similarity_features(mutation_mhci, mutation_mhcii, wild_type_mhci, wild_type_mhcii) - tmp_fasta = self.add_neoantigen_fitness_features(mutation_mhci, mutation_mhcii) + self.add_neoantigen_fitness_features(mutation_mhci, mutation_mhcii) self.add_tcell_predictor_features(gene) @@ -195,11 +195,11 @@ def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aa self.add_features( self.neoantigen_fitness_calculator.wrap_pathogensimilarity( - mutation=mutation_netmhcpan4_9mer, fastafile=tmp_fasta, iedb=self.references.iedb), + mutation=mutation_netmhcpan4_9mer, iedb=self.references.iedb), "Pathogensimiliarity_mhcI_9mer") self.add_features( self.neoantigen_fitness_calculator.wrap_pathogensimilarity( - mutation=mutation_netmhcpan4, fastafile=tmp_fasta, iedb=self.references.iedb), + mutation=mutation_netmhcpan4, iedb=self.references.iedb), "Pathogensimiliarity_mhcI_affinity_nmers") # recogntion potential with amplitude by affinity and netmhcpan4 score @@ -492,14 +492,13 @@ def add_tcell_predictor_features(self, gene): def add_neoantigen_fitness_features(self, mutation_mhci, mutation_mhcii): # neoantigen fitness - tmp_fasta = intermediate_files.create_temp_file(prefix="tmpseq", suffix=".fasta") self.add_features( self.neoantigen_fitness_calculator.wrap_pathogensimilarity( - mutation=mutation_mhci, fastafile=tmp_fasta, iedb=self.references.iedb), + mutation=mutation_mhci, iedb=self.references.iedb), "Pathogensimiliarity_mhcI") self.add_features( self.neoantigen_fitness_calculator.wrap_pathogensimilarity( - mutation=mutation_mhcii, fastafile=tmp_fasta, iedb=self.references.iedb), + mutation=mutation_mhcii, iedb=self.references.iedb), "Pathogensimiliarity_mhcII") score_mutation_mhci = self.properties["MHC_I_score_.best_prediction."].replace(",", ".") @@ -523,7 +522,6 @@ def add_neoantigen_fitness_features(self, mutation_mhci, mutation_mhcii): pathogen_similarity=self.properties["Pathogensimiliarity_mhcII"], mutation_in_anchor=self.properties["Mutation_in_anchor_netmhcpan"]), "Recognition_Potential_mhcII") - return tmp_fasta def add_self_similarity_features(self, mutation_mhci, mutation_mhcii, wild_type_mhci, wild_type_mhcii): # selfsimilarity diff --git a/input/neoantigen_fitness/neoantigen_fitness.py b/input/neoantigen_fitness/neoantigen_fitness.py index 452ab5b0..0323692e 100755 --- a/input/neoantigen_fitness/neoantigen_fitness.py +++ b/input/neoantigen_fitness/neoantigen_fitness.py @@ -40,11 +40,8 @@ def _calc_pathogensimilarity(self, fasta_file, n, iedb): os.remove(outfile) return x if x is not None else "NA" - def wrap_pathogensimilarity(self, mutation, fastafile, iedb): - with open(fastafile, "w") as f: - id = ">M_1" - f.write(id + "\n") - f.write(mutation + "\n") + def wrap_pathogensimilarity(self, mutation, iedb): + fastafile = intermediate_files.create_temp_fasta(sequences=[mutation], prefix="tmpseq") try: pathsim = self._calc_pathogensimilarity(fastafile, id, iedb) except: From 3359bded632a9f7827de0f14d190acea7f02b84f Mon Sep 17 00:00:00 2001 From: Pablo Riesgo Ferreiro Date: Mon, 25 May 2020 19:00:33 +0200 Subject: [PATCH 028/105] correct error overwriting parameter --- input/epitope.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/input/epitope.py b/input/epitope.py index 2db5e1b0..e3763771 100755 --- a/input/epitope.py +++ b/input/epitope.py @@ -162,10 +162,10 @@ def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aa self.add_tcell_predictor_features(gene) # DAI with affinity values - wild_type_netmhcpan4, mutation_netmhcpan4 = properties_manager.get_scores_netmhcpan4_affinity( + wild_type_netmhcpan4_affinity, mutation_netmhcpan4_affinity = properties_manager.get_scores_netmhcpan4_affinity( properties=self.properties, mhc=MHC_I) self.add_features( - FeatureLiterature.dai(score_mutation=mutation_netmhcpan4, score_wild_type=wild_type_netmhcpan4), + FeatureLiterature.dai(score_mutation=mutation_netmhcpan4_affinity, score_wild_type=wild_type_netmhcpan4_affinity), "DAI_affinity") # DAI wiht rank scores by netmhcpan4 From 2636120dd7ecfa0d9331868dd31733186d168de0 Mon Sep 17 00:00:00 2001 From: Pablo Riesgo Ferreiro Date: Thu, 28 May 2020 13:03:00 +0200 Subject: [PATCH 029/105] fix issue with blastp depending on comment format in input fasta --- .../dissimilaritycalculator.py | 38 ++++++++----------- input/epitope.py | 8 ++-- input/helpers/intermediate_files.py | 4 +- input/helpers/runner.py | 1 + .../neoantigen_fitness/neoantigen_fitness.py | 24 +++++++----- .../test_neoantigen_fitness.py | 17 +++++++-- 6 files changed, 50 insertions(+), 42 deletions(-) diff --git a/input/dissimilarity_garnish/dissimilaritycalculator.py b/input/dissimilarity_garnish/dissimilaritycalculator.py index ecb88555..bb1f95ac 100755 --- a/input/dissimilarity_garnish/dissimilaritycalculator.py +++ b/input/dissimilarity_garnish/dissimilaritycalculator.py @@ -17,10 +17,10 @@ def __init__(self, runner, configuration): self.runner = runner self.configuration = configuration - def _calc_dissimilarity(self, fasta_file, n, references): - ''' + def _calc_dissimilarity(self, fasta_file, references): + """ This function determines the dissimilarity to self-proteome of epitopes as described in Richman et al - ''' + """ outfile = intermediate_files.create_temp_file(prefix="tmp_prot_", suffix=".xml") self.runner.run_command(cmd=[ self.configuration.blastp, @@ -35,28 +35,20 @@ def _calc_dissimilarity(self, fasta_file, n, references): # set a to 32 for dissimilarity aligner.readAllBlastAlignments(outfile) aligner.computeR(a=32) - kk = int(n.split("_")[1]) - x = aligner.Ri.get(kk) - x_dis = "NA" - if x is not None: - x_dis = 1 - x + kk = 1 + similarity = aligner.Ri.get(kk, 1) # NOTE: returns 1 when not present + dissimilarity = 1 - similarity os.remove(fasta_file) os.remove(outfile) - return x_dis + return dissimilarity def calculate_dissimilarity(self, mhc_mutation, mhc_affinity, fastafile, references, filter_binder=False): - '''wrapper for dissimilarity calculation - ''' - with open(fastafile, "w") as f: - id = ">M_1" - f.write(id + "\n") - f.write(mhc_mutation + "\n") - dissim = self._calc_dissimilarity(fastafile, id, references) - if filter_binder: - if float(mhc_affinity) < 500: - sc = str(dissim) if dissim != "NA" else "0" - else: - sc = "NA" - else: - sc = str(dissim) if dissim != "NA" else "0" + """ + wrapper for dissimilarity calculation + """ + fastafile = intermediate_files.create_temp_fasta(sequences=[mhc_mutation], prefix="tmpseq", comment_prefix='M_') + dissim = self._calc_dissimilarity(fastafile, references) + sc = dissim + if filter_binder and float(mhc_affinity) >= 500: + sc = 0 return sc diff --git a/input/epitope.py b/input/epitope.py index e3763771..bdf1b870 100755 --- a/input/epitope.py +++ b/input/epitope.py @@ -194,11 +194,11 @@ def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aa apply_correction=True), "Amplitude_mhcI_affinity_9mer_netmhcpan4") self.add_features( - self.neoantigen_fitness_calculator.wrap_pathogensimilarity( + self.neoantigen_fitness_calculator.wrap_pathogen_similarity( mutation=mutation_netmhcpan4_9mer, iedb=self.references.iedb), "Pathogensimiliarity_mhcI_9mer") self.add_features( - self.neoantigen_fitness_calculator.wrap_pathogensimilarity( + self.neoantigen_fitness_calculator.wrap_pathogen_similarity( mutation=mutation_netmhcpan4, iedb=self.references.iedb), "Pathogensimiliarity_mhcI_affinity_nmers") @@ -493,11 +493,11 @@ def add_tcell_predictor_features(self, gene): def add_neoantigen_fitness_features(self, mutation_mhci, mutation_mhcii): # neoantigen fitness self.add_features( - self.neoantigen_fitness_calculator.wrap_pathogensimilarity( + self.neoantigen_fitness_calculator.wrap_pathogen_similarity( mutation=mutation_mhci, iedb=self.references.iedb), "Pathogensimiliarity_mhcI") self.add_features( - self.neoantigen_fitness_calculator.wrap_pathogensimilarity( + self.neoantigen_fitness_calculator.wrap_pathogen_similarity( mutation=mutation_mhcii, iedb=self.references.iedb), "Pathogensimiliarity_mhcII") diff --git a/input/helpers/intermediate_files.py b/input/helpers/intermediate_files.py index c5377e03..c62b2e60 100755 --- a/input/helpers/intermediate_files.py +++ b/input/helpers/intermediate_files.py @@ -6,7 +6,7 @@ def create_temp_file(prefix=None, suffix=None, dir=None): return temp_file.name -def create_temp_fasta(sequences, prefix=None): +def create_temp_fasta(sequences, prefix=None, comment_prefix='seq'): """ Writes seqs given in seqs list into fasta file """ @@ -14,7 +14,7 @@ def create_temp_fasta(sequences, prefix=None): counter = 1 with open(fasta_temp_file, "w") as f: for seq in sequences: - _id = ">seq{}".format(counter) + _id = ">{comment_prefix}{index}".format(comment_prefix=comment_prefix, index=counter) f.write(_id + "\n") f.write(seq + "\n") counter += 1 diff --git a/input/helpers/runner.py b/input/helpers/runner.py index ea4c1318..bfda1b02 100755 --- a/input/helpers/runner.py +++ b/input/helpers/runner.py @@ -14,6 +14,7 @@ def run_command(self, cmd, **kwargs): return_code = process.returncode if return_code == 0: logger.info("Finished command correctly!") + logger.info(self._decode(output)) else: logger.error("Finished command with return code {}".format(return_code)) logger.error(self._decode(errors)) diff --git a/input/neoantigen_fitness/neoantigen_fitness.py b/input/neoantigen_fitness/neoantigen_fitness.py index 0323692e..de212f2b 100755 --- a/input/neoantigen_fitness/neoantigen_fitness.py +++ b/input/neoantigen_fitness/neoantigen_fitness.py @@ -2,6 +2,7 @@ import os import os.path +from logzero import logger from input.helpers import intermediate_files from input.neoantigen_fitness.Aligner_modified import Aligner @@ -17,7 +18,7 @@ def __init__(self, runner, configuration): self.runner = runner self.configuration = configuration - def _calc_pathogensimilarity(self, fasta_file, n, iedb): + def _calc_pathogen_similarity(self, fasta_file, iedb): ''' This function determines the PATHOGENSIMILARITY of epitopes according to Balachandran et al. using a blast search against the IEDB pathogenepitope database ''' @@ -34,19 +35,22 @@ def _calc_pathogensimilarity(self, fasta_file, n, iedb): a = Aligner() a.readAllBlastAlignments(outfile) a.computeR() - kk = int(n.split("_")[1]) - x = a.Ri.get(kk) + kk = 1 + x = a.Ri.get(kk, 0) # NOTE: if not present it returns 0 os.remove(fasta_file) os.remove(outfile) - return x if x is not None else "NA" + return x - def wrap_pathogensimilarity(self, mutation, iedb): - fastafile = intermediate_files.create_temp_fasta(sequences=[mutation], prefix="tmpseq") + def wrap_pathogen_similarity(self, mutation, iedb): + fastafile = intermediate_files.create_temp_fasta(sequences=[mutation], prefix="tmpseq", comment_prefix='M_') try: - pathsim = self._calc_pathogensimilarity(fastafile, id, iedb) - except: - pathsim = "NA" - return str(pathsim) if pathsim != "NA" else "0" + pathsim = self._calc_pathogen_similarity(fastafile, iedb) + except Exception as ex: + # TODO: do we need this at all? it should not fail and if it fails we probably want to just stop execution + logger.exception(ex) + pathsim = 0 + logger.info("Peptide {} has a pathogen similarity of {}".format(mutation, pathsim)) + return str(pathsim) def calculate_amplitude_mhc(self, score_mutation, score_wild_type, apply_correction=False): """ diff --git a/input/tests/integration_tests/test_neoantigen_fitness.py b/input/tests/integration_tests/test_neoantigen_fitness.py index 60a592a4..3418b4a1 100755 --- a/input/tests/integration_tests/test_neoantigen_fitness.py +++ b/input/tests/integration_tests/test_neoantigen_fitness.py @@ -20,9 +20,20 @@ def _load_references(self): return references, configuration, fastafile def test_pathogen_similarity(self): - result = self.neoantigen_fitness_calculator.wrap_pathogensimilarity( - mutation='hey', - fastafile=self.fastafile.name, + # tests a pathogen sequence and expects 1.0 similarity + result = self.neoantigen_fitness_calculator.wrap_pathogen_similarity( + mutation='FIAGLIAIV', + iedb=self.references.iedb) + self.assertEqual('1.0', result) + # tests a modified pathogen sequence and expects something between 0 and 1 + result = self.neoantigen_fitness_calculator.wrap_pathogen_similarity( + mutation='FIAGDAAIV', + iedb=self.references.iedb) + self.assertLess(float(result), 1.0) + self.assertGreater(float(result), 0.0) + # tests a non pathogen sequence and expects 0 similarity + result = self.neoantigen_fitness_calculator.wrap_pathogen_similarity( + mutation='DDDDDMMDD', iedb=self.references.iedb) self.assertEqual('0', result) From 7d0450891ccdeef132fc00d64bd8c460b3018923 Mon Sep 17 00:00:00 2001 From: Pablo Riesgo Ferreiro Date: Thu, 28 May 2020 13:04:54 +0200 Subject: [PATCH 030/105] sets right default value to dissimilarity --- input/dissimilarity_garnish/dissimilaritycalculator.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/input/dissimilarity_garnish/dissimilaritycalculator.py b/input/dissimilarity_garnish/dissimilaritycalculator.py index bb1f95ac..be665c37 100755 --- a/input/dissimilarity_garnish/dissimilaritycalculator.py +++ b/input/dissimilarity_garnish/dissimilaritycalculator.py @@ -36,7 +36,7 @@ def _calc_dissimilarity(self, fasta_file, references): aligner.readAllBlastAlignments(outfile) aligner.computeR(a=32) kk = 1 - similarity = aligner.Ri.get(kk, 1) # NOTE: returns 1 when not present + similarity = aligner.Ri.get(kk, 0) # NOTE: returns 0 when not present dissimilarity = 1 - similarity os.remove(fasta_file) os.remove(outfile) From 67e522c0e5693500128262cd378b44e4eab49e7b Mon Sep 17 00:00:00 2001 From: Pablo Riesgo Ferreiro Date: Wed, 3 Jun 2020 13:33:24 +0200 Subject: [PATCH 031/105] remove unnecessaary parameter fastafile --- input/dissimilarity_garnish/dissimilaritycalculator.py | 4 ++-- input/epitope.py | 5 ++--- input/tests/integration_tests/test_dissimilarity.py | 1 - 3 files changed, 4 insertions(+), 6 deletions(-) diff --git a/input/dissimilarity_garnish/dissimilaritycalculator.py b/input/dissimilarity_garnish/dissimilaritycalculator.py index be665c37..12585ed5 100755 --- a/input/dissimilarity_garnish/dissimilaritycalculator.py +++ b/input/dissimilarity_garnish/dissimilaritycalculator.py @@ -42,11 +42,11 @@ def _calc_dissimilarity(self, fasta_file, references): os.remove(outfile) return dissimilarity - def calculate_dissimilarity(self, mhc_mutation, mhc_affinity, fastafile, references, filter_binder=False): + def calculate_dissimilarity(self, mhc_mutation, mhc_affinity, references, filter_binder=False): """ wrapper for dissimilarity calculation """ - fastafile = intermediate_files.create_temp_fasta(sequences=[mhc_mutation], prefix="tmpseq", comment_prefix='M_') + fastafile = intermediate_files.create_temp_fasta(sequences=[mhc_mutation], prefix="tmp_dissimilarity_", comment_prefix='M_') dissim = self._calc_dissimilarity(fastafile, references) sc = dissim if filter_binder and float(mhc_affinity) >= 500: diff --git a/input/epitope.py b/input/epitope.py index bdf1b870..5fc18ced 100755 --- a/input/epitope.py +++ b/input/epitope.py @@ -423,14 +423,13 @@ def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aa # dissimilarity to self-proteome # neoantigen fitness - tmp_fasta = intermediate_files.create_temp_file(prefix="tmpseq", suffix=".fasta") mhc_mutation = self.properties["best_affinity_epitope_netmhcpan4"] mhc_affinity = self.properties["best_affinity_netmhcpan4"] self.add_features(self.dissimilarity_calculator.calculate_dissimilarity( - mhc_mutation=mhc_mutation, mhc_affinity=mhc_affinity, fastafile=tmp_fasta, references=self.references), + mhc_mutation=mhc_mutation, mhc_affinity=mhc_affinity, references=self.references), "dissimilarity") self.add_features(self.dissimilarity_calculator.calculate_dissimilarity( - mhc_mutation=mhc_mutation, mhc_affinity=mhc_affinity, fastafile=tmp_fasta, references=self.references, + mhc_mutation=mhc_mutation, mhc_affinity=mhc_affinity, references=self.references, filter_binder=True), "dissimilarity_filter500") self.add_vax_rank_features() diff --git a/input/tests/integration_tests/test_dissimilarity.py b/input/tests/integration_tests/test_dissimilarity.py index ce8431b1..40574643 100755 --- a/input/tests/integration_tests/test_dissimilarity.py +++ b/input/tests/integration_tests/test_dissimilarity.py @@ -15,6 +15,5 @@ def setUp(self): def test_dissimilarity(self): result = DissimilarityCalculator(runner=self.runner, configuration=self.configuration).calculate_dissimilarity( mhc_mutation='hey', mhc_affinity='ho', - fastafile=self.fastafile.name, references=self.references) self.assertEqual('0', result) From 79553b7f32f9f54cfeb9a5fe74e33a5d61dcbec9 Mon Sep 17 00:00:00 2001 From: Pablo Riesgo Ferreiro Date: Wed, 3 Jun 2020 13:57:55 +0200 Subject: [PATCH 032/105] remove code from Balachndran 2016 --- .../.DS_Store | Bin 6148 -> 0 bytes .../__init__.py | 0 .../alignments/.DS_Store | Bin 6148 -> 0 bytes .../alignments/neoantigens_s_112032_1_T.fasta | 76 - .../neoantigens_s_112032_1_T_iedb.xml | 1246 - .../alignments/neoantigens_s_113413_1_T.fasta | 120 - .../neoantigens_s_113413_1_T_iedb.xml | 2156 - .../alignments/neoantigens_s_113520_1_T.fasta | 56 - .../neoantigens_s_113520_1_T_iedb.xml | 1106 - .../alignments/neoantigens_s_114296_1_T.fasta | 160 - .../neoantigens_s_114296_1_T_iedb.xml | 3362 -- .../alignments/neoantigens_s_114432_1_T.fasta | 198 - .../neoantigens_s_114432_1_T_iedb.xml | 3164 -- .../alignments/neoantigens_s_114445_1_T.fasta | 40 - .../neoantigens_s_114445_1_T_iedb.xml | 866 - 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input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_136587_1_T.fasta delete mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_136587_1_T_iedb.xml delete mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_137814_1_T.fasta delete mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_137814_1_T_iedb.xml delete mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_137854_2_T.fasta delete mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_137854_2_T_iedb.xml delete mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_138385_2_T.fasta delete mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_138385_2_T_iedb.xml delete mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_138625_1_T.fasta delete mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_138625_1_T_iedb.xml delete mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_138926_1_T.fasta delete mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_138926_1_T_iedb.xml delete mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_139381_1_T.fasta delete mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_139381_1_T_iedb.xml delete mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_139936_1_T.fasta delete mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_139936_1_T_iedb.xml delete mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_140531_2_T.fasta delete mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_140531_2_T_iedb.xml delete mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_141002_2_T.fasta delete mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_141002_2_T_iedb.xml delete mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_141146_2_T.fasta delete mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_141146_2_T_iedb.xml delete mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/data/.DS_Store delete mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/data/SupplementaryTable1.txt delete mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/data/iedb.fasta delete mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/output/NeoantigenQuality.txt delete mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/run.sh delete mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/src/.DS_Store delete mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/src/.project delete mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/src/.pydevproject delete mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/src/Aligner.py delete mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/src/__init__.py delete mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/src/main.py diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/.DS_Store b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/.DS_Store deleted file mode 100755 index 29498513331c9590ed766731a6b095eb0acf43ae..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 6148 zcmeHK%TB{U3>?!4RdDH%H1@V-^m;4Wg<&0T*E43hX&L&p$$qDprKhvt+--jT7}7np#A3 zem<@ulZcFPQ@L2!n>{z**++&mCkOWA81W14cNZlEfg7;MkzE(HCqgga^y>{tEnwC%0;vJ&^%eQ zLs35+`xjp>T0M_1 -HIQDLYTVL ->M_2 -GYYTLLNVF ->M_3 -LTLFGYYTL ->M_4 -TLFGYYTLL ->M_5 -YYTLLNVFL ->M_6 -LAVRPSKIK ->M_7 -PTYGNSTKL ->M_8 -TASNVEFAI ->M_9 -TSSDSISHM ->M_10 -RFRALNQEL ->M_11 -HRNHIDRAL ->M_12 -FALLFGHRF ->M_13 -HRFDYRDPV ->M_14 -VADSTLLLM ->M_15 -FKMGAHTEV ->M_16 -FEGFPQSLL ->M_17 -FEGFPQSLL ->M_18 -GAQDRNSSF ->M_19 -FTHLRLQEF ->M_20 -LAASGPTLV ->M_21 -MIVGRTYTL ->M_22 -VAAENEAVL ->M_23 -IERNLINSL ->M_24 -GEAGTIERV ->M_25 -VAIFLGFYV ->M_26 -YSIFQLAFV ->M_27 -MALNYNRAF ->M_28 -TVFGGLMAL ->M_29 -LSSRLSDTL ->M_30 -SRLSDTLSF ->M_31 -KRTSPEELL ->M_32 -HALHLRRMM ->M_33 -MAGFMGMAV ->M_34 -RMMAGFMGM ->M_35 -FVSTIIHLL ->M_36 -YLVPGFSPY ->M_37 -YLVPGFSPY ->M_38 -KASFDHACL diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_112032_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_112032_1_T_iedb.xml deleted file mode 100755 index 91a7ccb8..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_112032_1_T_iedb.xml +++ /dev/null @@ -1,1246 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_1 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_1 - 9 - - - 1 - gnl|BL_ORD_ID|86 - 6373|Genome polyprotein|SRC279960|Hepatitis C virus subtype 3a|356426 - 86 - 10 - - - 1 - 15.3938 - 28 - 0.84849 - 1 - 9 - 2 - 10 - 0 - 0 - 6 - 6 - 0 - 9 - HIQDLYTVL - HAQDATTVL - H QD TVL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 2 - Query_2 - M_2 - 9 - - - 1 - gnl|BL_ORD_ID|23 - 1516|Nucleoprotein|P03418.1|Human respiratory syncytial virus A2|11259 - 23 - 14 - - - 1 - 13.4678 - 23 - 7.59625 - 1 - 7 - 2 - 8 - 0 - 0 - 4 - 6 - 0 - 7 - GYYTLLN - GFYHILN - G+Y +LN - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 3 - Query_3 - M_3 - 9 - - - 1 - gnl|BL_ORD_ID|1677 - 149024|NS2 protein|NP_751923.1|Hepatitis C virus (isolate H77)|63746 - 1677 - 9 - - - 1 - 12.3122 - 20 - 64.7664 - 1 - 7 - 2 - 8 - 0 - 0 - 5 - 5 - 0 - 7 - LTLFGYY - LTLSPYY - LTL YY - - - - - 2 - gnl|BL_ORD_ID|639 - 37991|polyprotein|AAY82034.1|Hepatitis C virus genotype 1|41856 - 639 - 13 - - - 1 - 11.927 - 19 - 78.6478 - 1 - 7 - 4 - 10 - 0 - 0 - 5 - 5 - 0 - 7 - LTLFGYY - LTLSPYY - LTL YY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 4 - Query_4 - M_4 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_5 - 9 - - - 1 - gnl|BL_ORD_ID|1867 - 180464|polyprotein|CDF77361.1|Dengue virus 3|11069 - 1867 - 10 - - - 1 - 12.3122 - 20 - 44.794 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 7 - 0 - 8 - YTLLNVFL - FTILALFL - +T+L +FL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 6 - Query_6 - M_6 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_7 - 9 - - - 1 - gnl|BL_ORD_ID|1143 - 75436|Polyprotein|P90247|Hepatitis C virus|11103 - 1143 - 20 - - - 1 - 13.4678 - 23 - 11.6549 - 1 - 6 - 4 - 9 - 0 - 0 - 4 - 4 - 0 - 6 - PTYGNS - PLYGNE - P YGN - - - - - 2 - gnl|BL_ORD_ID|1144 - 75438|polyprotein|AAF65962.1|Hepatitis C virus|11103 - 1144 - 20 - - - 1 - 13.4678 - 23 - 11.8474 - 1 - 6 - 4 - 9 - 0 - 0 - 4 - 4 - 0 - 6 - PTYGNS - PLYGNE - P YGN - - - - - 3 - gnl|BL_ORD_ID|1142 - 75435|largest ORF|AAB02128.1|Hepatitis C virus|11103 - 1142 - 20 - - - 1 - 13.4678 - 23 - 12.0429 - 1 - 6 - 4 - 9 - 0 - 0 - 4 - 4 - 0 - 6 - PTYGNS - PLYGNE - P YGN - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 8 - Query_8 - M_8 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_9 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_10 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_11 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_12 - 9 - - - 1 - gnl|BL_ORD_ID|606 - 37251|||| - 606 - 9 - - - 1 - 13.853 - 24 - 4.4402 - 3 - 7 - 1 - 5 - 0 - 0 - 5 - 5 - 0 - 5 - LLFGH - LLFGH - LLFGH - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 13 - Query_13 - M_13 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_14 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_15 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_16 - 9 - - - 1 - gnl|BL_ORD_ID|389 - 23807|tax|AAG48731.1|Human T-lymphotropic virus 2|11909 - 389 - 23 - - - 1 - 15.779 - 29 - 0.429649 - 1 - 9 - 2 - 10 - 0 - 0 - 7 - 7 - 0 - 9 - FEGFPQSLL - FPGFGQSLL - F GF QSLL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 17 - Query_17 - M_17 - 9 - - - 1 - gnl|BL_ORD_ID|389 - 23807|tax|AAG48731.1|Human T-lymphotropic virus 2|11909 - 389 - 23 - - - 1 - 15.779 - 29 - 0.429649 - 1 - 9 - 2 - 10 - 0 - 0 - 7 - 7 - 0 - 9 - FEGFPQSLL - FPGFGQSLL - F GF QSLL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 18 - Query_18 - M_18 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_19 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_20 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_21 - 9 - - - 1 - gnl|BL_ORD_ID|301 - 20354|M1 protein|CAA30882.1|Influenza A virus|11320 - 301 - 9 - - - 1 - 11.927 - 19 - 70.3445 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 6 - 0 - 8 - IVGRTYTL - ILGFVFTL - I+G +TL - - - - - 2 - gnl|BL_ORD_ID|302 - 20355|Matrix protein 1|P03485.1|Influenza A virus (A/Puerto Rico/8/1934(H1N1))|211044 - 302 - 10 - - - 1 - 11.927 - 19 - 85.0569 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 6 - 0 - 8 - IVGRTYTL - ILGFVFTL - I+G +TL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 22 - Query_22 - M_22 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_23 - 9 - - - 1 - gnl|BL_ORD_ID|1972 - 182938|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1972 - 10 - - - 1 - 15.779 - 29 - 0.43293 - 2 - 9 - 3 - 10 - 0 - 0 - 6 - 7 - 0 - 8 - ERNLINSL - EENLVNSL - E NL+NSL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 24 - Query_24 - M_24 - 9 - - - 1 - gnl|BL_ORD_ID|2223 - 194242|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis|1773 - 2223 - 9 - - - 1 - 15.3938 - 28 - 0.819689 - 2 - 9 - 2 - 9 - 0 - 0 - 5 - 6 - 0 - 8 - EAGTIERV - EAGNFERI - EAG ER+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 25 - Query_25 - M_25 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_26 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_27 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 28 - Query_28 - M_28 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 29 - Query_29 - M_29 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 30 - Query_30 - M_30 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 31 - Query_31 - M_31 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 32 - Query_32 - M_32 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 33 - Query_33 - M_33 - 9 - - - 1 - gnl|BL_ORD_ID|1357 - 108153|polyprotein|AAF65950.1|Hepatitis C virus|11103 - 1357 - 10 - - - 1 - 12.6974 - 21 - 36.0093 - 1 - 6 - 5 - 10 - 0 - 0 - 4 - 4 - 0 - 6 - MAGFMG - MTGFTG - M GF G - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 34 - Query_34 - M_34 - 9 - - - 1 - gnl|BL_ORD_ID|1357 - 108153|polyprotein|AAF65950.1|Hepatitis C virus|11103 - 1357 - 10 - - - 1 - 13.0826 - 22 - 15.0326 - 2 - 8 - 4 - 10 - 0 - 0 - 4 - 5 - 0 - 7 - MMAGFMG - LMTGFTG - +M GF G - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 35 - Query_35 - M_35 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 36 - Query_36 - M_36 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 37 - Query_37 - M_37 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 38 - Query_38 - M_38 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_113413_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_113413_1_T.fasta deleted file mode 100755 index b7f441ce..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_113413_1_T.fasta +++ /dev/null @@ -1,120 +0,0 @@ ->M_39 -EFHDIASHV ->M_40 -MCDNGSGLV ->M_41 -IQNAGGSVI ->M_42 -TQDGALMNV ->M_43 -TLGIICLLL ->M_44 -WNDKVKEAL ->M_45 -QNAGGSVII ->M_46 -SDYLHWEVV ->M_47 -SSVPVLNML ->M_48 -WALEVLLNA ->M_49 -YETQDGALM ->M_50 -NMELPYFVL ->M_51 -LSTPAPQVF ->M_52 -VSDTEFHPL ->M_53 -MVVAGQRAV ->M_54 -YLHWEVVEL ->M_55 -ANFPWALEV ->M_56 -WYLRDVSEV ->M_57 -FHDIASHVK ->M_58 -FPWALEVLL ->M_59 -GTLGIICLL ->M_60 -YLHWEVVEL ->M_61 -LQFSRMEQL ->M_62 -VHLESNATV ->M_63 -QMFVHLQLL ->M_64 -VHLESNATV ->M_65 -TQDGALMNV ->M_66 -VAFCLKCNL ->M_67 -STDSLSTPA ->M_68 -DILEKSSSV ->M_69 -NMVGFSDRV ->M_70 -NLGSKLQLV ->M_71 -FPWALEVLL ->M_72 -TKDTFMMEL ->M_73 -HCANFPWAL ->M_74 -ESSSETSTY ->M_75 -QMFVHLQLL ->M_76 -QPLKYTWLL ->M_77 -SLTTLLQAL ->M_78 -SLSTPAPQV ->M_79 -FAINFFKEV ->M_80 -YTWLLAAKV ->M_81 -DLENMELPY ->M_82 -EKSSSVPVL ->M_83 -WLCDHPVPV ->M_84 -LLMSTLGIL ->M_85 -IQNAGGSVI ->M_86 -YTWLLAAKV ->M_87 -FSQEPADQM ->M_88 -ILSWLVSQL ->M_89 -LLLMSTLGI ->M_90 -FYIFNVSSI ->M_91 -GLGECITQV ->M_92 -LAMRRHSRI ->M_93 -LAKDSGAPV ->M_94 -YLHWEVVEL ->M_95 -FMMELLNRV ->M_96 -WLCDHPVPV ->M_97 -FAINFFKEV ->M_98 -FMMELLNRV diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_113413_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_113413_1_T_iedb.xml deleted file mode 100755 index 417ce7e1..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_113413_1_T_iedb.xml +++ /dev/null @@ -1,2156 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_39 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_39 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_40 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_41 - 9 - - - 1 - gnl|BL_ORD_ID|2016 - 183843|envelope protein|AGW23576.1|Dengue virus 3|11069 - 2016 - 10 - - - 1 - 15.779 - 29 - 0.401267 - 1 - 9 - 1 - 9 - 0 - 0 - 6 - 8 - 0 - 9 - IQNAGGSVI - IQNSGGTSI - IQN+GG+ I - - - - - 2 - gnl|BL_ORD_ID|461 - 27981|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 - 461 - 20 - - - 1 - 15.0086 - 27 - 1.13532 - 2 - 7 - 15 - 20 - 0 - 0 - 5 - 6 - 0 - 6 - QNAGGS - QNAGGT - QNAGG+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 4 - Query_4 - M_42 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_43 - 9 - - - 1 - gnl|BL_ORD_ID|979 - 64818|E7|AAD33253.1|Human papillomavirus type 16|333760 - 979 - 8 - - - 1 - 15.0086 - 27 - 1.52888 - 1 - 6 - 1 - 6 - 0 - 0 - 5 - 6 - 0 - 6 - TLGIIC - TLGIVC - TLGI+C - - - - - 2 - gnl|BL_ORD_ID|980 - 64819|E7 protein|ABL96585.1|Human papillomavirus type 16|333760 - 980 - 9 - - - 1 - 14.6234 - 26 - 2.04484 - 1 - 6 - 1 - 6 - 0 - 0 - 5 - 6 - 0 - 6 - TLGIIC - TLGIVC - TLGI+C - - - - - 3 - gnl|BL_ORD_ID|2102 - 185978|polyprotein|CDF77361.1|Dengue virus 3|11069 - 2102 - 10 - - - 1 - 14.6234 - 26 - 2.17971 - 1 - 7 - 1 - 7 - 0 - 0 - 4 - 7 - 0 - 7 - TLGIICL - TMGVLCL - T+G++CL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 6 - Query_6 - M_44 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_45 - 9 - - - 1 - gnl|BL_ORD_ID|461 - 27981|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 - 461 - 20 - - - 1 - 15.0086 - 27 - 1.13532 - 1 - 6 - 15 - 20 - 0 - 0 - 5 - 6 - 0 - 6 - QNAGGS - QNAGGT - QNAGG+ - - - - - 2 - gnl|BL_ORD_ID|2016 - 183843|envelope protein|AGW23576.1|Dengue virus 3|11069 - 2016 - 10 - - - 1 - 14.6234 - 26 - 1.84513 - 1 - 9 - 2 - 10 - 0 - 0 - 5 - 7 - 0 - 9 - QNAGGSVII - QNSGGTSIF - QN+GG+ I - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 8 - Query_8 - M_46 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_47 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_48 - 9 - - - 1 - gnl|BL_ORD_ID|637 - 37960|membrane protein|AAA45887.1|Human gammaherpesvirus 4|10376 - 637 - 9 - - - 1 - 12.3122 - 20 - 60.6092 - 1 - 7 - 3 - 9 - 0 - 0 - 5 - 5 - 0 - 7 - WALEVLL - WTLVVLL - W L VLL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 11 - Query_11 - M_49 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_50 - 9 - - - 1 - gnl|BL_ORD_ID|184 - 13518|HCV-1|AAA45676.1|Hepatitis C virus genotype 1|41856 - 184 - 20 - - - 1 - 12.6974 - 21 - 23.6647 - 4 - 8 - 3 - 7 - 0 - 0 - 4 - 4 - 0 - 5 - LPYFV - LPYLV - LPY V - - - - - 2 - gnl|BL_ORD_ID|183 - 13516|Genome polyprotein|P26664.3|Hepatitis C virus subtype 1a|31646 - 183 - 9 - - - 1 - 12.3122 - 20 - 47.1713 - 4 - 8 - 3 - 7 - 0 - 0 - 4 - 4 - 0 - 5 - LPYFV - LPYLV - LPY V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 13 - Query_13 - M_51 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_52 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_53 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_54 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_55 - 9 - - - 1 - gnl|BL_ORD_ID|561 - 34616|pol protein|BAA32832.1|Hepatitis B virus|10407 - 561 - 9 - - - 1 - 14.2382 - 25 - 3.05306 - 1 - 7 - 3 - 9 - 0 - 0 - 4 - 5 - 0 - 7 - ANFPWAL - TSFPWLL - +FPW L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 18 - Query_18 - M_56 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_57 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_58 - 9 - - - 1 - gnl|BL_ORD_ID|637 - 37960|membrane protein|AAA45887.1|Human gammaherpesvirus 4|10376 - 637 - 9 - - - 1 - 12.3122 - 20 - 66.9453 - 3 - 9 - 3 - 9 - 0 - 0 - 5 - 5 - 0 - 7 - WALEVLL - WTLVVLL - W L VLL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 21 - Query_21 - M_59 - 9 - - - 1 - gnl|BL_ORD_ID|979 - 64818|E7|AAD33253.1|Human papillomavirus type 16|333760 - 979 - 8 - - - 1 - 14.6234 - 26 - 1.73882 - 2 - 7 - 1 - 6 - 0 - 0 - 5 - 6 - 0 - 6 - TLGIIC - TLGIVC - TLGI+C - - - - - 2 - gnl|BL_ORD_ID|980 - 64819|E7 protein|ABL96585.1|Human papillomavirus type 16|333760 - 980 - 9 - - - 1 - 14.6234 - 26 - 2.33479 - 2 - 7 - 1 - 6 - 0 - 0 - 5 - 6 - 0 - 6 - TLGIIC - TLGIVC - TLGI+C - - - - - 3 - gnl|BL_ORD_ID|2102 - 185978|polyprotein|CDF77361.1|Dengue virus 3|11069 - 2102 - 10 - - - 1 - 14.6234 - 26 - 2.37049 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 7 - 0 - 7 - TLGIICL - TMGVLCL - T+G++CL - - - - - 4 - gnl|BL_ORD_ID|627 - 37573|E7 protein|ABL96585.1|Human papillomavirus type 16|333760 - 627 - 9 - - - 1 - 13.853 - 24 - 5.95161 - 1 - 6 - 4 - 9 - 0 - 0 - 5 - 6 - 0 - 6 - GTLGII - GTLGIV - GTLGI+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 22 - Query_22 - M_60 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_61 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_62 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_63 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_64 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_65 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 28 - Query_28 - M_66 - 9 - - - 1 - gnl|BL_ORD_ID|1382 - 110184|E7|AAD33253.1|Human papillomavirus type 16|333760 - 1382 - 35 - - - 1 - 13.4678 - 23 - 9.19861 - 1 - 8 - 14 - 21 - 0 - 0 - 5 - 6 - 0 - 8 - VAFCLKCN - VTFCCKCD - V FC KC+ - - - - - 2 - gnl|BL_ORD_ID|1400 - 110467|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1400 - 25 - - - 1 - 11.5418 - 18 - 93.0417 - 2 - 7 - 8 - 13 - 0 - 0 - 4 - 4 - 0 - 6 - AFCLKC - AVCDKC - A C KC - - - - - 3 - gnl|BL_ORD_ID|1387 - 110227|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1387 - 33 - - - 1 - 11.1566 - 17 - 143.577 - 2 - 7 - 15 - 20 - 0 - 0 - 4 - 4 - 0 - 6 - AFCLKC - AVCDKC - A C KC - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 29 - Query_29 - M_67 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 30 - Query_30 - M_68 - 9 - - - 1 - gnl|BL_ORD_ID|181 - 13456|circumsporozoite protein|AAN87606.1|Plasmodium falciparum|5833 - 181 - 20 - - - 1 - 13.4678 - 23 - 9.72555 - 3 - 9 - 11 - 17 - 0 - 0 - 5 - 6 - 0 - 7 - LEKSSSV - MEKCSSV - +EK SSV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 31 - Query_31 - M_69 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 32 - Query_32 - M_70 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 33 - Query_33 - M_71 - 9 - - - 1 - gnl|BL_ORD_ID|637 - 37960|membrane protein|AAA45887.1|Human gammaherpesvirus 4|10376 - 637 - 9 - - - 1 - 12.3122 - 20 - 66.9453 - 3 - 9 - 3 - 9 - 0 - 0 - 5 - 5 - 0 - 7 - WALEVLL - WTLVVLL - W L VLL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 34 - Query_34 - M_72 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 35 - Query_35 - M_73 - 9 - - - 1 - gnl|BL_ORD_ID|561 - 34616|pol protein|BAA32832.1|Hepatitis B virus|10407 - 561 - 9 - - - 1 - 14.2382 - 25 - 2.95178 - 3 - 9 - 3 - 9 - 0 - 0 - 4 - 5 - 0 - 7 - ANFPWAL - TSFPWLL - +FPW L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 36 - Query_36 - M_74 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 37 - Query_37 - M_75 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 38 - Query_38 - M_76 - 9 - - - 1 - gnl|BL_ORD_ID|1020 - 68229|EBNA3B (EBNA4A) latent protein|CAA24858.1|Human gammaherpesvirus 4|10376 - 1020 - 10 - - - 1 - 11.927 - 19 - 68.8532 - 2 - 7 - 5 - 10 - 0 - 0 - 4 - 4 - 0 - 6 - PLKYTW - PYKPTW - P K TW - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 39 - Query_39 - M_77 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 40 - Query_40 - M_78 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 41 - Query_41 - M_79 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 42 - Query_42 - M_80 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 43 - Query_43 - M_81 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 44 - Query_44 - M_82 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 45 - Query_45 - M_83 - 9 - - - 1 - gnl|BL_ORD_ID|1944 - 180818|Membrane glycoprotein precursor|NP_739582.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1944 - 15 - - - 1 - 13.4678 - 23 - 9.36117 - 1 - 6 - 1 - 6 - 0 - 0 - 3 - 4 - 0 - 6 - WLCDHP - WILRHP - W+ HP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 46 - Query_46 - M_84 - 9 - - - 1 - gnl|BL_ORD_ID|627 - 37573|E7 protein|ABL96585.1|Human papillomavirus type 16|333760 - 627 - 9 - - - 1 - 15.3938 - 28 - 0.565591 - 1 - 9 - 1 - 9 - 0 - 0 - 7 - 8 - 0 - 9 - LLMSTLGIL - LLMGTLGIV - LLM TLGI+ - - - - - 2 - gnl|BL_ORD_ID|1718 - 150391|polyprotein|AGS49173.1|Dengue virus 2|11060 - 1718 - 10 - - - 1 - 14.6234 - 26 - 1.64355 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 9 - 0 - 9 - LLMSTLGIL - LMMTTIGIV - L+M+T+GI+ - - - - - 3 - gnl|BL_ORD_ID|1722 - 150448|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1722 - 9 - - - 1 - 13.4678 - 23 - 8.56958 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 7 - 0 - 7 - LMSTLGI - MMATIGI - +M+T+GI - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 47 - Query_47 - M_85 - 9 - - - 1 - gnl|BL_ORD_ID|2016 - 183843|envelope protein|AGW23576.1|Dengue virus 3|11069 - 2016 - 10 - - - 1 - 15.779 - 29 - 0.401267 - 1 - 9 - 1 - 9 - 0 - 0 - 6 - 8 - 0 - 9 - IQNAGGSVI - IQNSGGTSI - IQN+GG+ I - - - - - 2 - gnl|BL_ORD_ID|461 - 27981|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 - 461 - 20 - - - 1 - 15.0086 - 27 - 1.13532 - 2 - 7 - 15 - 20 - 0 - 0 - 5 - 6 - 0 - 6 - QNAGGS - QNAGGT - QNAGG+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 48 - Query_48 - M_86 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 49 - Query_49 - M_87 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 50 - Query_50 - M_88 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 51 - Query_51 - M_89 - 9 - - - 1 - gnl|BL_ORD_ID|627 - 37573|E7 protein|ABL96585.1|Human papillomavirus type 16|333760 - 627 - 9 - - - 1 - 15.3938 - 28 - 0.690962 - 2 - 9 - 1 - 8 - 0 - 0 - 7 - 7 - 0 - 8 - LLMSTLGI - LLMGTLGI - LLM TLGI - - - - - 2 - gnl|BL_ORD_ID|1718 - 150391|polyprotein|AGS49173.1|Dengue virus 2|11060 - 1718 - 10 - - - 1 - 14.6234 - 26 - 2.17971 - 2 - 9 - 1 - 8 - 0 - 0 - 5 - 8 - 0 - 8 - LLMSTLGI - LMMTTIGI - L+M+T+GI - - - - - 3 - gnl|BL_ORD_ID|1722 - 150448|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1722 - 9 - - - 1 - 13.4678 - 23 - 8.56958 - 3 - 9 - 1 - 7 - 0 - 0 - 4 - 7 - 0 - 7 - LMSTLGI - MMATIGI - +M+T+GI - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 52 - Query_52 - M_90 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 53 - Query_53 - M_91 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 54 - Query_54 - M_92 - 9 - - - 1 - gnl|BL_ORD_ID|2274 - 419017|polyprotein|AFY10034.1|Dengue virus 4|11070 - 2274 - 10 - - - 1 - 13.4678 - 23 - 10.9961 - 2 - 7 - 3 - 8 - 0 - 0 - 4 - 6 - 0 - 6 - AMRRHS - AMKRYS - AM+R+S - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 55 - Query_55 - M_93 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 56 - Query_56 - M_94 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 57 - Query_57 - M_95 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 58 - Query_58 - M_96 - 9 - - - 1 - gnl|BL_ORD_ID|1944 - 180818|Membrane glycoprotein precursor|NP_739582.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1944 - 15 - - - 1 - 13.4678 - 23 - 9.36117 - 1 - 6 - 1 - 6 - 0 - 0 - 3 - 4 - 0 - 6 - WLCDHP - WILRHP - W+ HP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 59 - Query_59 - M_97 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 60 - Query_60 - M_98 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_113520_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_113520_1_T.fasta deleted file mode 100755 index 5c7319a5..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_113520_1_T.fasta +++ /dev/null @@ -1,56 +0,0 @@ ->M_99 -TVAEKRGWK ->M_100 -RLLPDTFVL ->M_101 -RLLPDTFVL ->M_102 -SSMAAGLEH ->M_103 -MIYRLAQAK ->M_104 -TPMYRTRPA ->M_105 -ITYYCHGGY ->M_106 -KLGSSITYY ->M_107 -FPVSYGVPA ->M_108 -IMFPVSYGV ->M_109 -ISDTILKTK ->M_110 -RLQTHTIYK ->M_111 -ELFHVDWHV ->M_112 -LPRQYWEAL ->M_113 -MPHRATVYA ->M_114 -KLLECSLTK ->M_115 -RPQGQRPAL ->M_116 -SSDCIIEKK ->M_117 -TSSDCIIEK ->M_118 -GLMGHTLHR ->M_119 -LPGHAPGIL ->M_120 -YAYHVEWEK ->M_121 -WVRWHKGCL ->M_122 -SSSIRIHER ->M_123 -FLSSSFSML ->M_124 -FSMLKDHIK ->M_125 -LSSSFSMLK ->M_126 -VVGADGVGK diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_113520_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_113520_1_T_iedb.xml deleted file mode 100755 index 8f3d16ac..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_113520_1_T_iedb.xml +++ /dev/null @@ -1,1106 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_99 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_99 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_100 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_101 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_102 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_103 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_104 - 9 - - - 1 - gnl|BL_ORD_ID|1284 - 102150|nef protein|ACR27119.1|Human immunodeficiency virus 1|11676 - 1284 - 9 - - - 1 - 10.7714 - 16 - 449.273 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 4 - 0 - 8 - TPMYRTRP - TPQVPLRP - TP RP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 7 - Query_7 - M_105 - 9 - - - 1 - gnl|BL_ORD_ID|1176 - 79454|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 1176 - 15 - - - 1 - 13.0826 - 22 - 20.7204 - 4 - 8 - 3 - 7 - 0 - 0 - 3 - 4 - 0 - 5 - YCHGG - FCHPG - +CH G - - - - - 2 - gnl|BL_ORD_ID|1160 - 76532|outer membrane protein|YP_170495.1|Francisella tularensis subsp. tularensis SCHU S4|177416 - 1160 - 10 - - - 1 - 11.5418 - 18 - 146.048 - 3 - 9 - 1 - 7 - 0 - 0 - 4 - 4 - 0 - 7 - YYCHGGY - YYLDRGY - YY GY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 8 - Query_8 - M_106 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_107 - 9 - - - 1 - gnl|BL_ORD_ID|1 - 118|envelope glycoprotein|ABS76372.1|Human immunodeficiency virus 1|11676 - 1 - 20 - - - 1 - 13.853 - 24 - 6.85717 - 3 - 8 - 9 - 14 - 0 - 0 - 5 - 5 - 0 - 6 - VSYGVP - VYYGVP - V YGVP - - - - - 2 - gnl|BL_ORD_ID|1831 - 179823|cell surface protein (associated with virulence)|NP_302372.1|Mycobacterium leprae TN|272631 - 1831 - 9 - - - 1 - 11.927 - 19 - 112.786 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 4 - 0 - 9 - FPVSYGVPA - IPASVSAPA - P S PA - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 10 - Query_10 - M_108 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_109 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_110 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_111 - 9 - - - 1 - gnl|BL_ORD_ID|686 - 41407|Envelope protein|NP_739583.2|Dengue virus 2|11060 - 686 - 15 - - - 1 - 10.3862 - 15 - 487.414 - 2 - 7 - 7 - 12 - 0 - 0 - 3 - 3 - 0 - 6 - LFHVDW - LVHRQW - L H W - - - - - 2 - gnl|BL_ORD_ID|1746 - 150725|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1746 - 9 - - - 1 - 10.001 - 14 - 843.115 - 2 - 7 - 2 - 7 - 0 - 0 - 3 - 3 - 0 - 6 - LFHVDW - LVHRQW - L H W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 14 - Query_14 - M_112 - 9 - - - 1 - gnl|BL_ORD_ID|502 - 31997|hypothetical protein FTT0484|YP_169522.1|Francisella tularensis subsp. tularensis SCHU S4|177416 - 502 - 9 - - - 1 - 13.853 - 24 - 5.65074 - 1 - 6 - 3 - 8 - 0 - 0 - 4 - 4 - 0 - 6 - LPRQYW - LPEGYW - LP YW - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 15 - Query_15 - M_113 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_114 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_115 - 9 - - - 1 - gnl|BL_ORD_ID|1739 - 150643|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1739 - 10 - - - 1 - 14.2382 - 25 - 3.50259 - 2 - 9 - 2 - 9 - 0 - 0 - 5 - 6 - 0 - 8 - PQGQRPAL - PEGIIPAL - P+G PAL - - - - - 2 - gnl|BL_ORD_ID|2075 - 185125|polyprotein|AGW21594.1|Dengue virus 1|11053 - 2075 - 10 - - - 1 - 14.2382 - 25 - 4.23087 - 2 - 9 - 3 - 10 - 0 - 0 - 5 - 6 - 0 - 8 - PQGQRPAL - PEGIIPAL - P+G PAL - - - - - 3 - gnl|BL_ORD_ID|577 - 36352|Polyprotein|P90247|Hepatitis C virus|11103 - 577 - 20 - - - 1 - 13.853 - 24 - 4.57317 - 2 - 9 - 10 - 17 - 0 - 0 - 4 - 6 - 0 - 8 - PQGQRPAL - PRGSRPSW - P+G RP+ - - - - - 4 - gnl|BL_ORD_ID|566 - 35237|nonstructural protein 3|NP_722463.1|Dengue virus type 1 Hawaii|10000440 - 566 - 20 - - - 1 - 13.853 - 24 - 5.14963 - 2 - 9 - 7 - 14 - 0 - 0 - 5 - 6 - 0 - 8 - PQGQRPAL - PEGIIPAL - P+G PAL - - - - - 5 - gnl|BL_ORD_ID|1107 - 72929|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 - 1107 - 15 - - - 1 - 13.0826 - 22 - 19.7105 - 2 - 6 - 4 - 8 - 0 - 0 - 4 - 4 - 0 - 5 - PQGQR - PQGSR - PQG R - - - - - 6 - gnl|BL_ORD_ID|131 - 9316|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 - 131 - 15 - - - 1 - 13.0826 - 22 - 20.0418 - 2 - 6 - 8 - 12 - 0 - 0 - 4 - 4 - 0 - 5 - PQGQR - PQGSR - PQG R - - - - - 7 - gnl|BL_ORD_ID|1933 - 180778|polyprotein|AFP27208.1|Dengue virus 4|11070 - 1933 - 10 - - - 1 - 12.6974 - 21 - 24.7764 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - PQGQRPAL - PEGIIPTL - P+G P L - - - - - 8 - gnl|BL_ORD_ID|1948 - 180850|polyprotein|AFP27208.1|Dengue virus 4|11070 - 1948 - 10 - - - 1 - 12.6974 - 21 - 26.5293 - 2 - 9 - 3 - 10 - 0 - 0 - 4 - 5 - 0 - 8 - PQGQRPAL - PEGIIPTL - P+G P L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 18 - Query_18 - M_116 - 9 - - - 1 - gnl|BL_ORD_ID|1007 - 66405|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 1007 - 20 - - - 1 - 10.7714 - 16 - 316.686 - 2 - 9 - 4 - 11 - 0 - 0 - 4 - 5 - 0 - 8 - SDCIIEKK - SACQRQKK - S C +KK - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 19 - Query_19 - M_117 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_118 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_119 - 9 - - - 1 - gnl|BL_ORD_ID|741 - 47760|EBNA-1 protein|Q777E1|Human gammaherpesvirus 4|10376 - 741 - 15 - - - 1 - 12.3122 - 20 - 43.2075 - 2 - 7 - 1 - 6 - 0 - 0 - 4 - 4 - 0 - 6 - PGHAPG - PGTGPG - PG PG - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 22 - Query_22 - M_120 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_121 - 9 - - - 1 - gnl|BL_ORD_ID|1944 - 180818|Membrane glycoprotein precursor|NP_739582.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1944 - 15 - - - 1 - 11.927 - 19 - 77.3377 - 1 - 7 - 1 - 7 - 0 - 0 - 3 - 4 - 0 - 7 - WVRWHKG - WILRHPG - W+ H G - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 24 - Query_24 - M_122 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_123 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_124 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_125 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 28 - Query_28 - M_126 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114296_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114296_1_T.fasta deleted file mode 100755 index 2b03eb9e..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114296_1_T.fasta +++ /dev/null @@ -1,160 +0,0 @@ ->M_127 -AVDLSSAGM ->M_128 -GMAGVLIGY ->M_129 -SSAGMAGVL ->M_130 -KAAPIYKLV ->M_131 -VTKAAPIYK ->M_132 -FLPSWLLGI ->M_133 -RMAFTDHQL ->M_134 -RMAFTDHQL ->M_135 -ALQPQLGCY ->M_136 -YQQALQPQL ->M_137 -YQQALQPQL ->M_138 -YQLKMLIKI ->M_139 -ILLVVYNNV ->M_140 -LLVVYNNVL ->M_141 -LLVVYNNVL ->M_142 -LVVYNNVLK ->M_143 -LSGHSTQDL ->M_144 -QALSKFKAM ->M_145 -LSVDRMRKV ->M_146 -LGVAARWDL ->M_147 -HAVQAAVQY ->M_148 -HAVQAAVQY ->M_149 -KIMNSLPEM ->M_150 -KIMNSLPEM ->M_151 -LPEMKVQLV ->M_152 -SLPEMKVQL ->M_153 -LTISGECPK ->M_154 -AMYDVLTFA ->M_155 -ATDQAMYDV ->M_156 -KIHATDQAM ->M_157 -QAMYDVLTF ->M_158 -QAMYDVLTF ->M_159 -LICFLTPVK ->M_160 -NLICFLTPV ->M_161 -IAHIFGGAR ->M_162 -LLEISKWFR ->M_163 -FSDDGVLGP ->M_164 -GSFSDDGVL ->M_165 -VLGPVLTTF ->M_166 -ATSIPAGSM ->M_167 -IPAGSMPTV ->M_168 -IMDLRNGTF ->M_169 -CLSGYCSVF ->M_170 -CSVFAYKPM ->M_171 -GYCSVFAYK ->M_172 -SGYCSVFAY ->M_173 -LIMALVWSL ->M_174 -LIMALVWSL ->M_175 -LIMALVWSL ->M_176 -LVWSLPCGF ->M_177 -ESDYLINEM ->M_178 -YLINEMYL* ->M_179 -TQMVDIWSV ->M_180 -MVAFFSSHT ->M_181 -VAFFSSHTY ->M_182 -VAFFSSHTY ->M_183 -VAFFSSHTY ->M_184 -VTFSTSSQL ->M_185 -WVDFADSVT ->M_186 -YQTFKDWGI ->M_187 -ISMGQEEKK ->M_188 -WISMGQEEK ->M_189 -FSWQSHLLI ->M_190 -QSHLLIHQR ->M_191 -FYIIECIAM ->M_192 -TAFYIIECI ->M_193 -YIIECIAMS ->M_194 -ASTYSQLKL ->M_195 -SASTYSQLK ->M_196 -VSASTYSQL ->M_197 -YSQLKLWNV ->M_198 -FYQHLNLMR ->M_199 -YQHLNLMRV ->M_200 -KPAPHPQAL ->M_201 -MADSGPIYN ->M_202 -GLGFYNDVV ->M_203 -FCENDAEVL ->M_204 -RTTQQENPR ->M_205 -AMDDLDTDM ->M_206 -EECGKTFYR diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114296_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114296_1_T_iedb.xml deleted file mode 100755 index 5a71dc1f..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114296_1_T_iedb.xml +++ /dev/null @@ -1,3362 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_127 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_127 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_128 - 9 - - - 1 - gnl|BL_ORD_ID|339 - 21275|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 - 339 - 9 - - - 1 - 11.5418 - 18 - 157.499 - 1 - 8 - 1 - 8 - 0 - 0 - 5 - 5 - 0 - 8 - GMAGVLIG - GMGPSLIG - GM LIG - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 3 - Query_3 - M_129 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_130 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_131 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_132 - 9 - - - 1 - gnl|BL_ORD_ID|174 - 13215|Antigen 85-B|P0C5B9.1|Mycobacterium tuberculosis|1773 - 174 - 10 - - - 1 - 13.4678 - 23 - 12.4198 - 2 - 6 - 2 - 6 - 0 - 0 - 4 - 4 - 0 - 5 - LPSWL - LPQWL - LP WL - - - - - 2 - gnl|BL_ORD_ID|2172 - 189727|Antigen 85-B|P0C5B9.1|Mycobacterium tuberculosis|1773 - 2172 - 9 - - - 1 - 13.0826 - 22 - 14.1983 - 2 - 6 - 1 - 5 - 0 - 0 - 4 - 4 - 0 - 5 - LPSWL - LPQWL - LP WL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 7 - Query_7 - M_133 - 9 - - - 1 - gnl|BL_ORD_ID|2185 - 190466|large surface antigen|CAL29876.1|Hepatitis B virus|10407 - 2185 - 15 - - - 1 - 15.3938 - 28 - 0.751673 - 4 - 9 - 4 - 9 - 0 - 0 - 5 - 5 - 0 - 6 - FTDHQL - FPDHQL - F DHQL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 8 - Query_8 - M_134 - 9 - - - 1 - gnl|BL_ORD_ID|2185 - 190466|large surface antigen|CAL29876.1|Hepatitis B virus|10407 - 2185 - 15 - - - 1 - 15.3938 - 28 - 0.751673 - 4 - 9 - 4 - 9 - 0 - 0 - 5 - 5 - 0 - 6 - FTDHQL - FPDHQL - F DHQL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 9 - Query_9 - M_135 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_136 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_137 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_138 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_139 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_140 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_141 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_142 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_143 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_144 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_145 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_146 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_147 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 22 - Query_22 - M_148 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_149 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_150 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_151 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_152 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_153 - 9 - - - 1 - gnl|BL_ORD_ID|2309 - 423011|polyprotein|AER51001.1|Hepatitis C virus genotype 1|41856 - 2309 - 9 - - - 1 - 13.4678 - 23 - 10.0233 - 3 - 8 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - ISGECP - MSGEVP - +SGE P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 28 - Query_28 - M_154 - 9 - - - 1 - gnl|BL_ORD_ID|45 - 3019|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 - 45 - 9 - - - 1 - 15.0086 - 27 - 1.12298 - 1 - 7 - 1 - 7 - 0 - 0 - 5 - 7 - 0 - 7 - AMYDVLT - ALYDVVT - A+YDV+T - - - - - 2 - gnl|BL_ORD_ID|1382 - 110184|E7|AAD33253.1|Human papillomavirus type 16|333760 - 1382 - 35 - - - 1 - 14.6234 - 26 - 2.14504 - 1 - 8 - 9 - 16 - 0 - 0 - 4 - 7 - 0 - 8 - AMYDVLTF - AHYNIVTF - A Y+++TF - - - - - 3 - gnl|BL_ORD_ID|43 - 3017|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 43 - 9 - - - 1 - 13.853 - 24 - 5.09494 - 1 - 7 - 1 - 7 - 0 - 0 - 4 - 7 - 0 - 7 - AMYDVLT - ALYDVVS - A+YDV++ - - - - - 4 - gnl|BL_ORD_ID|44 - 3018|polyprotein|BAA25076.1|Hepatitis C virus (isolate H77)|63746 - 44 - 9 - - - 1 - 13.853 - 24 - 6.37844 - 1 - 7 - 1 - 7 - 0 - 0 - 4 - 7 - 0 - 7 - AMYDVLT - ALYDVVS - A+YDV++ - - - - - 5 - gnl|BL_ORD_ID|682 - 41085|polyprotein|ABR25251.1|Hepatitis C virus|11103 - 682 - 15 - - - 1 - 13.853 - 24 - 6.52084 - 1 - 7 - 2 - 8 - 0 - 0 - 4 - 7 - 0 - 7 - AMYDVLT - ALYDVVS - A+YDV++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 29 - Query_29 - M_155 - 9 - - - 1 - gnl|BL_ORD_ID|1398 - 110431|E7|AAD33253.1|Human papillomavirus type 16|333760 - 1398 - 36 - - - 1 - 11.927 - 19 - 54.6787 - 3 - 9 - 29 - 35 - 0 - 0 - 3 - 6 - 0 - 7 - DQAMYDV - DRAHYNI - D+A Y++ - - - - - 2 - gnl|BL_ORD_ID|1382 - 110184|E7|AAD33253.1|Human papillomavirus type 16|333760 - 1382 - 35 - - - 1 - 11.927 - 19 - 69.4128 - 3 - 9 - 7 - 13 - 0 - 0 - 3 - 6 - 0 - 7 - DQAMYDV - DRAHYNI - D+A Y++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 30 - Query_30 - M_156 - 9 - - - 1 - gnl|BL_ORD_ID|1339 - 107925|polyprotein|AAF65964.1|Hepatitis C virus|11103 - 1339 - 10 - - - 1 - 12.6974 - 21 - 26.9859 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 4 - 0 - 6 - KIHATD - KAHGTD - K H TD - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 31 - Query_31 - M_157 - 9 - - - 1 - gnl|BL_ORD_ID|45 - 3019|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 - 45 - 9 - - - 1 - 15.0086 - 27 - 0.989407 - 2 - 8 - 1 - 7 - 0 - 0 - 5 - 7 - 0 - 7 - AMYDVLT - ALYDVVT - A+YDV+T - - - - - 2 - gnl|BL_ORD_ID|1382 - 110184|E7|AAD33253.1|Human papillomavirus type 16|333760 - 1382 - 35 - - - 1 - 15.0086 - 27 - 1.26448 - 1 - 9 - 8 - 16 - 0 - 0 - 4 - 8 - 0 - 9 - QAMYDVLTF - RAHYNIVTF - +A Y+++TF - - - - - 3 - gnl|BL_ORD_ID|43 - 3017|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 43 - 9 - - - 1 - 14.2382 - 25 - 4.3647 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 7 - 0 - 7 - AMYDVLT - ALYDVVS - A+YDV++ - - - - - 4 - gnl|BL_ORD_ID|44 - 3018|polyprotein|BAA25076.1|Hepatitis C virus (isolate H77)|63746 - 44 - 9 - - - 1 - 13.853 - 24 - 5.45887 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 7 - 0 - 7 - AMYDVLT - ALYDVVS - A+YDV++ - - - - - 5 - gnl|BL_ORD_ID|682 - 41085|polyprotein|ABR25251.1|Hepatitis C virus|11103 - 682 - 15 - - - 1 - 13.853 - 24 - 5.48445 - 2 - 8 - 2 - 8 - 0 - 0 - 4 - 7 - 0 - 7 - AMYDVLT - ALYDVVS - A+YDV++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 32 - Query_32 - M_158 - 9 - - - 1 - gnl|BL_ORD_ID|45 - 3019|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 - 45 - 9 - - - 1 - 15.0086 - 27 - 0.989407 - 2 - 8 - 1 - 7 - 0 - 0 - 5 - 7 - 0 - 7 - AMYDVLT - ALYDVVT - A+YDV+T - - - - - 2 - gnl|BL_ORD_ID|1382 - 110184|E7|AAD33253.1|Human papillomavirus type 16|333760 - 1382 - 35 - - - 1 - 15.0086 - 27 - 1.26448 - 1 - 9 - 8 - 16 - 0 - 0 - 4 - 8 - 0 - 9 - QAMYDVLTF - RAHYNIVTF - +A Y+++TF - - - - - 3 - gnl|BL_ORD_ID|43 - 3017|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 43 - 9 - - - 1 - 14.2382 - 25 - 4.3647 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 7 - 0 - 7 - AMYDVLT - ALYDVVS - A+YDV++ - - - - - 4 - gnl|BL_ORD_ID|44 - 3018|polyprotein|BAA25076.1|Hepatitis C virus (isolate H77)|63746 - 44 - 9 - - - 1 - 13.853 - 24 - 5.45887 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 7 - 0 - 7 - AMYDVLT - ALYDVVS - A+YDV++ - - - - - 5 - gnl|BL_ORD_ID|682 - 41085|polyprotein|ABR25251.1|Hepatitis C virus|11103 - 682 - 15 - - - 1 - 13.853 - 24 - 5.48445 - 2 - 8 - 2 - 8 - 0 - 0 - 4 - 7 - 0 - 7 - AMYDVLT - ALYDVVS - A+YDV++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 33 - Query_33 - M_159 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 34 - Query_34 - M_160 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 35 - Query_35 - M_161 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 36 - Query_36 - M_162 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 37 - Query_37 - M_163 - 9 - - - 1 - gnl|BL_ORD_ID|1136 - 75040|Protein P|P03159.1|Hepatitis B virus|10407 - 1136 - 9 - - - 1 - 13.4678 - 23 - 8.42175 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 6 - 0 - 9 - FSDDGVLGP - YMDDVVLGA - + DD VLG - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 38 - Query_38 - M_164 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 39 - Query_39 - M_165 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 40 - Query_40 - M_166 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 41 - Query_41 - M_167 - 9 - - - 1 - gnl|BL_ORD_ID|233 - 16796|HBcAg|ABE97049.1|Hepatitis B virus|10407 - 233 - 10 - - - 1 - 13.4678 - 23 - 11.9953 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 6 - 0 - 9 - IPAGSMPTV - LPADFFPSV - +PA P+V - - - - - 2 - gnl|BL_ORD_ID|1933 - 180778|polyprotein|AFP27208.1|Dengue virus 4|11070 - 1933 - 10 - - - 1 - 13.0826 - 22 - 20.8706 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 6 - 0 - 8 - PAGSMPTV - PEGIIPTL - P G +PT+ - - - - - 3 - gnl|BL_ORD_ID|1948 - 180850|polyprotein|AFP27208.1|Dengue virus 4|11070 - 1948 - 10 - - - 1 - 13.0826 - 22 - 21.9749 - 2 - 9 - 3 - 10 - 0 - 0 - 4 - 6 - 0 - 8 - PAGSMPTV - PEGIIPTL - P G +PT+ - - - - - 4 - gnl|BL_ORD_ID|232 - 16795|precore/core protein|AAP57273.1|Hepatitis B virus|10407 - 232 - 10 - - - 1 - 12.6974 - 21 - 23.5358 - 1 - 9 - 2 - 10 - 0 - 0 - 3 - 6 - 0 - 9 - IPAGSMPTV - LPADFFPSI - +PA P++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 42 - Query_42 - M_168 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 43 - Query_43 - M_169 - 9 - - - 1 - gnl|BL_ORD_ID|1196 - 95281|polyprotein|ACE82433.1|Hepatitis C virus genotype 1|41856 - 1196 - 9 - - - 1 - 13.4678 - 23 - 8.87313 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - CLSGYC - CISGVC - C+SG C - - - - - 2 - gnl|BL_ORD_ID|784 - 52509|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 - 784 - 15 - - - 1 - 12.6974 - 21 - 26.5542 - 1 - 6 - 7 - 12 - 0 - 0 - 3 - 5 - 0 - 6 - CLSGYC - CINGVC - C++G C - - - - - 3 - gnl|BL_ORD_ID|66 - 4910|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 66 - 20 - - - 1 - 12.6974 - 21 - 32.3697 - 1 - 6 - 3 - 8 - 0 - 0 - 3 - 5 - 0 - 6 - CLSGYC - CINGVC - C++G C - - - - - 4 - gnl|BL_ORD_ID|1674 - 148619|unnamed protein product|BAA14233.1|Hepatitis C virus|11103 - 1674 - 45 - - - 1 - 12.3122 - 20 - 32.7965 - 1 - 6 - 36 - 41 - 0 - 0 - 3 - 5 - 0 - 6 - CLSGYC - CVNGVC - C++G C - - - - - 5 - gnl|BL_ORD_ID|91 - 6435|polyprotein|BAB18806.1|Hepatitis C virus|11103 - 91 - 9 - - - 1 - 12.6974 - 21 - 35.3877 - 1 - 6 - 1 - 6 - 0 - 0 - 3 - 5 - 0 - 6 - CLSGYC - CINGVC - C++G C - - - - - 6 - gnl|BL_ORD_ID|90 - 6433|Genome polyprotein|SRC279960|Hepatitis C virus subtype 1a|31646 - 90 - 9 - - - 1 - 12.6974 - 21 - 39.1808 - 1 - 6 - 1 - 6 - 0 - 0 - 3 - 5 - 0 - 6 - CLSGYC - CINGVC - C++G C - - - - - 7 - gnl|BL_ORD_ID|89 - 6432|polyprotein [Hepatitis C virus]|CAL46125.1|Hepatitis C virus (isolate H77)|63746 - 89 - 9 - - - 1 - 12.6974 - 21 - 39.8499 - 1 - 6 - 1 - 6 - 0 - 0 - 3 - 5 - 0 - 6 - CLSGYC - CINGLC - C++G C - - - - - 8 - gnl|BL_ORD_ID|65 - 4909|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 - 65 - 15 - - - 1 - 12.3122 - 20 - 39.8759 - 1 - 6 - 3 - 8 - 0 - 0 - 3 - 5 - 0 - 6 - CLSGYC - CINGVC - C++G C - - - - - 9 - gnl|BL_ORD_ID|1194 - 95279|polyprotein|BAG31965.1|Hepatitis C virus|11103 - 1194 - 9 - - - 1 - 12.3122 - 20 - 40.5299 - 1 - 6 - 1 - 6 - 0 - 0 - 3 - 5 - 0 - 6 - CLSGYC - CINGVC - C++G C - - - - - 10 - gnl|BL_ORD_ID|1193 - 95278|polyprotein|BAC67110.1|Hepatitis C virus|11103 - 1193 - 9 - - - 1 - 12.3122 - 20 - 41.221 - 1 - 6 - 1 - 6 - 0 - 0 - 3 - 5 - 0 - 6 - CLSGYC - CINGVC - C++G C - - - - - 11 - gnl|BL_ORD_ID|87 - 6430|polyprotein|BAB18810.1|Hepatitis C virus genotype 1|41856 - 87 - 9 - - - 1 - 12.3122 - 20 - 49.6079 - 1 - 6 - 1 - 6 - 0 - 0 - 3 - 5 - 0 - 6 - CLSGYC - CINGAC - C++G C - - - - - 12 - gnl|BL_ORD_ID|107 - 7292|polyprotein|AAA75355.1|Hepatitis C virus subtype 1b|31647 - 107 - 9 - - - 1 - 12.3122 - 20 - 55.769 - 1 - 6 - 1 - 6 - 0 - 0 - 3 - 5 - 0 - 6 - CLSGYC - CVNGVC - C++G C - - - - - 13 - gnl|BL_ORD_ID|1632 - 146246|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 - 1632 - 17 - - - 1 - 11.927 - 19 - 62.8517 - 1 - 6 - 5 - 10 - 0 - 0 - 3 - 5 - 0 - 6 - CLSGYC - CVNGVC - C++G C - - - - - 14 - gnl|BL_ORD_ID|1198 - 95298|Genome polyprotein|Q913V3.1|Hepatitis C virus (isolate 1)|11104 - 1198 - 9 - - - 1 - 11.927 - 19 - 76.3762 - 1 - 6 - 1 - 6 - 0 - 0 - 3 - 5 - 0 - 6 - CLSGYC - CVNGAC - C++G C - - - - - 15 - gnl|BL_ORD_ID|106 - 7291|neuramindase|AAT73327.1|Influenza A virus (A/Puerto Rico/8/1934(H1N1))|211044 - 106 - 9 - - - 1 - 11.927 - 19 - 91.4136 - 1 - 6 - 1 - 6 - 0 - 0 - 3 - 5 - 0 - 6 - CLSGYC - CVNGSC - C++G C - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 44 - Query_44 - M_170 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 45 - Query_45 - M_171 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 46 - Query_46 - M_172 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 47 - Query_47 - M_173 - 9 - - - 1 - gnl|BL_ORD_ID|2038 - 184453|polyprotein|AFP27207.1|Dengue virus 4|11070 - 2038 - 10 - - - 1 - 11.5418 - 18 - 178.729 - 1 - 9 - 2 - 10 - 0 - 0 - 3 - 5 - 0 - 9 - LIMALVWSL - LLMRTTWAF - L+M W+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 48 - Query_48 - M_174 - 9 - - - 1 - gnl|BL_ORD_ID|2038 - 184453|polyprotein|AFP27207.1|Dengue virus 4|11070 - 2038 - 10 - - - 1 - 11.5418 - 18 - 178.729 - 1 - 9 - 2 - 10 - 0 - 0 - 3 - 5 - 0 - 9 - LIMALVWSL - LLMRTTWAF - L+M W+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 49 - Query_49 - M_175 - 9 - - - 1 - gnl|BL_ORD_ID|2038 - 184453|polyprotein|AFP27207.1|Dengue virus 4|11070 - 2038 - 10 - - - 1 - 11.5418 - 18 - 178.729 - 1 - 9 - 2 - 10 - 0 - 0 - 3 - 5 - 0 - 9 - LIMALVWSL - LLMRTTWAF - L+M W+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 50 - Query_50 - M_176 - 9 - - - 1 - gnl|BL_ORD_ID|832 - 54820|polyprotein precursor|BAA02756.1|Hepatitis C virus|11103 - 832 - 9 - - - 1 - 15.3938 - 28 - 0.794531 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - VWSLPCGF - LWHYPCTF - +W PC F - - - - - 2 - gnl|BL_ORD_ID|1149 - 75636|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 1149 - 10 - - - 1 - 13.4678 - 23 - 9.90554 - 2 - 7 - 3 - 8 - 0 - 0 - 3 - 4 - 0 - 6 - VWSLPC - LWHYPC - +W PC - - - - - 3 - gnl|BL_ORD_ID|831 - 54819|JK3|CAA43789.1|Hepatitis C virus|11103 - 831 - 9 - - - 1 - 13.4678 - 23 - 11.5219 - 2 - 7 - 2 - 7 - 0 - 0 - 3 - 4 - 0 - 6 - VWSLPC - LWHYPC - +W PC - - - - - 4 - gnl|BL_ORD_ID|834 - 54824|polyprotein precursor|BAA01583.1|Hepatitis C virus|11103 - 834 - 9 - - - 1 - 13.4678 - 23 - 12.1399 - 2 - 7 - 2 - 7 - 0 - 0 - 3 - 4 - 0 - 6 - VWSLPC - LWHYPC - +W PC - - - - - 5 - gnl|BL_ORD_ID|833 - 54821|E2 protein|AAM33354.1|Hepatitis C virus subtype 1a|31646 - 833 - 9 - - - 1 - 13.4678 - 23 - 12.3531 - 2 - 7 - 2 - 7 - 0 - 0 - 3 - 4 - 0 - 6 - VWSLPC - LWHYPC - +W PC - - - - - 6 - gnl|BL_ORD_ID|835 - 54825|polyprotein|BAA03375.1|Hepatitis C virus|11103 - 835 - 9 - - - 1 - 13.4678 - 23 - 13.2439 - 2 - 7 - 2 - 7 - 0 - 0 - 3 - 4 - 0 - 6 - VWSLPC - LWHYPC - +W PC - - - - - 7 - gnl|BL_ORD_ID|1372 - 108277|IE62|AAP32859.1|Human alphaherpesvirus 3|10335 - 1372 - 9 - - - 1 - 12.6974 - 21 - 30.8766 - 2 - 6 - 2 - 6 - 0 - 0 - 3 - 5 - 0 - 5 - VWSLP - LWALP - +W+LP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 51 - Query_51 - M_177 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 52 - Query_52 - M_178 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 53 - Query_53 - M_179 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 54 - Query_54 - M_180 - 9 - - - 1 - gnl|BL_ORD_ID|419 - 25275|Glutamate decarboxylase 2|Q05329.1|Homo sapiens|9606 - 419 - 13 - - - 1 - 12.6974 - 21 - 35.1136 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 6 - 0 - 8 - VAFFSSHT - IAFTSEHS - +AF S H+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 55 - Query_55 - M_181 - 9 - - - 1 - gnl|BL_ORD_ID|419 - 25275|Glutamate decarboxylase 2|Q05329.1|Homo sapiens|9606 - 419 - 13 - - - 1 - 13.0826 - 22 - 13.9136 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 7 - 0 - 9 - VAFFSSHTY - IAFTSEHSH - +AF S H++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 56 - Query_56 - M_182 - 9 - - - 1 - gnl|BL_ORD_ID|419 - 25275|Glutamate decarboxylase 2|Q05329.1|Homo sapiens|9606 - 419 - 13 - - - 1 - 13.0826 - 22 - 13.9136 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 7 - 0 - 9 - VAFFSSHTY - IAFTSEHSH - +AF S H++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 57 - Query_57 - M_183 - 9 - - - 1 - gnl|BL_ORD_ID|419 - 25275|Glutamate decarboxylase 2|Q05329.1|Homo sapiens|9606 - 419 - 13 - - - 1 - 13.0826 - 22 - 13.9136 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 7 - 0 - 9 - VAFFSSHTY - IAFTSEHSH - +AF S H++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 58 - Query_58 - M_184 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 59 - Query_59 - M_185 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 60 - Query_60 - M_186 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 61 - Query_61 - M_187 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 62 - Query_62 - M_188 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 63 - Query_63 - M_189 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 64 - Query_64 - M_190 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 65 - Query_65 - M_191 - 9 - - - 1 - gnl|BL_ORD_ID|399 - 24457|polyprotein|BAA09072.1|Hepatitis C virus|11103 - 399 - 15 - - - 1 - 12.3122 - 20 - 44.6122 - 2 - 8 - 6 - 12 - 0 - 0 - 3 - 6 - 0 - 7 - YIIECIA - YIMACMS - YI+ C++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 66 - Query_66 - M_192 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 67 - Query_67 - M_193 - 9 - - - 1 - gnl|BL_ORD_ID|399 - 24457|polyprotein|BAA09072.1|Hepatitis C virus|11103 - 399 - 15 - - - 1 - 12.3122 - 20 - 45.3306 - 1 - 7 - 6 - 12 - 0 - 0 - 3 - 6 - 0 - 7 - YIIECIA - YIMACMS - YI+ C++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 68 - Query_68 - M_194 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 69 - Query_69 - M_195 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 70 - Query_70 - M_196 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 71 - Query_71 - M_197 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 72 - Query_72 - M_198 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 73 - Query_73 - M_199 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 74 - Query_74 - M_200 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 75 - Query_75 - M_201 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 76 - Query_76 - M_202 - 9 - - - 1 - gnl|BL_ORD_ID|579 - 36358|ELAV-like protein 1|Q15717.2|Homo sapiens|9606 - 579 - 9 - - - 1 - 11.5418 - 18 - 130.247 - 1 - 8 - 2 - 9 - 0 - 0 - 5 - 5 - 0 - 8 - GLGFYNDV - GYGFVNYV - G GF N V - - - - - 2 - gnl|BL_ORD_ID|578 - 36357|ELAV-like protein 4 (Paraneoplastic encephalomyelitis antigen HuD) (Hu-antigen D)|P26378.1|Homo sapiens|9606 - 578 - 9 - - - 1 - 11.1566 - 17 - 215.083 - 1 - 8 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - GLGFYNDV - GYGFVNYI - G GF N + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 77 - Query_77 - M_203 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 78 - Query_78 - M_204 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 79 - Query_79 - M_205 - 9 - - - 1 - gnl|BL_ORD_ID|984 - 64967|Circumsporozoite protein precursor|P08677.2|Plasmodium vivax strain Belem|31273 - 984 - 9 - - - 1 - 13.4678 - 23 - 9.68021 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 8 - 0 - 9 - AMDDLDTDM - TLNDLETDV - ++DL+TD+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 80 - Query_80 - M_206 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114432_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114432_1_T.fasta deleted file mode 100755 index b6881013..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114432_1_T.fasta +++ /dev/null @@ -1,198 +0,0 @@ ->M_207 -MITQFELQK ->M_208 -CTAMRVAAK ->M_209 -HFERLTRAL ->M_210 -RLKFGNKHK ->M_211 -ASQQGMAAL ->M_212 -LDYASQQGM ->M_213 -YASQQGMAA ->M_214 -GVRAGRLQL ->M_215 -VRAGRLQLF ->M_216 -LFIHHIQGL ->M_217 -FCSIYITLL ->M_218 -HHSPSTHVM ->M_219 -RSFWSHVVR ->M_220 -AEVEVADKL ->M_221 -KLLENLAKV ->M_222 -MAEAKRMKL ->M_223 -SMAEAKRMK ->M_224 -SYESCDAHF ->M_225 -ASFVPSMGK ->M_226 -FVPSMGKNL ->M_227 -IPASFVPSM ->M_228 -SVSIPASFV ->M_229 -HLGVPVTLR ->M_230 -RVQHLGVPV ->M_231 -NPNTGSVYM ->M_232 -VYMNSQQSL ->M_233 -VYMNSQQSL ->M_234 -EMAKFKVTI ->M_235 -KLFGYEMAK ->M_236 -MAKFKVTIK ->M_237 -HRTIPYLDL ->M_238 -IVWEHRQKL ->M_239 -GMVAPDVVK ->M_240 -HPGVSSQFL ->M_241 -SPRGGPPPL ->M_242 -IVHPLKPQM ->M_243 -KPQMNYQTA ->M_244 -AYCSYCYYF ->M_245 -NAYCSYCYY ->M_246 -SPAPERCMV ->M_247 -ALMDMYPHV ->M_248 -IGVDDRRRL ->M_249 -RRRLCILRM ->M_250 -HFQWILFFV ->M_251 -HVPGAVPNL ->M_252 -SLTGDVSPL ->M_253 -HMVERIQFV ->M_254 -HFERLTRAL ->M_255 -ASQQGMAAL ->M_256 -LDYASQQGM ->M_257 -YASQQGMAA ->M_258 -GVRAGRLQL ->M_259 -VRAGRLQLF ->M_260 -APAGGTASA ->M_261 -HHSPSTHVM ->M_262 -FGHITHPCM ->M_263 -RSFWSHVVR ->M_264 -AAAAAAAAT ->M_265 -VSSKSQKLL ->M_266 -YSLSPVSSK ->M_267 -AEVEVADKL ->M_268 -KLLENLAKV ->M_269 -MAEAKRMKL ->M_270 -SMAEAKRMK ->M_271 -YRWCGFPQL ->M_272 -YRWCGFPQL ->M_273 -SYESCDAHF ->M_274 -FLVGLWSHL ->M_275 -KPRFLVGLW ->M_276 -LVGLWSHLL ->M_277 -MPPYYVGPL ->M_278 -TALPTYPPY ->M_279 -FEGFPQSPL ->M_280 -NPNTGSVYM ->M_281 -VYMNSQQSL ->M_282 -VYMNSQQSL ->M_283 -KRQQFGSQF ->M_284 -DPFALFFMA ->M_285 -EYAADPFAL ->M_286 -YAADPFALF ->M_287 -HRTIPYLDL ->M_288 -IVWEHRQKL ->M_289 -HSVAIVSPF ->M_290 -RIGFVGLFH ->M_291 -HPGVSSQFL ->M_292 -IVHPLKPQM ->M_293 -KPQMNYQTA ->M_294 -AYCSYCYYF ->M_295 -NAYCSYCYY ->M_296 -SPAPERCMV ->M_297 -LTLAVYLSF ->M_298 -ALMDMYPHV ->M_299 -IGVDDRRRL ->M_300 -RRRLCILRM ->M_301 -DTAWDTLEL ->M_302 -TAWDTLELI ->M_303 -TAWDTLELI ->M_304 -MSVSQKLTL ->M_305 -HQRAHTGEK diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114432_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114432_1_T_iedb.xml deleted file mode 100755 index 12a5b419..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114432_1_T_iedb.xml +++ /dev/null @@ -1,3164 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_207 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_207 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_208 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_209 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_210 - 9 - - - 1 - gnl|BL_ORD_ID|829 - 54741|gag polyprotein|BAA00992.1|Human immunodeficiency virus 1|11676 - 829 - 9 - - - 1 - 12.3122 - 20 - 52.1643 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 6 - 0 - 9 - RLKFGNKHK - RLRPGGKKK - RL+ G K K - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 5 - Query_5 - M_211 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_212 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_213 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_214 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_215 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_216 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_217 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_218 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_219 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_220 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_221 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_222 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_223 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_224 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_225 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_226 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_227 - 9 - - - 1 - gnl|BL_ORD_ID|232 - 16795|precore/core protein|AAP57273.1|Hepatitis B virus|10407 - 232 - 10 - - - 1 - 15.3938 - 28 - 0.822133 - 1 - 9 - 2 - 10 - 0 - 0 - 5 - 7 - 0 - 9 - IPASFVPSM - LPADFFPSI - +PA F PS+ - - - - - 2 - gnl|BL_ORD_ID|233 - 16796|HBcAg|ABE97049.1|Hepatitis B virus|10407 - 233 - 10 - - - 1 - 15.0086 - 27 - 1.04324 - 1 - 9 - 2 - 10 - 0 - 0 - 5 - 7 - 0 - 9 - IPASFVPSM - LPADFFPSV - +PA F PS+ - - - - - 3 - gnl|BL_ORD_ID|566 - 35237|nonstructural protein 3|NP_722463.1|Dengue virus type 1 Hawaii|10000440 - 566 - 20 - - - 1 - 13.4678 - 23 - 10.3889 - 1 - 8 - 11 - 18 - 0 - 0 - 5 - 5 - 0 - 8 - IPASFVPS - IPALFEPE - IPA F P - - - - - 4 - gnl|BL_ORD_ID|993 - 65550|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 993 - 15 - - - 1 - 12.3122 - 20 - 50.6727 - 1 - 8 - 6 - 13 - 0 - 0 - 4 - 5 - 0 - 8 - IPASFVPS - IPSMFEPE - IP+ F P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 22 - Query_22 - M_228 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_229 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_230 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_231 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_232 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_233 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 28 - Query_28 - M_234 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 29 - Query_29 - M_235 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 30 - Query_30 - M_236 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 31 - Query_31 - M_237 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 32 - Query_32 - M_238 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 33 - Query_33 - M_239 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 34 - Query_34 - M_240 - 9 - - - 1 - gnl|BL_ORD_ID|1152 - 75718|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 1152 - 11 - - - 1 - 14.6234 - 26 - 2.31378 - 1 - 8 - 4 - 11 - 0 - 0 - 4 - 6 - 0 - 8 - HPGVSSQF - HPTFTSQY - HP +SQ+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 35 - Query_35 - M_241 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 36 - Query_36 - M_242 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 37 - Query_37 - M_243 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 38 - Query_38 - M_244 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 39 - Query_39 - M_245 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 40 - Query_40 - M_246 - 9 - - - 1 - gnl|BL_ORD_ID|859 - 56310|polyprotein|AGO67248.1|Dengue virus 2|11060 - 859 - 10 - - - 1 - 13.853 - 24 - 5.38895 - 4 - 8 - 5 - 9 - 0 - 0 - 4 - 4 - 0 - 5 - PERCM - PRRCM - P RCM - - - - - 2 - gnl|BL_ORD_ID|2076 - 185200|polyprotein|AGO67248.1|Dengue virus 2|11060 - 2076 - 10 - - - 1 - 13.853 - 24 - 6.19145 - 4 - 8 - 1 - 5 - 0 - 0 - 4 - 4 - 0 - 5 - PERCM - PRRCM - P RCM - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 41 - Query_41 - M_247 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 42 - Query_42 - M_248 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 43 - Query_43 - M_249 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 44 - Query_44 - M_250 - 9 - - - 1 - gnl|BL_ORD_ID|325 - 21041|Membrane glycoprotein|Q692E0|SARS coronavirus TJF|284672 - 325 - 9 - - - 1 - 11.927 - 19 - 104.062 - 2 - 9 - 2 - 9 - 0 - 0 - 3 - 5 - 0 - 8 - FQWILFFV - LMWLSYFV - W+ +FV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 45 - Query_45 - M_251 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 46 - Query_46 - M_252 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 47 - Query_47 - M_253 - 9 - - - 1 - gnl|BL_ORD_ID|1799 - 164551|envelope glycoprotein B|NP_044629.1|Herpes simplex virus (type 1 / strain 17)|10299 - 1799 - 9 - - - 1 - 11.5418 - 18 - 159.996 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 6 - 0 - 8 - MVERIQFV - MLEDHEFV - M+E +FV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 48 - Query_48 - M_254 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 49 - Query_49 - M_255 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 50 - Query_50 - M_256 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 51 - Query_51 - M_257 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 52 - Query_52 - M_258 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 53 - Query_53 - M_259 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 54 - Query_54 - M_260 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 55 - Query_55 - M_261 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 56 - Query_56 - M_262 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 57 - Query_57 - M_263 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 58 - Query_58 - M_264 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 59 - Query_59 - M_265 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 60 - Query_60 - M_266 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 61 - Query_61 - M_267 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 62 - Query_62 - M_268 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 63 - Query_63 - M_269 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 64 - Query_64 - M_270 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 65 - Query_65 - M_271 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 66 - Query_66 - M_272 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 67 - Query_67 - M_273 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 68 - Query_68 - M_274 - 9 - - - 1 - gnl|BL_ORD_ID|1114 - 73862|EBNA-1 protein|Q777E1|Human gammaherpesvirus 4|10376 - 1114 - 15 - - - 1 - 13.0826 - 22 - 17.2424 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 7 - 0 - 9 - FLVGLWSHL - FMVFLQTHI - F+V L +H+ - - - - - 2 - gnl|BL_ORD_ID|254 - 17110|EBNA-1 protein|Q777E1|Human gammaherpesvirus 4|10376 - 254 - 9 - - - 1 - 13.0826 - 22 - 19.071 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 7 - 0 - 9 - FLVGLWSHL - FMVFLQTHI - F+V L +H+ - - - - - 3 - gnl|BL_ORD_ID|623 - 37498|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 - 623 - 10 - - - 1 - 12.6974 - 21 - 25.2038 - 1 - 7 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - FLVGLWS - LLLGLWG - L+GLW - - - - - 4 - gnl|BL_ORD_ID|616 - 37351|trans-sialidase, putative|EAN81560.1|Trypanosoma cruzi|5693 - 616 - 10 - - - 1 - 12.6974 - 21 - 34.2302 - 2 - 6 - 1 - 5 - 0 - 0 - 4 - 5 - 0 - 5 - LVGLW - LLGLW - L+GLW - - - - - 5 - gnl|BL_ORD_ID|615 - 37350|trans-sialidase|XP_818394.1|Trypanosoma cruzi|5693 - 615 - 10 - - - 1 - 12.6974 - 21 - 34.2302 - 2 - 7 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - LVGLWS - LLGLWG - L+GLW - - - - - 6 - gnl|BL_ORD_ID|614 - 37347|Sialidase 85-1.1 precursor|P18269.2|Trypanosoma cruzi|5693 - 614 - 10 - - - 1 - 12.6974 - 21 - 34.2302 - 2 - 7 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - LVGLWS - LLGLWG - L+GLW - - - - - 7 - gnl|BL_ORD_ID|1253 - 98223|trans-sialidase, putative|EAN80725.1|Trypanosoma cruzi|5693 - 1253 - 9 - - - 1 - 12.6974 - 21 - 35.3877 - 2 - 7 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - LVGLWS - LLGLWG - L+GLW - - - - - 8 - gnl|BL_ORD_ID|918 - 59766|Genome polyprotein|P27958.3|Hepatitis C virus (isolate H)|11108 - 918 - 9 - - - 1 - 12.3122 - 20 - 46.3849 - 2 - 9 - 2 - 9 - 0 - 0 - 3 - 6 - 0 - 8 - LVGLWSHL - MVGNWAKV - +VG W+ + - - - - - 9 - gnl|BL_ORD_ID|919 - 59767|polyprotein|BAB18806.1|Hepatitis C virus subtype 1a|31646 - 919 - 10 - - - 1 - 12.3122 - 20 - 56.5271 - 2 - 9 - 2 - 9 - 0 - 0 - 3 - 6 - 0 - 8 - LVGLWSHL - MVGNWAKV - +VG W+ + - - - - - 10 - gnl|BL_ORD_ID|1686 - 149052|E1 protein|NP_751920.1|Hepatitis C virus (isolate H77)|63746 - 1686 - 18 - - - 1 - 11.927 - 19 - 66.2126 - 2 - 9 - 7 - 14 - 0 - 0 - 3 - 6 - 0 - 8 - LVGLWSHL - MVGNWAKV - +VG W+ + - - - - - 11 - gnl|BL_ORD_ID|321 - 21004|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 - 321 - 10 - - - 1 - 7.30463 - 7 - 12470.7 - 5 - 6 - 7 - 8 - 0 - 0 - 2 - 2 - 0 - 2 - LW - LW - LW - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 69 - Query_69 - M_275 - 9 - - - 1 - gnl|BL_ORD_ID|2086 - 185468|polyprotein|AGW21594.1|Dengue virus 1|11053 - 2086 - 10 - - - 1 - 14.2382 - 25 - 3.44317 - 1 - 8 - 1 - 8 - 0 - 0 - 5 - 6 - 0 - 8 - KPRFLVGL - RPMFAVGL - +P F VGL - - - - - 2 - gnl|BL_ORD_ID|2277 - 419037|polyprotein|AEF01538.1|Dengue virus 1|11053 - 2277 - 10 - - - 1 - 13.4678 - 23 - 9.90554 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 6 - 0 - 8 - KPRFLVGL - RPMFAVGI - +P F VG+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 70 - Query_70 - M_276 - 9 - - - 1 - gnl|BL_ORD_ID|919 - 59767|polyprotein|BAB18806.1|Hepatitis C virus subtype 1a|31646 - 919 - 10 - - - 1 - 13.4678 - 23 - 9.23902 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 7 - 0 - 9 - LVGLWSHLL - MVGNWAKVL - +VG W+ +L - - - - - 2 - gnl|BL_ORD_ID|1686 - 149052|E1 protein|NP_751920.1|Hepatitis C virus (isolate H77)|63746 - 1686 - 18 - - - 1 - 13.0826 - 22 - 12.6766 - 1 - 9 - 7 - 15 - 0 - 0 - 4 - 7 - 0 - 9 - LVGLWSHLL - MVGNWAKVL - +VG W+ +L - - - - - 3 - gnl|BL_ORD_ID|623 - 37498|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 - 623 - 10 - - - 1 - 12.3122 - 20 - 39.1729 - 1 - 6 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - LVGLWS - LLGLWG - L+GLW - - - - - 4 - gnl|BL_ORD_ID|615 - 37350|trans-sialidase|XP_818394.1|Trypanosoma cruzi|5693 - 615 - 10 - - - 1 - 12.3122 - 20 - 39.1729 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - LVGLWS - LLGLWG - L+GLW - - - - - 5 - gnl|BL_ORD_ID|614 - 37347|Sialidase 85-1.1 precursor|P18269.2|Trypanosoma cruzi|5693 - 614 - 10 - - - 1 - 12.3122 - 20 - 39.1729 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - LVGLWS - LLGLWG - L+GLW - - - - - 6 - gnl|BL_ORD_ID|616 - 37351|trans-sialidase, putative|EAN81560.1|Trypanosoma cruzi|5693 - 616 - 10 - - - 1 - 12.3122 - 20 - 39.8368 - 1 - 5 - 1 - 5 - 0 - 0 - 4 - 5 - 0 - 5 - LVGLW - LLGLW - L+GLW - - - - - 7 - gnl|BL_ORD_ID|1253 - 98223|trans-sialidase, putative|EAN80725.1|Trypanosoma cruzi|5693 - 1253 - 9 - - - 1 - 12.3122 - 20 - 41.221 - 1 - 6 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - LVGLWS - LLGLWG - L+GLW - - - - - 8 - gnl|BL_ORD_ID|918 - 59766|Genome polyprotein|P27958.3|Hepatitis C virus (isolate H)|11108 - 918 - 9 - - - 1 - 12.3122 - 20 - 47.1713 - 1 - 8 - 2 - 9 - 0 - 0 - 3 - 6 - 0 - 8 - LVGLWSHL - MVGNWAKV - +VG W+ + - - - - - 9 - gnl|BL_ORD_ID|321 - 21004|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 - 321 - 10 - - - 1 - 7.68983 - 8 - 12187.2 - 4 - 5 - 7 - 8 - 0 - 0 - 2 - 2 - 0 - 2 - LW - LW - LW - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 71 - Query_71 - M_277 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 72 - Query_72 - M_278 - 9 - - - 1 - gnl|BL_ORD_ID|471 - 28594|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 - 471 - 20 - - - 1 - 12.3122 - 20 - 38.3641 - 2 - 8 - 2 - 8 - 0 - 0 - 4 - 6 - 0 - 7 - ALPTYPP - SLPSYYP - +LP+Y P - - - - - 2 - gnl|BL_ORD_ID|776 - 51643|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 - 776 - 20 - - - 1 - 12.3122 - 20 - 53.6149 - 2 - 8 - 12 - 18 - 0 - 0 - 4 - 6 - 0 - 7 - ALPTYPP - SLPSYYP - +LP+Y P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 73 - Query_73 - M_279 - 9 - - - 1 - gnl|BL_ORD_ID|273 - 18390|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 273 - 20 - - - 1 - 14.2382 - 25 - 3.85699 - 4 - 9 - 3 - 8 - 0 - 0 - 4 - 6 - 0 - 6 - FPQSPL - FPRAPL - FP++PL - - - - - 2 - gnl|BL_ORD_ID|946 - 62355|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 946 - 20 - - - 1 - 13.853 - 24 - 4.4203 - 4 - 9 - 10 - 15 - 0 - 0 - 4 - 6 - 0 - 6 - FPQSPL - FPRAPL - FP++PL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 74 - Query_74 - M_280 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 75 - Query_75 - M_281 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 76 - Query_76 - M_282 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 77 - Query_77 - M_283 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 78 - Query_78 - M_284 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 79 - Query_79 - M_285 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 80 - Query_80 - M_286 - 9 - - - 1 - gnl|BL_ORD_ID|1587 - 141484|capsid maturation protease|NP_044627.1|Human alphaherpesvirus 1|10298 - 1587 - 9 - - - 1 - 10.3862 - 15 - 583.315 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 5 - 0 - 9 - YAADPFALF - YVAGFLALY - Y A AL+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 81 - Query_81 - M_287 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 82 - Query_82 - M_288 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 83 - Query_83 - M_289 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 84 - Query_84 - M_290 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 85 - Query_85 - M_291 - 9 - - - 1 - gnl|BL_ORD_ID|1152 - 75718|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 1152 - 11 - - - 1 - 14.6234 - 26 - 2.31378 - 1 - 8 - 4 - 11 - 0 - 0 - 4 - 6 - 0 - 8 - HPGVSSQF - HPTFTSQY - HP +SQ+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 86 - Query_86 - M_292 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 87 - Query_87 - M_293 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 88 - Query_88 - M_294 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 89 - Query_89 - M_295 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 90 - Query_90 - M_296 - 9 - - - 1 - gnl|BL_ORD_ID|859 - 56310|polyprotein|AGO67248.1|Dengue virus 2|11060 - 859 - 10 - - - 1 - 13.853 - 24 - 5.38895 - 4 - 8 - 5 - 9 - 0 - 0 - 4 - 4 - 0 - 5 - PERCM - PRRCM - P RCM - - - - - 2 - gnl|BL_ORD_ID|2076 - 185200|polyprotein|AGO67248.1|Dengue virus 2|11060 - 2076 - 10 - - - 1 - 13.853 - 24 - 6.19145 - 4 - 8 - 1 - 5 - 0 - 0 - 4 - 4 - 0 - 5 - PERCM - PRRCM - P RCM - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 91 - Query_91 - M_297 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 92 - Query_92 - M_298 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 93 - Query_93 - M_299 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 94 - Query_94 - M_300 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 95 - Query_95 - M_301 - 9 - - - 1 - gnl|BL_ORD_ID|1924 - 180726|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1924 - 15 - - - 1 - 15.0086 - 27 - 0.917715 - 1 - 5 - 7 - 11 - 0 - 0 - 5 - 5 - 0 - 5 - DTAWD - DTAWD - DTAWD - - - - - 2 - gnl|BL_ORD_ID|439 - 27061|envelope glycoprotein|ABU89742.1|Dengue virus 2 Thailand/16681/84|31634 - 439 - 10 - - - 1 - 15.0086 - 27 - 1.37261 - 1 - 5 - 4 - 8 - 0 - 0 - 5 - 5 - 0 - 5 - DTAWD - DTAWD - DTAWD - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 96 - Query_96 - M_302 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 97 - Query_97 - M_303 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 98 - Query_98 - M_304 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 99 - Query_99 - M_305 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114445_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114445_1_T.fasta deleted file mode 100755 index 4d08ad1b..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114445_1_T.fasta +++ /dev/null @@ -1,40 +0,0 @@ ->M_306 -AVATITQAL ->M_307 -TTVNGNTAL ->M_308 -EYYSQTTGL ->M_309 -YYSQTTGLC ->M_310 -CPSEPNTPM ->M_311 -TPMARTFDW ->M_312 -GHYEVRASL ->M_313 -HYEVRASLL ->M_314 -MYWRRSQCC ->M_315 -DYPNAYTTW ->M_316 -RYSDYPNAY ->M_317 -AADLPILTW ->M_318 -WLLAADLPI ->M_319 -IPPEANITI ->M_320 -TVHNLCHIL ->M_321 -FFVEKRHAF ->M_322 -LPLTRSMSI ->M_323 -AAAAATSAL ->M_324 -SIYAYHVEW ->M_325 -AYPQYVIEY diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114445_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114445_1_T_iedb.xml deleted file mode 100755 index 59c917ba..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114445_1_T_iedb.xml +++ /dev/null @@ -1,866 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_306 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_306 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_307 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_308 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_309 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_310 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_311 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_312 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_313 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_314 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_315 - 9 - - - 1 - gnl|BL_ORD_ID|2124 - 186550|polyprotein|AFY10039.1|Dengue virus 4|11070 - 2124 - 10 - - - 1 - 14.2382 - 25 - 4.23087 - 1 - 9 - 2 - 10 - 0 - 0 - 5 - 5 - 0 - 9 - DYPNAYTTW - DQENPYRTW - D N Y TW - - - - - 2 - gnl|BL_ORD_ID|1174 - 79351|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 1174 - 17 - - - 1 - 13.4678 - 23 - 10.1282 - 3 - 9 - 1 - 7 - 0 - 0 - 4 - 4 - 0 - 7 - PNAYTTW - QNLYTLW - N YT W - - - - - 3 - gnl|BL_ORD_ID|1097 - 72563|polyprotein|AAB70696.1|Dengue virus type 1 Hawaii|10000440 - 1097 - 20 - - - 1 - 13.0826 - 22 - 14.6415 - 1 - 9 - 4 - 12 - 0 - 0 - 5 - 5 - 0 - 9 - DYPNAYTTW - DEDNPYKTW - D N Y TW - - - - - 4 - gnl|BL_ORD_ID|2189 - 190533|nucleocapsid protein|AAP49024.1|SARS coronavirus|227859 - 2189 - 15 - - - 1 - 12.3122 - 20 - 57.5015 - 3 - 9 - 7 - 13 - 0 - 0 - 3 - 4 - 0 - 7 - PNAYTTW - PNNIASW - PN +W - - - - - 5 - gnl|BL_ORD_ID|850 - 55683|nucleocapsid protein|ABI96968.1|SARS coronavirus|227859 - 850 - 15 - - - 1 - 11.5418 - 18 - 120.288 - 3 - 9 - 7 - 13 - 0 - 0 - 3 - 4 - 0 - 7 - PNAYTTW - PNNTASW - PN +W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 11 - Query_11 - M_316 - 9 - - - 1 - gnl|BL_ORD_ID|878 - 57703|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 - 878 - 15 - - - 1 - 13.4678 - 23 - 7.23267 - 3 - 7 - 1 - 5 - 0 - 0 - 4 - 5 - 0 - 5 - SDYPN - SEYPN - S+YPN - - - - - 2 - gnl|BL_ORD_ID|559 - 34598|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 559 - 15 - - - 1 - 12.6974 - 21 - 22.89 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 6 - 0 - 9 - RYSDYPNAY - KYSPFRNGY - +YS + N Y - - - - - 3 - gnl|BL_ORD_ID|657 - 38974|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 657 - 11 - - - 1 - 12.6974 - 21 - 27.7331 - 1 - 6 - 6 - 11 - 0 - 0 - 3 - 6 - 0 - 6 - RYSDYP - QYSEHP - +YS++P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 12 - Query_12 - M_317 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_318 - 9 - - - 1 - gnl|BL_ORD_ID|1438 - 120093|unnamed protein product|CAA33016.1|Rubella virus|11041 - 1438 - 21 - - - 1 - 11.927 - 19 - 61.829 - 1 - 8 - 4 - 11 - 0 - 0 - 3 - 4 - 0 - 8 - WLLAADLP - WCVEHDRP - W + D P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 14 - Query_14 - M_319 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_320 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_321 - 9 - - - 1 - gnl|BL_ORD_ID|2009 - 183781|polyprotein|AGO67248.1|Dengue virus 2|11060 - 2009 - 10 - - - 1 - 14.2382 - 25 - 4.15863 - 3 - 9 - 4 - 10 - 0 - 0 - 4 - 5 - 0 - 7 - VEKRHAF - LEKRHVL - +EKRH - - - - - 2 - gnl|BL_ORD_ID|2055 - 184755|polyprotein|AGO67248.1|Dengue virus 2|11060 - 2055 - 9 - - - 1 - 13.853 - 24 - 4.75595 - 3 - 9 - 3 - 9 - 0 - 0 - 4 - 5 - 0 - 7 - VEKRHAF - LEKRHVL - +EKRH - - - - - 3 - gnl|BL_ORD_ID|2031 - 184337|polyprotein|AGO67248.1|Dengue virus 2|11060 - 2031 - 10 - - - 1 - 13.853 - 24 - 5.38895 - 3 - 9 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - VEKRHAF - LEKRHVL - +EKRH - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 17 - Query_17 - M_322 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_323 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_324 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_325 - 9 - - - 1 - gnl|BL_ORD_ID|608 - 37254|||| - 608 - 9 - - - 1 - 13.853 - 24 - 7.58732 - 1 - 6 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - AYPQYV - GYPRYV - YP+YV - - - - - 2 - gnl|BL_ORD_ID|1170 - 79294|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 1170 - 15 - - - 1 - 12.3122 - 20 - 46.8002 - 1 - 6 - 4 - 9 - 0 - 0 - 4 - 4 - 0 - 6 - AYPQYV - GYPVYV - YP YV - - - - - 3 - gnl|BL_ORD_ID|389 - 23807|tax|AAG48731.1|Human T-lymphotropic virus 2|11909 - 389 - 23 - - - 1 - 12.3122 - 20 - 48.9251 - 1 - 7 - 12 - 18 - 0 - 0 - 4 - 4 - 0 - 7 - AYPQYVI - GYPVYVF - YP YV - - - - - 4 - gnl|BL_ORD_ID|572 - 35845|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 572 - 9 - - - 1 - 12.3122 - 20 - 61.624 - 1 - 6 - 3 - 8 - 0 - 0 - 4 - 4 - 0 - 6 - AYPQYV - GYPVYV - YP YV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114843_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114843_1_T.fasta deleted file mode 100755 index da28f85e..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114843_1_T.fasta +++ /dev/null @@ -1,10 +0,0 @@ ->M_326 -FSSKPSSIY ->M_327 -SIYGGLVLI ->M_328 -SAESGAQLL ->M_329 -GIICLDYKL ->M_330 -FEDIGDEDL diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114843_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114843_1_T_iedb.xml deleted file mode 100755 index 0b436b58..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114843_1_T_iedb.xml +++ /dev/null @@ -1,150 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_326 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_326 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_327 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_328 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_329 - 9 - - - 1 - gnl|BL_ORD_ID|2102 - 185978|polyprotein|CDF77361.1|Dengue virus 3|11069 - 2102 - 10 - - - 1 - 12.3122 - 20 - 44.0514 - 1 - 5 - 3 - 7 - 0 - 0 - 3 - 5 - 0 - 5 - GIICL - GVLCL - G++CL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 5 - Query_5 - M_330 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116261_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116261_1_T.fasta deleted file mode 100755 index 8d96174b..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116261_1_T.fasta +++ /dev/null @@ -1,64 +0,0 @@ ->M_331 -IRVEESMHL ->M_332 -AMEKLLSGK ->M_333 -ARTGHLPAM ->M_334 -GHLPAMEKL ->M_335 -QVYHWVCEK ->M_336 -HRWNRFTMI ->M_337 -THRWNRFTM ->M_338 -ITSGLEVIY ->M_339 -ARRFWGKIM ->M_340 -RFWGKIMAK ->M_341 -TYEEATVYI ->M_342 -EHAAALWAL ->M_343 -LVLMNWTKK ->M_344 -FTDTAAESA ->M_345 -NIEDSASFY ->M_346 -SRSDAAKHL ->M_347 -LRWRHCQRL ->M_348 -WRHCQRLDV ->M_349 -VRLGPVKSI ->M_350 -SMQAHIKAL ->M_351 -ESFKQTDFY ->M_352 -QTDFYSMAL ->M_353 -LPWMRLLLL ->M_354 -MRLLLLLLV ->M_355 -PRLPWMRLL ->M_356 -WMRLLLLLL ->M_357 -AIALHRLSL ->M_358 -MRGHDWRML ->M_359 -QMRGHDWRM ->M_360 -HLETHNTDK ->M_361 -CSKLKHRDL ->M_362 -VVGAVGVGK diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116261_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116261_1_T_iedb.xml deleted file mode 100755 index 4883d2fe..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116261_1_T_iedb.xml +++ /dev/null @@ -1,1019 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_331 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_331 - 9 - - - 1 - gnl|BL_ORD_ID|665 - 40158|polyprotein|AAA45534.1|Hepatitis C virus|11103 - 665 - 15 - - - 1 - 13.4678 - 23 - 7.74893 - 2 - 9 - 3 - 10 - 0 - 0 - 4 - 6 - 0 - 8 - RVEESMHL - RVEAQLHV - RVE +H+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 2 - Query_2 - M_332 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_333 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_334 - 9 - - - 1 - gnl|BL_ORD_ID|1271 - 101673|gag protein|ABO73990.1|Human immunodeficiency virus 1|11676 - 1271 - 9 - - - 1 - 13.853 - 24 - 6.83656 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 6 - 0 - 9 - GHLPAMEKL - GHQAAMQML - GH AM+ L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 5 - Query_5 - M_335 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_336 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_337 - 9 - - - 1 - gnl|BL_ORD_ID|1297 - 103389|unnamed protein product [Hepatitis C virus]|BAA14035.1|Hepatitis C virus|11103 - 1297 - 20 - - - 1 - 14.2382 - 25 - 3.035 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 5 - 0 - 9 - THRWNRFTM - THPITKFVM - TH +F M - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 8 - Query_8 - M_338 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_339 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_340 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_341 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_342 - 9 - - - 1 - gnl|BL_ORD_ID|1994 - 183594|polyprotein|AGT63075.1|Dengue virus 1|11053 - 1994 - 10 - - - 1 - 12.6974 - 21 - 30.9217 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 5 - 0 - 8 - HAAALWAL - HPASAWTL - H A+ W L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 13 - Query_13 - M_343 - 9 - - - 1 - gnl|BL_ORD_ID|692 - 42152|polyprotein|AAY82055.1|Hepatitis C virus (isolate H77)|63746 - 692 - 9 - - - 1 - 13.0826 - 22 - 13.4763 - 2 - 8 - 1 - 7 - 0 - 0 - 3 - 6 - 0 - 7 - VLMNWTK - MMMNWSP - ++MNW+ - - - - - 2 - gnl|BL_ORD_ID|1096 - 72322|polyprotein|AAA86907.1|Hepatitis C virus|11103 - 1096 - 15 - - - 1 - 13.0826 - 22 - 15.8531 - 2 - 8 - 3 - 9 - 0 - 0 - 3 - 6 - 0 - 7 - VLMNWTK - MMMNWSP - ++MNW+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 14 - Query_14 - M_344 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_345 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_346 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_347 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_348 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_349 - 9 - - - 1 - gnl|BL_ORD_ID|1651 - 146528|NS3/4A protein|CAM56207.1|Hepatitis C virus|11103 - 1651 - 9 - - - 1 - 15.779 - 29 - 0.508093 - 2 - 8 - 1 - 7 - 0 - 0 - 5 - 7 - 0 - 7 - RLGPVKS - RLGPVQN - RLGPV++ - - - - - 2 - gnl|BL_ORD_ID|2291 - 419325|Genome polyprotein|O92532.3|Hepatitis C virus|11103 - 2291 - 9 - - - 1 - 15.779 - 29 - 0.523878 - 2 - 8 - 1 - 7 - 0 - 0 - 5 - 7 - 0 - 7 - RLGPVKS - RLGPVQN - RLGPV++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 20 - Query_20 - M_350 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_351 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 22 - Query_22 - M_352 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_353 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_354 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_355 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_356 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_357 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 28 - Query_28 - M_358 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 29 - Query_29 - M_359 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 30 - Query_30 - M_360 - 9 - - - 1 - gnl|BL_ORD_ID|1224 - 97111|polyprotein|ABR25251.1|Hepatitis C virus (isolate H77)|63746 - 1224 - 18 - - - 1 - 13.4678 - 23 - 12.4678 - 3 - 9 - 8 - 14 - 0 - 0 - 4 - 5 - 0 - 7 - ETHNTDK - ECHSTDA - E H+TD - - - - - 2 - gnl|BL_ORD_ID|1337 - 107901|Genome polyprotein|P26664.3|Hepatitis C virus|11103 - 1337 - 10 - - - 1 - 13.0826 - 22 - 15.8345 - 3 - 8 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - ETHNTD - ECHSTD - E H+TD - - - - - 3 - gnl|BL_ORD_ID|1320 - 107780|Genome polyprotein|P26664.3|Hepatitis C virus|11103 - 1320 - 10 - - - 1 - 12.6974 - 21 - 30.4011 - 3 - 8 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - ETHNTD - ECHSTD - E H+TD - - - - - 4 - gnl|BL_ORD_ID|1321 - 107781|polyprotein|AAF65953.1|Hepatitis C virus|11103 - 1321 - 10 - - - 1 - 12.6974 - 21 - 35.4066 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - ETHNTDK - ECHSTDS - E H+TD - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 31 - Query_31 - M_361 - 9 - - - 1 - gnl|BL_ORD_ID|470 - 28508|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 470 - 15 - - - 1 - 11.5418 - 18 - 125.819 - 1 - 7 - 6 - 12 - 0 - 0 - 4 - 4 - 0 - 7 - CSKLKHR - CSARLHR - CS HR - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 32 - Query_32 - M_362 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116397_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116397_1_T.fasta deleted file mode 100755 index d653256b..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116397_1_T.fasta +++ /dev/null @@ -1,44 +0,0 @@ ->M_363 -AHPDGSWTF ->M_364 -WGRERGARV ->M_365 -KADIPRDSY ->M_366 -NVLQSSVPV ->M_367 -IITESGEVI ->M_368 -WVYDAIITE ->M_369 -FPPNILDDI ->M_370 -MASQRPLQF ->M_371 -DMHVAVKIV ->M_372 -FARPASPSR ->M_373 -IVFEVFGHH ->M_374 -TTAVLTATF ->M_375 -MAAAVVARL ->M_376 -FSLPPSRKK ->M_377 -LPMCWAMEV ->M_378 -LTYSCLDNK ->M_379 -LLNSGGDII ->M_380 -DIYCITDFV ->M_381 -FVEELADTV ->M_382 -TISCTSLKK ->M_383 -VTISCTSLK ->M_384 -IIIKCQLPK diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116397_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116397_1_T_iedb.xml deleted file mode 100755 index db2f2c3b..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116397_1_T_iedb.xml +++ /dev/null @@ -1,655 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_363 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_363 - 9 - - - 1 - gnl|BL_ORD_ID|1994 - 183594|polyprotein|AGT63075.1|Dengue virus 1|11053 - 1994 - 10 - - - 1 - 15.3938 - 28 - 0.809281 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 5 - 0 - 8 - HPDGSWTF - HPASAWTL - HP +WT - - - - - 2 - gnl|BL_ORD_ID|431 - 26273|nucleocapsid protein|ABI96968.1|SARS coronavirus|227859 - 431 - 15 - - - 1 - 13.4678 - 23 - 11.689 - 3 - 7 - 7 - 11 - 0 - 0 - 3 - 4 - 0 - 5 - PDGSW - PSGTW - P G+W - - - - - 3 - gnl|BL_ORD_ID|2187 - 190494|nucleocapsid protein|ABI96968.1|SARS coronavirus|227859 - 2187 - 10 - - - 1 - 13.0826 - 22 - 14.0252 - 3 - 7 - 5 - 9 - 0 - 0 - 3 - 4 - 0 - 5 - PDGSW - PSGTW - P G+W - - - - - 4 - gnl|BL_ORD_ID|1931 - 180758|Nonstructural protein NS5|NP_739590.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1931 - 15 - - - 1 - 13.0826 - 22 - 16.3955 - 2 - 9 - 8 - 15 - 0 - 0 - 3 - 5 - 0 - 8 - HPDGSWTF - HPYKTWAY - HP +W + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 2 - Query_2 - M_364 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_365 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_366 - 9 - - - 1 - gnl|BL_ORD_ID|1259 - 98308|trans-sialidase, putative|EAN80840.1|Trypanosoma cruzi|5693 - 1259 - 9 - - - 1 - 12.3122 - 20 - 52.1643 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 7 - 0 - 9 - NVLQSSVPV - NVMLVTLPV - NV+ ++PV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 5 - Query_5 - M_367 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_368 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_369 - 9 - - - 1 - gnl|BL_ORD_ID|1917 - 180682|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1917 - 9 - - - 1 - 12.6974 - 21 - 28.3449 - 3 - 9 - 2 - 8 - 0 - 0 - 5 - 5 - 0 - 7 - PNILDDI - PEIEDDI - P I DDI - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 8 - Query_8 - M_370 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_371 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_372 - 9 - - - 1 - gnl|BL_ORD_ID|803 - 53405|||| - 803 - 15 - - - 1 - 13.0826 - 22 - 16.6732 - 4 - 9 - 3 - 8 - 0 - 0 - 4 - 5 - 0 - 6 - PASPSR - PAKPAR - PA P+R - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 11 - Query_11 - M_373 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_374 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_375 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_376 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_377 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_378 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_379 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_380 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_381 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_382 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_383 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 22 - Query_22 - M_384 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116644_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116644_1_T.fasta deleted file mode 100755 index ca704e0b..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116644_1_T.fasta +++ /dev/null @@ -1,60 +0,0 @@ ->M_385 -RYGAGQQNL ->M_386 -TPYAACPAI ->M_387 -SPFNTTFPF ->M_388 -QVARRVQEL ->M_389 -HREARGRAL ->M_390 -AIFGPSNTY ->M_391 -DLFQFPKAY ->M_392 -LPEDPKCEF ->M_393 -SFQPKAAVF ->M_394 -PPSETGGIF ->M_395 -NAGEMVIEY ->M_396 -APTSSDYEF ->M_397 -LFCGLPFSI ->M_398 -VPVASSEAS ->M_399 -DPSPGIMAF ->M_400 -LTYSLLTPL ->M_401 -TYSLLTPLL ->M_402 -CYVAICNPF ->M_403 -LAAMAIDCY ->M_404 -MAIDCYVAI ->M_405 -YFFLGNLAF ->M_406 -FPVEDRRGV ->M_407 -FAQLINNKM ->M_408 -RVASVVVSF ->M_409 -RVASVVVSF ->M_410 -FYLRYFEK* ->M_411 -FFSSNLPTY ->M_412 -FSSNLPTYY ->M_413 -NPYKAPMAE ->M_414 -AFLQKAHLI diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116644_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116644_1_T_iedb.xml deleted file mode 100755 index d99c60f6..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116644_1_T_iedb.xml +++ /dev/null @@ -1,1173 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_385 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_385 - 9 - - - 1 - gnl|BL_ORD_ID|79 - 5783|Nucleoprotein|P03418.1|Human respiratory syncytial virus A2|11259 - 79 - 14 - - - 1 - 14.6234 - 26 - 1.47122 - 2 - 9 - 2 - 9 - 0 - 0 - 6 - 6 - 0 - 8 - YGAGQQNL - YGAGQVML - YGAGQ L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 2 - Query_2 - M_386 - 9 - - - 1 - gnl|BL_ORD_ID|1397 - 110401|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1397 - 25 - - - 1 - 13.853 - 24 - 4.88128 - 1 - 6 - 20 - 25 - 0 - 0 - 4 - 4 - 0 - 6 - TPYAAC - NPYAVC - PYA C - - - - - 2 - gnl|BL_ORD_ID|1387 - 110227|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1387 - 33 - - - 1 - 13.853 - 24 - 5.78904 - 2 - 6 - 13 - 17 - 0 - 0 - 4 - 4 - 0 - 5 - PYAAC - PYAVC - PYA C - - - - - 3 - gnl|BL_ORD_ID|1400 - 110467|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1400 - 25 - - - 1 - 13.853 - 24 - 5.83535 - 1 - 6 - 5 - 10 - 0 - 0 - 4 - 4 - 0 - 6 - TPYAAC - NPYAVC - PYA C - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 3 - Query_3 - M_387 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_388 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_389 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_390 - 9 - - - 1 - gnl|BL_ORD_ID|1205 - 96123|Genome polyprotein|P26664.3|Hepatitis C virus (isolate H77)|63746 - 1205 - 9 - - - 1 - 14.2382 - 25 - 3.80667 - 1 - 5 - 1 - 5 - 0 - 0 - 4 - 5 - 0 - 5 - AIFGP - AVFGP - A+FGP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 7 - Query_7 - M_391 - 9 - - - 1 - gnl|BL_ORD_ID|273 - 18390|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 273 - 20 - - - 1 - 13.0826 - 22 - 14.1742 - 3 - 8 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - FQFPKA - FYFPRA - F FP+A - - - - - 2 - gnl|BL_ORD_ID|946 - 62355|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 946 - 20 - - - 1 - 13.0826 - 22 - 20.1922 - 3 - 8 - 8 - 13 - 0 - 0 - 4 - 5 - 0 - 6 - FQFPKA - FYFPRA - F FP+A - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 8 - Query_8 - M_392 - 9 - - - 1 - gnl|BL_ORD_ID|1179 - 79628|E1 protein|BAA19893.1|Rubella virus|11041 - 1179 - 21 - - - 1 - 12.6974 - 21 - 24.4562 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 4 - 0 - 7 - PEDPKCE - PTDVSCE - P D CE - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 9 - Query_9 - M_393 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_394 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_395 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_396 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_397 - 9 - - - 1 - gnl|BL_ORD_ID|2182 - 190409|polymerase|AAD16253.1|Hepatitis B virus|10407 - 2182 - 15 - - - 1 - 16.5494 - 31 - 0.211832 - 2 - 8 - 8 - 14 - 0 - 0 - 5 - 6 - 0 - 7 - FCGLPFS - FCGSPYS - FCG P+S - - - - - 2 - gnl|BL_ORD_ID|390 - 23864|envelope glycoprotein(gp21, gp46) - human T-cell lymphotropic virus type 1|A45714|Human T-lymphotropic virus 1|11908 - 390 - 9 - - - 1 - 14.2382 - 25 - 3.37936 - 3 - 7 - 5 - 9 - 0 - 0 - 4 - 4 - 0 - 5 - CGLPF - CGFPF - CG PF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 14 - Query_14 - M_398 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_399 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_400 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_401 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_402 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_403 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_404 - 9 - - - 1 - gnl|BL_ORD_ID|2292 - 419366|polyprotein|BAA00792.1|Hepatitis C virus|11103 - 2292 - 9 - - - 1 - 14.2382 - 25 - 2.66858 - 3 - 9 - 3 - 9 - 0 - 0 - 5 - 6 - 0 - 7 - IDCYVAI - IDCNVAV - IDC VA+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 21 - Query_21 - M_405 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 22 - Query_22 - M_406 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_407 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_408 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_409 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_410 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_411 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 28 - Query_28 - M_412 - 9 - - - 1 - gnl|BL_ORD_ID|471 - 28594|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 - 471 - 20 - - - 1 - 13.4678 - 23 - 8.80594 - 4 - 9 - 2 - 7 - 0 - 0 - 4 - 6 - 0 - 6 - NLPTYY - SLPSYY - +LP+YY - - - - - 2 - gnl|BL_ORD_ID|1971 - 182926|polyprotein|AFP27208.1|Dengue virus 4|11070 - 1971 - 9 - - - 1 - 13.4678 - 23 - 9.18751 - 3 - 8 - 3 - 8 - 0 - 0 - 4 - 6 - 0 - 6 - SNLPTY - ASLPTY - ++LPTY - - - - - 3 - gnl|BL_ORD_ID|2100 - 185881|polyprotein|AFP27208.1|Dengue virus 4|11070 - 2100 - 10 - - - 1 - 13.4678 - 23 - 9.73455 - 3 - 8 - 4 - 9 - 0 - 0 - 4 - 6 - 0 - 6 - SNLPTY - ASLPTY - ++LPTY - - - - - 4 - gnl|BL_ORD_ID|776 - 51643|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 - 776 - 20 - - - 1 - 13.4678 - 23 - 10.5613 - 5 - 9 - 13 - 17 - 0 - 0 - 4 - 5 - 0 - 5 - LPTYY - LPSYY - LP+YY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 29 - Query_29 - M_413 - 9 - - - 1 - gnl|BL_ORD_ID|2141 - 187163|Gag polyprotein|P88150|Human immunodeficiency virus 1|11676 - 2141 - 11 - - - 1 - 11.5418 - 18 - 130.32 - 1 - 7 - 4 - 10 - 0 - 0 - 4 - 4 - 0 - 7 - NPYKAPM - NPEVIPM - NP PM - - - - - 2 - gnl|BL_ORD_ID|2139 - 187158|Gag protein|Q1KW74|Human immunodeficiency virus 1|11676 - 2139 - 11 - - - 1 - 11.5418 - 18 - 156.929 - 1 - 7 - 4 - 10 - 0 - 0 - 4 - 4 - 0 - 7 - NPYKAPM - NPEIIPM - NP PM - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 30 - Query_30 - M_414 - 9 - - - 1 - gnl|BL_ORD_ID|2055 - 184755|polyprotein|AGO67248.1|Dengue virus 2|11060 - 2055 - 9 - - - 1 - 11.927 - 19 - 104.062 - 3 - 9 - 3 - 9 - 0 - 0 - 3 - 6 - 0 - 7 - LQKAHLI - LEKRHVL - L+K H++ - - - - - 2 - gnl|BL_ORD_ID|2031 - 184337|polyprotein|AGO67248.1|Dengue virus 2|11060 - 2031 - 10 - - - 1 - 11.927 - 19 - 104.808 - 3 - 9 - 1 - 7 - 0 - 0 - 3 - 6 - 0 - 7 - LQKAHLI - LEKRHVL - L+K H++ - - - - - 3 - gnl|BL_ORD_ID|2009 - 183781|polyprotein|AGO67248.1|Dengue virus 2|11060 - 2009 - 10 - - - 1 - 11.927 - 19 - 108.205 - 3 - 9 - 4 - 10 - 0 - 0 - 3 - 6 - 0 - 7 - LQKAHLI - LEKRHVL - L+K H++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116732_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116732_1_T.fasta deleted file mode 100755 index ab50cfd0..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116732_1_T.fasta +++ /dev/null @@ -1,56 +0,0 @@ ->M_415 -FQGYLKDPV ->M_416 -SEVLGYWAF ->M_417 -SEVLGYWAF ->M_418 -RRFGWLQTA ->M_419 -GHEEKITFI ->M_420 -EESIAVGTM ->M_421 -EESIAVGTM ->M_422 -FRYLGKCNI ->M_423 -FEVGGAALF ->M_424 -FEVGGAALF ->M_425 -GMCVLEMAV ->M_426 -VLEMAVLEI ->M_427 -FLMVSRDCL ->M_428 -SRDCLRTVL ->M_429 -VSRDCLRTV ->M_430 -ALREFKFRV ->M_431 -REFKFRVSA ->M_432 -REFKFRVSA ->M_433 -YEALREFKF ->M_434 -NQMDKLAAF ->M_435 -YRMSPSNQM ->M_436 -KVISYPVAL ->M_437 -TERTKVISY ->M_438 -LHLRRKEIM ->M_439 -QTSCHVFMV ->M_440 -GEAGAGGTA ->M_441 -EHMPNNSRL ->M_442 -PRKPRSQNF diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116732_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116732_1_T_iedb.xml deleted file mode 100755 index 5aa795f9..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116732_1_T_iedb.xml +++ /dev/null @@ -1,832 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_415 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_415 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_416 - 9 - - - 1 - gnl|BL_ORD_ID|1253 - 98223|trans-sialidase, putative|EAN80725.1|Trypanosoma cruzi|5693 - 1253 - 9 - - - 1 - 13.853 - 24 - 7.58732 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - VLGYWAF - LLGLWGF - +LG W F - - - - - 2 - gnl|BL_ORD_ID|616 - 37351|trans-sialidase, putative|EAN81560.1|Trypanosoma cruzi|5693 - 616 - 10 - - - 1 - 13.4678 - 23 - 7.89871 - 3 - 9 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - VLGYWAF - LLGLWVF - +LG W F - - - - - 3 - gnl|BL_ORD_ID|614 - 37347|Sialidase 85-1.1 precursor|P18269.2|Trypanosoma cruzi|5693 - 614 - 10 - - - 1 - 11.927 - 19 - 77.1759 - 3 - 9 - 1 - 7 - 0 - 0 - 3 - 4 - 0 - 7 - VLGYWAF - LLGLWGL - +LG W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 3 - Query_3 - M_417 - 9 - - - 1 - gnl|BL_ORD_ID|1253 - 98223|trans-sialidase, putative|EAN80725.1|Trypanosoma cruzi|5693 - 1253 - 9 - - - 1 - 13.853 - 24 - 7.58732 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - VLGYWAF - LLGLWGF - +LG W F - - - - - 2 - gnl|BL_ORD_ID|616 - 37351|trans-sialidase, putative|EAN81560.1|Trypanosoma cruzi|5693 - 616 - 10 - - - 1 - 13.4678 - 23 - 7.89871 - 3 - 9 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - VLGYWAF - LLGLWVF - +LG W F - - - - - 3 - gnl|BL_ORD_ID|614 - 37347|Sialidase 85-1.1 precursor|P18269.2|Trypanosoma cruzi|5693 - 614 - 10 - - - 1 - 11.927 - 19 - 77.1759 - 3 - 9 - 1 - 7 - 0 - 0 - 3 - 4 - 0 - 7 - VLGYWAF - LLGLWGL - +LG W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 4 - Query_4 - M_418 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_419 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_420 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_421 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_422 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_423 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_424 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_425 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_426 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_427 - 9 - - - 1 - gnl|BL_ORD_ID|1492 - 136837|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 - 1492 - 11 - - - 1 - 11.5418 - 18 - 156.929 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 5 - 0 - 9 - FLMVSRDCL - FLLALLSCL - FL+ CL - - - - - 2 - gnl|BL_ORD_ID|428 - 26111|polyprotein|BAD73987.1|Hepatitis C virus subtype 1b|31647 - 428 - 10 - - - 1 - 11.5418 - 18 - 170.632 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 5 - 0 - 9 - FLMVSRDCL - FLLALLSCL - FL+ CL - - - - - 3 - gnl|BL_ORD_ID|225 - 16706|structural protein|BAA00705.1|Hepatitis C virus|11103 - 225 - 9 - - - 1 - 11.5418 - 18 - 187.089 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 5 - 0 - 9 - FLMVSRDCL - FLLALLSCL - FL+ CL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 14 - Query_14 - M_428 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_429 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_430 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_431 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_432 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_433 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_434 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_435 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 22 - Query_22 - M_436 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_437 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_438 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_439 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_440 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_441 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 28 - Query_28 - M_442 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116846_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116846_1_T.fasta deleted file mode 100755 index c4edc2b0..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116846_1_T.fasta +++ /dev/null @@ -1,56 +0,0 @@ ->M_443 -RQWPRLSHK ->M_444 -ISLAYLVKK ->M_445 -TISLAYLVK ->M_446 -MFLWTVAVI ->M_447 -TVAVIPILF ->M_448 -KIRQLKKKK ->M_449 -NEKTTPSPA ->M_450 -NENATPSPA ->M_451 -RERTANENA ->M_452 -CYLQIFATR ->M_453 -LPPSLQGAV ->M_454 -RVARSHCQR ->M_455 -VPSEPSSSV ->M_456 -EEWCSLWAG ->M_457 -WEEWCSLWA ->M_458 -RLPSYMVEK ->M_459 -SYMVEKREF ->M_460 -GENFCTAVK ->M_461 -MEGYMKAKV ->M_462 -CPLPRPPPI ->M_463 -AEEAGYPLS ->M_464 -EEAGYPLSC ->M_465 -GVYLLFALR ->M_466 -VYLLFALRL ->M_467 -QEASNKHAE ->M_468 -SEYSSSLGR ->M_469 -RESGSFLST ->M_470 -LYQLHNLVV diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116846_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116846_1_T_iedb.xml deleted file mode 100755 index d3bf813a..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116846_1_T_iedb.xml +++ /dev/null @@ -1,882 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_443 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_443 - 9 - - - 1 - gnl|BL_ORD_ID|1173 - 79337|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 1173 - 15 - - - 1 - 13.853 - 24 - 5.77703 - 2 - 8 - 4 - 10 - 0 - 0 - 4 - 4 - 0 - 7 - QWPRLSH - TWPLLPH - WP L H - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 2 - Query_2 - M_444 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_445 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_446 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_447 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_448 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_449 - 9 - - - 1 - gnl|BL_ORD_ID|2288 - 419298|RNA-dependent RNA polymerase|ACH97782.1|Hepatitis C virus|11103 - 2288 - 9 - - - 1 - 11.927 - 19 - 76.3762 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 4 - 0 - 6 - NEKTTP - NSKRTP - N K TP - - - - - 2 - gnl|BL_ORD_ID|1598 - 142244|polyprotein|ACJ37184.1|Hepatitis C virus subtype 1a|31646 - 1598 - 9 - - - 1 - 11.927 - 19 - 84.261 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 4 - 0 - 6 - NEKTTP - NSKKTP - N K TP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 8 - Query_8 - M_450 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_451 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_452 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_453 - 9 - - - 1 - gnl|BL_ORD_ID|746 - 48836|EBNA-1 protein|Q777E1|Human gammaherpesvirus 4|10376 - 746 - 15 - - - 1 - 13.4678 - 23 - 8.59146 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 6 - 0 - 8 - PPSLQGAV - PPMVEGAA - PP ++GA - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 12 - Query_12 - M_454 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_455 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_456 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_457 - 9 - - - 1 - gnl|BL_ORD_ID|2051 - 184702|non-structural protein 1|AGM49312.1|Dengue virus|12637 - 2051 - 9 - - - 1 - 10.7714 - 16 - 469.42 - 1 - 8 - 2 - 9 - 0 - 0 - 3 - 5 - 0 - 8 - WEEWCSLW - WPKTHTLW - W + +LW - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 16 - Query_16 - M_458 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_459 - 9 - - - 1 - gnl|BL_ORD_ID|1799 - 164551|envelope glycoprotein B|NP_044629.1|Herpes simplex virus (type 1 / strain 17)|10299 - 1799 - 9 - - - 1 - 12.6974 - 21 - 23.4633 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - MVEKREF - MLEDHEF - M+E EF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 18 - Query_18 - M_460 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_461 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_462 - 9 - - - 1 - gnl|BL_ORD_ID|1508 - 139406|polyprotein|ACT37184.1|Hepatitis C virus|11103 - 1508 - 10 - - - 1 - 12.3122 - 20 - 39.8368 - 3 - 8 - 3 - 8 - 0 - 0 - 5 - 5 - 0 - 6 - LPRPPP - LPRPGP - LPRP P - - - - - 2 - gnl|BL_ORD_ID|1438 - 120093|unnamed protein product|CAA33016.1|Rubella virus|11041 - 1438 - 21 - - - 1 - 11.927 - 19 - 68.5496 - 5 - 8 - 10 - 13 - 0 - 0 - 4 - 4 - 0 - 4 - RPPP - RPPP - RPPP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 21 - Query_21 - M_463 - 9 - - - 1 - gnl|BL_ORD_ID|2258 - 288104|nef protein|ACR27130.1|Human immunodeficiency virus 1|11676 - 2258 - 18 - - - 1 - 13.0826 - 22 - 13.7716 - 3 - 9 - 1 - 7 - 0 - 0 - 3 - 5 - 0 - 7 - EAGYPLS - EVGFPVR - E G+P+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 22 - Query_22 - M_464 - 9 - - - 1 - gnl|BL_ORD_ID|2258 - 288104|nef protein|ACR27130.1|Human immunodeficiency virus 1|11676 - 2258 - 18 - - - 1 - 13.0826 - 22 - 14.4713 - 2 - 8 - 1 - 7 - 0 - 0 - 3 - 5 - 0 - 7 - EAGYPLS - EVGFPVR - E G+P+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 23 - Query_23 - M_465 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_466 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_467 - 9 - - - 1 - gnl|BL_ORD_ID|53 - 3935|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis|1773 - 53 - 20 - - - 1 - 14.2382 - 25 - 3.6022 - 1 - 7 - 9 - 15 - 0 - 0 - 5 - 6 - 0 - 7 - QEASNKH - QEAANKQ - QEA+NK - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 26 - Query_26 - M_468 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_469 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 28 - Query_28 - M_470 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_118562_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_118562_1_T.fasta deleted file mode 100755 index babdc234..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_118562_1_T.fasta +++ /dev/null @@ -1,2712 +0,0 @@ ->M_471 -YAAPQLHSI ->M_472 -HLHDHYGPY ->M_473 -FAEDGACTV ->M_474 -HVIGTIGHF ->M_475 -FADDEHSMV ->M_476 -YANERPKSL ->M_477 -FACHFTVFV ->M_478 -NALDYICTV ->M_479 -LAYQELPTV ->M_480 -FVMEHSNIV ->M_481 -VAFCTMNVI ->M_482 -FTIRAIQVY ->M_483 -MAISVVKHI ->M_484 -RALEKLNHV ->M_485 -FADMERHHI ->M_486 -FANRRKEEV ->M_487 -LAIDSASPV ->M_488 -RALGPGHTV ->M_489 -FAKVLIRTY ->M_490 -SSDDNDAFY ->M_491 -YPKGRPSHI ->M_492 -WALPKTYTI ->M_493 -LARHWRVHI ->M_494 -FSYSASSEI ->M_495 -FSFFFVNIF ->M_496 -YSFDGMWKV ->M_497 -DSIHQVGMY ->M_498 -MTYDLASVV ->M_499 -LAFPVPLYY ->M_500 -YAALAMGTL ->M_501 -YLFRELATI ->M_502 -YMDLMGFSY ->M_503 -FAISHEGHM ->M_504 -FSSPRLRPI ->M_505 -FVYLHLNMV ->M_506 -MANNPDVMI ->M_507 -AALPAAQTV ->M_508 -FAWKNMDFL ->M_509 -FAAQGPTVF ->M_510 -LALSNLPTV ->M_511 -FTLEFLVCI ->M_512 -FSVDFPRIY ->M_513 -FTIFWTVYY ->M_514 -MADPNQCVI ->M_515 -RAFWAGSVV ->M_516 -YHFDAIRTF ->M_517 -FAKGWLLKL ->M_518 -NAQNMTITV ->M_519 -RALNRVHVL ->M_520 -MAPELISHL ->M_521 -KAFYHPRLI ->M_522 -LAFVIVLLV ->M_523 -CTAVVLLVY ->M_524 -FTEFCDSCY ->M_525 -LAREPVNEL ->M_526 -YTRKRTQSI ->M_527 -FAPSCANSL ->M_528 -KVYDLVHSV ->M_529 -QAPPLMGTI ->M_530 -QAFRRSISV ->M_531 -FVLDHSRLV ->M_532 -FIKRHIAPI ->M_533 -YSQPFYTSY ->M_534 -FAQDVDRMF ->M_535 -QAPEFLQTL ->M_536 -LSDISRSCY ->M_537 -NAYARVLRF ->M_538 -FANFFNTFL ->M_539 -FIYDAVGNM ->M_540 -LARECGSPL ->M_541 -WHGPARPSL ->M_542 -HVMFMVAFY ->M_543 -MAITSMNPV ->M_544 -TAVEFIMAI ->M_545 -QAYGGPRYL ->M_546 -FTIRAIQVY ->M_547 -YLDYVSISY ->M_548 -SAYMHHSKI ->M_549 -YLMEFGQLL ->M_550 -KAEELKETV ->M_551 -FALGVGTAL ->M_552 -LVFPNSDHV ->M_553 -FTLQNPSAV ->M_554 -EIVDQQGHM ->M_555 -FTIFWTVYY ->M_556 -FPNSCLSTL ->M_557 -YSISDWTSI ->M_558 -FTACYIRIV ->M_559 -FEFDHIRNF ->M_560 -YTPDELHAM ->M_561 -FVHPATRPL ->M_562 -KALRITNVY ->M_563 -QARDQGSPV ->M_564 -FIYDAVGNM ->M_565 -EAFPEDVAV ->M_566 -YATADSSSL ->M_567 -RAREHSDTF ->M_568 -IAIQLITHM ->M_569 -MAFENNAGL ->M_570 -FGHENRVSI ->M_571 -NATTIVTTV ->M_572 -VTFPGINLM ->M_573 -DAYPRQYSL ->M_574 -YIQEGFLAV ->M_575 -FATTACHTL ->M_576 -RANQCFAFV ->M_577 -MTQPVWSTI ->M_578 -FTEEGFCAI ->M_579 -FADHPQAPF ->M_580 -VAMGSAALV ->M_581 -TAKDYRVYV ->M_582 -EAEEWVVSY ->M_583 -FTLPLMDQV ->M_584 -MQMPCTIKI ->M_585 -YRYFCRVPV ->M_586 -WAHAWPSPY ->M_587 -IAIISVLVI ->M_588 -MASCPFAKV ->M_589 -NHDRFHYLL ->M_590 -FTIFWTVYY ->M_591 -VASQPAHVV ->M_592 -EAFNCESKM ->M_593 -FSSEVTVAL ->M_594 -ETIKQLQEL ->M_595 -YFMDPMVPL ->M_596 -NVYHVGMHI ->M_597 -AAMEGRLPV ->M_598 -NHDDDDVEI ->M_599 -NASVNVSHL ->M_600 -EALDAGAIY ->M_601 -YGRDDWEVI ->M_602 -VALDKDALV ->M_603 -LPFSLGKHV ->M_604 -MANNPCSRY ->M_605 -YEEPNTATF ->M_606 -MALYHCVAI ->M_607 -YTLAPGVPL ->M_608 -KIHPFFETI ->M_609 -NMDFLIAEY ->M_610 -LCIPWTNPV ->M_611 -SAQEHLLFV ->M_612 -QSVHPVVTV ->M_613 -YVASDIQYM ->M_614 -FHMRQVNIV ->M_615 -LAKHSTSAV ->M_616 -FSHQPKEKV ->M_617 -YLYIPALAV ->M_618 -VALFMAITI ->M_619 -VAFYGLGAV ->M_620 -EVDPIGNLY ->M_621 -WALSIHVSV ->M_622 -ITYPSQAPV ->M_623 -CIALWSLAY ->M_624 -FLFYVMTEV ->M_625 -HAEQDSTTV ->M_626 -DTNDNVPEF ->M_627 -NSYGSRRTL ->M_628 -NARCLIVHL ->M_629 -FWYRNCHHV ->M_630 -DADPSTPHL ->M_631 -DSYIHVTYI ->M_632 -DVFDALDLM ->M_633 -FSMDETGQM ->M_634 -RTFNKPESV ->M_635 -YSLQEMEVL ->M_636 -QTVMFMATM ->M_637 -VTIDGIRFI ->M_638 -RALSHPQSL ->M_639 -TAAGFWLMV ->M_640 -FMEELGECV ->M_641 -YLESNPGTI ->M_642 -VPSNFVEHV ->M_643 -FTEELRRTF ->M_644 -YGRSRGITV ->M_645 -FSMACNTPL ->M_646 -QAADEPQLL ->M_647 -YEFALQRIV ->M_648 -TAAPTSASV ->M_649 -LACRKAREI ->M_650 -FIEPLNDTI ->M_651 -SALRAITRV ->M_652 -RAAPKAMVL ->M_653 -VADEGLNNL ->M_654 -LSNDECKTI ->M_655 -NAWAVMNHF ->M_656 -VASNAWAVM ->M_657 -LSRNLIRTI ->M_658 -HSKEEIKVI ->M_659 -DSELNFNEY ->M_660 -DAAERECHL ->M_661 -ISYTEVPTY ->M_662 -IASDHVVDM ->M_663 -IAILICTMI ->M_664 -MAKTGRFHI ->M_665 -EVMEKVLPL ->M_666 -FENNAGLPV ->M_667 -FLHEMVAAM ->M_668 -QAEPKKKPV ->M_669 -YVLHSKEEI ->M_670 -FFFHNPKPL ->M_671 -FHWNWIIVL ->M_672 -YTMGIIFVL ->M_673 -YVGKDIESV ->M_674 -YQHYFRLLV ->M_675 -MSNSMINTM ->M_676 -FSMLSRVLI ->M_677 -FVDYPGDPV ->M_678 -STAPLYSGM ->M_679 -DTVQLNVKY ->M_680 -SAYMAATLL ->M_681 -QAWNFLRAM ->M_682 -CAFGAMCAV ->M_683 -IMEEEFSTI ->M_684 -HAANVTQAM ->M_685 -MAKQIKTKV ->M_686 -KAKGIYNSI ->M_687 -HAPVHFLVI ->M_688 -EVLQSMQRF ->M_689 -YVASDIQYM ->M_690 -YAAMDLSCL ->M_691 -TPMTCSNTI ->M_692 -EAPPGRVTF ->M_693 -DTHSGAGKF ->M_694 -YKYRYFCRV ->M_695 -LSDPHLTAV ->M_696 -WAGLGGRHV ->M_697 -QHTGTSVVL ->M_698 -STFCGTLEY ->M_699 -TMYRCGPLI ->M_700 -WHNQCSGHL ->M_701 -FPLRNRPFY ->M_702 -YVGPAQLSV ->M_703 -VAQHLATTY ->M_704 -LVYPRFLYL ->M_705 -FSREEMHNM ->M_706 -YYPPGVVFY ->M_707 -YLMSFFRLL ->M_708 -RVFPLRGKI ->M_709 -YPLPVANGM ->M_710 -RAVCFSMEI ->M_711 -QALPLDHHL ->M_712 -FIEPHARFY ->M_713 -FFYCIYASL ->M_714 -CHDDYLVML ->M_715 -KALFWTVAM ->M_716 -EYYEPPHRI ->M_717 -PTSPMPYTY ->M_718 -EAVEARGAI ->M_719 -NVVRLVATI ->M_720 -YLKNSMIAV ->M_721 -LQAEIVETM ->M_722 -FHHKSNFLL ->M_723 -KPIPAFEMV ->M_724 -FLVDSNLSV ->M_725 -FIDRQLTMV ->M_726 -YSASSEIII ->M_727 -YTPDELHAM ->M_728 -FFYLDYVSI ->M_729 -YIAPMMEKL ->M_730 -EAFDRTETH ->M_731 -SIVDVSIMY ->M_732 -IPYTTVLHL ->M_733 -EVFRHKLAM ->M_734 -VMDRWNETV ->M_735 -LLLDHGVHV ->M_736 -VIFNVVRLV ->M_737 -LAIKVTPSV ->M_738 -LTDRQPLMH ->M_739 -KPLPFNREV ->M_740 -LNFGDITTV ->M_741 -QAIDSTFYL ->M_742 -LALNKGRAY ->M_743 -IARQVVTAM ->M_744 -GAFAFGAVF ->M_745 -KSFPFQSLL ->M_746 -RAGGSSVVI ->M_747 -DTIPWYLRL ->M_748 -MAVDGKPEY ->M_749 -YLQDVVMQV ->M_750 -FMVRNYEFL ->M_751 -YMAGSDTTY ->M_752 -VVYVLMTSV ->M_753 -MPAERNGAI ->M_754 -WPLQPVDHI ->M_755 -MLDPHGHLI ->M_756 -FISNSLNIL ->M_757 -RADGDLTLI ->M_758 -YQEEMIQCY ->M_759 -FILDCHPKY ->M_760 -GAYVYPLPV ->M_761 -FKEAWKHTI ->M_762 -LAGVKMVMI ->M_763 -DAKQRIRLL ->M_764 -LYYPPGVVF ->M_765 -RASEDDRVL ->M_766 -SALEYLLPL ->M_767 -AAVEPERTL ->M_768 -GTDCLLLAF ->M_769 -FVQLPVPII ->M_770 -RIYPDRHRI ->M_771 -KVDKNISHI ->M_772 -RHSQWDHGL ->M_773 -MLYSRDHSV ->M_774 -AARPLSRMV ->M_775 -HAQVCSLYI ->M_776 -YSQPFYTSY ->M_777 -MSDFQYLVV ->M_778 -SANARCLIV ->M_779 -SAIAIVQIL ->M_780 -WMFYHFDAI ->M_781 -YSKVIKCVV ->M_782 -AARARGNKV ->M_783 -TAYERLYLW ->M_784 -TTASGVWAF ->M_785 -KVREEVVTM ->M_786 -MYYRVRDTM ->M_787 -YVDRLLQHF ->M_788 -PAIARPQAI ->M_789 -YLLRAGVHL ->M_790 -LVTPHMAEV ->M_791 -EHVSDDDLL ->M_792 -SFYHLVSTV ->M_793 -FSAGNEANV ->M_794 -KPGDRVVLV ->M_795 -YSRGSSRCI ->M_796 -YSTCVLVVL ->M_797 -YSTHQTFMV ->M_798 -WSLDGKYIV ->M_799 -HAWRDLSSM ->M_800 -FASSLWETT ->M_801 -FDYPSLFCI ->M_802 -KAPPLTDVL ->M_803 -DVFDALDLM ->M_804 -ALYCRLATV ->M_805 -MVYLQIGGF ->M_806 -EPFSGTASV ->M_807 -ETMDELELL ->M_808 -SMLNWFSPV ->M_809 -NMLNLTHTY ->M_810 -HSFNPEAQV ->M_811 -SAYGSSGEL ->M_812 -FSIPWAHAW ->M_813 -MASSAQEHL ->M_814 -RHSREMALL ->M_815 -WVLHHMGGM ->M_816 -VADSDRQLV ->M_817 -IAAAWALSF ->M_818 -KAESTPEIV ->M_819 -LHLGHMFSL ->M_820 -QRINLPHLL ->M_821 -YALMRHRHT ->M_822 -RLYPLANSL ->M_823 -DHFSHASSI ->M_824 -ISMEKGYNI ->M_825 -FLHEMVAAM ->M_826 -YVALEAQAI ->M_827 -YLMTRTLPM ->M_828 -QTFPQVSEL ->M_829 -YPESIKAPV ->M_830 -VHSKTSQLL ->M_831 -TSSDRMTSV ->M_832 -QMAERALYY ->M_833 -LASPFATTA ->M_834 -AAYTSYTPY ->M_835 -VSCRPVVYV ->M_836 -RTYHGRLAY ->M_837 -LARHSAAFL ->M_838 -RSEALPVSY ->M_839 -ETKPFGLVV ->M_840 -DVKNFWQGM ->M_841 -FAELKSARM ->M_842 -YMKPRLRTT ->M_843 -STFCGTLEY ->M_844 -HAATGPGEV ->M_845 -PSQNRFLTY ->M_846 -YISAWLDSL ->M_847 -VPFPPKEPL ->M_848 -KSHELVMYI ->M_849 -LMLGRTNTL ->M_850 -VARHTFSML ->M_851 -LAIFMPPTY ->M_852 -WAVVTMTAV ->M_853 -FPRASQSLV ->M_854 -YDFLCLSLV ->M_855 -NKFPGDSMV ->M_856 -FSLLATVIL ->M_857 -SSSDNRNFI ->M_858 -KSRNWLKSI ->M_859 -QALNLQVVL ->M_860 -FPVLLLDTI ->M_861 -VTDFHNHSV ->M_862 -LSDSMPLWM ->M_863 -QSTKVNMLY ->M_864 -MANHLGVGV ->M_865 -HMDVEESQY ->M_866 -LADPIEKEL ->M_867 -MAITILVAL ->M_868 -YRDNKMTRI ->M_869 -FQMAERALY ->M_870 -RINENTGIV ->M_871 -EAGEESTSV ->M_872 -RGMPPPPTV ->M_873 -RLFRMFVHV ->M_874 -FLTDMAKQI ->M_875 -ISMQFLSSL ->M_876 -HTDTNNLGI ->M_877 -LALAIYTLL ->M_878 -LAVCAFTVL ->M_879 -AAAPNLRAL ->M_880 -LVDSNLSVV ->M_881 -VSSVQGITY ->M_882 -HLMKQISSF ->M_883 -EARGAIRGF ->M_884 -LVSTSNHAY ->M_885 -IAPRRWLLL ->M_886 -RMAERRQEV ->M_887 -YVVATTKLM ->M_888 -FQDDFSPRF ->M_889 -IGFNGNQIV ->M_890 -KMFTCSKFV ->M_891 -VAEVCPREV ->M_892 -WAPLPGQML ->M_893 -DAQQLATAI ->M_894 -ILLNGDATV ->M_895 -TIYDEDVLV ->M_896 -WVKEDMGIV ->M_897 -RKYGSTSSI ->M_898 -MTDAQQLAT ->M_899 -GFDQYRTLL ->M_900 -NASGATAPL ->M_901 -FFPEMGTKI ->M_902 -NVHSSGKPI ->M_903 -AALVGAEVV ->M_904 -DHFSHASSI ->M_905 -RAMGERLLL ->M_906 -KIYDGKDKM ->M_907 -WASGNERSL ->M_908 -LATVRSHHM ->M_909 -LRDHGSFLL ->M_910 -TALETSAPF ->M_911 -HTFSMLSRV ->M_912 -KAFHGSSGL ->M_913 -LAKKPGCVF ->M_914 -IPNPQLGPV ->M_915 -QQHDGAFLI ->M_916 -AAFFYLDYV ->M_917 -FFPEMGTKI ->M_918 -SQWDHGLSI ->M_919 -MSCRKIAHL ->M_920 -MGFTVLTTV ->M_921 -NLEVLDCRY ->M_922 -LAQAVRAVL ->M_923 -FMQTRYNKL ->M_924 -LTHTGACPY ->M_925 -KAFSDRFSL ->M_926 -FLRDCSPRL ->M_927 -DIFTTLKMY ->M_928 -RAPPEAIAL ->M_929 -STQDTPVTV ->M_930 -QASSDWAAV ->M_931 -FTRGIQTLF ->M_932 -YRALNRVHV ->M_933 -YEARLLKHM ->M_934 -MELNSVNVM ->M_935 -TAARLRHKV ->M_936 -YAYFLDNVS ->M_937 -TVLENLAVL ->M_938 -HSFTHKQHL ->M_939 -NMEELILAI ->M_940 -IAPHRNEKL ->M_941 -MMNDIVKEF ->M_942 -FSVPLHIFL ->M_943 -TVMGRITTL ->M_944 -FAKYWEENF ->M_945 -VSDLLVLLL ->M_946 -FLHVGDLVI ->M_947 -EAFAHEARF ->M_948 -SSLGKTQTV ->M_949 -LVLIGISHV ->M_950 -FYFQVPFIY ->M_951 -WSFAVAICI ->M_952 -QHMIQQQAL ->M_953 -FPEGYGTQV ->M_954 -KPYGRNKPF ->M_955 -HGFNATYHV ->M_956 -YIRTRNEFV ->M_957 -YPEVFGPPL ->M_958 -MVACGGTVY ->M_959 -APSEHAQMV ->M_960 -TRTFVEFIL ->M_961 -LLSEVLLHY ->M_962 -IQVGTGVTV ->M_963 -LTLAFTVML ->M_964 -HVGDLVIVV ->M_965 -MTREELNAL ->M_966 -VAVQESARI ->M_967 -VPSPLFSIV ->M_968 -KAGGGSNEV ->M_969 -YMLIIVSIF ->M_970 -VAPHAPVHF ->M_971 -TPFHLASAV ->M_972 -SARDCKDPY ->M_973 -FMATMPPAV ->M_974 -TMVACGGTV ->M_975 -NSDHVMFMV ->M_976 -FMKNYFKDV ->M_977 -LNVEDPVTV ->M_978 -FIPINGCPI ->M_979 -YTSYFGYKM ->M_980 -WSPHPLQIV ->M_981 -YTTITPQII ->M_982 -CSFYRTHTL ->M_983 -NAAKNQVAM ->M_984 -FETDGRRFL ->M_985 -SVEINDIMY ->M_986 -DPAPRPSLL ->M_987 -QAVTEVEAV ->M_988 -TAFQKGYGI ->M_989 -ICFPVLVAL ->M_990 -NHVPVNHFW ->M_991 -DMNDHAPEV ->M_992 -SPLPPPEQI ->M_993 -LRLDGSVVI ->M_994 -HACSHLRQM ->M_995 -FPSSQGSLY ->M_996 -FNRDDCSVL ->M_997 -TSFPQKVHL ->M_998 -EAFAHEARF ->M_999 -DAKSHELVM ->M_1000 -TEYRALNRV ->M_1001 -KTIWHTAEY ->M_1002 -KAMLEEQLI ->M_1003 -DTSDGLAVL ->M_1004 -LEFGKPSTL ->M_1005 -TLLEFFITL ->M_1006 -FTKRQRKAM ->M_1007 -FCLSTENSI ->M_1008 -FQGFSVQLI ->M_1009 -RVAPGYYTL ->M_1010 -FYQDMMNDI ->M_1011 -CLYDSVLML ->M_1012 -YTCVVSNKL ->M_1013 -PAEEPTNEL ->M_1014 -QVYSWLLCL ->M_1015 -PANESFGHL ->M_1016 -SPFAAAAAV ->M_1017 -DVVHHLLSV ->M_1018 -MFYPERTAL ->M_1019 -VSDPACSSI ->M_1020 -WAKVRTAEF ->M_1021 -AALRHERAV ->M_1022 -YVVATTKLM ->M_1023 -RMLLDPNTV ->M_1024 -YYDYMKPRL ->M_1025 -FPRHCVSWM ->M_1026 -YLPPDPQPF ->M_1027 -HPATRPLHV ->M_1028 -MVTGILLYM ->M_1029 -KPISYMAII ->M_1030 -DSSQRFEVI ->M_1031 -STGYAISAY ->M_1032 -KQLEFHIEI ->M_1033 -FFCEVPVLL ->M_1034 -FSMDETGQM ->M_1035 -YPRQYSLKL ->M_1036 -ETAYTKDGF ->M_1037 -FSNHWTFWV ->M_1038 -IGYANAKIY ->M_1039 -DFFEDTEHY ->M_1040 -DPMKVEAHV ->M_1041 -GSGEHPMDY ->M_1042 -SHSRGNDTL ->M_1043 -FHTSSSLTV ->M_1044 -VVMRICNLI ->M_1045 -TALDSSLCL ->M_1046 -DSDDMDLEV ->M_1047 -HSYVGPAQL ->M_1048 -EMFQRYSAF ->M_1049 -MPVSIRLVV ->M_1050 -LVDGDLGKY ->M_1051 -RSLAFPVPL ->M_1052 -RAFHDLRVA ->M_1053 -IYDEDVLVV ->M_1054 -LAMHSIWEM ->M_1055 -YCRAWCQAL ->M_1056 -QAVTNHSVY ->M_1057 -HSQECGSFL ->M_1058 -LQHTGTSVV ->M_1059 -ETRAQLARH ->M_1060 -RAALVGAEV ->M_1061 -IPNAQNMTI ->M_1062 -LATCCRARY ->M_1063 -LMRHSMEKI ->M_1064 -VSARHPQHL ->M_1065 -YKYDAGSAA ->M_1066 -IIFLLGEIV ->M_1067 -LARSQRTQV ->M_1068 -NAAVETASL ->M_1069 -LACSICHVY ->M_1070 -DIYDVLICL ->M_1071 -LTMSWLTPL ->M_1072 -FHNDLMPSY ->M_1073 -VMVSPASAI ->M_1074 -VFFSLLATV ->M_1075 -EASLATQIV ->M_1076 -ETLVSTSTI ->M_1077 -FPYQITNEH ->M_1078 -RTFLPVHLL ->M_1079 -LPQPGVRSL ->M_1080 -VPNNCLGKV ->M_1081 -HPLEFCLLL ->M_1082 -MAFVTLTDL ->M_1083 -FSVQLIRKF ->M_1084 -FPQMRAMSL ->M_1085 -LRLNWGEPI ->M_1086 -YEEDSGEYF ->M_1087 -TAKGTAQLV ->M_1088 -LHFHWNWII ->M_1089 -DTDGQPLLL ->M_1090 -AHLLCTLLL ->M_1091 -KAPGFEKHL ->M_1092 -SSYGGTIRY ->M_1093 -YQDMMNDIV ->M_1094 -MQALNLQVV ->M_1095 -MHYLKNSMI ->M_1096 -NAKSRGWLI ->M_1097 -DSNRVVCPI ->M_1098 -ISNRSVLHL ->M_1099 -QAELRGRVL ->M_1100 -ASFDCAIEM ->M_1101 -LQIGGFSSV ->M_1102 -QTWRAVTTL ->M_1103 -FSAQTFYVL ->M_1104 -LGDDFSSAY ->M_1105 -FQCAPGYAL ->M_1106 -DRETGMHLL ->M_1107 -FALQRIVQK ->M_1108 -DAVGNMLNL ->M_1109 -FYRLHLGTY ->M_1110 -FELKSPVKM ->M_1111 -VLRPRWCPV ->M_1112 -HHSSFRRHL ->M_1113 -FSYLTMSWL ->M_1114 -WAESVEREI ->M_1115 -KADVVHVTL ->M_1116 -IMEENDSNI ->M_1117 -LRLPHWPII ->M_1118 -EAVQDPMKV ->M_1119 -LIRKFAQSI ->M_1120 -SHHQCGQSL ->M_1121 -CTLGLGSLY ->M_1122 -ELAHDSYFY ->M_1123 -HAANVTQAM ->M_1124 -WTFWVGPFI ->M_1125 -VVEHVLTTV ->M_1126 -NDHDNWCII ->M_1127 -IAPLLPVAV ->M_1128 -LSGPWGSPL ->M_1129 -DPADPTSNL ->M_1130 -FPNSDHVMF ->M_1131 -EVQDIQASL ->M_1132 -RPYKQGARL ->M_1133 -DVAQHGARL ->M_1134 -FLEKNKDAV ->M_1135 -DSELAHDSY ->M_1136 -MPLWMASII ->M_1137 -YHFDAIRTF ->M_1138 -VSTEHCLSV ->M_1139 -YEAAKLLLV ->M_1140 -LVQAGVDVV ->M_1141 -SATASMLSV ->M_1142 -DQFTKSISI ->M_1143 -CALCALSNI ->M_1144 -RAKPRWRVA ->M_1145 -AAMDAGFLY ->M_1146 -CAMTMNKYI ->M_1147 -NLEPHGYVV ->M_1148 -MLLSPGQNV ->M_1149 -WQIHRVDIL ->M_1150 -YAELGTTTK ->M_1151 -YKLNRAFML ->M_1152 -FAAAAAVAA ->M_1153 -KMADPNQCV ->M_1154 -DPYVKAHLL ->M_1155 -WPIINTPMV ->M_1156 -KYYTDPSTY ->M_1157 -RVSSYGGTI ->M_1158 -EALDAGAIY ->M_1159 -EFIMAITSM ->M_1160 -FPWWLARVL ->M_1161 -WTLASMELV ->M_1162 -IVRCLVTSV ->M_1163 -MPAFHFNIL ->M_1164 -YRTHTLQTL ->M_1165 -HASVVAAYL ->M_1166 -ISRPSSNAL ->M_1167 -RALLGCSCV ->M_1168 -DAVWSRATF ->M_1169 -DVVHHLLSV ->M_1170 -MSFFRLLQM ->M_1171 -KIIAFRKTL ->M_1172 -TVSSNLSHV ->M_1173 -MSVEINDIM ->M_1174 -IAICRQIGI ->M_1175 -ISKPSELPI ->M_1176 -DPIEKELSV ->M_1177 -DHSNDPTAI ->M_1178 -WRLAEAEML ->M_1179 -RGLPWTVRV ->M_1180 -KPMPTIQWI ->M_1181 -RRFNLTSTF ->M_1182 -RRSHTGTFL ->M_1183 -FALDENDNA ->M_1184 -NPEELEQVV ->M_1185 -QAMHSFGRF ->M_1186 -TAIAICRQI ->M_1187 -EVMEKVLPL ->M_1188 -DVLPDTFTL ->M_1189 -RTGDRPHTF ->M_1190 -QPAVFETTV ->M_1191 -VMDFRFGTI ->M_1192 -NEDDSTFTI ->M_1193 -TALGLCEEV ->M_1194 -SMLSRVLII ->M_1195 -DANLHKNEL ->M_1196 -DHYAVESAL ->M_1197 -EVKIGKMSY ->M_1198 -LANGGKVPF ->M_1199 -IGAKHTLTI ->M_1200 -EVVGGWPVV ->M_1201 -VANERISMQ ->M_1202 -LSLKQVISI ->M_1203 -VGFPVGDSV ->M_1204 -LPLDHHLAL ->M_1205 -GALPLFRKY ->M_1206 -VSYHPDLGI ->M_1207 -HLFGTSCPY ->M_1208 -TATTILIMI ->M_1209 -LSFMEAQSL ->M_1210 -FLSLGIASL ->M_1211 -RPPPTPRKV ->M_1212 -SQLEMPETL ->M_1213 -YCRLATVHM ->M_1214 -VPHEDTLSL ->M_1215 -KCYKQGAFI ->M_1216 -LVLAFKNQV ->M_1217 -TSDDFWYHA ->M_1218 -RAEHFGIA* ->M_1219 -QVLPWLKAF ->M_1220 -FSIVRADGV ->M_1221 -DVHDIARFL ->M_1222 -SAQRPWPRV ->M_1223 -CAFRSQLEM ->M_1224 -IIDCLVSMV ->M_1225 -NPTEARVQV ->M_1226 -MVLWHLPAV ->M_1227 -KVHDSVLAL ->M_1228 -FVLLLTYIL ->M_1229 -RSGEPMVSL ->M_1230 -LPHCGHRTL ->M_1231 -MTEHRGKCY ->M_1232 -RTLRISETL ->M_1233 -VSAKRVSVL ->M_1234 -SVYCIRKKY ->M_1235 -QSMPCLMSF ->M_1236 -HRYNLTQHF ->M_1237 -ISLMVIEKV ->M_1238 -EIYSLIDNF ->M_1239 -APSNHMNLV ->M_1240 -FAISHEGHM ->M_1241 -LTSVLTLMF ->M_1242 -YAIPSKQLE ->M_1243 -QALAQRNQL ->M_1244 -FNCSFVLEM ->M_1245 -SPRRRAASV ->M_1246 -AAGAPPAKI ->M_1247 -DTIPWYLRL ->M_1248 -FFGNNMPEF ->M_1249 -NPICCDCVI ->M_1250 -CPYSAWCVY ->M_1251 -QMCAVNSTV ->M_1252 -LQMVRLCSV ->M_1253 -LTRTFVEFI ->M_1254 -LSATVMLTV ->M_1255 -MVPREFKPI ->M_1256 -LVIQYTVKY ->M_1257 -LRFPRITFF ->M_1258 -TSMPVSKML ->M_1259 -LMKCPCNTF ->M_1260 -IHQAMFQLL ->M_1261 -VAGRRGQQL ->M_1262 -HASSIIDEL ->M_1263 -YARRRWPSQ ->M_1264 -SSLDHHMLV ->M_1265 -DLITNIEPF ->M_1266 -TTILIMIVF ->M_1267 -LLKSNTSTL ->M_1268 -LHDVYMFCI ->M_1269 -STRSPNSTV ->M_1270 -QELAGVKMV ->M_1271 -YVPYRDNKM ->M_1272 -DPADGIRLF ->M_1273 -WRCWFNGIM ->M_1274 -CALGLHNFV ->M_1275 -MEEEFSTIL ->M_1276 -MLDDAPRLL ->M_1277 -LGYDMFDCV ->M_1278 -FVYKSGMTS ->M_1279 -ESADKTAYL ->M_1280 -NLQRWVTAV ->M_1281 -WKLTDMSSI ->M_1282 -HTLEEIYSL ->M_1283 -DAFNSTERA ->M_1284 -YLYPLVLMS ->M_1285 -SPFKLDATY ->M_1286 -FPRIYSNSL ->M_1287 -YHISEEYGL ->M_1288 -ASMHRFGHI ->M_1289 -AIDSASPVY ->M_1290 -CTFDSPARL ->M_1291 -SFMEAQSLM ->M_1292 -LPYELGWLF ->M_1293 -NIWECNRNI ->M_1294 -SPAEETVVL ->M_1295 -RQIPVVGSM ->M_1296 -LVWALPKTY ->M_1297 -QARPKGKGL ->M_1298 -LHLCYEFLM ->M_1299 -HQEDGGKAL ->M_1300 -RPSSNALLI ->M_1301 -QKYDGKCPL ->M_1302 -YAQFRGRHR ->M_1303 -VAVYSTCVL ->M_1304 -FLPPARSGI ->M_1305 -QHGSLSETW ->M_1306 -LGLEKTTSI ->M_1307 -QTVMFMATM ->M_1308 -LLKPGDRVV ->M_1309 -MPGSPRDPV ->M_1310 -LTYCTTGGI ->M_1311 -FQSLLSQHM ->M_1312 -KEFHFNQYL ->M_1313 -SSTEWVAPL ->M_1314 -RSSPATHSL ->M_1315 -ELKEWAESV ->M_1316 -GVVEATLSY ->M_1317 -EIAELNRTI ->M_1318 -GAASMIHYI ->M_1319 -LVNTCIRFV ->M_1320 -QAVDTDEAL ->M_1321 -AATSRGQVL ->M_1322 -NPLRPRESL ->M_1323 -VSSNLSHVI ->M_1324 -FTFGETEVC ->M_1325 -FQDDFSPRF ->M_1326 -YTVKYEQKM ->M_1327 -EHSDTFINL ->M_1328 -YTPKLEIKV ->M_1329 -ETQETMDEL ->M_1330 -DLVHHTTTL ->M_1331 -LMFSGLWHL ->M_1332 -VPHQIPKAV ->M_1333 -MAPAAGTWV ->M_1334 -FLITNALHF ->M_1335 -SPKPPPQCV ->M_1336 -SIADGRAWF ->M_1337 -MGYRVESEV ->M_1338 -APAPDLVVV ->M_1339 -LSANARCLI ->M_1340 -DTSDGLAVL ->M_1341 -EARRQGAVF ->M_1342 -KVPEGDSIV ->M_1343 -WRPGCLWAL ->M_1344 -HGLEKVPVI ->M_1345 -ITIVVISLI ->M_1346 -FAMELDDLH ->M_1347 -LTDKVSTPA ->M_1348 -LMVSAGVFI ->M_1349 -LQLEVEEAV ->M_1350 -SMIHYIVLI ->M_1351 -FRMFVHVYI ->M_1352 -HIFLFAVLL ->M_1353 -QQHDGAFLI ->M_1354 -VELELWGVV ->M_1355 -WSLQTWRAV ->M_1356 -LVQEFTRGI ->M_1357 -VAAFFLSLF ->M_1358 -EAEEESLAL ->M_1359 -HVIVRTSRV ->M_1360 -ELLEPQKTY ->M_1361 -AMSDGRVPV ->M_1362 -RPPSPKDTV ->M_1363 -VPMCHLRLL ->M_1364 -LSARSVPSI ->M_1365 -QVHQRMNSL ->M_1366 -EALVQMQYL ->M_1367 -CAQSPWCLV ->M_1368 -LSCEAHNSM ->M_1369 -QARGVKKQI ->M_1370 -SHHSQCSSL ->M_1371 -YGGFFVISV ->M_1372 -YVYPLPVAN ->M_1373 -HSYWLLKLL ->M_1374 -YRTHTLQTL ->M_1375 -FTTLKMYSV ->M_1376 -EHMNHTCNL ->M_1377 -VAIYLYPLV ->M_1378 -YEGYKYEHI ->M_1379 -DRYVAVRHL ->M_1380 -DLIDYARYM ->M_1381 -NLLLWVLAI ->M_1382 -HLHDHYGPY ->M_1383 -NTDSTAALL ->M_1384 -YVKERQTVT ->M_1385 -TMECWGQKY ->M_1386 -KSDDSDFLA ->M_1387 -MAFVRLLHS ->M_1388 -LVDNLTYTL ->M_1389 -KHSATASML ->M_1390 -FEAHEVLKL ->M_1391 -LVLVGCFTI ->M_1392 -TTSGIGSSM ->M_1393 -KSRAPPEAI ->M_1394 -AALVPTQAM ->M_1395 -RQRNGVAKL ->M_1396 -SSDRMTSVA ->M_1397 -RPSPNRPKL ->M_1398 -SSVEVLVNY ->M_1399 -YCIYASLRI ->M_1400 -RLLPPVSP* ->M_1401 -FSLGKHVCL ->M_1402 -CTDKVGTEA ->M_1403 -FRRSISVRI ->M_1404 -LYLHTLLTI ->M_1405 -LEVPAPEAI ->M_1406 -LLSEMAVAV ->M_1407 -VPLVRWLKV ->M_1408 -DTLPMLGNI ->M_1409 -FAFGAVFSE ->M_1410 -RNYQAWNFL ->M_1411 -DATKNQVAM ->M_1412 -QTKHNAKVY ->M_1413 -IEWECTMML ->M_1414 -LELEFLCPL ->M_1415 -QLVNRPQSI ->M_1416 -TTKKSGGHY ->M_1417 -IVEHPAGHL ->M_1418 -HRYLWKILI ->M_1419 -SIFEVIWSV ->M_1420 -QHDDGYLEV ->M_1421 -GVAPGLQVV ->M_1422 -YLAMGEEIY ->M_1423 -SVVCHQLGF ->M_1424 -RTKRRVFII ->M_1425 -QMAERALYY ->M_1426 -LISPPQEKV ->M_1427 -HLIEERDTL ->M_1428 -ILKQPSQTL ->M_1429 -LQVVHLNAV ->M_1430 -VHDIARFLY ->M_1431 -RSLPIAIEM ->M_1432 -NVDEVNQIM ->M_1433 -GAGVEISTV ->M_1434 -VPREFKPIL ->M_1435 -GAQPPMPPY ->M_1436 -RADLLIVVF ->M_1437 -WKEDMAVHV ->M_1438 -FIEPHARFY ->M_1439 -DEFSGVPRV ->M_1440 -RVQPAVRAL ->M_1441 -ATTIVTTVY ->M_1442 -FFHNPKPLF ->M_1443 -VTASSGIMI ->M_1444 -HKAHFQYLL ->M_1445 -IGVEAGRTL ->M_1446 -ETMDNGFGH ->M_1447 -DFWYHAVVL ->M_1448 -FHLASAVAL ->M_1449 -LAMYLSKNY ->M_1450 -HLLELPQIL ->M_1451 -VSVHRAPSI ->M_1452 -DPAAASHPI ->M_1453 -SVYLRNNKL ->M_1454 -INREHIPTF ->M_1455 -AQYDDPRNL ->M_1456 -RPVNAYARV ->M_1457 -LARLGALLL ->M_1458 -SHTGTFLLV ->M_1459 -HTVAWSNGH ->M_1460 -TIPDSISKF ->M_1461 -AVFEEQIKV ->M_1462 -FCPLCHNPV ->M_1463 -RVLKCNVHL ->M_1464 -LLLPCPLLL ->M_1465 -QTAEQYVFV ->M_1466 -FLNSMDQQI ->M_1467 -GPARGIAII ->M_1468 -LASLSLKQV ->M_1469 -TSVPHEDTL ->M_1470 -EAEVETEAI ->M_1471 -SSLSNVSQV ->M_1472 -TVQNAMQIV ->M_1473 -WHFIKRHIA ->M_1474 -MTVAGMVLL ->M_1475 -YMAGSDTTY ->M_1476 -FRENFESIY ->M_1477 -LATVILGAV ->M_1478 -LSSGSFATM ->M_1479 -DTNNLGIRI ->M_1480 -CSGCVAQVY ->M_1481 -DHIRNFTTM ->M_1482 -KPFISRTMM ->M_1483 -PADPAQLAV ->M_1484 -YEPDTMEQY ->M_1485 -EPLNDTIAI ->M_1486 -QAPLAPTHM ->M_1487 -IHLDISSFV ->M_1488 -PLMDQVSVI ->M_1489 -HSLHPFPHF ->M_1490 -ITFKELGAL ->M_1491 -AAAREATEV ->M_1492 -RTYHGRLAY ->M_1493 -DADIYGKPM ->M_1494 -KGYRIVVAL ->M_1495 -FNMRDLSDI ->M_1496 -FRKTLLNPV ->M_1497 -YLAMGEEIY ->M_1498 -KPFSHSCNL ->M_1499 -DQATFINMY ->M_1500 -ARFRIRKTI ->M_1501 -RAFSFSLPC ->M_1502 -SHMCNSLLV ->M_1503 -EAEEWVVSY ->M_1504 -KASERFRTQ ->M_1505 -QIMPHAIIF ->M_1506 -LLKHMPKII ->M_1507 -ILSCNADII ->M_1508 -AAQCCHKKV ->M_1509 -TELDSVGPV ->M_1510 -STFCGTLEY ->M_1511 -GLIPPDATI ->M_1512 -SAQRNAAFF ->M_1513 -MDHPSGIAI ->M_1514 -FTVLENLAV ->M_1515 -KPPPQCVTL ->M_1516 -LAIYTLLSL ->M_1517 -RTVKFLMAI ->M_1518 -MCLEASIPL ->M_1519 -SAPQDSKAV ->M_1520 -FIIHHRTHT ->M_1521 -RKEENMESV ->M_1522 -FPQVSELVL ->M_1523 -YQVVAQHIY ->M_1524 -DSAQRNAAF ->M_1525 -KHFNNSSHF ->M_1526 -EANVHGIYF ->M_1527 -LSRVKAQVV ->M_1528 -LENSNRSMV ->M_1529 -ESKSGSPEY ->M_1530 -YTVKYEQKM ->M_1531 -LTYGHDRQL ->M_1532 -LHFHFTACY ->M_1533 -DCNKTAVTI ->M_1534 -QPLHSLSVL ->M_1535 -AACGIIQQV ->M_1536 -WDQRCLHTI ->M_1537 -QLQAFWKHV ->M_1538 -SPHPRRRRL ->M_1539 -FLDKASDLL ->M_1540 -SAWLFVTGI ->M_1541 -FMFEMPFMQ ->M_1542 -VSLQAAEEI ->M_1543 -RANGNPNPT ->M_1544 -ELPAFIEMM ->M_1545 -CVAKCGGTV ->M_1546 -LEYLAPEVL ->M_1547 -TMANNPDVM ->M_1548 -EAVSSASKL ->M_1549 -FSLYRGWAL ->M_1550 -VVIGAPYVV ->M_1551 -LHFHWNWII ->M_1552 -MSACWSFAV ->M_1553 -YIAQNDDEL ->M_1554 -ETINWTLLE ->M_1555 -DQYAICMKY ->M_1556 -HAKRKTATA ->M_1557 -LAAASSTAF ->M_1558 -KAYGRDNTP ->M_1559 -KHLQLYQLF ->M_1560 -WAVMNHFSM ->M_1561 -IERPGGSLL ->M_1562 -YCFGCLSHH ->M_1563 -QGYGGFFVI ->M_1564 -NENDLITNI ->M_1565 -LPVPIIQQL ->M_1566 -RLMHQLLVI ->M_1567 -FHKEVFGMF ->M_1568 -CTVEDGGHV ->M_1569 -EVAQHLATT ->M_1570 -VEHPAGHLV ->M_1571 -WKGSTECKL ->M_1572 -LSDPHLTAV ->M_1573 -ILTELLMVV ->M_1574 -MVHLVPALV ->M_1575 -TILENPYIM ->M_1576 -DHSDSDYDF ->M_1577 -NHLNIAWEL ->M_1578 -FPEDVAVYT ->M_1579 -YMTSSGRRF ->M_1580 -SSVPLRSSV ->M_1581 -LAAPPPLTE ->M_1582 -VVASQPAHV ->M_1583 -SMLDPHGHL ->M_1584 -LVVADIHSM ->M_1585 -LLYMAFVRL ->M_1586 -VVTVMVTTV ->M_1587 -KLIDVNHYV ->M_1588 -FTQYLGLSM ->M_1589 -FRGKHDCAL ->M_1590 -EVFRHKLAM ->M_1591 -RSIRLSQEI ->M_1592 -HTIQKAKHM ->M_1593 -PSGRPALAY ->M_1594 -WQDHIRLEV ->M_1595 -VLLDLRPSI ->M_1596 -AVYSTCVLV ->M_1597 -LALSLPACF ->M_1598 -NQCPCSSDI ->M_1599 -SIDPKTGVV ->M_1600 -AAASHPILL ->M_1601 -RLLKHMPKI ->M_1602 -LSLTGLQVL ->M_1603 -MSQEEKVAY ->M_1604 -MIENLEHHI ->M_1605 -IIATGLVTL ->M_1606 -SADCGCCPM ->M_1607 -CAELLSHTV ->M_1608 -HISEEYGLL ->M_1609 -YSFCPLCHN ->M_1610 -LPCRSLTRV ->M_1611 -KVLQHGRLY ->M_1612 -FLCDEEPLL ->M_1613 -IPCLDDVTV ->M_1614 -LASEAVSSA ->M_1615 -TPTPGFSSM ->M_1616 -FYLVAYAAM ->M_1617 -YLKSPECFL ->M_1618 -KVNTATTTM ->M_1619 -LPVSTKCTV ->M_1620 -SVRYAGPLY ->M_1621 -HTIQKAKHM ->M_1622 -TFRDVAVEF ->M_1623 -DEKDLWEYI ->M_1624 -DPADPTRDL ->M_1625 -EAEEWVVSY ->M_1626 -CAFTVLENL ->M_1627 -SWMEGQVTI ->M_1628 -MTAVGYGDM ->M_1629 -VSEDAKQRI ->M_1630 -DVDEDGYIM ->M_1631 -IVQCRVLNI ->M_1632 -IASLLENIL ->M_1633 -SRNWLKSIL ->M_1634 -KVKPTLAMY ->M_1635 -YTMGIIFVL ->M_1636 -ELKSPVKMI ->M_1637 -LSLGAPSPL ->M_1638 -QSIRAATEV ->M_1639 -YMAATLLEF ->M_1640 -CSDGSDEDA ->M_1641 -SYLEDVRLI ->M_1642 -QVYVGDSDI ->M_1643 -VIDQCLKKI ->M_1644 -YPDWIRDNM ->M_1645 -RATSFGKCF ->M_1646 -KAGSLGIIL ->M_1647 -VAQQSRLVF ->M_1648 -DCQSHRLTV ->M_1649 -MPNVLWDLV ->M_1650 -MSWLTPLMI ->M_1651 -DANNVTCVW ->M_1652 -KLLQCMSRV ->M_1653 -VHLPLAVAL ->M_1654 -SLYSLDATL ->M_1655 -FTTTQWSSL ->M_1656 -VALRDLGCL ->M_1657 -MVACGGTVY ->M_1658 -EMFQRYSAF ->M_1659 -DAACGIWSL ->M_1660 -FTILPCTCY ->M_1661 -IIYTMGIIF ->M_1662 -RVYNIRGDM ->M_1663 -RNDPELPTV ->M_1664 -HSDSDYDFV ->M_1665 -VLGEHHHHV ->M_1666 -HVVDEREQM ->M_1667 -GQFPYMGEV ->M_1668 -LPPEMYVYL ->M_1669 -EAYQKQLCF ->M_1670 -AATGPGEVL ->M_1671 -DLYATAFLV ->M_1672 -GFDWKSVFI ->M_1673 -FVVFSFFFV ->M_1674 -GRDVVHHLL ->M_1675 -VTLRWYLAM ->M_1676 -LVAQYDLTV ->M_1677 -RLIRGDAVV ->M_1678 -FQYLVVHTE ->M_1679 -KHYLMTRTL ->M_1680 -FVMEHSNIV ->M_1681 -HQMENNGWV ->M_1682 -NATYSGYVY ->M_1683 -KVKNSASVM ->M_1684 -KQDKCFAFI ->M_1685 -AQRPWPRVL ->M_1686 -MAATLLEFF ->M_1687 -DPNTVSNSI ->M_1688 -LPVSGGHVM ->M_1689 -MLDDAPRLL ->M_1690 -IPPDATIYF ->M_1691 -LHDALEVDL ->M_1692 -MMEKLYPGY ->M_1693 -IPFLFFTDM ->M_1694 -YKLCFNTFF ->M_1695 -YVTMVIDRL ->M_1696 -TIYFDVVLL ->M_1697 -SAWLRAISL ->M_1698 -HLWPGGLSL ->M_1699 -FGYMTQQRM ->M_1700 -HVYILRAVF ->M_1701 -LYIPALAVL ->M_1702 -DPMVPLQGV ->M_1703 -FTEEGFCAI ->M_1704 -FFNDDCCEL ->M_1705 -FLFHPLEFC ->M_1706 -VVMWWMGIL ->M_1707 -KTFHHKSNF ->M_1708 -QRPWPRVLL ->M_1709 -IRVQEASTI ->M_1710 -DLIDYARYM ->M_1711 -VTVRGFWIY ->M_1712 -FMDEHAAER ->M_1713 -SISDTYDPY ->M_1714 -DTNDNVPEF ->M_1715 -YNCTCGCSM ->M_1716 -LLLLASATV ->M_1717 -LYMAFVRLL ->M_1718 -SAEVQLSKI ->M_1719 -ITACLSVLI ->M_1720 -LPETKGVTL ->M_1721 -MSQEEKVAY ->M_1722 -MASPQAEST ->M_1723 -MSFELPYHC ->M_1724 -RWNDTRATV ->M_1725 -LRHERAVSM ->M_1726 -LHLLVACTI ->M_1727 -YGHDRQLCL ->M_1728 -DATIYFDVV ->M_1729 -IVCDIKEKL ->M_1730 -RPAQFLHEM ->M_1731 -WHFVYKSGM ->M_1732 -EVDPIGNLY ->M_1733 -RTDGNSHEA ->M_1734 -KHMPKIIHL ->M_1735 -DVHDIARFL ->M_1736 -PATRPLHVL ->M_1737 -LLHSNRSQI ->M_1738 -PARSGIFKI ->M_1739 -AALTPTEEM ->M_1740 -ISAYMAATL ->M_1741 -IMMSDEERI ->M_1742 -KRQEGMVPV ->M_1743 -LQKRATEEI ->M_1744 -GKDKMTHLL ->M_1745 -AQLPPWAPL ->M_1746 -FFCEVPVLL ->M_1747 -RAHKKAITT ->M_1748 -FDWKSVFII ->M_1749 -CLFRAARLI ->M_1750 -MIEDFLRRF ->M_1751 -TTTERWLRV ->M_1752 -FFKDKATSK ->M_1753 -HFFDAFRKF ->M_1754 -GALGLNRPV ->M_1755 -YRTKCTLGL ->M_1756 -MTVAGMVLL ->M_1757 -KTLSKTAHL ->M_1758 -NLYIFATCL ->M_1759 -GFDTSSSSL ->M_1760 -TPVLCGQPI ->M_1761 -WCAPGKPTL ->M_1762 -ILHNQIQQV ->M_1763 -VVLSPEVEV ->M_1764 -DSIHQVGMY ->M_1765 -NHSGVGAFW ->M_1766 -HNLEPHGYV ->M_1767 -PSLNATTIV ->M_1768 -ISGFKGDTV ->M_1769 -HIASSTTSI ->M_1770 -HTLHAHDPV ->M_1771 -WTDYGQVFT ->M_1772 -ELFRRGLRY ->M_1773 -SASRTKRRV ->M_1774 -NSGPSRSML ->M_1775 -ESADKTAYL ->M_1776 -TELEKFSKV ->M_1777 -FHAQVCSLY ->M_1778 -LVVEHVLTT ->M_1779 -RSYWLRLFL ->M_1780 -DVDEKQLLV ->M_1781 -CAIISLIFI ->M_1782 -SQLEMPETL ->M_1783 -NLEDVGRHL ->M_1784 -HLRRIGRFI ->M_1785 -KYDPDVVVM ->M_1786 -KDDDCITLV ->M_1787 -YDVTDSRII ->M_1788 -MLLHQVAAY ->M_1789 -THQSGFSVI ->M_1790 -DLQPVREAI ->M_1791 -FAGSTQSDL ->M_1792 -GSYREAQSL ->M_1793 -HFMPRIQRL ->M_1794 -LPLKRPGKL ->M_1795 -MAFPEGYGT ->M_1796 -DMQDLTEFL ->M_1797 -VDFSSEVTV ->M_1798 -MEVDPIGNL ->M_1799 -ISRNCNSRM ->M_1800 -YSLIDNFVM ->M_1801 -FEMPFMQTG ->M_1802 -SHELVMYIW ->M_1803 -IIVSYMLII ->M_1804 -AAAAAVAAL ->M_1805 -LVDQKAKEV ->M_1806 -FFSLLATVI ->M_1807 -IYGKPMPTI ->M_1808 -YMLERLIEQ ->M_1809 -CIADFLEHM ->M_1810 -LPYPGSSQA ->M_1811 -EAWQCQPVL ->M_1812 -VATSTAQLL ->M_1813 -VKYTPKLEI ->M_1814 -RVSAKRVSV ->M_1815 -NTWTRQMGY ->M_1816 -LDFACHFTV ->M_1817 -HVRIHPKLV ->M_1818 -LQQNCAAYL ->M_1819 -DAVGNMLNL ->M_1820 -WQAISLMVI ->M_1821 -WLWKLSAVV ->M_1822 -LAPTHMPEL ->M_1823 -YAQTPSKTP ->M_1824 -LLLCFLAAM ->M_1825 -HMPKIIHLV ->M_1826 -AQLPSYMHI diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_118562_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_118562_1_T_iedb.xml deleted file mode 100755 index e5875335..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_118562_1_T_iedb.xml +++ /dev/null @@ -1,45067 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_471 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_471 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_472 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_473 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_474 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_475 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_476 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_477 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_478 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_479 - 9 - - - 1 - gnl|BL_ORD_ID|1152 - 75718|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 1152 - 11 - - - 1 - 12.3122 - 20 - 42.1867 - 3 - 8 - 1 - 6 - 0 - 0 - 4 - 4 - 0 - 6 - YQELPT - YSEHPT - Y E PT - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 10 - Query_10 - M_480 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_481 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_482 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_483 - 9 - - - 1 - gnl|BL_ORD_ID|1903 - 180641|polyprotein|AFJ91714.1|Dengue virus 1|11053 - 1903 - 9 - - - 1 - 12.6974 - 21 - 37.875 - 1 - 7 - 1 - 7 - 0 - 0 - 4 - 6 - 0 - 7 - MAISVVK - MALSIVS - MA+S+V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 14 - Query_14 - M_484 - 9 - - - 1 - gnl|BL_ORD_ID|33 - 2506|M protein, serotype 5 precursor|P02977.2|Streptococcus pyogenes serotype M5|301449 - 33 - 9 - - - 1 - 14.6234 - 26 - 1.88321 - 2 - 7 - 1 - 6 - 0 - 0 - 6 - 6 - 0 - 6 - ALEKLN - ALEKLN - ALEKLN - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 15 - Query_15 - M_485 - 9 - - - 1 - gnl|BL_ORD_ID|2009 - 183781|polyprotein|AGO67248.1|Dengue virus 2|11060 - 2009 - 10 - - - 1 - 13.4678 - 23 - 8.61729 - 3 - 9 - 3 - 9 - 0 - 0 - 3 - 6 - 0 - 7 - DMERHHI - DLEKRHV - D+E+ H+ - - - - - 2 - gnl|BL_ORD_ID|2055 - 184755|polyprotein|AGO67248.1|Dengue virus 2|11060 - 2055 - 9 - - - 1 - 13.4678 - 23 - 8.87313 - 3 - 9 - 2 - 8 - 0 - 0 - 3 - 6 - 0 - 7 - DMERHHI - DLEKRHV - D+E+ H+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 16 - Query_16 - M_486 - 9 - - - 1 - gnl|BL_ORD_ID|4 - 327|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis|1773 - 4 - 20 - - - 1 - 13.853 - 24 - 4.4203 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 8 - 0 - 8 - ANRRKEEV - ANKQKQEL - AN++K+E+ - - - - - 2 - gnl|BL_ORD_ID|53 - 3935|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis|1773 - 53 - 20 - - - 1 - 13.853 - 24 - 4.97811 - 2 - 9 - 12 - 19 - 0 - 0 - 4 - 8 - 0 - 8 - ANRRKEEV - ANKQKQEL - AN++K+E+ - - - - - 3 - gnl|BL_ORD_ID|304 - 20415|circumsporozoite protein|AAN87606.1|Plasmodium falciparum|5833 - 304 - 20 - - - 1 - 13.4678 - 23 - 10.3889 - 2 - 9 - 11 - 18 - 0 - 0 - 4 - 7 - 0 - 8 - ANRRKEEV - ANKPKDEL - AN+ K+E+ - - - - - 4 - gnl|BL_ORD_ID|434 - 26870|Circumsporozoite protein precursor|P02893.1|Plasmodium falciparum|5833 - 434 - 20 - - - 1 - 13.4678 - 23 - 11.4655 - 2 - 9 - 6 - 13 - 0 - 0 - 4 - 7 - 0 - 8 - ANRRKEEV - ANKPKDEL - AN+ K+E+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 17 - Query_17 - M_487 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_488 - 9 - - - 1 - gnl|BL_ORD_ID|530 - 32663|small hydrophobic protein|AAM12943.1|Human metapneumovirus|162145 - 530 - 10 - - - 1 - 10.7714 - 16 - 390.249 - 2 - 9 - 3 - 10 - 0 - 0 - 4 - 5 - 0 - 8 - ALGPGHTV - AVGVYHIV - A+G H V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 19 - Query_19 - M_489 - 9 - - - 1 - gnl|BL_ORD_ID|1621 - 145860|Protein E6|P04019.1|Human papillomavirus type 11|10580 - 1621 - 9 - - - 1 - 15.3938 - 28 - 0.556982 - 3 - 9 - 1 - 7 - 0 - 0 - 6 - 6 - 0 - 7 - KVLIRTY - KVLIRCY - KVLIR Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 20 - Query_20 - M_490 - 9 - - - 1 - gnl|BL_ORD_ID|1265 - 98603|trans-sialidase, putative|EAN82716.1|Trypanosoma cruzi|5693 - 1265 - 9 - - - 1 - 14.2382 - 25 - 4.3647 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 7 - 0 - 8 - SDDNDAFY - TDNNRSFY - +D+N +FY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 21 - Query_21 - M_491 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 22 - Query_22 - M_492 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_493 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_494 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_495 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_496 - 9 - - - 1 - gnl|BL_ORD_ID|1654 - 146570|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 - 1654 - 17 - - - 1 - 15.3938 - 28 - 0.651332 - 2 - 9 - 1 - 8 - 0 - 0 - 5 - 6 - 0 - 8 - SFDGMWKV - SWDQMWKC - S+D MWK - - - - - 2 - gnl|BL_ORD_ID|1653 - 146569|polyprotein|ADF97231.1|Hepatitis C virus subtype 3a|356426 - 1653 - 17 - - - 1 - 13.0826 - 22 - 15.9108 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 5 - 0 - 8 - SFDGMWKV - SWDETWKC - S+D WK - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 27 - Query_27 - M_497 - 9 - - - 1 - gnl|BL_ORD_ID|382 - 23573|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 382 - 9 - - - 1 - 13.0826 - 22 - 14.7007 - 4 - 9 - 1 - 6 - 0 - 0 - 3 - 5 - 0 - 6 - HQVGMY - HAVGLF - H VG++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 28 - Query_28 - M_498 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 29 - Query_29 - M_499 - 9 - - - 1 - gnl|BL_ORD_ID|743 - 47946|envelope glycoprotein|AAC28452.1|Human immunodeficiency virus 1|11676 - 743 - 20 - - - 1 - 14.2382 - 25 - 4.20027 - 4 - 9 - 1 - 6 - 0 - 0 - 3 - 6 - 0 - 6 - PVPLYY - PIPIHY - P+P++Y - - - - - 2 - gnl|BL_ORD_ID|1001 - 65817|envelope glycoprotein|AAL59843.1|Human immunodeficiency virus 1|11676 - 1001 - 20 - - - 1 - 13.853 - 24 - 5.41768 - 4 - 9 - 11 - 16 - 0 - 0 - 3 - 6 - 0 - 6 - PVPLYY - PIPIHY - P+P++Y - - - - - 3 - gnl|BL_ORD_ID|1171 - 79300|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 1171 - 15 - - - 1 - 12.6974 - 21 - 29.7824 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - LAFPVP - LSFPDP - L+FP P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 30 - Query_30 - M_500 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 31 - Query_31 - M_501 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 32 - Query_32 - M_502 - 9 - - - 1 - gnl|BL_ORD_ID|255 - 17117|matrix protein|AAN09804.1|Measles virus strain Edmonston|11235 - 255 - 9 - - - 1 - 12.6974 - 21 - 27.8632 - 1 - 6 - 3 - 8 - 0 - 0 - 4 - 5 - 0 - 6 - YMDLMG - YMSLLG - YM L+G - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 33 - Query_33 - M_503 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 34 - Query_34 - M_504 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 35 - Query_35 - M_505 - 9 - - - 1 - gnl|BL_ORD_ID|41 - 2903|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 - 41 - 15 - - - 1 - 13.853 - 24 - 5.48445 - 1 - 9 - 6 - 14 - 0 - 0 - 4 - 7 - 0 - 9 - FVYLHLNMV - LIHLHQNIV - ++LH N+V - - - - - 2 - gnl|BL_ORD_ID|316 - 20921|polyprotein|BAA03375.1|Hepatitis C virus|11103 - 316 - 15 - - - 1 - 13.4678 - 23 - 11.2975 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 7 - 0 - 9 - FVYLHLNMV - LIHLHQNIV - ++LH N+V - - - - - 3 - gnl|BL_ORD_ID|1816 - 177843|polyprotein|ACZ60102.1|Hepatitis C virus subtype 3a|356426 - 1816 - 17 - - - 1 - 13.0826 - 22 - 17.2821 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 7 - 0 - 9 - FVYLHLNMV - LIHLHQNIV - ++LH N+V - - - - - 4 - gnl|BL_ORD_ID|1016 - 67503|Genome polyprotein|P26662.3|Hepatitis C virus|11103 - 1016 - 10 - - - 1 - 12.3122 - 20 - 47.8854 - 1 - 7 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - FVYLHLN - YVYDHLT - +VY HL - - - - - 5 - gnl|BL_ORD_ID|573 - 36062|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 573 - 20 - - - 1 - 12.3122 - 20 - 48.9705 - 1 - 7 - 8 - 14 - 0 - 0 - 4 - 5 - 0 - 7 - FVYLHLN - YVYNHLT - +VY HL - - - - - 6 - gnl|BL_ORD_ID|279 - 18678|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 - 279 - 15 - - - 1 - 12.3122 - 20 - 55.7176 - 1 - 7 - 7 - 13 - 0 - 0 - 4 - 5 - 0 - 7 - FVYLHLN - YVYNHLT - +VY HL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 36 - Query_36 - M_506 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 37 - Query_37 - M_507 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 38 - Query_38 - M_508 - 9 - - - 1 - gnl|BL_ORD_ID|949 - 62504|HBsAg protein|ABF71024.1|Hepatitis B virus|10407 - 949 - 9 - - - 1 - 12.6974 - 21 - 31.9494 - 3 - 9 - 3 - 9 - 0 - 0 - 3 - 6 - 0 - 7 - WKNMDFL - WTSLNFL - W +++FL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 39 - Query_39 - M_509 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 40 - Query_40 - M_510 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 41 - Query_41 - M_511 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 42 - Query_42 - M_512 - 9 - - - 1 - gnl|BL_ORD_ID|2137 - 187106|Vpr protein|BAA93983.1|Human immunodeficiency virus 1|11676 - 2137 - 9 - - - 1 - 14.2382 - 25 - 4.1461 - 5 - 9 - 5 - 9 - 0 - 0 - 4 - 5 - 0 - 5 - FPRIY - FPRIW - FPRI+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 43 - Query_43 - M_513 - 9 - - - 1 - gnl|BL_ORD_ID|1633 - 146249|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 - 1633 - 17 - - - 1 - 15.0086 - 27 - 0.838218 - 3 - 9 - 9 - 15 - 0 - 0 - 4 - 6 - 0 - 7 - IFWTVYY - VMWTVYH - + WTVY+ - - - - - 2 - gnl|BL_ORD_ID|66 - 4910|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 66 - 20 - - - 1 - 15.0086 - 27 - 1.19565 - 3 - 9 - 7 - 13 - 0 - 0 - 4 - 6 - 0 - 7 - IFWTVYY - VCWTVYH - + WTVY+ - - - - - 3 - gnl|BL_ORD_ID|65 - 4909|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 - 65 - 15 - - - 1 - 15.0086 - 27 - 1.24275 - 3 - 9 - 7 - 13 - 0 - 0 - 4 - 6 - 0 - 7 - IFWTVYY - VCWTVYH - + WTVY+ - - - - - 4 - gnl|BL_ORD_ID|1632 - 146246|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 - 1632 - 17 - - - 1 - 14.6234 - 26 - 1.81173 - 3 - 9 - 9 - 15 - 0 - 0 - 4 - 6 - 0 - 7 - IFWTVYY - VCWTVYH - + WTVY+ - - - - - 5 - gnl|BL_ORD_ID|1674 - 148619|unnamed protein product|BAA14233.1|Hepatitis C virus|11103 - 1674 - 45 - - - 1 - 14.2382 - 25 - 3.72943 - 3 - 8 - 40 - 45 - 0 - 0 - 4 - 5 - 0 - 6 - IFWTVY - VCWTVY - + WTVY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 44 - Query_44 - M_514 - 9 - - - 1 - gnl|BL_ORD_ID|1731 - 150556|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1731 - 10 - - - 1 - 13.853 - 24 - 6.99268 - 3 - 8 - 4 - 9 - 0 - 0 - 3 - 5 - 0 - 6 - DPNQCV - DPRRCL - DP +C+ - - - - - 2 - gnl|BL_ORD_ID|859 - 56310|polyprotein|AGO67248.1|Dengue virus 2|11060 - 859 - 10 - - - 1 - 13.4678 - 23 - 9.56649 - 3 - 8 - 4 - 9 - 0 - 0 - 3 - 5 - 0 - 6 - DPNQCV - DPRRCM - DP +C+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 45 - Query_45 - M_515 - 9 - - - 1 - gnl|BL_ORD_ID|1174 - 79351|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 1174 - 17 - - - 1 - 15.0086 - 27 - 1.02766 - 2 - 9 - 5 - 12 - 0 - 0 - 5 - 5 - 0 - 8 - AFWAGSVV - TLWGGSVV - W GSVV - - - - - 2 - gnl|BL_ORD_ID|2018 - 184130|polyprotein|AFP27208.1|Dengue virus 4|11070 - 2018 - 10 - - - 1 - 12.6974 - 21 - 24.356 - 3 - 8 - 5 - 10 - 0 - 0 - 3 - 4 - 0 - 6 - FWAGSV - LWCGSL - W GS+ - - - - - 3 - gnl|BL_ORD_ID|1921 - 180718|polyprotein|AFP27208.1|Dengue virus 4|11070 - 1921 - 9 - - - 1 - 12.6974 - 21 - 27.8632 - 3 - 8 - 4 - 9 - 0 - 0 - 3 - 4 - 0 - 6 - FWAGSV - LWCGSL - W GS+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 46 - Query_46 - M_516 - 9 - - - 1 - gnl|BL_ORD_ID|1756 - 154164|tegument protein|CAB06732.1|Human alphaherpesvirus 2|10310 - 1756 - 15 - - - 1 - 15.779 - 29 - 0.460848 - 3 - 9 - 9 - 15 - 0 - 0 - 4 - 7 - 0 - 7 - FDAIRTF - YDAVRTW - +DA+RT+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 47 - Query_47 - M_517 - 9 - - - 1 - gnl|BL_ORD_ID|120 - 8236|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 - 120 - 15 - - - 1 - 14.2382 - 25 - 2.60034 - 1 - 5 - 2 - 6 - 0 - 0 - 4 - 5 - 0 - 5 - FAKGW - FAQGW - FA+GW - - - - - 2 - gnl|BL_ORD_ID|2057 - 184814|polyprotein|AGO67248.1|Dengue virus 2|11060 - 2057 - 9 - - - 1 - 12.3122 - 20 - 43.3628 - 1 - 7 - 3 - 9 - 0 - 0 - 4 - 4 - 0 - 7 - FAKGWLL - LGKGWPL - KGW L - - - - - 3 - gnl|BL_ORD_ID|1716 - 150387|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1716 - 10 - - - 1 - 12.3122 - 20 - 46.3152 - 1 - 7 - 4 - 10 - 0 - 0 - 4 - 4 - 0 - 7 - FAKGWLL - LGKGWPL - KGW L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 48 - Query_48 - M_518 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 49 - Query_49 - M_519 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 50 - Query_50 - M_520 - 9 - - - 1 - gnl|BL_ORD_ID|1172 - 79308|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 1172 - 16 - - - 1 - 12.6974 - 21 - 24.3923 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 5 - 0 - 9 - MAPELISHL - MEPTLGQHL - M P L HL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 51 - Query_51 - M_521 - 9 - - - 1 - gnl|BL_ORD_ID|273 - 18390|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 273 - 20 - - - 1 - 13.4678 - 23 - 7.7086 - 3 - 7 - 1 - 5 - 0 - 0 - 4 - 4 - 0 - 5 - FYHPR - FYFPR - FY PR - - - - - 2 - gnl|BL_ORD_ID|946 - 62355|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 946 - 20 - - - 1 - 13.4678 - 23 - 9.25482 - 3 - 7 - 8 - 12 - 0 - 0 - 4 - 4 - 0 - 5 - FYHPR - FYFPR - FY PR - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 52 - Query_52 - M_522 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 53 - Query_53 - M_523 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 54 - Query_54 - M_524 - 9 - - - 1 - gnl|BL_ORD_ID|1338 - 107905|Genome polyprotein|P26664.3|Hepatitis C virus|11103 - 1338 - 10 - - - 1 - 13.0826 - 22 - 17.265 - 4 - 9 - 3 - 8 - 0 - 0 - 3 - 4 - 0 - 6 - FCDSCY - ICDECH - CD C+ - - - - - 2 - gnl|BL_ORD_ID|1323 - 107790|polyprotein|AAD56189.1|Hepatitis C virus|11103 - 1323 - 10 - - - 1 - 13.0826 - 22 - 19.1489 - 4 - 9 - 4 - 9 - 0 - 0 - 3 - 4 - 0 - 6 - FCDSCY - MCDECH - CD C+ - - - - - 3 - gnl|BL_ORD_ID|1337 - 107901|Genome polyprotein|P26664.3|Hepatitis C virus|11103 - 1337 - 10 - - - 1 - 13.0826 - 22 - 20.5146 - 4 - 9 - 1 - 6 - 0 - 0 - 3 - 4 - 0 - 6 - FCDSCY - ICDECH - CD C+ - - - - - 4 - gnl|BL_ORD_ID|1224 - 97111|polyprotein|ABR25251.1|Hepatitis C virus (isolate H77)|63746 - 1224 - 18 - - - 1 - 13.0826 - 22 - 21.0784 - 4 - 9 - 5 - 10 - 0 - 0 - 3 - 4 - 0 - 6 - FCDSCY - ICDECH - CD C+ - - - - - 5 - gnl|BL_ORD_ID|1366 - 108218|Genome polyprotein|P26664.3|Hepatitis C virus|11103 - 1366 - 10 - - - 1 - 12.6974 - 21 - 29.385 - 4 - 9 - 5 - 10 - 0 - 0 - 3 - 4 - 0 - 6 - FCDSCY - ICDECH - CD C+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 55 - Query_55 - M_525 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 56 - Query_56 - M_526 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 57 - Query_57 - M_527 - 9 - - - 1 - gnl|BL_ORD_ID|148 - 10962|envelope glycoprotein|AAU04921.1|Human T-lymphotropic virus 1|11908 - 148 - 9 - - - 1 - 13.0826 - 22 - 20.4374 - 1 - 7 - 2 - 8 - 0 - 0 - 3 - 5 - 0 - 7 - FAPSCAN - YSPSCCT - ++PSC - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 58 - Query_58 - M_528 - 9 - - - 1 - gnl|BL_ORD_ID|849 - 55620|EBNA3C latent protein|CAD53421.1|Human gammaherpesvirus 4|10376 - 849 - 9 - - - 1 - 14.2382 - 25 - 4.21767 - 1 - 7 - 2 - 8 - 0 - 0 - 3 - 6 - 0 - 7 - KVYDLVH - RIYDLIE - ++YDL+ - - - - - 2 - gnl|BL_ORD_ID|1518 - 140597|MCE-family protein MCE4A|YP_177977.1|Mycobacterium tuberculosis H37Rv|83332 - 1518 - 9 - - - 1 - 12.3122 - 20 - 63.7024 - 4 - 9 - 4 - 9 - 0 - 0 - 3 - 5 - 0 - 6 - DLVHSV - DLLHKI - DL+H + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 59 - Query_59 - M_529 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 60 - Query_60 - M_530 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 61 - Query_61 - M_531 - 9 - - - 1 - gnl|BL_ORD_ID|418 - 25237|Transcription activator BRLF1|P03209.1|Human herpesvirus 4 strain B95-8|10377 - 418 - 15 - - - 1 - 13.853 - 24 - 6.52084 - 1 - 5 - 9 - 13 - 0 - 0 - 4 - 5 - 0 - 5 - FVLDH - YVLDH - +VLDH - - - - - 2 - gnl|BL_ORD_ID|1156 - 76333|BRLF1|ABB89247.1|Human gammaherpesvirus 4|10376 - 1156 - 9 - - - 1 - 13.4678 - 23 - 9.85027 - 1 - 5 - 1 - 5 - 0 - 0 - 4 - 5 - 0 - 5 - FVLDH - YVLDH - +VLDH - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 62 - Query_62 - M_532 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 63 - Query_63 - M_533 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 64 - Query_64 - M_534 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 65 - Query_65 - M_535 - 9 - - - 1 - gnl|BL_ORD_ID|2045 - 184531|polyprotein|AFP27208.1|Dengue virus 4|11070 - 2045 - 10 - - - 1 - 13.4678 - 23 - 10.4367 - 3 - 9 - 2 - 8 - 0 - 0 - 5 - 6 - 0 - 7 - PEFLQTL - PESLETL - PE L+TL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 66 - Query_66 - M_536 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 67 - Query_67 - M_537 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 68 - Query_68 - M_538 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 69 - Query_69 - M_539 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 70 - Query_70 - M_540 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 71 - Query_71 - M_541 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 72 - Query_72 - M_542 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 73 - Query_73 - M_543 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 74 - Query_74 - M_544 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 75 - Query_75 - M_545 - 9 - - - 1 - gnl|BL_ORD_ID|654 - 38724|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 654 - 20 - - - 1 - 12.6974 - 21 - 29.0269 - 1 - 6 - 13 - 18 - 0 - 0 - 4 - 4 - 0 - 6 - QAYGGP - QLYRGP - Q Y GP - - - - - 2 - gnl|BL_ORD_ID|638 - 37970|tax|AAG48731.1|Human T-lymphotropic virus 2|11909 - 638 - 9 - - - 1 - 11.927 - 19 - 100.753 - 3 - 9 - 3 - 9 - 0 - 0 - 4 - 5 - 0 - 7 - YGGPRYL - YGYPVYV - YG P Y+ - - - - - 3 - gnl|BL_ORD_ID|389 - 23807|tax|AAG48731.1|Human T-lymphotropic virus 2|11909 - 389 - 23 - - - 1 - 11.5418 - 18 - 106.416 - 3 - 9 - 11 - 17 - 0 - 0 - 4 - 5 - 0 - 7 - YGGPRYL - YGYPVYV - YG P Y+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 76 - Query_76 - M_546 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 77 - Query_77 - M_547 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 78 - Query_78 - M_548 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 79 - Query_79 - M_549 - 9 - - - 1 - gnl|BL_ORD_ID|1040 - 69474|core protein|BAF42671.1|Hepatitis B virus|10407 - 1040 - 10 - - - 1 - 13.0826 - 22 - 13.5467 - 1 - 6 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - YLMEFG - YLVSFG - YL+ FG - - - - - 2 - gnl|BL_ORD_ID|201 - 15061|core protein|BAF42671.1|Hepatitis B virus|10407 - 201 - 9 - - - 1 - 13.0826 - 22 - 16.035 - 1 - 6 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - YLMEFG - YLVSFG - YL+ FG - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 80 - Query_80 - M_550 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 81 - Query_81 - M_551 - 9 - - - 1 - gnl|BL_ORD_ID|1351 - 108127|Genome polyprotein|P26664.3|Hepatitis C virus|11103 - 1351 - 10 - - - 1 - 14.2382 - 25 - 4.08767 - 3 - 9 - 3 - 9 - 0 - 0 - 5 - 6 - 0 - 7 - LGVGTAL - LGIGTVL - LG+GT L - - - - - 2 - gnl|BL_ORD_ID|1361 - 108169|Genome polyprotein|P26664.3|Hepatitis C virus|11103 - 1361 - 10 - - - 1 - 13.853 - 24 - 4.61192 - 3 - 9 - 4 - 10 - 0 - 0 - 5 - 6 - 0 - 7 - LGVGTAL - LGIGTVL - LG+GT L - - - - - 3 - gnl|BL_ORD_ID|1362 - 108171|polyprotein|AAF65953.1|Hepatitis C virus|11103 - 1362 - 10 - - - 1 - 13.853 - 24 - 4.94204 - 3 - 9 - 4 - 10 - 0 - 0 - 5 - 6 - 0 - 7 - LGVGTAL - LGIGTVL - LG+GT L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 82 - Query_82 - M_552 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 83 - Query_83 - M_553 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 84 - Query_84 - M_554 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 85 - Query_85 - M_555 - 9 - - - 1 - gnl|BL_ORD_ID|1633 - 146249|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 - 1633 - 17 - - - 1 - 15.0086 - 27 - 0.838218 - 3 - 9 - 9 - 15 - 0 - 0 - 4 - 6 - 0 - 7 - IFWTVYY - VMWTVYH - + WTVY+ - - - - - 2 - gnl|BL_ORD_ID|66 - 4910|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 66 - 20 - - - 1 - 15.0086 - 27 - 1.19565 - 3 - 9 - 7 - 13 - 0 - 0 - 4 - 6 - 0 - 7 - IFWTVYY - VCWTVYH - + WTVY+ - - - - - 3 - gnl|BL_ORD_ID|65 - 4909|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 - 65 - 15 - - - 1 - 15.0086 - 27 - 1.24275 - 3 - 9 - 7 - 13 - 0 - 0 - 4 - 6 - 0 - 7 - IFWTVYY - VCWTVYH - + WTVY+ - - - - - 4 - gnl|BL_ORD_ID|1632 - 146246|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 - 1632 - 17 - - - 1 - 14.6234 - 26 - 1.81173 - 3 - 9 - 9 - 15 - 0 - 0 - 4 - 6 - 0 - 7 - IFWTVYY - VCWTVYH - + WTVY+ - - - - - 5 - gnl|BL_ORD_ID|1674 - 148619|unnamed protein product|BAA14233.1|Hepatitis C virus|11103 - 1674 - 45 - - - 1 - 14.2382 - 25 - 3.72943 - 3 - 8 - 40 - 45 - 0 - 0 - 4 - 5 - 0 - 6 - IFWTVY - VCWTVY - + WTVY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 86 - Query_86 - M_556 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 87 - Query_87 - M_557 - 9 - - - 1 - gnl|BL_ORD_ID|949 - 62504|HBsAg protein|ABF71024.1|Hepatitis B virus|10407 - 949 - 9 - - - 1 - 11.1566 - 17 - 215.083 - 6 - 9 - 3 - 6 - 0 - 0 - 3 - 4 - 0 - 4 - WTSI - WTSL - WTS+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 88 - Query_88 - M_558 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 89 - Query_89 - M_559 - 9 - - - 1 - gnl|BL_ORD_ID|1758 - 154296|UL29|CAB06754.1|Human alphaherpesvirus 2|10310 - 1758 - 15 - - - 1 - 12.6974 - 21 - 24.0543 - 3 - 9 - 6 - 12 - 0 - 0 - 4 - 4 - 0 - 7 - FDHIRNF - FDRTRKF - FD R F - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 90 - Query_90 - M_560 - 9 - - - 1 - gnl|BL_ORD_ID|1474 - 130953|G1 and G2 surface glycoprotein precursor|AAG22532.1|Andes hantavirus|46607 - 1474 - 9 - - - 1 - 11.927 - 19 - 107.472 - 3 - 9 - 3 - 9 - 0 - 0 - 3 - 5 - 0 - 7 - PDELHAM - PDVAHSL - PD H++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 91 - Query_91 - M_561 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 92 - Query_92 - M_562 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 93 - Query_93 - M_563 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 94 - Query_94 - M_564 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 95 - Query_95 - M_565 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 96 - Query_96 - M_566 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 97 - Query_97 - M_567 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 98 - Query_98 - M_568 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 99 - Query_99 - M_569 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 100 - Query_100 - M_570 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 101 - Query_101 - M_571 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 102 - Query_102 - M_572 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 103 - Query_103 - M_573 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 104 - Query_104 - M_574 - 9 - - - 1 - gnl|BL_ORD_ID|777 - 51685|Nuclear antigen EBNA-3C|Q69140.1|Human gammaherpesvirus 4|10376 - 777 - 10 - - - 1 - 12.3122 - 20 - 49.5064 - 3 - 9 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - QEGFLAV - QNGALAI - Q G LA+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 105 - Query_105 - M_575 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 106 - Query_106 - M_576 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 107 - Query_107 - M_577 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 108 - Query_108 - M_578 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 109 - Query_109 - M_579 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 110 - Query_110 - M_580 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 111 - Query_111 - M_581 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 112 - Query_112 - M_582 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 113 - Query_113 - M_583 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 114 - Query_114 - M_584 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 115 - Query_115 - M_585 - 9 - - - 1 - gnl|BL_ORD_ID|1770 - 155131|ribonucleotide reductase large subunit|CAB06725.1|Human alphaherpesvirus 2|10310 - 1770 - 15 - - - 1 - 13.853 - 24 - 7.10896 - 3 - 6 - 5 - 8 - 0 - 0 - 4 - 4 - 0 - 4 - YFCR - YFCR - YFCR - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 116 - Query_116 - M_586 - 9 - - - 1 - gnl|BL_ORD_ID|1097 - 72563|polyprotein|AAB70696.1|Dengue virus type 1 Hawaii|10000440 - 1097 - 20 - - - 1 - 10.3862 - 15 - 509.034 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 5 - 0 - 9 - WAHAWPSPY - WHYDEDNPY - W + +PY - - - - - 2 - gnl|BL_ORD_ID|1943 - 180817|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1943 - 9 - - - 1 - 10.001 - 14 - 955.526 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 4 - 0 - 9 - WAHAWPSPY - WHYDQDHPY - W + PY - - - - - 3 - gnl|BL_ORD_ID|1931 - 180758|Nonstructural protein NS5|NP_739590.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1931 - 15 - - - 1 - 9.23063 - 12 - 1403.43 - 1 - 9 - 2 - 10 - 0 - 0 - 3 - 4 - 0 - 9 - WAHAWPSPY - WHYDQDHPY - W + PY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 117 - Query_117 - M_587 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 118 - Query_118 - M_588 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 119 - Query_119 - M_589 - 9 - - - 1 - gnl|BL_ORD_ID|134 - 9461|non structural protein 3|CAJ20172.1|Hepatitis C virus|11103 - 134 - 9 - - - 1 - 12.6974 - 21 - 31.4086 - 3 - 9 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - DRFHYLL - DNFPYLV - D F YL+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 120 - Query_120 - M_590 - 9 - - - 1 - gnl|BL_ORD_ID|1633 - 146249|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 - 1633 - 17 - - - 1 - 15.0086 - 27 - 0.838218 - 3 - 9 - 9 - 15 - 0 - 0 - 4 - 6 - 0 - 7 - IFWTVYY - VMWTVYH - + WTVY+ - - - - - 2 - gnl|BL_ORD_ID|66 - 4910|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 66 - 20 - - - 1 - 15.0086 - 27 - 1.19565 - 3 - 9 - 7 - 13 - 0 - 0 - 4 - 6 - 0 - 7 - IFWTVYY - VCWTVYH - + WTVY+ - - - - - 3 - gnl|BL_ORD_ID|65 - 4909|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 - 65 - 15 - - - 1 - 15.0086 - 27 - 1.24275 - 3 - 9 - 7 - 13 - 0 - 0 - 4 - 6 - 0 - 7 - IFWTVYY - VCWTVYH - + WTVY+ - - - - - 4 - gnl|BL_ORD_ID|1632 - 146246|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 - 1632 - 17 - - - 1 - 14.6234 - 26 - 1.81173 - 3 - 9 - 9 - 15 - 0 - 0 - 4 - 6 - 0 - 7 - IFWTVYY - VCWTVYH - + WTVY+ - - - - - 5 - gnl|BL_ORD_ID|1674 - 148619|unnamed protein product|BAA14233.1|Hepatitis C virus|11103 - 1674 - 45 - - - 1 - 14.2382 - 25 - 3.72943 - 3 - 8 - 40 - 45 - 0 - 0 - 4 - 5 - 0 - 6 - IFWTVY - VCWTVY - + WTVY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 121 - Query_121 - M_591 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 122 - Query_122 - M_592 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 123 - Query_123 - M_593 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 124 - Query_124 - M_594 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 125 - Query_125 - M_595 - 9 - - - 1 - gnl|BL_ORD_ID|1298 - 103392|polyprotein|BAB18806.1|Hepatitis C virus|11103 - 1298 - 9 - - - 1 - 13.0826 - 22 - 17.1877 - 4 - 9 - 4 - 9 - 0 - 0 - 4 - 4 - 0 - 6 - DPMVPL - DPTTPL - DP PL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 126 - Query_126 - M_596 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 127 - Query_127 - M_597 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 128 - Query_128 - M_598 - 9 - - - 1 - gnl|BL_ORD_ID|715 - 44133|Genome polyprotein|P26664.3|Hepatitis C virus genotype 1|41856 - 715 - 9 - - - 1 - 15.0086 - 27 - 1.21609 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 6 - 0 - 9 - NHDDDDVEI - NHDSPDAEL - NHD D E+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 129 - Query_129 - M_599 - 9 - - - 1 - gnl|BL_ORD_ID|1999 - 183670|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1999 - 10 - - - 1 - 14.2382 - 25 - 3.05549 - 1 - 7 - 3 - 9 - 0 - 0 - 6 - 7 - 0 - 7 - NASVNVS - NSSVNVS - N+SVNVS - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 130 - Query_130 - M_600 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 131 - Query_131 - M_601 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 132 - Query_132 - M_602 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 133 - Query_133 - M_603 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 134 - Query_134 - M_604 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 135 - Query_135 - M_605 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 136 - Query_136 - M_606 - 9 - - - 1 - gnl|BL_ORD_ID|2156 - 189292|gag protein|ABC40295.1|Human immunodeficiency virus 1|11676 - 2156 - 9 - - - 1 - 14.2382 - 25 - 3.05306 - 2 - 9 - 1 - 8 - 0 - 0 - 5 - 7 - 0 - 8 - ALYHCVAI - SLYNTVAI - +LY+ VAI - - - - - 2 - gnl|BL_ORD_ID|2201 - 190829|gag protein|BAB88077.1|Human immunodeficiency virus 1|11676 - 2201 - 10 - - - 1 - 13.853 - 24 - 5.77604 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 7 - 0 - 8 - ALYHCVAI - SLYNTVAV - +LY+ VA+ - - - - - 3 - gnl|BL_ORD_ID|1465 - 127003|gag polyprotein|BAB88551.1|Human immunodeficiency virus 1|11676 - 1465 - 10 - - - 1 - 13.853 - 24 - 6.19145 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 7 - 0 - 8 - ALYHCVAI - SLYNTVAV - +LY+ VA+ - - - - - 4 - gnl|BL_ORD_ID|2151 - 189287|gag protein|ADO94802.1|Human immunodeficiency virus 1|11676 - 2151 - 9 - - - 1 - 13.853 - 24 - 6.37844 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 7 - 0 - 8 - ALYHCVAI - SLYNTIAI - +LY+ +AI - - - - - 5 - gnl|BL_ORD_ID|2157 - 189293|gag protein|BAB88077.1|Human immunodeficiency virus 1|11676 - 2157 - 9 - - - 1 - 13.853 - 24 - 7.32819 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 7 - 0 - 8 - ALYHCVAI - SLYNTVAV - +LY+ VA+ - - - - - 6 - gnl|BL_ORD_ID|1466 - 127004|gag polyprotein|BAB88551.1|Human immunodeficiency virus 1|11676 - 1466 - 11 - - - 1 - 13.4678 - 23 - 7.61059 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 7 - 0 - 8 - ALYHCVAI - SLYNTVAV - +LY+ VA+ - - - - - 7 - gnl|BL_ORD_ID|1455 - 126492|gag protein|BAB88077.1|Human immunodeficiency virus 1|11676 - 1455 - 11 - - - 1 - 13.4678 - 23 - 7.61059 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 7 - 0 - 8 - ALYHCVAI - SLYNTVAV - +LY+ VA+ - - - - - 8 - gnl|BL_ORD_ID|2212 - 190981|gag protein|BAB88077.1|Human immunodeficiency virus 1|11676 - 2212 - 10 - - - 1 - 13.4678 - 23 - 9.40133 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 7 - 0 - 8 - ALYHCVAI - SLYNTVAV - +LY+ VA+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 137 - Query_137 - M_607 - 9 - - - 1 - gnl|BL_ORD_ID|974 - 64727|polyprotein precursor|NP_041724.2|West Nile virus|11082 - 974 - 9 - - - 1 - 13.4678 - 23 - 8.87313 - 2 - 9 - 1 - 8 - 0 - 0 - 5 - 5 - 0 - 8 - TLAPGVPL - TLARGFPF - TLA G P - - - - - 2 - gnl|BL_ORD_ID|652 - 38556|Genome polyprotein|Q00269.3|Hepatitis C virus|11103 - 652 - 9 - - - 1 - 12.6974 - 21 - 33.058 - 5 - 9 - 5 - 9 - 0 - 0 - 4 - 4 - 0 - 5 - PGVPL - PGVPF - PGVP - - - - - 3 - gnl|BL_ORD_ID|452 - 27345|Large envelope protein|P03138.3|Hepatitis B virus subtype ayw|10418 - 452 - 9 - - - 1 - 11.927 - 19 - 99.1366 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 6 - 0 - 7 - LAPGVPL - LSPFLPL - L+P +PL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 138 - Query_138 - M_608 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 139 - Query_139 - M_609 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 140 - Query_140 - M_610 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 141 - Query_141 - M_611 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 142 - Query_142 - M_612 - 9 - - - 1 - gnl|BL_ORD_ID|306 - 20686|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 - 306 - 11 - - - 1 - 15.779 - 29 - 0.466791 - 1 - 8 - 2 - 9 - 0 - 0 - 5 - 7 - 0 - 8 - QSVHPVVT - KSTHPMVT - +S HP+VT - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 143 - Query_143 - M_613 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 144 - Query_144 - M_614 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 145 - Query_145 - M_615 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 146 - Query_146 - M_616 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 147 - Query_147 - M_617 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 148 - Query_148 - M_618 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 149 - Query_149 - M_619 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 150 - Query_150 - M_620 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 151 - Query_151 - M_621 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 152 - Query_152 - M_622 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 153 - Query_153 - M_623 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 154 - Query_154 - M_624 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 155 - Query_155 - M_625 - 9 - - - 1 - gnl|BL_ORD_ID|86 - 6373|Genome polyprotein|SRC279960|Hepatitis C virus subtype 3a|356426 - 86 - 10 - - - 1 - 13.853 - 24 - 4.53299 - 4 - 9 - 4 - 9 - 0 - 0 - 5 - 6 - 0 - 6 - QDSTTV - QDATTV - QD+TTV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 156 - Query_156 - M_626 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 157 - Query_157 - M_627 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 158 - Query_158 - M_628 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 159 - Query_159 - M_629 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 160 - Query_160 - M_630 - 9 - - - 1 - gnl|BL_ORD_ID|1298 - 103392|polyprotein|BAB18806.1|Hepatitis C virus|11103 - 1298 - 9 - - - 1 - 13.0826 - 22 - 13.7128 - 3 - 7 - 4 - 8 - 0 - 0 - 4 - 5 - 0 - 5 - DPSTP - DPTTP - DP+TP - - - - - 2 - gnl|BL_ORD_ID|811 - 54342|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 - 811 - 20 - - - 1 - 12.3122 - 20 - 56.0891 - 2 - 9 - 11 - 18 - 0 - 0 - 4 - 4 - 0 - 8 - ADPSTPHL - GDPLFPEL - DP P L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 161 - Query_161 - M_631 - 9 - - - 1 - gnl|BL_ORD_ID|1083 - 71663|Spike glycoprotein precursor|P59594.1|SARS coronavirus|227859 - 1083 - 9 - - - 1 - 15.0086 - 27 - 1.17789 - 3 - 9 - 3 - 9 - 0 - 0 - 4 - 7 - 0 - 7 - YIHVTYI - FLHVTYV - ++HVTY+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 162 - Query_162 - M_632 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 163 - Query_163 - M_633 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 164 - Query_164 - M_634 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 165 - Query_165 - M_635 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 166 - Query_166 - M_636 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 167 - Query_167 - M_637 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 168 - Query_168 - M_638 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 169 - Query_169 - M_639 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 170 - Query_170 - M_640 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 171 - Query_171 - M_641 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 172 - Query_172 - M_642 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 173 - Query_173 - M_643 - 9 - - - 1 - gnl|BL_ORD_ID|658 - 39095|nonstructural protein 3|NP_722463.1|Dengue virus type 1 Hawaii|10000440 - 658 - 15 - - - 1 - 11.5418 - 18 - 108.251 - 1 - 7 - 9 - 15 - 0 - 0 - 4 - 5 - 0 - 7 - FTEELRR - FVELMRR - F E +RR - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 174 - Query_174 - M_644 - 9 - - - 1 - gnl|BL_ORD_ID|685 - 41269|kaposin|AAC57155.1|Human gammaherpesvirus 8|37296 - 685 - 15 - - - 1 - 12.6974 - 21 - 23.272 - 4 - 9 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - SRGITV - DRGLTV - RG+TV - - - - - 2 - gnl|BL_ORD_ID|1595 - 142231|Lipoprotein lpqH precursor|P0A5J0.1|Mycobacterium tuberculosis|1773 - 1595 - 24 - - - 1 - 12.6974 - 21 - 27.2634 - 5 - 9 - 3 - 7 - 0 - 0 - 4 - 5 - 0 - 5 - RGITV - RGLTV - RG+TV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 175 - Query_175 - M_645 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 176 - Query_176 - M_646 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 177 - Query_177 - M_647 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 178 - Query_178 - M_648 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 179 - Query_179 - M_649 - 9 - - - 1 - gnl|BL_ORD_ID|1770 - 155131|ribonucleotide reductase large subunit|CAB06725.1|Human alphaherpesvirus 2|10310 - 1770 - 15 - - - 1 - 13.0826 - 22 - 18.437 - 3 - 8 - 7 - 12 - 0 - 0 - 5 - 5 - 0 - 6 - CRKARE - CRCARE - CR ARE - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 180 - Query_180 - M_650 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 181 - Query_181 - M_651 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 182 - Query_182 - M_652 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 183 - Query_183 - M_653 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 184 - Query_184 - M_654 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 185 - Query_185 - M_655 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 186 - Query_186 - M_656 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 187 - Query_187 - M_657 - 9 - - - 1 - gnl|BL_ORD_ID|959 - 63010|6 kDa early secretory antigenic target|P0A564.2|Mycobacterium tuberculosis|1773 - 959 - 20 - - - 1 - 13.853 - 24 - 4.57317 - 3 - 9 - 10 - 16 - 0 - 0 - 5 - 6 - 0 - 7 - RNLIRTI - QNLARTI - +NL RTI - - - - - 2 - gnl|BL_ORD_ID|656 - 38922|6 kDa early secretory antigenic target|P0A564.2|Mycobacterium tuberculosis|1773 - 656 - 8 - - - 1 - 13.4678 - 23 - 11.0044 - 3 - 9 - 2 - 8 - 0 - 0 - 5 - 6 - 0 - 7 - RNLIRTI - QNLARTI - +NL RTI - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 188 - Query_188 - M_658 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 189 - Query_189 - M_659 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 190 - Query_190 - M_660 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 191 - Query_191 - M_661 - 9 - - - 1 - gnl|BL_ORD_ID|475 - 29186|polyprotein precursor|NP_041724.2|West Nile virus|11082 - 475 - 9 - - - 1 - 13.853 - 24 - 7.45662 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 7 - 0 - 9 - ISYTEVPTY - ITYTDVLRY - I+YT+V Y - - - - - 2 - gnl|BL_ORD_ID|1152 - 75718|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 1152 - 11 - - - 1 - 13.4678 - 23 - 11.9608 - 3 - 9 - 1 - 7 - 0 - 0 - 4 - 6 - 0 - 7 - YTEVPTY - YSEHPTF - Y+E PT+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 192 - Query_192 - M_662 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 193 - Query_193 - M_663 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 194 - Query_194 - M_664 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 195 - Query_195 - M_665 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 196 - Query_196 - M_666 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 197 - Query_197 - M_667 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 198 - Query_198 - M_668 - 9 - - - 1 - gnl|BL_ORD_ID|2282 - 419124|polyprotein|ACF49259.1|Dengue virus type 1 Hawaii|10000440 - 2282 - 9 - - - 1 - 11.927 - 19 - 84.261 - 3 - 8 - 3 - 8 - 0 - 0 - 4 - 4 - 0 - 6 - EPKKKP - EPGKNP - EP K P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 199 - Query_199 - M_669 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 200 - Query_200 - M_670 - 9 - - - 1 - gnl|BL_ORD_ID|707 - 43447|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 - 707 - 20 - - - 1 - 12.6974 - 21 - 22.9279 - 1 - 9 - 5 - 13 - 0 - 0 - 5 - 5 - 0 - 9 - FFFHNPKPL - IFFFNPGEL - FF NP L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 201 - Query_201 - M_671 - 9 - - - 1 - gnl|BL_ORD_ID|1121 - 74407|polyprotein|AAU89634.1|Hepatitis C virus subtype 2a|31649 - 1121 - 9 - - - 1 - 12.3122 - 20 - 54.8462 - 2 - 7 - 4 - 9 - 0 - 0 - 2 - 4 - 0 - 6 - HWNWII - RWEWVV - W W++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 202 - Query_202 - M_672 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 203 - Query_203 - M_673 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 204 - Query_204 - M_674 - 9 - - - 1 - gnl|BL_ORD_ID|1435 - 116781|Nucleoprotein|P05133.1|Hantaan virus 76-118|11602 - 1435 - 15 - - - 1 - 12.6974 - 21 - 26.9941 - 1 - 6 - 8 - 13 - 0 - 0 - 4 - 4 - 0 - 6 - YQHYFR - YQSYLR - YQ Y R - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 205 - Query_205 - M_675 - 9 - - - 1 - gnl|BL_ORD_ID|2259 - 294287|gag protein|ABI20203.1|Human immunodeficiency virus 1|11676 - 2259 - 17 - - - 1 - 13.4678 - 23 - 9.7917 - 3 - 9 - 8 - 14 - 0 - 0 - 4 - 7 - 0 - 7 - NSMINTM - NTMLNTV - N+M+NT+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 206 - Query_206 - M_676 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 207 - Query_207 - M_677 - 9 - - - 1 - gnl|BL_ORD_ID|1206 - 96156|polyprotein|ABR25251.1|Hepatitis C virus (isolate H77)|63746 - 1206 - 21 - - - 1 - 13.0826 - 22 - 17.0133 - 2 - 9 - 6 - 13 - 0 - 0 - 4 - 5 - 0 - 8 - VDYPGDPV - VDFSLDPT - VD+ DP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 208 - Query_208 - M_678 - 9 - - - 1 - gnl|BL_ORD_ID|1258 - 98254|trans-sialidase, putative|EAN81042.1|Trypanosoma cruzi|5693 - 1258 - 9 - - - 1 - 12.6974 - 21 - 26.4654 - 2 - 7 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - TAPLYS - TLPVYS - T P+YS - - - - - 2 - gnl|BL_ORD_ID|1255 - 98242|trans-sialidase, putative|EAN81042.1|Trypanosoma cruzi|5693 - 1255 - 9 - - - 1 - 12.6974 - 21 - 27.8632 - 2 - 7 - 3 - 8 - 0 - 0 - 4 - 5 - 0 - 6 - TAPLYS - TLPVYS - T P+YS - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 209 - Query_209 - M_679 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 210 - Query_210 - M_680 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 211 - Query_211 - M_681 - 9 - - - 1 - gnl|BL_ORD_ID|701 - 42797|6 kDa early secretory antigenic target|P0A564.2|Mycobacterium tuberculosis|1773 - 701 - 20 - - - 1 - 13.853 - 24 - 5.6992 - 1 - 5 - 4 - 8 - 0 - 0 - 4 - 4 - 0 - 5 - QAWNF - QQWNF - Q WNF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 212 - Query_212 - M_682 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 213 - Query_213 - M_683 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 214 - Query_214 - M_684 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 215 - Query_215 - M_685 - 9 - - - 1 - gnl|BL_ORD_ID|126 - 8920|M protein, serotype 5 precursor|P02977.2|Streptococcus pyogenes serotype M5|301449 - 126 - 18 - - - 1 - 11.5418 - 18 - 105.162 - 1 - 8 - 3 - 10 - 0 - 0 - 4 - 7 - 0 - 8 - MAKQIKTK - LAKEQKSK - +AK+ K+K - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 216 - Query_216 - M_686 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 217 - Query_217 - M_687 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 218 - Query_218 - M_688 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 219 - Query_219 - M_689 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 220 - Query_220 - M_690 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 221 - Query_221 - M_691 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 222 - Query_222 - M_692 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 223 - Query_223 - M_693 - 9 - - - 1 - gnl|BL_ORD_ID|386 - 23621|Genome polyprotein|P26664.3|Hepatitis C virus (isolate 1)|11104 - 386 - 11 - - - 1 - 14.2382 - 25 - 3.03901 - 3 - 8 - 1 - 6 - 0 - 0 - 5 - 5 - 0 - 6 - HSGAGK - HDGAGK - H GAGK - - - - - 2 - gnl|BL_ORD_ID|1874 - 180503|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1874 - 10 - - - 1 - 14.2382 - 25 - 3.21576 - 3 - 8 - 1 - 6 - 0 - 0 - 5 - 5 - 0 - 6 - HSGAGK - HPGAGK - H GAGK - - - - - 3 - gnl|BL_ORD_ID|385 - 23620|Genome polyprotein|SRC279960|Hepatitis C virus genotype 1|41856 - 385 - 10 - - - 1 - 14.2382 - 25 - 3.56308 - 3 - 8 - 1 - 6 - 0 - 0 - 5 - 5 - 0 - 6 - HSGAGK - HDGAGK - H GAGK - - - - - 4 - gnl|BL_ORD_ID|384 - 23619|Genome polyprotein|P27958.3|Hepatitis C virus (isolate H)|11108 - 384 - 9 - - - 1 - 14.2382 - 25 - 3.87216 - 3 - 8 - 1 - 6 - 0 - 0 - 5 - 5 - 0 - 6 - HSGAGK - HDGAGK - H GAGK - - - - - 5 - gnl|BL_ORD_ID|1015 - 67471|Genome polyprotein|Q99IB8.3|Hepatitis C virus JFH-1|356411 - 1015 - 9 - - - 1 - 13.853 - 24 - 5.45887 - 2 - 9 - 1 - 8 - 0 - 0 - 5 - 6 - 0 - 8 - THSGAGKF - TYSTYGKF - T+S GKF - - - - - 6 - gnl|BL_ORD_ID|474 - 29182|polyprotein|BAD73991.1|Hepatitis C virus subtype 1b|31647 - 474 - 9 - - - 1 - 13.853 - 24 - 5.45887 - 2 - 9 - 2 - 9 - 0 - 0 - 5 - 6 - 0 - 8 - THSGAGKF - TYSTYGKF - T+S GKF - - - - - 7 - gnl|BL_ORD_ID|1995 - 183598|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1995 - 10 - - - 1 - 13.0826 - 22 - 15.2954 - 3 - 8 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - HSGAGK - HPGSGK - H G+GK - - - - - 8 - gnl|BL_ORD_ID|847 - 55336|EBNA-1|YP_401677.1|Human gammaherpesvirus 4|10376 - 847 - 15 - - - 1 - 12.3122 - 20 - 58.4135 - 2 - 7 - 10 - 15 - 0 - 0 - 4 - 4 - 0 - 6 - THSGAG - THGGTG - TH G G - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 224 - Query_224 - M_694 - 9 - - - 1 - gnl|BL_ORD_ID|1770 - 155131|ribonucleotide reductase large subunit|CAB06725.1|Human alphaherpesvirus 2|10310 - 1770 - 15 - - - 1 - 13.4678 - 23 - 10.0248 - 4 - 8 - 4 - 8 - 0 - 0 - 4 - 4 - 0 - 5 - RYFCR - EYFCR - YFCR - - - - - 2 - gnl|BL_ORD_ID|469 - 28484|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 469 - 9 - - - 1 - 13.0826 - 22 - 21.8994 - 2 - 7 - 3 - 8 - 0 - 0 - 3 - 6 - 0 - 6 - KYRYFC - EYRHYC - +YR++C - - - - - 3 - gnl|BL_ORD_ID|1406 - 110846|E6 protein|CAB45108.1|Human papillomavirus type 16|333760 - 1406 - 9 - - - 1 - 13.0826 - 22 - 22.2806 - 2 - 7 - 1 - 6 - 0 - 0 - 3 - 6 - 0 - 6 - KYRYFC - EYRHYC - +YR++C - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 225 - Query_225 - M_695 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 226 - Query_226 - M_696 - 9 - - - 1 - gnl|BL_ORD_ID|160 - 12183|EBNA3C latent protein|CAD53421.1|Human gammaherpesvirus 4|10376 - 160 - 9 - - - 1 - 11.927 - 19 - 97.5444 - 3 - 8 - 3 - 8 - 0 - 0 - 4 - 5 - 0 - 6 - GLGGRH - GVGWRH - G+G RH - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 227 - Query_227 - M_697 - 9 - - - 1 - gnl|BL_ORD_ID|1760 - 154387|RL2|CAB06760.1|Human alphaherpesvirus 2|10310 - 1760 - 15 - - - 1 - 13.0826 - 22 - 13.39 - 2 - 9 - 6 - 13 - 0 - 0 - 5 - 5 - 0 - 8 - HTGTSVVL - HIGAYVVL - H G VVL - - - - - 2 - gnl|BL_ORD_ID|1764 - 154725|RL2|CAB06760.1|Human alphaherpesvirus 2|10310 - 1764 - 15 - - - 1 - 13.0826 - 22 - 17.5339 - 2 - 9 - 2 - 9 - 0 - 0 - 5 - 5 - 0 - 8 - HTGTSVVL - HIGAYVVL - H G VVL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 228 - Query_228 - M_698 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 229 - Query_229 - M_699 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 230 - Query_230 - M_700 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 231 - Query_231 - M_701 - 9 - - - 1 - gnl|BL_ORD_ID|1265 - 98603|trans-sialidase, putative|EAN82716.1|Trypanosoma cruzi|5693 - 1265 - 9 - - - 1 - 13.0826 - 22 - 15.7589 - 5 - 9 - 5 - 9 - 0 - 0 - 4 - 4 - 0 - 5 - NRPFY - NRSFY - NR FY - - - - - 2 - gnl|BL_ORD_ID|1981 - 183231|polyprotein|AFP27208.1|Dengue virus 4|11070 - 1981 - 10 - - - 1 - 13.0826 - 22 - 18.4997 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 4 - 0 - 8 - FPLRNRPF - FPQSNSPI - FP N P - - - - - 3 - gnl|BL_ORD_ID|1866 - 180460|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1866 - 10 - - - 1 - 12.6974 - 21 - 28.8893 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 4 - 0 - 8 - FPLRNRPF - FPQSNAPI - FP N P - - - - - 4 - gnl|BL_ORD_ID|1704 - 150217|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1704 - 9 - - - 1 - 12.6974 - 21 - 33.6262 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 4 - 0 - 8 - FPLRNRPF - FPQSNAPI - FP N P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 232 - Query_232 - M_702 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 233 - Query_233 - M_703 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 234 - Query_234 - M_704 - 9 - - - 1 - gnl|BL_ORD_ID|1755 - 154041|major capsid protein|CAB06743.1|Human alphaherpesvirus 2|10310 - 1755 - 15 - - - 1 - 11.927 - 19 - 87.4721 - 3 - 9 - 7 - 13 - 0 - 0 - 4 - 4 - 0 - 7 - YPRFLYL - YPAVFYL - YP YL - - - - - 2 - gnl|BL_ORD_ID|855 - 55779|fusion protein|BAB60865.1|Measles virus|11234 - 855 - 9 - - - 1 - 11.927 - 19 - 91.4136 - 3 - 9 - 3 - 9 - 0 - 0 - 4 - 5 - 0 - 7 - YPRFLYL - YPDAVYL - YP +YL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 235 - Query_235 - M_705 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 236 - Query_236 - M_706 - 9 - - - 1 - gnl|BL_ORD_ID|1948 - 180850|polyprotein|AFP27208.1|Dengue virus 4|11070 - 1948 - 10 - - - 1 - 12.3122 - 20 - 52.9061 - 1 - 7 - 1 - 7 - 0 - 0 - 3 - 5 - 0 - 7 - YYPPGVV - YTPEGII - Y P G++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 237 - Query_237 - M_707 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 238 - Query_238 - M_708 - 9 - - - 1 - gnl|BL_ORD_ID|1950 - 181035|||| - 1950 - 44 - - - 1 - 12.6974 - 21 - 25.8912 - 1 - 9 - 11 - 19 - 0 - 0 - 4 - 7 - 0 - 9 - RVFPLRGKI - KLFPGGGQI - ++FP G+I - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 239 - Query_239 - M_709 - 9 - - - 1 - gnl|BL_ORD_ID|1139 - 75356|EBNA3A nuclear protein|Q8AZJ8|Human gammaherpesvirus 4|10376 - 1139 - 9 - - - 1 - 14.6234 - 26 - 2.22125 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 6 - 0 - 9 - YPLPVANGM - YPLHEQHGM - YPL +GM - - - - - 2 - gnl|BL_ORD_ID|1144 - 75438|polyprotein|AAF65962.1|Hepatitis C virus|11103 - 1144 - 20 - - - 1 - 10.3862 - 15 - 376.551 - 1 - 9 - 3 - 11 - 0 - 0 - 4 - 5 - 0 - 9 - YPLPVANGM - WPLYGNEGM - +PL GM - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 240 - Query_240 - M_710 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 241 - Query_241 - M_711 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 242 - Query_242 - M_712 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 243 - Query_243 - M_713 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 244 - Query_244 - M_714 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 245 - Query_245 - M_715 - 9 - - - 1 - gnl|BL_ORD_ID|1449 - 126486|gag protein|ADK33372.1|Human immunodeficiency virus 1|11676 - 1449 - 10 - - - 1 - 15.0086 - 27 - 0.933082 - 1 - 9 - 1 - 9 - 0 - 0 - 6 - 8 - 0 - 9 - KALFWTVAM - KSLFNTVAV - K+LF TVA+ - - - - - 2 - gnl|BL_ORD_ID|1450 - 126487|gag protein|ADK33372.1|Human immunodeficiency virus 1|11676 - 1450 - 11 - - - 1 - 15.0086 - 27 - 1.06128 - 1 - 9 - 1 - 9 - 0 - 0 - 6 - 8 - 0 - 9 - KALFWTVAM - KSLFNTVAV - K+LF TVA+ - - - - - 3 - gnl|BL_ORD_ID|1447 - 126484|gag protein|AAW03034.1|Human immunodeficiency virus 1|11676 - 1447 - 10 - - - 1 - 15.0086 - 27 - 1.32867 - 1 - 8 - 1 - 8 - 0 - 0 - 6 - 7 - 0 - 8 - KALFWTVA - KSLFNTVA - K+LF TVA - - - - - 4 - gnl|BL_ORD_ID|1448 - 126485|gag protein|AAW03034.1|Human immunodeficiency virus 1|11676 - 1448 - 11 - - - 1 - 14.6234 - 26 - 1.54725 - 1 - 8 - 1 - 8 - 0 - 0 - 6 - 7 - 0 - 8 - KALFWTVA - KSLFNTVA - K+LF TVA - - - - - 5 - gnl|BL_ORD_ID|1445 - 126482|gag protein|AAY98604.1|Human immunodeficiency virus 1|11676 - 1445 - 10 - - - 1 - 14.6234 - 26 - 1.7557 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 8 - 0 - 9 - KALFWTVAM - KSLFNTIAV - K+LF T+A+ - - - - - 6 - gnl|BL_ORD_ID|1446 - 126483|gag protein|AAY98604.1|Human immunodeficiency virus 1|11676 - 1446 - 11 - - - 1 - 14.6234 - 26 - 2.02142 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 8 - 0 - 9 - KALFWTVAM - KSLFNTIAV - K+LF T+A+ - - - - - 7 - gnl|BL_ORD_ID|2198 - 190826|gag polyprotein|CAB81949.1|Human immunodeficiency virus 1|11676 - 2198 - 10 - - - 1 - 14.6234 - 26 - 2.33097 - 1 - 8 - 1 - 8 - 0 - 0 - 5 - 7 - 0 - 8 - KALFWTVA - KSLFNTIA - K+LF T+A - - - - - 8 - gnl|BL_ORD_ID|2204 - 190961|gag protein|BAC45024.1|Human immunodeficiency virus 1|11676 - 2204 - 10 - - - 1 - 14.2382 - 25 - 2.75947 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 8 - 0 - 9 - KALFWTVAM - RSLFNTVAV - ++LF TVA+ - - - - - 9 - gnl|BL_ORD_ID|1444 - 126481|gag polyprotein p17 region|BAA83653.1|Human immunodeficiency virus 1|11676 - 1444 - 11 - - - 1 - 14.2382 - 25 - 2.78989 - 1 - 8 - 1 - 8 - 0 - 0 - 5 - 7 - 0 - 8 - KALFWTVA - KSLFNTIA - K+LF T+A - - - - - 10 - gnl|BL_ORD_ID|1460 - 126997|gag protein|BAC45024.1|Human immunodeficiency virus 1|11676 - 1460 - 11 - - - 1 - 14.2382 - 25 - 3.14502 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 8 - 0 - 9 - KALFWTVAM - RSLFNTVAV - ++LF TVA+ - - - - - 11 - gnl|BL_ORD_ID|1458 - 126995|gag polyprotein|BAB19171.1|Human immunodeficiency virus 1|11676 - 1458 - 10 - - - 1 - 14.2382 - 25 - 4.08767 - 1 - 8 - 1 - 8 - 0 - 0 - 5 - 7 - 0 - 8 - KALFWTVA - RSLFNTVA - ++LF TVA - - - - - 12 - gnl|BL_ORD_ID|1459 - 126996|Gag protein|Q9YYH6|Human immunodeficiency virus 1|11676 - 1459 - 11 - - - 1 - 13.853 - 24 - 4.67708 - 1 - 8 - 1 - 8 - 0 - 0 - 5 - 7 - 0 - 8 - KALFWTVA - RSLFNTVA - ++LF TVA - - - - - 13 - gnl|BL_ORD_ID|2203 - 190960|gag-pol polyprotein|BAC02551.1|Human immunodeficiency virus 1|11676 - 2203 - 10 - - - 1 - 13.853 - 24 - 5.38895 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 8 - 0 - 9 - KALFWTVAM - RSLFNTIAV - ++LF T+A+ - - - - - 14 - gnl|BL_ORD_ID|1457 - 126994|gag-pol polyprotein|BAC02551.1|Human immunodeficiency virus 1|11676 - 1457 - 11 - - - 1 - 13.853 - 24 - 6.17581 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 8 - 0 - 9 - KALFWTVAM - RSLFNTIAV - ++LF T+A+ - - - - - 15 - gnl|BL_ORD_ID|2202 - 190959|gag polyprotein|BAB19174.1|Human immunodeficiency virus 1|11676 - 2202 - 10 - - - 1 - 13.4678 - 23 - 7.49677 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 7 - 0 - 8 - KALFWTVA - RSLFNTIA - ++LF T+A - - - - - 16 - gnl|BL_ORD_ID|1456 - 126993|gag polyprotein|BAB19174.1|Human immunodeficiency virus 1|11676 - 1456 - 11 - - - 1 - 13.4678 - 23 - 8.59697 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 7 - 0 - 8 - KALFWTVA - RSLFNTIA - ++LF T+A - - - - - 17 - gnl|BL_ORD_ID|1847 - 180236|gag|BAC81459.1|Human immunodeficiency virus 1|11676 - 1847 - 9 - - - 1 - 13.0826 - 22 - 17.1877 - 2 - 9 - 1 - 8 - 0 - 0 - 5 - 7 - 0 - 8 - ALFWTVAM - SLFNTVAV - +LF TVA+ - - - - - 18 - gnl|BL_ORD_ID|2208 - 190975|gag protein|BAC45024.1|Human immunodeficiency virus 1|11676 - 2208 - 10 - - - 1 - 13.0826 - 22 - 19.4818 - 2 - 9 - 1 - 8 - 0 - 0 - 5 - 7 - 0 - 8 - ALFWTVAM - SLFNTVAV - +LF TVA+ - - - - - 19 - gnl|BL_ORD_ID|1846 - 180233|gag protein|ACZ34075.1|Human immunodeficiency virus 1|11676 - 1846 - 9 - - - 1 - 13.0826 - 22 - 22.6682 - 2 - 8 - 1 - 7 - 0 - 0 - 5 - 6 - 0 - 7 - ALFWTVA - SLFNTVA - +LF TVA - - - - - 20 - gnl|BL_ORD_ID|1475 - 131070|Gag protein|Q9IN85|HIV-1 M:A|505184 - 1475 - 9 - - - 1 - 12.6974 - 21 - 23.4633 - 2 - 8 - 1 - 7 - 0 - 0 - 5 - 6 - 0 - 7 - ALFWTVA - SLFNTVA - +LF TVA - - - - - 21 - gnl|BL_ORD_ID|1468 - 127083|Gag protein|Q9YYH6|Human immunodeficiency virus 1|11676 - 1468 - 10 - - - 1 - 12.6974 - 21 - 26.9859 - 2 - 8 - 1 - 7 - 0 - 0 - 5 - 6 - 0 - 7 - ALFWTVA - SLFNTVA - +LF TVA - - - - - 22 - gnl|BL_ORD_ID|2145 - 189204|||| - 2145 - 9 - - - 1 - 12.6974 - 21 - 29.3325 - 2 - 8 - 1 - 7 - 0 - 0 - 5 - 6 - 0 - 7 - ALFWTVA - ALYNTVA - AL+ TVA - - - - - 23 - gnl|BL_ORD_ID|2147 - 189277|gag protein|AAY98604.1|Human immunodeficiency virus 1|11676 - 2147 - 9 - - - 1 - 12.6974 - 21 - 31.4086 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 7 - 0 - 8 - ALFWTVAM - SLFNTIAV - +LF T+A+ - - - - - 24 - gnl|BL_ORD_ID|1467 - 127082|gag-pol polyprotein|BAC02551.1|Human immunodeficiency virus 1|11676 - 1467 - 10 - - - 1 - 12.6974 - 21 - 36.0093 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 7 - 0 - 8 - ALFWTVAM - SLFNTIAV - +LF T+A+ - - - - - 25 - gnl|BL_ORD_ID|1845 - 180191|gag polyprotein|BAB19174.1|Human immunodeficiency virus 1|11676 - 1845 - 9 - - - 1 - 12.3122 - 20 - 44.1001 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 6 - 0 - 7 - ALFWTVA - SLFNTIA - +LF T+A - - - - - 26 - gnl|BL_ORD_ID|2207 - 190974|gag polyprotein|BAB19174.1|Human immunodeficiency virus 1|11676 - 2207 - 10 - - - 1 - 12.3122 - 20 - 50.3363 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 6 - 0 - 7 - ALFWTVA - SLFNTIA - +LF T+A - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 246 - Query_246 - M_716 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 247 - Query_247 - M_717 - 9 - - - 1 - gnl|BL_ORD_ID|545 - 33382|polyprotein|AAB67037.1|Hepatitis C virus|11103 - 545 - 15 - - - 1 - 12.6974 - 21 - 25.6947 - 3 - 9 - 5 - 11 - 0 - 0 - 3 - 6 - 0 - 7 - SPMPYTY - TPMGFSY - +PM ++Y - - - - - 2 - gnl|BL_ORD_ID|1068 - 70491|envelope glycoprotein|AAC28452.1|Human immunodeficiency virus 1|11676 - 1068 - 10 - - - 1 - 11.5418 - 18 - 141.547 - 1 - 6 - 2 - 7 - 0 - 0 - 4 - 4 - 0 - 6 - PTSPMP - PTDPNP - PT P P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 248 - Query_248 - M_718 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 249 - Query_249 - M_719 - 9 - - - 1 - gnl|BL_ORD_ID|722 - 44920|tegument protein pp65|YP_002608275.1|Human betaherpesvirus 5|10359 - 722 - 9 - - - 1 - 13.853 - 24 - 4.4402 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 8 - 0 - 9 - NVVRLVATI - NLVPMVATV - N+V +VAT+ - - - - - 2 - gnl|BL_ORD_ID|838 - 55029|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 838 - 11 - - - 1 - 13.853 - 24 - 4.75889 - 1 - 9 - 2 - 10 - 0 - 0 - 5 - 8 - 0 - 9 - NVVRLVATI - NLVPMVATV - N+V +VAT+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 250 - Query_250 - M_720 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 251 - Query_251 - M_721 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 252 - Query_252 - M_722 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 253 - Query_253 - M_723 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 254 - Query_254 - M_724 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 255 - Query_255 - M_725 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 256 - Query_256 - M_726 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 257 - Query_257 - M_727 - 9 - - - 1 - gnl|BL_ORD_ID|1474 - 130953|G1 and G2 surface glycoprotein precursor|AAG22532.1|Andes hantavirus|46607 - 1474 - 9 - - - 1 - 11.927 - 19 - 107.472 - 3 - 9 - 3 - 9 - 0 - 0 - 3 - 5 - 0 - 7 - PDELHAM - PDVAHSL - PD H++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 258 - Query_258 - M_728 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 259 - Query_259 - M_729 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 260 - Query_260 - M_730 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 261 - Query_261 - M_731 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 262 - Query_262 - M_732 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 263 - Query_263 - M_733 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 264 - Query_264 - M_734 - 9 - - - 1 - gnl|BL_ORD_ID|284 - 19337|gag protein|AAW57872.1|Human immunodeficiency virus 1|11676 - 284 - 9 - - - 1 - 13.0826 - 22 - 16.035 - 2 - 7 - 3 - 8 - 0 - 0 - 3 - 5 - 0 - 6 - MDRWNE - LDRWEK - +DRW + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 265 - Query_265 - M_735 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 266 - Query_266 - M_736 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 267 - Query_267 - M_737 - 9 - - - 1 - gnl|BL_ORD_ID|672 - 40288|kaposin|AAC57155.1|Human gammaherpesvirus 8|37296 - 672 - 15 - - - 1 - 13.0826 - 22 - 18.437 - 1 - 7 - 5 - 11 - 0 - 0 - 5 - 5 - 0 - 7 - LAIKVTP - LAISVVP - LAI V P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 268 - Query_268 - M_738 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 269 - Query_269 - M_739 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 270 - Query_270 - M_740 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 271 - Query_271 - M_741 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 272 - Query_272 - M_742 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 273 - Query_273 - M_743 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 274 - Query_274 - M_744 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 275 - Query_275 - M_745 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 276 - Query_276 - M_746 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 277 - Query_277 - M_747 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 278 - Query_278 - M_748 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 279 - Query_279 - M_749 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 280 - Query_280 - M_750 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 281 - Query_281 - M_751 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 282 - Query_282 - M_752 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 283 - Query_283 - M_753 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 284 - Query_284 - M_754 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 285 - Query_285 - M_755 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 286 - Query_286 - M_756 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 287 - Query_287 - M_757 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 288 - Query_288 - M_758 - 9 - - - 1 - gnl|BL_ORD_ID|1763 - 154585|ribonucleotide reductase large subunit|CAB06725.1|Human alphaherpesvirus 2|10310 - 1763 - 15 - - - 1 - 12.3122 - 20 - 42.5209 - 1 - 9 - 5 - 13 - 0 - 0 - 4 - 5 - 0 - 9 - YQEEMIQCY - YMESVFQMY - Y E + Q Y - - - - - 2 - gnl|BL_ORD_ID|1586 - 141480|ribonucleotide reductase subunit 1|NP_044641.1|Human alphaherpesvirus 1|10298 - 1586 - 9 - - - 1 - 11.927 - 19 - 77.6399 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 5 - 0 - 9 - YQEEMIQCY - YMESVFQMY - Y E + Q Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 289 - Query_289 - M_759 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 290 - Query_290 - M_760 - 9 - - - 1 - gnl|BL_ORD_ID|889 - 58463|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 889 - 20 - - - 1 - 13.853 - 24 - 5.89466 - 3 - 9 - 12 - 18 - 0 - 0 - 5 - 6 - 0 - 7 - YVYPLPV - YVYALPL - YVY LP+ - - - - - 2 - gnl|BL_ORD_ID|338 - 21242|polymerase|ACF94272.1|Hepatitis B virus|10407 - 338 - 9 - - - 1 - 11.1566 - 17 - 287.485 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 5 - 0 - 9 - GAYVYPLPV - GLYSSTVPV - G Y +PV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 291 - Query_291 - M_761 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 292 - Query_292 - M_762 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 293 - Query_293 - M_763 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 294 - Query_294 - M_764 - 9 - - - 1 - gnl|BL_ORD_ID|1948 - 180850|polyprotein|AFP27208.1|Dengue virus 4|11070 - 1948 - 10 - - - 1 - 12.3122 - 20 - 49.5064 - 2 - 8 - 1 - 7 - 0 - 0 - 3 - 5 - 0 - 7 - YYPPGVV - YTPEGII - Y P G++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 295 - Query_295 - M_765 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 296 - Query_296 - M_766 - 9 - - - 1 - gnl|BL_ORD_ID|356 - 22235|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 356 - 15 - - - 1 - 16.1642 - 30 - 0.297937 - 1 - 8 - 6 - 13 - 0 - 0 - 5 - 8 - 0 - 8 - SALEYLLP - SALQFLIP - SAL++L+P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 297 - Query_297 - M_767 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 298 - Query_298 - M_768 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 299 - Query_299 - M_769 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 300 - Query_300 - M_770 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 301 - Query_301 - M_771 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 302 - Query_302 - M_772 - 9 - - - 1 - gnl|BL_ORD_ID|1924 - 180726|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1924 - 15 - - - 1 - 13.0826 - 22 - 20.3784 - 3 - 8 - 8 - 13 - 0 - 0 - 3 - 4 - 0 - 6 - SQWDHG - TAWDFG - + WD G - - - - - 2 - gnl|BL_ORD_ID|439 - 27061|envelope glycoprotein|ABU89742.1|Dengue virus 2 Thailand/16681/84|31634 - 439 - 10 - - - 1 - 12.6974 - 21 - 29.385 - 3 - 8 - 5 - 10 - 0 - 0 - 3 - 4 - 0 - 6 - SQWDHG - TAWDFG - + WD G - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 303 - Query_303 - M_773 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 304 - Query_304 - M_774 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 305 - Query_305 - M_775 - 9 - - - 1 - gnl|BL_ORD_ID|1813 - 177701|polyprotein|ACZ60104.1|Hepatitis C virus subtype 3a|356426 - 1813 - 18 - - - 1 - 16.1642 - 30 - 0.340428 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 7 - 0 - 9 - HAQVCSLYI - KAKICGLYL - A++C LY+ - - - - - 2 - gnl|BL_ORD_ID|1793 - 164264|nucleocapsid protein|AAA43837.1|Hantaan virus 76-118|11602 - 1793 - 15 - - - 1 - 13.4678 - 23 - 11.1066 - 1 - 8 - 7 - 14 - 0 - 0 - 4 - 4 - 0 - 8 - HAQVCSLY - RTAVCGLY - VC LY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 306 - Query_306 - M_776 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 307 - Query_307 - M_777 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 308 - Query_308 - M_778 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 309 - Query_309 - M_779 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 310 - Query_310 - M_780 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 311 - Query_311 - M_781 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 312 - Query_312 - M_782 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 313 - Query_313 - M_783 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 314 - Query_314 - M_784 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 315 - Query_315 - M_785 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 316 - Query_316 - M_786 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 317 - Query_317 - M_787 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 318 - Query_318 - M_788 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 319 - Query_319 - M_789 - 9 - - - 1 - gnl|BL_ORD_ID|227 - 16751|pol protein|BAA32832.1|Hepatitis B virus|10407 - 227 - 9 - - - 1 - 15.0086 - 27 - 1.21609 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 7 - 0 - 9 - YLLRAGVHL - FLLSLGIHL - +LL G+HL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 320 - Query_320 - M_790 - 9 - - - 1 - gnl|BL_ORD_ID|1715 - 150378|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1715 - 9 - - - 1 - 13.4678 - 23 - 7.85574 - 1 - 6 - 4 - 9 - 0 - 0 - 5 - 5 - 0 - 6 - LVTPHM - LVTPSM - LVTP M - - - - - 2 - gnl|BL_ORD_ID|1908 - 180657|polyprotein|CDF77361.1|Dengue virus 3|11069 - 1908 - 9 - - - 1 - 13.4678 - 23 - 7.99354 - 1 - 7 - 2 - 8 - 0 - 0 - 5 - 5 - 0 - 7 - LVTPHMA - LVTPSMT - LVTP M - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 321 - Query_321 - M_791 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 322 - Query_322 - M_792 - 9 - - - 1 - gnl|BL_ORD_ID|23 - 1516|Nucleoprotein|P03418.1|Human respiratory syncytial virus A2|11259 - 23 - 14 - - - 1 - 13.853 - 24 - 6.4996 - 1 - 8 - 2 - 9 - 0 - 0 - 3 - 6 - 0 - 8 - SFYHLVST - GFYHILNN - FYH+++ - - - - - 2 - gnl|BL_ORD_ID|2158 - 189294|Gag|O89360|Human immunodeficiency virus 1|11676 - 2158 - 9 - - - 1 - 13.4678 - 23 - 10.1994 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 7 - 0 - 9 - SFYHLVSTV - SLYNTVSTL - S Y+ VST+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 323 - Query_323 - M_793 - 9 - - - 1 - gnl|BL_ORD_ID|14 - 1090|Transcription activator BRLF1|P03209.1|Human herpesvirus 4 strain B95-8|10377 - 14 - 9 - - - 1 - 11.927 - 19 - 88.4863 - 2 - 7 - 3 - 8 - 0 - 0 - 4 - 6 - 0 - 6 - SAGNEA - NAGNDA - +AGN+A - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 324 - Query_324 - M_794 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 325 - Query_325 - M_795 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 326 - Query_326 - M_796 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 327 - Query_327 - M_797 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 328 - Query_328 - M_798 - 9 - - - 1 - gnl|BL_ORD_ID|1092 - 72233|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 - 1092 - 15 - - - 1 - 13.0826 - 22 - 16.9555 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 7 - 0 - 9 - WSLDGKYIV - WAIKWEYVV - W++ +Y+V - - - - - 2 - gnl|BL_ORD_ID|1097 - 72563|polyprotein|AAB70696.1|Dengue virus type 1 Hawaii|10000440 - 1097 - 20 - - - 1 - 12.6974 - 21 - 22.9279 - 1 - 9 - 12 - 20 - 0 - 0 - 4 - 5 - 0 - 9 - WSLDGKYIV - WAYHGSYEV - W+ G Y V - - - - - 3 - gnl|BL_ORD_ID|2285 - 419170|polyprotein|ABR25251.1|Hepatitis C virus|11103 - 2285 - 9 - - - 1 - 12.6974 - 21 - 26.9236 - 1 - 7 - 3 - 9 - 0 - 0 - 4 - 5 - 0 - 7 - WSLDGKY - WYLKGKW - W L GK+ - - - - - 4 - gnl|BL_ORD_ID|1941 - 180814|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1941 - 9 - - - 1 - 12.3122 - 20 - 48.7826 - 1 - 7 - 1 - 7 - 0 - 0 - 3 - 4 - 0 - 7 - WSLDGKY - WAYHGSY - W+ G Y - - - - - 5 - gnl|BL_ORD_ID|1888 - 180582|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1888 - 15 - - - 1 - 12.3122 - 20 - 50.6727 - 1 - 7 - 3 - 9 - 0 - 0 - 3 - 4 - 0 - 7 - WSLDGKY - WAYHGSY - W+ G Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 329 - Query_329 - M_799 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 330 - Query_330 - M_800 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 331 - Query_331 - M_801 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 332 - Query_332 - M_802 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 333 - Query_333 - M_803 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 334 - Query_334 - M_804 - 9 - - - 1 - gnl|BL_ORD_ID|2199 - 190827|gag protein|AAN08336.1|Human immunodeficiency virus 1|11676 - 2199 - 10 - - - 1 - 12.3122 - 20 - 59.3959 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 7 - 0 - 9 - ALYCRLATV - SLYNTIATL - +LY +AT+ - - - - - 2 - gnl|BL_ORD_ID|2152 - 189288|gag protein|AAV53168.1|Human immunodeficiency virus 1|11676 - 2152 - 9 - - - 1 - 12.3122 - 20 - 64.7664 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 7 - 0 - 9 - ALYCRLATV - SLYNTIATL - +LY +AT+ - - - - - 3 - gnl|BL_ORD_ID|1451 - 126488|gag protein|AAV53168.1|Human immunodeficiency virus 1|11676 - 1451 - 11 - - - 1 - 11.927 - 19 - 67.9126 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 7 - 0 - 9 - ALYCRLATV - SLYNTIATL - +LY +AT+ - - - - - 4 - gnl|BL_ORD_ID|2209 - 190978|gag protein|AAV53168.1|Human immunodeficiency virus 1|11676 - 2209 - 10 - - - 1 - 11.927 - 19 - 73.4989 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 7 - 0 - 9 - ALYCRLATV - SLYNTIATL - +LY +AT+ - - - - - 5 - gnl|BL_ORD_ID|2205 - 190962|gag polyprotein|BAB88540.1|Human immunodeficiency virus 1|11676 - 2205 - 10 - - - 1 - 11.927 - 19 - 78.4397 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 7 - 0 - 9 - ALYCRLATV - SLYNTIATL - +LY +AT+ - - - - - 6 - gnl|BL_ORD_ID|1461 - 126999|gag polyprotein|BAB88540.1|Human immunodeficiency virus 1|11676 - 1461 - 11 - - - 1 - 11.927 - 19 - 85.0874 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 7 - 0 - 9 - ALYCRLATV - SLYNTIATL - +LY +AT+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 335 - Query_335 - M_805 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 336 - Query_336 - M_806 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 337 - Query_337 - M_807 - 9 - - - 1 - gnl|BL_ORD_ID|2083 - 185419|envelope protein|AGW23591.1|Dengue virus 3|11069 - 2083 - 9 - - - 1 - 13.4678 - 23 - 10.9354 - 3 - 8 - 4 - 9 - 0 - 0 - 5 - 6 - 0 - 6 - MDELEL - MDKLEL - MD+LEL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 338 - Query_338 - M_808 - 9 - - - 1 - gnl|BL_ORD_ID|624 - 37507|Large T antigen|P03071.1|Human polyomavirus 1|1891762 - 624 - 9 - - - 1 - 15.3938 - 28 - 0.690962 - 2 - 9 - 2 - 9 - 0 - 0 - 5 - 6 - 0 - 8 - MLNWFSPV - LLIWFRPV - +L WF PV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 339 - Query_339 - M_809 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 340 - Query_340 - M_810 - 9 - - - 1 - gnl|BL_ORD_ID|2139 - 187158|Gag protein|Q1KW74|Human immunodeficiency virus 1|11676 - 2139 - 11 - - - 1 - 13.853 - 24 - 5.66142 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - HSFNPE - KAFNPE - +FNPE - - - - - 2 - gnl|BL_ORD_ID|2141 - 187163|Gag polyprotein|P88150|Human immunodeficiency virus 1|11676 - 2141 - 11 - - - 1 - 13.4678 - 23 - 8.0187 - 1 - 7 - 1 - 7 - 0 - 0 - 4 - 4 - 0 - 7 - HSFNPEA - KGFNPEV - FNPE - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 341 - Query_341 - M_811 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 342 - Query_342 - M_812 - 9 - - - 1 - gnl|BL_ORD_ID|730 - 46480|DNA polymerase|CAA10434.1|Hepatitis B virus|10407 - 730 - 9 - - - 1 - 15.779 - 29 - 0.439716 - 1 - 7 - 2 - 8 - 0 - 0 - 5 - 5 - 0 - 7 - FSIPWAH - VSIPWTH - SIPW H - - - - - 2 - gnl|BL_ORD_ID|879 - 57723|polyprotein|CAB53095.1|Hepatitis C virus|11103 - 879 - 10 - - - 1 - 12.3122 - 20 - 44.0514 - 1 - 8 - 2 - 9 - 0 - 0 - 3 - 5 - 0 - 8 - FSIPWAHA - FAIKWEYV - F+I W + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 343 - Query_343 - M_813 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 344 - Query_344 - M_814 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 345 - Query_345 - M_815 - 9 - - - 1 - gnl|BL_ORD_ID|1944 - 180818|Membrane glycoprotein precursor|NP_739582.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1944 - 15 - - - 1 - 14.2382 - 25 - 3.31511 - 1 - 7 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - WVLHHMG - WILRHPG - W+L H G - - - - - 2 - gnl|BL_ORD_ID|1481 - 133645|cell surface protein|NP_302626.1|Mycobacterium leprae|1769 - 1481 - 15 - - - 1 - 11.5418 - 18 - 101.887 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 5 - 0 - 8 - VLHHMGGM - MLDHAGNM - +L H G M - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 346 - Query_346 - M_816 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 347 - Query_347 - M_817 - 9 - - - 1 - gnl|BL_ORD_ID|2014 - 183819|polyprotein|AGO67248.1|Dengue virus 2|11060 - 2014 - 10 - - - 1 - 12.3122 - 20 - 52.9061 - 2 - 7 - 5 - 10 - 0 - 0 - 5 - 5 - 0 - 6 - AAAWAL - AAAWYL - AAAW L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 348 - Query_348 - M_818 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 349 - Query_349 - M_819 - 9 - - - 1 - gnl|BL_ORD_ID|904 - 59459|Trans-sialidase|SRC7915|Trypanosoma cruzi|5693 - 904 - 9 - - - 1 - 12.3122 - 20 - 53.0441 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - LGHMFSL - LSHYFTL - L H F+L - - - - - 2 - gnl|BL_ORD_ID|1262 - 98466|Trans-sialidase|SRC7915|Trypanosoma cruzi|5693 - 1262 - 10 - - - 1 - 12.3122 - 20 - 56.5271 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - LGHMFSL - LSHYFTL - L H F+L - - - - - 3 - gnl|BL_ORD_ID|247 - 16890|trans-sialidase|XP_810777.1|Trypanosoma cruzi|5693 - 247 - 9 - - - 1 - 11.927 - 19 - 102.395 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - LGHMFSL - LSHNFTL - L H F+L - - - - - 4 - gnl|BL_ORD_ID|1242 - 98039|Trans-sialidase|SRC7915|Trypanosoma cruzi|5693 - 1242 - 10 - - - 1 - 11.5418 - 18 - 117.155 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - LGHMFSL - LSHNFTL - L H F+L - - - - - 5 - gnl|BL_ORD_ID|246 - 16889|trans-sialidase, putative|EAN82636.1|Trypanosoma cruzi|5693 - 246 - 9 - - - 1 - 11.5418 - 18 - 143.267 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - LGHMFSL - LSHDFTL - L H F+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 350 - Query_350 - M_820 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 351 - Query_351 - M_821 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 352 - Query_352 - M_822 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 353 - Query_353 - M_823 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 354 - Query_354 - M_824 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 355 - Query_355 - M_825 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 356 - Query_356 - M_826 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 357 - Query_357 - M_827 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 358 - Query_358 - M_828 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 359 - Query_359 - M_829 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 360 - Query_360 - M_830 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 361 - Query_361 - M_831 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 362 - Query_362 - M_832 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 363 - Query_363 - M_833 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 364 - Query_364 - M_834 - 9 - - - 1 - gnl|BL_ORD_ID|1916 - 180681|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1916 - 15 - - - 1 - 13.0826 - 22 - 14.8197 - 1 - 8 - 2 - 9 - 0 - 0 - 4 - 4 - 0 - 8 - AAYTSYTP - EEYTDYMP - YT Y P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 365 - Query_365 - M_835 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 366 - Query_366 - M_836 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 367 - Query_367 - M_837 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 368 - Query_368 - M_838 - 9 - - - 1 - gnl|BL_ORD_ID|2273 - 419006|PPE family protein PPE68|KAM81677.1|Mycobacterium tuberculosis H37Ra|419947 - 2273 - 10 - - - 1 - 13.4678 - 23 - 10.0795 - 1 - 6 - 3 - 8 - 0 - 0 - 4 - 6 - 0 - 6 - RSEALP - RAESLP - R+E+LP - - - - - 2 - gnl|BL_ORD_ID|328 - 21078|Antigen 85-B precursor|P21160.1|Mycobacterium kansasii|1768 - 328 - 9 - - - 1 - 13.0826 - 22 - 18.7436 - 4 - 9 - 1 - 6 - 0 - 0 - 4 - 4 - 0 - 6 - ALPVSY - GLPVEY - LPV Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 369 - Query_369 - M_839 - 9 - - - 1 - gnl|BL_ORD_ID|490 - 30946|HCV-1|AAA45676.1|Hepatitis C virus genotype 1|41856 - 490 - 20 - - - 1 - 11.1566 - 17 - 183.47 - 3 - 9 - 5 - 11 - 0 - 0 - 4 - 5 - 0 - 7 - KPFGLVV - KPARLIV - KP L+V - - - - - 2 - gnl|BL_ORD_ID|1414 - 111448|polyprotein precursor|BAA02756.1|Hepatitis C virus|11103 - 1414 - 15 - - - 1 - 11.1566 - 17 - 190.157 - 3 - 9 - 5 - 11 - 0 - 0 - 4 - 5 - 0 - 7 - KPFGLVV - KPARLIV - KP L+V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 370 - Query_370 - M_840 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 371 - Query_371 - M_841 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 372 - Query_372 - M_842 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 373 - Query_373 - M_843 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 374 - Query_374 - M_844 - 9 - - - 1 - gnl|BL_ORD_ID|1659 - 146644|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 - 1659 - 10 - - - 1 - 13.853 - 24 - 6.29996 - 1 - 8 - 3 - 10 - 0 - 0 - 5 - 6 - 0 - 8 - HAATGPGE - HAPTGSGK - HA TG G+ - - - - - 2 - gnl|BL_ORD_ID|394 - 24219|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 - 394 - 15 - - - 1 - 13.4678 - 23 - 7.61659 - 1 - 8 - 3 - 10 - 0 - 0 - 5 - 6 - 0 - 8 - HAATGPGE - HAPTGSGK - HA TG G+ - - - - - 3 - gnl|BL_ORD_ID|393 - 24218|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 - 393 - 10 - - - 1 - 13.4678 - 23 - 8.92274 - 1 - 8 - 3 - 10 - 0 - 0 - 5 - 6 - 0 - 8 - HAATGPGE - HAPTGSGK - HA TG G+ - - - - - 4 - gnl|BL_ORD_ID|741 - 47760|EBNA-1 protein|Q777E1|Human gammaherpesvirus 4|10376 - 741 - 15 - - - 1 - 12.3122 - 20 - 51.4826 - 3 - 8 - 2 - 7 - 0 - 0 - 4 - 4 - 0 - 6 - ATGPGE - GTGPGN - TGPG - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 375 - Query_375 - M_845 - 9 - - - 1 - gnl|BL_ORD_ID|1916 - 180681|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1916 - 15 - - - 1 - 13.0826 - 22 - 20.0418 - 1 - 6 - 9 - 14 - 0 - 0 - 4 - 4 - 0 - 6 - PSQNRF - PSMKRF - PS RF - - - - - 2 - gnl|BL_ORD_ID|1911 - 180667|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1911 - 10 - - - 1 - 13.0826 - 22 - 21.2326 - 1 - 6 - 2 - 7 - 0 - 0 - 4 - 4 - 0 - 6 - PSQNRF - PSMKRF - PS RF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 376 - Query_376 - M_846 - 9 - - - 1 - gnl|BL_ORD_ID|488 - 30903|prM protein|YP_001527879.1|West Nile virus NY-99|10000971 - 488 - 16 - - - 1 - 14.2382 - 25 - 3.11811 - 3 - 8 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - SAWLDS - GAWMDS - AW+DS - - - - - 2 - gnl|BL_ORD_ID|484 - 30266|Transcriptional regulator IE63 homolog|Q04360.1|Human herpesvirus 4 strain B95-8|10377 - 484 - 9 - - - 1 - 11.927 - 19 - 95.9763 - 4 - 8 - 3 - 7 - 0 - 0 - 3 - 4 - 0 - 5 - AWLDS - TWLDA - WLD+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 377 - Query_377 - M_847 - 9 - - - 1 - gnl|BL_ORD_ID|1936 - 180789|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1936 - 15 - - - 1 - 11.927 - 19 - 61.2314 - 1 - 6 - 8 - 13 - 0 - 0 - 3 - 5 - 0 - 6 - VPFPPK - IPYDPK - +P+ PK - - - - - 2 - gnl|BL_ORD_ID|1211 - 96366|polyprotein|ABR25251.1|Hepatitis C virus|11103 - 1211 - 12 - - - 1 - 11.1566 - 17 - 174.36 - 4 - 9 - 5 - 10 - 0 - 0 - 4 - 5 - 0 - 6 - PPKEPL - PPCKPL - PP +PL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 378 - Query_378 - M_848 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 379 - Query_379 - M_849 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 380 - Query_380 - M_850 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 381 - Query_381 - M_851 - 9 - - - 1 - gnl|BL_ORD_ID|1583 - 141469|envelope glycoprotein B|NP_044629.1|Human alphaherpesvirus 1|10298 - 1583 - 9 - - - 1 - 11.927 - 19 - 76.3762 - 3 - 9 - 1 - 7 - 0 - 0 - 3 - 5 - 0 - 7 - IFMPPTY - VYMSPFY - ++M P Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 382 - Query_382 - M_852 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 383 - Query_383 - M_853 - 9 - - - 1 - gnl|BL_ORD_ID|389 - 23807|tax|AAG48731.1|Human T-lymphotropic virus 2|11909 - 389 - 23 - - - 1 - 14.2382 - 25 - 4.20595 - 1 - 9 - 2 - 10 - 0 - 0 - 5 - 6 - 0 - 9 - FPRASQSLV - FPGFGQSLL - FP QSL+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 384 - Query_384 - M_854 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 385 - Query_385 - M_855 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 386 - Query_386 - M_856 - 9 - - - 1 - gnl|BL_ORD_ID|1266 - 98640|trans-sialidase, putative|EAN80840.1|Trypanosoma cruzi|5693 - 1266 - 9 - - - 1 - 13.853 - 24 - 7.20201 - 1 - 7 - 3 - 9 - 0 - 0 - 5 - 7 - 0 - 7 - FSLLATV - FTLVATV - F+L+ATV - - - - - 2 - gnl|BL_ORD_ID|1245 - 98044|trans-sialidase, putative|EAN80840.1|Trypanosoma cruzi|5693 - 1245 - 9 - - - 1 - 13.4678 - 23 - 7.99354 - 1 - 7 - 1 - 7 - 0 - 0 - 5 - 7 - 0 - 7 - FSLLATV - FTLVATV - F+L+ATV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 387 - Query_387 - M_857 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 388 - Query_388 - M_858 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 389 - Query_389 - M_859 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 390 - Query_390 - M_860 - 9 - - - 1 - gnl|BL_ORD_ID|1689 - 149063|NS3 protease/helicase'|NP_803144.1|Hepatitis C virus (isolate H77)|63746 - 1689 - 18 - - - 1 - 10.7714 - 16 - 272.739 - 2 - 8 - 7 - 13 - 0 - 0 - 4 - 5 - 0 - 7 - PVLLLDT - PVENLET - PV L+T - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 391 - Query_391 - M_861 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 392 - Query_392 - M_862 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 393 - Query_393 - M_863 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 394 - Query_394 - M_864 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 395 - Query_395 - M_865 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 396 - Query_396 - M_866 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 397 - Query_397 - M_867 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 398 - Query_398 - M_868 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 399 - Query_399 - M_869 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 400 - Query_400 - M_870 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 401 - Query_401 - M_871 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 402 - Query_402 - M_872 - 9 - - - 1 - gnl|BL_ORD_ID|1438 - 120093|unnamed protein product|CAA33016.1|Rubella virus|11041 - 1438 - 21 - - - 1 - 11.1566 - 17 - 146.584 - 4 - 8 - 11 - 15 - 0 - 0 - 4 - 4 - 0 - 5 - PPPPT - PPPAT - PPP T - - - - - 2 - gnl|BL_ORD_ID|1276 - 101821|vif protein|ACC96167.1|Human immunodeficiency virus 1|11676 - 1276 - 11 - - - 1 - 11.1566 - 17 - 185.696 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 6 - 0 - 9 - RGMPPPPTV - KTKPPLPSV - + PP P+V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 403 - Query_403 - M_873 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 404 - Query_404 - M_874 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 405 - Query_405 - M_875 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 406 - Query_406 - M_876 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 407 - Query_407 - M_877 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 408 - Query_408 - M_878 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 409 - Query_409 - M_879 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 410 - Query_410 - M_880 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 411 - Query_411 - M_881 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 412 - Query_412 - M_882 - 9 - - - 1 - gnl|BL_ORD_ID|392 - 24172|pX-rex-orf I {alternatively spliced}|AAB23359.1|Human T-lymphotropic virus 1|11908 - 392 - 9 - - - 1 - 12.6974 - 21 - 35.3877 - 1 - 8 - 1 - 8 - 0 - 0 - 5 - 6 - 0 - 8 - HLMKQISS - HLAFQLSS - HL Q+SS - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 413 - Query_413 - M_883 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 414 - Query_414 - M_884 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 415 - Query_415 - M_885 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 416 - Query_416 - M_886 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 417 - Query_417 - M_887 - 9 - - - 1 - gnl|BL_ORD_ID|2052 - 184713|polyprotein|AFP27208.1|Dengue virus 4|11070 - 2052 - 9 - - - 1 - 13.4678 - 23 - 10.1994 - 1 - 8 - 2 - 9 - 0 - 0 - 6 - 6 - 0 - 8 - YVVATTKL - YAVATTIL - Y VATT L - - - - - 2 - gnl|BL_ORD_ID|1484 - 133716|polyprotein|ABG75765.1|Dengue virus 1|11053 - 1484 - 9 - - - 1 - 12.6974 - 21 - 25.5715 - 1 - 6 - 3 - 8 - 0 - 0 - 5 - 5 - 0 - 6 - YVVATT - YAVATT - Y VATT - - - - - 3 - gnl|BL_ORD_ID|1738 - 150639|polyprotein|AGO67249.1|Dengue virus 2|11060 - 1738 - 10 - - - 1 - 12.6974 - 21 - 26.9859 - 1 - 6 - 3 - 8 - 0 - 0 - 5 - 5 - 0 - 6 - YVVATT - YAVATT - Y VATT - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 418 - Query_418 - M_888 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 419 - Query_419 - M_889 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 420 - Query_420 - M_890 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 421 - Query_421 - M_891 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 422 - Query_422 - M_892 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 423 - Query_423 - M_893 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 424 - Query_424 - M_894 - 9 - - - 1 - gnl|BL_ORD_ID|152 - 11214|possible regulatory protein|NP_302009.1|Mycobacterium leprae|1769 - 152 - 15 - - - 1 - 11.1566 - 17 - 239.5 - 1 - 8 - 3 - 10 - 0 - 0 - 4 - 5 - 0 - 8 - ILLNGDAT - VLLRLDGT - +LL D T - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 425 - Query_425 - M_895 - 9 - - - 1 - gnl|BL_ORD_ID|2225 - 194440|envelope glycoprotein B|NP_044629.1|Herpes simplex virus (type 1 / strain 17)|10299 - 2225 - 9 - - - 1 - 12.6974 - 21 - 27.8632 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 7 - 0 - 9 - TIYDEDVLV - TMYYKDVTV - T+Y +DV V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 426 - Query_426 - M_896 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 427 - Query_427 - M_897 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 428 - Query_428 - M_898 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 429 - Query_429 - M_899 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 430 - Query_430 - M_900 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 431 - Query_431 - M_901 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 432 - Query_432 - M_902 - 9 - - - 1 - gnl|BL_ORD_ID|367 - 22825|polyprotein|ABG75765.1|Dengue virus 1|11053 - 367 - 10 - - - 1 - 12.6974 - 21 - 30.9217 - 4 - 9 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - SSGKPI - TSGSPI - +SG PI - - - - - 2 - gnl|BL_ORD_ID|75 - 5542|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 75 - 15 - - - 1 - 12.6974 - 21 - 31.2769 - 4 - 9 - 10 - 15 - 0 - 0 - 4 - 5 - 0 - 6 - SSGKPI - TSGSPI - +SG PI - - - - - 3 - gnl|BL_ORD_ID|366 - 22824|polyprotein|AAG30730.1|Dengue virus 2|11060 - 366 - 10 - - - 1 - 12.6974 - 21 - 31.4509 - 4 - 9 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - SSGKPI - TSGSPI - +SG PI - - - - - 4 - gnl|BL_ORD_ID|363 - 22820|Nonstructural protein NS3|YP_001531172.2|Dengue virus 3|11069 - 363 - 10 - - - 1 - 12.6974 - 21 - 33.0913 - 4 - 9 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - SSGKPI - TSGSPI - +SG PI - - - - - 5 - gnl|BL_ORD_ID|365 - 22823|NS3 protein|NP_739587.1|Dengue virus 2|11060 - 365 - 10 - - - 1 - 12.6974 - 21 - 35.4066 - 4 - 9 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - SSGKPI - TSGSPI - +SG PI - - - - - 6 - gnl|BL_ORD_ID|364 - 22822|NS3 protein|NP_740321.1|Dengue virus 4|11070 - 364 - 11 - - - 1 - 12.6974 - 21 - 36.919 - 4 - 9 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - SSGKPI - TSGSPI - +SG PI - - - - - 7 - gnl|BL_ORD_ID|361 - 22818|Nonstructural protein NS3|NP_739587.2|Dengue virus 2|11060 - 361 - 10 - - - 1 - 12.6974 - 21 - 37.8768 - 4 - 9 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - SSGKPI - TSGSPI - +SG PI - - - - - 8 - gnl|BL_ORD_ID|360 - 22817|polyprotein|AAK49562.1|Dengue virus 2|11060 - 360 - 11 - - - 1 - 12.3122 - 20 - 38.8163 - 4 - 9 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - SSGKPI - TSGSPI - +SG PI - - - - - 9 - gnl|BL_ORD_ID|362 - 22819|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 362 - 11 - - - 1 - 12.3122 - 20 - 40.8064 - 4 - 9 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - SSGKPI - TSGSPI - +SG PI - - - - - 10 - gnl|BL_ORD_ID|260 - 17802|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 260 - 15 - - - 1 - 12.3122 - 20 - 51.4826 - 4 - 9 - 5 - 10 - 0 - 0 - 4 - 5 - 0 - 6 - SSGKPI - TSGSPI - +SG PI - - - - - 11 - gnl|BL_ORD_ID|1712 - 150341|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1712 - 9 - - - 1 - 12.3122 - 20 - 55.769 - 4 - 9 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - SSGKPI - TSGSPI - +SG PI - - - - - 12 - gnl|BL_ORD_ID|1929 - 180750|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1929 - 15 - - - 1 - 12.3122 - 20 - 59.339 - 4 - 9 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - SSGKPI - TSGSPI - +SG PI - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 433 - Query_433 - M_903 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 434 - Query_434 - M_904 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 435 - Query_435 - M_905 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 436 - Query_436 - M_906 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 437 - Query_437 - M_907 - 9 - - - 1 - gnl|BL_ORD_ID|1861 - 180440|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1861 - 15 - - - 1 - 12.6974 - 21 - 31.2769 - 1 - 6 - 9 - 14 - 0 - 0 - 4 - 5 - 0 - 6 - WASGNE - WNSGHE - W SG+E - - - - - 2 - gnl|BL_ORD_ID|1926 - 180734|Nonstructural protein NS3|NP_739587.2|Dengue virus 2|11060 - 1926 - 9 - - - 1 - 12.6974 - 21 - 39.8499 - 1 - 6 - 3 - 8 - 0 - 0 - 4 - 5 - 0 - 6 - WASGNE - WNSGHE - W SG+E - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 438 - Query_438 - M_908 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 439 - Query_439 - M_909 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 440 - Query_440 - M_910 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 441 - Query_441 - M_911 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 442 - Query_442 - M_912 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 443 - Query_443 - M_913 - 9 - - - 1 - gnl|BL_ORD_ID|721 - 44833|polyprotein|BAA03375.1|Hepatitis C virus subtype 1a|31646 - 721 - 9 - - - 1 - 14.2382 - 25 - 4.3647 - 5 - 9 - 3 - 7 - 0 - 0 - 4 - 4 - 0 - 5 - PGCVF - PGCSF - PGC F - - - - - 2 - gnl|BL_ORD_ID|651 - 38494|polyprotein|BAA03375.1|Hepatitis C virus|11103 - 651 - 9 - - - 1 - 13.853 - 24 - 6.26888 - 5 - 9 - 2 - 6 - 0 - 0 - 4 - 4 - 0 - 5 - PGCVF - PGCSF - PGC F - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 444 - Query_444 - M_914 - 9 - - - 1 - gnl|BL_ORD_ID|1766 - 154857|tegument protein|CAB06735.1|Human alphaherpesvirus 2|10310 - 1766 - 16 - - - 1 - 5.37863 - 2 - 67403 - 7 - 9 - 14 - 16 - 0 - 0 - 3 - 3 - 0 - 3 - GPV - GPV - GPV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 445 - Query_445 - M_915 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 446 - Query_446 - M_916 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 447 - Query_447 - M_917 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 448 - Query_448 - M_918 - 9 - - - 1 - gnl|BL_ORD_ID|1924 - 180726|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1924 - 15 - - - 1 - 12.6974 - 21 - 25.6947 - 1 - 6 - 8 - 13 - 0 - 0 - 3 - 4 - 0 - 6 - SQWDHG - TAWDFG - + WD G - - - - - 2 - gnl|BL_ORD_ID|439 - 27061|envelope glycoprotein|ABU89742.1|Dengue virus 2 Thailand/16681/84|31634 - 439 - 10 - - - 1 - 12.6974 - 21 - 37.8768 - 1 - 6 - 5 - 10 - 0 - 0 - 3 - 4 - 0 - 6 - SQWDHG - TAWDFG - + WD G - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 449 - Query_449 - M_919 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 450 - Query_450 - M_920 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 451 - Query_451 - M_921 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 452 - Query_452 - M_922 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 453 - Query_453 - M_923 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 454 - Query_454 - M_924 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 455 - Query_455 - M_925 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 456 - Query_456 - M_926 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 457 - Query_457 - M_927 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 458 - Query_458 - M_928 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 459 - Query_459 - M_929 - 9 - - - 1 - gnl|BL_ORD_ID|2165 - 189566|glycosyl transferase|WP_015631503.1|Mycobacterium tuberculosis|1773 - 2165 - 9 - - - 1 - 13.853 - 24 - 6.37844 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 6 - 0 - 9 - STQDTPVTV - ALADLPVTV - + D PVTV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 460 - Query_460 - M_930 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 461 - Query_461 - M_931 - 9 - - - 1 - gnl|BL_ORD_ID|786 - 52652|||| - 786 - 27 - - - 1 - 13.4678 - 23 - 11.7097 - 3 - 9 - 14 - 20 - 0 - 0 - 4 - 6 - 0 - 7 - RGIQTLF - RGLTSLF - RG+ +LF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 462 - Query_462 - M_932 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 463 - Query_463 - M_933 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 464 - Query_464 - M_934 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 465 - Query_465 - M_935 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 466 - Query_466 - M_936 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 467 - Query_467 - M_937 - 9 - - - 1 - gnl|BL_ORD_ID|2084 - 185447|polyprotein|AGK36298.1|Dengue virus 2|11060 - 2084 - 10 - - - 1 - 14.6234 - 26 - 1.93939 - 1 - 9 - 2 - 10 - 0 - 0 - 6 - 7 - 0 - 9 - TVLENLAVL - NALDNLAVL - L+NLAVL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 468 - Query_468 - M_938 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 469 - Query_469 - M_939 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 470 - Query_470 - M_940 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 471 - Query_471 - M_941 - 9 - - - 1 - gnl|BL_ORD_ID|2093 - 185710|Nonstructural protein NS5|YP_001531176.2|Dengue virus 3|11069 - 2093 - 9 - - - 1 - 13.0826 - 22 - 19.404 - 1 - 7 - 2 - 8 - 0 - 0 - 4 - 6 - 0 - 7 - MMNDIVK - MINGVVK - M+N +VK - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 472 - Query_472 - M_942 - 9 - - - 1 - gnl|BL_ORD_ID|1509 - 139746|Dense granule protein 3|B6KEU8.2|Toxoplasma gondii|5811 - 1509 - 9 - - - 1 - 12.6974 - 21 - 39.1808 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 6 - 0 - 9 - FSVPLHIFL - FLVPFVVFL - F VP +FL - - - - - 2 - gnl|BL_ORD_ID|1672 - 148397|Dense granule protein 3|B6KEU8.2|Toxoplasma gondii|5811 - 1672 - 9 - - - 1 - 11.5418 - 18 - 120.255 - 3 - 9 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - VPLHIFL - VPFVVFL - VP +FL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 473 - Query_473 - M_943 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 474 - Query_474 - M_944 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 475 - Query_475 - M_945 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 476 - Query_476 - M_946 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 477 - Query_477 - M_947 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 478 - Query_478 - M_948 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 479 - Query_479 - M_949 - 9 - - - 1 - gnl|BL_ORD_ID|901 - 59182|attachment glycoprotein|ABQ58821.1|Human metapneumovirus|162145 - 901 - 10 - - - 1 - 13.4678 - 23 - 9.23902 - 1 - 7 - 2 - 8 - 0 - 0 - 5 - 7 - 0 - 7 - LVLIGIS - LILIGIT - L+LIGI+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 480 - Query_480 - M_950 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 481 - Query_481 - M_951 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 482 - Query_482 - M_952 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 483 - Query_483 - M_953 - 9 - - - 1 - gnl|BL_ORD_ID|502 - 31997|hypothetical protein FTT0484|YP_169522.1|Francisella tularensis subsp. tularensis SCHU S4|177416 - 502 - 9 - - - 1 - 13.853 - 24 - 5.55396 - 1 - 5 - 3 - 7 - 0 - 0 - 4 - 4 - 0 - 5 - FPEGY - LPEGY - PEGY - - - - - 2 - gnl|BL_ORD_ID|1640 - 146287|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 - 1640 - 18 - - - 1 - 11.1566 - 17 - 184.539 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 6 - 0 - 8 - PEGYGTQV - PKGPITQM - P+G TQ+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 484 - Query_484 - M_954 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 485 - Query_485 - M_955 - 9 - - - 1 - gnl|BL_ORD_ID|1408 - 110940|Protein E7|P03129.1|Human papillomavirus type 16|333760 - 1408 - 15 - - - 1 - 11.927 - 19 - 60.2782 - 1 - 8 - 2 - 9 - 0 - 0 - 4 - 4 - 0 - 8 - HGFNATYH - HGDTPTLH - HG T H - - - - - 2 - gnl|BL_ORD_ID|1392 - 110335|E7|AAD33253.1|Human papillomavirus type 16|333760 - 1392 - 32 - - - 1 - 11.5418 - 18 - 87.5281 - 1 - 8 - 2 - 9 - 0 - 0 - 4 - 4 - 0 - 8 - HGFNATYH - HGDTPTLH - HG T H - - - - - 3 - gnl|BL_ORD_ID|2243 - 232152|rhoptry kinase family protein|AFO54841.1|Toxoplasma gondii type III|398031 - 2243 - 19 - - - 1 - 11.5418 - 18 - 130.88 - 1 - 7 - 7 - 13 - 0 - 0 - 3 - 4 - 0 - 7 - HGFNATY - HSYGVTY - H + TY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 486 - Query_486 - M_956 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 487 - Query_487 - M_957 - 9 - - - 1 - gnl|BL_ORD_ID|285 - 19348|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 - 285 - 20 - - - 1 - 12.6974 - 21 - 33.3894 - 2 - 7 - 5 - 10 - 0 - 0 - 4 - 4 - 0 - 6 - PEVFGP - PEAAGP - PE GP - - - - - 2 - gnl|BL_ORD_ID|866 - 56620|Nef protein|Q9YYU8|Human immunodeficiency virus 1|11676 - 866 - 10 - - - 1 - 12.6974 - 21 - 38.5196 - 1 - 6 - 2 - 7 - 0 - 0 - 4 - 4 - 0 - 6 - YPEVFG - YPLTFG - YP FG - - - - - 3 - gnl|BL_ORD_ID|1281 - 102046|nef protein|ACQ72180.1|Human immunodeficiency virus 1|11676 - 1281 - 8 - - - 1 - 12.6974 - 21 - 38.9267 - 1 - 6 - 2 - 7 - 0 - 0 - 4 - 4 - 0 - 6 - YPEVFG - YPLTFG - YP FG - - - - - 4 - gnl|BL_ORD_ID|1288 - 102254|nef protein|ACQ72180.1|Human immunodeficiency virus 1|11676 - 1288 - 9 - - - 1 - 12.3122 - 20 - 43.3628 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 4 - 0 - 6 - YPEVFG - YPLTFG - YP FG - - - - - 5 - gnl|BL_ORD_ID|707 - 43447|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 - 707 - 20 - - - 1 - 11.927 - 19 - 78.9367 - 2 - 7 - 15 - 20 - 0 - 0 - 4 - 4 - 0 - 6 - PEVFGP - PEAAGP - PE GP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 488 - Query_488 - M_958 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 489 - Query_489 - M_959 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 490 - Query_490 - M_960 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 491 - Query_491 - M_961 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 492 - Query_492 - M_962 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 493 - Query_493 - M_963 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 494 - Query_494 - M_964 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 495 - Query_495 - M_965 - 9 - - - 1 - gnl|BL_ORD_ID|1726 - 150461|polyprotein|AGK36298.1|Dengue virus 2|11060 - 1726 - 9 - - - 1 - 13.0826 - 22 - 14.4474 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 7 - 0 - 9 - MTREELNAL - MTQKARNAL - MT++ NAL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 496 - Query_496 - M_966 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 497 - Query_497 - M_967 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 498 - Query_498 - M_968 - 9 - - - 1 - gnl|BL_ORD_ID|2175 - 189750|Diacylglycerol acyltransferase/mycolyltransferase Ag85B|SRC280000|Mycobacterium tuberculosis|1773 - 2175 - 9 - - - 1 - 11.5418 - 18 - 147.871 - 1 - 7 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - KAGGGSN - PVGGGSS - GGGS+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 499 - Query_499 - M_969 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 500 - Query_500 - M_970 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 501 - Query_501 - M_971 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 502 - Query_502 - M_972 - 9 - - - 1 - gnl|BL_ORD_ID|2251 - 243835|glycosyl transferase|WP_015628558.1|Mycobacterium tuberculosis|1773 - 2251 - 9 - - - 1 - 13.0826 - 22 - 18.4218 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 5 - 0 - 9 - SARDCKDPY - SARLAGIPY - SAR PY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 503 - Query_503 - M_973 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 504 - Query_504 - M_974 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 505 - Query_505 - M_975 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 506 - Query_506 - M_976 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 507 - Query_507 - M_977 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 508 - Query_508 - M_978 - 9 - - - 1 - gnl|BL_ORD_ID|378 - 23365|polyprotein|BAB18806.1|Hepatitis C virus|11103 - 378 - 10 - - - 1 - 14.6234 - 26 - 2.00506 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 7 - 0 - 9 - FIPINGCPI - YIPLVGAPL - +IP+ G P+ - - - - - 2 - gnl|BL_ORD_ID|296 - 19493|polyprotein|BAA03375.1|Hepatitis C virus|11103 - 296 - 15 - - - 1 - 13.853 - 24 - 4.45371 - 1 - 8 - 8 - 15 - 0 - 0 - 4 - 6 - 0 - 8 - FIPINGCP - YIPLVGAP - +IP+ G P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 509 - Query_509 - M_979 - 9 - - - 1 - gnl|BL_ORD_ID|1153 - 76121|polyprotein precursor|NP_041724.2|West Nile virus|11082 - 1153 - 9 - - - 1 - 8.46023 - 10 - 5101.61 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 5 - 0 - 9 - YTSYFGYKM - YTMDGEYRL - YT Y++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 510 - Query_510 - M_980 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 511 - Query_511 - M_981 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 512 - Query_512 - M_982 - 9 - - - 1 - gnl|BL_ORD_ID|1175 - 79390|Protein Tax-1|P0C213.1|Human T-cell lymphotropic virus type 1 (african isolate)|39015 - 1175 - 15 - - - 1 - 11.927 - 19 - 69.3823 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 5 - 0 - 8 - SFYRTHTL - SFHNLHLL - SF+ H L - - - - - 2 - gnl|BL_ORD_ID|880 - 57790|Protein Tax-1|P03409.2|Human T-lymphotropic virus 1|11908 - 880 - 9 - - - 1 - 11.5418 - 18 - 122.194 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 5 - 0 - 8 - SFYRTHTL - SFHSLHLL - SF+ H L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 513 - Query_513 - M_983 - 9 - - - 1 - gnl|BL_ORD_ID|341 - 21385|polyprotein|AAY82034.1|Hepatitis C virus genotype 1|41856 - 341 - 10 - - - 1 - 13.853 - 24 - 7.36741 - 1 - 9 - 2 - 10 - 0 - 0 - 5 - 7 - 0 - 9 - NAAKNQVAM - NASRCWVAM - NA++ VAM - - - - - 2 - gnl|BL_ORD_ID|706 - 43310|polyprotein|AAW78019.1|Hepatitis C virus (isolate H77)|63746 - 706 - 9 - - - 1 - 13.4678 - 23 - 7.85574 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 7 - 0 - 9 - NAAKNQVAM - NASRCWVAM - NA++ VAM - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 514 - Query_514 - M_984 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 515 - Query_515 - M_985 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 516 - Query_516 - M_986 - 9 - - - 1 - gnl|BL_ORD_ID|1171 - 79300|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 1171 - 15 - - - 1 - 12.3122 - 20 - 43.2075 - 1 - 9 - 5 - 13 - 0 - 0 - 5 - 5 - 0 - 9 - DPAPRPSLL - DPGLRPQNL - DP RP L - - - - - 2 - gnl|BL_ORD_ID|1393 - 110338|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1393 - 33 - - - 1 - 11.927 - 19 - 64.3353 - 1 - 9 - 11 - 19 - 0 - 0 - 5 - 5 - 0 - 9 - DPAPRPSLL - DPQERPRKL - DP RP L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 517 - Query_517 - M_987 - 9 - - - 1 - gnl|BL_ORD_ID|29 - 2102|VP1|BAF93325.1|Human polyomavirus 1|1891762 - 29 - 9 - - - 1 - 13.853 - 24 - 5.00793 - 2 - 8 - 1 - 7 - 0 - 0 - 5 - 6 - 0 - 7 - AVTEVEA - AITEVEC - A+TEVE - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 518 - Query_518 - M_988 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 519 - Query_519 - M_989 - 9 - - - 1 - gnl|BL_ORD_ID|134 - 9461|non structural protein 3|CAJ20172.1|Hepatitis C virus|11103 - 134 - 9 - - - 1 - 13.4678 - 23 - 7.85574 - 3 - 8 - 3 - 8 - 0 - 0 - 5 - 5 - 0 - 6 - FPVLVA - FPYLVA - FP LVA - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 520 - Query_520 - M_990 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 521 - Query_521 - M_991 - 9 - - - 1 - gnl|BL_ORD_ID|235 - 16814|precore protein|CAM58990.1|Hepatitis B virus|10407 - 235 - 10 - - - 1 - 12.6974 - 21 - 28.8893 - 3 - 9 - 4 - 10 - 0 - 0 - 4 - 4 - 0 - 7 - NDHAPEV - NDFFPSV - ND P V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 522 - Query_522 - M_992 - 9 - - - 1 - gnl|BL_ORD_ID|1827 - 179766|cell surface protein (associated with virulence)|NP_302372.1|Mycobacterium leprae TN|272631 - 1827 - 9 - - - 1 - 12.3122 - 20 - 59.6102 - 1 - 5 - 1 - 5 - 0 - 0 - 4 - 5 - 0 - 5 - SPLPP - APLPP - +PLPP - - - - - 2 - gnl|BL_ORD_ID|1395 - 110394|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1395 - 32 - - - 1 - 11.927 - 19 - 60.6476 - 2 - 8 - 8 - 14 - 0 - 0 - 4 - 5 - 0 - 7 - PLPPPEQ - PLCPEEK - PL P E+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 523 - Query_523 - M_993 - 9 - - - 1 - gnl|BL_ORD_ID|152 - 11214|possible regulatory protein|NP_302009.1|Mycobacterium leprae|1769 - 152 - 15 - - - 1 - 15.0086 - 27 - 0.94895 - 1 - 8 - 5 - 12 - 0 - 0 - 5 - 7 - 0 - 8 - LRLDGSVV - LRLDGTTL - LRLDG+ + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 524 - Query_524 - M_994 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 525 - Query_525 - M_995 - 9 - - - 1 - gnl|BL_ORD_ID|745 - 48458|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 - 745 - 20 - - - 1 - 13.853 - 24 - 4.81213 - 1 - 8 - 6 - 13 - 0 - 0 - 5 - 5 - 0 - 8 - FPSSQGSL - FPIVQGEL - FP QG L - - - - - 2 - gnl|BL_ORD_ID|1994 - 183594|polyprotein|AGT63075.1|Dengue virus 1|11053 - 1994 - 10 - - - 1 - 13.0826 - 22 - 16.9691 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 6 - 0 - 8 - PSSQGSLY - PASAWTLY - P+S +LY - - - - - 3 - gnl|BL_ORD_ID|1729 - 150534|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1729 - 9 - - - 1 - 13.0826 - 22 - 18.1053 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 6 - 0 - 8 - PSSQGSLY - PASAWTLY - P+S +LY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 526 - Query_526 - M_996 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 527 - Query_527 - M_997 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 528 - Query_528 - M_998 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 529 - Query_529 - M_999 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 530 - Query_530 - M_1000 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 531 - Query_531 - M_1001 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 532 - Query_532 - M_1002 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 533 - Query_533 - M_1003 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 534 - Query_534 - M_1004 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 535 - Query_535 - M_1005 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 536 - Query_536 - M_1006 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 537 - Query_537 - M_1007 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 538 - Query_538 - M_1008 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 539 - Query_539 - M_1009 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 540 - Query_540 - M_1010 - 9 - - - 1 - gnl|BL_ORD_ID|1606 - 143680|Genome polyprotein|P06441.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 1606 - 21 - - - 1 - 13.853 - 24 - 5.97959 - 2 - 8 - 12 - 18 - 0 - 0 - 4 - 5 - 0 - 7 - YQDMMND - YQQQLND - YQ +ND - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 541 - Query_541 - M_1011 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 542 - Query_542 - M_1012 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 543 - Query_543 - M_1013 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 544 - Query_544 - M_1014 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 545 - Query_545 - M_1015 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 546 - Query_546 - M_1016 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 547 - Query_547 - M_1017 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 548 - Query_548 - M_1018 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 549 - Query_549 - M_1019 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 550 - Query_550 - M_1020 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 551 - Query_551 - M_1021 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 552 - Query_552 - M_1022 - 9 - - - 1 - gnl|BL_ORD_ID|2052 - 184713|polyprotein|AFP27208.1|Dengue virus 4|11070 - 2052 - 9 - - - 1 - 13.4678 - 23 - 10.1994 - 1 - 8 - 2 - 9 - 0 - 0 - 6 - 6 - 0 - 8 - YVVATTKL - YAVATTIL - Y VATT L - - - - - 2 - gnl|BL_ORD_ID|1484 - 133716|polyprotein|ABG75765.1|Dengue virus 1|11053 - 1484 - 9 - - - 1 - 12.6974 - 21 - 25.5715 - 1 - 6 - 3 - 8 - 0 - 0 - 5 - 5 - 0 - 6 - YVVATT - YAVATT - Y VATT - - - - - 3 - gnl|BL_ORD_ID|1738 - 150639|polyprotein|AGO67249.1|Dengue virus 2|11060 - 1738 - 10 - - - 1 - 12.6974 - 21 - 26.9859 - 1 - 6 - 3 - 8 - 0 - 0 - 5 - 5 - 0 - 6 - YVVATT - YAVATT - Y VATT - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 553 - Query_553 - M_1023 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 554 - Query_554 - M_1024 - 9 - - - 1 - gnl|BL_ORD_ID|1916 - 180681|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1916 - 15 - - - 1 - 11.927 - 19 - 61.2314 - 1 - 5 - 4 - 8 - 0 - 0 - 4 - 4 - 0 - 5 - YYDYM - YTDYM - Y DYM - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 555 - Query_555 - M_1025 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 556 - Query_556 - M_1026 - 9 - - - 1 - gnl|BL_ORD_ID|1068 - 70491|envelope glycoprotein|AAC28452.1|Human immunodeficiency virus 1|11676 - 1068 - 10 - - - 1 - 12.3122 - 20 - 65.5527 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - LPPDPQP - VPTDPNP - +P DP P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 557 - Query_557 - M_1027 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 558 - Query_558 - M_1028 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 559 - Query_559 - M_1029 - 9 - - - 1 - gnl|BL_ORD_ID|661 - 39571|polyprotein|BAD73987.1|Hepatitis C virus subtype 1b|31647 - 661 - 10 - - - 1 - 13.853 - 24 - 5.38895 - 1 - 6 - 4 - 9 - 0 - 0 - 3 - 6 - 0 - 6 - KPISYM - RPVSYL - +P+SY+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 560 - Query_560 - M_1030 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 561 - Query_561 - M_1031 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 562 - Query_562 - M_1032 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 563 - Query_563 - M_1033 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 564 - Query_564 - M_1034 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 565 - Query_565 - M_1035 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 566 - Query_566 - M_1036 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 567 - Query_567 - M_1037 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 568 - Query_568 - M_1038 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 569 - Query_569 - M_1039 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 570 - Query_570 - M_1040 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 571 - Query_571 - M_1041 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 572 - Query_572 - M_1042 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 573 - Query_573 - M_1043 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 574 - Query_574 - M_1044 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 575 - Query_575 - M_1045 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 576 - Query_576 - M_1046 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 577 - Query_577 - M_1047 - 9 - - - 1 - gnl|BL_ORD_ID|742 - 47854|Glycoprotein I precursor (Glycoprotein IV) (GI) (GPIV)|P09258.1|Human alphaherpesvirus 3|10335 - 742 - 10 - - - 1 - 12.6974 - 21 - 37.2442 - 1 - 6 - 2 - 7 - 0 - 0 - 4 - 4 - 0 - 6 - HSYVGP - HSVVNP - HS V P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 578 - Query_578 - M_1048 - 9 - - - 1 - gnl|BL_ORD_ID|716 - 44214|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 - 716 - 11 - - - 1 - 13.4678 - 23 - 7.61059 - 1 - 9 - 3 - 11 - 0 - 0 - 5 - 6 - 0 - 9 - EMFQRYSAF - EFFTKNSAF - E F + SAF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 579 - Query_579 - M_1049 - 9 - - - 1 - gnl|BL_ORD_ID|1184 - 93224|core protein|AAL31859.1|Hepatitis B virus|10407 - 1184 - 14 - - - 1 - 11.5418 - 18 - 149.079 - 2 - 9 - 4 - 11 - 0 - 0 - 5 - 5 - 0 - 8 - PVSIRLVV - PASRDLVV - P S LVV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 580 - Query_580 - M_1050 - 9 - - - 1 - gnl|BL_ORD_ID|50 - 3094|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 - 50 - 9 - - - 1 - 11.927 - 19 - 109.216 - 4 - 9 - 3 - 8 - 0 - 0 - 4 - 4 - 0 - 6 - GDLGKY - GDAGGY - GD G Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 581 - Query_581 - M_1051 - 9 - - - 1 - gnl|BL_ORD_ID|1171 - 79300|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 1171 - 15 - - - 1 - 12.6974 - 21 - 34.4815 - 3 - 8 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - LAFPVP - LSFPDP - L+FP P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 582 - Query_582 - M_1052 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 583 - Query_583 - M_1053 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 584 - Query_584 - M_1054 - 9 - - - 1 - gnl|BL_ORD_ID|413 - 24943|DNA polymerase|CAA10434.1|Hepatitis B virus|10407 - 413 - 11 - - - 1 - 12.3122 - 20 - 43.6113 - 4 - 8 - 1 - 5 - 0 - 0 - 2 - 5 - 0 - 5 - HSIWE - HTLWK - H++W+ - - - - - 2 - gnl|BL_ORD_ID|1983 - 183252|polyprotein|AGT63075.1|Dengue virus 1|11053 - 1983 - 10 - - - 1 - 11.5418 - 18 - 126.796 - 1 - 8 - 1 - 8 - 0 - 0 - 2 - 5 - 0 - 8 - LAMHSIWE - FSLHYAWK - ++H W+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 585 - Query_585 - M_1055 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 586 - Query_586 - M_1056 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 587 - Query_587 - M_1057 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 588 - Query_588 - M_1058 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 589 - Query_589 - M_1059 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 590 - Query_590 - M_1060 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 591 - Query_591 - M_1061 - 9 - - - 1 - gnl|BL_ORD_ID|1521 - 140615|amino acid decarboxylase|YP_177889.1|Mycobacterium tuberculosis H37Rv|83332 - 1521 - 9 - - - 1 - 13.853 - 24 - 5.65074 - 2 - 7 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - PNAQNM - PGAQNL - P AQN+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 592 - Query_592 - M_1062 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 593 - Query_593 - M_1063 - 9 - - - 1 - gnl|BL_ORD_ID|2284 - 419128|polyprotein|ACF49259.1|Dengue virus type 1 Hawaii|10000440 - 2284 - 9 - - - 1 - 14.6234 - 26 - 1.91441 - 3 - 9 - 3 - 9 - 0 - 0 - 4 - 7 - 0 - 7 - RHSMEKI - RHAMEEL - RH+ME++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 594 - Query_594 - M_1064 - 9 - - - 1 - gnl|BL_ORD_ID|1006 - 66195|Nucleoprotein|P41269.1|Puumala hantavirus|11604 - 1006 - 15 - - - 1 - 13.853 - 24 - 5.02902 - 4 - 9 - 10 - 15 - 0 - 0 - 4 - 5 - 0 - 6 - RHPQHL - RRPKHL - R P+HL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 595 - Query_595 - M_1065 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 596 - Query_596 - M_1066 - 9 - - - 1 - gnl|BL_ORD_ID|1781 - 156550|E3 ubiquitin-protein ligase Mdm2|Q00987.1|Homo sapiens|9606 - 1781 - 9 - - - 1 - 12.6974 - 21 - 26.9236 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 7 - 0 - 9 - IIFLLGEIV - VLFYLGQYI - ++F LG+ + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 597 - Query_597 - M_1067 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 598 - Query_598 - M_1068 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 599 - Query_599 - M_1069 - 9 - - - 1 - gnl|BL_ORD_ID|980 - 64819|E7 protein|ABL96585.1|Human papillomavirus type 16|333760 - 980 - 9 - - - 1 - 11.5418 - 18 - 147.871 - 1 - 6 - 4 - 9 - 0 - 0 - 3 - 4 - 0 - 6 - LACSIC - IVCPIC - + C IC - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 600 - Query_600 - M_1070 - 9 - - - 1 - gnl|BL_ORD_ID|1224 - 97111|polyprotein|ABR25251.1|Hepatitis C virus (isolate H77)|63746 - 1224 - 18 - - - 1 - 14.6234 - 26 - 2.18552 - 3 - 8 - 1 - 6 - 0 - 0 - 4 - 6 - 0 - 6 - YDVLIC - YDIIIC - YD++IC - - - - - 2 - gnl|BL_ORD_ID|1366 - 108218|Genome polyprotein|P26664.3|Hepatitis C virus|11103 - 1366 - 10 - - - 1 - 14.2382 - 25 - 3.38479 - 3 - 8 - 1 - 6 - 0 - 0 - 4 - 6 - 0 - 6 - YDVLIC - YDIIIC - YD++IC - - - - - 3 - gnl|BL_ORD_ID|1317 - 107760|polyprotein|AAD56189.1|Hepatitis C virus|11103 - 1317 - 10 - - - 1 - 13.4678 - 23 - 12.2057 - 3 - 8 - 2 - 7 - 0 - 0 - 3 - 6 - 0 - 6 - YDVLIC - YDIIMC - YD+++C - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 601 - Query_601 - M_1071 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 602 - Query_602 - M_1072 - 9 - - - 1 - gnl|BL_ORD_ID|234 - 16813|External core antigen|SRC279980|Hepatitis B virus|10407 - 234 - 10 - - - 1 - 13.0826 - 22 - 18.1832 - 3 - 8 - 4 - 9 - 0 - 0 - 4 - 4 - 0 - 6 - NDLMPS - NDFFPS - ND PS - - - - - 2 - gnl|BL_ORD_ID|235 - 16814|precore protein|CAM58990.1|Hepatitis B virus|10407 - 235 - 10 - - - 1 - 13.0826 - 22 - 19.1489 - 3 - 8 - 4 - 9 - 0 - 0 - 4 - 4 - 0 - 6 - NDLMPS - NDFFPS - ND PS - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 603 - Query_603 - M_1073 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 604 - Query_604 - M_1074 - 9 - - - 1 - gnl|BL_ORD_ID|1266 - 98640|trans-sialidase, putative|EAN80840.1|Trypanosoma cruzi|5693 - 1266 - 9 - - - 1 - 13.4678 - 23 - 9.02895 - 3 - 9 - 3 - 9 - 0 - 0 - 5 - 7 - 0 - 7 - FSLLATV - FTLVATV - F+L+ATV - - - - - 2 - gnl|BL_ORD_ID|1245 - 98044|trans-sialidase, putative|EAN80840.1|Trypanosoma cruzi|5693 - 1245 - 9 - - - 1 - 13.4678 - 23 - 10.561 - 3 - 9 - 1 - 7 - 0 - 0 - 5 - 7 - 0 - 7 - FSLLATV - FTLVATV - F+L+ATV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 605 - Query_605 - M_1075 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 606 - Query_606 - M_1076 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 607 - Query_607 - M_1077 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 608 - Query_608 - M_1078 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 609 - Query_609 - M_1079 - 9 - - - 1 - gnl|BL_ORD_ID|1171 - 79300|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 1171 - 15 - - - 1 - 14.2382 - 25 - 3.03951 - 1 - 7 - 3 - 9 - 0 - 0 - 4 - 5 - 0 - 7 - LPQPGVR - FPDPGLR - P PG+R - - - - - 2 - gnl|BL_ORD_ID|2238 - 230028|Protein Nef|P04603.3|Human immunodeficiency virus 1|11676 - 2238 - 10 - - - 1 - 13.853 - 24 - 5.02829 - 2 - 7 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - PQPGVR - PGPGIR - P PG+R - - - - - 3 - gnl|BL_ORD_ID|2239 - 230029|Protein Nef|P03404.4|Human immunodeficiency virus 1|11676 - 2239 - 10 - - - 1 - 13.853 - 24 - 5.11607 - 2 - 7 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - PQPGVR - PGPGIR - P PG+R - - - - - 4 - gnl|BL_ORD_ID|1508 - 139406|polyprotein|ACT37184.1|Hepatitis C virus|11103 - 1508 - 10 - - - 1 - 13.853 - 24 - 5.67669 - 1 - 7 - 3 - 9 - 0 - 0 - 5 - 6 - 0 - 7 - LPQPGVR - LPRPGPR - LP+PG R - - - - - 5 - gnl|BL_ORD_ID|1106 - 72928|Genome polyprotein|P26662.3|Hepatitis C virus (isolate Japanese)|11116 - 1106 - 10 - - - 1 - 13.853 - 24 - 7.36741 - 4 - 9 - 5 - 10 - 0 - 0 - 4 - 5 - 0 - 6 - PGVRSL - PGARSM - PG RS+ - - - - - 6 - gnl|BL_ORD_ID|2240 - 230030|Nef protein|BAA86664.1|Human immunodeficiency virus 1|11676 - 2240 - 10 - - - 1 - 13.0826 - 22 - 16.9691 - 2 - 7 - 4 - 9 - 0 - 0 - 4 - 4 - 0 - 6 - PQPGVR - PGPGTR - P PG R - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 610 - Query_610 - M_1080 - 9 - - - 1 - gnl|BL_ORD_ID|1862 - 180442|Chain B, Dengue Virus Rna Dependent Rna Polymerase With Residues From The Ns5 Linker Region|4C11_B|Dengue virus|12637 - 1862 - 10 - - - 1 - 13.4678 - 23 - 12.4198 - 5 - 9 - 4 - 8 - 0 - 0 - 4 - 4 - 0 - 5 - CLGKV - CLGKA - CLGK - - - - - 2 - gnl|BL_ORD_ID|193 - 14324|Chain B, Dengue Virus Rna Dependent Rna Polymerase With Residues From The Ns5 Linker Region|4C11_B|Dengue virus|12637 - 193 - 9 - - - 1 - 13.0826 - 22 - 14.1983 - 5 - 9 - 4 - 8 - 0 - 0 - 4 - 4 - 0 - 5 - CLGKV - CLGKA - CLGK - - - - - 3 - gnl|BL_ORD_ID|741 - 47760|EBNA-1 protein|Q777E1|Human gammaherpesvirus 4|10376 - 741 - 15 - - - 1 - 12.6974 - 21 - 22.89 - 2 - 8 - 5 - 11 - 0 - 0 - 4 - 5 - 0 - 7 - PNNCLGK - PGNGLGE - P N LG+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 611 - Query_611 - M_1081 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 612 - Query_612 - M_1082 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 613 - Query_613 - M_1083 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 614 - Query_614 - M_1084 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 615 - Query_615 - M_1085 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 616 - Query_616 - M_1086 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 617 - Query_617 - M_1087 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 618 - Query_618 - M_1088 - 9 - - - 1 - gnl|BL_ORD_ID|1121 - 74407|polyprotein|AAU89634.1|Hepatitis C virus subtype 2a|31649 - 1121 - 9 - - - 1 - 12.3122 - 20 - 44.8495 - 4 - 9 - 4 - 9 - 0 - 0 - 2 - 4 - 0 - 6 - HWNWII - RWEWVV - W W++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 619 - Query_619 - M_1089 - 9 - - - 1 - gnl|BL_ORD_ID|364 - 22822|NS3 protein|NP_740321.1|Dengue virus 4|11070 - 364 - 11 - - - 1 - 13.0826 - 22 - 15.2395 - 2 - 8 - 2 - 8 - 0 - 0 - 3 - 5 - 0 - 7 - TDGQPLL - TSGSPII - T G P++ - - - - - 2 - gnl|BL_ORD_ID|363 - 22820|Nonstructural protein NS3|YP_001531172.2|Dengue virus 3|11069 - 363 - 10 - - - 1 - 13.0826 - 22 - 16.9691 - 2 - 8 - 2 - 8 - 0 - 0 - 3 - 5 - 0 - 7 - TDGQPLL - TSGSPII - T G P++ - - - - - 3 - gnl|BL_ORD_ID|362 - 22819|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 362 - 11 - - - 1 - 13.0826 - 22 - 21.123 - 2 - 8 - 2 - 8 - 0 - 0 - 3 - 5 - 0 - 7 - TDGQPLL - TSGSPII - T G P++ - - - - - 4 - gnl|BL_ORD_ID|361 - 22818|Nonstructural protein NS3|NP_739587.2|Dengue virus 2|11060 - 361 - 10 - - - 1 - 13.0826 - 22 - 22.3554 - 2 - 8 - 2 - 8 - 0 - 0 - 3 - 5 - 0 - 7 - TDGQPLL - TSGSPII - T G P++ - - - - - 5 - gnl|BL_ORD_ID|1929 - 180750|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1929 - 15 - - - 1 - 12.6974 - 21 - 22.89 - 2 - 8 - 4 - 10 - 0 - 0 - 3 - 5 - 0 - 7 - TDGQPLL - TSGSPII - T G P++ - - - - - 6 - gnl|BL_ORD_ID|260 - 17802|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 260 - 15 - - - 1 - 12.6974 - 21 - 22.89 - 2 - 8 - 5 - 11 - 0 - 0 - 3 - 5 - 0 - 7 - TDGQPLL - TSGSPII - T G P++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 620 - Query_620 - M_1090 - 9 - - - 1 - gnl|BL_ORD_ID|688 - 41622|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 688 - 20 - - - 1 - 15.3938 - 28 - 0.534339 - 1 - 9 - 4 - 12 - 0 - 0 - 4 - 5 - 0 - 9 - AHLLCTLLL - SHFLCTFTF - +H LCT - - - - - 2 - gnl|BL_ORD_ID|123 - 8554|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 123 - 20 - - - 1 - 15.0086 - 27 - 1.09683 - 1 - 9 - 12 - 20 - 0 - 0 - 4 - 5 - 0 - 9 - AHLLCTLLL - SHFLCTFTF - +H LCT - - - - - 3 - gnl|BL_ORD_ID|388 - 23797|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 388 - 20 - - - 1 - 14.6234 - 26 - 1.80994 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 4 - 0 - 8 - HLLCTLLL - HFLCTFTF - H LCT - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 621 - Query_621 - M_1091 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 622 - Query_622 - M_1092 - 9 - - - 1 - gnl|BL_ORD_ID|1440 - 120127|unnamed protein product|CAA33016.1|Rubella virus|11041 - 1440 - 25 - - - 1 - 14.2382 - 25 - 3.45818 - 3 - 8 - 9 - 14 - 0 - 0 - 4 - 6 - 0 - 6 - YGGTIR - HGGTLR - +GGT+R - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 623 - Query_623 - M_1093 - 9 - - - 1 - gnl|BL_ORD_ID|1606 - 143680|Genome polyprotein|P06441.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 1606 - 21 - - - 1 - 15.0086 - 27 - 1.33185 - 1 - 9 - 12 - 20 - 0 - 0 - 5 - 6 - 0 - 9 - YQDMMNDIV - YQQQLNDPV - YQ +ND V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 624 - Query_624 - M_1094 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 625 - Query_625 - M_1095 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 626 - Query_626 - M_1096 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 627 - Query_627 - M_1097 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 628 - Query_628 - M_1098 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 629 - Query_629 - M_1099 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 630 - Query_630 - M_1100 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 631 - Query_631 - M_1101 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 632 - Query_632 - M_1102 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 633 - Query_633 - M_1103 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 634 - Query_634 - M_1104 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 635 - Query_635 - M_1105 - 9 - - - 1 - gnl|BL_ORD_ID|451 - 27295|polyprotein precursor|NP_041724.2|West Nile virus|11082 - 451 - 9 - - - 1 - 14.6234 - 26 - 1.76369 - 5 - 9 - 5 - 9 - 0 - 0 - 5 - 5 - 0 - 5 - PGYAL - PGYAL - PGYAL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 636 - Query_636 - M_1106 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 637 - Query_637 - M_1107 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 638 - Query_638 - M_1108 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 639 - Query_639 - M_1109 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 640 - Query_640 - M_1110 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 641 - Query_641 - M_1111 - 9 - - - 1 - gnl|BL_ORD_ID|577 - 36352|Polyprotein|P90247|Hepatitis C virus|11103 - 577 - 20 - - - 1 - 13.853 - 24 - 4.81213 - 3 - 9 - 14 - 20 - 0 - 0 - 4 - 4 - 0 - 7 - RPRWCPV - RPSWGPT - RP W P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 642 - Query_642 - M_1112 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 643 - Query_643 - M_1113 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 644 - Query_644 - M_1114 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 645 - Query_645 - M_1115 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 646 - Query_646 - M_1116 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 647 - Query_647 - M_1117 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 648 - Query_648 - M_1118 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 649 - Query_649 - M_1119 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 650 - Query_650 - M_1120 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 651 - Query_651 - M_1121 - 9 - - - 1 - gnl|BL_ORD_ID|104 - 7116|NS3|ABN45875.1|Hepatitis C virus (isolate H77)|63746 - 104 - 9 - - - 1 - 13.4678 - 23 - 9.02895 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 5 - 0 - 9 - CTLGLGSLY - CTCGSSDLY - CT G LY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 652 - Query_652 - M_1122 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 653 - Query_653 - M_1123 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 654 - Query_654 - M_1124 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 655 - Query_655 - M_1125 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 656 - Query_656 - M_1126 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 657 - Query_657 - M_1127 - 9 - - - 1 - gnl|BL_ORD_ID|2300 - 422989|polyprotein|ABY67644.1|Hepatitis C virus genotype 1|41856 - 2300 - 10 - - - 1 - 12.6974 - 21 - 37.8768 - 1 - 7 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - IAPLLPV - FAPALPI - AP LP+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 658 - Query_658 - M_1128 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 659 - Query_659 - M_1129 - 9 - - - 1 - gnl|BL_ORD_ID|448 - 27241|Spike glycoprotein precursor|P59594.1|SARS coronavirus|227859 - 448 - 9 - - - 1 - 12.3122 - 20 - 68.0606 - 1 - 6 - 4 - 9 - 0 - 0 - 4 - 4 - 0 - 6 - DPADPT - DPLKPT - DP PT - - - - - 2 - gnl|BL_ORD_ID|1635 - 146280|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 - 1635 - 10 - - - 1 - 10.7714 - 16 - 471.24 - 1 - 8 - 3 - 10 - 0 - 0 - 4 - 4 - 0 - 8 - DPADPTSN - DPNIRTGN - DP T N - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 660 - Query_660 - M_1130 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 661 - Query_661 - M_1131 - 9 - - - 1 - gnl|BL_ORD_ID|2307 - 423007|Genome polyprotein|P26664.3|Hepatitis C virus genotype 1|41856 - 2307 - 10 - - - 1 - 11.5418 - 18 - 175.991 - 2 - 9 - 2 - 9 - 0 - 0 - 5 - 6 - 0 - 8 - VQDIQASL - VQEDAASL - VQ+ ASL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 662 - Query_662 - M_1132 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 663 - Query_663 - M_1133 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 664 - Query_664 - M_1134 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 665 - Query_665 - M_1135 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 666 - Query_666 - M_1136 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 667 - Query_667 - M_1137 - 9 - - - 1 - gnl|BL_ORD_ID|1756 - 154164|tegument protein|CAB06732.1|Human alphaherpesvirus 2|10310 - 1756 - 15 - - - 1 - 15.779 - 29 - 0.460848 - 3 - 9 - 9 - 15 - 0 - 0 - 4 - 7 - 0 - 7 - FDAIRTF - YDAVRTW - +DA+RT+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 668 - Query_668 - M_1138 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 669 - Query_669 - M_1139 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 670 - Query_670 - M_1140 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 671 - Query_671 - M_1141 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 672 - Query_672 - M_1142 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 673 - Query_673 - M_1143 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 674 - Query_674 - M_1144 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 675 - Query_675 - M_1145 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 676 - Query_676 - M_1146 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 677 - Query_677 - M_1147 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 678 - Query_678 - M_1148 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 679 - Query_679 - M_1149 - 9 - - - 1 - gnl|BL_ORD_ID|686 - 41407|Envelope protein|NP_739583.2|Dengue virus 2|11060 - 686 - 15 - - - 1 - 12.3122 - 20 - 43.2075 - 1 - 5 - 6 - 10 - 0 - 0 - 3 - 4 - 0 - 5 - WQIHR - WLVHR - W +HR - - - - - 2 - gnl|BL_ORD_ID|1746 - 150725|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1746 - 9 - - - 1 - 12.3122 - 20 - 63.7024 - 1 - 5 - 1 - 5 - 0 - 0 - 3 - 4 - 0 - 5 - WQIHR - WLVHR - W +HR - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 680 - Query_680 - M_1150 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 681 - Query_681 - M_1151 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 682 - Query_682 - M_1152 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 683 - Query_683 - M_1153 - 9 - - - 1 - gnl|BL_ORD_ID|1731 - 150556|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1731 - 10 - - - 1 - 14.6234 - 26 - 2.108 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 7 - 0 - 9 - KMADPNQCV - RVIDPRRCL - ++ DP +C+ - - - - - 2 - gnl|BL_ORD_ID|859 - 56310|polyprotein|AGO67248.1|Dengue virus 2|11060 - 859 - 10 - - - 1 - 14.2382 - 25 - 3.75112 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 7 - 0 - 9 - KMADPNQCV - RVIDPRRCM - ++ DP +C+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 684 - Query_684 - M_1154 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 685 - Query_685 - M_1155 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 686 - Query_686 - M_1156 - 9 - - - 1 - gnl|BL_ORD_ID|527 - 32268|hemagglutinin|AAK38298.1|Influenza A virus (A/Bar-headed Goose/Qinghai/61/05(H5N1))|336238 - 527 - 10 - - - 1 - 15.0086 - 27 - 1.06007 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 7 - 0 - 9 - KYYTDPSTY - KLYQNPTTY - K Y +P+TY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 687 - Query_687 - M_1157 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 688 - Query_688 - M_1158 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 689 - Query_689 - M_1159 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 690 - Query_690 - M_1160 - 9 - - - 1 - gnl|BL_ORD_ID|2098 - 185817|envelope protein|AGW23590.1|Dengue virus 4|11070 - 2098 - 10 - - - 1 - 12.3122 - 20 - 48.6895 - 4 - 9 - 2 - 7 - 0 - 0 - 3 - 5 - 0 - 6 - WLARVL - WMIRIL - W+ R+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 691 - Query_691 - M_1161 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 692 - Query_692 - M_1162 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 693 - Query_693 - M_1163 - 9 - - - 1 - gnl|BL_ORD_ID|398 - 24427|polyprotein|ACX44238.1|Hepatitis C virus subtype 1a|31646 - 398 - 9 - - - 1 - 11.927 - 19 - 75.1319 - 2 - 8 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - PAFHFNI - PALVFDI - PA F+I - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 694 - Query_694 - M_1164 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 695 - Query_695 - M_1165 - 9 - - - 1 - gnl|BL_ORD_ID|3 - 194|Hypothetical protein esxG (PE family protein)|O53692.1|Mycobacterium tuberculosis|1773 - 3 - 9 - - - 1 - 11.927 - 19 - 102.395 - 1 - 7 - 3 - 9 - 0 - 0 - 5 - 5 - 0 - 7 - HASVVAA - HARFVAA - HA VAA - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 696 - Query_696 - M_1166 - 9 - - - 1 - gnl|BL_ORD_ID|1980 - 183229|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1980 - 10 - - - 1 - 13.0826 - 22 - 22.3554 - 4 - 9 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - PSSNAL - PQSNAV - P SNA+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 697 - Query_697 - M_1167 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 698 - Query_698 - M_1168 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 699 - Query_699 - M_1169 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 700 - Query_700 - M_1170 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 701 - Query_701 - M_1171 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 702 - Query_702 - M_1172 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 703 - Query_703 - M_1173 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 704 - Query_704 - M_1174 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 705 - Query_705 - M_1175 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 706 - Query_706 - M_1176 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 707 - Query_707 - M_1177 - 9 - - - 1 - gnl|BL_ORD_ID|2185 - 190466|large surface antigen|CAL29876.1|Hepatitis B virus|10407 - 2185 - 15 - - - 1 - 13.0826 - 22 - 16.6732 - 1 - 7 - 6 - 12 - 0 - 0 - 4 - 4 - 0 - 7 - DHSNDPT - DHQLDPA - DH DP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 708 - Query_708 - M_1178 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 709 - Query_709 - M_1179 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 710 - Query_710 - M_1180 - 9 - - - 1 - gnl|BL_ORD_ID|1207 - 96257|Genome polyprotein|SRC279960|Hepatitis C virus|11103 - 1207 - 8 - - - 1 - 13.4678 - 23 - 13.562 - 1 - 8 - 1 - 8 - 0 - 0 - 3 - 5 - 0 - 8 - KPMPTIQW - EPEPDVAW - +P P + W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 711 - Query_711 - M_1181 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 712 - Query_712 - M_1182 - 9 - - - 1 - gnl|BL_ORD_ID|931 - 61077|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 - 931 - 9 - - - 1 - 14.2382 - 25 - 3.61702 - 3 - 8 - 2 - 7 - 0 - 0 - 4 - 6 - 0 - 6 - SHTGTF - SHSGSF - SH+G+F - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 713 - Query_713 - M_1183 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 714 - Query_714 - M_1184 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 715 - Query_715 - M_1185 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 716 - Query_716 - M_1186 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 717 - Query_717 - M_1187 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 718 - Query_718 - M_1188 - 9 - - - 1 - gnl|BL_ORD_ID|1049 - 69679|polyprotein|BAD73987.1|Hepatitis C virus subtype 1b|31647 - 1049 - 9 - - - 1 - 13.853 - 24 - 6.26888 - 2 - 8 - 1 - 7 - 0 - 0 - 5 - 6 - 0 - 7 - VLPDTFT - VLPCSFT - VLP +FT - - - - - 2 - gnl|BL_ORD_ID|447 - 27239|polyprotein|BAB18806.1|Hepatitis C virus subtype 1b|31647 - 447 - 9 - - - 1 - 13.4678 - 23 - 11.7244 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 6 - 0 - 7 - VLPDTFT - ILPCSFT - +LP +FT - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 719 - Query_719 - M_1189 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 720 - Query_720 - M_1190 - 9 - - - 1 - gnl|BL_ORD_ID|922 - 59975|pol protein|ACJ76655.1|Human immunodeficiency virus 1|11676 - 922 - 9 - - - 1 - 14.6234 - 26 - 1.52328 - 2 - 9 - 2 - 9 - 0 - 0 - 3 - 8 - 0 - 8 - PAVFETTV - PAIFQSSM - PA+F++++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 721 - Query_721 - M_1191 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 722 - Query_722 - M_1192 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 723 - Query_723 - M_1193 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 724 - Query_724 - M_1194 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 725 - Query_725 - M_1195 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 726 - Query_726 - M_1196 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 727 - Query_727 - M_1197 - 9 - - - 1 - gnl|BL_ORD_ID|427 - 25929|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 427 - 15 - - - 1 - 10.7714 - 16 - 355.4 - 1 - 9 - 7 - 15 - 0 - 0 - 4 - 6 - 0 - 9 - EVKIGKMSY - DVKKDLISY - +VK +SY - - - - - 2 - gnl|BL_ORD_ID|9 - 790|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 9 - 15 - - - 1 - 10.001 - 14 - 663.673 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 6 - 0 - 9 - EVKIGKMSY - DVKKDLISY - +VK +SY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 728 - Query_728 - M_1198 - 9 - - - 1 - gnl|BL_ORD_ID|1346 - 108018|polyprotein|CAB41951.1|Hepatitis C virus|11103 - 1346 - 10 - - - 1 - 17.3198 - 33 - 0.18734 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 8 - 0 - 9 - LANGGKVPF - LSNTGEIPF - L+N G++PF - - - - - 2 - gnl|BL_ORD_ID|1312 - 107738|polyprotein|CAB41951.1|Hepatitis C virus|11103 - 1312 - 10 - - - 1 - 16.9346 - 32 - 0.197903 - 1 - 9 - 2 - 10 - 0 - 0 - 5 - 8 - 0 - 9 - LANGGKVPF - LSNTGEIPF - L+N G++PF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 729 - Query_729 - M_1199 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 730 - Query_730 - M_1200 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 731 - Query_731 - M_1201 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 732 - Query_732 - M_1202 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 733 - Query_733 - M_1203 - 9 - - - 1 - gnl|BL_ORD_ID|1141 - 75408|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 1141 - 20 - - - 1 - 13.853 - 24 - 5.99481 - 3 - 9 - 12 - 18 - 0 - 0 - 4 - 5 - 0 - 7 - FPVGDSV - LPVADAV - PV D+V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 734 - Query_734 - M_1204 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 735 - Query_735 - M_1205 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 736 - Query_736 - M_1206 - 9 - - - 1 - gnl|BL_ORD_ID|490 - 30946|HCV-1|AAA45676.1|Hepatitis C virus genotype 1|41856 - 490 - 20 - - - 1 - 14.2382 - 25 - 3.66432 - 5 - 9 - 13 - 17 - 0 - 0 - 4 - 5 - 0 - 5 - PDLGI - PDLGV - PDLG+ - - - - - 2 - gnl|BL_ORD_ID|816 - 54605|HCV-1|AAA45676.1|Hepatitis C virus|11103 - 816 - 10 - - - 1 - 14.2382 - 25 - 4.15863 - 5 - 9 - 6 - 10 - 0 - 0 - 4 - 5 - 0 - 5 - PDLGI - PDLGV - PDLG+ - - - - - 3 - gnl|BL_ORD_ID|471 - 28594|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 - 471 - 20 - - - 1 - 13.853 - 24 - 4.81213 - 2 - 6 - 5 - 9 - 0 - 0 - 4 - 5 - 0 - 5 - SYHPD - SYYPD - SY+PD - - - - - 4 - gnl|BL_ORD_ID|776 - 51643|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 - 776 - 20 - - - 1 - 13.4678 - 23 - 8.10378 - 2 - 6 - 15 - 19 - 0 - 0 - 4 - 5 - 0 - 5 - SYHPD - SYYPD - SY+PD - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 737 - Query_737 - M_1207 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 738 - Query_738 - M_1208 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 739 - Query_739 - M_1209 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 740 - Query_740 - M_1210 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 741 - Query_741 - M_1211 - 9 - - - 1 - gnl|BL_ORD_ID|1438 - 120093|unnamed protein product|CAA33016.1|Rubella virus|11041 - 1438 - 21 - - - 1 - 11.927 - 19 - 77.0667 - 2 - 9 - 12 - 19 - 0 - 0 - 4 - 5 - 0 - 8 - PPPTPRKV - PPATPTSL - PP TP + - - - - - 2 - gnl|BL_ORD_ID|1298 - 103392|polyprotein|BAB18806.1|Hepatitis C virus|11103 - 1298 - 9 - - - 1 - 11.1566 - 17 - 246.948 - 1 - 6 - 3 - 8 - 0 - 0 - 4 - 4 - 0 - 6 - RPPPTP - RDPTTP - R P TP - - - - - 3 - gnl|BL_ORD_ID|1573 - 141402|tegument protein VP22|NP_044651.1|Human alphaherpesvirus 1|10298 - 1573 - 10 - - - 1 - 10.001 - 14 - 1133.68 - 1 - 7 - 1 - 7 - 0 - 0 - 4 - 4 - 0 - 7 - RPPPTPR - RPTERPR - RP PR - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 742 - Query_742 - M_1212 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 743 - Query_743 - M_1213 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 744 - Query_744 - M_1214 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 745 - Query_745 - M_1215 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 746 - Query_746 - M_1216 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 747 - Query_747 - M_1217 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 748 - Query_748 - M_1218 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 749 - Query_749 - M_1219 - 9 - - - 1 - gnl|BL_ORD_ID|1035 - 69394|pol|AP_000202.1|Human adenovirus 5|28285 - 1035 - 9 - - - 1 - 15.0086 - 27 - 0.973936 - 2 - 9 - 1 - 8 - 0 - 0 - 5 - 6 - 0 - 8 - VLPWLKAF - VLAWTRAF - VL W +AF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 750 - Query_750 - M_1220 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 751 - Query_751 - M_1221 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 752 - Query_752 - M_1222 - 9 - - - 1 - gnl|BL_ORD_ID|1508 - 139406|polyprotein|ACT37184.1|Hepatitis C virus|11103 - 1508 - 10 - - - 1 - 12.6974 - 21 - 27.4501 - 4 - 9 - 5 - 10 - 0 - 0 - 4 - 5 - 0 - 6 - RPWPRV - RPGPRL - RP PR+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 753 - Query_753 - M_1223 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 754 - Query_754 - M_1224 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 755 - Query_755 - M_1225 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 756 - Query_756 - M_1226 - 9 - - - 1 - gnl|BL_ORD_ID|1149 - 75636|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 1149 - 10 - - - 1 - 15.0086 - 27 - 1.44144 - 3 - 9 - 3 - 9 - 0 - 0 - 4 - 4 - 0 - 7 - LWHLPAV - LWHYPCT - LWH P - - - - - 2 - gnl|BL_ORD_ID|832 - 54820|polyprotein precursor|BAA02756.1|Hepatitis C virus|11103 - 832 - 9 - - - 1 - 14.6234 - 26 - 1.52328 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 4 - 0 - 7 - LWHLPAV - LWHYPCT - LWH P - - - - - 3 - gnl|BL_ORD_ID|831 - 54819|JK3|CAA43789.1|Hepatitis C virus|11103 - 831 - 9 - - - 1 - 14.6234 - 26 - 1.6522 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 4 - 0 - 7 - LWHLPAV - LWHYPCT - LWH P - - - - - 4 - gnl|BL_ORD_ID|833 - 54821|E2 protein|AAM33354.1|Hepatitis C virus subtype 1a|31646 - 833 - 9 - - - 1 - 14.6234 - 26 - 1.67935 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 4 - 0 - 7 - LWHLPAV - LWHYPCT - LWH P - - - - - 5 - gnl|BL_ORD_ID|835 - 54825|polyprotein|BAA03375.1|Hepatitis C virus|11103 - 835 - 9 - - - 1 - 14.6234 - 26 - 1.73509 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 4 - 0 - 7 - LWHLPAV - LWHYPCT - LWH P - - - - - 6 - gnl|BL_ORD_ID|834 - 54824|polyprotein precursor|BAA01583.1|Hepatitis C virus|11103 - 834 - 9 - - - 1 - 14.6234 - 26 - 1.88321 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 4 - 0 - 7 - LWHLPAV - LWHYPCT - LWH P - - - - - 7 - gnl|BL_ORD_ID|1010 - 67210|NS3 protein|NP_739587.1|Dengue virus 2 Thailand/NGS-C/1944|11065 - 1010 - 9 - - - 1 - 12.6974 - 21 - 39.1808 - 3 - 9 - 2 - 8 - 0 - 0 - 2 - 6 - 0 - 7 - LWHLPAV - VWFVPSI - +W +P++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 757 - Query_757 - M_1227 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 758 - Query_758 - M_1228 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 759 - Query_759 - M_1229 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 760 - Query_760 - M_1230 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 761 - Query_761 - M_1231 - 9 - - - 1 - gnl|BL_ORD_ID|469 - 28484|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 469 - 9 - - - 1 - 14.2382 - 25 - 4.3647 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 7 - 0 - 9 - MTEHRGKCY - ISEYRHYCY - ++E+R CY - - - - - 2 - gnl|BL_ORD_ID|1406 - 110846|E6 protein|CAB45108.1|Human papillomavirus type 16|333760 - 1406 - 9 - - - 1 - 12.6974 - 21 - 30.8766 - 3 - 9 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - EHRGKCY - EYRHYCY - E+R CY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 762 - Query_762 - M_1232 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 763 - Query_763 - M_1233 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 764 - Query_764 - M_1234 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 765 - Query_765 - M_1235 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 766 - Query_766 - M_1236 - 9 - - - 1 - gnl|BL_ORD_ID|764 - 51250|nucleocapsid protein|ABI96968.1|SARS coronavirus|227859 - 764 - 15 - - - 1 - 15.779 - 29 - 0.411155 - 1 - 9 - 7 - 15 - 0 - 0 - 5 - 7 - 0 - 9 - HRYNLTQHF - KQYNVTQAF - +YN+TQ F - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 767 - Query_767 - M_1237 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 768 - Query_768 - M_1238 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 769 - Query_769 - M_1239 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 770 - Query_770 - M_1240 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 771 - Query_771 - M_1241 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 772 - Query_772 - M_1242 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 773 - Query_773 - M_1243 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 774 - Query_774 - M_1244 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 775 - Query_775 - M_1245 - 9 - - - 1 - gnl|BL_ORD_ID|135 - 9746|Genome polyprotein|P29846.3|Hepatitis C virus genotype 1|41856 - 135 - 9 - - - 1 - 13.0826 - 22 - 21.5246 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 7 - 0 - 9 - SPRRRAASV - DPRRRSRNL - PRRR+ ++ - - - - - 2 - gnl|BL_ORD_ID|1757 - 154196|tegument protein|CAB06735.1|Human alphaherpesvirus 2|10310 - 1757 - 16 - - - 1 - 12.6974 - 21 - 34.8463 - 4 - 9 - 4 - 9 - 0 - 0 - 5 - 6 - 0 - 6 - RRAASV - RRSASV - RR+ASV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 776 - Query_776 - M_1246 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 777 - Query_777 - M_1247 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 778 - Query_778 - M_1248 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 779 - Query_779 - M_1249 - 9 - - - 1 - gnl|BL_ORD_ID|750 - 49831|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 - 750 - 15 - - - 1 - 10.001 - 14 - 757.359 - 3 - 9 - 6 - 12 - 0 - 0 - 3 - 5 - 0 - 7 - ICCDCVI - ILCLCLV - I C C++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 780 - Query_780 - M_1250 - 9 - - - 1 - gnl|BL_ORD_ID|82 - 5952|PPE family protein|YP_177918.1|Mycobacterium tuberculosis H37Rv|83332 - 82 - 9 - - - 1 - 13.853 - 24 - 7.58732 - 1 - 7 - 3 - 9 - 0 - 0 - 4 - 4 - 0 - 7 - CPYSAWC - VPYVAWL - PY AW - - - - - 2 - gnl|BL_ORD_ID|1097 - 72563|polyprotein|AAB70696.1|Dengue virus type 1 Hawaii|10000440 - 1097 - 20 - - - 1 - 12.6974 - 21 - 21.8633 - 2 - 9 - 8 - 15 - 0 - 0 - 3 - 4 - 0 - 8 - PYSAWCVY - PYKTWAYH - PY W + - - - - - 3 - gnl|BL_ORD_ID|1931 - 180758|Nonstructural protein NS5|NP_739590.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1931 - 15 - - - 1 - 12.6974 - 21 - 27.8948 - 2 - 7 - 9 - 14 - 0 - 0 - 3 - 3 - 0 - 6 - PYSAWC - PYKTWA - PY W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 781 - Query_781 - M_1251 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 782 - Query_782 - M_1252 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 783 - Query_783 - M_1253 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 784 - Query_784 - M_1254 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 785 - Query_785 - M_1255 - 9 - - - 1 - gnl|BL_ORD_ID|566 - 35237|nonstructural protein 3|NP_722463.1|Dengue virus type 1 Hawaii|10000440 - 566 - 20 - - - 1 - 11.5418 - 18 - 95.4438 - 1 - 8 - 10 - 17 - 0 - 0 - 3 - 6 - 0 - 8 - MVPREFKP - IIPALFEP - ++P F+P - - - - - 2 - gnl|BL_ORD_ID|993 - 65550|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 993 - 15 - - - 1 - 11.5418 - 18 - 100.351 - 1 - 8 - 5 - 12 - 0 - 0 - 3 - 6 - 0 - 8 - MVPREFKP - IIPSMFEP - ++P F+P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 786 - Query_786 - M_1256 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 787 - Query_787 - M_1257 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 788 - Query_788 - M_1258 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 789 - Query_789 - M_1259 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 790 - Query_790 - M_1260 - 9 - - - 1 - gnl|BL_ORD_ID|1271 - 101673|gag protein|ABO73990.1|Human immunodeficiency virus 1|11676 - 1271 - 9 - - - 1 - 13.853 - 24 - 5.09494 - 2 - 9 - 2 - 9 - 0 - 0 - 5 - 6 - 0 - 8 - HQAMFQLL - HQAAMQML - HQA Q+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 791 - Query_791 - M_1261 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 792 - Query_792 - M_1262 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 793 - Query_793 - M_1263 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 794 - Query_794 - M_1264 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 795 - Query_795 - M_1265 - 9 - - - 1 - gnl|BL_ORD_ID|142 - 10650|Nucleoprotein|P05133.1|Hantaan virus 76-118|11602 - 142 - 15 - - - 1 - 13.0826 - 22 - 15.0718 - 3 - 9 - 7 - 13 - 0 - 0 - 4 - 5 - 0 - 7 - ITNIEPF - ISNQEPL - I+N EP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 796 - Query_796 - M_1266 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 797 - Query_797 - M_1267 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 798 - Query_798 - M_1268 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 799 - Query_799 - M_1269 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 800 - Query_800 - M_1270 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 801 - Query_801 - M_1271 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 802 - Query_802 - M_1272 - 9 - - - 1 - gnl|BL_ORD_ID|215 - 15914|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 - 215 - 15 - - - 1 - 13.4678 - 23 - 8.0204 - 4 - 8 - 6 - 10 - 0 - 0 - 4 - 5 - 0 - 5 - DGIRL - DGVRL - DG+RL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 803 - Query_803 - M_1273 - 9 - - - 1 - gnl|BL_ORD_ID|159 - 12108|polyprotein|AAP55688.1|Hepatitis C virus subtype 2a|31649 - 159 - 10 - - - 1 - 12.3122 - 20 - 49.5064 - 1 - 8 - 3 - 10 - 0 - 0 - 3 - 4 - 0 - 8 - WRCWFNGI - WEAVFTGL - W F G+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 804 - Query_804 - M_1274 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 805 - Query_805 - M_1275 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 806 - Query_806 - M_1276 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 807 - Query_807 - M_1277 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 808 - Query_808 - M_1278 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 809 - Query_809 - M_1279 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 810 - Query_810 - M_1280 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 811 - Query_811 - M_1281 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 812 - Query_812 - M_1282 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 813 - Query_813 - M_1283 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 814 - Query_814 - M_1284 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 815 - Query_815 - M_1285 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 816 - Query_816 - M_1286 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 817 - Query_817 - M_1287 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 818 - Query_818 - M_1288 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 819 - Query_819 - M_1289 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 820 - Query_820 - M_1290 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 821 - Query_821 - M_1291 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 822 - Query_822 - M_1292 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 823 - Query_823 - M_1293 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 824 - Query_824 - M_1294 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 825 - Query_825 - M_1295 - 9 - - - 1 - gnl|BL_ORD_ID|296 - 19493|polyprotein|BAA03375.1|Hepatitis C virus|11103 - 296 - 15 - - - 1 - 13.0826 - 22 - 14.8197 - 3 - 8 - 9 - 14 - 0 - 0 - 4 - 6 - 0 - 6 - IPVVGS - IPLVGA - IP+VG+ - - - - - 2 - gnl|BL_ORD_ID|378 - 23365|polyprotein|BAB18806.1|Hepatitis C virus|11103 - 378 - 10 - - - 1 - 13.0826 - 22 - 19.8203 - 3 - 8 - 3 - 8 - 0 - 0 - 4 - 6 - 0 - 6 - IPVVGS - IPLVGA - IP+VG+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 826 - Query_826 - M_1296 - 9 - - - 1 - gnl|BL_ORD_ID|1372 - 108277|IE62|AAP32859.1|Human alphaherpesvirus 3|10335 - 1372 - 9 - - - 1 - 13.853 - 24 - 7.20201 - 2 - 8 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - VWALPKT - LWALPHA - +WALP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 827 - Query_827 - M_1297 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 828 - Query_828 - M_1298 - 9 - - - 1 - gnl|BL_ORD_ID|621 - 37466|surface antigen|BAF44879.1|Hepatitis B virus|10407 - 621 - 9 - - - 1 - 11.5418 - 18 - 155.038 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 6 - 0 - 9 - LHLCYEFLM - LLLCLIFLL - L LC FL+ - - - - - 2 - gnl|BL_ORD_ID|596 - 37120|Major surface antigen precursor|P17399.3|Hepatitis B virus|10407 - 596 - 9 - - - 1 - 11.1566 - 17 - 208.544 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - LCYEFLM - LCLIFLL - LC FL+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 829 - Query_829 - M_1299 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 830 - Query_830 - M_1300 - 9 - - - 1 - gnl|BL_ORD_ID|1980 - 183229|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1980 - 10 - - - 1 - 13.853 - 24 - 6.8721 - 2 - 8 - 2 - 8 - 0 - 0 - 4 - 6 - 0 - 7 - PSSNALL - PQSNAVI - P SNA++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 831 - Query_831 - M_1301 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 832 - Query_832 - M_1302 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 833 - Query_833 - M_1303 - 9 - - - 1 - gnl|BL_ORD_ID|1688 - 149060|E2 protein|NP_751921.1|Hepatitis C virus (isolate H77)|63746 - 1688 - 9 - - - 1 - 12.6974 - 21 - 26.0147 - 2 - 7 - 4 - 9 - 0 - 0 - 4 - 4 - 0 - 6 - AVYSTC - ATYSRC - A YS C - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 834 - Query_834 - M_1304 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 835 - Query_835 - M_1305 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 836 - Query_836 - M_1306 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 837 - Query_837 - M_1307 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 838 - Query_838 - M_1308 - 9 - - - 1 - gnl|BL_ORD_ID|1778 - 155928|unnamed protein product|CAA30115.1|Trypanosoma cruzi|5693 - 1778 - 9 - - - 1 - 12.6974 - 21 - 23.8709 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 7 - 0 - 8 - LKPGDRVV - LQPVERVL - L+P +RV+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 839 - Query_839 - M_1309 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 840 - Query_840 - M_1310 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 841 - Query_841 - M_1311 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 842 - Query_842 - M_1312 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 843 - Query_843 - M_1313 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 844 - Query_844 - M_1314 - 9 - - - 1 - gnl|BL_ORD_ID|2051 - 184702|non-structural protein 1|AGM49312.1|Dengue virus|12637 - 2051 - 9 - - - 1 - 13.4678 - 23 - 9.02895 - 4 - 9 - 3 - 8 - 0 - 0 - 4 - 5 - 0 - 6 - PATHSL - PKTHTL - P TH+L - - - - - 2 - gnl|BL_ORD_ID|1333 - 107873|Genome polyprotein|P26664.3|Hepatitis C virus|11103 - 1333 - 10 - - - 1 - 12.3122 - 20 - 56.5271 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - SSPATHS - GSPITYS - SP T+S - - - - - 3 - gnl|BL_ORD_ID|965 - 63963|HCV-1|AAA45676.1|Hepatitis C virus|11103 - 965 - 10 - - - 1 - 12.3122 - 20 - 63.4362 - 3 - 8 - 3 - 8 - 0 - 0 - 4 - 5 - 0 - 6 - SPATHS - SPITYS - SP T+S - - - - - 4 - gnl|BL_ORD_ID|972 - 64489|polyprotein|BAA03375.1|Hepatitis C virus|11103 - 972 - 11 - - - 1 - 12.3122 - 20 - 63.6416 - 3 - 8 - 6 - 11 - 0 - 0 - 4 - 5 - 0 - 6 - SPATHS - SPITYS - SP T+S - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 845 - Query_845 - M_1315 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 846 - Query_846 - M_1316 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 847 - Query_847 - M_1317 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 848 - Query_848 - M_1318 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 849 - Query_849 - M_1319 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 850 - Query_850 - M_1320 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 851 - Query_851 - M_1321 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 852 - Query_852 - M_1322 - 9 - - - 1 - gnl|BL_ORD_ID|1395 - 110394|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1395 - 32 - - - 1 - 11.1566 - 17 - 134.202 - 2 - 8 - 8 - 14 - 0 - 0 - 4 - 4 - 0 - 7 - PLRPRES - PLCPEEK - PL P E - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 853 - Query_853 - M_1323 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 854 - Query_854 - M_1324 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 855 - Query_855 - M_1325 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 856 - Query_856 - M_1326 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 857 - Query_857 - M_1327 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 858 - Query_858 - M_1328 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 859 - Query_859 - M_1329 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 860 - Query_860 - M_1330 - 9 - - - 1 - gnl|BL_ORD_ID|1876 - 180507|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1876 - 15 - - - 1 - 11.5418 - 18 - 131.587 - 1 - 7 - 8 - 14 - 0 - 0 - 4 - 5 - 0 - 7 - DLVHHTT - DLMCHAT - DL+ H T - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 861 - Query_861 - M_1331 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 862 - Query_862 - M_1332 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 863 - Query_863 - M_1333 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 864 - Query_864 - M_1334 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 865 - Query_865 - M_1335 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 866 - Query_866 - M_1336 - 9 - - - 1 - gnl|BL_ORD_ID|2111 - 186219|polyprotein|AGK36298.1|Dengue virus 2|11060 - 2111 - 9 - - - 1 - 14.6234 - 26 - 2.33479 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - IADGRAW - VEDGRFW - + DGR W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 867 - Query_867 - M_1337 - 9 - - - 1 - gnl|BL_ORD_ID|1919 - 180689|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1919 - 15 - - - 1 - 15.3938 - 28 - 0.680841 - 1 - 7 - 8 - 14 - 0 - 0 - 5 - 6 - 0 - 7 - MGYRVES - MGYWIES - MGY +ES - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 868 - Query_868 - M_1338 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 869 - Query_869 - M_1339 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 870 - Query_870 - M_1340 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 871 - Query_871 - M_1341 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 872 - Query_872 - M_1342 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 873 - Query_873 - M_1343 - 9 - - - 1 - gnl|BL_ORD_ID|1729 - 150534|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1729 - 9 - - - 1 - 13.4678 - 23 - 9.02895 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 4 - 0 - 8 - RPGCLWAL - RPASAWTL - RP W L - - - - - 2 - gnl|BL_ORD_ID|88 - 6431|Genome polyprotein|SRC279960|Hepatitis C virus|11103 - 88 - 9 - - - 1 - 13.4678 - 23 - 12.1399 - 4 - 9 - 4 - 9 - 0 - 0 - 3 - 5 - 0 - 6 - GCLWAL - GCVWTV - GC+W + - - - - - 3 - gnl|BL_ORD_ID|708 - 43619|Genome polyprotein|P26664.3|Hepatitis C virus|11103 - 708 - 9 - - - 1 - 12.6974 - 21 - 26.4654 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 4 - 0 - 7 - RPGCLWA - NEGCGWA - GC WA - - - - - 4 - gnl|BL_ORD_ID|626 - 37536|Spike glycoprotein precursor|P15423.1|Human coronavirus 229E|11137 - 626 - 9 - - - 1 - 12.6974 - 21 - 34.7909 - 4 - 9 - 4 - 9 - 0 - 0 - 3 - 5 - 0 - 6 - GCLWAL - NCLWSV - CLW++ - - - - - 5 - gnl|BL_ORD_ID|664 - 39591|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 - 664 - 20 - - - 1 - 11.5418 - 18 - 101.139 - 5 - 9 - 12 - 16 - 0 - 0 - 4 - 4 - 0 - 5 - CLWAL - CLWWL - CLW L - - - - - 6 - gnl|BL_ORD_ID|1120 - 74387|Genome polyprotein|P26664.3|Hepatitis C virus (isolate 1)|11104 - 1120 - 9 - - - 1 - 11.5418 - 18 - 152.614 - 5 - 9 - 5 - 9 - 0 - 0 - 4 - 4 - 0 - 5 - CLWAL - CLWWL - CLW L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 874 - Query_874 - M_1344 - 9 - - - 1 - gnl|BL_ORD_ID|1476 - 131096|G1 and G2 surface glycoprotein precursor|AAG22532.1|Andes hantavirus|46607 - 1476 - 10 - - - 1 - 13.0826 - 22 - 15.0326 - 1 - 8 - 3 - 10 - 0 - 0 - 3 - 7 - 0 - 8 - HGLEKVPV - HGVGEIPM - HG+ ++P+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 875 - Query_875 - M_1345 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 876 - Query_876 - M_1346 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 877 - Query_877 - M_1347 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 878 - Query_878 - M_1348 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 879 - Query_879 - M_1349 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 880 - Query_880 - M_1350 - 9 - - - 1 - gnl|BL_ORD_ID|1394 - 110373|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1394 - 25 - - - 1 - 11.927 - 19 - 62.6597 - 1 - 8 - 13 - 20 - 0 - 0 - 4 - 6 - 0 - 8 - SMIHYIVL - TTIHDIIL - + IH I+L - - - - - 2 - gnl|BL_ORD_ID|1411 - 111251|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1411 - 15 - - - 1 - 11.5418 - 18 - 103.444 - 1 - 8 - 4 - 11 - 0 - 0 - 4 - 6 - 0 - 8 - SMIHYIVL - TTIHDIIL - + IH I+L - - - - - 3 - gnl|BL_ORD_ID|1390 - 110306|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1390 - 32 - - - 1 - 11.5418 - 18 - 109.949 - 1 - 8 - 11 - 18 - 0 - 0 - 4 - 6 - 0 - 8 - SMIHYIVL - TTIHDIIL - + IH I+L - - - - - 4 - gnl|BL_ORD_ID|1403 - 110720|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1403 - 9 - - - 1 - 11.1566 - 17 - 208.544 - 3 - 8 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - IHYIVL - IHDIIL - IH I+L - - - - - 5 - gnl|BL_ORD_ID|968 - 64320|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 968 - 10 - - - 1 - 11.1566 - 17 - 218.136 - 3 - 8 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - IHYIVL - IHDIIL - IH I+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 881 - Query_881 - M_1351 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 882 - Query_882 - M_1352 - 9 - - - 1 - gnl|BL_ORD_ID|1249 - 98100|trans-sialidase, putative|EAN81657.1|Trypanosoma cruzi|5693 - 1249 - 9 - - - 1 - 13.853 - 24 - 5.95161 - 1 - 9 - 1 - 9 - 0 - 0 - 6 - 7 - 0 - 9 - HIFLFAVLL - HLFYSAVLL - H+F AVLL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 883 - Query_883 - M_1353 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 884 - Query_884 - M_1354 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 885 - Query_885 - M_1355 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 886 - Query_886 - M_1356 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 887 - Query_887 - M_1357 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 888 - Query_888 - M_1358 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 889 - Query_889 - M_1359 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 890 - Query_890 - M_1360 - 9 - - - 1 - gnl|BL_ORD_ID|1563 - 141306|tegument host shutoff protein|NP_044643.1|Human alphaherpesvirus 1|10298 - 1563 - 10 - - - 1 - 13.853 - 24 - 5.98008 - 3 - 9 - 4 - 10 - 0 - 0 - 4 - 4 - 0 - 7 - LEPQKTY - LHPNNTY - L P TY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 891 - Query_891 - M_1361 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 892 - Query_892 - M_1362 - 9 - - - 1 - gnl|BL_ORD_ID|1820 - 177956|polyprotein|ACZ60102.1|Hepatitis C virus subtype 3a|356426 - 1820 - 17 - - - 1 - 11.927 - 19 - 68.8968 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 5 - 0 - 9 - RPPSPKDTV - RPSGMFDSV - RP D+V - - - - - 2 - gnl|BL_ORD_ID|1819 - 177955|polyprotein|ACZ60102.1|Hepatitis C virus subtype 3a|356426 - 1819 - 11 - - - 1 - 11.927 - 19 - 93.6338 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 5 - 0 - 9 - RPPSPKDTV - RPSGMFDSV - RP D+V - - - - - 3 - gnl|BL_ORD_ID|1656 - 146592|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 - 1656 - 16 - - - 1 - 11.5418 - 18 - 127.377 - 1 - 9 - 6 - 14 - 0 - 0 - 4 - 5 - 0 - 9 - RPPSPKDTV - RPSGMFDSV - RP D+V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 893 - Query_893 - M_1363 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 894 - Query_894 - M_1364 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 895 - Query_895 - M_1365 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 896 - Query_896 - M_1366 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 897 - Query_897 - M_1367 - 9 - - - 1 - gnl|BL_ORD_ID|281 - 18941|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 281 - 15 - - - 1 - 14.6234 - 26 - 1.39982 - 1 - 9 - 3 - 11 - 0 - 0 - 4 - 5 - 0 - 9 - CAQSPWCLV - CVQGDWCPI - C Q WC + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 898 - Query_898 - M_1368 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 899 - Query_899 - M_1369 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 900 - Query_900 - M_1370 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 901 - Query_901 - M_1371 - 9 - - - 1 - gnl|BL_ORD_ID|1050 - 69714|Large envelope protein|SRC279965|Hepatitis B virus|10407 - 1050 - 9 - - - 1 - 12.3122 - 20 - 54.8462 - 2 - 7 - 4 - 9 - 0 - 0 - 3 - 5 - 0 - 6 - GGFFVI - AGFFIL - GFF++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 902 - Query_902 - M_1372 - 9 - - - 1 - gnl|BL_ORD_ID|889 - 58463|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 889 - 20 - - - 1 - 13.853 - 24 - 5.41768 - 1 - 7 - 12 - 18 - 0 - 0 - 5 - 6 - 0 - 7 - YVYPLPV - YVYALPL - YVY LP+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 903 - Query_903 - M_1373 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 904 - Query_904 - M_1374 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 905 - Query_905 - M_1375 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 906 - Query_906 - M_1376 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 907 - Query_907 - M_1377 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 908 - Query_908 - M_1378 - 9 - - - 1 - gnl|BL_ORD_ID|659 - 39162|gag protein|AAV53308.1|Human immunodeficiency virus 1|11676 - 659 - 15 - - - 1 - 12.6974 - 21 - 23.6601 - 4 - 9 - 9 - 14 - 0 - 0 - 4 - 5 - 0 - 6 - YKYEHI - YKLKHI - YK +HI - - - - - 2 - gnl|BL_ORD_ID|2125 - 186551|polyprotein|AGW21594.1|Dengue virus 1|11053 - 2125 - 10 - - - 1 - 12.6974 - 21 - 26.5293 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 5 - 0 - 9 - YEGYKYEHI - YENLKYSVI - YE KY I - - - - - 3 - gnl|BL_ORD_ID|558 - 34482|gag polyprotein|BAA00992.1|Human immunodeficiency virus 1|11676 - 558 - 9 - - - 1 - 12.3122 - 20 - 40.5299 - 4 - 9 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - YKYEHI - YKLKHI - YK +HI - - - - - 4 - gnl|BL_ORD_ID|1016 - 67503|Genome polyprotein|P26662.3|Hepatitis C virus|11103 - 1016 - 10 - - - 1 - 11.927 - 19 - 66.6359 - 4 - 9 - 2 - 7 - 0 - 0 - 3 - 5 - 0 - 6 - YKYEHI - YVYDHL - Y Y+H+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 909 - Query_909 - M_1379 - 9 - - - 1 - gnl|BL_ORD_ID|929 - 60867|nucleoprotein|CAZ65591.1|Influenza A virus|11320 - 929 - 9 - - - 1 - 12.6974 - 21 - 24.2855 - 1 - 7 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - DRYVAVR - SRYWAIR - RY A+R - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 910 - Query_910 - M_1380 - 9 - - - 1 - gnl|BL_ORD_ID|601 - 37153|Nuclear antigen EBNA-3C|Q69140.1|Human gammaherpesvirus 4|10376 - 601 - 10 - - - 1 - 15.779 - 29 - 0.523411 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 7 - 0 - 8 - LIDYARYM - LLDFVRFM - L+D+ R+M - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 911 - Query_911 - M_1381 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 912 - Query_912 - M_1382 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 913 - Query_913 - M_1383 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 914 - Query_914 - M_1384 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 915 - Query_915 - M_1385 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 916 - Query_916 - M_1386 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 917 - Query_917 - M_1387 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 918 - Query_918 - M_1388 - 9 - - - 1 - gnl|BL_ORD_ID|2250 - 240808|polyprotein|AAB53095.1|Tick-borne encephalitis virus|11084 - 2250 - 9 - - - 1 - 12.3122 - 20 - 42.6373 - 1 - 6 - 2 - 7 - 0 - 0 - 4 - 6 - 0 - 6 - LVDNLT - LLDNIT - L+DN+T - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 919 - Query_919 - M_1389 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 920 - Query_920 - M_1390 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 921 - Query_921 - M_1391 - 9 - - - 1 - gnl|BL_ORD_ID|1621 - 145860|Protein E6|P04019.1|Human papillomavirus type 11|10580 - 1621 - 9 - - - 1 - 11.927 - 19 - 105.754 - 2 - 7 - 2 - 7 - 0 - 0 - 3 - 5 - 0 - 6 - VLVGCF - VLIRCY - VL+ C+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 922 - Query_922 - M_1392 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 923 - Query_923 - M_1393 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 924 - Query_924 - M_1394 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 925 - Query_925 - M_1395 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 926 - Query_926 - M_1396 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 927 - Query_927 - M_1397 - 9 - - - 1 - gnl|BL_ORD_ID|1936 - 180789|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1936 - 15 - - - 1 - 11.927 - 19 - 86.1406 - 2 - 9 - 7 - 14 - 0 - 0 - 4 - 4 - 0 - 8 - PSPNRPKL - PIPYDPKF - P P PK - - - - - 2 - gnl|BL_ORD_ID|1299 - 103563|polyprotein|BAB18806.1|Hepatitis C virus|11103 - 1299 - 9 - - - 1 - 11.1566 - 17 - 287.485 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 5 - 0 - 9 - RPSPNRPKL - RPDYNPPLL - RP N P L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 928 - Query_928 - M_1398 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 929 - Query_929 - M_1399 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 930 - Query_930 - M_1400 - 9 - - - 1 - gnl|BL_ORD_ID|819 - 54662|pX-rex-orf I {alternatively spliced}|AAB23359.1|Human T-lymphotropic virus 1|11908 - 819 - 9 - - - 1 - 15.0086 - 27 - 1.45111 - 1 - 8 - 1 - 8 - 0 - 0 - 6 - 7 - 0 - 8 - RLLPPVSP - RLLSPLSP - RLL P+SP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 931 - Query_931 - M_1401 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 932 - Query_932 - M_1402 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 933 - Query_933 - M_1403 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 934 - Query_934 - M_1404 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 935 - Query_935 - M_1405 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 936 - Query_936 - M_1406 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 937 - Query_937 - M_1407 - 9 - - - 1 - gnl|BL_ORD_ID|636 - 37919|envelope protein|BAF48755.1|Hepatitis B virus|10407 - 636 - 10 - - - 1 - 14.2382 - 25 - 3.16139 - 1 - 7 - 3 - 9 - 0 - 0 - 4 - 5 - 0 - 7 - VPLVRWL - VPFVQWF - VP V+W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 938 - Query_938 - M_1408 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 939 - Query_939 - M_1409 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 940 - Query_940 - M_1410 - 9 - - - 1 - gnl|BL_ORD_ID|701 - 42797|6 kDa early secretory antigenic target|P0A564.2|Mycobacterium tuberculosis|1773 - 701 - 20 - - - 1 - 13.4678 - 23 - 8.9532 - 4 - 8 - 4 - 8 - 0 - 0 - 4 - 4 - 0 - 5 - QAWNF - QQWNF - Q WNF - - - - - 2 - gnl|BL_ORD_ID|1538 - 140760|LOW MOLECULAR WEIGHT PROTEIN ANTIGEN 7 ESXH (10 kDa ANTIGEN) (CFP-7) (PROTEIN TB10.4)|CAA17363.1|Mycobacterium tuberculosis H37Rv|83332 - 1538 - 9 - - - 1 - 13.4678 - 23 - 11.9303 - 2 - 7 - 1 - 6 - 0 - 0 - 4 - 4 - 0 - 6 - NYQAWN - TYQAWQ - YQAW - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 941 - Query_941 - M_1411 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 942 - Query_942 - M_1412 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 943 - Query_943 - M_1413 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 944 - Query_944 - M_1414 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 945 - Query_945 - M_1415 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 946 - Query_946 - M_1416 - 9 - - - 1 - gnl|BL_ORD_ID|1008 - 66798|glycoprotein gp35/37|AAC59622.1|Human gammaherpesvirus 8|37296 - 1008 - 15 - - - 1 - 12.6974 - 21 - 27.8948 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 5 - 0 - 9 - TTKKSGGHY - TTRGRDAHY - TT+ HY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 947 - Query_947 - M_1417 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 948 - Query_948 - M_1418 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 949 - Query_949 - M_1419 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 950 - Query_950 - M_1420 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 951 - Query_951 - M_1421 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 952 - Query_952 - M_1422 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 953 - Query_953 - M_1423 - 9 - - - 1 - gnl|BL_ORD_ID|1111 - 73177|protein F [Hepatitis C virus subtype 1b]|ACA50643.1|Hepatitis C virus (isolate Japanese)|11116 - 1111 - 9 - - - 1 - 13.0826 - 22 - 20.7937 - 3 - 8 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - VCHQLG - VCARLG - VC +LG - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 954 - Query_954 - M_1424 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 955 - Query_955 - M_1425 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 956 - Query_956 - M_1426 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 957 - Query_957 - M_1427 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 958 - Query_958 - M_1428 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 959 - Query_959 - M_1429 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 960 - Query_960 - M_1430 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 961 - Query_961 - M_1431 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 962 - Query_962 - M_1432 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 963 - Query_963 - M_1433 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 964 - Query_964 - M_1434 - 9 - - - 1 - gnl|BL_ORD_ID|1581 - 141462|tegument protein UL21|NP_044622.1|Human alphaherpesvirus 1|10298 - 1581 - 9 - - - 1 - 13.4678 - 23 - 8.42175 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 6 - 0 - 9 - VPREFKPIL - VPRPDDPVL - VPR P+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 965 - Query_965 - M_1435 - 9 - - - 1 - gnl|BL_ORD_ID|747 - 48896|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 - 747 - 15 - - - 1 - 12.3122 - 20 - 53.9857 - 4 - 9 - 1 - 6 - 0 - 0 - 4 - 4 - 0 - 6 - PPMPPY - PPQPEY - PP P Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 966 - Query_966 - M_1436 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 967 - Query_967 - M_1437 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 968 - Query_968 - M_1438 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 969 - Query_969 - M_1439 - 9 - - - 1 - gnl|BL_ORD_ID|886 - 58122|pol protein|BAA32832.1|Hepatitis B virus|10407 - 886 - 10 - - - 1 - 13.4678 - 23 - 9.73455 - 4 - 8 - 1 - 5 - 0 - 0 - 4 - 5 - 0 - 5 - SGVPR - SGLPR - SG+PR - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 970 - Query_970 - M_1440 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 971 - Query_971 - M_1441 - 9 - - - 1 - gnl|BL_ORD_ID|1596 - 142232|POSSIBLE CONSERVED TRANSMEMBRANE PROTEIN|CAB00937.1|Mycobacterium tuberculosis|1773 - 1596 - 19 - - - 1 - 6.53423 - 5 - 16334.9 - 8 - 9 - 13 - 14 - 0 - 0 - 2 - 2 - 0 - 2 - VY - VY - VY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 972 - Query_972 - M_1442 - 9 - - - 1 - gnl|BL_ORD_ID|96 - 6591|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 96 - 18 - - - 1 - 14.2382 - 25 - 3.03664 - 2 - 9 - 9 - 16 - 0 - 0 - 4 - 4 - 0 - 8 - FHNPKPLF - LHGPTPLL - H P PL - - - - - 2 - gnl|BL_ORD_ID|707 - 43447|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 - 707 - 20 - - - 1 - 13.0826 - 22 - 19.8728 - 1 - 9 - 6 - 14 - 0 - 0 - 5 - 5 - 0 - 9 - FFHNPKPLF - FFFNPGELL - FF NP L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 973 - Query_973 - M_1443 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 974 - Query_974 - M_1444 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 975 - Query_975 - M_1445 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 976 - Query_976 - M_1446 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 977 - Query_977 - M_1447 - 9 - - - 1 - gnl|BL_ORD_ID|133 - 9415|Superoxide dismutase|P17670.1|Mycobacterium tuberculosis|1773 - 133 - 10 - - - 1 - 13.853 - 24 - 4.3044 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 5 - 0 - 9 - DFWYHAVVL - DMWEHAFYL - D W HA L - - - - - 2 - gnl|BL_ORD_ID|132 - 9414|Superoxide dismutase|P17670.1|Mycobacterium tuberculosis|1773 - 132 - 9 - - - 1 - 13.853 - 24 - 5.45887 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 5 - 0 - 9 - DFWYHAVVL - DMWEHAFYL - D W HA L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 978 - Query_978 - M_1448 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 979 - Query_979 - M_1449 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 980 - Query_980 - M_1450 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 981 - Query_981 - M_1451 - 9 - - - 1 - gnl|BL_ORD_ID|320 - 21000|glutamine synthetase GLNA1 (glutamine synthase) (GS-I)|NP_216736.1|Mycobacterium tuberculosis|1773 - 320 - 9 - - - 1 - 14.2382 - 25 - 4.07578 - 3 - 9 - 3 - 9 - 0 - 0 - 4 - 6 - 0 - 7 - VHRAPSI - LHHAPSL - +H APS+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 982 - Query_982 - M_1452 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 983 - Query_983 - M_1453 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 984 - Query_984 - M_1454 - 9 - - - 1 - gnl|BL_ORD_ID|981 - 64821|Protein Tax-1|P03409.2|Human T-lymphotropic virus 1|11908 - 981 - 9 - - - 1 - 13.853 - 24 - 7.20201 - 4 - 9 - 4 - 9 - 0 - 0 - 3 - 5 - 0 - 6 - EHIPTF - QHLPTL - +H+PT - - - - - 2 - gnl|BL_ORD_ID|1172 - 79308|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 1172 - 16 - - - 1 - 13.0826 - 22 - 12.7581 - 4 - 9 - 7 - 12 - 0 - 0 - 3 - 5 - 0 - 6 - EHIPTF - QHLPTL - +H+PT - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 985 - Query_985 - M_1455 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 986 - Query_986 - M_1456 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 987 - Query_987 - M_1457 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 988 - Query_988 - M_1458 - 9 - - - 1 - gnl|BL_ORD_ID|931 - 61077|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 - 931 - 9 - - - 1 - 14.6234 - 26 - 2.07889 - 1 - 8 - 2 - 9 - 0 - 0 - 4 - 7 - 0 - 8 - SHTGTFLL - SHSGSFQI - SH+G+F + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 989 - Query_989 - M_1459 - 9 - - - 1 - gnl|BL_ORD_ID|1861 - 180440|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1861 - 15 - - - 1 - 12.6974 - 21 - 22.514 - 4 - 9 - 8 - 13 - 0 - 0 - 3 - 6 - 0 - 6 - AWSNGH - SWNSGH - +W++GH - - - - - 2 - gnl|BL_ORD_ID|1926 - 180734|Nonstructural protein NS3|NP_739587.2|Dengue virus 2|11060 - 1926 - 9 - - - 1 - 12.3122 - 20 - 40.5299 - 4 - 9 - 2 - 7 - 0 - 0 - 3 - 6 - 0 - 6 - AWSNGH - SWNSGH - +W++GH - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 990 - Query_990 - M_1460 - 9 - - - 1 - gnl|BL_ORD_ID|163 - 12588|Glycoprotein B precursor (Glycoprotein II)|P09257.1|Human alphaherpesvirus 3|10335 - 163 - 11 - - - 1 - 14.2382 - 25 - 3.80034 - 2 - 9 - 2 - 9 - 0 - 0 - 5 - 6 - 0 - 8 - IPDSISKF - ITDTIDKF - I D+I KF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 991 - Query_991 - M_1461 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 992 - Query_992 - M_1462 - 9 - - - 1 - gnl|BL_ORD_ID|1036 - 69398|X protein|AAP06597.1|Hepatitis B virus|10407 - 1036 - 9 - - - 1 - 11.927 - 19 - 87.0561 - 4 - 9 - 2 - 7 - 0 - 0 - 4 - 4 - 0 - 6 - LCHNPV - LCLRPV - LC PV - - - - - 2 - gnl|BL_ORD_ID|310 - 20787|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 - 310 - 10 - - - 1 - 11.927 - 19 - 93.6922 - 1 - 7 - 2 - 8 - 0 - 0 - 4 - 4 - 0 - 7 - FCPLCHN - LCPHCIN - CP C N - - - - - 3 - gnl|BL_ORD_ID|309 - 20786|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 - 309 - 9 - - - 1 - 11.927 - 19 - 102.395 - 1 - 7 - 2 - 8 - 0 - 0 - 4 - 4 - 0 - 7 - FCPLCHN - LCPHCIN - CP C N - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 993 - Query_993 - M_1463 - 9 - - - 1 - gnl|BL_ORD_ID|743 - 47946|envelope glycoprotein|AAC28452.1|Human immunodeficiency virus 1|11676 - 743 - 20 - - - 1 - 13.853 - 24 - 5.6992 - 2 - 6 - 14 - 18 - 0 - 0 - 4 - 5 - 0 - 5 - VLKCN - ILKCN - +LKCN - - - - - 2 - gnl|BL_ORD_ID|1570 - 141396|ribonucleotide reductase subunit 1|NP_044641.1|Human alphaherpesvirus 1|10298 - 1570 - 9 - - - 1 - 13.0826 - 22 - 22.6682 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 6 - 0 - 9 - RVLKCNVHL - RILGVLVHL - R+L VHL - - - - - 3 - gnl|BL_ORD_ID|156 - 11956|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 - 156 - 11 - - - 1 - 11.927 - 19 - 69.0218 - 1 - 7 - 4 - 10 - 0 - 0 - 5 - 5 - 0 - 7 - RVLKCNV - RVLCCYV - RVL C V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 994 - Query_994 - M_1464 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 995 - Query_995 - M_1465 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 996 - Query_996 - M_1466 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 997 - Query_997 - M_1467 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 998 - Query_998 - M_1468 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 999 - Query_999 - M_1469 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1000 - Query_1000 - M_1470 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1001 - Query_1001 - M_1471 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1002 - Query_1002 - M_1472 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1003 - Query_1003 - M_1473 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1004 - Query_1004 - M_1474 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1005 - Query_1005 - M_1475 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1006 - Query_1006 - M_1476 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1007 - Query_1007 - M_1477 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1008 - Query_1008 - M_1478 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1009 - Query_1009 - M_1479 - 9 - - - 1 - gnl|BL_ORD_ID|490 - 30946|HCV-1|AAA45676.1|Hepatitis C virus genotype 1|41856 - 490 - 20 - - - 1 - 12.6974 - 21 - 22.5677 - 4 - 9 - 14 - 19 - 0 - 0 - 3 - 6 - 0 - 6 - NLGIRI - DLGVRV - +LG+R+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1010 - Query_1010 - M_1480 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1011 - Query_1011 - M_1481 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1012 - Query_1012 - M_1482 - 9 - - - 1 - gnl|BL_ORD_ID|1432 - 116123|nucleocapsid protein|ABP49342.1|Influenza A virus (A/California/10/1978(H1N1))|425557 - 1432 - 9 - - - 1 - 11.927 - 19 - 82.8955 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - PFISRTMM - PFDKSTVM - PF T+M - - - - - 2 - gnl|BL_ORD_ID|1232 - 97467|nucleocapsid protein|ACP44251.1|Influenza A virus (A/Fujian/411/2002(H3N2))|293090 - 1232 - 9 - - - 1 - 11.927 - 19 - 94.432 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - PFISRTMM - PFEKSTIM - PF T+M - - - - - 3 - gnl|BL_ORD_ID|649 - 38471|nucleocapsid protein|ABC46569.1|Influenza A virus (A/Memphis/4/1980(H3N2))|383578 - 649 - 9 - - - 1 - 11.927 - 19 - 99.1366 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - PFISRTMM - PFEKSTVM - PF T+M - - - - - 4 - gnl|BL_ORD_ID|647 - 38466|nucleocapsid protein|ABF21284.1|Influenza A virus (A/Iran/1/1957(H2N2))|488233 - 647 - 9 - - - 1 - 11.5418 - 18 - 165.102 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - PFISRTMM - PFDKPTIM - PF T+M - - - - - 5 - gnl|BL_ORD_ID|648 - 38468|nucleoprotein|CAA24268.1|Influenza A virus (A/Puerto Rico/8/1934(H1N1))|211044 - 648 - 9 - - - 1 - 11.5418 - 18 - 181.349 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - PFISRTMM - PFDRTTIM - PF T+M - - - - - 6 - gnl|BL_ORD_ID|650 - 38472|nucleoprotein|AAV48837.1|Influenza A virus (A/Brevig Mission/1/1918(H1N1))|88776 - 650 - 9 - - - 1 - 11.5418 - 18 - 187.089 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - PFISRTMM - PFERATIM - PF T+M - - - - - 7 - gnl|BL_ORD_ID|1434 - 116136|nucleocapsid protein|ACS34671.1|Influenza A virus (A/Auckland/1/2009(H1N1))|642794 - 1434 - 9 - - - 1 - 11.1566 - 17 - 199.082 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - PFISRTMM - PFERATVM - PF T+M - - - - - 8 - gnl|BL_ORD_ID|1433 - 116127|Nucleoprotein|P15682.1|Influenza A virus (A/Wilson-Smith/1933(H1N1))|381518 - 1433 - 9 - - - 1 - 11.1566 - 17 - 291.863 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - PFISRTMM - PFDRPTIM - PF T+M - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1013 - Query_1013 - M_1483 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1014 - Query_1014 - M_1484 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1015 - Query_1015 - M_1485 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1016 - Query_1016 - M_1486 - 9 - - - 1 - gnl|BL_ORD_ID|1395 - 110394|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1395 - 32 - - - 1 - 13.4678 - 23 - 8.60866 - 1 - 6 - 6 - 11 - 0 - 0 - 4 - 4 - 0 - 6 - QAPLAP - QKPLCP - Q PL P - - - - - 2 - gnl|BL_ORD_ID|52 - 3889|||| - 52 - 9 - - - 1 - 13.0826 - 22 - 16.035 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 6 - 0 - 7 - APLAPTH - APVFPSH - AP+ P+H - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1017 - Query_1017 - M_1487 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1018 - Query_1018 - M_1488 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1019 - Query_1019 - M_1489 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1020 - Query_1020 - M_1490 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1021 - Query_1021 - M_1491 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1022 - Query_1022 - M_1492 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1023 - Query_1023 - M_1493 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1024 - Query_1024 - M_1494 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1025 - Query_1025 - M_1495 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1026 - Query_1026 - M_1496 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1027 - Query_1027 - M_1497 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1028 - Query_1028 - M_1498 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1029 - Query_1029 - M_1499 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1030 - Query_1030 - M_1500 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1031 - Query_1031 - M_1501 - 9 - - - 1 - gnl|BL_ORD_ID|755 - 50253|DNA polymerase|CAA10434.1|Hepatitis B virus|10407 - 755 - 10 - - - 1 - 12.6974 - 21 - 29.8889 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 6 - 0 - 6 - RAFSFS - QAFTFS - +AF+FS - - - - - 2 - gnl|BL_ORD_ID|539 - 32955|P protein|P31870.1|Hepatitis B virus|10407 - 539 - 15 - - - 1 - 12.6974 - 21 - 32.8422 - 1 - 6 - 2 - 7 - 0 - 0 - 4 - 6 - 0 - 6 - RAFSFS - QAFTFS - +AF+FS - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1032 - Query_1032 - M_1502 - 9 - - - 1 - gnl|BL_ORD_ID|494 - 31771|Nucleoprotein|P03418.1|Human respiratory syncytial virus A2|11259 - 494 - 14 - - - 1 - 11.5418 - 18 - 158.243 - 3 - 9 - 2 - 8 - 0 - 0 - 3 - 5 - 0 - 7 - MCNSLLV - LCGMLLI - +C LL+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1033 - Query_1033 - M_1503 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1034 - Query_1034 - M_1504 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1035 - Query_1035 - M_1505 - 9 - - - 1 - gnl|BL_ORD_ID|1173 - 79337|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 1173 - 15 - - - 1 - 11.927 - 19 - 66.2133 - 2 - 7 - 7 - 12 - 0 - 0 - 3 - 5 - 0 - 6 - IMPHAI - LLPHVI - ++PH I - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1036 - Query_1036 - M_1506 - 9 - - - 1 - gnl|BL_ORD_ID|2137 - 187106|Vpr protein|BAA93983.1|Human immunodeficiency virus 1|11676 - 2137 - 9 - - - 1 - 14.2382 - 25 - 4.1461 - 2 - 8 - 2 - 8 - 0 - 0 - 3 - 6 - 0 - 7 - LKHMPKI - VRHFPRI - ++H P+I - - - - - 2 - gnl|BL_ORD_ID|798 - 53148|Transcription activator BRLF1|P03209.1|Human herpesvirus 4 strain B95-8|10377 - 798 - 15 - - - 1 - 11.927 - 19 - 90.193 - 1 - 7 - 3 - 9 - 0 - 0 - 3 - 6 - 0 - 7 - LLKHMPK - LIKTLPR - L+K +P+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1037 - Query_1037 - M_1507 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1038 - Query_1038 - M_1508 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1039 - Query_1039 - M_1509 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1040 - Query_1040 - M_1510 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1041 - Query_1041 - M_1511 - 9 - - - 1 - gnl|BL_ORD_ID|838 - 55029|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 838 - 11 - - - 1 - 12.3122 - 20 - 44.3407 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 6 - 0 - 9 - GLIPPDATI - NLVPMVATV - L+P AT+ - - - - - 2 - gnl|BL_ORD_ID|722 - 44920|tegument protein pp65|YP_002608275.1|Human betaherpesvirus 5|10359 - 722 - 9 - - - 1 - 12.3122 - 20 - 60.6092 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 6 - 0 - 9 - GLIPPDATI - NLVPMVATV - L+P AT+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1042 - Query_1042 - M_1512 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1043 - Query_1043 - M_1513 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1044 - Query_1044 - M_1514 - 9 - - - 1 - gnl|BL_ORD_ID|2084 - 185447|polyprotein|AGK36298.1|Dengue virus 2|11060 - 2084 - 10 - - - 1 - 13.4678 - 23 - 11.1891 - 2 - 9 - 2 - 9 - 0 - 0 - 5 - 6 - 0 - 8 - TVLENLAV - NALDNLAV - L+NLAV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1045 - Query_1045 - M_1515 - 9 - - - 1 - gnl|BL_ORD_ID|516 - 32201|Gp160|Q0ED31|Human immunodeficiency virus 1|11676 - 516 - 9 - - - 1 - 14.6234 - 26 - 2.37398 - 1 - 9 - 1 - 9 - 0 - 0 - 6 - 6 - 0 - 9 - KPPPQCVTL - KLTPLCVTL - K P CVTL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1046 - Query_1046 - M_1516 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1047 - Query_1047 - M_1517 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1048 - Query_1048 - M_1518 - 9 - - - 1 - gnl|BL_ORD_ID|1769 - 155096|RL2|CAB06760.1|Human alphaherpesvirus 2|10310 - 1769 - 15 - - - 1 - 13.4678 - 23 - 8.30114 - 2 - 9 - 8 - 15 - 0 - 0 - 4 - 6 - 0 - 8 - CLEASIPL - CMKTWIPL - C++ IPL - - - - - 2 - gnl|BL_ORD_ID|1381 - 110125|E2 protein|ACS92695.1|Human papillomavirus type 16|333760 - 1381 - 10 - - - 1 - 13.4678 - 23 - 10.0795 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 7 - 0 - 9 - MCLEASIPL - ICEEASVTV - +C EAS+ + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1049 - Query_1049 - M_1519 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1050 - Query_1050 - M_1520 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1051 - Query_1051 - M_1521 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1052 - Query_1052 - M_1522 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1053 - Query_1053 - M_1523 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1054 - Query_1054 - M_1524 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1055 - Query_1055 - M_1525 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1056 - Query_1056 - M_1526 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1057 - Query_1057 - M_1527 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1058 - Query_1058 - M_1528 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1059 - Query_1059 - M_1529 - 9 - - - 1 - gnl|BL_ORD_ID|1289 - 102368|E2 protein|NP_751921.1|Hepatitis C virus subtype 1a|31646 - 1289 - 15 - - - 1 - 14.6234 - 26 - 2.26419 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 6 - 0 - 7 - KSGSPEY - RSGAPTY - +SG+P Y - - - - - 2 - gnl|BL_ORD_ID|1696 - 149098|E2 protein|NP_751921.1|Hepatitis C virus (isolate H77)|63746 - 1696 - 9 - - - 1 - 14.2382 - 25 - 2.80642 - 3 - 9 - 1 - 7 - 0 - 0 - 4 - 6 - 0 - 7 - KSGSPEY - RSGAPTY - +SG+P Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1060 - Query_1060 - M_1530 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1061 - Query_1061 - M_1531 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1062 - Query_1062 - M_1532 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1063 - Query_1063 - M_1533 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1064 - Query_1064 - M_1534 - 9 - - - 1 - gnl|BL_ORD_ID|2243 - 232152|rhoptry kinase family protein|AFO54841.1|Toxoplasma gondii type III|398031 - 2243 - 19 - - - 1 - 15.779 - 29 - 0.404157 - 1 - 8 - 4 - 11 - 0 - 0 - 5 - 5 - 0 - 8 - QPLHSLSV - QPFHSYGV - QP HS V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1065 - Query_1065 - M_1535 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1066 - Query_1066 - M_1536 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1067 - Query_1067 - M_1537 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1068 - Query_1068 - M_1538 - 9 - - - 1 - gnl|BL_ORD_ID|2013 - 183813|polyprotein|AGW21594.1|Dengue virus 1|11053 - 2013 - 10 - - - 1 - 12.3122 - 20 - 53.7901 - 2 - 8 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - PHPRRRR - PEPDRQR - P P R+R - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1069 - Query_1069 - M_1539 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1070 - Query_1070 - M_1540 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1071 - Query_1071 - M_1541 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1072 - Query_1072 - M_1542 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1073 - Query_1073 - M_1543 - 9 - - - 1 - gnl|BL_ORD_ID|1767 - 154980|tegument protein|CAB06735.1|Human alphaherpesvirus 2|10310 - 1767 - 15 - - - 1 - 11.927 - 19 - 78.5415 - 1 - 8 - 6 - 13 - 0 - 0 - 5 - 5 - 0 - 8 - RANGNPNP - RANELVNP - RAN NP - - - - - 2 - gnl|BL_ORD_ID|559 - 34598|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 559 - 15 - - - 1 - 11.5418 - 18 - 143.868 - 3 - 9 - 7 - 13 - 0 - 0 - 4 - 4 - 0 - 7 - NGNPNPT - NGYMEPT - NG PT - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1074 - Query_1074 - M_1544 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1075 - Query_1075 - M_1545 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1076 - Query_1076 - M_1546 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1077 - Query_1077 - M_1547 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1078 - Query_1078 - M_1548 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1079 - Query_1079 - M_1549 - 9 - - - 1 - gnl|BL_ORD_ID|1686 - 149052|E1 protein|NP_751920.1|Hepatitis C virus (isolate H77)|63746 - 1686 - 18 - - - 1 - 13.0826 - 22 - 19.4353 - 1 - 8 - 5 - 12 - 0 - 0 - 4 - 5 - 0 - 8 - FSLYRGWA - FSMVGNWA - FS+ WA - - - - - 2 - gnl|BL_ORD_ID|2312 - 423020|polyprotein|ACE82359.1|Hepatitis C virus genotype 1|41856 - 2312 - 9 - - - 1 - 11.927 - 19 - 71.5135 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 4 - 0 - 8 - SLYRGWAL - KLYISWCL - LY W L - - - - - 3 - gnl|BL_ORD_ID|164 - 12616|gag protein|AAV53308.1|Human immunodeficiency virus 1|11676 - 164 - 8 - - - 1 - 11.927 - 19 - 100.945 - 2 - 9 - 1 - 8 - 0 - 0 - 2 - 5 - 0 - 8 - SLYRGWAL - EIYKRWII - +Y+ W + - - - - - 4 - gnl|BL_ORD_ID|47 - 3026|polyprotein|CAB53095.1|Hepatitis C virus subtype 1b|31647 - 47 - 9 - - - 1 - 11.5418 - 18 - 155.038 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 5 - 0 - 8 - SLYRGWAL - ALYGVWPL - +LY W L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1080 - Query_1080 - M_1550 - 9 - - - 1 - gnl|BL_ORD_ID|1387 - 110227|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1387 - 33 - - - 1 - 13.853 - 24 - 8.26714 - 4 - 9 - 11 - 16 - 0 - 0 - 4 - 4 - 0 - 6 - GAPYVV - GNPYAV - G PY V - - - - - 2 - gnl|BL_ORD_ID|1400 - 110467|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1400 - 25 - - - 1 - 13.0826 - 22 - 17.2955 - 4 - 9 - 4 - 9 - 0 - 0 - 4 - 4 - 0 - 6 - GAPYVV - GNPYAV - G PY V - - - - - 3 - gnl|BL_ORD_ID|1397 - 110401|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1397 - 25 - - - 1 - 13.0826 - 22 - 21.086 - 4 - 9 - 19 - 24 - 0 - 0 - 4 - 4 - 0 - 6 - GAPYVV - GNPYAV - G PY V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1081 - Query_1081 - M_1551 - 9 - - - 1 - gnl|BL_ORD_ID|1121 - 74407|polyprotein|AAU89634.1|Hepatitis C virus subtype 2a|31649 - 1121 - 9 - - - 1 - 12.3122 - 20 - 44.8495 - 4 - 9 - 4 - 9 - 0 - 0 - 2 - 4 - 0 - 6 - HWNWII - RWEWVV - W W++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1082 - Query_1082 - M_1552 - 9 - - - 1 - gnl|BL_ORD_ID|1177 - 79506|E1 protein|BAA19893.1|Rubella virus|11041 - 1177 - 20 - - - 1 - 15.0086 - 27 - 1.42104 - 2 - 7 - 7 - 12 - 0 - 0 - 4 - 5 - 0 - 6 - SACWSF - AACWGF - +ACW F - - - - - 2 - gnl|BL_ORD_ID|1198 - 95298|Genome polyprotein|Q913V3.1|Hepatitis C virus (isolate 1)|11104 - 1198 - 9 - - - 1 - 12.6974 - 21 - 35.3877 - 2 - 6 - 4 - 8 - 0 - 0 - 3 - 4 - 0 - 5 - SACWS - GACWT - ACW+ - - - - - 3 - gnl|BL_ORD_ID|87 - 6430|polyprotein|BAB18810.1|Hepatitis C virus genotype 1|41856 - 87 - 9 - - - 1 - 12.6974 - 21 - 35.3877 - 2 - 6 - 4 - 8 - 0 - 0 - 3 - 4 - 0 - 5 - SACWS - GACWT - ACW+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1083 - Query_1083 - M_1553 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1084 - Query_1084 - M_1554 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1085 - Query_1085 - M_1555 - 9 - - - 1 - gnl|BL_ORD_ID|1400 - 110467|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1400 - 25 - - - 1 - 13.4678 - 23 - 11.7461 - 1 - 8 - 5 - 12 - 0 - 0 - 4 - 6 - 0 - 8 - DQYAICMK - NPYAVCDK - + YA+C K - - - - - 2 - gnl|BL_ORD_ID|1387 - 110227|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1387 - 33 - - - 1 - 13.0826 - 22 - 15.9056 - 1 - 8 - 12 - 19 - 0 - 0 - 4 - 6 - 0 - 8 - DQYAICMK - NPYAVCDK - + YA+C K - - - - - 3 - gnl|BL_ORD_ID|2035 - 184412|envelope protein|AGW23591.1|Dengue virus 3|11069 - 2035 - 10 - - - 1 - 12.6974 - 21 - 36.0093 - 2 - 7 - 5 - 10 - 0 - 0 - 3 - 5 - 0 - 6 - QYAICM - SYAMCL - YA+C+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1086 - Query_1086 - M_1556 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1087 - Query_1087 - M_1557 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1088 - Query_1088 - M_1558 - 9 - - - 1 - gnl|BL_ORD_ID|1370 - 108230|polyprotein|AAF65953.1|Hepatitis C virus|11103 - 1370 - 10 - - - 1 - 14.2382 - 25 - 3.62465 - 1 - 6 - 4 - 9 - 0 - 0 - 5 - 5 - 0 - 6 - KAYGRD - KAYGTD - KAYG D - - - - - 2 - gnl|BL_ORD_ID|1339 - 107925|polyprotein|AAF65964.1|Hepatitis C virus|11103 - 1339 - 10 - - - 1 - 12.6974 - 21 - 32.5356 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - KAYGRD - KAHGTD - KA+G D - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1089 - Query_1089 - M_1559 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1090 - Query_1090 - M_1560 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1091 - Query_1091 - M_1561 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1092 - Query_1092 - M_1562 - 9 - - - 1 - gnl|BL_ORD_ID|1769 - 155096|RL2|CAB06760.1|Human alphaherpesvirus 2|10310 - 1769 - 15 - - - 1 - 11.927 - 19 - 86.1406 - 1 - 7 - 4 - 10 - 0 - 0 - 2 - 4 - 0 - 7 - YCFGCLS - FCIPCMK - +C C+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1093 - Query_1093 - M_1563 - 9 - - - 1 - gnl|BL_ORD_ID|1050 - 69714|Large envelope protein|SRC279965|Hepatitis B virus|10407 - 1050 - 9 - - - 1 - 12.3122 - 20 - 53.938 - 4 - 9 - 4 - 9 - 0 - 0 - 3 - 5 - 0 - 6 - GGFFVI - AGFFIL - GFF++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1094 - Query_1094 - M_1564 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1095 - Query_1095 - M_1565 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1096 - Query_1096 - M_1566 - 9 - - - 1 - gnl|BL_ORD_ID|1186 - 93431|pre-C/C protein|ABY54138.1|Hepatitis B virus|10407 - 1186 - 20 - - - 1 - 11.5418 - 18 - 98.2529 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 6 - 0 - 9 - RLMHQLLVI - QLFHLCLII - +L H L+I - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1097 - Query_1097 - M_1567 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1098 - Query_1098 - M_1568 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1099 - Query_1099 - M_1569 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1100 - Query_1100 - M_1570 - 9 - - - 1 - gnl|BL_ORD_ID|383 - 23601|Genome polyprotein|SRC279960|Hepatitis C virus (isolate H77)|63746 - 383 - 21 - - - 1 - 14.2382 - 25 - 3.66708 - 4 - 9 - 3 - 8 - 0 - 0 - 5 - 5 - 0 - 6 - PAGHLV - PAGHAV - PAGH V - - - - - 2 - gnl|BL_ORD_ID|597 - 37127|polyprotein|AAY82030.1|Hepatitis C virus genotype 1|41856 - 597 - 9 - - - 1 - 13.853 - 24 - 5.00793 - 4 - 9 - 4 - 9 - 0 - 0 - 5 - 5 - 0 - 6 - PAGHLV - PAGHAV - PAGH V - - - - - 3 - gnl|BL_ORD_ID|598 - 37136|Genome polyprotein|P27958.3|Hepatitis C virus|11103 - 598 - 9 - - - 1 - 12.6974 - 21 - 38.5226 - 4 - 9 - 4 - 9 - 0 - 0 - 4 - 4 - 0 - 6 - PAGHLV - PTGHAV - P GH V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1101 - Query_1101 - M_1571 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1102 - Query_1102 - M_1572 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1103 - Query_1103 - M_1573 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1104 - Query_1104 - M_1574 - 9 - - - 1 - gnl|BL_ORD_ID|320 - 21000|glutamine synthetase GLNA1 (glutamine synthase) (GS-I)|NP_216736.1|Mycobacterium tuberculosis|1773 - 320 - 9 - - - 1 - 11.5418 - 18 - 150.225 - 1 - 8 - 2 - 9 - 0 - 0 - 3 - 6 - 0 - 8 - MVHLVPAL - LLHHAPSL - ++H P+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1105 - Query_1105 - M_1575 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1106 - Query_1106 - M_1576 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1107 - Query_1107 - M_1577 - 9 - - - 1 - gnl|BL_ORD_ID|10 - 1000|glycoprotein gp35/37|AAC59622.1|Human gammaherpesvirus 8|37296 - 10 - 15 - - - 1 - 13.0826 - 22 - 21.0678 - 1 - 9 - 5 - 13 - 0 - 0 - 4 - 5 - 0 - 9 - NHLNIAWEL - THLYILWAV - HL I W + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1108 - Query_1108 - M_1578 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1109 - Query_1109 - M_1579 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1110 - Query_1110 - M_1580 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1111 - Query_1111 - M_1581 - 9 - - - 1 - gnl|BL_ORD_ID|1438 - 120093|unnamed protein product|CAA33016.1|Rubella virus|11041 - 1438 - 21 - - - 1 - 11.5418 - 18 - 101.431 - 4 - 8 - 11 - 15 - 0 - 0 - 4 - 4 - 0 - 5 - PPPLT - PPPAT - PPP T - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1112 - Query_1112 - M_1582 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1113 - Query_1113 - M_1583 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1114 - Query_1114 - M_1584 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1115 - Query_1115 - M_1585 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1116 - Query_1116 - M_1586 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1117 - Query_1117 - M_1587 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1118 - Query_1118 - M_1588 - 9 - - - 1 - gnl|BL_ORD_ID|1561 - 141277|transactivating tegument protein VP16|NP_044650.1|Human alphaherpesvirus 1|10298 - 1561 - 10 - - - 1 - 12.6974 - 21 - 26.0802 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 5 - 0 - 8 - FTQYLGLS - FTDALGID - FT LG+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1119 - Query_1119 - M_1589 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1120 - Query_1120 - M_1590 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1121 - Query_1121 - M_1591 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1122 - Query_1122 - M_1592 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1123 - Query_1123 - M_1593 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1124 - Query_1124 - M_1594 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1125 - Query_1125 - M_1595 - 9 - - - 1 - gnl|BL_ORD_ID|1392 - 110335|E7|AAD33253.1|Human papillomavirus type 16|333760 - 1392 - 32 - - - 1 - 14.2382 - 25 - 4.6455 - 2 - 7 - 12 - 17 - 0 - 0 - 4 - 6 - 0 - 6 - LLDLRP - MLDLQP - +LDL+P - - - - - 2 - gnl|BL_ORD_ID|1138 - 75075|E7 protein|ABL96585.1|Human papillomavirus type 16|333760 - 1138 - 10 - - - 1 - 13.853 - 24 - 6.08483 - 2 - 8 - 2 - 8 - 0 - 0 - 4 - 6 - 0 - 7 - LLDLRPS - MLDLQPE - +LDL+P - - - - - 3 - gnl|BL_ORD_ID|1823 - 178351|Protein E7|P03129.1|Human papillomavirus type 16|333760 - 1823 - 15 - - - 1 - 13.853 - 24 - 6.40908 - 2 - 8 - 8 - 14 - 0 - 0 - 4 - 6 - 0 - 7 - LLDLRPS - MLDLQPE - +LDL+P - - - - - 4 - gnl|BL_ORD_ID|1137 - 75074|Protein E7|P03129.1|Human papillomavirus type 16|333760 - 1137 - 9 - - - 1 - 13.853 - 24 - 6.83656 - 2 - 8 - 2 - 8 - 0 - 0 - 4 - 6 - 0 - 7 - LLDLRPS - MLDLQPE - +LDL+P - - - - - 5 - gnl|BL_ORD_ID|1117 - 74288|Protein E7|P36831.1|Human papillomavirus type 52|10618 - 1117 - 10 - - - 1 - 13.4678 - 23 - 9.07951 - 2 - 8 - 2 - 8 - 0 - 0 - 4 - 6 - 0 - 7 - LLDLRPS - ILDLQPE - +LDL+P - - - - - 6 - gnl|BL_ORD_ID|1157 - 76334|Protein E7|P17387.1|Human papillomavirus type 31|10585 - 1157 - 10 - - - 1 - 13.4678 - 23 - 12.2057 - 2 - 8 - 2 - 8 - 0 - 0 - 4 - 6 - 0 - 7 - LLDLRPS - VLDLQPE - +LDL+P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1126 - Query_1126 - M_1596 - 9 - - - 1 - gnl|BL_ORD_ID|1688 - 149060|E2 protein|NP_751921.1|Hepatitis C virus (isolate H77)|63746 - 1688 - 9 - - - 1 - 12.6974 - 21 - 26.0147 - 1 - 6 - 4 - 9 - 0 - 0 - 4 - 4 - 0 - 6 - AVYSTC - ATYSRC - A YS C - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1127 - Query_1127 - M_1597 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1128 - Query_1128 - M_1598 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1129 - Query_1129 - M_1599 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1130 - Query_1130 - M_1600 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1131 - Query_1131 - M_1601 - 9 - - - 1 - gnl|BL_ORD_ID|2137 - 187106|Vpr protein|BAA93983.1|Human immunodeficiency virus 1|11676 - 2137 - 9 - - - 1 - 13.853 - 24 - 5.74926 - 3 - 9 - 2 - 8 - 0 - 0 - 3 - 6 - 0 - 7 - LKHMPKI - VRHFPRI - ++H P+I - - - - - 2 - gnl|BL_ORD_ID|798 - 53148|Transcription activator BRLF1|P03209.1|Human herpesvirus 4 strain B95-8|10377 - 798 - 15 - - - 1 - 11.927 - 19 - 90.193 - 2 - 8 - 3 - 9 - 0 - 0 - 3 - 6 - 0 - 7 - LLKHMPK - LIKTLPR - L+K +P+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1132 - Query_1132 - M_1602 - 9 - - - 1 - gnl|BL_ORD_ID|2136 - 187086|polyprotein|ABG67747.1|West Nile virus|11082 - 2136 - 9 - - - 1 - 12.6974 - 21 - 33.058 - 1 - 7 - 3 - 9 - 0 - 0 - 5 - 6 - 0 - 7 - LSLTGLQ - LSLIGLK - LSL GL+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1133 - Query_1133 - M_1603 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1134 - Query_1134 - M_1604 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1135 - Query_1135 - M_1605 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1136 - Query_1136 - M_1606 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1137 - Query_1137 - M_1607 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1138 - Query_1138 - M_1608 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1139 - Query_1139 - M_1609 - 9 - - - 1 - gnl|BL_ORD_ID|310 - 20787|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 - 310 - 10 - - - 1 - 12.3122 - 20 - 42.6014 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 4 - 0 - 8 - SFCPLCHN - GLCPHCIN - CP C N - - - - - 2 - gnl|BL_ORD_ID|309 - 20786|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 - 309 - 9 - - - 1 - 12.3122 - 20 - 51.2985 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 4 - 0 - 8 - SFCPLCHN - GLCPHCIN - CP C N - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1140 - Query_1140 - M_1610 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1141 - Query_1141 - M_1611 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1142 - Query_1142 - M_1612 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1143 - Query_1143 - M_1613 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1144 - Query_1144 - M_1614 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1145 - Query_1145 - M_1615 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1146 - Query_1146 - M_1616 - 9 - - - 1 - gnl|BL_ORD_ID|1122 - 74545|TcP2beta|CAA52943.1|Trypanosoma cruzi|5693 - 1122 - 10 - - - 1 - 12.6974 - 21 - 37.8768 - 2 - 7 - 1 - 6 - 0 - 0 - 5 - 5 - 0 - 6 - YLVAYA - YLAAYA - YL AYA - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1147 - Query_1147 - M_1617 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1148 - Query_1148 - M_1618 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1149 - Query_1149 - M_1619 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1150 - Query_1150 - M_1620 - 9 - - - 1 - gnl|BL_ORD_ID|703 - 42897|RNA polymerase beta-subunit|AAA21416.1|Mycobacterium tuberculosis|1773 - 703 - 9 - - - 1 - 14.2382 - 25 - 4.1461 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 6 - 0 - 8 - VRYAGPLY - MTYAAPLF - + YA PL+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1151 - Query_1151 - M_1621 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1152 - Query_1152 - M_1622 - 9 - - - 1 - gnl|BL_ORD_ID|2108 - 186175|polyprotein|AFY10053.1|Dengue virus 3|11069 - 2108 - 10 - - - 1 - 13.853 - 24 - 6.08483 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 6 - 0 - 6 - TFRDVA - TWRDMA - T+RD+A - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1153 - Query_1153 - M_1623 - 9 - - - 1 - gnl|BL_ORD_ID|471 - 28594|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 - 471 - 20 - - - 1 - 13.853 - 24 - 4.57317 - 1 - 9 - 9 - 17 - 0 - 0 - 5 - 6 - 0 - 9 - DEKDLWEYI - DQKSLENYI - D+K L YI - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1154 - Query_1154 - M_1624 - 9 - - - 1 - gnl|BL_ORD_ID|803 - 53405|||| - 803 - 15 - - - 1 - 15.3938 - 28 - 0.751673 - 1 - 9 - 2 - 10 - 0 - 0 - 6 - 6 - 0 - 9 - DPADPTRDL - DPAKPARLL - DPA P R L - - - - - 2 - gnl|BL_ORD_ID|694 - 42295|Circumsporozoite protein precursor|P02893.1|Plasmodium falciparum|5833 - 694 - 9 - - - 1 - 13.853 - 24 - 4.6749 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 6 - 0 - 8 - PADPTRDL - PNDPNRNV - P DP R++ - - - - - 3 - gnl|BL_ORD_ID|765 - 51311|X protein|ABR68906.1|Hepatitis B virus|10407 - 765 - 9 - - - 1 - 13.0826 - 22 - 17.1877 - 4 - 9 - 3 - 8 - 0 - 0 - 4 - 5 - 0 - 6 - DPTRDL - DPARDV - DP RD+ - - - - - 4 - gnl|BL_ORD_ID|448 - 27241|Spike glycoprotein precursor|P59594.1|SARS coronavirus|227859 - 448 - 9 - - - 1 - 11.927 - 19 - 82.8955 - 1 - 6 - 4 - 9 - 0 - 0 - 4 - 4 - 0 - 6 - DPADPT - DPLKPT - DP PT - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1155 - Query_1155 - M_1625 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1156 - Query_1156 - M_1626 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1157 - Query_1157 - M_1627 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1158 - Query_1158 - M_1628 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1159 - Query_1159 - M_1629 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1160 - Query_1160 - M_1630 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1161 - Query_1161 - M_1631 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1162 - Query_1162 - M_1632 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1163 - Query_1163 - M_1633 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1164 - Query_1164 - M_1634 - 9 - - - 1 - gnl|BL_ORD_ID|1634 - 146260|polyprotein|ADF97231.1|Hepatitis C virus subtype 3a|356426 - 1634 - 18 - - - 1 - 13.0826 - 22 - 13.1042 - 4 - 9 - 5 - 10 - 0 - 0 - 4 - 4 - 0 - 6 - PTLAMY - PALQMY - P L MY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1165 - Query_1165 - M_1635 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1166 - Query_1166 - M_1636 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1167 - Query_1167 - M_1637 - 9 - - - 1 - gnl|BL_ORD_ID|811 - 54342|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 - 811 - 20 - - - 1 - 13.0826 - 22 - 16.1327 - 1 - 6 - 8 - 13 - 0 - 0 - 5 - 5 - 0 - 6 - LSLGAP - LSLGDP - LSLG P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1168 - Query_1168 - M_1638 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1169 - Query_1169 - M_1639 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1170 - Query_1170 - M_1640 - 9 - - - 1 - gnl|BL_ORD_ID|83 - 6094|Genome polyprotein|Q81495.3|Hepatitis C virus (isolate HCV-K3a/650)|356416 - 83 - 15 - - - 1 - 10.7714 - 16 - 331.488 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 5 - 0 - 9 - CSDGSDEDA - CDDCHAQDA - C D +DA - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1171 - Query_1171 - M_1641 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1172 - Query_1172 - M_1642 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1173 - Query_1173 - M_1643 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1174 - Query_1174 - M_1644 - 9 - - - 1 - gnl|BL_ORD_ID|376 - 23288|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 - 376 - 15 - - - 1 - 12.6974 - 21 - 22.1438 - 1 - 5 - 7 - 11 - 0 - 0 - 3 - 4 - 0 - 5 - YPDWI - YQDWL - Y DW+ - - - - - 2 - gnl|BL_ORD_ID|1256 - 98244|trans-sialidase, putative|EAN80840.1|Trypanosoma cruzi|5693 - 1256 - 9 - - - 1 - 12.3122 - 20 - 43.3628 - 4 - 8 - 2 - 6 - 0 - 0 - 3 - 4 - 0 - 5 - WIRDN - WLTDN - W+ DN - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1175 - Query_1175 - M_1645 - 9 - - - 1 - gnl|BL_ORD_ID|866 - 56620|Nef protein|Q9YYU8|Human immunodeficiency virus 1|11676 - 866 - 10 - - - 1 - 13.853 - 24 - 7.36741 - 4 - 9 - 5 - 10 - 0 - 0 - 4 - 5 - 0 - 6 - SFGKCF - TFGWCF - +FG CF - - - - - 2 - gnl|BL_ORD_ID|2214 - 193060|Nef protein|Q9YYU3|Human immunodeficiency virus 1|11676 - 2214 - 10 - - - 1 - 13.4678 - 23 - 9.07951 - 4 - 9 - 5 - 10 - 0 - 0 - 4 - 5 - 0 - 6 - SFGKCF - TFGWCF - +FG CF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1176 - Query_1176 - M_1646 - 9 - - - 1 - gnl|BL_ORD_ID|627 - 37573|E7 protein|ABL96585.1|Human papillomavirus type 16|333760 - 627 - 9 - - - 1 - 13.0826 - 22 - 21.1561 - 3 - 8 - 4 - 9 - 0 - 0 - 4 - 6 - 0 - 6 - GSLGII - GTLGIV - G+LGI+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1177 - Query_1177 - M_1647 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1178 - Query_1178 - M_1648 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1179 - Query_1179 - M_1649 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1180 - Query_1180 - M_1650 - 9 - - - 1 - gnl|BL_ORD_ID|1956 - 181733|Antigen 85-B|P0C5B9.1|Mycobacterium tuberculosis|1773 - 1956 - 40 - - - 1 - 11.5418 - 18 - 88.9423 - 2 - 9 - 10 - 17 - 0 - 0 - 4 - 5 - 0 - 8 - SWLTPLMI - AWGRRLMI - +W LMI - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1181 - Query_1181 - M_1651 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1182 - Query_1182 - M_1652 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1183 - Query_1183 - M_1653 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1184 - Query_1184 - M_1654 - 9 - - - 1 - gnl|BL_ORD_ID|2150 - 189286|||| - 2150 - 9 - - - 1 - 13.4678 - 23 - 8.87313 - 1 - 9 - 1 - 9 - 0 - 0 - 6 - 7 - 0 - 9 - SLYSLDATL - SLYNTAATL - SLY+ ATL - - - - - 2 - gnl|BL_ORD_ID|1463 - 127001|gag polyprotein|BAA00992.1|Human immunodeficiency virus 1|11676 - 1463 - 10 - - - 1 - 13.0826 - 22 - 14.0252 - 1 - 9 - 2 - 10 - 0 - 0 - 6 - 7 - 0 - 9 - SLYSLDATL - SLYNTVATL - SLY+ ATL - - - - - 3 - gnl|BL_ORD_ID|1453 - 126490|Gag protein|Q1KW74|Human immunodeficiency virus 1|11676 - 1453 - 10 - - - 1 - 13.0826 - 22 - 14.5203 - 1 - 9 - 2 - 10 - 0 - 0 - 6 - 7 - 0 - 9 - SLYSLDATL - SLYNTVATL - SLY+ ATL - - - - - 4 - gnl|BL_ORD_ID|2205 - 190962|gag polyprotein|BAB88540.1|Human immunodeficiency virus 1|11676 - 2205 - 10 - - - 1 - 13.0826 - 22 - 15.0326 - 1 - 9 - 2 - 10 - 0 - 0 - 6 - 7 - 0 - 9 - SLYSLDATL - SLYNTIATL - SLY+ ATL - - - - - 5 - gnl|BL_ORD_ID|2199 - 190827|gag protein|AAN08336.1|Human immunodeficiency virus 1|11676 - 2199 - 10 - - - 1 - 13.0826 - 22 - 15.5626 - 1 - 9 - 2 - 10 - 0 - 0 - 6 - 7 - 0 - 9 - SLYSLDATL - SLYNTIATL - SLY+ ATL - - - - - 6 - gnl|BL_ORD_ID|1464 - 127002|gag protein|AAV53342.1|Human immunodeficiency virus 1|11676 - 1464 - 11 - - - 1 - 13.0826 - 22 - 15.7745 - 1 - 9 - 2 - 10 - 0 - 0 - 6 - 7 - 0 - 9 - SLYSLDATL - SLYNTVATL - SLY+ ATL - - - - - 7 - gnl|BL_ORD_ID|1454 - 126491|gag protein|AAV53216.1|Human immunodeficiency virus 1|11676 - 1454 - 11 - - - 1 - 13.0826 - 22 - 16.0488 - 1 - 9 - 2 - 10 - 0 - 0 - 6 - 7 - 0 - 9 - SLYSLDATL - SLYNTVATL - SLY+ ATL - - - - - 8 - gnl|BL_ORD_ID|913 - 59613|Gag polyprotein|P03347.3|Human immunodeficiency virus 1|11676 - 913 - 9 - - - 1 - 13.0826 - 22 - 16.3158 - 1 - 9 - 1 - 9 - 0 - 0 - 6 - 7 - 0 - 9 - SLYSLDATL - SLYNTVATL - SLY+ ATL - - - - - 9 - gnl|BL_ORD_ID|1461 - 126999|gag polyprotein|BAB88540.1|Human immunodeficiency virus 1|11676 - 1461 - 11 - - - 1 - 13.0826 - 22 - 16.3278 - 1 - 9 - 2 - 10 - 0 - 0 - 6 - 7 - 0 - 9 - SLYSLDATL - SLYNTIATL - SLY+ ATL - - - - - 10 - gnl|BL_ORD_ID|2152 - 189288|gag protein|AAV53168.1|Human immunodeficiency virus 1|11676 - 2152 - 9 - - - 1 - 13.0826 - 22 - 17.1877 - 1 - 9 - 1 - 9 - 0 - 0 - 6 - 7 - 0 - 9 - SLYSLDATL - SLYNTIATL - SLY+ ATL - - - - - 11 - gnl|BL_ORD_ID|1451 - 126488|gag protein|AAV53168.1|Human immunodeficiency virus 1|11676 - 1451 - 11 - - - 1 - 13.0826 - 22 - 17.1933 - 1 - 9 - 2 - 10 - 0 - 0 - 6 - 7 - 0 - 9 - SLYSLDATL - SLYNTIATL - SLY+ ATL - - - - - 12 - gnl|BL_ORD_ID|2211 - 190980|gag protein|AAV53216.1|Human immunodeficiency virus 1|11676 - 2211 - 10 - - - 1 - 13.0826 - 22 - 18.8216 - 1 - 9 - 1 - 9 - 0 - 0 - 6 - 7 - 0 - 9 - SLYSLDATL - SLYNTVATL - SLY+ ATL - - - - - 13 - gnl|BL_ORD_ID|2209 - 190978|gag protein|AAV53168.1|Human immunodeficiency virus 1|11676 - 2209 - 10 - - - 1 - 13.0826 - 22 - 19.4818 - 1 - 9 - 1 - 9 - 0 - 0 - 6 - 7 - 0 - 9 - SLYSLDATL - SLYNTIATL - SLY+ ATL - - - - - 14 - gnl|BL_ORD_ID|2160 - 189297|||| - 2160 - 9 - - - 1 - 12.6974 - 21 - 23.4633 - 1 - 9 - 1 - 9 - 0 - 0 - 6 - 6 - 0 - 9 - SLYSLDATL - SLYQTVATL - SLY ATL - - - - - 15 - gnl|BL_ORD_ID|2149 - 189285|gag protein|AAK30999.1|Human immunodeficiency virus 1|11676 - 2149 - 9 - - - 1 - 12.3122 - 20 - 41.221 - 1 - 9 - 1 - 9 - 0 - 0 - 6 - 7 - 0 - 9 - SLYSLDATL - SLYNSVATL - SLY+ ATL - - - - - 16 - gnl|BL_ORD_ID|2161 - 189300|gag polyprotein|BAB88548.1|Human immunodeficiency virus 1|11676 - 2161 - 9 - - - 1 - 12.3122 - 20 - 52.1643 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 7 - 0 - 9 - SLYSLDATL - SVYNTVATL - S+Y+ ATL - - - - - 17 - gnl|BL_ORD_ID|2145 - 189204|||| - 2145 - 9 - - - 1 - 12.3122 - 20 - 64.7664 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 7 - 0 - 9 - SLYSLDATL - ALYNTVATL - +LY+ ATL - - - - - 18 - gnl|BL_ORD_ID|1458 - 126995|gag polyprotein|BAB19171.1|Human immunodeficiency virus 1|11676 - 1458 - 10 - - - 1 - 12.3122 - 20 - 65.5527 - 1 - 9 - 2 - 10 - 0 - 0 - 5 - 7 - 0 - 9 - SLYSLDATL - SLFNTVATL - SL++ ATL - - - - - 19 - gnl|BL_ORD_ID|1447 - 126484|gag protein|AAW03034.1|Human immunodeficiency virus 1|11676 - 1447 - 10 - - - 1 - 11.927 - 19 - 66.6359 - 1 - 9 - 2 - 10 - 0 - 0 - 5 - 7 - 0 - 9 - SLYSLDATL - SLFNTVATL - SL++ ATL - - - - - 20 - gnl|BL_ORD_ID|2202 - 190959|gag polyprotein|BAB19174.1|Human immunodeficiency virus 1|11676 - 2202 - 10 - - - 1 - 11.927 - 19 - 67.736 - 1 - 9 - 2 - 10 - 0 - 0 - 5 - 7 - 0 - 9 - SLYSLDATL - SLFNTIATL - SL++ ATL - - - - - 21 - gnl|BL_ORD_ID|2198 - 190826|gag polyprotein|CAB81949.1|Human immunodeficiency virus 1|11676 - 2198 - 10 - - - 1 - 11.927 - 19 - 68.8532 - 1 - 9 - 2 - 10 - 0 - 0 - 5 - 7 - 0 - 9 - SLYSLDATL - SLFNTIATL - SL++ ATL - - - - - 22 - gnl|BL_ORD_ID|1845 - 180191|gag polyprotein|BAB19174.1|Human immunodeficiency virus 1|11676 - 1845 - 9 - - - 1 - 11.927 - 19 - 80.227 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 7 - 0 - 9 - SLYSLDATL - SLFNTIATL - SL++ ATL - - - - - 23 - gnl|BL_ORD_ID|1475 - 131070|Gag protein|Q9IN85|HIV-1 M:A|505184 - 1475 - 9 - - - 1 - 11.927 - 19 - 80.227 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 7 - 0 - 9 - SLYSLDATL - SLFNTVATL - SL++ ATL - - - - - 24 - gnl|BL_ORD_ID|1844 - 180168|gag protein|ABO14878.1|Human immunodeficiency virus 1|11676 - 1844 - 9 - - - 1 - 11.927 - 19 - 81.5509 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 7 - 0 - 9 - SLYSLDATL - SLFNAVATL - SL++ ATL - - - - - 25 - gnl|BL_ORD_ID|1459 - 126996|Gag protein|Q9YYH6|Human immunodeficiency virus 1|11676 - 1459 - 11 - - - 1 - 11.927 - 19 - 86.4589 - 1 - 9 - 2 - 10 - 0 - 0 - 5 - 7 - 0 - 9 - SLYSLDATL - SLFNTVATL - SL++ ATL - - - - - 26 - gnl|BL_ORD_ID|1448 - 126485|gag protein|AAW03034.1|Human immunodeficiency virus 1|11676 - 1448 - 11 - - - 1 - 11.927 - 19 - 87.8512 - 1 - 9 - 2 - 10 - 0 - 0 - 5 - 7 - 0 - 9 - SLYSLDATL - SLFNTVATL - SL++ ATL - - - - - 27 - gnl|BL_ORD_ID|1456 - 126993|gag polyprotein|BAB19174.1|Human immunodeficiency virus 1|11676 - 1456 - 11 - - - 1 - 11.927 - 19 - 89.2645 - 1 - 9 - 2 - 10 - 0 - 0 - 5 - 7 - 0 - 9 - SLYSLDATL - SLFNTIATL - SL++ ATL - - - - - 28 - gnl|BL_ORD_ID|1444 - 126481|gag polyprotein p17 region|BAA83653.1|Human immunodeficiency virus 1|11676 - 1444 - 11 - - - 1 - 11.927 - 19 - 89.2645 - 1 - 9 - 2 - 10 - 0 - 0 - 5 - 7 - 0 - 9 - SLYSLDATL - SLFNTIATL - SL++ ATL - - - - - 29 - gnl|BL_ORD_ID|2207 - 190974|gag polyprotein|BAB19174.1|Human immunodeficiency virus 1|11676 - 2207 - 10 - - - 1 - 11.927 - 19 - 99.9004 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 7 - 0 - 9 - SLYSLDATL - SLFNTIATL - SL++ ATL - - - - - 30 - gnl|BL_ORD_ID|1468 - 127083|Gag protein|Q9YYH6|Human immunodeficiency virus 1|11676 - 1468 - 10 - - - 1 - 11.927 - 19 - 99.9004 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 7 - 0 - 9 - SLYSLDATL - SLFNTVATL - SL++ ATL - - - - - 31 - gnl|BL_ORD_ID|2148 - 189280|||| - 2148 - 9 - - - 1 - 11.5418 - 18 - 152.614 - 1 - 9 - 1 - 9 - 0 - 0 - 6 - 6 - 0 - 9 - SLYSLDATL - SLYLTVATL - SLY ATL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1185 - Query_1185 - M_1655 - 9 - - - 1 - gnl|BL_ORD_ID|634 - 37830|polyprotein|BAB18806.1|Hepatitis C virus subtype 1b|31647 - 634 - 9 - - - 1 - 12.3122 - 20 - 62.655 - 1 - 6 - 2 - 7 - 0 - 0 - 3 - 5 - 0 - 6 - FTTTQW - LSTTEW - +TT+W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1186 - Query_1186 - M_1656 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1187 - Query_1187 - M_1657 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1188 - Query_1188 - M_1658 - 9 - - - 1 - gnl|BL_ORD_ID|716 - 44214|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 - 716 - 11 - - - 1 - 13.4678 - 23 - 7.61059 - 1 - 9 - 3 - 11 - 0 - 0 - 5 - 6 - 0 - 9 - EMFQRYSAF - EFFTKNSAF - E F + SAF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1189 - Query_1189 - M_1659 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1190 - Query_1190 - M_1660 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1191 - Query_1191 - M_1661 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1192 - Query_1192 - M_1662 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1193 - Query_1193 - M_1663 - 9 - - - 1 - gnl|BL_ORD_ID|990 - 65497|HCV-1|AAA45676.1|Hepatitis C virus genotype 1|41856 - 990 - 20 - - - 1 - 12.3122 - 20 - 40.7919 - 2 - 7 - 14 - 19 - 0 - 0 - 4 - 4 - 0 - 6 - NDPELP - NTPGLP - N P LP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1194 - Query_1194 - M_1664 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1195 - Query_1195 - M_1665 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1196 - Query_1196 - M_1666 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1197 - Query_1197 - M_1667 - 9 - - - 1 - gnl|BL_ORD_ID|1950 - 181035|||| - 1950 - 44 - - - 1 - 10.7714 - 16 - 169.864 - 3 - 9 - 13 - 19 - 0 - 0 - 3 - 5 - 0 - 7 - FPYMGEV - FPGGGQI - FP G++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1198 - Query_1198 - M_1668 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1199 - Query_1199 - M_1669 - 9 - - - 1 - gnl|BL_ORD_ID|1409 - 110982|E6 protein|CAB45108.1|Human papillomavirus type 16|333760 - 1409 - 10 - - - 1 - 13.0826 - 22 - 17.5659 - 3 - 8 - 2 - 7 - 0 - 0 - 4 - 4 - 0 - 6 - YQKQLC - YNKPLC - Y K LC - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1200 - Query_1200 - M_1670 - 9 - - - 1 - gnl|BL_ORD_ID|741 - 47760|EBNA-1 protein|Q777E1|Human gammaherpesvirus 4|10376 - 741 - 15 - - - 1 - 13.0826 - 22 - 14.3275 - 2 - 9 - 2 - 9 - 0 - 0 - 5 - 5 - 0 - 8 - ATGPGEVL - GTGPGNGL - TGPG L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1201 - Query_1201 - M_1671 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1202 - Query_1202 - M_1672 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1203 - Query_1203 - M_1673 - 9 - - - 1 - gnl|BL_ORD_ID|2305 - 422999|polyprotein|ABD97104.1|Hepatitis C virus genotype 3|356114 - 2305 - 9 - - - 1 - 11.1566 - 17 - 211.79 - 1 - 7 - 3 - 9 - 0 - 0 - 4 - 5 - 0 - 7 - FVVFSFF - LVLFGFF - V+F FF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1204 - Query_1204 - M_1674 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1205 - Query_1205 - M_1675 - 9 - - - 1 - gnl|BL_ORD_ID|654 - 38724|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 654 - 20 - - - 1 - 15.0086 - 27 - 1.19565 - 2 - 9 - 4 - 11 - 0 - 0 - 4 - 6 - 0 - 8 - TLRWYLAM - TLRWFFNL - TLRW+ + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1206 - Query_1206 - M_1676 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1207 - Query_1207 - M_1677 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1208 - Query_1208 - M_1678 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1209 - Query_1209 - M_1679 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1210 - Query_1210 - M_1680 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1211 - Query_1211 - M_1681 - 9 - - - 1 - gnl|BL_ORD_ID|1719 - 150399|polyprotein|AGV76873.1|Dengue virus 2|11060 - 1719 - 10 - - - 1 - 16.5494 - 31 - 0.283519 - 2 - 9 - 2 - 9 - 0 - 0 - 5 - 6 - 0 - 8 - QMENNGWV - QMENKAWL - QMEN W+ - - - - - 2 - gnl|BL_ORD_ID|2040 - 184467|polyprotein|AGO67248.1|Dengue virus 2|11060 - 2040 - 10 - - - 1 - 15.779 - 29 - 0.499796 - 2 - 9 - 3 - 10 - 0 - 0 - 4 - 6 - 0 - 8 - QMENNGWV - QMEDKAWL - QME+ W+ - - - - - 3 - gnl|BL_ORD_ID|686 - 41407|Envelope protein|NP_739583.2|Dengue virus 2|11060 - 686 - 15 - - - 1 - 14.6234 - 26 - 2.07692 - 3 - 9 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - MENNGWV - MENKAWL - MEN W+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1212 - Query_1212 - M_1682 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1213 - Query_1213 - M_1683 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1214 - Query_1214 - M_1684 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1215 - Query_1215 - M_1685 - 9 - - - 1 - gnl|BL_ORD_ID|1508 - 139406|polyprotein|ACT37184.1|Hepatitis C virus|11103 - 1508 - 10 - - - 1 - 12.6974 - 21 - 29.8889 - 3 - 8 - 5 - 10 - 0 - 0 - 4 - 5 - 0 - 6 - RPWPRV - RPGPRL - RP PR+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1216 - Query_1216 - M_1686 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1217 - Query_1217 - M_1687 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1218 - Query_1218 - M_1688 - 9 - - - 1 - gnl|BL_ORD_ID|2175 - 189750|Diacylglycerol acyltransferase/mycolyltransferase Ag85B|SRC280000|Mycobacterium tuberculosis|1773 - 2175 - 9 - - - 1 - 12.6974 - 21 - 26.0147 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - LPVSGG - MPVGGG - +PV GG - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1219 - Query_1219 - M_1689 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1220 - Query_1220 - M_1690 - 9 - - - 1 - gnl|BL_ORD_ID|1274 - 101812|Pol polyprotein|Q9YLQ7|Human immunodeficiency virus 1|11676 - 1274 - 9 - - - 1 - 12.6974 - 21 - 35.9943 - 3 - 8 - 4 - 9 - 0 - 0 - 4 - 4 - 0 - 6 - PDATIY - PDIVIY - PD IY - - - - - 2 - gnl|BL_ORD_ID|1275 - 101813|Pol polyprotein|Q9YLQ7|Human immunodeficiency virus 1|11676 - 1275 - 11 - - - 1 - 12.6974 - 21 - 37.5414 - 3 - 8 - 4 - 9 - 0 - 0 - 4 - 4 - 0 - 6 - PDATIY - PDIVIY - PD IY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1221 - Query_1221 - M_1691 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1222 - Query_1222 - M_1692 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1223 - Query_1223 - M_1693 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1224 - Query_1224 - M_1694 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1225 - Query_1225 - M_1695 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1226 - Query_1226 - M_1696 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1227 - Query_1227 - M_1697 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1228 - Query_1228 - M_1698 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1229 - Query_1229 - M_1699 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1230 - Query_1230 - M_1700 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1231 - Query_1231 - M_1701 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1232 - Query_1232 - M_1702 - 9 - - - 1 - gnl|BL_ORD_ID|1298 - 103392|polyprotein|BAB18806.1|Hepatitis C virus|11103 - 1298 - 9 - - - 1 - 13.0826 - 22 - 20.0871 - 1 - 6 - 4 - 9 - 0 - 0 - 4 - 4 - 0 - 6 - DPMVPL - DPTTPL - DP PL - - - - - 2 - gnl|BL_ORD_ID|2258 - 288104|nef protein|ACR27130.1|Human immunodeficiency virus 1|11676 - 2258 - 18 - - - 1 - 11.927 - 19 - 58.6274 - 2 - 7 - 8 - 13 - 0 - 0 - 4 - 5 - 0 - 6 - PMVPLQ - PQVPLR - P VPL+ - - - - - 3 - gnl|BL_ORD_ID|1284 - 102150|nef protein|ACR27119.1|Human immunodeficiency virus 1|11676 - 1284 - 9 - - - 1 - 11.927 - 19 - 87.0561 - 2 - 7 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - PMVPLQ - PQVPLR - P VPL+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1233 - Query_1233 - M_1703 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1234 - Query_1234 - M_1704 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1235 - Query_1235 - M_1705 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1236 - Query_1236 - M_1706 - 9 - - - 1 - gnl|BL_ORD_ID|413 - 24943|DNA polymerase|CAA10434.1|Hepatitis B virus|10407 - 413 - 11 - - - 1 - 12.3122 - 20 - 39.4691 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - VMWWMGIL - TLWKAGIL - +W GIL - - - - - 2 - gnl|BL_ORD_ID|988 - 65148|DNA polymerase|CAA10434.1|Hepatitis B virus|10407 - 988 - 10 - - - 1 - 12.3122 - 20 - 48.6895 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 5 - 0 - 8 - VMWWMGIL - TLWKAGIL - +W GIL - - - - - 3 - gnl|BL_ORD_ID|664 - 39591|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 - 664 - 20 - - - 1 - 11.5418 - 18 - 132.799 - 2 - 9 - 12 - 19 - 0 - 0 - 2 - 4 - 0 - 8 - VMWWMGIL - CLWWLQYF - +WW+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1237 - Query_1237 - M_1707 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1238 - Query_1238 - M_1708 - 9 - - - 1 - gnl|BL_ORD_ID|1508 - 139406|polyprotein|ACT37184.1|Hepatitis C virus|11103 - 1508 - 10 - - - 1 - 12.6974 - 21 - 31.4509 - 2 - 7 - 5 - 10 - 0 - 0 - 4 - 5 - 0 - 6 - RPWPRV - RPGPRL - RP PR+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1239 - Query_1239 - M_1709 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1240 - Query_1240 - M_1710 - 9 - - - 1 - gnl|BL_ORD_ID|601 - 37153|Nuclear antigen EBNA-3C|Q69140.1|Human gammaherpesvirus 4|10376 - 601 - 10 - - - 1 - 15.779 - 29 - 0.523411 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 7 - 0 - 8 - LIDYARYM - LLDFVRFM - L+D+ R+M - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1241 - Query_1241 - M_1711 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1242 - Query_1242 - M_1712 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1243 - Query_1243 - M_1713 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1244 - Query_1244 - M_1714 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1245 - Query_1245 - M_1715 - 9 - - - 1 - gnl|BL_ORD_ID|1296 - 103322|polyprotein|BAB18806.1|Hepatitis C virus|11103 - 1296 - 20 - - - 1 - 11.1566 - 17 - 199.383 - 2 - 8 - 10 - 16 - 0 - 0 - 3 - 5 - 0 - 7 - NCTCGCS - DCSTPCS - +C+ CS - - - - - 2 - gnl|BL_ORD_ID|873 - 57364|Genome polyprotein|P26664.3|Hepatitis C virus|11103 - 873 - 11 - - - 1 - 11.1566 - 17 - 222.638 - 2 - 8 - 2 - 8 - 0 - 0 - 4 - 4 - 0 - 7 - NCTCGCS - ECTTPCS - CT CS - - - - - 3 - gnl|BL_ORD_ID|1679 - 149029|polyprotein|ABR25251.1|Hepatitis C virus (isolate H77)|63746 - 1679 - 9 - - - 1 - 10.7714 - 16 - 354.707 - 3 - 8 - 1 - 6 - 0 - 0 - 4 - 4 - 0 - 6 - CTCGCS - CTTPCS - CT CS - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1246 - Query_1246 - M_1716 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1247 - Query_1247 - M_1717 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1248 - Query_1248 - M_1718 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1249 - Query_1249 - M_1719 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1250 - Query_1250 - M_1720 - 9 - - - 1 - gnl|BL_ORD_ID|1801 - 168240|major paraflagellar rod protein|AAA30221.1|Trypanosoma cruzi|5693 - 1801 - 10 - - - 1 - 13.4678 - 23 - 8.76869 - 1 - 9 - 2 - 10 - 0 - 0 - 5 - 6 - 0 - 9 - LPETKGVTL - VPEVTDVTL - +PE VTL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1251 - Query_1251 - M_1721 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1252 - Query_1252 - M_1722 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1253 - Query_1253 - M_1723 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1254 - Query_1254 - M_1724 - 9 - - - 1 - gnl|BL_ORD_ID|1730 - 150538|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1730 - 9 - - - 1 - 12.3122 - 20 - 46.3849 - 1 - 6 - 3 - 8 - 0 - 0 - 4 - 4 - 0 - 6 - RWNDTR - RWLDAR - RW D R - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1255 - Query_1255 - M_1725 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1256 - Query_1256 - M_1726 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1257 - Query_1257 - M_1727 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1258 - Query_1258 - M_1728 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1259 - Query_1259 - M_1729 - 9 - - - 1 - gnl|BL_ORD_ID|582 - 36504|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 - 582 - 9 - - - 1 - 11.5418 - 18 - 126.161 - 1 - 8 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - IVCDIKEK - IFCHSKKK - I C K+K - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1260 - Query_1260 - M_1730 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1261 - Query_1261 - M_1731 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1262 - Query_1262 - M_1732 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1263 - Query_1263 - M_1733 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1264 - Query_1264 - M_1734 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1265 - Query_1265 - M_1735 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1266 - Query_1266 - M_1736 - 9 - - - 1 - gnl|BL_ORD_ID|530 - 32663|small hydrophobic protein|AAM12943.1|Human metapneumovirus|162145 - 530 - 10 - - - 1 - 11.1566 - 17 - 238.931 - 1 - 9 - 2 - 10 - 0 - 0 - 3 - 5 - 0 - 9 - PATRPLHVL - PAVGVYHIV - PA H++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1267 - Query_1267 - M_1737 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1268 - Query_1268 - M_1738 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1269 - Query_1269 - M_1739 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1270 - Query_1270 - M_1740 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1271 - Query_1271 - M_1741 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1272 - Query_1272 - M_1742 - 9 - - - 1 - gnl|BL_ORD_ID|1512 - 140541|hypothetical protein|NP_218210.1|Mycobacterium tuberculosis H37Rv|83332 - 1512 - 9 - - - 1 - 14.2382 - 25 - 3.00197 - 3 - 9 - 3 - 9 - 0 - 0 - 4 - 6 - 0 - 7 - QEGMVPV - DEGLLPV - EG++PV - - - - - 2 - gnl|BL_ORD_ID|604 - 37187|surface antigen|BAF44879.1|Hepatitis B virus|10407 - 604 - 10 - - - 1 - 13.853 - 24 - 4.3044 - 4 - 9 - 5 - 10 - 0 - 0 - 4 - 6 - 0 - 6 - EGMVPV - QGMLPV - +GM+PV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1273 - Query_1273 - M_1743 - 9 - - - 1 - gnl|BL_ORD_ID|4 - 327|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis|1773 - 4 - 20 - - - 1 - 11.1566 - 17 - 210.697 - 2 - 9 - 5 - 12 - 0 - 0 - 4 - 6 - 0 - 8 - QKRATEEI - QKQELDEI - QK+ +EI - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1274 - Query_1274 - M_1744 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1275 - Query_1275 - M_1745 - 9 - - - 1 - gnl|BL_ORD_ID|665 - 40158|polyprotein|AAA45534.1|Hepatitis C virus|11103 - 665 - 15 - - - 1 - 13.853 - 24 - 5.87794 - 1 - 8 - 6 - 13 - 0 - 0 - 5 - 5 - 0 - 8 - AQLPPWAP - AQLHVWVP - AQL W P - - - - - 2 - gnl|BL_ORD_ID|1187 - 93536|core protein|AAL31859.1|Hepatitis B virus|10407 - 1187 - 11 - - - 1 - 12.3122 - 20 - 55.8493 - 1 - 9 - 2 - 10 - 0 - 0 - 5 - 6 - 0 - 9 - AQLPPWAPL - AYRPPNAPI - A PP AP+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1276 - Query_1276 - M_1746 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1277 - Query_1277 - M_1747 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1278 - Query_1278 - M_1748 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1279 - Query_1279 - M_1749 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1280 - Query_1280 - M_1750 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1281 - Query_1281 - M_1751 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1282 - Query_1282 - M_1752 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1283 - Query_1283 - M_1753 - 9 - - - 1 - gnl|BL_ORD_ID|1758 - 154296|UL29|CAB06754.1|Human alphaherpesvirus 2|10310 - 1758 - 15 - - - 1 - 13.0826 - 22 - 17.8301 - 2 - 9 - 5 - 12 - 0 - 0 - 5 - 5 - 0 - 8 - FFDAFRKF - IFDRTRKF - FD RKF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1284 - Query_1284 - M_1754 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1285 - Query_1285 - M_1755 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1286 - Query_1286 - M_1756 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1287 - Query_1287 - M_1757 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1288 - Query_1288 - M_1758 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1289 - Query_1289 - M_1759 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1290 - Query_1290 - M_1760 - 9 - - - 1 - gnl|BL_ORD_ID|1036 - 69398|X protein|AAP06597.1|Hepatitis B virus|10407 - 1036 - 9 - - - 1 - 13.0826 - 22 - 20.7937 - 3 - 9 - 1 - 7 - 0 - 0 - 4 - 6 - 0 - 7 - VLCGQPI - VLCLRPV - VLC +P+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1291 - Query_1291 - M_1761 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1292 - Query_1292 - M_1762 - 9 - - - 1 - gnl|BL_ORD_ID|619 - 37398|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 - 619 - 10 - - - 1 - 13.853 - 24 - 6.52279 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 6 - 0 - 9 - ILHNQIQQV - LLHTDFEQV - +LH +QV - - - - - 2 - gnl|BL_ORD_ID|618 - 37397|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 - 618 - 9 - - - 1 - 13.853 - 24 - 6.83656 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 6 - 0 - 9 - ILHNQIQQV - LLHTDFEQV - +LH +QV - - - - - 3 - gnl|BL_ORD_ID|581 - 36432|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 - 581 - 9 - - - 1 - 13.0826 - 22 - 16.8921 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 5 - 0 - 8 - LHNQIQQV - LHTDFEQV - LH +QV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1293 - Query_1293 - M_1763 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1294 - Query_1294 - M_1764 - 9 - - - 1 - gnl|BL_ORD_ID|382 - 23573|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 382 - 9 - - - 1 - 13.0826 - 22 - 14.7007 - 4 - 9 - 1 - 6 - 0 - 0 - 3 - 5 - 0 - 6 - HQVGMY - HAVGLF - H VG++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1295 - Query_1295 - M_1765 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1296 - Query_1296 - M_1766 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1297 - Query_1297 - M_1767 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1298 - Query_1298 - M_1768 - 9 - - - 1 - gnl|BL_ORD_ID|1177 - 79506|E1 protein|BAA19893.1|Rubella virus|11041 - 1177 - 20 - - - 1 - 13.853 - 24 - 7.09074 - 3 - 9 - 11 - 17 - 0 - 0 - 5 - 5 - 0 - 7 - GFKGDTV - GFPTDTV - GF DTV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1299 - Query_1299 - M_1769 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1300 - Query_1300 - M_1770 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1301 - Query_1301 - M_1771 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1302 - Query_1302 - M_1772 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1303 - Query_1303 - M_1773 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1304 - Query_1304 - M_1774 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1305 - Query_1305 - M_1775 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1306 - Query_1306 - M_1776 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1307 - Query_1307 - M_1777 - 9 - - - 1 - gnl|BL_ORD_ID|1813 - 177701|polyprotein|ACZ60104.1|Hepatitis C virus subtype 3a|356426 - 1813 - 18 - - - 1 - 15.3938 - 28 - 0.594437 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 6 - 0 - 8 - HAQVCSLY - KAKICGLY - A++C LY - - - - - 2 - gnl|BL_ORD_ID|1793 - 164264|nucleocapsid protein|AAA43837.1|Hantaan virus 76-118|11602 - 1793 - 15 - - - 1 - 14.6234 - 26 - 2.07692 - 1 - 9 - 6 - 14 - 0 - 0 - 4 - 5 - 0 - 9 - FHAQVCSLY - YRTAVCGLY - + VC LY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1308 - Query_1308 - M_1778 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1309 - Query_1309 - M_1779 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1310 - Query_1310 - M_1780 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1311 - Query_1311 - M_1781 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1312 - Query_1312 - M_1782 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1313 - Query_1313 - M_1783 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1314 - Query_1314 - M_1784 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1315 - Query_1315 - M_1785 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1316 - Query_1316 - M_1786 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1317 - Query_1317 - M_1787 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1318 - Query_1318 - M_1788 - 9 - - - 1 - gnl|BL_ORD_ID|2232 - 196087|PPE family protein PPE54|YP_177960.1|Mycobacterium tuberculosis H37Rv|83332 - 2232 - 11 - - - 1 - 13.0826 - 22 - 14.9787 - 1 - 6 - 5 - 10 - 0 - 0 - 3 - 6 - 0 - 6 - MLLHQV - MILHEI - M+LH++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1319 - Query_1319 - M_1789 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1320 - Query_1320 - M_1790 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1321 - Query_1321 - M_1791 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1322 - Query_1322 - M_1792 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1323 - Query_1323 - M_1793 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1324 - Query_1324 - M_1794 - 9 - - - 1 - gnl|BL_ORD_ID|1433 - 116127|Nucleoprotein|P15682.1|Influenza A virus (A/Wilson-Smith/1933(H1N1))|381518 - 1433 - 9 - - - 1 - 13.0826 - 22 - 19.7427 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 4 - 0 - 6 - LPLKRP - LPFDRP - LP RP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1325 - Query_1325 - M_1795 - 9 - - - 1 - gnl|BL_ORD_ID|502 - 31997|hypothetical protein FTT0484|YP_169522.1|Francisella tularensis subsp. tularensis SCHU S4|177416 - 502 - 9 - - - 1 - 13.853 - 24 - 5.55396 - 3 - 7 - 3 - 7 - 0 - 0 - 4 - 4 - 0 - 5 - FPEGY - LPEGY - PEGY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1326 - Query_1326 - M_1796 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1327 - Query_1327 - M_1797 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1328 - Query_1328 - M_1798 - 9 - - - 1 - gnl|BL_ORD_ID|431 - 26273|nucleocapsid protein|ABI96968.1|SARS coronavirus|227859 - 431 - 15 - - - 1 - 14.2382 - 25 - 2.55569 - 1 - 9 - 3 - 11 - 0 - 0 - 5 - 5 - 0 - 9 - MEVDPIGNL - MEVTPSGTW - MEV P G - - - - - 2 - gnl|BL_ORD_ID|2187 - 190494|nucleocapsid protein|ABI96968.1|SARS coronavirus|227859 - 2187 - 10 - - - 1 - 14.2382 - 25 - 3.10797 - 1 - 8 - 1 - 8 - 0 - 0 - 5 - 5 - 0 - 8 - MEVDPIGN - MEVTPSGT - MEV P G - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1329 - Query_1329 - M_1799 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1330 - Query_1330 - M_1800 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1331 - Query_1331 - M_1801 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1332 - Query_1332 - M_1802 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1333 - Query_1333 - M_1803 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1334 - Query_1334 - M_1804 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1335 - Query_1335 - M_1805 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1336 - Query_1336 - M_1806 - 9 - - - 1 - gnl|BL_ORD_ID|1266 - 98640|trans-sialidase, putative|EAN80840.1|Trypanosoma cruzi|5693 - 1266 - 9 - - - 1 - 13.4678 - 23 - 8.13377 - 2 - 8 - 3 - 9 - 0 - 0 - 5 - 7 - 0 - 7 - FSLLATV - FTLVATV - F+L+ATV - - - - - 2 - gnl|BL_ORD_ID|1245 - 98044|trans-sialidase, putative|EAN80840.1|Trypanosoma cruzi|5693 - 1245 - 9 - - - 1 - 13.4678 - 23 - 9.34888 - 2 - 8 - 1 - 7 - 0 - 0 - 5 - 7 - 0 - 7 - FSLLATV - FTLVATV - F+L+ATV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1337 - Query_1337 - M_1807 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1338 - Query_1338 - M_1808 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1339 - Query_1339 - M_1809 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1340 - Query_1340 - M_1810 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1341 - Query_1341 - M_1811 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1342 - Query_1342 - M_1812 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1343 - Query_1343 - M_1813 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1344 - Query_1344 - M_1814 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1345 - Query_1345 - M_1815 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1346 - Query_1346 - M_1816 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1347 - Query_1347 - M_1817 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1348 - Query_1348 - M_1818 - 9 - - - 1 - gnl|BL_ORD_ID|1741 - 150649|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1741 - 10 - - - 1 - 11.1566 - 17 - 228.313 - 2 - 9 - 3 - 10 - 0 - 0 - 4 - 5 - 0 - 8 - QQNCAAYL - QDNQLAYV - Q N AY+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1349 - Query_1349 - M_1819 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1350 - Query_1350 - M_1820 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1351 - Query_1351 - M_1821 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1352 - Query_1352 - M_1822 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1353 - Query_1353 - M_1823 - 9 - - - 1 - gnl|BL_ORD_ID|910 - 59585|polymerase|AAD16253.1|Hepatitis B virus|10407 - 910 - 9 - - - 1 - 13.0826 - 22 - 18.4218 - 1 - 6 - 3 - 8 - 0 - 0 - 4 - 5 - 0 - 6 - YAQTPS - YADSPS - YA +PS - - - - - 2 - gnl|BL_ORD_ID|793 - 53041|phosphorylated matrix protein (pp65)|AAA45996.1|Human betaherpesvirus 5|10359 - 793 - 11 - - - 1 - 12.3122 - 20 - 59.6252 - 4 - 9 - 3 - 8 - 0 - 0 - 4 - 4 - 0 - 6 - TPSKTP - TPDSTP - TP TP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1354 - Query_1354 - M_1824 - 9 - - - 1 - gnl|BL_ORD_ID|442 - 27168|envelope protein|BAF48755.1|Hepatitis B virus|10407 - 442 - 9 - - - 1 - 10.7714 - 16 - 411.363 - 1 - 6 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - LLLCFL - LLLCLI - LLLC + - - - - - 2 - gnl|BL_ORD_ID|621 - 37466|surface antigen|BAF44879.1|Hepatitis B virus|10407 - 621 - 9 - - - 1 - 10.7714 - 16 - 497.585 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - LLLCFL - LLLCLI - LLLC + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1355 - Query_1355 - M_1825 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1356 - Query_1356 - M_1826 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_118813_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_118813_1_T.fasta deleted file mode 100755 index 6e1ccdb0..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_118813_1_T.fasta +++ /dev/null @@ -1,188 +0,0 @@ ->M_1827 -IKLHNPSTI ->M_1828 -TLLTTHYMA ->M_1829 -SYEVVIPEW ->M_1830 -WVNEFGEVF ->M_1831 -LTYRHCQNF ->M_1832 -LTYRHCQNF ->M_1833 -RHCQNFSIL ->M_1834 -YRHCQNFSI ->M_1835 -YRHCQNFSI ->M_1836 -FSLERIAES ->M_1837 -CLHYIMGDY ->M_1838 -LLACLHYIM ->M_1839 -RLLACLHYI ->M_1840 -RLLACLHYI ->M_1841 -SQSADAHSI ->M_1842 -TFFSSSQSA ->M_1843 -YANNHCIRT ->M_1844 -FYGMTEMNY ->M_1845 -LQFYGMTEM ->M_1846 -LQFYGMTEM ->M_1847 -ALWMYRSLM ->M_1848 -ALWMYRSLM ->M_1849 -QALWMYRSL ->M_1850 -SFRKEKRNL ->M_1851 -LTSQDLAGY ->M_1852 -MAGHGWGAL ->M_1853 -VMSYGEQPY ->M_1854 -SVSDVFHGI ->M_1855 -IPNDNTLSL ->M_1856 -KTIPNDNTL ->M_1857 -KTIPNDNTL ->M_1858 -TLSLRICTI ->M_1859 -FSMRARIDV ->M_1860 -RLLGQKFSM ->M_1861 -IYMENERRM ->M_1862 -QFLLELYSL ->M_1863 -RVIRYVIGV ->M_1864 -QYLSLINYY ->M_1865 -STLQYLSLI ->M_1866 -IAQGKPVTL ->M_1867 -SVIAQGKPV ->M_1868 -FAIMHAQRT ->M_1869 -HTNAVFAIM ->M_1870 -NHTNAVFAI ->M_1871 -HHHHHHQAW ->M_1872 -QAWPPPSSA ->M_1873 -AHTVARGPV ->M_1874 -ALQTFAHTV ->M_1875 -EIYTKNHAY ->M_1876 -FGYQLKEIY ->M_1877 -IYTKNHAYI ->M_1878 -YTKNHAYII ->M_1879 -YTKNHAYII ->M_1880 -HAFDRYETT ->M_1881 -TTHSRPVTL ->M_1882 -TTHSRPVTL ->M_1883 -YETTHSRPV ->M_1884 -VLFDVAGQV ->M_1885 -VLFDVAGQV ->M_1886 -ESKPAPAEV ->M_1887 -LNVEKTEKI ->M_1888 -MVIVFYGTL ->M_1889 -MVIVFYGTL ->M_1890 -SAHLTMVIV ->M_1891 -YETFGAASF ->M_1892 -RGVPPLRTV ->M_1893 -TAESCRSTL ->M_1894 -TAESCRSTL ->M_1895 -RVRAAGQRL ->M_1896 -DVHARESKI ->M_1897 -NVPPTVQKV ->M_1898 -CYYPMAGYI ->M_1899 -CYYPMAGYI ->M_1900 -NTRQCYYPM ->M_1901 -LGYRWCLHV ->M_1902 -LLLGYRWCL ->M_1903 -TAHSSVLTL ->M_1904 -TAHSSVLTL ->M_1905 -FPSNHLGDL ->M_1906 -LLLAHKKKV ->M_1907 -AQILEQVEV ->M_1908 -QIFKCKGTL ->M_1909 -QIFKCKGTL ->M_1910 -TLVGHQGPV ->M_1911 -TLVGHQGPV ->M_1912 -DAVELWAIV ->M_1913 -VDLPLTSTI ->M_1914 -NVVNGQMRF ->M_1915 -MGAPGSEII ->M_1916 -FSQFSNLKV ->M_1917 -KAFSQFSNL ->M_1918 -HFSVSSNLL ->M_1919 -KHFSVSSNL ->M_1920 -KHFSVSSNL diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_118813_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_118813_1_T_iedb.xml deleted file mode 100755 index 0c91beb3..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_118813_1_T_iedb.xml +++ /dev/null @@ -1,2608 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_1827 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_1827 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_1828 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_1829 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_1830 - 9 - - - 1 - gnl|BL_ORD_ID|1103 - 72790|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 - 1103 - 9 - - - 1 - 13.853 - 24 - 5.65074 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 6 - 0 - 9 - WVNEFGEVF - WLSDCGEAL - W+++ GE - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 5 - Query_5 - M_1831 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_1832 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_1833 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_1834 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_1835 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_1836 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_1837 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_1838 - 9 - - - 1 - gnl|BL_ORD_ID|669 - 40262|Cytochrome P450 2A7|P20853.1|Homo sapiens|9606 - 669 - 10 - - - 1 - 12.6974 - 21 - 31.4509 - 1 - 5 - 4 - 8 - 0 - 0 - 5 - 5 - 0 - 5 - LLACL - LLACL - LLACL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 13 - Query_13 - M_1839 - 9 - - - 1 - gnl|BL_ORD_ID|669 - 40262|Cytochrome P450 2A7|P20853.1|Homo sapiens|9606 - 669 - 10 - - - 1 - 12.6974 - 21 - 28.8893 - 2 - 6 - 4 - 8 - 0 - 0 - 5 - 5 - 0 - 5 - LLACL - LLACL - LLACL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 14 - Query_14 - M_1840 - 9 - - - 1 - gnl|BL_ORD_ID|669 - 40262|Cytochrome P450 2A7|P20853.1|Homo sapiens|9606 - 669 - 10 - - - 1 - 12.6974 - 21 - 28.8893 - 2 - 6 - 4 - 8 - 0 - 0 - 5 - 5 - 0 - 5 - LLACL - LLACL - LLACL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 15 - Query_15 - M_1841 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_1842 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_1843 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_1844 - 9 - - - 1 - gnl|BL_ORD_ID|2264 - 418945|PPE family protein PPE68|KAM81677.1|Mycobacterium tuberculosis H37Ra|419947 - 2264 - 9 - - - 1 - 14.2382 - 25 - 2.62424 - 3 - 9 - 1 - 7 - 0 - 0 - 4 - 6 - 0 - 7 - GMTEMNY - ALTEMDY - +TEM+Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 19 - Query_19 - M_1845 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_1846 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_1847 - 9 - - - 1 - gnl|BL_ORD_ID|1951 - 181036|||| - 1951 - 20 - - - 1 - 13.0826 - 22 - 13.0672 - 2 - 9 - 7 - 14 - 0 - 0 - 3 - 7 - 0 - 8 - LWMYRSLM - VWLKKSMM - +W+ +S+M - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 22 - Query_22 - M_1848 - 9 - - - 1 - gnl|BL_ORD_ID|1951 - 181036|||| - 1951 - 20 - - - 1 - 13.0826 - 22 - 13.0672 - 2 - 9 - 7 - 14 - 0 - 0 - 3 - 7 - 0 - 8 - LWMYRSLM - VWLKKSMM - +W+ +S+M - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 23 - Query_23 - M_1849 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_1850 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_1851 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_1852 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_1853 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 28 - Query_28 - M_1854 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 29 - Query_29 - M_1855 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 30 - Query_30 - M_1856 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 31 - Query_31 - M_1857 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 32 - Query_32 - M_1858 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 33 - Query_33 - M_1859 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 34 - Query_34 - M_1860 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 35 - Query_35 - M_1861 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 36 - Query_36 - M_1862 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 37 - Query_37 - M_1863 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 38 - Query_38 - M_1864 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 39 - Query_39 - M_1865 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 40 - Query_40 - M_1866 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 41 - Query_41 - M_1867 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 42 - Query_42 - M_1868 - 9 - - - 1 - gnl|BL_ORD_ID|1393 - 110338|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1393 - 33 - - - 1 - 13.0826 - 22 - 15.4552 - 4 - 9 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - MHAQRT - MHQKRT - MH +RT - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 43 - Query_43 - M_1869 - 9 - - - 1 - gnl|BL_ORD_ID|414 - 24986|polyprotein precursor|NP_041724.2|West Nile virus|11082 - 414 - 9 - - - 1 - 11.1566 - 17 - 221.814 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 5 - 0 - 9 - HTNAVFAIM - HTTKGAALM - HT A+M - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 44 - Query_44 - M_1870 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 45 - Query_45 - M_1871 - 9 - - - 1 - gnl|BL_ORD_ID|1975 - 183147|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1975 - 9 - - - 1 - 10.7714 - 16 - 349.459 - 3 - 7 - 4 - 8 - 0 - 0 - 4 - 4 - 0 - 5 - HHHHQ - HHFHQ - HH HQ - - - - - 2 - gnl|BL_ORD_ID|1576 - 141418|tegument protein VP11/12|NP_044648.1|Human alphaherpesvirus 1|10298 - 1576 - 9 - - - 1 - 10.3862 - 15 - 574.99 - 3 - 7 - 4 - 8 - 0 - 0 - 4 - 4 - 0 - 5 - HHHHQ - HHHAQ - HHH Q - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 46 - Query_46 - M_1872 - 9 - - - 1 - gnl|BL_ORD_ID|1618 - 144544|polyprotein precursor|BAA01728.1|Hepatitis C virus|11103 - 1618 - 10 - - - 1 - 14.2382 - 25 - 4.01795 - 3 - 9 - 1 - 7 - 0 - 0 - 5 - 5 - 0 - 7 - WPPPSSA - WPAPSGA - WP PS A - - - - - 2 - gnl|BL_ORD_ID|665 - 40158|polyprotein|AAA45534.1|Hepatitis C virus|11103 - 665 - 15 - - - 1 - 12.3122 - 20 - 51.4826 - 1 - 6 - 9 - 14 - 0 - 0 - 3 - 3 - 0 - 6 - QAWPPP - HVWVPP - W PP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 47 - Query_47 - M_1873 - 9 - - - 1 - gnl|BL_ORD_ID|403 - 24557|Gag polyprotein|P03347.3|Human immunodeficiency virus 1|11676 - 403 - 9 - - - 1 - 12.6974 - 21 - 39.8499 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 5 - 0 - 8 - HTVARGPV - HPVHAGPI - H V GP+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 48 - Query_48 - M_1874 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 49 - Query_49 - M_1875 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 50 - Query_50 - M_1876 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 51 - Query_51 - M_1877 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 52 - Query_52 - M_1878 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 53 - Query_53 - M_1879 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 54 - Query_54 - M_1880 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 55 - Query_55 - M_1881 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 56 - Query_56 - M_1882 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 57 - Query_57 - M_1883 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 58 - Query_58 - M_1884 - 9 - - - 1 - gnl|BL_ORD_ID|1176 - 79454|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 1176 - 15 - - - 1 - 11.5418 - 18 - 141.75 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 6 - 0 - 9 - VLFDVAGQV - VIFCHPGQL - V+F GQ+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 59 - Query_59 - M_1885 - 9 - - - 1 - gnl|BL_ORD_ID|1176 - 79454|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 1176 - 15 - - - 1 - 11.5418 - 18 - 141.75 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 6 - 0 - 9 - VLFDVAGQV - VIFCHPGQL - V+F GQ+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 60 - Query_60 - M_1886 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 61 - Query_61 - M_1887 - 9 - - - 1 - gnl|BL_ORD_ID|569 - 35568|Polyprotein|Q9J8D4|Dengue virus 2|11060 - 569 - 8 - - - 1 - 11.5418 - 18 - 135.128 - 3 - 8 - 1 - 6 - 0 - 0 - 4 - 6 - 0 - 6 - VEKTEK - LEKTKK - +EKT+K - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 62 - Query_62 - M_1888 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 63 - Query_63 - M_1889 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 64 - Query_64 - M_1890 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 65 - Query_65 - M_1891 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 66 - Query_66 - M_1892 - 9 - - - 1 - gnl|BL_ORD_ID|576 - 36345|polyprotein|ABR25251.1|Hepatitis C virus (isolate H77)|63746 - 576 - 10 - - - 1 - 16.1642 - 30 - 0.338287 - 2 - 8 - 2 - 8 - 0 - 0 - 6 - 6 - 0 - 7 - GVPPLRT - GVPPLRA - GVPPLR - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 67 - Query_67 - M_1893 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 68 - Query_68 - M_1894 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 69 - Query_69 - M_1895 - 9 - - - 1 - gnl|BL_ORD_ID|1956 - 181733|Antigen 85-B|P0C5B9.1|Mycobacterium tuberculosis|1773 - 1956 - 40 - - - 1 - 14.6234 - 26 - 2.9583 - 1 - 9 - 7 - 15 - 0 - 0 - 5 - 8 - 0 - 9 - RVRAAGQRL - KIRAWGRRL - ++RA G+RL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 70 - Query_70 - M_1896 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 71 - Query_71 - M_1897 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 72 - Query_72 - M_1898 - 9 - - - 1 - gnl|BL_ORD_ID|1160 - 76532|outer membrane protein|YP_170495.1|Francisella tularensis subsp. tularensis SCHU S4|177416 - 1160 - 10 - - - 1 - 11.1566 - 17 - 190.083 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 5 - 0 - 8 - YYPMAGYI - YYLDRGYL - YY GY+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 73 - Query_73 - M_1899 - 9 - - - 1 - gnl|BL_ORD_ID|1160 - 76532|outer membrane protein|YP_170495.1|Francisella tularensis subsp. tularensis SCHU S4|177416 - 1160 - 10 - - - 1 - 11.1566 - 17 - 190.083 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 5 - 0 - 8 - YYPMAGYI - YYLDRGYL - YY GY+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 74 - Query_74 - M_1900 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 75 - Query_75 - M_1901 - 9 - - - 1 - gnl|BL_ORD_ID|629 - 37607|kaposin|AAC57155.1|Human gammaherpesvirus 8|37296 - 629 - 9 - - - 1 - 12.6974 - 21 - 23.4633 - 2 - 7 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - GYRWCL - GWRWRL - G+RW L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 76 - Query_76 - M_1902 - 9 - - - 1 - gnl|BL_ORD_ID|629 - 37607|kaposin|AAC57155.1|Human gammaherpesvirus 8|37296 - 629 - 9 - - - 1 - 14.2382 - 25 - 3.87216 - 1 - 9 - 1 - 9 - 0 - 0 - 6 - 7 - 0 - 9 - LLLGYRWCL - LLNGWRWRL - LL G+RW L - - - - - 2 - gnl|BL_ORD_ID|626 - 37536|Spike glycoprotein precursor|P15423.1|Human coronavirus 229E|11137 - 626 - 9 - - - 1 - 9.61583 - 13 - 1239.7 - 1 - 7 - 1 - 7 - 0 - 0 - 4 - 4 - 0 - 7 - LLLGYRW - LLLNCLW - LLL W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 77 - Query_77 - M_1903 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 78 - Query_78 - M_1904 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 79 - Query_79 - M_1905 - 9 - - - 1 - gnl|BL_ORD_ID|741 - 47760|EBNA-1 protein|Q777E1|Human gammaherpesvirus 4|10376 - 741 - 15 - - - 1 - 13.0826 - 22 - 16.6732 - 2 - 8 - 5 - 11 - 0 - 0 - 4 - 5 - 0 - 7 - PSNHLGD - PGNGLGE - P N LG+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 80 - Query_80 - M_1906 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 81 - Query_81 - M_1907 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 82 - Query_82 - M_1908 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 83 - Query_83 - M_1909 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 84 - Query_84 - M_1910 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 85 - Query_85 - M_1911 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 86 - Query_86 - M_1912 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 87 - Query_87 - M_1913 - 9 - - - 1 - gnl|BL_ORD_ID|322 - 21007|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 322 - 9 - - - 1 - 12.3122 - 20 - 56.7066 - 3 - 9 - 3 - 9 - 0 - 0 - 4 - 5 - 0 - 7 - LPLTSTI - LPFHSTL - LP ST+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 88 - Query_88 - M_1914 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 89 - Query_89 - M_1915 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 90 - Query_90 - M_1916 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 91 - Query_91 - M_1917 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 92 - Query_92 - M_1918 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 93 - Query_93 - M_1919 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 94 - Query_94 - M_1920 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_119118_2_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_119118_2_T.fasta deleted file mode 100755 index a2c43fcd..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_119118_2_T.fasta +++ /dev/null @@ -1,50 +0,0 @@ ->M_1921 -YQVLAMSTK ->M_1922 -KLSSEAKTK ->M_1923 -TVLRLFPFR ->M_1924 -TVLRLFPFR ->M_1925 -TVKDVHKAK ->M_1926 -TIHNVNFSK ->M_1927 -TIHNVNFSK ->M_1928 -SETTFDIFV ->M_1929 -GMHFSPGAR ->M_1930 -FLTQPVAPK ->M_1931 -KAISFYMKR ->M_1932 -RTVAQVTKK ->M_1933 -RTVAQVTKK ->M_1934 -SEDKKNTKL ->M_1935 -RVAAGVQIK ->M_1936 -RVAAGVQIK ->M_1937 -VVGAVGVGK ->M_1938 -VVGAVGVGK ->M_1939 -TTTPTLKEK ->M_1940 -QSLYIDRLK ->M_1941 -TTIHYNYMY ->M_1942 -TECIIAMSF ->M_1943 -IESSYLESL ->M_1944 -AEEEEEEVV ->M_1945 -TENHQPVCL diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_119118_2_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_119118_2_T_iedb.xml deleted file mode 100755 index 6c7a7c78..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_119118_2_T_iedb.xml +++ /dev/null @@ -1,577 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_1921 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_1921 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_1922 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_1923 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_1924 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_1925 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_1926 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_1927 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_1928 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_1929 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_1930 - 9 - - - 1 - gnl|BL_ORD_ID|2271 - 419002|PPE family protein PPE68|KAM81677.1|Mycobacterium tuberculosis H37Ra|419947 - 2271 - 10 - - - 1 - 13.4678 - 23 - 7.76238 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 6 - 0 - 8 - FLTQPVAP - LIEKPVAP - + +PVAP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 11 - Query_11 - M_1931 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_1932 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_1933 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_1934 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_1935 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_1936 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_1937 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_1938 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_1939 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_1940 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_1941 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 22 - Query_22 - M_1942 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_1943 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_1944 - 9 - - - 1 - gnl|BL_ORD_ID|1398 - 110431|E7|AAD33253.1|Human papillomavirus type 16|333760 - 1398 - 36 - - - 1 - 10.7714 - 16 - 242.357 - 1 - 6 - 13 - 18 - 0 - 0 - 4 - 6 - 0 - 6 - AEEEEE - SEEEDE - +EEE+E - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 25 - Query_25 - M_1945 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_119914_2_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_119914_2_T.fasta deleted file mode 100755 index 34547d25..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_119914_2_T.fasta +++ /dev/null @@ -1,58 +0,0 @@ ->M_1946 -GQLGGLAGK ->M_1947 -LSDWGPHFK ->M_1948 -LSDWGPHFK ->M_1949 -KPASKKEWI ->M_1950 -TTKSEAIEK ->M_1951 -IVRASGCEL ->M_1952 -VPTELNGSM ->M_1953 -VPLFPARVL ->M_1954 -APAQPPMLA ->M_1955 -VVGARGVGK ->M_1956 -VVGARGVGK ->M_1957 -KLCNSGDFR ->M_1958 -HPLTENSPL ->M_1959 -STVRKSPWK ->M_1960 -STVRKSPWK ->M_1961 -LIRMYNINK ->M_1962 -LIRMYNINK ->M_1963 -SPWPLSSLT ->M_1964 -SLKSTRAVF ->M_1965 -SVGSASSLK ->M_1966 -SVGSASSLK ->M_1967 -KGYGGFSRY ->M_1968 -KGYGGFSRY ->M_1969 -KAIGKSRPY ->M_1970 -KTLRKAIGK ->M_1971 -KTLRKAIGK ->M_1972 -QALQKTLRK ->M_1973 -SYQSTGDPK ->M_1974 -VPEWSNNS* diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_119914_2_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_119914_2_T_iedb.xml deleted file mode 100755 index 6278990d..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_119914_2_T_iedb.xml +++ /dev/null @@ -1,739 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_1946 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_1946 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_1947 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_1948 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_1949 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_1950 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_1951 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_1952 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_1953 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_1954 - 9 - - - 1 - gnl|BL_ORD_ID|889 - 58463|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 889 - 20 - - - 1 - 13.0826 - 22 - 16.1327 - 1 - 7 - 3 - 9 - 0 - 0 - 4 - 5 - 0 - 7 - APAQPPM - CPSQEPM - P+Q PM - - - - - 2 - gnl|BL_ORD_ID|749 - 49485|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 749 - 11 - - - 1 - 13.0826 - 22 - 16.8999 - 2 - 7 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - PAQPPM - PSQEPM - P+Q PM - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 10 - Query_10 - M_1955 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_1956 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_1957 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_1958 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_1959 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_1960 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_1961 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_1962 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_1963 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_1964 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_1965 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_1966 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 22 - Query_22 - M_1967 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_1968 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_1969 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_1970 - 9 - - - 1 - gnl|BL_ORD_ID|115 - 7708|gag polyprotein|BAA00992.1|Human immunodeficiency virus 1|11676 - 115 - 9 - - - 1 - 11.5418 - 18 - 165.102 - 1 - 7 - 3 - 9 - 0 - 0 - 4 - 6 - 0 - 7 - KTLRKAI - KTILKAL - KT+ KA+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 26 - Query_26 - M_1971 - 9 - - - 1 - gnl|BL_ORD_ID|115 - 7708|gag polyprotein|BAA00992.1|Human immunodeficiency virus 1|11676 - 115 - 9 - - - 1 - 11.5418 - 18 - 165.102 - 1 - 7 - 3 - 9 - 0 - 0 - 4 - 6 - 0 - 7 - KTLRKAI - KTILKAL - KT+ KA+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 27 - Query_27 - M_1972 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 28 - Query_28 - M_1973 - 9 - - - 1 - gnl|BL_ORD_ID|26 - 2002|Large envelope protein|SRC279965|Hepatitis B virus|10407 - 26 - 10 - - - 1 - 13.4678 - 23 - 10.0795 - 5 - 8 - 6 - 9 - 0 - 0 - 4 - 4 - 0 - 4 - TGDP - TGDP - TGDP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 29 - Query_29 - M_1974 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_119995_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_119995_1_T.fasta deleted file mode 100755 index f889c16c..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_119995_1_T.fasta +++ /dev/null @@ -1,172 +0,0 @@ ->M_1975 -VLETAAPGV ->M_1976 -AVLDAIPLV ->M_1977 -VLDAIPLVA ->M_1978 -KPVVTEVRM ->M_1979 -MPTNTWSGL ->M_1980 -VFQGHSASI ->M_1981 -SLYDFGELR ->M_1982 -DSMLQTVER ->M_1983 -MLQTVEREK ->M_1984 -LLWKDFDQA ->M_1985 -HVPQVADAI ->M_1986 -LLEMNLMHV ->M_1987 -NLMHVPQVA ->M_1988 -VPQVADAIL ->M_1989 -FLIDGSQSV ->M_1990 -FLIDGSQSV ->M_1991 -SVGPEFQYV ->M_1992 -LALSVTEMV ->M_1993 -RLALSVTEM ->M_1994 -TILQIKEEK ->M_1995 -DYEAVCGHR ->M_1996 -EAVCGHRAR ->M_1997 -ILFQKITNR ->M_1998 -KITNRGDEL ->M_1999 -SPTPALGPA ->M_2000 -LTPQQAQEL ->M_2001 -APLGAPPPL ->M_2002 -SKTPPGAPL ->M_2003 -SKTPPGAPL ->M_2004 -MFQSLGEHI ->M_2005 -SLGEHINTL ->M_2006 -SLGEHINTL ->M_2007 -AVGVGKSAL ->M_2008 -YKLVVVGAV ->M_2009 -AMLWALGFI ->M_2010 -FIWSVLITA ->M_2011 -MLWALGFIF ->M_2012 -QTPLFIWSV ->M_2013 -TPLFIWSVL ->M_2014 -TQYQTPLFI ->M_2015 -IINDGKHHV ->M_2016 -GLSAEEFQL ->M_2017 -SAEEFQLIR ->M_2018 -APTTPKEPA ->M_2019 -LLLLLLLLV ->M_2020 -LLLLLLLVV ->M_2021 -LLLLLLVVV ->M_2022 -LLVVVPWGV ->M_2023 -SRRHSRSPL ->M_2024 -SRRHSRSPL ->M_2025 -GSYSMAIPL ->M_2026 -MAIPLLCSY ->M_2027 -NPGSYSMAI ->M_2028 -RYNPGSYSM ->M_2029 -RYNPGSYSM ->M_2030 -SYSMAIPLL ->M_2031 -CQPHAHCSL ->M_2032 -HAHCSLWRR ->M_2033 -IIQELTIFK ->M_2034 -LPPKPVQVL ->M_2035 -QLPPKPVQV ->M_2036 -GLYASLFPA ->M_2037 -LFPAIIYLF ->M_2038 -LYASLFPAI ->M_2039 -PVYGLYASL ->M_2040 -SLFPAIIYL ->M_2041 -SLFPAIIYL ->M_2042 -SLFPAIIYL ->M_2043 -VYGLYASLF ->M_2044 -VYGLYASLF ->M_2045 -RYNVADVSV ->M_2046 -VSVAICMSL ->M_2047 -YTISDDESF ->M_2048 -YVQYWYYTI ->M_2049 -YVQYWYYTI ->M_2050 -SFYNSNRDF ->M_2051 -SFYNSNRDF ->M_2052 -TISFYNSNR ->M_2053 -CRFELMHFK ->M_2054 -ELMHFKTLY ->M_2055 -ILGDWSNGI ->M_2056 -NGISALYCR ->M_2057 -HIHGGTNQV ->M_2058 -AFTCTSSLL ->M_2059 -KAFTCTSSL ->M_2060 -KAFTCTSSL diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_119995_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_119995_1_T_iedb.xml deleted file mode 100755 index 2c8c8541..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_119995_1_T_iedb.xml +++ /dev/null @@ -1,3002 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_1975 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_1975 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_1976 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_1977 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_1978 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_1979 - 9 - - - 1 - gnl|BL_ORD_ID|1289 - 102368|E2 protein|NP_751921.1|Hepatitis C virus subtype 1a|31646 - 1289 - 15 - - - 1 - 11.5418 - 18 - 98.8375 - 2 - 6 - 6 - 10 - 0 - 0 - 3 - 4 - 0 - 5 - PTNTW - PTYSW - PT +W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 6 - Query_6 - M_1980 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_1981 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_1982 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_1983 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_1984 - 9 - - - 1 - gnl|BL_ORD_ID|1699 - 149117|envelope glycoprotein|AAV74049.1|Hepatitis C virus (isolate H77)|63746 - 1699 - 18 - - - 1 - 13.4678 - 23 - 11.4723 - 5 - 9 - 2 - 6 - 0 - 0 - 4 - 4 - 0 - 5 - DFDQA - DFDQG - DFDQ - - - - - 2 - gnl|BL_ORD_ID|103 - 6936|Genome polyprotein|P26664.3|Hepatitis C virus (isolate 1)|11104 - 103 - 11 - - - 1 - 13.0826 - 22 - 18.7359 - 5 - 9 - 6 - 10 - 0 - 0 - 4 - 4 - 0 - 5 - DFDQA - DFDQG - DFDQ - - - - - 3 - gnl|BL_ORD_ID|841 - 55226|HCV-1|AAA45676.1|Hepatitis C virus|11103 - 841 - 10 - - - 1 - 13.0826 - 22 - 19.8203 - 5 - 9 - 5 - 9 - 0 - 0 - 4 - 4 - 0 - 5 - DFDQA - DFDQG - DFDQ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 11 - Query_11 - M_1985 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_1986 - 9 - - - 1 - gnl|BL_ORD_ID|2280 - 419095|polyprotein|ABR25251.1|Hepatitis C virus|11103 - 2280 - 10 - - - 1 - 11.927 - 19 - 66.6359 - 1 - 7 - 3 - 9 - 0 - 0 - 4 - 6 - 0 - 7 - LLEMNLM - LIEANLL - L+E NL+ - - - - - 2 - gnl|BL_ORD_ID|168 - 13091|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 168 - 9 - - - 1 - 11.927 - 19 - 82.8955 - 1 - 7 - 2 - 8 - 0 - 0 - 4 - 6 - 0 - 7 - LLEMNLM - LIEANLL - L+E NL+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 13 - Query_13 - M_1987 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_1988 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_1989 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_1990 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_1991 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_1992 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_1993 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_1994 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_1995 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 22 - Query_22 - M_1996 - 9 - - - 1 - gnl|BL_ORD_ID|343 - 21635|gag protein|ABO73990.1|Human immunodeficiency virus 1|11676 - 343 - 9 - - - 1 - 13.4678 - 23 - 10.3786 - 5 - 9 - 3 - 7 - 0 - 0 - 4 - 5 - 0 - 5 - GHRAR - GHKAR - GH+AR - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 23 - Query_23 - M_1997 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_1998 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_1999 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_2000 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_2001 - 9 - - - 1 - gnl|BL_ORD_ID|1110 - 73059|kaposin|AAC57155.1|Human gammaherpesvirus 8|37296 - 1110 - 15 - - - 1 - 14.2382 - 25 - 2.93584 - 3 - 9 - 5 - 11 - 0 - 0 - 6 - 6 - 0 - 7 - LGAPPPL - LGAIPPL - LGA PPL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 28 - Query_28 - M_2002 - 9 - - - 1 - gnl|BL_ORD_ID|1187 - 93536|core protein|AAL31859.1|Hepatitis B virus|10407 - 1187 - 11 - - - 1 - 12.6974 - 21 - 26.8092 - 4 - 9 - 5 - 10 - 0 - 0 - 4 - 5 - 0 - 6 - PPGAPL - PPNAPI - PP AP+ - - - - - 2 - gnl|BL_ORD_ID|1316 - 107754|Genome polyprotein|P26664.3|Hepatitis C virus|11103 - 1316 - 10 - - - 1 - 12.6974 - 21 - 30.9217 - 3 - 7 - 2 - 6 - 0 - 0 - 4 - 5 - 0 - 5 - TPPGA - TPPGS - TPPG+ - - - - - 3 - gnl|BL_ORD_ID|1766 - 154857|tegument protein|CAB06735.1|Human alphaherpesvirus 2|10310 - 1766 - 16 - - - 1 - 4.99343 - 1 - 101281 - 8 - 9 - 15 - 16 - 0 - 0 - 1 - 2 - 0 - 2 - PL - PV - P+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 29 - Query_29 - M_2003 - 9 - - - 1 - gnl|BL_ORD_ID|1187 - 93536|core protein|AAL31859.1|Hepatitis B virus|10407 - 1187 - 11 - - - 1 - 12.6974 - 21 - 26.8092 - 4 - 9 - 5 - 10 - 0 - 0 - 4 - 5 - 0 - 6 - PPGAPL - PPNAPI - PP AP+ - - - - - 2 - gnl|BL_ORD_ID|1316 - 107754|Genome polyprotein|P26664.3|Hepatitis C virus|11103 - 1316 - 10 - - - 1 - 12.6974 - 21 - 30.9217 - 3 - 7 - 2 - 6 - 0 - 0 - 4 - 5 - 0 - 5 - TPPGA - TPPGS - TPPG+ - - - - - 3 - gnl|BL_ORD_ID|1766 - 154857|tegument protein|CAB06735.1|Human alphaherpesvirus 2|10310 - 1766 - 16 - - - 1 - 4.99343 - 1 - 101281 - 8 - 9 - 15 - 16 - 0 - 0 - 1 - 2 - 0 - 2 - PL - PV - P+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 30 - Query_30 - M_2004 - 9 - - - 1 - gnl|BL_ORD_ID|1172 - 79308|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 1172 - 16 - - - 1 - 13.853 - 24 - 7.02995 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 7 - 0 - 9 - MFQSLGEHI - MEPTLGQHL - M +LG+H+ - - - - - 2 - gnl|BL_ORD_ID|981 - 64821|Protein Tax-1|P03409.2|Human T-lymphotropic virus 1|11908 - 981 - 9 - - - 1 - 13.0826 - 22 - 20.0871 - 4 - 9 - 1 - 6 - 0 - 0 - 3 - 6 - 0 - 6 - SLGEHI - TLGQHL - +LG+H+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 31 - Query_31 - M_2005 - 9 - - - 1 - gnl|BL_ORD_ID|1172 - 79308|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 1172 - 16 - - - 1 - 16.1642 - 30 - 0.328782 - 1 - 9 - 4 - 12 - 0 - 0 - 5 - 8 - 0 - 9 - SLGEHINTL - TLGQHLPTL - +LG+H+ TL - - - - - 2 - gnl|BL_ORD_ID|981 - 64821|Protein Tax-1|P03409.2|Human T-lymphotropic virus 1|11908 - 981 - 9 - - - 1 - 15.779 - 29 - 0.48278 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 8 - 0 - 9 - SLGEHINTL - TLGQHLPTL - +LG+H+ TL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 32 - Query_32 - M_2006 - 9 - - - 1 - gnl|BL_ORD_ID|1172 - 79308|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 1172 - 16 - - - 1 - 16.1642 - 30 - 0.328782 - 1 - 9 - 4 - 12 - 0 - 0 - 5 - 8 - 0 - 9 - SLGEHINTL - TLGQHLPTL - +LG+H+ TL - - - - - 2 - gnl|BL_ORD_ID|981 - 64821|Protein Tax-1|P03409.2|Human T-lymphotropic virus 1|11908 - 981 - 9 - - - 1 - 15.779 - 29 - 0.48278 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 8 - 0 - 9 - SLGEHINTL - TLGQHLPTL - +LG+H+ TL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 33 - Query_33 - M_2007 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 34 - Query_34 - M_2008 - 9 - - - 1 - gnl|BL_ORD_ID|524 - 32238|polyprotein [Hepatitis C virus subtype 1a]|ABV46251.2|Hepatitis C virus (isolate H77)|63746 - 524 - 10 - - - 1 - 12.6974 - 21 - 30.9217 - 2 - 7 - 1 - 6 - 0 - 0 - 5 - 6 - 0 - 6 - KLVVVG - KLVVLG - KLVV+G - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 35 - Query_35 - M_2009 - 9 - - - 1 - gnl|BL_ORD_ID|10 - 1000|glycoprotein gp35/37|AAC59622.1|Human gammaherpesvirus 8|37296 - 10 - 15 - - - 1 - 13.853 - 24 - 5.67783 - 2 - 8 - 9 - 15 - 0 - 0 - 4 - 6 - 0 - 7 - MLWALGF - ILWAVGL - +LWA+G - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 36 - Query_36 - M_2010 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 37 - Query_37 - M_2011 - 9 - - - 1 - gnl|BL_ORD_ID|10 - 1000|glycoprotein gp35/37|AAC59622.1|Human gammaherpesvirus 8|37296 - 10 - 15 - - - 1 - 13.853 - 24 - 4.94253 - 1 - 7 - 9 - 15 - 0 - 0 - 4 - 6 - 0 - 7 - MLWALGF - ILWAVGL - +LWA+G - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 38 - Query_38 - M_2012 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 39 - Query_39 - M_2013 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 40 - Query_40 - M_2014 - 9 - - - 1 - gnl|BL_ORD_ID|1897 - 180617|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1897 - 10 - - - 1 - 13.4678 - 23 - 9.40133 - 2 - 6 - 4 - 8 - 0 - 0 - 4 - 5 - 0 - 5 - QYQTP - RYQTP - +YQTP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 41 - Query_41 - M_2015 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 42 - Query_42 - M_2016 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 43 - Query_43 - M_2017 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 44 - Query_44 - M_2018 - 9 - - - 1 - gnl|BL_ORD_ID|305 - 20417|HCV-1|AAA45676.1|Hepatitis C virus genotype 1|41856 - 305 - 20 - - - 1 - 11.927 - 19 - 61.3622 - 3 - 9 - 10 - 16 - 0 - 0 - 4 - 4 - 0 - 7 - TTPKEPA - TLPGNPA - T P PA - - - - - 2 - gnl|BL_ORD_ID|1545 - 141216|envelope glycoprotein I|NP_044669.1|Human alphaherpesvirus 1|10298 - 1545 - 9 - - - 1 - 11.5418 - 18 - 134.458 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 6 - 0 - 9 - APTTPKEPA - APASVYQPA - AP + +PA - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 45 - Query_45 - M_2019 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 46 - Query_46 - M_2020 - 9 - - - 1 - gnl|BL_ORD_ID|1263 - 98540|trans-sialidase, putative|EAN88532.1|Trypanosoma cruzi|5693 - 1263 - 10 - - - 1 - 11.1566 - 17 - 242.571 - 3 - 9 - 4 - 10 - 0 - 0 - 6 - 7 - 0 - 7 - LLLLLVV - VLLLLVV - +LLLLVV - - - - - 2 - gnl|BL_ORD_ID|1254 - 98224|trans-sialidase, putative|EAN82076.1|Trypanosoma cruzi|5693 - 1254 - 10 - - - 1 - 11.1566 - 17 - 286.165 - 4 - 9 - 1 - 6 - 0 - 0 - 6 - 6 - 0 - 6 - LLLLVV - LLLLVV - LLLLVV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 47 - Query_47 - M_2021 - 9 - - - 1 - gnl|BL_ORD_ID|1263 - 98540|trans-sialidase, putative|EAN88532.1|Trypanosoma cruzi|5693 - 1263 - 10 - - - 1 - 11.1566 - 17 - 231.802 - 3 - 8 - 5 - 10 - 0 - 0 - 6 - 6 - 0 - 6 - LLLLVV - LLLLVV - LLLLVV - - - - - 2 - gnl|BL_ORD_ID|1254 - 98224|trans-sialidase, putative|EAN82076.1|Trypanosoma cruzi|5693 - 1254 - 10 - - - 1 - 11.1566 - 17 - 250.006 - 3 - 9 - 1 - 7 - 0 - 0 - 6 - 7 - 0 - 7 - LLLLVVV - LLLLVVM - LLLLVV+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 48 - Query_48 - M_2022 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 49 - Query_49 - M_2023 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 50 - Query_50 - M_2024 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 51 - Query_51 - M_2025 - 9 - - - 1 - gnl|BL_ORD_ID|338 - 21242|polymerase|ACF94272.1|Hepatitis B virus|10407 - 338 - 9 - - - 1 - 13.0826 - 22 - 19.071 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 6 - 0 - 9 - GSYSMAIPL - GLYSSTVPV - G YS +P+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 52 - Query_52 - M_2026 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 53 - Query_53 - M_2027 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 54 - Query_54 - M_2028 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 55 - Query_55 - M_2029 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 56 - Query_56 - M_2030 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 57 - Query_57 - M_2031 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 58 - Query_58 - M_2032 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 59 - Query_59 - M_2033 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 60 - Query_60 - M_2034 - 9 - - - 1 - gnl|BL_ORD_ID|1140 - 75376|Genome polyprotein|P26664.3|Hepatitis C virus|11103 - 1140 - 8 - - - 1 - 13.0826 - 22 - 15.3199 - 2 - 8 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - PPKPVQV - PPKPCGI - PPKP + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 61 - Query_61 - M_2035 - 9 - - - 1 - gnl|BL_ORD_ID|1140 - 75376|Genome polyprotein|P26664.3|Hepatitis C virus|11103 - 1140 - 8 - - - 1 - 13.0826 - 22 - 14.7957 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - PPKPVQV - PPKPCGI - PPKP + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 62 - Query_62 - M_2036 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 63 - Query_63 - M_2037 - 9 - - - 1 - gnl|BL_ORD_ID|1755 - 154041|major capsid protein|CAB06743.1|Human alphaherpesvirus 2|10310 - 1755 - 15 - - - 1 - 14.2382 - 25 - 3.03951 - 2 - 8 - 7 - 13 - 0 - 0 - 4 - 6 - 0 - 7 - FPAIIYL - YPAVFYL - +PA+ YL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 64 - Query_64 - M_2038 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 65 - Query_65 - M_2039 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 66 - Query_66 - M_2040 - 9 - - - 1 - gnl|BL_ORD_ID|1755 - 154041|major capsid protein|CAB06743.1|Human alphaherpesvirus 2|10310 - 1755 - 15 - - - 1 - 14.6234 - 26 - 2.04141 - 3 - 9 - 7 - 13 - 0 - 0 - 4 - 6 - 0 - 7 - FPAIIYL - YPAVFYL - +PA+ YL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 67 - Query_67 - M_2041 - 9 - - - 1 - gnl|BL_ORD_ID|1755 - 154041|major capsid protein|CAB06743.1|Human alphaherpesvirus 2|10310 - 1755 - 15 - - - 1 - 14.6234 - 26 - 2.04141 - 3 - 9 - 7 - 13 - 0 - 0 - 4 - 6 - 0 - 7 - FPAIIYL - YPAVFYL - +PA+ YL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 68 - Query_68 - M_2042 - 9 - - - 1 - gnl|BL_ORD_ID|1755 - 154041|major capsid protein|CAB06743.1|Human alphaherpesvirus 2|10310 - 1755 - 15 - - - 1 - 14.6234 - 26 - 2.04141 - 3 - 9 - 7 - 13 - 0 - 0 - 4 - 6 - 0 - 7 - FPAIIYL - YPAVFYL - +PA+ YL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 69 - Query_69 - M_2043 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 70 - Query_70 - M_2044 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 71 - Query_71 - M_2045 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 72 - Query_72 - M_2046 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 73 - Query_73 - M_2047 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 74 - Query_74 - M_2048 - 9 - - - 1 - gnl|BL_ORD_ID|1541 - 141206|tegument protein VP11/12|NP_044648.1|Human alphaherpesvirus 1|10298 - 1541 - 9 - - - 1 - 12.6974 - 21 - 31.9494 - 2 - 7 - 4 - 9 - 0 - 0 - 4 - 4 - 0 - 6 - VQYWYY - TQYWKY - QYW Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 75 - Query_75 - M_2049 - 9 - - - 1 - gnl|BL_ORD_ID|1541 - 141206|tegument protein VP11/12|NP_044648.1|Human alphaherpesvirus 1|10298 - 1541 - 9 - - - 1 - 12.6974 - 21 - 31.9494 - 2 - 7 - 4 - 9 - 0 - 0 - 4 - 4 - 0 - 6 - VQYWYY - TQYWKY - QYW Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 76 - Query_76 - M_2050 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 77 - Query_77 - M_2051 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 78 - Query_78 - M_2052 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 79 - Query_79 - M_2053 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 80 - Query_80 - M_2054 - 9 - - - 1 - gnl|BL_ORD_ID|555 - 34101|X protein|ACH95876.1|Hepatitis B virus|10407 - 555 - 10 - - - 1 - 11.5418 - 18 - 115.311 - 1 - 8 - 1 - 8 - 0 - 0 - 3 - 7 - 0 - 8 - ELMHFKTL - KVLHKRTL - +++H +TL - - - - - 2 - gnl|BL_ORD_ID|1042 - 69524|X protein|ACH95876.1|Hepatitis B virus|10407 - 1042 - 9 - - - 1 - 11.1566 - 17 - 221.814 - 2 - 8 - 1 - 7 - 0 - 0 - 3 - 6 - 0 - 7 - LMHFKTL - VLHKRTL - ++H +TL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 81 - Query_81 - M_2055 - 9 - - - 1 - gnl|BL_ORD_ID|775 - 51604|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 - 775 - 10 - - - 1 - 14.6234 - 26 - 1.78499 - 4 - 9 - 3 - 8 - 0 - 0 - 4 - 6 - 0 - 6 - DWSNGI - DYSNGL - D+SNG+ - - - - - 2 - gnl|BL_ORD_ID|623 - 37498|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 - 623 - 10 - - - 1 - 10.7714 - 16 - 303.747 - 1 - 8 - 2 - 9 - 0 - 0 - 3 - 4 - 0 - 8 - ILGDWSNG - LLGLWGTA - +LG W - - - - - 3 - gnl|BL_ORD_ID|615 - 37350|trans-sialidase|XP_818394.1|Trypanosoma cruzi|5693 - 615 - 10 - - - 1 - 10.7714 - 16 - 303.747 - 1 - 8 - 1 - 8 - 0 - 0 - 3 - 4 - 0 - 8 - ILGDWSNG - LLGLWGTA - +LG W - - - - - 4 - gnl|BL_ORD_ID|321 - 21004|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 - 321 - 10 - - - 1 - 7.30463 - 7 - 14472.4 - 4 - 5 - 7 - 8 - 0 - 0 - 1 - 1 - 0 - 2 - DW - LW - W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 82 - Query_82 - M_2056 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 83 - Query_83 - M_2057 - 9 - - - 1 - gnl|BL_ORD_ID|847 - 55336|EBNA-1|YP_401677.1|Human gammaherpesvirus 4|10376 - 847 - 15 - - - 1 - 12.3122 - 20 - 58.4135 - 3 - 7 - 11 - 15 - 0 - 0 - 4 - 4 - 0 - 5 - HGGTN - HGGTG - HGGT - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 84 - Query_84 - M_2058 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 85 - Query_85 - M_2059 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 86 - Query_86 - M_2060 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_120070_2_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_120070_2_T.fasta deleted file mode 100755 index 415651ea..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_120070_2_T.fasta +++ /dev/null @@ -1,76 +0,0 @@ ->M_2061 -GDASKVWVW ->M_2062 -STFVHGNKI ->M_2063 -GEEAEASAV ->M_2064 -TTSPSNTLV ->M_2065 -STGLQYATK ->M_2066 -SVLRCVHLL ->M_2067 -GRNSFKVRV ->M_2068 -MRTLLGDLV ->M_2069 -RWDRKPMQI ->M_2070 -SRSTIFMRL ->M_2071 -PHLTQGNEI ->M_2072 -ASTFVHGNK ->M_2073 -ENAGPQNMK ->M_2074 -MGQEIAALK ->M_2075 -NLLGRNSFK ->M_2076 -QAVCVTKPK ->M_2077 -LRCVHLLRI ->M_2078 -FVHGNKIYV ->M_2079 -ATKFIKKRR ->M_2080 -VHLLRIFKV ->M_2081 -LANAPRTLK ->M_2082 -WRLTWDRHL ->M_2083 -CTGPPLAPR ->M_2084 -NLTRASSKR ->M_2085 -RRSGPSPTV ->M_2086 -DLVAHYVHR ->M_2087 -SSLEGFATR ->M_2088 -LEDLGWANW ->M_2089 -CVHLLRIFK ->M_2090 -TIQAVCVTK ->M_2091 -ITCMPGSVR ->M_2092 -CSIPSICEK ->M_2093 -SSRSTIFMR ->M_2094 -SVTKASNLK ->M_2095 -YATKFIKKR ->M_2096 -FSSSDDSPR ->M_2097 -VHGNKIYVL ->M_2098 -WANWVLSPR diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_120070_2_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_120070_2_T_iedb.xml deleted file mode 100755 index 22e96f0f..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_120070_2_T_iedb.xml +++ /dev/null @@ -1,1584 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_2061 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_2061 - 9 - - - 1 - gnl|BL_ORD_ID|341 - 21385|polyprotein|AAY82034.1|Hepatitis C virus genotype 1|41856 - 341 - 10 - - - 1 - 15.779 - 29 - 0.401267 - 1 - 8 - 1 - 8 - 0 - 0 - 5 - 7 - 0 - 8 - GDASKVWV - GNASRCWV - G+AS+ WV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 2 - Query_2 - M_2062 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_2063 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_2064 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_2065 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_2066 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_2067 - 9 - - - 1 - gnl|BL_ORD_ID|617 - 37364|P53_HUMAN Cellular tumor antigen p53 (Tumor suppressor p53) (Phosphoprotein p53) (Antigen NY-CO-13)|P04637.2|Homo sapiens|9606 - 617 - 9 - - - 1 - 16.5494 - 31 - 0.265948 - 1 - 7 - 3 - 9 - 0 - 0 - 6 - 7 - 0 - 7 - GRNSFKV - GRNSFEV - GRNSF+V - - - - - 2 - gnl|BL_ORD_ID|1613 - 143740|polyprotein|ACF60462.1|Hepatovirus A|12092 - 1613 - 9 - - - 1 - 13.0826 - 22 - 14.4474 - 2 - 7 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - RNSFKV - RNEFRV - RN F+V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 8 - Query_8 - M_2068 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_2069 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_2070 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_2071 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_2072 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_2073 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_2074 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_2075 - 9 - - - 1 - gnl|BL_ORD_ID|617 - 37364|P53_HUMAN Cellular tumor antigen p53 (Tumor suppressor p53) (Phosphoprotein p53) (Antigen NY-CO-13)|P04637.2|Homo sapiens|9606 - 617 - 9 - - - 1 - 18.0902 - 35 - 0.111589 - 2 - 9 - 1 - 8 - 0 - 0 - 7 - 8 - 0 - 8 - LLGRNSFK - LLGRNSFE - LLGRNSF+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 16 - Query_16 - M_2076 - 9 - - - 1 - gnl|BL_ORD_ID|1645 - 146317|polyprotein|ADF97231.1|Hepatitis C virus subtype 3a|356426 - 1645 - 9 - - - 1 - 13.0826 - 22 - 13.7128 - 3 - 8 - 1 - 6 - 0 - 0 - 3 - 5 - 0 - 6 - VCVTKP - ICLTHP - +C+T P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 17 - Query_17 - M_2077 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_2078 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_2079 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_2080 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_2081 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 22 - Query_22 - M_2082 - 9 - - - 1 - gnl|BL_ORD_ID|1539 - 140769|LOW MOLECULAR WEIGHT PROTEIN ANTIGEN 7 ESXH (10 kDa ANTIGEN) (CFP-7) (PROTEIN TB10.4)|CAA17363.1|Mycobacterium tuberculosis H37Rv|83332 - 1539 - 9 - - - 1 - 12.3122 - 20 - 59.6102 - 1 - 9 - 1 - 9 - 0 - 0 - 2 - 6 - 0 - 9 - WRLTWDRHL - WQAQWNQAM - W+ W++ + - - - - - 2 - gnl|BL_ORD_ID|1092 - 72233|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 - 1092 - 15 - - - 1 - 11.1566 - 17 - 190.157 - 1 - 6 - 1 - 6 - 0 - 0 - 2 - 4 - 0 - 6 - WRLTWD - WAIKWE - W + W+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 23 - Query_23 - M_2083 - 9 - - - 1 - gnl|BL_ORD_ID|1950 - 181035|||| - 1950 - 44 - - - 1 - 13.4678 - 23 - 10.2905 - 1 - 9 - 20 - 28 - 0 - 0 - 5 - 5 - 0 - 9 - CTGPPLAPR - CGGVYLLPR - C G L PR - - - - - 2 - gnl|BL_ORD_ID|344 - 21638|protein F|ABV46152.2|Hepatitis C virus (isolate Japanese)|11116 - 344 - 9 - - - 1 - 11.927 - 19 - 95.9763 - 3 - 8 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - GPPLAP - GPGLSP - GP L+P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 24 - Query_24 - M_2084 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_2085 - 9 - - - 1 - gnl|BL_ORD_ID|1829 - 179799|hypothetical protein|NP_301670.1|Mycobacterium leprae TN|272631 - 1829 - 9 - - - 1 - 12.3122 - 20 - 53.938 - 4 - 9 - 1 - 6 - 0 - 0 - 4 - 4 - 0 - 6 - GPSPTV - GPVPAV - GP P V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 26 - Query_26 - M_2086 - 9 - - - 1 - gnl|BL_ORD_ID|1714 - 150377|polyprotein|AGS49173.1|Dengue virus 2|11060 - 1714 - 9 - - - 1 - 13.853 - 24 - 7.45662 - 2 - 6 - 3 - 7 - 0 - 0 - 5 - 5 - 0 - 5 - LVAHY - LVAHY - LVAHY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 27 - Query_27 - M_2087 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 28 - Query_28 - M_2088 - 9 - - - 1 - gnl|BL_ORD_ID|1143 - 75436|Polyprotein|P90247|Hepatitis C virus|11103 - 1143 - 20 - - - 1 - 16.5494 - 31 - 0.231862 - 2 - 9 - 9 - 16 - 0 - 0 - 6 - 6 - 0 - 8 - EDLGWANW - EGLGWAGW - E LGWA W - - - - - 2 - gnl|BL_ORD_ID|1144 - 75438|polyprotein|AAF65962.1|Hepatitis C virus|11103 - 1144 - 20 - - - 1 - 16.1642 - 30 - 0.347768 - 2 - 9 - 9 - 16 - 0 - 0 - 5 - 6 - 0 - 8 - EDLGWANW - EGMGWAGW - E +GWA W - - - - - 3 - gnl|BL_ORD_ID|710 - 43624|Genome polyprotein|P26660.3|Hepatitis C virus isolate HC-J6|11113 - 710 - 9 - - - 1 - 16.1642 - 30 - 0.349175 - 2 - 9 - 2 - 9 - 0 - 0 - 6 - 6 - 0 - 8 - EDLGWANW - EGLGWAGW - E LGWA W - - - - - 4 - gnl|BL_ORD_ID|116 - 7999|core protein|BAA82580.1|Hepatitis C virus|11103 - 116 - 9 - - - 1 - 16.1642 - 30 - 0.356759 - 2 - 9 - 2 - 9 - 0 - 0 - 6 - 6 - 0 - 8 - EDLGWANW - EGLGWAGW - E LGWA W - - - - - 5 - gnl|BL_ORD_ID|712 - 43628|polyprotein|BAA03375.1|Hepatitis C virus subtype 1b|31647 - 712 - 9 - - - 1 - 15.779 - 29 - 0.457844 - 2 - 9 - 2 - 9 - 0 - 0 - 5 - 6 - 0 - 8 - EDLGWANW - EGMGWAGW - E +GWA W - - - - - 6 - gnl|BL_ORD_ID|713 - 43756|Genome polyprotein|SRC279960|Hepatitis C virus subtype 2a|31649 - 713 - 9 - - - 1 - 15.0086 - 27 - 1.05395 - 2 - 9 - 2 - 9 - 0 - 0 - 5 - 5 - 0 - 8 - EDLGWANW - ETCGWAGW - E GWA W - - - - - 7 - gnl|BL_ORD_ID|577 - 36352|Polyprotein|P90247|Hepatitis C virus|11103 - 577 - 20 - - - 1 - 15.0086 - 27 - 1.17519 - 4 - 9 - 1 - 6 - 0 - 0 - 5 - 5 - 0 - 6 - LGWANW - LGWAGW - LGWA W - - - - - 8 - gnl|BL_ORD_ID|708 - 43619|Genome polyprotein|P26664.3|Hepatitis C virus|11103 - 708 - 9 - - - 1 - 15.0086 - 27 - 1.21609 - 2 - 9 - 2 - 9 - 0 - 0 - 5 - 5 - 0 - 8 - EDLGWANW - EGCGWAGW - E GWA W - - - - - 9 - gnl|BL_ORD_ID|711 - 43627|core protein|AAX68853.1|Hepatitis C virus subtype 1b|31647 - 711 - 9 - - - 1 - 15.0086 - 27 - 1.2556 - 2 - 9 - 2 - 9 - 0 - 0 - 5 - 5 - 0 - 8 - EDLGWANW - EGLGWTGW - E LGW W - - - - - 10 - gnl|BL_ORD_ID|2120 - 186453|polyprotein|AFP27208.1|Dengue virus 4|11070 - 2120 - 10 - - - 1 - 13.4678 - 23 - 7.76238 - 5 - 9 - 6 - 10 - 0 - 0 - 4 - 4 - 0 - 5 - GWANW - GWKNW - GW NW - - - - - 11 - gnl|BL_ORD_ID|315 - 20894|polyprotein [Hepatitis C virus]|BAF91806.1|Hepatitis C virus|11103 - 315 - 9 - - - 1 - 13.4678 - 23 - 10.0233 - 4 - 9 - 2 - 7 - 0 - 0 - 4 - 4 - 0 - 6 - LGWANW - LGWVGW - LGW W - - - - - 12 - gnl|BL_ORD_ID|160 - 12183|EBNA3C latent protein|CAD53421.1|Human gammaherpesvirus 4|10376 - 160 - 9 - - - 1 - 12.6974 - 21 - 32.4991 - 4 - 9 - 4 - 9 - 0 - 0 - 3 - 5 - 0 - 6 - LGWANW - VGWRHW - +GW +W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 29 - Query_29 - M_2089 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 30 - Query_30 - M_2090 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 31 - Query_31 - M_2091 - 9 - - - 1 - gnl|BL_ORD_ID|1176 - 79454|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 1176 - 15 - - - 1 - 13.853 - 24 - 7.10896 - 1 - 8 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - ITCMPGSV - IFCHPGQL - I C PG + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 32 - Query_32 - M_2092 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 33 - Query_33 - M_2093 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 34 - Query_34 - M_2094 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 35 - Query_35 - M_2095 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 36 - Query_36 - M_2096 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 37 - Query_37 - M_2097 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 38 - Query_38 - M_2098 - 9 - - - 1 - gnl|BL_ORD_ID|577 - 36352|Polyprotein|P90247|Hepatitis C virus|11103 - 577 - 20 - - - 1 - 19.631 - 39 - 0.0260695 - 1 - 9 - 3 - 11 - 0 - 0 - 7 - 8 - 0 - 9 - WANWVLSPR - WAGWLLSPR - WA W+LSPR - - - - - 2 - gnl|BL_ORD_ID|1144 - 75438|polyprotein|AAF65962.1|Hepatitis C virus|11103 - 1144 - 20 - - - 1 - 17.3198 - 33 - 0.118837 - 1 - 8 - 13 - 20 - 0 - 0 - 6 - 7 - 0 - 8 - WANWVLSP - WAGWLLSP - WA W+LSP - - - - - 3 - gnl|BL_ORD_ID|1143 - 75436|Polyprotein|P90247|Hepatitis C virus|11103 - 1143 - 20 - - - 1 - 17.3198 - 33 - 0.120923 - 1 - 8 - 13 - 20 - 0 - 0 - 6 - 7 - 0 - 8 - WANWVLSP - WAGWLLSP - WA W+LSP - - - - - 4 - gnl|BL_ORD_ID|1142 - 75435|largest ORF|AAB02128.1|Hepatitis C virus|11103 - 1142 - 20 - - - 1 - 15.779 - 29 - 0.412688 - 1 - 8 - 13 - 20 - 0 - 0 - 5 - 6 - 0 - 8 - WANWVLSP - WMGWLLSP - W W+LSP - - - - - 5 - gnl|BL_ORD_ID|315 - 20894|polyprotein [Hepatitis C virus]|BAF91806.1|Hepatitis C virus|11103 - 315 - 9 - - - 1 - 12.3122 - 20 - 65.8473 - 1 - 6 - 4 - 9 - 0 - 0 - 3 - 4 - 0 - 6 - WANWVL - WVGWLL - W W+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_120920_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_120920_1_T.fasta deleted file mode 100755 index bb5924de..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_120920_1_T.fasta +++ /dev/null @@ -1,126 +0,0 @@ ->M_2099 -LSLPGGHTA ->M_2100 -FRAAAEAAV ->M_2101 -FRAAAEAAV ->M_2102 -TSSDHSFSL ->M_2103 -TSSDHSFSL ->M_2104 -NHQQFYHSV ->M_2105 -NHQQFYHSV ->M_2106 -DYSELPHHV ->M_2107 -HHVSTEQEI ->M_2108 -HHVSTEQEI ->M_2109 -EIISLWSPW ->M_2110 -NQDPISPSL ->M_2111 -ENASAYLTL ->M_2112 -KKMENASAY ->M_2113 -RRHSLPRRC ->M_2114 -NMCRCLVTV ->M_2115 -RLMSARLAI ->M_2116 -SYSYLGLRL ->M_2117 -YSYLGLRLM ->M_2118 -YSYLGLRLM ->M_2119 -RFSQAFFYM ->M_2120 -RRFSQAFFY ->M_2121 -FMMPRSSSC ->M_2122 -FMMPRSSSC ->M_2123 -IPAMEIFMV ->M_2124 -LMAASIPAM ->M_2125 -DTLQATAML ->M_2126 -QATAMLDIV ->M_2127 -TVTRTTATV ->M_2128 -EHFPLCKTV ->M_2129 -EHFPLCKTV ->M_2130 -WPQCHPEEI ->M_2131 -YSYSCGHYE ->M_2132 -SHFERDYRV ->M_2133 -FQTLMPDVV ->M_2134 -FQTLMPDVV ->M_2135 -MPDVVHQSL ->M_2136 -LWYTLYLMI ->M_2137 -LYLMITTFF ->M_2138 -MITTFFFPL ->M_2139 -TLYLMITTF ->M_2140 -YLMITTFFF ->M_2141 -YTLYLMITT ->M_2142 -PTSPFQTTI ->M_2143 -TAERSIPTV ->M_2144 -ERPCHREPL ->M_2145 -SSSSGPFPL ->M_2146 -ELATFAKAY ->M_2147 -RWDEELATF ->M_2148 -ELIDLISRV ->M_2149 -ELIDLISRV ->M_2150 -QVNQKSSVV ->M_2151 -VRLELIDLI ->M_2152 -YEEYRGRLL ->M_2153 -YEEYRGRLL ->M_2154 -CRNVHTPDL ->M_2155 -YSRDQAQAL ->M_2156 -YSRDQAQAL ->M_2157 -FEVEGRDLL ->M_2158 -FFFLCVCVF ->M_2159 -FFLCVCVFV ->M_2160 -RRYPHKRCI ->M_2161 -RRYPHKRCI diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_120920_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_120920_1_T_iedb.xml deleted file mode 100755 index ae438936..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_120920_1_T_iedb.xml +++ /dev/null @@ -1,1853 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_2099 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_2099 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_2100 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_2101 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_2102 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_2103 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_2104 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_2105 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_2106 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_2107 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_2108 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_2109 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_2110 - 9 - - - 1 - gnl|BL_ORD_ID|2271 - 419002|PPE family protein PPE68|KAM81677.1|Mycobacterium tuberculosis H37Ra|419947 - 2271 - 10 - - - 1 - 13.4678 - 23 - 9.40133 - 2 - 9 - 3 - 10 - 0 - 0 - 3 - 7 - 0 - 8 - QDPISPSL - EKPVAPSV - + P++PS+ - - - - - 2 - gnl|BL_ORD_ID|811 - 54342|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 - 811 - 20 - - - 1 - 13.0826 - 22 - 14.406 - 3 - 9 - 12 - 18 - 0 - 0 - 4 - 5 - 0 - 7 - DPISPSL - DPLFPEL - DP+ P L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 13 - Query_13 - M_2111 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_2112 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_2113 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_2114 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_2115 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_2116 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_2117 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_2118 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_2119 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 22 - Query_22 - M_2120 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_2121 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_2122 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_2123 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_2124 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_2125 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 28 - Query_28 - M_2126 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 29 - Query_29 - M_2127 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 30 - Query_30 - M_2128 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 31 - Query_31 - M_2129 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 32 - Query_32 - M_2130 - 9 - - - 1 - gnl|BL_ORD_ID|48 - 3051|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 - 48 - 20 - - - 1 - 18.8606 - 37 - 0.0470713 - 1 - 9 - 8 - 16 - 0 - 0 - 6 - 7 - 0 - 9 - WPQCHPEEI - LPQCSPDEI - PQC P+EI - - - - - 2 - gnl|BL_ORD_ID|20 - 1230|gag protein|AAW03034.1|Human immunodeficiency virus 1|11676 - 20 - 9 - - - 1 - 13.0826 - 22 - 14.9585 - 1 - 6 - 3 - 8 - 0 - 0 - 3 - 4 - 0 - 6 - WPQCHP - WDRVHP - W + HP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 33 - Query_33 - M_2131 - 9 - - - 1 - gnl|BL_ORD_ID|147 - 10939|polyprotein|BAB18806.1|Hepatitis C virus subtype 1a|31646 - 147 - 9 - - - 1 - 12.3122 - 20 - 42.6373 - 1 - 8 - 2 - 9 - 0 - 0 - 4 - 4 - 0 - 8 - YSYSCGHY - YPYRLWHY - Y Y HY - - - - - 2 - gnl|BL_ORD_ID|1145 - 75448|polyprotein|BAB18806.1|Hepatitis C virus|11103 - 1145 - 8 - - - 1 - 12.3122 - 20 - 45.3667 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 4 - 0 - 8 - YSYSCGHY - YPYRLWHY - Y Y HY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 34 - Query_34 - M_2132 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 35 - Query_35 - M_2133 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 36 - Query_36 - M_2134 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 37 - Query_37 - M_2135 - 9 - - - 1 - gnl|BL_ORD_ID|1474 - 130953|G1 and G2 surface glycoprotein precursor|AAG22532.1|Andes hantavirus|46607 - 1474 - 9 - - - 1 - 15.3938 - 28 - 0.556982 - 1 - 7 - 2 - 8 - 0 - 0 - 5 - 5 - 0 - 7 - MPDVVHQ - MPDVAHS - MPDV H - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 38 - Query_38 - M_2136 - 9 - - - 1 - gnl|BL_ORD_ID|1 - 118|envelope glycoprotein|ABS76372.1|Human immunodeficiency virus 1|11676 - 1 - 20 - - - 1 - 12.6974 - 21 - 24.4238 - 1 - 6 - 5 - 10 - 0 - 0 - 4 - 5 - 0 - 6 - LWYTLY - LWVTVY - LW T+Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 39 - Query_39 - M_2137 - 9 - - - 1 - gnl|BL_ORD_ID|1525 - 140651|granule antigen protein GRA6|XP_002371939.1|Toxoplasma gondii ME49|508771 - 1525 - 9 - - - 1 - 12.6974 - 21 - 28.8346 - 4 - 9 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - MITTFF - MLTAFF - M+T FF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 40 - Query_40 - M_2138 - 9 - - - 1 - gnl|BL_ORD_ID|1525 - 140651|granule antigen protein GRA6|XP_002371939.1|Toxoplasma gondii ME49|508771 - 1525 - 9 - - - 1 - 12.6974 - 21 - 33.058 - 1 - 6 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - MITTFF - MLTAFF - M+T FF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 41 - Query_41 - M_2139 - 9 - - - 1 - gnl|BL_ORD_ID|1738 - 150639|polyprotein|AGO67249.1|Dengue virus 2|11060 - 1738 - 10 - - - 1 - 14.6234 - 26 - 1.97194 - 1 - 9 - 1 - 9 - 0 - 0 - 6 - 7 - 0 - 9 - TLYLMITTF - TLYAVATTF - TLY + TTF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 42 - Query_42 - M_2140 - 9 - - - 1 - gnl|BL_ORD_ID|1525 - 140651|granule antigen protein GRA6|XP_002371939.1|Toxoplasma gondii ME49|508771 - 1525 - 9 - - - 1 - 12.6974 - 21 - 35.3877 - 3 - 8 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - MITTFF - MLTAFF - M+T FF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 43 - Query_43 - M_2141 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 44 - Query_44 - M_2142 - 9 - - - 1 - gnl|BL_ORD_ID|2245 - 232154|rhoptry protein, putative / protein kinase domain-containing protein|XP_002367757.1|Toxoplasma gondii type II|1209523 - 2245 - 19 - - - 1 - 13.0826 - 22 - 18.5716 - 1 - 6 - 2 - 7 - 0 - 0 - 4 - 4 - 0 - 6 - PTSPFQ - PERPFQ - P PFQ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 45 - Query_45 - M_2143 - 9 - - - 1 - gnl|BL_ORD_ID|1755 - 154041|major capsid protein|CAB06743.1|Human alphaherpesvirus 2|10310 - 1755 - 15 - - - 1 - 13.4678 - 23 - 11.1066 - 3 - 9 - 4 - 10 - 0 - 0 - 4 - 5 - 0 - 7 - ERSIPTV - DRSYPAV - +RS P V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 46 - Query_46 - M_2144 - 9 - - - 1 - gnl|BL_ORD_ID|1871 - 180488|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1871 - 10 - - - 1 - 13.853 - 24 - 6.41039 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - PCHREPL - PGHEEPI - P H EP+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 47 - Query_47 - M_2145 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 48 - Query_48 - M_2146 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 49 - Query_49 - M_2147 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 50 - Query_50 - M_2148 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 51 - Query_51 - M_2149 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 52 - Query_52 - M_2150 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 53 - Query_53 - M_2151 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 54 - Query_54 - M_2152 - 9 - - - 1 - gnl|BL_ORD_ID|376 - 23288|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 - 376 - 15 - - - 1 - 13.853 - 24 - 5.98058 - 1 - 8 - 7 - 14 - 0 - 0 - 3 - 7 - 0 - 8 - YEEYRGRL - YQDWLGRM - Y+++ GR+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 55 - Query_55 - M_2153 - 9 - - - 1 - gnl|BL_ORD_ID|376 - 23288|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 - 376 - 15 - - - 1 - 13.853 - 24 - 5.98058 - 1 - 8 - 7 - 14 - 0 - 0 - 3 - 7 - 0 - 8 - YEEYRGRL - YQDWLGRM - Y+++ GR+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 56 - Query_56 - M_2154 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 57 - Query_57 - M_2155 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 58 - Query_58 - M_2156 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 59 - Query_59 - M_2157 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 60 - Query_60 - M_2158 - 9 - - - 1 - gnl|BL_ORD_ID|750 - 49831|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 - 750 - 15 - - - 1 - 11.927 - 19 - 74.9817 - 1 - 8 - 4 - 11 - 0 - 0 - 3 - 5 - 0 - 8 - FFFLCVCV - LLILCLCL - LC+C+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 61 - Query_61 - M_2159 - 9 - - - 1 - gnl|BL_ORD_ID|750 - 49831|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 - 750 - 15 - - - 1 - 11.5418 - 18 - 131.587 - 1 - 7 - 5 - 11 - 0 - 0 - 3 - 5 - 0 - 7 - FFLCVCV - LILCLCL - LC+C+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 62 - Query_62 - M_2160 - 9 - - - 1 - gnl|BL_ORD_ID|1140 - 75376|Genome polyprotein|P26664.3|Hepatitis C virus|11103 - 1140 - 8 - - - 1 - 12.6974 - 21 - 24.9053 - 3 - 8 - 1 - 6 - 0 - 0 - 4 - 4 - 0 - 6 - YPHKRC - YPPKPC - YP K C - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 63 - Query_63 - M_2161 - 9 - - - 1 - gnl|BL_ORD_ID|1140 - 75376|Genome polyprotein|P26664.3|Hepatitis C virus|11103 - 1140 - 8 - - - 1 - 12.6974 - 21 - 24.9053 - 3 - 8 - 1 - 6 - 0 - 0 - 4 - 4 - 0 - 6 - YPHKRC - YPPKPC - YP K C - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_121511_2_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_121511_2_T.fasta deleted file mode 100755 index ac5e8004..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_121511_2_T.fasta +++ /dev/null @@ -1,116 +0,0 @@ ->M_2162 -NMSRCCIRV ->M_2163 -GLLGNGIGY ->M_2164 -LLGNGIGYV ->M_2165 -KILSLHLLL ->M_2166 -HPAFISLAF ->M_2167 -FPREKTPEV ->M_2168 -WPPWLKGKY ->M_2169 -IVLTGHNAY ->M_2170 -IVLTGHNAY ->M_2171 -VLTGHNAYL ->M_2172 -QAQALGIPL ->M_2173 -IVFFANNGF ->M_2174 -HSESSDSEV ->M_2175 -RRGSGHSEY ->M_2176 -LIMEDLVCY ->M_2177 -MEDLPAACM ->M_2178 -HPMASNSGG ->M_2179 -DVEWRWHSY ->M_2180 -DVEWRWHSY ->M_2181 -ILPTCSPLV ->M_2182 -LPTCSPLVF ->M_2183 -VHFWPGYEY ->M_2184 -SPEGDDTLY ->M_2185 -TLVPTAPEL ->M_2186 -HLIGSTTLA ->M_2187 -LIGSTTLAM ->M_2188 -LLMHLIGST ->M_2189 -IAHQWYWTY ->M_2190 -IAHQWYWTY ->M_2191 -LLEENGDVF ->M_2192 -QRCACPHGY ->M_2193 -CMYDPLGTI ->M_2194 -GPHRITCMY ->M_2195 -NESCLSMSE ->M_2196 -VANESCLSM ->M_2197 -EESELYAQL ->M_2198 -RTAQCFLCV ->M_2199 -KYSNYVWPI ->M_2200 -FIFEIVGFT ->M_2201 -DSSGQSNRY ->M_2202 -DSSSWSNRY ->M_2203 -DSSSWSNRY ->M_2204 -NRYGGGGRY ->M_2205 -NRYGGGGRY ->M_2206 -NEHGHRRKI ->M_2207 -HTSLRGFLY ->M_2208 -ALNEMFCQL ->M_2209 -NEMFCQLAK ->M_2210 -GLYAIAVML ->M_2211 -MLSFSRIAY ->M_2212 -MLSFSRIAY ->M_2213 -YAIAVMLSF ->M_2214 -AEWDSLYVL ->M_2215 -LAEWDSLYV ->M_2216 -VLAEWDSLY ->M_2217 -VLAEWDSLY ->M_2218 -GKAFSQSAY ->M_2219 -KAFSQSAYL diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_121511_2_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_121511_2_T_iedb.xml deleted file mode 100755 index bbcebff2..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_121511_2_T_iedb.xml +++ /dev/null @@ -1,1923 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_2162 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_2162 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_2163 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_2164 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_2165 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_2166 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_2167 - 9 - - - 1 - gnl|BL_ORD_ID|1181 - 88849|IE62|AAP32859.1|Human alphaherpesvirus 3|10335 - 1181 - 9 - - - 1 - 14.2382 - 25 - 2.85402 - 1 - 7 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - FPREKTP - LPRSRTP - PR +TP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 7 - Query_7 - M_2168 - 9 - - - 1 - gnl|BL_ORD_ID|2285 - 419170|polyprotein|ABR25251.1|Hepatitis C virus|11103 - 2285 - 9 - - - 1 - 11.1566 - 17 - 202.191 - 4 - 8 - 4 - 8 - 0 - 0 - 4 - 5 - 0 - 5 - WLKGK - YLKGK - +LKGK - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 8 - Query_8 - M_2169 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_2170 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_2171 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_2172 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_2173 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_2174 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_2175 - 9 - - - 1 - gnl|BL_ORD_ID|1871 - 180488|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1871 - 10 - - - 1 - 13.0826 - 22 - 16.3922 - 3 - 8 - 1 - 6 - 0 - 0 - 4 - 4 - 0 - 6 - GSGHSE - GPGHEE - G GH E - - - - - 2 - gnl|BL_ORD_ID|657 - 38974|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 657 - 11 - - - 1 - 12.3122 - 20 - 38.8163 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 7 - 0 - 9 - RRGSGHSEY - QRGPQYSEH - +RG +SE+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 15 - Query_15 - M_2176 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_2177 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_2178 - 9 - - - 1 - gnl|BL_ORD_ID|1636 - 146282|polyprotein|ADF97231.1|Hepatitis C virus subtype 3a|356426 - 1636 - 17 - - - 1 - 12.3122 - 20 - 54.7088 - 2 - 9 - 5 - 12 - 0 - 0 - 4 - 5 - 0 - 8 - PMASNSGG - PIALLKGG - P+A GG - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 18 - Query_18 - M_2179 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_2180 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_2181 - 9 - - - 1 - gnl|BL_ORD_ID|863 - 56502|polyprotein|BAD73994.1|Hepatitis C virus subtype 1b|31647 - 863 - 9 - - - 1 - 13.853 - 24 - 6.16125 - 3 - 8 - 4 - 9 - 0 - 0 - 4 - 4 - 0 - 6 - PTCSPL - PACKPL - P C PL - - - - - 2 - gnl|BL_ORD_ID|1211 - 96366|polyprotein|ABR25251.1|Hepatitis C virus|11103 - 1211 - 12 - - - 1 - 13.4678 - 23 - 11.0162 - 3 - 9 - 5 - 11 - 0 - 0 - 4 - 5 - 0 - 7 - PTCSPLV - PPCKPLL - P C PL+ - - - - - 3 - gnl|BL_ORD_ID|745 - 48458|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 - 745 - 20 - - - 1 - 11.5418 - 18 - 98.2529 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - LPTCSPLV - LPVVFPIV - LP P+V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 21 - Query_21 - M_2182 - 9 - - - 1 - gnl|BL_ORD_ID|863 - 56502|polyprotein|BAD73994.1|Hepatitis C virus subtype 1b|31647 - 863 - 9 - - - 1 - 13.853 - 24 - 6.16125 - 2 - 7 - 4 - 9 - 0 - 0 - 4 - 4 - 0 - 6 - PTCSPL - PACKPL - P C PL - - - - - 2 - gnl|BL_ORD_ID|1211 - 96366|polyprotein|ABR25251.1|Hepatitis C virus|11103 - 1211 - 12 - - - 1 - 13.4678 - 23 - 11.0162 - 2 - 8 - 5 - 11 - 0 - 0 - 4 - 5 - 0 - 7 - PTCSPLV - PPCKPLL - P C PL+ - - - - - 3 - gnl|BL_ORD_ID|745 - 48458|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 - 745 - 20 - - - 1 - 11.5418 - 18 - 107.151 - 1 - 8 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - LPTCSPLV - LPVVFPIV - LP P+V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 22 - Query_22 - M_2183 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_2184 - 9 - - - 1 - gnl|BL_ORD_ID|186 - 13701|Trans-activator protein BZLF1|P03206.2|Human gammaherpesvirus 4|10376 - 186 - 11 - - - 1 - 12.6974 - 21 - 24.627 - 2 - 9 - 4 - 11 - 0 - 0 - 4 - 5 - 0 - 8 - PEGDDTLY - PQGQLTAY - P+G T Y - - - - - 2 - gnl|BL_ORD_ID|2045 - 184531|polyprotein|AFP27208.1|Dengue virus 4|11070 - 2045 - 10 - - - 1 - 12.3122 - 20 - 61.3845 - 2 - 8 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - PEGDDTL - PESLETL - PE +TL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 24 - Query_24 - M_2185 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_2186 - 9 - - - 1 - gnl|BL_ORD_ID|901 - 59182|attachment glycoprotein|ABQ58821.1|Human metapneumovirus|162145 - 901 - 10 - - - 1 - 13.4678 - 23 - 12.859 - 2 - 8 - 4 - 10 - 0 - 0 - 6 - 6 - 0 - 7 - LIGSTTL - LIGITTL - LIG TTL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 26 - Query_26 - M_2187 - 9 - - - 1 - gnl|BL_ORD_ID|901 - 59182|attachment glycoprotein|ABQ58821.1|Human metapneumovirus|162145 - 901 - 10 - - - 1 - 13.0826 - 22 - 16.3922 - 1 - 7 - 4 - 10 - 0 - 0 - 6 - 6 - 0 - 7 - LIGSTTL - LIGITTL - LIG TTL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 27 - Query_27 - M_2188 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 28 - Query_28 - M_2189 - 9 - - - 1 - gnl|BL_ORD_ID|957 - 62903|Genome polyprotein|P27909.2|Dengue virus type 1 Hawaii|10000440 - 957 - 20 - - - 1 - 11.5418 - 18 - 98.2529 - 4 - 9 - 3 - 8 - 0 - 0 - 2 - 4 - 0 - 6 - QWYWTY - KWLWGF - +W W + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 29 - Query_29 - M_2190 - 9 - - - 1 - gnl|BL_ORD_ID|957 - 62903|Genome polyprotein|P27909.2|Dengue virus type 1 Hawaii|10000440 - 957 - 20 - - - 1 - 11.5418 - 18 - 98.2529 - 4 - 9 - 3 - 8 - 0 - 0 - 2 - 4 - 0 - 6 - QWYWTY - KWLWGF - +W W + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 30 - Query_30 - M_2191 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 31 - Query_31 - M_2192 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 32 - Query_32 - M_2193 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 33 - Query_33 - M_2194 - 9 - - - 1 - gnl|BL_ORD_ID|1173 - 79337|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 1173 - 15 - - - 1 - 12.3122 - 20 - 38.6124 - 2 - 7 - 9 - 14 - 0 - 0 - 4 - 4 - 0 - 6 - PHRITC - PHVIFC - PH I C - - - - - 2 - gnl|BL_ORD_ID|1332 - 107872|Genome polyprotein|P26664.3|Hepatitis C virus|11103 - 1332 - 10 - - - 1 - 11.927 - 19 - 106.494 - 1 - 7 - 1 - 7 - 0 - 0 - 4 - 4 - 0 - 7 - GPHRITC - GRHLIFC - G H I C - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 34 - Query_34 - M_2195 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 35 - Query_35 - M_2196 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 36 - Query_36 - M_2197 - 9 - - - 1 - gnl|BL_ORD_ID|946 - 62355|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 946 - 20 - - - 1 - 13.0826 - 22 - 20.1922 - 1 - 6 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - EESELY - EQSEFY - E+SE Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 37 - Query_37 - M_2198 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 38 - Query_38 - M_2199 - 9 - - - 1 - gnl|BL_ORD_ID|561 - 34616|pol protein|BAA32832.1|Hepatitis B virus|10407 - 561 - 9 - - - 1 - 12.6974 - 21 - 26.4654 - 1 - 7 - 1 - 7 - 0 - 0 - 3 - 6 - 0 - 7 - KYSNYVW - KYTSFPW - KY+++ W - - - - - 2 - gnl|BL_ORD_ID|1915 - 180675|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1915 - 15 - - - 1 - 10.7714 - 16 - 257.204 - 3 - 9 - 2 - 8 - 0 - 0 - 3 - 4 - 0 - 7 - SNYVWPI - STYGWNL - S Y W + - - - - - 3 - gnl|BL_ORD_ID|1711 - 150309|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1711 - 10 - - - 1 - 10.3862 - 15 - 485 - 3 - 7 - 4 - 8 - 0 - 0 - 3 - 3 - 0 - 5 - SNYVW - STYGW - S Y W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 39 - Query_39 - M_2200 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 40 - Query_40 - M_2201 - 9 - - - 1 - gnl|BL_ORD_ID|1995 - 183598|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1995 - 10 - - - 1 - 13.4678 - 23 - 9.90554 - 3 - 9 - 4 - 10 - 0 - 0 - 4 - 6 - 0 - 7 - SGQSNRY - SGKTRRY - SG++ RY - - - - - 2 - gnl|BL_ORD_ID|15 - 1095|glycoprotein gp35/37|AAC59622.1|Human gammaherpesvirus 8|37296 - 15 - 15 - - - 1 - 13.0826 - 22 - 16.6732 - 2 - 8 - 6 - 12 - 0 - 0 - 5 - 6 - 0 - 7 - SSGQSNR - NSGASNR - +SG SNR - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 41 - Query_41 - M_2202 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 42 - Query_42 - M_2203 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 43 - Query_43 - M_2204 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 44 - Query_44 - M_2205 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 45 - Query_45 - M_2206 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 46 - Query_46 - M_2207 - 9 - - - 1 - gnl|BL_ORD_ID|396 - 24302|X protein|AAP06597.1|Hepatitis B virus|10407 - 396 - 9 - - - 1 - 14.2382 - 25 - 2.75966 - 1 - 7 - 1 - 7 - 0 - 0 - 5 - 5 - 0 - 7 - HTSLRGF - HLSLRGL - H SLRG - - - - - 2 - gnl|BL_ORD_ID|395 - 24299|X protein|BAF81690.1|Hepatitis B virus|10407 - 395 - 9 - - - 1 - 14.2382 - 25 - 3.74233 - 1 - 7 - 1 - 7 - 0 - 0 - 5 - 5 - 0 - 7 - HTSLRGF - HLSLRGL - H SLRG - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 47 - Query_47 - M_2208 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 48 - Query_48 - M_2209 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 49 - Query_49 - M_2210 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 50 - Query_50 - M_2211 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 51 - Query_51 - M_2212 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 52 - Query_52 - M_2213 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 53 - Query_53 - M_2214 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 54 - Query_54 - M_2215 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 55 - Query_55 - M_2216 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 56 - Query_56 - M_2217 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 57 - Query_57 - M_2218 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 58 - Query_58 - M_2219 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_122176_2_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_122176_2_T.fasta deleted file mode 100755 index 5fe42885..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_122176_2_T.fasta +++ /dev/null @@ -1,54 +0,0 @@ ->M_2220 -RREDLTHTL ->M_2221 -RREDLTHTL ->M_2222 -ERWLRQAAF ->M_2223 -RKREEEERW ->M_2224 -THCSPNLLF ->M_2225 -HQYNIYAAL ->M_2226 -RSFTESHQY ->M_2227 -ISAKIMQQW ->M_2228 -YTDTISAKI ->M_2229 -AAVLGMLLW ->M_2230 -ISGRVVQHF ->M_2231 -IAFNHGDLL ->M_2232 -KYHYYGLHI ->M_2233 -LSRRVTQSL ->M_2234 -RRVTQSLEA ->M_2235 -KTYAPLFIW ->M_2236 -TYAPLFIWV ->M_2237 -KYIAFCINI ->M_2238 -YIAFCINIF ->M_2239 -FHYPQSIFS ->M_2240 -MKFHYPQSI ->M_2241 -NTNSNRSLI ->M_2242 -FRAYQDYFL ->M_2243 -FRAYQDYFL ->M_2244 -LHIGKDVQL ->M_2245 -QVFAAVHEW ->M_2246 -RRHTDEKPY diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_122176_2_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_122176_2_T_iedb.xml deleted file mode 100755 index 503d1aad..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_122176_2_T_iedb.xml +++ /dev/null @@ -1,1281 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_2220 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_2220 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_2221 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_2222 - 9 - - - 1 - gnl|BL_ORD_ID|357 - 22255|polyprotein|ABR27377.1|Hepatitis C virus|11103 - 357 - 9 - - - 1 - 13.853 - 24 - 5.95161 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 6 - 0 - 8 - RWLRQAAF - RWVPGAAY - RW+ AA+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 4 - Query_4 - M_2223 - 9 - - - 1 - gnl|BL_ORD_ID|2088 - 185491|polyprotein|AGO67248.1|Dengue virus 2|11060 - 2088 - 10 - - - 1 - 12.3122 - 20 - 62.4024 - 2 - 7 - 1 - 6 - 0 - 0 - 5 - 6 - 0 - 6 - KREEEE - RREEEE - +REEEE - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 5 - Query_5 - M_2224 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_2225 - 9 - - - 1 - gnl|BL_ORD_ID|790 - 52886|pp65|AAA45994.1|Human betaherpesvirus 5|10359 - 790 - 9 - - - 1 - 12.6974 - 21 - 23.4633 - 2 - 9 - 1 - 8 - 0 - 0 - 5 - 6 - 0 - 8 - QYNIYAAL - QYDPVAAL - QY+ AAL - - - - - 2 - gnl|BL_ORD_ID|2155 - 189291|||| - 2155 - 9 - - - 1 - 12.6974 - 21 - 26.0147 - 3 - 9 - 3 - 9 - 0 - 0 - 5 - 5 - 0 - 7 - YNIYAAL - YNTVAAL - YN AAL - - - - - 3 - gnl|BL_ORD_ID|791 - 52888|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 791 - 11 - - - 1 - 12.6974 - 21 - 29.1766 - 2 - 9 - 1 - 8 - 0 - 0 - 5 - 6 - 0 - 8 - QYNIYAAL - QYDPVAAL - QY+ AAL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 7 - Query_7 - M_2226 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_2227 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_2228 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_2229 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_2230 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_2231 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_2232 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_2233 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_2234 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_2235 - 9 - - - 1 - gnl|BL_ORD_ID|1011 - 67349|Latent membrane protein 2|Q69135|Human gammaherpesvirus 4|10376 - 1011 - 9 - - - 1 - 14.6234 - 26 - 1.85254 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 6 - 0 - 7 - TYAPLFI - TYGPVFM - TY P+F+ - - - - - 2 - gnl|BL_ORD_ID|2312 - 423020|polyprotein|ACE82359.1|Hepatitis C virus genotype 1|41856 - 2312 - 9 - - - 1 - 10.001 - 14 - 866.983 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 4 - 0 - 9 - KTYAPLFIW - KLYISWCLW - K Y +W - - - - - 3 - gnl|BL_ORD_ID|664 - 39591|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 - 664 - 20 - - - 1 - 9.61583 - 13 - 985.051 - 1 - 9 - 6 - 14 - 0 - 0 - 3 - 4 - 0 - 9 - KTYAPLFIW - KRYISWCLW - K Y +W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 17 - Query_17 - M_2236 - 9 - - - 1 - gnl|BL_ORD_ID|1011 - 67349|Latent membrane protein 2|Q69135|Human gammaherpesvirus 4|10376 - 1011 - 9 - - - 1 - 14.6234 - 26 - 1.62552 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 7 - 0 - 9 - TYAPLFIWV - TYGPVFMCL - TY P+F+ + - - - - - 2 - gnl|BL_ORD_ID|82 - 5952|PPE family protein|YP_177918.1|Mycobacterium tuberculosis H37Rv|83332 - 82 - 9 - - - 1 - 11.1566 - 17 - 211.79 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 4 - 0 - 9 - TYAPLFIWV - AYVPYVAWL - Y P W+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 18 - Query_18 - M_2237 - 9 - - - 1 - gnl|BL_ORD_ID|664 - 39591|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 - 664 - 20 - - - 1 - 14.2382 - 25 - 3.035 - 1 - 7 - 7 - 13 - 0 - 0 - 3 - 7 - 0 - 7 - KYIAFCI - RYISWCL - +YI++C+ - - - - - 2 - gnl|BL_ORD_ID|2312 - 423020|polyprotein|ACE82359.1|Hepatitis C virus genotype 1|41856 - 2312 - 9 - - - 1 - 13.4678 - 23 - 10.7466 - 2 - 7 - 3 - 8 - 0 - 0 - 3 - 6 - 0 - 6 - YIAFCI - YISWCL - YI++C+ - - - - - 3 - gnl|BL_ORD_ID|1120 - 74387|Genome polyprotein|P26664.3|Hepatitis C virus (isolate 1)|11104 - 1120 - 9 - - - 1 - 13.4678 - 23 - 11.5219 - 2 - 7 - 1 - 6 - 0 - 0 - 3 - 6 - 0 - 6 - YIAFCI - YISWCL - YI++C+ - - - - - 4 - gnl|BL_ORD_ID|1119 - 74386|HCV-1|AAA45676.1|Hepatitis C virus|11103 - 1119 - 8 - - - 1 - 13.4678 - 23 - 12.8716 - 2 - 7 - 1 - 6 - 0 - 0 - 3 - 6 - 0 - 6 - YIAFCI - YISWCL - YI++C+ - - - - - 5 - gnl|BL_ORD_ID|399 - 24457|polyprotein|BAA09072.1|Hepatitis C virus|11103 - 399 - 15 - - - 1 - 13.0826 - 22 - 13.39 - 1 - 8 - 5 - 12 - 0 - 0 - 4 - 6 - 0 - 8 - KYIAFCIN - KYIMACMS - KYI C++ - - - - - 6 - gnl|BL_ORD_ID|1297 - 103389|unnamed protein product [Hepatitis C virus]|BAA14035.1|Hepatitis C virus|11103 - 1297 - 20 - - - 1 - 11.5418 - 18 - 116.798 - 1 - 8 - 7 - 14 - 0 - 0 - 2 - 6 - 0 - 8 - KYIAFCIN - KFVMACMS - K++ C++ - - - - - 7 - gnl|BL_ORD_ID|1502 - 137660|L1|ACL12325.1|Human papillomavirus type 58|10598 - 1502 - 9 - - - 1 - 11.5418 - 18 - 150.225 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 6 - 0 - 9 - KYIAFCINI - KYTFWEVNL - KY + +N+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 19 - Query_19 - M_2238 - 9 - - - 1 - gnl|BL_ORD_ID|2312 - 423020|polyprotein|ACE82359.1|Hepatitis C virus genotype 1|41856 - 2312 - 9 - - - 1 - 13.4678 - 23 - 11.5219 - 1 - 6 - 3 - 8 - 0 - 0 - 3 - 6 - 0 - 6 - YIAFCI - YISWCL - YI++C+ - - - - - 2 - gnl|BL_ORD_ID|1120 - 74387|Genome polyprotein|P26664.3|Hepatitis C virus (isolate 1)|11104 - 1120 - 9 - - - 1 - 13.4678 - 23 - 13.0154 - 1 - 6 - 1 - 6 - 0 - 0 - 3 - 6 - 0 - 6 - YIAFCI - YISWCL - YI++C+ - - - - - 3 - gnl|BL_ORD_ID|664 - 39591|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 - 664 - 20 - - - 1 - 13.0826 - 22 - 13.0672 - 1 - 6 - 8 - 13 - 0 - 0 - 3 - 6 - 0 - 6 - YIAFCI - YISWCL - YI++C+ - - - - - 4 - gnl|BL_ORD_ID|1119 - 74386|HCV-1|AAA45676.1|Hepatitis C virus|11103 - 1119 - 8 - - - 1 - 13.4678 - 23 - 13.8002 - 1 - 6 - 1 - 6 - 0 - 0 - 3 - 6 - 0 - 6 - YIAFCI - YISWCL - YI++C+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 20 - Query_20 - M_2239 - 9 - - - 1 - gnl|BL_ORD_ID|1763 - 154585|ribonucleotide reductase large subunit|CAB06725.1|Human alphaherpesvirus 2|10310 - 1763 - 15 - - - 1 - 14.2382 - 25 - 2.38473 - 2 - 8 - 4 - 10 - 0 - 0 - 4 - 6 - 0 - 7 - HYPQSIF - HYMESVF - HY +S+F - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 21 - Query_21 - M_2240 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 22 - Query_22 - M_2241 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_2242 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_2243 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_2244 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_2245 - 9 - - - 1 - gnl|BL_ORD_ID|1596 - 142232|POSSIBLE CONSERVED TRANSMEMBRANE PROTEIN|CAB00937.1|Mycobacterium tuberculosis|1773 - 1596 - 19 - - - 1 - 10.001 - 14 - 683.554 - 3 - 7 - 14 - 18 - 0 - 0 - 3 - 4 - 0 - 5 - FAAVH - YAFVH - +A VH - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 27 - Query_27 - M_2246 - 9 - - - 1 - gnl|BL_ORD_ID|1395 - 110394|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1395 - 32 - - - 1 - 12.6974 - 21 - 25.5546 - 1 - 7 - 15 - 21 - 0 - 0 - 4 - 6 - 0 - 7 - RRHTDEK - QRHLDKK - +RH D+K - - - - - 2 - gnl|BL_ORD_ID|1405 - 110829|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1405 - 15 - - - 1 - 12.6974 - 21 - 26.1211 - 1 - 7 - 3 - 9 - 0 - 0 - 4 - 6 - 0 - 7 - RRHTDEK - QRHLDKK - +RH D+K - - - - - 3 - gnl|BL_ORD_ID|1385 - 110215|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1385 - 25 - - - 1 - 12.6974 - 21 - 28.4868 - 2 - 8 - 4 - 10 - 0 - 0 - 4 - 5 - 0 - 7 - RHTDEKP - RHLDKKQ - RH D+K - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_123126_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_123126_1_T.fasta deleted file mode 100755 index eda51dc1..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_123126_1_T.fasta +++ /dev/null @@ -1,120 +0,0 @@ ->M_2247 -FNGNFLLSM ->M_2248 -GSADNTVQF ->M_2249 -SADNTVQFI ->M_2250 -KVQREDIFY ->M_2251 -YLWPSGTPA ->M_2252 -LKMVSPSPC ->M_2253 -SRVARDVAM ->M_2254 -QNGYSWSQF ->M_2255 -SYKLSQNGY ->M_2256 -WKRGKRRYF ->M_2257 -CFGHCFSLY ->M_2258 -CSAIRLRNY ->M_2259 -FGHCFSLYI ->M_2260 -IRLRNYLCF ->M_2261 -IRLRNYLCF ->M_2262 -LCFGHCFSL ->M_2263 -NHLCFGHCF ->M_2264 -DFVECLMWF ->M_2265 -DFVECLMWF ->M_2266 -NKFEPSTDL ->M_2267 -AYLCCRVPL ->M_2268 -SKGTTDTPV ->M_2269 -KQSNSVEPI ->M_2270 -AMSAQEYYI ->M_2271 -SAQEYYIDY ->M_2272 -YIDYKPNHI ->M_2273 -LMLLAAAIY ->M_2274 -LMLLAAAIY ->M_2275 -SEDDTSYFV ->M_2276 -RESVKHIGY ->M_2277 -YQKVVRESV ->M_2278 -SSVKTPETL ->M_2279 -VIHHELQVL ->M_2280 -KTDATPGRL ->M_2281 -IKRLTAGSL ->M_2282 -KRLTAGSLF ->M_2283 -KQLSHHIGA ->M_2284 -FHVNWFRRY ->M_2285 -FRRYEAGHF ->M_2286 -RRYEAGHFL ->M_2287 -RYEAGHFLW ->M_2288 -VSDHTPEQH ->M_2289 -SFHMDTQNF ->M_2290 -SFHMDTQNF ->M_2291 -TQNFCDIGY ->M_2292 -LALSVFSKL ->M_2293 -TVKLALSVF ->M_2294 -LQFAVGQEV ->M_2295 -PQVPEHLQF ->M_2296 -QFAVGQEVF ->M_2297 -NRYGGGGRY ->M_2298 -EQLKLGAIF ->M_2299 -LLMPYPVIV ->M_2300 -TLLMPYPVI ->M_2301 -RALKPVNKI ->M_2302 -KEAMENEQF ->M_2303 -LTEENKEAM ->M_2304 -MEVPNIASS ->M_2305 -RRFASGEKV ->M_2306 -TFRDVAVEF diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_123126_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_123126_1_T_iedb.xml deleted file mode 100755 index 6f4861f5..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_123126_1_T_iedb.xml +++ /dev/null @@ -1,2774 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_2247 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_2247 - 9 - - - 1 - gnl|BL_ORD_ID|2229 - 194567|envelope glycoprotein B|NP_044629.1|Herpes simplex virus (type 1 / strain 17)|10299 - 2229 - 9 - - - 1 - 12.6974 - 21 - 35.9943 - 2 - 7 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - NGNFLL - NGGFLI - NG FL+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 2 - Query_2 - M_2248 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_2249 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_2250 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_2251 - 9 - - - 1 - gnl|BL_ORD_ID|1520 - 140600|glutamine synthetase GLNA1 (glutamine synthase) (GS-I)|NP_216736.1|Mycobacterium tuberculosis H37Rv|83332 - 1520 - 9 - - - 1 - 13.853 - 24 - 6.48995 - 2 - 8 - 2 - 8 - 0 - 0 - 4 - 4 - 0 - 7 - LWPSGTP - LWKDGAP - LW G P - - - - - 2 - gnl|BL_ORD_ID|2041 - 184512|polyprotein|AGO67248.1|Dengue virus 2|11060 - 2041 - 10 - - - 1 - 11.927 - 19 - 90.726 - 2 - 8 - 2 - 8 - 0 - 0 - 3 - 4 - 0 - 7 - LWPSGTP - MWKQITP - +W TP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 6 - Query_6 - M_2252 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_2253 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_2254 - 9 - - - 1 - gnl|BL_ORD_ID|101 - 6889|Agglutinin isolectin 1 precursor|P10968.2|Triticum aestivum|4565 - 101 - 9 - - - 1 - 14.2382 - 25 - 3.49608 - 1 - 7 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - QNGYSWS - QNGACWT - QNG W+ - - - - - 2 - gnl|BL_ORD_ID|1194 - 95279|polyprotein|BAG31965.1|Hepatitis C virus|11103 - 1194 - 9 - - - 1 - 13.853 - 24 - 6.48995 - 2 - 7 - 3 - 8 - 0 - 0 - 4 - 4 - 0 - 6 - NGYSWS - NGVCWS - NG WS - - - - - 3 - gnl|BL_ORD_ID|1193 - 95278|polyprotein|BAC67110.1|Hepatitis C virus|11103 - 1193 - 9 - - - 1 - 13.853 - 24 - 6.48995 - 2 - 7 - 3 - 8 - 0 - 0 - 4 - 4 - 0 - 6 - NGYSWS - NGVCWS - NG WS - - - - - 4 - gnl|BL_ORD_ID|66 - 4910|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 66 - 20 - - - 1 - 13.4678 - 23 - 8.23977 - 2 - 9 - 5 - 12 - 0 - 0 - 3 - 5 - 0 - 8 - NGYSWSQF - NGVCWTVY - NG W+ + - - - - - 5 - gnl|BL_ORD_ID|65 - 4909|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 - 65 - 15 - - - 1 - 13.4678 - 23 - 9.20205 - 2 - 9 - 5 - 12 - 0 - 0 - 3 - 5 - 0 - 8 - NGYSWSQF - NGVCWTVY - NG W+ + - - - - - 6 - gnl|BL_ORD_ID|1632 - 146246|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 - 1632 - 17 - - - 1 - 13.4678 - 23 - 10.4757 - 2 - 9 - 7 - 14 - 0 - 0 - 3 - 5 - 0 - 8 - NGYSWSQF - NGVCWTVY - NG W+ + - - - - - 7 - gnl|BL_ORD_ID|784 - 52509|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 - 784 - 15 - - - 1 - 13.4678 - 23 - 12.0936 - 2 - 7 - 9 - 14 - 0 - 0 - 3 - 4 - 0 - 6 - NGYSWS - NGVCWT - NG W+ - - - - - 8 - gnl|BL_ORD_ID|107 - 7292|polyprotein|AAA75355.1|Hepatitis C virus subtype 1b|31647 - 107 - 9 - - - 1 - 13.0826 - 22 - 16.035 - 2 - 7 - 3 - 8 - 0 - 0 - 3 - 4 - 0 - 6 - NGYSWS - NGVCWT - NG W+ - - - - - 9 - gnl|BL_ORD_ID|89 - 6432|polyprotein [Hepatitis C virus]|CAL46125.1|Hepatitis C virus (isolate H77)|63746 - 89 - 9 - - - 1 - 13.0826 - 22 - 16.035 - 2 - 7 - 3 - 8 - 0 - 0 - 3 - 4 - 0 - 6 - NGYSWS - NGLCWT - NG W+ - - - - - 10 - gnl|BL_ORD_ID|1674 - 148619|unnamed protein product|BAA14233.1|Hepatitis C virus|11103 - 1674 - 45 - - - 1 - 13.0826 - 22 - 16.0472 - 2 - 9 - 38 - 45 - 0 - 0 - 3 - 5 - 0 - 8 - NGYSWSQF - NGVCWTVY - NG W+ + - - - - - 11 - gnl|BL_ORD_ID|91 - 6435|polyprotein|BAB18806.1|Hepatitis C virus|11103 - 91 - 9 - - - 1 - 13.0826 - 22 - 16.6015 - 2 - 7 - 3 - 8 - 0 - 0 - 3 - 4 - 0 - 6 - NGYSWS - NGVCWT - NG W+ - - - - - 12 - gnl|BL_ORD_ID|1197 - 95297|polyprotein|BAA09072.1|Hepatitis C virus genotype 1|41856 - 1197 - 9 - - - 1 - 13.0826 - 22 - 18.4218 - 2 - 7 - 3 - 8 - 0 - 0 - 3 - 4 - 0 - 6 - NGYSWS - NGVCWT - NG W+ - - - - - 13 - gnl|BL_ORD_ID|90 - 6433|Genome polyprotein|SRC279960|Hepatitis C virus subtype 1a|31646 - 90 - 9 - - - 1 - 13.0826 - 22 - 19.404 - 2 - 7 - 3 - 8 - 0 - 0 - 3 - 4 - 0 - 6 - NGYSWS - NGVCWT - NG W+ - - - - - 14 - gnl|BL_ORD_ID|1195 - 95280|Genome polyprotein|O39928.3|Hepatitis C virus genotype 5|33746 - 1195 - 9 - - - 1 - 12.6974 - 21 - 38.5226 - 2 - 7 - 3 - 8 - 0 - 0 - 3 - 4 - 0 - 6 - NGYSWS - NGVMWT - NG W+ - - - - - 15 - gnl|BL_ORD_ID|1192 - 95265|polyprotein|ABL63009.1|Hepatitis C virus genotype 4|33745 - 1192 - 9 - - - 1 - 12.3122 - 20 - 40.5299 - 2 - 7 - 3 - 8 - 0 - 0 - 3 - 4 - 0 - 6 - NGYSWS - NGVMWT - NG W+ - - - - - 16 - gnl|BL_ORD_ID|27 - 2033|polyprotein|BAA32665.1|Hepatitis C virus genotype 6|42182 - 27 - 9 - - - 1 - 12.3122 - 20 - 40.5299 - 2 - 7 - 3 - 8 - 0 - 0 - 3 - 4 - 0 - 6 - NGYSWS - NGVMWT - NG W+ - - - - - 17 - gnl|BL_ORD_ID|1199 - 95854|Genome polyprotein|O39927.3|Hepatitis C virus genotype 6|42182 - 1199 - 9 - - - 1 - 12.3122 - 20 - 49.6079 - 2 - 7 - 3 - 8 - 0 - 0 - 3 - 4 - 0 - 6 - NGYSWS - NGVMWT - NG W+ - - - - - 18 - gnl|BL_ORD_ID|1200 - 95890|polyprotein|ABE98152.1|Hepatitis C virus genotype 6|42182 - 1200 - 9 - - - 1 - 12.3122 - 20 - 51.2985 - 2 - 7 - 3 - 8 - 0 - 0 - 3 - 4 - 0 - 6 - NGYSWS - NGVMWT - NG W+ - - - - - 19 - gnl|BL_ORD_ID|397 - 24390|Major capsid protein L1|P50816.2|Human papillomavirus type 44|10592 - 397 - 9 - - - 1 - 11.927 - 19 - 102.395 - 1 - 8 - 2 - 9 - 0 - 0 - 3 - 3 - 0 - 8 - QNGYSWSQ - NNGICWGN - NG W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 9 - Query_9 - M_2255 - 9 - - - 1 - gnl|BL_ORD_ID|1961 - 182687|polyprotein|AGK36298.1|Dengue virus 2|11060 - 1961 - 10 - - - 1 - 13.4678 - 23 - 9.40133 - 1 - 8 - 1 - 8 - 0 - 0 - 3 - 6 - 0 - 8 - SYKLSQNG - AYRIKQRG - +Y++ Q G - - - - - 2 - gnl|BL_ORD_ID|1888 - 180582|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1888 - 15 - - - 1 - 12.3122 - 20 - 41.1784 - 1 - 8 - 8 - 15 - 0 - 0 - 4 - 5 - 0 - 8 - SYKLSQNG - SYETKQTG - SY+ Q G - - - - - 3 - gnl|BL_ORD_ID|2287 - 419229|polyprotein|ACF49259.1|Dengue virus type 1 Hawaii|10000440 - 2287 - 9 - - - 1 - 12.3122 - 20 - 61.624 - 2 - 8 - 2 - 8 - 0 - 0 - 3 - 5 - 0 - 7 - YKLSQNG - YRILQRG - Y++ Q G - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 10 - Query_10 - M_2256 - 9 - - - 1 - gnl|BL_ORD_ID|1811 - 170063|polyprotein|ABU97067.1|Hepatitis C virus subtype 1b|31647 - 1811 - 9 - - - 1 - 13.853 - 24 - 7.07804 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - WKRGKR - WTRGER - W RG+R - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 11 - Query_11 - M_2257 - 9 - - - 1 - gnl|BL_ORD_ID|866 - 56620|Nef protein|Q9YYU8|Human immunodeficiency virus 1|11676 - 866 - 10 - - - 1 - 12.6974 - 21 - 25.6384 - 2 - 6 - 6 - 10 - 0 - 0 - 4 - 4 - 0 - 5 - FGHCF - FGWCF - FG CF - - - - - 2 - gnl|BL_ORD_ID|2214 - 193060|Nef protein|Q9YYU3|Human immunodeficiency virus 1|11676 - 2214 - 10 - - - 1 - 12.6974 - 21 - 30.4011 - 2 - 6 - 6 - 10 - 0 - 0 - 4 - 4 - 0 - 5 - FGHCF - FGWCF - FG CF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 12 - Query_12 - M_2258 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_2259 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_2260 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_2261 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_2262 - 9 - - - 1 - gnl|BL_ORD_ID|866 - 56620|Nef protein|Q9YYU8|Human immunodeficiency virus 1|11676 - 866 - 10 - - - 1 - 14.2382 - 25 - 3.50259 - 1 - 7 - 4 - 10 - 0 - 0 - 5 - 5 - 0 - 7 - LCFGHCF - LTFGWCF - L FG CF - - - - - 2 - gnl|BL_ORD_ID|2214 - 193060|Nef protein|Q9YYU3|Human immunodeficiency virus 1|11676 - 2214 - 10 - - - 1 - 14.2382 - 25 - 4.15863 - 1 - 7 - 4 - 10 - 0 - 0 - 5 - 5 - 0 - 7 - LCFGHCF - LTFGWCF - L FG CF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 17 - Query_17 - M_2263 - 9 - - - 1 - gnl|BL_ORD_ID|866 - 56620|Nef protein|Q9YYU8|Human immunodeficiency virus 1|11676 - 866 - 10 - - - 1 - 14.2382 - 25 - 2.66759 - 3 - 9 - 4 - 10 - 0 - 0 - 5 - 5 - 0 - 7 - LCFGHCF - LTFGWCF - L FG CF - - - - - 2 - gnl|BL_ORD_ID|2214 - 193060|Nef protein|Q9YYU3|Human immunodeficiency virus 1|11676 - 2214 - 10 - - - 1 - 14.2382 - 25 - 3.16139 - 3 - 9 - 4 - 10 - 0 - 0 - 5 - 5 - 0 - 7 - LCFGHCF - LTFGWCF - L FG CF - - - - - 3 - gnl|BL_ORD_ID|1332 - 107872|Genome polyprotein|P26664.3|Hepatitis C virus|11103 - 1332 - 10 - - - 1 - 10.7714 - 16 - 373.491 - 1 - 7 - 2 - 8 - 0 - 0 - 4 - 4 - 0 - 7 - NHLCFGH - RHLIFCH - HL F H - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 18 - Query_18 - M_2264 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_2265 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_2266 - 9 - - - 1 - gnl|BL_ORD_ID|235 - 16814|precore protein|CAM58990.1|Hepatitis B virus|10407 - 235 - 10 - - - 1 - 11.5418 - 18 - 113.495 - 1 - 7 - 4 - 10 - 0 - 0 - 4 - 4 - 0 - 7 - NKFEPST - NDFFPSV - N F PS - - - - - 2 - gnl|BL_ORD_ID|234 - 16813|External core antigen|SRC279980|Hepatitis B virus|10407 - 234 - 10 - - - 1 - 11.5418 - 18 - 137.176 - 1 - 7 - 4 - 10 - 0 - 0 - 4 - 4 - 0 - 7 - NKFEPST - NDFFPSA - N F PS - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 21 - Query_21 - M_2267 - 9 - - - 1 - gnl|BL_ORD_ID|156 - 11956|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 - 156 - 11 - - - 1 - 11.1566 - 17 - 203.388 - 3 - 7 - 6 - 10 - 0 - 0 - 4 - 4 - 0 - 5 - LCCRV - LCCYV - LCC V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 22 - Query_22 - M_2268 - 9 - - - 1 - gnl|BL_ORD_ID|75 - 5542|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 75 - 15 - - - 1 - 13.4678 - 23 - 10.9188 - 1 - 9 - 7 - 15 - 0 - 0 - 4 - 7 - 0 - 9 - SKGTTDTPV - SPGTSGSPI - S GT+ +P+ - - - - - 2 - gnl|BL_ORD_ID|260 - 17802|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 260 - 15 - - - 1 - 13.0826 - 22 - 13.6187 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 7 - 0 - 9 - SKGTTDTPV - SPGTSGSPI - S GT+ +P+ - - - - - 3 - gnl|BL_ORD_ID|1929 - 180750|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1929 - 15 - - - 1 - 13.0826 - 22 - 15.8531 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 7 - 0 - 9 - SKGTTDTPV - SPGTSGSPI - S GT+ +P+ - - - - - 4 - gnl|BL_ORD_ID|364 - 22822|NS3 protein|NP_740321.1|Dengue virus 4|11070 - 364 - 11 - - - 1 - 12.6974 - 21 - 29.6736 - 3 - 9 - 1 - 7 - 0 - 0 - 3 - 6 - 0 - 7 - GTTDTPV - GTSGSPI - GT+ +P+ - - - - - 5 - gnl|BL_ORD_ID|363 - 22820|Nonstructural protein NS3|YP_001531172.2|Dengue virus 3|11069 - 363 - 10 - - - 1 - 12.6974 - 21 - 33.6561 - 3 - 9 - 1 - 7 - 0 - 0 - 3 - 6 - 0 - 7 - GTTDTPV - GTSGSPI - GT+ +P+ - - - - - 6 - gnl|BL_ORD_ID|367 - 22825|polyprotein|ABG75765.1|Dengue virus 1|11053 - 367 - 10 - - - 1 - 12.6974 - 21 - 37.2442 - 3 - 9 - 1 - 7 - 0 - 0 - 3 - 6 - 0 - 7 - GTTDTPV - GTSGSPI - GT+ +P+ - - - - - 7 - gnl|BL_ORD_ID|360 - 22817|polyprotein|AAK49562.1|Dengue virus 2|11060 - 360 - 11 - - - 1 - 12.6974 - 21 - 37.5414 - 3 - 9 - 1 - 7 - 0 - 0 - 3 - 6 - 0 - 7 - GTTDTPV - GTSGSPI - GT+ +P+ - - - - - 8 - gnl|BL_ORD_ID|362 - 22819|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 362 - 11 - - - 1 - 12.3122 - 20 - 40.1325 - 3 - 9 - 1 - 7 - 0 - 0 - 3 - 6 - 0 - 7 - GTTDTPV - GTSGSPI - GT+ +P+ - - - - - 9 - gnl|BL_ORD_ID|361 - 22818|Nonstructural protein NS3|NP_739587.2|Dengue virus 2|11060 - 361 - 10 - - - 1 - 12.3122 - 20 - 46.3152 - 3 - 9 - 1 - 7 - 0 - 0 - 3 - 6 - 0 - 7 - GTTDTPV - GTSGSPI - GT+ +P+ - - - - - 10 - gnl|BL_ORD_ID|1712 - 150341|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1712 - 9 - - - 1 - 12.3122 - 20 - 47.1713 - 3 - 9 - 3 - 9 - 0 - 0 - 3 - 6 - 0 - 7 - GTTDTPV - GTSGSPI - GT+ +P+ - - - - - 11 - gnl|BL_ORD_ID|366 - 22824|polyprotein|AAG30730.1|Dengue virus 2|11060 - 366 - 10 - - - 1 - 12.3122 - 20 - 50.3363 - 3 - 9 - 1 - 7 - 0 - 0 - 3 - 6 - 0 - 7 - GTTDTPV - GTSGSPI - GT+ +P+ - - - - - 12 - gnl|BL_ORD_ID|365 - 22823|NS3 protein|NP_739587.1|Dengue virus 2|11060 - 365 - 10 - - - 1 - 12.3122 - 20 - 51.1794 - 3 - 9 - 1 - 7 - 0 - 0 - 3 - 6 - 0 - 7 - GTTDTPV - GTSGSPI - GT+ +P+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 23 - Query_23 - M_2269 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_2270 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_2271 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_2272 - 9 - - - 1 - gnl|BL_ORD_ID|1916 - 180681|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1916 - 15 - - - 1 - 13.4678 - 23 - 9.20205 - 1 - 7 - 4 - 10 - 0 - 0 - 4 - 5 - 0 - 7 - YIDYKPN - YTDYMPS - Y DY P+ - - - - - 2 - gnl|BL_ORD_ID|558 - 34482|gag polyprotein|BAA00992.1|Human immunodeficiency virus 1|11676 - 558 - 9 - - - 1 - 11.927 - 19 - 84.261 - 3 - 9 - 1 - 7 - 0 - 0 - 4 - 4 - 0 - 7 - DYKPNHI - KYKLKHI - YK HI - - - - - 3 - gnl|BL_ORD_ID|659 - 39162|gag protein|AAV53308.1|Human immunodeficiency virus 1|11676 - 659 - 15 - - - 1 - 11.5418 - 18 - 108.251 - 3 - 9 - 8 - 14 - 0 - 0 - 4 - 4 - 0 - 7 - DYKPNHI - KYKLKHI - YK HI - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 27 - Query_27 - M_2273 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 28 - Query_28 - M_2274 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 29 - Query_29 - M_2275 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 30 - Query_30 - M_2276 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 31 - Query_31 - M_2277 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 32 - Query_32 - M_2278 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 33 - Query_33 - M_2279 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 34 - Query_34 - M_2280 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 35 - Query_35 - M_2281 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 36 - Query_36 - M_2282 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 37 - Query_37 - M_2283 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 38 - Query_38 - M_2284 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 39 - Query_39 - M_2285 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 40 - Query_40 - M_2286 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 41 - Query_41 - M_2287 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 42 - Query_42 - M_2288 - 9 - - - 1 - gnl|BL_ORD_ID|1057 - 69754|Lipoprotein lpqH precursor|P46733.1|Mycobacterium avium|1764 - 1057 - 10 - - - 1 - 12.6974 - 21 - 36.6217 - 1 - 8 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - VSDHTPEQ - LSDGNPPQ - +SD P Q - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 43 - Query_43 - M_2289 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 44 - Query_44 - M_2290 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 45 - Query_45 - M_2291 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 46 - Query_46 - M_2292 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 47 - Query_47 - M_2293 - 9 - - - 1 - gnl|BL_ORD_ID|786 - 52652|||| - 786 - 27 - - - 1 - 10.3862 - 15 - 322.823 - 1 - 9 - 12 - 20 - 0 - 0 - 4 - 6 - 0 - 9 - TVKLALSVF - TVRGLTSLF - TV+ S+F - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 48 - Query_48 - M_2294 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 49 - Query_49 - M_2295 - 9 - - - 1 - gnl|BL_ORD_ID|657 - 38974|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 657 - 11 - - - 1 - 12.3122 - 20 - 51.4474 - 1 - 6 - 5 - 10 - 0 - 0 - 4 - 4 - 0 - 6 - PQVPEH - PQYSEH - PQ EH - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 50 - Query_50 - M_2296 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 51 - Query_51 - M_2297 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 52 - Query_52 - M_2298 - 9 - - - 1 - gnl|BL_ORD_ID|2319 - 423046|polyprotein|ACX44272.1|Hepatitis C virus genotype 1|41856 - 2319 - 10 - - - 1 - 12.6974 - 21 - 37.8768 - 3 - 8 - 5 - 10 - 0 - 0 - 4 - 6 - 0 - 6 - LKLGAI - IKLGAL - +KLGA+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 53 - Query_53 - M_2299 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 54 - Query_54 - M_2300 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 55 - Query_55 - M_2301 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 56 - Query_56 - M_2302 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 57 - Query_57 - M_2303 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 58 - Query_58 - M_2304 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 59 - Query_59 - M_2305 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 60 - Query_60 - M_2306 - 9 - - - 1 - gnl|BL_ORD_ID|2108 - 186175|polyprotein|AFY10053.1|Dengue virus 3|11069 - 2108 - 10 - - - 1 - 13.853 - 24 - 6.08483 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 6 - 0 - 6 - TFRDVA - TWRDMA - T+RD+A - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_124242_3_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_124242_3_T.fasta deleted file mode 100755 index bd231bd7..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_124242_3_T.fasta +++ /dev/null @@ -1,92 +0,0 @@ ->M_2307 -FHISLFQYM ->M_2308 -LIIDEDFHI ->M_2309 -VLETAAPGV ->M_2310 -ESHEKGCFW ->M_2311 -MADAKGYTV ->M_2312 -KQLPRILEA ->M_2313 -HTCQVNGRW ->M_2314 -PLLPSIISL ->M_2315 -AIWEAVMSA ->M_2316 -AVMSALPSL ->M_2317 -MSALPSLNW ->M_2318 -GLDGPLVHV ->M_2319 -SIRVSQKGW ->M_2320 -PTDPGHFLV ->M_2321 -MRGEHRFHM ->M_2322 -KLSHCLSKA ->M_2323 -CRPQCCQSV ->M_2324 -VRNPEPSPL ->M_2325 -VLVVSPWPA ->M_2326 -GMLWAMMSI ->M_2327 -YMGMLWAMM ->M_2328 -SRAVTSTTI ->M_2329 -KTASWAEVV ->M_2330 -WTFALTSGL ->M_2331 -TDFNNGSYL ->M_2332 -VTDFNNGSY ->M_2333 -LLDTIPWYL ->M_2334 -ASSDHTTHL ->M_2335 -SHSSCVWLW ->M_2336 -TGSHSSCVW ->M_2337 -SIGELLQVL ->M_2338 -TGFVRRPLW ->M_2339 -DAEPFQRGW ->M_2340 -FIFSDTVVL ->M_2341 -FIFSDTVVL ->M_2342 -FSDTVVLLF ->M_2343 -MHFIFSDTV ->M_2344 -TVVLLFDFW ->M_2345 -YHPGAMHCV ->M_2346 -CAFSGTLPW ->M_2347 -FMCAFSGTL ->M_2348 -STHPSLSQW ->M_2349 -SRKDRAPKC ->M_2350 -LMGLASTTV ->M_2351 -SLLAIHQWV ->M_2352 -SSLLAIHQW diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_124242_3_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_124242_3_T_iedb.xml deleted file mode 100755 index 1e232a20..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_124242_3_T_iedb.xml +++ /dev/null @@ -1,1631 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_2307 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_2307 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_2308 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_2309 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_2310 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_2311 - 9 - - - 1 - gnl|BL_ORD_ID|50 - 3094|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 - 50 - 9 - - - 1 - 14.2382 - 25 - 3.37936 - 1 - 7 - 2 - 8 - 0 - 0 - 5 - 5 - 0 - 7 - MADAKGY - MGDAGGY - M DA GY - - - - - 2 - gnl|BL_ORD_ID|1639 - 146285|polyprotein|ADF97231.1|Hepatitis C virus subtype 3a|356426 - 1639 - 18 - - - 1 - 12.6974 - 21 - 28.603 - 4 - 9 - 12 - 17 - 0 - 0 - 4 - 5 - 0 - 6 - AKGYTV - AQGYNV - A+GY V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 6 - Query_6 - M_2312 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_2313 - 9 - - - 1 - gnl|BL_ORD_ID|1179 - 79628|E1 protein|BAA19893.1|Rubella virus|11041 - 1179 - 21 - - - 1 - 11.927 - 19 - 77.0667 - 2 - 9 - 5 - 12 - 0 - 0 - 3 - 5 - 0 - 8 - TCQVNGRW - SCEGLGAW - +C+ G W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 8 - Query_8 - M_2314 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_2315 - 9 - - - 1 - gnl|BL_ORD_ID|628 - 37590|VP1|BAF93325.1|Human polyomavirus 1|1891762 - 628 - 9 - - - 1 - 13.0826 - 22 - 21.8994 - 2 - 6 - 3 - 7 - 0 - 0 - 4 - 5 - 0 - 5 - IWEAV - MWEAV - +WEAV - - - - - 2 - gnl|BL_ORD_ID|446 - 27217|VP1|AAL37677.1|JC polyomavirus|10632 - 446 - 9 - - - 1 - 13.0826 - 22 - 22.6682 - 2 - 6 - 3 - 7 - 0 - 0 - 4 - 5 - 0 - 5 - IWEAV - MWEAV - +WEAV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 10 - Query_10 - M_2316 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_2317 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_2318 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_2319 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_2320 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_2321 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_2322 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_2323 - 9 - - - 1 - gnl|BL_ORD_ID|156 - 11956|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 - 156 - 11 - - - 1 - 12.3122 - 20 - 38.8163 - 1 - 9 - 3 - 11 - 0 - 0 - 4 - 5 - 0 - 9 - CRPQCCQSV - CRVLCCYVL - CR CC + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 18 - Query_18 - M_2324 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_2325 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_2326 - 9 - - - 1 - gnl|BL_ORD_ID|1203 - 95940|polyprotein|BAA32666.1|Hepatitis C virus genotype 6|42182 - 1203 - 9 - - - 1 - 12.3122 - 20 - 43.3628 - 1 - 6 - 4 - 9 - 0 - 0 - 3 - 5 - 0 - 6 - GMLWAM - GVLWTV - G+LW + - - - - - 2 - gnl|BL_ORD_ID|1201 - 95908|Genome polyprotein|O92529.3|Hepatitis C virus genotype 6|42182 - 1201 - 9 - - - 1 - 12.3122 - 20 - 44.8495 - 1 - 6 - 4 - 9 - 0 - 0 - 3 - 5 - 0 - 6 - GMLWAM - GVLWTV - G+LW + - - - - - 3 - gnl|BL_ORD_ID|1191 - 95264|Genome polyprotein|O92532.3|Hepatitis C virus genotype 6|42182 - 1191 - 9 - - - 1 - 12.3122 - 20 - 53.0441 - 1 - 6 - 4 - 9 - 0 - 0 - 3 - 5 - 0 - 6 - GMLWAM - GVLWTV - G+LW + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 21 - Query_21 - M_2327 - 9 - - - 1 - gnl|BL_ORD_ID|1201 - 95908|Genome polyprotein|O92529.3|Hepatitis C virus genotype 6|42182 - 1201 - 9 - - - 1 - 12.6974 - 21 - 39.1808 - 3 - 8 - 4 - 9 - 0 - 0 - 3 - 5 - 0 - 6 - GMLWAM - GVLWTV - G+LW + - - - - - 2 - gnl|BL_ORD_ID|1203 - 95940|polyprotein|BAA32666.1|Hepatitis C virus genotype 6|42182 - 1203 - 9 - - - 1 - 12.6974 - 21 - 39.8499 - 3 - 8 - 4 - 9 - 0 - 0 - 3 - 5 - 0 - 6 - GMLWAM - GVLWTV - G+LW + - - - - - 3 - gnl|BL_ORD_ID|223 - 16623|gag protein|AAV53308.1|Human immunodeficiency virus 1|11676 - 223 - 10 - - - 1 - 12.3122 - 20 - 44.794 - 1 - 7 - 1 - 7 - 0 - 0 - 2 - 5 - 0 - 7 - YMGMLWA - FLGKIWP - ++G +W - - - - - 4 - gnl|BL_ORD_ID|1191 - 95264|Genome polyprotein|O92532.3|Hepatitis C virus genotype 6|42182 - 1191 - 9 - - - 1 - 12.3122 - 20 - 47.1713 - 3 - 8 - 4 - 9 - 0 - 0 - 3 - 5 - 0 - 6 - GMLWAM - GVLWTV - G+LW + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 22 - Query_22 - M_2328 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_2329 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_2330 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_2331 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_2332 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_2333 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 28 - Query_28 - M_2334 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 29 - Query_29 - M_2335 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 30 - Query_30 - M_2336 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 31 - Query_31 - M_2337 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 32 - Query_32 - M_2338 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 33 - Query_33 - M_2339 - 9 - - - 1 - gnl|BL_ORD_ID|381 - 23566|tegument protein UL7|NP_044476.1|Human alphaherpesvirus 2|10310 - 381 - 13 - - - 1 - 13.853 - 24 - 5.01075 - 1 - 7 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - DAEPFQR - HASPFER - A PF+R - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 34 - Query_34 - M_2340 - 9 - - - 1 - gnl|BL_ORD_ID|760 - 50779|N protein|AAP13445.1|SARS coronavirus Urbani|228330 - 760 - 9 - - - 1 - 13.0826 - 22 - 15.4875 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - FSDTVVL - FKDNVIL - F D V+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 35 - Query_35 - M_2341 - 9 - - - 1 - gnl|BL_ORD_ID|760 - 50779|N protein|AAP13445.1|SARS coronavirus Urbani|228330 - 760 - 9 - - - 1 - 13.0826 - 22 - 15.4875 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - FSDTVVL - FKDNVIL - F D V+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 36 - Query_36 - M_2342 - 9 - - - 1 - gnl|BL_ORD_ID|760 - 50779|N protein|AAP13445.1|SARS coronavirus Urbani|228330 - 760 - 9 - - - 1 - 14.6234 - 26 - 2.01137 - 1 - 8 - 2 - 9 - 0 - 0 - 5 - 6 - 0 - 8 - FSDTVVLL - FKDNVILL - F D V+LL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 37 - Query_37 - M_2343 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 38 - Query_38 - M_2344 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 39 - Query_39 - M_2345 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 40 - Query_40 - M_2346 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 41 - Query_41 - M_2347 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 42 - Query_42 - M_2348 - 9 - - - 1 - gnl|BL_ORD_ID|1028 - 68601|polyprotein|AAA45534.1|Hepatitis C virus|11103 - 1028 - 15 - - - 1 - 14.6234 - 26 - 2.00652 - 1 - 9 - 6 - 14 - 0 - 0 - 4 - 5 - 0 - 9 - STHPSLSQW - NTRPPLGNW - +T P L W - - - - - 2 - gnl|BL_ORD_ID|729 - 46243|E2 protein|NP_751921.1|Hepatitis C virus (isolate H77)|63746 - 729 - 10 - - - 1 - 14.2382 - 25 - 2.80664 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 5 - 0 - 9 - STHPSLSQW - NTRPPLGNW - +T P L W - - - - - 3 - gnl|BL_ORD_ID|1600 - 142246|polyprotein|BAB18810.1|Hepatitis C virus subtype 1a|31646 - 1600 - 9 - - - 1 - 14.2382 - 25 - 3.10506 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 5 - 0 - 9 - STHPSLSQW - NTRPPLGNW - +T P L W - - - - - 4 - gnl|BL_ORD_ID|1601 - 142247|envelope protein 2|ACY64760.1|Hepatitis C virus subtype 1a|31646 - 1601 - 9 - - - 1 - 13.4678 - 23 - 7.72035 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 5 - 0 - 9 - STHPSLSQW - NTRPPMGNW - +T P + W - - - - - 5 - gnl|BL_ORD_ID|1599 - 142245|polyprotein|ACJ37204.1|Hepatitis C virus subtype 1a|31646 - 1599 - 9 - - - 1 - 12.3122 - 20 - 56.7066 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 4 - 0 - 9 - STHPSLSQW - NTRPPAGNW - +T P W - - - - - 6 - gnl|BL_ORD_ID|1603 - 142249|polyprotein|AAY82036.1|Hepatitis C virus subtype 1a|31646 - 1603 - 9 - - - 1 - 12.3122 - 20 - 60.6092 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 4 - 0 - 9 - STHPSLSQW - NTRPPRGNW - +T P W - - - - - 7 - gnl|BL_ORD_ID|1602 - 142248|polyprotein|BAB18806.1|Hepatitis C virus subtype 1a|31646 - 1602 - 9 - - - 1 - 11.927 - 19 - 110.987 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 4 - 0 - 9 - STHPSLSQW - NTRPPQGNW - +T P W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 43 - Query_43 - M_2349 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 44 - Query_44 - M_2350 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 45 - Query_45 - M_2351 - 9 - - - 1 - gnl|BL_ORD_ID|1607 - 143690|Genome polyprotein|P06441.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 1607 - 9 - - - 1 - 13.4678 - 23 - 13.0154 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - LAIHQWV - LAVDPWV - LA+ WV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 46 - Query_46 - M_2352 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_124756_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_124756_1_T.fasta deleted file mode 100755 index 90bf1be6..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_124756_1_T.fasta +++ /dev/null @@ -1,174 +0,0 @@ ->M_2353 -AIHIVAEKK ->M_2354 -ESLPPSPTW ->M_2355 -WAGNVLAPY ->M_2356 -QIIAGHFRK ->M_2357 -STSSRSHRY ->M_2358 -FHQCLSIYY ->M_2359 -IYYWDIRYK ->M_2360 -LFHQCLSIY ->M_2361 -SIYYWDIRY ->M_2362 -SIYYWDIRY ->M_2363 -SRHTIRELL ->M_2364 -QINIPIGPY ->M_2365 -GGMQALGLY ->M_2366 -FLNLSQPRK ->M_2367 -RLNSHFLNL ->M_2368 -ERSLQVKRV ->M_2369 -LQVKRVFVK ->M_2370 -RSLQVKRVF ->M_2371 -RVFVKGMKK ->M_2372 -CSSSIGTIW ->M_2373 -WSHASASLY ->M_2374 -WSHASASLY ->M_2375 -KESNAGRYY ->M_2376 -VKESNAGRY ->M_2377 -IVSVKPNMK ->M_2378 -FSYPKRPII ->M_2379 -MSHPPNILK ->M_2380 -GARPGLGRY ->M_2381 -ITSRDATRF ->M_2382 -TRFPIIASC ->M_2383 -RLLSSGTAK ->M_2384 -KVLELADRF ->M_2385 -RVSTGSVHK ->M_2386 -VVGAVGVGK ->M_2387 -LSFRSSSCR ->M_2388 -EMFEHLFGK ->M_2389 -TRAHCHLPV ->M_2390 -ILDYMQLRK ->M_2391 -KILDYMQLR ->M_2392 -TTMLDRGPK ->M_2393 -IHITEEEAV ->M_2394 -LVSMTYDRY ->M_2395 -MTYDRYVAI ->M_2396 -MVLLVSMTY ->M_2397 -MVLLVSMTY ->M_2398 -MVLLVSMTY ->M_2399 -VSMTYDRYV ->M_2400 -IHMDARLHT ->M_2401 -MGMALLIHM ->M_2402 -FKSKVPQTW ->M_2403 -VGQQQQVLW ->M_2404 -DSSSWSDRY ->M_2405 -SGGHDSSSW ->M_2406 -YEEYRGHSL ->M_2407 -HTSTVRESY ->M_2408 -HTSTVRESY ->M_2409 -SHYGQPDRQ ->M_2410 -DHEVYLKHL ->M_2411 -GGLFIASNW ->M_2412 -KVTRLHRRK ->M_2413 -LMSTSEEEF ->M_2414 -LSNNCVPQM ->M_2415 -STRDEIEGL ->M_2416 -RMCTVTNYF ->M_2417 -VMVSLKPDK ->M_2418 -CRQEQERKF ->M_2419 -EQEERREQL ->M_2420 -FRLEEQKVC ->M_2421 -QSLCGTRFY ->M_2422 -TAAAAPTPF ->M_2423 -DRNTFRHSL ->M_2424 -NTFRHSLVV ->M_2425 -RMNSFLHIL ->M_2426 -RMNSFLHIL ->M_2427 -SRMNSFLHI ->M_2428 -GSFPTEYIL ->M_2429 -VTNCHKNYW ->M_2430 -VVTNCHKNY ->M_2431 -DMAPTRPRW ->M_2432 -FRRPQESLL ->M_2433 -GINNKVCFW ->M_2434 -LLTDTNSWW ->M_2435 -QLLTDTNSW ->M_2436 -HQRVHSGEK ->M_2437 -QRYSHQRVH ->M_2438 -VKSKLIAHY ->M_2439 -SVDECELHK diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_124756_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_124756_1_T_iedb.xml deleted file mode 100755 index 2842ee1f..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_124756_1_T_iedb.xml +++ /dev/null @@ -1,2615 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_2353 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_2353 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_2354 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_2355 - 9 - - - 1 - gnl|BL_ORD_ID|577 - 36352|Polyprotein|P90247|Hepatitis C virus|11103 - 577 - 20 - - - 1 - 14.2382 - 25 - 2.6 - 1 - 8 - 3 - 10 - 0 - 0 - 5 - 7 - 0 - 8 - WAGNVLAP - WAGWLLSP - WAG +L+P - - - - - 2 - gnl|BL_ORD_ID|1144 - 75438|polyprotein|AAF65962.1|Hepatitis C virus|11103 - 1144 - 20 - - - 1 - 14.2382 - 25 - 2.64513 - 1 - 8 - 13 - 20 - 0 - 0 - 5 - 7 - 0 - 8 - WAGNVLAP - WAGWLLSP - WAG +L+P - - - - - 3 - gnl|BL_ORD_ID|1143 - 75436|Polyprotein|P90247|Hepatitis C virus|11103 - 1143 - 20 - - - 1 - 14.2382 - 25 - 2.69103 - 1 - 8 - 13 - 20 - 0 - 0 - 5 - 7 - 0 - 8 - WAGNVLAP - WAGWLLSP - WAG +L+P - - - - - 4 - gnl|BL_ORD_ID|2293 - 419410|polyprotein|ABR25251.1|Hepatitis C virus|11103 - 2293 - 9 - - - 1 - 13.4678 - 23 - 11.1275 - 1 - 6 - 1 - 6 - 0 - 0 - 3 - 5 - 0 - 6 - WAGNVL - WLGNII - W GN++ - - - - - 5 - gnl|BL_ORD_ID|1102 - 72722|polyprotein|AAF01178.1|Hepatitis C virus subtype 2a|31649 - 1102 - 9 - - - 1 - 13.4678 - 23 - 11.5219 - 1 - 6 - 1 - 6 - 0 - 0 - 3 - 5 - 0 - 6 - WAGNVL - WLGNII - W GN++ - - - - - 6 - gnl|BL_ORD_ID|1142 - 75435|largest ORF|AAB02128.1|Hepatitis C virus|11103 - 1142 - 20 - - - 1 - 12.6974 - 21 - 22.9279 - 1 - 8 - 13 - 20 - 0 - 0 - 4 - 6 - 0 - 8 - WAGNVLAP - WMGWLLSP - W G +L+P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 4 - Query_4 - M_2356 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_2357 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_2358 - 9 - - - 1 - gnl|BL_ORD_ID|1186 - 93431|pre-C/C protein|ABY54138.1|Hepatitis B virus|10407 - 1186 - 20 - - - 1 - 13.4678 - 23 - 12.4431 - 1 - 7 - 4 - 10 - 0 - 0 - 5 - 5 - 0 - 7 - FHQCLSI - FHLCLII - FH CL I - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 7 - Query_7 - M_2359 - 9 - - - 1 - gnl|BL_ORD_ID|1996 - 183619|nonstructural protein NS1|1802191G|Dengue virus|12637 - 1996 - 9 - - - 1 - 11.1566 - 17 - 266.5 - 2 - 9 - 1 - 8 - 0 - 0 - 3 - 5 - 0 - 8 - YYWDIRYK - HTWTEQYK - + W +YK - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 8 - Query_8 - M_2360 - 9 - - - 1 - gnl|BL_ORD_ID|1186 - 93431|pre-C/C protein|ABY54138.1|Hepatitis B virus|10407 - 1186 - 20 - - - 1 - 14.6234 - 26 - 2.38548 - 1 - 8 - 3 - 10 - 0 - 0 - 6 - 6 - 0 - 8 - LFHQCLSI - LFHLCLII - LFH CL I - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 9 - Query_9 - M_2361 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_2362 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_2363 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_2364 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_2365 - 9 - - - 1 - gnl|BL_ORD_ID|938 - 61861|Nucleoprotein|P03418.1|Human respiratory syncytial virus A2|11259 - 938 - 14 - - - 1 - 11.5418 - 18 - 140.41 - 1 - 9 - 4 - 12 - 0 - 0 - 3 - 6 - 0 - 9 - GGMQALGLY - GGSRVEGIF - GG + G++ - - - - - 2 - gnl|BL_ORD_ID|1950 - 181035|||| - 1950 - 44 - - - 1 - 9.61583 - 13 - 724.877 - 1 - 9 - 16 - 24 - 0 - 0 - 4 - 5 - 0 - 9 - GGMQALGLY - GGQICGGVY - GG G+Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 14 - Query_14 - M_2366 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_2367 - 9 - - - 1 - gnl|BL_ORD_ID|1437 - 119822|110 kd polyprotein precursor|CAA28880.1|Rubella virus|11041 - 1437 - 29 - - - 1 - 16.9346 - 32 - 0.172633 - 1 - 9 - 19 - 27 - 0 - 0 - 5 - 8 - 0 - 9 - RLNSHFLNL - RVDLHFINL - R++ HF+NL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 16 - Query_16 - M_2368 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_2369 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_2370 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_2371 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_2372 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_2373 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 22 - Query_22 - M_2374 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_2375 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_2376 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_2377 - 9 - - - 1 - gnl|BL_ORD_ID|287 - 19359|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 - 287 - 20 - - - 1 - 13.4678 - 23 - 9.25482 - 2 - 7 - 11 - 16 - 0 - 0 - 4 - 5 - 0 - 6 - VSVKPN - VSIAPN - VS+ PN - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 26 - Query_26 - M_2378 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_2379 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 28 - Query_28 - M_2380 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 29 - Query_29 - M_2381 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 30 - Query_30 - M_2382 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 31 - Query_31 - M_2383 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 32 - Query_32 - M_2384 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 33 - Query_33 - M_2385 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 34 - Query_34 - M_2386 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 35 - Query_35 - M_2387 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 36 - Query_36 - M_2388 - 9 - - - 1 - gnl|BL_ORD_ID|133 - 9415|Superoxide dismutase|P17670.1|Mycobacterium tuberculosis|1773 - 133 - 10 - - - 1 - 13.853 - 24 - 5.02829 - 1 - 7 - 1 - 7 - 0 - 0 - 4 - 6 - 0 - 7 - EMFEHLF - DMWEHAF - +M+EH F - - - - - 2 - gnl|BL_ORD_ID|132 - 9414|Superoxide dismutase|P17670.1|Mycobacterium tuberculosis|1773 - 132 - 9 - - - 1 - 13.853 - 24 - 5.65074 - 1 - 7 - 1 - 7 - 0 - 0 - 4 - 6 - 0 - 7 - EMFEHLF - DMWEHAF - +M+EH F - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 37 - Query_37 - M_2389 - 9 - - - 1 - gnl|BL_ORD_ID|1141 - 75408|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 1141 - 20 - - - 1 - 15.779 - 29 - 0.419784 - 2 - 9 - 7 - 14 - 0 - 0 - 6 - 6 - 0 - 8 - RAHCHLPV - RKHRHLPV - R H HLPV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 38 - Query_38 - M_2390 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 39 - Query_39 - M_2391 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 40 - Query_40 - M_2392 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 41 - Query_41 - M_2393 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 42 - Query_42 - M_2394 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 43 - Query_43 - M_2395 - 9 - - - 1 - gnl|BL_ORD_ID|664 - 39591|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 - 664 - 20 - - - 1 - 12.6974 - 21 - 32.8758 - 3 - 8 - 5 - 10 - 0 - 0 - 3 - 5 - 0 - 6 - YDRYVA - YKRYIS - Y RY++ - - - - - 2 - gnl|BL_ORD_ID|663 - 39590|polyprotein|AAY82030.1|Hepatitis C virus|11103 - 663 - 11 - - - 1 - 12.3122 - 20 - 45.0816 - 3 - 8 - 5 - 10 - 0 - 0 - 3 - 5 - 0 - 6 - YDRYVA - YKRYIS - Y RY++ - - - - - 3 - gnl|BL_ORD_ID|662 - 39589|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 662 - 10 - - - 1 - 12.3122 - 20 - 45.5485 - 3 - 8 - 5 - 10 - 0 - 0 - 3 - 5 - 0 - 6 - YDRYVA - YKRYIS - Y RY++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 44 - Query_44 - M_2396 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 45 - Query_45 - M_2397 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 46 - Query_46 - M_2398 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 47 - Query_47 - M_2399 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 48 - Query_48 - M_2400 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 49 - Query_49 - M_2401 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 50 - Query_50 - M_2402 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 51 - Query_51 - M_2403 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 52 - Query_52 - M_2404 - 9 - - - 1 - gnl|BL_ORD_ID|552 - 33912|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 - 552 - 10 - - - 1 - 13.4678 - 23 - 8.03745 - 4 - 9 - 2 - 7 - 0 - 0 - 3 - 5 - 0 - 6 - SWSDRY - TWADEY - +W+D Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 53 - Query_53 - M_2405 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 54 - Query_54 - M_2406 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 55 - Query_55 - M_2407 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 56 - Query_56 - M_2408 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 57 - Query_57 - M_2409 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 58 - Query_58 - M_2410 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 59 - Query_59 - M_2411 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 60 - Query_60 - M_2412 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 61 - Query_61 - M_2413 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 62 - Query_62 - M_2414 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 63 - Query_63 - M_2415 - 9 - - - 1 - gnl|BL_ORD_ID|1398 - 110431|E7|AAD33253.1|Human papillomavirus type 16|333760 - 1398 - 36 - - - 1 - 12.6974 - 21 - 32.5473 - 3 - 8 - 16 - 21 - 0 - 0 - 4 - 5 - 0 - 6 - RDEIEG - EDEIDG - DEI+G - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 64 - Query_64 - M_2416 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 65 - Query_65 - M_2417 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 66 - Query_66 - M_2418 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 67 - Query_67 - M_2419 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 68 - Query_68 - M_2420 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 69 - Query_69 - M_2421 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 70 - Query_70 - M_2422 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 71 - Query_71 - M_2423 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 72 - Query_72 - M_2424 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 73 - Query_73 - M_2425 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 74 - Query_74 - M_2426 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 75 - Query_75 - M_2427 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 76 - Query_76 - M_2428 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 77 - Query_77 - M_2429 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 78 - Query_78 - M_2430 - 9 - - - 1 - gnl|BL_ORD_ID|1382 - 110184|E7|AAD33253.1|Human papillomavirus type 16|333760 - 1382 - 35 - - - 1 - 11.1566 - 17 - 179.88 - 1 - 7 - 13 - 19 - 0 - 0 - 4 - 5 - 0 - 7 - VVTNCHK - IVTFCCK - +VT C K - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 79 - Query_79 - M_2431 - 9 - - - 1 - gnl|BL_ORD_ID|2300 - 422989|polyprotein|ABY67644.1|Hepatitis C virus genotype 1|41856 - 2300 - 10 - - - 1 - 12.6974 - 21 - 26.9859 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 4 - 0 - 8 - MAPTRPRW - FAPALPIW - AP P W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 80 - Query_80 - M_2432 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 81 - Query_81 - M_2433 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 82 - Query_82 - M_2434 - 9 - - - 1 - gnl|BL_ORD_ID|1054 - 69750|polyprotein|AAC03058.1|Hepatitis C virus genotype 3|356114 - 1054 - 9 - - - 1 - 13.0826 - 22 - 19.7427 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 6 - 0 - 8 - LLTDTNSW - VLSDFKSW - +L+D SW - - - - - 2 - gnl|BL_ORD_ID|1058 - 69797|polyprotein|BAA09073.1|Hepatitis C virus subtype 1b|31647 - 1058 - 9 - - - 1 - 12.6974 - 21 - 24.707 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 6 - 0 - 8 - LLTDTNSW - VLTDFKTW - +LTD +W - - - - - 3 - gnl|BL_ORD_ID|1055 - 69751|polyprotein|BAB18806.1|Hepatitis C virus genotype 1|41856 - 1055 - 9 - - - 1 - 11.927 - 19 - 114.611 - 1 - 8 - 1 - 8 - 0 - 0 - 3 - 6 - 0 - 8 - LLTDTNSW - VLSDFKTW - +L+D +W - - - - - 4 - gnl|BL_ORD_ID|1056 - 69753|polyprotein|AAK49500.1|Hepatitis C virus genotype 3|356114 - 1056 - 9 - - - 1 - 11.5418 - 18 - 120.255 - 1 - 8 - 1 - 8 - 0 - 0 - 3 - 6 - 0 - 8 - LLTDTNSW - VLSDFRTW - +L+D +W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 83 - Query_83 - M_2435 - 9 - - - 1 - gnl|BL_ORD_ID|1054 - 69750|polyprotein|AAC03058.1|Hepatitis C virus genotype 3|356114 - 1054 - 9 - - - 1 - 13.4678 - 23 - 10.561 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 6 - 0 - 8 - LLTDTNSW - VLSDFKSW - +L+D SW - - - - - 2 - gnl|BL_ORD_ID|1058 - 69797|polyprotein|BAA09073.1|Hepatitis C virus subtype 1b|31647 - 1058 - 9 - - - 1 - 13.4678 - 23 - 13.2439 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 6 - 0 - 8 - LLTDTNSW - VLTDFKTW - +LTD +W - - - - - 3 - gnl|BL_ORD_ID|1055 - 69751|polyprotein|BAB18806.1|Hepatitis C virus genotype 1|41856 - 1055 - 9 - - - 1 - 12.3122 - 20 - 61.624 - 2 - 9 - 1 - 8 - 0 - 0 - 3 - 6 - 0 - 8 - LLTDTNSW - VLSDFKTW - +L+D +W - - - - - 4 - gnl|BL_ORD_ID|1056 - 69753|polyprotein|AAK49500.1|Hepatitis C virus genotype 3|356114 - 1056 - 9 - - - 1 - 12.3122 - 20 - 66.9453 - 2 - 9 - 1 - 8 - 0 - 0 - 3 - 6 - 0 - 8 - LLTDTNSW - VLSDFRTW - +L+D +W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 84 - Query_84 - M_2436 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 85 - Query_85 - M_2437 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 86 - Query_86 - M_2438 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 87 - Query_87 - M_2439 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_125196_3_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_125196_3_T.fasta deleted file mode 100755 index 67783270..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_125196_3_T.fasta +++ /dev/null @@ -1,126 +0,0 @@ ->M_2440 -PMPPPLEPI ->M_2441 -KEIDVIAIP ->M_2442 -YKDYAAELV ->M_2443 -DNLDSDNTY ->M_2444 -LAVTLGLAL ->M_2445 -HNNNRPLTM ->M_2446 -WAVPPLLLA ->M_2447 -RCYVRGLFH ->M_2448 -KITAQRLSH ->M_2449 -SSLHSEPPK ->M_2450 -QAQALGIPL ->M_2451 -QAQALGIPL ->M_2452 -IPKSPEEAI ->M_2453 -PEEPTSPAA ->M_2454 -RVQSRPIPI ->M_2455 -HSLQQAQSV ->M_2456 -PLFTTQCGK ->M_2457 -HMEAEMAQK ->M_2458 -VQLPKVSEM ->M_2459 -ITAQRLSHL ->M_2460 -LLLSPPVEV ->M_2461 -IPILPLIYI ->M_2462 -AEAQTPEDS ->M_2463 -LLSPPVEVK ->M_2464 -TEHDVQIYV ->M_2465 -FISLKFSSK ->M_2466 -IPGPIPGPI ->M_2467 -KTRRTSSLH ->M_2468 -EEPTSPAAA ->M_2469 -WILSARLLK ->M_2470 -QQFPSLELL ->M_2471 -RPIPILPLI ->M_2472 -NMKEQVVIL ->M_2473 -AQRLSHLNK ->M_2474 -RAYRDDTDL ->M_2475 -NVFWGEHFK ->M_2476 -YYKDYAAEL ->M_2477 -QQFPSLELL ->M_2478 -SLKFSSKIK ->M_2479 -FLFGLAQNL ->M_2480 -YVRGLFHSL ->M_2481 -TENSETTTA ->M_2482 -ALGIPLTPK ->M_2483 -NENTTPSPA ->M_2484 -RLPEVQLPK ->M_2485 -ISLKFSSKI ->M_2486 -KEGARNVLA ->M_2487 -MPNDFWARL ->M_2488 -FTEHDVQIY ->M_2489 -FKFHNLPPL ->M_2490 -NTYRTPSVL ->M_2491 -IAIPSKCLL ->M_2492 -EASSAVPTV ->M_2493 -MAAAVVARL ->M_2494 -QEFENIKSY ->M_2495 -FQKDPPADI ->M_2496 -DMYDGRFLV ->M_2497 -PLYKVRFSK ->M_2498 -VTRPFISLK ->M_2499 -IILFNRLLK ->M_2500 -IPYRDSVLI ->M_2501 -AEASSAVPT ->M_2502 -EEMPNDFWA diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_125196_3_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_125196_3_T_iedb.xml deleted file mode 100755 index 0ae81462..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_125196_3_T_iedb.xml +++ /dev/null @@ -1,2325 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_2440 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_2440 - 9 - - - 1 - gnl|BL_ORD_ID|448 - 27241|Spike glycoprotein precursor|P59594.1|SARS coronavirus|227859 - 448 - 9 - - - 1 - 11.927 - 19 - 77.6399 - 2 - 8 - 2 - 8 - 0 - 0 - 4 - 6 - 0 - 7 - MPPPLEP - LPDPLKP - +P PL+P - - - - - 2 - gnl|BL_ORD_ID|1581 - 141462|tegument protein UL21|NP_044622.1|Human alphaherpesvirus 1|10298 - 1581 - 9 - - - 1 - 10.3862 - 15 - 702.182 - 2 - 9 - 1 - 8 - 0 - 0 - 3 - 6 - 0 - 8 - MPPPLEPI - VPRPDDPV - +P P +P+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 2 - Query_2 - M_2441 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_2442 - 9 - - - 1 - gnl|BL_ORD_ID|1970 - 182917|polyprotein|CDF77361.1|Dengue virus 3|11069 - 1970 - 9 - - - 1 - 14.2382 - 25 - 4.1461 - 1 - 6 - 2 - 7 - 0 - 0 - 4 - 6 - 0 - 6 - YKDYAA - FKDFAA - +KD+AA - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 4 - Query_4 - M_2443 - 9 - - - 1 - gnl|BL_ORD_ID|1097 - 72563|polyprotein|AAB70696.1|Dengue virus type 1 Hawaii|10000440 - 1097 - 20 - - - 1 - 12.6974 - 21 - 29.0269 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - NLDSDNTY - HYDEDNPY - + D DN Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 5 - Query_5 - M_2444 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_2445 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_2446 - 9 - - - 1 - gnl|BL_ORD_ID|1110 - 73059|kaposin|AAC57155.1|Human gammaherpesvirus 8|37296 - 1110 - 15 - - - 1 - 13.0826 - 22 - 17.5339 - 2 - 7 - 7 - 12 - 0 - 0 - 4 - 6 - 0 - 6 - AVPPLL - AIPPLV - A+PPL+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 8 - Query_8 - M_2447 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_2448 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_2449 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_2450 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_2451 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_2452 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_2453 - 9 - - - 1 - gnl|BL_ORD_ID|1179 - 79628|E1 protein|BAA19893.1|Rubella virus|11041 - 1179 - 21 - - - 1 - 12.3122 - 20 - 39.4328 - 4 - 9 - 14 - 19 - 0 - 0 - 4 - 5 - 0 - 6 - PTSPAA - PTAPCA - PT+P A - - - - - 2 - gnl|BL_ORD_ID|1573 - 141402|tegument protein VP22|NP_044651.1|Human alphaherpesvirus 1|10298 - 1573 - 10 - - - 1 - 11.927 - 19 - 68.8532 - 2 - 8 - 4 - 10 - 0 - 0 - 4 - 5 - 0 - 7 - EEPTSPA - ERPRAPA - E P +PA - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 15 - Query_15 - M_2454 - 9 - - - 1 - gnl|BL_ORD_ID|876 - 57591|Cobalamin (vitamin B12) synthesis protein/P47K family protein|YP_169986.1|Francisella tularensis subsp. tularensis SCHU S4|177416 - 876 - 10 - - - 1 - 12.6974 - 21 - 25.2038 - 4 - 9 - 1 - 6 - 0 - 0 - 3 - 5 - 0 - 6 - SRPIPI - SEPLPV - S P+P+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 16 - Query_16 - M_2455 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_2456 - 9 - - - 1 - gnl|BL_ORD_ID|1152 - 75718|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 1152 - 11 - - - 1 - 13.0826 - 22 - 16.3278 - 1 - 6 - 5 - 10 - 0 - 0 - 4 - 5 - 0 - 6 - PLFTTQ - PTFTSQ - P FT+Q - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 18 - Query_18 - M_2457 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_2458 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_2459 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_2460 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 22 - Query_22 - M_2461 - 9 - - - 1 - gnl|BL_ORD_ID|452 - 27345|Large envelope protein|P03138.3|Hepatitis B virus subtype ayw|10418 - 452 - 9 - - - 1 - 11.927 - 19 - 82.8955 - 2 - 7 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - PILPLI - PFLPLL - P LPL+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 23 - Query_23 - M_2462 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_2463 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_2464 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_2465 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_2466 - 9 - - - 1 - gnl|BL_ORD_ID|741 - 47760|EBNA-1 protein|Q777E1|Human gammaherpesvirus 4|10376 - 741 - 15 - - - 1 - 10.3862 - 15 - 419.458 - 2 - 7 - 1 - 6 - 0 - 0 - 4 - 4 - 0 - 6 - PGPIPG - PGTGPG - PG PG - - - - - 2 - gnl|BL_ORD_ID|75 - 5542|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 75 - 15 - - - 1 - 10.001 - 14 - 709.084 - 2 - 9 - 8 - 15 - 0 - 0 - 4 - 4 - 0 - 8 - PGPIPGPI - PGTSGSPI - PG PI - - - - - 3 - gnl|BL_ORD_ID|1929 - 180750|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1929 - 15 - - - 1 - 10.001 - 14 - 819.307 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 4 - 0 - 8 - PGPIPGPI - PGTSGSPI - PG PI - - - - - 4 - gnl|BL_ORD_ID|260 - 17802|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 260 - 15 - - - 1 - 10.001 - 14 - 830.077 - 2 - 9 - 3 - 10 - 0 - 0 - 4 - 4 - 0 - 8 - PGPIPGPI - PGTSGSPI - PG PI - - - - - 5 - gnl|BL_ORD_ID|1712 - 150341|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1712 - 9 - - - 1 - 9.61583 - 13 - 1362.74 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 4 - 0 - 8 - PGPIPGPI - PGTSGSPI - PG PI - - - - - 6 - gnl|BL_ORD_ID|1766 - 154857|tegument protein|CAB06735.1|Human alphaherpesvirus 2|10310 - 1766 - 16 - - - 1 - 4.99343 - 1 - 89081.4 - 7 - 9 - 14 - 16 - 0 - 0 - 2 - 3 - 0 - 3 - GPI - GPV - GP+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 28 - Query_28 - M_2467 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 29 - Query_29 - M_2468 - 9 - - - 1 - gnl|BL_ORD_ID|1179 - 79628|E1 protein|BAA19893.1|Rubella virus|11041 - 1179 - 21 - - - 1 - 12.6974 - 21 - 30.3943 - 3 - 8 - 14 - 19 - 0 - 0 - 4 - 5 - 0 - 6 - PTSPAA - PTAPCA - PT+P A - - - - - 2 - gnl|BL_ORD_ID|1573 - 141402|tegument protein VP22|NP_044651.1|Human alphaherpesvirus 1|10298 - 1573 - 10 - - - 1 - 12.3122 - 20 - 62.4024 - 1 - 7 - 4 - 10 - 0 - 0 - 4 - 5 - 0 - 7 - EEPTSPA - ERPRAPA - E P +PA - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 30 - Query_30 - M_2469 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 31 - Query_31 - M_2470 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 32 - Query_32 - M_2471 - 9 - - - 1 - gnl|BL_ORD_ID|452 - 27345|Large envelope protein|P03138.3|Hepatitis B virus subtype ayw|10418 - 452 - 9 - - - 1 - 11.927 - 19 - 105.754 - 4 - 9 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - PILPLI - PFLPLL - P LPL+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 33 - Query_33 - M_2472 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 34 - Query_34 - M_2473 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 35 - Query_35 - M_2474 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 36 - Query_36 - M_2475 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 37 - Query_37 - M_2476 - 9 - - - 1 - gnl|BL_ORD_ID|1970 - 182917|polyprotein|CDF77361.1|Dengue virus 3|11069 - 1970 - 9 - - - 1 - 13.853 - 24 - 4.59527 - 2 - 7 - 2 - 7 - 0 - 0 - 4 - 6 - 0 - 6 - YKDYAA - FKDFAA - +KD+AA - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 38 - Query_38 - M_2477 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 39 - Query_39 - M_2478 - 9 - - - 1 - gnl|BL_ORD_ID|1387 - 110227|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1387 - 33 - - - 1 - 14.6234 - 26 - 2.38904 - 2 - 8 - 21 - 27 - 0 - 0 - 6 - 6 - 0 - 7 - LKFSSKI - LKFYSKI - LKF SKI - - - - - 2 - gnl|BL_ORD_ID|1400 - 110467|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1400 - 25 - - - 1 - 14.6234 - 26 - 2.651 - 1 - 8 - 13 - 20 - 0 - 0 - 6 - 6 - 0 - 8 - SLKFSSKI - CLKFYSKI - LKF SKI - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 40 - Query_40 - M_2479 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 41 - Query_41 - M_2480 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 42 - Query_42 - M_2481 - 9 - - - 1 - gnl|BL_ORD_ID|1689 - 149063|NS3 protease/helicase'|NP_803144.1|Hepatitis C virus (isolate H77)|63746 - 1689 - 18 - - - 1 - 12.6974 - 21 - 27.7051 - 1 - 7 - 8 - 14 - 0 - 0 - 5 - 5 - 0 - 7 - TENSETT - VENLETT - EN ETT - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 43 - Query_43 - M_2482 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 44 - Query_44 - M_2483 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 45 - Query_45 - M_2484 - 9 - - - 1 - gnl|BL_ORD_ID|241 - 16836|precore/core protein [Hepatitis B virus]|AAR03815.1|Hepatitis B virus|10407 - 241 - 10 - - - 1 - 10.3862 - 15 - 499.131 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 4 - 0 - 8 - LPEVQLPK - LPSDFLPS - LP LP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 46 - Query_46 - M_2485 - 9 - - - 1 - gnl|BL_ORD_ID|1387 - 110227|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1387 - 33 - - - 1 - 15.0086 - 27 - 1.24899 - 3 - 9 - 21 - 27 - 0 - 0 - 6 - 6 - 0 - 7 - LKFSSKI - LKFYSKI - LKF SKI - - - - - 2 - gnl|BL_ORD_ID|1400 - 110467|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1400 - 25 - - - 1 - 14.2382 - 25 - 2.9789 - 3 - 9 - 14 - 20 - 0 - 0 - 6 - 6 - 0 - 7 - LKFSSKI - LKFYSKI - LKF SKI - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 47 - Query_47 - M_2486 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 48 - Query_48 - M_2487 - 9 - - - 1 - gnl|BL_ORD_ID|235 - 16814|precore protein|CAM58990.1|Hepatitis B virus|10407 - 235 - 10 - - - 1 - 15.3938 - 28 - 0.822133 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 7 - 0 - 9 - MPNDFWARL - LPNDFFPSV - +PNDF+ + - - - - - 2 - gnl|BL_ORD_ID|234 - 16813|External core antigen|SRC279980|Hepatitis B virus|10407 - 234 - 10 - - - 1 - 15.0086 - 27 - 1.18631 - 1 - 6 - 2 - 7 - 0 - 0 - 4 - 6 - 0 - 6 - MPNDFW - LPNDFF - +PNDF+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 49 - Query_49 - M_2488 - 9 - - - 1 - gnl|BL_ORD_ID|1984 - 183275|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1984 - 10 - - - 1 - 13.0826 - 22 - 16.111 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 6 - 0 - 8 - FTEHDVQI - FTNMEVQL - FT +VQ+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 50 - Query_50 - M_2489 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 51 - Query_51 - M_2490 - 9 - - - 1 - gnl|BL_ORD_ID|1897 - 180617|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1897 - 10 - - - 1 - 13.4678 - 23 - 12.2057 - 3 - 8 - 5 - 10 - 0 - 0 - 3 - 6 - 0 - 6 - YRTPSV - YQTPAI - Y+TP++ - - - - - 2 - gnl|BL_ORD_ID|2153 - 189289|gag protein|ADO93742.1|Human immunodeficiency virus 1|11676 - 2153 - 9 - - - 1 - 12.3122 - 20 - 44.8495 - 3 - 9 - 3 - 9 - 0 - 0 - 5 - 5 - 0 - 7 - YRTPSVL - YNTISVL - Y T SVL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 52 - Query_52 - M_2491 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 53 - Query_53 - M_2492 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 54 - Query_54 - M_2493 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 55 - Query_55 - M_2494 - 9 - - - 1 - gnl|BL_ORD_ID|1822 - 178247|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1822 - 15 - - - 1 - 14.2382 - 25 - 3.43226 - 1 - 8 - 6 - 13 - 0 - 0 - 4 - 5 - 0 - 8 - QEFENIKS - QRFHNIRG - Q F NI+ - - - - - 2 - gnl|BL_ORD_ID|1384 - 110205|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1384 - 32 - - - 1 - 14.2382 - 25 - 4.11038 - 1 - 7 - 4 - 10 - 0 - 0 - 4 - 5 - 0 - 7 - QEFENIK - QRFHNIR - Q F NI+ - - - - - 3 - gnl|BL_ORD_ID|1385 - 110215|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1385 - 25 - - - 1 - 14.2382 - 25 - 4.57287 - 1 - 8 - 10 - 17 - 0 - 0 - 4 - 5 - 0 - 8 - QEFENIKS - QRFHNIRG - Q F NI+ - - - - - 4 - gnl|BL_ORD_ID|1395 - 110394|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1395 - 32 - - - 1 - 13.0826 - 22 - 18.1365 - 1 - 7 - 22 - 28 - 0 - 0 - 4 - 5 - 0 - 7 - QEFENIK - QRFHNIR - Q F NI+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 56 - Query_56 - M_2495 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 57 - Query_57 - M_2496 - 9 - - - 1 - gnl|BL_ORD_ID|1185 - 93270|hypothetical protein|NP_218356.1|Mycobacterium tuberculosis H37Rv|83332 - 1185 - 9 - - - 1 - 15.0086 - 27 - 0.92904 - 2 - 9 - 2 - 9 - 0 - 0 - 5 - 6 - 0 - 8 - MYDGRFLV - LYDGSFAV - +YDG F V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 58 - Query_58 - M_2497 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 59 - Query_59 - M_2498 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 60 - Query_60 - M_2499 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 61 - Query_61 - M_2500 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 62 - Query_62 - M_2501 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 63 - Query_63 - M_2502 - 9 - - - 1 - gnl|BL_ORD_ID|235 - 16814|precore protein|CAM58990.1|Hepatitis B virus|10407 - 235 - 10 - - - 1 - 15.0086 - 27 - 0.948031 - 3 - 8 - 2 - 7 - 0 - 0 - 4 - 6 - 0 - 6 - MPNDFW - LPNDFF - +PNDF+ - - - - - 2 - gnl|BL_ORD_ID|234 - 16813|External core antigen|SRC279980|Hepatitis B virus|10407 - 234 - 10 - - - 1 - 15.0086 - 27 - 0.978697 - 3 - 8 - 2 - 7 - 0 - 0 - 4 - 6 - 0 - 6 - MPNDFW - LPNDFF - +PNDF+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_126613_2_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_126613_2_T.fasta deleted file mode 100755 index 73fb9895..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_126613_2_T.fasta +++ /dev/null @@ -1,70 +0,0 @@ ->M_2503 -KMPEMHFKA ->M_2504 -AYSKCFISV ->M_2505 -LYLKTSQDV ->M_2506 -DLLTNLMYV ->M_2507 -LLTNLMYVL ->M_2508 -YQFPQSIDL ->M_2509 -VWQRPVLNF ->M_2510 -VEGTFISDY ->M_2511 -EELEIFMAR ->M_2512 -YEMIRTFYI ->M_2513 -EEFPCHKCV ->M_2514 -NYMAHLVAV ->M_2515 -FADFEWHFL ->M_2516 -SFADFEWHF ->M_2517 -FEQTLEELY ->M_2518 -IYVKPLPIL ->M_2519 -VLQIYVKPL ->M_2520 -RQWRSLTTL ->M_2521 -FCLGLVVTI ->M_2522 -GVFCLGLVV ->M_2523 -TLGVFCLGL ->M_2524 -IVPRLIMNF ->M_2525 -LIMNFTLGV ->M_2526 -GEHPYQCPY ->M_2527 -VLHRHMTTI ->M_2528 -HEIDFYRED ->M_2529 -KLDASVQHL ->M_2530 -RQLKLDASV ->M_2531 -FLWLWPLDF ->M_2532 -SEDGFLWLW ->M_2533 -WLWPLDFSS ->M_2534 -TFRDVAVEF ->M_2535 -AFSQSAYLI ->M_2536 -AYLIQHQRF ->M_2537 -KAFSQSAYL diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_126613_2_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_126613_2_T_iedb.xml deleted file mode 100755 index 2a4695b8..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_126613_2_T_iedb.xml +++ /dev/null @@ -1,1190 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_2503 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_2503 - 9 - - - 1 - gnl|BL_ORD_ID|2244 - 232153|rhoptry protein 18|CAJ27113.1|Toxoplasma gondii type I|1209525 - 2244 - 19 - - - 1 - 12.3122 - 20 - 38.4826 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - PEMHFKA - PERPFQA - PE F+A - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 2 - Query_2 - M_2504 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_2505 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_2506 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_2507 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_2508 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_2509 - 9 - - - 1 - gnl|BL_ORD_ID|624 - 37507|Large T antigen|P03071.1|Human polyomavirus 1|1891762 - 624 - 9 - - - 1 - 13.853 - 24 - 5.95161 - 1 - 6 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - VWQRPV - IWFRPV - +W RPV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 8 - Query_8 - M_2510 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_2511 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_2512 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_2513 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_2514 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_2515 - 9 - - - 1 - gnl|BL_ORD_ID|732 - 46575|polyprotein|AAG30730.1|Dengue virus 2|11060 - 732 - 9 - - - 1 - 13.4678 - 23 - 7.85574 - 1 - 8 - 2 - 9 - 0 - 0 - 4 - 6 - 0 - 8 - FADFEWHF - YADRKWCF - +AD +W F - - - - - 2 - gnl|BL_ORD_ID|456 - 27770|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 456 - 10 - - - 1 - 13.4678 - 23 - 10.4367 - 1 - 8 - 3 - 10 - 0 - 0 - 4 - 5 - 0 - 8 - FADFEWHF - YADRRWCF - +AD W F - - - - - 3 - gnl|BL_ORD_ID|1850 - 180360|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1850 - 15 - - - 1 - 13.4678 - 23 - 11.2975 - 1 - 8 - 7 - 14 - 0 - 0 - 4 - 5 - 0 - 8 - FADFEWHF - YADRRWCF - +AD W F - - - - - 4 - gnl|BL_ORD_ID|733 - 46576|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 733 - 9 - - - 1 - 13.4678 - 23 - 11.9303 - 1 - 8 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - FADFEWHF - YADRRWCF - +AD W F - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 14 - Query_14 - M_2516 - 9 - - - 1 - gnl|BL_ORD_ID|732 - 46575|polyprotein|AAG30730.1|Dengue virus 2|11060 - 732 - 9 - - - 1 - 13.853 - 24 - 4.92244 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 7 - 0 - 9 - SFADFEWHF - NYADRKWCF - ++AD +W F - - - - - 2 - gnl|BL_ORD_ID|456 - 27770|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 456 - 10 - - - 1 - 13.853 - 24 - 5.98008 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 6 - 0 - 9 - SFADFEWHF - NYADRRWCF - ++AD W F - - - - - 3 - gnl|BL_ORD_ID|1850 - 180360|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1850 - 15 - - - 1 - 13.853 - 24 - 6.40908 - 1 - 9 - 6 - 14 - 0 - 0 - 4 - 6 - 0 - 9 - SFADFEWHF - NYADRRWCF - ++AD W F - - - - - 4 - gnl|BL_ORD_ID|733 - 46576|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 733 - 9 - - - 1 - 13.853 - 24 - 6.95623 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 6 - 0 - 9 - SFADFEWHF - NYADRRWCF - ++AD W F - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 15 - Query_15 - M_2517 - 9 - - - 1 - gnl|BL_ORD_ID|697 - 42430|Major surface antigen precursor|P03141.3|Hepatitis B virus|10407 - 697 - 15 - - - 1 - 13.4678 - 23 - 7.23267 - 1 - 7 - 8 - 14 - 0 - 0 - 4 - 6 - 0 - 7 - FEQTLEE - FHQTLQD - F QTL++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 16 - Query_16 - M_2518 - 9 - - - 1 - gnl|BL_ORD_ID|889 - 58463|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 889 - 20 - - - 1 - 12.6974 - 21 - 31.8709 - 1 - 8 - 11 - 18 - 0 - 0 - 5 - 6 - 0 - 8 - IYVKPLPI - IYVYALPL - IYV LP+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 17 - Query_17 - M_2519 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_2520 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_2521 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_2522 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_2523 - 9 - - - 1 - gnl|BL_ORD_ID|2102 - 185978|polyprotein|CDF77361.1|Dengue virus 3|11069 - 2102 - 10 - - - 1 - 15.3938 - 28 - 0.539796 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 7 - 0 - 9 - TLGVFCLGL - TMGVLCLAI - T+GV CL + - - - - - 2 - gnl|BL_ORD_ID|979 - 64818|E7|AAD33253.1|Human papillomavirus type 16|333760 - 979 - 8 - - - 1 - 13.4678 - 23 - 12.6494 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - TLGVFC - TLGIVC - TLG+ C - - - - - 3 - gnl|BL_ORD_ID|980 - 64819|E7 protein|ABL96585.1|Human papillomavirus type 16|333760 - 980 - 9 - - - 1 - 13.0826 - 22 - 17.1877 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - TLGVFC - TLGIVC - TLG+ C - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 22 - Query_22 - M_2524 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_2525 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_2526 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_2527 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_2528 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_2529 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 28 - Query_28 - M_2530 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 29 - Query_29 - M_2531 - 9 - - - 1 - gnl|BL_ORD_ID|1243 - 98040|trans-sialidase, putative|EAN80725.1|Trypanosoma cruzi|5693 - 1243 - 9 - - - 1 - 13.0826 - 22 - 22.6682 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 6 - 0 - 8 - FLWLWPLD - FLYNRPLN - FL+ PL+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 30 - Query_30 - M_2532 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 31 - Query_31 - M_2533 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 32 - Query_32 - M_2534 - 9 - - - 1 - gnl|BL_ORD_ID|2108 - 186175|polyprotein|AFY10053.1|Dengue virus 3|11069 - 2108 - 10 - - - 1 - 13.853 - 24 - 6.08483 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 6 - 0 - 6 - TFRDVA - TWRDMA - T+RD+A - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 33 - Query_33 - M_2535 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 34 - Query_34 - M_2536 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 35 - Query_35 - M_2537 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_126796_3_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_126796_3_T.fasta deleted file mode 100755 index d1c98dee..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_126796_3_T.fasta +++ /dev/null @@ -1,132 +0,0 @@ ->M_2538 -QEEQQQQQL ->M_2539 -YLFSPQNQF ->M_2540 -YLFSPQNQF ->M_2541 -QARKIDHPL ->M_2542 -QARKIDHPL ->M_2543 -GLFVHTPCL ->M_2544 -RVLPAGLFV ->M_2545 -VHTPCLVGL ->M_2546 -AGLDSYPEL ->M_2547 -LVVSRSVSL ->M_2548 -LVVSRSVSL ->M_2549 -CSVDHRSVL ->M_2550 -HRSVLQRIM ->M_2551 -KMWEQEEKI ->M_2552 -FGIISIIFV ->M_2553 -GIISIIFVV ->M_2554 -IFGIISIIF ->M_2555 -RIFGIISII ->M_2556 -STAARIFGI ->M_2557 -TAARIFGII ->M_2558 -LSVQLGPTV ->M_2559 -CYTFNSIII ->M_2560 -SIIIFGPFL ->M_2561 -SIIIFGPFL ->M_2562 -YTFNSIIIF ->M_2563 -LEIQTPEAV ->M_2564 -YLALAAQCL ->M_2565 -YLALAAQCL ->M_2566 -AGCPAAQEL ->M_2567 -RARPAGCPA ->M_2568 -RPAGCPAAQ ->M_2569 -AGVDHIITM ->M_2570 -LSIAGVDHI ->M_2571 -PPRYIGIPI ->M_2572 -CMLVGDSAV ->M_2573 -MLSSIKCML ->M_2574 -MLSSIKCML ->M_2575 -FGHTYVPAF ->M_2576 -GQDFGHTYV ->M_2577 -YSTPQGQDF ->M_2578 -FVGLAIGTL ->M_2579 -IGTLSGDAL ->M_2580 -NMFEISNRL ->M_2581 -VDLGSTTPL ->M_2582 -IPLWGSPVT ->M_2583 -FVLSMQPVV ->M_2584 -FVLSMQPVV ->M_2585 -SMQPVVFQA ->M_2586 -YYDPFVLSM ->M_2587 -YYDPFVLSM ->M_2588 -YSHQNGASY ->M_2589 -AGVLLVLAL ->M_2590 -RFAGVLLVL ->M_2591 -VLALILPGT ->M_2592 -VLLVLALIL ->M_2593 -RQIPAQRDL ->M_2594 -SYRKSVRQI ->M_2595 -CYYELNQCL ->M_2596 -CYYELNQCL ->M_2597 -CPLCPFLTM ->M_2598 -FMNRFQCPL ->M_2599 -FMNRFQCPL ->M_2600 -FQCPLCPFL ->M_2601 -FQCPLCPFL ->M_2602 -RFQCPLCPF ->M_2603 -RFQCPLCPF diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_126796_3_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_126796_3_T_iedb.xml deleted file mode 100755 index fed7e106..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_126796_3_T_iedb.xml +++ /dev/null @@ -1,2526 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_2538 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_2538 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_2539 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_2540 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_2541 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_2542 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_2543 - 9 - - - 1 - gnl|BL_ORD_ID|1562 - 141281|tegument protein UL21|NP_044622.1|Human alphaherpesvirus 1|10298 - 1562 - 10 - - - 1 - 13.4678 - 23 - 10.6199 - 3 - 8 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - FVHTPC - FVYTPS - FV+TP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 7 - Query_7 - M_2544 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_2545 - 9 - - - 1 - gnl|BL_ORD_ID|1099 - 72566|polyprotein|BAD73987.1|Hepatitis C virus subtype 1b|31647 - 1099 - 9 - - - 1 - 14.2382 - 25 - 3.61702 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 4 - 0 - 8 - HTPCLVGL - HYPCTVNF - H PC V - - - - - 2 - gnl|BL_ORD_ID|417 - 25186|polyprotein|AAK32686.1|Hepatitis C virus|11103 - 417 - 10 - - - 1 - 13.853 - 24 - 4.3044 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 4 - 0 - 8 - HTPCLVGL - HYPCTVNF - H PC V - - - - - 3 - gnl|BL_ORD_ID|1413 - 111407|polyprotein|BAA00792.1|Hepatitis C virus|11103 - 1413 - 10 - - - 1 - 13.4678 - 23 - 8.46851 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 4 - 0 - 7 - HTPCLVG - HYPCTVN - H PC V - - - - - 4 - gnl|BL_ORD_ID|835 - 54825|polyprotein|BAA03375.1|Hepatitis C virus|11103 - 835 - 9 - - - 1 - 13.0826 - 22 - 14.1983 - 2 - 7 - 4 - 9 - 0 - 0 - 4 - 4 - 0 - 6 - HTPCLV - HYPCTV - H PC V - - - - - 5 - gnl|BL_ORD_ID|1149 - 75636|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 1149 - 10 - - - 1 - 13.0826 - 22 - 20.1646 - 2 - 7 - 5 - 10 - 0 - 0 - 3 - 4 - 0 - 6 - HTPCLV - HYPCTI - H PC + - - - - - 6 - gnl|BL_ORD_ID|833 - 54821|E2 protein|AAM33354.1|Hepatitis C virus subtype 1a|31646 - 833 - 9 - - - 1 - 12.6974 - 21 - 24.2855 - 2 - 7 - 4 - 9 - 0 - 0 - 3 - 4 - 0 - 6 - HTPCLV - HYPCTI - H PC + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 9 - Query_9 - M_2546 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_2547 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_2548 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_2549 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_2550 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_2551 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_2552 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_2553 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_2554 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_2555 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_2556 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_2557 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_2558 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 22 - Query_22 - M_2559 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_2560 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_2561 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_2562 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_2563 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_2564 - 9 - - - 1 - gnl|BL_ORD_ID|1292 - 102636|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 - 1292 - 15 - - - 1 - 13.4678 - 23 - 10.1977 - 3 - 9 - 8 - 14 - 0 - 0 - 6 - 6 - 0 - 7 - ALAAQCL - ALAAYCL - ALAA CL - - - - - 2 - gnl|BL_ORD_ID|1033 - 69349|Genome polyprotein|P29846.3|Hepatitis C virus (isolate Taiwan)|31645 - 1033 - 10 - - - 1 - 13.4678 - 23 - 12.859 - 3 - 9 - 4 - 10 - 0 - 0 - 6 - 6 - 0 - 7 - ALAAQCL - ALAAYCL - ALAA CL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 28 - Query_28 - M_2565 - 9 - - - 1 - gnl|BL_ORD_ID|1292 - 102636|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 - 1292 - 15 - - - 1 - 13.4678 - 23 - 10.1977 - 3 - 9 - 8 - 14 - 0 - 0 - 6 - 6 - 0 - 7 - ALAAQCL - ALAAYCL - ALAA CL - - - - - 2 - gnl|BL_ORD_ID|1033 - 69349|Genome polyprotein|P29846.3|Hepatitis C virus (isolate Taiwan)|31645 - 1033 - 10 - - - 1 - 13.4678 - 23 - 12.859 - 3 - 9 - 4 - 10 - 0 - 0 - 6 - 6 - 0 - 7 - ALAAQCL - ALAAYCL - ALAA CL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 29 - Query_29 - M_2566 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 30 - Query_30 - M_2567 - 9 - - - 1 - gnl|BL_ORD_ID|1493 - 136865|tegument protein|CAB06735.1|Human alphaherpesvirus 2|10310 - 1493 - 15 - - - 1 - 13.4678 - 23 - 10.1977 - 1 - 6 - 3 - 8 - 0 - 0 - 5 - 5 - 0 - 6 - RARPAG - RARPRG - RARP G - - - - - 2 - gnl|BL_ORD_ID|2189 - 190533|nucleocapsid protein|AAP49024.1|SARS coronavirus|227859 - 2189 - 15 - - - 1 - 13.4678 - 23 - 10.3735 - 3 - 8 - 2 - 7 - 0 - 0 - 4 - 4 - 0 - 6 - RPAGCP - RPQGLP - RP G P - - - - - 3 - gnl|BL_ORD_ID|850 - 55683|nucleocapsid protein|ABI96968.1|SARS coronavirus|227859 - 850 - 15 - - - 1 - 13.4678 - 23 - 10.9188 - 3 - 8 - 2 - 7 - 0 - 0 - 4 - 4 - 0 - 6 - RPAGCP - RPQGLP - RP G P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 31 - Query_31 - M_2568 - 9 - - - 1 - gnl|BL_ORD_ID|2189 - 190533|nucleocapsid protein|AAP49024.1|SARS coronavirus|227859 - 2189 - 15 - - - 1 - 13.4678 - 23 - 11.1066 - 1 - 6 - 2 - 7 - 0 - 0 - 4 - 4 - 0 - 6 - RPAGCP - RPQGLP - RP G P - - - - - 2 - gnl|BL_ORD_ID|850 - 55683|nucleocapsid protein|ABI96968.1|SARS coronavirus|227859 - 850 - 15 - - - 1 - 13.4678 - 23 - 11.689 - 1 - 6 - 2 - 7 - 0 - 0 - 4 - 4 - 0 - 6 - RPAGCP - RPQGLP - RP G P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 32 - Query_32 - M_2569 - 9 - - - 1 - gnl|BL_ORD_ID|698 - 42455|Probable Na(+)-translocating NADH-quinone reductase subunit A|O84639.1|Chlamydia trachomatis|813 - 698 - 9 - - - 1 - 13.0826 - 22 - 20.4374 - 4 - 9 - 3 - 8 - 0 - 0 - 4 - 5 - 0 - 6 - DHIITM - DHTITL - DH IT+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 33 - Query_33 - M_2570 - 9 - - - 1 - gnl|BL_ORD_ID|1441 - 120187|E1 protein|BAA19893.1|Rubella virus|11041 - 1441 - 21 - - - 1 - 14.2382 - 25 - 3.04044 - 1 - 7 - 14 - 20 - 0 - 0 - 5 - 6 - 0 - 7 - LSIAGVD - LSVAGVS - LS+AGV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 34 - Query_34 - M_2571 - 9 - - - 1 - gnl|BL_ORD_ID|1 - 118|envelope glycoprotein|ABS76372.1|Human immunodeficiency virus 1|11676 - 1 - 20 - - - 1 - 13.0826 - 22 - 14.6415 - 4 - 9 - 10 - 15 - 0 - 0 - 3 - 5 - 0 - 6 - YIGIPI - YYGVPV - Y G+P+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 35 - Query_35 - M_2572 - 9 - - - 1 - gnl|BL_ORD_ID|1792 - 164258|nucleocapsid protein|AAA43837.1|Hantaan virus 76-118|11602 - 1792 - 15 - - - 1 - 13.4678 - 23 - 11.689 - 1 - 8 - 4 - 11 - 0 - 0 - 4 - 6 - 0 - 8 - CMLVGDSA - CKLLPDTA - C L+ D+A - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 36 - Query_36 - M_2573 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 37 - Query_37 - M_2574 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 38 - Query_38 - M_2575 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 39 - Query_39 - M_2576 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 40 - Query_40 - M_2577 - 9 - - - 1 - gnl|BL_ORD_ID|1904 - 180643|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1904 - 15 - - - 1 - 11.927 - 19 - 61.2314 - 2 - 7 - 6 - 11 - 0 - 0 - 4 - 5 - 0 - 6 - STPQGQ - TTPFGQ - +TP GQ - - - - - 2 - gnl|BL_ORD_ID|1856 - 180411|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1856 - 9 - - - 1 - 11.5418 - 18 - 138.797 - 2 - 7 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - STPQGQ - TTPFGQ - +TP GQ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 41 - Query_41 - M_2578 - 9 - - - 1 - gnl|BL_ORD_ID|344 - 21638|protein F|ABV46152.2|Hepatitis C virus (isolate Japanese)|11116 - 344 - 9 - - - 1 - 13.0826 - 22 - 18.7436 - 3 - 9 - 3 - 9 - 0 - 0 - 5 - 6 - 0 - 7 - GLAIGTL - GLSPGTL - GL+ GTL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 42 - Query_42 - M_2579 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 43 - Query_43 - M_2580 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 44 - Query_44 - M_2581 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 45 - Query_45 - M_2582 - 9 - - - 1 - gnl|BL_ORD_ID|744 - 48321|||| - 744 - 9 - - - 1 - 15.0086 - 27 - 1.49881 - 2 - 8 - 1 - 7 - 0 - 0 - 5 - 6 - 0 - 7 - PLWGSPV - PLFGYPV - PL+G PV - - - - - 2 - gnl|BL_ORD_ID|378 - 23365|polyprotein|BAB18806.1|Hepatitis C virus|11103 - 378 - 10 - - - 1 - 14.2382 - 25 - 2.57891 - 1 - 8 - 3 - 10 - 0 - 0 - 5 - 7 - 0 - 8 - IPLWGSPV - IPLVGAPL - IPL G+P+ - - - - - 3 - gnl|BL_ORD_ID|296 - 19493|polyprotein|BAA03375.1|Hepatitis C virus|11103 - 296 - 15 - - - 1 - 14.2382 - 25 - 3.14687 - 1 - 7 - 9 - 15 - 0 - 0 - 5 - 6 - 0 - 7 - IPLWGSP - IPLVGAP - IPL G+P - - - - - 4 - gnl|BL_ORD_ID|1149 - 75636|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 1149 - 10 - - - 1 - 13.0826 - 22 - 15.0326 - 3 - 9 - 3 - 9 - 0 - 0 - 4 - 4 - 0 - 7 - LWGSPVT - LWHYPCT - LW P T - - - - - 5 - gnl|BL_ORD_ID|832 - 54820|polyprotein precursor|BAA02756.1|Hepatitis C virus|11103 - 832 - 9 - - - 1 - 13.0826 - 22 - 16.6015 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 4 - 0 - 7 - LWGSPVT - LWHYPCT - LW P T - - - - - 6 - gnl|BL_ORD_ID|833 - 54821|E2 protein|AAM33354.1|Hepatitis C virus subtype 1a|31646 - 833 - 9 - - - 1 - 13.0826 - 22 - 18.4218 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 4 - 0 - 7 - LWGSPVT - LWHYPCT - LW P T - - - - - 7 - gnl|BL_ORD_ID|831 - 54819|JK3|CAA43789.1|Hepatitis C virus|11103 - 831 - 9 - - - 1 - 13.0826 - 22 - 18.4218 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 4 - 0 - 7 - LWGSPVT - LWHYPCT - LW P T - - - - - 8 - gnl|BL_ORD_ID|834 - 54824|polyprotein precursor|BAA01583.1|Hepatitis C virus|11103 - 834 - 9 - - - 1 - 13.0826 - 22 - 18.7436 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 4 - 0 - 7 - LWGSPVT - LWHYPCT - LW P T - - - - - 9 - gnl|BL_ORD_ID|835 - 54825|polyprotein|BAA03375.1|Hepatitis C virus|11103 - 835 - 9 - - - 1 - 13.0826 - 22 - 19.7427 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 4 - 0 - 7 - LWGSPVT - LWHYPCT - LW P T - - - - - 10 - gnl|BL_ORD_ID|609 - 37255|||| - 609 - 9 - - - 1 - 12.6974 - 21 - 26.0147 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - LWGSPVT - LFGYPVA - L+G PV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 46 - Query_46 - M_2583 - 9 - - - 1 - gnl|BL_ORD_ID|1157 - 76334|Protein E7|P17387.1|Human papillomavirus type 31|10585 - 1157 - 10 - - - 1 - 14.6234 - 26 - 1.81479 - 1 - 7 - 1 - 7 - 0 - 0 - 4 - 6 - 0 - 7 - FVLSMQP - YVLDLQP - +VL +QP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 47 - Query_47 - M_2584 - 9 - - - 1 - gnl|BL_ORD_ID|1157 - 76334|Protein E7|P17387.1|Human papillomavirus type 31|10585 - 1157 - 10 - - - 1 - 14.6234 - 26 - 1.81479 - 1 - 7 - 1 - 7 - 0 - 0 - 4 - 6 - 0 - 7 - FVLSMQP - YVLDLQP - +VL +QP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 48 - Query_48 - M_2585 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 49 - Query_49 - M_2586 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 50 - Query_50 - M_2587 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 51 - Query_51 - M_2588 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 52 - Query_52 - M_2589 - 9 - - - 1 - gnl|BL_ORD_ID|336 - 21199|Circumsporozoite protein precursor|P08677.2|Plasmodium vivax strain Belem|31273 - 336 - 10 - - - 1 - 12.6974 - 21 - 30.4011 - 3 - 9 - 4 - 10 - 0 - 0 - 6 - 7 - 0 - 7 - VLLVLAL - ILLVLAL - +LLVLAL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 53 - Query_53 - M_2590 - 9 - - - 1 - gnl|BL_ORD_ID|1824 - 178829|envelope protein|BAJ51675.1|HBV genotype D|489483 - 1824 - 10 - - - 1 - 12.6974 - 21 - 25.6384 - 2 - 9 - 1 - 8 - 0 - 0 - 6 - 6 - 0 - 8 - FAGVLLVL - FLGPLLVL - F G LLVL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 54 - Query_54 - M_2591 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 55 - Query_55 - M_2592 - 9 - - - 1 - gnl|BL_ORD_ID|336 - 21199|Circumsporozoite protein precursor|P08677.2|Plasmodium vivax strain Belem|31273 - 336 - 10 - - - 1 - 12.3122 - 20 - 46.3152 - 1 - 7 - 4 - 10 - 0 - 0 - 6 - 7 - 0 - 7 - VLLVLAL - ILLVLAL - +LLVLAL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 56 - Query_56 - M_2593 - 9 - - - 1 - gnl|BL_ORD_ID|1184 - 93224|core protein|AAL31859.1|Hepatitis B virus|10407 - 1184 - 14 - - - 1 - 15.0086 - 27 - 1.285 - 4 - 9 - 4 - 9 - 0 - 0 - 5 - 5 - 0 - 6 - PAQRDL - PASRDL - PA RDL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 57 - Query_57 - M_2594 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 58 - Query_58 - M_2595 - 9 - - - 1 - gnl|BL_ORD_ID|1398 - 110431|E7|AAD33253.1|Human papillomavirus type 16|333760 - 1398 - 36 - - - 1 - 13.0826 - 22 - 14.7121 - 1 - 8 - 5 - 12 - 0 - 0 - 4 - 5 - 0 - 8 - CYYELNQC - CYEQLNDS - CY +LN - - - - - 2 - gnl|BL_ORD_ID|1392 - 110335|E7|AAD33253.1|Human papillomavirus type 16|333760 - 1392 - 32 - - - 1 - 13.0826 - 22 - 19.4872 - 1 - 8 - 24 - 31 - 0 - 0 - 4 - 5 - 0 - 8 - CYYELNQC - CYEQLNDS - CY +LN - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 59 - Query_59 - M_2596 - 9 - - - 1 - gnl|BL_ORD_ID|1398 - 110431|E7|AAD33253.1|Human papillomavirus type 16|333760 - 1398 - 36 - - - 1 - 13.0826 - 22 - 14.7121 - 1 - 8 - 5 - 12 - 0 - 0 - 4 - 5 - 0 - 8 - CYYELNQC - CYEQLNDS - CY +LN - - - - - 2 - gnl|BL_ORD_ID|1392 - 110335|E7|AAD33253.1|Human papillomavirus type 16|333760 - 1392 - 32 - - - 1 - 13.0826 - 22 - 19.4872 - 1 - 8 - 24 - 31 - 0 - 0 - 4 - 5 - 0 - 8 - CYYELNQC - CYEQLNDS - CY +LN - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 60 - Query_60 - M_2597 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 61 - Query_61 - M_2598 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 62 - Query_62 - M_2599 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 63 - Query_63 - M_2600 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 64 - Query_64 - M_2601 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 65 - Query_65 - M_2602 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 66 - Query_66 - M_2603 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_127486_2_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_127486_2_T.fasta deleted file mode 100755 index 86c0b387..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_127486_2_T.fasta +++ /dev/null @@ -1,62 +0,0 @@ ->M_2604 -APEPLLLSW ->M_2605 -ASLHHHHHR ->M_2606 -RPPPSQASL ->M_2607 -FPDHMACDL ->M_2608 -ALLGNRTAL ->M_2609 -GPVSAPGLL ->M_2610 -HVYRNFLNK ->M_2611 -RPRGDNGYT ->M_2612 -SNSESEILK ->M_2613 -AVDRYVAMR ->M_2614 -RYVAMRHPL ->M_2615 -YVAMRHPLR ->M_2616 -RAGESVWPK ->M_2617 -VWPKKINNI ->M_2618 -VVGADGVGK ->M_2619 -KTETYDNYK ->M_2620 -RQLTVESDK ->M_2621 -ITLTATSQK ->M_2622 -HPTASTLST ->M_2623 -NPSHPTAST ->M_2624 -LMLLQSGYK ->M_2625 -HFPIYHLLL ->M_2626 -LASSFVFLY ->M_2627 -LISEGQRLK ->M_2628 -KPLPLVTDL ->M_2629 -LPLVTDLSL ->M_2630 -APIAPTFYK ->M_2631 -APTFYKPKL ->M_2632 -IAPTFYKPK ->M_2633 -TFYKPKLLK ->M_2634 -VFQHIFDLI diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_127486_2_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_127486_2_T_iedb.xml deleted file mode 100755 index cb107982..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_127486_2_T_iedb.xml +++ /dev/null @@ -1,724 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_2604 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_2604 - 9 - - - 1 - gnl|BL_ORD_ID|1682 - 149036|E2 protein|NP_751921.1|Hepatitis C virus (isolate H77)|63746 - 1682 - 9 - - - 1 - 12.3122 - 20 - 55.769 - 4 - 8 - 4 - 8 - 0 - 0 - 5 - 5 - 0 - 5 - PLLLS - PLLLS - PLLLS - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 2 - Query_2 - M_2605 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_2606 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_2607 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_2608 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_2609 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_2610 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_2611 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_2612 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_2613 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_2614 - 9 - - - 1 - gnl|BL_ORD_ID|2080 - 185327|polyprotein|ACF49259.1|Dengue virus type 1 Hawaii|10000440 - 2080 - 9 - - - 1 - 13.853 - 24 - 5.18352 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 6 - 0 - 9 - RYVAMRHPL - QYIYMGQPL - +Y+ M PL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 12 - Query_12 - M_2615 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_2616 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_2617 - 9 - - - 1 - gnl|BL_ORD_ID|1950 - 181035|||| - 1950 - 44 - - - 1 - 13.4678 - 23 - 8.97754 - 1 - 6 - 7 - 12 - 0 - 0 - 4 - 5 - 0 - 6 - VWPKKI - VWLKKL - VW KK+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 15 - Query_15 - M_2618 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_2619 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_2620 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_2621 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_2622 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_2623 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_2624 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 22 - Query_22 - M_2625 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_2626 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_2627 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_2628 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_2629 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_2630 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 28 - Query_28 - M_2631 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 29 - Query_29 - M_2632 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 30 - Query_30 - M_2633 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 31 - Query_31 - M_2634 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_128984_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_128984_1_T.fasta deleted file mode 100755 index 288816ea..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_128984_1_T.fasta +++ /dev/null @@ -1,216 +0,0 @@ ->M_2635 -AAATAVVAF ->M_2636 -ALLRATDTI ->M_2637 -APFDKHCAV ->M_2638 -APFLNSVSI ->M_2639 -APHGEEAHL ->M_2640 -APLLPRTHL ->M_2641 -APRRHSGRV ->M_2642 -APSLPSPTA ->M_2643 -APVTLRGSY ->M_2644 -ATGGHHQPL ->M_2645 -AVMAFDLCV ->M_2646 -AVMAFDRSV ->M_2647 -AYQVSVCAF ->M_2648 -CTTPVTVEI ->M_2649 -CYYYFLCLL ->M_2650 -DTPRHRLLV ->M_2651 -EAQQSSHCL ->M_2652 -EPRITRSFV ->M_2653 -ETGLALKYL ->M_2654 -FSFQVDSPV ->M_2655 -FSILSTALL ->M_2656 -GLRKTNMSL ->M_2657 -GPNAMRYSL ->M_2658 -GPRNCIGQA ->M_2659 -HMSACHHSI ->M_2660 -HPNAHSNST ->M_2661 -HPWTTDMPA ->M_2662 -HSNSTSFIF ->M_2663 -HSNSTSFIF ->M_2664 -HTWQMRNTV ->M_2665 -HTWQMRNTV ->M_2666 -IFSLGRHTW ->M_2667 -INALIIFIF ->M_2668 -IPHLLKLAC ->M_2669 -ISASVCIQV ->M_2670 -ITSTVMLEV ->M_2671 -KAFNCSSFV ->M_2672 -KAFSQSSNL ->M_2673 -KLFSILSTA ->M_2674 -KLWATAEAL ->M_2675 -KTHRIVRRL ->M_2676 -KTHRIVRRL ->M_2677 -KTLRKSLPA ->M_2678 -KTLRKSLPA ->M_2679 -KYIFNNSII ->M_2680 -KYTSAAILV ->M_2681 -LALSVTEMV ->M_2682 -LHSPMYFFL ->M_2683 -LHTPVYFLL ->M_2684 -LLVSLTVTF ->M_2685 -LPGGVGRTL ->M_2686 -LPSDDRGSL ->M_2687 -LSVADQEKV ->M_2688 -LWGKHQFIL ->M_2689 -MAFDLCVAI ->M_2690 -MAFDRSVAI ->M_2691 -MAFDRSVAI ->M_2692 -MIISASVCI ->M_2693 -MIISASVCI ->M_2694 -MLDLLTNTL ->M_2695 -MTNGLCIWL ->M_2696 -MVNATACAV ->M_2697 -NAFQEARRL ->M_2698 -PSAPKPSTL ->M_2699 -QALRAGLAL ->M_2700 -QALRAGLAL ->M_2701 -QAVEFCQRV ->M_2702 -QILVKICTI ->M_2703 -QLHFIFHIL ->M_2704 -QLWGKHQFI ->M_2705 -QPWEHVNAF ->M_2706 -QQQMASRPF ->M_2707 -QTSMSQSQV ->M_2708 -RIIKLLVSL ->M_2709 -RLALSTFEW ->M_2710 -RLHSPMYFF ->M_2711 -RLHSPMYFF ->M_2712 -RLHTPVYFL ->M_2713 -RSFTEENHM ->M_2714 -RSFVPHLEI ->M_2715 -RSFVPHLEI ->M_2716 -RSVAICKPL ->M_2717 -RVVLINNNL ->M_2718 -SASSQSSSI ->M_2719 -SASVCIQVV ->M_2720 -SIIQDFFAW ->M_2721 -SINALIIFI ->M_2722 -SMSQSQVAL ->M_2723 -SPAQAPIPY ->M_2724 -SPGGWRSGW ->M_2725 -SSEQSIFVV ->M_2726 -SSIPENEAI ->M_2727 -STVMLEVPL ->M_2728 -STVMLEVPL ->M_2729 -SYSSLDEDF ->M_2730 -TPRHRLLVL ->M_2731 -TSMYNEILI ->M_2732 -TSVPVTTAV ->M_2733 -VPADSTQTL ->M_2734 -VSIETHLLF ->M_2735 -VSIETHLLF ->M_2736 -VSLTVTFVL ->M_2737 -VTTAVSTFV ->M_2738 -VTTGLMGAV ->M_2739 -YSSLDEDFL ->M_2740 -YVQKRSSQI ->M_2741 -YYFLCLLL* ->M_2742 -YYYFLCLLL diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_128984_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_128984_1_T_iedb.xml deleted file mode 100755 index ef42d15d..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_128984_1_T_iedb.xml +++ /dev/null @@ -1,3116 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_2635 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_2635 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_2636 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_2637 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_2638 - 9 - - - 1 - gnl|BL_ORD_ID|1826 - 179765|cell surface protein (associated with virulence)|NP_302372.1|Mycobacterium leprae TN|272631 - 1826 - 9 - - - 1 - 11.1566 - 17 - 202.191 - 1 - 8 - 1 - 8 - 0 - 0 - 5 - 5 - 0 - 8 - APFLNSVS - APIPASVS - AP SVS - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 5 - Query_5 - M_2639 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_2640 - 9 - - - 1 - gnl|BL_ORD_ID|1827 - 179766|cell surface protein (associated with virulence)|NP_302372.1|Mycobacterium leprae TN|272631 - 1827 - 9 - - - 1 - 12.3122 - 20 - 57.6592 - 1 - 7 - 1 - 7 - 0 - 0 - 5 - 5 - 0 - 7 - APLLPRT - APLPPST - APL P T - - - - - 2 - gnl|BL_ORD_ID|789 - 52760|nef protein|ACR27174.1|Human immunodeficiency virus 1|11676 - 789 - 10 - - - 1 - 11.927 - 19 - 86.442 - 1 - 8 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - APLLPRTH - VPLRPMTY - PL P T+ - - - - - 3 - gnl|BL_ORD_ID|1067 - 70365|Truncated Nef protein|P04601.4|Human immunodeficiency virus 1|11676 - 1067 - 9 - - - 1 - 11.927 - 19 - 97.5444 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 5 - 0 - 8 - APLLPRTH - VPLRPMTY - PL P T+ - - - - - 4 - gnl|BL_ORD_ID|2258 - 288104|nef protein|ACR27130.1|Human immunodeficiency virus 1|11676 - 2258 - 18 - - - 1 - 10.7714 - 16 - 330.264 - 1 - 7 - 10 - 16 - 0 - 0 - 4 - 4 - 0 - 7 - APLLPRT - VPLRPMT - PL P T - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 7 - Query_7 - M_2641 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_2642 - 9 - - - 1 - gnl|BL_ORD_ID|96 - 6591|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 96 - 18 - - - 1 - 11.927 - 19 - 82.9694 - 2 - 8 - 7 - 13 - 0 - 0 - 4 - 5 - 0 - 7 - PSLPSPT - PTLHGPT - P+L PT - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 9 - Query_9 - M_2643 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_2644 - 9 - - - 1 - gnl|BL_ORD_ID|1871 - 180488|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1871 - 10 - - - 1 - 12.6974 - 21 - 22.7423 - 4 - 9 - 3 - 8 - 0 - 0 - 3 - 5 - 0 - 6 - GHHQPL - GHEEPI - GH +P+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 11 - Query_11 - M_2645 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_2646 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_2647 - 9 - - - 1 - gnl|BL_ORD_ID|184 - 13518|HCV-1|AAA45676.1|Hepatitis C virus genotype 1|41856 - 184 - 20 - - - 1 - 16.5494 - 31 - 0.218227 - 1 - 8 - 8 - 15 - 0 - 0 - 6 - 7 - 0 - 8 - AYQVSVCA - AYQATVCA - AYQ +VCA - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 14 - Query_14 - M_2648 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_2649 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_2650 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_2651 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_2652 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_2653 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_2654 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_2655 - 9 - - - 1 - gnl|BL_ORD_ID|883 - 57894|polyprotein|BAD73987.1|Hepatitis C virus subtype 1b|31647 - 883 - 10 - - - 1 - 11.927 - 19 - 79.723 - 1 - 9 - 2 - 10 - 0 - 0 - 6 - 6 - 0 - 9 - FSILSTALL - FSIFLLALL - FSI ALL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 22 - Query_22 - M_2656 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_2657 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_2658 - 9 - - - 1 - gnl|BL_ORD_ID|1731 - 150556|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1731 - 10 - - - 1 - 12.6974 - 21 - 25.6384 - 1 - 6 - 4 - 9 - 0 - 0 - 3 - 4 - 0 - 6 - GPRNCI - DPRRCL - PR C+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 25 - Query_25 - M_2659 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_2660 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_2661 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 28 - Query_28 - M_2662 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 29 - Query_29 - M_2663 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 30 - Query_30 - M_2664 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 31 - Query_31 - M_2665 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 32 - Query_32 - M_2666 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 33 - Query_33 - M_2667 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 34 - Query_34 - M_2668 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 35 - Query_35 - M_2669 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 36 - Query_36 - M_2670 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 37 - Query_37 - M_2671 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 38 - Query_38 - M_2672 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 39 - Query_39 - M_2673 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 40 - Query_40 - M_2674 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 41 - Query_41 - M_2675 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 42 - Query_42 - M_2676 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 43 - Query_43 - M_2677 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 44 - Query_44 - M_2678 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 45 - Query_45 - M_2679 - 9 - - - 1 - gnl|BL_ORD_ID|1565 - 141323|multifunctional expression regulator|NP_044657.1|Human alphaherpesvirus 1|10298 - 1565 - 9 - - - 1 - 13.0826 - 22 - 15.7589 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 6 - 0 - 9 - KYIFNNSII - KYFYCNSLF - KY + NS+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 46 - Query_46 - M_2680 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 47 - Query_47 - M_2681 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 48 - Query_48 - M_2682 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 49 - Query_49 - M_2683 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 50 - Query_50 - M_2684 - 9 - - - 1 - gnl|BL_ORD_ID|670 - 40264|Cytochrome P450 2A6|P11509.3|Homo sapiens|9606 - 670 - 10 - - - 1 - 12.6974 - 21 - 34.8136 - 1 - 7 - 4 - 10 - 0 - 0 - 6 - 6 - 0 - 7 - LLVSLTV - LLVCLTV - LLV LTV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 51 - Query_51 - M_2685 - 9 - - - 1 - gnl|BL_ORD_ID|1580 - 141461|ubiquitin E3 ligase ICP0|NP_044601.1|Human alphaherpesvirus 1|10298 - 1580 - 9 - - - 1 - 13.0826 - 22 - 14.4474 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 6 - 0 - 9 - LPGGVGRTL - VPGWSRRTL - +PG RTL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 52 - Query_52 - M_2686 - 9 - - - 1 - gnl|BL_ORD_ID|851 - 55709|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 - 851 - 15 - - - 1 - 13.0826 - 22 - 12.5116 - 4 - 9 - 5 - 10 - 0 - 0 - 5 - 5 - 0 - 6 - DDRGSL - DSRGSL - D RGSL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 53 - Query_53 - M_2687 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 54 - Query_54 - M_2688 - 9 - - - 1 - gnl|BL_ORD_ID|691 - 42094|telomer length regulation protein TEL1|EDV12172.1|Saccharomyces cerevisiae|4932 - 691 - 9 - - - 1 - 14.2382 - 25 - 3.87216 - 1 - 8 - 2 - 9 - 0 - 0 - 4 - 6 - 0 - 8 - LWGKHQFI - LWGYLQYV - LWG Q++ - - - - - 2 - gnl|BL_ORD_ID|1295 - 103020|polyprotein|ABR25251.1|Hepatitis C virus|11103 - 1295 - 10 - - - 1 - 12.6974 - 21 - 38.5196 - 1 - 5 - 2 - 6 - 0 - 0 - 3 - 3 - 0 - 5 - LWGKH - FWAKH - W KH - - - - - 3 - gnl|BL_ORD_ID|1029 - 68605|Genome polyprotein|P26662.3|Hepatitis C virus|11103 - 1029 - 10 - - - 1 - 12.3122 - 20 - 39.1729 - 1 - 5 - 2 - 6 - 0 - 0 - 3 - 3 - 0 - 5 - LWGKH - FWAKH - W KH - - - - - 4 - gnl|BL_ORD_ID|195 - 14381|polyprotein|BAA25076.1|Hepatitis C virus|11103 - 195 - 9 - - - 1 - 12.3122 - 20 - 41.221 - 1 - 7 - 3 - 9 - 0 - 0 - 3 - 4 - 0 - 7 - LWGKHQF - FWAKHMW - W KH + - - - - - 5 - gnl|BL_ORD_ID|272 - 18337|polyprotein|BAD73987.1|Hepatitis C virus subtype 1b|31647 - 272 - 9 - - - 1 - 12.3122 - 20 - 43.3628 - 1 - 5 - 1 - 5 - 0 - 0 - 3 - 3 - 0 - 5 - LWGKH - FWAKH - W KH - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 55 - Query_55 - M_2689 - 9 - - - 1 - gnl|BL_ORD_ID|1422 - 112503|E6 protein|ACV53993.1|Human papillomavirus type 35|10587 - 1422 - 10 - - - 1 - 13.0826 - 22 - 18.1832 - 3 - 7 - 4 - 8 - 0 - 0 - 3 - 5 - 0 - 5 - FDLCV - YDLCI - +DLC+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 56 - Query_56 - M_2690 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 57 - Query_57 - M_2691 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 58 - Query_58 - M_2692 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 59 - Query_59 - M_2693 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 60 - Query_60 - M_2694 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 61 - Query_61 - M_2695 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 62 - Query_62 - M_2696 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 63 - Query_63 - M_2697 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 64 - Query_64 - M_2698 - 9 - - - 1 - gnl|BL_ORD_ID|1180 - 88377|IE62|AAP32859.1|Human alphaherpesvirus 3|10335 - 1180 - 9 - - - 1 - 12.3122 - 20 - 55.769 - 2 - 8 - 1 - 7 - 0 - 0 - 5 - 5 - 0 - 7 - SAPKPST - SAPLPSN - SAP PS - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 65 - Query_65 - M_2699 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 66 - Query_66 - M_2700 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 67 - Query_67 - M_2701 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 68 - Query_68 - M_2702 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 69 - Query_69 - M_2703 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 70 - Query_70 - M_2704 - 9 - - - 1 - gnl|BL_ORD_ID|691 - 42094|telomer length regulation protein TEL1|EDV12172.1|Saccharomyces cerevisiae|4932 - 691 - 9 - - - 1 - 14.2382 - 25 - 3.26672 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 6 - 0 - 8 - LWGKHQFI - LWGYLQYV - LWG Q++ - - - - - 2 - gnl|BL_ORD_ID|195 - 14381|polyprotein|BAA25076.1|Hepatitis C virus|11103 - 195 - 9 - - - 1 - 12.6974 - 21 - 37.875 - 2 - 8 - 3 - 9 - 0 - 0 - 3 - 4 - 0 - 7 - LWGKHQF - FWAKHMW - W KH + - - - - - 3 - gnl|BL_ORD_ID|1029 - 68605|Genome polyprotein|P26662.3|Hepatitis C virus|11103 - 1029 - 10 - - - 1 - 12.6974 - 21 - 38.5196 - 2 - 7 - 2 - 7 - 0 - 0 - 3 - 3 - 0 - 6 - LWGKHQ - FWAKHM - W KH - - - - - 4 - gnl|BL_ORD_ID|1295 - 103020|polyprotein|ABR25251.1|Hepatitis C virus|11103 - 1295 - 10 - - - 1 - 12.3122 - 20 - 39.1729 - 2 - 6 - 2 - 6 - 0 - 0 - 3 - 3 - 0 - 5 - LWGKH - FWAKH - W KH - - - - - 5 - gnl|BL_ORD_ID|272 - 18337|polyprotein|BAD73987.1|Hepatitis C virus subtype 1b|31647 - 272 - 9 - - - 1 - 12.3122 - 20 - 44.8495 - 2 - 6 - 1 - 5 - 0 - 0 - 3 - 3 - 0 - 5 - LWGKH - FWAKH - W KH - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 71 - Query_71 - M_2705 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 72 - Query_72 - M_2706 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 73 - Query_73 - M_2707 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 74 - Query_74 - M_2708 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 75 - Query_75 - M_2709 - 9 - - - 1 - gnl|BL_ORD_ID|1711 - 150309|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1711 - 10 - - - 1 - 13.4678 - 23 - 7.76238 - 2 - 9 - 1 - 8 - 0 - 0 - 3 - 6 - 0 - 8 - LALSTFEW - IPMSTYGW - + +ST+ W - - - - - 2 - gnl|BL_ORD_ID|634 - 37830|polyprotein|BAB18806.1|Hepatitis C virus subtype 1b|31647 - 634 - 9 - - - 1 - 13.4678 - 23 - 8.13377 - 4 - 9 - 2 - 7 - 0 - 0 - 5 - 5 - 0 - 6 - LSTFEW - LSTTEW - LST EW - - - - - 3 - gnl|BL_ORD_ID|1915 - 180675|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1915 - 15 - - - 1 - 13.0826 - 22 - 17.2424 - 4 - 9 - 1 - 6 - 0 - 0 - 3 - 5 - 0 - 6 - LSTFEW - MSTYGW - +ST+ W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 76 - Query_76 - M_2710 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 77 - Query_77 - M_2711 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 78 - Query_78 - M_2712 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 79 - Query_79 - M_2713 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 80 - Query_80 - M_2714 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 81 - Query_81 - M_2715 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 82 - Query_82 - M_2716 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 83 - Query_83 - M_2717 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 84 - Query_84 - M_2718 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 85 - Query_85 - M_2719 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 86 - Query_86 - M_2720 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 87 - Query_87 - M_2721 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 88 - Query_88 - M_2722 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 89 - Query_89 - M_2723 - 9 - - - 1 - gnl|BL_ORD_ID|1694 - 149096|polyprotein|BAB18801.1|Hepatitis C virus|11103 - 1694 - 9 - - - 1 - 11.927 - 19 - 95.9763 - 3 - 8 - 2 - 7 - 0 - 0 - 5 - 5 - 0 - 6 - AQAPIP - AQAPPP - AQAP P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 90 - Query_90 - M_2724 - 9 - - - 1 - gnl|BL_ORD_ID|1151 - 75674|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 - 1151 - 15 - - - 1 - 13.0826 - 22 - 16.1221 - 3 - 9 - 6 - 12 - 0 - 0 - 4 - 5 - 0 - 7 - GGWRSGW - GFWQEGW - G W+ GW - - - - - 2 - gnl|BL_ORD_ID|800 - 53246|polyprotein precursor|AAF20092.2|West Nile virus|11082 - 800 - 9 - - - 1 - 10.7714 - 16 - 393.541 - 4 - 9 - 2 - 7 - 0 - 0 - 3 - 4 - 0 - 6 - GWRSGW - AWNSGY - W SG+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 91 - Query_91 - M_2725 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 92 - Query_92 - M_2726 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 93 - Query_93 - M_2727 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 94 - Query_94 - M_2728 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 95 - Query_95 - M_2729 - 9 - - - 1 - gnl|BL_ORD_ID|162 - 12585|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis|1773 - 162 - 20 - - - 1 - 12.6974 - 21 - 34.4393 - 2 - 8 - 13 - 19 - 0 - 0 - 4 - 5 - 0 - 7 - YSSLDED - YSRADEE - YS DE+ - - - - - 2 - gnl|BL_ORD_ID|1071 - 70687|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis|1773 - 1071 - 20 - - - 1 - 12.3122 - 20 - 42.7067 - 2 - 8 - 3 - 9 - 0 - 0 - 4 - 5 - 0 - 7 - YSSLDED - YSRADEE - YS DE+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 96 - Query_96 - M_2730 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 97 - Query_97 - M_2731 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 98 - Query_98 - M_2732 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 99 - Query_99 - M_2733 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 100 - Query_100 - M_2734 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 101 - Query_101 - M_2735 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 102 - Query_102 - M_2736 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 103 - Query_103 - M_2737 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 104 - Query_104 - M_2738 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 105 - Query_105 - M_2739 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 106 - Query_106 - M_2740 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 107 - Query_107 - M_2741 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 108 - Query_108 - M_2742 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_129049_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_129049_1_T.fasta deleted file mode 100755 index 29de5645..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_129049_1_T.fasta +++ /dev/null @@ -1,54 +0,0 @@ ->M_2743 -ASLDVTLRL ->M_2744 -ISSHLSTLV ->M_2745 -LSTLVDFAI ->M_2746 -KTSVGSTKY ->M_2747 -HPCERSDEV ->M_2748 -ITVEEQHRI ->M_2749 -ITVEEQHRI ->M_2750 -MTAVQTLHL ->M_2751 -PAMTAVQTL ->M_2752 -RQLPAMTAV ->M_2753 -ETVFTRSSW ->M_2754 -FTRSSWDWI ->M_2755 -VFTRSSWDW ->M_2756 -EPPPPPSPL ->M_2757 -QTTQLSLNF ->M_2758 -GAMDGATYI ->M_2759 -MAFVKSVWL ->M_2760 -CAVRRAAQV ->M_2761 -QAVAQAVNW ->M_2762 -NPKTWNTMV ->M_2763 -QLYMNPKTW ->M_2764 -RQVGFCVQW ->M_2765 -KMLLAPGRF ->M_2766 -MLLAPGRFI ->M_2767 -FTMPEDEYM ->M_2768 -FTMPEDEYM ->M_2769 -MPEDEYMVY diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_129049_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_129049_1_T_iedb.xml deleted file mode 100755 index 30ba0cad..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_129049_1_T_iedb.xml +++ /dev/null @@ -1,754 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_2743 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_2743 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_2744 - 9 - - - 1 - gnl|BL_ORD_ID|1262 - 98466|Trans-sialidase|SRC7915|Trypanosoma cruzi|5693 - 1262 - 10 - - - 1 - 12.3122 - 20 - 49.5064 - 3 - 9 - 3 - 9 - 0 - 0 - 5 - 5 - 0 - 7 - SHLSTLV - SHYFTLV - SH TLV - - - - - 2 - gnl|BL_ORD_ID|904 - 59459|Trans-sialidase|SRC7915|Trypanosoma cruzi|5693 - 904 - 9 - - - 1 - 12.3122 - 20 - 63.7024 - 3 - 9 - 3 - 9 - 0 - 0 - 5 - 5 - 0 - 7 - SHLSTLV - SHYFTLV - SH TLV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 3 - Query_3 - M_2745 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_2746 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_2747 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_2748 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_2749 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_2750 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_2751 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_2752 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_2753 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_2754 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_2755 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_2756 - 9 - - - 1 - gnl|BL_ORD_ID|1211 - 96366|polyprotein|ABR25251.1|Hepatitis C virus|11103 - 1211 - 12 - - - 1 - 10.3862 - 15 - 463.357 - 4 - 9 - 5 - 10 - 0 - 0 - 4 - 4 - 0 - 6 - PPPSPL - PPCKPL - PP PL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 15 - Query_15 - M_2757 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_2758 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_2759 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_2760 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_2761 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_2762 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_2763 - 9 - - - 1 - gnl|BL_ORD_ID|1486 - 135263|hemagglutinin|ACX31970.1|Influenza A virus (A/Bar-headed Goose/Qinghai/61/05(H5N1))|336238 - 1486 - 10 - - - 1 - 16.1642 - 30 - 0.390189 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 7 - 0 - 9 - QLYMNPKTW - RLYQNPTTY - +LY NP T+ - - - - - 2 - gnl|BL_ORD_ID|527 - 32268|hemagglutinin|AAK38298.1|Influenza A virus (A/Bar-headed Goose/Qinghai/61/05(H5N1))|336238 - 527 - 10 - - - 1 - 15.779 - 29 - 0.412579 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 7 - 0 - 9 - QLYMNPKTW - KLYQNPTTY - +LY NP T+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 22 - Query_22 - M_2764 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_2765 - 9 - - - 1 - gnl|BL_ORD_ID|902 - 59240|HCV-1|AAA45676.1|Hepatitis C virus genotype 1|41856 - 902 - 11 - - - 1 - 13.853 - 24 - 5.19029 - 3 - 7 - 2 - 6 - 0 - 0 - 5 - 5 - 0 - 5 - LLAPG - LLAPG - LLAPG - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 24 - Query_24 - M_2766 - 9 - - - 1 - gnl|BL_ORD_ID|902 - 59240|HCV-1|AAA45676.1|Hepatitis C virus genotype 1|41856 - 902 - 11 - - - 1 - 13.853 - 24 - 5.28123 - 2 - 6 - 2 - 6 - 0 - 0 - 5 - 5 - 0 - 5 - LLAPG - LLAPG - LLAPG - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 25 - Query_25 - M_2767 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_2768 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_2769 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_129675_2_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_129675_2_T.fasta deleted file mode 100755 index 708278e5..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_129675_2_T.fasta +++ /dev/null @@ -1,38 +0,0 @@ ->M_2770 -IAWPADRTA ->M_2771 -QALIRPTTF ->M_2772 -FPEYDGVDH ->M_2773 -EIAEIEYSI ->M_2774 -FVVSACNAT ->M_2775 -WITPAQREY ->M_2776 -EPVWGLEAI ->M_2777 -RLSWQASSL ->M_2778 -KIKELAAEF ->M_2779 -VPILQSTPV ->M_2780 -APRGFLTNY ->M_2781 -RAAEQRRAY ->M_2782 -KSASWITWI ->M_2783 -TPWSFTGTV ->M_2784 -GPLADATPL ->M_2785 -LAGERRFAF ->M_2786 -IAASAMCVF ->M_2787 -SSYGRNHYI ->M_2788 -IIHTGARPY diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_129675_2_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_129675_2_T_iedb.xml deleted file mode 100755 index c4cadf10..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_129675_2_T_iedb.xml +++ /dev/null @@ -1,845 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_2770 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_2770 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_2771 - 9 - - - 1 - gnl|BL_ORD_ID|172 - 13165|trans-sialidase, putative|EAN81972.1|Trypanosoma cruzi|5693 - 172 - 9 - - - 1 - 15.0086 - 27 - 1.19683 - 3 - 9 - 2 - 8 - 0 - 0 - 5 - 6 - 0 - 7 - LIRPTTF - LLRPTTL - L+RPTT - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 3 - Query_3 - M_2772 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_2773 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_2774 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_2775 - 9 - - - 1 - gnl|BL_ORD_ID|1408 - 110940|Protein E7|P03129.1|Human papillomavirus type 16|333760 - 1408 - 15 - - - 1 - 13.0826 - 22 - 13.39 - 3 - 9 - 5 - 11 - 0 - 0 - 4 - 4 - 0 - 7 - TPAQREY - TPTLHEY - TP EY - - - - - 2 - gnl|BL_ORD_ID|1392 - 110335|E7|AAD33253.1|Human papillomavirus type 16|333760 - 1392 - 32 - - - 1 - 13.0826 - 22 - 19.7687 - 3 - 9 - 5 - 11 - 0 - 0 - 4 - 4 - 0 - 7 - TPAQREY - TPTLHEY - TP EY - - - - - 3 - gnl|BL_ORD_ID|1823 - 178351|Protein E7|P03129.1|Human papillomavirus type 16|333760 - 1823 - 15 - - - 1 - 12.6974 - 21 - 31.7906 - 3 - 9 - 1 - 7 - 0 - 0 - 4 - 4 - 0 - 7 - TPAQREY - TPTLHEY - TP EY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 7 - Query_7 - M_2776 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_2777 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_2778 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_2779 - 9 - - - 1 - gnl|BL_ORD_ID|1906 - 180647|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1906 - 15 - - - 1 - 11.927 - 19 - 77.3377 - 1 - 8 - 8 - 15 - 0 - 0 - 4 - 5 - 0 - 8 - VPILQSTP - LPIRYQTP - +PI TP - - - - - 2 - gnl|BL_ORD_ID|1897 - 180617|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1897 - 10 - - - 1 - 11.5418 - 18 - 128.811 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 5 - 0 - 9 - VPILQSTPV - LPIRYQTPA - +PI TP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 11 - Query_11 - M_2780 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_2781 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_2782 - 9 - - - 1 - gnl|BL_ORD_ID|1142 - 75435|largest ORF|AAB02128.1|Hepatitis C virus|11103 - 1142 - 20 - - - 1 - 12.6974 - 21 - 27.6963 - 1 - 9 - 9 - 17 - 0 - 0 - 2 - 5 - 0 - 9 - KSASWITWI - EGCGWMGWL - + W+ W+ - - - - - 2 - gnl|BL_ORD_ID|1070 - 70634|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 - 1070 - 9 - - - 1 - 12.6974 - 21 - 35.3877 - 4 - 8 - 3 - 7 - 0 - 0 - 3 - 4 - 0 - 5 - SWITW - QWLTW - W+TW - - - - - 3 - gnl|BL_ORD_ID|315 - 20894|polyprotein [Hepatitis C virus]|BAF91806.1|Hepatitis C virus|11103 - 315 - 9 - - - 1 - 11.927 - 19 - 82.8955 - 4 - 9 - 3 - 8 - 0 - 0 - 2 - 4 - 0 - 6 - SWITWI - GWVGWL - W+ W+ - - - - - 4 - gnl|BL_ORD_ID|1277 - 101967|pol protein|ACJ76655.1|Human immunodeficiency virus 1|11676 - 1277 - 10 - - - 1 - 11.927 - 19 - 108.205 - 1 - 8 - 3 - 10 - 0 - 0 - 3 - 5 - 0 - 8 - KSASWITW - QKETWETW - + +W TW - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 14 - Query_14 - M_2783 - 9 - - - 1 - gnl|BL_ORD_ID|701 - 42797|6 kDa early secretory antigenic target|P0A564.2|Mycobacterium tuberculosis|1773 - 701 - 20 - - - 1 - 13.0826 - 22 - 15.1234 - 2 - 7 - 5 - 10 - 0 - 0 - 3 - 4 - 0 - 6 - PWSFTG - QWNFAG - W+F G - - - - - 2 - gnl|BL_ORD_ID|1471 - 127792|6 kDa early secretory antigenic target|P0A564.2|Mycobacterium tuberculosis|1773 - 1471 - 10 - - - 1 - 13.0826 - 22 - 21.2326 - 3 - 7 - 2 - 6 - 0 - 0 - 3 - 4 - 0 - 5 - WSFTG - WNFAG - W+F G - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 15 - Query_15 - M_2784 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_2785 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_2786 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_2787 - 9 - - - 1 - gnl|BL_ORD_ID|123 - 8554|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 123 - 20 - - - 1 - 13.853 - 24 - 5.06317 - 4 - 9 - 10 - 15 - 0 - 0 - 3 - 6 - 0 - 6 - GRNHYI - GRSHFL - GR+H++ - - - - - 2 - gnl|BL_ORD_ID|688 - 41622|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 688 - 20 - - - 1 - 13.853 - 24 - 6.41204 - 4 - 9 - 2 - 7 - 0 - 0 - 3 - 6 - 0 - 6 - GRNHYI - GRSHFL - GR+H++ - - - - - 3 - gnl|BL_ORD_ID|578 - 36357|ELAV-like protein 4 (Paraneoplastic encephalomyelitis antigen HuD) (Hu-antigen D)|P26378.1|Homo sapiens|9606 - 578 - 9 - - - 1 - 10.7714 - 16 - 324.284 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - SYGRNHYI - GYGFVNYI - YG +YI - - - - - 4 - gnl|BL_ORD_ID|579 - 36358|ELAV-like protein 1|Q15717.2|Homo sapiens|9606 - 579 - 9 - - - 1 - 10.3862 - 15 - 617.74 - 2 - 9 - 2 - 9 - 0 - 0 - 3 - 5 - 0 - 8 - SYGRNHYI - GYGFVNYV - YG +Y+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 19 - Query_19 - M_2788 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_131144_2_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_131144_2_T.fasta deleted file mode 100755 index 3e7a8fb1..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_131144_2_T.fasta +++ /dev/null @@ -1,120 +0,0 @@ ->M_2789 -DTATGNCLR ->M_2790 -GPYENCSVF ->M_2791 -ETYQQALGK ->M_2792 -YQQALGKRF ->M_2793 -YQQALGKRF ->M_2794 -FAIHKIKQF ->M_2795 -GYTVNIPTI ->M_2796 -HSPSVASMK ->M_2797 -YTDCHASNL ->M_2798 -TYSSPTPNM ->M_2799 -DAIPFGNVP ->M_2800 -IPFGNVPVL ->M_2801 -NYFGVQDAI ->M_2802 -ETLGRGNPM ->M_2803 -MALQLFLQI ->M_2804 -MALQLFLQI ->M_2805 -MALQLFLQI ->M_2806 -KVHSAVITI ->M_2807 -QAGEYSRVV ->M_2808 -RVVDCYLKV ->M_2809 -WQRPTLESI ->M_2810 -WQRPTLESI ->M_2811 -VAQLGFQPL ->M_2812 -EAINCLNVA ->M_2813 -VAIDIYTDM ->M_2814 -HFLHSWTNL ->M_2815 -TFKHLVHFL ->M_2816 -YTFKHLVHF ->M_2817 -YTFKHLVHF ->M_2818 -IIMSRNAYV ->M_2819 -LRYPIIMSR ->M_2820 -MSRNAYVPM ->M_2821 -NAPALLTPR ->M_2822 -RAGSAGGTV ->M_2823 -EAFTLKATV ->M_2824 -YSVIRGEAF ->M_2825 -DIYSMPEGK ->M_2826 -IYSMPEGKL ->M_2827 -SMPEGKLHV ->M_2828 -YSMPEGKLH ->M_2829 -FFFLCVCVF ->M_2830 -FFFLCVCVF ->M_2831 -FFLCVCVFV ->M_2832 -FFLCVCVFV ->M_2833 -HLLQRYNEF ->M_2834 -RAEERRRHL ->M_2835 -ITTTGQKLR ->M_2836 -IMALAVLII ->M_2837 -TALVVVSIM ->M_2838 -DVLPYDAFV ->M_2839 -LTLATFSRI ->M_2840 -VLTLATFSR ->M_2841 -MNQRPILTI ->M_2842 -NQRPILTII ->M_2843 -FNVNAPDLY ->M_2844 -NVNAPDLYI ->M_2845 -RFNVNAPDL ->M_2846 -FHWRVNFIR ->M_2847 -IFHWRVNFI ->M_2848 -KIFHWRVNF diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_131144_2_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_131144_2_T_iedb.xml deleted file mode 100755 index 7034a12b..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_131144_2_T_iedb.xml +++ /dev/null @@ -1,1820 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_2789 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_2789 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_2790 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_2791 - 9 - - - 1 - gnl|BL_ORD_ID|376 - 23288|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 - 376 - 15 - - - 1 - 13.853 - 24 - 5.58032 - 1 - 9 - 5 - 13 - 0 - 0 - 4 - 6 - 0 - 9 - ETYQQALGK - QVYQDWLGR - + YQ LG+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 4 - Query_4 - M_2792 - 9 - - - 1 - gnl|BL_ORD_ID|376 - 23288|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 - 376 - 15 - - - 1 - 12.6974 - 21 - 26.9941 - 1 - 7 - 7 - 13 - 0 - 0 - 4 - 5 - 0 - 7 - YQQALGK - YQDWLGR - YQ LG+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 5 - Query_5 - M_2793 - 9 - - - 1 - gnl|BL_ORD_ID|376 - 23288|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 - 376 - 15 - - - 1 - 12.6974 - 21 - 26.9941 - 1 - 7 - 7 - 13 - 0 - 0 - 4 - 5 - 0 - 7 - YQQALGK - YQDWLGR - YQ LG+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 6 - Query_6 - M_2794 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_2795 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_2796 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_2797 - 9 - - - 1 - gnl|BL_ORD_ID|83 - 6094|Genome polyprotein|Q81495.3|Hepatitis C virus (isolate HCV-K3a/650)|356416 - 83 - 15 - - - 1 - 14.2382 - 25 - 3.49239 - 3 - 8 - 3 - 8 - 0 - 0 - 4 - 5 - 0 - 6 - DCHASN - DCHAQD - DCHA + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 10 - Query_10 - M_2798 - 9 - - - 1 - gnl|BL_ORD_ID|2244 - 232153|rhoptry protein 18|CAJ27113.1|Toxoplasma gondii type I|1209525 - 2244 - 19 - - - 1 - 11.927 - 19 - 88.393 - 1 - 6 - 12 - 17 - 0 - 0 - 4 - 5 - 0 - 6 - TYSSPT - TYTFPT - TY+ PT - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 11 - Query_11 - M_2799 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_2800 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_2801 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_2802 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_2803 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_2804 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_2805 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_2806 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_2807 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_2808 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_2809 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 22 - Query_22 - M_2810 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_2811 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_2812 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_2813 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_2814 - 9 - - - 1 - gnl|BL_ORD_ID|1296 - 103322|polyprotein|BAB18806.1|Hepatitis C virus|11103 - 1296 - 20 - - - 1 - 13.4678 - 23 - 11.4655 - 3 - 8 - 3 - 8 - 0 - 0 - 4 - 4 - 0 - 6 - LHSWTN - LHQWIN - LH W N - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 27 - Query_27 - M_2815 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 28 - Query_28 - M_2816 - 9 - - - 1 - gnl|BL_ORD_ID|123 - 8554|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 123 - 20 - - - 1 - 10.001 - 14 - 536.103 - 1 - 9 - 6 - 14 - 0 - 0 - 4 - 4 - 0 - 9 - YTFKHLVHF - YKFMGRSHF - Y F HF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 29 - Query_29 - M_2817 - 9 - - - 1 - gnl|BL_ORD_ID|123 - 8554|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 123 - 20 - - - 1 - 10.001 - 14 - 536.103 - 1 - 9 - 6 - 14 - 0 - 0 - 4 - 4 - 0 - 9 - YTFKHLVHF - YKFMGRSHF - Y F HF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 30 - Query_30 - M_2818 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 31 - Query_31 - M_2819 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 32 - Query_32 - M_2820 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 33 - Query_33 - M_2821 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 34 - Query_34 - M_2822 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 35 - Query_35 - M_2823 - 9 - - - 1 - gnl|BL_ORD_ID|1266 - 98640|trans-sialidase, putative|EAN80840.1|Trypanosoma cruzi|5693 - 1266 - 9 - - - 1 - 13.853 - 24 - 5.65074 - 3 - 9 - 3 - 9 - 0 - 0 - 6 - 6 - 0 - 7 - FTLKATV - FTLVATV - FTL ATV - - - - - 2 - gnl|BL_ORD_ID|1245 - 98044|trans-sialidase, putative|EAN80840.1|Trypanosoma cruzi|5693 - 1245 - 9 - - - 1 - 13.853 - 24 - 5.65074 - 3 - 9 - 1 - 7 - 0 - 0 - 6 - 6 - 0 - 7 - FTLKATV - FTLVATV - FTL ATV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 36 - Query_36 - M_2824 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 37 - Query_37 - M_2825 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 38 - Query_38 - M_2826 - 9 - - - 1 - gnl|BL_ORD_ID|1725 - 150456|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1725 - 10 - - - 1 - 14.2382 - 25 - 2.71312 - 2 - 9 - 3 - 10 - 0 - 0 - 5 - 5 - 0 - 8 - YSMPEGKL - YSMCTGKF - YSM GK - - - - - 2 - gnl|BL_ORD_ID|186 - 13701|Trans-activator protein BZLF1|P03206.2|Human gammaherpesvirus 4|10376 - 186 - 11 - - - 1 - 13.0826 - 22 - 18.1034 - 4 - 9 - 3 - 8 - 0 - 0 - 3 - 6 - 0 - 6 - MPEGKL - LPQGQL - +P+G+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 39 - Query_39 - M_2827 - 9 - - - 1 - gnl|BL_ORD_ID|186 - 13701|Trans-activator protein BZLF1|P03206.2|Human gammaherpesvirus 4|10376 - 186 - 11 - - - 1 - 13.0826 - 22 - 16.6114 - 2 - 7 - 3 - 8 - 0 - 0 - 3 - 6 - 0 - 6 - MPEGKL - LPQGQL - +P+G+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 40 - Query_40 - M_2828 - 9 - - - 1 - gnl|BL_ORD_ID|1725 - 150456|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1725 - 10 - - - 1 - 14.2382 - 25 - 2.75947 - 1 - 8 - 3 - 10 - 0 - 0 - 5 - 5 - 0 - 8 - YSMPEGKL - YSMCTGKF - YSM GK - - - - - 2 - gnl|BL_ORD_ID|186 - 13701|Trans-activator protein BZLF1|P03206.2|Human gammaherpesvirus 4|10376 - 186 - 11 - - - 1 - 13.0826 - 22 - 17.4916 - 3 - 8 - 3 - 8 - 0 - 0 - 3 - 6 - 0 - 6 - MPEGKL - LPQGQL - +P+G+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 41 - Query_41 - M_2829 - 9 - - - 1 - gnl|BL_ORD_ID|750 - 49831|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 - 750 - 15 - - - 1 - 11.927 - 19 - 74.9817 - 1 - 8 - 4 - 11 - 0 - 0 - 3 - 5 - 0 - 8 - FFFLCVCV - LLILCLCL - LC+C+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 42 - Query_42 - M_2830 - 9 - - - 1 - gnl|BL_ORD_ID|750 - 49831|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 - 750 - 15 - - - 1 - 11.927 - 19 - 74.9817 - 1 - 8 - 4 - 11 - 0 - 0 - 3 - 5 - 0 - 8 - FFFLCVCV - LLILCLCL - LC+C+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 43 - Query_43 - M_2831 - 9 - - - 1 - gnl|BL_ORD_ID|750 - 49831|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 - 750 - 15 - - - 1 - 11.5418 - 18 - 131.587 - 1 - 7 - 5 - 11 - 0 - 0 - 3 - 5 - 0 - 7 - FFLCVCV - LILCLCL - LC+C+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 44 - Query_44 - M_2832 - 9 - - - 1 - gnl|BL_ORD_ID|750 - 49831|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 - 750 - 15 - - - 1 - 11.5418 - 18 - 131.587 - 1 - 7 - 5 - 11 - 0 - 0 - 3 - 5 - 0 - 7 - FFLCVCV - LILCLCL - LC+C+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 45 - Query_45 - M_2833 - 9 - - - 1 - gnl|BL_ORD_ID|1767 - 154980|tegument protein|CAB06735.1|Human alphaherpesvirus 2|10310 - 1767 - 15 - - - 1 - 16.1642 - 30 - 0.279828 - 1 - 9 - 2 - 10 - 0 - 0 - 6 - 7 - 0 - 9 - HLLQRYNEF - NLLQRANEL - +LLQR NE - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 46 - Query_46 - M_2834 - 9 - - - 1 - gnl|BL_ORD_ID|1395 - 110394|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1395 - 32 - - - 1 - 15.0086 - 27 - 1.766 - 2 - 9 - 11 - 18 - 0 - 0 - 5 - 7 - 0 - 8 - AEERRRHL - PEEKQRHL - EE++RHL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 47 - Query_47 - M_2835 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 48 - Query_48 - M_2836 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 49 - Query_49 - M_2837 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 50 - Query_50 - M_2838 - 9 - - - 1 - gnl|BL_ORD_ID|1578 - 141423|envelope glycoprotein B|NP_044629.1|Human alphaherpesvirus 1|10298 - 1578 - 9 - - - 1 - 15.779 - 29 - 0.442703 - 2 - 9 - 2 - 9 - 0 - 0 - 6 - 6 - 0 - 8 - VLPYDAFV - VYPYDEFV - V PYD FV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 51 - Query_51 - M_2839 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 52 - Query_52 - M_2840 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 53 - Query_53 - M_2841 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 54 - Query_54 - M_2842 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 55 - Query_55 - M_2843 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 56 - Query_56 - M_2844 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 57 - Query_57 - M_2845 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 58 - Query_58 - M_2846 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 59 - Query_59 - M_2847 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 60 - Query_60 - M_2848 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_131327_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_131327_1_T.fasta deleted file mode 100755 index ec8b2bf3..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_131327_1_T.fasta +++ /dev/null @@ -1,224 +0,0 @@ ->M_2849 -LHDTTTRSV ->M_2850 -LHNNTTRSV ->M_2851 -TTTRSVHAK ->M_2852 -HFKAPKISM ->M_2853 -GTSSTSCSW ->M_2854 -GVRAQGCYM ->M_2855 -GVRAQGCYM ->M_2856 -RAQGCYMDI ->M_2857 -VAEKGTSKL ->M_2858 -EAFSVSPEW ->M_2859 -FSVSPEWAV ->M_2860 -LTRPVHGAA ->M_2861 -MARTAPASG ->M_2862 -AHQYFAQLL ->M_2863 -AHQYFAQLL ->M_2864 -HQYFAQLLA ->M_2865 -LALQRQRTY ->M_2866 -LALQRQRTY ->M_2867 -ATVCRDPGV ->M_2868 -VCRDPGVPM ->M_2869 -DAPLFNTIV ->M_2870 -VDAPLFNTI ->M_2871 -LSETISPLW ->M_2872 -WPQRPKSQV ->M_2873 -MVLPGGVDI ->M_2874 -FELEWLLYT ->M_2875 -HSHTTGINL ->M_2876 -HSHTTGINL ->M_2877 -SHTTGINLV ->M_2878 -STHSHTTGI ->M_2879 -STHSHTTGI ->M_2880 -STHSHTTGI ->M_2881 -LTLVGVVVY ->M_2882 -LTLVGVVVY ->M_2883 -SEYFLGLTL ->M_2884 -EAHSFEEEM ->M_2885 -SSLQEAHSF ->M_2886 -SHTTLSLDL ->M_2887 -KLREFFKCA ->M_2888 -VAYCPAYVV ->M_2889 -VAYCPAYVV ->M_2890 -VLIPDVVAY ->M_2891 -VVAYCPAYV ->M_2892 -YLVLIPDVV ->M_2893 -FGIGVENFI ->M_2894 -IGVENFITL ->M_2895 -ITLVVFGLI ->M_2896 -KVARSKPYA ->M_2897 -VARSKPYAM ->M_2898 -KFRCDAGLG ->M_2899 -GSRESNMSR ->M_2900 -MSRKKKAVK ->M_2901 -RKKKAVKEK ->M_2902 -QSNTWSLSK ->M_2903 -YQQSNTWSL ->M_2904 -YQQSNTWSL ->M_2905 -YKLVVVGAV ->M_2906 -AVRYSRGCL ->M_2907 -VRYSRGCLT ->M_2908 -YSRGCLTVM ->M_2909 -YSRGCLTVM ->M_2910 -YSRGCLTVM ->M_2911 -VQYASGNRW ->M_2912 -YASGNRWTF ->M_2913 -YASGNRWTF ->M_2914 -AVRNAITST ->M_2915 -NAITSTSVI ->M_2916 -TSIAVRNAI ->M_2917 -VVLPTEAPI ->M_2918 -VVLPTEAPI ->M_2919 -LVATSPSPV ->M_2920 -LSENAVLIL ->M_2921 -LSENAVLIL ->M_2922 -MALSENAVL ->M_2923 -MALSENAVL ->M_2924 -SSSGWRKSF ->M_2925 -FSEASQLDF ->M_2926 -FSEASQLDF ->M_2927 -RTKQFSEAS ->M_2928 -RGFSRQSVL ->M_2929 -LTRSTLSSV ->M_2930 -LTRSTLSSV ->M_2931 -RADHDLGRL ->M_2932 -YRADHDLGR ->M_2933 -ALRVNPVLA ->M_2934 -RVNPVLAEL ->M_2935 -RVNPVLAEL ->M_2936 -SALRVNPVL ->M_2937 -SSALRVNPV ->M_2938 -LLYRRTKAF ->M_2939 -LLYRRTKAF ->M_2940 -LYRRTKAFI ->M_2941 -RTKAFIDYE ->M_2942 -ATSYELHKF ->M_2943 -RTQILATSY ->M_2944 -TSYELHKFY ->M_2945 -TSYELHKFY ->M_2946 -IQKITSPNI ->M_2947 -TSVKPSQPK ->M_2948 -AIFASMAHA ->M_2949 -ASMAHAMQK ->M_2950 -MAHAMQKYL ->M_2951 -MAHAMQKYL ->M_2952 -MAHAMQKYL ->M_2953 -SMAHAMQKY ->M_2954 -RQRLSAPPS ->M_2955 -TAHGLSPTA ->M_2956 -GLIEGYGGW ->M_2957 -QVLGLGGHI ->M_2958 -AAFNPTRDF ->M_2959 -AAFNPTRDF ->M_2960 -KGFVCKAHF diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_131327_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_131327_1_T_iedb.xml deleted file mode 100755 index 651f706c..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_131327_1_T_iedb.xml +++ /dev/null @@ -1,3217 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_2849 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_2849 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_2850 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_2851 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_2852 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_2853 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_2854 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_2855 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_2856 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_2857 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_2858 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_2859 - 9 - - - 1 - gnl|BL_ORD_ID|1686 - 149052|E1 protein|NP_751920.1|Hepatitis C virus (isolate H77)|63746 - 1686 - 18 - - - 1 - 13.0826 - 22 - 17.338 - 1 - 8 - 5 - 12 - 0 - 0 - 4 - 5 - 0 - 8 - FSVSPEWA - FSMVGNWA - FS+ WA - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 12 - Query_12 - M_2860 - 9 - - - 1 - gnl|BL_ORD_ID|441 - 27125|gag-pol fusion polyprotein|AAN73817.1|Human immunodeficiency virus 1|11676 - 441 - 9 - - - 1 - 15.3938 - 28 - 0.845687 - 1 - 8 - 2 - 9 - 0 - 0 - 5 - 5 - 0 - 8 - LTRPVHGA - LKEPVHGV - L PVHG - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 13 - Query_13 - M_2861 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_2862 - 9 - - - 1 - gnl|BL_ORD_ID|1271 - 101673|gag protein|ABO73990.1|Human immunodeficiency virus 1|11676 - 1271 - 9 - - - 1 - 11.5418 - 18 - 152.614 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 5 - 0 - 9 - AHQYFAQLL - GHQAAMQML - HQ Q+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 15 - Query_15 - M_2863 - 9 - - - 1 - gnl|BL_ORD_ID|1271 - 101673|gag protein|ABO73990.1|Human immunodeficiency virus 1|11676 - 1271 - 9 - - - 1 - 11.5418 - 18 - 152.614 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 5 - 0 - 9 - AHQYFAQLL - GHQAAMQML - HQ Q+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 16 - Query_16 - M_2864 - 9 - - - 1 - gnl|BL_ORD_ID|1271 - 101673|gag protein|ABO73990.1|Human immunodeficiency virus 1|11676 - 1271 - 9 - - - 1 - 11.1566 - 17 - 199.082 - 1 - 8 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - HQYFAQLL - HQAAMQML - HQ Q+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 17 - Query_17 - M_2865 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_2866 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_2867 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_2868 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_2869 - 9 - - - 1 - gnl|BL_ORD_ID|1848 - 180255|gag protein|AAT90688.1|Human immunodeficiency virus 1|11676 - 1848 - 9 - - - 1 - 14.6234 - 26 - 1.85254 - 3 - 9 - 1 - 7 - 0 - 0 - 5 - 6 - 0 - 7 - PLFNTIV - SLFNTVV - LFNT+V - - - - - 2 - gnl|BL_ORD_ID|2159 - 189295|gag protein|AEB70304.1|Human immunodeficiency virus 1|11676 - 2159 - 9 - - - 1 - 13.853 - 24 - 6.16125 - 3 - 9 - 1 - 7 - 0 - 0 - 4 - 6 - 0 - 7 - PLFNTIV - SLYNTVV - L+NT+V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 22 - Query_22 - M_2870 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_2871 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_2872 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_2873 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_2874 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_2875 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 28 - Query_28 - M_2876 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 29 - Query_29 - M_2877 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 30 - Query_30 - M_2878 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 31 - Query_31 - M_2879 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 32 - Query_32 - M_2880 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 33 - Query_33 - M_2881 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 34 - Query_34 - M_2882 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 35 - Query_35 - M_2883 - 9 - - - 1 - gnl|BL_ORD_ID|1608 - 143705|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 1608 - 9 - - - 1 - 11.5418 - 18 - 132.337 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 5 - 0 - 9 - SEYFLGLTL - KEYTFPITL - EY +TL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 36 - Query_36 - M_2884 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 37 - Query_37 - M_2885 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 38 - Query_38 - M_2886 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 39 - Query_39 - M_2887 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 40 - Query_40 - M_2888 - 9 - - - 1 - gnl|BL_ORD_ID|668 - 40253|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 - 668 - 15 - - - 1 - 13.0826 - 22 - 15.3281 - 2 - 7 - 6 - 11 - 0 - 0 - 4 - 4 - 0 - 6 - AYCPAY - ANCPTY - A CP Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 41 - Query_41 - M_2889 - 9 - - - 1 - gnl|BL_ORD_ID|668 - 40253|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 - 668 - 15 - - - 1 - 13.0826 - 22 - 15.3281 - 2 - 7 - 6 - 11 - 0 - 0 - 4 - 4 - 0 - 6 - AYCPAY - ANCPTY - A CP Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 42 - Query_42 - M_2890 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 43 - Query_43 - M_2891 - 9 - - - 1 - gnl|BL_ORD_ID|668 - 40253|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 - 668 - 15 - - - 1 - 13.0826 - 22 - 15.3281 - 3 - 8 - 6 - 11 - 0 - 0 - 4 - 4 - 0 - 6 - AYCPAY - ANCPTY - A CP Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 44 - Query_44 - M_2892 - 9 - - - 1 - gnl|BL_ORD_ID|737 - 46755|HCV-1|AAA45676.1|Hepatitis C virus genotype 1|41856 - 737 - 20 - - - 1 - 12.3122 - 20 - 47.5082 - 2 - 9 - 12 - 19 - 0 - 0 - 5 - 5 - 0 - 8 - LVLIPDVV - LVLNPSVA - LVL P V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 45 - Query_45 - M_2893 - 9 - - - 1 - gnl|BL_ORD_ID|578 - 36357|ELAV-like protein 4 (Paraneoplastic encephalomyelitis antigen HuD) (Hu-antigen D)|P26378.1|Homo sapiens|9606 - 578 - 9 - - - 1 - 11.5418 - 18 - 187.089 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 5 - 0 - 9 - FGIGVENFI - LGYGFVNYI - G G N+I - - - - - 2 - gnl|BL_ORD_ID|579 - 36358|ELAV-like protein 1|Q15717.2|Homo sapiens|9606 - 579 - 9 - - - 1 - 10.7714 - 16 - 339.179 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 5 - 0 - 9 - FGIGVENFI - LGYGFVNYV - G G N++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 46 - Query_46 - M_2894 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 47 - Query_47 - M_2895 - 9 - - - 1 - gnl|BL_ORD_ID|2326 - 423068|polyprotein|ACX44241.1|Hepatitis C virus genotype 1|41856 - 2326 - 10 - - - 1 - 12.3122 - 20 - 51.1794 - 4 - 9 - 1 - 6 - 0 - 0 - 4 - 6 - 0 - 6 - VVFGLI - VLFGLM - V+FGL+ - - - - - 2 - gnl|BL_ORD_ID|1269 - 101380|BNLF2a|YP_401721.1|Human herpesvirus 4 type 1|36352 - 1269 - 9 - - - 1 - 12.3122 - 20 - 58.627 - 4 - 9 - 1 - 6 - 0 - 0 - 4 - 6 - 0 - 6 - VVFGLI - VLFGLL - V+FGL+ - - - - - 3 - gnl|BL_ORD_ID|2331 - 423075|polyprotein|ACX44241.1|Hepatitis C virus genotype 1|41856 - 2331 - 9 - - - 1 - 12.3122 - 20 - 68.0606 - 4 - 9 - 2 - 7 - 0 - 0 - 4 - 6 - 0 - 6 - VVFGLI - VLFGLM - V+FGL+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 48 - Query_48 - M_2896 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 49 - Query_49 - M_2897 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 50 - Query_50 - M_2898 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 51 - Query_51 - M_2899 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 52 - Query_52 - M_2900 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 53 - Query_53 - M_2901 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 54 - Query_54 - M_2902 - 9 - - - 1 - gnl|BL_ORD_ID|1132 - 74886|latent membrane protein 1|AAS99606.1|Human gammaherpesvirus 4|10376 - 1132 - 9 - - - 1 - 12.6974 - 21 - 33.058 - 1 - 7 - 3 - 9 - 0 - 0 - 4 - 5 - 0 - 7 - QSNTWSL - QQNWWTL - Q N W+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 55 - Query_55 - M_2903 - 9 - - - 1 - gnl|BL_ORD_ID|1132 - 74886|latent membrane protein 1|AAS99606.1|Human gammaherpesvirus 4|10376 - 1132 - 9 - - - 1 - 13.853 - 24 - 7.20201 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 6 - 0 - 9 - YQQSNTWSL - YLQQNWWTL - Y Q N W+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 56 - Query_56 - M_2904 - 9 - - - 1 - gnl|BL_ORD_ID|1132 - 74886|latent membrane protein 1|AAS99606.1|Human gammaherpesvirus 4|10376 - 1132 - 9 - - - 1 - 13.853 - 24 - 7.20201 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 6 - 0 - 9 - YQQSNTWSL - YLQQNWWTL - Y Q N W+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 57 - Query_57 - M_2905 - 9 - - - 1 - gnl|BL_ORD_ID|524 - 32238|polyprotein [Hepatitis C virus subtype 1a]|ABV46251.2|Hepatitis C virus (isolate H77)|63746 - 524 - 10 - - - 1 - 12.6974 - 21 - 30.9217 - 2 - 7 - 1 - 6 - 0 - 0 - 5 - 6 - 0 - 6 - KLVVVG - KLVVLG - KLVV+G - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 58 - Query_58 - M_2906 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 59 - Query_59 - M_2907 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 60 - Query_60 - M_2908 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 61 - Query_61 - M_2909 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 62 - Query_62 - M_2910 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 63 - Query_63 - M_2911 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 64 - Query_64 - M_2912 - 9 - - - 1 - gnl|BL_ORD_ID|2244 - 232153|rhoptry protein 18|CAJ27113.1|Toxoplasma gondii type I|1209525 - 2244 - 19 - - - 1 - 12.3122 - 20 - 39.084 - 2 - 9 - 8 - 15 - 0 - 0 - 4 - 6 - 0 - 8 - ASGNRWTF - ATGITYTF - A+G +TF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 65 - Query_65 - M_2913 - 9 - - - 1 - gnl|BL_ORD_ID|2244 - 232153|rhoptry protein 18|CAJ27113.1|Toxoplasma gondii type I|1209525 - 2244 - 19 - - - 1 - 12.3122 - 20 - 39.084 - 2 - 9 - 8 - 15 - 0 - 0 - 4 - 6 - 0 - 8 - ASGNRWTF - ATGITYTF - A+G +TF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 66 - Query_66 - M_2914 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 67 - Query_67 - M_2915 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 68 - Query_68 - M_2916 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 69 - Query_69 - M_2917 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 70 - Query_70 - M_2918 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 71 - Query_71 - M_2919 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 72 - Query_72 - M_2920 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 73 - Query_73 - M_2921 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 74 - Query_74 - M_2922 - 9 - - - 1 - gnl|BL_ORD_ID|40 - 2884|cysteine proteinase cruzipain (EC 3.4.22.-) - Trypanosoma cruzi|A45629|Trypanosoma cruzi|5693 - 40 - 10 - - - 1 - 11.5418 - 18 - 139.346 - 2 - 9 - 1 - 8 - 0 - 0 - 6 - 6 - 0 - 8 - ALSENAVL - ALSLAAVL - ALS AVL - - - - - 2 - gnl|BL_ORD_ID|39 - 2883|cysteine proteinase cruzipain (EC 3.4.22.-) - Trypanosoma cruzi|A45629|Trypanosoma cruzi|5693 - 39 - 9 - - - 1 - 11.5418 - 18 - 157.499 - 2 - 9 - 1 - 8 - 0 - 0 - 6 - 6 - 0 - 8 - ALSENAVL - ALSLAAVL - ALS AVL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 75 - Query_75 - M_2923 - 9 - - - 1 - gnl|BL_ORD_ID|40 - 2884|cysteine proteinase cruzipain (EC 3.4.22.-) - Trypanosoma cruzi|A45629|Trypanosoma cruzi|5693 - 40 - 10 - - - 1 - 11.5418 - 18 - 139.346 - 2 - 9 - 1 - 8 - 0 - 0 - 6 - 6 - 0 - 8 - ALSENAVL - ALSLAAVL - ALS AVL - - - - - 2 - gnl|BL_ORD_ID|39 - 2883|cysteine proteinase cruzipain (EC 3.4.22.-) - Trypanosoma cruzi|A45629|Trypanosoma cruzi|5693 - 39 - 9 - - - 1 - 11.5418 - 18 - 157.499 - 2 - 9 - 1 - 8 - 0 - 0 - 6 - 6 - 0 - 8 - ALSENAVL - ALSLAAVL - ALS AVL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 76 - Query_76 - M_2924 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 77 - Query_77 - M_2925 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 78 - Query_78 - M_2926 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 79 - Query_79 - M_2927 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 80 - Query_80 - M_2928 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 81 - Query_81 - M_2929 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 82 - Query_82 - M_2930 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 83 - Query_83 - M_2931 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 84 - Query_84 - M_2932 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 85 - Query_85 - M_2933 - 9 - - - 1 - gnl|BL_ORD_ID|857 - 56198|glycoprotein gp35/37|AAC59622.1|Human gammaherpesvirus 8|37296 - 857 - 15 - - - 1 - 13.0826 - 22 - 17.2424 - 2 - 7 - 5 - 10 - 0 - 0 - 4 - 6 - 0 - 6 - LRVNPV - IRVSPV - +RV+PV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 86 - Query_86 - M_2934 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 87 - Query_87 - M_2935 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 88 - Query_88 - M_2936 - 9 - - - 1 - gnl|BL_ORD_ID|857 - 56198|glycoprotein gp35/37|AAC59622.1|Human gammaherpesvirus 8|37296 - 857 - 15 - - - 1 - 13.0826 - 22 - 17.2424 - 1 - 8 - 3 - 10 - 0 - 0 - 4 - 7 - 0 - 8 - SALRVNPV - TRIRVSPV - + +RV+PV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 89 - Query_89 - M_2937 - 9 - - - 1 - gnl|BL_ORD_ID|857 - 56198|glycoprotein gp35/37|AAC59622.1|Human gammaherpesvirus 8|37296 - 857 - 15 - - - 1 - 13.4678 - 23 - 8.0204 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 8 - 0 - 9 - SSALRVNPV - TTRIRVSPV - ++ +RV+PV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 90 - Query_90 - M_2938 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 91 - Query_91 - M_2939 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 92 - Query_92 - M_2940 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 93 - Query_93 - M_2941 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 94 - Query_94 - M_2942 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 95 - Query_95 - M_2943 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 96 - Query_96 - M_2944 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 97 - Query_97 - M_2945 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 98 - Query_98 - M_2946 - 9 - - - 1 - gnl|BL_ORD_ID|2271 - 419002|PPE family protein PPE68|KAM81677.1|Mycobacterium tuberculosis H37Ra|419947 - 2271 - 10 - - - 1 - 11.927 - 19 - 81.0261 - 1 - 9 - 2 - 10 - 0 - 0 - 3 - 7 - 0 - 9 - IQKITSPNI - IEKPVAPSV - I+K +P++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 99 - Query_99 - M_2947 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 100 - Query_100 - M_2948 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 101 - Query_101 - M_2949 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 102 - Query_102 - M_2950 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 103 - Query_103 - M_2951 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 104 - Query_104 - M_2952 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 105 - Query_105 - M_2953 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 106 - Query_106 - M_2954 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 107 - Query_107 - M_2955 - 9 - - - 1 - gnl|BL_ORD_ID|332 - 21139|envelope protein|BAF48755.1|Hepatitis B virus|10407 - 332 - 10 - - - 1 - 14.2382 - 25 - 3.10797 - 4 - 9 - 1 - 6 - 0 - 0 - 5 - 5 - 0 - 6 - GLSPTA - GLSPTV - GLSPT - - - - - 2 - gnl|BL_ORD_ID|331 - 21137|Major surface antigen precursor|P03142.4|Hepatitis B virus subtype adw|106821 - 331 - 10 - - - 1 - 14.2382 - 25 - 3.68732 - 4 - 9 - 1 - 6 - 0 - 0 - 5 - 5 - 0 - 6 - GLSPTA - GLSPTV - GLSPT - - - - - 3 - gnl|BL_ORD_ID|1392 - 110335|E7|AAD33253.1|Human papillomavirus type 16|333760 - 1392 - 32 - - - 1 - 13.0826 - 22 - 19.2096 - 3 - 8 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - HGLSPT - HGDTPT - HG +PT - - - - - 4 - gnl|BL_ORD_ID|1408 - 110940|Protein E7|P03129.1|Human papillomavirus type 16|333760 - 1408 - 15 - - - 1 - 12.6974 - 21 - 27.8948 - 3 - 8 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - HGLSPT - HGDTPT - HG +PT - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 108 - Query_108 - M_2956 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 109 - Query_109 - M_2957 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 110 - Query_110 - M_2958 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 111 - Query_111 - M_2959 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 112 - Query_112 - M_2960 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_131909_2_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_131909_2_T.fasta deleted file mode 100755 index c4488424..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_131909_2_T.fasta +++ /dev/null @@ -1,76 +0,0 @@ ->M_2961 -SRRACSSEL ->M_2962 -SPKLKMPEM ->M_2963 -SNKEKWISL ->M_2964 -KRWESEHIL ->M_2965 -LHNEIKTLL ->M_2966 -FSDKMGTLT ->M_2967 -LAAERKAAL ->M_2968 -TPRRSRWQL ->M_2969 -MNCIRQASV ->M_2970 -DQRCRLCPA ->M_2971 -HTTRSLFQY ->M_2972 -PHCPQPLVY ->M_2973 -SLEGRIWAL ->M_2974 -YTDFLLCAS ->M_2975 -VVGARGVGK ->M_2976 -RGRKNRSSV ->M_2977 -FEKMHQMDL ->M_2978 -QVFEKMHQM ->M_2979 -ARWPFGNTM ->M_2980 -GALKKALAK ->M_2981 -RLIAISWPL ->M_2982 -WPLRYVTVM ->M_2983 -HILGNFLTK ->M_2984 -IRCGYPTHI ->M_2985 -EAGPRKGPL ->M_2986 -RLEEAGPRK ->M_2987 -KLPEMKLPK ->M_2988 -MKLPKVPEM ->M_2989 -DRQDQSSHY ->M_2990 -SHYGQPDRQ ->M_2991 -GIMPGHIQK ->M_2992 -IMPGHIQKK ->M_2993 -STMRESSPK ->M_2994 -FPLFAIWPM ->M_2995 -PTDPMLGLA ->M_2996 -EARSRATLA ->M_2997 -FHEARSRAT ->M_2998 -FSIFSTLTK diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_131909_2_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_131909_2_T_iedb.xml deleted file mode 100755 index 40c7799e..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_131909_2_T_iedb.xml +++ /dev/null @@ -1,1221 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_2961 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_2961 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_2962 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_2963 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_2964 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_2965 - 9 - - - 1 - gnl|BL_ORD_ID|1378 - 109332|L1 protein|ACG75893.1|Human papillomavirus type 16|333760 - 1378 - 9 - - - 1 - 9.61583 - 13 - 1457.43 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 6 - 0 - 9 - LHNEIKTLL - IHSMNSTIL - +H+ T+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 6 - Query_6 - M_2966 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_2967 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_2968 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_2969 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_2970 - 9 - - - 1 - gnl|BL_ORD_ID|1621 - 145860|Protein E6|P04019.1|Human papillomavirus type 11|10580 - 1621 - 9 - - - 1 - 12.6974 - 21 - 39.1808 - 3 - 7 - 5 - 9 - 0 - 0 - 4 - 4 - 0 - 5 - RCRLC - RCYLC - RC LC - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 11 - Query_11 - M_2971 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_2972 - 9 - - - 1 - gnl|BL_ORD_ID|96 - 6591|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 96 - 18 - - - 1 - 15.0086 - 27 - 1.3941 - 2 - 9 - 10 - 17 - 0 - 0 - 5 - 6 - 0 - 8 - HCPQPLVY - HGPTPLLY - H P PL+Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 13 - Query_13 - M_2973 - 9 - - - 1 - gnl|BL_ORD_ID|2111 - 186219|polyprotein|AGK36298.1|Dengue virus 2|11060 - 2111 - 9 - - - 1 - 14.2382 - 25 - 3.43721 - 3 - 9 - 3 - 9 - 0 - 0 - 4 - 5 - 0 - 7 - EGRIWAL - DGRFWEL - +GR W L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 14 - Query_14 - M_2974 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_2975 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_2976 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_2977 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_2978 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_2979 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_2980 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_2981 - 9 - - - 1 - gnl|BL_ORD_ID|1787 - 161186|Nonstructural protein NS5|NP_739590.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1787 - 15 - - - 1 - 11.1566 - 17 - 239.5 - 1 - 7 - 1 - 7 - 0 - 0 - 3 - 4 - 0 - 7 - RLIAISW - RLLTKPW - RL+ W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 22 - Query_22 - M_2982 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_2983 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_2984 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_2985 - 9 - - - 1 - gnl|BL_ORD_ID|1950 - 181035|||| - 1950 - 44 - - - 1 - 14.2382 - 25 - 5.04563 - 4 - 8 - 27 - 31 - 0 - 0 - 4 - 5 - 0 - 5 - PRKGP - PRRGP - PR+GP - - - - - 2 - gnl|BL_ORD_ID|1130 - 74798|polyprotein|BAA03375.1|Hepatitis C virus|11103 - 1130 - 10 - - - 1 - 13.853 - 24 - 5.77604 - 4 - 8 - 4 - 8 - 0 - 0 - 4 - 5 - 0 - 5 - PRKGP - PRRGP - PR+GP - - - - - 3 - gnl|BL_ORD_ID|374 - 23224|polyprotein|BAB18806.1|Hepatitis C virus|11103 - 374 - 15 - - - 1 - 13.853 - 24 - 5.77703 - 4 - 8 - 6 - 10 - 0 - 0 - 4 - 5 - 0 - 5 - PRKGP - PRRGP - PR+GP - - - - - 4 - gnl|BL_ORD_ID|630 - 37685|polyprotein|BAA03375.1|Hepatitis C virus|11103 - 630 - 9 - - - 1 - 13.853 - 24 - 6.83656 - 4 - 8 - 3 - 7 - 0 - 0 - 4 - 5 - 0 - 5 - PRKGP - PRRGP - PR+GP - - - - - 5 - gnl|BL_ORD_ID|1129 - 74797|polyprotein|BAA09073.1|Hepatitis C virus subtype 1b|31647 - 1129 - 9 - - - 1 - 13.853 - 24 - 6.95623 - 4 - 8 - 4 - 8 - 0 - 0 - 4 - 5 - 0 - 5 - PRKGP - PRRGP - PR+GP - - - - - 6 - gnl|BL_ORD_ID|1508 - 139406|polyprotein|ACT37184.1|Hepatitis C virus|11103 - 1508 - 10 - - - 1 - 12.3122 - 20 - 54.6881 - 4 - 8 - 4 - 8 - 0 - 0 - 4 - 4 - 0 - 5 - PRKGP - PRPGP - PR GP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 26 - Query_26 - M_2986 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_2987 - 9 - - - 1 - gnl|BL_ORD_ID|241 - 16836|precore/core protein [Hepatitis B virus]|AAR03815.1|Hepatitis B virus|10407 - 241 - 10 - - - 1 - 10.7714 - 16 - 451.277 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 4 - 0 - 8 - LPEMKLPK - LPSDFLPS - LP LP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 28 - Query_28 - M_2988 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 29 - Query_29 - M_2989 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 30 - Query_30 - M_2990 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 31 - Query_31 - M_2991 - 9 - - - 1 - gnl|BL_ORD_ID|1912 - 180668|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1912 - 10 - - - 1 - 12.6974 - 21 - 26.0802 - 3 - 9 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - MPGHIQK - MPSVIEK - MP I+K - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 32 - Query_32 - M_2992 - 9 - - - 1 - gnl|BL_ORD_ID|1912 - 180668|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1912 - 10 - - - 1 - 12.6974 - 21 - 35.4066 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - MPGHIQK - MPSVIEK - MP I+K - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 33 - Query_33 - M_2993 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 34 - Query_34 - M_2994 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 35 - Query_35 - M_2995 - 9 - - - 1 - gnl|BL_ORD_ID|242 - 16839|External core antigen|SRC279980|Hepatitis B virus|10407 - 242 - 10 - - - 1 - 12.6974 - 21 - 26.0802 - 1 - 8 - 3 - 10 - 0 - 0 - 4 - 6 - 0 - 8 - PTDPMLGL - PSDTNMGL - P+D +GL - - - - - 2 - gnl|BL_ORD_ID|1581 - 141462|tegument protein UL21|NP_044622.1|Human alphaherpesvirus 1|10298 - 1581 - 9 - - - 1 - 12.3122 - 20 - 40.5299 - 1 - 6 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - PTDPML - PDDPVL - P DP+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 36 - Query_36 - M_2996 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 37 - Query_37 - M_2997 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 38 - Query_38 - M_2998 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132080_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132080_1_T.fasta deleted file mode 100755 index 7703bccd..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132080_1_T.fasta +++ /dev/null @@ -1,80 +0,0 @@ ->M_2999 -LPDRLTLEF ->M_3000 -LPDRLTLEF ->M_3001 -FSDHQSFVV ->M_3002 -LLSQVQFPY ->M_3003 -GELSVDVSF ->M_3004 -LSVDVSFFF ->M_3005 -LSVDVSFFF ->M_3006 -SVDVSFFFK ->M_3007 -VVDQGNIGK ->M_3008 -MVFHKHGEK ->M_3009 -NAYTMVFHK ->M_3010 -MESNNMPFL ->M_3011 -VMESNNMPF ->M_3012 -IPVPVGATA ->M_3013 -VPVGATASF ->M_3014 -SLDLSQTNL ->M_3015 -TETSSSMPG ->M_3016 -HTDPHLCDF ->M_3017 -SLGFKLLLR ->M_3018 -HEQCDSSSL ->M_3019 -AEKSQGPVL ->M_3020 -RLLSTQAEK ->M_3021 -LSDIGGLLL ->M_3022 -LYLYVLSDI ->M_3023 -SELSSDINL ->M_3024 -MPHSQYLSA ->M_3025 -EEAFVPILY ->M_3026 -QVTVSFTEM ->M_3027 -TVSFTEMLK ->M_3028 -VSFTEMLKK ->M_3029 -LGYRCRFNK ->M_3030 -LPDLFTPPL ->M_3031 -HTDGDTLLQ ->M_3032 -ILAKHKSLF ->M_3033 -KLTILAKHK ->M_3034 -AQTHEPRQW ->M_3035 -EAVAGHIPA ->M_3036 -VAGHIPAIF ->M_3037 -VADLLAFTH ->M_3038 -VVGAVGVGK diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132080_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132080_1_T_iedb.xml deleted file mode 100755 index 5a5e9535..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132080_1_T_iedb.xml +++ /dev/null @@ -1,1566 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_2999 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_2999 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_3000 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_3001 - 9 - - - 1 - gnl|BL_ORD_ID|2185 - 190466|large surface antigen|CAL29876.1|Hepatitis B virus|10407 - 2185 - 15 - - - 1 - 13.4678 - 23 - 7.48645 - 1 - 5 - 4 - 8 - 0 - 0 - 4 - 4 - 0 - 5 - FSDHQ - FPDHQ - F DHQ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 4 - Query_4 - M_3002 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_3003 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_3004 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_3005 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_3006 - 9 - - - 1 - gnl|BL_ORD_ID|72 - 5295|nef protein|ACR27174.1|Human immunodeficiency virus 1|11676 - 72 - 9 - - - 1 - 14.6234 - 26 - 1.88321 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 7 - 0 - 9 - SVDVSFFFK - AVDLSHFLK - +VD+S F K - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 9 - Query_9 - M_3007 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_3008 - 9 - - - 1 - gnl|BL_ORD_ID|1090 - 72039|polyprotein|CAB53095.1|Hepatitis C virus subtype 1b|31647 - 1090 - 10 - - - 1 - 12.6974 - 21 - 23.5358 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 5 - 0 - 8 - VFHKHGEK - VYHGAGSK - V+H G K - - - - - 2 - gnl|BL_ORD_ID|1089 - 72038|Polyprotein|Q9IZA3|Hepatitis C virus subtype 2a|31649 - 1089 - 10 - - - 1 - 12.6974 - 21 - 27.922 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 5 - 0 - 8 - VFHKHGEK - VYHGAGNK - V+H G K - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 11 - Query_11 - M_3009 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_3010 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_3011 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_3012 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_3013 - 9 - - - 1 - gnl|BL_ORD_ID|696 - 42342|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 - 696 - 9 - - - 1 - 15.3938 - 28 - 0.610749 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 7 - 0 - 9 - VPVGATASF - MPVGGQSSF - +PVG +SF - - - - - 2 - gnl|BL_ORD_ID|2175 - 189750|Diacylglycerol acyltransferase/mycolyltransferase Ag85B|SRC280000|Mycobacterium tuberculosis|1773 - 2175 - 9 - - - 1 - 15.0086 - 27 - 1.15928 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 7 - 0 - 9 - VPVGATASF - MPVGGGSSF - +PVG +SF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 16 - Query_16 - M_3014 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_3015 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_3016 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_3017 - 9 - - - 1 - gnl|BL_ORD_ID|785 - 52578|liver stage antigen-1|CAA82974.1|Plasmodium falciparum|5833 - 785 - 9 - - - 1 - 12.6974 - 21 - 30.8766 - 3 - 9 - 3 - 9 - 0 - 0 - 5 - 5 - 0 - 7 - GFKLLLR - NFKSLLR - FK LLR - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 20 - Query_20 - M_3018 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_3019 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 22 - Query_22 - M_3020 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_3021 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_3022 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_3023 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_3024 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_3025 - 9 - - - 1 - gnl|BL_ORD_ID|1553 - 141228|tegument protein VP11/12|NP_044648.1|Human alphaherpesvirus 1|10298 - 1553 - 9 - - - 1 - 13.4678 - 23 - 8.56958 - 3 - 9 - 1 - 7 - 0 - 0 - 4 - 6 - 0 - 7 - AFVPILY - AYVSVLY - A+V +LY - - - - - 2 - gnl|BL_ORD_ID|1568 - 141341|tegument protein VP11/12|NP_044648.1|Human alphaherpesvirus 1|10298 - 1568 - 9 - - - 1 - 13.4678 - 23 - 11.9303 - 3 - 9 - 3 - 9 - 0 - 0 - 4 - 6 - 0 - 7 - AFVPILY - AYVSVLY - A+V +LY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 28 - Query_28 - M_3026 - 9 - - - 1 - gnl|BL_ORD_ID|1427 - 112697|Protein E6|P26554.1|Human papillomavirus type 51|10595 - 1427 - 10 - - - 1 - 13.0826 - 22 - 16.6782 - 4 - 9 - 1 - 6 - 0 - 0 - 4 - 6 - 0 - 6 - VSFTEM - VAFTEI - V+FTE+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 29 - Query_29 - M_3027 - 9 - - - 1 - gnl|BL_ORD_ID|1427 - 112697|Protein E6|P26554.1|Human papillomavirus type 51|10595 - 1427 - 10 - - - 1 - 13.0826 - 22 - 14.2707 - 2 - 7 - 1 - 6 - 0 - 0 - 4 - 6 - 0 - 6 - VSFTEM - VAFTEI - V+FTE+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 30 - Query_30 - M_3028 - 9 - - - 1 - gnl|BL_ORD_ID|1427 - 112697|Protein E6|P26554.1|Human papillomavirus type 51|10595 - 1427 - 10 - - - 1 - 13.4678 - 23 - 11.9953 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 6 - 0 - 6 - VSFTEM - VAFTEI - V+FTE+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 31 - Query_31 - M_3029 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 32 - Query_32 - M_3030 - 9 - - - 1 - gnl|BL_ORD_ID|141 - 10587|viral polyprotein|AAA42941.1|Dengue virus 2 Thailand/NGS-C/1944|11065 - 141 - 9 - - - 1 - 13.0826 - 22 - 23.0624 - 4 - 8 - 3 - 7 - 0 - 0 - 4 - 4 - 0 - 5 - LFTPP - FFTPP - FTPP - - - - - 2 - gnl|BL_ORD_ID|235 - 16814|precore protein|CAM58990.1|Hepatitis B virus|10407 - 235 - 10 - - - 1 - 10.7714 - 16 - 347.035 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 6 - 0 - 9 - LPDLFTPPL - LPNDFFPSV - LP+ F P + - - - - - 3 - gnl|BL_ORD_ID|234 - 16813|External core antigen|SRC279980|Hepatitis B virus|10407 - 234 - 10 - - - 1 - 10.7714 - 16 - 384.587 - 1 - 7 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - LPDLFTP - LPNDFFP - LP+ F P - - - - - 4 - gnl|BL_ORD_ID|239 - 16832|core protein|BAF42671.1|Hepatitis B virus|10407 - 239 - 10 - - - 1 - 10.3862 - 15 - 626.674 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 5 - 0 - 9 - LPDLFTPPL - LPSDFFPSI - LP F P + - - - - - 5 - gnl|BL_ORD_ID|69 - 5191|core protein|AAL31859.1|Hepatitis B virus|10407 - 69 - 17 - - - 1 - 10.001 - 14 - 641.761 - 1 - 9 - 9 - 17 - 0 - 0 - 4 - 5 - 0 - 9 - LPDLFTPPL - LPSDFFPSV - LP F P + - - - - - 6 - gnl|BL_ORD_ID|241 - 16836|precore/core protein [Hepatitis B virus]|AAR03815.1|Hepatitis B virus|10407 - 241 - 10 - - - 1 - 10.3862 - 15 - 731.165 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 5 - 0 - 9 - LPDLFTPPL - LPSDFLPSV - LP F P + - - - - - 7 - gnl|BL_ORD_ID|240 - 16833|core protein|CAL29866.1|Hepatitis B virus|10407 - 240 - 10 - - - 1 - 10.001 - 14 - 817.025 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 5 - 0 - 9 - LPDLFTPPL - LPSDFFPSV - LP F P + - - - - - 8 - gnl|BL_ORD_ID|653 - 38701|core protein|AAL31859.1|Hepatitis B virus|10407 - 653 - 9 - - - 1 - 10.001 - 14 - 831.41 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 5 - 0 - 9 - LPDLFTPPL - LPSDFFPSV - LP F P + - - - - - 9 - gnl|BL_ORD_ID|238 - 16831|External core antigen|SRC279980|Hepatitis B virus|10407 - 238 - 10 - - - 1 - 10.001 - 14 - 887.43 - 1 - 7 - 2 - 8 - 0 - 0 - 4 - 4 - 0 - 7 - LPDLFTP - LPSDFFP - LP F P - - - - - 10 - gnl|BL_ORD_ID|237 - 16827|External core antigen|SRC279980|Hepatitis B virus|10407 - 237 - 10 - - - 1 - 10.001 - 14 - 887.43 - 1 - 7 - 2 - 8 - 0 - 0 - 4 - 4 - 0 - 7 - LPDLFTP - LPSDFFP - LP F P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 33 - Query_33 - M_3031 - 9 - - - 1 - gnl|BL_ORD_ID|1355 - 108148|polyprotein|AAF65953.1|Hepatitis C virus|11103 - 1355 - 10 - - - 1 - 11.5418 - 18 - 175.991 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 5 - 0 - 8 - HTDGDTLL - STDSTTIL - TD T+L - - - - - 2 - gnl|BL_ORD_ID|1359 - 108158|polyprotein|AAF65953.1|Hepatitis C virus|11103 - 1359 - 10 - - - 1 - 11.1566 - 17 - 253.803 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - TDGDTLL - TDSTTIL - TD T+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 34 - Query_34 - M_3032 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 35 - Query_35 - M_3033 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 36 - Query_36 - M_3034 - 9 - - - 1 - gnl|BL_ORD_ID|2137 - 187106|Vpr protein|BAA93983.1|Human immunodeficiency virus 1|11676 - 2137 - 9 - - - 1 - 14.2382 - 25 - 3.55601 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 5 - 0 - 9 - AQTHEPRQW - AVRHFPRIW - A H PR W - - - - - 2 - gnl|BL_ORD_ID|1931 - 180758|Nonstructural protein NS5|NP_739590.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1931 - 15 - - - 1 - 10.7714 - 16 - 365.404 - 2 - 9 - 6 - 13 - 0 - 0 - 3 - 4 - 0 - 8 - QTHEPRQW - QDHPYKTW - Q H + W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 37 - Query_37 - M_3035 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 38 - Query_38 - M_3036 - 9 - - - 1 - gnl|BL_ORD_ID|128 - 9199|E1 protein|ABB77003.1|Hepatitis C virus|11103 - 128 - 9 - - - 1 - 14.2382 - 25 - 3.32254 - 1 - 8 - 2 - 9 - 0 - 0 - 4 - 7 - 0 - 8 - VAGHIPAI - LMGYIPAV - + G+IPA+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 39 - Query_39 - M_3037 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 40 - Query_40 - M_3038 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132221_2_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132221_2_T.fasta deleted file mode 100755 index 04e045d2..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132221_2_T.fasta +++ /dev/null @@ -1,74 +0,0 @@ ->M_3039 -KLTSYKCKL ->M_3040 -WLRVGNGAL ->M_3041 -SLQLSAHRL ->M_3042 -IVVISIWEI ->M_3043 -SIWEIVGQA ->M_3044 -YLKRGYLTL ->M_3045 -MLHVDRHTL ->M_3046 -VLERGQFDY ->M_3047 -AALSIDHWV ->M_3048 -SIDHWVAVV ->M_3049 -ATAAAAAAL ->M_3050 -GPATAAAAA ->M_3051 -LLLDTPTQL ->M_3052 -HLYDTLGST ->M_3053 -LPLHLYDTL ->M_3054 -EEYTVWIQL ->M_3055 -WEEEYTVWI ->M_3056 -TPEDNRQPL ->M_3057 -LPEQQEGQL ->M_3058 -KPMQVKTPC ->M_3059 -NLQNSPLEI ->M_3060 -VPNLQNSPL ->M_3061 -NELYFAHVL ->M_3062 -YFAHVLFSA ->M_3063 -AVTRPFISL ->M_3064 -FLWPLRVLS ->M_3065 -ISMKFLWPL ->M_3066 -WPLRVLSQF ->M_3067 -REIVWEQGL ->M_3068 -TLAEKRPFM ->M_3069 -LPGHLSRAL ->M_3070 -SLPGHLSRA ->M_3071 -SPSSLPGHL ->M_3072 -ALNNMFCQL ->M_3073 -GPRRGSSPQ ->M_3074 -SPQGAAGAA ->M_3075 -KAFSQSAYL diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132221_2_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132221_2_T_iedb.xml deleted file mode 100755 index 1c80711c..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132221_2_T_iedb.xml +++ /dev/null @@ -1,1367 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_3039 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_3039 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_3040 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_3041 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_3042 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_3043 - 9 - - - 1 - gnl|BL_ORD_ID|939 - 62004|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 - 939 - 15 - - - 1 - 12.6974 - 21 - 27.8948 - 1 - 7 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - SIWEIVG - STWVLVG - S W +VG - - - - - 2 - gnl|BL_ORD_ID|2122 - 186474|polyprotein|AGO67248.1|Dengue virus 2|11060 - 2122 - 10 - - - 1 - 11.5418 - 18 - 155.455 - 3 - 9 - 1 - 7 - 0 - 0 - 3 - 5 - 0 - 7 - WEIVGQA - WKTWGKA - W+ G+A - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 6 - Query_6 - M_3044 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_3045 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_3046 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_3047 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_3048 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_3049 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_3050 - 9 - - - 1 - gnl|BL_ORD_ID|2014 - 183819|polyprotein|AGO67248.1|Dengue virus 2|11060 - 2014 - 10 - - - 1 - 11.927 - 19 - 68.8532 - 2 - 7 - 2 - 7 - 0 - 0 - 5 - 5 - 0 - 6 - PATAAA - PITAAA - P TAAA - - - - - 2 - gnl|BL_ORD_ID|1882 - 180538|Nonstructural protein NS2B|NP_739586.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1882 - 15 - - - 1 - 11.927 - 19 - 73.829 - 2 - 7 - 10 - 15 - 0 - 0 - 5 - 5 - 0 - 6 - PATAAA - PITAAA - P TAAA - - - - - 3 - gnl|BL_ORD_ID|1880 - 180529|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1880 - 9 - - - 1 - 11.927 - 19 - 82.8955 - 2 - 7 - 2 - 7 - 0 - 0 - 5 - 5 - 0 - 6 - PATAAA - PITAAA - P TAAA - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 13 - Query_13 - M_3051 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_3052 - 9 - - - 1 - gnl|BL_ORD_ID|1808 - 169658|major paraflagellar rod protein|AAA30221.1|Trypanosoma cruzi|5693 - 1808 - 9 - - - 1 - 14.2382 - 25 - 3.05306 - 1 - 8 - 1 - 8 - 0 - 0 - 5 - 5 - 0 - 8 - HLYDTLGS - RLYKTLGQ - LY TLG - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 15 - Query_15 - M_3053 - 9 - - - 1 - gnl|BL_ORD_ID|2191 - 190568|polymerase|AAD16253.1|Hepatitis B virus|10407 - 2191 - 20 - - - 1 - 12.3122 - 20 - 44.0299 - 3 - 7 - 6 - 10 - 0 - 0 - 4 - 4 - 0 - 5 - LHLYD - LHLYS - LHLY - - - - - 2 - gnl|BL_ORD_ID|498 - 31898|P protein|P17100.1|Hepatitis B virus|10407 - 498 - 9 - - - 1 - 11.927 - 19 - 75.1319 - 3 - 7 - 2 - 6 - 0 - 0 - 4 - 4 - 0 - 5 - LHLYD - LHLYS - LHLY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 16 - Query_16 - M_3054 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_3055 - 9 - - - 1 - gnl|BL_ORD_ID|2051 - 184702|non-structural protein 1|AGM49312.1|Dengue virus|12637 - 2051 - 9 - - - 1 - 13.4678 - 23 - 9.85027 - 1 - 8 - 2 - 9 - 0 - 0 - 3 - 6 - 0 - 8 - WEEEYTVW - WPKTHTLW - W + +T+W - - - - - 2 - gnl|BL_ORD_ID|552 - 33912|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 - 552 - 10 - - - 1 - 11.927 - 19 - 81.0261 - 1 - 5 - 3 - 7 - 0 - 0 - 3 - 4 - 0 - 5 - WEEEY - WADEY - W +EY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 18 - Query_18 - M_3056 - 9 - - - 1 - gnl|BL_ORD_ID|1741 - 150649|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1741 - 10 - - - 1 - 14.2382 - 25 - 3.44317 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 6 - 0 - 6 - TPEDNR - TPQDNQ - TP+DN+ - - - - - 2 - gnl|BL_ORD_ID|1934 - 180780|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1934 - 9 - - - 1 - 14.2382 - 25 - 4.0067 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 6 - 0 - 6 - TPEDNR - TPQDNQ - TP+DN+ - - - - - 3 - gnl|BL_ORD_ID|1935 - 180781|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1935 - 9 - - - 1 - 13.853 - 24 - 4.75595 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 6 - 0 - 6 - TPEDNR - TPQDNQ - TP+DN+ - - - - - 4 - gnl|BL_ORD_ID|2105 - 186029|envelope protein|ABV59122.1|Dengue virus 3|11069 - 2105 - 9 - - - 1 - 13.0826 - 22 - 13.9535 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 6 - 0 - 9 - TPEDNRQPL - TPTWNRKEL - TP NR+ L - - - - - 5 - gnl|BL_ORD_ID|1494 - 136890|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1494 - 9 - - - 1 - 12.6974 - 21 - 30.3534 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 5 - 0 - 9 - TPEDNRQPL - TPPGSRDPF - TP +R P - - - - - 6 - gnl|BL_ORD_ID|2013 - 183813|polyprotein|AGW21594.1|Dengue virus 1|11053 - 2013 - 10 - - - 1 - 11.927 - 19 - 75.9314 - 2 - 7 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - PEDNRQ - PEPDRQ - PE +RQ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 19 - Query_19 - M_3057 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_3058 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_3059 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 22 - Query_22 - M_3060 - 9 - - - 1 - gnl|BL_ORD_ID|1068 - 70491|envelope glycoprotein|AAC28452.1|Human immunodeficiency virus 1|11676 - 1068 - 10 - - - 1 - 10.3862 - 15 - 691.436 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 4 - 0 - 8 - VPNLQNSP - VPTDPNPP - VP N P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 23 - Query_23 - M_3061 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_3062 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_3063 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_3064 - 9 - - - 1 - gnl|BL_ORD_ID|2098 - 185817|envelope protein|AGW23590.1|Dengue virus 4|11070 - 2098 - 10 - - - 1 - 12.3122 - 20 - 52.9061 - 3 - 8 - 2 - 7 - 0 - 0 - 3 - 5 - 0 - 6 - WPLRVL - WMIRIL - W +R+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 27 - Query_27 - M_3065 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 28 - Query_28 - M_3066 - 9 - - - 1 - gnl|BL_ORD_ID|2098 - 185817|envelope protein|AGW23590.1|Dengue virus 4|11070 - 2098 - 10 - - - 1 - 13.4678 - 23 - 7.62841 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 6 - 0 - 9 - WPLRVLSQF - WMIRILIGF - W +R+L F - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 29 - Query_29 - M_3067 - 9 - - - 1 - gnl|BL_ORD_ID|588 - 36717|nonstructural protein 4B|YP_001527886.1|West Nile virus NY-99|10000971 - 588 - 18 - - - 1 - 12.3122 - 20 - 41.1077 - 4 - 8 - 9 - 13 - 0 - 0 - 3 - 4 - 0 - 5 - VWEQG - LWENG - +WE G - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 30 - Query_30 - M_3068 - 9 - - - 1 - gnl|BL_ORD_ID|974 - 64727|polyprotein precursor|NP_041724.2|West Nile virus|11082 - 974 - 9 - - - 1 - 13.4678 - 23 - 10.7466 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 6 - 0 - 9 - TLAEKRPFM - TLARGFPFV - TLA PF+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 31 - Query_31 - M_3069 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 32 - Query_32 - M_3070 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 33 - Query_33 - M_3071 - 9 - - - 1 - gnl|BL_ORD_ID|793 - 53041|phosphorylated matrix protein (pp65)|AAA45996.1|Human betaherpesvirus 5|10359 - 793 - 11 - - - 1 - 13.0826 - 22 - 14.7222 - 1 - 8 - 3 - 10 - 0 - 0 - 4 - 5 - 0 - 8 - SPSSLPGH - TPDSTPCH - +P S P H - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 34 - Query_34 - M_3072 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 35 - Query_35 - M_3073 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 36 - Query_36 - M_3074 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 37 - Query_37 - M_3075 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132607_2_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132607_2_T.fasta deleted file mode 100755 index 517f5990..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132607_2_T.fasta +++ /dev/null @@ -1,98 +0,0 @@ ->M_3076 -FADHTVVTI ->M_3077 -FADHTVVTI ->M_3078 -MTAFADHTV ->M_3079 -TAFADHTVV ->M_3080 -GLSPRTSRH ->M_3081 -LSPRTSRHI ->M_3082 -RTSRHILER ->M_3083 -SVQACGWRK ->M_3084 -CLLSPSYYH ->M_3085 -LASDRFNHI ->M_3086 -QVASSPAGK ->M_3087 -VASSPAGKL ->M_3088 -IEYDTFGEV ->M_3089 -APSSVALSL ->M_3090 -NTAPSSVAL ->M_3091 -EMKRHKVHI ->M_3092 -ELLDYIRAV ->M_3093 -PQIPPYSTF ->M_3094 -ISHLHRESV ->M_3095 -NLLSPDNMV ->M_3096 -FASDHFLYA ->M_3097 -FASDHFLYA ->M_3098 -ATYVRILQR ->M_3099 -FVVITATYV ->M_3100 -LASSSLDIV ->M_3101 -FAYTILQSV ->M_3102 -TILQSVPNK ->M_3103 -FTLFFMAEY ->M_3104 -FTLFFMAEY ->M_3105 -YAAGPFTLF ->M_3106 -YAAGPFTLF ->M_3107 -YAAGPFTLF ->M_3108 -ICSEATAAI ->M_3109 -SLFNALRGK ->M_3110 -VAIMGSTQV ->M_3111 -SAYVALSNK ->M_3112 -YAISARSDL ->M_3113 -ATKTLRNYK ->M_3114 -DVFFATKTL ->M_3115 -FATKTLRNY ->M_3116 -FATKTLRNY ->M_3117 -FLSWCRRVV ->M_3118 -LSWCRRVVL ->M_3119 -RVVLELSPK ->M_3120 -VVLELSPKV ->M_3121 -IAIAIGAVL ->M_3122 -IAIGAVLLV ->M_3123 -RGMQCAICK ->M_3124 -FSNADVNRL diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132607_2_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132607_2_T_iedb.xml deleted file mode 100755 index 29c73261..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132607_2_T_iedb.xml +++ /dev/null @@ -1,1665 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_3076 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_3076 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_3077 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_3078 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_3079 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_3080 - 9 - - - 1 - gnl|BL_ORD_ID|256 - 17278|Genome polyprotein|P06441.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 256 - 20 - - - 1 - 13.4678 - 23 - 10.9145 - 2 - 9 - 4 - 11 - 0 - 0 - 5 - 5 - 0 - 8 - LSPRTSRH - LKPGESRH - L P SRH - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 6 - Query_6 - M_3081 - 9 - - - 1 - gnl|BL_ORD_ID|664 - 39591|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 - 664 - 20 - - - 1 - 15.0086 - 27 - 1.23765 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 6 - 0 - 9 - LSPRTSRHI - LSPYYKRYI - LSP R+I - - - - - 2 - gnl|BL_ORD_ID|663 - 39590|polyprotein|AAY82030.1|Hepatitis C virus|11103 - 663 - 11 - - - 1 - 14.2382 - 25 - 2.83796 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 6 - 0 - 9 - LSPRTSRHI - LSPYYKRYI - LSP R+I - - - - - 3 - gnl|BL_ORD_ID|662 - 39589|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 662 - 10 - - - 1 - 14.2382 - 25 - 3.68732 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 6 - 0 - 9 - LSPRTSRHI - LSPYYKRYI - LSP R+I - - - - - 4 - gnl|BL_ORD_ID|256 - 17278|Genome polyprotein|P06441.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 256 - 20 - - - 1 - 13.853 - 24 - 6.63101 - 1 - 8 - 4 - 11 - 0 - 0 - 5 - 5 - 0 - 8 - LSPRTSRH - LKPGESRH - L P SRH - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 7 - Query_7 - M_3082 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_3083 - 9 - - - 1 - gnl|BL_ORD_ID|1142 - 75435|largest ORF|AAB02128.1|Hepatitis C virus|11103 - 1142 - 20 - - - 1 - 13.4678 - 23 - 8.80594 - 3 - 7 - 9 - 13 - 0 - 0 - 3 - 4 - 0 - 5 - QACGW - EGCGW - + CGW - - - - - 2 - gnl|BL_ORD_ID|709 - 43621|largest ORF|AAB02128.1|Hepatitis C virus (isolate H77)|63746 - 709 - 9 - - - 1 - 13.4678 - 23 - 12.1399 - 3 - 7 - 2 - 6 - 0 - 0 - 3 - 4 - 0 - 5 - QACGW - EGCGW - + CGW - - - - - 3 - gnl|BL_ORD_ID|708 - 43619|Genome polyprotein|P26664.3|Hepatitis C virus|11103 - 708 - 9 - - - 1 - 13.0826 - 22 - 14.1983 - 3 - 7 - 2 - 6 - 0 - 0 - 3 - 4 - 0 - 5 - QACGW - EGCGW - + CGW - - - - - 4 - gnl|BL_ORD_ID|713 - 43756|Genome polyprotein|SRC279960|Hepatitis C virus subtype 2a|31649 - 713 - 9 - - - 1 - 13.0826 - 22 - 14.7007 - 3 - 7 - 2 - 6 - 0 - 0 - 3 - 4 - 0 - 5 - QACGW - ETCGW - + CGW - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 9 - Query_9 - M_3084 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_3085 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_3086 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_3087 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_3088 - 9 - - - 1 - gnl|BL_ORD_ID|531 - 32738|Liver stage antigen|Q25893|Plasmodium falciparum|5833 - 531 - 9 - - - 1 - 13.4678 - 23 - 10.7466 - 1 - 6 - 4 - 9 - 0 - 0 - 3 - 5 - 0 - 6 - IEYDTF - VQYDNF - ++YD F - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 14 - Query_14 - M_3089 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_3090 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_3091 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_3092 - 9 - - - 1 - gnl|BL_ORD_ID|155 - 11804|EBNA3C latent protein|CAD53421.1|Human gammaherpesvirus 4|10376 - 155 - 10 - - - 1 - 14.2382 - 25 - 3.88217 - 2 - 7 - 4 - 9 - 0 - 0 - 4 - 6 - 0 - 6 - LLDYIR - LLDFVR - LLD++R - - - - - 2 - gnl|BL_ORD_ID|601 - 37153|Nuclear antigen EBNA-3C|Q69140.1|Human gammaherpesvirus 4|10376 - 601 - 10 - - - 1 - 14.2382 - 25 - 4.01795 - 2 - 7 - 1 - 6 - 0 - 0 - 4 - 6 - 0 - 6 - LLDYIR - LLDFVR - LLD++R - - - - - 3 - gnl|BL_ORD_ID|1127 - 74768|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 - 1127 - 9 - - - 1 - 12.6974 - 21 - 26.0147 - 2 - 8 - 2 - 8 - 0 - 0 - 5 - 6 - 0 - 7 - LLDYIRA - LLDGLRA - LLD +RA - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 18 - Query_18 - M_3093 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_3094 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_3095 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_3096 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 22 - Query_22 - M_3097 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_3098 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_3099 - 9 - - - 1 - gnl|BL_ORD_ID|200 - 14902|Genome polyprotein|P26664.3|Hepatitis C virus subtype 1a|31646 - 200 - 9 - - - 1 - 13.0826 - 22 - 16.6015 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 7 - 0 - 7 - VITATYV - VVTSTWV - V+T+T+V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 25 - Query_25 - M_3100 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_3101 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_3102 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 28 - Query_28 - M_3103 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 29 - Query_29 - M_3104 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 30 - Query_30 - M_3105 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 31 - Query_31 - M_3106 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 32 - Query_32 - M_3107 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 33 - Query_33 - M_3108 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 34 - Query_34 - M_3109 - 9 - - - 1 - gnl|BL_ORD_ID|1844 - 180168|gag protein|ABO14878.1|Human immunodeficiency virus 1|11676 - 1844 - 9 - - - 1 - 13.853 - 24 - 5.36545 - 1 - 6 - 1 - 6 - 0 - 0 - 5 - 6 - 0 - 6 - SLFNAL - SLFNAV - SLFNA+ - - - - - 2 - gnl|BL_ORD_ID|2146 - 189275|gag protein|AAO84847.1|Human immunodeficiency virus 1|11676 - 2146 - 9 - - - 1 - 13.853 - 24 - 5.45887 - 1 - 6 - 1 - 6 - 0 - 0 - 5 - 6 - 0 - 6 - SLFNAL - SLFNAV - SLFNA+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 35 - Query_35 - M_3110 - 9 - - - 1 - gnl|BL_ORD_ID|1290 - 102376|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 - 1290 - 15 - - - 1 - 13.853 - 24 - 5.77703 - 1 - 7 - 8 - 14 - 0 - 0 - 4 - 7 - 0 - 7 - VAIMGST - LAVMGSS - +A+MGS+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 36 - Query_36 - M_3111 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 37 - Query_37 - M_3112 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 38 - Query_38 - M_3113 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 39 - Query_39 - M_3114 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 40 - Query_40 - M_3115 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 41 - Query_41 - M_3116 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 42 - Query_42 - M_3117 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 43 - Query_43 - M_3118 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 44 - Query_44 - M_3119 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 45 - Query_45 - M_3120 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 46 - Query_46 - M_3121 - 9 - - - 1 - gnl|BL_ORD_ID|1595 - 142231|Lipoprotein lpqH precursor|P0A5J0.1|Mycobacterium tuberculosis|1773 - 1595 - 24 - - - 1 - 10.3862 - 15 - 335.171 - 1 - 9 - 7 - 15 - 0 - 0 - 4 - 7 - 0 - 9 - IAIAIGAVL - VAVAGAAIL - +A+A A+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 47 - Query_47 - M_3122 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 48 - Query_48 - M_3123 - 9 - - - 1 - gnl|BL_ORD_ID|2035 - 184412|envelope protein|AGW23591.1|Dengue virus 3|11069 - 2035 - 10 - - - 1 - 13.4678 - 23 - 8.32231 - 1 - 8 - 2 - 9 - 0 - 0 - 4 - 6 - 0 - 8 - RGMQCAIC - KGMSYAMC - +GM A+C - - - - - 2 - gnl|BL_ORD_ID|1388 - 110282|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1388 - 25 - - - 1 - 13.0826 - 22 - 15.2941 - 3 - 9 - 5 - 11 - 0 - 0 - 3 - 5 - 0 - 7 - MQCAICK - LECVYCK - ++C CK - - - - - 3 - gnl|BL_ORD_ID|1671 - 148177|early protein|CAA52585.1|Human papillomavirus type 52|10618 - 1671 - 9 - - - 1 - 12.6974 - 21 - 24.707 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - MQCAICK - LQCVQCK - +QC CK - - - - - 4 - gnl|BL_ORD_ID|1661 - 147835|early protein|CAA52585.1|Human papillomavirus type 52|10618 - 1661 - 9 - - - 1 - 11.927 - 19 - 85.6478 - 3 - 9 - 3 - 9 - 0 - 0 - 3 - 6 - 0 - 7 - MQCAICK - IRCIICQ - ++C IC+ - - - - - 5 - gnl|BL_ORD_ID|1499 - 137656|E6 protein|ACT36477.1|Human papillomavirus type 58|10598 - 1499 - 9 - - - 1 - 11.927 - 19 - 87.0561 - 3 - 9 - 3 - 9 - 0 - 0 - 3 - 6 - 0 - 7 - MQCAICK - IRCIICQ - ++C IC+ - - - - - 6 - gnl|BL_ORD_ID|1390 - 110306|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1390 - 32 - - - 1 - 11.5418 - 18 - 120.694 - 3 - 9 - 18 - 24 - 0 - 0 - 3 - 5 - 0 - 7 - MQCAICK - LECVYCK - ++C CK - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 49 - Query_49 - M_3124 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132916_2_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132916_2_T.fasta deleted file mode 100755 index 797c1d82..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132916_2_T.fasta +++ /dev/null @@ -1,38 +0,0 @@ ->M_3125 -MLLKPSERR ->M_3126 -QLAWVPSPY ->M_3127 -QLAWVPSPY ->M_3128 -SSSEYMHHK ->M_3129 -HIASEEPAK ->M_3130 -STGFPHMLF ->M_3131 -YFSTGFPHM ->M_3132 -LVYMMERGK ->M_3133 -VATPGRLVY ->M_3134 -LLIPVAAVY ->M_3135 -SAPLMELLY ->M_3136 -LAMEDTGEY ->M_3137 -MYLHFSDTY ->M_3138 -SVSLMYLHF ->M_3139 -RLSISQWYR ->M_3140 -SQWYRVMVK ->M_3141 -STWIGNKLY ->M_3142 -YMYVCTPLL ->M_3143 -HQRIHTGEK diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132916_2_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132916_2_T_iedb.xml deleted file mode 100755 index fc0cf64a..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132916_2_T_iedb.xml +++ /dev/null @@ -1,511 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_3125 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_3125 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_3126 - 9 - - - 1 - gnl|BL_ORD_ID|1179 - 79628|E1 protein|BAA19893.1|Rubella virus|11041 - 1179 - 21 - - - 1 - 13.853 - 24 - 6.94735 - 3 - 7 - 11 - 15 - 0 - 0 - 4 - 5 - 0 - 5 - AWVPS - AWVPT - AWVP+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 3 - Query_3 - M_3127 - 9 - - - 1 - gnl|BL_ORD_ID|1179 - 79628|E1 protein|BAA19893.1|Rubella virus|11041 - 1179 - 21 - - - 1 - 13.853 - 24 - 6.94735 - 3 - 7 - 11 - 15 - 0 - 0 - 4 - 5 - 0 - 5 - AWVPS - AWVPT - AWVP+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 4 - Query_4 - M_3128 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_3129 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_3130 - 9 - - - 1 - gnl|BL_ORD_ID|23 - 1516|Nucleoprotein|P03418.1|Human respiratory syncytial virus A2|11259 - 23 - 14 - - - 1 - 12.6974 - 21 - 30.4718 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - TGFPHML - AGFYHIL - GF H+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 7 - Query_7 - M_3131 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_3132 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_3133 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_3134 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_3135 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_3136 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_3137 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_3138 - 9 - - - 1 - gnl|BL_ORD_ID|1887 - 180579|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1887 - 15 - - - 1 - 14.6234 - 26 - 2.26419 - 3 - 8 - 8 - 13 - 0 - 0 - 5 - 5 - 0 - 6 - SLMYLH - SLMYFH - SLMY H - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 15 - Query_15 - M_3139 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_3140 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_3141 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_3142 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_3143 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132940_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132940_1_T.fasta deleted file mode 100755 index 4ee0029b..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132940_1_T.fasta +++ /dev/null @@ -1,262 +0,0 @@ ->M_3144 -ALGLAQGTF ->M_3145 -GLAQGTFVF ->M_3146 -GTFVFIAHF ->M_3147 -KLHQVFHSI ->M_3148 -VTVPEKLSF ->M_3149 -HPCSQPVWL ->M_3150 -FPLVRSCQM ->M_3151 -MMCRDLPGF ->M_3152 -RVKATIVAM ->M_3153 -AQGEPLGAL ->M_3154 -FQVPDLHIL ->M_3155 -GMQARSVEM ->M_3156 -MLHLYPGPM ->M_3157 -SPYSEELPL ->M_3158 -YAQEGFLPH ->M_3159 -HLLFRVIPY ->M_3160 -RVIPYDQSF ->M_3161 -SIGSSATLY ->M_3162 -VQKQDNSTY ->M_3163 -AQVGFTLPL ->M_3164 -LPTPPPPPL ->M_3165 -YSCAGGRLF ->M_3166 -FQLDVASVI ->M_3167 -LDVASVIPF ->M_3168 -SVIPFDICY ->M_3169 -RLPNLHPSF ->M_3170 -LMVAVARSA ->M_3171 -TQHTSFQGY ->M_3172 -EQRCSLQAF ->M_3173 -KSKEREHSF ->M_3174 -NIDLAREAY ->M_3175 -IMSFLLSSL ->M_3176 -SEKEASLLY ->M_3177 -YLKEHASSL ->M_3178 -LVLSGSSSL ->M_3179 -FWRSSCSLF ->M_3180 -QLADQCLTM ->M_3181 -LPIKDGNTL ->M_3182 -LLVDRKDAM ->M_3183 -TPAIRHIML ->M_3184 -MQIHMGLAL ->M_3185 -ALARSSDAF ->M_3186 -HQGGATRVY ->M_3187 -FPNAGKSSF ->M_3188 -ILQEHIGAM ->M_3189 -SASAGLAAM ->M_3190 -HPCVPQALV ->M_3191 -ATIMETLTM ->M_3192 -PSDINVSSY ->M_3193 -VSSYNIYWY ->M_3194 -ESSEHEGTY ->M_3195 -QAWQPTASF ->M_3196 -FLNDRLANY ->M_3197 -LQIMAGRHG ->M_3198 -WLFPTGGSV ->M_3199 -LMYLQKLWM ->M_3200 -SIQSPFEGF ->M_3201 -LALLVSTAF ->M_3202 -GLIATQLLF ->M_3203 -LIATQLLFY ->M_3204 -LIATQLLFY ->M_3205 -AVRPTFGVL ->M_3206 -AMRFHFHSM ->M_3207 -MTSGLAMRF ->M_3208 -FPTTTFMCL ->M_3209 -ISLFPTTTF ->M_3210 -SLFPTTTFM ->M_3211 -SMRSSSISG ->M_3212 -VQHITGPVW ->M_3213 -ASDSQEALF ->M_3214 -FSDISEMRT ->M_3215 -TLAELLGPY ->M_3216 -LVNPWGEVL ->M_3217 -LPVVLQLKL ->M_3218 -AQADQVDPL ->M_3219 -FCDTAPVLK ->M_3220 -RLHSPMYFF ->M_3221 -TMCMYFRPL ->M_3222 -FLVFPFTSI ->M_3223 -LMADMYLLL ->M_3224 -HSHLLSHSY ->M_3225 -HSHLLSHSY ->M_3226 -TQYLVFCGM ->M_3227 -YLVFCGMGL ->M_3228 -LIFMYLCPA ->M_3229 -VAICHPLHY ->M_3230 -VLVQSLMVL ->M_3231 -QAQNQSITY ->M_3232 -TILTFCLSY ->M_3233 -CSIQDDLPF ->M_3234 -RMSRALWTL ->M_3235 -KQGWCYLVY ->M_3236 -YLVYVLLPL ->M_3237 -TINSAGDLF ->M_3238 -FPLDEVHAK ->M_3239 -LTLPPLATY ->M_3240 -PPAPPSLSL ->M_3241 -MQRASRHSQ ->M_3242 -QQSQSSGPG ->M_3243 -MLGDPSADY ->M_3244 -SADYINANY ->M_3245 -GVHKGRKPF ->M_3246 -ALACFARAF ->M_3247 -LTGDCCFDY ->M_3248 -YPKPQVSFL ->M_3249 -HPLGSLQIF ->M_3250 -AVGGMIASF ->M_3251 -PTEQSLTEY ->M_3252 -LLMGFSLTL ->M_3253 -TQGMQCSSL ->M_3254 -LLNLVVTSL ->M_3255 -YVKIYLLPY ->M_3256 -YVKIYLLPY ->M_3257 -ISVFSGSEM ->M_3258 -LLDEDISVF ->M_3259 -STVELVPIF ->M_3260 -KSADFEGLY ->M_3261 -CLFSLYTAY ->M_3262 -SLYTAYHVF ->M_3263 -SSHLHSDHY ->M_3264 -RQKHGEAPI ->M_3265 -RQDVGTYTF ->M_3266 -VERQDVGTY ->M_3267 -HSNSTSFIF ->M_3268 -NAHSNSTSF ->M_3269 -ATTESDQSF ->M_3270 -FPSETKVII ->M_3271 -HQVASSPGH ->M_3272 -SQGGPRGTF ->M_3273 -GGAPHFGHF ->M_3274 -GAIALIRRY diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132940_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132940_1_T_iedb.xml deleted file mode 100755 index ca2e9615..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132940_1_T_iedb.xml +++ /dev/null @@ -1,4011 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_3144 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_3144 - 9 - - - 1 - gnl|BL_ORD_ID|344 - 21638|protein F|ABV46152.2|Hepatitis C virus (isolate Japanese)|11116 - 344 - 9 - - - 1 - 12.3122 - 20 - 49.6079 - 3 - 9 - 3 - 9 - 0 - 0 - 4 - 5 - 0 - 7 - GLAQGTF - GLSPGTL - GL+ GT - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 2 - Query_2 - M_3145 - 9 - - - 1 - gnl|BL_ORD_ID|344 - 21638|protein F|ABV46152.2|Hepatitis C virus (isolate Japanese)|11116 - 344 - 9 - - - 1 - 12.6974 - 21 - 37.2378 - 1 - 7 - 3 - 9 - 0 - 0 - 4 - 5 - 0 - 7 - GLAQGTF - GLSPGTL - GL+ GT - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 3 - Query_3 - M_3146 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_3147 - 9 - - - 1 - gnl|BL_ORD_ID|2191 - 190568|polymerase|AAD16253.1|Hepatitis B virus|10407 - 2191 - 20 - - - 1 - 11.927 - 19 - 77.7846 - 1 - 9 - 5 - 13 - 0 - 0 - 5 - 5 - 0 - 9 - KLHQVFHSI - KLHLYSHPI - KLH H I - - - - - 2 - gnl|BL_ORD_ID|498 - 31898|P protein|P17100.1|Hepatitis B virus|10407 - 498 - 9 - - - 1 - 11.927 - 19 - 92.9112 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 5 - 0 - 9 - KLHQVFHSI - KLHLYSHPI - KLH H I - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 5 - Query_5 - M_3148 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_3149 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_3150 - 9 - - - 1 - gnl|BL_ORD_ID|586 - 36676|polyprotein|BAA09073.1|Hepatitis C virus subtype 1b|31647 - 586 - 9 - - - 1 - 13.0826 - 22 - 18.1053 - 3 - 9 - 1 - 7 - 0 - 0 - 3 - 6 - 0 - 7 - LVRSCQM - LIRACML - L+R+C + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 8 - Query_8 - M_3151 - 9 - - - 1 - gnl|BL_ORD_ID|799 - 53201|Fusion glycoprotein F0 precursor|P03420.1|Human respiratory syncytial virus A2|11259 - 799 - 9 - - - 1 - 13.0826 - 22 - 14.1983 - 4 - 9 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - RDLPGF - RELPRF - R+LP F - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 9 - Query_9 - M_3152 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_3153 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_3154 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_3155 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_3156 - 9 - - - 1 - gnl|BL_ORD_ID|654 - 38724|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 654 - 20 - - - 1 - 14.2382 - 25 - 2.55563 - 1 - 9 - 11 - 19 - 0 - 0 - 4 - 6 - 0 - 9 - MLHLYPGPM - LFQLYRGPL - + LY GP+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 14 - Query_14 - M_3157 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_3158 - 9 - - - 1 - gnl|BL_ORD_ID|1512 - 140541|hypothetical protein|NP_218210.1|Mycobacterium tuberculosis H37Rv|83332 - 1512 - 9 - - - 1 - 13.4678 - 23 - 11.1275 - 3 - 8 - 3 - 8 - 0 - 0 - 4 - 4 - 0 - 6 - QEGFLP - DEGLLP - EG LP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 16 - Query_16 - M_3159 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_3160 - 9 - - - 1 - gnl|BL_ORD_ID|1432 - 116123|nucleocapsid protein|ABP49342.1|Influenza A virus (A/California/10/1978(H1N1))|425557 - 1432 - 9 - - - 1 - 13.4678 - 23 - 7.72035 - 3 - 8 - 1 - 6 - 0 - 0 - 3 - 6 - 0 - 6 - IPYDQS - LPFDKS - +P+D+S - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 18 - Query_18 - M_3161 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_3162 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_3163 - 9 - - - 1 - gnl|BL_ORD_ID|1841 - 179898|cell surface protein (associated with virulence)|NP_302372.1|Mycobacterium leprae TN|272631 - 1841 - 9 - - - 1 - 13.853 - 24 - 5.18352 - 4 - 9 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - GFTLPL - AFTMPL - FT+PL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 21 - Query_21 - M_3164 - 9 - - - 1 - gnl|BL_ORD_ID|1068 - 70491|envelope glycoprotein|AAC28452.1|Human immunodeficiency virus 1|11676 - 1068 - 10 - - - 1 - 11.927 - 19 - 95.2093 - 1 - 8 - 1 - 8 - 0 - 0 - 5 - 6 - 0 - 8 - LPTPPPPP - VPTDPNPP - +PT P PP - - - - - 2 - gnl|BL_ORD_ID|1276 - 101821|vif protein|ACC96167.1|Human immunodeficiency virus 1|11676 - 1276 - 11 - - - 1 - 9.61583 - 13 - 1292.96 - 3 - 8 - 2 - 7 - 0 - 0 - 4 - 4 - 0 - 6 - TPPPPP - TKPPLP - T PP P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 22 - Query_22 - M_3165 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_3166 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_3167 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_3168 - 9 - - - 1 - gnl|BL_ORD_ID|1110 - 73059|kaposin|AAC57155.1|Human gammaherpesvirus 8|37296 - 1110 - 15 - - - 1 - 10.3862 - 15 - 500.815 - 1 - 8 - 6 - 13 - 0 - 0 - 3 - 4 - 0 - 8 - SVIPFDIC - GAIPPLVC - IP +C - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 26 - Query_26 - M_3169 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_3170 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 28 - Query_28 - M_3171 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 29 - Query_29 - M_3172 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 30 - Query_30 - M_3173 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 31 - Query_31 - M_3174 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 32 - Query_32 - M_3175 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 33 - Query_33 - M_3176 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 34 - Query_34 - M_3177 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 35 - Query_35 - M_3178 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 36 - Query_36 - M_3179 - 9 - - - 1 - gnl|BL_ORD_ID|834 - 54824|polyprotein precursor|BAA01583.1|Hepatitis C virus|11103 - 834 - 9 - - - 1 - 12.6974 - 21 - 25.1356 - 1 - 8 - 2 - 9 - 0 - 0 - 3 - 4 - 0 - 8 - FWRSSCSL - LWHYPCTL - W C+L - - - - - 2 - gnl|BL_ORD_ID|1149 - 75636|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 1149 - 10 - - - 1 - 11.927 - 19 - 66.6359 - 1 - 8 - 3 - 10 - 0 - 0 - 2 - 4 - 0 - 8 - FWRSSCSL - LWHYPCTI - W C++ - - - - - 3 - gnl|BL_ORD_ID|833 - 54821|E2 protein|AAM33354.1|Hepatitis C virus subtype 1a|31646 - 833 - 9 - - - 1 - 11.927 - 19 - 73.9069 - 1 - 8 - 2 - 9 - 0 - 0 - 2 - 4 - 0 - 8 - FWRSSCSL - LWHYPCTI - W C++ - - - - - 4 - gnl|BL_ORD_ID|835 - 54825|polyprotein|BAA03375.1|Hepatitis C virus|11103 - 835 - 9 - - - 1 - 11.927 - 19 - 110.987 - 1 - 8 - 2 - 9 - 0 - 0 - 2 - 4 - 0 - 8 - FWRSSCSL - LWHYPCTV - W C++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 37 - Query_37 - M_3180 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 38 - Query_38 - M_3181 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 39 - Query_39 - M_3182 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 40 - Query_40 - M_3183 - 9 - - - 1 - gnl|BL_ORD_ID|2103 - 186002|polyprotein|AGO67248.1|Dengue virus 2|11060 - 2103 - 9 - - - 1 - 13.853 - 24 - 5.74926 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - TPAIRH - TPMLRH - TP +RH - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 41 - Query_41 - M_3184 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 42 - Query_42 - M_3185 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 43 - Query_43 - M_3186 - 9 - - - 1 - gnl|BL_ORD_ID|385 - 23620|Genome polyprotein|SRC279960|Hepatitis C virus genotype 1|41856 - 385 - 10 - - - 1 - 15.0086 - 27 - 1.14868 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 5 - 0 - 9 - HQGGATRVY - HDGAGKRVY - H G RVY - - - - - 2 - gnl|BL_ORD_ID|386 - 23621|Genome polyprotein|P26664.3|Hepatitis C virus (isolate 1)|11104 - 386 - 11 - - - 1 - 15.0086 - 27 - 1.29055 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 5 - 0 - 9 - HQGGATRVY - HDGAGKRVY - H G RVY - - - - - 3 - gnl|BL_ORD_ID|384 - 23619|Genome polyprotein|P27958.3|Hepatitis C virus (isolate H)|11108 - 384 - 9 - - - 1 - 15.0086 - 27 - 1.33879 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 5 - 0 - 9 - HQGGATRVY - HDGAGKRVY - H G RVY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 44 - Query_44 - M_3187 - 9 - - - 1 - gnl|BL_ORD_ID|1874 - 180503|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1874 - 10 - - - 1 - 13.0826 - 22 - 18.1832 - 2 - 7 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - PNAGKS - PGAGKT - P AGK+ - - - - - 2 - gnl|BL_ORD_ID|389 - 23807|tax|AAG48731.1|Human T-lymphotropic virus 2|11909 - 389 - 23 - - - 1 - 12.6974 - 21 - 26.0558 - 1 - 7 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - FPNAGKS - FPGFGQS - FP G+S - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 45 - Query_45 - M_3188 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 46 - Query_46 - M_3189 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 47 - Query_47 - M_3190 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 48 - Query_48 - M_3191 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 49 - Query_49 - M_3192 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 50 - Query_50 - M_3193 - 9 - - - 1 - gnl|BL_ORD_ID|469 - 28484|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 469 - 9 - - - 1 - 11.5418 - 18 - 150.225 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 5 - 0 - 9 - VSSYNIYWY - ISEYRHYCY - +S Y Y Y - - - - - 2 - gnl|BL_ORD_ID|353 - 21960|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 - 353 - 10 - - - 1 - 10.001 - 14 - 976.635 - 2 - 9 - 3 - 10 - 0 - 0 - 4 - 5 - 0 - 8 - SSYNIYWY - SSFYSDWY - SS+ WY - - - - - 3 - gnl|BL_ORD_ID|782 - 52431|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 - 782 - 9 - - - 1 - 10.001 - 14 - 1142.49 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - SSYNIYWY - SSFYSDWY - SS+ WY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 51 - Query_51 - M_3194 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 52 - Query_52 - M_3195 - 9 - - - 1 - gnl|BL_ORD_ID|1179 - 79628|E1 protein|BAA19893.1|Rubella virus|11041 - 1179 - 21 - - - 1 - 14.2382 - 25 - 2.93831 - 2 - 7 - 11 - 16 - 0 - 0 - 5 - 5 - 0 - 6 - AWQPTA - AWVPTA - AW PTA - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 53 - Query_53 - M_3196 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 54 - Query_54 - M_3197 - 9 - - - 1 - gnl|BL_ORD_ID|1757 - 154196|tegument protein|CAB06735.1|Human alphaherpesvirus 2|10310 - 1757 - 16 - - - 1 - 12.6974 - 21 - 35.41 - 4 - 9 - 9 - 14 - 0 - 0 - 4 - 5 - 0 - 6 - MAGRHG - VAGSHG - +AG HG - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 55 - Query_55 - M_3198 - 9 - - - 1 - gnl|BL_ORD_ID|1950 - 181035|||| - 1950 - 44 - - - 1 - 15.3938 - 28 - 1.11573 - 2 - 9 - 12 - 19 - 0 - 0 - 5 - 6 - 0 - 8 - LFPTGGSV - LFPGGGQI - LFP GG + - - - - - 2 - gnl|BL_ORD_ID|1177 - 79506|E1 protein|BAA19893.1|Rubella virus|11041 - 1177 - 20 - - - 1 - 13.0826 - 22 - 15.1234 - 1 - 5 - 10 - 14 - 0 - 0 - 4 - 4 - 0 - 5 - WLFPT - WGFPT - W FPT - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 56 - Query_56 - M_3199 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 57 - Query_57 - M_3200 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 58 - Query_58 - M_3201 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 59 - Query_59 - M_3202 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 60 - Query_60 - M_3203 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 61 - Query_61 - M_3204 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 62 - Query_62 - M_3205 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 63 - Query_63 - M_3206 - 9 - - - 1 - gnl|BL_ORD_ID|470 - 28508|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 470 - 15 - - - 1 - 12.3122 - 20 - 46.8002 - 1 - 9 - 7 - 15 - 0 - 0 - 3 - 6 - 0 - 9 - AMRFHFHSM - SARLHRHAL - + R H H++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 64 - Query_64 - M_3207 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 65 - Query_65 - M_3208 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 66 - Query_66 - M_3209 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 67 - Query_67 - M_3210 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 68 - Query_68 - M_3211 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 69 - Query_69 - M_3212 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 70 - Query_70 - M_3213 - 9 - - - 1 - gnl|BL_ORD_ID|783 - 52496|polyprotein precursor|NP_041724.2|West Nile virus|11082 - 783 - 9 - - - 1 - 13.0826 - 22 - 21.5246 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 7 - 0 - 8 - SDSQEALF - TDNQLAVF - +D+Q A+F - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 71 - Query_71 - M_3214 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 72 - Query_72 - M_3215 - 9 - - - 1 - gnl|BL_ORD_ID|391 - 23883|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 - 391 - 15 - - - 1 - 11.927 - 19 - 68.3105 - 1 - 8 - 7 - 14 - 0 - 0 - 4 - 5 - 0 - 8 - TLAELLGP - TIASPKGP - T+A GP - - - - - 2 - gnl|BL_ORD_ID|1005 - 66106|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 - 1005 - 15 - - - 1 - 11.927 - 19 - 74.9817 - 1 - 8 - 3 - 10 - 0 - 0 - 4 - 5 - 0 - 8 - TLAELLGP - TIASPKGP - T+A GP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 73 - Query_73 - M_3216 - 9 - - - 1 - gnl|BL_ORD_ID|1607 - 143690|Genome polyprotein|P06441.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 1607 - 9 - - - 1 - 13.0826 - 22 - 16.035 - 2 - 7 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - VNPWGE - VDPWVE - V+PW E - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 74 - Query_74 - M_3217 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 75 - Query_75 - M_3218 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 76 - Query_76 - M_3219 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 77 - Query_77 - M_3220 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 78 - Query_78 - M_3221 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 79 - Query_79 - M_3222 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 80 - Query_80 - M_3223 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 81 - Query_81 - M_3224 - 9 - - - 1 - gnl|BL_ORD_ID|2191 - 190568|polymerase|AAD16253.1|Hepatitis B virus|10407 - 2191 - 20 - - - 1 - 11.1566 - 17 - 207.813 - 3 - 8 - 7 - 12 - 0 - 0 - 4 - 4 - 0 - 6 - HLLSHS - HLYSHP - HL SH - - - - - 2 - gnl|BL_ORD_ID|580 - 36402|P protein|Q05486.1|Hepatitis B virus|10407 - 580 - 15 - - - 1 - 10.7714 - 16 - 300.51 - 3 - 8 - 2 - 7 - 0 - 0 - 4 - 4 - 0 - 6 - HLLSHS - HLYSHP - HL SH - - - - - 3 - gnl|BL_ORD_ID|498 - 31898|P protein|P17100.1|Hepatitis B virus|10407 - 498 - 9 - - - 1 - 10.7714 - 16 - 354.707 - 3 - 8 - 3 - 8 - 0 - 0 - 4 - 4 - 0 - 6 - HLLSHS - HLYSHP - HL SH - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 82 - Query_82 - M_3225 - 9 - - - 1 - gnl|BL_ORD_ID|2191 - 190568|polymerase|AAD16253.1|Hepatitis B virus|10407 - 2191 - 20 - - - 1 - 11.1566 - 17 - 207.813 - 3 - 8 - 7 - 12 - 0 - 0 - 4 - 4 - 0 - 6 - HLLSHS - HLYSHP - HL SH - - - - - 2 - gnl|BL_ORD_ID|580 - 36402|P protein|Q05486.1|Hepatitis B virus|10407 - 580 - 15 - - - 1 - 10.7714 - 16 - 300.51 - 3 - 8 - 2 - 7 - 0 - 0 - 4 - 4 - 0 - 6 - HLLSHS - HLYSHP - HL SH - - - - - 3 - gnl|BL_ORD_ID|498 - 31898|P protein|P17100.1|Hepatitis B virus|10407 - 498 - 9 - - - 1 - 10.7714 - 16 - 354.707 - 3 - 8 - 3 - 8 - 0 - 0 - 4 - 4 - 0 - 6 - HLLSHS - HLYSHP - HL SH - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 83 - Query_83 - M_3226 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 84 - Query_84 - M_3227 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 85 - Query_85 - M_3228 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 86 - Query_86 - M_3229 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 87 - Query_87 - M_3230 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 88 - Query_88 - M_3231 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 89 - Query_89 - M_3232 - 9 - - - 1 - gnl|BL_ORD_ID|1705 - 150224|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1705 - 10 - - - 1 - 11.927 - 19 - 86.442 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 6 - 0 - 9 - TILTFCLSY - TIMAAILAY - TI+ L+Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 90 - Query_90 - M_3233 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 91 - Query_91 - M_3234 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 92 - Query_92 - M_3235 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 93 - Query_93 - M_3236 - 9 - - - 1 - gnl|BL_ORD_ID|1404 - 110744|E5 protein|AAD24036.1|Human papillomavirus type 16|333760 - 1404 - 9 - - - 1 - 13.853 - 24 - 5.65074 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 8 - 0 - 9 - YLVYVLLPL - YIIFVYIPL - Y+++V +PL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 94 - Query_94 - M_3237 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 95 - Query_95 - M_3238 - 9 - - - 1 - gnl|BL_ORD_ID|1139 - 75356|EBNA3A nuclear protein|Q8AZJ8|Human gammaherpesvirus 4|10376 - 1139 - 9 - - - 1 - 13.853 - 24 - 5.55396 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 5 - 0 - 8 - FPLDEVHA - YPLHEQHG - +PL E H - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 96 - Query_96 - M_3239 - 9 - - - 1 - gnl|BL_ORD_ID|2049 - 184643|polyprotein|AGW24534.1|Dengue virus 2|11060 - 2049 - 10 - - - 1 - 13.4678 - 23 - 8.32231 - 1 - 7 - 1 - 7 - 0 - 0 - 5 - 6 - 0 - 7 - LTLPPLA - LTIPPTA - LT+PP A - - - - - 2 - gnl|BL_ORD_ID|1560 - 141276|tegument protein VP13/14|NP_044649.1|Human alphaherpesvirus 1|10298 - 1560 - 9 - - - 1 - 13.0826 - 22 - 14.4474 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 5 - 0 - 9 - LTLPPLATY - FTAPEVGTY - T P + TY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 97 - Query_97 - M_3240 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 98 - Query_98 - M_3241 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 99 - Query_99 - M_3242 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 100 - Query_100 - M_3243 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 101 - Query_101 - M_3244 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 102 - Query_102 - M_3245 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 103 - Query_103 - M_3246 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 104 - Query_104 - M_3247 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 105 - Query_105 - M_3248 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 106 - Query_106 - M_3249 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 107 - Query_107 - M_3250 - 9 - - - 1 - gnl|BL_ORD_ID|1248 - 98085|trans-sialidase, putative|EAN82636.1|Trypanosoma cruzi|5693 - 1248 - 10 - - - 1 - 12.3122 - 20 - 40.5114 - 4 - 9 - 1 - 6 - 0 - 0 - 4 - 6 - 0 - 6 - GMIASF - GVIAAF - G+IA+F - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 108 - Query_108 - M_3251 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 109 - Query_109 - M_3252 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 110 - Query_110 - M_3253 - 9 - - - 1 - gnl|BL_ORD_ID|1811 - 170063|polyprotein|ABU97067.1|Hepatitis C virus subtype 1b|31647 - 1811 - 9 - - - 1 - 12.3122 - 20 - 44.1001 - 1 - 7 - 2 - 8 - 0 - 0 - 3 - 6 - 0 - 7 - TQGMQCS - TRGERCN - T+G +C+ - - - - - 2 - gnl|BL_ORD_ID|714 - 43937|polyprotein|AAF01178.1|Hepatitis C virus subtype 2a|31649 - 714 - 10 - - - 1 - 12.3122 - 20 - 51.1794 - 1 - 7 - 3 - 9 - 0 - 0 - 3 - 6 - 0 - 7 - TQGMQCS - TRGDRCN - T+G +C+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 111 - Query_111 - M_3254 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 112 - Query_112 - M_3255 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 113 - Query_113 - M_3256 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 114 - Query_114 - M_3257 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 115 - Query_115 - M_3258 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 116 - Query_116 - M_3259 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 117 - Query_117 - M_3260 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 118 - Query_118 - M_3261 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 119 - Query_119 - M_3262 - 9 - - - 1 - gnl|BL_ORD_ID|526 - 32250|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 - 526 - 9 - - - 1 - 12.6974 - 21 - 33.058 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 5 - 0 - 8 - SLYTAYHV - KLYCSYEV - LY +Y V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 120 - Query_120 - M_3263 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 121 - Query_121 - M_3264 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 122 - Query_122 - M_3265 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 123 - Query_123 - M_3266 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 124 - Query_124 - M_3267 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 125 - Query_125 - M_3268 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 126 - Query_126 - M_3269 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 127 - Query_127 - M_3270 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 128 - Query_128 - M_3271 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 129 - Query_129 - M_3272 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 130 - Query_130 - M_3273 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 131 - Query_131 - M_3274 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_133761_2_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_133761_2_T.fasta deleted file mode 100755 index ef93e997..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_133761_2_T.fasta +++ /dev/null @@ -1,86 +0,0 @@ ->M_3275 -DTTRYVTSK ->M_3276 -EPSESDTTR ->M_3277 -PSESDTTRY ->M_3278 -TRYVTSKIL ->M_3279 -TTRYVTSKI ->M_3280 -TSCSCQSSR ->M_3281 -TGDSEAAPV ->M_3282 -LSMEETLLL ->M_3283 -WWNPALWKR ->M_3284 -LFQDNSSQL ->M_3285 -LTPPQAQEL ->M_3286 -LTPQQAQEL ->M_3287 -QAQALGIPL ->M_3288 -ASRPDRLSL ->M_3289 -EAQGQEASR ->M_3290 -WVEPQNPVL ->M_3291 -HLPHLTHTL ->M_3292 -HTLATSCRR ->M_3293 -ITSFDNLFR ->M_3294 -SHFHKTHEV ->M_3295 -YKLVVVGAV ->M_3296 -FHRRLSSSL ->M_3297 -FHRRLSSSL ->M_3298 -FSRRSFHRR ->M_3299 -RSDVWNLGI ->M_3300 -VYILILPSF ->M_3301 -STTIPILTL ->M_3302 -TIPILTLSL ->M_3303 -LSHISHLEL ->M_3304 -SHLELVESL ->M_3305 -SAEVRIEPM ->M_3306 -QSHLLIHQR ->M_3307 -QVITLRKSL ->M_3308 -TKKQVITLR ->M_3309 -MFDASKANF ->M_3310 -FLDWLRTMT ->M_3311 -VDWFLDWLR ->M_3312 -WFLDWLRTM ->M_3313 -WLRTMTNVL ->M_3314 -KFLQEEPQL ->M_3315 -DVFRFSPYR ->M_3316 -RFSPYRGLL ->M_3317 -DSTRPPGTR diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_133761_2_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_133761_2_T_iedb.xml deleted file mode 100755 index 6e8c146f..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_133761_2_T_iedb.xml +++ /dev/null @@ -1,1517 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_3275 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_3275 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_3276 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_3277 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_3278 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_3279 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_3280 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_3281 - 9 - - - 1 - gnl|BL_ORD_ID|1759 - 154346|RL2|CAB06760.1|Human alphaherpesvirus 2|10310 - 1759 - 15 - - - 1 - 13.0826 - 22 - 18.437 - 1 - 8 - 5 - 12 - 0 - 0 - 4 - 5 - 0 - 8 - TGDSEAAP - TGNPRTAP - TG+ AP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 8 - Query_8 - M_3282 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_3283 - 9 - - - 1 - gnl|BL_ORD_ID|549 - 33681|||| - 549 - 10 - - - 1 - 15.0086 - 27 - 0.933082 - 3 - 9 - 4 - 10 - 0 - 0 - 4 - 6 - 0 - 7 - NPALWKR - GPAIYKR - PA++KR - - - - - 2 - gnl|BL_ORD_ID|1678 - 149027|NS5 protein|BAA00702.1|Hepatitis C virus (isolate H77)|63746 - 1678 - 18 - - - 1 - 13.4678 - 23 - 8.48241 - 4 - 9 - 2 - 7 - 0 - 0 - 4 - 4 - 0 - 6 - PALWKR - PTLWAR - P LW R - - - - - 3 - gnl|BL_ORD_ID|1615 - 144207|polyprotein|CAB41951.1|Hepatitis C virus|11103 - 1615 - 10 - - - 1 - 13.0826 - 22 - 14.7743 - 4 - 9 - 2 - 7 - 0 - 0 - 4 - 4 - 0 - 6 - PALWKR - PTLWAR - P LW R - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 10 - Query_10 - M_3284 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_3285 - 9 - - - 1 - gnl|BL_ORD_ID|1060 - 69799|envelope glycoprotein|BAE96221.1|Human immunodeficiency virus 1|11676 - 1060 - 10 - - - 1 - 13.0826 - 22 - 16.6782 - 1 - 9 - 2 - 10 - 0 - 0 - 5 - 6 - 0 - 9 - LTPPQAQEL - LTDPNPQEV - LT P QE+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 12 - Query_12 - M_3286 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_3287 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_3288 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_3289 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_3290 - 9 - - - 1 - gnl|BL_ORD_ID|891 - 58740|Major surface antigen precursor|P03142.4|Hepatitis B virus|10407 - 891 - 10 - - - 1 - 10.7714 - 16 - 368.054 - 2 - 9 - 3 - 10 - 0 - 0 - 4 - 5 - 0 - 8 - VEPQNPVL - VSPFIPLL - V P P+L - - - - - 2 - gnl|BL_ORD_ID|478 - 29455|Major surface antigen precursor|P03141.3|Hepatitis B virus subtype adw2|10408 - 478 - 9 - - - 1 - 10.7714 - 16 - 393.541 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - VEPQNPVL - VSPFIPLL - V P P+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 17 - Query_17 - M_3291 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_3292 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_3293 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_3294 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_3295 - 9 - - - 1 - gnl|BL_ORD_ID|524 - 32238|polyprotein [Hepatitis C virus subtype 1a]|ABV46251.2|Hepatitis C virus (isolate H77)|63746 - 524 - 10 - - - 1 - 12.6974 - 21 - 30.9217 - 2 - 7 - 1 - 6 - 0 - 0 - 5 - 6 - 0 - 6 - KLVVVG - KLVVLG - KLVV+G - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 22 - Query_22 - M_3296 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_3297 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_3298 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_3299 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_3300 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_3301 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 28 - Query_28 - M_3302 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 29 - Query_29 - M_3303 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 30 - Query_30 - M_3304 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 31 - Query_31 - M_3305 - 9 - - - 1 - gnl|BL_ORD_ID|1075 - 71266|Circumsporozoite protein precursor|P02893.1|Plasmodium falciparum|5833 - 1075 - 20 - - - 1 - 13.853 - 24 - 4.4203 - 3 - 8 - 8 - 13 - 0 - 0 - 4 - 6 - 0 - 6 - EVRIEP - QVRIKP - +VRI+P - - - - - 2 - gnl|BL_ORD_ID|304 - 20415|circumsporozoite protein|AAN87606.1|Plasmodium falciparum|5833 - 304 - 20 - - - 1 - 13.853 - 24 - 7.45549 - 3 - 8 - 3 - 8 - 0 - 0 - 4 - 6 - 0 - 6 - EVRIEP - QVRIKP - +VRI+P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 32 - Query_32 - M_3306 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 33 - Query_33 - M_3307 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 34 - Query_34 - M_3308 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 35 - Query_35 - M_3309 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 36 - Query_36 - M_3310 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 37 - Query_37 - M_3311 - 9 - - - 1 - gnl|BL_ORD_ID|664 - 39591|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 - 664 - 20 - - - 1 - 12.3122 - 20 - 56.0891 - 1 - 9 - 9 - 17 - 0 - 0 - 4 - 6 - 0 - 9 - VDWFLDWLR - ISWCLWWLQ - + W L WL+ - - - - - 2 - gnl|BL_ORD_ID|1120 - 74387|Genome polyprotein|P26664.3|Hepatitis C virus (isolate 1)|11104 - 1120 - 9 - - - 1 - 11.5418 - 18 - 138.797 - 1 - 8 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - VDWFLDWL - ISWCLWWL - + W L WL - - - - - 3 - gnl|BL_ORD_ID|1697 - 149105|E2 protein|NP_751921.1|Hepatitis C virus (isolate H77)|63746 - 1697 - 9 - - - 1 - 10.7714 - 16 - 365.422 - 1 - 7 - 3 - 9 - 0 - 0 - 2 - 3 - 0 - 7 - VDWFLDW - ASWAIKW - W + W - - - - - 4 - gnl|BL_ORD_ID|1119 - 74386|HCV-1|AAA45676.1|Hepatitis C virus|11103 - 1119 - 8 - - - 1 - 10.3862 - 15 - 795.381 - 1 - 7 - 2 - 8 - 0 - 0 - 3 - 4 - 0 - 7 - VDWFLDW - ISWCLWW - + W L W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 38 - Query_38 - M_3312 - 9 - - - 1 - gnl|BL_ORD_ID|664 - 39591|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 - 664 - 20 - - - 1 - 10.3862 - 15 - 413.002 - 1 - 7 - 11 - 17 - 0 - 0 - 4 - 5 - 0 - 7 - WFLDWLR - WCLWWLQ - W L WL+ - - - - - 2 - gnl|BL_ORD_ID|1120 - 74387|Genome polyprotein|P26664.3|Hepatitis C virus (isolate 1)|11104 - 1120 - 9 - - - 1 - 10.001 - 14 - 968.836 - 1 - 6 - 4 - 9 - 0 - 0 - 4 - 4 - 0 - 6 - WFLDWL - WCLWWL - W L WL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 39 - Query_39 - M_3313 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 40 - Query_40 - M_3314 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 41 - Query_41 - M_3315 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 42 - Query_42 - M_3316 - 9 - - - 1 - gnl|BL_ORD_ID|421 - 25388|matrix protein|ABP96803.1|Human metapneumovirus|162145 - 421 - 10 - - - 1 - 14.6234 - 26 - 1.59035 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 6 - 0 - 8 - FSPYRGLL - IAPYAGLI - +PY GL+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 43 - Query_43 - M_3317 - 9 - - - 1 - gnl|BL_ORD_ID|1494 - 136890|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1494 - 9 - - - 1 - 13.0826 - 22 - 13.4763 - 5 - 9 - 2 - 6 - 0 - 0 - 4 - 5 - 0 - 5 - PPGTR - PPGSR - PPG+R - - - - - 2 - gnl|BL_ORD_ID|1106 - 72928|Genome polyprotein|P26662.3|Hepatitis C virus (isolate Japanese)|11116 - 1106 - 10 - - - 1 - 13.0826 - 22 - 15.8345 - 5 - 9 - 4 - 8 - 0 - 0 - 4 - 4 - 0 - 5 - PPGTR - PPGAR - PPG R - - - - - 3 - gnl|BL_ORD_ID|1599 - 142245|polyprotein|ACJ37204.1|Hepatitis C virus subtype 1a|31646 - 1599 - 9 - - - 1 - 13.0826 - 22 - 18.1053 - 2 - 7 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - STRPPG - NTRPPA - +TRPP - - - - - 4 - gnl|BL_ORD_ID|1601 - 142247|envelope protein 2|ACY64760.1|Hepatitis C virus subtype 1a|31646 - 1601 - 9 - - - 1 - 13.0826 - 22 - 19.071 - 2 - 6 - 1 - 5 - 0 - 0 - 4 - 5 - 0 - 5 - STRPP - NTRPP - +TRPP - - - - - 5 - gnl|BL_ORD_ID|1602 - 142248|polyprotein|BAB18806.1|Hepatitis C virus subtype 1a|31646 - 1602 - 9 - - - 1 - 13.0826 - 22 - 19.404 - 2 - 6 - 1 - 5 - 0 - 0 - 4 - 5 - 0 - 5 - STRPP - NTRPP - +TRPP - - - - - 6 - gnl|BL_ORD_ID|1603 - 142249|polyprotein|AAY82036.1|Hepatitis C virus subtype 1a|31646 - 1603 - 9 - - - 1 - 13.0826 - 22 - 23.0624 - 2 - 6 - 1 - 5 - 0 - 0 - 4 - 5 - 0 - 5 - STRPP - NTRPP - +TRPP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_133954_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_133954_1_T.fasta deleted file mode 100755 index 43cd5767..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_133954_1_T.fasta +++ /dev/null @@ -1,336 +0,0 @@ ->M_3318 -YLGVPVFYA ->M_3319 -AIHIVAEKK ->M_3320 -TQFELQRNK ->M_3321 -VRGTDWHLK ->M_3322 -GFHPDPEAL ->M_3323 -HIRTDTYVK ->M_3324 -SRWQVHGIV ->M_3325 -VPACSRAHV ->M_3326 -VPACSYAHV ->M_3327 -MLFFRTRYI ->M_3328 -TRYICTTVF ->M_3329 -YICTTVFYT ->M_3330 -AALVPTQAM ->M_3331 -MPGSPRDPV ->M_3332 -RRGSGHSEY ->M_3333 -RICGHIFCY ->M_3334 -GIAPLNQWV ->M_3335 -KIIATCFAV ->M_3336 -KMNEPKCLK ->M_3337 -SFVPWNSYV ->M_3338 -VPWNSYVRL ->M_3339 -YQLKLFACM ->M_3340 -YQLKLFACM ->M_3341 -RGRGGSVSI ->M_3342 -IPHTAILVT ->M_3343 -SIPHTAILV ->M_3344 -GLSDLELRL ->M_3345 -VLLRCPNKL ->M_3346 -TRLAFGLFA ->M_3347 -ILIACRLNK ->M_3348 -LIACRLNKK ->M_3349 -RLNKKKGAY ->M_3350 -TLAHEASPL ->M_3351 -SAWWSFGSL ->M_3352 -NPEAMCSDL ->M_3353 -AMHPLFRKL ->M_3354 -CRAMHPLFR ->M_3355 -GPCRAMHPL ->M_3356 -RAMHPLFRK ->M_3357 -GYIHYVFYL ->M_3358 -GYIHYVFYL ->M_3359 -KGYIHYVFY ->M_3360 -YLGNGPNVI ->M_3361 -SLSNKEVKK ->M_3362 -GPRAINNFF ->M_3363 -FRFSSQEAA ->M_3364 -LLPPQDPHL ->M_3365 -PPQDPHLPL ->M_3366 -HVDPGTIGV ->M_3367 -GLMGAVNVA ->M_3368 -LMGAVNVAK ->M_3369 -PRMAIPWPR ->M_3370 -WPRDVRKLV ->M_3371 -KYYEALPEL ->M_3372 -HYYHNVHAV ->M_3373 -MVEHYYHNV ->M_3374 -YHNVHAVVF ->M_3375 -YYHNVHAVV ->M_3376 -ARVWKFGPK ->M_3377 -RVWKFGPKL ->M_3378 -RVWKFGPKL ->M_3379 -VLDKARVWK ->M_3380 -CYEEYRGRL ->M_3381 -GRYEEYRGH ->M_3382 -APRGACYRA ->M_3383 -YRADHDLGR ->M_3384 -SYVCVVRNY ->M_3385 -ARPFFFFLL ->M_3386 -FFFFLLDKV ->M_3387 -FFFLLDKVL ->M_3388 -FLLDKVLAS ->M_3389 -HARPFFFFL ->M_3390 -APSWRGLAE ->M_3391 -LRLALMKKK ->M_3392 -WLRLALMKK ->M_3393 -VLIQQLEKV ->M_3394 -YPGQVNRTA ->M_3395 -MADVAMYGV ->M_3396 -GLYYAEFGA ->M_3397 -SVLAGLYYA ->M_3398 -TMWRREESL ->M_3399 -CLWQLKAPV ->M_3400 -RPRKAWAWC ->M_3401 -QRLKREEEK ->M_3402 -VYHMSQSPL ->M_3403 -FTMLLSLLA ->M_3404 -GLAGFTMLL ->M_3405 -MLLSLLAFA ->M_3406 -KVHQLAITV ->M_3407 -LPKSSEKAI ->M_3408 -STQEPTAYV ->M_3409 -ARMRKHIKR ->M_3410 -GPARMRKHI ->M_3411 -RMRKHIKRL ->M_3412 -HVGKASSSM ->M_3413 -QQMEAHVGK ->M_3414 -VILLPQPPK ->M_3415 -YLGVPVFYA ->M_3416 -AIHIVAEKK ->M_3417 -IVGHTGSGK ->M_3418 -LPAPPGAPP ->M_3419 -VRGTDWHLK ->M_3420 -RRHHSPSQR ->M_3421 -WLQQENHEL ->M_3422 -SLQPIHHDL ->M_3423 -VPACSRAHV ->M_3424 -VPACSYAHV ->M_3425 -LLLSPPVEV ->M_3426 -LLSPPVEVK ->M_3427 -RPEPPETGV ->M_3428 -RRGSGHSEY ->M_3429 -GLLQRPVHL ->M_3430 -HLALGRLSR ->M_3431 -KIIATCFAV ->M_3432 -SFVPWNSYV ->M_3433 -VPWNSYVRL ->M_3434 -YQLKLFACM ->M_3435 -YQLKLFACM ->M_3436 -IPHTAILVT ->M_3437 -SIPHTAILV ->M_3438 -SVSSCCQPV ->M_3439 -WLLEWTEAA ->M_3440 -GLSDLELRL ->M_3441 -VLLRCPNKL ->M_3442 -TLAHEASPL ->M_3443 -ILPATILVL ->M_3444 -TILPATILV ->M_3445 -SAWWSFGSL ->M_3446 -NPEAMCSDL ->M_3447 -AMHPLFRKL ->M_3448 -CRAMHPLFR ->M_3449 -GPCRAMHPL ->M_3450 -RAMHPLFRK ->M_3451 -SLSNKEVKK ->M_3452 -GPRAINNFF ->M_3453 -LLPPQDPHL ->M_3454 -PPQDPHLPL ->M_3455 -GLMGAVNVA ->M_3456 -LMGAVNVAK ->M_3457 -KLPEVQLPK ->M_3458 -ARVWKFGPK ->M_3459 -RVWKFGPKL ->M_3460 -RVWKFGPKL ->M_3461 -VLDKARVWK ->M_3462 -APRGACYRA ->M_3463 -YRADHDLGR ->M_3464 -SYVCVVRNY ->M_3465 -APSWRGLAE ->M_3466 -VLIQQLEKV ->M_3467 -GLYYAEFGA ->M_3468 -SVLAGLYYA ->M_3469 -KPVNKILQI ->M_3470 -CLWQLKAPV ->M_3471 -RPRKAWAWC ->M_3472 -SLDTVAQAV ->M_3473 -QRLKREEEK ->M_3474 -RREQQLRRK ->M_3475 -VYHMSQSPL ->M_3476 -FTMLLSLLA ->M_3477 -GLAGFTMLL ->M_3478 -MLLSLLAFA ->M_3479 -KVHQLAITV ->M_3480 -KIMHGPFMK ->M_3481 -RPRWNTHGH ->M_3482 -ARMRKHIKR ->M_3483 -GPARMRKHI ->M_3484 -RMRKHIKRL ->M_3485 -VILLPQPPK diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_133954_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_133954_1_T_iedb.xml deleted file mode 100755 index 23b6434e..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_133954_1_T_iedb.xml +++ /dev/null @@ -1,6405 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_3318 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_3318 - 9 - - - 1 - gnl|BL_ORD_ID|1 - 118|envelope glycoprotein|ABS76372.1|Human immunodeficiency virus 1|11676 - 1 - 20 - - - 1 - 14.6234 - 26 - 1.57628 - 1 - 7 - 10 - 16 - 0 - 0 - 5 - 6 - 0 - 7 - YLGVPVF - YYGVPVW - Y GVPV+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 2 - Query_2 - M_3319 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_3320 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_3321 - 9 - - - 1 - gnl|BL_ORD_ID|1008 - 66798|glycoprotein gp35/37|AAC59622.1|Human gammaherpesvirus 8|37296 - 1008 - 15 - - - 1 - 12.6974 - 21 - 22.1438 - 1 - 7 - 2 - 8 - 0 - 0 - 4 - 4 - 0 - 7 - VRGTDWH - TRGRDAH - RG D H - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 5 - Query_5 - M_3322 - 9 - - - 1 - gnl|BL_ORD_ID|2185 - 190466|large surface antigen|CAL29876.1|Hepatitis B virus|10407 - 2185 - 15 - - - 1 - 12.6974 - 21 - 30.2729 - 1 - 5 - 2 - 6 - 0 - 0 - 4 - 4 - 0 - 5 - GFHPD - GFFPD - GF PD - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 6 - Query_6 - M_3323 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_3324 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_3325 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_3326 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_3327 - 9 - - - 1 - gnl|BL_ORD_ID|1781 - 156550|E3 ubiquitin-protein ligase Mdm2|Q00987.1|Homo sapiens|9606 - 1781 - 9 - - - 1 - 12.6974 - 21 - 30.3534 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 7 - 0 - 9 - MLFFRTRYI - VLFYLGQYI - +LF+ +YI - - - - - 2 - gnl|BL_ORD_ID|608 - 37254|||| - 608 - 9 - - - 1 - 12.3122 - 20 - 62.655 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 6 - 0 - 9 - MLFFRTRYI - LLFGYPRYV - +LF RY+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 11 - Query_11 - M_3328 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_3329 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_3330 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_3331 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_3332 - 9 - - - 1 - gnl|BL_ORD_ID|1871 - 180488|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1871 - 10 - - - 1 - 13.0826 - 22 - 16.3922 - 3 - 8 - 1 - 6 - 0 - 0 - 4 - 4 - 0 - 6 - GSGHSE - GPGHEE - G GH E - - - - - 2 - gnl|BL_ORD_ID|657 - 38974|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 657 - 11 - - - 1 - 12.3122 - 20 - 38.8163 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 7 - 0 - 9 - RRGSGHSEY - QRGPQYSEH - +RG +SE+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 16 - Query_16 - M_3333 - 9 - - - 1 - gnl|BL_ORD_ID|1186 - 93431|pre-C/C protein|ABY54138.1|Hepatitis B virus|10407 - 1186 - 20 - - - 1 - 8.84543 - 11 - 2528.11 - 2 - 8 - 6 - 12 - 0 - 0 - 3 - 4 - 0 - 7 - ICGHIFC - LCLIISC - +C I C - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 17 - Query_17 - M_3334 - 9 - - - 1 - gnl|BL_ORD_ID|573 - 36062|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 573 - 20 - - - 1 - 13.0826 - 22 - 15.1234 - 2 - 8 - 13 - 19 - 0 - 0 - 3 - 4 - 0 - 7 - IAPLNQW - LTPLRDW - + PL W - - - - - 2 - gnl|BL_ORD_ID|996 - 65654|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 - 996 - 15 - - - 1 - 12.3122 - 20 - 41.8446 - 3 - 9 - 1 - 7 - 0 - 0 - 3 - 3 - 0 - 7 - APLNQWV - TPLRDWA - PL W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 18 - Query_18 - M_3335 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_3336 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_3337 - 9 - - - 1 - gnl|BL_ORD_ID|1610 - 143728|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 1610 - 9 - - - 1 - 14.2382 - 25 - 3.00197 - 3 - 9 - 1 - 7 - 0 - 0 - 4 - 6 - 0 - 7 - VPWNSYV - LPWYSYL - +PW SY+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 21 - Query_21 - M_3338 - 9 - - - 1 - gnl|BL_ORD_ID|1610 - 143728|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 1610 - 9 - - - 1 - 14.2382 - 25 - 3.05306 - 1 - 7 - 1 - 7 - 0 - 0 - 4 - 6 - 0 - 7 - VPWNSYV - LPWYSYL - +PW SY+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 22 - Query_22 - M_3339 - 9 - - - 1 - gnl|BL_ORD_ID|1149 - 75636|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 1149 - 10 - - - 1 - 11.5418 - 18 - 153.051 - 1 - 8 - 1 - 8 - 0 - 0 - 3 - 5 - 0 - 8 - YQLKLFAC - YRLWHYPC - Y+L + C - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 23 - Query_23 - M_3340 - 9 - - - 1 - gnl|BL_ORD_ID|1149 - 75636|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 1149 - 10 - - - 1 - 11.5418 - 18 - 153.051 - 1 - 8 - 1 - 8 - 0 - 0 - 3 - 5 - 0 - 8 - YQLKLFAC - YRLWHYPC - Y+L + C - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 24 - Query_24 - M_3341 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_3342 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_3343 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_3344 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 28 - Query_28 - M_3345 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 29 - Query_29 - M_3346 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 30 - Query_30 - M_3347 - 9 - - - 1 - gnl|BL_ORD_ID|1621 - 145860|Protein E6|P04019.1|Human papillomavirus type 11|10580 - 1621 - 9 - - - 1 - 11.1566 - 17 - 208.544 - 1 - 7 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - ILIACRL - VLIRCYL - +LI C L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 31 - Query_31 - M_3348 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 32 - Query_32 - M_3349 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 33 - Query_33 - M_3350 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 34 - Query_34 - M_3351 - 9 - - - 1 - gnl|BL_ORD_ID|1924 - 180726|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1924 - 15 - - - 1 - 15.0086 - 27 - 1.14188 - 4 - 9 - 10 - 15 - 0 - 0 - 5 - 5 - 0 - 6 - WSFGSL - WDFGSL - W FGSL - - - - - 2 - gnl|BL_ORD_ID|1095 - 72301|envelope protein|YP_001527880.1|West Nile virus NY-99|10000971 - 1095 - 18 - - - 1 - 13.4678 - 23 - 7.53558 - 4 - 9 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - WSFGSL - WDFGSV - W FGS+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 35 - Query_35 - M_3352 - 9 - - - 1 - gnl|BL_ORD_ID|1397 - 110401|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1397 - 25 - - - 1 - 14.2382 - 25 - 3.81797 - 1 - 6 - 20 - 25 - 0 - 0 - 4 - 5 - 0 - 6 - NPEAMC - NPYAVC - NP A+C - - - - - 2 - gnl|BL_ORD_ID|1400 - 110467|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1400 - 25 - - - 1 - 14.2382 - 25 - 3.88133 - 1 - 6 - 5 - 10 - 0 - 0 - 4 - 5 - 0 - 6 - NPEAMC - NPYAVC - NP A+C - - - - - 3 - gnl|BL_ORD_ID|1387 - 110227|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1387 - 33 - - - 1 - 14.2382 - 25 - 4.76191 - 1 - 6 - 12 - 17 - 0 - 0 - 4 - 5 - 0 - 6 - NPEAMC - NPYAVC - NP A+C - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 36 - Query_36 - M_3353 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 37 - Query_37 - M_3354 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 38 - Query_38 - M_3355 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 39 - Query_39 - M_3356 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 40 - Query_40 - M_3357 - 9 - - - 1 - gnl|BL_ORD_ID|691 - 42094|telomer length regulation protein TEL1|EDV12172.1|Saccharomyces cerevisiae|4932 - 691 - 9 - - - 1 - 13.0826 - 22 - 15.4875 - 1 - 6 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - GYIHYV - GYLQYV - GY+ YV - - - - - 2 - gnl|BL_ORD_ID|579 - 36358|ELAV-like protein 1|Q15717.2|Homo sapiens|9606 - 579 - 9 - - - 1 - 12.3122 - 20 - 53.0441 - 1 - 6 - 4 - 9 - 0 - 0 - 3 - 6 - 0 - 6 - GYIHYV - GFVNYV - G+++YV - - - - - 3 - gnl|BL_ORD_ID|578 - 36357|ELAV-like protein 4 (Paraneoplastic encephalomyelitis antigen HuD) (Hu-antigen D)|P26378.1|Homo sapiens|9606 - 578 - 9 - - - 1 - 11.927 - 19 - 109.216 - 1 - 6 - 4 - 9 - 0 - 0 - 2 - 6 - 0 - 6 - GYIHYV - GFVNYI - G+++Y+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 41 - Query_41 - M_3358 - 9 - - - 1 - gnl|BL_ORD_ID|691 - 42094|telomer length regulation protein TEL1|EDV12172.1|Saccharomyces cerevisiae|4932 - 691 - 9 - - - 1 - 13.0826 - 22 - 15.4875 - 1 - 6 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - GYIHYV - GYLQYV - GY+ YV - - - - - 2 - gnl|BL_ORD_ID|579 - 36358|ELAV-like protein 1|Q15717.2|Homo sapiens|9606 - 579 - 9 - - - 1 - 12.3122 - 20 - 53.0441 - 1 - 6 - 4 - 9 - 0 - 0 - 3 - 6 - 0 - 6 - GYIHYV - GFVNYV - G+++YV - - - - - 3 - gnl|BL_ORD_ID|578 - 36357|ELAV-like protein 4 (Paraneoplastic encephalomyelitis antigen HuD) (Hu-antigen D)|P26378.1|Homo sapiens|9606 - 578 - 9 - - - 1 - 11.927 - 19 - 109.216 - 1 - 6 - 4 - 9 - 0 - 0 - 2 - 6 - 0 - 6 - GYIHYV - GFVNYI - G+++Y+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 42 - Query_42 - M_3359 - 9 - - - 1 - gnl|BL_ORD_ID|691 - 42094|telomer length regulation protein TEL1|EDV12172.1|Saccharomyces cerevisiae|4932 - 691 - 9 - - - 1 - 13.0826 - 22 - 14.7007 - 2 - 7 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - GYIHYV - GYLQYV - GY+ YV - - - - - 2 - gnl|BL_ORD_ID|579 - 36358|ELAV-like protein 1|Q15717.2|Homo sapiens|9606 - 579 - 9 - - - 1 - 12.3122 - 20 - 51.2985 - 2 - 7 - 4 - 9 - 0 - 0 - 3 - 6 - 0 - 6 - GYIHYV - GFVNYV - G+++YV - - - - - 3 - gnl|BL_ORD_ID|389 - 23807|tax|AAG48731.1|Human T-lymphotropic virus 2|11909 - 389 - 23 - - - 1 - 11.927 - 19 - 72.4855 - 2 - 8 - 12 - 18 - 0 - 0 - 5 - 5 - 0 - 7 - GYIHYVF - GYPVYVF - GY YVF - - - - - 4 - gnl|BL_ORD_ID|578 - 36357|ELAV-like protein 4 (Paraneoplastic encephalomyelitis antigen HuD) (Hu-antigen D)|P26378.1|Homo sapiens|9606 - 578 - 9 - - - 1 - 11.927 - 19 - 104.062 - 2 - 7 - 4 - 9 - 0 - 0 - 2 - 6 - 0 - 6 - GYIHYV - GFVNYI - G+++Y+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 43 - Query_43 - M_3360 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 44 - Query_44 - M_3361 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 45 - Query_45 - M_3362 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 46 - Query_46 - M_3363 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 47 - Query_47 - M_3364 - 9 - - - 1 - gnl|BL_ORD_ID|374 - 23224|polyprotein|BAB18806.1|Hepatitis C virus|11103 - 374 - 15 - - - 1 - 13.853 - 24 - 6.75013 - 1 - 9 - 4 - 12 - 0 - 0 - 5 - 6 - 0 - 9 - LLPPQDPHL - LLPRRGPRL - LLP + P L - - - - - 2 - gnl|BL_ORD_ID|1950 - 181035|||| - 1950 - 44 - - - 1 - 13.4678 - 23 - 10.7201 - 1 - 9 - 25 - 33 - 0 - 0 - 5 - 6 - 0 - 9 - LLPPQDPHL - LLPRRGPRL - LLP + P L - - - - - 3 - gnl|BL_ORD_ID|1130 - 74798|polyprotein|BAA03375.1|Hepatitis C virus|11103 - 1130 - 10 - - - 1 - 13.0826 - 22 - 16.3922 - 1 - 9 - 2 - 10 - 0 - 0 - 5 - 6 - 0 - 9 - LLPPQDPHL - LLPRRGPRL - LLP + P L - - - - - 4 - gnl|BL_ORD_ID|630 - 37685|polyprotein|BAA03375.1|Hepatitis C virus|11103 - 630 - 9 - - - 1 - 13.0826 - 22 - 18.1053 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 6 - 0 - 9 - LLPPQDPHL - LLPRRGPRL - LLP + P L - - - - - 5 - gnl|BL_ORD_ID|1508 - 139406|polyprotein|ACT37184.1|Hepatitis C virus|11103 - 1508 - 10 - - - 1 - 10.7714 - 16 - 299.259 - 1 - 9 - 2 - 10 - 0 - 0 - 5 - 5 - 0 - 9 - LLPPQDPHL - LLPRPGPRL - LLP P L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 48 - Query_48 - M_3365 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 49 - Query_49 - M_3366 - 9 - - - 1 - gnl|BL_ORD_ID|2183 - 190443|core protein|BAF42671.1|Hepatitis B virus|10407 - 2183 - 9 - - - 1 - 10.7714 - 16 - 370.892 - 1 - 8 - 1 - 8 - 0 - 0 - 3 - 4 - 0 - 8 - HVDPGTIG - HISCLTFG - H+ T G - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 50 - Query_50 - M_3367 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 51 - Query_51 - M_3368 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 52 - Query_52 - M_3369 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 53 - Query_53 - M_3370 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 54 - Query_54 - M_3371 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 55 - Query_55 - M_3372 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 56 - Query_56 - M_3373 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 57 - Query_57 - M_3374 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 58 - Query_58 - M_3375 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 59 - Query_59 - M_3376 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 60 - Query_60 - M_3377 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 61 - Query_61 - M_3378 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 62 - Query_62 - M_3379 - 9 - - - 1 - gnl|BL_ORD_ID|1038 - 69435|Genome polyprotein|SRC279960|Hepatitis C virus (isolate H77)|63746 - 1038 - 9 - - - 1 - 13.4678 - 23 - 11.5219 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 5 - 0 - 8 - VLDKARVW - VLDSFKTW - VLD + W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 63 - Query_63 - M_3380 - 9 - - - 1 - gnl|BL_ORD_ID|376 - 23288|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 - 376 - 15 - - - 1 - 14.2382 - 25 - 3.37317 - 1 - 9 - 6 - 14 - 0 - 0 - 3 - 7 - 0 - 9 - CYEEYRGRL - VYQDWLGRM - Y+++ GR+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 64 - Query_64 - M_3381 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 65 - Query_65 - M_3382 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 66 - Query_66 - M_3383 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 67 - Query_67 - M_3384 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 68 - Query_68 - M_3385 - 9 - - - 1 - gnl|BL_ORD_ID|1672 - 148397|Dense granule protein 3|B6KEU8.2|Toxoplasma gondii|5811 - 1672 - 9 - - - 1 - 11.927 - 19 - 76.3762 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - PFFFFLL - PFVVFLV - PF FL+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 69 - Query_69 - M_3386 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 70 - Query_70 - M_3387 - 9 - - - 1 - gnl|BL_ORD_ID|228 - 16753|Pre-S/S protein|AAR99337.1|Hepatitis B virus|10407 - 228 - 9 - - - 1 - 13.0826 - 22 - 18.4218 - 3 - 9 - 1 - 7 - 0 - 0 - 5 - 6 - 0 - 7 - FLLDKVL - FLLTKIL - FLL K+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 71 - Query_71 - M_3388 - 9 - - - 1 - gnl|BL_ORD_ID|228 - 16753|Pre-S/S protein|AAR99337.1|Hepatitis B virus|10407 - 228 - 9 - - - 1 - 13.853 - 24 - 7.07804 - 1 - 8 - 1 - 8 - 0 - 0 - 5 - 6 - 0 - 8 - FLLDKVLA - FLLTKILT - FLL K+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 72 - Query_72 - M_3389 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 73 - Query_73 - M_3390 - 9 - - - 1 - gnl|BL_ORD_ID|350 - 21780|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 - 350 - 9 - - - 1 - 13.0826 - 22 - 17.4884 - 1 - 8 - 1 - 8 - 0 - 0 - 5 - 5 - 0 - 8 - APSWRGLA - GPSLIGLA - PS GLA - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 74 - Query_74 - M_3391 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 75 - Query_75 - M_3392 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 76 - Query_76 - M_3393 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 77 - Query_77 - M_3394 - 9 - - - 1 - gnl|BL_ORD_ID|899 - 59153|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 - 899 - 15 - - - 1 - 17.705 - 34 - 0.120504 - 2 - 9 - 7 - 14 - 0 - 0 - 5 - 7 - 0 - 8 - PGQVNRTA - PGEINRVA - PG++NR A - - - - - 2 - gnl|BL_ORD_ID|925 - 60059|Genome polyprotein|P27958.3|Hepatitis C virus genotype 1|41856 - 925 - 10 - - - 1 - 17.3198 - 33 - 0.174505 - 2 - 9 - 2 - 9 - 0 - 0 - 5 - 7 - 0 - 8 - PGQVNRTA - PGEINRVA - PG++NR A - - - - - 3 - gnl|BL_ORD_ID|1089 - 72038|Polyprotein|Q9IZA3|Hepatitis C virus subtype 2a|31649 - 1089 - 10 - - - 1 - 12.3122 - 20 - 64.4862 - 1 - 8 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - YPGQVNRT - YHGAGNKT - Y G N+T - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 78 - Query_78 - M_3395 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 79 - Query_79 - M_3396 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 80 - Query_80 - M_3397 - 9 - - - 1 - gnl|BL_ORD_ID|375 - 23270|polyprotein|AAB67036.1|Hepatitis C virus (isolate H77)|63746 - 375 - 15 - - - 1 - 14.6234 - 26 - 2.2254 - 3 - 8 - 3 - 8 - 0 - 0 - 5 - 6 - 0 - 6 - LAGLYY - LAGLFY - LAGL+Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 81 - Query_81 - M_3398 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 82 - Query_82 - M_3399 - 9 - - - 1 - gnl|BL_ORD_ID|1520 - 140600|glutamine synthetase GLNA1 (glutamine synthase) (GS-I)|NP_216736.1|Mycobacterium tuberculosis H37Rv|83332 - 1520 - 9 - - - 1 - 13.0826 - 22 - 18.1053 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 6 - 0 - 9 - CLWQLKAPV - SLWKDGAPL - LW+ AP+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 83 - Query_83 - M_3400 - 9 - - - 1 - gnl|BL_ORD_ID|1729 - 150534|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1729 - 9 - - - 1 - 12.6974 - 21 - 24.707 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 4 - 0 - 6 - RPRKAW - RPASAW - RP AW - - - - - 2 - gnl|BL_ORD_ID|928 - 60238|Gag polyprotein|P03347.3|Human immunodeficiency virus 1|11676 - 928 - 9 - - - 1 - 11.927 - 19 - 80.227 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 4 - 0 - 8 - PRKAWAWC - PRTLNAWV - PR AW - - - - - 3 - gnl|BL_ORD_ID|756 - 50292|gag protein|ACR27140.1|Human immunodeficiency virus 1|11676 - 756 - 11 - - - 1 - 11.927 - 19 - 106.287 - 2 - 8 - 5 - 11 - 0 - 0 - 4 - 4 - 0 - 7 - PRKAWAW - PRTLNAW - PR AW - - - - - 4 - gnl|BL_ORD_ID|472 - 28657|gag protein|CAB00235.1|Human immunodeficiency virus 1|11676 - 472 - 9 - - - 1 - 11.927 - 19 - 107.472 - 2 - 8 - 3 - 9 - 0 - 0 - 4 - 4 - 0 - 7 - PRKAWAW - PRTLNAW - PR AW - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 84 - Query_84 - M_3401 - 9 - - - 1 - gnl|BL_ORD_ID|2088 - 185491|polyprotein|AGO67248.1|Dengue virus 2|11060 - 2088 - 10 - - - 1 - 11.1566 - 17 - 205.223 - 4 - 9 - 1 - 6 - 0 - 0 - 4 - 6 - 0 - 6 - KREEEK - RREEEE - +REEE+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 85 - Query_85 - M_3402 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 86 - Query_86 - M_3403 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 87 - Query_87 - M_3404 - 9 - - - 1 - gnl|BL_ORD_ID|1944 - 180818|Membrane glycoprotein precursor|NP_739582.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1944 - 15 - - - 1 - 13.0826 - 22 - 12.5116 - 4 - 8 - 7 - 11 - 0 - 0 - 4 - 5 - 0 - 5 - GFTML - GFTMM - GFTM+ - - - - - 2 - gnl|BL_ORD_ID|1686 - 149052|E1 protein|NP_751920.1|Hepatitis C virus (isolate H77)|63746 - 1686 - 18 - - - 1 - 13.0826 - 22 - 15.2048 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 7 - 0 - 8 - GLAGFTML - GIAYFSMV - G+A F+M+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 88 - Query_88 - M_3405 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 89 - Query_89 - M_3406 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 90 - Query_90 - M_3407 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 91 - Query_91 - M_3408 - 9 - - - 1 - gnl|BL_ORD_ID|1486 - 135263|hemagglutinin|ACX31970.1|Influenza A virus (A/Bar-headed Goose/Qinghai/61/05(H5N1))|336238 - 1486 - 10 - - - 1 - 14.2382 - 25 - 2.71312 - 3 - 9 - 4 - 10 - 0 - 0 - 4 - 5 - 0 - 7 - QEPTAYV - QNPTTYI - Q PT Y+ - - - - - 2 - gnl|BL_ORD_ID|527 - 32268|hemagglutinin|AAK38298.1|Influenza A virus (A/Bar-headed Goose/Qinghai/61/05(H5N1))|336238 - 527 - 10 - - - 1 - 14.2382 - 25 - 2.71312 - 3 - 9 - 4 - 10 - 0 - 0 - 4 - 5 - 0 - 7 - QEPTAYV - QNPTTYI - Q PT Y+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 92 - Query_92 - M_3409 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 93 - Query_93 - M_3410 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 94 - Query_94 - M_3411 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 95 - Query_95 - M_3412 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 96 - Query_96 - M_3413 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 97 - Query_97 - M_3414 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 98 - Query_98 - M_3415 - 9 - - - 1 - gnl|BL_ORD_ID|1 - 118|envelope glycoprotein|ABS76372.1|Human immunodeficiency virus 1|11676 - 1 - 20 - - - 1 - 14.6234 - 26 - 1.57628 - 1 - 7 - 10 - 16 - 0 - 0 - 5 - 6 - 0 - 7 - YLGVPVF - YYGVPVW - Y GVPV+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 99 - Query_99 - M_3416 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 100 - Query_100 - M_3417 - 9 - - - 1 - gnl|BL_ORD_ID|1995 - 183598|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1995 - 10 - - - 1 - 13.853 - 24 - 5.02829 - 4 - 9 - 1 - 6 - 0 - 0 - 5 - 5 - 0 - 6 - HTGSGK - HPGSGK - H GSGK - - - - - 2 - gnl|BL_ORD_ID|386 - 23621|Genome polyprotein|P26664.3|Hepatitis C virus (isolate 1)|11104 - 386 - 11 - - - 1 - 13.0826 - 22 - 16.0488 - 4 - 9 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - HTGSGK - HDGAGK - H G+GK - - - - - 3 - gnl|BL_ORD_ID|385 - 23620|Genome polyprotein|SRC279960|Hepatitis C virus genotype 1|41856 - 385 - 10 - - - 1 - 13.0826 - 22 - 17.5659 - 4 - 9 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - HTGSGK - HDGAGK - H G+GK - - - - - 4 - gnl|BL_ORD_ID|384 - 23619|Genome polyprotein|P27958.3|Hepatitis C virus (isolate H)|11108 - 384 - 9 - - - 1 - 13.0826 - 22 - 20.4374 - 4 - 9 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - HTGSGK - HDGAGK - H G+GK - - - - - 5 - gnl|BL_ORD_ID|1874 - 180503|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1874 - 10 - - - 1 - 12.6974 - 21 - 23.1358 - 4 - 9 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - HTGSGK - HPGAGK - H G+GK - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 101 - Query_101 - M_3418 - 9 - - - 1 - gnl|BL_ORD_ID|1106 - 72928|Genome polyprotein|P26662.3|Hepatitis C virus (isolate Japanese)|11116 - 1106 - 10 - - - 1 - 14.6234 - 26 - 1.61671 - 1 - 7 - 1 - 7 - 0 - 0 - 6 - 6 - 0 - 7 - LPAPPGA - WPAPPGA - PAPPGA - - - - - 2 - gnl|BL_ORD_ID|1187 - 93536|core protein|AAL31859.1|Hepatitis B virus|10407 - 1187 - 11 - - - 1 - 11.1566 - 17 - 185.696 - 4 - 8 - 5 - 9 - 0 - 0 - 4 - 4 - 0 - 5 - PPGAP - PPNAP - PP AP - - - - - 3 - gnl|BL_ORD_ID|1831 - 179823|cell surface protein (associated with virulence)|NP_302372.1|Mycobacterium leprae TN|272631 - 1831 - 9 - - - 1 - 10.7714 - 16 - 339.179 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 5 - 0 - 8 - LPAPPGAP - IPASVSAP - +PA AP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 102 - Query_102 - M_3419 - 9 - - - 1 - gnl|BL_ORD_ID|1008 - 66798|glycoprotein gp35/37|AAC59622.1|Human gammaherpesvirus 8|37296 - 1008 - 15 - - - 1 - 12.6974 - 21 - 22.1438 - 1 - 7 - 2 - 8 - 0 - 0 - 4 - 4 - 0 - 7 - VRGTDWH - TRGRDAH - RG D H - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 103 - Query_103 - M_3420 - 9 - - - 1 - gnl|BL_ORD_ID|320 - 21000|glutamine synthetase GLNA1 (glutamine synthase) (GS-I)|NP_216736.1|Mycobacterium tuberculosis|1773 - 320 - 9 - - - 1 - 13.853 - 24 - 6.71897 - 3 - 7 - 4 - 8 - 0 - 0 - 4 - 5 - 0 - 5 - HHSPS - HHAPS - HH+PS - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 104 - Query_104 - M_3421 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 105 - Query_105 - M_3422 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 106 - Query_106 - M_3423 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 107 - Query_107 - M_3424 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 108 - Query_108 - M_3425 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 109 - Query_109 - M_3426 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 110 - Query_110 - M_3427 - 9 - - - 1 - gnl|BL_ORD_ID|1827 - 179766|cell surface protein (associated with virulence)|NP_302372.1|Mycobacterium leprae TN|272631 - 1827 - 9 - - - 1 - 11.927 - 19 - 82.8955 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 4 - 0 - 8 - PEPPETGV - PLPPSTAT - P PP T - - - - - 2 - gnl|BL_ORD_ID|1068 - 70491|envelope glycoprotein|AAC28452.1|Human immunodeficiency virus 1|11676 - 1068 - 10 - - - 1 - 11.927 - 19 - 85.0569 - 2 - 7 - 5 - 10 - 0 - 0 - 4 - 4 - 0 - 6 - PEPPET - PNPPEV - P PPE - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 111 - Query_111 - M_3428 - 9 - - - 1 - gnl|BL_ORD_ID|1871 - 180488|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1871 - 10 - - - 1 - 13.0826 - 22 - 16.3922 - 3 - 8 - 1 - 6 - 0 - 0 - 4 - 4 - 0 - 6 - GSGHSE - GPGHEE - G GH E - - - - - 2 - gnl|BL_ORD_ID|657 - 38974|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 657 - 11 - - - 1 - 12.3122 - 20 - 38.8163 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 7 - 0 - 9 - RRGSGHSEY - QRGPQYSEH - +RG +SE+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 112 - Query_112 - M_3429 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 113 - Query_113 - M_3430 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 114 - Query_114 - M_3431 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 115 - Query_115 - M_3432 - 9 - - - 1 - gnl|BL_ORD_ID|1610 - 143728|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 1610 - 9 - - - 1 - 14.2382 - 25 - 3.00197 - 3 - 9 - 1 - 7 - 0 - 0 - 4 - 6 - 0 - 7 - VPWNSYV - LPWYSYL - +PW SY+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 116 - Query_116 - M_3433 - 9 - - - 1 - gnl|BL_ORD_ID|1610 - 143728|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 1610 - 9 - - - 1 - 14.2382 - 25 - 3.05306 - 1 - 7 - 1 - 7 - 0 - 0 - 4 - 6 - 0 - 7 - VPWNSYV - LPWYSYL - +PW SY+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 117 - Query_117 - M_3434 - 9 - - - 1 - gnl|BL_ORD_ID|1149 - 75636|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 1149 - 10 - - - 1 - 11.5418 - 18 - 153.051 - 1 - 8 - 1 - 8 - 0 - 0 - 3 - 5 - 0 - 8 - YQLKLFAC - YRLWHYPC - Y+L + C - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 118 - Query_118 - M_3435 - 9 - - - 1 - gnl|BL_ORD_ID|1149 - 75636|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 1149 - 10 - - - 1 - 11.5418 - 18 - 153.051 - 1 - 8 - 1 - 8 - 0 - 0 - 3 - 5 - 0 - 8 - YQLKLFAC - YRLWHYPC - Y+L + C - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 119 - Query_119 - M_3436 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 120 - Query_120 - M_3437 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 121 - Query_121 - M_3438 - 9 - - - 1 - gnl|BL_ORD_ID|872 - 57361|Genome polyprotein|SRC279960|Hepatitis C virus (isolate H77)|63746 - 872 - 11 - - - 1 - 12.6974 - 21 - 28.2065 - 3 - 8 - 1 - 6 - 0 - 0 - 4 - 4 - 0 - 6 - SSCCQP - SECCTP - S CC P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 122 - Query_122 - M_3439 - 9 - - - 1 - gnl|BL_ORD_ID|664 - 39591|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 - 664 - 20 - - - 1 - 10.3862 - 15 - 495.983 - 1 - 7 - 11 - 17 - 0 - 0 - 3 - 4 - 0 - 7 - WLLEWTE - WCLWWLQ - W L W + - - - - - 2 - gnl|BL_ORD_ID|1092 - 72233|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 - 1092 - 15 - - - 1 - 10.001 - 14 - 852.012 - 1 - 5 - 1 - 5 - 0 - 0 - 2 - 4 - 0 - 5 - WLLEW - WAIKW - W ++W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 123 - Query_123 - M_3440 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 124 - Query_124 - M_3441 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 125 - Query_125 - M_3442 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 126 - Query_126 - M_3443 - 9 - - - 1 - gnl|BL_ORD_ID|1910 - 180662|polyprotein|CDF77361.1|Dengue virus 3|11069 - 1910 - 10 - - - 1 - 13.0826 - 22 - 22.3554 - 1 - 6 - 3 - 8 - 0 - 0 - 4 - 6 - 0 - 6 - ILPATI - MLPATL - +LPAT+ - - - - - 2 - gnl|BL_ORD_ID|1853 - 180390|polyprotein|CDF77361.1|Dengue virus 3|11069 - 1853 - 10 - - - 1 - 12.6974 - 21 - 22.7423 - 1 - 6 - 5 - 10 - 0 - 0 - 4 - 6 - 0 - 6 - ILPATI - MLPATL - +LPAT+ - - - - - 3 - gnl|BL_ORD_ID|1894 - 180609|polyprotein|ABK30845.1|Dengue virus 3|11069 - 1894 - 9 - - - 1 - 12.6974 - 21 - 24.2855 - 1 - 6 - 4 - 9 - 0 - 0 - 4 - 6 - 0 - 6 - ILPATI - MLPATL - +LPAT+ - - - - - 4 - gnl|BL_ORD_ID|1909 - 180660|polyprotein|CDF77361.1|Dengue virus 3|11069 - 1909 - 9 - - - 1 - 12.6974 - 21 - 24.707 - 1 - 6 - 2 - 7 - 0 - 0 - 4 - 6 - 0 - 6 - ILPATI - MLPATL - +LPAT+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 127 - Query_127 - M_3444 - 9 - - - 1 - gnl|BL_ORD_ID|1910 - 180662|polyprotein|CDF77361.1|Dengue virus 3|11069 - 1910 - 10 - - - 1 - 13.0826 - 22 - 20.1646 - 2 - 7 - 3 - 8 - 0 - 0 - 4 - 6 - 0 - 6 - ILPATI - MLPATL - +LPAT+ - - - - - 2 - gnl|BL_ORD_ID|1853 - 180390|polyprotein|CDF77361.1|Dengue virus 3|11069 - 1853 - 10 - - - 1 - 13.0826 - 22 - 21.6006 - 2 - 7 - 5 - 10 - 0 - 0 - 4 - 6 - 0 - 6 - ILPATI - MLPATL - +LPAT+ - - - - - 3 - gnl|BL_ORD_ID|1909 - 180660|polyprotein|CDF77361.1|Dengue virus 3|11069 - 1909 - 9 - - - 1 - 13.0826 - 22 - 21.8994 - 2 - 7 - 2 - 7 - 0 - 0 - 4 - 6 - 0 - 6 - ILPATI - MLPATL - +LPAT+ - - - - - 4 - gnl|BL_ORD_ID|1894 - 180609|polyprotein|ABK30845.1|Dengue virus 3|11069 - 1894 - 9 - - - 1 - 13.0826 - 22 - 22.2806 - 2 - 7 - 4 - 9 - 0 - 0 - 4 - 6 - 0 - 6 - ILPATI - MLPATL - +LPAT+ - - - - - 5 - gnl|BL_ORD_ID|983 - 64948|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 - 983 - 9 - - - 1 - 11.927 - 19 - 104.062 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 7 - 0 - 9 - TILPATILV - TLLYATVEV - T+L AT+ V - - - - - 6 - gnl|BL_ORD_ID|6 - 449|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 - 6 - 10 - - - 1 - 11.5418 - 18 - 157.893 - 1 - 7 - 4 - 10 - 0 - 0 - 4 - 6 - 0 - 7 - TILPATI - TLLYATV - T+L AT+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 128 - Query_128 - M_3445 - 9 - - - 1 - gnl|BL_ORD_ID|1924 - 180726|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1924 - 15 - - - 1 - 15.0086 - 27 - 1.14188 - 4 - 9 - 10 - 15 - 0 - 0 - 5 - 5 - 0 - 6 - WSFGSL - WDFGSL - W FGSL - - - - - 2 - gnl|BL_ORD_ID|1095 - 72301|envelope protein|YP_001527880.1|West Nile virus NY-99|10000971 - 1095 - 18 - - - 1 - 13.4678 - 23 - 7.53558 - 4 - 9 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - WSFGSL - WDFGSV - W FGS+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 129 - Query_129 - M_3446 - 9 - - - 1 - gnl|BL_ORD_ID|1397 - 110401|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1397 - 25 - - - 1 - 14.2382 - 25 - 3.81797 - 1 - 6 - 20 - 25 - 0 - 0 - 4 - 5 - 0 - 6 - NPEAMC - NPYAVC - NP A+C - - - - - 2 - gnl|BL_ORD_ID|1400 - 110467|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1400 - 25 - - - 1 - 14.2382 - 25 - 3.88133 - 1 - 6 - 5 - 10 - 0 - 0 - 4 - 5 - 0 - 6 - NPEAMC - NPYAVC - NP A+C - - - - - 3 - gnl|BL_ORD_ID|1387 - 110227|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1387 - 33 - - - 1 - 14.2382 - 25 - 4.76191 - 1 - 6 - 12 - 17 - 0 - 0 - 4 - 5 - 0 - 6 - NPEAMC - NPYAVC - NP A+C - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 130 - Query_130 - M_3447 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 131 - Query_131 - M_3448 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 132 - Query_132 - M_3449 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 133 - Query_133 - M_3450 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 134 - Query_134 - M_3451 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 135 - Query_135 - M_3452 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 136 - Query_136 - M_3453 - 9 - - - 1 - gnl|BL_ORD_ID|374 - 23224|polyprotein|BAB18806.1|Hepatitis C virus|11103 - 374 - 15 - - - 1 - 13.853 - 24 - 6.75013 - 1 - 9 - 4 - 12 - 0 - 0 - 5 - 6 - 0 - 9 - LLPPQDPHL - LLPRRGPRL - LLP + P L - - - - - 2 - gnl|BL_ORD_ID|1950 - 181035|||| - 1950 - 44 - - - 1 - 13.4678 - 23 - 10.7201 - 1 - 9 - 25 - 33 - 0 - 0 - 5 - 6 - 0 - 9 - LLPPQDPHL - LLPRRGPRL - LLP + P L - - - - - 3 - gnl|BL_ORD_ID|1130 - 74798|polyprotein|BAA03375.1|Hepatitis C virus|11103 - 1130 - 10 - - - 1 - 13.0826 - 22 - 16.3922 - 1 - 9 - 2 - 10 - 0 - 0 - 5 - 6 - 0 - 9 - LLPPQDPHL - LLPRRGPRL - LLP + P L - - - - - 4 - gnl|BL_ORD_ID|630 - 37685|polyprotein|BAA03375.1|Hepatitis C virus|11103 - 630 - 9 - - - 1 - 13.0826 - 22 - 18.1053 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 6 - 0 - 9 - LLPPQDPHL - LLPRRGPRL - LLP + P L - - - - - 5 - gnl|BL_ORD_ID|1508 - 139406|polyprotein|ACT37184.1|Hepatitis C virus|11103 - 1508 - 10 - - - 1 - 10.7714 - 16 - 299.259 - 1 - 9 - 2 - 10 - 0 - 0 - 5 - 5 - 0 - 9 - LLPPQDPHL - LLPRPGPRL - LLP P L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 137 - Query_137 - M_3454 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 138 - Query_138 - M_3455 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 139 - Query_139 - M_3456 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 140 - Query_140 - M_3457 - 9 - - - 1 - gnl|BL_ORD_ID|241 - 16836|precore/core protein [Hepatitis B virus]|AAR03815.1|Hepatitis B virus|10407 - 241 - 10 - - - 1 - 10.3862 - 15 - 506.338 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 4 - 0 - 8 - LPEVQLPK - LPSDFLPS - LP LP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 141 - Query_141 - M_3458 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 142 - Query_142 - M_3459 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 143 - Query_143 - M_3460 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 144 - Query_144 - M_3461 - 9 - - - 1 - gnl|BL_ORD_ID|1038 - 69435|Genome polyprotein|SRC279960|Hepatitis C virus (isolate H77)|63746 - 1038 - 9 - - - 1 - 13.4678 - 23 - 11.5219 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 5 - 0 - 8 - VLDKARVW - VLDSFKTW - VLD + W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 145 - Query_145 - M_3462 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 146 - Query_146 - M_3463 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 147 - Query_147 - M_3464 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 148 - Query_148 - M_3465 - 9 - - - 1 - gnl|BL_ORD_ID|350 - 21780|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 - 350 - 9 - - - 1 - 13.0826 - 22 - 17.4884 - 1 - 8 - 1 - 8 - 0 - 0 - 5 - 5 - 0 - 8 - APSWRGLA - GPSLIGLA - PS GLA - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 149 - Query_149 - M_3466 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 150 - Query_150 - M_3467 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 151 - Query_151 - M_3468 - 9 - - - 1 - gnl|BL_ORD_ID|375 - 23270|polyprotein|AAB67036.1|Hepatitis C virus (isolate H77)|63746 - 375 - 15 - - - 1 - 14.6234 - 26 - 2.2254 - 3 - 8 - 3 - 8 - 0 - 0 - 5 - 6 - 0 - 6 - LAGLYY - LAGLFY - LAGL+Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 152 - Query_152 - M_3469 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 153 - Query_153 - M_3470 - 9 - - - 1 - gnl|BL_ORD_ID|1520 - 140600|glutamine synthetase GLNA1 (glutamine synthase) (GS-I)|NP_216736.1|Mycobacterium tuberculosis H37Rv|83332 - 1520 - 9 - - - 1 - 13.0826 - 22 - 18.1053 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 6 - 0 - 9 - CLWQLKAPV - SLWKDGAPL - LW+ AP+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 154 - Query_154 - M_3471 - 9 - - - 1 - gnl|BL_ORD_ID|1729 - 150534|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1729 - 9 - - - 1 - 12.6974 - 21 - 24.707 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 4 - 0 - 6 - RPRKAW - RPASAW - RP AW - - - - - 2 - gnl|BL_ORD_ID|928 - 60238|Gag polyprotein|P03347.3|Human immunodeficiency virus 1|11676 - 928 - 9 - - - 1 - 11.927 - 19 - 80.227 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 4 - 0 - 8 - PRKAWAWC - PRTLNAWV - PR AW - - - - - 3 - gnl|BL_ORD_ID|756 - 50292|gag protein|ACR27140.1|Human immunodeficiency virus 1|11676 - 756 - 11 - - - 1 - 11.927 - 19 - 106.287 - 2 - 8 - 5 - 11 - 0 - 0 - 4 - 4 - 0 - 7 - PRKAWAW - PRTLNAW - PR AW - - - - - 4 - gnl|BL_ORD_ID|472 - 28657|gag protein|CAB00235.1|Human immunodeficiency virus 1|11676 - 472 - 9 - - - 1 - 11.927 - 19 - 107.472 - 2 - 8 - 3 - 9 - 0 - 0 - 4 - 4 - 0 - 7 - PRKAWAW - PRTLNAW - PR AW - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 155 - Query_155 - M_3472 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 156 - Query_156 - M_3473 - 9 - - - 1 - gnl|BL_ORD_ID|2088 - 185491|polyprotein|AGO67248.1|Dengue virus 2|11060 - 2088 - 10 - - - 1 - 11.1566 - 17 - 205.223 - 4 - 9 - 1 - 6 - 0 - 0 - 4 - 6 - 0 - 6 - KREEEK - RREEEE - +REEE+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 157 - Query_157 - M_3474 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 158 - Query_158 - M_3475 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 159 - Query_159 - M_3476 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 160 - Query_160 - M_3477 - 9 - - - 1 - gnl|BL_ORD_ID|1944 - 180818|Membrane glycoprotein precursor|NP_739582.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1944 - 15 - - - 1 - 13.0826 - 22 - 12.5116 - 4 - 8 - 7 - 11 - 0 - 0 - 4 - 5 - 0 - 5 - GFTML - GFTMM - GFTM+ - - - - - 2 - gnl|BL_ORD_ID|1686 - 149052|E1 protein|NP_751920.1|Hepatitis C virus (isolate H77)|63746 - 1686 - 18 - - - 1 - 13.0826 - 22 - 15.2048 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 7 - 0 - 8 - GLAGFTML - GIAYFSMV - G+A F+M+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 161 - Query_161 - M_3478 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 162 - Query_162 - M_3479 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 163 - Query_163 - M_3480 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 164 - Query_164 - M_3481 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 165 - Query_165 - M_3482 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 166 - Query_166 - M_3483 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 167 - Query_167 - M_3484 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 168 - Query_168 - M_3485 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134127_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134127_1_T.fasta deleted file mode 100755 index b2113c0f..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134127_1_T.fasta +++ /dev/null @@ -1,108 +0,0 @@ ->M_3486 -TPCHCTGTL ->M_3487 -TPCHCTGTL ->M_3488 -IPFFGQVHL ->M_3489 -ILMENKSNI ->M_3490 -ILMENKSNI ->M_3491 -LAYLVKKMM ->M_3492 -VTISLAYLV ->M_3493 -LLIESKEEM ->M_3494 -WVGPWHTIV ->M_3495 -WWVGPWHTI ->M_3496 -KTFCGDVEY ->M_3497 -AVMEQINSV ->M_3498 -AVMEQINSV ->M_3499 -HPRINTLGS ->M_3500 -FLVAFIKKI ->M_3501 -FLVAFIKKI ->M_3502 -GIVSWDTFL ->M_3503 -IVSWDTFLV ->M_3504 -SAKLTTLVV ->M_3505 -KLIWHPFSI ->M_3506 -YFDENIQKL ->M_3507 -SPSSGQRST ->M_3508 -SAQNELTEM ->M_3509 -VATNSETAM ->M_3510 -PLWGGIIYI ->M_3511 -YPLWGGIIY ->M_3512 -AALATLHPL ->M_3513 -AALATLHPL ->M_3514 -LATLHPLFL ->M_3515 -GLNMLITAL ->M_3516 -LLTGLNMLI ->M_3517 -LMWLTYTMA ->M_3518 -LTYTMAFMV ->M_3519 -LTYTMAFMV ->M_3520 -MLITALYSL ->M_3521 -NLMWLTYTM ->M_3522 -WLTYTMAFM ->M_3523 -SANTGSSVV ->M_3524 -AMGSGIQPL ->M_3525 -HLLEPGQAM ->M_3526 -TVVGNLGII ->M_3527 -HGKPTLSTV ->M_3528 -LEYNTRNAY ->M_3529 -LLGLTWPVV ->M_3530 -QLLGLTWPV ->M_3531 -RVLFWGHIL ->M_3532 -RVLFWGHIL ->M_3533 -KVFNNGADL ->M_3534 -LAGEWRERL ->M_3535 -MNWRPILTI ->M_3536 -FSDLRSSIV ->M_3537 -FSDLRSSIV ->M_3538 -YFSDLRSSI ->M_3539 -EANFSASRV diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134127_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134127_1_T_iedb.xml deleted file mode 100755 index 70b4f12a..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134127_1_T_iedb.xml +++ /dev/null @@ -1,1681 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_3486 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_3486 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_3487 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_3488 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_3489 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_3490 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_3491 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_3492 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_3493 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_3494 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_3495 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_3496 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_3497 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_3498 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_3499 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_3500 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_3501 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_3502 - 9 - - - 1 - gnl|BL_ORD_ID|787 - 52666|Antigen 85-B|P0C5B9.1|Mycobacterium tuberculosis|1773 - 787 - 9 - - - 1 - 14.2382 - 25 - 3.10506 - 4 - 9 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - SWDTFL - KWETFL - W+TFL - - - - - 2 - gnl|BL_ORD_ID|317 - 20929|Circumsporozoite protein precursor|P02893.1|Plasmodium falciparum|5833 - 317 - 9 - - - 1 - 10.3862 - 15 - 712.196 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 6 - 0 - 9 - GIVSWDTFL - GLIMVLSFL - G++ +FL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 18 - Query_18 - M_3503 - 9 - - - 1 - gnl|BL_ORD_ID|787 - 52666|Antigen 85-B|P0C5B9.1|Mycobacterium tuberculosis|1773 - 787 - 9 - - - 1 - 14.2382 - 25 - 3.05306 - 3 - 8 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - SWDTFL - KWETFL - W+TFL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 19 - Query_19 - M_3504 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_3505 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_3506 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 22 - Query_22 - M_3507 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_3508 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_3509 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_3510 - 9 - - - 1 - gnl|BL_ORD_ID|744 - 48321|||| - 744 - 9 - - - 1 - 13.4678 - 23 - 12.57 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 7 - 0 - 9 - PLWGGIIYI - PLFGYPVYV - PL+G +Y+ - - - - - 2 - gnl|BL_ORD_ID|606 - 37251|||| - 606 - 9 - - - 1 - 11.5418 - 18 - 165.102 - 2 - 9 - 2 - 9 - 0 - 0 - 3 - 6 - 0 - 8 - LWGGIIYI - LFGHPVYV - L+G +Y+ - - - - - 3 - gnl|BL_ORD_ID|607 - 37253|||| - 607 - 9 - - - 1 - 11.1566 - 17 - 202.191 - 2 - 9 - 2 - 9 - 0 - 0 - 3 - 6 - 0 - 8 - LWGGIIYI - LFGYAVYV - L+G +Y+ - - - - - 4 - gnl|BL_ORD_ID|389 - 23807|tax|AAG48731.1|Human T-lymphotropic virus 2|11909 - 389 - 23 - - - 1 - 10.7714 - 16 - 238.868 - 2 - 9 - 10 - 17 - 0 - 0 - 3 - 6 - 0 - 8 - LWGGIIYI - LYGYPVYV - L+G +Y+ - - - - - 5 - gnl|BL_ORD_ID|638 - 37970|tax|AAG48731.1|Human T-lymphotropic virus 2|11909 - 638 - 9 - - - 1 - 10.7714 - 16 - 376.438 - 2 - 9 - 2 - 9 - 0 - 0 - 3 - 6 - 0 - 8 - LWGGIIYI - LYGYPVYV - L+G +Y+ - - - - - 6 - gnl|BL_ORD_ID|2036 - 184429|||| - 2036 - 9 - - - 1 - 10.7714 - 16 - 393.541 - 2 - 9 - 2 - 9 - 0 - 0 - 3 - 6 - 0 - 8 - LWGGIIYI - LFGFPVYV - L+G +Y+ - - - - - 7 - gnl|BL_ORD_ID|1170 - 79294|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 1170 - 15 - - - 1 - 10.3862 - 15 - 443.083 - 2 - 9 - 2 - 9 - 0 - 0 - 3 - 6 - 0 - 8 - LWGGIIYI - LFGYPVYV - L+G +Y+ - - - - - 8 - gnl|BL_ORD_ID|572 - 35845|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 572 - 9 - - - 1 - 10.7714 - 16 - 497.585 - 2 - 9 - 1 - 8 - 0 - 0 - 3 - 6 - 0 - 8 - LWGGIIYI - LFGYPVYV - L+G +Y+ - - - - - 9 - gnl|BL_ORD_ID|571 - 35844|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 571 - 8 - - - 1 - 10.7714 - 16 - 522.979 - 2 - 9 - 1 - 8 - 0 - 0 - 3 - 6 - 0 - 8 - LWGGIIYI - LFGYPVYV - L+G +Y+ - - - - - 10 - gnl|BL_ORD_ID|610 - 37257|Protein Tax-1|P03409.2|Human T-lymphotropic virus 1|11908 - 610 - 9 - - - 1 - 10.3862 - 15 - 534.993 - 2 - 9 - 2 - 9 - 0 - 0 - 3 - 6 - 0 - 8 - LWGGIIYI - LFGYPVYV - L+G +Y+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 26 - Query_26 - M_3511 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_3512 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 28 - Query_28 - M_3513 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 29 - Query_29 - M_3514 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 30 - Query_30 - M_3515 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 31 - Query_31 - M_3516 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 32 - Query_32 - M_3517 - 9 - - - 1 - gnl|BL_ORD_ID|325 - 21041|Membrane glycoprotein|Q692E0|SARS coronavirus TJF|284672 - 325 - 9 - - - 1 - 15.3938 - 28 - 0.807007 - 1 - 6 - 2 - 7 - 0 - 0 - 5 - 6 - 0 - 6 - LMWLTY - LMWLSY - LMWL+Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 33 - Query_33 - M_3518 - 9 - - - 1 - gnl|BL_ORD_ID|1162 - 76621|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 1162 - 11 - - - 1 - 11.927 - 19 - 70.1482 - 3 - 8 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - YTMAFM - YTSAFV - YT AF+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 34 - Query_34 - M_3519 - 9 - - - 1 - gnl|BL_ORD_ID|1162 - 76621|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 1162 - 11 - - - 1 - 11.927 - 19 - 70.1482 - 3 - 8 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - YTMAFM - YTSAFV - YT AF+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 35 - Query_35 - M_3520 - 9 - - - 1 - gnl|BL_ORD_ID|1596 - 142232|POSSIBLE CONSERVED TRANSMEMBRANE PROTEIN|CAB00937.1|Mycobacterium tuberculosis|1773 - 1596 - 19 - - - 1 - 7.68983 - 8 - 7255.43 - 6 - 9 - 13 - 16 - 0 - 0 - 1 - 3 - 0 - 4 - LYSL - VYAF - +Y+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 36 - Query_36 - M_3521 - 9 - - - 1 - gnl|BL_ORD_ID|325 - 21041|Membrane glycoprotein|Q692E0|SARS coronavirus TJF|284672 - 325 - 9 - - - 1 - 15.779 - 29 - 0.548509 - 1 - 7 - 1 - 7 - 0 - 0 - 5 - 6 - 0 - 7 - NLMWLTY - GLMWLSY - LMWL+Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 37 - Query_37 - M_3522 - 9 - - - 1 - gnl|BL_ORD_ID|1812 - 177647|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 - 1812 - 16 - - - 1 - 12.3122 - 20 - 47.9018 - 1 - 8 - 6 - 13 - 0 - 0 - 3 - 5 - 0 - 8 - WLTYTMAF - WMNRLIAF - W+ +AF - - - - - 2 - gnl|BL_ORD_ID|1162 - 76621|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 1162 - 11 - - - 1 - 11.927 - 19 - 65.7443 - 4 - 9 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - YTMAFM - YTSAFV - YT AF+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 38 - Query_38 - M_3523 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 39 - Query_39 - M_3524 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 40 - Query_40 - M_3525 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 41 - Query_41 - M_3526 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 42 - Query_42 - M_3527 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 43 - Query_43 - M_3528 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 44 - Query_44 - M_3529 - 9 - - - 1 - gnl|BL_ORD_ID|645 - 38427|BZLF1|AAA66529.1|Human gammaherpesvirus 4|10376 - 645 - 9 - - - 1 - 11.5418 - 18 - 132.337 - 6 - 9 - 6 - 9 - 0 - 0 - 3 - 4 - 0 - 4 - WPVV - WPVL - WPV+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 45 - Query_45 - M_3530 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 46 - Query_46 - M_3531 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 47 - Query_47 - M_3532 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 48 - Query_48 - M_3533 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 49 - Query_49 - M_3534 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 50 - Query_50 - M_3535 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 51 - Query_51 - M_3536 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 52 - Query_52 - M_3537 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 53 - Query_53 - M_3538 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 54 - Query_54 - M_3539 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134510_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134510_1_T.fasta deleted file mode 100755 index 9d7ce536..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134510_1_T.fasta +++ /dev/null @@ -1,26 +0,0 @@ ->M_3540 -TLEGFFESL ->M_3541 -KILKAQEHV ->M_3542 -LLQPTPPAA ->M_3543 -SLQVKRVFV ->M_3544 -FTLEGFFES ->M_3545 -PLLRDVFNV ->M_3546 -AQSEIHFQV ->M_3547 -LQAHSMHEV ->M_3548 -LLLQPTPPA ->M_3549 -SLSFSFPLL ->M_3550 -RVWDIVPTL ->M_3551 -IVMCAMCGV ->M_3552 -AMCGVPFSV diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134510_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134510_1_T_iedb.xml deleted file mode 100755 index 32faa078..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134510_1_T_iedb.xml +++ /dev/null @@ -1,615 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_3540 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_3540 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_3541 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_3542 - 9 - - - 1 - gnl|BL_ORD_ID|1106 - 72928|Genome polyprotein|P26662.3|Hepatitis C virus (isolate Japanese)|11116 - 1106 - 10 - - - 1 - 12.3122 - 20 - 62.4024 - 4 - 9 - 2 - 7 - 0 - 0 - 4 - 4 - 0 - 6 - PTPPAA - PAPPGA - P PP A - - - - - 2 - gnl|BL_ORD_ID|1179 - 79628|E1 protein|BAA19893.1|Rubella virus|11041 - 1179 - 21 - - - 1 - 11.5418 - 18 - 116.985 - 4 - 9 - 14 - 19 - 0 - 0 - 4 - 4 - 0 - 6 - PTPPAA - PTAPCA - PT P A - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 4 - Query_4 - M_3543 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_3544 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_3545 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_3546 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_3547 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_3548 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_3549 - 9 - - - 1 - gnl|BL_ORD_ID|660 - 39339|Nucleocapsid protein|Q89462|Sin Nombre hantavirus|37705 - 660 - 15 - - - 1 - 13.853 - 24 - 7.10896 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 7 - 0 - 8 - LSFSFPLL - LSFALPII - LSF+ P++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 11 - Query_11 - M_3550 - 9 - - - 1 - gnl|BL_ORD_ID|538 - 32944|polyprotein|AAW51418.1|Dengue virus 3|11069 - 538 - 9 - - - 1 - 16.9346 - 32 - 0.261971 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 8 - 0 - 9 - RVWDIVPTL - KPWDVVPTV - + WD+VPT+ - - - - - 2 - gnl|BL_ORD_ID|536 - 32942|Polyprotein|Q9J8D4|Dengue virus 2|11060 - 536 - 9 - - - 1 - 15.779 - 29 - 0.485957 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 8 - 0 - 9 - RVWDIVPTL - KPWDVLPTV - + WD++PT+ - - - - - 3 - gnl|BL_ORD_ID|1787 - 161186|Nonstructural protein NS5|NP_739590.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1787 - 15 - - - 1 - 15.0086 - 27 - 1.12275 - 3 - 7 - 7 - 11 - 0 - 0 - 4 - 5 - 0 - 5 - WDIVP - WDVVP - WD+VP - - - - - 4 - gnl|BL_ORD_ID|533 - 32939|polyprotein|AAK67712.1|Dengue virus 2|11060 - 533 - 9 - - - 1 - 15.0086 - 27 - 1.17789 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 7 - 0 - 9 - RVWDIVPTL - KPWDIIPMV - + WDI+P + - - - - - 5 - gnl|BL_ORD_ID|537 - 32943|polyprotein|AAL96681.1|Dengue virus 2|11060 - 537 - 9 - - - 1 - 15.0086 - 27 - 1.45111 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 7 - 0 - 9 - RVWDIVPTL - KPWDVVPMV - + WD+VP + - - - - - 6 - gnl|BL_ORD_ID|534 - 32940|polyprotein|ABG75765.1|Dengue virus type 1 Hawaii|10000440 - 534 - 9 - - - 1 - 14.2382 - 25 - 2.71372 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 7 - 0 - 9 - RVWDIVPTL - KPWDVIPMV - + WD++P + - - - - - 7 - gnl|BL_ORD_ID|535 - 32941|DEN polyprotein|AAC40835.1|Dengue virus 2|11060 - 535 - 9 - - - 1 - 13.853 - 24 - 5.95161 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 7 - 0 - 9 - RVWDIVPTL - KPWDVLPMV - + WD++P + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 12 - Query_12 - M_3551 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_3552 - 9 - - - 1 - gnl|BL_ORD_ID|2182 - 190409|polymerase|AAD16253.1|Hepatitis B virus|10407 - 2182 - 15 - - - 1 - 15.3938 - 28 - 0.658828 - 1 - 8 - 7 - 14 - 0 - 0 - 4 - 6 - 0 - 8 - AMCGVPFS - SFCGSPYS - + CG P+S - - - - - 2 - gnl|BL_ORD_ID|390 - 23864|envelope glycoprotein(gp21, gp46) - human T-cell lymphotropic virus type 1|A45714|Human T-lymphotropic virus 1|11908 - 390 - 9 - - - 1 - 14.6234 - 26 - 2.45448 - 1 - 7 - 3 - 9 - 0 - 0 - 4 - 5 - 0 - 7 - AMCGVPF - SKCGFPF - + CG PF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134611_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134611_1_T.fasta deleted file mode 100755 index 9830ebcb..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134611_1_T.fasta +++ /dev/null @@ -1,38 +0,0 @@ ->M_3553 -RQMAARECK ->M_3554 -FLVYQNILK ->M_3555 -FLVYQNILK ->M_3556 -KVERERLEK ->M_3557 -KQIEMLEYK ->M_3558 -KQIEMLEYK ->M_3559 -VVGAVGVGK ->M_3560 -VVGAVGVGK ->M_3561 -FIDTYPPVL ->M_3562 -RSAFPCAHR ->M_3563 -GTPRAATMK ->M_3564 -TMKAKTDLK ->M_3565 -TMKAKTDLK ->M_3566 -GLLFAAIKR ->M_3567 -LLFAAIKRR ->M_3568 -YQIDRDLHK ->M_3569 -QTGEKLMAK ->M_3570 -QTGEKLMAK ->M_3571 -SSNLIAHVR diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134611_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134611_1_T_iedb.xml deleted file mode 100755 index 155a1ef3..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134611_1_T_iedb.xml +++ /dev/null @@ -1,403 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_3553 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_3553 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_3554 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_3555 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_3556 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_3557 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_3558 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_3559 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_3560 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_3561 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_3562 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_3563 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_3564 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_3565 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_3566 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_3567 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_3568 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_3569 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_3570 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_3571 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134702_2_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134702_2_T.fasta deleted file mode 100755 index d6a788c6..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134702_2_T.fasta +++ /dev/null @@ -1,36 +0,0 @@ ->M_3572 -GEDVDSLAL ->M_3573 -AELVYILKH ->M_3574 -KVAELVYIL ->M_3575 -ISMKLVLRF ->M_3576 -KSPGWSFQV ->M_3577 -SWKSPGWSF ->M_3578 -LTVDNITFL ->M_3579 -DAATRVAMV ->M_3580 -DSVDAATRV ->M_3581 -VGAQIYHTI ->M_3582 -GELSMLVTT ->M_3583 -EELQLICQA ->M_3584 -SEEELQLIC ->M_3585 -CELHAQAAT ->M_3586 -FTLRPGEVM ->M_3587 -VYMPPPRLL ->M_3588 -TFKKQWFYL ->M_3589 -KANRESQSL diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134702_2_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134702_2_T_iedb.xml deleted file mode 100755 index da61382f..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134702_2_T_iedb.xml +++ /dev/null @@ -1,519 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_3572 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_3572 - 9 - - - 1 - gnl|BL_ORD_ID|1858 - 180428|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1858 - 15 - - - 1 - 15.0086 - 27 - 1.35294 - 1 - 9 - 7 - 15 - 0 - 0 - 6 - 7 - 0 - 9 - GEDVDSLAL - GEEVQVLAL - GE+V LAL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 2 - Query_2 - M_3573 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_3574 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_3575 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_3576 - 9 - - - 1 - gnl|BL_ORD_ID|1580 - 141461|ubiquitin E3 ligase ICP0|NP_044601.1|Human alphaherpesvirus 1|10298 - 1580 - 9 - - - 1 - 13.853 - 24 - 4.51705 - 3 - 6 - 2 - 5 - 0 - 0 - 4 - 4 - 0 - 4 - PGWS - PGWS - PGWS - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 6 - Query_6 - M_3577 - 9 - - - 1 - gnl|BL_ORD_ID|1580 - 141461|ubiquitin E3 ligase ICP0|NP_044601.1|Human alphaherpesvirus 1|10298 - 1580 - 9 - - - 1 - 13.4678 - 23 - 9.18751 - 5 - 8 - 2 - 5 - 0 - 0 - 4 - 4 - 0 - 4 - PGWS - PGWS - PGWS - - - - - 2 - gnl|BL_ORD_ID|951 - 62616|Chain A, Dengue Virus 4 Ns3 Helicase In Complex With Ssrna|2JLU_A|Dengue virus 4 Thailand/0348/1991|408688 - 951 - 9 - - - 1 - 13.0826 - 22 - 22.6682 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 5 - 0 - 9 - SWKSPGWSF - SYKDREWCF - S+K W F - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 7 - Query_7 - M_3578 - 9 - - - 1 - gnl|BL_ORD_ID|69 - 5191|core protein|AAL31859.1|Hepatitis B virus|10407 - 69 - 17 - - - 1 - 11.927 - 19 - 75.4827 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 7 - 0 - 8 - TVDNITFL - TVELLSFL - TV+ ++FL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 8 - Query_8 - M_3579 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_3580 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_3581 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_3582 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_3583 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_3584 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_3585 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_3586 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_3587 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_3588 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_3589 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_135773_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_135773_1_T.fasta deleted file mode 100755 index c0cf645e..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_135773_1_T.fasta +++ /dev/null @@ -1,2572 +0,0 @@ ->M_3590 -AAKARDREL ->M_3591 -AARLRFFST ->M_3592 -AFFSLSYIF ->M_3593 -AHASLIPEF ->M_3594 -AHCGLGKIL ->M_3595 -AHIERRLHI ->M_3596 -AHMETMAKL ->M_3597 -AHMGVFTEL ->M_3598 -AHQDALMLA ->M_3599 -AHRPRARLA ->M_3600 -AHTSAILTV ->M_3601 -AIRPKSLAI ->M_3602 -ALQRRRLSL ->M_3603 -ALQRRVQRL ->M_3604 -AMACMSSVF ->M_3605 -AMCVIHFSF ->M_3606 -AMYLRASSL ->M_3607 -APASRHLSA ->M_3608 -APRLLRSPV ->M_3609 -AQKEHSHLL ->M_3610 -ARAAQVAGI ->M_3611 -ARDPSPIQI ->M_3612 -ARHERIHTK ->M_3613 -ARINSIYGL ->M_3614 -ARKPRTREC ->M_3615 -ARLQHCSAL ->M_3616 -ARLQHCSAL ->M_3617 -ARLYRGQAL ->M_3618 -ARLYRGQAL ->M_3619 -ARMQSYSTI ->M_3620 -ARPEKLPEL ->M_3621 -ARQHLLQRM ->M_3622 -ARRARLQHC ->M_3623 -ARRKQSEMY ->M_3624 -ARTRAKQNI ->M_3625 -ARVQMQVTM ->M_3626 -ASFSNHQRV ->M_3627 -ATDDKMTIF ->M_3628 -AVDPMRAAY ->M_3629 -AVMGRSWEV ->M_3630 -AYATQLFFF ->M_3631 -AYEDTVRQV ->M_3632 -AYFTHSLSF ->M_3633 -CAFSRRRPI ->M_3634 -CFPLHGLQF ->M_3635 -CGDKISDRY ->M_3636 -CHFSCNNGF ->M_3637 -CHQDHWSQL ->M_3638 -CHQRCGGRV ->M_3639 -CHSNSRDHL ->M_3640 -CHYEKKTDL ->M_3641 -CLKPHQGPV ->M_3642 -CLLRNSACL ->M_3643 -CLPSRTSSV ->M_3644 -CLRDLFFPL ->M_3645 -CMKQRDEEF ->M_3646 -CPPNHIVSL ->M_3647 -CQFGTVQLV ->M_3648 -CRAETRKTF ->M_3649 -CRCPIRGLV ->M_3650 -CREELAVHL ->M_3651 -CREQHPAQL ->M_3652 -CRKMFRRSA ->M_3653 -CRKMGLRVM ->M_3654 -CRPQCCQSV ->M_3655 -CRRGLEQLL ->M_3656 -CRYGRFHKF ->M_3657 -CSDTHTNEL ->M_3658 -CVLYKYVPI ->M_3659 -CVMTKIFSL ->M_3660 -CYLITVTPI ->M_3661 -CYLVFIGCF ->M_3662 -CYNSAIQAL ->M_3663 -CYSRDQIYI ->M_3664 -CYVAICGPL ->M_3665 -CYYYFLCLL ->M_3666 -DAKRHRKVL ->M_3667 -DALCRLLGL ->M_3668 -DFKKKKGSM ->M_3669 -DHRDLGLSV ->M_3670 -DILVHHLAV ->M_3671 -DLGDKILAL ->M_3672 -DLHTRHGSI ->M_3673 -DLKMGKKPV ->M_3674 -DLLGHPQAL ->M_3675 -DLPTKRPAL ->M_3676 -DLQQKILCM ->M_3677 -DMMKEFISM ->M_3678 -DPKERIKVA ->M_3679 -DPRLKWVVL ->M_3680 -DRGGCVAGV ->M_3681 -DRMQRVISV ->M_3682 -DRMQRVISV ->M_3683 -DRNDFPVVL ->M_3684 -DRQLAAQLL ->M_3685 -DRSGARPHL ->M_3686 -DRSHTLQRM ->M_3687 -DRVERNCLL ->M_3688 -DSDGEEPCY ->M_3689 -DSHDYVFYL ->M_3690 -DTDILSYSY ->M_3691 -DTDLYHCTA ->M_3692 -DTEGILTEY ->M_3693 -DYMGFTLKI ->M_3694 -DYPCCIFPF ->M_3695 -DYRTVNNLI ->M_3696 -EAEPYYCSL ->M_3697 -EAKRQNLRL ->M_3698 -EALIRHLNA ->M_3699 -EAMNNAQKI ->M_3700 -EASRRYKKV ->M_3701 -EFPQKYYWW ->M_3702 -EGQRRPSSV ->M_3703 -EHEEDGSEI ->M_3704 -EHGGKTVKV ->M_3705 -EHLAAPRLV ->M_3706 -EHNVTVLVV ->M_3707 -EHQIGPQEI ->M_3708 -EHRLHTPMY ->M_3709 -EIKTIVKAI ->M_3710 -EIMNRVVNA ->M_3711 -EKRFKRKSV ->M_3712 -ELACYNSAI ->M_3713 -ELEHMRLRY ->M_3714 -ELHARGHQV ->M_3715 -ELHRQVKTL ->M_3716 -ELKQMCNPI ->M_3717 -ELLLKVFAL ->M_3718 -ELQARLAAL ->M_3719 -ELRAHCETL ->M_3720 -ELRRYLKSG ->M_3721 -EMKCREKGF ->M_3722 -EMLRRQIRL ->M_3723 -EMRCQYETV ->M_3724 -EMYEKGLSV ->M_3725 -EPKKKEKGM ->M_3726 -EPKKRKVVP ->M_3727 -EPRFRLNLF ->M_3728 -ERDGLERAL ->M_3729 -ERDGLHSVV ->M_3730 -ERDQLKETL ->M_3731 -EREKMGVTM ->M_3732 -ERFWRIILL ->M_3733 -ERHVAVEGV ->M_3734 -ERIDTNQKC ->M_3735 -ERKTMIKKI ->M_3736 -ERLQALYMI ->M_3737 -ERLQNPLRV ->M_3738 -ERQCHNTAL ->M_3739 -ERQCHNTAL ->M_3740 -ERRDCIICC ->M_3741 -ERSCWVRAI ->M_3742 -ERSEQPLSV ->M_3743 -ERSPQAAAV ->M_3744 -ERTNQKWSV ->M_3745 -ERTSATLTI ->M_3746 -ERTTWVQKI ->M_3747 -ERYGPVFTI ->M_3748 -ETMLHGQVM ->M_3749 -ETRPTPRLL ->M_3750 -ETVSTTLCY ->M_3751 -EYIVIPSTF ->M_3752 -EYLLGSWVI ->M_3753 -EYNANTSVL ->M_3754 -EYRPRTFCF ->M_3755 -EYVKFLHTF ->M_3756 -EYVTELPSF ->M_3757 -FAAQHGLAV ->M_3758 -FAKLRHNTQ ->M_3759 -FARGQRWRL ->M_3760 -FARGQRWRL ->M_3761 -FCLRYGAAL ->M_3762 -FCSLHCLLY ->M_3763 -FCYYYFLCL ->M_3764 -FEESKSYEV ->M_3765 -FEFSQVLAL ->M_3766 -FESHRILHL ->M_3767 -FFLSYLKSL ->M_3768 -FFLSYLSLV ->M_3769 -FGAIRRSDA ->M_3770 -FGYENSPEL ->M_3771 -FHFRRPWSF ->M_3772 -FHFRRPWSF ->M_3773 -FHFRRPWSF ->M_3774 -FHHCHPKYS ->M_3775 -FHHIDSAYL ->M_3776 -FHIGSAESM ->M_3777 -FHLHNAHVL ->M_3778 -FHLPYLEQK ->M_3779 -FHLQHWKQI ->M_3780 -FHLSIHLLY ->M_3781 -FHMASGEAL ->M_3782 -FHPMRTLPM ->M_3783 -FHVDQATTV ->M_3784 -FHYDTQLSL ->M_3785 -FHYLKKQET ->M_3786 -FIADKLSTL ->M_3787 -FIADKLSTL ->M_3788 -FICLQFWCI ->M_3789 -FIMFLFVYI ->M_3790 -FINNSIVYL ->M_3791 -FKKARWTII ->M_3792 -FKNHHNRTV ->M_3793 -FLARTVSTL ->M_3794 -FLEHGEQAY ->M_3795 -FLHERKQAS ->M_3796 -FLKTLWAGL ->M_3797 -FLLAMLLSI ->M_3798 -FLLEFLLPL ->M_3799 -FLLFSFLFL ->M_3800 -FLRTYKNSV ->M_3801 -FLSDLTPGY ->M_3802 -FLSVFYTAV ->M_3803 -FLTVMLLAL ->M_3804 -FLVERKTIA ->M_3805 -FMAYATQLF ->M_3806 -FMKYLVNFI ->M_3807 -FMLVMICIL ->M_3808 -FMWPLHWSM ->M_3809 -FPAMLQAPI ->M_3810 -FPIIIAWAI ->M_3811 -FPKKSLMLM ->M_3812 -FPLVRSCQM ->M_3813 -FPNGRLTFL ->M_3814 -FPQKYYWWF ->M_3815 -FPQNRYTQE ->M_3816 -FPTDCVYVM ->M_3817 -FPYCRAHVL ->M_3818 -FPYCRAHVL ->M_3819 -FPYCRSHVF ->M_3820 -FPYGSSTAL ->M_3821 -FPYNSDLSL ->M_3822 -FQFGAGTQV ->M_3823 -FQGRRSPSF ->M_3824 -FQRKKRRKF ->M_3825 -FREDPVAWV ->M_3826 -FREGRPREW ->M_3827 -FRGALPVQI ->M_3828 -FRGDGRTCC ->M_3829 -FRHSPRNLI ->M_3830 -FRKELRYFL ->M_3831 -FRKELRYFL ->M_3832 -FRLMHNLNF ->M_3833 -FRLRRVASA ->M_3834 -FRLWMTTEV ->M_3835 -FRNDQEETT ->M_3836 -FRNGLGTGM ->M_3837 -FRNSRLKQC ->M_3838 -FRPPAWNRL ->M_3839 -FRQGHQLFH ->M_3840 -FRQLEDSQV ->M_3841 -FRQSRSQVV ->M_3842 -FRQSRSQVV ->M_3843 -FRSHVPSHL ->M_3844 -FRSLQGSVF ->M_3845 -FRSPEDLSL ->M_3846 -FRSSASGAL ->M_3847 -FRTKDGSFV ->M_3848 -FRVSISQTA ->M_3849 -FRYEGSLTT ->M_3850 -FSDKKTITY ->M_3851 -FSFINNSIV ->M_3852 -FSIPTCLMY ->M_3853 -FSKAQAEYL ->M_3854 -FSYPSIHRF ->M_3855 -FTDVSRFTL ->M_3856 -FTFDLYRVL ->M_3857 -FTSFLLLMY ->M_3858 -FVEEWTESL ->M_3859 -FVQKLLFPY ->M_3860 -FWCAQFTSF ->M_3861 -FWKKILFVI ->M_3862 -FWKLFYCKF ->M_3863 -FYADSHHCV ->M_3864 -FYAIVVPML ->M_3865 -FYCDDLPLL ->M_3866 -FYLGTYQAV ->M_3867 -FYMLTCIDL ->M_3868 -FYQAGSLCI ->M_3869 -FYTDSSSVL ->M_3870 -FYTPALFSF ->M_3871 -GAGPRFLEL ->M_3872 -GDKQHFTTL ->M_3873 -GGATRVYAL ->M_3874 -GHDAPRRTL ->M_3875 -GHKEDAGVV ->M_3876 -GHKGLNQCV ->M_3877 -GHLEAASCI ->M_3878 -GHLQIRSLL ->M_3879 -GHLSKKMTL ->M_3880 -GHNSWGFGV ->M_3881 -GHPQDGSGL ->M_3882 -GHPSLSQHL ->M_3883 -GHTGERHRV ->M_3884 -GHTPNGRHF ->M_3885 -GHVAGEQML ->M_3886 -GLHSSFMPL ->M_3887 -GLSVRPHAI ->M_3888 -GMFTLRMAL ->M_3889 -GNYSRSSHV ->M_3890 -GPCRRRFSF ->M_3891 -GPLPKSYAV ->M_3892 -GPRTKAWFL ->M_3893 -GRAEESVVL ->M_3894 -GRAPCWQRL ->M_3895 -GREAEMQEL ->M_3896 -GRMHIGDEL ->M_3897 -GRMMFVGTL ->M_3898 -GRNGQKAAL ->M_3899 -GRVEKLLDL ->M_3900 -GSDSSNGAV ->M_3901 -GSEDFEDTY ->M_3902 -GTNIVILEY ->M_3903 -GVLECPRLI ->M_3904 -HAKKKPNPV ->M_3905 -HHIDSAYLY ->M_3906 -HHKGKMKAL ->M_3907 -HHKHKELQV ->M_3908 -HHRFNNFML ->M_3909 -HIKDKKLPL ->M_3910 -HLLSHSYCL ->M_3911 -HLMGQLSSL ->M_3912 -HMRLRYLAA ->M_3913 -HPKYSFRRL ->M_3914 -HPLRYTLIM ->M_3915 -HRADVYVGV ->M_3916 -HREDFEARL ->M_3917 -HRGTGAVYV ->M_3918 -HRLGESQTL ->M_3919 -HRLHTPMYL ->M_3920 -HRQAEVHKV ->M_3921 -HRQQRGQQL ->M_3922 -HRSKRGSSV ->M_3923 -HRTRCLSKL ->M_3924 -HRYPRVMAA ->M_3925 -HRYPRVMAA ->M_3926 -HSHLLSHSY ->M_3927 -HSYEAGTEI ->M_3928 -HTPNGRHFY ->M_3929 -HWSMWLGVF ->M_3930 -HYATILTSL ->M_3931 -HYHHRFNNF ->M_3932 -HYISIFYAL ->M_3933 -HYLRDVLPL ->M_3934 -HYQGTWYLT ->M_3935 -HYRKRGAHL ->M_3936 -IAHAWWAHF ->M_3937 -IAMYFYTTL ->M_3938 -IEYGSPEEL ->M_3939 -IFIASIYLL ->M_3940 -IFLFVIVTI ->M_3941 -IFPFALIFF ->M_3942 -IFPFILIFF ->M_3943 -IFSEKNRLV ->M_3944 -IFSFINNSI ->M_3945 -IFVSSYINI ->M_3946 -IGRNRSPCM ->M_3947 -IHDGAVHTI ->M_3948 -IHDRQLRSF ->M_3949 -IHEDEVDDM ->M_3950 -IHFTKKDYV ->M_3951 -IHGASNHCL ->M_3952 -IHIDDNKWV ->M_3953 -IHLLDSLRL ->M_3954 -IHLLYPPSL ->M_3955 -IHPRDRSTV ->M_3956 -IHTDDNKCV ->M_3957 -ILAVLPSLF ->M_3958 -ILKKRQQAA ->M_3959 -ILKRRYQEP ->M_3960 -ILLTQFHFL ->M_3961 -ILMRQPLPA ->M_3962 -ILRSKMKTV ->M_3963 -ILRVYSGVL ->M_3964 -ILSSRSRQL ->M_3965 -ILSSRSRQL ->M_3966 -INFNHDSSI ->M_3967 -IQWSYWGVF ->M_3968 -IRAANRRGL ->M_3969 -IRDGSTMTF ->M_3970 -IREYCPYTY ->M_3971 -IRFLRQYEF ->M_3972 -IRHGNVIAC ->M_3973 -IRHLNATSF ->M_3974 -IRIDTIHLL ->M_3975 -IRLNRQRHT ->M_3976 -IRNMAPDSL ->M_3977 -IRPPDSRSL ->M_3978 -IRRGGKHQL ->M_3979 -IRRLRPSSI ->M_3980 -IRRLRPSSI ->M_3981 -IRRRGSTSL ->M_3982 -IRYLHSLQI ->M_3983 -ISELLFECY ->M_3984 -ISFSMSEKM ->M_3985 -ISKRKVSVA ->M_3986 -ISLGFFLVF ->M_3987 -ISSSAGLPY ->M_3988 -ITIRNPLRY ->M_3989 -ITMDQKKTI ->M_3990 -ITMRYIHFL ->M_3991 -ITTFDRLAY ->M_3992 -IVHRQFYLF ->M_3993 -IVMGYSSGI ->M_3994 -IWFSIPTCL ->M_3995 -IYAALPYVK ->M_3996 -IYAFMGTPM ->M_3997 -IYCRPFTTL ->M_3998 -IYCVYPDSL ->M_3999 -IYGLCVVIV ->M_4000 -IYHDSRIHV ->M_4001 -IYTIVNIKI ->M_4002 -IYVDKVRHV ->M_4003 -KAFKRSSYL ->M_4004 -KAFKRSSYL ->M_4005 -KAMERSSLM ->M_4006 -KHFIHLITV ->M_4007 -KHLSRSNWL ->M_4008 -KHNEEIRFL ->M_4009 -KHRNMHCKI ->M_4010 -KHRSEISMM ->M_4011 -KIHIRETAI ->M_4012 -KILKKRQQA ->M_4013 -KISKRKVSV ->M_4014 -KKRRKFWKA ->M_4015 -KLKPKKPTL ->M_4016 -KLQPYFQTL ->M_4017 -KMFRRSAHL ->M_4018 -KRCALRLLV ->M_4019 -KRFKRKSVV ->M_4020 -KRILMPQVM ->M_4021 -KRISHKAAL ->M_4022 -KRQNLRLAL ->M_4023 -KRQRAMETL ->M_4024 -KRSPAWNEM ->M_4025 -KRYLSQREV ->M_4026 -KSDGLSLAV ->M_4027 -KSFSKYASF ->M_4028 -KWIREGYLV ->M_4029 -KYMPPCSLV ->M_4030 -KYPYWYQQK ->M_4031 -KYSTGIGWI ->M_4032 -KYSTPPYLL ->M_4033 -LAGQKRCAL ->M_4034 -LAKVKYTAS ->M_4035 -LALLKQVSV ->M_4036 -LANDPIQVV ->M_4037 -LAQSFFNCL ->M_4038 -LCAIYFLSI ->M_4039 -LCIKHFNIL ->M_4040 -LEHMRLRYL ->M_4041 -LFAAVVLLI ->M_4042 -LFKKARWTI ->M_4043 -LFLLFSFLF ->M_4044 -LFPRLPSIL ->M_4045 -LFSFMTHCF ->M_4046 -LFSFMTHRF ->M_4047 -LGRNRHFGF ->M_4048 -LHAPMYNLL ->M_4049 -LHAPMYNLL ->M_4050 -LHEQLGDRL ->M_4051 -LHFDAVQIC ->M_4052 -LHFMPCVYI ->M_4053 -LHFVQKLLF ->M_4054 -LHHKHKELQ ->M_4055 -LHHTHIALL ->M_4056 -LHKDSNMPV ->M_4057 -LHMNLLSYF ->M_4058 -LHNAHVLDV ->M_4059 -LHQCVLRFL ->M_4060 -LHQGGATRV ->M_4061 -LHRASGVGV ->M_4062 -LHSGLQILI ->M_4063 -LHTPVYFLL ->M_4064 -LHTPVYFLL ->M_4065 -LHTRHGSIL ->M_4066 -LHVGCDEVY ->M_4067 -LHYEEIPEY ->M_4068 -LIATQLLFY ->M_4069 -LIKHKKTHI ->M_4070 -LIKYRQNHA ->M_4071 -LIMNKRLGL ->M_4072 -LKKRQQAAL ->M_4073 -LKLVKRNSL ->M_4074 -LLCARAWLL ->M_4075 -LLDRRPHGY ->M_4076 -LLESYSASL ->M_4077 -LLGHKTVTI ->M_4078 -LLGKKGTSA ->M_4079 -LLHTIITPM ->M_4080 -LLKKLCIKL ->M_4081 -LLKSDGLSL ->M_4082 -LLKTAFHPV ->M_4083 -LLLMYSYAV ->M_4084 -LLLQALQAL ->M_4085 -LLMNKPYLA ->M_4086 -LLMYTKLVV ->M_4087 -LLNVHLSKL ->M_4088 -LLRDFVAPL ->M_4089 -LLRGHDQSA ->M_4090 -LLRLLRKAM ->M_4091 -LLRNDARSL ->M_4092 -LLSFKRQRA ->M_4093 -LLSRKDSIF ->M_4094 -LLTQRLQGL ->M_4095 -LMACATQLF ->M_4096 -LMGQLSSLY ->M_4097 -LMKMDDPSI ->M_4098 -LMKQKKSSC ->M_4099 -LNKLDFYVL ->M_4100 -LNRQRHTPM ->M_4101 -LPALRKTGV ->M_4102 -LPAVHALRL ->M_4103 -LPGLHFMPG ->M_4104 -LPGMRGPPG ->M_4105 -LPKDRFFAV ->M_4106 -LPKEKLAAA ->M_4107 -LPMTLLLLL ->M_4108 -LPQGRESPI ->M_4109 -LPRSKDTIL ->M_4110 -LPRVRGTTL ->M_4111 -LPSCRLAPA ->M_4112 -LPTLKFQTF ->M_4113 -LPYVKKTGM ->M_4114 -LQKVRQEVL ->M_4115 -LQLYRFSPI ->M_4116 -LQRRRLSLL ->M_4117 -LRADTSFFL ->M_4118 -LRAKYRESL ->M_4119 -LRAKYRESL ->M_4120 -LRAPPGPQL ->M_4121 -LRCHYHHRF ->M_4122 -LRETRDQPL ->M_4123 -LRIMLGEIL ->M_4124 -LRINEVMVY ->M_4125 -LRKGPIMEV ->M_4126 -LRKHQILHL ->M_4127 -LRKHQITHL ->M_4128 -LRKPQNSEC ->M_4129 -LRKQNFQPA ->M_4130 -LRLALDQYL ->M_4131 -LRLEINHTI ->M_4132 -LRLPGGSCM ->M_4133 -LRLRWGQII ->M_4134 -LRLSEPAEI ->M_4135 -LRMSDPSHI ->M_4136 -LRMSRSYPT ->M_4137 -LRNDARSLY ->M_4138 -LRPSSIETY ->M_4139 -LRQWIVVTM ->M_4140 -LRRHRDVSA ->M_4141 -LRRMNSFQV ->M_4142 -LRRNYRCAI ->M_4143 -LRRNYRCAI ->M_4144 -LRRQDYQEI ->M_4145 -LRRVASALL ->M_4146 -LRSDAPAQL ->M_4147 -LRSEEDGLV ->M_4148 -LRSERNNTM ->M_4149 -LRSIRVRLL ->M_4150 -LRSQAALSL ->M_4151 -LRSQFPLIL ->M_4152 -LRTEQNDFI ->M_4153 -LRVSDGSLL ->M_4154 -LRWEYGSIL ->M_4155 -LRYFLKHGI ->M_4156 -LRYGAALIY ->M_4157 -LSEFPEDSY ->M_4158 -LSFKRQRAM ->M_4159 -LSIIRFKGL ->M_4160 -LSPMNHLCY ->M_4161 -LSSLWYHTY ->M_4162 -LSTCRKLSL ->M_4163 -LTDYDTRFY ->M_4164 -LTEPHLRLL ->M_4165 -LTGLVWQRY ->M_4166 -LTIYAALPY ->M_4167 -LTMCMKKSL ->M_4168 -LTQKQVLNY ->M_4169 -LVAQHYAAL ->M_4170 -LVDTVIDAY ->M_4171 -LVQNSCWLI ->M_4172 -LVRDRMKEL ->M_4173 -LWQSCEESF ->M_4174 -LYAVMGRSW ->M_4175 -LYEDTLYTV ->M_4176 -LYEDWCQTV ->M_4177 -LYEDWCQTV ->M_4178 -LYFHSFIRI ->M_4179 -LYFLAGQSL ->M_4180 -LYFTRPVPL ->M_4181 -LYGEQGHRW ->M_4182 -LYGHSTHDL ->M_4183 -LYHRDLAKW ->M_4184 -LYMINHFFC ->M_4185 -LYPDINNPF ->M_4186 -LYPPSLPPF ->M_4187 -LYTAYHVFF ->M_4188 -LYVWKSELV ->M_4189 -MACDRYVAI ->M_4190 -MAEVNITYV ->M_4191 -MAFDRYVAI ->M_4192 -MAFDRYVAI ->M_4193 -MAHERRDQL ->M_4194 -MAHERRDQL ->M_4195 -MAIGHFGQL ->M_4196 -MAKYWNQFL ->M_4197 -MAMSSRLAL ->M_4198 -MATAYIRSM ->M_4199 -MAYDQFLAI ->M_4200 -MAYDQFLAI ->M_4201 -MAYSITCPI ->M_4202 -MCMKKSLRL ->M_4203 -MERERKAIA ->M_4204 -MEVEAEQLL ->M_4205 -MFATDYTTI ->M_4206 -MFTLRMALF ->M_4207 -MGHLQIRSL ->M_4208 -MGKSTHTSM ->M_4209 -MHEEGYNKL ->M_4210 -MHEYKIQGL ->M_4211 -MHFCGGSFI ->M_4212 -MHHPGSRKF ->M_4213 -MHKTGLLGL ->M_4214 -MHNLLIHRV ->M_4215 -MHPDGRFEC ->M_4216 -MIFILFLVI ->M_4217 -MIRVKDSLI ->M_4218 -MKQKKSSCL ->M_4219 -MLCFYTPAL ->M_4220 -MLHLYPGPM ->M_4221 -MLKTGISTV ->M_4222 -MLLMNLATA ->M_4223 -MLLSILLPL ->M_4224 -MLLSQNASI ->M_4225 -MLNKVLYRL ->M_4226 -MLRELSSAF ->M_4227 -MLRRQIRLL ->M_4228 -MLRRQIRLL ->M_4229 -MLSLRESPM ->M_4230 -MLTSKVTVL ->M_4231 -MLYRTVREL ->M_4232 -MLYRTVREL ->M_4233 -MMQCHRLSW ->M_4234 -MNKRLGLEL ->M_4235 -MNYKKGRAF ->M_4236 -MPILKSVLI ->M_4237 -MPKKVISAL ->M_4238 -MPLLKLSCS ->M_4239 -MPQYLASPL ->M_4240 -MQFTQALEV ->M_4241 -MRAAYLDDL ->M_4242 -MRCQYETVL ->M_4243 -MREQRERQL ->M_4244 -MRLRGGRMI ->M_4245 -MRPISGVML ->M_4246 -MRQPLPASM ->M_4247 -MRRRQCEEV ->M_4248 -MRRYQSRVI ->M_4249 -MRRYQSRVI ->M_4250 -MRSCLRLAL ->M_4251 -MRSCLRLAL ->M_4252 -MSEGIVKLY ->M_4253 -MSPRVFFLL ->M_4254 -MSQSQVALL ->M_4255 -MSRSYPTGL ->M_4256 -MWPLHWSMW ->M_4257 -MYCLMLQCW ->M_4258 -MYCMVFLVL ->M_4259 -MYGAETEKF ->M_4260 -MYMSVLSLI ->M_4261 -MYMSVLSLI ->M_4262 -MYSVVPQMV ->M_4263 -MYSVVPQMV ->M_4264 -MYSYAVPPL ->M_4265 -MYTKLVVGF ->M_4266 -NEILRRYSV ->M_4267 -NFIERFWRI ->M_4268 -NFIERFWRI ->M_4269 -NFSINWWPI ->M_4270 -NHHNRTVEV ->M_4271 -NHKDNSRIR ->M_4272 -NHPYWANTV ->M_4273 -NHSDLAAEL ->M_4274 -NIDLAREAY ->M_4275 -NILPHYLEL ->M_4276 -NIVYHTASI ->M_4277 -NIYSRIREY ->M_4278 -NLARKEYTI ->M_4279 -NLGFRFHMA ->M_4280 -NLKHRKTAA ->M_4281 -NLLANFSFL ->M_4282 -NLLSYFNNL ->M_4283 -NLMAKNNQA ->M_4284 -NLNYRDLYY ->M_4285 -NLPSKRVSL ->M_4286 -NMHCKISLL ->M_4287 -NPLLHMVTM ->M_4288 -NPLRYLAVM ->M_4289 -NPLRYTSIL ->M_4290 -NQKRRSESF ->M_4291 -NRDKLGLQI ->M_4292 -NRFSSKLLA ->M_4293 -NRGPATAEV ->M_4294 -NRLDLVRFY ->M_4295 -NRNYCVSVY ->M_4296 -NRPEEEEQV ->M_4297 -NRQRHTPMY ->M_4298 -NRVGVSSKL ->M_4299 -NSDSFTGFI ->M_4300 -NSINQVKLL ->M_4301 -NTHRSRLSL ->M_4302 -NTMAFSTDY ->M_4303 -NVKKQRAGL ->M_4304 -NVNQRFLNV ->M_4305 -NYLEKVRSL ->M_4306 -NYRDLYYFL ->M_4307 -NYSPRPICV ->M_4308 -PASTLSLGY ->M_4309 -PFPRWLKII ->M_4310 -PHWASSIVL ->M_4311 -PHYDFERSC ->M_4312 -PIEMNPEGY ->M_4313 -PRIGYSLLL ->M_4314 -PRLKWVVLV ->M_4315 -PRNRKPLTV ->M_4316 -PRPSRCLLL ->M_4317 -PRSEEAAVL ->M_4318 -PRSKDTILL ->M_4319 -PRSRWRDQL ->M_4320 -PRWSCQEKL ->M_4321 -PSQPANSFY ->M_4322 -PTALSSLWY ->M_4323 -PTDVLNGAA ->M_4324 -PYPETPPRW ->M_4325 -PYQGRPKLL ->M_4326 -PYQGRPKLL ->M_4327 -PYTSVFLSV ->M_4328 -QAEARLLAL ->M_4329 -QAKVKFIGV ->M_4330 -QEHVRCSAI ->M_4331 -QFSFDGWKF ->M_4332 -QGRPKLLQL ->M_4333 -QHCYMSRLL ->M_4334 -QHDFCGLYM ->M_4335 -QHLLQRMSI ->M_4336 -QHMHCLQDL ->M_4337 -QHPNNSKDV ->M_4338 -QHQRLLEVL ->M_4339 -QHTESLEYM ->M_4340 -QHYAALQEY ->M_4341 -QILSRVAAL ->M_4342 -QLMMSLLQL ->M_4343 -QLREHAATL ->M_4344 -QLRRSKVSV ->M_4345 -QLYPRLKML ->M_4346 -QLYPRLKML ->M_4347 -QMLRIFKEM ->M_4348 -QMYMSVLSL ->M_4349 -QPAWRKASA ->M_4350 -QPLRNFISV ->M_4351 -QPMCRICHE ->M_4352 -QRAPVGKLL ->M_4353 -QRAVSRNLM ->M_4354 -QRFLFIMFL ->M_4355 -QRFLNVQEL ->M_4356 -QRGEGILDM ->M_4357 -QRHGFGEEI ->M_4358 -QRIQMYMSV ->M_4359 -QRIVKPTSI ->M_4360 -QRLEPVYFV ->M_4361 -QRLEVPIEM ->M_4362 -QRMELLITF ->M_4363 -QRQARQYQL ->M_4364 -QRRPSSVGL ->M_4365 -QRRSIPFQM ->M_4366 -QRSGKPVLM ->M_4367 -QRSNSETKV ->M_4368 -QRSRKGDLL ->M_4369 -QSEDRSHTL ->M_4370 -QSQPFSMQY ->M_4371 -QSQPGNALY ->M_4372 -QTCKANLCY ->M_4373 -QTLACNLCY ->M_4374 -QVKRKVQAL ->M_4375 -QYMLTLFTA ->M_4376 -RAEDTALYY ->M_4377 -RAIYHSCSL ->M_4378 -RAKYRESLL ->M_4379 -RAPQRIPSL ->M_4380 -RARLQHCSA ->M_4381 -RARYYIQVA ->M_4382 -RASQRMSSV ->M_4383 -RATARFHQL ->M_4384 -RFFSRFTAV ->M_4385 -RFHRVIKDF ->M_4386 -RFKRKSVVA ->M_4387 -RFLFIMFLF ->M_4388 -RFLRNFPQI ->M_4389 -RFMKYLVNF ->M_4390 -RFNMLNQIF ->M_4391 -RFQDHRWEL ->M_4392 -RHFEEALQT ->M_4393 -RHFRLMHNL ->M_4394 -RHIRHGNVI ->M_4395 -RHLGDQMEV ->M_4396 -RHRCRNRFV ->M_4397 -RHSPRNLIY ->M_4398 -RHTPMYYFL ->M_4399 -RHTPMYYFL ->M_4400 -RLIVKSREL ->M_4401 -RLKQEIKRL ->M_4402 -RLMCGPNTI ->M_4403 -RLRRVASAL ->M_4404 -RMCKFLQYF ->M_4405 -RMSSVGANF ->M_4406 -RNFPQIYIL ->M_4407 -RNPQELWHF ->M_4408 -RNRKRFCVP ->M_4409 -RPGSRGCPM ->M_4410 -RPKYSFHRL ->M_4411 -RPRARLAAL ->M_4412 -RPRARYYIQ ->M_4413 -RPRQGRWWL ->M_4414 -RQFPKKSLM ->M_4415 -RQFYLFYNF ->M_4416 -RQMISELLF ->M_4417 -RQQQDYWLM ->M_4418 -RRENSLSEI ->M_4419 -RRFNMLNQI ->M_4420 -RRGEAEKRL ->M_4421 -RRGGSGAMV ->M_4422 -RRKQSEMYI ->M_4423 -RRLDYDHKL ->M_4424 -RRPSRAMWL ->M_4425 -RRQDYQEIL ->M_4426 -RRSDAEKQL ->M_4427 -RRSKVSVEM ->M_4428 -RRSPSFSRV ->M_4429 -RRVASALLL ->M_4430 -RRVPYRGSV ->M_4431 -RRYLKSGVV ->M_4432 -RSADWQRKI ->M_4433 -RSELNSVEY ->M_4434 -RSFPAGVEM ->M_4435 -RTQDAIHEL ->M_4436 -RTSSIFYSF ->M_4437 -RVGQMAFVF ->M_4438 -RVNDCILQV ->M_4439 -RVRRRGQKL ->M_4440 -RVSDGSLLY ->M_4441 -RWQGRVRTL ->M_4442 -RYAALLKCW ->M_4443 -RYARPSRLV ->M_4444 -RYCLTTLTI ->M_4445 -RYFDEPVEL ->M_4446 -RYFDEPVEL ->M_4447 -RYFLKHGIL ->M_4448 -RYILLKRSL ->M_4449 -RYLENGKEM ->M_4450 -RYLKSGVVL ->M_4451 -RYLPDCDYL ->M_4452 -RYRSIISDI ->M_4453 -RYVAICAPL ->M_4454 -RYVASCKPL ->M_4455 -SADYINANY ->M_4456 -SAEECRTEL ->M_4457 -SAKQQNQIL ->M_4458 -SAKQQNQIL ->M_4459 -SALGREHPA ->M_4460 -SARDQPSSV ->M_4461 -SARLRQRAV ->M_4462 -SASNNNSEL ->M_4463 -SAVRRDLTF ->M_4464 -SAYDGKDYI ->M_4465 -SCSSNPHLL ->M_4466 -SEEERGLEL ->M_4467 -SEKDRPVKV ->M_4468 -SESHRTSLL ->M_4469 -SEVERLDVL ->M_4470 -SFFNCLWEV ->M_4471 -SFPGRVREL ->M_4472 -SFQTITEQF ->M_4473 -SFVDAIHTF ->M_4474 -SGFEFSQVL ->M_4475 -SGMARVGSL ->M_4476 -SHKEAITAL ->M_4477 -SHKKQSSVI ->M_4478 -SHLQRIGTI ->M_4479 -SHLTIVILF ->M_4480 -SHMYVATGI ->M_4481 -SHNRHVPKI ->M_4482 -SHPLHYTTI ->M_4483 -SHPLHYTTI ->M_4484 -SHQPLPGTL ->M_4485 -SHRNPLLDL ->M_4486 -SHSPAGELT ->M_4487 -SHSSNPHLL ->M_4488 -SHTLLLTQL ->M_4489 -SIFYSFLPL ->M_4490 -SKFGQGTGL ->M_4491 -SKQNMPQYL ->M_4492 -SLAKFDAPL ->M_4493 -SLDTTTWEY ->M_4494 -SLFTCVLQL ->M_4495 -SLGDNSEYL ->M_4496 -SLHHKHKEL ->M_4497 -SLIDSSRVV ->M_4498 -SLKLTQSSA ->M_4499 -SLLRKHQIL ->M_4500 -SLLRKHQIT ->M_4501 -SLLVHGGPL ->M_4502 -SLNHRGRVM ->M_4503 -SLNHRGRVM ->M_4504 -SLNPKKFSI ->M_4505 -SLRAEDTAL ->M_4506 -SLSETVRLV ->M_4507 -SLSVRTSGL ->M_4508 -SLWYHTYGL ->M_4509 -SLYTAYHVF ->M_4510 -SLYVWKSEL ->M_4511 -SMAKYWNQF ->M_4512 -SMKAERPPA ->M_4513 -SMKNLQRAV ->M_4514 -SMKVHIKAM ->M_4515 -SMMTATIVF ->M_4516 -SMPANFETI ->M_4517 -SMREALREL ->M_4518 -SMREAVREL ->M_4519 -SMRYFITSV ->M_4520 -SPGPFFWMF ->M_4521 -SPLFYSTCM ->M_4522 -SPLQLPAPL ->M_4523 -SPLRYISIL ->M_4524 -SPMYFFLSY ->M_4525 -SPRSRPSDI ->M_4526 -SPRVFFLLM ->M_4527 -SPSSAYLLF ->M_4528 -SQHPAQQQI ->M_4529 -SQMSQLMGL ->M_4530 -SQPGNALYF ->M_4531 -SRAMWLSLF ->M_4532 -SRATADPEV ->M_4533 -SRCLLLPLL ->M_4534 -SREDDNRER ->M_4535 -SRENRWTTV ->M_4536 -SRFCSLHCL ->M_4537 -SRFTAVREF ->M_4538 -SRFTLRCMV ->M_4539 -SRFVVRPLL ->M_4540 -SRGQEIKTI ->M_4541 -SRHDFHVDL ->M_4542 -SRKGDLLRI ->M_4543 -SRKKRRSPP ->M_4544 -SRKLRKLPT ->M_4545 -SRLHTPVYF ->M_4546 -SRNAYSLEI ->M_4547 -SRNDFEWVY ->M_4548 -SRPGALEHL ->M_4549 -SRPSSKQNM ->M_4550 -SRQMISELL ->M_4551 -SRRARGREK ->M_4552 -SRRSFWSEL ->M_4553 -SRSRNAYSL ->M_4554 -SRSVDVTNI ->M_4555 -SRTVWEEMV ->M_4556 -SRWRDQLLF ->M_4557 -SRYARPSRL ->M_4558 -SSASLNSNY ->M_4559 -SSDEIVQEL ->M_4560 -SSKQHLKPA ->M_4561 -SSLARELSL ->M_4562 -SSLRRMNSF ->M_4563 -SSRGNGKMM ->M_4564 -SSTSHIPEV ->M_4565 -SSYSRVALV ->M_4566 -STDDATWAA ->M_4567 -STERPKMTY ->M_4568 -STIYIFALF ->M_4569 -STKVHIKVL ->M_4570 -STQTHPLTL ->M_4571 -STSHVYHLF ->M_4572 -STYNETNLI ->M_4573 -STYPDQQHV ->M_4574 -SVEEKGKLL ->M_4575 -SVFPTQLQL ->M_4576 -SVFSEQWIF ->M_4577 -SVRENCCSL ->M_4578 -SWMPALECL ->M_4579 -SWPLWTAIF ->M_4580 -SWVSSTLGF ->M_4581 -SYAKNAQDL ->M_4582 -SYARILGTV ->M_4583 -SYAVICNNF ->M_4584 -SYFCILRTI ->M_4585 -SYFGLATVF ->M_4586 -SYFLATDTI ->M_4587 -SYFNNLHLW ->M_4588 -SYGVNLYQF ->M_4589 -SYIYILITI ->M_4590 -SYKFLAPWI ->M_4591 -SYPSIHRFI ->M_4592 -SYPSQPDGF ->M_4593 -SYSLISEKL ->M_4594 -SYVMDHFDI ->M_4595 -SYVRIGATI ->M_4596 -SYWGVFAPI ->M_4597 -SYYKIVSSI ->M_4598 -TAAIRPKSL ->M_4599 -TADVGLAGY ->M_4600 -TAFDESISL ->M_4601 -TAMAYDQFL ->M_4602 -TDKERQRLL ->M_4603 -TDYDTRFYM ->M_4604 -TEFGQKQKL ->M_4605 -TERDQIELL ->M_4606 -TFDRLAYLW ->M_4607 -TFEDNLRSL ->M_4608 -TFGEVNYFF ->M_4609 -TFITSVIRF ->M_4610 -TFLIAMVFI ->M_4611 -TFNDWFEII ->M_4612 -TFSCQLHKF ->M_4613 -THAPERDLC ->M_4614 -THASLSNHV ->M_4615 -THHGPAFSI ->M_4616 -THIFGLMVI ->M_4617 -THIHAAACI ->M_4618 -THMERVLSL ->M_4619 -THMERVLSL ->M_4620 -THPIYYLKI ->M_4621 -THQEALMKL ->M_4622 -THREGISAI ->M_4623 -THRSRLSLG ->M_4624 -THTSYQLSA ->M_4625 -THYQGTWYL ->M_4626 -TIKQRPKPT ->M_4627 -TKFESNLCV ->M_4628 -TLDKKLEYY ->M_4629 -TLERAALRY ->M_4630 -TLGLIFLCL ->M_4631 -TLMVVVWVL ->M_4632 -TLTIRALPA ->M_4633 -TMCMYFRPL ->M_4634 -TMETSFFSF ->M_4635 -TMGSWTCLF ->M_4636 -TMRTRHFTG ->M_4637 -TMRYIHFLF ->M_4638 -TMSPRVFFL ->M_4639 -TPGNRTKCF ->M_4640 -TPKSMQSTL ->M_4641 -TPNFRRRAI ->M_4642 -TPSERSKPL ->M_4643 -TPSTQTHPL ->M_4644 -TRAERLTWL ->M_4645 -TRALHRLIV ->M_4646 -TRASDRRGI ->M_4647 -TRDAPGLRV ->M_4648 -TREVTVNVL ->M_4649 -TRFPLKTAF ->M_4650 -TRFPLPEAF ->M_4651 -TRFRSFSSL ->M_4652 -TRFYMYEIL ->M_4653 -TRGPCRRRF ->M_4654 -TRGPQRQIL ->M_4655 -TRGRHQKKI ->M_4656 -TRHGSILAC ->M_4657 -TRHRCRNRF ->M_4658 -TRNCNRHLC ->M_4659 -TRPSEELEL ->M_4660 -TRPTASSSV ->M_4661 -TRRSQKRLQ ->M_4662 -TRSAEPGYL ->M_4663 -TRSSKPSDM ->M_4664 -TRSWGTPQL ->M_4665 -TRTPHSTRC ->M_4666 -TRVGSKLLI ->M_4667 -TRYSAQADI ->M_4668 -TSMWRTYVM ->M_4669 -TSMWRTYVM ->M_4670 -TTDGRNYIV ->M_4671 -TTFDRLAYL ->M_4672 -TTMEDQLLF ->M_4673 -TVHTRNHTA ->M_4674 -TVIDAYMNF ->M_4675 -TVLHRPHSA ->M_4676 -TVSPQPQEV ->M_4677 -TWLQVLEAI ->M_4678 -TYEEPCQAI ->M_4679 -TYLADRVQI ->M_4680 -TYLYPPKHW ->M_4681 -TYVLYYDAL ->M_4682 -TYYPLKPEI ->M_4683 -TYYPLKPEI ->M_4684 -VAKKKEAPA ->M_4685 -VARERRKAE ->M_4686 -VFERDFFKI ->M_4687 -VFETGTFLI ->M_4688 -VFLPMTLLL ->M_4689 -VFRQGHQLF ->M_4690 -VFTRVSAYI ->M_4691 -VFYTIFTPI ->M_4692 -VGKKRHDPL ->M_4693 -VHALRLHLY ->M_4694 -VHFDHFHPC ->M_4695 -VHFLREVTV ->M_4696 -VHHLAVSGV ->M_4697 -VHIKAMQTV ->M_4698 -VHIKVLQTV ->M_4699 -VHKKGYNKL ->M_4700 -VHKQFPITL ->M_4701 -VHKTDLERM ->M_4702 -VHRGTGAVY ->M_4703 -VHSENLQNW ->M_4704 -VLAIQRCPM ->M_4705 -VLDEMRCQY ->M_4706 -VLKSTSCSI ->M_4707 -VMKHLLSPL ->M_4708 -VMSCVWFTI ->M_4709 -VQMYRGHPA ->M_4710 -VQNEDVTLL ->M_4711 -VQPSQWASI ->M_4712 -VRDRMKELL ->M_4713 -VRELRDMGI ->M_4714 -VRFQDESVV ->M_4715 -VRFVTRYIY ->M_4716 -VRFVVTITV ->M_4717 -VRGTTLHLL ->M_4718 -VRHQRVHQA ->M_4719 -VRLKRSIQF ->M_4720 -VRLSYKLTF ->M_4721 -VRMEVISVT ->M_4722 -VRMEVVSIT ->M_4723 -VRNDHMNLR ->M_4724 -VRNRCNIYI ->M_4725 -VRPRARYYI ->M_4726 -VRQGGVFRL ->M_4727 -VRRLGPKLL ->M_4728 -VRRLHCSAA ->M_4729 -VRRMLTSKV ->M_4730 -VRRRRRCPG ->M_4731 -VRSLNLVLM ->M_4732 -VRSNLEPLF ->M_4733 -VRVGSDMLI ->M_4734 -VRVTQKFHM ->M_4735 -VSDDLVKQY ->M_4736 -VSGHVSMKY ->M_4737 -VSSSSSGGY ->M_4738 -VTADSDPAY ->M_4739 -VTAPRATTL ->M_4740 -VTDVLTEPH ->M_4741 -VTMDWLVRI ->M_4742 -VVAPRTLLL ->M_4743 -VVESLVEAY ->M_4744 -VVHEVQRYL ->M_4745 -VVKSKQVAL ->M_4746 -VVPQMVNPF ->M_4747 -VVSDVPEEL ->M_4748 -VYFHMTLSF ->M_4749 -VYHLFCALL ->M_4750 -VYISLFTCV ->M_4751 -VYLRRHRDV ->M_4752 -VYPRGFQEK ->M_4753 -VYQVLSGGW ->M_4754 -VYSEYGMDV ->M_4755 -VYSLRTRAI ->M_4756 -VYSLYWSIL ->M_4757 -VYVVSNNNL ->M_4758 -VYVVTKFLM ->M_4759 -VYYLLELLL ->M_4760 -WAGSHSMRY ->M_4761 -WARRKQSEM ->M_4762 -WASRFSTPY ->M_4763 -WFLWKQFCW ->M_4764 -WGMLNSLSL ->M_4765 -WHLQGPEDL ->M_4766 -WHREYNFKY ->M_4767 -WHSVVIQRL ->M_4768 -WHVPNKPPM ->M_4769 -WIEREGPEY ->M_4770 -WLNENQRLV ->M_4771 -WLSFRSSAS ->M_4772 -WLSNFQGRY ->M_4773 -WMEKRYLSQ ->M_4774 -WMEQEGPEY ->M_4775 -WPLTHSQGM ->M_4776 -WQRQHKLTI ->M_4777 -WRPEAVQYY ->M_4778 -WSDQLSAFS ->M_4779 -WTDVFQIGI ->M_4780 -WTESLAAVF ->M_4781 -WVKRQKISF ->M_4782 -WVRPRRRLL ->M_4783 -WVRPRRRLL ->M_4784 -WYHTCGGTL ->M_4785 -WYIWILLVL ->M_4786 -YAFTGLTLM ->M_4787 -YAMQRSWQE ->M_4788 -YARILGTVL ->M_4789 -YCDDLPLLA ->M_4790 -YDDARVELV ->M_4791 -YEHHHSARL ->M_4792 -YFGLATVFI ->M_4793 -YFHSFIRIV ->M_4794 -YFTSSSRYF ->M_4795 -YFYNQEEYV ->M_4796 -YGVTRSKAM ->M_4797 -YHCTAVNAY ->M_4798 -YHDACIEEA ->M_4799 -YHDVSGCYI ->M_4800 -YHEAGVTAL ->M_4801 -YHFSWTSDR ->M_4802 -YHHRFNNFM ->M_4803 -YHQQNVPWA ->M_4804 -YICDLRRQV ->M_4805 -YINNSVLPY ->M_4806 -YKGSRFHRV ->M_4807 -YLADRVQIV ->M_4808 -YLADRVQIV ->M_4809 -YLENRKETL ->M_4810 -YLENRKETL ->M_4811 -YLEQKPCIY ->M_4812 -YLFRKELRY ->M_4813 -YLKEELMCL ->M_4814 -YLKENFLPW ->M_4815 -YLRRHRDVS ->M_4816 -YLSLVEISY ->M_4817 -YLTVVSLSY ->M_4818 -YMDRTPGPA ->M_4819 -YMKTQSKSS ->M_4820 -YMLTLFTAM ->M_4821 -YNFKYVDLI ->M_4822 -YNVFRQLSL ->M_4823 -YPMRRRQCE ->M_4824 -YPRLKMLAF ->M_4825 -YPSIHRFIL ->M_4826 -YQLHNIQVI ->M_4827 -YQMQFTQAL ->M_4828 -YQMQFTQAL ->M_4829 -YQSEKLCSL ->M_4830 -YRAGKPTLV ->M_4831 -YRASEQKLC ->M_4832 -YRDNTELPY ->M_4833 -YRDVHVQKV ->M_4834 -YRGPLSTTI ->M_4835 -YRGSVAPIL ->M_4836 -YRITVVESL ->M_4837 -YRLEAVHAL ->M_4838 -YRLEGDTLI ->M_4839 -YRQFPKKSL ->M_4840 -YRRHSLRAI ->M_4841 -YRTVNNLIL ->M_4842 -YSFDSLCQY ->M_4843 -YSRDQIYIY ->M_4844 -YSRQMISEL ->M_4845 -YSRQMISEL ->M_4846 -YTCEQNDQL ->M_4847 -YTDSSSVLN ->M_4848 -YTEDHSASL ->M_4849 -YTELWFLGL ->M_4850 -YTLLAFSVF ->M_4851 -YTRKCTQAI ->M_4852 -YTSMWRTYV ->M_4853 -YTSMWRTYV ->M_4854 -YVAICSPLF ->M_4855 -YVDYMMCEF ->M_4856 -YVFLHQCVL ->M_4857 -YVFLHQCVL ->M_4858 -YVGENVRFV ->M_4859 -YVGIFHFQF ->M_4860 -YVLTRSKAM ->M_4861 -YVTVLCLTF ->M_4862 -YVYSLYWSI ->M_4863 -YWGVFAPIW ->M_4864 -YWPPQSQPF ->M_4865 -YYEKIFSTL ->M_4866 -YYFLCLLL* ->M_4867 -YYFLRPLL* ->M_4868 -YYFLRPLL* ->M_4869 -YYKIVSSIL ->M_4870 -YYLVANTKF ->M_4871 -YYTNFSLEL ->M_4872 -YYTNFSLEL ->M_4873 -YYYFLCLLL ->M_4874 -YYYFLRPLL ->M_4875 -YYYFLRPLL diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_135773_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_135773_1_T_iedb.xml deleted file mode 100755 index c0028a47..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_135773_1_T_iedb.xml +++ /dev/null @@ -1,41743 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_3590 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_3590 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_3591 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_3592 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_3593 - 9 - - - 1 - gnl|BL_ORD_ID|1223 - 97093|polyprotein|AAB66324.1|Hepatitis C virus (isolate H77)|63746 - 1223 - 10 - - - 1 - 13.4678 - 23 - 8.17864 - 2 - 7 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - HASLIP - HADVIP - HA +IP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 5 - Query_5 - M_3594 - 9 - - - 1 - gnl|BL_ORD_ID|99 - 6808|membrane protein|AAA45887.1|Human gammaherpesvirus 4|10376 - 99 - 8 - - - 1 - 13.853 - 24 - 7.77379 - 3 - 9 - 1 - 7 - 0 - 0 - 5 - 5 - 0 - 7 - CGLGKIL - CPLSKIL - C L KIL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 6 - Query_6 - M_3595 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_3596 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_3597 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_3598 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_3599 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_3600 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_3601 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_3602 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_3603 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_3604 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_3605 - 9 - - - 1 - gnl|BL_ORD_ID|114 - 7660|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 - 114 - 20 - - - 1 - 13.0826 - 22 - 16.9313 - 2 - 9 - 7 - 14 - 0 - 0 - 3 - 5 - 0 - 8 - MCVIHFSF - MCAVHPTL - MC +H + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 17 - Query_17 - M_3606 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_3607 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_3608 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_3609 - 9 - - - 1 - gnl|BL_ORD_ID|1141 - 75408|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 1141 - 20 - - - 1 - 13.853 - 24 - 5.60382 - 1 - 8 - 5 - 12 - 0 - 0 - 4 - 7 - 0 - 8 - AQKEHSHL - AERKHRHL - A+++H HL - - - - - 2 - gnl|BL_ORD_ID|419 - 25275|Glutamate decarboxylase 2|Q05329.1|Homo sapiens|9606 - 419 - 13 - - - 1 - 13.0826 - 22 - 16.789 - 4 - 8 - 6 - 10 - 0 - 0 - 4 - 4 - 0 - 5 - EHSHL - EHSHF - EHSH - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 21 - Query_21 - M_3610 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 22 - Query_22 - M_3611 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_3612 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_3613 - 9 - - - 1 - gnl|BL_ORD_ID|2266 - 418964|PPE family protein PPE68|KAM81677.1|Mycobacterium tuberculosis H37Ra|419947 - 2266 - 9 - - - 1 - 13.4678 - 23 - 10.0233 - 1 - 6 - 4 - 9 - 0 - 0 - 4 - 6 - 0 - 6 - ARINSI - ARLNSL - AR+NS+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 25 - Query_25 - M_3614 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_3615 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_3616 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 28 - Query_28 - M_3617 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 29 - Query_29 - M_3618 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 30 - Query_30 - M_3619 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 31 - Query_31 - M_3620 - 9 - - - 1 - gnl|BL_ORD_ID|1393 - 110338|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1393 - 33 - - - 1 - 16.5494 - 31 - 0.25572 - 2 - 9 - 15 - 22 - 0 - 0 - 6 - 7 - 0 - 8 - RPEKLPEL - RPRKLPQL - RP KLP+L - - - - - 2 - gnl|BL_ORD_ID|1428 - 113122|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1428 - 10 - - - 1 - 16.1642 - 30 - 0.350719 - 2 - 9 - 3 - 10 - 0 - 0 - 6 - 7 - 0 - 8 - RPEKLPEL - RPRKLPQL - RP KLP+L - - - - - 3 - gnl|BL_ORD_ID|1394 - 110373|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1394 - 25 - - - 1 - 14.6234 - 26 - 1.89486 - 3 - 9 - 1 - 7 - 0 - 0 - 5 - 6 - 0 - 7 - PEKLPEL - PRKLPQL - P KLP+L - - - - - 4 - gnl|BL_ORD_ID|2189 - 190533|nucleocapsid protein|AAP49024.1|SARS coronavirus|227859 - 2189 - 15 - - - 1 - 13.853 - 24 - 6.19118 - 2 - 8 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - RPEKLPE - RPQGLPN - RP+ LP - - - - - 5 - gnl|BL_ORD_ID|850 - 55683|nucleocapsid protein|ABI96968.1|SARS coronavirus|227859 - 850 - 15 - - - 1 - 13.853 - 24 - 6.40908 - 2 - 8 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - RPEKLPE - RPQGLPN - RP+ LP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 32 - Query_32 - M_3621 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 33 - Query_33 - M_3622 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 34 - Query_34 - M_3623 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 35 - Query_35 - M_3624 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 36 - Query_36 - M_3625 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 37 - Query_37 - M_3626 - 9 - - - 1 - gnl|BL_ORD_ID|798 - 53148|Transcription activator BRLF1|P03209.1|Human herpesvirus 4 strain B95-8|10377 - 798 - 15 - - - 1 - 13.4678 - 23 - 12.0936 - 1 - 6 - 10 - 15 - 0 - 0 - 4 - 6 - 0 - 6 - ASFSNH - ASYSSH - AS+S+H - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 38 - Query_38 - M_3627 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 39 - Query_39 - M_3628 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 40 - Query_40 - M_3629 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 41 - Query_41 - M_3630 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 42 - Query_42 - M_3631 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 43 - Query_43 - M_3632 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 44 - Query_44 - M_3633 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 45 - Query_45 - M_3634 - 9 - - - 1 - gnl|BL_ORD_ID|1171 - 79300|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 1171 - 15 - - - 1 - 11.927 - 19 - 83.5344 - 1 - 8 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - CFPLHGLQ - SFPDPGLR - FP GL+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 46 - Query_46 - M_3635 - 9 - - - 1 - gnl|BL_ORD_ID|2252 - 244160|surface antigen 2 (CA-2)|XP_818927.1|Trypanosoma cruzi strain CL Brener|353153 - 2252 - 9 - - - 1 - 13.0826 - 22 - 13.4763 - 1 - 6 - 3 - 8 - 0 - 0 - 4 - 5 - 0 - 6 - CGDKIS - AGDKLS - GDK+S - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 47 - Query_47 - M_3636 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 48 - Query_48 - M_3637 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 49 - Query_49 - M_3638 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 50 - Query_50 - M_3639 - 9 - - - 1 - gnl|BL_ORD_ID|109 - 7353|Early antigen protein D|P03191.1|Human herpesvirus 4 strain B95-8|10377 - 109 - 9 - - - 1 - 12.3122 - 20 - 45.611 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 7 - 0 - 9 - CHSNSRDHL - CYDHAQTHL - C+ +++ HL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 51 - Query_51 - M_3640 - 9 - - - 1 - gnl|BL_ORD_ID|582 - 36504|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 - 582 - 9 - - - 1 - 12.6974 - 21 - 26.0147 - 1 - 6 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - CHYEKK - CHSKKK - CH +KK - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 52 - Query_52 - M_3641 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 53 - Query_53 - M_3642 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 54 - Query_54 - M_3643 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 55 - Query_55 - M_3644 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 56 - Query_56 - M_3645 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 57 - Query_57 - M_3646 - 9 - - - 1 - gnl|BL_ORD_ID|383 - 23601|Genome polyprotein|SRC279960|Hepatitis C virus (isolate H77)|63746 - 383 - 21 - - - 1 - 15.0086 - 27 - 1.18025 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 5 - 0 - 9 - CPPNHIVSL - CPAGHAVGI - CP H V + - - - - - 2 - gnl|BL_ORD_ID|597 - 37127|polyprotein|AAY82030.1|Hepatitis C virus genotype 1|41856 - 597 - 9 - - - 1 - 13.853 - 24 - 7.07804 - 1 - 7 - 3 - 9 - 0 - 0 - 4 - 4 - 0 - 7 - CPPNHIV - CPAGHAV - CP H V - - - - - 3 - gnl|BL_ORD_ID|598 - 37136|Genome polyprotein|P27958.3|Hepatitis C virus|11103 - 598 - 9 - - - 1 - 13.4678 - 23 - 9.5131 - 1 - 7 - 3 - 9 - 0 - 0 - 4 - 4 - 0 - 7 - CPPNHIV - CPTGHAV - CP H V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 58 - Query_58 - M_3647 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 59 - Query_59 - M_3648 - 9 - - - 1 - gnl|BL_ORD_ID|291 - 19435|polyprotein|CDF77361.1|Dengue virus 3|11069 - 291 - 10 - - - 1 - 15.0086 - 27 - 1.14868 - 3 - 9 - 1 - 7 - 0 - 0 - 5 - 6 - 0 - 7 - AETRKTF - GESRKTF - E+RKTF - - - - - 2 - gnl|BL_ORD_ID|290 - 19434|Genome polyprotein|P27915.1|Dengue virus 3|11069 - 290 - 9 - - - 1 - 15.0086 - 27 - 1.29649 - 3 - 9 - 1 - 7 - 0 - 0 - 5 - 6 - 0 - 7 - AETRKTF - GESRKTF - E+RKTF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 60 - Query_60 - M_3649 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 61 - Query_61 - M_3650 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 62 - Query_62 - M_3651 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 63 - Query_63 - M_3652 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 64 - Query_64 - M_3653 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 65 - Query_65 - M_3654 - 9 - - - 1 - gnl|BL_ORD_ID|156 - 11956|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 - 156 - 11 - - - 1 - 12.3122 - 20 - 38.8163 - 1 - 9 - 3 - 11 - 0 - 0 - 4 - 5 - 0 - 9 - CRPQCCQSV - CRVLCCYVL - CR CC + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 66 - Query_66 - M_3655 - 9 - - - 1 - gnl|BL_ORD_ID|810 - 54330|BZLF1|AAA66529.1|Human gammaherpesvirus 4|10376 - 810 - 13 - - - 1 - 13.853 - 24 - 5.6596 - 1 - 9 - 3 - 11 - 0 - 0 - 5 - 6 - 0 - 9 - CRRGLEQLL - CRAKFKQLL - CR +QLL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 67 - Query_67 - M_3656 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 68 - Query_68 - M_3657 - 9 - - - 1 - gnl|BL_ORD_ID|61 - 4371|tegument protein VP11/12|NP_044516.1|Human alphaherpesvirus 2|10310 - 61 - 9 - - - 1 - 11.927 - 19 - 112.786 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 5 - 0 - 8 - CSDTHTNE - ASDSLNNE - SD+ NE - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 69 - Query_69 - M_3658 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 70 - Query_70 - M_3659 - 9 - - - 1 - gnl|BL_ORD_ID|2118 - 186354|polyprotein|AGO67248.1|Dengue virus 2|11060 - 2118 - 10 - - - 1 - 13.4678 - 23 - 10.9961 - 3 - 9 - 4 - 10 - 0 - 0 - 5 - 6 - 0 - 7 - MTKIFSL - LTKRFSL - +TK FSL - - - - - 2 - gnl|BL_ORD_ID|445 - 27216|polyprotein|BAD73987.1|Hepatitis C virus subtype 1b|31647 - 445 - 9 - - - 1 - 12.6974 - 21 - 31.4086 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 6 - 0 - 8 - VMTKIFSL - LMTHFFSI - +MT FS+ - - - - - 3 - gnl|BL_ORD_ID|1678 - 149027|NS5 protein|BAA00702.1|Hepatitis C virus (isolate H77)|63746 - 1678 - 18 - - - 1 - 12.3122 - 20 - 40.471 - 2 - 9 - 10 - 17 - 0 - 0 - 4 - 6 - 0 - 8 - VMTKIFSL - LMTHFFSV - +MT FS+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 71 - Query_71 - M_3660 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 72 - Query_72 - M_3661 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 73 - Query_73 - M_3662 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 74 - Query_74 - M_3663 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 75 - Query_75 - M_3664 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 76 - Query_76 - M_3665 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 77 - Query_77 - M_3666 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 78 - Query_78 - M_3667 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 79 - Query_79 - M_3668 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 80 - Query_80 - M_3669 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 81 - Query_81 - M_3670 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 82 - Query_82 - M_3671 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 83 - Query_83 - M_3672 - 9 - - - 1 - gnl|BL_ORD_ID|1139 - 75356|EBNA3A nuclear protein|Q8AZJ8|Human gammaherpesvirus 4|10376 - 1139 - 9 - - - 1 - 13.4678 - 23 - 12.7908 - 2 - 7 - 3 - 8 - 0 - 0 - 4 - 5 - 0 - 6 - LHTRHG - LHEQHG - LH +HG - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 84 - Query_84 - M_3673 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 85 - Query_85 - M_3674 - 9 - - - 1 - gnl|BL_ORD_ID|131 - 9316|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 - 131 - 15 - - - 1 - 13.4678 - 23 - 11.8896 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - DLLGHP - DLVGWP - DL+G P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 86 - Query_86 - M_3675 - 9 - - - 1 - gnl|BL_ORD_ID|1573 - 141402|tegument protein VP22|NP_044651.1|Human alphaherpesvirus 1|10298 - 1573 - 10 - - - 1 - 12.6974 - 21 - 27.4501 - 3 - 7 - 2 - 6 - 0 - 0 - 4 - 5 - 0 - 5 - PTKRP - PTERP - PT+RP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 87 - Query_87 - M_3676 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 88 - Query_88 - M_3677 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 89 - Query_89 - M_3678 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 90 - Query_90 - M_3679 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 91 - Query_91 - M_3680 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 92 - Query_92 - M_3681 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 93 - Query_93 - M_3682 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 94 - Query_94 - M_3683 - 9 - - - 1 - gnl|BL_ORD_ID|1895 - 180611|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1895 - 15 - - - 1 - 14.2382 - 25 - 3.25804 - 2 - 9 - 4 - 11 - 0 - 0 - 5 - 5 - 0 - 8 - RNDFPVVL - RGDLPVWL - R D PV L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 95 - Query_95 - M_3684 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 96 - Query_96 - M_3685 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 97 - Query_97 - M_3686 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 98 - Query_98 - M_3687 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 99 - Query_99 - M_3688 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 100 - Query_100 - M_3689 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 101 - Query_101 - M_3690 - 9 - - - 1 - gnl|BL_ORD_ID|1275 - 101813|Pol polyprotein|Q9YLQ7|Human immunodeficiency virus 1|11676 - 1275 - 11 - - - 1 - 13.0826 - 22 - 19.3899 - 1 - 9 - 3 - 11 - 0 - 0 - 4 - 6 - 0 - 9 - DTDILSYSY - NPDIVIYQY - + DI+ Y Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 102 - Query_102 - M_3691 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 103 - Query_103 - M_3692 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 104 - Query_104 - M_3693 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 105 - Query_105 - M_3694 - 9 - - - 1 - gnl|BL_ORD_ID|833 - 54821|E2 protein|AAM33354.1|Hepatitis C virus subtype 1a|31646 - 833 - 9 - - - 1 - 13.0826 - 22 - 15.4875 - 1 - 6 - 4 - 9 - 0 - 0 - 4 - 4 - 0 - 6 - DYPCCI - HYPCTI - YPC I - - - - - 2 - gnl|BL_ORD_ID|1149 - 75636|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 1149 - 10 - - - 1 - 13.0826 - 22 - 16.111 - 1 - 6 - 5 - 10 - 0 - 0 - 4 - 4 - 0 - 6 - DYPCCI - HYPCTI - YPC I - - - - - 3 - gnl|BL_ORD_ID|835 - 54825|polyprotein|BAA03375.1|Hepatitis C virus|11103 - 835 - 9 - - - 1 - 12.6974 - 21 - 29.3325 - 1 - 6 - 4 - 9 - 0 - 0 - 3 - 4 - 0 - 6 - DYPCCI - HYPCTV - YPC + - - - - - 4 - gnl|BL_ORD_ID|417 - 25186|polyprotein|AAK32686.1|Hepatitis C virus|11103 - 417 - 10 - - - 1 - 12.6974 - 21 - 29.385 - 2 - 6 - 2 - 6 - 0 - 0 - 3 - 4 - 0 - 5 - YPCCI - YPCTV - YPC + - - - - - 5 - gnl|BL_ORD_ID|1099 - 72566|polyprotein|BAD73987.1|Hepatitis C virus subtype 1b|31647 - 1099 - 9 - - - 1 - 12.6974 - 21 - 30.8766 - 1 - 6 - 2 - 7 - 0 - 0 - 3 - 4 - 0 - 6 - DYPCCI - HYPCTV - YPC + - - - - - 6 - gnl|BL_ORD_ID|1413 - 111407|polyprotein|BAA00792.1|Hepatitis C virus|11103 - 1413 - 10 - - - 1 - 12.6974 - 21 - 33.6561 - 2 - 6 - 2 - 6 - 0 - 0 - 3 - 4 - 0 - 5 - YPCCI - YPCTV - YPC + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 106 - Query_106 - M_3695 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 107 - Query_107 - M_3696 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 108 - Query_108 - M_3697 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 109 - Query_109 - M_3698 - 9 - - - 1 - gnl|BL_ORD_ID|1218 - 96897|polyprotein|ABR25251.1|Hepatitis C virus (isolate H77)|63746 - 1218 - 17 - - - 1 - 12.6974 - 21 - 22.1036 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 6 - 0 - 7 - ALIRHLN - SLLRHHN - +L+RH N - - - - - 2 - gnl|BL_ORD_ID|1616 - 144403|polyprotein|AAK08509.1|Hepatitis C virus subtype 1b|31647 - 1616 - 9 - - - 1 - 11.927 - 19 - 95.9763 - 3 - 8 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - LIRHLN - LLRHHN - L+RH N - - - - - 3 - gnl|BL_ORD_ID|1785 - 159290|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 - 1785 - 9 - - - 1 - 11.927 - 19 - 109.216 - 3 - 8 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - LIRHLN - LLRHHN - L+RH N - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 110 - Query_110 - M_3699 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 111 - Query_111 - M_3700 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 112 - Query_112 - M_3701 - 9 - - - 1 - gnl|BL_ORD_ID|1979 - 183223|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1979 - 10 - - - 1 - 13.0826 - 22 - 16.6782 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 5 - 0 - 8 - FPQKYYWW - FPGKTVWF - FP K W+ - - - - - 2 - gnl|BL_ORD_ID|2214 - 193060|Nef protein|Q9YYU3|Human immunodeficiency virus 1|11676 - 2214 - 10 - - - 1 - 11.927 - 19 - 86.442 - 1 - 8 - 1 - 8 - 0 - 0 - 3 - 4 - 0 - 8 - EFPQKYYW - RFPLTFGW - FP + W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 113 - Query_113 - M_3702 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 114 - Query_114 - M_3703 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 115 - Query_115 - M_3704 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 116 - Query_116 - M_3705 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 117 - Query_117 - M_3706 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 118 - Query_118 - M_3707 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 119 - Query_119 - M_3708 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 120 - Query_120 - M_3709 - 9 - - - 1 - gnl|BL_ORD_ID|115 - 7708|gag polyprotein|BAA00992.1|Human immunodeficiency virus 1|11676 - 115 - 9 - - - 1 - 14.6234 - 26 - 2.04484 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 8 - 0 - 9 - EIKTIVKAI - DCKTILKAL - + KTI+KA+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 121 - Query_121 - M_3710 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 122 - Query_122 - M_3711 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 123 - Query_123 - M_3712 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 124 - Query_124 - M_3713 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 125 - Query_125 - M_3714 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 126 - Query_126 - M_3715 - 9 - - - 1 - gnl|BL_ORD_ID|1983 - 183252|polyprotein|AGT63075.1|Dengue virus 1|11053 - 1983 - 10 - - - 1 - 12.6974 - 21 - 36.0093 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 5 - 0 - 9 - ELHRQVKTL - SLHYAWKTM - LH KT+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 127 - Query_127 - M_3716 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 128 - Query_128 - M_3717 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 129 - Query_129 - M_3718 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 130 - Query_130 - M_3719 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 131 - Query_131 - M_3720 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 132 - Query_132 - M_3721 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 133 - Query_133 - M_3722 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 134 - Query_134 - M_3723 - 9 - - - 1 - gnl|BL_ORD_ID|176 - 13262|gag polyprotein|BAA00992.1|Human immunodeficiency virus 1|11676 - 176 - 9 - - - 1 - 14.6234 - 26 - 1.76369 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 6 - 0 - 9 - EMRCQYETV - ELRSLYNTV - E+R Y TV - - - - - 2 - gnl|BL_ORD_ID|575 - 36306|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 - 575 - 15 - - - 1 - 14.2382 - 25 - 2.38473 - 2 - 9 - 4 - 11 - 0 - 0 - 4 - 5 - 0 - 8 - MRCQYETV - MNCSYENM - M C YE + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 135 - Query_135 - M_3724 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 136 - Query_136 - M_3725 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 137 - Query_137 - M_3726 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 138 - Query_138 - M_3727 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 139 - Query_139 - M_3728 - 9 - - - 1 - gnl|BL_ORD_ID|1857 - 180423|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1857 - 10 - - - 1 - 12.6974 - 21 - 37.2442 - 1 - 9 - 2 - 10 - 0 - 0 - 5 - 6 - 0 - 9 - ERDGLERAL - ERDIPERSW - ERD ER+ - - - - - 2 - gnl|BL_ORD_ID|1861 - 180440|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1861 - 15 - - - 1 - 10.7714 - 16 - 260.888 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 6 - 0 - 9 - ERDGLERAL - EREIPERSW - ER+ ER+ - - - - - 3 - gnl|BL_ORD_ID|1968 - 182898|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1968 - 10 - - - 1 - 10.7714 - 16 - 362.692 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 6 - 0 - 9 - ERDGLERAL - EREIPERSW - ER+ ER+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 140 - Query_140 - M_3729 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 141 - Query_141 - M_3730 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 142 - Query_142 - M_3731 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 143 - Query_143 - M_3732 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 144 - Query_144 - M_3733 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 145 - Query_145 - M_3734 - 9 - - - 1 - gnl|BL_ORD_ID|358 - 22633|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 - 358 - 20 - - - 1 - 13.4678 - 23 - 12.2414 - 4 - 9 - 3 - 8 - 0 - 0 - 4 - 4 - 0 - 6 - DTNQKC - DTGQAC - DT Q C - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 146 - Query_146 - M_3735 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 147 - Query_147 - M_3736 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 148 - Query_148 - M_3737 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 149 - Query_149 - M_3738 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 150 - Query_150 - M_3739 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 151 - Query_151 - M_3740 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 152 - Query_152 - M_3741 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 153 - Query_153 - M_3742 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 154 - Query_154 - M_3743 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 155 - Query_155 - M_3744 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 156 - Query_156 - M_3745 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 157 - Query_157 - M_3746 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 158 - Query_158 - M_3747 - 9 - - - 1 - gnl|BL_ORD_ID|1011 - 67349|Latent membrane protein 2|Q69135|Human gammaherpesvirus 4|10376 - 1011 - 9 - - - 1 - 15.3938 - 28 - 0.690962 - 3 - 7 - 2 - 6 - 0 - 0 - 5 - 5 - 0 - 5 - YGPVF - YGPVF - YGPVF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 159 - Query_159 - M_3748 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 160 - Query_160 - M_3749 - 9 - - - 1 - gnl|BL_ORD_ID|1508 - 139406|polyprotein|ACT37184.1|Hepatitis C virus|11103 - 1508 - 10 - - - 1 - 13.853 - 24 - 6.99268 - 3 - 8 - 5 - 10 - 0 - 0 - 5 - 5 - 0 - 6 - RPTPRL - RPGPRL - RP PRL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 161 - Query_161 - M_3750 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 162 - Query_162 - M_3751 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 163 - Query_163 - M_3752 - 9 - - - 1 - gnl|BL_ORD_ID|1179 - 79628|E1 protein|BAA19893.1|Rubella virus|11041 - 1179 - 21 - - - 1 - 13.853 - 24 - 7.30211 - 4 - 8 - 9 - 13 - 0 - 0 - 4 - 5 - 0 - 5 - LGSWV - LGAWV - LG+WV - - - - - 2 - gnl|BL_ORD_ID|1022 - 68461|polyprotein|ACZ60108.1|Hepatitis C virus|11103 - 1022 - 10 - - - 1 - 13.4678 - 23 - 12.6375 - 3 - 8 - 5 - 10 - 0 - 0 - 4 - 5 - 0 - 6 - LLGSWV - ILGGWV - +LG WV - - - - - 3 - gnl|BL_ORD_ID|1213 - 96547|Genome polyprotein|Q913D4.3|Hepatitis C virus (isolate H77)|63746 - 1213 - 10 - - - 1 - 13.0826 - 22 - 13.7839 - 3 - 8 - 5 - 10 - 0 - 0 - 4 - 5 - 0 - 6 - LLGSWV - ILGGWV - +LG WV - - - - - 4 - gnl|BL_ORD_ID|616 - 37351|trans-sialidase, putative|EAN81560.1|Trypanosoma cruzi|5693 - 616 - 10 - - - 1 - 13.0826 - 22 - 15.8345 - 3 - 8 - 1 - 6 - 0 - 0 - 5 - 5 - 0 - 6 - LLGSWV - LLGLWV - LLG WV - - - - - 5 - gnl|BL_ORD_ID|612 - 37286|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 - 612 - 10 - - - 1 - 13.0826 - 22 - 16.3922 - 3 - 8 - 5 - 10 - 0 - 0 - 4 - 5 - 0 - 6 - LLGSWV - ILGGWV - +LG WV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 164 - Query_164 - M_3753 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 165 - Query_165 - M_3754 - 9 - - - 1 - gnl|BL_ORD_ID|1547 - 141218|regulatory protein ICP22|NP_044663.1|Human alphaherpesvirus 1|10298 - 1547 - 9 - - - 1 - 14.6234 - 26 - 2.04484 - 4 - 8 - 2 - 6 - 0 - 0 - 4 - 5 - 0 - 5 - PRTFC - PRTWC - PRT+C - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 166 - Query_166 - M_3755 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 167 - Query_167 - M_3756 - 9 - - - 1 - gnl|BL_ORD_ID|1916 - 180681|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1916 - 15 - - - 1 - 12.6974 - 21 - 30.771 - 1 - 8 - 3 - 10 - 0 - 0 - 4 - 5 - 0 - 8 - EYVTELPS - EYTDYMPS - EY +PS - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 168 - Query_168 - M_3757 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 169 - Query_169 - M_3758 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 170 - Query_170 - M_3759 - 9 - - - 1 - gnl|BL_ORD_ID|714 - 43937|polyprotein|AAF01178.1|Hepatitis C virus subtype 2a|31649 - 714 - 10 - - - 1 - 14.6234 - 26 - 1.7557 - 1 - 9 - 2 - 10 - 0 - 0 - 5 - 5 - 0 - 9 - FARGQRWRL - FTRGDRCNL - F RG R L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 171 - Query_171 - M_3760 - 9 - - - 1 - gnl|BL_ORD_ID|714 - 43937|polyprotein|AAF01178.1|Hepatitis C virus subtype 2a|31649 - 714 - 10 - - - 1 - 14.6234 - 26 - 1.7557 - 1 - 9 - 2 - 10 - 0 - 0 - 5 - 5 - 0 - 9 - FARGQRWRL - FTRGDRCNL - F RG R L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 172 - Query_172 - M_3761 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 173 - Query_173 - M_3762 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 174 - Query_174 - M_3763 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 175 - Query_175 - M_3764 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 176 - Query_176 - M_3765 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 177 - Query_177 - M_3766 - 9 - - - 1 - gnl|BL_ORD_ID|1982 - 183245|polyprotein|AGT63074.1|Dengue virus 1|11053 - 1982 - 10 - - - 1 - 13.0826 - 22 - 20.1646 - 1 - 6 - 1 - 6 - 0 - 0 - 3 - 6 - 0 - 6 - FESHRI - FQSHQL - F+SH++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 178 - Query_178 - M_3767 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 179 - Query_179 - M_3768 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 180 - Query_180 - M_3769 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 181 - Query_181 - M_3770 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 182 - Query_182 - M_3771 - 9 - - - 1 - gnl|BL_ORD_ID|2137 - 187106|Vpr protein|BAA93983.1|Human immunodeficiency virus 1|11676 - 2137 - 9 - - - 1 - 11.927 - 19 - 80.227 - 2 - 7 - 4 - 9 - 0 - 0 - 4 - 4 - 0 - 6 - HFRRPW - HFPRIW - HF R W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 183 - Query_183 - M_3772 - 9 - - - 1 - gnl|BL_ORD_ID|2137 - 187106|Vpr protein|BAA93983.1|Human immunodeficiency virus 1|11676 - 2137 - 9 - - - 1 - 11.927 - 19 - 80.227 - 2 - 7 - 4 - 9 - 0 - 0 - 4 - 4 - 0 - 6 - HFRRPW - HFPRIW - HF R W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 184 - Query_184 - M_3773 - 9 - - - 1 - gnl|BL_ORD_ID|2137 - 187106|Vpr protein|BAA93983.1|Human immunodeficiency virus 1|11676 - 2137 - 9 - - - 1 - 11.927 - 19 - 80.227 - 2 - 7 - 4 - 9 - 0 - 0 - 4 - 4 - 0 - 6 - HFRRPW - HFPRIW - HF R W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 185 - Query_185 - M_3774 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 186 - Query_186 - M_3775 - 9 - - - 1 - gnl|BL_ORD_ID|1177 - 79506|E1 protein|BAA19893.1|Rubella virus|11041 - 1177 - 20 - - - 1 - 12.3122 - 20 - 52.8131 - 1 - 7 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - FHHIDSA - FGHSDAA - F H D+A - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 187 - Query_187 - M_3776 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 188 - Query_188 - M_3777 - 9 - - - 1 - gnl|BL_ORD_ID|1175 - 79390|Protein Tax-1|P0C213.1|Human T-cell lymphotropic virus type 1 (african isolate)|39015 - 1175 - 15 - - - 1 - 12.3122 - 20 - 53.1389 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - LHNAHVL - FHNLHLL - HN H+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 189 - Query_189 - M_3778 - 9 - - - 1 - gnl|BL_ORD_ID|1293 - 102819|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 - 1293 - 15 - - - 1 - 18.0902 - 35 - 0.0792643 - 2 - 8 - 3 - 9 - 0 - 0 - 6 - 7 - 0 - 7 - HLPYLEQ - HLPYIEQ - HLPY+EQ - - - - - 2 - gnl|BL_ORD_ID|1214 - 96601|polyprotein|ABR25251.1|Hepatitis C virus (isolate H77)|63746 - 1214 - 10 - - - 1 - 15.3938 - 28 - 0.630146 - 3 - 8 - 1 - 6 - 0 - 0 - 5 - 6 - 0 - 6 - LPYLEQ - LPYIEQ - LPY+EQ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 190 - Query_190 - M_3779 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 191 - Query_191 - M_3780 - 9 - - - 1 - gnl|BL_ORD_ID|880 - 57790|Protein Tax-1|P03409.2|Human T-lymphotropic virus 1|11908 - 880 - 9 - - - 1 - 12.3122 - 20 - 43.3628 - 4 - 9 - 4 - 9 - 0 - 0 - 4 - 6 - 0 - 6 - SIHLLY - SLHLLF - S+HLL+ - - - - - 2 - gnl|BL_ORD_ID|1175 - 79390|Protein Tax-1|P0C213.1|Human T-cell lymphotropic virus type 1 (african isolate)|39015 - 1175 - 15 - - - 1 - 11.1566 - 17 - 161.906 - 4 - 9 - 4 - 9 - 0 - 0 - 3 - 6 - 0 - 6 - SIHLLY - NLHLLF - ++HLL+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 192 - Query_192 - M_3781 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 193 - Query_193 - M_3782 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 194 - Query_194 - M_3783 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 195 - Query_195 - M_3784 - 9 - - - 1 - gnl|BL_ORD_ID|545 - 33382|polyprotein|AAB67037.1|Hepatitis C virus|11103 - 545 - 15 - - - 1 - 13.853 - 24 - 4.45371 - 1 - 7 - 9 - 15 - 0 - 0 - 4 - 5 - 0 - 7 - FHYDTQL - FSYDTRC - F YDT+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 196 - Query_196 - M_3785 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 197 - Query_197 - M_3786 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 198 - Query_198 - M_3787 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 199 - Query_199 - M_3788 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 200 - Query_200 - M_3789 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 201 - Query_201 - M_3790 - 9 - - - 1 - gnl|BL_ORD_ID|100 - 6817|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 100 - 8 - - - 1 - 13.4678 - 23 - 9.40947 - 3 - 8 - 3 - 8 - 0 - 0 - 5 - 6 - 0 - 6 - NNSIVY - NSSIVY - N+SIVY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 202 - Query_202 - M_3791 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 203 - Query_203 - M_3792 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 204 - Query_204 - M_3793 - 9 - - - 1 - gnl|BL_ORD_ID|719 - 44653|6 kDa early secretory antigenic target|P0A564.2|Mycobacterium tuberculosis|1773 - 719 - 20 - - - 1 - 14.2382 - 25 - 3.36386 - 2 - 7 - 2 - 7 - 0 - 0 - 5 - 6 - 0 - 6 - LARTVS - LARTIS - LART+S - - - - - 2 - gnl|BL_ORD_ID|959 - 63010|6 kDa early secretory antigenic target|P0A564.2|Mycobacterium tuberculosis|1773 - 959 - 20 - - - 1 - 14.2382 - 25 - 3.42196 - 2 - 7 - 12 - 17 - 0 - 0 - 5 - 6 - 0 - 6 - LARTVS - LARTIS - LART+S - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 205 - Query_205 - M_3794 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 206 - Query_206 - M_3795 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 207 - Query_207 - M_3796 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 208 - Query_208 - M_3797 - 9 - - - 1 - gnl|BL_ORD_ID|2053 - 184736|polyprotein|AGW21594.1|Dengue virus 1|11053 - 2053 - 9 - - - 1 - 13.0826 - 22 - 16.3158 - 3 - 9 - 1 - 7 - 0 - 0 - 5 - 7 - 0 - 7 - LAMLLSI - MAMVLSI - +AM+LSI - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 209 - Query_209 - M_3798 - 9 - - - 1 - gnl|BL_ORD_ID|356 - 22235|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 356 - 15 - - - 1 - 13.4678 - 23 - 9.68748 - 3 - 8 - 8 - 13 - 0 - 0 - 4 - 6 - 0 - 6 - LEFLLP - LQFLIP - L+FL+P - - - - - 2 - gnl|BL_ORD_ID|1976 - 183162|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1976 - 10 - - - 1 - 11.1566 - 17 - 202.108 - 1 - 8 - 2 - 9 - 0 - 0 - 4 - 6 - 0 - 8 - FLLEFLLP - FLMVLLIP - FL+ L+P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 210 - Query_210 - M_3799 - 9 - - - 1 - gnl|BL_ORD_ID|1509 - 139746|Dense granule protein 3|B6KEU8.2|Toxoplasma gondii|5811 - 1509 - 9 - - - 1 - 7.68983 - 8 - 11881 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 6 - 0 - 9 - FLLFSFLFL - FLVPFVVFL - FL+ +FL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 211 - Query_211 - M_3800 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 212 - Query_212 - M_3801 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 213 - Query_213 - M_3802 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 214 - Query_214 - M_3803 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 215 - Query_215 - M_3804 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 216 - Query_216 - M_3805 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 217 - Query_217 - M_3806 - 9 - - - 1 - gnl|BL_ORD_ID|1040 - 69474|core protein|BAF42671.1|Hepatitis B virus|10407 - 1040 - 10 - - - 1 - 13.853 - 24 - 6.8721 - 2 - 8 - 2 - 8 - 0 - 0 - 4 - 7 - 0 - 7 - MKYLVNF - LEYLVSF - ++YLV+F - - - - - 2 - gnl|BL_ORD_ID|2322 - 423053|core protein|AAL31859.1|Hepatitis B virus|10407 - 2322 - 11 - - - 1 - 13.4678 - 23 - 9.05775 - 2 - 8 - 5 - 11 - 0 - 0 - 4 - 7 - 0 - 7 - MKYLVNF - IEYLVSF - ++YLV+F - - - - - 3 - gnl|BL_ORD_ID|201 - 15061|core protein|BAF42671.1|Hepatitis B virus|10407 - 201 - 9 - - - 1 - 13.0826 - 22 - 21.5246 - 3 - 8 - 1 - 6 - 0 - 0 - 4 - 6 - 0 - 6 - KYLVNF - EYLVSF - +YLV+F - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 218 - Query_218 - M_3807 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 219 - Query_219 - M_3808 - 9 - - - 1 - gnl|BL_ORD_ID|1143 - 75436|Polyprotein|P90247|Hepatitis C virus|11103 - 1143 - 20 - - - 1 - 12.3122 - 20 - 38.3641 - 1 - 6 - 1 - 6 - 0 - 0 - 3 - 5 - 0 - 6 - FMWPLH - YPWPLY - + WPL+ - - - - - 2 - gnl|BL_ORD_ID|1144 - 75438|polyprotein|AAF65962.1|Hepatitis C virus|11103 - 1144 - 20 - - - 1 - 12.3122 - 20 - 39.5605 - 1 - 6 - 1 - 6 - 0 - 0 - 3 - 5 - 0 - 6 - FMWPLH - YPWPLY - + WPL+ - - - - - 3 - gnl|BL_ORD_ID|1142 - 75435|largest ORF|AAB02128.1|Hepatitis C virus|11103 - 1142 - 20 - - - 1 - 12.3122 - 20 - 41.421 - 1 - 6 - 1 - 6 - 0 - 0 - 3 - 5 - 0 - 6 - FMWPLH - YPWPLY - + WPL+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 220 - Query_220 - M_3809 - 9 - - - 1 - gnl|BL_ORD_ID|2258 - 288104|nef protein|ACR27130.1|Human immunodeficiency virus 1|11676 - 2258 - 18 - - - 1 - 12.3122 - 20 - 45.1301 - 1 - 9 - 4 - 12 - 0 - 0 - 4 - 5 - 0 - 9 - FPAMLQAPI - FPVRPQVPL - FP Q P+ - - - - - 2 - gnl|BL_ORD_ID|1831 - 179823|cell surface protein (associated with virulence)|NP_302372.1|Mycobacterium leprae TN|272631 - 1831 - 9 - - - 1 - 12.3122 - 20 - 50.4464 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 5 - 0 - 8 - FPAMLQAP - IPASVSAP - PA + AP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 221 - Query_221 - M_3810 - 9 - - - 1 - gnl|BL_ORD_ID|2214 - 193060|Nef protein|Q9YYU3|Human immunodeficiency virus 1|11676 - 2214 - 10 - - - 1 - 14.2382 - 25 - 4.08767 - 1 - 9 - 2 - 10 - 0 - 0 - 3 - 4 - 0 - 9 - FPIIIAWAI - FPLTFGWCF - FP+ W - - - - - 2 - gnl|BL_ORD_ID|2215 - 193071|Nef protein|Q9WPU2|Human immunodeficiency virus 1|11676 - 2215 - 10 - - - 1 - 13.853 - 24 - 6.29996 - 1 - 9 - 2 - 10 - 0 - 0 - 2 - 5 - 0 - 9 - FPIIIAWAI - YPLTLGWCF - +P+ + W - - - - - 3 - gnl|BL_ORD_ID|866 - 56620|Nef protein|Q9YYU8|Human immunodeficiency virus 1|11676 - 866 - 10 - - - 1 - 13.0826 - 22 - 16.111 - 1 - 9 - 2 - 10 - 0 - 0 - 2 - 4 - 0 - 9 - FPIIIAWAI - YPLTFGWCF - +P+ W - - - - - 4 - gnl|BL_ORD_ID|1288 - 102254|nef protein|ACQ72180.1|Human immunodeficiency virus 1|11676 - 1288 - 9 - - - 1 - 13.0826 - 22 - 18.7436 - 1 - 8 - 1 - 8 - 0 - 0 - 2 - 4 - 0 - 8 - FPIIIAWA - YPLTFGWC - +P+ W - - - - - 5 - gnl|BL_ORD_ID|1281 - 102046|nef protein|ACQ72180.1|Human immunodeficiency virus 1|11676 - 1281 - 8 - - - 1 - 12.6974 - 21 - 26.6862 - 1 - 7 - 2 - 8 - 0 - 0 - 2 - 4 - 0 - 7 - FPIIIAW - YPLTFGW - +P+ W - - - - - 6 - gnl|BL_ORD_ID|459 - 27878|large surface antigen|CAC87019.1|Hepatitis B virus|10407 - 459 - 9 - - - 1 - 11.927 - 19 - 92.9112 - 2 - 8 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - PIIIAWA - PIPSSWA - PI +WA - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 222 - Query_222 - M_3811 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 223 - Query_223 - M_3812 - 9 - - - 1 - gnl|BL_ORD_ID|586 - 36676|polyprotein|BAA09073.1|Hepatitis C virus subtype 1b|31647 - 586 - 9 - - - 1 - 13.0826 - 22 - 18.1053 - 3 - 9 - 1 - 7 - 0 - 0 - 3 - 6 - 0 - 7 - LVRSCQM - LIRACML - L+R+C + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 224 - Query_224 - M_3813 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 225 - Query_225 - M_3814 - 9 - - - 1 - gnl|BL_ORD_ID|1979 - 183223|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1979 - 10 - - - 1 - 12.6974 - 21 - 23.5358 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 5 - 0 - 8 - FPQKYYWW - FPGKTVWF - FP K W+ - - - - - 2 - gnl|BL_ORD_ID|2214 - 193060|Nef protein|Q9YYU3|Human immunodeficiency virus 1|11676 - 2214 - 10 - - - 1 - 12.6974 - 21 - 27.922 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 5 - 0 - 9 - FPQKYYWWF - FPLTFGWCF - FP + W F - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 226 - Query_226 - M_3815 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 227 - Query_227 - M_3816 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 228 - Query_228 - M_3817 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 229 - Query_229 - M_3818 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 230 - Query_230 - M_3819 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 231 - Query_231 - M_3820 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 232 - Query_232 - M_3821 - 9 - - - 1 - gnl|BL_ORD_ID|1575 - 141411|transactivating tegument protein VP16|NP_044650.1|Human alphaherpesvirus 1|10298 - 1575 - 10 - - - 1 - 13.0826 - 22 - 13.3135 - 1 - 7 - 3 - 9 - 0 - 0 - 4 - 5 - 0 - 7 - FPYNSDL - LPTNADL - P N+DL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 233 - Query_233 - M_3822 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 234 - Query_234 - M_3823 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 235 - Query_235 - M_3824 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 236 - Query_236 - M_3825 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 237 - Query_237 - M_3826 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 238 - Query_238 - M_3827 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 239 - Query_239 - M_3828 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 240 - Query_240 - M_3829 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 241 - Query_241 - M_3830 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 242 - Query_242 - M_3831 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 243 - Query_243 - M_3832 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 244 - Query_244 - M_3833 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 245 - Query_245 - M_3834 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 246 - Query_246 - M_3835 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 247 - Query_247 - M_3836 - 9 - - - 1 - gnl|BL_ORD_ID|1817 - 177884|polyprotein|ACZ60102.1|Hepatitis C virus genotype 1|41856 - 1817 - 18 - - - 1 - 13.4678 - 23 - 12.4678 - 1 - 9 - 7 - 15 - 0 - 0 - 4 - 7 - 0 - 9 - FRNGLGTGM - YLYGVGSGM - + G+G+GM - - - - - 2 - gnl|BL_ORD_ID|807 - 53953|kaposin|AAC57155.1|Human gammaherpesvirus 8|37296 - 807 - 15 - - - 1 - 12.6974 - 21 - 31.2769 - 1 - 8 - 6 - 13 - 0 - 0 - 4 - 5 - 0 - 8 - FRNGLGTG - FRTRVATG - FR + TG - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 248 - Query_248 - M_3837 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 249 - Query_249 - M_3838 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 250 - Query_250 - M_3839 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 251 - Query_251 - M_3840 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 252 - Query_252 - M_3841 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 253 - Query_253 - M_3842 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 254 - Query_254 - M_3843 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 255 - Query_255 - M_3844 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 256 - Query_256 - M_3845 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 257 - Query_257 - M_3846 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 258 - Query_258 - M_3847 - 9 - - - 1 - gnl|BL_ORD_ID|1732 - 150571|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1732 - 10 - - - 1 - 14.2382 - 25 - 3.00394 - 1 - 6 - 4 - 9 - 0 - 0 - 4 - 6 - 0 - 6 - FRTKDG - FKTEDG - F+T+DG - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 259 - Query_259 - M_3848 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 260 - Query_260 - M_3849 - 9 - - - 1 - gnl|BL_ORD_ID|1443 - 126028|ATP-dependent helicase|NP_217813.1|Mycobacterium tuberculosis H37Rv|83332 - 1443 - 9 - - - 1 - 13.0826 - 22 - 15.4875 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 4 - 0 - 6 - FRYEGS - FMYEGD - F YEG - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 261 - Query_261 - M_3850 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 262 - Query_262 - M_3851 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 263 - Query_263 - M_3852 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 264 - Query_264 - M_3853 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 265 - Query_265 - M_3854 - 9 - - - 1 - gnl|BL_ORD_ID|355 - 22046|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 - 355 - 10 - - - 1 - 13.853 - 24 - 5.67669 - 4 - 9 - 5 - 10 - 0 - 0 - 4 - 5 - 0 - 6 - PSIHRF - PGIYRF - P I+RF - - - - - 2 - gnl|BL_ORD_ID|1687 - 149053|NS3 gene product|AAB02124.1|Hepatitis C virus|11103 - 1687 - 18 - - - 1 - 13.4678 - 23 - 8.34044 - 4 - 9 - 5 - 10 - 0 - 0 - 4 - 5 - 0 - 6 - PSIHRF - PGIYRF - P I+RF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 266 - Query_266 - M_3855 - 9 - - - 1 - gnl|BL_ORD_ID|1956 - 181733|Antigen 85-B|P0C5B9.1|Mycobacterium tuberculosis|1773 - 1956 - 40 - - - 1 - 14.6234 - 26 - 3.22525 - 2 - 6 - 2 - 6 - 0 - 0 - 5 - 5 - 0 - 5 - TDVSR - TDVSR - TDVSR - - - - - 2 - gnl|BL_ORD_ID|221 - 16548|Glycoprotein GP110 precursor|P03188.1|Human herpesvirus 4 strain B95-8|10377 - 221 - 9 - - - 1 - 11.5418 - 18 - 159.996 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 5 - 0 - 9 - FTDVSRFTL - FLDKGTYTL - F D +TL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 267 - Query_267 - M_3856 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 268 - Query_268 - M_3857 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 269 - Query_269 - M_3858 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 270 - Query_270 - M_3859 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 271 - Query_271 - M_3860 - 9 - - - 1 - gnl|BL_ORD_ID|159 - 12108|polyprotein|AAP55688.1|Hepatitis C virus subtype 2a|31649 - 159 - 10 - - - 1 - 13.4678 - 23 - 8.46851 - 1 - 9 - 2 - 10 - 0 - 0 - 5 - 5 - 0 - 9 - FWCAQFTSF - FWEAVFTGL - FW A FT - - - - - 2 - gnl|BL_ORD_ID|1628 - 146188|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 - 1628 - 18 - - - 1 - 12.3122 - 20 - 36.8413 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 5 - 0 - 9 - FWCAQFTSF - FWESVFTGL - FW + FT - - - - - 3 - gnl|BL_ORD_ID|1630 - 146213|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 - 1630 - 18 - - - 1 - 12.3122 - 20 - 38.0157 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 5 - 0 - 9 - FWCAQFTSF - FWESVFTGL - FW + FT - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 272 - Query_272 - M_3861 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 273 - Query_273 - M_3862 - 9 - - - 1 - gnl|BL_ORD_ID|422 - 25460|Fusion glycoprotein F0 precursor|P03420.1|Human respiratory syncytial virus A2|11259 - 422 - 11 - - - 1 - 13.4678 - 23 - 10.7778 - 4 - 8 - 6 - 10 - 0 - 0 - 4 - 4 - 0 - 5 - LFYCK - LLYCK - L YCK - - - - - 2 - gnl|BL_ORD_ID|1960 - 182599|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1960 - 9 - - - 1 - 12.3122 - 20 - 45.611 - 1 - 6 - 3 - 8 - 0 - 0 - 3 - 4 - 0 - 6 - FWKLFY - MWQLMY - W+L Y - - - - - 3 - gnl|BL_ORD_ID|1887 - 180579|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1887 - 15 - - - 1 - 11.5418 - 18 - 98.8375 - 1 - 6 - 6 - 11 - 0 - 0 - 3 - 3 - 0 - 6 - FWKLFY - MWSLMY - W L Y - - - - - 4 - gnl|BL_ORD_ID|1945 - 180828|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1945 - 10 - - - 1 - 11.5418 - 18 - 137.176 - 1 - 6 - 4 - 9 - 0 - 0 - 3 - 3 - 0 - 6 - FWKLFY - MWSLMY - W L Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 274 - Query_274 - M_3863 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 275 - Query_275 - M_3864 - 9 - - - 1 - gnl|BL_ORD_ID|1231 - 97400|Genome polyprotein|P26664.3|Hepatitis C virus|11103 - 1231 - 10 - - - 1 - 12.6974 - 21 - 25.2038 - 1 - 8 - 3 - 10 - 0 - 0 - 3 - 5 - 0 - 8 - FYAIVVPM - FYGKAIPL - FY +P+ - - - - - 2 - gnl|BL_ORD_ID|274 - 18397|Genome polyprotein|P26662.3|Hepatitis C virus|11103 - 274 - 11 - - - 1 - 12.6974 - 21 - 35.1103 - 1 - 8 - 1 - 8 - 0 - 0 - 3 - 5 - 0 - 8 - FYAIVVPM - FYGKAIPI - FY +P+ - - - - - 3 - gnl|BL_ORD_ID|1230 - 97399|polyprotein|ACZ60108.1|Hepatitis C virus subtype 3a|356426 - 1230 - 10 - - - 1 - 12.3122 - 20 - 51.1794 - 1 - 8 - 3 - 10 - 0 - 0 - 3 - 5 - 0 - 8 - FYAIVVPM - FYGKAIPI - FY +P+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 276 - Query_276 - M_3865 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 277 - Query_277 - M_3866 - 9 - - - 1 - gnl|BL_ORD_ID|1781 - 156550|E3 ubiquitin-protein ligase Mdm2|Q00987.1|Homo sapiens|9606 - 1781 - 9 - - - 1 - 14.2382 - 25 - 3.55601 - 1 - 6 - 3 - 8 - 0 - 0 - 5 - 5 - 0 - 6 - FYLGTY - FYLGQY - FYLG Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 278 - Query_278 - M_3867 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 279 - Query_279 - M_3868 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 280 - Query_280 - M_3869 - 9 - - - 1 - gnl|BL_ORD_ID|1336 - 107894|polyprotein|CAB41951.1|Hepatitis C virus|11103 - 1336 - 10 - - - 1 - 14.2382 - 25 - 4.23087 - 3 - 9 - 3 - 9 - 0 - 0 - 5 - 7 - 0 - 7 - TDSSSVL - TDSTSIL - TDS+S+L - - - - - 2 - gnl|BL_ORD_ID|1226 - 97227|polyprotein|CAB41951.1|Hepatitis C virus|11103 - 1226 - 10 - - - 1 - 14.2382 - 25 - 4.23087 - 3 - 9 - 4 - 10 - 0 - 0 - 5 - 7 - 0 - 7 - TDSSSVL - TDSTSIL - TDS+S+L - - - - - 3 - gnl|BL_ORD_ID|1224 - 97111|polyprotein|ABR25251.1|Hepatitis C virus (isolate H77)|63746 - 1224 - 18 - - - 1 - 13.4678 - 23 - 11.4723 - 3 - 9 - 12 - 18 - 0 - 0 - 4 - 7 - 0 - 7 - TDSSSVL - TDATSIL - TD++S+L - - - - - 4 - gnl|BL_ORD_ID|1225 - 97226|Genome polyprotein|P26664.3|Hepatitis C virus|11103 - 1225 - 10 - - - 1 - 13.4678 - 23 - 12.4198 - 3 - 9 - 4 - 10 - 0 - 0 - 4 - 7 - 0 - 7 - TDSSSVL - TDATSIL - TD++S+L - - - - - 5 - gnl|BL_ORD_ID|1354 - 108147|Genome polyprotein|P26664.3|Hepatitis C virus|11103 - 1354 - 10 - - - 1 - 13.4678 - 23 - 12.859 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 7 - 0 - 7 - TDSSSVL - TDATSIL - TD++S+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 281 - Query_281 - M_3870 - 9 - - - 1 - gnl|BL_ORD_ID|1565 - 141323|multifunctional expression regulator|NP_044657.1|Human alphaherpesvirus 1|10298 - 1565 - 9 - - - 1 - 12.3122 - 20 - 60.6092 - 1 - 7 - 3 - 9 - 0 - 0 - 4 - 5 - 0 - 7 - FYTPALF - FYCNSLF - FY +LF - - - - - 2 - gnl|BL_ORD_ID|545 - 33382|polyprotein|AAB67037.1|Hepatitis C virus|11103 - 545 - 15 - - - 1 - 11.927 - 19 - 65.1875 - 3 - 9 - 5 - 11 - 0 - 0 - 4 - 5 - 0 - 7 - TPALFSF - TPMGFSY - TP FS+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 282 - Query_282 - M_3871 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 283 - Query_283 - M_3872 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 284 - Query_284 - M_3873 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 285 - Query_285 - M_3874 - 9 - - - 1 - gnl|BL_ORD_ID|66 - 4910|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 66 - 20 - - - 1 - 12.6974 - 21 - 27.2657 - 2 - 9 - 13 - 20 - 0 - 0 - 4 - 5 - 0 - 8 - HDAPRRTL - HGAGTRTI - H A RT+ - - - - - 2 - gnl|BL_ORD_ID|1089 - 72038|Polyprotein|Q9IZA3|Hepatitis C virus subtype 2a|31649 - 1089 - 10 - - - 1 - 12.6974 - 21 - 35.4066 - 2 - 9 - 3 - 10 - 0 - 0 - 4 - 5 - 0 - 8 - HDAPRRTL - HGAGNKTL - H A +TL - - - - - 3 - gnl|BL_ORD_ID|1090 - 72039|polyprotein|CAB53095.1|Hepatitis C virus subtype 1b|31647 - 1090 - 10 - - - 1 - 12.3122 - 20 - 41.8935 - 2 - 9 - 3 - 10 - 0 - 0 - 4 - 5 - 0 - 8 - HDAPRRTL - HGAGSKTL - H A +TL - - - - - 4 - gnl|BL_ORD_ID|391 - 23883|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 - 391 - 15 - - - 1 - 11.5418 - 18 - 100.351 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 5 - 0 - 8 - HDAPRRTL - HGAGTRTI - H A RT+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 286 - Query_286 - M_3875 - 9 - - - 1 - gnl|BL_ORD_ID|2088 - 185491|polyprotein|AGO67248.1|Dengue virus 2|11060 - 2088 - 10 - - - 1 - 13.0826 - 22 - 19.8203 - 2 - 9 - 3 - 10 - 0 - 0 - 4 - 7 - 0 - 8 - HKEDAGVV - EEEEAGVL - +E+AGV+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 287 - Query_287 - M_3876 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 288 - Query_288 - M_3877 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 289 - Query_289 - M_3878 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 290 - Query_290 - M_3879 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 291 - Query_291 - M_3880 - 9 - - - 1 - gnl|BL_ORD_ID|1924 - 180726|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1924 - 15 - - - 1 - 14.2382 - 25 - 2.60034 - 1 - 8 - 6 - 13 - 0 - 0 - 4 - 5 - 0 - 8 - GHNSWGFG - GDTAWDFG - G +W FG - - - - - 2 - gnl|BL_ORD_ID|439 - 27061|envelope glycoprotein|ABU89742.1|Dengue virus 2 Thailand/16681/84|31634 - 439 - 10 - - - 1 - 14.2382 - 25 - 4.15863 - 1 - 8 - 3 - 10 - 0 - 0 - 4 - 5 - 0 - 8 - GHNSWGFG - GDTAWDFG - G +W FG - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 292 - Query_292 - M_3881 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 293 - Query_293 - M_3882 - 9 - - - 1 - gnl|BL_ORD_ID|1172 - 79308|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 1172 - 16 - - - 1 - 14.6234 - 26 - 1.40835 - 2 - 9 - 2 - 9 - 0 - 0 - 5 - 6 - 0 - 8 - HPSLSQHL - EPTLGQHL - P+L QHL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 294 - Query_294 - M_3883 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 295 - Query_295 - M_3884 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 296 - Query_296 - M_3885 - 9 - - - 1 - gnl|BL_ORD_ID|1271 - 101673|gag protein|ABO73990.1|Human immunodeficiency virus 1|11676 - 1271 - 9 - - - 1 - 14.2382 - 25 - 2.75966 - 1 - 9 - 1 - 9 - 0 - 0 - 6 - 6 - 0 - 9 - GHVAGEQML - GHQAAMQML - GH A QML - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 297 - Query_297 - M_3886 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 298 - Query_298 - M_3887 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 299 - Query_299 - M_3888 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 300 - Query_300 - M_3889 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 301 - Query_301 - M_3890 - 9 - - - 1 - gnl|BL_ORD_ID|1775 - 155637|tegument protein|CAB06732.1|Human alphaherpesvirus 2|10310 - 1775 - 15 - - - 1 - 14.6234 - 26 - 1.37617 - 1 - 7 - 3 - 9 - 0 - 0 - 5 - 5 - 0 - 7 - GPCRRRF - GPADRRF - GP RRF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 302 - Query_302 - M_3891 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 303 - Query_303 - M_3892 - 9 - - - 1 - gnl|BL_ORD_ID|654 - 38724|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 654 - 20 - - - 1 - 13.0826 - 22 - 20.5164 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 4 - 0 - 8 - PRTKAWFL - PSTLRWFF - P T WF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 304 - Query_304 - M_3893 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 305 - Query_305 - M_3894 - 9 - - - 1 - gnl|BL_ORD_ID|1774 - 155554|RL2|CAB06760.1|Human alphaherpesvirus 2|10310 - 1774 - 15 - - - 1 - 13.853 - 24 - 4.61107 - 3 - 8 - 4 - 9 - 0 - 0 - 4 - 4 - 0 - 6 - APCWQR - APAWSR - AP W R - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 306 - Query_306 - M_3895 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 307 - Query_307 - M_3896 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 308 - Query_308 - M_3897 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 309 - Query_309 - M_3898 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 310 - Query_310 - M_3899 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 311 - Query_311 - M_3900 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 312 - Query_312 - M_3901 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 313 - Query_313 - M_3902 - 9 - - - 1 - gnl|BL_ORD_ID|461 - 27981|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 - 461 - 20 - - - 1 - 12.6974 - 21 - 21.519 - 1 - 8 - 5 - 12 - 0 - 0 - 4 - 6 - 0 - 8 - GTNIVILE - GTQAVVLK - GT V+L+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 314 - Query_314 - M_3903 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 315 - Query_315 - M_3904 - 9 - - - 1 - gnl|BL_ORD_ID|1589 - 142203|polyprotein|BAD73974.1|Hepatitis C virus subtype 1b|31647 - 1589 - 9 - - - 1 - 13.0826 - 22 - 16.6015 - 3 - 9 - 1 - 7 - 0 - 0 - 5 - 6 - 0 - 7 - KKKPNPV - KKKKNPM - KKK NP+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 316 - Query_316 - M_3905 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 317 - Query_317 - M_3906 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 318 - Query_318 - M_3907 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 319 - Query_319 - M_3908 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 320 - Query_320 - M_3909 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 321 - Query_321 - M_3910 - 9 - - - 1 - gnl|BL_ORD_ID|2191 - 190568|polymerase|AAD16253.1|Hepatitis B virus|10407 - 2191 - 20 - - - 1 - 12.3122 - 20 - 44.7058 - 1 - 9 - 7 - 15 - 0 - 0 - 5 - 5 - 0 - 9 - HLLSHSYCL - HLYSHPIIL - HL SH L - - - - - 2 - gnl|BL_ORD_ID|580 - 36402|P protein|Q05486.1|Hepatitis B virus|10407 - 580 - 15 - - - 1 - 12.3122 - 20 - 49.8749 - 1 - 9 - 2 - 10 - 0 - 0 - 5 - 5 - 0 - 9 - HLLSHSYCL - HLYSHPIIL - HL SH L - - - - - 3 - gnl|BL_ORD_ID|498 - 31898|P protein|P17100.1|Hepatitis B virus|10407 - 498 - 9 - - - 1 - 11.1566 - 17 - 199.082 - 1 - 6 - 3 - 8 - 0 - 0 - 4 - 4 - 0 - 6 - HLLSHS - HLYSHP - HL SH - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 322 - Query_322 - M_3911 - 9 - - - 1 - gnl|BL_ORD_ID|392 - 24172|pX-rex-orf I {alternatively spliced}|AAB23359.1|Human T-lymphotropic virus 1|11908 - 392 - 9 - - - 1 - 14.2382 - 25 - 3.21187 - 1 - 9 - 1 - 9 - 0 - 0 - 6 - 7 - 0 - 9 - HLMGQLSSL - HLAFQLSSI - HL QLSS+ - - - - - 2 - gnl|BL_ORD_ID|2031 - 184337|polyprotein|AGO67248.1|Dengue virus 2|11060 - 2031 - 10 - - - 1 - 12.3122 - 20 - 44.0514 - 1 - 6 - 5 - 10 - 0 - 0 - 3 - 6 - 0 - 6 - HLMGQL - HVLGRL - H++G+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 323 - Query_323 - M_3912 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 324 - Query_324 - M_3913 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 325 - Query_325 - M_3914 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 326 - Query_326 - M_3915 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 327 - Query_327 - M_3916 - 9 - - - 1 - gnl|BL_ORD_ID|1776 - 155811|ribonucleotide reductase large subunit|CAB06725.1|Human alphaherpesvirus 2|10310 - 1776 - 15 - - - 1 - 12.6974 - 21 - 28.3557 - 1 - 6 - 8 - 13 - 0 - 0 - 4 - 5 - 0 - 6 - HREDFE - HGEEFE - H E+FE - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 328 - Query_328 - M_3917 - 9 - - - 1 - gnl|BL_ORD_ID|450 - 27285|pol protein|BAA32832.1|Hepatitis B virus|10407 - 450 - 10 - - - 1 - 15.0086 - 27 - 0.948031 - 2 - 9 - 3 - 10 - 0 - 0 - 6 - 6 - 0 - 8 - RGTGAVYV - RGTSFVYV - RGT VYV - - - - - 2 - gnl|BL_ORD_ID|1437 - 119822|110 kd polyprotein precursor|CAA28880.1|Rubella virus|11041 - 1437 - 29 - - - 1 - 13.0826 - 22 - 19.5886 - 2 - 8 - 11 - 17 - 0 - 0 - 4 - 5 - 0 - 7 - RGTGAVY - EGEGAVF - G GAV+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 329 - Query_329 - M_3918 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 330 - Query_330 - M_3919 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 331 - Query_331 - M_3920 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 332 - Query_332 - M_3921 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 333 - Query_333 - M_3922 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 334 - Query_334 - M_3923 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 335 - Query_335 - M_3924 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 336 - Query_336 - M_3925 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 337 - Query_337 - M_3926 - 9 - - - 1 - gnl|BL_ORD_ID|2191 - 190568|polymerase|AAD16253.1|Hepatitis B virus|10407 - 2191 - 20 - - - 1 - 11.1566 - 17 - 207.813 - 3 - 8 - 7 - 12 - 0 - 0 - 4 - 4 - 0 - 6 - HLLSHS - HLYSHP - HL SH - - - - - 2 - gnl|BL_ORD_ID|580 - 36402|P protein|Q05486.1|Hepatitis B virus|10407 - 580 - 15 - - - 1 - 10.7714 - 16 - 300.51 - 3 - 8 - 2 - 7 - 0 - 0 - 4 - 4 - 0 - 6 - HLLSHS - HLYSHP - HL SH - - - - - 3 - gnl|BL_ORD_ID|498 - 31898|P protein|P17100.1|Hepatitis B virus|10407 - 498 - 9 - - - 1 - 10.7714 - 16 - 354.707 - 3 - 8 - 3 - 8 - 0 - 0 - 4 - 4 - 0 - 6 - HLLSHS - HLYSHP - HL SH - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 338 - Query_338 - M_3927 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 339 - Query_339 - M_3928 - 9 - - - 1 - gnl|BL_ORD_ID|1265 - 98603|trans-sialidase, putative|EAN82716.1|Trypanosoma cruzi|5693 - 1265 - 9 - - - 1 - 14.6234 - 26 - 1.6522 - 2 - 9 - 2 - 9 - 0 - 0 - 5 - 5 - 0 - 8 - TPNGRHFY - TDNNRSFY - T N R FY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 340 - Query_340 - M_3929 - 9 - - - 1 - gnl|BL_ORD_ID|2123 - 186524|polyprotein|AGW21594.1|Dengue virus 1|11053 - 2123 - 10 - - - 1 - 12.6974 - 21 - 23.5358 - 2 - 8 - 1 - 7 - 0 - 0 - 3 - 6 - 0 - 7 - WSMWLGV - WTMKIGI - W+M +G+ - - - - - 2 - gnl|BL_ORD_ID|2121 - 186470|envelope protein|AGT63061.1|Dengue virus 3|11069 - 2121 - 10 - - - 1 - 11.1566 - 17 - 184.324 - 2 - 8 - 1 - 7 - 0 - 0 - 3 - 5 - 0 - 7 - WSMWLGV - WIMKIGI - W M +G+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 341 - Query_341 - M_3930 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 342 - Query_342 - M_3931 - 9 - - - 1 - gnl|BL_ORD_ID|375 - 23270|polyprotein|AAB67036.1|Hepatitis C virus (isolate H77)|63746 - 375 - 15 - - - 1 - 14.6234 - 26 - 1.57759 - 2 - 8 - 8 - 14 - 0 - 0 - 4 - 6 - 0 - 7 - YHHRFNN - YQHKFNS - Y H+FN+ - - - - - 2 - gnl|BL_ORD_ID|23 - 1516|Nucleoprotein|P03418.1|Human respiratory syncytial virus A2|11259 - 23 - 14 - - - 1 - 11.1566 - 17 - 170.435 - 2 - 8 - 3 - 9 - 0 - 0 - 3 - 5 - 0 - 7 - YHHRFNN - FYHILNN - ++H NN - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 343 - Query_343 - M_3932 - 9 - - - 1 - gnl|BL_ORD_ID|1583 - 141469|envelope glycoprotein B|NP_044629.1|Human alphaherpesvirus 1|10298 - 1583 - 9 - - - 1 - 12.3122 - 20 - 46.3849 - 2 - 8 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - YISIFYA - YMSPFYG - Y+S FY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 344 - Query_344 - M_3933 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 345 - Query_345 - M_3934 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 346 - Query_346 - M_3935 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 347 - Query_347 - M_3936 - 9 - - - 1 - gnl|BL_ORD_ID|1556 - 141262|DNA polymerase catalytic subunit|NP_044632.1|Human alphaherpesvirus 1|10298 - 1556 - 10 - - - 1 - 12.6974 - 21 - 25.6384 - 3 - 9 - 4 - 10 - 0 - 0 - 5 - 5 - 0 - 7 - HAWWAHF - HARWAAF - HA WA F - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 348 - Query_348 - M_3937 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 349 - Query_349 - M_3938 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 350 - Query_350 - M_3939 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 351 - Query_351 - M_3940 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 352 - Query_352 - M_3941 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 353 - Query_353 - M_3942 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 354 - Query_354 - M_3943 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 355 - Query_355 - M_3944 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 356 - Query_356 - M_3945 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 357 - Query_357 - M_3946 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 358 - Query_358 - M_3947 - 9 - - - 1 - gnl|BL_ORD_ID|759 - 50596|polyprotein|ABG75765.1|Dengue virus 1|11053 - 759 - 9 - - - 1 - 14.2382 - 25 - 4.0067 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 6 - 0 - 7 - HDGAVHT - QEGAMHT - +GA+HT - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 359 - Query_359 - M_3948 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 360 - Query_360 - M_3949 - 9 - - - 1 - gnl|BL_ORD_ID|1398 - 110431|E7|AAD33253.1|Human papillomavirus type 16|333760 - 1398 - 36 - - - 1 - 12.3122 - 20 - 43.3992 - 3 - 7 - 16 - 20 - 0 - 0 - 4 - 5 - 0 - 5 - EDEVD - EDEID - EDE+D - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 361 - Query_361 - M_3950 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 362 - Query_362 - M_3951 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 363 - Query_363 - M_3952 - 9 - - - 1 - gnl|BL_ORD_ID|495 - 31802|large delta antigen|AAG26087.1|Hepatitis delta virus TW2667|10000523 - 495 - 9 - - - 1 - 13.0826 - 22 - 21.8994 - 4 - 9 - 4 - 9 - 0 - 0 - 3 - 5 - 0 - 6 - DDNKWV - DENPWL - D+N W+ - - - - - 2 - gnl|BL_ORD_ID|1919 - 180689|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1919 - 15 - - - 1 - 12.6974 - 21 - 22.89 - 1 - 9 - 4 - 12 - 0 - 0 - 3 - 5 - 0 - 9 - IHIDDNKWV - VHADMGYWI - +H D W+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 364 - Query_364 - M_3953 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 365 - Query_365 - M_3954 - 9 - - - 1 - gnl|BL_ORD_ID|665 - 40158|polyprotein|AAA45534.1|Hepatitis C virus|11103 - 665 - 15 - - - 1 - 12.3122 - 20 - 57.5015 - 1 - 7 - 8 - 14 - 0 - 0 - 3 - 5 - 0 - 7 - IHLLYPP - LHVWVPP - +H+ PP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 366 - Query_366 - M_3955 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 367 - Query_367 - M_3956 - 9 - - - 1 - gnl|BL_ORD_ID|1390 - 110306|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1390 - 32 - - - 1 - 10.001 - 14 - 635.848 - 1 - 9 - 13 - 21 - 0 - 0 - 4 - 5 - 0 - 9 - IHTDDNKCV - IHDIILECV - IH +CV - - - - - 2 - gnl|BL_ORD_ID|1394 - 110373|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1394 - 25 - - - 1 - 9.61583 - 13 - 777.964 - 1 - 9 - 15 - 23 - 0 - 0 - 4 - 5 - 0 - 9 - IHTDDNKCV - IHDIILECV - IH +CV - - - - - 3 - gnl|BL_ORD_ID|1411 - 111251|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1411 - 15 - - - 1 - 10.001 - 14 - 909.224 - 1 - 9 - 6 - 14 - 0 - 0 - 4 - 5 - 0 - 9 - IHTDDNKCV - IHDIILECV - IH +CV - - - - - 4 - gnl|BL_ORD_ID|968 - 64320|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 968 - 10 - - - 1 - 9.61583 - 13 - 1245.43 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 5 - 0 - 9 - IHTDDNKCV - IHDIILECV - IH +CV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 368 - Query_368 - M_3957 - 9 - - - 1 - gnl|BL_ORD_ID|1854 - 180407|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1854 - 15 - - - 1 - 13.853 - 24 - 4.3017 - 3 - 9 - 8 - 14 - 0 - 0 - 3 - 6 - 0 - 7 - AVLPSLF - GIIPSMF - ++PS+F - - - - - 2 - gnl|BL_ORD_ID|567 - 35238|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 567 - 15 - - - 1 - 13.853 - 24 - 5.39022 - 3 - 9 - 9 - 15 - 0 - 0 - 3 - 6 - 0 - 7 - AVLPSLF - GIIPSMF - ++PS+F - - - - - 3 - gnl|BL_ORD_ID|993 - 65550|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 993 - 15 - - - 1 - 13.853 - 24 - 5.67783 - 3 - 9 - 4 - 10 - 0 - 0 - 3 - 6 - 0 - 7 - AVLPSLF - GIIPSMF - ++PS+F - - - - - 4 - gnl|BL_ORD_ID|1740 - 150644|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1740 - 10 - - - 1 - 13.853 - 24 - 6.99268 - 3 - 9 - 4 - 10 - 0 - 0 - 3 - 6 - 0 - 7 - AVLPSLF - GIIPSMF - ++PS+F - - - - - 5 - gnl|BL_ORD_ID|1933 - 180778|polyprotein|AFP27208.1|Dengue virus 4|11070 - 1933 - 10 - - - 1 - 13.0826 - 22 - 13.0843 - 3 - 9 - 4 - 10 - 0 - 0 - 3 - 6 - 0 - 7 - AVLPSLF - GIIPTLF - ++P+LF - - - - - 6 - gnl|BL_ORD_ID|566 - 35237|nonstructural protein 3|NP_722463.1|Dengue virus type 1 Hawaii|10000440 - 566 - 20 - - - 1 - 13.0826 - 22 - 15.8745 - 3 - 9 - 9 - 15 - 0 - 0 - 3 - 6 - 0 - 7 - AVLPSLF - GIIPALF - ++P+LF - - - - - 7 - gnl|BL_ORD_ID|1739 - 150643|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1739 - 10 - - - 1 - 13.0826 - 22 - 20.8706 - 3 - 9 - 4 - 10 - 0 - 0 - 3 - 6 - 0 - 7 - AVLPSLF - GIIPALF - ++P+LF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 369 - Query_369 - M_3958 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 370 - Query_370 - M_3959 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 371 - Query_371 - M_3960 - 9 - - - 1 - gnl|BL_ORD_ID|2298 - 422984|NS5B protein|ABB72740.1|Hepatitis C virus genotype 1|41856 - 2298 - 9 - - - 1 - 12.6974 - 21 - 35.3877 - 1 - 6 - 4 - 9 - 0 - 0 - 5 - 5 - 0 - 6 - ILLTQF - ILLTHF - ILLT F - - - - - 2 - gnl|BL_ORD_ID|2329 - 423072|polyprotein|ACJ37172.1|Hepatitis C virus genotype 1|41856 - 2329 - 9 - - - 1 - 12.6974 - 21 - 39.1808 - 1 - 6 - 4 - 9 - 0 - 0 - 5 - 5 - 0 - 6 - ILLTQF - ILLTHF - ILLT F - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 372 - Query_372 - M_3961 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 373 - Query_373 - M_3962 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 374 - Query_374 - M_3963 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 375 - Query_375 - M_3964 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 376 - Query_376 - M_3965 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 377 - Query_377 - M_3966 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 378 - Query_378 - M_3967 - 9 - - - 1 - gnl|BL_ORD_ID|1888 - 180582|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1888 - 15 - - - 1 - 12.3122 - 20 - 38.6124 - 3 - 9 - 3 - 9 - 0 - 0 - 3 - 5 - 0 - 7 - WSYWGVF - WAYHGSY - W+Y G + - - - - - 2 - gnl|BL_ORD_ID|1097 - 72563|polyprotein|AAB70696.1|Dengue virus type 1 Hawaii|10000440 - 1097 - 20 - - - 1 - 11.927 - 19 - 78.9367 - 3 - 9 - 12 - 18 - 0 - 0 - 3 - 5 - 0 - 7 - WSYWGVF - WAYHGSY - W+Y G + - - - - - 3 - gnl|BL_ORD_ID|160 - 12183|EBNA3C latent protein|CAD53421.1|Human gammaherpesvirus 4|10376 - 160 - 9 - - - 1 - 11.5418 - 18 - 145.552 - 1 - 6 - 4 - 9 - 0 - 0 - 2 - 4 - 0 - 6 - IQWSYW - VGWRHW - + W +W - - - - - 4 - gnl|BL_ORD_ID|1244 - 98042|trans-sialidase, putative|EAN80840.1|Trypanosoma cruzi|5693 - 1244 - 10 - - - 1 - 11.1566 - 17 - 265.518 - 3 - 8 - 5 - 10 - 0 - 0 - 3 - 4 - 0 - 6 - WSYWGV - WAEWPV - W+ W V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 379 - Query_379 - M_3968 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 380 - Query_380 - M_3969 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 381 - Query_381 - M_3970 - 9 - - - 1 - gnl|BL_ORD_ID|469 - 28484|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 469 - 9 - - - 1 - 10.7714 - 16 - 354.707 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 5 - 0 - 9 - IREYCPYTY - ISEYRHYCY - I EY Y Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 382 - Query_382 - M_3971 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 383 - Query_383 - M_3972 - 9 - - - 1 - gnl|BL_ORD_ID|1481 - 133645|cell surface protein|NP_302626.1|Mycobacterium leprae|1769 - 1481 - 15 - - - 1 - 13.0826 - 22 - 17.8301 - 4 - 9 - 6 - 11 - 0 - 0 - 4 - 5 - 0 - 6 - GNVIAC - GNMSAC - GN+ AC - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 384 - Query_384 - M_3973 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 385 - Query_385 - M_3974 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 386 - Query_386 - M_3975 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 387 - Query_387 - M_3976 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 388 - Query_388 - M_3977 - 9 - - - 1 - gnl|BL_ORD_ID|1106 - 72928|Genome polyprotein|P26662.3|Hepatitis C virus (isolate Japanese)|11116 - 1106 - 10 - - - 1 - 13.853 - 24 - 6.75361 - 3 - 9 - 4 - 10 - 0 - 0 - 4 - 6 - 0 - 7 - PPDSRSL - PPGARSM - PP +RS+ - - - - - 2 - gnl|BL_ORD_ID|256 - 17278|Genome polyprotein|P06441.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 256 - 20 - - - 1 - 11.927 - 19 - 67.0972 - 1 - 7 - 4 - 10 - 0 - 0 - 3 - 6 - 0 - 7 - IRPPDSR - LKPGESR - ++P +SR - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 389 - Query_389 - M_3978 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 390 - Query_390 - M_3979 - 9 - - - 1 - gnl|BL_ORD_ID|761 - 50894|Genome polyprotein|P27909.2|Dengue virus type 1 Hawaii|10000440 - 761 - 20 - - - 1 - 13.4678 - 23 - 11.8474 - 2 - 7 - 3 - 8 - 0 - 0 - 4 - 5 - 0 - 6 - RRLRPS - KRLEPS - +RL PS - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 391 - Query_391 - M_3980 - 9 - - - 1 - gnl|BL_ORD_ID|761 - 50894|Genome polyprotein|P27909.2|Dengue virus type 1 Hawaii|10000440 - 761 - 20 - - - 1 - 13.4678 - 23 - 11.8474 - 2 - 7 - 3 - 8 - 0 - 0 - 4 - 5 - 0 - 6 - RRLRPS - KRLEPS - +RL PS - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 392 - Query_392 - M_3981 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 393 - Query_393 - M_3982 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 394 - Query_394 - M_3983 - 9 - - - 1 - gnl|BL_ORD_ID|469 - 28484|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 469 - 9 - - - 1 - 12.6974 - 21 - 31.4086 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 5 - 0 - 9 - ISELLFECY - ISEYRHYCY - ISE CY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 395 - Query_395 - M_3984 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 396 - Query_396 - M_3985 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 397 - Query_397 - M_3986 - 9 - - - 1 - gnl|BL_ORD_ID|1051 - 69715|envelope protein|BAF48755.1|Hepatitis B virus|10407 - 1051 - 9 - - - 1 - 11.927 - 19 - 72.7009 - 1 - 8 - 2 - 9 - 0 - 0 - 4 - 6 - 0 - 8 - ISLGFFLV - LQAGFFLL - + GFFL+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 398 - Query_398 - M_3987 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 399 - Query_399 - M_3988 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 400 - Query_400 - M_3989 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 401 - Query_401 - M_3990 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 402 - Query_402 - M_3991 - 9 - - - 1 - gnl|BL_ORD_ID|1007 - 66405|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 1007 - 20 - - - 1 - 14.6234 - 26 - 1.71852 - 3 - 7 - 13 - 17 - 0 - 0 - 5 - 5 - 0 - 5 - TFDRL - TFDRL - TFDRL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 403 - Query_403 - M_3992 - 9 - - - 1 - gnl|BL_ORD_ID|686 - 41407|Envelope protein|NP_739583.2|Dengue virus 2|11060 - 686 - 15 - - - 1 - 16.9346 - 32 - 0.201842 - 1 - 8 - 7 - 14 - 0 - 0 - 5 - 8 - 0 - 8 - IVHRQFYL - LVHRQWFL - +VHRQ++L - - - - - 2 - gnl|BL_ORD_ID|1746 - 150725|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1746 - 9 - - - 1 - 16.5494 - 31 - 0.331977 - 1 - 8 - 2 - 9 - 0 - 0 - 5 - 8 - 0 - 8 - IVHRQFYL - LVHRQWFL - +VHRQ++L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 404 - Query_404 - M_3993 - 9 - - - 1 - gnl|BL_ORD_ID|775 - 51604|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 - 775 - 10 - - - 1 - 13.4678 - 23 - 8.92274 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 6 - 0 - 7 - MGYSSGI - MDYSNGL - M YS+G+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 405 - Query_405 - M_3994 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 406 - Query_406 - M_3995 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 407 - Query_407 - M_3996 - 9 - - - 1 - gnl|BL_ORD_ID|990 - 65497|HCV-1|AAA45676.1|Hepatitis C virus genotype 1|41856 - 990 - 20 - - - 1 - 13.853 - 24 - 5.50999 - 1 - 8 - 9 - 16 - 0 - 0 - 4 - 6 - 0 - 8 - IYAFMGTP - LRAYMNTP - + A+M TP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 408 - Query_408 - M_3997 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 409 - Query_409 - M_3998 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 410 - Query_410 - M_3999 - 9 - - - 1 - gnl|BL_ORD_ID|1667 - 148117|early protein|CAA52585.1|Human papillomavirus type 52|10618 - 1667 - 9 - - - 1 - 12.6974 - 21 - 26.0147 - 2 - 7 - 2 - 7 - 0 - 0 - 3 - 6 - 0 - 6 - YGLCVV - YGVCIM - YG+C++ - - - - - 2 - gnl|BL_ORD_ID|389 - 23807|tax|AAG48731.1|Human T-lymphotropic virus 2|11909 - 389 - 23 - - - 1 - 11.5418 - 18 - 117.383 - 1 - 6 - 17 - 22 - 0 - 0 - 3 - 5 - 0 - 6 - IYGLCV - VFGDCV - ++G CV - - - - - 3 - gnl|BL_ORD_ID|1170 - 79294|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 1170 - 15 - - - 1 - 11.5418 - 18 - 135.568 - 1 - 6 - 9 - 14 - 0 - 0 - 3 - 5 - 0 - 6 - IYGLCV - VFGDCV - ++G CV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 411 - Query_411 - M_4000 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 412 - Query_412 - M_4001 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 413 - Query_413 - M_4002 - 9 - - - 1 - gnl|BL_ORD_ID|1125 - 74605|Circumsporozoite protein precursor|P08677.2|Plasmodium vivax strain Belem|31273 - 1125 - 9 - - - 1 - 14.6234 - 26 - 1.6522 - 2 - 7 - 1 - 6 - 0 - 0 - 5 - 6 - 0 - 6 - YVDKVR - YLDKVR - Y+DKVR - - - - - 2 - gnl|BL_ORD_ID|837 - 54965|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 - 837 - 10 - - - 1 - 12.3122 - 20 - 39.1729 - 1 - 8 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - IYVDKVRH - MYVGGVEH - +YV V H - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 414 - Query_414 - M_4003 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 415 - Query_415 - M_4004 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 416 - Query_416 - M_4005 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 417 - Query_417 - M_4006 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 418 - Query_418 - M_4007 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 419 - Query_419 - M_4008 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 420 - Query_420 - M_4009 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 421 - Query_421 - M_4010 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 422 - Query_422 - M_4011 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 423 - Query_423 - M_4012 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 424 - Query_424 - M_4013 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 425 - Query_425 - M_4014 - 9 - - - 1 - gnl|BL_ORD_ID|852 - 55718|Probable membrane glycoprotein precursor|P03218.1|Human herpesvirus 4 strain B95-8|10377 - 852 - 9 - - - 1 - 11.927 - 19 - 70.3445 - 2 - 7 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - KRRKFW - RRRKGW - +RRK W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 426 - Query_426 - M_4015 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 427 - Query_427 - M_4016 - 9 - - - 1 - gnl|BL_ORD_ID|1677 - 149024|NS2 protein|NP_751923.1|Hepatitis C virus (isolate H77)|63746 - 1677 - 9 - - - 1 - 12.6974 - 21 - 25.1356 - 2 - 7 - 4 - 9 - 0 - 0 - 3 - 5 - 0 - 6 - LQPYFQ - LSPYYK - L PY++ - - - - - 2 - gnl|BL_ORD_ID|639 - 37991|polyprotein|AAY82034.1|Hepatitis C virus genotype 1|41856 - 639 - 13 - - - 1 - 12.6974 - 21 - 26.4786 - 2 - 7 - 6 - 11 - 0 - 0 - 3 - 5 - 0 - 6 - LQPYFQ - LSPYYK - L PY++ - - - - - 3 - gnl|BL_ORD_ID|662 - 39589|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 662 - 10 - - - 1 - 12.6974 - 21 - 28.8893 - 2 - 7 - 1 - 6 - 0 - 0 - 3 - 5 - 0 - 6 - LQPYFQ - LSPYYK - L PY++ - - - - - 4 - gnl|BL_ORD_ID|663 - 39590|polyprotein|AAY82030.1|Hepatitis C virus|11103 - 663 - 11 - - - 1 - 12.6974 - 21 - 29.6736 - 2 - 7 - 1 - 6 - 0 - 0 - 3 - 5 - 0 - 6 - LQPYFQ - LSPYYK - L PY++ - - - - - 5 - gnl|BL_ORD_ID|664 - 39591|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 - 664 - 20 - - - 1 - 12.3122 - 20 - 49.7173 - 2 - 7 - 1 - 6 - 0 - 0 - 3 - 5 - 0 - 6 - LQPYFQ - LSPYYK - L PY++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 428 - Query_428 - M_4017 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 429 - Query_429 - M_4018 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 430 - Query_430 - M_4019 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 431 - Query_431 - M_4020 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 432 - Query_432 - M_4021 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 433 - Query_433 - M_4022 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 434 - Query_434 - M_4023 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 435 - Query_435 - M_4024 - 9 - - - 1 - gnl|BL_ORD_ID|1774 - 155554|RL2|CAB06760.1|Human alphaherpesvirus 2|10310 - 1774 - 15 - - - 1 - 12.6974 - 21 - 26.5542 - 3 - 7 - 4 - 8 - 0 - 0 - 3 - 5 - 0 - 5 - SPAWN - APAWS - +PAW+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 436 - Query_436 - M_4025 - 9 - - - 1 - gnl|BL_ORD_ID|1745 - 150698|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1745 - 10 - - - 1 - 13.0826 - 22 - 20.5146 - 3 - 8 - 3 - 8 - 0 - 0 - 4 - 5 - 0 - 6 - YLSQRE - YLGKRE - YL +RE - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 437 - Query_437 - M_4026 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 438 - Query_438 - M_4027 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 439 - Query_439 - M_4028 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 440 - Query_440 - M_4029 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 441 - Query_441 - M_4030 - 9 - - - 1 - gnl|BL_ORD_ID|1502 - 137660|L1|ACL12325.1|Human papillomavirus type 58|10598 - 1502 - 9 - - - 1 - 12.6974 - 21 - 36.611 - 1 - 5 - 1 - 5 - 0 - 0 - 3 - 4 - 0 - 5 - KYPYW - KYTFW - KY +W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 442 - Query_442 - M_4031 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 443 - Query_443 - M_4032 - 9 - - - 1 - gnl|BL_ORD_ID|561 - 34616|pol protein|BAA32832.1|Hepatitis B virus|10407 - 561 - 9 - - - 1 - 14.6234 - 26 - 1.91441 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 8 - 0 - 9 - KYSTPPYLL - KYTSFPWLL - KY++ P+LL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 444 - Query_444 - M_4033 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 445 - Query_445 - M_4034 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 446 - Query_446 - M_4035 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 447 - Query_447 - M_4036 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 448 - Query_448 - M_4037 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 449 - Query_449 - M_4038 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 450 - Query_450 - M_4039 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 451 - Query_451 - M_4040 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 452 - Query_452 - M_4041 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 453 - Query_453 - M_4042 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 454 - Query_454 - M_4043 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 455 - Query_455 - M_4044 - 9 - - - 1 - gnl|BL_ORD_ID|946 - 62355|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 946 - 20 - - - 1 - 13.853 - 24 - 7.33195 - 2 - 6 - 10 - 14 - 0 - 0 - 4 - 4 - 0 - 5 - FPRLP - FPRAP - FPR P - - - - - 2 - gnl|BL_ORD_ID|273 - 18390|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 273 - 20 - - - 1 - 13.4678 - 23 - 9.40925 - 2 - 6 - 3 - 7 - 0 - 0 - 4 - 4 - 0 - 5 - FPRLP - FPRAP - FPR P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 456 - Query_456 - M_4045 - 9 - - - 1 - gnl|BL_ORD_ID|545 - 33382|polyprotein|AAB67037.1|Hepatitis C virus|11103 - 545 - 15 - - - 1 - 13.4678 - 23 - 9.20205 - 2 - 8 - 9 - 15 - 0 - 0 - 4 - 5 - 0 - 7 - FSFMTHC - FSYDTRC - FS+ T C - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 457 - Query_457 - M_4046 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 458 - Query_458 - M_4047 - 9 - - - 1 - gnl|BL_ORD_ID|1008 - 66798|glycoprotein gp35/37|AAC59622.1|Human gammaherpesvirus 8|37296 - 1008 - 15 - - - 1 - 12.3122 - 20 - 37.995 - 2 - 7 - 4 - 9 - 0 - 0 - 3 - 5 - 0 - 6 - GRNRHF - GRDAHY - GR+ H+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 459 - Query_459 - M_4048 - 9 - - - 1 - gnl|BL_ORD_ID|1744 - 150693|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1744 - 9 - - - 1 - 12.6974 - 21 - 26.4654 - 3 - 9 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - APMYNLL - VPNYNLI - P YNL+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 460 - Query_460 - M_4049 - 9 - - - 1 - gnl|BL_ORD_ID|1744 - 150693|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1744 - 9 - - - 1 - 12.6974 - 21 - 26.4654 - 3 - 9 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - APMYNLL - VPNYNLI - P YNL+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 461 - Query_461 - M_4050 - 9 - - - 1 - gnl|BL_ORD_ID|1660 - 147561|early protein|CAA52586.1|Human papillomavirus type 52|10618 - 1660 - 9 - - - 1 - 15.3938 - 28 - 0.819689 - 1 - 7 - 1 - 7 - 0 - 0 - 5 - 6 - 0 - 7 - LHEQLGD - CYEQLGD - +EQLGD - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 462 - Query_462 - M_4051 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 463 - Query_463 - M_4052 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 464 - Query_464 - M_4053 - 9 - - - 1 - gnl|BL_ORD_ID|1992 - 183577|polyprotein|AGK36298.1|Dengue virus 2|11060 - 1992 - 10 - - - 1 - 12.3122 - 20 - 43.3206 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 6 - 0 - 8 - HFVQKLLF - HFQRALIF - HF + L+F - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 465 - Query_465 - M_4054 - 9 - - - 1 - gnl|BL_ORD_ID|1392 - 110335|E7|AAD33253.1|Human papillomavirus type 16|333760 - 1392 - 32 - - - 1 - 10.001 - 14 - 438.401 - 1 - 9 - 8 - 16 - 0 - 0 - 4 - 5 - 0 - 9 - LHHKHKELQ - LHEYMLDLQ - LH +LQ - - - - - 2 - gnl|BL_ORD_ID|1823 - 178351|Protein E7|P03129.1|Human papillomavirus type 16|333760 - 1823 - 15 - - - 1 - 10.3862 - 15 - 565.448 - 1 - 9 - 4 - 12 - 0 - 0 - 4 - 5 - 0 - 9 - LHHKHKELQ - LHEYMLDLQ - LH +LQ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 466 - Query_466 - M_4055 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 467 - Query_467 - M_4056 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 468 - Query_468 - M_4057 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 469 - Query_469 - M_4058 - 9 - - - 1 - gnl|BL_ORD_ID|1175 - 79390|Protein Tax-1|P0C213.1|Human T-cell lymphotropic virus type 1 (african isolate)|39015 - 1175 - 15 - - - 1 - 12.6974 - 21 - 21.4208 - 1 - 7 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - LHNAHVL - FHNLHLL - HN H+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 470 - Query_470 - M_4059 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 471 - Query_471 - M_4060 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 472 - Query_472 - M_4061 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 473 - Query_473 - M_4062 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 474 - Query_474 - M_4063 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 475 - Query_475 - M_4064 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 476 - Query_476 - M_4065 - 9 - - - 1 - gnl|BL_ORD_ID|1139 - 75356|EBNA3A nuclear protein|Q8AZJ8|Human gammaherpesvirus 4|10376 - 1139 - 9 - - - 1 - 13.4678 - 23 - 12.57 - 1 - 6 - 3 - 8 - 0 - 0 - 4 - 5 - 0 - 6 - LHTRHG - LHEQHG - LH +HG - - - - - 2 - gnl|BL_ORD_ID|1377 - 109331|L1|ABP99807.1|Human papillomavirus type 18|333761 - 1377 - 9 - - - 1 - 12.6974 - 21 - 33.058 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 7 - 0 - 9 - LHTRHGSIL - IHSMNSSIL - +H+ + SIL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 477 - Query_477 - M_4066 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 478 - Query_478 - M_4067 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 479 - Query_479 - M_4068 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 480 - Query_480 - M_4069 - 9 - - - 1 - gnl|BL_ORD_ID|558 - 34482|gag polyprotein|BAA00992.1|Human immunodeficiency virus 1|11676 - 558 - 9 - - - 1 - 10.7714 - 16 - 497.585 - 3 - 9 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - KHKKTHI - KYKLKHI - K+K HI - - - - - 2 - gnl|BL_ORD_ID|659 - 39162|gag protein|AAV53308.1|Human immunodeficiency virus 1|11676 - 659 - 15 - - - 1 - 10.3862 - 15 - 507.643 - 3 - 9 - 8 - 14 - 0 - 0 - 4 - 5 - 0 - 7 - KHKKTHI - KYKLKHI - K+K HI - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 481 - Query_481 - M_4070 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 482 - Query_482 - M_4071 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 483 - Query_483 - M_4072 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 484 - Query_484 - M_4073 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 485 - Query_485 - M_4074 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 486 - Query_486 - M_4075 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 487 - Query_487 - M_4076 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 488 - Query_488 - M_4077 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 489 - Query_489 - M_4078 - 9 - - - 1 - gnl|BL_ORD_ID|623 - 37498|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 - 623 - 10 - - - 1 - 13.853 - 24 - 4.69227 - 1 - 9 - 2 - 10 - 0 - 0 - 6 - 7 - 0 - 9 - LLGKKGTSA - LLGLWGTAA - LLG GT+A - - - - - 2 - gnl|BL_ORD_ID|615 - 37350|trans-sialidase|XP_818394.1|Trypanosoma cruzi|5693 - 615 - 10 - - - 1 - 13.853 - 24 - 4.69227 - 1 - 9 - 1 - 9 - 0 - 0 - 6 - 7 - 0 - 9 - LLGKKGTSA - LLGLWGTAA - LLG GT+A - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 490 - Query_490 - M_4079 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 491 - Query_491 - M_4080 - 9 - - - 1 - gnl|BL_ORD_ID|2027 - 184299|envelope protein|AGT63061.1|Dengue virus 3|11069 - 2027 - 9 - - - 1 - 13.853 - 24 - 5.00793 - 2 - 7 - 4 - 9 - 0 - 0 - 5 - 6 - 0 - 6 - LKKLCI - LRKLCI - L+KLCI - - - - - 2 - gnl|BL_ORD_ID|2028 - 184300|envelope protein|AFN87749.1|Dengue virus 2|11060 - 2028 - 9 - - - 1 - 12.6974 - 21 - 34.7909 - 2 - 7 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - LKKLCI - LRKYCI - L+K CI - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 492 - Query_492 - M_4081 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 493 - Query_493 - M_4082 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 494 - Query_494 - M_4083 - 9 - - - 1 - gnl|BL_ORD_ID|1714 - 150377|polyprotein|AGS49173.1|Dengue virus 2|11060 - 1714 - 9 - - - 1 - 12.3122 - 20 - 51.2985 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 7 - 0 - 9 - LLLMYSYAV - LLLVAHYAI - LLL+ YA+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 495 - Query_495 - M_4084 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 496 - Query_496 - M_4085 - 9 - - - 1 - gnl|BL_ORD_ID|184 - 13518|HCV-1|AAA45676.1|Hepatitis C virus genotype 1|41856 - 184 - 20 - - - 1 - 11.927 - 19 - 57.7977 - 4 - 8 - 2 - 6 - 0 - 0 - 4 - 4 - 0 - 5 - NKPYL - NLPYL - N PYL - - - - - 2 - gnl|BL_ORD_ID|183 - 13516|Genome polyprotein|P26664.3|Hepatitis C virus subtype 1a|31646 - 183 - 9 - - - 1 - 11.927 - 19 - 88.4863 - 4 - 8 - 2 - 6 - 0 - 0 - 4 - 4 - 0 - 5 - NKPYL - NLPYL - N PYL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 497 - Query_497 - M_4086 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 498 - Query_498 - M_4087 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 499 - Query_499 - M_4088 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 500 - Query_500 - M_4089 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 501 - Query_501 - M_4090 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 502 - Query_502 - M_4091 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 503 - Query_503 - M_4092 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 504 - Query_504 - M_4093 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 505 - Query_505 - M_4094 - 9 - - - 1 - gnl|BL_ORD_ID|590 - 36724|Spike glycoprotein precursor|P59594.1|SARS coronavirus|227859 - 590 - 9 - - - 1 - 13.853 - 24 - 6.48995 - 1 - 9 - 1 - 9 - 0 - 0 - 6 - 7 - 0 - 9 - LLTQRLQGL - LITGRLQSL - L+T RLQ L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 506 - Query_506 - M_4095 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 507 - Query_507 - M_4096 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 508 - Query_508 - M_4097 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 509 - Query_509 - M_4098 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 510 - Query_510 - M_4099 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 511 - Query_511 - M_4100 - 9 - - - 1 - gnl|BL_ORD_ID|55 - 4156|polyprotein|ABR25251.1|Hepatitis C virus|11103 - 55 - 9 - - - 1 - 14.2382 - 25 - 4.29054 - 5 - 9 - 2 - 6 - 0 - 0 - 4 - 5 - 0 - 5 - RHTPM - RHTPV - RHTP+ - - - - - 2 - gnl|BL_ORD_ID|958 - 62977|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 958 - 10 - - - 1 - 13.853 - 24 - 4.37925 - 5 - 9 - 3 - 7 - 0 - 0 - 4 - 5 - 0 - 5 - RHTPM - RHTPV - RHTP+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 512 - Query_512 - M_4101 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 513 - Query_513 - M_4102 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 514 - Query_514 - M_4103 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 515 - Query_515 - M_4104 - 9 - - - 1 - gnl|BL_ORD_ID|75 - 5542|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 75 - 15 - - - 1 - 12.3122 - 20 - 41.1784 - 2 - 8 - 8 - 14 - 0 - 0 - 4 - 4 - 0 - 7 - PGMRGPP - PGTSGSP - PG G P - - - - - 2 - gnl|BL_ORD_ID|748 - 48915|kaposin|AAC57155.1|Human gammaherpesvirus 8|37296 - 748 - 15 - - - 1 - 12.3122 - 20 - 46.8002 - 3 - 7 - 4 - 8 - 0 - 0 - 4 - 4 - 0 - 5 - GMRGP - GQRGP - G RGP - - - - - 3 - gnl|BL_ORD_ID|260 - 17802|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 260 - 15 - - - 1 - 12.3122 - 20 - 55.7176 - 2 - 8 - 3 - 9 - 0 - 0 - 4 - 4 - 0 - 7 - PGMRGPP - PGTSGSP - PG G P - - - - - 4 - gnl|BL_ORD_ID|1929 - 180750|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1929 - 15 - - - 1 - 12.3122 - 20 - 57.5015 - 2 - 8 - 2 - 8 - 0 - 0 - 4 - 4 - 0 - 7 - PGMRGPP - PGTSGSP - PG G P - - - - - 5 - gnl|BL_ORD_ID|1494 - 136890|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1494 - 9 - - - 1 - 11.927 - 19 - 78.9234 - 2 - 7 - 3 - 8 - 0 - 0 - 4 - 4 - 0 - 6 - PGMRGP - PGSRDP - PG R P - - - - - 6 - gnl|BL_ORD_ID|1712 - 150341|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1712 - 9 - - - 1 - 11.927 - 19 - 92.9112 - 2 - 8 - 2 - 8 - 0 - 0 - 4 - 4 - 0 - 7 - PGMRGPP - PGTSGSP - PG G P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 516 - Query_516 - M_4105 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 517 - Query_517 - M_4106 - 9 - - - 1 - gnl|BL_ORD_ID|825 - 54706|matrix protein 2-1|AAS22094.1|Human metapneumovirus|162145 - 825 - 9 - - - 1 - 14.2382 - 25 - 3.32254 - 1 - 6 - 2 - 7 - 0 - 0 - 5 - 6 - 0 - 6 - LPKEKL - LPREKL - LP+EKL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 518 - Query_518 - M_4107 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 519 - Query_519 - M_4108 - 9 - - - 1 - gnl|BL_ORD_ID|826 - 54709|protein F [Hepatitis C virus subtype 1b]|ACA50643.1|Hepatitis C virus (isolate Japanese)|11116 - 826 - 9 - - - 1 - 12.6974 - 21 - 24.2855 - 1 - 6 - 2 - 7 - 0 - 0 - 4 - 4 - 0 - 6 - LPQGRE - LPSGRN - LP GR - - - - - 2 - gnl|BL_ORD_ID|1871 - 180488|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1871 - 10 - - - 1 - 12.3122 - 20 - 41.8935 - 4 - 9 - 3 - 8 - 0 - 0 - 4 - 4 - 0 - 6 - GRESPI - GHEEPI - G E PI - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 520 - Query_520 - M_4109 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 521 - Query_521 - M_4110 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 522 - Query_522 - M_4111 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 523 - Query_523 - M_4112 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 524 - Query_524 - M_4113 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 525 - Query_525 - M_4114 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 526 - Query_526 - M_4115 - 9 - - - 1 - gnl|BL_ORD_ID|215 - 15914|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 - 215 - 15 - - - 1 - 15.0086 - 27 - 0.858443 - 1 - 8 - 8 - 15 - 0 - 0 - 4 - 8 - 0 - 8 - LQLYRFSP - VRLHRFAP - ++L+RF+P - - - - - 2 - gnl|BL_ORD_ID|767 - 51346|Genome polyprotein|P29846.3|Hepatitis C virus|11103 - 767 - 9 - - - 1 - 14.6234 - 26 - 1.62552 - 2 - 8 - 1 - 7 - 0 - 0 - 5 - 6 - 0 - 7 - QLYRFSP - QLFTFSP - QL+ FSP - - - - - 3 - gnl|BL_ORD_ID|1079 - 71616|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 1079 - 15 - - - 1 - 13.0826 - 22 - 14.3275 - 1 - 8 - 4 - 11 - 0 - 0 - 4 - 6 - 0 - 8 - LQLYRFSP - MYLYQLSP - + LY+ SP - - - - - 4 - gnl|BL_ORD_ID|1135 - 75024|Protein Tax-1|P03409.2|Human T-lymphotropic virus 1|11908 - 1135 - 9 - - - 1 - 12.6974 - 21 - 26.9236 - 3 - 8 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - LYRFSP - LYQLSP - LY+ SP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 527 - Query_527 - M_4116 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 528 - Query_528 - M_4117 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 529 - Query_529 - M_4118 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 530 - Query_530 - M_4119 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 531 - Query_531 - M_4120 - 9 - - - 1 - gnl|BL_ORD_ID|1508 - 139406|polyprotein|ACT37184.1|Hepatitis C virus|11103 - 1508 - 10 - - - 1 - 12.6974 - 21 - 34.2302 - 5 - 9 - 6 - 10 - 0 - 0 - 4 - 5 - 0 - 5 - PGPQL - PGPRL - PGP+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 532 - Query_532 - M_4121 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 533 - Query_533 - M_4122 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 534 - Query_534 - M_4123 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 535 - Query_535 - M_4124 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 536 - Query_536 - M_4125 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 537 - Query_537 - M_4126 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 538 - Query_538 - M_4127 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 539 - Query_539 - M_4128 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 540 - Query_540 - M_4129 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 541 - Query_541 - M_4130 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 542 - Query_542 - M_4131 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 543 - Query_543 - M_4132 - 9 - - - 1 - gnl|BL_ORD_ID|1077 - 71409|cysteine proteinase cruzipain (EC 3.4.22.-) - Trypanosoma cruzi|A45629|Trypanosoma cruzi|5693 - 1077 - 9 - - - 1 - 14.2382 - 25 - 3.43721 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 6 - 0 - 9 - LRLPGGSCM - VTLPTGQCL - + LP G C+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 544 - Query_544 - M_4133 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 545 - Query_545 - M_4134 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 546 - Query_546 - M_4135 - 9 - - - 1 - gnl|BL_ORD_ID|915 - 59709|polyprotein|BAD73987.1|Hepatitis C virus subtype 1b|31647 - 915 - 9 - - - 1 - 16.1642 - 30 - 0.354217 - 3 - 9 - 3 - 9 - 0 - 0 - 5 - 7 - 0 - 7 - MSDPSHI - LTDPSHI - ++DPSHI - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 547 - Query_547 - M_4136 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 548 - Query_548 - M_4137 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 549 - Query_549 - M_4138 - 9 - - - 1 - gnl|BL_ORD_ID|2045 - 184531|polyprotein|AFP27208.1|Dengue virus 4|11070 - 2045 - 10 - - - 1 - 13.0826 - 22 - 18.4997 - 3 - 8 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - PSSIET - PESLET - P S+ET - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 550 - Query_550 - M_4139 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 551 - Query_551 - M_4140 - 9 - - - 1 - gnl|BL_ORD_ID|771 - 51526|HCV-1|AAA45676.1|Hepatitis C virus|11103 - 771 - 10 - - - 1 - 13.853 - 24 - 7.36741 - 1 - 7 - 2 - 8 - 0 - 0 - 5 - 6 - 0 - 7 - LRRHRDV - LRRHIDL - LRRH D+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 552 - Query_552 - M_4141 - 9 - - - 1 - gnl|BL_ORD_ID|1435 - 116781|Nucleoprotein|P05133.1|Hantaan virus 76-118|11602 - 1435 - 15 - - - 1 - 12.3122 - 20 - 41.1784 - 1 - 7 - 1 - 7 - 0 - 0 - 4 - 6 - 0 - 7 - LRRMNSF - LRKKSSF - LR+ +SF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 553 - Query_553 - M_4142 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 554 - Query_554 - M_4143 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 555 - Query_555 - M_4144 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 556 - Query_556 - M_4145 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 557 - Query_557 - M_4146 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 558 - Query_558 - M_4147 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 559 - Query_559 - M_4148 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 560 - Query_560 - M_4149 - 9 - - - 1 - gnl|BL_ORD_ID|1698 - 149115|NS5 protein|BAA00702.1|Hepatitis C virus (isolate H77)|63746 - 1698 - 9 - - - 1 - 13.4678 - 23 - 11.9303 - 3 - 9 - 1 - 7 - 0 - 0 - 5 - 6 - 0 - 7 - SIRVRLL - SVRARLL - S+R RLL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 561 - Query_561 - M_4150 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 562 - Query_562 - M_4151 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 563 - Query_563 - M_4152 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 564 - Query_564 - M_4153 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 565 - Query_565 - M_4154 - 9 - - - 1 - gnl|BL_ORD_ID|1095 - 72301|envelope protein|YP_001527880.1|West Nile virus NY-99|10000971 - 1095 - 18 - - - 1 - 15.0086 - 27 - 1.37027 - 3 - 8 - 1 - 6 - 0 - 0 - 3 - 6 - 0 - 6 - WEYGSI - WDFGSV - W++GS+ - - - - - 2 - gnl|BL_ORD_ID|1924 - 180726|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1924 - 15 - - - 1 - 14.6234 - 26 - 2.14985 - 3 - 8 - 10 - 15 - 0 - 0 - 3 - 6 - 0 - 6 - WEYGSI - WDFGSL - W++GS+ - - - - - 3 - gnl|BL_ORD_ID|1110 - 73059|kaposin|AAC57155.1|Human gammaherpesvirus 8|37296 - 1110 - 15 - - - 1 - 13.853 - 24 - 4.45371 - 2 - 8 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - RWEYGSI - RWRLGAI - RW G+I - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 566 - Query_566 - M_4155 - 9 - - - 1 - gnl|BL_ORD_ID|418 - 25237|Transcription activator BRLF1|P03209.1|Human herpesvirus 4 strain B95-8|10377 - 418 - 15 - - - 1 - 14.2382 - 25 - 2.88535 - 1 - 9 - 7 - 15 - 0 - 0 - 5 - 6 - 0 - 9 - LRYFLKHGI - MRYVLDHLI - +RY L H I - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 567 - Query_567 - M_4156 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 568 - Query_568 - M_4157 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 569 - Query_569 - M_4158 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 570 - Query_570 - M_4159 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 571 - Query_571 - M_4160 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 572 - Query_572 - M_4161 - 9 - - - 1 - gnl|BL_ORD_ID|133 - 9415|Superoxide dismutase|P17670.1|Mycobacterium tuberculosis|1773 - 133 - 10 - - - 1 - 11.927 - 19 - 75.9314 - 3 - 9 - 1 - 7 - 0 - 0 - 2 - 4 - 0 - 7 - SLWYHTY - DMWEHAF - +W H + - - - - - 2 - gnl|BL_ORD_ID|132 - 9414|Superoxide dismutase|P17670.1|Mycobacterium tuberculosis|1773 - 132 - 9 - - - 1 - 11.927 - 19 - 91.4136 - 3 - 9 - 1 - 7 - 0 - 0 - 2 - 4 - 0 - 7 - SLWYHTY - DMWEHAF - +W H + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 573 - Query_573 - M_4162 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 574 - Query_574 - M_4163 - 9 - - - 1 - gnl|BL_ORD_ID|1265 - 98603|trans-sialidase, putative|EAN82716.1|Trypanosoma cruzi|5693 - 1265 - 9 - - - 1 - 12.3122 - 20 - 62.655 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 6 - 0 - 9 - LTDYDTRFY - VTDNNRSFY - +TD + FY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 575 - Query_575 - M_4164 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 576 - Query_576 - M_4165 - 9 - - - 1 - gnl|BL_ORD_ID|830 - 54797|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 830 - 11 - - - 1 - 14.2382 - 25 - 3.36866 - 1 - 8 - 4 - 11 - 0 - 0 - 4 - 6 - 0 - 8 - LTGLVWQR - VSGLAWTR - ++GL W R - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 577 - Query_577 - M_4166 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 578 - Query_578 - M_4167 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 579 - Query_579 - M_4168 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 580 - Query_580 - M_4169 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 581 - Query_581 - M_4170 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 582 - Query_582 - M_4171 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 583 - Query_583 - M_4172 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 584 - Query_584 - M_4173 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 585 - Query_585 - M_4174 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 586 - Query_586 - M_4175 - 9 - - - 1 - gnl|BL_ORD_ID|2125 - 186551|polyprotein|AGW21594.1|Dengue virus 1|11053 - 2125 - 10 - - - 1 - 12.3122 - 20 - 48.6895 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 6 - 0 - 8 - YEDTLYTV - YENLKYSV - YE+ Y+V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 587 - Query_587 - M_4176 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 588 - Query_588 - M_4177 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 589 - Query_589 - M_4178 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 590 - Query_590 - M_4179 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 591 - Query_591 - M_4180 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 592 - Query_592 - M_4181 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 593 - Query_593 - M_4182 - 9 - - - 1 - gnl|BL_ORD_ID|1619 - 144913|Hexon protein|P04133.3|Human adenovirus 5|28285 - 1619 - 10 - - - 1 - 14.2382 - 25 - 3.62465 - 1 - 9 - 2 - 10 - 0 - 0 - 5 - 6 - 0 - 9 - LYGHSTHDL - LYANSAHAL - LY +S H L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 594 - Query_594 - M_4183 - 9 - - - 1 - gnl|BL_ORD_ID|1177 - 79506|E1 protein|BAA19893.1|Rubella virus|11041 - 1177 - 20 - - - 1 - 13.4678 - 23 - 8.37795 - 3 - 9 - 4 - 10 - 0 - 0 - 4 - 4 - 0 - 7 - HRDLAKW - HSDAACW - H D A W - - - - - 2 - gnl|BL_ORD_ID|1384 - 110205|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1384 - 32 - - - 1 - 10.7714 - 16 - 223.475 - 2 - 9 - 6 - 13 - 0 - 0 - 2 - 4 - 0 - 8 - YHRDLAKW - FHNIRGRW - +H +W - - - - - 3 - gnl|BL_ORD_ID|1395 - 110394|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1395 - 32 - - - 1 - 10.7714 - 16 - 260.809 - 2 - 9 - 24 - 31 - 0 - 0 - 2 - 4 - 0 - 8 - YHRDLAKW - FHNIRGRW - +H +W - - - - - 4 - gnl|BL_ORD_ID|1385 - 110215|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1385 - 25 - - - 1 - 10.7714 - 16 - 308.682 - 2 - 9 - 12 - 19 - 0 - 0 - 2 - 4 - 0 - 8 - YHRDLAKW - FHNIRGRW - +H +W - - - - - 5 - gnl|BL_ORD_ID|1822 - 178247|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1822 - 15 - - - 1 - 10.3862 - 15 - 443.083 - 2 - 9 - 8 - 15 - 0 - 0 - 2 - 4 - 0 - 8 - YHRDLAKW - FHNIRGRW - +H +W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 595 - Query_595 - M_4184 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 596 - Query_596 - M_4185 - 9 - - - 1 - gnl|BL_ORD_ID|1299 - 103563|polyprotein|BAB18806.1|Hepatitis C virus|11103 - 1299 - 9 - - - 1 - 11.927 - 19 - 114.611 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 4 - 0 - 7 - PDINNPF - PDYNPPL - PD N P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 597 - Query_597 - M_4186 - 9 - - - 1 - gnl|BL_ORD_ID|486 - 30815|Genome polyprotein|P26662.3|Hepatitis C virus|11103 - 486 - 9 - - - 1 - 13.4678 - 23 - 13.2439 - 2 - 7 - 2 - 7 - 0 - 0 - 4 - 6 - 0 - 6 - YPPSLP - FPPALP - +PP+LP - - - - - 2 - gnl|BL_ORD_ID|1882 - 180538|Nonstructural protein NS2B|NP_739586.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1882 - 15 - - - 1 - 12.6974 - 21 - 21.7795 - 1 - 7 - 4 - 10 - 0 - 0 - 4 - 6 - 0 - 7 - LYPPSLP - LFPVSIP - L+P S+P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 598 - Query_598 - M_4187 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 599 - Query_599 - M_4188 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 600 - Query_600 - M_4189 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 601 - Query_601 - M_4190 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 602 - Query_602 - M_4191 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 603 - Query_603 - M_4192 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 604 - Query_604 - M_4193 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 605 - Query_605 - M_4194 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 606 - Query_606 - M_4195 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 607 - Query_607 - M_4196 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 608 - Query_608 - M_4197 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 609 - Query_609 - M_4198 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 610 - Query_610 - M_4199 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 611 - Query_611 - M_4200 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 612 - Query_612 - M_4201 - 9 - - - 1 - gnl|BL_ORD_ID|259 - 17620|Early antigen protein D|P03191.1|Human herpesvirus 4 strain B95-8|10377 - 259 - 15 - - - 1 - 13.853 - 24 - 5.11701 - 1 - 9 - 4 - 12 - 0 - 0 - 4 - 6 - 0 - 9 - MAYSITCPI - LAYGRTCVL - +AY TC + - - - - - 2 - gnl|BL_ORD_ID|258 - 17619|Early antigen protein D|P03191.1|Human herpesvirus 4 strain B95-8|10377 - 258 - 14 - - - 1 - 13.853 - 24 - 5.3697 - 1 - 9 - 4 - 12 - 0 - 0 - 4 - 6 - 0 - 9 - MAYSITCPI - LAYGRTCVL - +AY TC + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 613 - Query_613 - M_4202 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 614 - Query_614 - M_4203 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 615 - Query_615 - M_4204 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 616 - Query_616 - M_4205 - 9 - - - 1 - gnl|BL_ORD_ID|1355 - 108148|polyprotein|AAF65953.1|Hepatitis C virus|11103 - 1355 - 10 - - - 1 - 13.0826 - 22 - 20.8706 - 3 - 9 - 1 - 7 - 0 - 0 - 5 - 6 - 0 - 7 - ATDYTTI - STDSTTI - +TD TTI - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 617 - Query_617 - M_4206 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 618 - Query_618 - M_4207 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 619 - Query_619 - M_4208 - 9 - - - 1 - gnl|BL_ORD_ID|306 - 20686|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 - 306 - 11 - - - 1 - 14.2382 - 25 - 3.14502 - 2 - 6 - 1 - 5 - 0 - 0 - 5 - 5 - 0 - 5 - GKSTH - GKSTH - GKSTH - - - - - 2 - gnl|BL_ORD_ID|256 - 17278|Genome polyprotein|P06441.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 256 - 20 - - - 1 - 13.853 - 24 - 5.14963 - 2 - 8 - 7 - 13 - 0 - 0 - 5 - 6 - 0 - 7 - GKSTHTS - GESRHTS - G+S HTS - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 620 - Query_620 - M_4209 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 621 - Query_621 - M_4210 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 622 - Query_622 - M_4211 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 623 - Query_623 - M_4212 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 624 - Query_624 - M_4213 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 625 - Query_625 - M_4214 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 626 - Query_626 - M_4215 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 627 - Query_627 - M_4216 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 628 - Query_628 - M_4217 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 629 - Query_629 - M_4218 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 630 - Query_630 - M_4219 - 9 - - - 1 - gnl|BL_ORD_ID|114 - 7660|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 - 114 - 20 - - - 1 - 11.1566 - 17 - 164.091 - 1 - 9 - 6 - 14 - 0 - 0 - 3 - 5 - 0 - 9 - MLCFYTPAL - LMCAVHPTL - ++C P L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 631 - Query_631 - M_4220 - 9 - - - 1 - gnl|BL_ORD_ID|654 - 38724|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 654 - 20 - - - 1 - 14.2382 - 25 - 2.55563 - 1 - 9 - 11 - 19 - 0 - 0 - 4 - 6 - 0 - 9 - MLHLYPGPM - LFQLYRGPL - + LY GP+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 632 - Query_632 - M_4221 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 633 - Query_633 - M_4222 - 9 - - - 1 - gnl|BL_ORD_ID|2303 - 422997|preC/core protein|CAJ33968.1|Hepatitis B virus|10407 - 2303 - 9 - - - 1 - 14.6234 - 26 - 2.11355 - 3 - 8 - 3 - 8 - 0 - 0 - 6 - 6 - 0 - 6 - LMNLAT - LMNLAT - LMNLAT - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 634 - Query_634 - M_4223 - 9 - - - 1 - gnl|BL_ORD_ID|690 - 41971|putative D-ribose-binding protein|NP_301386.1|Mycobacterium leprae|1769 - 690 - 15 - - - 1 - 10.001 - 14 - 757.359 - 1 - 8 - 1 - 8 - 0 - 0 - 5 - 6 - 0 - 8 - MLLSILLP - MLILGLLP - ML+ LLP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 635 - Query_635 - M_4224 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 636 - Query_636 - M_4225 - 9 - - - 1 - gnl|BL_ORD_ID|629 - 37607|kaposin|AAC57155.1|Human gammaherpesvirus 8|37296 - 629 - 9 - - - 1 - 11.5418 - 18 - 124.163 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 6 - 0 - 9 - MLNKVLYRL - LLNGWRWRL - +LN +RL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 637 - Query_637 - M_4226 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 638 - Query_638 - M_4227 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 639 - Query_639 - M_4228 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 640 - Query_640 - M_4229 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 641 - Query_641 - M_4230 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 642 - Query_642 - M_4231 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 643 - Query_643 - M_4232 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 644 - Query_644 - M_4233 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 645 - Query_645 - M_4234 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 646 - Query_646 - M_4235 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 647 - Query_647 - M_4236 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 648 - Query_648 - M_4237 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 649 - Query_649 - M_4238 - 9 - - - 1 - gnl|BL_ORD_ID|1938 - 180802|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1938 - 9 - - - 1 - 13.853 - 24 - 4.92244 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 6 - 0 - 8 - MPLLKLSC - VPLLAIGC - +PLL + C - - - - - 2 - gnl|BL_ORD_ID|1939 - 180803|polyprotein|AFP27208.1|Dengue virus 4|11070 - 1939 - 9 - - - 1 - 13.853 - 24 - 6.71897 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 6 - 0 - 8 - MPLLKLSC - VPLLAMGC - +PLL + C - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 650 - Query_650 - M_4239 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 651 - Query_651 - M_4240 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 652 - Query_652 - M_4241 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 653 - Query_653 - M_4242 - 9 - - - 1 - gnl|BL_ORD_ID|575 - 36306|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 - 575 - 15 - - - 1 - 14.6234 - 26 - 2.07692 - 1 - 8 - 4 - 11 - 0 - 0 - 4 - 5 - 0 - 8 - MRCQYETV - MNCSYENM - M C YE + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 654 - Query_654 - M_4243 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 655 - Query_655 - M_4244 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 656 - Query_656 - M_4245 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 657 - Query_657 - M_4246 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 658 - Query_658 - M_4247 - 9 - - - 1 - gnl|BL_ORD_ID|409 - 24765|polyprotein [Hepatitis C virus]|ABR27360.1|Hepatitis C virus|11103 - 409 - 9 - - - 1 - 13.853 - 24 - 6.37844 - 3 - 9 - 3 - 9 - 0 - 0 - 3 - 7 - 0 - 7 - RRQCEEV - KKKCDEV - +++C+EV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 659 - Query_659 - M_4248 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 660 - Query_660 - M_4249 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 661 - Query_661 - M_4250 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 662 - Query_662 - M_4251 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 663 - Query_663 - M_4252 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 664 - Query_664 - M_4253 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 665 - Query_665 - M_4254 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 666 - Query_666 - M_4255 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 667 - Query_667 - M_4256 - 9 - - - 1 - gnl|BL_ORD_ID|2051 - 184702|non-structural protein 1|AGM49312.1|Dengue virus|12637 - 2051 - 9 - - - 1 - 11.5418 - 18 - 130.247 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 6 - 0 - 9 - MWPLHWSMW - LWPKTHTLW - +WP ++W - - - - - 2 - gnl|BL_ORD_ID|2310 - 423016|NS5A|ACX46481.1|Hepatitis C virus genotype 1|41856 - 2310 - 9 - - - 1 - 11.1566 - 17 - 296.302 - 2 - 9 - 2 - 9 - 0 - 0 - 3 - 5 - 0 - 8 - WPLHWSMW - FPLAMPVW - +PL +W - - - - - 3 - gnl|BL_ORD_ID|664 - 39591|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 - 664 - 20 - - - 1 - 10.7714 - 16 - 334.087 - 4 - 9 - 9 - 14 - 0 - 0 - 2 - 4 - 0 - 6 - LHWSMW - ISWCLW - + W +W - - - - - 4 - gnl|BL_ORD_ID|2312 - 423020|polyprotein|ACE82359.1|Hepatitis C virus genotype 1|41856 - 2312 - 9 - - - 1 - 10.7714 - 16 - 365.422 - 4 - 9 - 4 - 9 - 0 - 0 - 2 - 4 - 0 - 6 - LHWSMW - ISWCLW - + W +W - - - - - 5 - gnl|BL_ORD_ID|1120 - 74387|Genome polyprotein|P26664.3|Hepatitis C virus (isolate 1)|11104 - 1120 - 9 - - - 1 - 10.3862 - 15 - 504.867 - 4 - 9 - 2 - 7 - 0 - 0 - 2 - 4 - 0 - 6 - LHWSMW - ISWCLW - + W +W - - - - - 6 - gnl|BL_ORD_ID|1119 - 74386|HCV-1|AAA45676.1|Hepatitis C virus|11103 - 1119 - 8 - - - 1 - 10.7714 - 16 - 530.711 - 4 - 9 - 2 - 7 - 0 - 0 - 2 - 4 - 0 - 6 - LHWSMW - ISWCLW - + W +W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 668 - Query_668 - M_4257 - 9 - - - 1 - gnl|BL_ORD_ID|1186 - 93431|pre-C/C protein|ABY54138.1|Hepatitis B virus|10407 - 1186 - 20 - - - 1 - 11.927 - 19 - 74.4218 - 3 - 8 - 7 - 12 - 0 - 0 - 3 - 5 - 0 - 6 - CLMLQC - CLIISC - CL++ C - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 669 - Query_669 - M_4258 - 9 - - - 1 - gnl|BL_ORD_ID|621 - 37466|surface antigen|BAF44879.1|Hepatitis B virus|10407 - 621 - 9 - - - 1 - 12.6974 - 21 - 28.8346 - 1 - 8 - 2 - 9 - 0 - 0 - 3 - 7 - 0 - 8 - MYCMVFLV - LLCLIFLL - + C++FL+ - - - - - 2 - gnl|BL_ORD_ID|596 - 37120|Major surface antigen precursor|P17399.3|Hepatitis B virus|10407 - 596 - 9 - - - 1 - 12.6974 - 21 - 33.6262 - 1 - 8 - 1 - 8 - 0 - 0 - 3 - 7 - 0 - 8 - MYCMVFLV - LLCLIFLL - + C++FL+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 670 - Query_670 - M_4259 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 671 - Query_671 - M_4260 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 672 - Query_672 - M_4261 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 673 - Query_673 - M_4262 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 674 - Query_674 - M_4263 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 675 - Query_675 - M_4264 - 9 - - - 1 - gnl|BL_ORD_ID|889 - 58463|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 889 - 20 - - - 1 - 12.6974 - 21 - 25.6057 - 1 - 7 - 11 - 17 - 0 - 0 - 4 - 6 - 0 - 7 - MYSYAVP - IYVYALP - +Y YA+P - - - - - 2 - gnl|BL_ORD_ID|338 - 21242|polymerase|ACF94272.1|Hepatitis B virus|10407 - 338 - 9 - - - 1 - 12.3122 - 20 - 45.611 - 1 - 7 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - MYSYAVP - LYSSTVP - +YS VP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 676 - Query_676 - M_4265 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 677 - Query_677 - M_4266 - 9 - - - 1 - gnl|BL_ORD_ID|557 - 34304|Gag polyprotein|P88150|Human immunodeficiency virus 1|11676 - 557 - 14 - - - 1 - 13.0826 - 22 - 17.8721 - 1 - 7 - 8 - 14 - 0 - 0 - 4 - 6 - 0 - 7 - NEILRRY - NKIVRMY - N+I+R Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 678 - Query_678 - M_4267 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 679 - Query_679 - M_4268 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 680 - Query_680 - M_4269 - 9 - - - 1 - gnl|BL_ORD_ID|1132 - 74886|latent membrane protein 1|AAS99606.1|Human gammaherpesvirus 4|10376 - 1132 - 9 - - - 1 - 12.6974 - 21 - 31.9494 - 5 - 9 - 5 - 9 - 0 - 0 - 3 - 4 - 0 - 5 - NWWPI - NWWTL - NWW + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 681 - Query_681 - M_4270 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 682 - Query_682 - M_4271 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 683 - Query_683 - M_4272 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 684 - Query_684 - M_4273 - 9 - - - 1 - gnl|BL_ORD_ID|715 - 44133|Genome polyprotein|P26664.3|Hepatitis C virus genotype 1|41856 - 715 - 9 - - - 1 - 11.927 - 19 - 69.1936 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 5 - 0 - 9 - NHSDLAAEL - NHDSPDAEL - NH AEL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 685 - Query_685 - M_4274 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 686 - Query_686 - M_4275 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 687 - Query_687 - M_4276 - 9 - - - 1 - gnl|BL_ORD_ID|1219 - 96898|Genome polyprotein|SRC279960|Hepatitis C virus|11103 - 1219 - 17 - - - 1 - 13.853 - 24 - 4.23286 - 1 - 8 - 7 - 14 - 0 - 0 - 5 - 6 - 0 - 8 - NIVYHTAS - NLVYSTTS - N+VY T S - - - - - 2 - gnl|BL_ORD_ID|1218 - 96897|polyprotein|ABR25251.1|Hepatitis C virus (isolate H77)|63746 - 1218 - 17 - - - 1 - 13.853 - 24 - 5.7721 - 1 - 8 - 7 - 14 - 0 - 0 - 5 - 6 - 0 - 8 - NIVYHTAS - NLVYSTTS - N+VY T S - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 688 - Query_688 - M_4277 - 9 - - - 1 - gnl|BL_ORD_ID|487 - 30892|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 487 - 9 - - - 1 - 14.6234 - 26 - 1.76369 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 6 - 0 - 9 - NIYSRIREY - KFYSKISEY - YS+I EY - - - - - 2 - gnl|BL_ORD_ID|1400 - 110467|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1400 - 25 - - - 1 - 14.6234 - 26 - 2.69562 - 2 - 9 - 16 - 23 - 0 - 0 - 5 - 6 - 0 - 8 - IYSRIREY - FYSKISEY - YS+I EY - - - - - 3 - gnl|BL_ORD_ID|1387 - 110227|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1387 - 33 - - - 1 - 14.2382 - 25 - 3.62324 - 1 - 9 - 22 - 30 - 0 - 0 - 5 - 6 - 0 - 9 - NIYSRIREY - KFYSKISEY - YS+I EY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 689 - Query_689 - M_4278 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 690 - Query_690 - M_4279 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 691 - Query_691 - M_4280 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 692 - Query_692 - M_4281 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 693 - Query_693 - M_4282 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 694 - Query_694 - M_4283 - 9 - - - 1 - gnl|BL_ORD_ID|1300 - 103654|polyprotein|BAB18806.1|Hepatitis C virus|11103 - 1300 - 9 - - - 1 - 12.6974 - 21 - 26.0147 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - NLMAKN - TIMAKN - +MAKN - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 695 - Query_695 - M_4284 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 696 - Query_696 - M_4285 - 9 - - - 1 - gnl|BL_ORD_ID|21 - 1356|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 21 - 15 - - - 1 - 14.6234 - 26 - 1.63256 - 1 - 8 - 5 - 12 - 0 - 0 - 4 - 6 - 0 - 8 - NLPSKRVS - NVPYKRIE - N+P KR+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 697 - Query_697 - M_4286 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 698 - Query_698 - M_4287 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 699 - Query_699 - M_4288 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 700 - Query_700 - M_4289 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 701 - Query_701 - M_4290 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 702 - Query_702 - M_4291 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 703 - Query_703 - M_4292 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 704 - Query_704 - M_4293 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 705 - Query_705 - M_4294 - 9 - - - 1 - gnl|BL_ORD_ID|540 - 32998|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 - 540 - 11 - - - 1 - 13.4678 - 23 - 12.17 - 2 - 7 - 6 - 11 - 0 - 0 - 4 - 6 - 0 - 6 - RLDLVR - RVDMVR - R+D+VR - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 706 - Query_706 - M_4295 - 9 - - - 1 - gnl|BL_ORD_ID|1406 - 110846|E6 protein|CAB45108.1|Human papillomavirus type 16|333760 - 1406 - 9 - - - 1 - 13.853 - 24 - 6.71897 - 2 - 8 - 3 - 9 - 0 - 0 - 4 - 6 - 0 - 7 - RNYCVSV - RHYCYSL - R+YC S+ - - - - - 2 - gnl|BL_ORD_ID|855 - 55779|fusion protein|BAB60865.1|Measles virus|11234 - 855 - 9 - - - 1 - 11.5418 - 18 - 175.774 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 5 - 0 - 8 - RNYCVSVY - RRYPDAVY - R Y +VY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 707 - Query_707 - M_4296 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 708 - Query_708 - M_4297 - 9 - - - 1 - gnl|BL_ORD_ID|958 - 62977|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 958 - 10 - - - 1 - 13.853 - 24 - 4.37925 - 4 - 8 - 3 - 7 - 0 - 0 - 4 - 5 - 0 - 5 - RHTPM - RHTPV - RHTP+ - - - - - 2 - gnl|BL_ORD_ID|55 - 4156|polyprotein|ABR25251.1|Hepatitis C virus|11103 - 55 - 9 - - - 1 - 13.853 - 24 - 4.51705 - 4 - 8 - 2 - 6 - 0 - 0 - 4 - 5 - 0 - 5 - RHTPM - RHTPV - RHTP+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 709 - Query_709 - M_4298 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 710 - Query_710 - M_4299 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 711 - Query_711 - M_4300 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 712 - Query_712 - M_4301 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 713 - Query_713 - M_4302 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 714 - Query_714 - M_4303 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 715 - Query_715 - M_4304 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 716 - Query_716 - M_4305 - 9 - - - 1 - gnl|BL_ORD_ID|1125 - 74605|Circumsporozoite protein precursor|P08677.2|Plasmodium vivax strain Belem|31273 - 1125 - 9 - - - 1 - 15.3938 - 28 - 0.735125 - 2 - 8 - 1 - 7 - 0 - 0 - 5 - 7 - 0 - 7 - YLEKVRS - YLDKVRA - YL+KVR+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 717 - Query_717 - M_4306 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 718 - Query_718 - M_4307 - 9 - - - 1 - gnl|BL_ORD_ID|416 - 25149|polyprotein|BAD73994.1|Hepatitis C virus subtype 1b|31647 - 416 - 9 - - - 1 - 14.6234 - 26 - 2.07889 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 6 - 0 - 6 - NYSPRP - HYAPRP - +Y+PRP - - - - - 2 - gnl|BL_ORD_ID|1551 - 141226|tegument protein UL37|ADD60080.1|Human alphaherpesvirus 1|10298 - 1551 - 9 - - - 1 - 13.853 - 24 - 5.84954 - 2 - 7 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - YSPRPI - YLPRPV - Y PRP+ - - - - - 3 - gnl|BL_ORD_ID|2240 - 230030|Nef protein|BAA86664.1|Human immunodeficiency virus 1|11676 - 2240 - 10 - - - 1 - 13.4678 - 23 - 7.76238 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - NYSPRP - NYTPGP - NY+P P - - - - - 4 - gnl|BL_ORD_ID|2238 - 230028|Protein Nef|P04603.3|Human immunodeficiency virus 1|11676 - 2238 - 10 - - - 1 - 13.4678 - 23 - 7.89871 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - NYSPRP - NYTPGP - NY+P P - - - - - 5 - gnl|BL_ORD_ID|2239 - 230029|Protein Nef|P03404.4|Human immunodeficiency virus 1|11676 - 2239 - 10 - - - 1 - 13.4678 - 23 - 9.73455 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - NYSPRP - NYTPGP - NY+P P - - - - - 6 - gnl|BL_ORD_ID|1011 - 67349|Latent membrane protein 2|Q69135|Human gammaherpesvirus 4|10376 - 1011 - 9 - - - 1 - 11.927 - 19 - 92.9112 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 5 - 0 - 9 - NYSPRPICV - TYGPVFMCL - Y P +C+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 719 - Query_719 - M_4308 - 9 - - - 1 - gnl|BL_ORD_ID|150 - 11063|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 150 - 15 - - - 1 - 14.2382 - 25 - 4.08331 - 1 - 9 - 7 - 15 - 0 - 0 - 5 - 6 - 0 - 9 - PASTLSLGY - PASIAARGY - PAS + GY - - - - - 2 - gnl|BL_ORD_ID|1855 - 180408|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1855 - 10 - - - 1 - 13.853 - 24 - 4.61192 - 1 - 9 - 2 - 10 - 0 - 0 - 5 - 6 - 0 - 9 - PASTLSLGY - PASIAARGY - PAS + GY - - - - - 3 - gnl|BL_ORD_ID|1639 - 146285|polyprotein|ADF97231.1|Hepatitis C virus subtype 3a|356426 - 1639 - 18 - - - 1 - 13.4678 - 23 - 11.4723 - 1 - 9 - 7 - 15 - 0 - 0 - 4 - 7 - 0 - 9 - PASTLSLGY - PAAYVAQGY - PA+ ++ GY - - - - - 4 - gnl|BL_ORD_ID|1638 - 146284|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 - 1638 - 18 - - - 1 - 12.3122 - 20 - 44.435 - 1 - 9 - 7 - 15 - 0 - 0 - 4 - 6 - 0 - 9 - PASTLSLGY - PAAYAAQGY - PA+ + GY - - - - - 5 - gnl|BL_ORD_ID|737 - 46755|HCV-1|AAA45676.1|Hepatitis C virus genotype 1|41856 - 737 - 20 - - - 1 - 11.927 - 19 - 58.6701 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 6 - 0 - 9 - PASTLSLGY - PAAYAAQGY - PA+ + GY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 720 - Query_720 - M_4309 - 9 - - - 1 - gnl|BL_ORD_ID|636 - 37919|envelope protein|BAF48755.1|Hepatitis B virus|10407 - 636 - 10 - - - 1 - 12.3122 - 20 - 47.0941 - 1 - 6 - 4 - 9 - 0 - 0 - 3 - 4 - 0 - 6 - PFPRWL - PFVQWF - PF +W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 721 - Query_721 - M_4310 - 9 - - - 1 - gnl|BL_ORD_ID|1174 - 79351|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 1174 - 17 - - - 1 - 12.6974 - 21 - 34.1537 - 3 - 8 - 7 - 12 - 0 - 0 - 3 - 4 - 0 - 6 - WASSIV - WGGSVV - W S+V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 722 - Query_722 - M_4311 - 9 - - - 1 - gnl|BL_ORD_ID|747 - 48896|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 - 747 - 15 - - - 1 - 13.853 - 24 - 4.22764 - 1 - 6 - 4 - 9 - 0 - 0 - 4 - 4 - 0 - 6 - PHYDFE - PEYDLE - P YD E - - - - - 2 - gnl|BL_ORD_ID|619 - 37398|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 - 619 - 10 - - - 1 - 13.853 - 24 - 7.36741 - 2 - 7 - 3 - 8 - 0 - 0 - 4 - 5 - 0 - 6 - HYDFER - HTDFEQ - H DFE+ - - - - - 3 - gnl|BL_ORD_ID|581 - 36432|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 - 581 - 9 - - - 1 - 13.4678 - 23 - 8.56958 - 2 - 7 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - HYDFER - HTDFEQ - H DFE+ - - - - - 4 - gnl|BL_ORD_ID|618 - 37397|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 - 618 - 9 - - - 1 - 13.4678 - 23 - 8.72003 - 2 - 7 - 3 - 8 - 0 - 0 - 4 - 5 - 0 - 6 - HYDFER - HTDFEQ - H DFE+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 723 - Query_723 - M_4312 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 724 - Query_724 - M_4313 - 9 - - - 1 - gnl|BL_ORD_ID|798 - 53148|Transcription activator BRLF1|P03209.1|Human herpesvirus 4 strain B95-8|10377 - 798 - 15 - - - 1 - 13.4678 - 23 - 12.0936 - 1 - 6 - 8 - 13 - 0 - 0 - 4 - 4 - 0 - 6 - PRIGYS - PRASYS - PR YS - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 725 - Query_725 - M_4314 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 726 - Query_726 - M_4315 - 9 - - - 1 - gnl|BL_ORD_ID|854 - 55744|polyprotein precursor|NP_041724.2|West Nile virus|11082 - 854 - 9 - - - 1 - 14.2382 - 25 - 3.74233 - 2 - 9 - 2 - 9 - 0 - 0 - 5 - 7 - 0 - 8 - RNRKPLTV - RSRRSLTV - R+R+ LTV - - - - - 2 - gnl|BL_ORD_ID|1181 - 88849|IE62|AAP32859.1|Human alphaherpesvirus 3|10335 - 1181 - 9 - - - 1 - 13.853 - 24 - 7.20201 - 1 - 7 - 3 - 9 - 0 - 0 - 4 - 6 - 0 - 7 - PRNRKPL - PRSRTPI - PR+R P+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 727 - Query_727 - M_4316 - 9 - - - 1 - gnl|BL_ORD_ID|381 - 23566|tegument protein UL7|NP_044476.1|Human alphaherpesvirus 2|10310 - 381 - 13 - - - 1 - 13.4678 - 23 - 10.7509 - 5 - 9 - 9 - 13 - 0 - 0 - 5 - 5 - 0 - 5 - RCLLL - RCLLL - RCLLL - - - - - 2 - gnl|BL_ORD_ID|1731 - 150556|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1731 - 10 - - - 1 - 12.6974 - 21 - 26.5293 - 3 - 7 - 5 - 9 - 0 - 0 - 4 - 4 - 0 - 5 - PSRCL - PRRCL - P RCL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 728 - Query_728 - M_4317 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 729 - Query_729 - M_4318 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 730 - Query_730 - M_4319 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 731 - Query_731 - M_4320 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 732 - Query_732 - M_4321 - 9 - - - 1 - gnl|BL_ORD_ID|889 - 58463|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 889 - 20 - - - 1 - 12.6974 - 21 - 33.9105 - 1 - 9 - 4 - 12 - 0 - 0 - 5 - 5 - 0 - 9 - PSQPANSFY - PSQEPMSIY - PSQ S Y - - - - - 2 - gnl|BL_ORD_ID|749 - 49485|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 749 - 11 - - - 1 - 12.3122 - 20 - 50.6074 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 5 - 0 - 9 - PSQPANSFY - PSQEPMSIY - PSQ S Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 733 - Query_733 - M_4322 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 734 - Query_734 - M_4323 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 735 - Query_735 - M_4324 - 9 - - - 1 - gnl|BL_ORD_ID|1569 - 141354|transcriptional regulator ICP4|NP_044662.1|Human alphaherpesvirus 1|10298 - 1569 - 10 - - - 1 - 13.4678 - 23 - 8.46851 - 2 - 7 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - YPETPP - YPDAPP - YP+ PP - - - - - 2 - gnl|BL_ORD_ID|1759 - 154346|RL2|CAB06760.1|Human alphaherpesvirus 2|10310 - 1759 - 15 - - - 1 - 12.3122 - 20 - 59.339 - 3 - 8 - 8 - 13 - 0 - 0 - 4 - 4 - 0 - 6 - PETPPR - PRTAPR - P T PR - - - - - 3 - gnl|BL_ORD_ID|1438 - 120093|unnamed protein product|CAA33016.1|Rubella virus|11041 - 1438 - 21 - - - 1 - 10.001 - 14 - 777.216 - 1 - 6 - 11 - 16 - 0 - 0 - 4 - 4 - 0 - 6 - PYPETP - PPPATP - P P TP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 736 - Query_736 - M_4325 - 9 - - - 1 - gnl|BL_ORD_ID|1000 - 65810|sporozoite surface protein 2|NP_705260.1|Plasmodium falciparum 3D7|36329 - 1000 - 10 - - - 1 - 13.4678 - 23 - 8.61729 - 1 - 6 - 2 - 7 - 0 - 0 - 4 - 4 - 0 - 6 - PYQGRP - PYAGEP - PY G P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 737 - Query_737 - M_4326 - 9 - - - 1 - gnl|BL_ORD_ID|1000 - 65810|sporozoite surface protein 2|NP_705260.1|Plasmodium falciparum 3D7|36329 - 1000 - 10 - - - 1 - 13.4678 - 23 - 8.61729 - 1 - 6 - 2 - 7 - 0 - 0 - 4 - 4 - 0 - 6 - PYQGRP - PYAGEP - PY G P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 738 - Query_738 - M_4327 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 739 - Query_739 - M_4328 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 740 - Query_740 - M_4329 - 9 - - - 1 - gnl|BL_ORD_ID|601 - 37153|Nuclear antigen EBNA-3C|Q69140.1|Human gammaherpesvirus 4|10376 - 601 - 10 - - - 1 - 13.0826 - 22 - 14.2707 - 4 - 9 - 5 - 10 - 0 - 0 - 4 - 6 - 0 - 6 - VKFIGV - VRFMGV - V+F+GV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 741 - Query_741 - M_4330 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 742 - Query_742 - M_4331 - 9 - - - 1 - gnl|BL_ORD_ID|792 - 53027|nonstructural protein 3|NP_722463.1|Dengue virus 1 Singapore/S275/1990|33741 - 792 - 9 - - - 1 - 11.1566 - 17 - 254.603 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 5 - 0 - 9 - QFSFDGWKF - QYSDRRWCF - Q+S W F - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 743 - Query_743 - M_4332 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 744 - Query_744 - M_4333 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 745 - Query_745 - M_4334 - 9 - - - 1 - gnl|BL_ORD_ID|1813 - 177701|polyprotein|ACZ60104.1|Hepatitis C virus subtype 3a|356426 - 1813 - 18 - - - 1 - 15.3938 - 28 - 0.691719 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 6 - 0 - 9 - QHDFCGLYM - KAKICGLYL - + CGLY+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 746 - Query_746 - M_4335 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 747 - Query_747 - M_4336 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 748 - Query_748 - M_4337 - 9 - - - 1 - gnl|BL_ORD_ID|1563 - 141306|tegument host shutoff protein|NP_044643.1|Human alphaherpesvirus 1|10298 - 1563 - 10 - - - 1 - 13.853 - 24 - 5.48318 - 2 - 6 - 5 - 9 - 0 - 0 - 4 - 5 - 0 - 5 - HPNNS - HPNNT - HPNN+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 749 - Query_749 - M_4338 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 750 - Query_750 - M_4339 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 751 - Query_751 - M_4340 - 9 - - - 1 - gnl|BL_ORD_ID|1271 - 101673|gag protein|ABO73990.1|Human immunodeficiency virus 1|11676 - 1271 - 9 - - - 1 - 11.927 - 19 - 71.5135 - 2 - 7 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - HYAALQ - HQAAMQ - H AA+Q - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 752 - Query_752 - M_4341 - 9 - - - 1 - gnl|BL_ORD_ID|1257 - 98253|trans-sialidase, putative|EAN81042.1|Trypanosoma cruzi|5693 - 1257 - 9 - - - 1 - 14.6234 - 26 - 1.57352 - 2 - 9 - 1 - 8 - 0 - 0 - 6 - 8 - 0 - 8 - ILSRVAAL - MLSRVAAV - +LSRVAA+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 753 - Query_753 - M_4342 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 754 - Query_754 - M_4343 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 755 - Query_755 - M_4344 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 756 - Query_756 - M_4345 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 757 - Query_757 - M_4346 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 758 - Query_758 - M_4347 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 759 - Query_759 - M_4348 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 760 - Query_760 - M_4349 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 761 - Query_761 - M_4350 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 762 - Query_762 - M_4351 - 9 - - - 1 - gnl|BL_ORD_ID|1323 - 107790|polyprotein|AAD56189.1|Hepatitis C virus|11103 - 1323 - 10 - - - 1 - 12.6974 - 21 - 37.8768 - 3 - 8 - 4 - 9 - 0 - 0 - 4 - 4 - 0 - 6 - MCRICH - MCDECH - MC CH - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 763 - Query_763 - M_4352 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 764 - Query_764 - M_4353 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 765 - Query_765 - M_4354 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 766 - Query_766 - M_4355 - 9 - - - 1 - gnl|BL_ORD_ID|191 - 14101|envelope glycoprotein|ABI16336.1|Human immunodeficiency virus 1|11676 - 191 - 9 - - - 1 - 12.6974 - 21 - 30.8766 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 7 - 0 - 9 - QRFLNVQEL - ERYLKDQQL - +R+L Q+L - - - - - 2 - gnl|BL_ORD_ID|864 - 56574|envelope glycoprotein|ABI16336.1|Human immunodeficiency virus 1|11676 - 864 - 9 - - - 1 - 11.927 - 19 - 69.1936 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 6 - 0 - 8 - RFLNVQEL - RYLKDQQL - R+L Q+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 767 - Query_767 - M_4356 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 768 - Query_768 - M_4357 - 9 - - - 1 - gnl|BL_ORD_ID|1114 - 73862|EBNA-1 protein|Q777E1|Human gammaherpesvirus 4|10376 - 1114 - 15 - - - 1 - 13.0826 - 22 - 16.3955 - 1 - 9 - 7 - 15 - 0 - 0 - 4 - 5 - 0 - 9 - QRHGFGEEI - QTHIFAEVL - Q H F E + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 769 - Query_769 - M_4358 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 770 - Query_770 - M_4359 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 771 - Query_771 - M_4360 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 772 - Query_772 - M_4361 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 773 - Query_773 - M_4362 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 774 - Query_774 - M_4363 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 775 - Query_775 - M_4364 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 776 - Query_776 - M_4365 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 777 - Query_777 - M_4366 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 778 - Query_778 - M_4367 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 779 - Query_779 - M_4368 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 780 - Query_780 - M_4369 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 781 - Query_781 - M_4370 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 782 - Query_782 - M_4371 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 783 - Query_783 - M_4372 - 9 - - - 1 - gnl|BL_ORD_ID|1674 - 148619|unnamed protein product|BAA14233.1|Hepatitis C virus|11103 - 1674 - 45 - - - 1 - 11.927 - 19 - 52.3928 - 2 - 9 - 35 - 42 - 0 - 0 - 3 - 5 - 0 - 8 - TCKANLCY - TCVNGVCW - TC +C+ - - - - - 2 - gnl|BL_ORD_ID|1632 - 146246|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 - 1632 - 17 - - - 1 - 11.927 - 19 - 83.9093 - 2 - 9 - 4 - 11 - 0 - 0 - 3 - 5 - 0 - 8 - TCKANLCY - TCVNGVCW - TC +C+ - - - - - 3 - gnl|BL_ORD_ID|66 - 4910|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 66 - 20 - - - 1 - 11.927 - 19 - 86.1921 - 2 - 9 - 2 - 9 - 0 - 0 - 3 - 5 - 0 - 8 - TCKANLCY - TCINGVCW - TC +C+ - - - - - 4 - gnl|BL_ORD_ID|784 - 52509|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 - 784 - 15 - - - 1 - 11.927 - 19 - 94.4229 - 2 - 9 - 6 - 13 - 0 - 0 - 3 - 5 - 0 - 8 - TCKANLCY - TCINGVCW - TC +C+ - - - - - 5 - gnl|BL_ORD_ID|65 - 4909|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 - 65 - 15 - - - 1 - 11.5418 - 18 - 101.887 - 2 - 9 - 2 - 9 - 0 - 0 - 3 - 5 - 0 - 8 - TCKANLCY - TCINGVCW - TC +C+ - - - - - 6 - gnl|BL_ORD_ID|156 - 11956|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 - 156 - 11 - - - 1 - 11.5418 - 18 - 152.168 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 5 - 0 - 9 - QTCKANLCY - EFCRVLCCY - + C+ CY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 784 - Query_784 - M_4373 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 785 - Query_785 - M_4374 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 786 - Query_786 - M_4375 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 787 - Query_787 - M_4376 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 788 - Query_788 - M_4377 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 789 - Query_789 - M_4378 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 790 - Query_790 - M_4379 - 9 - - - 1 - gnl|BL_ORD_ID|1131 - 74800|Genome polyprotein|SRC279960|Hepatitis C virus subtype 2b|31650 - 1131 - 10 - - - 1 - 11.1566 - 17 - 199.037 - 3 - 9 - 4 - 10 - 0 - 0 - 4 - 4 - 0 - 7 - PQRIPSL - PSRGPKL - P R P L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 791 - Query_791 - M_4380 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 792 - Query_792 - M_4381 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 793 - Query_793 - M_4382 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 794 - Query_794 - M_4383 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 795 - Query_795 - M_4384 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 796 - Query_796 - M_4385 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 797 - Query_797 - M_4386 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 798 - Query_798 - M_4387 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 799 - Query_799 - M_4388 - 9 - - - 1 - gnl|BL_ORD_ID|2137 - 187106|Vpr protein|BAA93983.1|Human immunodeficiency virus 1|11676 - 2137 - 9 - - - 1 - 14.2382 - 25 - 4.21767 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 7 - 0 - 7 - LRNFPQI - VRHFPRI - +R+FP+I - - - - - 2 - gnl|BL_ORD_ID|48 - 3051|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 - 48 - 20 - - - 1 - 14.2382 - 25 - 4.2724 - 3 - 8 - 5 - 10 - 0 - 0 - 4 - 5 - 0 - 6 - LRNFPQ - LQNLPQ - L+N PQ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 800 - Query_800 - M_4389 - 9 - - - 1 - gnl|BL_ORD_ID|1040 - 69474|core protein|BAF42671.1|Hepatitis B virus|10407 - 1040 - 10 - - - 1 - 13.853 - 24 - 5.87716 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 7 - 0 - 7 - MKYLVNF - LEYLVSF - ++YLV+F - - - - - 2 - gnl|BL_ORD_ID|2322 - 423053|core protein|AAL31859.1|Hepatitis B virus|10407 - 2322 - 11 - - - 1 - 13.853 - 24 - 6.85565 - 3 - 9 - 5 - 11 - 0 - 0 - 4 - 7 - 0 - 7 - MKYLVNF - IEYLVSF - ++YLV+F - - - - - 3 - gnl|BL_ORD_ID|201 - 15061|core protein|BAF42671.1|Hepatitis B virus|10407 - 201 - 9 - - - 1 - 13.0826 - 22 - 19.404 - 4 - 9 - 1 - 6 - 0 - 0 - 4 - 6 - 0 - 6 - KYLVNF - EYLVSF - +YLV+F - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 801 - Query_801 - M_4390 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 802 - Query_802 - M_4391 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 803 - Query_803 - M_4392 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 804 - Query_804 - M_4393 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 805 - Query_805 - M_4394 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 806 - Query_806 - M_4395 - 9 - - - 1 - gnl|BL_ORD_ID|256 - 17278|Genome polyprotein|P06441.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 256 - 20 - - - 1 - 14.6234 - 26 - 1.54928 - 1 - 9 - 10 - 18 - 0 - 0 - 4 - 5 - 0 - 9 - RHLGDQMEV - RHTSDHMSI - RH D M + - - - - - 2 - gnl|BL_ORD_ID|864 - 56574|envelope glycoprotein|ABI16336.1|Human immunodeficiency virus 1|11676 - 864 - 9 - - - 1 - 13.0826 - 22 - 23.0624 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - RHLGDQ - RYLKDQ - R+L DQ - - - - - 3 - gnl|BL_ORD_ID|191 - 14101|envelope glycoprotein|ABI16336.1|Human immunodeficiency virus 1|11676 - 191 - 9 - - - 1 - 13.0826 - 22 - 23.0624 - 1 - 6 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - RHLGDQ - RYLKDQ - R+L DQ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 807 - Query_807 - M_4396 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 808 - Query_808 - M_4397 - 9 - - - 1 - gnl|BL_ORD_ID|96 - 6591|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 96 - 18 - - - 1 - 13.4678 - 23 - 8.6267 - 2 - 9 - 10 - 17 - 0 - 0 - 4 - 5 - 0 - 8 - HSPRNLIY - HGPTPLLY - H P L+Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 809 - Query_809 - M_4398 - 9 - - - 1 - gnl|BL_ORD_ID|1616 - 144403|polyprotein|AAK08509.1|Hepatitis C virus subtype 1b|31647 - 1616 - 9 - - - 1 - 11.5418 - 18 - 120.255 - 1 - 7 - 3 - 9 - 0 - 0 - 4 - 4 - 0 - 7 - RHTPMYY - RHHNMVY - RH M Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 810 - Query_810 - M_4399 - 9 - - - 1 - gnl|BL_ORD_ID|1616 - 144403|polyprotein|AAK08509.1|Hepatitis C virus subtype 1b|31647 - 1616 - 9 - - - 1 - 11.5418 - 18 - 120.255 - 1 - 7 - 3 - 9 - 0 - 0 - 4 - 4 - 0 - 7 - RHTPMYY - RHHNMVY - RH M Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 811 - Query_811 - M_4400 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 812 - Query_812 - M_4401 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 813 - Query_813 - M_4402 - 9 - - - 1 - gnl|BL_ORD_ID|2005 - 183741|polyprotein|AGS49173.1|Dengue virus 2|11060 - 2005 - 10 - - - 1 - 13.853 - 24 - 5.48318 - 2 - 9 - 1 - 8 - 0 - 0 - 3 - 6 - 0 - 8 - LMCGPNTI - ILCVPNAV - ++C PN + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 814 - Query_814 - M_4403 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 815 - Query_815 - M_4404 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 816 - Query_816 - M_4405 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 817 - Query_817 - M_4406 - 9 - - - 1 - gnl|BL_ORD_ID|2137 - 187106|Vpr protein|BAA93983.1|Human immunodeficiency virus 1|11676 - 2137 - 9 - - - 1 - 15.0086 - 27 - 0.914566 - 1 - 7 - 3 - 9 - 0 - 0 - 4 - 7 - 0 - 7 - RNFPQIY - RHFPRIW - R+FP+I+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 818 - Query_818 - M_4407 - 9 - - - 1 - gnl|BL_ORD_ID|1060 - 69799|envelope glycoprotein|BAE96221.1|Human immunodeficiency virus 1|11676 - 1060 - 10 - - - 1 - 13.4678 - 23 - 10.0795 - 2 - 6 - 6 - 10 - 0 - 0 - 4 - 5 - 0 - 5 - NPQEL - NPQEV - NPQE+ - - - - - 2 - gnl|BL_ORD_ID|1097 - 72563|polyprotein|AAB70696.1|Dengue virus type 1 Hawaii|10000440 - 1097 - 20 - - - 1 - 12.6974 - 21 - 28.5768 - 2 - 9 - 7 - 14 - 0 - 0 - 3 - 5 - 0 - 8 - NPQELWHF - NPYKTWAY - NP + W + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 819 - Query_819 - M_4408 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 820 - Query_820 - M_4409 - 9 - - - 1 - gnl|BL_ORD_ID|1712 - 150341|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1712 - 9 - - - 1 - 15.0086 - 27 - 1.14097 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 7 - 0 - 9 - RPGSRGCPM - KPGTSGSPI - +PG+ G P+ - - - - - 2 - gnl|BL_ORD_ID|75 - 5542|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 75 - 15 - - - 1 - 14.2382 - 25 - 2.38473 - 1 - 9 - 7 - 15 - 0 - 0 - 4 - 6 - 0 - 9 - RPGSRGCPM - SPGTSGSPI - PG+ G P+ - - - - - 3 - gnl|BL_ORD_ID|260 - 17802|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 260 - 15 - - - 1 - 14.2382 - 25 - 3.14687 - 2 - 9 - 3 - 10 - 0 - 0 - 4 - 6 - 0 - 8 - PGSRGCPM - PGTSGSPI - PG+ G P+ - - - - - 4 - gnl|BL_ORD_ID|1929 - 180750|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1929 - 15 - - - 1 - 14.2382 - 25 - 3.37317 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 6 - 0 - 8 - PGSRGCPM - PGTSGSPI - PG+ G P+ - - - - - 5 - gnl|BL_ORD_ID|847 - 55336|EBNA-1|YP_401677.1|Human gammaherpesvirus 4|10376 - 847 - 15 - - - 1 - 11.1566 - 17 - 174.225 - 1 - 7 - 1 - 7 - 0 - 0 - 4 - 4 - 0 - 7 - RPGSRGC - RPSCIGC - RP GC - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 821 - Query_821 - M_4410 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 822 - Query_822 - M_4411 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 823 - Query_823 - M_4412 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 824 - Query_824 - M_4413 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 825 - Query_825 - M_4414 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 826 - Query_826 - M_4415 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 827 - Query_827 - M_4416 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 828 - Query_828 - M_4417 - 9 - - - 1 - gnl|BL_ORD_ID|1132 - 74886|latent membrane protein 1|AAS99606.1|Human gammaherpesvirus 4|10376 - 1132 - 9 - - - 1 - 12.3122 - 20 - 42.6373 - 3 - 9 - 3 - 9 - 0 - 0 - 3 - 6 - 0 - 7 - QQDYWLM - QQNWWTL - QQ++W + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 829 - Query_829 - M_4418 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 830 - Query_830 - M_4419 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 831 - Query_831 - M_4420 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 832 - Query_832 - M_4421 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 833 - Query_833 - M_4422 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 834 - Query_834 - M_4423 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 835 - Query_835 - M_4424 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 836 - Query_836 - M_4425 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 837 - Query_837 - M_4426 - 9 - - - 1 - gnl|BL_ORD_ID|1071 - 70687|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis|1773 - 1071 - 20 - - - 1 - 12.6974 - 21 - 32.3697 - 2 - 8 - 5 - 11 - 0 - 0 - 4 - 6 - 0 - 7 - RSDAEKQ - RADEEQQ - R+D E+Q - - - - - 2 - gnl|BL_ORD_ID|73 - 5316|EBNA-3B nuclear protein|CAD53420.1|Human gammaherpesvirus 4|10376 - 73 - 10 - - - 1 - 12.6974 - 21 - 36.6217 - 1 - 6 - 5 - 10 - 0 - 0 - 4 - 6 - 0 - 6 - RRSDAE - RKSDAK - R+SDA+ - - - - - 3 - gnl|BL_ORD_ID|794 - 53077|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis|1773 - 794 - 10 - - - 1 - 12.3122 - 20 - 40.5114 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 6 - 0 - 7 - RSDAEKQ - RADEEQQ - R+D E+Q - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 838 - Query_838 - M_4427 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 839 - Query_839 - M_4428 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 840 - Query_840 - M_4429 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 841 - Query_841 - M_4430 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 842 - Query_842 - M_4431 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 843 - Query_843 - M_4432 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 844 - Query_844 - M_4433 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 845 - Query_845 - M_4434 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 846 - Query_846 - M_4435 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 847 - Query_847 - M_4436 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 848 - Query_848 - M_4437 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 849 - Query_849 - M_4438 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 850 - Query_850 - M_4439 - 9 - - - 1 - gnl|BL_ORD_ID|829 - 54741|gag polyprotein|BAA00992.1|Human immunodeficiency virus 1|11676 - 829 - 9 - - - 1 - 10.3862 - 15 - 600.299 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 6 - 0 - 8 - RVRRRGQK - RLRPGGKK - R+R G+K - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 851 - Query_851 - M_4440 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 852 - Query_852 - M_4441 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 853 - Query_853 - M_4442 - 9 - - - 1 - gnl|BL_ORD_ID|2090 - 185573|polyprotein|CDF77361.1|Dengue virus 3|11069 - 2090 - 9 - - - 1 - 13.4678 - 23 - 10.7466 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 4 - 0 - 9 - RYAALLKCW - RYMGEDGCW - RY CW - - - - - 2 - gnl|BL_ORD_ID|1928 - 180738|polyprotein|CDF77361.1|Dengue virus 3|11069 - 1928 - 10 - - - 1 - 13.4678 - 23 - 12.859 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 4 - 0 - 9 - RYAALLKCW - RYMGEDGCW - RY CW - - - - - 3 - gnl|BL_ORD_ID|1387 - 110227|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1387 - 33 - - - 1 - 11.1566 - 17 - 129.204 - 2 - 8 - 14 - 20 - 0 - 0 - 4 - 4 - 0 - 7 - YAALLKC - YAVCDKC - YA KC - - - - - 4 - gnl|BL_ORD_ID|1400 - 110467|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1400 - 25 - - - 1 - 11.5418 - 18 - 133.249 - 2 - 8 - 7 - 13 - 0 - 0 - 4 - 4 - 0 - 7 - YAALLKC - YAVCDKC - YA KC - - - - - 5 - gnl|BL_ORD_ID|865 - 56589|polyprotein precursor|NP_041724.2|West Nile virus|11082 - 865 - 9 - - - 1 - 11.1566 - 17 - 287.485 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 4 - 0 - 9 - RYAALLKCW - RYLVKTESW - RY + W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 854 - Query_854 - M_4443 - 9 - - - 1 - gnl|BL_ORD_ID|1597 - 142233|ATP-dependent helicase|NP_217813.1|Mycobacterium tuberculosis|1773 - 1597 - 32 - - - 1 - 15.3938 - 28 - 1.12437 - 1 - 8 - 2 - 9 - 0 - 0 - 5 - 7 - 0 - 8 - RYARPSRL - RFAQPSAL - R+A+PS L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 855 - Query_855 - M_4444 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 856 - Query_856 - M_4445 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 857 - Query_857 - M_4446 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 858 - Query_858 - M_4447 - 9 - - - 1 - gnl|BL_ORD_ID|418 - 25237|Transcription activator BRLF1|P03209.1|Human herpesvirus 4 strain B95-8|10377 - 418 - 15 - - - 1 - 13.4678 - 23 - 7.61659 - 1 - 8 - 8 - 15 - 0 - 0 - 5 - 5 - 0 - 8 - RYFLKHGI - RYVLDHLI - RY L H I - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 859 - Query_859 - M_4448 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 860 - Query_860 - M_4449 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 861 - Query_861 - M_4450 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 862 - Query_862 - M_4451 - 9 - - - 1 - gnl|BL_ORD_ID|863 - 56502|polyprotein|BAD73994.1|Hepatitis C virus subtype 1b|31647 - 863 - 9 - - - 1 - 14.2382 - 25 - 3.55601 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 5 - 0 - 9 - RYLPDCDYL - RYAPACKPL - RY P C L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 863 - Query_863 - M_4452 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 864 - Query_864 - M_4453 - 9 - - - 1 - gnl|BL_ORD_ID|863 - 56502|polyprotein|BAD73994.1|Hepatitis C virus subtype 1b|31647 - 863 - 9 - - - 1 - 15.0086 - 27 - 1.2556 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 5 - 0 - 9 - RYVAICAPL - RYAPACKPL - RY C PL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 865 - Query_865 - M_4454 - 9 - - - 1 - gnl|BL_ORD_ID|863 - 56502|polyprotein|BAD73994.1|Hepatitis C virus subtype 1b|31647 - 863 - 9 - - - 1 - 17.705 - 34 - 0.13901 - 1 - 9 - 1 - 9 - 0 - 0 - 6 - 7 - 0 - 9 - RYVASCKPL - RYAPACKPL - RY +CKPL - - - - - 2 - gnl|BL_ORD_ID|2080 - 185327|polyprotein|ACF49259.1|Dengue virus type 1 Hawaii|10000440 - 2080 - 9 - - - 1 - 12.3122 - 20 - 60.6092 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 6 - 0 - 9 - RYVASCKPL - QYIYMGQPL - +Y+ +PL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 866 - Query_866 - M_4455 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 867 - Query_867 - M_4456 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 868 - Query_868 - M_4457 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 869 - Query_869 - M_4458 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 870 - Query_870 - M_4459 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 871 - Query_871 - M_4460 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 872 - Query_872 - M_4461 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 873 - Query_873 - M_4462 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 874 - Query_874 - M_4463 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 875 - Query_875 - M_4464 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 876 - Query_876 - M_4465 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 877 - Query_877 - M_4466 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 878 - Query_878 - M_4467 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 879 - Query_879 - M_4468 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 880 - Query_880 - M_4469 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 881 - Query_881 - M_4470 - 9 - - - 1 - gnl|BL_ORD_ID|626 - 37536|Spike glycoprotein precursor|P15423.1|Human coronavirus 229E|11137 - 626 - 9 - - - 1 - 16.5494 - 31 - 0.306344 - 2 - 9 - 2 - 9 - 0 - 0 - 5 - 5 - 0 - 8 - FFNCLWEV - LLNCLWSV - NCLW V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 882 - Query_882 - M_4471 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 883 - Query_883 - M_4472 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 884 - Query_884 - M_4473 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 885 - Query_885 - M_4474 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 886 - Query_886 - M_4475 - 9 - - - 1 - gnl|BL_ORD_ID|340 - 21347|Nucleoprotein|P59595.1|SARS coronavirus|227859 - 340 - 9 - - - 1 - 13.853 - 24 - 5.36545 - 2 - 7 - 1 - 6 - 0 - 0 - 4 - 6 - 0 - 6 - GMARVG - GMSRIG - GM+R+G - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 887 - Query_887 - M_4476 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 888 - Query_888 - M_4477 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 889 - Query_889 - M_4478 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 890 - Query_890 - M_4479 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 891 - Query_891 - M_4480 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 892 - Query_892 - M_4481 - 9 - - - 1 - gnl|BL_ORD_ID|2137 - 187106|Vpr protein|BAA93983.1|Human immunodeficiency virus 1|11676 - 2137 - 9 - - - 1 - 13.853 - 24 - 5.74926 - 4 - 9 - 3 - 8 - 0 - 0 - 4 - 5 - 0 - 6 - RHVPKI - RHFPRI - RH P+I - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 893 - Query_893 - M_4482 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 894 - Query_894 - M_4483 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 895 - Query_895 - M_4484 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 896 - Query_896 - M_4485 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 897 - Query_897 - M_4486 - 9 - - - 1 - gnl|BL_ORD_ID|186 - 13701|Trans-activator protein BZLF1|P03206.2|Human gammaherpesvirus 4|10376 - 186 - 11 - - - 1 - 13.0826 - 22 - 15.2395 - 4 - 9 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - PAGELT - PQGQLT - P G+LT - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 898 - Query_898 - M_4487 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 899 - Query_899 - M_4488 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 900 - Query_900 - M_4489 - 9 - - - 1 - gnl|BL_ORD_ID|889 - 58463|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 889 - 20 - - - 1 - 11.927 - 19 - 87.4603 - 1 - 9 - 10 - 18 - 0 - 0 - 5 - 6 - 0 - 9 - SIFYSFLPL - SIYVYALPL - SI+ LPL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 901 - Query_901 - M_4490 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 902 - Query_902 - M_4491 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 903 - Query_903 - M_4492 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 904 - Query_904 - M_4493 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 905 - Query_905 - M_4494 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 906 - Query_906 - M_4495 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 907 - Query_907 - M_4496 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 908 - Query_908 - M_4497 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 909 - Query_909 - M_4498 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 910 - Query_910 - M_4499 - 9 - - - 1 - gnl|BL_ORD_ID|1219 - 96898|Genome polyprotein|SRC279960|Hepatitis C virus|11103 - 1219 - 17 - - - 1 - 15.0086 - 27 - 0.976474 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 7 - 0 - 9 - SLLRKHQIL - SLLRNHNLV - SLLR H ++ - - - - - 2 - gnl|BL_ORD_ID|1218 - 96897|polyprotein|ABR25251.1|Hepatitis C virus (isolate H77)|63746 - 1218 - 17 - - - 1 - 14.2382 - 25 - 3.04646 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 7 - 0 - 9 - SLLRKHQIL - SLLRHHNLV - SLLR H ++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 911 - Query_911 - M_4500 - 9 - - - 1 - gnl|BL_ORD_ID|1219 - 96898|Genome polyprotein|SRC279960|Hepatitis C virus|11103 - 1219 - 17 - - - 1 - 15.0086 - 27 - 1.13851 - 1 - 8 - 1 - 8 - 0 - 0 - 5 - 6 - 0 - 8 - SLLRKHQI - SLLRNHNL - SLLR H + - - - - - 2 - gnl|BL_ORD_ID|1218 - 96897|polyprotein|ABR25251.1|Hepatitis C virus (isolate H77)|63746 - 1218 - 17 - - - 1 - 14.2382 - 25 - 3.43929 - 1 - 8 - 1 - 8 - 0 - 0 - 5 - 6 - 0 - 8 - SLLRKHQI - SLLRHHNL - SLLR H + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 912 - Query_912 - M_4501 - 9 - - - 1 - gnl|BL_ORD_ID|403 - 24557|Gag polyprotein|P03347.3|Human immunodeficiency virus 1|11676 - 403 - 9 - - - 1 - 13.853 - 24 - 5.84954 - 4 - 9 - 3 - 8 - 0 - 0 - 4 - 5 - 0 - 6 - VHGGPL - VHAGPI - VH GP+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 913 - Query_913 - M_4502 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 914 - Query_914 - M_4503 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 915 - Query_915 - M_4504 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 916 - Query_916 - M_4505 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 917 - Query_917 - M_4506 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 918 - Query_918 - M_4507 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 919 - Query_919 - M_4508 - 9 - - - 1 - gnl|BL_ORD_ID|2243 - 232152|rhoptry kinase family protein|AFO54841.1|Toxoplasma gondii type III|398031 - 2243 - 19 - - - 1 - 13.853 - 24 - 6.77098 - 4 - 9 - 6 - 11 - 0 - 0 - 3 - 6 - 0 - 6 - YHTYGL - FHSYGV - +H+YG+ - - - - - 2 - gnl|BL_ORD_ID|474 - 29182|polyprotein|BAD73991.1|Hepatitis C virus subtype 1b|31647 - 474 - 9 - - - 1 - 12.6974 - 21 - 37.2378 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - LWYHTYG - ITYSTYG - + Y TYG - - - - - 3 - gnl|BL_ORD_ID|1371 - 108232|Genome polyprotein|P26664.3|Hepatitis C virus|11103 - 1371 - 10 - - - 1 - 12.3122 - 20 - 43.3206 - 4 - 8 - 1 - 5 - 0 - 0 - 4 - 4 - 0 - 5 - YHTYG - YSTYG - Y TYG - - - - - 4 - gnl|BL_ORD_ID|1015 - 67471|Genome polyprotein|Q99IB8.3|Hepatitis C virus JFH-1|356411 - 1015 - 9 - - - 1 - 12.3122 - 20 - 56.7066 - 4 - 8 - 2 - 6 - 0 - 0 - 4 - 4 - 0 - 5 - YHTYG - YSTYG - Y TYG - - - - - 5 - gnl|BL_ORD_ID|133 - 9415|Superoxide dismutase|P17670.1|Mycobacterium tuberculosis|1773 - 133 - 10 - - - 1 - 12.3122 - 20 - 63.4362 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 5 - 0 - 9 - SLWYHTYGL - DMWEHAFYL - +W H + L - - - - - 6 - gnl|BL_ORD_ID|132 - 9414|Superoxide dismutase|P17670.1|Mycobacterium tuberculosis|1773 - 132 - 9 - - - 1 - 11.927 - 19 - 76.3762 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 5 - 0 - 9 - SLWYHTYGL - DMWEHAFYL - +W H + L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 920 - Query_920 - M_4509 - 9 - - - 1 - gnl|BL_ORD_ID|526 - 32250|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 - 526 - 9 - - - 1 - 12.6974 - 21 - 33.058 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 5 - 0 - 8 - SLYTAYHV - KLYCSYEV - LY +Y V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 921 - Query_921 - M_4510 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 922 - Query_922 - M_4511 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 923 - Query_923 - M_4512 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 924 - Query_924 - M_4513 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 925 - Query_925 - M_4514 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 926 - Query_926 - M_4515 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 927 - Query_927 - M_4516 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 928 - Query_928 - M_4517 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 929 - Query_929 - M_4518 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 930 - Query_930 - M_4519 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 931 - Query_931 - M_4520 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 932 - Query_932 - M_4521 - 9 - - - 1 - gnl|BL_ORD_ID|1333 - 107873|Genome polyprotein|P26664.3|Hepatitis C virus|11103 - 1333 - 10 - - - 1 - 13.853 - 24 - 5.48318 - 1 - 7 - 2 - 8 - 0 - 0 - 5 - 6 - 0 - 7 - SPLFYST - SPITYST - SP+ YST - - - - - 2 - gnl|BL_ORD_ID|965 - 63963|HCV-1|AAA45676.1|Hepatitis C virus|11103 - 965 - 10 - - - 1 - 13.853 - 24 - 6.08483 - 1 - 7 - 3 - 9 - 0 - 0 - 5 - 6 - 0 - 7 - SPLFYST - SPITYST - SP+ YST - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 933 - Query_933 - M_4522 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 934 - Query_934 - M_4523 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 935 - Query_935 - M_4524 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 936 - Query_936 - M_4525 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 937 - Query_937 - M_4526 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 938 - Query_938 - M_4527 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 939 - Query_939 - M_4528 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 940 - Query_940 - M_4529 - 9 - - - 1 - gnl|BL_ORD_ID|1960 - 182599|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1960 - 9 - - - 1 - 13.4678 - 23 - 11.5219 - 1 - 7 - 1 - 7 - 0 - 0 - 5 - 6 - 0 - 7 - SQMSQLM - AQMWQLM - +QM QLM - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 941 - Query_941 - M_4530 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 942 - Query_942 - M_4531 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 943 - Query_943 - M_4532 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 944 - Query_944 - M_4533 - 9 - - - 1 - gnl|BL_ORD_ID|381 - 23566|tegument protein UL7|NP_044476.1|Human alphaherpesvirus 2|10310 - 381 - 13 - - - 1 - 13.0826 - 22 - 15.9524 - 2 - 6 - 9 - 13 - 0 - 0 - 5 - 5 - 0 - 5 - RCLLL - RCLLL - RCLLL - - - - - 2 - gnl|BL_ORD_ID|645 - 38427|BZLF1|AAA66529.1|Human gammaherpesvirus 4|10376 - 645 - 9 - - - 1 - 12.6974 - 21 - 39.1808 - 3 - 9 - 3 - 9 - 0 - 0 - 4 - 6 - 0 - 7 - CLLLPLL - CVLWPVL - C+L P+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 945 - Query_945 - M_4534 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 946 - Query_946 - M_4535 - 9 - - - 1 - gnl|BL_ORD_ID|805 - 53476|polyprotein|AGO67248.1|Dengue virus 2|11060 - 805 - 9 - - - 1 - 13.0826 - 22 - 20.0871 - 2 - 7 - 1 - 6 - 0 - 0 - 3 - 5 - 0 - 6 - RENRWT - REDQWC - RE++W - - - - - 2 - gnl|BL_ORD_ID|2019 - 184131|polyprotein|AGO67248.1|Dengue virus 2|11060 - 2019 - 10 - - - 1 - 13.0826 - 22 - 20.1646 - 2 - 7 - 2 - 7 - 0 - 0 - 3 - 5 - 0 - 6 - RENRWT - REDQWC - RE++W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 947 - Query_947 - M_4536 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 948 - Query_948 - M_4537 - 9 - - - 1 - gnl|BL_ORD_ID|929 - 60867|nucleoprotein|CAZ65591.1|Influenza A virus|11320 - 929 - 9 - - - 1 - 13.0826 - 22 - 14.7007 - 1 - 7 - 1 - 7 - 0 - 0 - 4 - 6 - 0 - 7 - SRFTAVR - SRYWAIR - SR+ A+R - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 949 - Query_949 - M_4538 - 9 - - - 1 - gnl|BL_ORD_ID|1385 - 110215|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1385 - 25 - - - 1 - 15.3938 - 28 - 0.880103 - 1 - 8 - 17 - 24 - 0 - 0 - 5 - 6 - 0 - 8 - SRFTLRCM - GRWTGRCM - R+T RCM - - - - - 2 - gnl|BL_ORD_ID|1429 - 113154|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1429 - 10 - - - 1 - 14.6234 - 26 - 2.14354 - 2 - 8 - 1 - 7 - 0 - 0 - 5 - 6 - 0 - 7 - RFTLRCM - RWTGRCM - R+T RCM - - - - - 3 - gnl|BL_ORD_ID|1396 - 110399|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1396 - 23 - - - 1 - 14.6234 - 26 - 2.49651 - 2 - 8 - 3 - 9 - 0 - 0 - 5 - 6 - 0 - 7 - RFTLRCM - RWTGRCM - R+T RCM - - - - - 4 - gnl|BL_ORD_ID|1384 - 110205|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1384 - 32 - - - 1 - 14.6234 - 26 - 2.74814 - 1 - 8 - 11 - 18 - 0 - 0 - 5 - 6 - 0 - 8 - SRFTLRCM - GRWTGRCM - R+T RCM - - - - - 5 - gnl|BL_ORD_ID|2060 - 184840|polyprotein|AGS49173.1|Dengue virus 2|11060 - 2060 - 9 - - - 1 - 13.4678 - 23 - 9.02895 - 1 - 6 - 4 - 9 - 0 - 0 - 4 - 6 - 0 - 6 - SRFTLR - NRFTMR - +RFT+R - - - - - 6 - gnl|BL_ORD_ID|1661 - 147835|early protein|CAA52585.1|Human papillomavirus type 52|10618 - 1661 - 9 - - - 1 - 13.4678 - 23 - 11.9303 - 3 - 9 - 1 - 7 - 0 - 0 - 3 - 6 - 0 - 7 - FTLRCMV - ITIRCII - T+RC++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 950 - Query_950 - M_4539 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 951 - Query_951 - M_4540 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 952 - Query_952 - M_4541 - 9 - - - 1 - gnl|BL_ORD_ID|1823 - 178351|Protein E7|P03129.1|Human papillomavirus type 16|333760 - 1823 - 15 - - - 1 - 12.6974 - 21 - 26.5542 - 1 - 9 - 3 - 11 - 0 - 0 - 3 - 7 - 0 - 9 - SRHDFHVDL - TLHEYMLDL - + H++ +DL - - - - - 2 - gnl|BL_ORD_ID|982 - 64830|E7 protein|ABL96585.1|Human papillomavirus type 16|333760 - 982 - 9 - - - 1 - 12.3122 - 20 - 40.5299 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 7 - 0 - 9 - SRHDFHVDL - TLHEYMLDL - + H++ +DL - - - - - 3 - gnl|BL_ORD_ID|1408 - 110940|Protein E7|P03129.1|Human papillomavirus type 16|333760 - 1408 - 15 - - - 1 - 12.3122 - 20 - 54.8452 - 1 - 9 - 7 - 15 - 0 - 0 - 3 - 7 - 0 - 9 - SRHDFHVDL - TLHEYMLDL - + H++ +DL - - - - - 4 - gnl|BL_ORD_ID|1392 - 110335|E7|AAD33253.1|Human papillomavirus type 16|333760 - 1392 - 32 - - - 1 - 11.1566 - 17 - 167.857 - 3 - 9 - 9 - 15 - 0 - 0 - 3 - 6 - 0 - 7 - HDFHVDL - HEYMLDL - H++ +DL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 953 - Query_953 - M_4542 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 954 - Query_954 - M_4543 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 955 - Query_955 - M_4544 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 956 - Query_956 - M_4545 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 957 - Query_957 - M_4546 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 958 - Query_958 - M_4547 - 9 - - - 1 - gnl|BL_ORD_ID|617 - 37364|P53_HUMAN Cellular tumor antigen p53 (Tumor suppressor p53) (Phosphoprotein p53) (Antigen NY-CO-13)|P04637.2|Homo sapiens|9606 - 617 - 9 - - - 1 - 13.0826 - 22 - 17.1877 - 1 - 6 - 3 - 8 - 0 - 0 - 4 - 4 - 0 - 6 - SRNDFE - GRNSFE - RN FE - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 959 - Query_959 - M_4548 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 960 - Query_960 - M_4549 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 961 - Query_961 - M_4550 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 962 - Query_962 - M_4551 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 963 - Query_963 - M_4552 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 964 - Query_964 - M_4553 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 965 - Query_965 - M_4554 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 966 - Query_966 - M_4555 - 9 - - - 1 - gnl|BL_ORD_ID|1441 - 120187|E1 protein|BAA19893.1|Rubella virus|11041 - 1441 - 21 - - - 1 - 14.6234 - 26 - 2.56229 - 1 - 6 - 8 - 13 - 0 - 0 - 4 - 6 - 0 - 6 - SRTVWE - TRTVWQ - +RTVW+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 967 - Query_967 - M_4556 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 968 - Query_968 - M_4557 - 9 - - - 1 - gnl|BL_ORD_ID|1597 - 142233|ATP-dependent helicase|NP_217813.1|Mycobacterium tuberculosis|1773 - 1597 - 32 - - - 1 - 15.0086 - 27 - 1.21962 - 2 - 9 - 2 - 9 - 0 - 0 - 5 - 7 - 0 - 8 - RYARPSRL - RFAQPSAL - R+A+PS L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 969 - Query_969 - M_4558 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 970 - Query_970 - M_4559 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 971 - Query_971 - M_4560 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 972 - Query_972 - M_4561 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 973 - Query_973 - M_4562 - 9 - - - 1 - gnl|BL_ORD_ID|1435 - 116781|Nucleoprotein|P05133.1|Hantaan virus 76-118|11602 - 1435 - 15 - - - 1 - 11.927 - 19 - 64.1766 - 3 - 9 - 1 - 7 - 0 - 0 - 4 - 6 - 0 - 7 - LRRMNSF - LRKKSSF - LR+ +SF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 974 - Query_974 - M_4563 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 975 - Query_975 - M_4564 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 976 - Query_976 - M_4565 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 977 - Query_977 - M_4566 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 978 - Query_978 - M_4567 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 979 - Query_979 - M_4568 - 9 - - - 1 - gnl|BL_ORD_ID|889 - 58463|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 889 - 20 - - - 1 - 14.6234 - 26 - 2.46911 - 2 - 8 - 10 - 16 - 0 - 0 - 4 - 7 - 0 - 7 - TIYIFAL - SIYVYAL - +IY++AL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 980 - Query_980 - M_4569 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 981 - Query_981 - M_4570 - 9 - - - 1 - gnl|BL_ORD_ID|1078 - 71412|polyprotein [Hepatitis C virus subtype 1a]|ABV46251.2|Hepatitis C virus subtype 1a|31646 - 1078 - 9 - - - 1 - 13.853 - 24 - 4.51705 - 2 - 8 - 2 - 8 - 0 - 0 - 5 - 6 - 0 - 7 - TQTHPLT - TLTHPIT - T THP+T - - - - - 2 - gnl|BL_ORD_ID|1297 - 103389|unnamed protein product [Hepatitis C virus]|BAA14035.1|Hepatitis C virus|11103 - 1297 - 20 - - - 1 - 13.853 - 24 - 4.73116 - 4 - 8 - 2 - 6 - 0 - 0 - 4 - 5 - 0 - 5 - THPLT - THPIT - THP+T - - - - - 3 - gnl|BL_ORD_ID|985 - 65090|polyprotein|BAB18810.1|Hepatitis C virus (isolate H77)|63746 - 985 - 8 - - - 1 - 13.853 - 24 - 5.69712 - 2 - 8 - 1 - 7 - 0 - 0 - 5 - 6 - 0 - 7 - TQTHPLT - TLTHPIT - T THP+T - - - - - 4 - gnl|BL_ORD_ID|986 - 65092|Genome polyprotein|P26664.3|Hepatitis C virus genotype 1|41856 - 986 - 8 - - - 1 - 13.4678 - 23 - 8.77767 - 2 - 8 - 1 - 7 - 0 - 0 - 5 - 6 - 0 - 7 - TQTHPLT - TLTHPVT - T THP+T - - - - - 5 - gnl|BL_ORD_ID|1645 - 146317|polyprotein|ADF97231.1|Hepatitis C virus subtype 3a|356426 - 1645 - 9 - - - 1 - 13.0826 - 22 - 13.9535 - 4 - 8 - 4 - 8 - 0 - 0 - 4 - 5 - 0 - 5 - THPLT - THPVT - THP+T - - - - - 6 - gnl|BL_ORD_ID|1627 - 146182|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 - 1627 - 8 - - - 1 - 13.0826 - 22 - 15.0555 - 4 - 8 - 3 - 7 - 0 - 0 - 4 - 5 - 0 - 5 - THPLT - THPVT - THP+T - - - - - 7 - gnl|BL_ORD_ID|1608 - 143705|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 1608 - 9 - - - 1 - 12.3122 - 20 - 44.8495 - 4 - 9 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - THPLTL - TFPITL - T P+TL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 982 - Query_982 - M_4571 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 983 - Query_983 - M_4572 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 984 - Query_984 - M_4573 - 9 - - - 1 - gnl|BL_ORD_ID|471 - 28594|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 - 471 - 20 - - - 1 - 15.0086 - 27 - 1.02375 - 1 - 9 - 5 - 13 - 0 - 0 - 5 - 7 - 0 - 9 - STYPDQQHV - SYYPDQKSL - S YPDQ+ + - - - - - 2 - gnl|BL_ORD_ID|1173 - 79337|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 1173 - 15 - - - 1 - 12.6974 - 21 - 28.3557 - 2 - 9 - 4 - 11 - 0 - 0 - 4 - 5 - 0 - 8 - TYPDQQHV - TWPLLPHV - T+P HV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 985 - Query_985 - M_4574 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 986 - Query_986 - M_4575 - 9 - - - 1 - gnl|BL_ORD_ID|313 - 20865|Nucleoprotein|P41269.1|Puumala hantavirus|11604 - 313 - 9 - - - 1 - 16.1642 - 30 - 0.361887 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 8 - 0 - 9 - SVFPTQLQL - GLFPTQIQV - +FPTQ+Q+ - - - - - 2 - gnl|BL_ORD_ID|1416 - 111604|L1|ABP99807.1|Human papillomavirus type 18|333761 - 1416 - 9 - - - 1 - 14.2382 - 25 - 3.93883 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 7 - 0 - 9 - SVFPTQLQL - NVFPIFLQM - +VFP LQ+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 987 - Query_987 - M_4576 - 9 - - - 1 - gnl|BL_ORD_ID|1205 - 96123|Genome polyprotein|P26664.3|Hepatitis C virus (isolate H77)|63746 - 1205 - 9 - - - 1 - 13.4678 - 23 - 7.85574 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 5 - 0 - 9 - SVFSEQWIF - AVFGPLWIL - +VF WI - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 988 - Query_988 - M_4577 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 989 - Query_989 - M_4578 - 9 - - - 1 - gnl|BL_ORD_ID|1653 - 146569|polyprotein|ADF97231.1|Hepatitis C virus subtype 3a|356426 - 1653 - 17 - - - 1 - 12.3122 - 20 - 57.3063 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 5 - 0 - 9 - SWMPALECL - SWDETWKCL - SW +CL - - - - - 2 - gnl|BL_ORD_ID|1654 - 146570|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 - 1654 - 17 - - - 1 - 11.5418 - 18 - 129.081 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 5 - 0 - 9 - SWMPALECL - SWDQMWKCL - SW +CL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 990 - Query_990 - M_4579 - 9 - - - 1 - gnl|BL_ORD_ID|664 - 39591|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 - 664 - 20 - - - 1 - 11.927 - 19 - 59.5549 - 1 - 5 - 10 - 14 - 0 - 0 - 4 - 4 - 0 - 5 - SWPLW - SWCLW - SW LW - - - - - 2 - gnl|BL_ORD_ID|1120 - 74387|Genome polyprotein|P26664.3|Hepatitis C virus (isolate 1)|11104 - 1120 - 9 - - - 1 - 11.927 - 19 - 76.3762 - 1 - 5 - 3 - 7 - 0 - 0 - 4 - 4 - 0 - 5 - SWPLW - SWCLW - SW LW - - - - - 3 - gnl|BL_ORD_ID|1119 - 74386|HCV-1|AAA45676.1|Hepatitis C virus|11103 - 1119 - 8 - - - 1 - 11.927 - 19 - 82.8897 - 1 - 5 - 3 - 7 - 0 - 0 - 4 - 4 - 0 - 5 - SWPLW - SWCLW - SW LW - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 991 - Query_991 - M_4580 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 992 - Query_992 - M_4581 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 993 - Query_993 - M_4582 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 994 - Query_994 - M_4583 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 995 - Query_995 - M_4584 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 996 - Query_996 - M_4585 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 997 - Query_997 - M_4586 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 998 - Query_998 - M_4587 - 9 - - - 1 - gnl|BL_ORD_ID|1175 - 79390|Protein Tax-1|P0C213.1|Human T-cell lymphotropic virus type 1 (african isolate)|39015 - 1175 - 15 - - - 1 - 13.853 - 24 - 5.77703 - 3 - 8 - 2 - 7 - 0 - 0 - 5 - 6 - 0 - 6 - FNNLHL - FHNLHL - F+NLHL - - - - - 2 - gnl|BL_ORD_ID|2167 - 189571|Antigen 85-B|P0C5B9.1|Mycobacterium tuberculosis|1773 - 2167 - 9 - - - 1 - 13.0826 - 22 - 20.7937 - 4 - 9 - 2 - 7 - 0 - 0 - 4 - 4 - 0 - 6 - NNLHLW - NNTRLW - NN LW - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 999 - Query_999 - M_4588 - 9 - - - 1 - gnl|BL_ORD_ID|389 - 23807|tax|AAG48731.1|Human T-lymphotropic virus 2|11909 - 389 - 23 - - - 1 - 11.1566 - 17 - 170.423 - 2 - 9 - 11 - 18 - 0 - 0 - 4 - 5 - 0 - 8 - YGVNLYQF - YGYPVYVF - YG +Y F - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1000 - Query_1000 - M_4589 - 9 - - - 1 - gnl|BL_ORD_ID|2128 - 186620|polyprotein|AFP27208.1|Dengue virus 4|11070 - 2128 - 9 - - - 1 - 11.1566 - 17 - 291.863 - 4 - 9 - 1 - 6 - 0 - 0 - 3 - 6 - 0 - 6 - YILITI - YVILTI - Y+++TI - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1001 - Query_1001 - M_4590 - 9 - - - 1 - gnl|BL_ORD_ID|1687 - 149053|NS3 gene product|AAB02124.1|Hepatitis C virus|11103 - 1687 - 18 - - - 1 - 15.0086 - 27 - 1.25718 - 2 - 8 - 8 - 14 - 0 - 0 - 4 - 6 - 0 - 7 - YKFLAPW - YRFVAPG - Y+F+AP - - - - - 2 - gnl|BL_ORD_ID|2333 - 423082|Genome polyprotein|P26664.3|Hepatitis C virus genotype 1|41856 - 2333 - 9 - - - 1 - 15.0086 - 27 - 1.49881 - 2 - 7 - 1 - 6 - 0 - 0 - 4 - 6 - 0 - 6 - YKFLAP - YRFVAP - Y+F+AP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1002 - Query_1002 - M_4591 - 9 - - - 1 - gnl|BL_ORD_ID|1687 - 149053|NS3 gene product|AAB02124.1|Hepatitis C virus|11103 - 1687 - 18 - - - 1 - 15.0086 - 27 - 1.19394 - 3 - 9 - 5 - 11 - 0 - 0 - 4 - 6 - 0 - 7 - PSIHRFI - PGIYRFV - P I+RF+ - - - - - 2 - gnl|BL_ORD_ID|355 - 22046|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 - 355 - 10 - - - 1 - 13.853 - 24 - 4.53299 - 3 - 8 - 5 - 10 - 0 - 0 - 4 - 5 - 0 - 6 - PSIHRF - PGIYRF - P I+RF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1003 - Query_1003 - M_4592 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1004 - Query_1004 - M_4593 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1005 - Query_1005 - M_4594 - 9 - - - 1 - gnl|BL_ORD_ID|418 - 25237|Transcription activator BRLF1|P03209.1|Human herpesvirus 4 strain B95-8|10377 - 418 - 15 - - - 1 - 14.6234 - 26 - 2.30367 - 2 - 7 - 9 - 14 - 0 - 0 - 4 - 5 - 0 - 6 - YVMDHF - YVLDHL - YV+DH - - - - - 2 - gnl|BL_ORD_ID|1156 - 76333|BRLF1|ABB89247.1|Human gammaherpesvirus 4|10376 - 1156 - 9 - - - 1 - 14.2382 - 25 - 3.49608 - 2 - 7 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - YVMDHF - YVLDHL - YV+DH - - - - - 3 - gnl|BL_ORD_ID|1016 - 67503|Genome polyprotein|P26662.3|Hepatitis C virus|11103 - 1016 - 10 - - - 1 - 13.4678 - 23 - 10.2566 - 1 - 7 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - SYVMDHF - TYVYDHL - +YV DH - - - - - 4 - gnl|BL_ORD_ID|438 - 27011|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 - 438 - 9 - - - 1 - 12.6974 - 21 - 39.8499 - 3 - 8 - 1 - 6 - 0 - 0 - 3 - 5 - 0 - 6 - VMDHFD - ILDSFD - ++D FD - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1006 - Query_1006 - M_4595 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1007 - Query_1007 - M_4596 - 9 - - - 1 - gnl|BL_ORD_ID|1520 - 140600|glutamine synthetase GLNA1 (glutamine synthase) (GS-I)|NP_216736.1|Mycobacterium tuberculosis H37Rv|83332 - 1520 - 9 - - - 1 - 11.927 - 19 - 89.9387 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 5 - 0 - 9 - SYWGVFAPI - SLWKDGAPL - S W AP+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1008 - Query_1008 - M_4597 - 9 - - - 1 - gnl|BL_ORD_ID|1190 - 95262|LAMP|AAK72632.1|Human gammaherpesvirus 8|37296 - 1190 - 15 - - - 1 - 12.3122 - 20 - 59.339 - 4 - 9 - 9 - 14 - 0 - 0 - 4 - 6 - 0 - 6 - KIVSSI - KLVSSV - K+VSS+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1009 - Query_1009 - M_4598 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1010 - Query_1010 - M_4599 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1011 - Query_1011 - M_4600 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1012 - Query_1012 - M_4601 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1013 - Query_1013 - M_4602 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1014 - Query_1014 - M_4603 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1015 - Query_1015 - M_4604 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1016 - Query_1016 - M_4605 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1017 - Query_1017 - M_4606 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1018 - Query_1018 - M_4607 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1019 - Query_1019 - M_4608 - 9 - - - 1 - gnl|BL_ORD_ID|401 - 24535|EBNA-1 protein|Q777E1|Human gammaherpesvirus 4|10376 - 401 - 9 - - - 1 - 13.853 - 24 - 7.07804 - 3 - 8 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - GEVNYF - GEADYF - GE +YF - - - - - 2 - gnl|BL_ORD_ID|402 - 24536|EBNA-1|YP_401677.1|Human gammaherpesvirus 4|10376 - 402 - 11 - - - 1 - 13.4678 - 23 - 8.44862 - 3 - 8 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - GEVNYF - GEADYF - GE +YF - - - - - 3 - gnl|BL_ORD_ID|1170 - 79294|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 1170 - 15 - - - 1 - 9.61583 - 13 - 1034.49 - 2 - 9 - 3 - 10 - 0 - 0 - 4 - 4 - 0 - 8 - FGEVNYFF - FGYPVYVF - FG Y F - - - - - 4 - gnl|BL_ORD_ID|572 - 35845|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 572 - 9 - - - 1 - 9.61583 - 13 - 1600.23 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 4 - 0 - 8 - FGEVNYFF - FGYPVYVF - FG Y F - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1020 - Query_1020 - M_4609 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1021 - Query_1021 - M_4610 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1022 - Query_1022 - M_4611 - 9 - - - 1 - gnl|BL_ORD_ID|94 - 6556|X protein|AAP06597.1|Hepatitis B virus|10407 - 94 - 9 - - - 1 - 13.4678 - 23 - 9.02895 - 2 - 8 - 3 - 9 - 0 - 0 - 4 - 5 - 0 - 7 - FNDWFEI - FKDWEEL - F DW E+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1023 - Query_1023 - M_4612 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1024 - Query_1024 - M_4613 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1025 - Query_1025 - M_4614 - 9 - - - 1 - gnl|BL_ORD_ID|1528 - 140686|ESAT-6-like protein esxH|P0A568.2|Mycobacterium tuberculosis|1773 - 1528 - 9 - - - 1 - 10.001 - 14 - 831.41 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 4 - 0 - 7 - HASLSNH - HAMSSTH - HA S H - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1026 - Query_1026 - M_4615 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1027 - Query_1027 - M_4616 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1028 - Query_1028 - M_4617 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1029 - Query_1029 - M_4618 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1030 - Query_1030 - M_4619 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1031 - Query_1031 - M_4620 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1032 - Query_1032 - M_4621 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1033 - Query_1033 - M_4622 - 9 - - - 1 - gnl|BL_ORD_ID|563 - 34642|methionine sulfoxide reductase B|YP_169878.1|Francisella tularensis subsp. tularensis SCHU S4|177416 - 563 - 10 - - - 1 - 14.2382 - 25 - 3.05549 - 1 - 6 - 5 - 10 - 0 - 0 - 4 - 5 - 0 - 6 - THREGI - NHRQGI - HR+GI - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1034 - Query_1034 - M_4623 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1035 - Query_1035 - M_4624 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1036 - Query_1036 - M_4625 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1037 - Query_1037 - M_4626 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1038 - Query_1038 - M_4627 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1039 - Query_1039 - M_4628 - 9 - - - 1 - gnl|BL_ORD_ID|437 - 27000|Heat shock protein HSP 90-beta|P08238.4|Homo sapiens|9606 - 437 - 9 - - - 1 - 13.853 - 24 - 7.32819 - 2 - 7 - 2 - 7 - 0 - 0 - 5 - 6 - 0 - 6 - LDKKLE - LDKKVE - LDKK+E - - - - - 2 - gnl|BL_ORD_ID|1126 - 74635|matrix protein|AEQ63649.1|Respiratory syncytial virus|12814 - 1126 - 9 - - - 1 - 10.3862 - 15 - 663.415 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 6 - 0 - 8 - LDKKLEYY - LEKESIYY - L+K+ YY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1040 - Query_1040 - M_4629 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1041 - Query_1041 - M_4630 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1042 - Query_1042 - M_4631 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1043 - Query_1043 - M_4632 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1044 - Query_1044 - M_4633 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1045 - Query_1045 - M_4634 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1046 - Query_1046 - M_4635 - 9 - - - 1 - gnl|BL_ORD_ID|1653 - 146569|polyprotein|ADF97231.1|Hepatitis C virus subtype 3a|356426 - 1653 - 17 - - - 1 - 12.3122 - 20 - 41.9577 - 4 - 8 - 5 - 9 - 0 - 0 - 3 - 4 - 0 - 5 - SWTCL - TWKCL - +W CL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1047 - Query_1047 - M_4636 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1048 - Query_1048 - M_4637 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1049 - Query_1049 - M_4638 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1050 - Query_1050 - M_4639 - 9 - - - 1 - gnl|BL_ORD_ID|341 - 21385|polyprotein|AAY82034.1|Hepatitis C virus genotype 1|41856 - 341 - 10 - - - 1 - 13.853 - 24 - 5.29638 - 3 - 9 - 1 - 7 - 0 - 0 - 3 - 6 - 0 - 7 - GNRTKCF - GNASRCW - GN ++C+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1051 - Query_1051 - M_4640 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1052 - Query_1052 - M_4641 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1053 - Query_1053 - M_4642 - 9 - - - 1 - gnl|BL_ORD_ID|551 - 33856|polyprotein|BAA03375.1|Hepatitis C virus|11103 - 551 - 9 - - - 1 - 13.853 - 24 - 5.55396 - 3 - 8 - 3 - 8 - 0 - 0 - 5 - 6 - 0 - 6 - SERSKP - SERSQP - SERS+P - - - - - 2 - gnl|BL_ORD_ID|1284 - 102150|nef protein|ACR27119.1|Human immunodeficiency virus 1|11676 - 1284 - 9 - - - 1 - 9.61583 - 13 - 1256.63 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 5 - 0 - 9 - TPSERSKPL - TPQVPLRPM - TP +P+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1054 - Query_1054 - M_4643 - 9 - - - 1 - gnl|BL_ORD_ID|1683 - 149037|NS4B protein|NP_751926.1|Hepatitis C virus (isolate H77)|63746 - 1683 - 11 - - - 1 - 13.0826 - 22 - 13.9783 - 1 - 7 - 4 - 10 - 0 - 0 - 4 - 6 - 0 - 7 - TPSTQTH - TPAVQTN - TP+ QT+ - - - - - 2 - gnl|BL_ORD_ID|2104 - 186008|polyprotein|AGI95993.1|Dengue virus 4|11070 - 2104 - 9 - - - 1 - 11.1566 - 17 - 221.814 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 4 - 0 - 9 - TPSTQTHPL - TPPGATDPF - TP T P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1055 - Query_1055 - M_4644 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1056 - Query_1056 - M_4645 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1057 - Query_1057 - M_4646 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1058 - Query_1058 - M_4647 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1059 - Query_1059 - M_4648 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1060 - Query_1060 - M_4649 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1061 - Query_1061 - M_4650 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1062 - Query_1062 - M_4651 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1063 - Query_1063 - M_4652 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1064 - Query_1064 - M_4653 - 9 - - - 1 - gnl|BL_ORD_ID|1775 - 155637|tegument protein|CAB06732.1|Human alphaherpesvirus 2|10310 - 1775 - 15 - - - 1 - 15.0086 - 27 - 1.24275 - 3 - 9 - 3 - 9 - 0 - 0 - 5 - 5 - 0 - 7 - GPCRRRF - GPADRRF - GP RRF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1065 - Query_1065 - M_4654 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1066 - Query_1066 - M_4655 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1067 - Query_1067 - M_4656 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1068 - Query_1068 - M_4657 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1069 - Query_1069 - M_4658 - 9 - - - 1 - gnl|BL_ORD_ID|1395 - 110394|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1395 - 32 - - - 1 - 13.4678 - 23 - 12.8091 - 3 - 9 - 4 - 10 - 0 - 0 - 4 - 5 - 0 - 7 - NCNRHLC - NCQKPLC - NC + LC - - - - - 2 - gnl|BL_ORD_ID|957 - 62903|Genome polyprotein|P27909.2|Dengue virus type 1 Hawaii|10000440 - 957 - 20 - - - 1 - 10.7714 - 16 - 300.133 - 1 - 9 - 10 - 18 - 0 - 0 - 3 - 5 - 0 - 9 - TRNCNRHLC - SRNKKPRIC - +RN +C - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1070 - Query_1070 - M_4659 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1071 - Query_1071 - M_4660 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1072 - Query_1072 - M_4661 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1073 - Query_1073 - M_4662 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1074 - Query_1074 - M_4663 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1075 - Query_1075 - M_4664 - 9 - - - 1 - gnl|BL_ORD_ID|525 - 32243|C protein|BAB60863.1|Measles virus|11234 - 525 - 9 - - - 1 - 12.6974 - 21 - 33.6262 - 2 - 8 - 1 - 7 - 0 - 0 - 3 - 5 - 0 - 7 - RSWGTPQ - KLWESPQ - + W +PQ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1076 - Query_1076 - M_4665 - 9 - - - 1 - gnl|BL_ORD_ID|793 - 53041|phosphorylated matrix protein (pp65)|AAA45996.1|Human betaherpesvirus 5|10359 - 793 - 11 - - - 1 - 13.0826 - 22 - 17.7949 - 3 - 9 - 3 - 9 - 0 - 0 - 5 - 5 - 0 - 7 - TPHSTRC - TPDSTPC - TP ST C - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1077 - Query_1077 - M_4666 - 9 - - - 1 - gnl|BL_ORD_ID|2106 - 186041|polyprotein|AGO67248.1|Dengue virus 2|11060 - 2106 - 10 - - - 1 - 14.6234 - 26 - 1.69864 - 1 - 9 - 1 - 9 - 0 - 0 - 6 - 7 - 0 - 9 - TRVGSKLLI - TRVGTKHAI - TRVG+K I - - - - - 2 - gnl|BL_ORD_ID|2064 - 184864|polyprotein|AGO67248.1|Dengue virus 2|11060 - 2064 - 9 - - - 1 - 14.2382 - 25 - 3.21187 - 1 - 6 - 4 - 9 - 0 - 0 - 5 - 6 - 0 - 6 - TRVGSK - TRVGTK - TRVG+K - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1078 - Query_1078 - M_4667 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1079 - Query_1079 - M_4668 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1080 - Query_1080 - M_4669 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1081 - Query_1081 - M_4670 - 9 - - - 1 - gnl|BL_ORD_ID|860 - 56343|structural protein|BAA00705.1|Hepatitis C virus|11103 - 860 - 10 - - - 1 - 12.3122 - 20 - 40.5114 - 3 - 7 - 5 - 9 - 0 - 0 - 4 - 4 - 0 - 5 - DGRNY - DGVNY - DG NY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1082 - Query_1082 - M_4671 - 9 - - - 1 - gnl|BL_ORD_ID|1007 - 66405|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 1007 - 20 - - - 1 - 15.779 - 29 - 0.372461 - 2 - 9 - 13 - 20 - 0 - 0 - 6 - 6 - 0 - 8 - TFDRLAYL - TFDRLQVL - TFDRL L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1083 - Query_1083 - M_4672 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1084 - Query_1084 - M_4673 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1085 - Query_1085 - M_4674 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1086 - Query_1086 - M_4675 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1087 - Query_1087 - M_4676 - 9 - - - 1 - gnl|BL_ORD_ID|1060 - 69799|envelope glycoprotein|BAE96221.1|Human immunodeficiency virus 1|11676 - 1060 - 10 - - - 1 - 14.6234 - 26 - 2.37049 - 3 - 9 - 4 - 10 - 0 - 0 - 5 - 5 - 0 - 7 - SPQPQEV - DPNPQEV - P PQEV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1088 - Query_1088 - M_4677 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1089 - Query_1089 - M_4678 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1090 - Query_1090 - M_4679 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1091 - Query_1091 - M_4680 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1092 - Query_1092 - M_4681 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1093 - Query_1093 - M_4682 - 9 - - - 1 - gnl|BL_ORD_ID|2258 - 288104|nef protein|ACR27130.1|Human immunodeficiency virus 1|11676 - 2258 - 18 - - - 1 - 13.4678 - 23 - 7.92816 - 3 - 9 - 4 - 10 - 0 - 0 - 2 - 7 - 0 - 7 - YPLKPEI - FPVRPQV - +P++P++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1094 - Query_1094 - M_4683 - 9 - - - 1 - gnl|BL_ORD_ID|2258 - 288104|nef protein|ACR27130.1|Human immunodeficiency virus 1|11676 - 2258 - 18 - - - 1 - 13.4678 - 23 - 7.92816 - 3 - 9 - 4 - 10 - 0 - 0 - 2 - 7 - 0 - 7 - YPLKPEI - FPVRPQV - +P++P++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1095 - Query_1095 - M_4684 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1096 - Query_1096 - M_4685 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1097 - Query_1097 - M_4686 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1098 - Query_1098 - M_4687 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1099 - Query_1099 - M_4688 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1100 - Query_1100 - M_4689 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1101 - Query_1101 - M_4690 - 9 - - - 1 - gnl|BL_ORD_ID|716 - 44214|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 - 716 - 11 - - - 1 - 13.0826 - 22 - 18.7359 - 2 - 8 - 5 - 11 - 0 - 0 - 4 - 6 - 0 - 7 - FTRVSAY - FTKNSAF - FT+ SA+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1102 - Query_1102 - M_4691 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1103 - Query_1103 - M_4692 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1104 - Query_1104 - M_4693 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1105 - Query_1105 - M_4694 - 9 - - - 1 - gnl|BL_ORD_ID|1931 - 180758|Nonstructural protein NS5|NP_739590.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1931 - 15 - - - 1 - 13.4678 - 23 - 8.59146 - 2 - 8 - 3 - 9 - 0 - 0 - 4 - 5 - 0 - 7 - HFDHFHP - HYDQDHP - H+D HP - - - - - 2 - gnl|BL_ORD_ID|1943 - 180817|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1943 - 9 - - - 1 - 13.0826 - 22 - 13.9535 - 2 - 8 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - HFDHFHP - HYDQDHP - H+D HP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1106 - Query_1106 - M_4695 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1107 - Query_1107 - M_4696 - 9 - - - 1 - gnl|BL_ORD_ID|2272 - 419005|polyprotein|AGW21594.1|Dengue virus 1|11053 - 2272 - 10 - - - 1 - 14.2382 - 25 - 3.68732 - 4 - 9 - 2 - 7 - 0 - 0 - 6 - 6 - 0 - 6 - LAVSGV - LAVSGV - LAVSGV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1108 - Query_1108 - M_4697 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1109 - Query_1109 - M_4698 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1110 - Query_1110 - M_4699 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1111 - Query_1111 - M_4700 - 9 - - - 1 - gnl|BL_ORD_ID|1608 - 143705|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 1608 - 9 - - - 1 - 14.2382 - 25 - 3.10506 - 5 - 9 - 5 - 9 - 0 - 0 - 5 - 5 - 0 - 5 - FPITL - FPITL - FPITL - - - - - 2 - gnl|BL_ORD_ID|2215 - 193071|Nef protein|Q9WPU2|Human immunodeficiency virus 1|11676 - 2215 - 10 - - - 1 - 13.0826 - 22 - 22.3554 - 4 - 9 - 1 - 6 - 0 - 0 - 3 - 6 - 0 - 6 - QFPITL - RYPLTL - ++P+TL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1112 - Query_1112 - M_4701 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1113 - Query_1113 - M_4702 - 9 - - - 1 - gnl|BL_ORD_ID|1437 - 119822|110 kd polyprotein precursor|CAA28880.1|Rubella virus|11041 - 1437 - 29 - - - 1 - 13.0826 - 22 - 19.5886 - 3 - 9 - 11 - 17 - 0 - 0 - 4 - 5 - 0 - 7 - RGTGAVY - EGEGAVF - G GAV+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1114 - Query_1114 - M_4703 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1115 - Query_1115 - M_4704 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1116 - Query_1116 - M_4705 - 9 - - - 1 - gnl|BL_ORD_ID|1731 - 150556|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1731 - 10 - - - 1 - 13.4678 - 23 - 11.9953 - 1 - 7 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - VLDEMRC - VIDPRRC - V+D RC - - - - - 2 - gnl|BL_ORD_ID|859 - 56310|polyprotein|AGO67248.1|Dengue virus 2|11060 - 859 - 10 - - - 1 - 13.0826 - 22 - 13.0843 - 1 - 7 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - VLDEMRC - VIDPRRC - V+D RC - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1117 - Query_1117 - M_4706 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1118 - Query_1118 - M_4707 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1119 - Query_1119 - M_4708 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1120 - Query_1120 - M_4709 - 9 - - - 1 - gnl|BL_ORD_ID|1000 - 65810|sporozoite surface protein 2|NP_705260.1|Plasmodium falciparum 3D7|36329 - 1000 - 10 - - - 1 - 12.6974 - 21 - 26.9859 - 4 - 9 - 3 - 8 - 0 - 0 - 4 - 4 - 0 - 6 - YRGHPA - YAGEPA - Y G PA - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1121 - Query_1121 - M_4710 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1122 - Query_1122 - M_4711 - 9 - - - 1 - gnl|BL_ORD_ID|459 - 27878|large surface antigen|CAC87019.1|Hepatitis B virus|10407 - 459 - 9 - - - 1 - 13.0826 - 22 - 16.8921 - 3 - 7 - 4 - 8 - 0 - 0 - 4 - 4 - 0 - 5 - PSQWA - PSSWA - PS WA - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1123 - Query_1123 - M_4712 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1124 - Query_1124 - M_4713 - 9 - - - 1 - gnl|BL_ORD_ID|897 - 59090|nonstructural protein 4B|YP_001527886.1|West Nile virus NY-99|10000971 - 897 - 18 - - - 1 - 11.1566 - 17 - 174.368 - 1 - 8 - 9 - 16 - 0 - 0 - 4 - 5 - 0 - 8 - VRELRDMG - VKENFSMG - V+E MG - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1125 - Query_1125 - M_4714 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1126 - Query_1126 - M_4715 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1127 - Query_1127 - M_4716 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1128 - Query_1128 - M_4717 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1129 - Query_1129 - M_4718 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1130 - Query_1130 - M_4719 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1131 - Query_1131 - M_4720 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1132 - Query_1132 - M_4721 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1133 - Query_1133 - M_4722 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1134 - Query_1134 - M_4723 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1135 - Query_1135 - M_4724 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1136 - Query_1136 - M_4725 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1137 - Query_1137 - M_4726 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1138 - Query_1138 - M_4727 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1139 - Query_1139 - M_4728 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1140 - Query_1140 - M_4729 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1141 - Query_1141 - M_4730 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1142 - Query_1142 - M_4731 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1143 - Query_1143 - M_4732 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1144 - Query_1144 - M_4733 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1145 - Query_1145 - M_4734 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1146 - Query_1146 - M_4735 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1147 - Query_1147 - M_4736 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1148 - Query_1148 - M_4737 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1149 - Query_1149 - M_4738 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1150 - Query_1150 - M_4739 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1151 - Query_1151 - M_4740 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1152 - Query_1152 - M_4741 - 9 - - - 1 - gnl|BL_ORD_ID|2098 - 185817|envelope protein|AGW23590.1|Dengue virus 4|11070 - 2098 - 10 - - - 1 - 13.0826 - 22 - 16.3922 - 4 - 9 - 1 - 6 - 0 - 0 - 3 - 5 - 0 - 6 - DWLVRI - SWMIRI - W++RI - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1153 - Query_1153 - M_4742 - 9 - - - 1 - gnl|BL_ORD_ID|756 - 50292|gag protein|ACR27140.1|Human immunodeficiency virus 1|11676 - 756 - 11 - - - 1 - 14.2382 - 25 - 3.03901 - 1 - 7 - 2 - 8 - 0 - 0 - 4 - 6 - 0 - 7 - VVAPRTL - AISPRTL - ++PRTL - - - - - 2 - gnl|BL_ORD_ID|472 - 28657|gag protein|CAB00235.1|Human immunodeficiency virus 1|11676 - 472 - 9 - - - 1 - 14.2382 - 25 - 3.74233 - 2 - 7 - 1 - 6 - 0 - 0 - 4 - 6 - 0 - 6 - VAPRTL - ISPRTL - ++PRTL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1154 - Query_1154 - M_4743 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1155 - Query_1155 - M_4744 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1156 - Query_1156 - M_4745 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1157 - Query_1157 - M_4746 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1158 - Query_1158 - M_4747 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1159 - Query_1159 - M_4748 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1160 - Query_1160 - M_4749 - 9 - - - 1 - gnl|BL_ORD_ID|834 - 54824|polyprotein precursor|BAA01583.1|Hepatitis C virus|11103 - 834 - 9 - - - 1 - 11.5418 - 18 - 173.047 - 1 - 8 - 2 - 9 - 0 - 0 - 3 - 5 - 0 - 8 - VYHLFCAL - LWHYPCTL - ++H C L - - - - - 2 - gnl|BL_ORD_ID|833 - 54821|E2 protein|AAM33354.1|Hepatitis C virus subtype 1a|31646 - 833 - 9 - - - 1 - 10.7714 - 16 - 429.931 - 1 - 8 - 2 - 9 - 0 - 0 - 2 - 5 - 0 - 8 - VYHLFCAL - LWHYPCTI - ++H C + - - - - - 3 - gnl|BL_ORD_ID|1149 - 75636|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 1149 - 10 - - - 1 - 10.3862 - 15 - 485 - 1 - 8 - 3 - 10 - 0 - 0 - 2 - 5 - 0 - 8 - VYHLFCAL - LWHYPCTI - ++H C + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1161 - Query_1161 - M_4750 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1162 - Query_1162 - M_4751 - 9 - - - 1 - gnl|BL_ORD_ID|771 - 51526|HCV-1|AAA45676.1|Hepatitis C virus|11103 - 771 - 10 - - - 1 - 13.4678 - 23 - 10.0795 - 3 - 9 - 2 - 8 - 0 - 0 - 5 - 6 - 0 - 7 - LRRHRDV - LRRHIDL - LRRH D+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1163 - Query_1163 - M_4752 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1164 - Query_1164 - M_4753 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1165 - Query_1165 - M_4754 - 9 - - - 1 - gnl|BL_ORD_ID|1015 - 67471|Genome polyprotein|Q99IB8.3|Hepatitis C virus JFH-1|356411 - 1015 - 9 - - - 1 - 12.6974 - 21 - 36.611 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 4 - 0 - 6 - VYSEYG - TYSTYG - YS YG - - - - - 2 - gnl|BL_ORD_ID|474 - 29182|polyprotein|BAD73991.1|Hepatitis C virus subtype 1b|31647 - 474 - 9 - - - 1 - 12.6974 - 21 - 39.8499 - 1 - 6 - 2 - 7 - 0 - 0 - 4 - 4 - 0 - 6 - VYSEYG - TYSTYG - YS YG - - - - - 3 - gnl|BL_ORD_ID|1333 - 107873|Genome polyprotein|P26664.3|Hepatitis C virus|11103 - 1333 - 10 - - - 1 - 12.3122 - 20 - 41.1969 - 1 - 6 - 5 - 10 - 0 - 0 - 4 - 4 - 0 - 6 - VYSEYG - TYSTYG - YS YG - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1166 - Query_1166 - M_4755 - 9 - - - 1 - gnl|BL_ORD_ID|1418 - 111816|polyprotein|BAA09072.1|Hepatitis C virus|11103 - 1418 - 12 - - - 1 - 13.4678 - 23 - 11.0162 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 6 - 0 - 9 - VYSLRTRAI - AYSQQTRGL - YS +TR + - - - - - 2 - gnl|BL_ORD_ID|80 - 5934|polyprotein|CAB53095.1|Hepatitis C virus subtype 1b|31647 - 80 - 9 - - - 1 - 13.4678 - 23 - 12.57 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 6 - 0 - 9 - VYSLRTRAI - AYSQQTRGL - YS +TR + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1167 - Query_1167 - M_4756 - 9 - - - 1 - gnl|BL_ORD_ID|1376 - 108965|Prolipoprotein diacylglyceryl transferase|O06131.1|Mycobacterium tuberculosis|1773 - 1376 - 9 - - - 1 - 12.3122 - 20 - 41.9234 - 1 - 8 - 2 - 9 - 0 - 0 - 3 - 6 - 0 - 8 - VYSLYWSI - LYELIWNV - +Y L W++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1168 - Query_1168 - M_4757 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1169 - Query_1169 - M_4758 - 9 - - - 1 - gnl|BL_ORD_ID|1297 - 103389|unnamed protein product [Hepatitis C virus]|BAA14035.1|Hepatitis C virus|11103 - 1297 - 20 - - - 1 - 13.853 - 24 - 4.89444 - 2 - 9 - 3 - 10 - 0 - 0 - 4 - 7 - 0 - 8 - YVVTKFLM - HPITKFVM - + +TKF+M - - - - - 2 - gnl|BL_ORD_ID|1092 - 72233|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 - 1092 - 15 - - - 1 - 12.6974 - 21 - 31.7906 - 2 - 9 - 7 - 14 - 0 - 0 - 5 - 6 - 0 - 8 - YVVTKFLM - YVVLLFLL - YVV FL+ - - - - - 3 - gnl|BL_ORD_ID|203 - 15110|Genome polyprotein|P26663.3|Hepatitis C virus|11103 - 203 - 9 - - - 1 - 11.5418 - 18 - 152.614 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 6 - 0 - 8 - YVVTKFLM - YVLLLFLL - YV+ FL+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1170 - Query_1170 - M_4759 - 9 - - - 1 - gnl|BL_ORD_ID|1128 - 74774|LMP1 protein (Epstein-Barr virus, putative LYDMA gene)|Q777A4|Human gammaherpesvirus 4|10376 - 1128 - 9 - - - 1 - 12.6974 - 21 - 35.9943 - 3 - 8 - 1 - 6 - 0 - 0 - 5 - 6 - 0 - 6 - YLLELL - YLLEML - YLLE+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1171 - Query_1171 - M_4760 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1172 - Query_1172 - M_4761 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1173 - Query_1173 - M_4762 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1174 - Query_1174 - M_4763 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1175 - Query_1175 - M_4764 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1176 - Query_1176 - M_4765 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1177 - Query_1177 - M_4766 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1178 - Query_1178 - M_4767 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1179 - Query_1179 - M_4768 - 9 - - - 1 - gnl|BL_ORD_ID|23 - 1516|Nucleoprotein|P03418.1|Human respiratory syncytial virus A2|11259 - 23 - 14 - - - 1 - 13.4678 - 23 - 10.3614 - 1 - 7 - 4 - 10 - 0 - 0 - 3 - 5 - 0 - 7 - WHVPNKP - YHILNNP - +H+ N P - - - - - 2 - gnl|BL_ORD_ID|1110 - 73059|kaposin|AAC57155.1|Human gammaherpesvirus 8|37296 - 1110 - 15 - - - 1 - 12.3122 - 20 - 58.4135 - 1 - 9 - 3 - 11 - 0 - 0 - 3 - 5 - 0 - 9 - WHVPNKPPM - WRLGAIPPL - W + PP+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1180 - Query_1180 - M_4769 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1181 - Query_1181 - M_4770 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1182 - Query_1182 - M_4771 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1183 - Query_1183 - M_4772 - 9 - - - 1 - gnl|BL_ORD_ID|554 - 34027|DNA polymerase|CAA10434.1|Hepatitis B virus|10407 - 554 - 9 - - - 1 - 13.0826 - 22 - 20.0871 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - LSNFQGRY - VGNFTGLY - + NF G Y - - - - - 2 - gnl|BL_ORD_ID|1630 - 146213|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 - 1630 - 18 - - - 1 - 11.927 - 19 - 86.7645 - 1 - 7 - 3 - 9 - 0 - 0 - 4 - 4 - 0 - 7 - WLSNFQG - WESVFTG - W S F G - - - - - 3 - gnl|BL_ORD_ID|1628 - 146188|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 - 1628 - 18 - - - 1 - 11.927 - 19 - 88.0652 - 1 - 7 - 3 - 9 - 0 - 0 - 4 - 4 - 0 - 7 - WLSNFQG - WESVFTG - W S F G - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1184 - Query_1184 - M_4773 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1185 - Query_1185 - M_4774 - 9 - - - 1 - gnl|BL_ORD_ID|657 - 38974|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 657 - 11 - - - 1 - 13.853 - 24 - 4.28904 - 4 - 9 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - QEGPEY - QRGPQY - Q GP+Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1186 - Query_1186 - M_4775 - 9 - - - 1 - gnl|BL_ORD_ID|1144 - 75438|polyprotein|AAF65962.1|Hepatitis C virus|11103 - 1144 - 20 - - - 1 - 15.779 - 29 - 0.398839 - 1 - 9 - 3 - 11 - 0 - 0 - 5 - 7 - 0 - 9 - WPLTHSQGM - WPLYGNEGM - WPL ++GM - - - - - 2 - gnl|BL_ORD_ID|1723 - 150450|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1723 - 9 - - - 1 - 14.2382 - 25 - 4.3647 - 2 - 8 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - PLTHSQG - PVTHSSA - P+THS - - - - - 3 - gnl|BL_ORD_ID|1724 - 150451|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1724 - 10 - - - 1 - 13.853 - 24 - 4.8573 - 2 - 8 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - PLTHSQG - PVTHSSA - P+THS - - - - - 4 - gnl|BL_ORD_ID|2051 - 184702|non-structural protein 1|AGM49312.1|Dengue virus|12637 - 2051 - 9 - - - 1 - 13.853 - 24 - 5.65074 - 1 - 6 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - WPLTHS - WPKTHT - WP TH+ - - - - - 5 - gnl|BL_ORD_ID|1139 - 75356|EBNA3A nuclear protein|Q8AZJ8|Human gammaherpesvirus 4|10376 - 1139 - 9 - - - 1 - 13.4678 - 23 - 13.0154 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 5 - 0 - 9 - WPLTHSQGM - YPLHEQHGM - +PL GM - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1187 - Query_1187 - M_4776 - 9 - - - 1 - gnl|BL_ORD_ID|1786 - 159299|polyprotein|AAC03058.1|Hepatitis C virus subtype 3a|356426 - 1786 - 9 - - - 1 - 14.2382 - 25 - 4.21767 - 2 - 9 - 2 - 9 - 0 - 0 - 5 - 6 - 0 - 8 - QRQHKLTI - QRQRKVTF - QRQ K+T - - - - - 2 - gnl|BL_ORD_ID|1007 - 66405|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 1007 - 20 - - - 1 - 13.853 - 24 - 4.65152 - 1 - 9 - 6 - 14 - 0 - 0 - 5 - 6 - 0 - 9 - WQRQHKLTI - CQRQKKVTF - QRQ K+T - - - - - 3 - gnl|BL_ORD_ID|1617 - 144480|polyprotein|ACA50684.1|Hepatitis C virus subtype 1b|31647 - 1617 - 9 - - - 1 - 13.853 - 24 - 5.00793 - 2 - 9 - 2 - 9 - 0 - 0 - 5 - 6 - 0 - 8 - QRQHKLTI - QRQKKVTF - QRQ K+T - - - - - 4 - gnl|BL_ORD_ID|2051 - 184702|non-structural protein 1|AGM49312.1|Dengue virus|12637 - 2051 - 9 - - - 1 - 11.927 - 19 - 75.1319 - 1 - 7 - 2 - 8 - 0 - 0 - 3 - 4 - 0 - 7 - WQRQHKL - WPKTHTL - W + H L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1188 - Query_1188 - M_4777 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1189 - Query_1189 - M_4778 - 9 - - - 1 - gnl|BL_ORD_ID|1812 - 177647|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 - 1812 - 16 - - - 1 - 13.853 - 24 - 4.97938 - 1 - 9 - 6 - 14 - 0 - 0 - 4 - 7 - 0 - 9 - WSDQLSAFS - WMNRLIAFA - W ++L AF+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1190 - Query_1190 - M_4779 - 9 - - - 1 - gnl|BL_ORD_ID|921 - 59787|Hemagglutinin glycoprotein|P08362.1|Measles virus strain Edmonston|11235 - 921 - 10 - - - 1 - 13.0826 - 22 - 13.3135 - 4 - 9 - 5 - 10 - 0 - 0 - 3 - 6 - 0 - 6 - VFQIGI - VFEVGV - VF++G+ - - - - - 2 - gnl|BL_ORD_ID|2123 - 186524|polyprotein|AGW21594.1|Dengue virus 1|11053 - 2123 - 10 - - - 1 - 12.3122 - 20 - 61.3845 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 5 - 0 - 9 - WTDVFQIGI - WTMKIGIGI - WT IGI - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1191 - Query_1191 - M_4780 - 9 - - - 1 - gnl|BL_ORD_ID|1437 - 119822|110 kd polyprotein precursor|CAA28880.1|Rubella virus|11041 - 1437 - 29 - - - 1 - 14.6234 - 26 - 2.01102 - 1 - 9 - 9 - 17 - 0 - 0 - 5 - 6 - 0 - 9 - WTESLAAVF - WSEGEGAVF - W+E AVF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1192 - Query_1192 - M_4781 - 9 - - - 1 - gnl|BL_ORD_ID|427 - 25929|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 427 - 15 - - - 1 - 12.3122 - 20 - 50.6727 - 2 - 9 - 8 - 15 - 0 - 0 - 4 - 6 - 0 - 8 - VKRQKISF - VKKDLISY - VK+ IS+ - - - - - 2 - gnl|BL_ORD_ID|9 - 790|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 9 - 15 - - - 1 - 12.3122 - 20 - 51.4826 - 2 - 9 - 3 - 10 - 0 - 0 - 4 - 6 - 0 - 8 - VKRQKISF - VKKDLISY - VK+ IS+ - - - - - 3 - gnl|BL_ORD_ID|943 - 62184|nonstructural protein 3|NP_722463.1|Dengue virus type 1 Hawaii|10000440 - 943 - 15 - - - 1 - 11.927 - 19 - 74.9817 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 6 - 0 - 8 - VKRQKISF - VKKDLISY - VK+ IS+ - - - - - 4 - gnl|BL_ORD_ID|761 - 50894|Genome polyprotein|P27909.2|Dengue virus type 1 Hawaii|10000440 - 761 - 20 - - - 1 - 11.927 - 19 - 76.6481 - 2 - 9 - 12 - 19 - 0 - 0 - 4 - 6 - 0 - 8 - VKRQKISF - VKKDLISY - VK+ IS+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1193 - Query_1193 - M_4782 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1194 - Query_1194 - M_4783 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1195 - Query_1195 - M_4784 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1196 - Query_1196 - M_4785 - 9 - - - 1 - gnl|BL_ORD_ID|885 - 57987|envelope protein|YP_001527880.1|West Nile virus NY-99|10000971 - 885 - 18 - - - 1 - 11.5418 - 18 - 116.517 - 4 - 9 - 5 - 10 - 0 - 0 - 4 - 5 - 0 - 6 - WILLVL - WVDLVL - W+ LVL - - - - - 2 - gnl|BL_ORD_ID|801 - 53341|envelope protein|YP_001527880.1|West Nile virus NY-99|10000971 - 801 - 17 - - - 1 - 11.5418 - 18 - 136.848 - 4 - 9 - 12 - 17 - 0 - 0 - 4 - 5 - 0 - 6 - WILLVL - WVDLVL - W+ LVL - - - - - 3 - gnl|BL_ORD_ID|637 - 37960|membrane protein|AAA45887.1|Human gammaherpesvirus 4|10376 - 637 - 9 - - - 1 - 9.61583 - 13 - 1779.2 - 1 - 7 - 3 - 9 - 0 - 0 - 3 - 5 - 0 - 7 - WYIWILL - WTLVVLL - W + +LL - - - - - 4 - gnl|BL_ORD_ID|664 - 39591|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 - 664 - 20 - - - 1 - 8.84543 - 11 - 1791.35 - 1 - 4 - 11 - 14 - 0 - 0 - 2 - 3 - 0 - 4 - WYIW - WCLW - W +W - - - - - 5 - gnl|BL_ORD_ID|1120 - 74387|Genome polyprotein|P26664.3|Hepatitis C virus (isolate 1)|11104 - 1120 - 9 - - - 1 - 9.23063 - 12 - 2628.29 - 1 - 6 - 4 - 9 - 0 - 0 - 3 - 4 - 0 - 6 - WYIWIL - WCLWWL - W +W L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1197 - Query_1197 - M_4786 - 9 - - - 1 - gnl|BL_ORD_ID|1630 - 146213|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 - 1630 - 18 - - - 1 - 13.853 - 24 - 6.14503 - 3 - 7 - 7 - 11 - 0 - 0 - 5 - 5 - 0 - 5 - FTGLT - FTGLT - FTGLT - - - - - 2 - gnl|BL_ORD_ID|1027 - 68581|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 1027 - 20 - - - 1 - 13.853 - 24 - 6.30518 - 3 - 7 - 2 - 6 - 0 - 0 - 5 - 5 - 0 - 5 - FTGLT - FTGLT - FTGLT - - - - - 3 - gnl|BL_ORD_ID|1628 - 146188|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 - 1628 - 18 - - - 1 - 13.853 - 24 - 6.46733 - 3 - 7 - 7 - 11 - 0 - 0 - 5 - 5 - 0 - 5 - FTGLT - FTGLT - FTGLT - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1198 - Query_1198 - M_4787 - 9 - - - 1 - gnl|BL_ORD_ID|1861 - 180440|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1861 - 15 - - - 1 - 11.927 - 19 - 82.259 - 4 - 8 - 6 - 10 - 0 - 0 - 3 - 4 - 0 - 5 - QRSWQ - ERSWN - +RSW - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1199 - Query_1199 - M_4788 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1200 - Query_1200 - M_4789 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1201 - Query_1201 - M_4790 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1202 - Query_1202 - M_4791 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1203 - Query_1203 - M_4792 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1204 - Query_1204 - M_4793 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1205 - Query_1205 - M_4794 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1206 - Query_1206 - M_4795 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1207 - Query_1207 - M_4796 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1208 - Query_1208 - M_4797 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1209 - Query_1209 - M_4798 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1210 - Query_1210 - M_4799 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1211 - Query_1211 - M_4800 - 9 - - - 1 - gnl|BL_ORD_ID|2243 - 232152|rhoptry kinase family protein|AFO54841.1|Toxoplasma gondii type III|398031 - 2243 - 19 - - - 1 - 13.0826 - 22 - 17.6919 - 1 - 7 - 6 - 12 - 0 - 0 - 4 - 5 - 0 - 7 - YHEAGVT - FHSYGVT - +H GVT - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1212 - Query_1212 - M_4801 - 9 - - - 1 - gnl|BL_ORD_ID|1983 - 183252|polyprotein|AGT63075.1|Dengue virus 1|11053 - 1983 - 10 - - - 1 - 11.927 - 19 - 78.4397 - 2 - 7 - 4 - 9 - 0 - 0 - 2 - 5 - 0 - 6 - HFSWTS - HYAWKT - H++W + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1213 - Query_1213 - M_4802 - 9 - - - 1 - gnl|BL_ORD_ID|375 - 23270|polyprotein|AAB67036.1|Hepatitis C virus (isolate H77)|63746 - 375 - 15 - - - 1 - 15.0086 - 27 - 1.20133 - 1 - 7 - 8 - 14 - 0 - 0 - 4 - 6 - 0 - 7 - YHHRFNN - YQHKFNS - Y H+FN+ - - - - - 2 - gnl|BL_ORD_ID|23 - 1516|Nucleoprotein|P03418.1|Human respiratory syncytial virus A2|11259 - 23 - 14 - - - 1 - 11.1566 - 17 - 165.457 - 1 - 7 - 3 - 9 - 0 - 0 - 3 - 5 - 0 - 7 - YHHRFNN - FYHILNN - ++H NN - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1214 - Query_1214 - M_4803 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1215 - Query_1215 - M_4804 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1216 - Query_1216 - M_4805 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1217 - Query_1217 - M_4806 - 9 - - - 1 - gnl|BL_ORD_ID|1405 - 110829|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1405 - 15 - - - 1 - 13.4678 - 23 - 7.74893 - 2 - 9 - 8 - 15 - 0 - 0 - 4 - 5 - 0 - 8 - KGSRFHRV - KKQRFHNI - K RFH + - - - - - 2 - gnl|BL_ORD_ID|1822 - 178247|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1822 - 15 - - - 1 - 13.0826 - 22 - 14.0874 - 2 - 9 - 4 - 11 - 0 - 0 - 4 - 5 - 0 - 8 - KGSRFHRV - KKQRFHNI - K RFH + - - - - - 3 - gnl|BL_ORD_ID|1385 - 110215|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1385 - 25 - - - 1 - 13.0826 - 22 - 16.7731 - 2 - 9 - 8 - 15 - 0 - 0 - 4 - 5 - 0 - 8 - KGSRFHRV - KKQRFHNI - K RFH + - - - - - 4 - gnl|BL_ORD_ID|1384 - 110205|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1384 - 32 - - - 1 - 13.0826 - 22 - 17.6218 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - KGSRFHRV - KKQRFHNI - K RFH + - - - - - 5 - gnl|BL_ORD_ID|1395 - 110394|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1395 - 32 - - - 1 - 12.3122 - 20 - 36.3427 - 2 - 9 - 20 - 27 - 0 - 0 - 4 - 5 - 0 - 8 - KGSRFHRV - KKQRFHNI - K RFH + - - - - - 6 - gnl|BL_ORD_ID|786 - 52652|||| - 786 - 27 - - - 1 - 12.3122 - 20 - 45.1033 - 3 - 9 - 7 - 13 - 0 - 0 - 4 - 5 - 0 - 7 - GSRFHRV - GSQSHTV - GS+ H V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1218 - Query_1218 - M_4807 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1219 - Query_1219 - M_4808 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1220 - Query_1220 - M_4809 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1221 - Query_1221 - M_4810 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1222 - Query_1222 - M_4811 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1223 - Query_1223 - M_4812 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1224 - Query_1224 - M_4813 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1225 - Query_1225 - M_4814 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1226 - Query_1226 - M_4815 - 9 - - - 1 - gnl|BL_ORD_ID|771 - 51526|HCV-1|AAA45676.1|Hepatitis C virus|11103 - 771 - 10 - - - 1 - 13.4678 - 23 - 8.32231 - 2 - 8 - 2 - 8 - 0 - 0 - 5 - 6 - 0 - 7 - LRRHRDV - LRRHIDL - LRRH D+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1227 - Query_1227 - M_4816 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1228 - Query_1228 - M_4817 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1229 - Query_1229 - M_4818 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1230 - Query_1230 - M_4819 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1231 - Query_1231 - M_4820 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1232 - Query_1232 - M_4821 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1233 - Query_1233 - M_4822 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1234 - Query_1234 - M_4823 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1235 - Query_1235 - M_4824 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1236 - Query_1236 - M_4825 - 9 - - - 1 - gnl|BL_ORD_ID|1687 - 149053|NS3 gene product|AAB02124.1|Hepatitis C virus|11103 - 1687 - 18 - - - 1 - 15.0086 - 27 - 1.32384 - 2 - 8 - 5 - 11 - 0 - 0 - 4 - 6 - 0 - 7 - PSIHRFI - PGIYRFV - P I+RF+ - - - - - 2 - gnl|BL_ORD_ID|355 - 22046|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 - 355 - 10 - - - 1 - 13.853 - 24 - 4.94204 - 2 - 7 - 5 - 10 - 0 - 0 - 4 - 5 - 0 - 6 - PSIHRF - PGIYRF - P I+RF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1237 - Query_1237 - M_4826 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1238 - Query_1238 - M_4827 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1239 - Query_1239 - M_4828 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1240 - Query_1240 - M_4829 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1241 - Query_1241 - M_4830 - 9 - - - 1 - gnl|BL_ORD_ID|1289 - 102368|E2 protein|NP_751921.1|Hepatitis C virus subtype 1a|31646 - 1289 - 15 - - - 1 - 13.4678 - 23 - 9.36117 - 2 - 7 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - RAGKPT - RSGAPT - R+G PT - - - - - 2 - gnl|BL_ORD_ID|1696 - 149098|E2 protein|NP_751921.1|Hepatitis C virus (isolate H77)|63746 - 1696 - 9 - - - 1 - 13.4678 - 23 - 10.561 - 2 - 7 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - RAGKPT - RSGAPT - R+G PT - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1242 - Query_1242 - M_4831 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1243 - Query_1243 - M_4832 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1244 - Query_1244 - M_4833 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1245 - Query_1245 - M_4834 - 9 - - - 1 - gnl|BL_ORD_ID|654 - 38724|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 654 - 20 - - - 1 - 15.3938 - 28 - 0.507864 - 1 - 6 - 15 - 20 - 0 - 0 - 5 - 5 - 0 - 6 - YRGPLS - YRGPLD - YRGPL - - - - - 2 - gnl|BL_ORD_ID|1852 - 180387|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1852 - 15 - - - 1 - 13.0826 - 22 - 14.8197 - 3 - 7 - 9 - 13 - 0 - 0 - 4 - 5 - 0 - 5 - GPLST - GPIST - GP+ST - - - - - 3 - gnl|BL_ORD_ID|1946 - 180836|polyprotein|AGT63075.1|Dengue virus 1|11053 - 1946 - 10 - - - 1 - 13.0826 - 22 - 17.265 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - YRGPLS - YGGPIS - Y GP+S - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1246 - Query_1246 - M_4835 - 9 - - - 1 - gnl|BL_ORD_ID|1000 - 65810|sporozoite surface protein 2|NP_705260.1|Plasmodium falciparum 3D7|36329 - 1000 - 10 - - - 1 - 12.3122 - 20 - 52.9061 - 1 - 8 - 3 - 10 - 0 - 0 - 4 - 4 - 0 - 8 - YRGSVAPI - YAGEPAPF - Y G AP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1247 - Query_1247 - M_4836 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1248 - Query_1248 - M_4837 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1249 - Query_1249 - M_4838 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1250 - Query_1250 - M_4839 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1251 - Query_1251 - M_4840 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1252 - Query_1252 - M_4841 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1253 - Query_1253 - M_4842 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1254 - Query_1254 - M_4843 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1255 - Query_1255 - M_4844 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1256 - Query_1256 - M_4845 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1257 - Query_1257 - M_4846 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1258 - Query_1258 - M_4847 - 9 - - - 1 - gnl|BL_ORD_ID|1336 - 107894|polyprotein|CAB41951.1|Hepatitis C virus|11103 - 1336 - 10 - - - 1 - 14.2382 - 25 - 3.62465 - 2 - 9 - 3 - 10 - 0 - 0 - 5 - 7 - 0 - 8 - TDSSSVLN - TDSTSILG - TDS+S+L - - - - - 2 - gnl|BL_ORD_ID|1226 - 97227|polyprotein|CAB41951.1|Hepatitis C virus|11103 - 1226 - 10 - - - 1 - 14.2382 - 25 - 4.23087 - 2 - 8 - 4 - 10 - 0 - 0 - 5 - 7 - 0 - 7 - TDSSSVL - TDSTSIL - TDS+S+L - - - - - 3 - gnl|BL_ORD_ID|1354 - 108147|Genome polyprotein|P26664.3|Hepatitis C virus|11103 - 1354 - 10 - - - 1 - 13.4678 - 23 - 9.73455 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 7 - 0 - 8 - TDSSSVLN - TDATSILG - TD++S+L - - - - - 4 - gnl|BL_ORD_ID|1224 - 97111|polyprotein|ABR25251.1|Hepatitis C virus (isolate H77)|63746 - 1224 - 18 - - - 1 - 13.4678 - 23 - 11.2826 - 2 - 8 - 12 - 18 - 0 - 0 - 4 - 7 - 0 - 7 - TDSSSVL - TDATSIL - TD++S+L - - - - - 5 - gnl|BL_ORD_ID|1225 - 97226|Genome polyprotein|P26664.3|Hepatitis C virus|11103 - 1225 - 10 - - - 1 - 13.4678 - 23 - 12.4198 - 2 - 8 - 4 - 10 - 0 - 0 - 4 - 7 - 0 - 7 - TDSSSVL - TDATSIL - TD++S+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1259 - Query_1259 - M_4848 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1260 - Query_1260 - M_4849 - 9 - - - 1 - gnl|BL_ORD_ID|1843 - 180077|PPE family protein|YP_177935.1|Mycobacterium tuberculosis H37Rv|83332 - 1843 - 9 - - - 1 - 13.0826 - 22 - 14.9585 - 1 - 5 - 1 - 5 - 0 - 0 - 3 - 4 - 0 - 5 - YTELW - YAEMW - Y E+W - - - - - 2 - gnl|BL_ORD_ID|10 - 1000|glycoprotein gp35/37|AAC59622.1|Human gammaherpesvirus 8|37296 - 10 - 15 - - - 1 - 12.6974 - 21 - 34.4815 - 4 - 9 - 10 - 15 - 0 - 0 - 4 - 5 - 0 - 6 - LWFLGL - LWAVGL - LW +GL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1261 - Query_1261 - M_4850 - 9 - - - 1 - gnl|BL_ORD_ID|1959 - 182554|polyprotein|ACF49259.1|Dengue virus type 1 Hawaii|10000440 - 1959 - 9 - - - 1 - 12.6974 - 21 - 26.9236 - 3 - 9 - 2 - 8 - 0 - 0 - 5 - 6 - 0 - 7 - LLAFSVF - LLATSIF - LLA S+F - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1262 - Query_1262 - M_4851 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1263 - Query_1263 - M_4852 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1264 - Query_1264 - M_4853 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1265 - Query_1265 - M_4854 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1266 - Query_1266 - M_4855 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1267 - Query_1267 - M_4856 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1268 - Query_1268 - M_4857 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1269 - Query_1269 - M_4858 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1270 - Query_1270 - M_4859 - 9 - - - 1 - gnl|BL_ORD_ID|530 - 32663|small hydrophobic protein|AAM12943.1|Human metapneumovirus|162145 - 530 - 10 - - - 1 - 13.0826 - 22 - 19.8203 - 2 - 7 - 4 - 9 - 0 - 0 - 3 - 5 - 0 - 6 - VGIFHF - VGVYHI - VG++H - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1271 - Query_1271 - M_4860 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1272 - Query_1272 - M_4861 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1273 - Query_1273 - M_4862 - 9 - - - 1 - gnl|BL_ORD_ID|1376 - 108965|Prolipoprotein diacylglyceryl transferase|O06131.1|Mycobacterium tuberculosis|1773 - 1376 - 9 - - - 1 - 13.4678 - 23 - 7.72035 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 7 - 0 - 9 - YVYSLYWSI - FLYELIWNV - ++Y L W++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1274 - Query_1274 - M_4863 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1275 - Query_1275 - M_4864 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1276 - Query_1276 - M_4865 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1277 - Query_1277 - M_4866 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1278 - Query_1278 - M_4867 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1279 - Query_1279 - M_4868 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1280 - Query_1280 - M_4869 - 9 - - - 1 - gnl|BL_ORD_ID|1190 - 95262|LAMP|AAK72632.1|Human gammaherpesvirus 8|37296 - 1190 - 15 - - - 1 - 11.927 - 19 - 60.2782 - 3 - 8 - 9 - 14 - 0 - 0 - 4 - 6 - 0 - 6 - KIVSSI - KLVSSV - K+VSS+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1281 - Query_1281 - M_4870 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1282 - Query_1282 - M_4871 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1283 - Query_1283 - M_4872 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1284 - Query_1284 - M_4873 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1285 - Query_1285 - M_4874 - 9 - - - 1 - gnl|BL_ORD_ID|2080 - 185327|polyprotein|ACF49259.1|Dengue virus type 1 Hawaii|10000440 - 2080 - 9 - - - 1 - 11.5418 - 18 - 141.015 - 1 - 8 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - YYYFLRPL - YIYMGQPL - Y Y +PL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1286 - Query_1286 - M_4875 - 9 - - - 1 - gnl|BL_ORD_ID|2080 - 185327|polyprotein|ACF49259.1|Dengue virus type 1 Hawaii|10000440 - 2080 - 9 - - - 1 - 11.5418 - 18 - 141.015 - 1 - 8 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - YYYFLRPL - YIYMGQPL - Y Y +PL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_136103_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_136103_1_T.fasta deleted file mode 100755 index 6a70b850..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_136103_1_T.fasta +++ /dev/null @@ -1,36 +0,0 @@ ->M_4876 -LSILVDWMI ->M_4877 -LVMFLSILV ->M_4878 -HWPEKEWPI ->M_4879 -WLEAMQGVI ->M_4880 -MNRGRRSSL ->M_4881 -RADHAAEQV ->M_4882 -TTLSPAEPT ->M_4883 -CLMVLYSLI ->M_4884 -MTPSVYGGA ->M_4885 -FCFLVVASA ->M_4886 -FLVVASAYI ->M_4887 -VVASAYIKL ->M_4888 -NSTIIPTLI ->M_4889 -SSSGVNSTI ->M_4890 -STIIPTLIL ->M_4891 -NLAMCFGPV ->M_4892 -MVAFINEKM ->M_4893 -RHSNMVAFI diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_136103_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_136103_1_T_iedb.xml deleted file mode 100755 index 8d9d2dc7..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_136103_1_T_iedb.xml +++ /dev/null @@ -1,742 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_4876 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_4876 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_4877 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_4878 - 9 - - - 1 - gnl|BL_ORD_ID|958 - 62977|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 958 - 10 - - - 1 - 11.5418 - 18 - 153.051 - 1 - 7 - 4 - 10 - 0 - 0 - 3 - 3 - 0 - 7 - HWPEKEW - HTPVNSW - H P W - - - - - 2 - gnl|BL_ORD_ID|55 - 4156|polyprotein|ABR25251.1|Hepatitis C virus|11103 - 55 - 9 - - - 1 - 11.5418 - 18 - 184.198 - 1 - 7 - 3 - 9 - 0 - 0 - 3 - 3 - 0 - 7 - HWPEKEW - HTPVNSW - H P W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 4 - Query_4 - M_4879 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_4880 - 9 - - - 1 - gnl|BL_ORD_ID|2115 - 186301|polyprotein|AGO67248.1|Dengue virus 2|11060 - 2115 - 9 - - - 1 - 13.4678 - 23 - 9.5131 - 1 - 6 - 3 - 8 - 0 - 0 - 4 - 6 - 0 - 6 - MNRGRR - MHRGKR - M+RG+R - - - - - 2 - gnl|BL_ORD_ID|2011 - 183800|polyprotein|AGT63075.1|Dengue virus 1|11053 - 2011 - 9 - - - 1 - 13.0826 - 22 - 17.7942 - 1 - 7 - 2 - 8 - 0 - 0 - 5 - 6 - 0 - 7 - MNRGRRS - MNRRKRS - MNR +RS - - - - - 3 - gnl|BL_ORD_ID|2065 - 184880|polyprotein|AGT63075.1|Dengue virus 1|11053 - 2065 - 9 - - - 1 - 13.0826 - 22 - 18.4218 - 1 - 7 - 1 - 7 - 0 - 0 - 5 - 6 - 0 - 7 - MNRGRRS - MNRRKRS - MNR +RS - - - - - 4 - gnl|BL_ORD_ID|2007 - 183766|polyprotein|AGO67248.1|Dengue virus 2|11060 - 2007 - 9 - - - 1 - 12.6974 - 21 - 31.9494 - 1 - 8 - 2 - 9 - 0 - 0 - 4 - 7 - 0 - 8 - MNRGRRSS - LNRRRRTA - +NR RR++ - - - - - 5 - gnl|BL_ORD_ID|2042 - 184518|polyprotein|AGO67248.1|Dengue virus 2|11060 - 2042 - 9 - - - 1 - 12.3122 - 20 - 56.7066 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 7 - 0 - 8 - MNRGRRSS - LNRRRRTA - +NR RR++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 6 - Query_6 - M_4881 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_4882 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_4883 - 9 - - - 1 - gnl|BL_ORD_ID|1549 - 141222|DNA packaging tegument protein UL25|NP_044626.1|Human alphaherpesvirus 1|10298 - 1549 - 9 - - - 1 - 11.5418 - 18 - 118.346 - 1 - 6 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - CLMVLY - CLYLLY - CL +LY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 9 - Query_9 - M_4884 - 9 - - - 1 - gnl|BL_ORD_ID|999 - 65749|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 999 - 11 - - - 1 - 13.4678 - 23 - 7.47922 - 2 - 8 - 1 - 7 - 0 - 0 - 5 - 5 - 0 - 7 - TPSVYGG - TPRVTGG - TP V GG - - - - - 2 - gnl|BL_ORD_ID|998 - 65748|pp65|AAA45994.1|Human betaherpesvirus 5|10359 - 998 - 10 - - - 1 - 13.4678 - 23 - 8.46851 - 2 - 8 - 1 - 7 - 0 - 0 - 5 - 5 - 0 - 7 - TPSVYGG - TPRVTGG - TP V GG - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 10 - Query_10 - M_4885 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_4886 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_4887 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_4888 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_4889 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_4890 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_4891 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_4892 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_4893 - 9 - - - 1 - gnl|BL_ORD_ID|1616 - 144403|polyprotein|AAK08509.1|Hepatitis C virus subtype 1b|31647 - 1616 - 9 - - - 1 - 14.6234 - 26 - 2.53786 - 1 - 6 - 3 - 8 - 0 - 0 - 5 - 5 - 0 - 6 - RHSNMV - RHHNMV - RH NMV - - - - - 2 - gnl|BL_ORD_ID|1785 - 159290|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 - 1785 - 9 - - - 1 - 13.4678 - 23 - 11.7244 - 1 - 6 - 3 - 8 - 0 - 0 - 4 - 5 - 0 - 6 - RHSNMV - RHHNLV - RH N+V - - - - - 3 - gnl|BL_ORD_ID|1218 - 96897|polyprotein|ABR25251.1|Hepatitis C virus (isolate H77)|63746 - 1218 - 17 - - - 1 - 13.0826 - 22 - 13.7 - 1 - 6 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - RHSNMV - RHHNLV - RH N+V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_136546_2_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_136546_2_T.fasta deleted file mode 100755 index f6e6c44a..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_136546_2_T.fasta +++ /dev/null @@ -1,78 +0,0 @@ ->M_4894 -SILASLSTL ->M_4895 -TLQQMWISK ->M_4896 -RAFADTLEV ->M_4897 -VLLPVSLFI ->M_4898 -LLFSVTMPK ->M_4899 -VPVPPAPPL ->M_4900 -EIFMGLPTK ->M_4901 -VYTEIFMGL ->M_4902 -YYASVYTEI ->M_4903 -HMWNYMQSK ->M_4904 -QTYQHMWNY ->M_4905 -SRYQTYQHM ->M_4906 -MIMAQMRRI ->M_4907 -RRISPFSCL ->M_4908 -ILFDEAVKL ->M_4909 -MKYPVKSIL ->M_4910 -TLIHQFQEK ->M_4911 -KLGADFIGH ->M_4912 -ALGPPVLLR ->M_4913 -PPVLLRCSL ->M_4914 -FTRENTLTF ->M_4915 -LTFMHLSPI ->M_4916 -TFMHLSPIL ->M_4917 -EFVERYHVL ->M_4918 -RLWARGLTV ->M_4919 -RLWARGLTV ->M_4920 -LVWRPLREV ->M_4921 -SYVMLPCAL ->M_4922 -VMLPCALPV ->M_4923 -RLPEVQLPK ->M_4924 -APRGACYRA ->M_4925 -APRGVCYGA ->M_4926 -GLTWAVVLI ->M_4927 -QPLGLTWAV ->M_4928 -YRNEDHWAW ->M_4929 -KCAEPSTRK ->M_4930 -LLTDDLRSV ->M_4931 -QMPTDYAEV ->M_4932 -VVGARGVGK diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_136546_2_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_136546_2_T_iedb.xml deleted file mode 100755 index b982e37c..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_136546_2_T_iedb.xml +++ /dev/null @@ -1,1402 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_4894 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_4894 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_4895 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_4896 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_4897 - 9 - - - 1 - gnl|BL_ORD_ID|1168 - 79180|tax protein|AAF37566.1|Human T-lymphotropic virus 1|11908 - 1168 - 15 - - - 1 - 12.6974 - 21 - 24.4548 - 3 - 8 - 3 - 8 - 0 - 0 - 4 - 5 - 0 - 6 - LPVSLF - LPTTLF - LP +LF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 5 - Query_5 - M_4898 - 9 - - - 1 - gnl|BL_ORD_ID|338 - 21242|polymerase|ACF94272.1|Hepatitis B virus|10407 - 338 - 9 - - - 1 - 13.0826 - 22 - 19.7427 - 2 - 8 - 2 - 8 - 0 - 0 - 4 - 6 - 0 - 7 - LFSVTMP - LYSSTVP - L+S T+P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 6 - Query_6 - M_4899 - 9 - - - 1 - gnl|BL_ORD_ID|1068 - 70491|envelope glycoprotein|AAC28452.1|Human immunodeficiency virus 1|11676 - 1068 - 10 - - - 1 - 11.927 - 19 - 86.442 - 1 - 8 - 1 - 8 - 0 - 0 - 5 - 5 - 0 - 8 - VPVPPAPP - VPTDPNPP - VP P PP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 7 - Query_7 - M_4900 - 9 - - - 1 - gnl|BL_ORD_ID|2080 - 185327|polyprotein|ACF49259.1|Dengue virus type 1 Hawaii|10000440 - 2080 - 9 - - - 1 - 13.4678 - 23 - 8.87313 - 2 - 7 - 3 - 8 - 0 - 0 - 4 - 5 - 0 - 6 - IFMGLP - IYMGQP - I+MG P - - - - - 2 - gnl|BL_ORD_ID|141 - 10587|viral polyprotein|AAA42941.1|Dengue virus 2 Thailand/NGS-C/1944|11065 - 141 - 9 - - - 1 - 11.1566 - 17 - 232.278 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 5 - 0 - 9 - EIFMGLPTK - DVFFTPPEK - ++F P K - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 8 - Query_8 - M_4901 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_4902 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_4903 - 9 - - - 1 - gnl|BL_ORD_ID|691 - 42094|telomer length regulation protein TEL1|EDV12172.1|Saccharomyces cerevisiae|4932 - 691 - 9 - - - 1 - 13.853 - 24 - 6.60345 - 2 - 7 - 2 - 7 - 0 - 0 - 3 - 5 - 0 - 6 - MWNYMQ - LWGYLQ - +W Y+Q - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 11 - Query_11 - M_4904 - 9 - - - 1 - gnl|BL_ORD_ID|1295 - 103020|polyprotein|ABR25251.1|Hepatitis C virus|11103 - 1295 - 10 - - - 1 - 16.1642 - 30 - 0.390189 - 4 - 9 - 5 - 10 - 0 - 0 - 4 - 6 - 0 - 6 - QHMWNY - KHMWNF - +HMWN+ - - - - - 2 - gnl|BL_ORD_ID|1029 - 68605|Genome polyprotein|P26662.3|Hepatitis C virus|11103 - 1029 - 10 - - - 1 - 16.1642 - 30 - 0.392937 - 4 - 9 - 5 - 10 - 0 - 0 - 4 - 6 - 0 - 6 - QHMWNY - KHMWNF - +HMWN+ - - - - - 3 - gnl|BL_ORD_ID|272 - 18337|polyprotein|BAD73987.1|Hepatitis C virus subtype 1b|31647 - 272 - 9 - - - 1 - 15.779 - 29 - 0.436744 - 4 - 9 - 4 - 9 - 0 - 0 - 4 - 6 - 0 - 6 - QHMWNY - KHMWNF - +HMWN+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 12 - Query_12 - M_4905 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_4906 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_4907 - 9 - - - 1 - gnl|BL_ORD_ID|1731 - 150556|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1731 - 10 - - - 1 - 12.6974 - 21 - 26.0802 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 5 - 0 - 9 - RRISPFSCL - RVIDPRRCL - R I P CL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 15 - Query_15 - M_4908 - 9 - - - 1 - gnl|BL_ORD_ID|1807 - 169050|polyprotein|ABU97067.1|Hepatitis C virus subtype 1b|31647 - 1807 - 9 - - - 1 - 13.4678 - 23 - 8.13377 - 2 - 8 - 3 - 9 - 0 - 0 - 5 - 6 - 0 - 7 - LFDEAVK - LFNWAVK - LF+ AVK - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 16 - Query_16 - M_4909 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_4910 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_4911 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_4912 - 9 - - - 1 - gnl|BL_ORD_ID|898 - 59141|Circumsporozoite protein precursor|P08677.2|Plasmodium vivax strain Belem|31273 - 898 - 10 - - - 1 - 10.7714 - 16 - 303.747 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 6 - 0 - 8 - ALGPPVLL - SLGLVILL - +LG +LL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 20 - Query_20 - M_4913 - 9 - - - 1 - gnl|BL_ORD_ID|1621 - 145860|Protein E6|P04019.1|Human papillomavirus type 11|10580 - 1621 - 9 - - - 1 - 13.853 - 24 - 5.84954 - 2 - 9 - 1 - 8 - 0 - 0 - 5 - 6 - 0 - 8 - PVLLRCSL - KVLIRCYL - VL+RC L - - - - - 2 - gnl|BL_ORD_ID|114 - 7660|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 - 114 - 20 - - - 1 - 11.927 - 19 - 83.707 - 3 - 9 - 4 - 10 - 0 - 0 - 3 - 6 - 0 - 7 - VLLRCSL - ILLMCAV - +LL C++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 21 - Query_21 - M_4914 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 22 - Query_22 - M_4915 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_4916 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_4917 - 9 - - - 1 - gnl|BL_ORD_ID|2142 - 187188|PE family protein PE9|YP_177784.1|Mycobacterium tuberculosis H37Rv|83332 - 2142 - 15 - - - 1 - 13.4678 - 23 - 10.3735 - 3 - 9 - 7 - 13 - 0 - 0 - 4 - 4 - 0 - 7 - VERYHVL - AEEYHAL - E YH L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 25 - Query_25 - M_4918 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_4919 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_4920 - 9 - - - 1 - gnl|BL_ORD_ID|1872 - 180496|Polyprotein|NP_056776.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1872 - 15 - - - 1 - 12.3122 - 20 - 36.7879 - 2 - 8 - 7 - 13 - 0 - 0 - 3 - 5 - 0 - 7 - VWRPLRE - IWLKLKE - +W L+E - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 28 - Query_28 - M_4921 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 29 - Query_29 - M_4922 - 9 - - - 1 - gnl|BL_ORD_ID|690 - 41971|putative D-ribose-binding protein|NP_301386.1|Mycobacterium leprae|1769 - 690 - 15 - - - 1 - 11.5418 - 18 - 154.909 - 2 - 8 - 6 - 12 - 0 - 0 - 4 - 5 - 0 - 7 - MLPCALP - LLPAILP - +LP LP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 30 - Query_30 - M_4923 - 9 - - - 1 - gnl|BL_ORD_ID|241 - 16836|precore/core protein [Hepatitis B virus]|AAR03815.1|Hepatitis B virus|10407 - 241 - 10 - - - 1 - 10.3862 - 15 - 499.131 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 4 - 0 - 8 - LPEVQLPK - LPSDFLPS - LP LP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 31 - Query_31 - M_4924 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 32 - Query_32 - M_4925 - 9 - - - 1 - gnl|BL_ORD_ID|1667 - 148117|early protein|CAA52585.1|Human papillomavirus type 52|10618 - 1667 - 9 - - - 1 - 12.6974 - 21 - 26.9236 - 2 - 6 - 1 - 5 - 0 - 0 - 4 - 4 - 0 - 5 - PRGVC - PYGVC - P GVC - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 33 - Query_33 - M_4926 - 9 - - - 1 - gnl|BL_ORD_ID|1686 - 149052|E1 protein|NP_751920.1|Hepatitis C virus (isolate H77)|63746 - 1686 - 18 - - - 1 - 12.3122 - 20 - 44.435 - 3 - 9 - 10 - 16 - 0 - 0 - 4 - 5 - 0 - 7 - TWAVVLI - NWAKVLV - WA VL+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 34 - Query_34 - M_4927 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 35 - Query_35 - M_4928 - 9 - - - 1 - gnl|BL_ORD_ID|2019 - 184131|polyprotein|AGO67248.1|Dengue virus 2|11060 - 2019 - 10 - - - 1 - 12.6974 - 21 - 23.5358 - 2 - 8 - 1 - 7 - 0 - 0 - 3 - 4 - 0 - 7 - RNEDHWA - KREDQWC - + ED W - - - - - 2 - gnl|BL_ORD_ID|805 - 53476|polyprotein|AGO67248.1|Dengue virus 2|11060 - 805 - 9 - - - 1 - 12.3122 - 20 - 65.8473 - 4 - 8 - 2 - 6 - 0 - 0 - 3 - 3 - 0 - 5 - EDHWA - EDQWC - ED W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 36 - Query_36 - M_4929 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 37 - Query_37 - M_4930 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 38 - Query_38 - M_4931 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 39 - Query_39 - M_4932 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_136587_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_136587_1_T.fasta deleted file mode 100755 index 13a39e09..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_136587_1_T.fasta +++ /dev/null @@ -1,50 +0,0 @@ ->M_4933 -ALFCGRSDY ->M_4934 -SFLCHKALF ->M_4935 -SFLCHKALF ->M_4936 -SFLCHKALF ->M_4937 -HHLLSLQYV ->M_4938 -NHHLLSLQY ->M_4939 -LRLLDRELL ->M_4940 -QMPPMPPPL ->M_4941 -SRVSGGTPL ->M_4942 -IPLEVMEPF ->M_4943 -RHAACSVLV ->M_4944 -TRHAACSVL ->M_4945 -TRHAACSVL ->M_4946 -IYLGAVNWI ->M_4947 -YLGAVNWIY ->M_4948 -MWALGIIAY ->M_4949 -SPALNKMFY ->M_4950 -IPGPIPGPI ->M_4951 -IPGPIPGPI ->M_4952 -NPGPIPGPI ->M_4953 -AEYIVVARN ->M_4954 -YIVVARNKY ->M_4955 -IFWDLSKPM ->M_4956 -IFWDLSKPM ->M_4957 -IPTEKPTIL diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_136587_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_136587_1_T_iedb.xml deleted file mode 100755 index 4479cd1c..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_136587_1_T_iedb.xml +++ /dev/null @@ -1,1298 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_4933 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_4933 - 9 - - - 1 - gnl|BL_ORD_ID|73 - 5316|EBNA-3B nuclear protein|CAD53420.1|Human gammaherpesvirus 4|10376 - 73 - 10 - - - 1 - 11.927 - 19 - 106.494 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 6 - 0 - 8 - ALFCGRSD - AVFDRKSD - A+F +SD - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 2 - Query_2 - M_4934 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_4935 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_4936 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_4937 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_4938 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_4939 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_4940 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_4941 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_4942 - 9 - - - 1 - gnl|BL_ORD_ID|1879 - 180528|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1879 - 10 - - - 1 - 13.853 - 24 - 6.41039 - 1 - 7 - 1 - 7 - 0 - 0 - 4 - 6 - 0 - 7 - IPLEVME - IPFEIMD - IP E+M+ - - - - - 2 - gnl|BL_ORD_ID|1733 - 150578|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1733 - 10 - - - 1 - 13.0826 - 22 - 15.2954 - 1 - 6 - 5 - 10 - 0 - 0 - 4 - 5 - 0 - 6 - IPLEVM - IPFEIM - IP E+M - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 11 - Query_11 - M_4943 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_4944 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_4945 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_4946 - 9 - - - 1 - gnl|BL_ORD_ID|1812 - 177647|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 - 1812 - 16 - - - 1 - 13.853 - 24 - 5.42889 - 4 - 9 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - GAVNWI - GAVQWM - GAV W+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 15 - Query_15 - M_4947 - 9 - - - 1 - gnl|BL_ORD_ID|1812 - 177647|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 - 1812 - 16 - - - 1 - 13.853 - 24 - 5.3359 - 3 - 8 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - GAVNWI - GAVQWM - GAV W+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 16 - Query_16 - M_4948 - 9 - - - 1 - gnl|BL_ORD_ID|413 - 24943|DNA polymerase|CAA10434.1|Hepatitis B virus|10407 - 413 - 11 - - - 1 - 12.3122 - 20 - 60.6062 - 1 - 7 - 3 - 9 - 0 - 0 - 3 - 5 - 0 - 7 - MWALGII - LWKAGIL - +W GI+ - - - - - 2 - gnl|BL_ORD_ID|988 - 65148|DNA polymerase|CAA10434.1|Hepatitis B virus|10407 - 988 - 10 - - - 1 - 11.927 - 19 - 69.9879 - 1 - 7 - 2 - 8 - 0 - 0 - 3 - 5 - 0 - 7 - MWALGII - LWKAGIL - +W GI+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 17 - Query_17 - M_4949 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_4950 - 9 - - - 1 - gnl|BL_ORD_ID|741 - 47760|EBNA-1 protein|Q777E1|Human gammaherpesvirus 4|10376 - 741 - 15 - - - 1 - 10.3862 - 15 - 419.458 - 2 - 7 - 1 - 6 - 0 - 0 - 4 - 4 - 0 - 6 - PGPIPG - PGTGPG - PG PG - - - - - 2 - gnl|BL_ORD_ID|75 - 5542|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 75 - 15 - - - 1 - 10.001 - 14 - 709.084 - 2 - 9 - 8 - 15 - 0 - 0 - 4 - 4 - 0 - 8 - PGPIPGPI - PGTSGSPI - PG PI - - - - - 3 - gnl|BL_ORD_ID|1929 - 180750|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1929 - 15 - - - 1 - 10.001 - 14 - 819.307 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 4 - 0 - 8 - PGPIPGPI - PGTSGSPI - PG PI - - - - - 4 - gnl|BL_ORD_ID|260 - 17802|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 260 - 15 - - - 1 - 10.001 - 14 - 830.077 - 2 - 9 - 3 - 10 - 0 - 0 - 4 - 4 - 0 - 8 - PGPIPGPI - PGTSGSPI - PG PI - - - - - 5 - gnl|BL_ORD_ID|1712 - 150341|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1712 - 9 - - - 1 - 9.61583 - 13 - 1362.74 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 4 - 0 - 8 - PGPIPGPI - PGTSGSPI - PG PI - - - - - 6 - gnl|BL_ORD_ID|1766 - 154857|tegument protein|CAB06735.1|Human alphaherpesvirus 2|10310 - 1766 - 16 - - - 1 - 4.99343 - 1 - 89081.4 - 7 - 9 - 14 - 16 - 0 - 0 - 2 - 3 - 0 - 3 - GPI - GPV - GP+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 19 - Query_19 - M_4951 - 9 - - - 1 - gnl|BL_ORD_ID|741 - 47760|EBNA-1 protein|Q777E1|Human gammaherpesvirus 4|10376 - 741 - 15 - - - 1 - 10.3862 - 15 - 419.458 - 2 - 7 - 1 - 6 - 0 - 0 - 4 - 4 - 0 - 6 - PGPIPG - PGTGPG - PG PG - - - - - 2 - gnl|BL_ORD_ID|75 - 5542|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 75 - 15 - - - 1 - 10.001 - 14 - 709.084 - 2 - 9 - 8 - 15 - 0 - 0 - 4 - 4 - 0 - 8 - PGPIPGPI - PGTSGSPI - PG PI - - - - - 3 - gnl|BL_ORD_ID|1929 - 180750|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1929 - 15 - - - 1 - 10.001 - 14 - 819.307 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 4 - 0 - 8 - PGPIPGPI - PGTSGSPI - PG PI - - - - - 4 - gnl|BL_ORD_ID|260 - 17802|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 260 - 15 - - - 1 - 10.001 - 14 - 830.077 - 2 - 9 - 3 - 10 - 0 - 0 - 4 - 4 - 0 - 8 - PGPIPGPI - PGTSGSPI - PG PI - - - - - 5 - gnl|BL_ORD_ID|1712 - 150341|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1712 - 9 - - - 1 - 9.61583 - 13 - 1362.74 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 4 - 0 - 8 - PGPIPGPI - PGTSGSPI - PG PI - - - - - 6 - gnl|BL_ORD_ID|1766 - 154857|tegument protein|CAB06735.1|Human alphaherpesvirus 2|10310 - 1766 - 16 - - - 1 - 4.99343 - 1 - 89081.4 - 7 - 9 - 14 - 16 - 0 - 0 - 2 - 3 - 0 - 3 - GPI - GPV - GP+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 20 - Query_20 - M_4952 - 9 - - - 1 - gnl|BL_ORD_ID|344 - 21638|protein F|ABV46152.2|Hepatitis C virus (isolate Japanese)|11116 - 344 - 9 - - - 1 - 10.7714 - 16 - 376.438 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - PGPIPGPI - PGLSPGTL - PG PG + - - - - - 2 - gnl|BL_ORD_ID|741 - 47760|EBNA-1 protein|Q777E1|Human gammaherpesvirus 4|10376 - 741 - 15 - - - 1 - 10.3862 - 15 - 449.179 - 2 - 7 - 1 - 6 - 0 - 0 - 4 - 4 - 0 - 6 - PGPIPG - PGTGPG - PG PG - - - - - 3 - gnl|BL_ORD_ID|75 - 5542|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 75 - 15 - - - 1 - 10.3862 - 15 - 461.604 - 1 - 9 - 7 - 15 - 0 - 0 - 4 - 5 - 0 - 9 - NPGPIPGPI - SPGTSGSPI - +PG PI - - - - - 4 - gnl|BL_ORD_ID|260 - 17802|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 260 - 15 - - - 1 - 10.3862 - 15 - 550.452 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 5 - 0 - 9 - NPGPIPGPI - SPGTSGSPI - +PG PI - - - - - 5 - gnl|BL_ORD_ID|1929 - 180750|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1929 - 15 - - - 1 - 10.3862 - 15 - 557.903 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 5 - 0 - 9 - NPGPIPGPI - SPGTSGSPI - +PG PI - - - - - 6 - gnl|BL_ORD_ID|1712 - 150341|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1712 - 9 - - - 1 - 10.001 - 14 - 1206.48 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 4 - 0 - 9 - NPGPIPGPI - KPGTSGSPI - PG PI - - - - - 7 - gnl|BL_ORD_ID|1766 - 154857|tegument protein|CAB06735.1|Human alphaherpesvirus 2|10310 - 1766 - 16 - - - 1 - 4.99343 - 1 - 83537.4 - 7 - 9 - 14 - 16 - 0 - 0 - 2 - 3 - 0 - 3 - GPI - GPV - GP+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 21 - Query_21 - M_4953 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 22 - Query_22 - M_4954 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_4955 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_4956 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_4957 - 9 - - - 1 - gnl|BL_ORD_ID|647 - 38466|nucleocapsid protein|ABF21284.1|Influenza A virus (A/Iran/1/1957(H2N2))|488233 - 647 - 9 - - - 1 - 15.779 - 29 - 0.476466 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 8 - 0 - 9 - IPTEKPTIL - LPFDKPTIM - +P +KPTI+ - - - - - 2 - gnl|BL_ORD_ID|1433 - 116127|Nucleoprotein|P15682.1|Influenza A virus (A/Wilson-Smith/1933(H1N1))|381518 - 1433 - 9 - - - 1 - 15.0086 - 27 - 1.10528 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 8 - 0 - 9 - IPTEKPTIL - LPFDRPTIM - +P ++PTI+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_137814_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_137814_1_T.fasta deleted file mode 100755 index 452ea838..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_137814_1_T.fasta +++ /dev/null @@ -1,50 +0,0 @@ ->M_4958 -FLNRWMANT ->M_4959 -WMANTLDAV ->M_4960 -ALHTAVLLL ->M_4961 -KMWDAVLYR ->M_4962 -LSIESLTLV ->M_4963 -TLSIESLTL ->M_4964 -HRVNWVVFL ->M_4965 -FLYQPNWRF ->M_4966 -LRKRRSRKR ->M_4967 -RQLRKRRSR ->M_4968 -RRQEQPSIK ->M_4969 -FQYKFTVQA ->M_4970 -ILGTPLSKV ->M_4971 -VLSGAKIWL ->M_4972 -AVLIVTTTV ->M_4973 -LLESSNTNV ->M_4974 -VVWATKYFL ->M_4975 -AMCSAQEEI ->M_4976 -KLTPYMVVL ->M_4977 -FRVRGAVSH ->M_4978 -FRHSMVVPY ->M_4979 -KRRRLWAAL ->M_4980 -RRLWAALGP ->M_4981 -YLIISTFFL ->M_4982 -KIFNHPSTL diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_137814_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_137814_1_T_iedb.xml deleted file mode 100755 index d612c630..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_137814_1_T_iedb.xml +++ /dev/null @@ -1,1072 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_4958 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_4958 - 9 - - - 1 - gnl|BL_ORD_ID|1516 - 140561|metal cation transporter P-type ATPase A CtpF|NP_216513.1|Mycobacterium tuberculosis H37Rv|83332 - 1516 - 9 - - - 1 - 13.853 - 24 - 4.4402 - 1 - 6 - 3 - 8 - 0 - 0 - 4 - 5 - 0 - 6 - FLNRWM - FANRWI - F NRW+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 2 - Query_2 - M_4959 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_4960 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_4961 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_4962 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_4963 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_4964 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_4965 - 9 - - - 1 - gnl|BL_ORD_ID|1272 - 101721|nef|AAA02639.1|Human immunodeficiency virus 1|11676 - 1272 - 10 - - - 1 - 11.927 - 19 - 78.4397 - 3 - 8 - 5 - 10 - 0 - 0 - 3 - 5 - 0 - 6 - YQPNWR - YFPDWQ - Y P+W+ - - - - - 2 - gnl|BL_ORD_ID|1287 - 102235|nef protein|ACR27119.1|Human immunodeficiency virus 1|11676 - 1287 - 9 - - - 1 - 11.927 - 19 - 91.4136 - 3 - 8 - 1 - 6 - 0 - 0 - 3 - 5 - 0 - 6 - YQPNWR - YFPDWQ - Y P+W+ - - - - - 3 - gnl|BL_ORD_ID|1285 - 102151|nef protein|ACR27128.1|Human immunodeficiency virus 1|11676 - 1285 - 11 - - - 1 - 11.927 - 19 - 98.2033 - 3 - 8 - 4 - 9 - 0 - 0 - 3 - 5 - 0 - 6 - YQPNWR - YFPDWQ - Y P+W+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 9 - Query_9 - M_4966 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_4967 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_4968 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_4969 - 9 - - - 1 - gnl|BL_ORD_ID|210 - 15242|trans-sialidase, putative|EAN81560.1|Trypanosoma cruzi|5693 - 210 - 9 - - - 1 - 13.0826 - 22 - 15.4875 - 2 - 7 - 3 - 8 - 0 - 0 - 4 - 5 - 0 - 6 - QYKFTV - NYKFTL - YKFT+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 13 - Query_13 - M_4970 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_4971 - 9 - - - 1 - gnl|BL_ORD_ID|1951 - 181036|||| - 1951 - 20 - - - 1 - 15.779 - 29 - 0.402259 - 1 - 9 - 1 - 9 - 0 - 0 - 6 - 7 - 0 - 9 - VLSGAKIWL - VLSDFKVWL - VLS K+WL - - - - - 2 - gnl|BL_ORD_ID|1950 - 181035|||| - 1950 - 44 - - - 1 - 15.3938 - 28 - 1.34675 - 1 - 9 - 1 - 9 - 0 - 0 - 6 - 7 - 0 - 9 - VLSGAKIWL - VLSDFKVWL - VLS K+WL - - - - - 3 - gnl|BL_ORD_ID|1055 - 69751|polyprotein|BAB18806.1|Hepatitis C virus genotype 1|41856 - 1055 - 9 - - - 1 - 14.6234 - 26 - 1.82241 - 1 - 9 - 1 - 9 - 0 - 0 - 6 - 6 - 0 - 9 - VLSGAKIWL - VLSDFKTWL - VLS K WL - - - - - 4 - gnl|BL_ORD_ID|1056 - 69753|polyprotein|AAK49500.1|Hepatitis C virus genotype 3|356114 - 1056 - 9 - - - 1 - 13.853 - 24 - 5.09494 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 6 - 0 - 9 - VLSGAKIWL - VLSDFRTWL - VLS + WL - - - - - 5 - gnl|BL_ORD_ID|1054 - 69750|polyprotein|AAC03058.1|Hepatitis C virus genotype 3|356114 - 1054 - 9 - - - 1 - 13.853 - 24 - 5.74926 - 1 - 9 - 1 - 9 - 0 - 0 - 6 - 6 - 0 - 9 - VLSGAKIWL - VLSDFKSWL - VLS K WL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 15 - Query_15 - M_4972 - 9 - - - 1 - gnl|BL_ORD_ID|901 - 59182|attachment glycoprotein|ABQ58821.1|Human metapneumovirus|162145 - 901 - 10 - - - 1 - 9.61583 - 13 - 1296.37 - 2 - 9 - 3 - 10 - 0 - 0 - 4 - 6 - 0 - 8 - VLIVTTTV - ILIGITTL - +LI TT+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 16 - Query_16 - M_4973 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_4974 - 9 - - - 1 - gnl|BL_ORD_ID|664 - 39591|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 - 664 - 20 - - - 1 - 13.0826 - 22 - 15.6203 - 1 - 9 - 12 - 20 - 0 - 0 - 4 - 6 - 0 - 9 - VVWATKYFL - CLWWLQYFL - +W +YFL - - - - - 2 - gnl|BL_ORD_ID|1945 - 180828|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1945 - 10 - - - 1 - 12.3122 - 20 - 52.036 - 2 - 8 - 4 - 10 - 0 - 0 - 3 - 5 - 0 - 7 - VWATKYF - MWSLMYF - +W+ YF - - - - - 3 - gnl|BL_ORD_ID|1887 - 180579|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1887 - 15 - - - 1 - 12.3122 - 20 - 53.1389 - 2 - 8 - 6 - 12 - 0 - 0 - 3 - 5 - 0 - 7 - VWATKYF - MWSLMYF - +W+ YF - - - - - 4 - gnl|BL_ORD_ID|1960 - 182599|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1960 - 9 - - - 1 - 11.927 - 19 - 110.987 - 2 - 8 - 3 - 9 - 0 - 0 - 3 - 4 - 0 - 7 - VWATKYF - MWQLMYF - +W YF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 18 - Query_18 - M_4975 - 9 - - - 1 - gnl|BL_ORD_ID|889 - 58463|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 889 - 20 - - - 1 - 13.0826 - 22 - 16.661 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 7 - 0 - 9 - AMCSAQEEI - SICPSQEPM - ++C +QE + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 19 - Query_19 - M_4976 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_4977 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_4978 - 9 - - - 1 - gnl|BL_ORD_ID|1223 - 97093|polyprotein|AAB66324.1|Hepatitis C virus (isolate H77)|63746 - 1223 - 10 - - - 1 - 13.853 - 24 - 5.20543 - 2 - 8 - 3 - 9 - 0 - 0 - 4 - 6 - 0 - 7 - RHSMVVP - RHADVIP - RH+ V+P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 22 - Query_22 - M_4979 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_4980 - 9 - - - 1 - gnl|BL_ORD_ID|909 - 59569|Genome polyprotein|P26662.3|Hepatitis C virus (isolate Japanese)|11116 - 909 - 10 - - - 1 - 11.927 - 19 - 99.9004 - 4 - 9 - 5 - 10 - 0 - 0 - 3 - 4 - 0 - 6 - WAALGP - WLSQGP - W + GP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 24 - Query_24 - M_4981 - 9 - - - 1 - gnl|BL_ORD_ID|1522 - 140616|membrane-associated phospholipase C|NP_216866.1|Mycobacterium tuberculosis H37Rv|83332 - 1522 - 9 - - - 1 - 12.3122 - 20 - 48.7826 - 1 - 7 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - YLIISTF - YLLADTF - YL+ TF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 25 - Query_25 - M_4982 - 9 - - - 1 - gnl|BL_ORD_ID|2158 - 189294|Gag|O89360|Human immunodeficiency virus 1|11676 - 2158 - 9 - - - 1 - 12.3122 - 20 - 52.1643 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 6 - 0 - 9 - KIFNHPSTL - SLYNTVSTL - ++N STL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_137854_2_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_137854_2_T.fasta deleted file mode 100755 index 3d9bfe8d..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_137854_2_T.fasta +++ /dev/null @@ -1,160 +0,0 @@ ->M_4983 -RSPKKHGYM ->M_4984 -YMKMFEIPA ->M_4985 -LSSIGRSPM ->M_4986 -MVFCDFHGH ->M_4987 -RSPMVFCDF ->M_4988 -SIGRSPMVF ->M_4989 -SSIGRSPMV ->M_4990 -ATATAYLCR ->M_4991 -ATAYLCRVK ->M_4992 -RVKGNFQTI ->M_4993 -TATAYLCRV ->M_4994 -YLCRVKGNF ->M_4995 -CVSCWNVSR ->M_4996 -RLASLYKTL ->M_4997 -TLPQSVDPL ->M_4998 -SSSYAIEKR ->M_4999 -ISRSTFAEV ->M_5000 -RLPISRSTF ->M_5001 -STFAEVTGL ->M_5002 -STFAEVTGL ->M_5003 -FSWNGGSFV ->M_5004 -FSWNGGSFV ->M_5005 -TINEECSEI ->M_5006 -ILACRWVEM ->M_5007 -ESPFSSGKV ->M_5008 -MLAIGCALL ->M_5009 -ESIRHNVLY ->M_5010 -SIRHNVLYR ->M_5011 -LQFGPTAEG ->M_5012 -QPIPSVHER ->M_5013 -SVHERTDWV ->M_5014 -SVHERTDWV ->M_5015 -RAPSPVSFV ->M_5016 -GVLVLLFTL ->M_5017 -VLAPGVLVL ->M_5018 -VLAPGVLVL ->M_5019 -VLVLLFTLV ->M_5020 -FTFLVSLYL ->M_5021 -FTFLVSLYL ->M_5022 -IQAYVFTFL ->M_5023 -IQAYVFTFL ->M_5024 -LIQAYVFTF ->M_5025 -QAYVFTFLV ->M_5026 -QAYVFTFLV ->M_5027 -YVFTFLVSL ->M_5028 -YVFTFLVSL ->M_5029 -SSSPTCSLM ->M_5030 -ENWDLVTYR ->M_5031 -GAMENWDLV ->M_5032 -LEHPGSTRF ->M_5033 -QTDYVLSPL ->M_5034 -VLSPLTGGL ->M_5035 -ITEILDRYV ->M_5036 -FNKSGFKHY ->M_5037 -KSGFKHYQM ->M_5038 -PVFNKSGFK ->M_5039 -VLVSGIQVL ->M_5040 -VLVSGIQVL ->M_5041 -RSRTGEDEV ->M_5042 -LGQGELSAF ->M_5043 -EAQPESEGV ->M_5044 -LQDFYLGTY ->M_5045 -VAFPLQDFY ->M_5046 -ESVNILSVL ->M_5047 -GLVESVNIL ->M_5048 -FTVGQTEKY ->M_5049 -ESFKQTYVY ->M_5050 -ESFKQTYVY ->M_5051 -QTYVYSMAL ->M_5052 -YVYSMALVL ->M_5053 -YVYSMALVL ->M_5054 -YVYSMALVL ->M_5055 -FSLHKDRPV ->M_5056 -ATRKLIGKV ->M_5057 -HLKVRTATR ->M_5058 -TATRKLIGK ->M_5059 -LLPWAHSML ->M_5060 -QQNAPLLPW ->M_5061 -RIHSDEQPY ->M_5062 -AVHTVPQTI diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_137854_2_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_137854_2_T_iedb.xml deleted file mode 100755 index 77954074..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_137854_2_T_iedb.xml +++ /dev/null @@ -1,2720 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_4983 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_4983 - 9 - - - 1 - gnl|BL_ORD_ID|924 - 60031|SAG1 protein|AAO72426.1|Toxoplasma gondii RH|383379 - 924 - 9 - - - 1 - 13.0826 - 22 - 16.035 - 2 - 6 - 1 - 5 - 0 - 0 - 4 - 5 - 0 - 5 - SPKKH - SPEKH - SP+KH - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 2 - Query_2 - M_4984 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_4985 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_4986 - 9 - - - 1 - gnl|BL_ORD_ID|1776 - 155811|ribonucleotide reductase large subunit|CAB06725.1|Human alphaherpesvirus 2|10310 - 1776 - 15 - - - 1 - 16.1642 - 30 - 0.342581 - 1 - 9 - 2 - 10 - 0 - 0 - 5 - 5 - 0 - 9 - MVFCDFHGH - MSLADFHGE - M DFHG - - - - - 2 - gnl|BL_ORD_ID|1975 - 183147|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1975 - 9 - - - 1 - 11.5418 - 18 - 116.464 - 3 - 9 - 1 - 7 - 0 - 0 - 4 - 4 - 0 - 7 - FCDFHGH - FCSHHFH - FC H H - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 5 - Query_5 - M_4987 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_4988 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_4989 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_4990 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_4991 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_4992 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_4993 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_4994 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_4995 - 9 - - - 1 - gnl|BL_ORD_ID|181 - 13456|circumsporozoite protein|AAN87606.1|Plasmodium falciparum|5833 - 181 - 20 - - - 1 - 11.927 - 19 - 62.285 - 1 - 7 - 14 - 20 - 0 - 0 - 4 - 5 - 0 - 7 - CVSCWNV - CSSVFNV - C S +NV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 14 - Query_14 - M_4996 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_4997 - 9 - - - 1 - gnl|BL_ORD_ID|646 - 38446|Glycoprotein B precursor (Glycoprotein II)|P09257.1|Human alphaherpesvirus 3|10335 - 646 - 11 - - - 1 - 15.0086 - 27 - 1.31191 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 6 - 0 - 8 - LPQSVDPL - LPEGMDPF - LP+ +DP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 16 - Query_16 - M_4998 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_4999 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_5000 - 9 - - - 1 - gnl|BL_ORD_ID|1333 - 107873|Genome polyprotein|P26664.3|Hepatitis C virus|11103 - 1333 - 10 - - - 1 - 13.4678 - 23 - 10.2566 - 3 - 9 - 3 - 9 - 0 - 0 - 4 - 6 - 0 - 7 - PISRSTF - PITYSTY - PI+ ST+ - - - - - 2 - gnl|BL_ORD_ID|965 - 63963|HCV-1|AAA45676.1|Hepatitis C virus|11103 - 965 - 10 - - - 1 - 13.4678 - 23 - 11.3855 - 3 - 9 - 4 - 10 - 0 - 0 - 4 - 6 - 0 - 7 - PISRSTF - PITYSTY - PI+ ST+ - - - - - 3 - gnl|BL_ORD_ID|1434 - 116136|nucleocapsid protein|ACS34671.1|Influenza A virus (A/Auckland/1/2009(H1N1))|642794 - 1434 - 9 - - - 1 - 13.0826 - 22 - 16.6015 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - LPISRST - LPFERAT - LP R+T - - - - - 4 - gnl|BL_ORD_ID|650 - 38472|nucleoprotein|AAV48837.1|Influenza A virus (A/Brevig Mission/1/1918(H1N1))|88776 - 650 - 9 - - - 1 - 13.0826 - 22 - 18.1053 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - LPISRST - LPFERAT - LP R+T - - - - - 5 - gnl|BL_ORD_ID|964 - 63784|Genome polyprotein|P26663.3|Hepatitis C virus|11103 - 964 - 10 - - - 1 - 13.0826 - 22 - 18.1832 - 3 - 9 - 4 - 10 - 0 - 0 - 3 - 6 - 0 - 7 - PISRSTF - PVTYSTY - P++ ST+ - - - - - 6 - gnl|BL_ORD_ID|1432 - 116123|nucleocapsid protein|ABP49342.1|Influenza A virus (A/California/10/1978(H1N1))|425557 - 1432 - 9 - - - 1 - 13.0826 - 22 - 20.0871 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - LPISRST - LPFDKST - LP +ST - - - - - 7 - gnl|BL_ORD_ID|649 - 38471|nucleocapsid protein|ABC46569.1|Influenza A virus (A/Memphis/4/1980(H3N2))|383578 - 649 - 9 - - - 1 - 13.0826 - 22 - 21.1561 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - LPISRST - LPFEKST - LP +ST - - - - - 8 - gnl|BL_ORD_ID|648 - 38468|nucleoprotein|CAA24268.1|Influenza A virus (A/Puerto Rico/8/1934(H1N1))|211044 - 648 - 9 - - - 1 - 13.0826 - 22 - 21.5246 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - LPISRST - LPFDRTT - LP R+T - - - - - 9 - gnl|BL_ORD_ID|1232 - 97467|nucleocapsid protein|ACP44251.1|Influenza A virus (A/Fujian/411/2002(H3N2))|293090 - 1232 - 9 - - - 1 - 13.0826 - 22 - 22.6682 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - LPISRST - LPFEKST - LP +ST - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 19 - Query_19 - M_5001 - 9 - - - 1 - gnl|BL_ORD_ID|192 - 14198|UL123; IE1|AAR31390.1|Human betaherpesvirus 5|10359 - 192 - 11 - - - 1 - 11.927 - 19 - 64.6849 - 1 - 7 - 4 - 10 - 0 - 0 - 4 - 5 - 0 - 7 - STFAEVT - KTFEQVT - TF +VT - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 20 - Query_20 - M_5002 - 9 - - - 1 - gnl|BL_ORD_ID|192 - 14198|UL123; IE1|AAR31390.1|Human betaherpesvirus 5|10359 - 192 - 11 - - - 1 - 11.927 - 19 - 64.6849 - 1 - 7 - 4 - 10 - 0 - 0 - 4 - 5 - 0 - 7 - STFAEVT - KTFEQVT - TF +VT - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 21 - Query_21 - M_5003 - 9 - - - 1 - gnl|BL_ORD_ID|1861 - 180440|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1861 - 15 - - - 1 - 13.0826 - 22 - 16.1221 - 2 - 6 - 8 - 12 - 0 - 0 - 4 - 4 - 0 - 5 - SWNGG - SWNSG - SWN G - - - - - 2 - gnl|BL_ORD_ID|1926 - 180734|Nonstructural protein NS3|NP_739587.2|Dengue virus 2|11060 - 1926 - 9 - - - 1 - 12.6974 - 21 - 33.058 - 2 - 6 - 2 - 6 - 0 - 0 - 4 - 4 - 0 - 5 - SWNGG - SWNSG - SWN G - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 22 - Query_22 - M_5004 - 9 - - - 1 - gnl|BL_ORD_ID|1861 - 180440|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1861 - 15 - - - 1 - 13.0826 - 22 - 16.1221 - 2 - 6 - 8 - 12 - 0 - 0 - 4 - 4 - 0 - 5 - SWNGG - SWNSG - SWN G - - - - - 2 - gnl|BL_ORD_ID|1926 - 180734|Nonstructural protein NS3|NP_739587.2|Dengue virus 2|11060 - 1926 - 9 - - - 1 - 12.6974 - 21 - 33.058 - 2 - 6 - 2 - 6 - 0 - 0 - 4 - 4 - 0 - 5 - SWNGG - SWNSG - SWN G - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 23 - Query_23 - M_5005 - 9 - - - 1 - gnl|BL_ORD_ID|1296 - 103322|polyprotein|BAB18806.1|Hepatitis C virus|11103 - 1296 - 20 - - - 1 - 15.0086 - 27 - 1.00627 - 2 - 7 - 7 - 12 - 0 - 0 - 5 - 6 - 0 - 6 - INEECS - INEDCS - INE+CS - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 24 - Query_24 - M_5006 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_5007 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_5008 - 9 - - - 1 - gnl|BL_ORD_ID|1938 - 180802|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1938 - 9 - - - 1 - 14.6234 - 26 - 2.22125 - 1 - 6 - 3 - 8 - 0 - 0 - 5 - 6 - 0 - 6 - MLAIGC - LLAIGC - +LAIGC - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 27 - Query_27 - M_5009 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 28 - Query_28 - M_5010 - 9 - - - 1 - gnl|BL_ORD_ID|312 - 20861|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 - 312 - 9 - - - 1 - 11.927 - 19 - 75.1319 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 6 - 0 - 8 - SIRHNVLY - GLFNNVLY - + +NVLY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 29 - Query_29 - M_5011 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 30 - Query_30 - M_5012 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 31 - Query_31 - M_5013 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 32 - Query_32 - M_5014 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 33 - Query_33 - M_5015 - 9 - - - 1 - gnl|BL_ORD_ID|661 - 39571|polyprotein|BAD73987.1|Hepatitis C virus subtype 1b|31647 - 661 - 10 - - - 1 - 13.853 - 24 - 4.77406 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 7 - 0 - 8 - APSPVSFV - SPRPVSYL - +P PVS++ - - - - - 2 - gnl|BL_ORD_ID|2163 - 189546|glycosyl transferase|WP_015631503.1|Mycobacterium tuberculosis|1773 - 2163 - 9 - - - 1 - 12.6974 - 21 - 37.875 - 2 - 7 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - APSPVS - APEPVA - AP PV+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 34 - Query_34 - M_5016 - 9 - - - 1 - gnl|BL_ORD_ID|301 - 20354|M1 protein|CAA30882.1|Influenza A virus|11320 - 301 - 9 - - - 1 - 13.0826 - 22 - 20.7937 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 7 - 0 - 9 - GVLVLLFTL - GILGFVFTL - G+L +FTL - - - - - 2 - gnl|BL_ORD_ID|302 - 20355|Matrix protein 1|P03485.1|Influenza A virus (A/Puerto Rico/8/1934(H1N1))|211044 - 302 - 10 - - - 1 - 13.0826 - 22 - 21.2326 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 7 - 0 - 9 - GVLVLLFTL - GILGFVFTL - G+L +FTL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 35 - Query_35 - M_5017 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 36 - Query_36 - M_5018 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 37 - Query_37 - M_5019 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 38 - Query_38 - M_5020 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 39 - Query_39 - M_5021 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 40 - Query_40 - M_5022 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 41 - Query_41 - M_5023 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 42 - Query_42 - M_5024 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 43 - Query_43 - M_5025 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 44 - Query_44 - M_5026 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 45 - Query_45 - M_5027 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 46 - Query_46 - M_5028 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 47 - Query_47 - M_5029 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 48 - Query_48 - M_5030 - 9 - - - 1 - gnl|BL_ORD_ID|120 - 8236|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 - 120 - 15 - - - 1 - 12.6974 - 21 - 29.2994 - 1 - 8 - 4 - 11 - 0 - 0 - 2 - 5 - 0 - 8 - ENWDLVTY - QGWGPISY - + W ++Y - - - - - 2 - gnl|BL_ORD_ID|1699 - 149117|envelope glycoprotein|AAV74049.1|Hepatitis C virus (isolate H77)|63746 - 1699 - 18 - - - 1 - 12.6974 - 21 - 29.5284 - 1 - 8 - 5 - 12 - 0 - 0 - 2 - 5 - 0 - 8 - ENWDLVTY - QGWGPISY - + W ++Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 49 - Query_49 - M_5031 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 50 - Query_50 - M_5032 - 9 - - - 1 - gnl|BL_ORD_ID|1944 - 180818|Membrane glycoprotein precursor|NP_739582.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1944 - 15 - - - 1 - 15.0086 - 27 - 1.30769 - 1 - 7 - 3 - 9 - 0 - 0 - 5 - 5 - 0 - 7 - LEHPGST - LRHPGFT - L HPG T - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 51 - Query_51 - M_5033 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 52 - Query_52 - M_5034 - 9 - - - 1 - gnl|BL_ORD_ID|260 - 17802|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 260 - 15 - - - 1 - 11.1566 - 17 - 219.749 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 4 - 0 - 7 - LSPLTGG - FSPGTSG - SP T G - - - - - 2 - gnl|BL_ORD_ID|75 - 5542|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 75 - 15 - - - 1 - 11.1566 - 17 - 246.442 - 2 - 8 - 6 - 12 - 0 - 0 - 4 - 4 - 0 - 7 - LSPLTGG - FSPGTSG - SP T G - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 53 - Query_53 - M_5035 - 9 - - - 1 - gnl|BL_ORD_ID|163 - 12588|Glycoprotein B precursor (Glycoprotein II)|P09257.1|Human alphaherpesvirus 3|10335 - 163 - 11 - - - 1 - 13.0826 - 22 - 14.9787 - 1 - 8 - 2 - 9 - 0 - 0 - 3 - 7 - 0 - 8 - ITEILDRY - ITDTIDKF - IT+ +D++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 54 - Query_54 - M_5036 - 9 - - - 1 - gnl|BL_ORD_ID|390 - 23864|envelope glycoprotein(gp21, gp46) - human T-cell lymphotropic virus type 1|A45714|Human T-lymphotropic virus 1|11908 - 390 - 9 - - - 1 - 12.6974 - 21 - 37.875 - 1 - 7 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - FNKSGFK - FSKCGFP - F+K GF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 55 - Query_55 - M_5037 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 56 - Query_56 - M_5038 - 9 - - - 1 - gnl|BL_ORD_ID|390 - 23864|envelope glycoprotein(gp21, gp46) - human T-cell lymphotropic virus type 1|A45714|Human T-lymphotropic virus 1|11908 - 390 - 9 - - - 1 - 12.6974 - 21 - 37.875 - 3 - 8 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - FNKSGF - FSKCGF - F+K GF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 57 - Query_57 - M_5039 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 58 - Query_58 - M_5040 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 59 - Query_59 - M_5041 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 60 - Query_60 - M_5042 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 61 - Query_61 - M_5043 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 62 - Query_62 - M_5044 - 9 - - - 1 - gnl|BL_ORD_ID|1412 - 111404|Protein E7|P03129.1|Human papillomavirus type 16|333760 - 1412 - 15 - - - 1 - 14.2382 - 25 - 3.74365 - 1 - 8 - 7 - 14 - 0 - 0 - 4 - 6 - 0 - 8 - LQDFYLGT - LEDLLMGT - L+D +GT - - - - - 2 - gnl|BL_ORD_ID|1781 - 156550|E3 ubiquitin-protein ligase Mdm2|Q00987.1|Homo sapiens|9606 - 1781 - 9 - - - 1 - 14.2382 - 25 - 4.29054 - 4 - 9 - 3 - 8 - 0 - 0 - 5 - 5 - 0 - 6 - FYLGTY - FYLGQY - FYLG Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 63 - Query_63 - M_5045 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 64 - Query_64 - M_5046 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 65 - Query_65 - M_5047 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 66 - Query_66 - M_5048 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 67 - Query_67 - M_5049 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 68 - Query_68 - M_5050 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 69 - Query_69 - M_5051 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 70 - Query_70 - M_5052 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 71 - Query_71 - M_5053 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 72 - Query_72 - M_5054 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 73 - Query_73 - M_5055 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 74 - Query_74 - M_5056 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 75 - Query_75 - M_5057 - 9 - - - 1 - gnl|BL_ORD_ID|1765 - 154822|ribonucleotide reductase large subunit|CAB06725.1|Human alphaherpesvirus 2|10310 - 1765 - 15 - - - 1 - 14.2382 - 25 - 3.37317 - 1 - 6 - 5 - 10 - 0 - 0 - 4 - 6 - 0 - 6 - HLKVRT - HLRIRT - HL++RT - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 76 - Query_76 - M_5058 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 77 - Query_77 - M_5059 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 78 - Query_78 - M_5060 - 9 - - - 1 - gnl|BL_ORD_ID|1866 - 180460|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1866 - 10 - - - 1 - 14.2382 - 25 - 3.50259 - 1 - 7 - 3 - 9 - 0 - 0 - 4 - 6 - 0 - 7 - QQNAPLL - QSNAPIM - Q NAP++ - - - - - 2 - gnl|BL_ORD_ID|1704 - 150217|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1704 - 9 - - - 1 - 14.2382 - 25 - 3.93883 - 1 - 7 - 3 - 9 - 0 - 0 - 4 - 6 - 0 - 7 - QQNAPLL - QSNAPIM - Q NAP++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 79 - Query_79 - M_5061 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 80 - Query_80 - M_5062 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_138385_2_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_138385_2_T.fasta deleted file mode 100755 index 89206968..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_138385_2_T.fasta +++ /dev/null @@ -1,104 +0,0 @@ ->M_5063 -DPIRRHLHI ->M_5064 -HILYHCYGV ->M_5065 -WTRPGSEVL ->M_5066 -FPYVRNFVM ->M_5067 -YVRNFVMNL ->M_5068 -VAHEGMRPM ->M_5069 -RPDKMVPVV ->M_5070 -ILYLLSLFT ->M_5071 -LTILYLLSL ->M_5072 -YLLSLFTQT ->M_5073 -AAGPHVTVL ->M_5074 -RASAAGPHV ->M_5075 -SAAGPHVTV ->M_5076 -AVADLSCML ->M_5077 -CMLVLPTRL ->M_5078 -LAVADLSCM ->M_5079 -MLVLPTRLV ->M_5080 -VAVGTEHTL ->M_5081 -SVAWTTMDV ->M_5082 -TMDVATPSV ->M_5083 -NLYKGSVLY ->M_5084 -DEYNFVRTY ->M_5085 -RTYECFQHR ->M_5086 -LPSDPRLHL ->M_5087 -FLADITHLR ->M_5088 -GMRYWNMMV ->M_5089 -NMMVQWWLA ->M_5090 -TPLGKGDIV ->M_5091 -KVRSCIDLI ->M_5092 -YEQKVRSCI ->M_5093 -ALLAFATIM ->M_5094 -ATIMYVPAL ->M_5095 -LAFATIMYV ->M_5096 -LAFATIMYV ->M_5097 -YALLAFATI ->M_5098 -YALLAFATI ->M_5099 -LLLLLLLLV ->M_5100 -LLLLLLLVV ->M_5101 -LLLLLLVVV ->M_5102 -LLVVVPWGV ->M_5103 -IAATPIPAM ->M_5104 -HVLEIDESV ->M_5105 -HVLEIDESV ->M_5106 -YFNGSTNHV ->M_5107 -TPLCPGELL ->M_5108 -LMLGLVWTI ->M_5109 -LMLGLVWTI ->M_5110 -RLMLGLVWT ->M_5111 -SLTADDAFV ->M_5112 -PAFSLDVLM ->M_5113 -YLQAEIEPV ->M_5114 -YLQAEIEPV diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_138385_2_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_138385_2_T_iedb.xml deleted file mode 100755 index 385d1a53..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_138385_2_T_iedb.xml +++ /dev/null @@ -1,1610 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_5063 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_5063 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_5064 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_5065 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_5066 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_5067 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_5068 - 9 - - - 1 - gnl|BL_ORD_ID|996 - 65654|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 - 996 - 15 - - - 1 - 14.6234 - 26 - 1.57759 - 2 - 9 - 7 - 14 - 0 - 0 - 4 - 6 - 0 - 8 - AHEGMRPM - AHNGLRDL - AH G+R + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 7 - Query_7 - M_5069 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_5070 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_5071 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_5072 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_5073 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_5074 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_5075 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_5076 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_5077 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_5078 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_5079 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_5080 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_5081 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_5082 - 9 - - - 1 - gnl|BL_ORD_ID|1762 - 154448|RL2|CAB06760.1|Human alphaherpesvirus 2|10310 - 1762 - 16 - - - 1 - 8.46023 - 10 - 4206.81 - 2 - 5 - 5 - 8 - 0 - 0 - 3 - 3 - 0 - 4 - MDVA - MDAA - MD A - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 21 - Query_21 - M_5083 - 9 - - - 1 - gnl|BL_ORD_ID|413 - 24943|DNA polymerase|CAA10434.1|Hepatitis B virus|10407 - 413 - 11 - - - 1 - 13.853 - 24 - 4.51774 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 6 - 0 - 9 - NLYKGSVLY - TLWKAGILY - L+K +LY - - - - - 2 - gnl|BL_ORD_ID|988 - 65148|DNA polymerase|CAA10434.1|Hepatitis B virus|10407 - 988 - 10 - - - 1 - 13.853 - 24 - 4.53299 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 6 - 0 - 9 - NLYKGSVLY - TLWKAGILY - L+K +LY - - - - - 3 - gnl|BL_ORD_ID|683 - 41093|polyprotein|AGO67248.1|Dengue virus 2|11060 - 683 - 9 - - - 1 - 13.4678 - 23 - 11.1275 - 1 - 6 - 3 - 8 - 0 - 0 - 3 - 6 - 0 - 6 - NLYKGS - NIFRGS - N+++GS - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 22 - Query_22 - M_5084 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_5085 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_5086 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_5087 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_5088 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_5089 - 9 - - - 1 - gnl|BL_ORD_ID|1096 - 72322|polyprotein|AAA86907.1|Hepatitis C virus|11103 - 1096 - 15 - - - 1 - 11.5418 - 18 - 139.661 - 1 - 6 - 2 - 7 - 0 - 0 - 3 - 5 - 0 - 6 - NMMVQW - DMMMNW - +MM+ W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 28 - Query_28 - M_5090 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 29 - Query_29 - M_5091 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 30 - Query_30 - M_5092 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 31 - Query_31 - M_5093 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 32 - Query_32 - M_5094 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 33 - Query_33 - M_5095 - 9 - - - 1 - gnl|BL_ORD_ID|1568 - 141341|tegument protein VP11/12|NP_044648.1|Human alphaherpesvirus 1|10298 - 1568 - 9 - - - 1 - 13.0826 - 22 - 18.4218 - 1 - 8 - 2 - 9 - 0 - 0 - 3 - 7 - 0 - 8 - LAFATIMY - LAYVSVLY - LA+ +++Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 34 - Query_34 - M_5096 - 9 - - - 1 - gnl|BL_ORD_ID|1568 - 141341|tegument protein VP11/12|NP_044648.1|Human alphaherpesvirus 1|10298 - 1568 - 9 - - - 1 - 13.0826 - 22 - 18.4218 - 1 - 8 - 2 - 9 - 0 - 0 - 3 - 7 - 0 - 8 - LAFATIMY - LAYVSVLY - LA+ +++Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 35 - Query_35 - M_5097 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 36 - Query_36 - M_5098 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 37 - Query_37 - M_5099 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 38 - Query_38 - M_5100 - 9 - - - 1 - gnl|BL_ORD_ID|1263 - 98540|trans-sialidase, putative|EAN88532.1|Trypanosoma cruzi|5693 - 1263 - 10 - - - 1 - 11.1566 - 17 - 242.571 - 3 - 9 - 4 - 10 - 0 - 0 - 6 - 7 - 0 - 7 - LLLLLVV - VLLLLVV - +LLLLVV - - - - - 2 - gnl|BL_ORD_ID|1254 - 98224|trans-sialidase, putative|EAN82076.1|Trypanosoma cruzi|5693 - 1254 - 10 - - - 1 - 11.1566 - 17 - 286.165 - 4 - 9 - 1 - 6 - 0 - 0 - 6 - 6 - 0 - 6 - LLLLVV - LLLLVV - LLLLVV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 39 - Query_39 - M_5101 - 9 - - - 1 - gnl|BL_ORD_ID|1263 - 98540|trans-sialidase, putative|EAN88532.1|Trypanosoma cruzi|5693 - 1263 - 10 - - - 1 - 11.1566 - 17 - 231.802 - 3 - 8 - 5 - 10 - 0 - 0 - 6 - 6 - 0 - 6 - LLLLVV - LLLLVV - LLLLVV - - - - - 2 - gnl|BL_ORD_ID|1254 - 98224|trans-sialidase, putative|EAN82076.1|Trypanosoma cruzi|5693 - 1254 - 10 - - - 1 - 11.1566 - 17 - 250.006 - 3 - 9 - 1 - 7 - 0 - 0 - 6 - 7 - 0 - 7 - LLLLVVV - LLLLVVM - LLLLVV+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 40 - Query_40 - M_5102 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 41 - Query_41 - M_5103 - 9 - - - 1 - gnl|BL_ORD_ID|1815 - 177806|polyprotein|ACZ60104.1|Hepatitis C virus subtype 3a|356426 - 1815 - 11 - - - 1 - 13.0826 - 22 - 14.9787 - 4 - 8 - 3 - 7 - 0 - 0 - 4 - 5 - 0 - 5 - TPIPA - TPLPA - TP+PA - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 42 - Query_42 - M_5104 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 43 - Query_43 - M_5105 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 44 - Query_44 - M_5106 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 45 - Query_45 - M_5107 - 9 - - - 1 - gnl|BL_ORD_ID|2144 - 187197|Core protein|Q9QAC5|Hepatitis B virus|10407 - 2144 - 9 - - - 1 - 13.4678 - 23 - 8.42175 - 3 - 9 - 1 - 7 - 0 - 0 - 4 - 6 - 0 - 7 - LCPGELL - VCWGELM - +C GEL+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 46 - Query_46 - M_5108 - 9 - - - 1 - gnl|BL_ORD_ID|1717 - 150389|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1717 - 9 - - - 1 - 10.7714 - 16 - 354.707 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 5 - 0 - 9 - LMLGLVWTI - LMMRTTWAL - LM+ W + - - - - - 2 - gnl|BL_ORD_ID|1743 - 150686|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1743 - 9 - - - 1 - 10.7714 - 16 - 442.738 - 1 - 7 - 2 - 8 - 0 - 0 - 3 - 4 - 0 - 7 - LMLGLVW - LMMRTTW - LM+ W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 47 - Query_47 - M_5109 - 9 - - - 1 - gnl|BL_ORD_ID|1717 - 150389|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1717 - 9 - - - 1 - 10.7714 - 16 - 354.707 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 5 - 0 - 9 - LMLGLVWTI - LMMRTTWAL - LM+ W + - - - - - 2 - gnl|BL_ORD_ID|1743 - 150686|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1743 - 9 - - - 1 - 10.7714 - 16 - 442.738 - 1 - 7 - 2 - 8 - 0 - 0 - 3 - 4 - 0 - 7 - LMLGLVW - LMMRTTW - LM+ W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 48 - Query_48 - M_5110 - 9 - - - 1 - gnl|BL_ORD_ID|1743 - 150686|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1743 - 9 - - - 1 - 10.3862 - 15 - 654.037 - 2 - 8 - 2 - 8 - 0 - 0 - 3 - 4 - 0 - 7 - LMLGLVW - LMMRTTW - LM+ W - - - - - 2 - gnl|BL_ORD_ID|1717 - 150389|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1717 - 9 - - - 1 - 10.3862 - 15 - 732.621 - 2 - 8 - 1 - 7 - 0 - 0 - 3 - 4 - 0 - 7 - LMLGLVW - LMMRTTW - LM+ W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 49 - Query_49 - M_5111 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 50 - Query_50 - M_5112 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 51 - Query_51 - M_5113 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 52 - Query_52 - M_5114 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_138625_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_138625_1_T.fasta deleted file mode 100755 index 764f3386..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_138625_1_T.fasta +++ /dev/null @@ -1,106 +0,0 @@ ->M_5115 -LFFVDKLYK ->M_5116 -ALLPLFVVL ->M_5117 -ALLPLFVVL ->M_5118 -KALLPLFVV ->M_5119 -VVLCGNDHV ->M_5120 -TEMKRKAPF ->M_5121 -AMATYHFHF ->M_5122 -ATYHFHFNL ->M_5123 -ATYHFHFNL ->M_5124 -KAMATYHFH ->M_5125 -LKAMATYHF ->M_5126 -NVFVEVVLV ->M_5127 -GVKGVNSLF ->M_5128 -KGVNSLFKK ->M_5129 -AMSTPIYQM ->M_5130 -AMSTPIYQM ->M_5131 -SMAMSTPIY ->M_5132 -SMAMSTPIY ->M_5133 -SSMAMSTPI ->M_5134 -KMADEVPLK ->M_5135 -FLLAFRSGA ->M_5136 -LLAFRSGAL ->M_5137 -RVAEVAAQV ->M_5138 -KIFWFPTGL ->M_5139 -AGIFLLIHF ->M_5140 -FLLIHFHPL ->M_5141 -FLLIHFHPL ->M_5142 -GIFLLIHFH ->M_5143 -LLIHFHPLA ->M_5144 -SIVTSTFII ->M_5145 -VTSTFIISL ->M_5146 -LQIHGLAVE ->M_5147 -ATVLTLPHV ->M_5148 -VLTLPHVTK ->M_5149 -AVSNFYLPL ->M_5150 -HISAVSNFY ->M_5151 -HISAVSNFY ->M_5152 -SVVVIIDVK ->M_5153 -VVIIDVKPK ->M_5154 -FQRALVQPG ->M_5155 -ESFTATVEF ->M_5156 -LAAPRGVCY ->M_5157 -ATGATSLCF ->M_5158 -GLAMCHQEL ->M_5159 -LLTLAGLAM ->M_5160 -TVWPSLAPL ->M_5161 -CQHKLGKRY ->M_5162 -AVWRHLLLA ->M_5163 -HLLLALLLL ->M_5164 -LLALLLLVL ->M_5165 -LLALLLLVL ->M_5166 -LLLALLLLV ->M_5167 -LTRHQRTHM diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_138625_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_138625_1_T_iedb.xml deleted file mode 100755 index 24e9475d..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_138625_1_T_iedb.xml +++ /dev/null @@ -1,1766 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_5115 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_5115 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_5116 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_5117 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_5118 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_5119 - 9 - - - 1 - gnl|BL_ORD_ID|987 - 65118|SAG1 protein|AAO72426.1|Toxoplasma gondii RH|383379 - 987 - 9 - - - 1 - 13.4678 - 23 - 13.0154 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 6 - 0 - 9 - VVLCGNDHV - TLVCGKDGV - ++CG D V - - - - - 2 - gnl|BL_ORD_ID|671 - 40286|SAG1 protein|AAO72426.1|Toxoplasma gondii RH|383379 - 671 - 9 - - - 1 - 13.4678 - 23 - 13.0154 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 6 - 0 - 8 - VLCGNDHV - LVCGKDGV - ++CG D V - - - - - 3 - gnl|BL_ORD_ID|1075 - 71266|Circumsporozoite protein precursor|P02893.1|Plasmodium falciparum|5833 - 1075 - 20 - - - 1 - 13.0826 - 22 - 16.3948 - 2 - 6 - 1 - 5 - 0 - 0 - 4 - 4 - 0 - 5 - VLCGN - VTCGN - V CGN - - - - - 4 - gnl|BL_ORD_ID|1074 - 71265|Circumsporozoite protein precursor|P02893.1|Plasmodium falciparum|5833 - 1074 - 10 - - - 1 - 12.6974 - 21 - 28.4017 - 2 - 6 - 1 - 5 - 0 - 0 - 4 - 4 - 0 - 5 - VLCGN - VTCGN - V CGN - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 6 - Query_6 - M_5120 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_5121 - 9 - - - 1 - gnl|BL_ORD_ID|1975 - 183147|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1975 - 9 - - - 1 - 11.927 - 19 - 69.1936 - 3 - 8 - 2 - 7 - 0 - 0 - 3 - 5 - 0 - 6 - ATYHFH - CSHHFH - ++HFH - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 8 - Query_8 - M_5122 - 9 - - - 1 - gnl|BL_ORD_ID|419 - 25275|Glutamate decarboxylase 2|Q05329.1|Homo sapiens|9606 - 419 - 13 - - - 1 - 12.3122 - 20 - 42.7536 - 2 - 9 - 5 - 12 - 0 - 0 - 4 - 6 - 0 - 8 - TYHFHFNL - SEHSHFSL - + H HF+L - - - - - 2 - gnl|BL_ORD_ID|1975 - 183147|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1975 - 9 - - - 1 - 11.927 - 19 - 76.3762 - 1 - 6 - 2 - 7 - 0 - 0 - 3 - 5 - 0 - 6 - ATYHFH - CSHHFH - ++HFH - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 9 - Query_9 - M_5123 - 9 - - - 1 - gnl|BL_ORD_ID|419 - 25275|Glutamate decarboxylase 2|Q05329.1|Homo sapiens|9606 - 419 - 13 - - - 1 - 12.3122 - 20 - 42.7536 - 2 - 9 - 5 - 12 - 0 - 0 - 4 - 6 - 0 - 8 - TYHFHFNL - SEHSHFSL - + H HF+L - - - - - 2 - gnl|BL_ORD_ID|1975 - 183147|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1975 - 9 - - - 1 - 11.927 - 19 - 76.3762 - 1 - 6 - 2 - 7 - 0 - 0 - 3 - 5 - 0 - 6 - ATYHFH - CSHHFH - ++HFH - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 10 - Query_10 - M_5124 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_5125 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_5126 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_5127 - 9 - - - 1 - gnl|BL_ORD_ID|786 - 52652|||| - 786 - 27 - - - 1 - 15.0086 - 27 - 1.22232 - 2 - 9 - 13 - 20 - 0 - 0 - 5 - 7 - 0 - 8 - VKGVNSLF - VRGLTSLF - V+G+ SLF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 14 - Query_14 - M_5128 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_5129 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_5130 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_5131 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_5132 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_5133 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_5134 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_5135 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 22 - Query_22 - M_5136 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_5137 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_5138 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_5139 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_5140 - 9 - - - 1 - gnl|BL_ORD_ID|624 - 37507|Large T antigen|P03071.1|Human polyomavirus 1|1891762 - 624 - 9 - - - 1 - 13.853 - 24 - 6.71897 - 2 - 9 - 2 - 9 - 0 - 0 - 5 - 6 - 0 - 8 - LLIHFHPL - LLIWFRPV - LLI F P+ - - - - - 2 - gnl|BL_ORD_ID|1975 - 183147|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1975 - 9 - - - 1 - 12.3122 - 20 - 61.624 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 5 - 0 - 9 - FLLIHFHPL - FCSHHFHQL - F HFH L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 27 - Query_27 - M_5141 - 9 - - - 1 - gnl|BL_ORD_ID|624 - 37507|Large T antigen|P03071.1|Human polyomavirus 1|1891762 - 624 - 9 - - - 1 - 13.853 - 24 - 6.71897 - 2 - 9 - 2 - 9 - 0 - 0 - 5 - 6 - 0 - 8 - LLIHFHPL - LLIWFRPV - LLI F P+ - - - - - 2 - gnl|BL_ORD_ID|1975 - 183147|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1975 - 9 - - - 1 - 12.3122 - 20 - 61.624 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 5 - 0 - 9 - FLLIHFHPL - FCSHHFHQL - F HFH L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 28 - Query_28 - M_5142 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 29 - Query_29 - M_5143 - 9 - - - 1 - gnl|BL_ORD_ID|624 - 37507|Large T antigen|P03071.1|Human polyomavirus 1|1891762 - 624 - 9 - - - 1 - 13.853 - 24 - 4.83846 - 1 - 8 - 2 - 9 - 0 - 0 - 5 - 6 - 0 - 8 - LLIHFHPL - LLIWFRPV - LLI F P+ - - - - - 2 - gnl|BL_ORD_ID|1975 - 183147|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1975 - 9 - - - 1 - 12.3122 - 20 - 59.6102 - 4 - 8 - 5 - 9 - 0 - 0 - 4 - 4 - 0 - 5 - HFHPL - HFHQL - HFH L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 30 - Query_30 - M_5144 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 31 - Query_31 - M_5145 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 32 - Query_32 - M_5146 - 9 - - - 1 - gnl|BL_ORD_ID|2320 - 423047|Genome polyprotein|P27958.3|Hepatitis C virus genotype 1|41856 - 2320 - 9 - - - 1 - 12.6974 - 21 - 35.9943 - 2 - 8 - 2 - 8 - 0 - 0 - 3 - 6 - 0 - 7 - QIHGLAV - RLHGLSA - ++HGL+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 33 - Query_33 - M_5147 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 34 - Query_34 - M_5148 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 35 - Query_35 - M_5149 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 36 - Query_36 - M_5150 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 37 - Query_37 - M_5151 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 38 - Query_38 - M_5152 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 39 - Query_39 - M_5153 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 40 - Query_40 - M_5154 - 9 - - - 1 - gnl|BL_ORD_ID|1992 - 183577|polyprotein|AGK36298.1|Dengue virus 2|11060 - 1992 - 10 - - - 1 - 15.0086 - 27 - 1.28623 - 1 - 6 - 2 - 7 - 0 - 0 - 5 - 6 - 0 - 6 - FQRALV - FQRALI - FQRAL+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 41 - Query_41 - M_5155 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 42 - Query_42 - M_5156 - 9 - - - 1 - gnl|BL_ORD_ID|1667 - 148117|early protein|CAA52585.1|Human papillomavirus type 52|10618 - 1667 - 9 - - - 1 - 13.0826 - 22 - 22.6682 - 4 - 8 - 1 - 5 - 0 - 0 - 4 - 4 - 0 - 5 - PRGVC - PYGVC - P GVC - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 43 - Query_43 - M_5157 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 44 - Query_44 - M_5158 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 45 - Query_45 - M_5159 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 46 - Query_46 - M_5160 - 9 - - - 1 - gnl|BL_ORD_ID|1520 - 140600|glutamine synthetase GLNA1 (glutamine synthase) (GS-I)|NP_216736.1|Mycobacterium tuberculosis H37Rv|83332 - 1520 - 9 - - - 1 - 13.0826 - 22 - 21.1561 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 6 - 0 - 9 - TVWPSLAPL - SLWKDGAPL - ++W APL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 47 - Query_47 - M_5161 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 48 - Query_48 - M_5162 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 49 - Query_49 - M_5163 - 9 - - - 1 - gnl|BL_ORD_ID|292 - 19442|nucleocapsid protein|ABI96968.1|SARS coronavirus|227859 - 292 - 10 - - - 1 - 11.1566 - 17 - 246.263 - 4 - 9 - 5 - 10 - 0 - 0 - 6 - 6 - 0 - 6 - LALLLL - LALLLL - LALLLL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 50 - Query_50 - M_5164 - 9 - - - 1 - gnl|BL_ORD_ID|292 - 19442|nucleocapsid protein|ABI96968.1|SARS coronavirus|227859 - 292 - 10 - - - 1 - 11.1566 - 17 - 265.518 - 2 - 7 - 5 - 10 - 0 - 0 - 6 - 6 - 0 - 6 - LALLLL - LALLLL - LALLLL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 51 - Query_51 - M_5165 - 9 - - - 1 - gnl|BL_ORD_ID|292 - 19442|nucleocapsid protein|ABI96968.1|SARS coronavirus|227859 - 292 - 10 - - - 1 - 11.1566 - 17 - 265.518 - 2 - 7 - 5 - 10 - 0 - 0 - 6 - 6 - 0 - 6 - LALLLL - LALLLL - LALLLL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 52 - Query_52 - M_5166 - 9 - - - 1 - gnl|BL_ORD_ID|292 - 19442|nucleocapsid protein|ABI96968.1|SARS coronavirus|227859 - 292 - 10 - - - 1 - 11.1566 - 17 - 265.518 - 3 - 8 - 5 - 10 - 0 - 0 - 6 - 6 - 0 - 6 - LALLLL - LALLLL - LALLLL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 53 - Query_53 - M_5167 - 9 - - - 1 - gnl|BL_ORD_ID|256 - 17278|Genome polyprotein|P06441.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 256 - 20 - - - 1 - 13.0826 - 22 - 15.3699 - 2 - 9 - 9 - 16 - 0 - 0 - 4 - 5 - 0 - 8 - TRHQRTHM - SRHTSDHM - +RH HM - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_138926_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_138926_1_T.fasta deleted file mode 100755 index c2a8f427..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_138926_1_T.fasta +++ /dev/null @@ -1,108 +0,0 @@ ->M_5168 -EAWLFLEWV ->M_5169 -SEAWLFLEW ->M_5170 -WILSHTVAL ->M_5171 -WILSHTVAL ->M_5172 -SVRKSVSTV ->M_5173 -MTVTVCPPT ->M_5174 -SPMVLLLAA ->M_5175 -VERGSPMVL ->M_5176 -VVERGSPMV ->M_5177 -FEAFDHTET ->M_5178 -RLFEAFDHT ->M_5179 -HTCRVMGAL ->M_5180 -YKIGGIGMV ->M_5181 -EELTQLNEA ->M_5182 -LQSRLEEEL ->M_5183 -RLEEELTQL ->M_5184 -FPRLGCPWF ->M_5185 -RLGCPWFTL ->M_5186 -RLGCPWFTL ->M_5187 -DWPVFPGLF ->M_5188 -FNVGDDWPV ->M_5189 -NYASRTQNI ->M_5190 -SVSSCCQPV ->M_5191 -SVSSCCQPV ->M_5192 -CTLGDQLSL ->M_5193 -STAPQAHGV ->M_5194 -STAPQAHGV ->M_5195 -VSLFYSTAI ->M_5196 -VSLFYSTAI ->M_5197 -YSTAISVYL ->M_5198 -YSTAISVYL ->M_5199 -DTAPDIVEI ->M_5200 -FLWDRHVRF ->M_5201 -LWDRHVRFF ->M_5202 -FTCLPLGSL ->M_5203 -HVWLCDLPV ->M_5204 -HVWLCDLPV ->M_5205 -APRGVCYGA ->M_5206 -DPEYSPGAL ->M_5207 -YSPGALATF ->M_5208 -VLGDFLGTV ->M_5209 -AVVGTVWNV ->M_5210 -NVATTGLSL ->M_5211 -DTTDKGALM ->M_5212 -KAVSVCPEA ->M_5213 -SVCPEAAPA ->M_5214 -VLVVGMGPV ->M_5215 -IFATKPELL ->M_5216 -RIFATKPEL ->M_5217 -AFSQSAYLI ->M_5218 -AYLIQHQRF ->M_5219 -KAFSQSAYL ->M_5220 -KAFSQSAYL ->M_5221 -FPAPARDDF diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_138926_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_138926_1_T_iedb.xml deleted file mode 100755 index 4e49d0f8..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_138926_1_T_iedb.xml +++ /dev/null @@ -1,1429 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_5168 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_5168 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_5169 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_5170 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_5171 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_5172 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_5173 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_5174 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_5175 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_5176 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_5177 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_5178 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_5179 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_5180 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_5181 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_5182 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_5183 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_5184 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_5185 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_5186 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_5187 - 9 - - - 1 - gnl|BL_ORD_ID|1106 - 72928|Genome polyprotein|P26662.3|Hepatitis C virus (isolate Japanese)|11116 - 1106 - 10 - - - 1 - 13.4678 - 23 - 12.4198 - 2 - 7 - 1 - 6 - 0 - 0 - 4 - 4 - 0 - 6 - WPVFPG - WPAPPG - WP PG - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 21 - Query_21 - M_5188 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 22 - Query_22 - M_5189 - 9 - - - 1 - gnl|BL_ORD_ID|84 - 6308|HCV-1|AAA45676.1|Hepatitis C virus genotype 1|41856 - 84 - 20 - - - 1 - 13.853 - 24 - 7.21037 - 1 - 7 - 7 - 13 - 0 - 0 - 4 - 6 - 0 - 7 - NYASRTQ - NWAVRTK - N+A RT+ - - - - - 2 - gnl|BL_ORD_ID|1813 - 177701|polyprotein|ACZ60104.1|Hepatitis C virus subtype 3a|356426 - 1813 - 18 - - - 1 - 13.853 - 24 - 7.28436 - 1 - 7 - 12 - 18 - 0 - 0 - 4 - 6 - 0 - 7 - NYASRTQ - NWAVRTK - N+A RT+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 23 - Query_23 - M_5190 - 9 - - - 1 - gnl|BL_ORD_ID|872 - 57361|Genome polyprotein|SRC279960|Hepatitis C virus (isolate H77)|63746 - 872 - 11 - - - 1 - 12.6974 - 21 - 28.2065 - 3 - 8 - 1 - 6 - 0 - 0 - 4 - 4 - 0 - 6 - SSCCQP - SECCTP - S CC P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 24 - Query_24 - M_5191 - 9 - - - 1 - gnl|BL_ORD_ID|872 - 57361|Genome polyprotein|SRC279960|Hepatitis C virus (isolate H77)|63746 - 872 - 11 - - - 1 - 12.6974 - 21 - 28.2065 - 3 - 8 - 1 - 6 - 0 - 0 - 4 - 4 - 0 - 6 - SSCCQP - SECCTP - S CC P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 25 - Query_25 - M_5192 - 9 - - - 1 - gnl|BL_ORD_ID|2252 - 244160|surface antigen 2 (CA-2)|XP_818927.1|Trypanosoma cruzi strain CL Brener|353153 - 2252 - 9 - - - 1 - 14.2382 - 25 - 4.0067 - 4 - 9 - 4 - 9 - 0 - 0 - 5 - 6 - 0 - 6 - GDQLSL - GDKLSL - GD+LSL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 26 - Query_26 - M_5193 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_5194 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 28 - Query_28 - M_5195 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 29 - Query_29 - M_5196 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 30 - Query_30 - M_5197 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 31 - Query_31 - M_5198 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 32 - Query_32 - M_5199 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 33 - Query_33 - M_5200 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 34 - Query_34 - M_5201 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 35 - Query_35 - M_5202 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 36 - Query_36 - M_5203 - 9 - - - 1 - gnl|BL_ORD_ID|57 - 4172|Glycoprotein I precursor (Glycoprotein IV) (GI) (GPIV)|P09258.1|Human alphaherpesvirus 3|10335 - 57 - 11 - - - 1 - 15.3938 - 28 - 0.668034 - 2 - 9 - 1 - 8 - 0 - 0 - 5 - 5 - 0 - 8 - VWLCDLPV - ARLCDLPA - LCDLP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 37 - Query_37 - M_5204 - 9 - - - 1 - gnl|BL_ORD_ID|57 - 4172|Glycoprotein I precursor (Glycoprotein IV) (GI) (GPIV)|P09258.1|Human alphaherpesvirus 3|10335 - 57 - 11 - - - 1 - 15.3938 - 28 - 0.668034 - 2 - 9 - 1 - 8 - 0 - 0 - 5 - 5 - 0 - 8 - VWLCDLPV - ARLCDLPA - LCDLP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 38 - Query_38 - M_5205 - 9 - - - 1 - gnl|BL_ORD_ID|1667 - 148117|early protein|CAA52585.1|Human papillomavirus type 52|10618 - 1667 - 9 - - - 1 - 12.6974 - 21 - 26.9236 - 2 - 6 - 1 - 5 - 0 - 0 - 4 - 4 - 0 - 5 - PRGVC - PYGVC - P GVC - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 39 - Query_39 - M_5206 - 9 - - - 1 - gnl|BL_ORD_ID|899 - 59153|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 - 899 - 15 - - - 1 - 13.4678 - 23 - 10.0248 - 4 - 9 - 5 - 10 - 0 - 0 - 4 - 5 - 0 - 6 - YSPGAL - YSPGEI - YSPG + - - - - - 2 - gnl|BL_ORD_ID|256 - 17278|Genome polyprotein|P06441.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 256 - 20 - - - 1 - 12.6974 - 21 - 21.519 - 2 - 7 - 2 - 7 - 0 - 0 - 4 - 4 - 0 - 6 - PEYSPG - PELKPG - PE PG - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 40 - Query_40 - M_5207 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 41 - Query_41 - M_5208 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 42 - Query_42 - M_5209 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 43 - Query_43 - M_5210 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 44 - Query_44 - M_5211 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 45 - Query_45 - M_5212 - 9 - - - 1 - gnl|BL_ORD_ID|287 - 19359|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 - 287 - 20 - - - 1 - 13.4678 - 23 - 8.9532 - 1 - 9 - 9 - 17 - 0 - 0 - 4 - 6 - 0 - 9 - KAVSVCPEA - QQVSIAPNA - + VS+ P A - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 46 - Query_46 - M_5213 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 47 - Query_47 - M_5214 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 48 - Query_48 - M_5215 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 49 - Query_49 - M_5216 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 50 - Query_50 - M_5217 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 51 - Query_51 - M_5218 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 52 - Query_52 - M_5219 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 53 - Query_53 - M_5220 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 54 - Query_54 - M_5221 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_139381_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_139381_1_T.fasta deleted file mode 100755 index a16d5f0c..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_139381_1_T.fasta +++ /dev/null @@ -1,78 +0,0 @@ ->M_5222 -SPSVMWLVH ->M_5223 -LAVRDVFEL ->M_5224 -LAVRDVFEL ->M_5225 -KTLTLAKNY ->M_5226 -SSGSMCNRW ->M_5227 -TTKNDIGPY ->M_5228 -LGLTNNTAM ->M_5229 -FTTELTAPF ->M_5230 -FTTELTAPF ->M_5231 -FTTELTAPF ->M_5232 -MPAFTTELT ->M_5233 -LMALHPALF ->M_5234 -QCSEHDVLF ->M_5235 -EPYIDNEEF ->M_5236 -VVIKAIEPY ->M_5237 -QVQDSNLEY ->M_5238 -QVQDSNLEY ->M_5239 -LASSCGCTF ->M_5240 -LASSCGCTF ->M_5241 -IQLLGVFVW ->M_5242 -ISIQLLGVF ->M_5243 -EVDFTCWKY ->M_5244 -HPTAASQSR ->M_5245 -IIETANVSY ->M_5246 -VSYTNAWAL ->M_5247 -FFIHSFTLM ->M_5248 -MFFIHSFTL ->M_5249 -MFNPIIYIF ->M_5250 -LPTPVEPTV ->M_5251 -TPVEPTVAC ->M_5252 -HPDNVSSSY ->M_5253 -LLAAARPLW ->M_5254 -SPVALQLRY ->M_5255 -YQIGTDSAL ->M_5256 -EAHHHFPSL ->M_5257 -EAHHHFPSL ->M_5258 -GSGEAHHHF ->M_5259 -RVSSLTLHF ->M_5260 -KPFSQSCEF diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_139381_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_139381_1_T_iedb.xml deleted file mode 100755 index fcd36868..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_139381_1_T_iedb.xml +++ /dev/null @@ -1,1822 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_5222 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_5222 - 9 - - - 1 - gnl|BL_ORD_ID|431 - 26273|nucleocapsid protein|ABI96968.1|SARS coronavirus|227859 - 431 - 15 - - - 1 - 13.853 - 24 - 5.29758 - 1 - 9 - 6 - 14 - 0 - 0 - 4 - 6 - 0 - 9 - SPSVMWLVH - TPSGTWLTY - +PS WL + - - - - - 2 - gnl|BL_ORD_ID|1436 - 116835|Nucleoprotein|P05133.1|Hantaan virus 76-118|11602 - 1436 - 15 - - - 1 - 13.4678 - 23 - 9.36117 - 1 - 7 - 1 - 7 - 0 - 0 - 4 - 6 - 0 - 7 - SPSVMWL - SPSSIWV - SPS +W+ - - - - - 3 - gnl|BL_ORD_ID|2187 - 190494|nucleocapsid protein|ABI96968.1|SARS coronavirus|227859 - 2187 - 10 - - - 1 - 12.6974 - 21 - 24.356 - 1 - 7 - 4 - 10 - 0 - 0 - 4 - 5 - 0 - 7 - SPSVMWL - TPSGTWL - +PS WL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 2 - Query_2 - M_5223 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_5224 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_5225 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_5226 - 9 - - - 1 - gnl|BL_ORD_ID|136 - 9920|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis|1773 - 136 - 18 - - - 1 - 13.0826 - 22 - 15.4571 - 1 - 9 - 6 - 14 - 0 - 0 - 3 - 7 - 0 - 9 - SSGSMCNRW - TAGSLQGQW - ++GS+ +W - - - - - 2 - gnl|BL_ORD_ID|2224 - 194400|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis|1773 - 2224 - 9 - - - 1 - 13.0826 - 22 - 18.4218 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 7 - 0 - 9 - SSGSMCNRW - TAGSLQGQW - ++GS+ +W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 6 - Query_6 - M_5227 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_5228 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_5229 - 9 - - - 1 - gnl|BL_ORD_ID|1818 - 177903|polyprotein|ACZ60102.1|Hepatitis C virus subtype 3a|356426 - 1818 - 17 - - - 1 - 13.4678 - 23 - 9.62753 - 1 - 9 - 9 - 17 - 0 - 0 - 4 - 6 - 0 - 9 - FTTELTAPF - FTASVTSPL - FT +T+P - - - - - 2 - gnl|BL_ORD_ID|1597 - 142233|ATP-dependent helicase|NP_217813.1|Mycobacterium tuberculosis|1773 - 1597 - 32 - - - 1 - 11.927 - 19 - 52.8651 - 1 - 8 - 20 - 27 - 0 - 0 - 4 - 5 - 0 - 8 - FTTELTAP - FTSTFAAP - FT+ AP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 9 - Query_9 - M_5230 - 9 - - - 1 - gnl|BL_ORD_ID|1818 - 177903|polyprotein|ACZ60102.1|Hepatitis C virus subtype 3a|356426 - 1818 - 17 - - - 1 - 13.4678 - 23 - 9.62753 - 1 - 9 - 9 - 17 - 0 - 0 - 4 - 6 - 0 - 9 - FTTELTAPF - FTASVTSPL - FT +T+P - - - - - 2 - gnl|BL_ORD_ID|1597 - 142233|ATP-dependent helicase|NP_217813.1|Mycobacterium tuberculosis|1773 - 1597 - 32 - - - 1 - 11.927 - 19 - 52.8651 - 1 - 8 - 20 - 27 - 0 - 0 - 4 - 5 - 0 - 8 - FTTELTAP - FTSTFAAP - FT+ AP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 10 - Query_10 - M_5231 - 9 - - - 1 - gnl|BL_ORD_ID|1818 - 177903|polyprotein|ACZ60102.1|Hepatitis C virus subtype 3a|356426 - 1818 - 17 - - - 1 - 13.4678 - 23 - 9.62753 - 1 - 9 - 9 - 17 - 0 - 0 - 4 - 6 - 0 - 9 - FTTELTAPF - FTASVTSPL - FT +T+P - - - - - 2 - gnl|BL_ORD_ID|1597 - 142233|ATP-dependent helicase|NP_217813.1|Mycobacterium tuberculosis|1773 - 1597 - 32 - - - 1 - 11.927 - 19 - 52.8651 - 1 - 8 - 20 - 27 - 0 - 0 - 4 - 5 - 0 - 8 - FTTELTAP - FTSTFAAP - FT+ AP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 11 - Query_11 - M_5232 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_5233 - 9 - - - 1 - gnl|BL_ORD_ID|114 - 7660|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 - 114 - 20 - - - 1 - 13.4678 - 23 - 8.10378 - 1 - 8 - 7 - 14 - 0 - 0 - 4 - 6 - 0 - 8 - LMALHPAL - MCAVHPTL - + A+HP L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 13 - Query_13 - M_5234 - 9 - - - 1 - gnl|BL_ORD_ID|1438 - 120093|unnamed protein product|CAA33016.1|Rubella virus|11041 - 1438 - 21 - - - 1 - 13.853 - 24 - 6.7201 - 2 - 6 - 5 - 9 - 0 - 0 - 4 - 4 - 0 - 5 - CSEHD - CVEHD - C EHD - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 14 - Query_14 - M_5235 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_5236 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_5237 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_5238 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_5239 - 9 - - - 1 - gnl|BL_ORD_ID|920 - 59786|Large envelope protein|P03138.3|Hepatitis B virus ayw/France/Tiollais/1979|490133 - 920 - 10 - - - 1 - 11.5418 - 18 - 148.349 - 1 - 8 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - LASSCGCT - MYPSCCCT - + SC CT - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 19 - Query_19 - M_5240 - 9 - - - 1 - gnl|BL_ORD_ID|920 - 59786|Large envelope protein|P03138.3|Hepatitis B virus ayw/France/Tiollais/1979|490133 - 920 - 10 - - - 1 - 11.5418 - 18 - 148.349 - 1 - 8 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - LASSCGCT - MYPSCCCT - + SC CT - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 20 - Query_20 - M_5241 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_5242 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 22 - Query_22 - M_5243 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_5244 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_5245 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_5246 - 9 - - - 1 - gnl|BL_ORD_ID|1887 - 180579|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1887 - 15 - - - 1 - 13.4678 - 23 - 7.35849 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - SYTNAWAL - SYAQMWSL - SY W+L - - - - - 2 - gnl|BL_ORD_ID|943 - 62184|nonstructural protein 3|NP_722463.1|Dengue virus type 1 Hawaii|10000440 - 943 - 15 - - - 1 - 13.4678 - 23 - 9.36117 - 1 - 9 - 7 - 15 - 0 - 0 - 3 - 4 - 0 - 9 - VSYTNAWAL - ISYGGGWRF - +SY W - - - - - 3 - gnl|BL_ORD_ID|9 - 790|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 9 - 15 - - - 1 - 13.4678 - 23 - 9.36117 - 1 - 7 - 8 - 14 - 0 - 0 - 3 - 4 - 0 - 7 - VSYTNAW - ISYGGGW - +SY W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 26 - Query_26 - M_5247 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_5248 - 9 - - - 1 - gnl|BL_ORD_ID|375 - 23270|polyprotein|AAB67036.1|Hepatitis C virus (isolate H77)|63746 - 375 - 15 - - - 1 - 12.3122 - 20 - 38.6124 - 1 - 8 - 6 - 13 - 0 - 0 - 3 - 5 - 0 - 8 - MFFIHSFT - LFYQHKFN - +F+ H F - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 28 - Query_28 - M_5249 - 9 - - - 1 - gnl|BL_ORD_ID|312 - 20861|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 - 312 - 9 - - - 1 - 13.0826 - 22 - 18.4218 - 1 - 7 - 2 - 8 - 0 - 0 - 3 - 6 - 0 - 7 - MFNPIIY - LFNNVLY - +FN ++Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 29 - Query_29 - M_5250 - 9 - - - 1 - gnl|BL_ORD_ID|448 - 27241|Spike glycoprotein precursor|P59594.1|SARS coronavirus|227859 - 448 - 9 - - - 1 - 14.2382 - 25 - 2.90246 - 1 - 8 - 2 - 9 - 0 - 0 - 5 - 7 - 0 - 8 - LPTPVEPT - LPDPLKPT - LP P++PT - - - - - 2 - gnl|BL_ORD_ID|1020 - 68229|EBNA3B (EBNA4A) latent protein|CAA24858.1|Human gammaherpesvirus 4|10376 - 1020 - 10 - - - 1 - 12.3122 - 20 - 63.4362 - 3 - 8 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - TPVEPT - TPYKPT - TP +PT - - - - - 3 - gnl|BL_ORD_ID|240 - 16833|core protein|CAL29866.1|Hepatitis B virus|10407 - 240 - 10 - - - 1 - 11.927 - 19 - 78.4397 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 6 - 0 - 9 - LPTPVEPTV - LPSDFFPSV - LP+ P+V - - - - - 4 - gnl|BL_ORD_ID|69 - 5191|core protein|AAL31859.1|Hepatitis B virus|10407 - 69 - 17 - - - 1 - 11.927 - 19 - 93.2086 - 1 - 9 - 9 - 17 - 0 - 0 - 4 - 6 - 0 - 9 - LPTPVEPTV - LPSDFFPSV - LP+ P+V - - - - - 5 - gnl|BL_ORD_ID|653 - 38701|core protein|AAL31859.1|Hepatitis B virus|10407 - 653 - 9 - - - 1 - 11.927 - 19 - 107.472 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 6 - 0 - 9 - LPTPVEPTV - LPSDFFPSV - LP+ P+V - - - - - 6 - gnl|BL_ORD_ID|239 - 16832|core protein|BAF42671.1|Hepatitis B virus|10407 - 239 - 10 - - - 1 - 11.5418 - 18 - 119.026 - 1 - 9 - 2 - 10 - 0 - 0 - 3 - 6 - 0 - 9 - LPTPVEPTV - LPSDFFPSI - LP+ P++ - - - - - 7 - gnl|BL_ORD_ID|241 - 16836|precore/core protein [Hepatitis B virus]|AAR03815.1|Hepatitis B virus|10407 - 241 - 10 - - - 1 - 11.5418 - 18 - 124.81 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 6 - 0 - 9 - LPTPVEPTV - LPSDFLPSV - LP+ P+V - - - - - 8 - gnl|BL_ORD_ID|235 - 16814|precore protein|CAM58990.1|Hepatitis B virus|10407 - 235 - 10 - - - 1 - 11.5418 - 18 - 128.811 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 5 - 0 - 9 - LPTPVEPTV - LPNDFFPSV - LP P+V - - - - - 9 - gnl|BL_ORD_ID|233 - 16796|HBcAg|ABE97049.1|Hepatitis B virus|10407 - 233 - 10 - - - 1 - 11.5418 - 18 - 162.878 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 5 - 0 - 9 - LPTPVEPTV - LPADFFPSV - LP P+V - - - - - 10 - gnl|BL_ORD_ID|244 - 16857|pre-c/core|CAA59565.1|Hepatitis B virus|10407 - 244 - 10 - - - 1 - 11.1566 - 17 - 224.873 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 5 - 0 - 9 - LPTPVEPTV - LPVDFFPSV - LP P+V - - - - - 11 - gnl|BL_ORD_ID|232 - 16795|precore/core protein|AAP57273.1|Hepatitis B virus|10407 - 232 - 10 - - - 1 - 11.1566 - 17 - 235.341 - 1 - 9 - 2 - 10 - 0 - 0 - 3 - 5 - 0 - 9 - LPTPVEPTV - LPADFFPSI - LP P++ - - - - - 12 - gnl|BL_ORD_ID|1438 - 120093|unnamed protein product|CAA33016.1|Rubella virus|11041 - 1438 - 21 - - - 1 - 10.7714 - 16 - 331.885 - 2 - 8 - 11 - 17 - 0 - 0 - 4 - 4 - 0 - 7 - PTPVEPT - PPPATPT - P P PT - - - - - 13 - gnl|BL_ORD_ID|243 - 16856|||| - 243 - 10 - - - 1 - 10.7714 - 16 - 336.948 - 1 - 9 - 2 - 10 - 0 - 0 - 3 - 5 - 0 - 9 - LPTPVEPTV - LPVDFFPSI - LP P++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 30 - Query_30 - M_5251 - 9 - - - 1 - gnl|BL_ORD_ID|1020 - 68229|EBNA3B (EBNA4A) latent protein|CAA24858.1|Human gammaherpesvirus 4|10376 - 1020 - 10 - - - 1 - 12.3122 - 20 - 40.5114 - 1 - 6 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - TPVEPT - TPYKPT - TP +PT - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 31 - Query_31 - M_5252 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 32 - Query_32 - M_5253 - 9 - - - 1 - gnl|BL_ORD_ID|588 - 36717|nonstructural protein 4B|YP_001527886.1|West Nile virus NY-99|10000971 - 588 - 18 - - - 1 - 12.6974 - 21 - 25.1685 - 1 - 9 - 2 - 10 - 0 - 0 - 5 - 6 - 0 - 9 - LLAAARPLW - ITAAAVTLW - + AAA LW - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 33 - Query_33 - M_5254 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 34 - Query_34 - M_5255 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 35 - Query_35 - M_5256 - 9 - - - 1 - gnl|BL_ORD_ID|320 - 21000|glutamine synthetase GLNA1 (glutamine synthase) (GS-I)|NP_216736.1|Mycobacterium tuberculosis|1773 - 320 - 9 - - - 1 - 13.4678 - 23 - 8.13377 - 4 - 9 - 4 - 9 - 0 - 0 - 5 - 5 - 0 - 6 - HHFPSL - HHAPSL - HH PSL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 36 - Query_36 - M_5257 - 9 - - - 1 - gnl|BL_ORD_ID|320 - 21000|glutamine synthetase GLNA1 (glutamine synthase) (GS-I)|NP_216736.1|Mycobacterium tuberculosis|1773 - 320 - 9 - - - 1 - 13.4678 - 23 - 8.13377 - 4 - 9 - 4 - 9 - 0 - 0 - 5 - 5 - 0 - 6 - HHFPSL - HHAPSL - HH PSL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 37 - Query_37 - M_5258 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 38 - Query_38 - M_5259 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 39 - Query_39 - M_5260 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_139936_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_139936_1_T.fasta deleted file mode 100755 index 837993b7..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_139936_1_T.fasta +++ /dev/null @@ -1,70 +0,0 @@ ->M_5261 -KPLLSGPWA ->M_5262 -LSMTSITSV ->M_5263 -IDTDQVHTL ->M_5264 -TWKDTPYYI ->M_5265 -KLILTLSAI ->M_5266 -SYQMSNKLI ->M_5267 -YQMSNKLIL ->M_5268 -YQMSNKLIL ->M_5269 -LMWSVTWPK ->M_5270 -SQSETNSAV ->M_5271 -SHASHLHLF ->M_5272 -SHASHLHLF ->M_5273 -KVLISVHLI ->M_5274 -DHYLVDRTL ->M_5275 -YIKPLVPPA ->M_5276 -RPGQSPGQL ->M_5277 -HLFESSQLV ->M_5278 -HLFESSQLV ->M_5279 -GVYLWEDPV ->M_5280 -YLWEDPVCG ->M_5281 -RILYMADEV ->M_5282 -SLLDACLIL ->M_5283 -APLPMPNPL ->M_5284 -LLLWAPLPM ->M_5285 -MQLRKAPNV ->M_5286 -AHACAHALL ->M_5287 -GAHACAHAL ->M_5288 -VLNGWLRSV ->M_5289 -AIDDHVCMA ->M_5290 -LMVPRLEYV ->M_5291 -FINARGRLL ->M_5292 -AIPLRGFPV ->M_5293 -FVDENNEKL ->M_5294 -FVDENNEKL ->M_5295 -HTARLFYFV diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_139936_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_139936_1_T_iedb.xml deleted file mode 100755 index e696aaad..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_139936_1_T_iedb.xml +++ /dev/null @@ -1,1051 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_5261 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_5261 - 9 - - - 1 - gnl|BL_ORD_ID|96 - 6591|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 96 - 18 - - - 1 - 13.853 - 24 - 5.73946 - 1 - 7 - 6 - 12 - 0 - 0 - 5 - 5 - 0 - 7 - KPLLSGP - KPTLHGP - KP L GP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 2 - Query_2 - M_5262 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_5263 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_5264 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_5265 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_5266 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_5267 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_5268 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_5269 - 9 - - - 1 - gnl|BL_ORD_ID|1697 - 149105|E2 protein|NP_751921.1|Hepatitis C virus (isolate H77)|63746 - 1697 - 9 - - - 1 - 11.1566 - 17 - 225.252 - 3 - 7 - 5 - 9 - 0 - 0 - 2 - 4 - 0 - 5 - WSVTW - WAIKW - W++ W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 10 - Query_10 - M_5270 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_5271 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_5272 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_5273 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_5274 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_5275 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_5276 - 9 - - - 1 - gnl|BL_ORD_ID|344 - 21638|protein F|ABV46152.2|Hepatitis C virus (isolate Japanese)|11116 - 344 - 9 - - - 1 - 15.0086 - 27 - 0.92904 - 2 - 9 - 2 - 9 - 0 - 0 - 6 - 6 - 0 - 8 - PGQSPGQL - PGLSPGTL - PG SPG L - - - - - 2 - gnl|BL_ORD_ID|741 - 47760|EBNA-1 protein|Q777E1|Human gammaherpesvirus 4|10376 - 741 - 15 - - - 1 - 12.6974 - 21 - 27.4409 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 4 - 0 - 7 - PGQSPGQ - PGTGPGN - PG PG - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 17 - Query_17 - M_5277 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_5278 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_5279 - 9 - - - 1 - gnl|BL_ORD_ID|525 - 32243|C protein|BAB60863.1|Measles virus|11234 - 525 - 9 - - - 1 - 13.853 - 24 - 6.16125 - 4 - 8 - 2 - 6 - 0 - 0 - 4 - 4 - 0 - 5 - LWEDP - LWESP - LWE P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 20 - Query_20 - M_5280 - 9 - - - 1 - gnl|BL_ORD_ID|525 - 32243|C protein|BAB60863.1|Measles virus|11234 - 525 - 9 - - - 1 - 13.853 - 24 - 6.48995 - 2 - 6 - 2 - 6 - 0 - 0 - 4 - 4 - 0 - 5 - LWEDP - LWESP - LWE P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 21 - Query_21 - M_5281 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 22 - Query_22 - M_5282 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_5283 - 9 - - - 1 - gnl|BL_ORD_ID|1881 - 180531|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1881 - 10 - - - 1 - 12.6974 - 21 - 30.9217 - 3 - 9 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - LPMPNPL - IPMTGPL - +PM PL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 24 - Query_24 - M_5284 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_5285 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_5286 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_5287 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 28 - Query_28 - M_5288 - 9 - - - 1 - gnl|BL_ORD_ID|629 - 37607|kaposin|AAC57155.1|Human gammaherpesvirus 8|37296 - 629 - 9 - - - 1 - 13.4678 - 23 - 10.7466 - 1 - 5 - 1 - 5 - 0 - 0 - 4 - 5 - 0 - 5 - VLNGW - LLNGW - +LNGW - - - - - 2 - gnl|BL_ORD_ID|2011 - 183800|polyprotein|AGT63075.1|Dengue virus 1|11053 - 2011 - 9 - - - 1 - 11.927 - 19 - 78.9234 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 6 - 0 - 9 - VLNGWLRSV - IMNRRKRSV - ++N RSV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 29 - Query_29 - M_5289 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 30 - Query_30 - M_5290 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 31 - Query_31 - M_5291 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 32 - Query_32 - M_5292 - 9 - - - 1 - gnl|BL_ORD_ID|396 - 24302|X protein|AAP06597.1|Hepatitis B virus|10407 - 396 - 9 - - - 1 - 15.0086 - 27 - 1.17789 - 2 - 9 - 2 - 9 - 0 - 0 - 5 - 6 - 0 - 8 - IPLRGFPV - LSLRGLPV - + LRG PV - - - - - 2 - gnl|BL_ORD_ID|378 - 23365|polyprotein|BAB18806.1|Hepatitis C virus|11103 - 378 - 10 - - - 1 - 12.6974 - 21 - 22.7423 - 2 - 9 - 3 - 10 - 0 - 0 - 5 - 6 - 0 - 8 - IPLRGFPV - IPLVGAPL - IPL G P+ - - - - - 3 - gnl|BL_ORD_ID|296 - 19493|polyprotein|BAA03375.1|Hepatitis C virus|11103 - 296 - 15 - - - 1 - 12.6974 - 21 - 31.7906 - 2 - 8 - 9 - 15 - 0 - 0 - 5 - 5 - 0 - 7 - IPLRGFP - IPLVGAP - IPL G P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 33 - Query_33 - M_5293 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 34 - Query_34 - M_5294 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 35 - Query_35 - M_5295 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_140531_2_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_140531_2_T.fasta deleted file mode 100755 index 1a080f0a..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_140531_2_T.fasta +++ /dev/null @@ -1,52 +0,0 @@ ->M_5296 -LPSTAGPEM ->M_5297 -LPSTAGPEM ->M_5298 -TAANGSEVM ->M_5299 -TAANGSEVM ->M_5300 -MADATFQSL ->M_5301 -MADATFQSL ->M_5302 -WFNMADATF ->M_5303 -ICIWNVSKL ->M_5304 -EPTITDASL ->M_5305 -IFDEWLKRF ->M_5306 -FTGGIVNKL ->M_5307 -GIVNKLCAL ->M_5308 -FGSLLGTCL ->M_5309 -ISGPRSPTY ->M_5310 -MSLNSYIKL ->M_5311 -YMVIMSPRL ->M_5312 -EILWTTELY ->M_5313 -LEILWTTEL ->M_5314 -LGTSDVRIL ->M_5315 -VAFLGTSDV ->M_5316 -IMIAVVDSM ->M_5317 -IMIAVVDSM ->M_5318 -EASVHSVPI ->M_5319 -FFSSNLPTY ->M_5320 -FSSNLPTYY ->M_5321 -VALVPESSV diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_140531_2_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_140531_2_T_iedb.xml deleted file mode 100755 index 20155b14..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_140531_2_T_iedb.xml +++ /dev/null @@ -1,874 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_5296 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_5296 - 9 - - - 1 - gnl|BL_ORD_ID|707 - 43447|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 - 707 - 20 - - - 1 - 14.2382 - 25 - 2.73772 - 1 - 7 - 14 - 20 - 0 - 0 - 5 - 5 - 0 - 7 - LPSTAGP - LPEAAGP - LP AGP - - - - - 2 - gnl|BL_ORD_ID|285 - 19348|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 - 285 - 20 - - - 1 - 14.2382 - 25 - 3.42196 - 1 - 7 - 4 - 10 - 0 - 0 - 5 - 5 - 0 - 7 - LPSTAGP - LPEAAGP - LP AGP - - - - - 3 - gnl|BL_ORD_ID|993 - 65550|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 993 - 15 - - - 1 - 11.5418 - 18 - 141.75 - 1 - 8 - 6 - 13 - 0 - 0 - 4 - 5 - 0 - 8 - LPSTAGPE - IPSMFEPE - +PS PE - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 2 - Query_2 - M_5297 - 9 - - - 1 - gnl|BL_ORD_ID|707 - 43447|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 - 707 - 20 - - - 1 - 14.2382 - 25 - 2.73772 - 1 - 7 - 14 - 20 - 0 - 0 - 5 - 5 - 0 - 7 - LPSTAGP - LPEAAGP - LP AGP - - - - - 2 - gnl|BL_ORD_ID|285 - 19348|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 - 285 - 20 - - - 1 - 14.2382 - 25 - 3.42196 - 1 - 7 - 4 - 10 - 0 - 0 - 5 - 5 - 0 - 7 - LPSTAGP - LPEAAGP - LP AGP - - - - - 3 - gnl|BL_ORD_ID|993 - 65550|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 993 - 15 - - - 1 - 11.5418 - 18 - 141.75 - 1 - 8 - 6 - 13 - 0 - 0 - 4 - 5 - 0 - 8 - LPSTAGPE - IPSMFEPE - +PS PE - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 3 - Query_3 - M_5298 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_5299 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_5300 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_5301 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_5302 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_5303 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_5304 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_5305 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_5306 - 9 - - - 1 - gnl|BL_ORD_ID|1510 - 139747|granule antigen protein GRA6|XP_002371939.1|Toxoplasma gondii ME49|508771 - 1510 - 9 - - - 1 - 13.4678 - 23 - 10.9354 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 6 - 0 - 9 - FTGGIVNKL - FMGVLVNSL - F G +VN L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 12 - Query_12 - M_5307 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_5308 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_5309 - 9 - - - 1 - gnl|BL_ORD_ID|1006 - 66195|Nucleoprotein|P41269.1|Puumala hantavirus|11604 - 1006 - 15 - - - 1 - 13.0826 - 22 - 16.1221 - 1 - 9 - 6 - 14 - 0 - 0 - 4 - 6 - 0 - 9 - ISGPRSPTY - INGIRRPKH - I+G R P + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 15 - Query_15 - M_5310 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_5311 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_5312 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_5313 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_5314 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_5315 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_5316 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 22 - Query_22 - M_5317 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_5318 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_5319 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_5320 - 9 - - - 1 - gnl|BL_ORD_ID|471 - 28594|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 - 471 - 20 - - - 1 - 13.4678 - 23 - 8.80594 - 4 - 9 - 2 - 7 - 0 - 0 - 4 - 6 - 0 - 6 - NLPTYY - SLPSYY - +LP+YY - - - - - 2 - gnl|BL_ORD_ID|1971 - 182926|polyprotein|AFP27208.1|Dengue virus 4|11070 - 1971 - 9 - - - 1 - 13.4678 - 23 - 9.18751 - 3 - 8 - 3 - 8 - 0 - 0 - 4 - 6 - 0 - 6 - SNLPTY - ASLPTY - ++LPTY - - - - - 3 - gnl|BL_ORD_ID|2100 - 185881|polyprotein|AFP27208.1|Dengue virus 4|11070 - 2100 - 10 - - - 1 - 13.4678 - 23 - 9.73455 - 3 - 8 - 4 - 9 - 0 - 0 - 4 - 6 - 0 - 6 - SNLPTY - ASLPTY - ++LPTY - - - - - 4 - gnl|BL_ORD_ID|776 - 51643|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 - 776 - 20 - - - 1 - 13.4678 - 23 - 10.5613 - 5 - 9 - 13 - 17 - 0 - 0 - 4 - 5 - 0 - 5 - LPTYY - LPSYY - LP+YY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 26 - Query_26 - M_5321 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_141002_2_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_141002_2_T.fasta deleted file mode 100755 index 77f5f7f7..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_141002_2_T.fasta +++ /dev/null @@ -1,62 +0,0 @@ ->M_5322 -ISRNHNSRM ->M_5323 -KTFGISRNH ->M_5324 -RNHNSRMNK ->M_5325 -LTDLQGVIV ->M_5326 -IRHEMSTFA ->M_5327 -VVSDSWGSK ->M_5328 -IRAANVSAL ->M_5329 -IRAANVSAL ->M_5330 -RAANVSALY ->M_5331 -GYRERGHPY ->M_5332 -VVGAVGVGK ->M_5333 -LTNTLTTSK ->M_5334 -AAASTSSPK ->M_5335 -TSITTSTQK ->M_5336 -SHPGSAEIV ->M_5337 -SYYSCVAAM ->M_5338 -SYYSCVAAM ->M_5339 -AHTFKQRRI ->M_5340 -HTFKQRRIK ->M_5341 -RYEEYRGRF ->M_5342 -YEEYRGRFL ->M_5343 -MTTGSVFFY ->M_5344 -MTTGSVFFY ->M_5345 -HVLSLAETK ->M_5346 -SLAETKTLY ->M_5347 -KLKTVSQTK ->M_5348 -ASYDQSLRV ->M_5349 -FSASYDQSL ->M_5350 -HLKEPLQKL ->M_5351 -HLYEQGGHL ->M_5352 -HQCVHTGAK diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_141002_2_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_141002_2_T_iedb.xml deleted file mode 100755 index 41672e73..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_141002_2_T_iedb.xml +++ /dev/null @@ -1,697 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_5322 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_5322 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_5323 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_5324 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_5325 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_5326 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_5327 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_5328 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_5329 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_5330 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_5331 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_5332 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_5333 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_5334 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_5335 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_5336 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_5337 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_5338 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_5339 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_5340 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_5341 - 9 - - - 1 - gnl|BL_ORD_ID|376 - 23288|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 - 376 - 15 - - - 1 - 13.0826 - 22 - 12.7259 - 2 - 9 - 7 - 14 - 0 - 0 - 3 - 6 - 0 - 8 - YEEYRGRF - YQDWLGRM - Y+++ GR - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 21 - Query_21 - M_5342 - 9 - - - 1 - gnl|BL_ORD_ID|376 - 23288|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 - 376 - 15 - - - 1 - 13.0826 - 22 - 15.0718 - 1 - 8 - 7 - 14 - 0 - 0 - 3 - 6 - 0 - 8 - YEEYRGRF - YQDWLGRM - Y+++ GR - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 22 - Query_22 - M_5343 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_5344 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_5345 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_5346 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_5347 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_5348 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 28 - Query_28 - M_5349 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 29 - Query_29 - M_5350 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 30 - Query_30 - M_5351 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 31 - Query_31 - M_5352 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_141146_2_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_141146_2_T.fasta deleted file mode 100755 index 93f95ae9..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_141146_2_T.fasta +++ /dev/null @@ -1,76 +0,0 @@ ->M_5353 -IAHAWWACF ->M_5354 -AMWNRCADL ->M_5355 -AYTFWTYIM ->M_5356 -IMNARSKNV ->M_5357 -YAYTFWTYI ->M_5358 -YAYTFWTYI ->M_5359 -KAARIAAKV ->M_5360 -KVGQSSMWI ->M_5361 -PSTSTSRPV ->M_5362 -CLAAMALSI ->M_5363 -WLTPVIPTL ->M_5364 -GLFHCTRSV ->M_5365 -RNWDVCKVI ->M_5366 -KIPIRLPPV ->M_5367 -FMLGITPNL ->M_5368 -HRHHHRCRR ->M_5369 -FLAGSSLPV ->M_5370 -FLAGSSLPV ->M_5371 -SSFLAGSSL ->M_5372 -KLPSDPDAL ->M_5373 -VYAVTVVTL ->M_5374 -YAVTVVTLL ->M_5375 -YAVTVVTLL ->M_5376 -FILICCLII ->M_5377 -ILICCLIIL ->M_5378 -LIILENIFV ->M_5379 -VFILICCLI ->M_5380 -PAMKFSCSL ->M_5381 -FLSLIIDAT ->M_5382 -LIIDATKFI ->M_5383 -LIIDATKFI ->M_5384 -IMMSSEDDI ->M_5385 -YLDGQPQEA ->M_5386 -GLAPPQLLI ->M_5387 -ARIERPHNY ->M_5388 -FTSSEPSRM ->M_5389 -ESEGHTIEL ->M_5390 -KMQEGLLAV diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_141146_2_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_141146_2_T_iedb.xml deleted file mode 100755 index 0bb39458..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_141146_2_T_iedb.xml +++ /dev/null @@ -1,1557 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_5353 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_5353 - 9 - - - 1 - gnl|BL_ORD_ID|1556 - 141262|DNA polymerase catalytic subunit|NP_044632.1|Human alphaherpesvirus 1|10298 - 1556 - 10 - - - 1 - 13.853 - 24 - 4.45544 - 3 - 9 - 4 - 10 - 0 - 0 - 5 - 5 - 0 - 7 - HAWWACF - HARWAAF - HA WA F - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 2 - Query_2 - M_5354 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_5355 - 9 - - - 1 - gnl|BL_ORD_ID|1502 - 137660|L1|ACL12325.1|Human papillomavirus type 58|10598 - 1502 - 9 - - - 1 - 13.853 - 24 - 7.07804 - 1 - 5 - 1 - 5 - 0 - 0 - 4 - 4 - 0 - 5 - AYTFW - KYTFW - YTFW - - - - - 2 - gnl|BL_ORD_ID|81 - 5938|EBNA3A nuclear protein|Q8AZJ8|Human gammaherpesvirus 4|10376 - 81 - 9 - - - 1 - 12.6974 - 21 - 39.8499 - 1 - 7 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - AYTFWTY - AYSSWMY - AY+ W Y - - - - - 3 - gnl|BL_ORD_ID|578 - 36357|ELAV-like protein 4 (Paraneoplastic encephalomyelitis antigen HuD) (Hu-antigen D)|P26378.1|Homo sapiens|9606 - 578 - 9 - - - 1 - 12.3122 - 20 - 57.6592 - 1 - 8 - 2 - 9 - 0 - 0 - 4 - 4 - 0 - 8 - AYTFWTYI - GYGFVNYI - Y F YI - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 4 - Query_4 - M_5356 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_5357 - 9 - - - 1 - gnl|BL_ORD_ID|1502 - 137660|L1|ACL12325.1|Human papillomavirus type 58|10598 - 1502 - 9 - - - 1 - 13.4678 - 23 - 10.0233 - 2 - 6 - 1 - 5 - 0 - 0 - 4 - 4 - 0 - 5 - AYTFW - KYTFW - YTFW - - - - - 2 - gnl|BL_ORD_ID|147 - 10939|polyprotein|BAB18806.1|Hepatitis C virus subtype 1a|31646 - 147 - 9 - - - 1 - 13.0826 - 22 - 18.7436 - 1 - 8 - 2 - 9 - 0 - 0 - 4 - 4 - 0 - 8 - YAYTFWTY - YPYRLWHY - Y Y W Y - - - - - 3 - gnl|BL_ORD_ID|1145 - 75448|polyprotein|BAB18806.1|Hepatitis C virus|11103 - 1145 - 8 - - - 1 - 13.0826 - 22 - 22.4497 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 4 - 0 - 8 - YAYTFWTY - YPYRLWHY - Y Y W Y - - - - - 4 - gnl|BL_ORD_ID|81 - 5938|EBNA3A nuclear protein|Q8AZJ8|Human gammaherpesvirus 4|10376 - 81 - 9 - - - 1 - 12.6974 - 21 - 36.611 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - AYTFWTY - AYSSWMY - AY+ W Y - - - - - 5 - gnl|BL_ORD_ID|578 - 36357|ELAV-like protein 4 (Paraneoplastic encephalomyelitis antigen HuD) (Hu-antigen D)|P26378.1|Homo sapiens|9606 - 578 - 9 - - - 1 - 11.927 - 19 - 78.9234 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 4 - 0 - 8 - AYTFWTYI - GYGFVNYI - Y F YI - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 6 - Query_6 - M_5358 - 9 - - - 1 - gnl|BL_ORD_ID|1502 - 137660|L1|ACL12325.1|Human papillomavirus type 58|10598 - 1502 - 9 - - - 1 - 13.4678 - 23 - 10.0233 - 2 - 6 - 1 - 5 - 0 - 0 - 4 - 4 - 0 - 5 - AYTFW - KYTFW - YTFW - - - - - 2 - gnl|BL_ORD_ID|147 - 10939|polyprotein|BAB18806.1|Hepatitis C virus subtype 1a|31646 - 147 - 9 - - - 1 - 13.0826 - 22 - 18.7436 - 1 - 8 - 2 - 9 - 0 - 0 - 4 - 4 - 0 - 8 - YAYTFWTY - YPYRLWHY - Y Y W Y - - - - - 3 - gnl|BL_ORD_ID|1145 - 75448|polyprotein|BAB18806.1|Hepatitis C virus|11103 - 1145 - 8 - - - 1 - 13.0826 - 22 - 22.4497 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 4 - 0 - 8 - YAYTFWTY - YPYRLWHY - Y Y W Y - - - - - 4 - gnl|BL_ORD_ID|81 - 5938|EBNA3A nuclear protein|Q8AZJ8|Human gammaherpesvirus 4|10376 - 81 - 9 - - - 1 - 12.6974 - 21 - 36.611 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - AYTFWTY - AYSSWMY - AY+ W Y - - - - - 5 - gnl|BL_ORD_ID|578 - 36357|ELAV-like protein 4 (Paraneoplastic encephalomyelitis antigen HuD) (Hu-antigen D)|P26378.1|Homo sapiens|9606 - 578 - 9 - - - 1 - 11.927 - 19 - 78.9234 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 4 - 0 - 8 - AYTFWTYI - GYGFVNYI - Y F YI - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 7 - Query_7 - M_5359 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_5360 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_5361 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_5362 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_5363 - 9 - - - 1 - gnl|BL_ORD_ID|948 - 62477|HBsAg protein|ABF71024.1|Hepatitis B virus|10407 - 948 - 9 - - - 1 - 12.3122 - 20 - 48.7826 - 1 - 7 - 2 - 8 - 0 - 0 - 3 - 6 - 0 - 7 - WLTPVIP - WLSLLVP - WL+ ++P - - - - - 2 - gnl|BL_ORD_ID|1104 - 72794|Large envelope protein|P03138.3|Hepatitis B virus|10407 - 1104 - 9 - - - 1 - 12.3122 - 20 - 56.7066 - 1 - 7 - 1 - 7 - 0 - 0 - 3 - 6 - 0 - 7 - WLTPVIP - WLSLLVP - WL+ ++P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 12 - Query_12 - M_5364 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_5365 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_5366 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_5367 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_5368 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_5369 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_5370 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_5371 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_5372 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_5373 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 22 - Query_22 - M_5374 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_5375 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_5376 - 9 - - - 1 - gnl|BL_ORD_ID|156 - 11956|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 - 156 - 11 - - - 1 - 10.7714 - 16 - 322.541 - 3 - 9 - 5 - 11 - 0 - 0 - 2 - 6 - 0 - 7 - LICCLII - VLCCYVL - ++CC ++ - - - - - 2 - gnl|BL_ORD_ID|1499 - 137656|E6 protein|ACT36477.1|Human papillomavirus type 58|10598 - 1499 - 9 - - - 1 - 10.3862 - 15 - 519.728 - 2 - 8 - 1 - 7 - 0 - 0 - 5 - 6 - 0 - 7 - ILICCLI - ILIRCII - ILI C+I - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 25 - Query_25 - M_5377 - 9 - - - 1 - gnl|BL_ORD_ID|156 - 11956|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 - 156 - 11 - - - 1 - 10.7714 - 16 - 341.939 - 2 - 8 - 5 - 11 - 0 - 0 - 2 - 6 - 0 - 7 - LICCLII - VLCCYVL - ++CC ++ - - - - - 2 - gnl|BL_ORD_ID|1499 - 137656|E6 protein|ACT36477.1|Human papillomavirus type 58|10598 - 1499 - 9 - - - 1 - 10.3862 - 15 - 600.299 - 1 - 7 - 1 - 7 - 0 - 0 - 5 - 6 - 0 - 7 - ILICCLI - ILIRCII - ILI C+I - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 26 - Query_26 - M_5378 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_5379 - 9 - - - 1 - gnl|BL_ORD_ID|1499 - 137656|E6 protein|ACT36477.1|Human papillomavirus type 58|10598 - 1499 - 9 - - - 1 - 10.7714 - 16 - 462.613 - 3 - 9 - 1 - 7 - 0 - 0 - 5 - 6 - 0 - 7 - ILICCLI - ILIRCII - ILI C+I - - - - - 2 - gnl|BL_ORD_ID|156 - 11956|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 - 156 - 11 - - - 1 - 10.3862 - 15 - 596.566 - 4 - 9 - 5 - 10 - 0 - 0 - 2 - 5 - 0 - 6 - LICCLI - VLCCYV - ++CC + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 28 - Query_28 - M_5380 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 29 - Query_29 - M_5381 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 30 - Query_30 - M_5382 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 31 - Query_31 - M_5383 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 32 - Query_32 - M_5384 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 33 - Query_33 - M_5385 - 9 - - - 1 - gnl|BL_ORD_ID|1387 - 110227|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1387 - 33 - - - 1 - 14.2382 - 25 - 3.73557 - 1 - 6 - 8 - 13 - 0 - 0 - 4 - 4 - 0 - 6 - YLDGQP - YRDGNP - Y DG P - - - - - 2 - gnl|BL_ORD_ID|1400 - 110467|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1400 - 25 - - - 1 - 13.853 - 24 - 7.91622 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 4 - 0 - 6 - YLDGQP - YRDGNP - Y DG P - - - - - 3 - gnl|BL_ORD_ID|1397 - 110401|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1397 - 25 - - - 1 - 13.4678 - 23 - 8.70865 - 1 - 6 - 16 - 21 - 0 - 0 - 4 - 4 - 0 - 6 - YLDGQP - YRDGNP - Y DG P - - - - - 4 - gnl|BL_ORD_ID|1821 - 178185|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1821 - 15 - - - 1 - 13.4678 - 23 - 10.5523 - 1 - 6 - 9 - 14 - 0 - 0 - 4 - 4 - 0 - 6 - YLDGQP - YRDGNP - Y DG P - - - - - 5 - gnl|BL_ORD_ID|1059 - 69798|Lipoprotein lpqH precursor|P0A5J0.1|Mycobacterium tuberculosis|1773 - 1059 - 10 - - - 1 - 13.4678 - 23 - 12.6375 - 3 - 9 - 4 - 10 - 0 - 0 - 4 - 4 - 0 - 7 - DGQPQEA - DGNPPEV - DG P E - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 34 - Query_34 - M_5386 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 35 - Query_35 - M_5387 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 36 - Query_36 - M_5388 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 37 - Query_37 - M_5389 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 38 - Query_38 - M_5390 - 9 - - - 1 - gnl|BL_ORD_ID|777 - 51685|Nuclear antigen EBNA-3C|Q69140.1|Human gammaherpesvirus 4|10376 - 777 - 10 - - - 1 - 12.6974 - 21 - 30.4011 - 3 - 9 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - QEGLLAV - QNGALAI - Q G LA+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/data/.DS_Store b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/data/.DS_Store deleted file mode 100755 index 5008ddfcf53c02e82d7eee2e57c38e5672ef89f6..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 6148 zcmeH~Jr2S!425mzP>H1@V-^m;4Wg<&0T*E43hX&L&p$$qDprKhvt+--jT7}7np#A3 zem<@ulZcFPQ@L2!n>{z**++&mCkOWA81W14cNZlEfg7;MkzE(HCqgga^y>{tEnwC%0;vJ&^%eQ zLs35+`xjp>T046|hypothetical protein ML1057|NP_301777.1|Mycobacterium leprae|1769 -AAALEQLLGQTADVA ->118|envelope glycoprotein|ABS76372.1|Human immunodeficiency virus 1|11676 -AAEQLWVTVYYGVPVWKEAT ->140|Accessory protein p30II|SRC276210|Human T-lymphotropic virus 1|11908 -AAFSSARFL ->194|Hypothetical protein esxG (PE family protein)|O53692.1|Mycobacterium tuberculosis|1773 -AAHARFVAA ->327|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis|1773 -AANKQKQELDEISTNIRQAG ->420|Genome polyprotein|P26664.3|Hepatitis C virus genotype 1|41856 -AARVTAIL ->449|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 -AASTLLYATV ->465|polyprotein|BAA09072.1|Hepatitis C virus|11103 -AATLGFGAYMSKAHG ->716|polyprotein|BAB18806.1|Hepatitis C virus subtype 1a|31646 -ADLMGYIPLV ->790|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 -ADVKKDLISYGGGWK ->1000|glycoprotein gp35/37|AAC59622.1|Human gammaherpesvirus 8|37296 -AEIRTHLYILWAVGL ->1078|10 kda culture filtrate antigen esxB (cfp10)|ZP_04982462.1|Mycobacterium tuberculosis|1773 -AEMKTDAA ->1079|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis H37Rv|83332 -AEMKTDAATL ->1080|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis H37Rv|83332 -AEMKTDAATLA ->1090|Transcription activator BRLF1|P03209.1|Human herpesvirus 4 strain B95-8|10377 -AENAGNDAC ->1095|glycoprotein gp35/37|AAC59622.1|Human gammaherpesvirus 8|37296 -AENGRNSGASNRVPF ->1129|gag protein|AAV53342.1|Human immunodeficiency virus 1|11676 -AEQASQDVKNW ->1154|RL2|NP_044469.1|Human herpesvirus 2 strain HG52|10315 -AERQGSPTPA ->1211|polyprotein precursor|NP_041724.2|West Nile virus|11082 -AEVEEHRTV ->1226|Polyprotein|Q9IZA3|Hepatitis C virus|11103 -AEVTQHGSY ->1230|gag protein|AAW03034.1|Human immunodeficiency virus 1|11676 -AEWDRVHPV ->1356|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 -AFLTNVPYKRIEELL ->1421|polyprotein|BAD73991.1|Hepatitis C virus subtype 1b|31647 -AFYGVWPLL ->1516|Nucleoprotein|P03418.1|Human respiratory syncytial virus A2|11259 -AGFYHILNNPKASL ->1658|Nucleoprotein|P03418.1|Human respiratory syncytial virus A2|11259 -AGQVMLRWGVLAKS ->1994|structural protein|BAA00705.1|Hepatitis C virus subtype 1a|31646 -AILHTPGCV ->2002|Large envelope protein|SRC279965|Hepatitis B virus|10407 -AILSKTGDPV ->2033|polyprotein|BAA32665.1|Hepatitis C virus genotype 6|42182 -AINGVMWTV ->2058|6 kDa early secretory antigenic target|P0A564.2|Mycobacterium tuberculosis|1773 -AIQGNVTSI ->2102|VP1|BAF93325.1|Human polyomavirus 1|1891762 -AITEVECFL ->2154|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 -AKARAKKDELR ->2244|polyprotein|NP_671491.1|Hepatitis C virus|11103 -AKLVALGINAVAYYR ->2387|Genome polyprotein|O39929.3|Hepatitis C virus|11103 -ALAHGVRAL ->2506|M protein, serotype 5 precursor|P02977.2|Streptococcus pyogenes serotype M5|301449 -ALEKLNKEL ->2527|Circumsporozoite protein-related antigen precursor|P04923.2|Plasmodium falciparum|5833 -ALFFIIFNK ->2556|PE_PGRS 33|AAU10330.1|Mycobacterium tuberculosis|1773 -ALGGGATGV ->2758|pol protein|BAA32832.1|Hepatitis B virus|10407 -ALMPLYACI ->2860|polyprotein|AAU89634.1|Hepatitis C virus|11103 -ALRGMGLNA ->2861|Genome polyprotein|P26661.3|Hepatitis C virus isolate HC-J8|11115 -ALRGMGVNAV ->2883|cysteine proteinase cruzipain (EC 3.4.22.-) - Trypanosoma cruzi|A45629|Trypanosoma cruzi|5693 -ALSLAAVLV ->2884|cysteine proteinase cruzipain (EC 3.4.22.-) - Trypanosoma cruzi|A45629|Trypanosoma cruzi|5693 -ALSLAAVLVV ->2903|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 -ALSTGLIHLHQNIVD ->2957|||| -ALVFPSHHH ->3017|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 -ALYDVVSKL ->3018|polyprotein|BAA25076.1|Hepatitis C virus (isolate H77)|63746 -ALYDVVSTL ->3019|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 -ALYDVVTKL ->3024|precursor protein|AAB02126.1|Hepatitis C virus (isolate H77)|63746 -ALYEVVSKL ->3026|polyprotein|CAB53095.1|Hepatitis C virus subtype 1b|31647 -ALYGVWPLL ->3051|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 -AMAALQNLPQCSPDEIMAYA ->3064|6 kDa early secretory antigenic target|P0A564.2|Mycobacterium tuberculosis|1773 -AMASTEGNV ->3094|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 -AMGDAGGYK ->3587|protein F [Hepatitis C virus subtype 1b]|ACA50643.1|Hepatitis C virus (isolate Japanese)|11116 -APGWVCARL ->3889|||| -APVFPSHHP ->3935|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis|1773 -AQAAVVRFQEAANKQKQELD ->4002|PPE family protein|YP_177918.1|Mycobacterium tuberculosis H37Rv|83332 -AQLLTEFAI ->4156|polyprotein|ABR25251.1|Hepatitis C virus|11103 -ARHTPVNSW ->4169|PqqC-like protein|O84616.1|Chlamydia trachomatis|813 -ARKLLLDNL ->4172|Glycoprotein I precursor (Glycoprotein IV) (GI) (GPIV)|P09258.1|Human alphaherpesvirus 3|10335 -ARLCDLPATPK ->4197|polyprotein|ACB87119.1|Hepatitis C virus subtype 1a|31646 -ARMILMTHF ->4236|polyprotein|BAA03375.1|Hepatitis C virus|11103 -ARRGREILL ->4289|Major DNA-binding protein|P03227.1|Human herpesvirus 4 strain B95-8|10377 -ARYAYYLQF ->4371|tegument protein VP11/12|NP_044516.1|Human alphaherpesvirus 2|10310 -ASDSLNNEY ->4668|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 -ASPKGPVIQMYTNVD ->4682|LOW MOLECULAR WEIGHT T-CELL ANTIGEN TB8.4 (Hypothetical protein)|O50430|Mycobacterium tuberculosis H37Rv|83332 -ASPVAQSYL ->4735|polyprotein|AAY82034.1|Hepatitis C virus|11103 -ASRCWVAM ->4909|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 -ATCINGVCWTVYHGA ->4910|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 -ATCINGVCWTVYHGAGTRTI ->4916|NS3|AAU44857.1|Hepatitis C virus|11103 -ATDALMTGF ->4917|Genome polyprotein|P26664.3|Hepatitis C virus genotype 1|41856 -ATDALMTGY ->5191|core protein|AAL31859.1|Hepatitis B virus|10407 -ATVELLSFLPSDFFPSV ->5196|60 kDa chaperonin 2|P0A520.2|Mycobacterium tuberculosis|1773 -ATVLAQALVREGLRN ->5213|nonstructural protein 5|YP_001527887.1|West Nile virus NY-99|10000971 -ATWAENIQV ->5295|nef protein|ACR27174.1|Human immunodeficiency virus 1|11676 -AVDLSHFLK ->5316|EBNA-3B nuclear protein|CAD53420.1|Human gammaherpesvirus 4|10376 -AVFDRKSDAK ->5381|LOW MOLECULAR WEIGHT T-CELL ANTIGEN TB8.4 (Hypothetical protein)|O50430|Mycobacterium tuberculosis|1773 -AVINTTCNYGQ ->5542|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 -AVSLDFSPGTSGSPI ->5623|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 -AVYLLDGLR ->5714|Genome polyprotein|P26662.3|Hepatitis C virus|11103 -AYAAQGYKVL ->5727|Polyprotein|Q9IZA3|Hepatitis C virus subtype 2a|31649 -AYAMRVPEVI ->5783|Nucleoprotein|P03418.1|Human respiratory syncytial virus A2|11259 -AYGAGQVMLRWGVL ->5934|polyprotein|CAB53095.1|Hepatitis C virus subtype 1b|31647 -AYSQQTRGL ->5938|EBNA3A nuclear protein|Q8AZJ8|Human gammaherpesvirus 4|10376 -AYSSWMYSY ->5952|PPE family protein|YP_177918.1|Mycobacterium tuberculosis H37Rv|83332 -AYVPYVAWL ->6094|Genome polyprotein|Q81495.3|Hepatitis C virus (isolate HCV-K3a/650)|356416 -CDDCHAQDATSILGI ->6308|HCV-1|AAA45676.1|Hepatitis C virus genotype 1|41856 -CGKYLFNWAVRTKLKLTPIA ->6372|Genome polyprotein|SRC279960|Hepatitis C virus|11103 -CHAQDATSVL ->6373|Genome polyprotein|SRC279960|Hepatitis C virus subtype 3a|356426 -CHAQDATTVL ->6430|polyprotein|BAB18810.1|Hepatitis C virus genotype 1|41856 -CINGACWTV ->6431|Genome polyprotein|SRC279960|Hepatitis C virus|11103 -CINGCVWTV ->6432|polyprotein [Hepatitis C virus]|CAL46125.1|Hepatitis C virus (isolate H77)|63746 -CINGLCWTV ->6433|Genome polyprotein|SRC279960|Hepatitis C virus subtype 1a|31646 -CINGVCWTA ->6435|polyprotein|BAB18806.1|Hepatitis C virus|11103 -CINGVCWTV ->6437|Genome polyprotein|SRC279960|Hepatitis C virus|11103 -CINGVWCTV ->6511|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 -CKPLLREEVSFRVGL ->6556|X protein|AAP06597.1|Hepatitis B virus|10407 -CLFKDWEEL ->6568|latent membrane protein 2|AAB59844.1|Human gammaherpesvirus 4|10376 -CLGGLLTMV ->6591|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 -CLIRLKPTLHGPTPLLYR ->6631|core protein|AAL31859.1|Hepatitis B virus|10407 -CLTFGRETV ->6636|polyprotein|ABU97067.1|Hepatitis C virus subtype 1b|31647 -CLVDYPYRL ->6808|membrane protein|AAA45887.1|Human gammaherpesvirus 4|10376 -CPLSKILL ->6817|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 -CPNSSIVY ->6889|Agglutinin isolectin 1 precursor|P10968.2|Triticum aestivum|4565 -CQNGACWTS ->6901|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 -CQTYKWETF ->6936|Genome polyprotein|P26664.3|Hepatitis C virus (isolate 1)|11104 -CRPLTDFDQGW ->7116|NS3|ABN45875.1|Hepatitis C virus (isolate H77)|63746 -CTCGSSDLY ->7270|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -CVIGGAGNNT ->7291|neuramindase|AAT73327.1|Influenza A virus (A/Puerto Rico/8/1934(H1N1))|211044 -CVNGSCFTV ->7292|polyprotein|AAA75355.1|Hepatitis C virus subtype 1b|31647 -CVNGVCWTV ->7338|nonstructural protein 4A|YP_001527885.1|West Nile virus NY-99|10000971 -CWMAEVPGTKIAGMLLL ->7353|Early antigen protein D|P03191.1|Human herpesvirus 4 strain B95-8|10377 -CYDHAQTHL ->7436|Genome polyprotein|P26663.3|Hepatitis C virus|11103 -CYSIEPLDL ->7447|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 -CYVLEETSVML ->7481|Major outer membrane porin, serovar E precursor|P17451.1|Chlamydia trachomatis|813 -DADKYAVTV ->7538|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 -DAIDESGSGEEERPV ->7660|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 -DAVILLMCAVHPTLVFDITK ->7708|gag polyprotein|BAA00992.1|Human immunodeficiency virus 1|11676 -DCKTILKAL ->7999|core protein|BAA82580.1|Hepatitis C virus|11103 -DEGLGWAGW ->8052|polyprotein|NP_671491.1|Hepatitis C virus|11103 -DELAAKLVALGINAV ->8064|circumsporozoite protein|AAN87606.1|Plasmodium falciparum|5833 -DELDYENDIEKKICKMEKCS ->8191|Transcriptional regulator IE63 homolog|Q04360.1|Human herpesvirus 4 strain B95-8|10377 -DEVEFLGHY ->8236|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 -DFAQGWGPISYANGS ->8285|Genome polyprotein|P26662.3|Hepatitis C virus|11103 -DFKTWLQSKL ->8293|Polyprotein|Q9IZA3|Hepatitis C virus subtype 2a|31649 -DFNASTDLL ->8554|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 -DHMSIYKFMGRSHFLCTFTF ->8685|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 -DIKVQFQSG ->8910|Polyprotein|Q9J8D4|Dengue virus 2|11060 -DKKGKVVGL ->8920|M protein, serotype 5 precursor|P02977.2|Streptococcus pyogenes serotype M5|301449 -DKLAKEQKSKQNIGALKQ ->9114|Genome polyprotein|SRC279960|Hepatitis C virus subtype 1a|31646 -DLIAQPIRLL ->9199|E1 protein|ABB77003.1|Hepatitis C virus|11103 -DLMGYIPAV ->9203|polyprotein|BAA03375.1|Hepatitis C virus|11103 -DLMGYIPLV ->9209|polyprotein|CAB53095.1|Hepatitis C virus|11103 -DLMGYLPLV ->9316|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 -DLVGWPAPQGSRSLT ->9414|Superoxide dismutase|P17670.1|Mycobacterium tuberculosis|1773 -DMWEHAFYL ->9415|Superoxide dismutase|P17670.1|Mycobacterium tuberculosis|1773 -DMWEHAFYLQ ->9461|non structural protein 3|CAJ20172.1|Hepatitis C virus|11103 -DNFPYLVAY ->9746|Genome polyprotein|P29846.3|Hepatitis C virus genotype 1|41856 -DPRRRSRNL ->9920|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis|1773 -DQVESTAGSLQGQWRGAA ->9974|gag polyprotein|BAA00992.1|Human immunodeficiency virus 1|11676 -DRFYKTLRA ->9995|Exodeoxyribonuclease V, Gamma|NP_220158.1|Chlamydia trachomatis|813 -DRLALLANL ->9999|DNA packaging tegument protein UL25|NP_044494.1|Human alphaherpesvirus 2|10310 -DRLDNRLQL ->10448|nuclear protein EBNA2|AAA45903.1|Human gammaherpesvirus 4|10376 -DTPLIPLTIF ->10587|viral polyprotein|AAA42941.1|Dengue virus 2 Thailand/NGS-C/1944|11065 -DVFFTPPEK ->10650|Nucleoprotein|P05133.1|Hantaan virus 76-118|11602 -DVKVKEISNQEPLKL ->10681|nucleocapsid protein|AAA43837.1|Hantaan hantavirus|11599 -DVNGIRKPK ->10736|trans-sialidase|XP_814755.1|Trypanosoma cruzi|5693 -DVSRPTAVV ->10763|polyprotein|ABV46054.1|Hepatitis C virus subtype 1a|31646 -DVVCCSMSY ->10790|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 -DVVVVATDALMTGYT ->10939|polyprotein|BAB18806.1|Hepatitis C virus subtype 1a|31646 -DYPYRLWHY ->10962|envelope glycoprotein|AAU04921.1|Human T-lymphotropic virus 1|11908 -DYSPSCCTL ->11014|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 -EADVQQWLT ->11063|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 -EAHFTDPASIAARGY ->11125|NS3 protein|NP_739587.1|Dengue virus 2 Thailand/NGS-C/1944|11065 -EALRGLPIR ->11214|possible regulatory protein|NP_302009.1|Mycobacterium leprae|1769 -EAVLLRLDGTTLEVE ->11258|Nucleoprotein|P41269.1|Puumala hantavirus|11604 -ECPFIKPEV ->11455|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 -EDTSASGSGEDAIDE ->11804|EBNA3C latent protein|CAD53421.1|Human gammaherpesvirus 4|10376 -EENLLDFVRF ->11956|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 -EFCRVLCCYVL ->12060|Myosin heavy chain, skeletal muscle, adult 2 (Myosin heavy chain IIa) (MyHC-IIa)|Q9UKX2.1|Homo sapiens|9606 -EFQKMRRDL ->12062|hypothetical glycine-rich protein Rv3812 - Mycobacterium tuberculosis (strain H37RV)|H70520|Mycobacterium tuberculosis|1773 -EFQTVSNQL ->12108|polyprotein|AAP55688.1|Hepatitis C virus subtype 2a|31649 -EFWEAVFTGL ->12183|EBNA3C latent protein|CAD53421.1|Human gammaherpesvirus 4|10376 -EGGVGWRHW ->12583|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis H37Rv|83332 -EISTNIRQA ->12585|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis|1773 -EISTNIRQAGVQYSRADEEQ ->12588|Glycoprotein B precursor (Glycoprotein II)|P09257.1|Human alphaherpesvirus 3|10335 -EITDTIDKFGK ->12616|gag protein|AAV53308.1|Human immunodeficiency virus 1|11676 -EIYKRWII ->12926|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 -ELAAKLVAL ->12928|Genome polyprotein|Q81754.3|Hepatitis C virus|11103 -ELAAKLVGL ->12941|||| -ELAGIGILTV ->13091|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 -ELIEANLLW ->13119|envelope protein|AGW23591.1|Dengue virus 3|11069 -ELKGMSYAM ->13133|UL123; IE1|AAR31419.1|Human herpesvirus 5 TB40|10000408 -ELKRKMIYM ->13135|UL123; IE1|AAR31504.1|Human betaherpesvirus 5|10359 -ELKRKMMYM ->13165|trans-sialidase, putative|EAN81972.1|Trypanosoma cruzi|5693 -ELLRPTTLV ->13195|6 kDa early secretory antigenic target|P0A564.2|Mycobacterium tuberculosis|1773 -ELNNALQNL ->13215|Antigen 85-B|P0C5B9.1|Mycobacterium tuberculosis|1773 -ELPQWLSANR ->13257|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 -ELRRKMMYM ->13262|gag polyprotein|BAA00992.1|Human immunodeficiency virus 1|11676 -ELRSLYNTV ->13283|glycoprotein gp35/37|AAC59622.1|Human gammaherpesvirus 8|37296 -ELTDALISAFSGSYS ->13346|nonstructural protein 3|NP_722463.1|Dengue virus 1|11053 -EMAEALKGMPIRYQT ->13358|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 -EMEEALRGLPIRYQT ->13386|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis|1773 -EMKTDAATL ->13456|circumsporozoite protein|AAN87606.1|Plasmodium falciparum|5833 -ENDIEKKICKMEKCSSVFNV ->13473|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 -ENFVRSSNL ->13516|Genome polyprotein|P26664.3|Hepatitis C virus subtype 1a|31646 -ENLPYLVAY ->13518|HCV-1|AAA45676.1|Hepatitis C virus genotype 1|41856 -ENLPYLVAYQATVCARAQAP ->13638|polyprotein|BAB18810.1|Hepatitis C virus (isolate H77)|63746 -EPEPDVAVL ->13701|Trans-activator protein BZLF1|P03206.2|Human gammaherpesvirus 4|10376 -EPLPQGQLTAY ->13946|UL123; IE1|AAR31390.1|Human betaherpesvirus 5|10359 -EQVTEDCNENP ->13983|ATP-dependent zinc protease|NP_220362.1|Chlamydia trachomatis|813 -EREQTLNQL ->13991|hypothetical protein CT850|NP_220372.1|Chlamydia trachomatis|813 -ERFLAQEQL ->14001|Nucleocapsid protein|Q89462|Sin Nombre hantavirus|37705 -ERIDDFLAA ->14101|envelope glycoprotein|ABI16336.1|Human immunodeficiency virus 1|11676 -ERYLKDQQL ->14198|UL123; IE1|AAR31390.1|Human betaherpesvirus 5|10359 -ESLKTFEQVTE ->14324|Chain B, Dengue Virus Rna Dependent Rna Polymerase With Residues From The Ns5 Linker Region|4C11_B|Dengue virus|12637 -ETACLGKAY ->14325|polyprotein|AGO67248.1|Dengue virus 2|11060 -ETACLGKSY ->14381|polyprotein|BAA25076.1|Hepatitis C virus|11103 -ETFWAKHMW ->14427|polyprotein|BAD73974.1|Hepatitis C virus subtype 1b|31647 -ETIKGGRHL ->14720|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 -EVIAPAVQTNW ->14727|polyprotein|AAB67036.1|Hepatitis C virus subtype 1a|31646 -EVIKGGRHL ->14731|gag protein|ACD85912.1|Human immunodeficiency virus 1|11676 -EVIPMFSAL ->14902|Genome polyprotein|P26664.3|Hepatitis C virus subtype 1a|31646 -EVVTSTWVL ->15061|core protein|BAF42671.1|Hepatitis B virus|10407 -EYLVSFGVW ->15100|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 -EYTNIPISL ->15110|Genome polyprotein|P26663.3|Hepatitis C virus|11103 -EYVLLLFLL ->15226|trans-sialidase|XP_810383.1|Trypanosoma cruzi|5693 -FANCNFTLV ->15230|Trans-sialidase|SRC7915|Trypanosoma cruzi|5693 -FANHDFTLV ->15231|trans-sialidase|XP_817875.1|Trypanosoma cruzi|5693 -FANHKFTLV ->15232|trans-sialidase, putative|EAN82291.1|Trypanosoma cruzi|5693 -FANHNFTLV ->15233|trans-sialidase, putative|EAN81456.1|Trypanosoma cruzi|5693 -FANNEFTLV ->15234|trans-sialidase|XP_815749.1|Trypanosoma cruzi|5693 -FANNKFTLV ->15242|trans-sialidase, putative|EAN81560.1|Trypanosoma cruzi|5693 -FANYKFTLV ->15244|trans-sialidase|XP_818893.1|Trypanosoma cruzi|5693 -FANYNFTLV ->15787|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 -FFCFAWYLKGRWVPG ->15879|Core antigen|P69708.1|Hepatitis B virus|10407 -FFPSIRDLL ->15885|envelope|BAK20487.1|Human T-lymphotropic virus 1|11908 -FFQFCPLIF ->15914|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 -FFTELDGVRLHRFAP ->16156|Spike glycoprotein precursor|P59594.1|SARS coronavirus|227859 -FIAGLIAIV ->16250|liver stage antigen-1|CAA82974.1|Plasmodium falciparum|5833 -FILVNLLIFH ->16332|secreted antigen Ag85B|AAO62005.1|Mycobacterium tuberculosis|1773 -FIYAGSLSA ->16333|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 -FIYAGSLSAL ->16521|polyprotein|ABU97067.1|Hepatitis C virus subtype 1b|31647 -FLARLIWWL ->16548|Glycoprotein GP110 precursor|P03188.1|Human herpesvirus 4 strain B95-8|10377 -FLDKGTYTL ->16617|Large envelope protein|SRC279965|Hepatitis B virus|10407 -FLGGTRVCL ->16623|gag protein|AAV53308.1|Human immunodeficiency virus 1|11676 -FLGKIWPSYK ->16685|Gag-Pol polyprotein|SRC279958|Human immunodeficiency virus 1|11676 -FLKEKKGL ->16706|structural protein|BAA00705.1|Hepatitis C virus|11103 -FLLALLSCL ->16725|Genome polyprotein|P26664.3|Hepatitis C virus subtype 1a|31646 -FLLLADARV ->16751|pol protein|BAA32832.1|Hepatitis B virus|10407 -FLLSLGIHL ->16753|Pre-S/S protein|AAR99337.1|Hepatitis B virus|10407 -FLLTKILTI ->16755|envelope protein|BAF48755.1|Hepatitis B virus|10407 -FLLTRILTI ->16756|Large envelope protein|SRC279965|Hepatitis B virus|10407 -FLLTRILTL ->16772|Type IV pili glycosylation protein|YP_169902.1|Francisella tularensis subsp. tularensis SCHU S4|177416 -FLMPFMHYIV ->16795|precore/core protein|AAP57273.1|Hepatitis B virus|10407 -FLPADFFPSI ->16796|HBcAg|ABE97049.1|Hepatitis B virus|10407 -FLPADFFPSV ->16813|External core antigen|SRC279980|Hepatitis B virus|10407 -FLPNDFFPSA ->16814|precore protein|CAM58990.1|Hepatitis B virus|10407 -FLPNDFFPSV ->16815|core protein [Hepatitis B virus]|AAR19324.1|Hepatitis B virus|10407 -FLPPDFFPSV ->16827|External core antigen|SRC279980|Hepatitis B virus|10407 -FLPSDFFPGV ->16831|External core antigen|SRC279980|Hepatitis B virus|10407 -FLPSDFFPSA ->16832|core protein|BAF42671.1|Hepatitis B virus|10407 -FLPSDFFPSI ->16833|core protein|CAL29866.1|Hepatitis B virus|10407 -FLPSDFFPSV ->16836|precore/core protein [Hepatitis B virus]|AAR03815.1|Hepatitis B virus|10407 -FLPSDFLPSV ->16839|External core antigen|SRC279980|Hepatitis B virus|10407 -FLPSDTNMGL ->16856|||| -FLPVDFFPSI ->16857|pre-c/core|CAA59565.1|Hepatitis B virus|10407 -FLPVDFFPSV ->16878|EBNA-3A|AFY97830.1|Human gammaherpesvirus 4|10376 -FLRGRAYGL ->16889|trans-sialidase, putative|EAN82636.1|Trypanosoma cruzi|5693 -FLSHDFTLV ->16890|trans-sialidase|XP_810777.1|Trypanosoma cruzi|5693 -FLSHNFTLV ->16924|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 -FLTSELPQW ->16936|tegument protein VP13/14|NP_044517.1|Human alphaherpesvirus 2|10310 -FLVDAIVRV ->16937|tegument protein VP13/14|NP_044517.1|Human alphaherpesvirus 2|10310 -FLVDAIVRVA ->16966|polyprotein|BAA03375.1|Hepatitis C virus|11103 -FLVSQLFTF ->16979|Latent membrane protein 2|Q69135|Human gammaherpesvirus 4|10376 -FLYALALLL ->17079|hypothetical protein FTT1095c|YP_170074.1|Francisella tularensis subsp. tularensis SCHU S4|177416 -FMPKVNFEV ->17110|EBNA-1 protein|Q777E1|Human gammaherpesvirus 4|10376 -FMVFLQTHI ->17117|matrix protein|AAN09804.1|Measles virus strain Edmonston|11235 -FMYMSLLGV ->17278|Genome polyprotein|P06441.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 -FPELKPGESRHTSDHMSIYK ->17321|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 -FPKTTNGCSQA ->17619|Early antigen protein D|P03191.1|Human herpesvirus 4 strain B95-8|10377 -FRNLAYGRTCVLGK ->17620|Early antigen protein D|P03191.1|Human herpesvirus 4 strain B95-8|10377 -FRNLAYGRTCVLGKE ->17802|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 -FSPGTSGSPIIDKKG ->18011|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 -FTLVAPVSI ->18062|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 -FTSAVLLLV ->18142|polyprotein precursor|NP_041724.2|West Nile virus|11082 -FVDVGVSAL ->18144|trans-sialidase|XP_804884.1|Trypanosoma cruzi|5693 -FVDYNFSLV ->18145|trypomastigote surface glycoprotein|AAA30259.1|Trypanosoma cruzi|5693 -FVDYNFTIV ->18242|trans-sialidase, putative|EAN80731.1|Trypanosoma cruzi|5693 -FVNHRFTLV ->18250|Trans-sialidase|SRC7915|Trypanosoma cruzi|5693 -FVNYDFALV ->18251|trans-sialidase|XP_820181.1|Trypanosoma cruzi|5693 -FVNYDFTIV ->18252|trans-sialidase|XP_814186.1|Trypanosoma cruzi|5693 -FVNYNFTLV ->18276|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 -FVRSSNLKF ->18284|Trans-sialidase|SRC7915|Trypanosoma cruzi|5693 -FVSCDFTIV ->18337|polyprotein|BAD73987.1|Hepatitis C virus subtype 1b|31647 -FWAKHMWNF ->18390|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 -FYFPRAPLNSNAMLSTESMM ->18397|Genome polyprotein|P26662.3|Hepatitis C virus|11103 -FYGKAIPIEAI ->18400|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 -FYGMWPLL ->18401|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 -FYGMWPLLL ->18474|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 -FYTPLADQF ->18507|10 kDa culture filtrate antigen EsxB|NP_218391.1|Mycobacterium tuberculosis H37Rv|83332 -GAAGTAAQAAVVRFQ ->18678|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 -GALTGTYVYNHLTPL ->18847|polyprotein|AEH28241.1|Hepatitis C virus subtype 1b|31647 -GAYMSKAHGV ->18941|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 -GDCVQGDWCPISGGL ->19225|polyprotein|AGO67248.1|Dengue virus 2|11060 -GEDGCWYGM ->19305|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -GEIPFYGKAI ->19337|gag protein|AAW57872.1|Human immunodeficiency virus 1|11676 -GELDRWEKI ->19348|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 -GELLPEAAGPTQVLVPRSAI ->19351|core protein|AAL31859.1|Hepatitis B virus|10407 -GELMTLATW ->19359|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 -GELSKQTGQQVSIAPNAGLD ->19366|Hepatitis C virus core, matrix, envelope and non-structural protein RNA.|AAA72945.1|Hepatitis C virus|11103 -GEMPSTEDL ->19370|Genome polyprotein|P26664.3|Hepatitis C virus genotype 6|42182 -GENDTDVFVL ->19434|Genome polyprotein|P27915.1|Dengue virus 3|11069 -GESRKTFVE ->19435|polyprotein|CDF77361.1|Dengue virus 3|11069 -GESRKTFVEL ->19442|nucleocapsid protein|ABI96968.1|SARS coronavirus|227859 -GETALALLLL ->19463|Carbamoyl-phosphate synthase large chain|YP_170571.1|Francisella tularensis subsp. tularensis SCHU S4|177416 -GEVLGVIVQF ->19490|Genome polyprotein|P26663.3|Hepatitis C virus (isolate BK)|11105 -GFADLMGYI ->19492|Genome polyprotein|P29846.3|Hepatitis C virus|11103 -GFADLMGYIPL ->19493|polyprotein|BAA03375.1|Hepatitis C virus|11103 -GFADLMGYIPLVGAP ->19575|glycoprotein B precursor|AAB72100.1|Human alphaherpesvirus 2|10310 -GFLIAYQPLL ->19628|Genome polyprotein|P26662.3|Hepatitis C virus|11103 -GFTGDFDSV ->19898|gag protein|AAV53308.1|Human immunodeficiency virus 1|11676 -GGKKKYKLK ->20023|EBNA-1|YP_401677.1|Human gammaherpesvirus 4|10376 -GGSKTSLYNLRRGTA ->20354|M1 protein|CAA30882.1|Influenza A virus|11320 -GILGFVFTL ->20355|Matrix protein 1|P03485.1|Influenza A virus (A/Puerto Rico/8/1934(H1N1))|211044 -GILGFVFTLT ->20369|HEAT SHOCK PROTEIN HSPX (ALPHA-CRSTALLIN HOMOLOG) (14 kDa ANTIGEN) (HSP16.3)|NP_216547.1|Mycobacterium tuberculosis H37Rv|83332 -GILTVSVAV ->20415|circumsporozoite protein|AAN87606.1|Plasmodium falciparum|5833 -GIQVRIKPGSANKPKDELDY ->20417|HCV-1|AAA45676.1|Hepatitis C virus genotype 1|41856 -GIQYLAGLSTLPGNPAIASL ->20686|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 -GKSTHPMVTRS ->20752|tegument protein VP13/14|NP_044517.1|Human alphaherpesvirus 2|10310 -GLADTVVAC ->20772|Genome polyprotein|SRC279960|Hepatitis C virus|11103 -GLASLFTQGA ->20786|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 -GLCPHCINV ->20787|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 -GLCPHCINVG ->20788|BMLF1 protein|CAD53409.1|Human gammaherpesvirus 4|10376 -GLCTLVAML ->20861|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 -GLFNNVLYH ->20865|Nucleoprotein|P41269.1|Puumala hantavirus|11604 -GLFPTQIQV ->20892|latent membrane protein 2|AAB59844.1|Human gammaherpesvirus 4|10376 -GLGTLGAAL ->20894|polyprotein [Hepatitis C virus]|BAF91806.1|Hepatitis C virus|11103 -GLGWVGWLL ->20921|polyprotein|BAA03375.1|Hepatitis C virus|11103 -GLIHLHQNIVDVQYL ->20929|Circumsporozoite protein precursor|P02893.1|Plasmodium falciparum|5833 -GLIMVLSFL ->20988|Genome polyprotein|P26662.3|Hepatitis C virus (isolate Japanese)|11116 -GLLGCIITSL ->20994|Circumsporozoite-related antigen|SRC280086|Plasmodium falciparum|5833 -GLLGNVSTV ->21000|glutamine synthetase GLNA1 (glutamine synthase) (GS-I)|NP_216736.1|Mycobacterium tuberculosis|1773 -GLLHHAPSL ->21004|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 -GLLLLGLWGT ->21007|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 -GLLPFHSTL ->21013|trans-sialidase, putative|EAN80935.1|Trypanosoma cruzi|5693 -GLLPSLLLLL ->21038|cysteine proteinase cruzipain (EC 3.4.22.-) - Trypanosoma cruzi|A45629|Trypanosoma cruzi|5693 -GLMNNAFEWI ->21041|Membrane glycoprotein|Q692E0|SARS coronavirus TJF|284672 -GLMWLSYFV ->21070|polymerase|CAA53358.1|Hepatitis B virus subtype AYR|10000437 -GLPRYVARL ->21071|Protein P|SRC279982|Hepatitis B virus subtype adr|106820 -GLPRYVVCL ->21078|Antigen 85-B precursor|P21160.1|Mycobacterium kansasii|1768 -GLPVEYLQV ->21079|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 -GLQDCTMLV ->21116|X protein|BAG70907.1|Hepatitis B virus|10407 -GLSAMSTTDL ->21137|Major surface antigen precursor|P03142.4|Hepatitis B virus subtype adw|106821 -GLSPTVWLSA ->21139|envelope protein|BAF48755.1|Hepatitis B virus|10407 -GLSPTVWLSV ->21145|DNA polymerase|CAA10434.1|Hepatitis B virus|10407 -GLSRYVARL ->21146|polymerase|AAD16253.1|Hepatitis B virus|10407 -GLSRYVARLS ->21190|Genome polyprotein|P27958.3|Hepatitis C virus (isolate H)|11108 -GLVGLLTPGA ->21199|Circumsporozoite protein precursor|P08677.2|Plasmodium vivax strain Belem|31273 -GLVILLVLAL ->21230|polyprotein precursor|AAP22088.1|West Nile virus|11082 -GLYKSAPRR ->21242|polymerase|ACF94272.1|Hepatitis B virus|10407 -GLYSSTVPV ->21275|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 -GMGPSLIGL ->21347|Nucleoprotein|P59595.1|SARS coronavirus|227859 -GMSRIGMEV ->21385|polyprotein|AAY82034.1|Hepatitis C virus genotype 1|41856 -GNASRCWVAM ->21576|nucleocapsid protein|AAA43837.1|Hantaan virus 76-118|11602 -GPATNRDYL ->21635|gag protein|ABO73990.1|Human immunodeficiency virus 1|11676 -GPGHKARVL ->21638|protein F|ABV46152.2|Hepatitis C virus (isolate Japanese)|11116 -GPGLSPGTL ->21656|protease|CAB06750.1|Human alphaherpesvirus 2|10310 -GPHETITAL ->21663|polyprotein precursor|NP_041724.2|West Nile virus|11082 -GPIRFVLAL ->21754|Genome polyprotein|SRC279960|Hepatitis C virus genotype 1|41856 -GPRLGFRAT ->21757|polyprotein|BAA09072.1|Hepatitis C virus|11103 -GPRLGVRAT ->21762|Genome polyprotein|Q99IB8.3|Hepatitis C virus|11103 -GPRLGVRTT ->21780|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 -GPSLIGLAM ->21894|Polyprotein|P90247|Hepatitis C virus|11103 -GQIVGGVYL ->21895|core protein|AAS15195.1|Hepatitis C virus (isolate H77)|63746 -GQIVGGVYLL ->21960|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 -GQSSFYSDWY ->21982|HCV-1|AAA45676.1|Hepatitis C virus|11103 -GRAAICGKY ->22046|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 -GRGKPGIYRF ->22235|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 -GRVIGSALQFLIPRL ->22255|polyprotein|ABR27377.1|Hepatitis C virus|11103 -GRWVPGAAY ->22633|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 -GTDTGQACQIQMSDPAYNIN ->22801|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 -GTRLAAGSPSSEYPN ->22817|polyprotein|AAK49562.1|Dengue virus 2|11060 -GTSGSPIADKK ->22818|Nonstructural protein NS3|NP_739587.2|Dengue virus 2|11060 -GTSGSPIIDK ->22819|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 -GTSGSPIIDKK ->22820|Nonstructural protein NS3|YP_001531172.2|Dengue virus 3|11069 -GTSGSPIINR ->22822|NS3 protein|NP_740321.1|Dengue virus 4|11070 -GTSGSPIINRK ->22823|NS3 protein|NP_739587.1|Dengue virus 2|11060 -GTSGSPIVDK ->22824|polyprotein|AAG30730.1|Dengue virus 2|11060 -GTSGSPIVDR ->22825|polyprotein|ABG75765.1|Dengue virus 1|11053 -GTSGSPIVNR ->22910|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 -GVAGALVAFK ->22919|Genome polyprotein|SRC279960|Hepatitis C virus|11103 -GVASFFTPGA ->22976|nuclear antigen EBNA-1|AAA67277.1|Human gammaherpesvirus 4|10376 -GVFVYGGSKTSLYNL ->23129|polyprotein|BAB18806.1|Hepatitis C virus subtype 1a|31646 -GVRVLEDGV ->23137|liver stage antigen-1|CAA82974.1|Plasmodium falciparum|5833 -GVSENIFLK ->23151|polymerase ORF|CAA46356.1|Hepatitis B virus subtype ayw|10418 -GVSRYVARL ->23224|polyprotein|BAB18806.1|Hepatitis C virus|11103 -GVYLLPRRGPRLGVR ->23270|polyprotein|AAB67036.1|Hepatitis C virus (isolate H77)|63746 -GWLAGLFYQHKFNSS ->23288|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 -GWSGQVYQDWLGRMN ->23306|LOW MOLECULAR WEIGHT PROTEIN ANTIGEN 7 ESXH (10 kDa ANTIGEN) (CFP-7) (PROTEIN TB10.4)|CAA17363.1|Mycobacterium tuberculosis H37Rv|83332 -GYAGTLQSL ->23365|polyprotein|BAB18806.1|Hepatitis C virus|11103 -GYIPLVGAPL ->23474|polyprotein|AAP55688.1|Hepatitis C virus subtype 2a|31649 -GYTGDFDSVI ->23542|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 -HAKALKERMV ->23566|tegument protein UL7|NP_044476.1|Human alphaherpesvirus 2|10310 -HASPFERVRCLLL ->23573|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 -HAVGLFRAA ->23601|Genome polyprotein|SRC279960|Hepatitis C virus (isolate H77)|63746 -HCPAGHAVGIFRAAVCTRGVA ->23619|Genome polyprotein|P27958.3|Hepatitis C virus (isolate H)|11108 -HDGAGKRVY ->23620|Genome polyprotein|SRC279960|Hepatitis C virus genotype 1|41856 -HDGAGKRVYL ->23621|Genome polyprotein|P26664.3|Hepatitis C virus (isolate 1)|11104 -HDGAGKRVYYL ->23754|Genome polyprotein|P26664.3|Hepatitis C virus genotype 1|41856 -HEYPVGSQL ->23797|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 -HFLCTFTFNSNNKEYTFPIT ->23807|tax|AAG48731.1|Human T-lymphotropic virus 2|11909 -HFPGFGQSLLYGYPVYVFGDCVQ ->23864|envelope glycoprotein(gp21, gp46) - human T-cell lymphotropic virus type 1|A45714|Human T-lymphotropic virus 1|11908 -HFSKCGFPF ->23883|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 -HGAGTRTIASPKGPV ->24172|pX-rex-orf I {alternatively spliced}|AAB23359.1|Human T-lymphotropic virus 1|11908 -HLAFQLSSI ->24218|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 -HLHAPTGSGK ->24219|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 -HLHAPTGSGKSTKVP ->24299|X protein|BAF81690.1|Hepatitis B virus|10407 -HLSLRGLFV ->24302|X protein|AAP06597.1|Hepatitis B virus|10407 -HLSLRGLPV ->24390|Major capsid protein L1|P50816.2|Human papillomavirus type 44|10592 -HNNGICWGN ->24427|polyprotein|ACX44238.1|Hepatitis C virus subtype 1a|31646 -HPALVFDIT ->24457|polyprotein|BAA09072.1|Hepatitis C virus|11103 -HPITKYIMACMSADL ->24479|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 -HPNIEEVAL ->24535|EBNA-1 protein|Q777E1|Human gammaherpesvirus 4|10376 -HPVGEADYF ->24536|EBNA-1|YP_401677.1|Human gammaherpesvirus 4|10376 -HPVGEADYFEY ->24557|Gag polyprotein|P03347.3|Human immunodeficiency virus 1|11676 -HPVHAGPIA ->24759|polyprotein|AAY82031.1|Hepatitis C virus|11103 -HSKKKCDDL ->24760|polyprotein|ACP19428.1|Hepatitis C virus subtype 1b|31647 -HSKKKCDEF ->24761|polyprotein|ACZ60102.1|Hepatitis C virus subtype 3a|356426 -HSKKKCDEI ->24762|NS3|ABW71987.1|Hepatitis C virus subtype 1b|31647 -HSKKKCDEL ->24764|polyprotein [Hepatitis C virus subtype 1b]|ABV46195.2|Hepatitis C virus|11103 -HSKKKCDELT ->24765|polyprotein [Hepatitis C virus]|ABR27360.1|Hepatitis C virus|11103 -HSKKKCDEV ->24768|NS3 [Hepatitis C virus]|AAU44886.1|Hepatitis C virus subtype 1b|31647 -HSKRKCDEF ->24769|polyprotein|AAY82032.1|Hepatitis C virus subtype 1b|31647 -HSKRKCDEL ->24818|polyprotein|ABL63011.1|Hepatitis C virus|11103 -HSNIEEVAL ->24943|DNA polymerase|CAA10434.1|Hepatitis B virus|10407 -HTLWKAGILYK ->24986|polyprotein precursor|NP_041724.2|West Nile virus|11082 -HTTKGAALM ->25133|Envelope glycoprotein precursor|P27312.1|Puumala hantavirus|11604 -HWMDATFNL ->25149|polyprotein|BAD73994.1|Hepatitis C virus subtype 1b|31647 -HYAPRPCGI ->25186|polyprotein|AAK32686.1|Hepatitis C virus|11103 -HYPCTVNFTI ->25237|Transcription activator BRLF1|P03209.1|Human herpesvirus 4 strain B95-8|10377 -IACPIVMRYVLDHLI ->25275|Glutamate decarboxylase 2|Q05329.1|Homo sapiens|9606 -IAFTSEHSHFSLK ->25370|Trans-sialidase|SRC7915|Trypanosoma cruzi|5693 -IANYNFTLV ->25388|matrix protein|ABP96803.1|Human metapneumovirus|162145 -IAPYAGLIMI ->25460|Fusion glycoprotein F0 precursor|P03420.1|Human respiratory syncytial virus A2|11259 -IAVGLLLYCKA ->25677|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 -IDTCISATFR ->25756|membrane protein|AAA45887.1|Human gammaherpesvirus 4|10376 -IEDPPFNSL ->25782|pol protein|ACJ76655.1|Human immunodeficiency virus 1|11676 -IEELRQHLL ->25839|gag protein|ACN42927.1|Human immunodeficiency virus 1|11676 -IEIKDTKEAL ->25929|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 -IEPSWADVKKDLISY ->26111|polyprotein|BAD73987.1|Hepatitis C virus subtype 1b|31647 -IFLLALLSCL ->26174|Genome polyprotein|Q9WMX2.3|Hepatitis C virus|11103 -IFTITKILL ->26186|UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-me so-diaminopimelate ligase|YP_169478.1|Francisella tularensis subsp. tularensis SCHU S4|177416 -IFWQFHQLL ->26273|nucleocapsid protein|ABI96968.1|SARS coronavirus|227859 -IGMEVTPSGTWLTYH ->26579|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 -IILNGSLLTL ->26666|Receptor tyrosine-protein kinase erbB-2 precursor|P04626.1|Homo sapiens|9606 -IISAVVGIL ->26870|Circumsporozoite protein precursor|P02893.1|Plasmodium falciparum|5833 -IKPGSANKPKDELDYENDIE ->26954|HCV-1|AAA45676.1|Hepatitis C virus genotype 1|41856 -ILAGYGAGV ->26965|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 -ILAPTRVVAAEMEEA ->27000|Heat shock protein HSP 90-beta|P08238.4|Homo sapiens|9606 -ILDKKVEKV ->27011|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 -ILDSFDPLV ->27061|envelope glycoprotein|ABU89742.1|Dengue virus 2 Thailand/16681/84|31634 -ILGDTAWDFG ->27096|HCV-1|AAA45676.1|Hepatitis C virus (isolate H)|11108 -ILHTPGCV ->27125|gag-pol fusion polyprotein|AAN73817.1|Human immunodeficiency virus 1|11676 -ILKEPVHGV ->27168|envelope protein|BAF48755.1|Hepatitis B virus|10407 -ILLLCLIFL ->27169|envelope protein|BAF48755.1|Hepatitis B virus|10407 -ILLLCLIFLL ->27195|polyprotein|ABG67747.1|West Nile virus|11082 -ILLWEIPDV ->27216|polyprotein|BAD73987.1|Hepatitis C virus subtype 1b|31647 -ILMTHFFSI ->27217|VP1|AAL37677.1|JC polyomavirus|10632 -ILMWEAVTL ->27239|polyprotein|BAB18806.1|Hepatitis C virus subtype 1b|31647 -ILPCSFTTL ->27241|Spike glycoprotein precursor|P59594.1|SARS coronavirus|227859 -ILPDPLKPT ->27245|Hemagglutinin glycoprotein|P08362.1|Measles virus strain Edmonston|11235 -ILPGQDLQYV ->27285|pol protein|BAA32832.1|Hepatitis B virus|10407 -ILRGTSFVYV ->27295|polyprotein precursor|NP_041724.2|West Nile virus|11082 -ILRNPGYAL ->27345|Large envelope protein|P03138.3|Hepatitis B virus subtype ayw|10418 -ILSPFLPLL ->27365|precore/core protein|BAE97616.1|Hepatitis B virus|10407 -ILSTLPETTV ->27564|organic solvent tolerance protein|YP_169505.1|Francisella tularensis subsp. tularensis SCHU S4|177416 -IMSSFEFQV ->27586|ESAT-6-like protein esxH|P0A568.2|Mycobacterium tuberculosis|1773 -IMYNYPAML ->27770|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 -INYADRRWCF ->27811|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 -IPDREVLY ->27847|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 -IPFYGKAI ->27878|large surface antigen|CAC87019.1|Hepatitis B virus|10407 -IPIPSSWAF ->27901|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 -IPKLVANNT ->27981|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 -IPPRGTQAVVLKVYQNAGGT ->27983|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 -IPPSFLQAMRKYSPF ->28126|matrix protein|ABP96803.1|Human metapneumovirus|162145 -IPYTAAVQV ->28222|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 -IQSALKLAIYKAT ->28282|Nucleoprotein|P41269.1|Puumala hantavirus|11604 -IREFMEKECPFIKPE ->28338|hypothetical protein CT339|NP_219846.1|Chlamydia trachomatis|813 -IRMFKILPL ->28364|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis H37Rv|83332 -IRQAGVQYSR ->28403|Invasin repeat family phosphatase|NP_220117.1|Chlamydia trachomatis|813 -IRSSVQNKL ->28484|Protein E6|P03126.1|Human papillomavirus type 16|333760 -ISEYRHYCY ->28508|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 -ISGGLCSARLHRHAL ->28594|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 -ISLPSYYPDQKSLENYIAQT ->28657|gag protein|CAB00235.1|Human immunodeficiency virus 1|11676 -ISPRTLNAW ->29181|unnamed protein product|BAA14233.1|Hepatitis C virus subtype 1b|31647 -ITYSTYCKF ->29182|polyprotein|BAD73991.1|Hepatitis C virus subtype 1b|31647 -ITYSTYGKF ->29186|polyprotein precursor|NP_041724.2|West Nile virus|11082 -ITYTDVLRY ->29287|polyprotein|BAA09073.1|Hepatitis C virus subtype 1b|31647 -IVGGVYLLPR ->29352|pol protein|AAS38336.1|Human immunodeficiency virus 1|11676 -IVLPEKDSW ->29455|Major surface antigen precursor|P03141.3|Hepatitis B virus subtype adw2|10408 -IVSPFIPLL ->29466|Epstein-Barr nuclear antigen 4|P03203.3|Human herpesvirus 4 strain B95-8|10377 -IVTDFSVIK ->29558|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 -IYAGSLSAL ->29655|pol protein|ACJ76655.1|Human immunodeficiency virus 1|11676 -IYQEPFKNLK ->29804|p24|AAB82828.1|Human immunodeficiency virus 1|11676 -KAFSPEVIPMF ->30138|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 -KDELRRKMMYM ->30266|Transcriptional regulator IE63 homolog|Q04360.1|Human herpesvirus 4 strain B95-8|10377 -KDTWLDARM ->30464|nef protein|ACR27130.1|Human immunodeficiency virus 1|11676 -KEKGGLEGL ->30815|Genome polyprotein|P26662.3|Hepatitis C virus|11103 -KFPPALPIW ->30892|Protein E6|P03126.1|Human papillomavirus type 16|333760 -KFYSKISEY ->30903|prM protein|YP_001527879.1|West Nile virus NY-99|10000971 -KGAWMDSTKATRYLVK ->30913|polyprotein precursor|NP_041724.2|West Nile virus|11082 -KGDTTTGVY ->30946|HCV-1|AAA45676.1|Hepatitis C virus genotype 1|41856 -KGGRKPARLIVFPDLGVRVC ->31004|M protein, serotype 5 precursor|P02977.2|Streptococcus pyogenes serotype M5|301449 -KGLRRDLDA ->31747|polyprotein|AGO67248.1|Dengue virus 2|11060 -KLAEAIFKL ->31756|matrix protein 2-1|AAS22094.1|Human metapneumovirus|162145 -KLAKLIIDL ->31771|Nucleoprotein|P03418.1|Human respiratory syncytial virus A2|11259 -KLCGMLLITEDANH ->31802|large delta antigen|AAG26087.1|Hepatitis delta virus TW2667|10000523 -KLEDENPWL ->31803|large delta antigen|AAG26087.1|Hepatitis delta virus TW2667|10000523 -KLEDLERDL ->31884|HAD superfamily protein|YP_169641.1|Francisella tularensis subsp. tularensis SCHU S4|177416 -KLGGYVSFV ->31898|P protein|P17100.1|Hepatitis B virus|10407 -KLHLYSHPI ->31902|Secreted antigen Ag85A|Q847N5|Mycobacterium tuberculosis|1773 -KLIANNTRV ->31974|short chain dehydrogenase|YP_169584.1|Francisella tularensis subsp. tularensis SCHU S4|177416 -KLLGQINLV ->31996|nucleocapsid protein|AAA43837.1|Hantaan virus 76-118|11602 -KLLPDTAAV ->31997|hypothetical protein FTT0484|YP_169522.1|Francisella tularensis subsp. tularensis SCHU S4|177416 -KLLPEGYWV ->32047|M protein, serotype 5 precursor|P02977.2|Streptococcus pyogenes serotype M5|301449 -KLNKELEES ->32069|Spike glycoprotein precursor|P59594.1|SARS coronavirus BJ01|228407 -KLPDDFMGCV ->32073|Protein E6|P06463.1|Human papillomavirus type 18|333761 -KLPDLCTEL ->32085|Protein E6|P03126.1|Human papillomavirus type 16|333760 -KLPQLCTEL ->32103|60 kDa chaperonin 2|P0A520.2|Mycobacterium tuberculosis|1773 -KLQERLAKL ->32147|nonstructural protein 3|NP_722463.1|Dengue virus type 1 Hawaii|10000440 -KLRTLVLAPTRVVAS ->32150|polyprotein|AAF65953.1|Hepatitis C virus|11103 -KLSALGLNAV ->32165|Hepatitis C virus core, matrix, envelope and non-structural protein RNA.|AAA72945.1|Hepatitis C virus (isolate BK)|11105 -KLSGLGINAV ->32166|Genome polyprotein|SRC279960|Hepatitis C virus (isolate H77)|63746 -KLSGLGLNAI ->32167|polyprotein|BAB18806.1|Hepatitis C virus|11103 -KLSGLGLNAV ->32174|non structural protein 3|CAJ20172.1|Hepatitis C virus|11103 -KLSNLGLNAV ->32179|polyprotein|ABU97067.1|Hepatitis C virus (isolate H77)|63746 -KLSSLGLNAV ->32187|polyprotein [Hepatitis C virus subtype 1a]|ACA50630.1|Hepatitis C virus (isolate H77)|63746 -KLTALGVNAV ->32201|Gp160|Q0ED31|Human immunodeficiency virus 1|11676 -KLTPLCVTL ->32208|Genome polyprotein|P26664.3|Hepatitis C virus subtype 1a|31646 -KLVALGINAV ->32209|polyprotein precursor|BAA01582.1|Hepatitis C virus (isolate H77)|63746 -KLVALGVNAV ->32210|polyprotein|AAY82027.1|Hepatitis C virus|11103 -KLVAMGINAV ->32212|polyprotein [Hepatitis C virus subtype 1a]|ACA50667.1|Hepatitis C virus (isolate H77)|63746 -KLVAMGVNAV ->32213|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 -KLVANNTRL ->32223|polyprotein [Hepatitis C virus subtype 1a]|ABW86969.1|Hepatitis C virus (isolate H77)|63746 -KLVGLGLNAV ->32237|polyprotein|ABV46286.2|Hepatitis C virus subtype 1b|31647 -KLVSLGVNAV ->32238|polyprotein [Hepatitis C virus subtype 1a]|ABV46251.2|Hepatitis C virus (isolate H77)|63746 -KLVVLGINAV ->32243|C protein|BAB60863.1|Measles virus|11234 -KLWESPQEI ->32250|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 -KLYCSYEVA ->32268|hemagglutinin|AAK38298.1|Influenza A virus (A/Bar-headed Goose/Qinghai/61/05(H5N1))|336238 -KLYQNPTTYI ->32393|Myosin heavy chain, skeletal muscle, adult 2 (Myosin heavy chain IIa) (MyHC-IIa)|Q9UKX2.1|Homo sapiens|9606 -KMRRDLEEA ->32605|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 -KNSAFPKTTNG ->32663|small hydrophobic protein|AAM12943.1|Human metapneumovirus|162145 -KPAVGVYHIV ->32738|Liver stage antigen|Q25893|Plasmodium falciparum|5833 -KPIVQYDNF ->32741|circumsporozoite protein|ABF83988.1|Plasmodium falciparum|5833 -KPKDELDY ->32939|polyprotein|AAK67712.1|Dengue virus 2|11060 -KPWDIIPMV ->32940|polyprotein|ABG75765.1|Dengue virus type 1 Hawaii|10000440 -KPWDVIPMV ->32941|DEN polyprotein|AAC40835.1|Dengue virus 2|11060 -KPWDVLPMV ->32942|Polyprotein|Q9J8D4|Dengue virus 2|11060 -KPWDVLPTV ->32943|polyprotein|AAL96681.1|Dengue virus 2|11060 -KPWDVVPMV ->32944|polyprotein|AAW51418.1|Dengue virus 3|11069 -KPWDVVPTV ->32955|P protein|P31870.1|Hepatitis B virus|10407 -KQAFTFSPTYKAFLC ->32998|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 -KQIKVRVDMVR ->33245|60 kDa chaperonin|P48219.1|Yersinia enterocolitica|630 -KRVVINKDT ->33250|gag protein|ABO73990.1|Human immunodeficiency virus 1|11676 -KRWIILGLNK ->33362|Circumsporozoite protein|Q27325|Plasmodium falciparum|5833 -KSKDELDY ->33381|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 -KSKKTPMGF ->33382|polyprotein|AAB67037.1|Hepatitis C virus|11103 -KSKKTPMGFSYDTRC ->33502|envelope glycoprotein E|NP_044538.1|Human alphaherpesvirus 2|10310 -KSRRPLTTF ->33576|polyprotein|ABG67747.1|West Nile virus|11082 -KSYETEYPK ->33618|pol protein|ACJ76655.1|Human immunodeficiency virus 1|11676 -KTAVQMAVF ->33681|||| -KTGGPAIYKR ->33749|nonstructural protein 4B|YP_001527886.1|West Nile virus NY-99|10000971 -KTKSDISSLFGQRIEVK ->33856|polyprotein|BAA03375.1|Hepatitis C virus|11103 -KTSERSQPR ->33912|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 -KTWADEYLCV ->33979|fusion protein|ABQ58820.1|Human metapneumovirus|162145 -KVEGEQHVIK ->34027|DNA polymerase|CAA10434.1|Hepatitis B virus|10407 -KVGNFTGLY ->34101|X protein|ACH95876.1|Hepatitis B virus|10407 -KVLHKRTLGL ->34251|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 -KVVSLVILA ->34304|Gag polyprotein|P88150|Human immunodeficiency virus 1|11676 -KWIILGLNKIVRMY ->34482|gag polyprotein|BAA00992.1|Human immunodeficiency virus 1|11676 -KYKLKHIVW ->34598|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 -KYSPFRNGYMEPTLG ->34605|NS3 protein|Q3LXL6|Dengue virus 3|11069 -KYTDRKWCF ->34616|pol protein|BAA32832.1|Hepatitis B virus|10407 -KYTSFPWLL ->34637|Polyprotein|Q9IZA3|Hepatitis C virus subtype 2a|31649 -KYVQMALLAL ->34642|methionine sulfoxide reductase B|YP_169878.1|Francisella tularensis subsp. tularensis SCHU S4|177416 -KYWNNHRQGI ->34671|polyprotein|NP_671491.1|Hepatitis C virus|11103 -LAAKLVALGINAVAY ->34918|polyprotein precursor|AAG45435.1|Dengue virus 4|11070 -LAPTRVVAAEME ->35237|nonstructural protein 3|NP_722463.1|Dengue virus type 1 Hawaii|10000440 -LDNINTPEGIIPALFEPERE ->35238|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 -LDNINTPEGIIPSMF ->35407|polyprotein|ACE82359.1|Hepatitis C virus subtype 1a|31646 -LEDRDRSEL ->35568|Polyprotein|Q9J8D4|Dengue virus 2|11060 -LEKTKKDL ->35785|14 kDa antigen|P0A5B7.2|Mycobacterium tuberculosis|1773 -LFAAFPSFA ->35844|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 -LFGYPVYV ->35845|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 -LFGYPVYVF ->36062|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 -LGALTGTYVYNHLTPLRDWA ->36102|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 -LGFGAYMSK ->36306|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 -LGRMNCSYENMTALE ->36345|polyprotein|ABR25251.1|Hepatitis C virus (isolate H77)|63746 -LGVPPLRAWR ->36352|Polyprotein|P90247|Hepatitis C virus|11103 -LGWAGWLLSPRGSRPSWGPT ->36357|ELAV-like protein 4 (Paraneoplastic encephalomyelitis antigen HuD) (Hu-antigen D)|P26378.1|Homo sapiens|9606 -LGYGFVNYI ->36358|ELAV-like protein 1|Q15717.2|Homo sapiens|9606 -LGYGFVNYV ->36402|P protein|Q05486.1|Hepatitis B virus|10407 -LHLYSHPIILGFRKI ->36432|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 -LHTDFEQVM ->36504|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 -LIFCHSKKK ->36563|Accessory protein p30II|P0C214.1|Human T-lymphotropic virus 1|11908 -LIISPLPRV ->36599|putative D-ribose-binding protein|NP_301386.1|Mycobacterium leprae|1769 -LILGLLPAI ->36621|glycoprotein gp35/37|AAC59622.1|Human gammaherpesvirus 8|37296 -LILYLCVPRCRRKKP ->36676|polyprotein|BAA09073.1|Hepatitis C virus subtype 1b|31647 -LIRACMLVR ->36688|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 -LIRLKPTL ->36717|nonstructural protein 4B|YP_001527886.1|West Nile virus NY-99|10000971 -LITAAAVTLWENGASSVW ->36723|Spike glycoprotein precursor|P15423.1|Human coronavirus 229E|11137 -LITGRLAAL ->36724|Spike glycoprotein precursor|P59594.1|SARS coronavirus|227859 -LITGRLQSL ->37073|sporozoite surface protein 2|NP_705260.1|Plasmodium falciparum 3D7|36329 -LLACAGLAY ->37074|sporozoite surface protein 2|NP_705260.1|Plasmodium falciparum 3D7|36329 -LLACAGLAYK ->37079|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -LLADARVCSC ->37097|polyprotein|AAY82030.1|Hepatitis C virus genotype 1|41856 -LLALLSCLTV ->37115|Circumsporozoite|SRC280011|Plasmodium falciparum|5833 -LLAVSSILLL ->37120|Major surface antigen precursor|P17399.3|Hepatitis B virus|10407 -LLCLIFLLV ->37127|polyprotein|AAY82030.1|Hepatitis C virus genotype 1|41856 -LLCPAGHAV ->37136|Genome polyprotein|P27958.3|Hepatitis C virus|11103 -LLCPTGHAV ->37140|Hypothetical protein esxG (PE family protein)|O53692.1|Mycobacterium tuberculosis|1773 -LLDAHIPQL ->37146|6 kDa early secretory antigenic target|P0A564.2|Mycobacterium tuberculosis|1773 -LLDEGKQSL ->37153|Nuclear antigen EBNA-3C|Q69140.1|Human gammaherpesvirus 4|10376 -LLDFVRFMGV ->37170|Major surface antigen precursor|P12934.3|Hepatitis B virus|10407 -LLDPRVRGL ->37181|core|CAA59522.1|Hepatitis B virus|10407 -LLDTASALY ->37187|surface antigen|BAF44879.1|Hepatitis B virus|10407 -LLDYQGMLPV ->37246|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 -LLFEEYTNI ->37251|||| -LLFGHPVYV ->37253|||| -LLFGYAVYV ->37254|||| -LLFGYPRYV ->37255|||| -LLFGYPVAV ->37257|Protein Tax-1|P03409.2|Human T-lymphotropic virus 1|11908 -LLFGYPVYV ->37273|Genome polyprotein|P26664.3|Hepatitis C virus (isolate 1)|11104 -LLFLLLADA ->37286|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 -LLFNILGGWV ->37317|Genome polyprotein|P26662.3|Hepatitis C virus (isolate Japanese)|11116 -LLGCIITSL ->37347|Sialidase 85-1.1 precursor|P18269.2|Trypanosoma cruzi|5693 -LLGLWGLATA ->37350|trans-sialidase|XP_818394.1|Trypanosoma cruzi|5693 -LLGLWGTAAL ->37351|trans-sialidase, putative|EAN81560.1|Trypanosoma cruzi|5693 -LLGLWVFAAL ->37364|P53_HUMAN Cellular tumor antigen p53 (Tumor suppressor p53) (Phosphoprotein p53) (Antigen NY-CO-13)|P04637.2|Homo sapiens|9606 -LLGRNSFEV ->37397|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 -LLHTDFEQV ->37398|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 -LLHTDFEQVM ->37453|polyprotein|BAD73987.1|Hepatitis C virus subtype 1b|31647 -LLKRLHQWI ->37466|surface antigen|BAF44879.1|Hepatitis B virus|10407 -LLLCLIFLL ->37473|Nucleoprotein|P59595.1|SARS coronavirus|227859 -LLLDRLNQL ->37498|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 -LLLGLWGTAA ->37507|Large T antigen|P03071.1|Human polyomavirus 1|1891762 -LLLIWFRPV ->37511|||| -LLLKATLCI ->37536|Spike glycoprotein precursor|P15423.1|Human coronavirus 229E|11137 -LLLNCLWSV ->37573|E7 protein|ABL96585.1|Human papillomavirus type 16|333760 -LLMGTLGIV ->37590|VP1|BAF93325.1|Human polyomavirus 1|1891762 -LLMWEAVTV ->37607|kaposin|AAC57155.1|Human gammaherpesvirus 8|37296 -LLNGWRWRL ->37685|polyprotein|BAA03375.1|Hepatitis C virus|11103 -LLPRRGPRL ->37700|vimentin|NP_003371.1|Homo sapiens|9606 -LLQDSVDFSL ->37738|polyprotein|AAA45534.1|Hepatitis C virus (isolate Taiwan)|31645 -LLREEVSFRV ->37769|Latent membrane protein 2|Q69135|Human gammaherpesvirus 4|10376 -LLSAWILTA ->37830|polyprotein|BAB18806.1|Hepatitis C virus subtype 1b|31647 -LLSTTEWQI ->37877|cysteine proteinase cruzipain (EC 3.4.22.-) - Trypanosoma cruzi|A45629|Trypanosoma cruzi|5693 -LLTTSGVSA ->37919|envelope protein|BAF48755.1|Hepatitis B virus|10407 -LLVPFVQWFV ->37960|membrane protein|AAA45887.1|Human gammaherpesvirus 4|10376 -LLWTLVVLL ->37970|tax|AAG48731.1|Human T-lymphotropic virus 2|11909 -LLYGYPVYV ->37991|polyprotein|AAY82034.1|Hepatitis C virus genotype 1|41856 -LMALTLSPYYKRY ->38052|Glycoprotein GP85 precursor|P03231.1|Human gammaherpesvirus 4|10376 -LMIIPLINV ->38082|cysteine proteinase cruzipain (EC 3.4.22.-) - Trypanosoma cruzi|A45629|Trypanosoma cruzi|5693 -LMNNAFEWI ->38083|cysteine proteinase cruzipain (EC 3.4.22.-) - Trypanosoma cruzi|A45629|Trypanosoma cruzi|5693 -LMNNAFEWIV ->38152|L-aspartate oxidase|YP_170403.1|Francisella tularensis subsp. tularensis SCHU S4|177416 -LMWDNVGLV ->38400|polyprotein|ABG75765.1|Dengue virus 1|11053 -LPAIVREAI ->38427|BZLF1|AAA66529.1|Human gammaherpesvirus 4|10376 -LPCVLWPVL ->38446|Glycoprotein B precursor (Glycoprotein II)|P09257.1|Human alphaherpesvirus 3|10335 -LPEGMDPFAEK ->38466|nucleocapsid protein|ABF21284.1|Influenza A virus (A/Iran/1/1957(H2N2))|488233 -LPFDKPTIM ->38468|nucleoprotein|CAA24268.1|Influenza A virus (A/Puerto Rico/8/1934(H1N1))|211044 -LPFDRTTIM ->38471|nucleocapsid protein|ABC46569.1|Influenza A virus (A/Memphis/4/1980(H3N2))|383578 -LPFEKSTVM ->38472|nucleoprotein|AAV48837.1|Influenza A virus (A/Brevig Mission/1/1918(H1N1))|88776 -LPFERATIM ->38494|polyprotein|BAA03375.1|Hepatitis C virus|11103 -LPGCSFSIF ->38556|Genome polyprotein|Q00269.3|Hepatitis C virus|11103 -LPKLPGVPF ->38701|core protein|AAL31859.1|Hepatitis B virus|10407 -LPSDFFPSV ->38724|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 -LPSTLRWFFNLFQLYRGPLD ->38851|Trans-activator protein BZLF1|P03206.2|Human herpesvirus 4 strain B95-8|10377 -LQHYREVAA ->38922|6 kDa early secretory antigenic target|P0A564.2|Mycobacterium tuberculosis|1773 -LQNLARTI ->38974|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 -LQRGPQYSEHP ->39095|nonstructural protein 3|NP_722463.1|Dengue virus type 1 Hawaii|10000440 -LRGEARKTFVELMRR ->39162|gag protein|AAV53308.1|Human immunodeficiency virus 1|11676 -LRPGGKKKYKLKHIV ->39339|Nucleocapsid protein|Q89462|Sin Nombre hantavirus|37705 -LSFALPIILKALYML ->39571|polyprotein|BAD73987.1|Hepatitis C virus subtype 1b|31647 -LSPRPVSYLK ->39589|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 -LSPYYKRYIS ->39590|polyprotein|AAY82030.1|Hepatitis C virus|11103 -LSPYYKRYISW ->39591|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 -LSPYYKRYISWCLWWLQYFL ->40158|polyprotein|AAA45534.1|Hepatitis C virus|11103 -LTRVEAQLHVWVPPL ->40210|polyprotein|ABR25251.1|Hepatitis C virus (isolate H77)|63746 -LTTSQTLLF ->40247|polyprotein precursor|NP_041724.2|West Nile virus|11082 -LTYRHKVVK ->40253|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 -LVACHANCPTYRSHL ->40262|Cytochrome P450 2A7|P20853.1|Homo sapiens|9606 -LVALLACLTV ->40264|Cytochrome P450 2A6|P11509.3|Homo sapiens|9606 -LVALLVCLTV ->40286|SAG1 protein|AAO72426.1|Toxoplasma gondii RH|383379 -LVCGKDGVK ->40288|kaposin|AAC57155.1|Human gammaherpesvirus 8|37296 -LVCLLAISVVPPSGQ ->40447|Major surface antigen precursor|P12934.3|Hepatitis B virus|10407 -LVLLDYQGML ->40468|structural protein|BAA00705.1|Hepatitis C virus subtype 1a|31646 -LVMAQLLRI ->40470|Genome polyprotein|SRC279960|Hepatitis C virus|11103 -LVMAQLLRT ->40559|polyprotein|ADF97231.1|Hepatitis C virus subtype 3a|356426 -LVRLKPTL ->40624|DNA polymerase|CAA10434.1|Hepatitis B virus|10407 -LVVDFSQFSR ->40637|polyprotein|BAA03375.1|Hepatitis C virus|11103 -LVVSQLLRI ->40664|core|CAA59522.1|Hepatitis B virus|10407 -LWFHISCLTF ->40784|Genome polyprotein|P26662.3|Hepatitis C virus|11103 -LYGVWPLLL ->41082|Genome polyprotein|P26664.3|Hepatitis C virus (isolate 1)|11104 -MALTLSPY ->41085|polyprotein|ABR25251.1|Hepatitis C virus|11103 -MALYDVVSKLPLAVM ->41093|polyprotein|AGO67248.1|Dengue virus 2|11060 -MANIFRGSY ->41174|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 -MAYAQKIFKIL ->41269|kaposin|AAC57155.1|Human gammaherpesvirus 8|37296 -MDRGLTVFVAVHVPD ->41407|Envelope protein|NP_739583.2|Dengue virus 2|11060 -MENKAWLVHRQWFLD ->41482|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 -MFDSSVLCECYDAGC ->41622|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 -MGRSHFLCTFTFNSNNKEYT ->41898|polyprotein|AAF01178.1|Hepatitis C virus subtype 2a|31649 -MLAAQMFIV ->41971|putative D-ribose-binding protein|NP_301386.1|Mycobacterium leprae|1769 -MLILGLLPAILPACG ->42094|telomer length regulation protein TEL1|EDV12172.1|Saccharomyces cerevisiae|4932 -MLWGYLQYV ->42152|polyprotein|AAY82055.1|Hepatitis C virus (isolate H77)|63746 -MMMNWSPTT ->42290|protein antigen|AAA29733.1|Plasmodium falciparum|5833 -MPLETQLAI ->42295|Circumsporozoite protein precursor|P02893.1|Plasmodium falciparum|5833 -MPNDPNRNV ->42299|nonstructural protein 3|YP_001527884.1|West Nile virus|11082 -MPNGLIAQF ->42342|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 -MPVGGQSSF ->42430|Major surface antigen precursor|P03141.3|Hepatitis B virus|10407 -MQWNSTAFHQTLQDP ->42455|Probable Na(+)-translocating NADH-quinone reductase subunit A|O84639.1|Chlamydia trachomatis|813 -MRDHTITLL ->42672|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 -MSSTQIRTEIPVALL ->42737|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 -MTALEAVSLNGTRLA ->42797|6 kDa early secretory antigenic target|P0A564.2|Mycobacterium tuberculosis|1773 -MTEQQWNFAGIEAAASAIQG ->42819|polyprotein precursor|NP_041724.2|West Nile virus|11082 -MTKEEFTRY ->42897|RNA polymerase beta-subunit|AAA21416.1|Mycobacterium tuberculosis|1773 -MTYAAPLFV ->43089|Polyprotein|Q9IZA3|Hepatitis C virus subtype 2a|31649 -MYSSAEGDL ->43108|Major outer membrane porin, serovar E precursor|P17451.1|Chlamydia trachomatis|813 -NAACMALNI ->43310|polyprotein|AAW78019.1|Hepatitis C virus (isolate H77)|63746 -NASRCWVAM ->43447|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 -NDGVIFFFNPGELLPEAAGP ->43619|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -NEGCGWAGW ->43621|largest ORF|AAB02128.1|Hepatitis C virus (isolate H77)|63746 -NEGCGWMGW ->43624|Genome polyprotein|P26660.3|Hepatitis C virus isolate HC-J6|11113 -NEGLGWAGW ->43627|core protein|AAX68853.1|Hepatitis C virus subtype 1b|31647 -NEGLGWTGW ->43628|polyprotein|BAA03375.1|Hepatitis C virus subtype 1b|31647 -NEGMGWAGW ->43756|Genome polyprotein|SRC279960|Hepatitis C virus subtype 2a|31649 -NETCGWAGW ->43937|polyprotein|AAF01178.1|Hepatitis C virus subtype 2a|31649 -NFTRGDRCNL ->44133|Genome polyprotein|P26664.3|Hepatitis C virus genotype 1|41856 -NHDSPDAEL ->44214|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 -NIEFFTKNSAF ->44327|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis H37Rv|83332 -NIRQAGVQY ->44649|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 -NLAMAIAKSVPVYGM ->44653|6 kDa early secretory antigenic target|P0A564.2|Mycobacterium tuberculosis|1773 -NLARTISEAGQAMASTEGNV ->44802|PE-PGRS family protein|ZP_02552202.1|Mycobacterium tuberculosis|1773 -NLLVTGFDT ->44833|polyprotein|BAA03375.1|Hepatitis C virus subtype 1a|31646 -NLPGCSFSI ->44920|tegument protein pp65|YP_002608275.1|Human betaherpesvirus 5|10359 -NLVPMVATV ->44976|Major outer membrane porin, serovar A precursor|P23732.1|Chlamydia trachomatis|813 -NMFTPYIGV ->45374|nucleocapsid protein|AEQ63625.1|Respiratory syncytial virus|12814 -NPKASLLSL ->45652|Probable ATP-dependent Clp protease ATP-binding subunit|O84288.1|Chlamydia trachomatis|813 -NRAKQVIKL ->45672|hypothetical protein CT847|NP_220368.1|Chlamydia trachomatis|813 -NRELIQQEL ->45677|Probable outer membrane protein pmpC precursor|O84419.1|Chlamydia trachomatis|813 -NRFSVAYML ->45749|glycoprotein gp35/37|AAC59622.1|Human gammaherpesvirus 8|37296 -NRVPFSATTTTTRGR ->46243|E2 protein|NP_751921.1|Hepatitis C virus (isolate H77)|63746 -NTRPPLGNWF ->46480|DNA polymerase|CAA10434.1|Hepatitis B virus|10407 -NVSIPWTHK ->46499|6 kDa early secretory antigenic target|P0A564.2|Mycobacterium tuberculosis|1773 -NVTSIHSLL ->46575|polyprotein|AAG30730.1|Dengue virus 2|11060 -NYADRKWCF ->46576|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 -NYADRRWCF ->46625|hypothetical glycine-rich protein Rv3812 - Mycobacterium tuberculosis (strain H37RV)|H70520|Mycobacterium tuberculosis|1773 -NYIPQQLAL ->46672|Periplasmic L-asparaginase II precursor|YP_169502.1|Francisella tularensis subsp. tularensis SCHU S4|177416 -NYNNLDDKF ->46713|Polyprotein|Q9IZA3|Hepatitis C virus subtype 2a|31649 -NYTIFKIRM ->46755|HCV-1|AAA45676.1|Hepatitis C virus genotype 1|41856 -PAAYAAQGYKVLVLNPSVAA ->46931|||| -PARLLLKATLCIPHV ->47005|RL2|CAB06705.1|Human alphaherpesvirus 2|10310 -PAWSRRTLL ->47017|Genome polyprotein|P26664.3|Hepatitis C virus genotype 1|41856 -PCEPEPDVAVL ->47760|EBNA-1 protein|Q777E1|Human gammaherpesvirus 4|10376 -PGTGPGNGLGEKGDT ->47854|Glycoprotein I precursor (Glycoprotein IV) (GI) (GPIV)|P09258.1|Human alphaherpesvirus 3|10335 -PHSVVNPFVK ->47946|envelope glycoprotein|AAC28452.1|Human immunodeficiency virus 1|11676 -PIPIHYCAPAGFAILKCNNK ->48321|||| -PLFGYPVYV ->48458|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 -PLPVVFPIVQGELSKQTGQQ ->48836|EBNA-1 protein|Q777E1|Human gammaherpesvirus 4|10376 -PPMVEGAAAEGDDGD ->48896|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 -PPQPEYDLELITSCS ->48915|kaposin|AAC57155.1|Human gammaherpesvirus 8|37296 -PPSGQRGPVAFRTRV ->49485|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 -PSQEPMSIYVY ->49831|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 -PVALLILCLCLVACH ->50089|Genome polyprotein|P26662.3|Hepatitis C virus|11103 -PYFVRAQGLI ->50104|polyprotein|BAA25076.1|Hepatitis C virus|11103 -PYIEQGMQL ->50124|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 -PYKRIEELL ->50130|membrane protein|AAA45887.1|Human gammaherpesvirus 4|10376 -PYLFWLAAIA ->50253|DNA polymerase|CAA10434.1|Hepatitis B virus|10407 -QAFTFSPTYK ->50292|gag protein|ACR27140.1|Human immunodeficiency virus 1|11676 -QAISPRTLNAW ->50298|EBNA3A nuclear protein|Q8AZJ8|Human gammaherpesvirus 4|10376 -QAKWRLQTL ->50586|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 -QEFFWDANDIY ->50596|polyprotein|ABG75765.1|Dengue virus 1|11053 -QEGAMHTAL ->50779|N protein|AAP13445.1|SARS coronavirus Urbani|228330 -QFKDNVILL ->50894|Genome polyprotein|P27909.2|Dengue virus type 1 Hawaii|10000440 -QGKRLEPSWASVKKDLISYG ->51089|UL123; IE1|AAR31390.1|Human betaherpesvirus 5|10359 -QIKVRVDMV ->51104|LOW MOLECULAR WEIGHT PROTEIN ANTIGEN 7 ESXH (10 kDa ANTIGEN) (CFP-7) (PROTEIN TB10.4)|CAA17363.1|Mycobacterium tuberculosis H37Rv|83332 -QIMYNYPAM ->51250|nucleocapsid protein|ABI96968.1|SARS coronavirus|227859 -QKRTATKQYNVTQAF ->51311|X protein|ABR68906.1|Hepatitis B virus|10407 -QLDPARDVL ->51342|myosin-9|NP_002464.1|Homo sapiens|9606 -QLFNHTMFI ->51346|Genome polyprotein|P29846.3|Hepatitis C virus|11103 -QLFTFSPRR ->51351|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 -QLGAFLTNV ->51388|polyprotein|AGO67248.1|Dengue virus 2|11060 -QLKGMSYSM ->51410|hypothetical protein ML1057|NP_301777.1|Mycobacterium leprae|1769 -QLLGQTADV ->51526|HCV-1|AAA45676.1|Hepatitis C virus|11103 -QLRRHIDLLV ->51528|Genome polyprotein|SRC279960|Hepatitis C virus genotype 1|41856 -QLRRIDLLV ->51532|polyprotein|AAA45534.1|Hepatitis C virus|11103 -QLSAPSLKATCTANH ->51562|polyprotein|AGO67248.1|Dengue virus 2|11060 -QLTYVVIAIL ->51604|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 -QMDYSNGLFV ->51643|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 -QMSDPAYNINISLPSYYPDQ ->51685|Nuclear antigen EBNA-3C|Q69140.1|Human gammaherpesvirus 4|10376 -QNGALAINTF ->51805|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 -QPEKGGRKPA ->51946|EBNA3C latent protein|CAD53421.1|Human gammaherpesvirus 4|10376 -QPRAPIRPI ->51947|EBNA3C latent protein|CAD53421.1|Human gammaherpesvirus 4|10376 -QPRAPIRPIPT ->52287|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 -QSALKLAIYK ->52431|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 -QSSFYSDWY ->52496|polyprotein precursor|NP_041724.2|West Nile virus|11082 -QTDNQLAVF ->52509|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 -QTFLATCINGVCWTV ->52578|liver stage antigen-1|CAA82974.1|Plasmodium falciparum|5833 -QTNFKSLLR ->52652|||| -QTTVVGGSQSHTVRGLTSLFSPGASQN ->52666|Antigen 85-B|P0C5B9.1|Mycobacterium tuberculosis|1773 -QTYKWETFL ->52746|Nucleoprotein|P03418.1|Human respiratory syncytial virus A2|11259 -QVMLRWGVL ->52760|nef protein|ACR27174.1|Human immunodeficiency virus 1|11676 -QVPLRPMTYK ->52886|pp65|AAA45994.1|Human betaherpesvirus 5|10359 -QYDPVAALF ->52888|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 -QYDPVAALFFF ->53027|nonstructural protein 3|NP_722463.1|Dengue virus 1 Singapore/S275/1990|33741 -QYSDRRWCF ->53041|phosphorylated matrix protein (pp65)|AAA45996.1|Human betaherpesvirus 5|10359 -QYTPDSTPCHR ->53077|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis|1773 -RADEEQQQAL ->53114|envelope glycoprotein|ABI16336.1|Human immunodeficiency virus 1|11676 -RAIEAQQHL ->53128|BZLF1|AAA66529.1|Human gammaherpesvirus 4|10376 -RAKFKQLL ->53129|BZLF1|AAA66529.1|Human gammaherpesvirus 4|10376 -RAKFKQLLQ ->53148|Transcription activator BRLF1|P03209.1|Human herpesvirus 4 strain B95-8|10377 -RALIKTLPRASYSSH ->53201|Fusion glycoprotein F0 precursor|P03420.1|Human respiratory syncytial virus A2|11259 -RARRELPRF ->53246|polyprotein precursor|AAF20092.2|West Nile virus|11082 -RAWNSGYEW ->53341|envelope protein|YP_001527880.1|West Nile virus NY-99|10000971 -RDFLEGVSGATWVDLVL ->53370|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 -RDKFLSAATSSTPREAPYEL ->53405|||| -RDPAKPARLLLKATL ->53437|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 -RDWAHNGL ->53476|polyprotein|AGO67248.1|Dengue virus 2|11060 -REDQWCGSL ->53541|Genome polyprotein|P26664.3|Hepatitis C virus (isolate 1)|11104 -REISVPAEIL ->53953|kaposin|AAC57155.1|Human gammaherpesvirus 8|37296 -RGPVAFRTRVATGAH ->54175|envelope glycoprotein|ACR43875.1|Human immunodeficiency virus 1|11676 -RIKQIINMW ->54176|Polyprotein|Q9J8D4|Dengue virus 2|11060 -RIKQKGIL ->54330|BZLF1|AAA66529.1|Human gammaherpesvirus 4|10376 -RKCRAKFKQLLQH ->54342|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 -RKEVNSQLSLGDPLFPELAE ->54501|nonstructural protein 2B|YP_001527883.1|West Nile virus NY-99|10000971 -RLDDDGNFQL ->54504|possible regulatory protein|NP_302009.1|Mycobacterium leprae|1769 -RLDGTTLEV ->54568|polyprotein|BAA03375.1|Hepatitis C virus|11103 -RLGVRATRK ->54587|monooxygenase family protein|YP_170175.1|Francisella tularensis subsp. tularensis SCHU S4|177416 -RLIGHISTL ->54605|HCV-1|AAA45676.1|Hepatitis C virus|11103 -RLIVFPDLGV ->54650|polyprotein|AAU89634.1|Hepatitis C virus subtype 2a|31649 -RLLLLGLLLL ->54654|trans-sialidase|XP_816729.1|Trypanosoma cruzi|5693 -RLLPSLLLLL ->54662|pX-rex-orf I {alternatively spliced}|AAB23359.1|Human T-lymphotropic virus 1|11908 -RLLSPLSPL ->54664|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 -RLLSPTTIV ->54680|Spike glycoprotein precursor|P59594.1|SARS coronavirus|227859 -RLNEVAKNL ->54686|Major outer membrane porin, serovar E precursor|P17451.1|Chlamydia trachomatis|813 -RLNMFTPYI ->54690|Nucleoprotein|P59595.1|SARS coronavirus|227859 -RLNQLESKV ->54704|hydrolase|WP_015628351.1|Mycobacterium tuberculosis|1773 -RLPLVLPAV ->54706|matrix protein 2-1|AAS22094.1|Human metapneumovirus|162145 -RLPREKLKK ->54709|protein F [Hepatitis C virus subtype 1b]|ACA50643.1|Hepatitis C virus (isolate Japanese)|11116 -RLPSGRNLV ->54728|EBNA3A nuclear protein|Q8AZJ8|Human gammaherpesvirus 4|10376 -RLRAEAQVK ->54730|envelope glycoprotein|AAB06256.1|Human immunodeficiency virus 1|11676 -RLRDLLLIVTR ->54741|gag polyprotein|BAA00992.1|Human immunodeficiency virus 1|11676 -RLRPGGKKK ->54797|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 -RLTVSGLAWTR ->54819|JK3|CAA43789.1|Hepatitis C virus|11103 -RLWHYPCTA ->54820|polyprotein precursor|BAA02756.1|Hepatitis C virus|11103 -RLWHYPCTF ->54821|E2 protein|AAM33354.1|Hepatitis C virus subtype 1a|31646 -RLWHYPCTI ->54824|polyprotein precursor|BAA01583.1|Hepatitis C virus|11103 -RLWHYPCTL ->54825|polyprotein|BAA03375.1|Hepatitis C virus|11103 -RLWHYPCTV ->54903|Genome polyprotein|P26663.3|Hepatitis C virus|11103 -RMILMTHFF ->54965|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 -RMYVGGVEHR ->55029|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 -RNLVPMVATVQ ->55102|polyprotein precursor|NP_041724.2|West Nile virus|11082 -RPAADGKTV ->55184|Nucleoprotein|P41269.1|Puumala hantavirus|11604 -RPKHLYVSM ->55226|HCV-1|AAA45676.1|Hepatitis C virus|11103 -RPLTDFDQGW ->55251|Epstein-Barr nuclear antigen 3|SRC279942|Human gammaherpesvirus 4|10376 -RPPIFIRLL ->55252|EBNA3A nuclear protein|Q8AZJ8|Human gammaherpesvirus 4|10376 -RPPIFIRRL ->55253|EBNA3A nuclear protein|Q8AZJ8|Human gammaherpesvirus 4|10376 -RPPIFIRRLH ->55295|Early antigen protein D|P03191.1|Human herpesvirus 4 strain B95-8|10377 -RPQGGSRPEFVKL ->55320|tegument protein VP22|NP_044519.1|Human alphaherpesvirus 2|10310 -RPRGEVRFL ->55336|EBNA-1|YP_401677.1|Human gammaherpesvirus 4|10376 -RPSCIGCKGTHGGTG ->55526|glycoprotein D|AAB60552.1|Human alphaherpesvirus 2|10310 -RRAQMAPKR ->55620|EBNA3C latent protein|CAD53421.1|Human gammaherpesvirus 4|10376 -RRIYDLIEL ->55683|nucleocapsid protein|ABI96968.1|SARS coronavirus|227859 -RRPQGLPNNTASWFT ->55709|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 -RRRGDSRGSLLSPRP ->55718|Probable membrane glycoprotein precursor|P03218.1|Human herpesvirus 4 strain B95-8|10377 -RRRKGWIPL ->55734|membrane protein|AAA45887.1|Human gammaherpesvirus 4|10376 -RRRWRRLTV ->55744|polyprotein precursor|NP_041724.2|West Nile virus|11082 -RRSRRSLTV ->55779|fusion protein|BAB60865.1|Measles virus|11234 -RRYPDAVYL ->55881|polyprotein precursor|NP_041724.2|West Nile virus|11082 -RSLFGGMSW ->56198|glycoprotein gp35/37|AAC59622.1|Human gammaherpesvirus 8|37296 -RTTRIRVSPVAENGR ->56247|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 -RVCEKMALY ->56310|polyprotein|AGO67248.1|Dengue virus 2|11060 -RVIDPRRCMK ->56343|structural protein|BAA00705.1|Hepatitis C virus|11103 -RVLEDGVNYA ->56344|polyprotein precursor|NP_041724.2|West Nile virus|11082 -RVLEMVEDW ->56390|Transcription activator BRLF1|P03209.1|Human herpesvirus 4 strain B95-8|10377 -RVRAYTYSK ->56502|polyprotein|BAD73994.1|Hepatitis C virus subtype 1b|31647 -RYAPACKPL ->56574|envelope glycoprotein|ABI16336.1|Human immunodeficiency virus 1|11676 -RYLKDQQLL ->56589|polyprotein precursor|NP_041724.2|West Nile virus|11082 -RYLVKTESW ->56620|Nef protein|Q9YYU8|Human immunodeficiency virus 1|11676 -RYPLTFGWCF ->56646|nucleocapsid protein|AAA43837.1|Hantaan virus 76-118|11602 -RYRTAVCGL ->56650|EBNA3A nuclear protein|Q8AZJ8|Human gammaherpesvirus 4|10376 -RYSIFFDY ->56814|DNA polymerase|CAA10434.1|Hepatitis B virus|10407 -SAICSVVRR ->56861|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 -SALKLAIYKA ->57313|Polyprotein|Q9IZA3|Hepatitis C virus|11103 -SDWAANGL ->57361|Genome polyprotein|SRC279960|Hepatitis C virus (isolate H77)|63746 -SECCTPCSGSW ->57364|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -SECTTPCSGSW ->57438|gag protein|ABO73990.1|Human immunodeficiency virus 1|11676 -SEGATPQDL ->57560|BZLF1|AAA66529.1|Human gammaherpesvirus 4|10376 -SENDRLRLL ->57591|Cobalamin (vitamin B12) synthesis protein/P47K family protein|YP_169986.1|Francisella tularensis subsp. tularensis SCHU S4|177416 -SEPLPVATTF ->57628|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 -SESSFFNLI ->57703|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 -SEYPNVSVSVEDTSA ->57723|polyprotein|CAB53095.1|Hepatitis C virus|11103 -SFAIKWEYVL ->57790|Protein Tax-1|P03409.2|Human T-lymphotropic virus 1|11908 -SFHSLHLLF ->57828|Protein Tax-1|P03409.2|Human T-lymphotropic virus 1|11908 -SFLLSHGLI ->57893|polyprotein|BAA03375.1|Hepatitis C virus|11103 -SFSIFLLAL ->57894|polyprotein|BAD73987.1|Hepatitis C virus subtype 1b|31647 -SFSIFLLALL ->57986|envelope glycoprotein|AAK62756.1|West Nile virus|11082 -SGATWVDLV ->57987|envelope protein|YP_001527880.1|West Nile virus NY-99|10000971 -SGATWVDLVLEGDSCVTI ->58122|pol protein|BAA32832.1|Hepatitis B virus|10407 -SGLPRYVARL ->58249|glycoprotein gp35/37|AAC59622.1|Human gammaherpesvirus 8|37296 -SGSYSSGEPSRTTRI ->58446|pX-rex-orf I|SRC240587|Human T-lymphotropic virus 1|11908 -SIAINPQLL ->58463|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 -SICPSQEPMSIYVYALPLKM ->58721|VP1|BAB68863.1|JC polyomavirus|10632 -SITEVECFL ->58740|Major surface antigen precursor|P03142.4|Hepatitis B virus|10407 -SIVSPFIPLL ->59020|Genome polyprotein|P29846.3|Hepatitis C virus (isolate Taiwan)|31645 -SLASLFTQGA ->59021|polyprotein|AAN40570.2|Hepatitis C virus|11103 -SLASLFTSGA ->59044|Major outer membrane porin, serovar E precursor|P17451.1|Chlamydia trachomatis|813 -SLDQSVVEL ->59088|polyprotein precursor|NP_041724.2|West Nile virus|11082 -SLFGGMSWI ->59089|nonstructural protein 4B|YP_001527886.1|West Nile virus NY-99|10000971 -SLFGQRIEV ->59090|nonstructural protein 4B|YP_001527886.1|West Nile virus NY-99|10000971 -SLFGQRIEVKENFSMGEF ->59141|Circumsporozoite protein precursor|P08677.2|Plasmodium vivax strain Belem|31273 -SLGLVILLVL ->59153|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 -SLHSYSPGEINRVAA ->59154|polyprotein|AAP55688.1|Hepatitis C virus subtype 2a|31649 -SLHTGFLASL ->59182|attachment glycoprotein|ABQ58821.1|Human metapneumovirus|162145 -SLILIGITTL ->59240|HCV-1|AAA45676.1|Hepatitis C virus genotype 1|41856 -SLLAPGAKQNV ->59336|polyprotein|AAA45534.1|Hepatitis C virus genotype 1|41856 -SLMAFTAAV ->59459|Trans-sialidase|SRC7915|Trypanosoma cruzi|5693 -SLSHYFTLV ->59521|polyprotein|ACB87121.1|Hepatitis C virus subtype 1a|31646 -SLTPPHSAK ->59524|nonstructural protein 4B|YP_001527886.1|West Nile virus NY-99|10000971 -SLTSINVQA ->59551|Glycoprotein GP85 precursor|P03231.1|Human gammaherpesvirus 4|10376 -SLVIVTTFV ->59561|polyprotein precursor|NP_041724.2|West Nile virus|11082 -SLVNGVVRL ->59569|Genome polyprotein|P26662.3|Hepatitis C virus (isolate Japanese)|11116 -SLVSWLSQGP ->59585|polymerase|AAD16253.1|Hepatitis B virus|10407 -SLYADSPSV ->59594|Phosphate transport system permease protein PstA 1|SRC280197|Mycobacterium tuberculosis|1773 -SLYFGGICV ->59612|gag protein|ABI20203.1|Human immunodeficiency virus 1|11676 -SLYNTIAVL ->59613|Gag polyprotein|P03347.3|Human immunodeficiency virus 1|11676 -SLYNTVATL ->59627|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 -SMAGSSAMI ->59709|polyprotein|BAD73987.1|Hepatitis C virus subtype 1b|31647 -SMLTDPSHI ->59722|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 -SMNATLVQA ->59765|Genome polyprotein|SRC279960|Hepatitis C virus|11103 -SMVGNMAKV ->59766|Genome polyprotein|P27958.3|Hepatitis C virus (isolate H)|11108 -SMVGNWAKV ->59767|polyprotein|BAB18806.1|Hepatitis C virus subtype 1a|31646 -SMVGNWAKVL ->59786|Large envelope protein|P03138.3|Hepatitis B virus ayw/France/Tiollais/1979|490133 -SMYPSCCCTK ->59787|Hemagglutinin glycoprotein|P08362.1|Measles virus strain Edmonston|11235 -SMYRVFEVGV ->59975|pol protein|ACJ76655.1|Human immunodeficiency virus 1|11676 -SPAIFQSSM ->60009|Genome polyprotein|P26664.3|Hepatitis C virus genotype 1|41856 -SPDAELIEANL ->60031|SAG1 protein|AAO72426.1|Toxoplasma gondii RH|383379 -SPEKHHCTV ->60059|Genome polyprotein|P27958.3|Hepatitis C virus genotype 1|41856 -SPGEINRVAA ->60092|nucleocapsid protein|ABK96997.1|Human metapneumovirus|162145 -SPKAGLLSL ->60104|polyprotein|AGW21594.1|Dengue virus 1|11053 -SPKRLSAAI ->60238|Gag polyprotein|P03347.3|Human immunodeficiency virus 1|11676 -SPRTLNAWV ->60867|nucleoprotein|CAZ65591.1|Influenza A virus|11320 -SRYWAIRTR ->60931|latent membrane protein 2|AAB59844.1|Human gammaherpesvirus 4|10376 -SSCSSCPLSKI ->61077|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 -SSHSGSFQI ->61622|polyprotein|BAA03375.1|Hepatitis C virus|11103 -STGLIHLHQ ->61741|Core protein|Q9QAC5|Hepatitis B virus|10407 -STLPETTVV ->61745|C protein|CAB41699.1|Hepatitis B virus|10407 -STLPETTVVRR ->61787|HCV-1|AAA45676.1|Hepatitis C virus|11103 -STNPKPQK ->61788|HCV-1|AAA45676.1|Hepatitis C virus|11103 -STNPKPQKK ->61790|polyprotein|BAB18806.1|Hepatitis C virus|11103 -STNPKPQRK ->61861|Nucleoprotein|P03418.1|Human respiratory syncytial virus A2|11259 -STRGGSRVEGIFAG ->62004|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 -STWVLVGGVLAALAA ->62052|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 -SVASSSASQLSA ->62127|cysteine proteinase cruzipain (EC 3.4.22.-) - Trypanosoma cruzi|A45629|Trypanosoma cruzi|5693 -SVFRENLFL ->62139|envelope glycoprotein|AAK62756.1|West Nile virus|11082 -SVGGVFTSV ->62184|nonstructural protein 3|NP_722463.1|Dengue virus type 1 Hawaii|10000440 -SVKKDLISYGGGWRF ->62244|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 -SVMKRRIEEIC ->62305|EBNA3A nuclear protein|Q8AZJ8|Human gammaherpesvirus 4|10376 -SVRDRLARL ->62355|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 -SVTEQSEFYFPRAPLNSNAM ->62367|Genome polyprotein|SRC279960|Hepatitis C virus|11103 -SVTSFFTQGA ->62477|HBsAg protein|ABF71024.1|Hepatitis B virus|10407 -SWLSLLVPF ->62504|HBsAg protein|ABF71024.1|Hepatitis B virus|10407 -SWWTSLNFL ->62564|polyprotein precursor|AAF20092.2|West Nile virus|11082 -SYHDRRWCF ->62616|Chain A, Dengue Virus 4 Ns3 Helicase In Complex With Ssrna|2JLU_A|Dengue virus 4 Thailand/0348/1991|408688 -SYKDREWCF ->62713|polyprotein|AAP55688.1|Hepatitis C virus subtype 2a|31649 -SYSWTGALI ->62731|polyprotein|BAD73987.1|Hepatitis C virus subtype 1b|31647 -SYTWTGALI ->62797|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis|1773 -TAAQAAVVRF ->62799|10 kDa culture filtrate antigen EsxB|NP_218391.1|Mycobacterium tuberculosis H37Rv|83332 -TAAQAAVVRFQEAAN ->62900|viral protein 2|CAG70336.1|Human parvovirus B19|10798 -TAKSRVHPL ->62903|Genome polyprotein|P27909.2|Dengue virus type 1 Hawaii|10000440 -TAKWLWGFLSRNKKPRICTR ->62977|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 -TARHTPVNSW ->63010|6 kDa early secretory antigenic target|P0A564.2|Mycobacterium tuberculosis|1773 -TATELNNALQNLARTISEAG ->63285|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 -TEADVQQWL ->63286|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 -TEADVQQWLTW ->63508|gag protein|AAN03145.1|Human immunodeficiency virus 1|11676 -TERQANFL ->63582|polyprotein precursor|NP_041724.2|West Nile virus|11082 -TEVMTAVGL ->63784|Genome polyprotein|P26663.3|Hepatitis C virus|11103 -TGAPVTYSTY ->63963|HCV-1|AAA45676.1|Hepatitis C virus|11103 -TGSPITYSTY ->64286|polyprotein|AAB70696.1|Dengue virus type 1 Hawaii|10000440 -TIENTTANISLTAIA ->64312|M protein, serotype 5 precursor|P02977.2|Streptococcus pyogenes serotype M5|301449 -TIGTLKKILDETVKDKIA ->64320|Protein E6|P03126.1|Human papillomavirus type 16|333760 -TIHDIILECV ->64404|Genome polyprotein|P26664.3|Hepatitis C virus genotype 1|41856 -TINYTIFK ->64405|polyprotein|ACB87121.1|Hepatitis C virus|11103 -TINYTIFKI ->64412|PE_PGRS 33|AAU10330.1|Mycobacterium tuberculosis|1773 -TIPEALAAV ->64489|polyprotein|BAA03375.1|Hepatitis C virus|11103 -TITTGSPITYS ->64710|Membrane glycoprotein|Q692E0|SARS coronavirus TJF|284672 -TLACFVLAAV ->64727|polyprotein precursor|NP_041724.2|West Nile virus|11082 -TLARGFPFV ->64763|Early antigen protein D|P03191.1|Human herpesvirus 4 strain B95-8|10377 -TLDYKPLSV ->64769|kinetoplastid membrane protein KMP-11|EAN87014.1|Trypanosoma cruzi|5693 -TLEEFSAKL ->64794|Glycoprotein GP85 precursor|P03231.1|Human gammaherpesvirus 4|10376 -TLFIGSHVV ->64810|polyprotein|BAB18806.1|Hepatitis C virus|11103 -TLGFGAYMSK ->64818|E7|AAD33253.1|Human papillomavirus type 16|333760 -TLGIVCPI ->64819|E7 protein|ABL96585.1|Human papillomavirus type 16|333760 -TLGIVCPIC ->64821|Protein Tax-1|P03409.2|Human T-lymphotropic virus 1|11908 -TLGQHLPTL ->64830|E7 protein|ABL96585.1|Human papillomavirus type 16|333760 -TLHEYMLDL ->64948|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 -TLLYATVEV ->64967|Circumsporozoite protein precursor|P08677.2|Plasmodium vivax strain Belem|31273 -TLNDLETDV ->65090|polyprotein|BAB18810.1|Hepatitis C virus (isolate H77)|63746 -TLTHPITK ->65092|Genome polyprotein|P26664.3|Hepatitis C virus genotype 1|41856 -TLTHPVTK ->65118|SAG1 protein|AAO72426.1|Toxoplasma gondii RH|383379 -TLVCGKDGV ->65148|DNA polymerase|CAA10434.1|Hepatitis B virus|10407 -TLWKAGILYK ->65494|polyprotein|AAY82030.1|Hepatitis C virus|11103 -TPAETTVRL ->65497|HCV-1|AAA45676.1|Hepatitis C virus genotype 1|41856 -TPAETTVRLRAYMNTPGLPV ->65509|DNA polymerase|CAA10434.1|Hepatitis B virus|10407 -TPARVTGGVF ->65549|polyprotein|AGO67248.1|Dengue virus 2|11060 -TPEGIIPSM ->65550|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 -TPEGIIPSMFEPERE ->65567|polyprotein|AJE59927.1|Japanese encephalitis virus|11072 -TPFGQQRVF ->65589|nucleocapsid protein|AAA43837.1|Hantaan virus 76-118|11602 -TPGRYRTAV ->65654|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 -TPLRDWAHNGLRDLA ->65703|gag protein|CAB00235.1|Human immunodeficiency virus 1|11676 -TPQDLNTM ->65748|pp65|AAA45994.1|Human betaherpesvirus 5|10359 -TPRVTGGGAM ->65749|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 -TPRVTGGGAMA ->65810|sporozoite surface protein 2|NP_705260.1|Plasmodium falciparum 3D7|36329 -TPYAGEPAPF ->65817|envelope glycoprotein|AAL59843.1|Human immunodeficiency virus 1|11676 -TQACPKVSFEPIPIHYCAPA ->65929|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 -TQRTSKTLKVLTPPIT ->65965|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 -TQVLVPRSAIDSMLA ->66084|M protein, serotype 5 precursor|P02977.2|Streptococcus pyogenes serotype M5|301449 -TRQELANKQQESKENEKAL ->66106|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 -TRTIASPKGPVIQMY ->66195|Nucleoprotein|P41269.1|Puumala hantavirus|11604 -TSFEDINGIRRPKHL ->66405|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 -TSRSACQRQKKVTFDRLQVL ->66798|glycoprotein gp35/37|AAC59622.1|Human gammaherpesvirus 8|37296 -TTRGRDAHYNAEIRT ->67087|polyprotein|AAK32686.1|Hepatitis C virus|11103 -TVNFTIFKV ->67210|NS3 protein|NP_739587.1|Dengue virus 2 Thailand/NGS-C/1944|11065 -TVWFVPSIK ->67349|Latent membrane protein 2|Q69135|Human gammaherpesvirus 4|10376 -TYGPVFMCL ->67362|polyprotein|AGW21594.1|Dengue virus 1|11053 -TYGWNLVKL ->67382|Type IV pili associated protein|YP_170126.1|Francisella tularensis subsp. tularensis SCHU S4|177416 -TYLGIDLGF ->67385|HER2 receptor|AAA75493.1|Homo sapiens|9606 -TYLPTNASL ->67471|Genome polyprotein|Q99IB8.3|Hepatitis C virus JFH-1|356411 -TYSTYGKFL ->67503|Genome polyprotein|P26662.3|Hepatitis C virus|11103 -TYVYDHLTPL ->67596|Genome polyprotein|P26664.3|Hepatitis C virus (isolate 1)|11104 -VAGALVAFK ->67764|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 -VATDALMTGYTGDFD ->68194|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 -VEGEVQIVSTAAQTF ->68229|EBNA3B (EBNA4A) latent protein|CAA24858.1|Human gammaherpesvirus 4|10376 -VEITPYKPTW ->68443|polyprotein|AAF01178.1|Hepatitis C virus subtype 2a|31649 -VFDITKWLL ->68461|polyprotein|ACZ60108.1|Hepatitis C virus|11103 -VFFNILGGWV ->68521|Genome polyprotein|P26662.3|Hepatitis C virus|11103 -VFLVSQLFTF ->68549|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 -VFPTKDVALRH ->68562|unnamed protein product|BAA14233.1|Hepatitis C virus subtype 1b|31647 -VFSDMETKL ->68563|polyprotein|CAB53095.1|Hepatitis C virus subtype 1b|31647 -VFSDMETKV ->68581|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 -VFTGLTHIDAHFLSQTKQSG ->68601|polyprotein|AAA45534.1|Hepatitis C virus|11103 -VFVLNNTRPPLGNWF ->68605|Genome polyprotein|P26662.3|Hepatitis C virus|11103 -VFWAKHMWNF ->68694|Genome polyprotein|P26664.3|Hepatitis C virus (isolate 1)|11104 -VGIYLLPNR ->68908|nonstructural protein|AAC53959.1|Hepatitis C virus (isolate H77)|63746 -VIAPAVQTNW ->69076|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -VIPTSGDVVV ->69349|Genome polyprotein|P29846.3|Hepatitis C virus (isolate Taiwan)|31645 -VLAALAAYCL ->69387|fusion protein|ABQ58820.1|Human metapneumovirus|162145 -VLATAVREL ->69394|pol|AP_000202.1|Human adenovirus 5|28285 -VLAWTRAFV ->69398|X protein|AAP06597.1|Hepatitis B virus|10407 -VLCLRPVGA ->69404|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 -VLCPKNMIIKP ->69435|Genome polyprotein|SRC279960|Hepatitis C virus (isolate H77)|63746 -VLDSFKTWL ->69452|UL123; IE1|AAR31666.1|Human betaherpesvirus 5|10359 -VLEETSVML ->69474|core protein|BAF42671.1|Hepatitis B virus|10407 -VLEYLVSFGV ->69500|X protein|BAG70907.1|Hepatitis B virus|10407 -VLGGCRHKL ->69524|X protein|ACH95876.1|Hepatitis B virus|10407 -VLHKRTLGL ->69558|EBNA-1 protein|Q777E1|Human gammaherpesvirus 4|10376 -VLKDAIKDL ->69581|Major surface antigen precursor|P12934.3|Hepatitis B virus|10407 -VLLDYQGML ->69646|Alanine dehydrogenase|P30234.2|Mycobacterium tuberculosis|1773 -VLMGGVPGVE ->69649|myosin-9|NP_002464.1|Homo sapiens|9606 -VLMIKALEL ->69661|polyprotein precursor|NP_041724.2|West Nile virus|11082 -VLNETTNWL ->69671|polyprotein|AGO67248.1|Dengue virus 2|11060 -VLNPYMPSV ->69679|polyprotein|BAD73987.1|Hepatitis C virus subtype 1b|31647 -VLPCSFTTL ->69714|Large envelope protein|SRC279965|Hepatitis B virus|10407 -VLQAGFFIL ->69715|envelope protein|BAF48755.1|Hepatitis B virus|10407 -VLQAGFFLL ->69719|proteinase 3|AAH96184.1|Homo sapiens|9606 -VLQELNVTV ->69731|Major outer envelope glycoprotein gp350|Q66537|Human gammaherpesvirus 4|10376 -VLQWASLAV ->69750|polyprotein|AAC03058.1|Hepatitis C virus genotype 3|356114 -VLSDFKSWL ->69751|polyprotein|BAB18806.1|Hepatitis C virus genotype 1|41856 -VLSDFKTWL ->69753|polyprotein|AAK49500.1|Hepatitis C virus genotype 3|356114 -VLSDFRTWL ->69754|Lipoprotein lpqH precursor|P46733.1|Mycobacterium avium|1764 -VLSDGNPPQV ->69797|polyprotein|BAA09073.1|Hepatitis C virus subtype 1b|31647 -VLTDFKTWL ->69798|Lipoprotein lpqH precursor|P0A5J0.1|Mycobacterium tuberculosis|1773 -VLTDGNPPEV ->69799|envelope glycoprotein|BAE96221.1|Human immunodeficiency virus 1|11676 -VLTDPNPQEV ->69907|envelope|BAK20487.1|Human T-lymphotropic virus 1|11908 -VLYSPNVSV ->69913|cysteine proteinase cruzipain (EC 3.4.22.-) - Trypanosoma cruzi|A45629|Trypanosoma cruzi|5693 -VMACLVPAA ->69980|polyprotein|AAF01178.1|Hepatitis C virus subtype 2a|31649 -VMLAAQMFIV ->69991|Nucleoprotein|P03418.1|Human respiratory syncytial virus A2|11259 -VMLRWGVLAKSVKN ->69996|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 -VMMSCSSEA ->70017|membrane protein|AAA45887.1|Human gammaherpesvirus 4|10376 -VMSNTLLSAW ->70365|Truncated Nef protein|P04601.4|Human immunodeficiency virus 1|11676 -VPLRPMTYK ->70491|envelope glycoprotein|AAC28452.1|Human immunodeficiency virus 1|11676 -VPTDPNPPEV ->70516|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 -VPYKRIEEL ->70634|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 -VQQWLTWCN ->70687|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis|1773 -VQYSRADEEQQQALSSQMGF ->70789|Nucleoprotein|P41269.1|Puumala hantavirus|11604 -VRNIMSPVM ->70932|EBNA-3B nuclear protein|CAD53420.1|Human gammaherpesvirus 4|10376 -VSFIEFVGW ->71265|Circumsporozoite protein precursor|P02893.1|Plasmodium falciparum|5833 -VTCGNGIQVR ->71266|Circumsporozoite protein precursor|P02893.1|Plasmodium falciparum|5833 -VTCGNGIQVRIKPGSANKPK ->71290|DNA processivity factor|AAO73452.1|Human betaherpesvirus 5|10359 -VTEHDTLLY ->71409|cysteine proteinase cruzipain (EC 3.4.22.-) - Trypanosoma cruzi|A45629|Trypanosoma cruzi|5693 -VTLPTGQCL ->71412|polyprotein [Hepatitis C virus subtype 1a]|ABV46251.2|Hepatitis C virus subtype 1a|31646 -VTLTHPITK ->71616|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 -VVCMYLYQLSPPITW ->71631|polymerase|ACT90735.1|Hepatitis B virus|10407 -VVDFSQFSR ->71650|polyprotein precursor|AAP22088.1|West Nile virus|11082 -VVEKQSGLY ->71657|polyprotein|AAF01178.1|Hepatitis C virus subtype 2a|31649 -VVFDITKWLL ->71663|Spike glycoprotein precursor|P59594.1|SARS coronavirus|227859 -VVFLHVTYV ->71734|polyprotein|AAF01178.1|Hepatitis C virus subtype 2a|31649 -VVLDSLDPMV ->71756|cysteine proteinase cruzipain (EC 3.4.22.-) - Trypanosoma cruzi|A45629|Trypanosoma cruzi|5693 -VVMACLVPAA ->71847|core protein|AAL31859.1|Hepatitis B virus|10407 -VVSYVNTNMGLKFRQL ->71988|Protein E6|P03126.1|Human papillomavirus type 16|333760 -VYDFAFRDL ->72006|polyprotein|BAD73994.1|Hepatitis C virus subtype 1b|31647 -VYEAADMIM ->72038|Polyprotein|Q9IZA3|Hepatitis C virus subtype 2a|31649 -VYHGAGNKTL ->72039|polyprotein|CAB53095.1|Hepatitis C virus subtype 1b|31647 -VYHGAGSKTL ->72165|Genome polyprotein|P26662.3|Hepatitis C virus|11103 -VYSTTSRSASL ->72233|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 -WAIKWEYVVLLFLLL ->72261|Gag polyprotein|P03347.3|Human immunodeficiency virus 1|11676 -WASRELERF ->72269|glycoprotein gp35/37|AAC59622.1|Human gammaherpesvirus 8|37296 -WAVGLLLGLVLILYL ->72301|envelope protein|YP_001527880.1|West Nile virus NY-99|10000971 -WDFGSVGGVFTSVGKAVH ->72322|polyprotein|AAA86907.1|Hepatitis C virus|11103 -WDMMMNWSPTAALVV ->72563|polyprotein|AAB70696.1|Dengue virus type 1 Hawaii|10000440 -WHYDEDNPYKTWAYHGSYEV ->72564|JK3|CAA43789.1|Hepatitis C virus subtype 1b|31647 -WHYPCTANF ->72566|polyprotein|BAD73987.1|Hepatitis C virus subtype 1b|31647 -WHYPCTVNF ->72621|cysteine proteinase cruzipain (EC 3.4.22.-) - Trypanosoma cruzi|A45629|Trypanosoma cruzi|5693 -WIIKNSWTA ->72721|hypothetical protein FTT0869|YP_169869.1|Francisella tularensis subsp. tularensis SCHU S4|177416 -WLGNHGFEV ->72722|polyprotein|AAF01178.1|Hepatitis C virus subtype 2a|31649 -WLGNIIQYA ->72790|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 -WLSDCGEAL ->72794|Large envelope protein|P03138.3|Hepatitis B virus|10407 -WLSLLVPFV ->72842|polyprotein|ABG67747.1|West Nile virus|11082 -WMDSTKATRY ->72928|Genome polyprotein|P26662.3|Hepatitis C virus (isolate Japanese)|11116 -WPAPPGARSM ->72929|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 -WPAPQGSRSLTPCTC ->72979|Major outer membrane porin, serovar A precursor|P23732.1|Chlamydia trachomatis|813 -WQASLALSY ->72985|LOW MOLECULAR WEIGHT PROTEIN ANTIGEN 7 ESXH (10 kDa ANTIGEN) (CFP-7) (PROTEIN TB10.4)|CAA17363.1|Mycobacterium tuberculosis H37Rv|83332 -WQGDTGITY ->73059|kaposin|AAC57155.1|Human gammaherpesvirus 8|37296 -WRWRLGAIPPLVCLL ->73177|protein F [Hepatitis C virus subtype 1b]|ACA50643.1|Hepatitis C virus (isolate Japanese)|11116 -WVCARLGRL ->73296|hemK protein homolog|YP_169235.1|Francisella tularensis subsp. tularensis SCHU S4|177416 -WYTNLDTDKF ->73306|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 -WYYQSGLSI ->73862|EBNA-1 protein|Q777E1|Human gammaherpesvirus 4|10376 -YFMVFLQTHIFAEVL ->74020|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -YGKAIPLEVI ->74180|reverse transcriptase|CAJ26826.1|Hepatitis B virus|10407 -YIDDVVLGA ->74288|Protein E7|P36831.1|Human papillomavirus type 52|10618 -YILDLQPETT ->74305|Nonstructural protein NS5|NP_739590.2|Dengue virus 2 Thailand/NGS-C/1944|11065 -YILRDVSKK ->74386|HCV-1|AAA45676.1|Hepatitis C virus|11103 -YISWCLWW ->74387|Genome polyprotein|P26664.3|Hepatitis C virus (isolate 1)|11104 -YISWCLWWL ->74407|polyprotein|AAU89634.1|Hepatitis C virus subtype 2a|31649 -YIVRWEWVV ->74545|TcP2beta|CAA52943.1|Trypanosoma cruzi|5693 -YLAAYALVGL ->74558|polyprotein|AGW21594.1|Dengue virus 1|11053 -YLAGAGLAF ->74590|glycoprotein gp35/37|AAC59622.1|Human gammaherpesvirus 8|37296 -YLCVPRCRRKKPYIV ->74605|Circumsporozoite protein precursor|P08677.2|Plasmodium vivax strain Belem|31273 -YLDKVRATV ->74635|matrix protein|AEQ63649.1|Respiratory syncytial virus|12814 -YLEKESIYY ->74768|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 -YLLDGLRAQ ->74774|LMP1 protein (Epstein-Barr virus, putative LYDMA gene)|Q777A4|Human gammaherpesvirus 4|10376 -YLLEMLWRL ->74797|polyprotein|BAA09073.1|Hepatitis C virus subtype 1b|31647 -YLLPRRGPR ->74798|polyprotein|BAA03375.1|Hepatitis C virus|11103 -YLLPRRGPRL ->74800|Genome polyprotein|SRC279960|Hepatitis C virus subtype 2b|31650 -YLLPSRGPKL ->74886|latent membrane protein 1|AAS99606.1|Human gammaherpesvirus 4|10376 -YLQQNWWTL ->74961|polyprotein|ABU97067.1|Hepatitis C virus subtype 1b|31647 -YLVAYQATV ->74988|polyprotein|BAB18806.1|Hepatitis C virus|11103 -YLVTRHADV ->75024|Protein Tax-1|P03409.2|Human T-lymphotropic virus 1|11908 -YLYQLSPPI ->75040|Protein P|P03159.1|Hepatitis B virus|10407 -YMDDVVLGA ->75074|Protein E7|P03129.1|Human papillomavirus type 16|333760 -YMLDLQPET ->75075|E7 protein|ABL96585.1|Human papillomavirus type 16|333760 -YMLDLQPETT ->75356|EBNA3A nuclear protein|Q8AZJ8|Human gammaherpesvirus 4|10376 -YPLHEQHGM ->75376|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -YPPKPCGI ->75408|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 -YPSAAERKHRHLPVADAVIH ->75435|largest ORF|AAB02128.1|Hepatitis C virus|11103 -YPWPLYGNEGCGWMGWLLSP ->75436|Polyprotein|P90247|Hepatitis C virus|11103 -YPWPLYGNEGLGWAGWLLSP ->75438|polyprotein|AAF65962.1|Hepatitis C virus|11103 -YPWPLYGNEGMGWAGWLLSP ->75448|polyprotein|BAB18806.1|Hepatitis C virus|11103 -YPYRLWHY ->75495|6 kDa early secretory antigenic target|P0A564.2|Mycobacterium tuberculosis|1773 -YQGVQQKWDATATELNNALQ ->75614|polyprotein precursor|NP_041724.2|West Nile virus|11082 -YRHKVVKVM ->75632|predicted Efflux Protein|NP_220159.1|Chlamydia trachomatis|813 -YRLLLTRVL ->75636|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 -YRLWHYPCTI ->75673|Early antigen protein D|P03191.1|Human herpesvirus 4 strain B95-8|10377 -YRSGIIAVV ->75674|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 -YRSHLGFWQEGWSGQ ->75718|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 -YSEHPTFTSQY ->76121|polyprotein precursor|NP_041724.2|West Nile virus|11082 -YTMDGEYRL ->76245|reverse transcriptase|CAJ26474.1|Hepatitis B virus|10407 -YVDDVVLGA ->76277|Genome polyprotein|SRC279960|Hepatitis C virus|11103 -YVGDLCGCV ->76333|BRLF1|ABB89247.1|Human gammaherpesvirus 4|10376 -YVLDHLIVV ->76334|Protein E7|P17387.1|Human papillomavirus type 31|10585 -YVLDLQPEAT ->76370|core protein|BAF42671.1|Hepatitis B virus|10407 -YVNVNMGLK ->76529|polyprotein|ABU97067.1|Hepatitis C virus subtype 1b|31647 -YYKVFLARL ->76532|outer membrane protein|YP_170495.1|Francisella tularensis subsp. tularensis SCHU S4|177416 -YYLDRGYLDF ->76591|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -YYRGLDVSVI ->76621|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 -YYTSAFVFPTK ->78346|BARF1 protein|CAD53469.1|Human gammaherpesvirus 4|10376 -AFLGERVTL ->78382|BARF1 protein|CAD53469.1|Human gammaherpesvirus 4|10376 -FLGERVTLT ->78432|BARF1 protein|CAD53469.1|Human gammaherpesvirus 4|10376 -KLGPGEEQV ->78501|BARF1 protein|CAD53469.1|Human gammaherpesvirus 4|10376 -RFIAQLLLL ->78534|BARF1 protein|CAD53469.1|Human gammaherpesvirus 4|10376 -TLTSYWRRV ->79180|tax protein|AAF37566.1|Human T-lymphotropic virus 1|11908 -DCLPTTLFQPVRAPV ->79208|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 -EYTNIPISLLFNEKEA ->79294|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 -LLFGYPVYVFGDCVQ ->79300|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 -LSFPDPGLRPQNLYT ->79308|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 -MEPTLGQHLPTLSFPD ->79337|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 -PPITWPLLPHVIFCH ->79351|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 -QNLYTLWGGSVVCMYLY ->79390|Protein Tax-1|P0C213.1|Human T-cell lymphotropic virus type 1 (african isolate)|39015 -SFHNLHLLFEEYTNI ->79454|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 -VIFCHPGQLGAFLTN ->79506|E1 protein|BAA19893.1|Rubella virus|11041 -AFGHSDAACWGFPTDTVMSV ->79601|envelope protein|BAF48755.1|Hepatitis B virus|10407 -LLCLIFLLVL ->79628|E1 protein|BAA19893.1|Rubella virus|11041 -PTDVSCEGLGAWVPTAPCARI ->88377|IE62|AAP32859.1|Human alphaherpesvirus 3|10335 -SAPLPSNRV ->88849|IE62|AAP32859.1|Human alphaherpesvirus 3|10335 -SLPRSRTPI ->92301|ATP-dependent Clp protease proteolytic subunit|NP_216976.1|Mycobacterium tuberculosis H37Rv|83332 -AIYDTMQYV ->92817|secreted antigen 85-B fbpB (85B) (antigen 85 complex B) (Mycolyl transferase 85B) (fibronectin-binding protein B) (extracellular alpha-antigen)|NP_216402.1|Mycobacterium tuberculosis H37Rv|83332 -GLAGGAATA ->93224|core protein|AAL31859.1|Hepatitis B virus|10407 -LEDPASRDLVVSYV ->93270|hypothetical protein|NP_218356.1|Mycobacterium tuberculosis H37Rv|83332 -LLYDGSFAV ->93431|pre-C/C protein|ABY54138.1|Hepatitis B virus|10407 -MQLFHLCLIISCTCPTVQAS ->93536|core protein|AAL31859.1|Hepatitis B virus|10407 -PAYRPPNAPIL ->95234|latent membrane protein 1|AAS99606.1|Human gammaherpesvirus 4|10376 -ALLVLYSFA ->95261|LAMP|AAK72632.1|Human gammaherpesvirus 8|37296 -ATVKTGNIKL ->95262|LAMP|AAK72632.1|Human gammaherpesvirus 8|37296 -ATVKTGNIKLVSSVS ->95264|Genome polyprotein|O92532.3|Hepatitis C virus genotype 6|42182 -AVNGVLWTV ->95265|polyprotein|ABL63009.1|Hepatitis C virus genotype 4|33745 -AVNGVMWTV ->95278|polyprotein|BAC67110.1|Hepatitis C virus|11103 -CINGVCWSI ->95279|polyprotein|BAG31965.1|Hepatitis C virus|11103 -CINGVCWSV ->95280|Genome polyprotein|O39928.3|Hepatitis C virus genotype 5|33746 -CINGVMWTL ->95281|polyprotein|ACE82433.1|Hepatitis C virus genotype 1|41856 -CISGVCWTV ->95297|polyprotein|BAA09072.1|Hepatitis C virus genotype 1|41856 -CTNGVCWTV ->95298|Genome polyprotein|Q913V3.1|Hepatitis C virus (isolate 1)|11104 -CVNGACWTV ->95854|Genome polyprotein|O39927.3|Hepatitis C virus genotype 6|42182 -SINGVMWTV ->95890|polyprotein|ABE98152.1|Hepatitis C virus genotype 6|42182 -SVNGVMWTV ->95908|Genome polyprotein|O92529.3|Hepatitis C virus genotype 6|42182 -TINGVLWTV ->95937|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 -TVGGVMWTV ->95940|polyprotein|BAA32666.1|Hepatitis C virus genotype 6|42182 -TVNGVLWTV ->96120|polyprotein|BAB18806.1|Hepatitis C virus (isolate H77)|63746 -ATLGFGAYMSKA ->96123|Genome polyprotein|P26664.3|Hepatitis C virus (isolate H77)|63746 -AVFGPLWIL ->96156|polyprotein|ABR25251.1|Hepatitis C virus (isolate H77)|63746 -CVTQTVDFSLDPTFTIETTTL ->96257|Genome polyprotein|SRC279960|Hepatitis C virus|11103 -EPEPDVAW ->96346|Genome polyprotein|SRC279960|Hepatitis C virus (isolate H77)|63746 -GVDPNVRTGVRT ->96358|polyprotein|BAB18806.1|Hepatitis C virus (isolate H77)|63746 -HAVGIFRAA ->96365|polyprotein|AAB66324.1|Hepatitis C virus (isolate H77)|63746 -HPTLVFDITKL ->96366|polyprotein|ABR25251.1|Hepatitis C virus|11103 -HRFAPPCKPLLR ->96369|polyprotein|BAB18810.1|Hepatitis C virus|11103 -HVVGIFRAA ->96547|Genome polyprotein|Q913D4.3|Hepatitis C virus (isolate H77)|63746 -LFFNILGGWV ->96601|polyprotein|ABR25251.1|Hepatitis C virus (isolate H77)|63746 -LPYIEQGMML ->96633|polyprotein|ABR25251.1|Hepatitis C virus (isolate H77)|63746 -LYGMWPLLL ->96827|Genome polyprotein|SRC279960|Hepatitis C virus (isolate H77)|63746 -RLADFAQGW ->96836|polyprotein|ABR25251.1|Hepatitis C virus (isolate H77)|63746 -RQVGDFHYV ->96897|polyprotein|ABR25251.1|Hepatitis C virus (isolate H77)|63746 -SLLRHHNLVYSTTSRSA ->96898|Genome polyprotein|SRC279960|Hepatitis C virus|11103 -SLLRNHNLVYSTTSRSA ->96957|polyprotein|ABR25251.1|Hepatitis C virus (isolate H77)|63746 -THFFSVLIARDQ ->96958|Genome polyprotein|SRC279960|Hepatitis C virus|11103 -THLFSVLMARDQ ->97044|Genome polyprotein|SRC279960|Hepatitis C virus (isolate H77)|63746 -VITPVVQTNW ->97093|polyprotein|AAB66324.1|Hepatitis C virus (isolate H77)|63746 -VTRHADVIPV ->97111|polyprotein|ABR25251.1|Hepatitis C virus (isolate H77)|63746 -YDIIICDECHSTDATSIL ->97226|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -CHSTDATSIL ->97227|polyprotein|CAB41951.1|Hepatitis C virus|11103 -CHSTDSTSIL ->97338|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -GIDPNIRTGV ->97365|polyprotein|CAA03854.1|Hepatitis C virus|11103 -GTDPNIRTGV ->97373|polyprotein|ACE82359.1|Hepatitis C virus subtype 1a|31646 -GVDPNIRTGV ->97399|polyprotein|ACZ60108.1|Hepatitis C virus subtype 3a|356426 -IPFYGKAIPI ->97400|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -IPFYGKAIPL ->97467|nucleocapsid protein|ACP44251.1|Influenza A virus (A/Fujian/411/2002(H3N2))|293090 -LPFEKSTIM ->97558|Genome polyprotein|SRC279960|Hepatitis C virus|11103 -PPHPNIEEVA ->97630|polyprotein|AAF65953.1|Hepatitis C virus|11103 -SALGLNAVAY ->97641|polyprotein|CAA03854.1|Hepatitis C virus|11103 -SGLGLNAVAY ->97719|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -VALGINAVAY ->97720|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 -VALGVNAVAY ->97750|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -VPHPNIEEVA ->97876|trans-sialidase, putative|EAN81705.1|Trypanosoma cruzi|5693 -ALSSSLGNV ->97905|trans-sialidase, putative|EAN88532.1|Trypanosoma cruzi|5693 -AVAEAQCKK ->97961|trans-sialidase, putative|EAN81042.1|Trypanosoma cruzi|5693 -DVAASSLLY ->98039|Trans-sialidase|SRC7915|Trypanosoma cruzi|5693 -FLSHNFTLVF ->98040|trans-sialidase, putative|EAN80725.1|Trypanosoma cruzi|5693 -FLYNRPLNS ->98042|trans-sialidase, putative|EAN80840.1|Trypanosoma cruzi|5693 -FQGAWAEWPV ->98044|trans-sialidase, putative|EAN80840.1|Trypanosoma cruzi|5693 -FTLVATVSI ->98046|trans-sialidase, putative|EAN82835.1|Trypanosoma cruzi|5693 -FTSAVLLLL ->98051|trans-sialidase, putative|EAN82716.1|Trypanosoma cruzi|5693 -FVSPSLVSA ->98085|trans-sialidase, putative|EAN82636.1|Trypanosoma cruzi|5693 -GVIAAFAEGH ->98100|trans-sialidase, putative|EAN81657.1|Trypanosoma cruzi|5693 -HLFYSAVLL ->98101|trans-sialidase, putative|EAN80725.1|Trypanosoma cruzi|5693 -HNFTLVASV ->98126|trans-sialidase, putative|EAN81650.1|Trypanosoma cruzi|5693 -ITATIEGRK ->98138|trans-sialidase, putative|EAN81657.1|Trypanosoma cruzi|5693 -IYMLVGKYS ->98223|trans-sialidase, putative|EAN80725.1|Trypanosoma cruzi|5693 -LLLGLWGFA ->98224|trans-sialidase, putative|EAN82076.1|Trypanosoma cruzi|5693 -LLLLVVMMCC ->98242|trans-sialidase, putative|EAN81042.1|Trypanosoma cruzi|5693 -LVTLPVYSK ->98244|trans-sialidase, putative|EAN80840.1|Trypanosoma cruzi|5693 -LWLTDNTHI ->98253|trans-sialidase, putative|EAN81042.1|Trypanosoma cruzi|5693 -MLSRVAAVK ->98254|trans-sialidase, putative|EAN81042.1|Trypanosoma cruzi|5693 -MLVTLPVYS ->98308|trans-sialidase, putative|EAN80840.1|Trypanosoma cruzi|5693 -NVMLVTLPV ->98431|trans-sialidase, putative|EAN82235.1|Trypanosoma cruzi|5693 -RVLLLLLLGL ->98459|trans-sialidase, putative|EAN80725.1|Trypanosoma cruzi|5693 -SIPTAGLVAV ->98466|Trans-sialidase|SRC7915|Trypanosoma cruzi|5693 -SLSHYFTLVF ->98540|trans-sialidase, putative|EAN88532.1|Trypanosoma cruzi|5693 -TSAVLLLLVV ->98560|trans-sialidase, putative|EAN80918.1|Trypanosoma cruzi|5693 -VALMLQGNK ->98603|trans-sialidase, putative|EAN82716.1|Trypanosoma cruzi|5693 -VTDNNRSFY ->98640|trans-sialidase, putative|EAN80840.1|Trypanosoma cruzi|5693 -YNFTLVATV ->98757|G1 and G2 surface glycoprotein precursor|AAG22532.1|Andes hantavirus|46607 -ELGLISIEAASDIKL ->100124|polyprotein|BAD73977.1|Hepatitis C virus subtype 1b|31647 -HSRKKCDEL ->101380|BNLF2a|YP_401721.1|Human herpesvirus 4 type 1|36352 -VLFGLLCLL ->101645|Protein Vpr|P69728.1|Human immunodeficiency virus 1|11676 -FPRIWLHGL ->101673|gag protein|ABO73990.1|Human immunodeficiency virus 1|11676 -GHQAAMQML ->101721|nef|AAA02639.1|Human immunodeficiency virus 1|11676 -HTQGYFPDWQ ->101766|nef protein|ACQ77160.1|Human immunodeficiency virus 1|11676 -KAAVDLSHFL ->101812|Pol polyprotein|Q9YLQ7|Human immunodeficiency virus 1|11676 -KQNPDIVIY ->101813|Pol polyprotein|Q9YLQ7|Human immunodeficiency virus 1|11676 -KQNPDIVIYQY ->101821|vif protein|ACC96167.1|Human immunodeficiency virus 1|11676 -KTKPPLPSVKK ->101967|pol protein|ACJ76655.1|Human immunodeficiency virus 1|11676 -PIQKETWETW ->101990|gag polyprotein|BAH60623.1|Human immunodeficiency virus 1|11676 -QASQEVKNW ->102032|nef protein|AAA87476.1|Human immunodeficiency virus 1|11676 -RPMTYKAAV ->102037|Gag polyprotein|P15832.3|Human immunodeficiency virus 2|11709 -RRWIQLGLQK ->102046|nef protein|ACQ72180.1|Human immunodeficiency virus 1|11676 -RYPLTFGW ->102104|Gag-Pol polyprotein|P03366.3|Human immunodeficiency virus 1|11676 -TAFTIPSI ->102149|Gag polyprotein|P03347.3|Human immunodeficiency virus 1|11676 -TPQDLNTML ->102150|nef protein|ACR27119.1|Human immunodeficiency virus 1|11676 -TPQVPLRPM ->102151|nef protein|ACR27128.1|Human immunodeficiency virus 1|11676 -TQGYFPDWQNY ->102205|envelope glycoprotein|ACR43875.1|Human immunodeficiency virus 1|11676 -VPVWKEATTTL ->102235|nef protein|ACR27119.1|Human immunodeficiency virus 1|11676 -YFPDWQNYT ->102254|nef protein|ACQ72180.1|Human immunodeficiency virus 1|11676 -YPLTFGWCY ->102368|E2 protein|NP_751921.1|Hepatitis C virus subtype 1a|31646 -DRSGAPTYSWGANDT ->102376|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 -DVVSKLPLAVMGSSY ->102611|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 -LHQNIVDVQYLYGVG ->102636|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 -LVGGVLAALAAYCLS ->102819|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 -SQHLPYIEQGMMLAE ->102922|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 -VTVSHPNIEEVALST ->103020|polyprotein|ABR25251.1|Hepatitis C virus|11103 -AFWAKHMWNF ->103322|polyprotein|BAB18806.1|Hepatitis C virus|11103 -KRLHQWINEDCSTPCSGSWL ->103389|unnamed protein product [Hepatitis C virus]|BAA14035.1|Hepatitis C virus|11103 -LTHPITKFVMACMSADLEVV ->103392|polyprotein|BAB18806.1|Hepatitis C virus|11103 -LTRDPTTPL ->103563|polyprotein|BAB18806.1|Hepatitis C virus|11103 -RPDYNPPLL ->103654|polyprotein|BAB18806.1|Hepatitis C virus|11103 -TIMAKNEVF ->104114|Glutamate decarboxylase 2|Q05329.1|Homo sapiens|9606 -MIARFKMFPEVKEKG ->104419|polyprotein|BAA00792.1|Hepatitis C virus|11103 -ALYDITQKL ->105333|Latent membrane protein 2|P0C729.1|Human gammaherpesvirus 4|10376 -MGSLEMVPM ->107720|polyprotein|AAF65953.1|Hepatitis C virus|11103 -AAKLSALGLN ->107721|polyprotein|AAD56189.1|Hepatitis C virus|11103 -AAKLSALGVN ->107722|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -AAKLVALGIN ->107727|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -AETAGARLVV ->107732|polyprotein|AAF65964.1|Hepatitis C virus|11103 -AHGTDPNIRT ->107733|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -ALGINAVAYY ->107734|polyprotein|AAF65953.1|Hepatitis C virus|11103 -ALGLNAVAYY ->107735|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 -ALGVNAVAYY ->107738|polyprotein|CAB41951.1|Hepatitis C virus|11103 -ALSNTGEIPF ->107748|polyprotein|AAF65950.1|Hepatitis C virus|11103 -ATDALMTGFT ->107749|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -ATDALMTGYT ->107752|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -ATLGFGAYMS ->107754|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -ATPPGSVTVP ->107760|polyprotein|AAD56189.1|Hepatitis C virus|11103 -AYDIIMCDEC ->107762|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -AYYRGLDVSV ->107777|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -DATSILGIGT ->107780|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -DECHSTDATS ->107781|polyprotein|AAF65953.1|Hepatitis C virus|11103 -DECHSTDSTT ->107782|Genome polyprotein|SRC279960|Hepatitis C virus|11103 -DELAAKLSLG ->107790|polyprotein|AAD56189.1|Hepatitis C virus|11103 -DIIMCDECHS ->107801|polyprotein|AAF65953.1|Hepatitis C virus|11103 -DSTTILGIGT ->107802|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -DVSVIPTSGD ->107818|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -EIPFYGKAIP ->107821|polyprotein|AAF65953.1|Hepatitis C virus|11103 -ELAAKLSALG ->107822|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -ELAAKLVALG ->107840|polyprotein|AAF65950.1|Hepatitis C virus|11103 -FTGDFDSVID ->107862|polyprotein|AAA86907.1|Hepatitis C virus|11103 -GLGINAVAYY ->107863|polyprotein|AAF65950.1|Hepatitis C virus|11103 -GLGLNAVAYY ->107872|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -GRHLIFCHSK ->107873|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -GSPITYSTYG ->107877|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 -GVNAVAYYRG ->107888|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -HPNIEEVALS ->107894|polyprotein|CAB41951.1|Hepatitis C virus|11103 -HSTDSTSILG ->107901|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -ICDECHSTDA ->107905|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -IIICDECHST ->107925|polyprotein|AAF65964.1|Hepatitis C virus|11103 -KAHGTDPNIR ->107945|polyprotein|BAA09073.1|Hepatitis C virus|11103 -KLSALGVNAV ->107984|polyprotein|AAF65953.1|Hepatitis C virus|11103 -LAAKLSALGL ->107985|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -LADGGCSGGA ->108001|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 -LGVNAVAYYR ->108016|polyprotein|AAF65953.1|Hepatitis C virus|11103 -LSALGLNAVA ->108017|polyprotein|BAA09073.1|Hepatitis C virus|11103 -LSALGVNAVA ->108018|polyprotein|CAB41951.1|Hepatitis C virus|11103 -LSNTGEIPFY ->108020|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -LSTTGEIPFY ->108067|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -PHPNIEEVAL ->108079|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -QAETAGARLV ->108100|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -RLVVLATATP ->108127|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -SILGIGTVLD ->108130|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -SKAHGIDPNI ->108139|polyprotein|CAB41951.1|Hepatitis C virus|11103 -SNTGEIPFYG ->108147|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -STDATSILGI ->108148|polyprotein|AAF65953.1|Hepatitis C virus|11103 -STDSTTILGI ->108149|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -STTGEIPFYG ->108153|polyprotein|AAF65950.1|Hepatitis C virus|11103 -TDALMTGFTG ->108154|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -TDALMTGYTG ->108158|polyprotein|AAF65953.1|Hepatitis C virus|11103 -TDSTTILGIG ->108163|polyprotein|CAB41951.1|Hepatitis C virus|11103 -TLSFGAYMSK ->108169|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -TSILGIGTVL ->108171|polyprotein|AAF65953.1|Hepatitis C virus|11103 -TTILGIGTVL ->108175|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -TYGKFLADGG ->108180|polyprotein|AAF65950.1|Hepatitis C virus|11103 -VATDALMTGF ->108181|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -VATDALMTGY ->108218|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -YDIIICDECH ->108225|polyprotein|ABR25251.1|Hepatitis C virus|11103 -YGKAIPLEAI ->108226|polyprotein|AAF65953.1|Hepatitis C virus|11103 -YGTDPNIRTG ->108229|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -YMSKAHGIDP ->108230|polyprotein|AAF65953.1|Hepatitis C virus|11103 -YMSKAYGTDP ->108232|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -YSTYGKFLAD ->108277|IE62|AAP32859.1|Human alphaherpesvirus 3|10335 -ALWALPHAA ->108687|Genome polyprotein|Q81495.3|Hepatitis C virus|11103 -VVSDFKTWL ->108770|E2 protein|ACS92695.1|Human papillomavirus type 16|333760 -ALQAIELQL ->108957|hypothetical protein|NP_216006.1|Mycobacterium tuberculosis|1773 -FLLGLLFFV ->108965|Prolipoprotein diacylglyceryl transferase|O06131.1|Mycobacterium tuberculosis|1773 -FLYELIWNV ->109331|L1|ABP99807.1|Human papillomavirus type 18|333761 -IHSMNSSIL ->109332|L1 protein|ACG75893.1|Human papillomavirus type 16|333760 -IHSMNSTIL ->109984|E2 protein|ACS92695.1|Human papillomavirus type 16|333760 -TLQDVSLEV ->110018|polyprotein|AGO67248.1|Dengue virus 2|11060 -VAFLRFLTI ->110125|E2 protein|ACS92695.1|Human papillomavirus type 16|333760 -YICEEASVTV ->110184|E7|AAD33253.1|Human papillomavirus type 16|333760 -AGQAEPDRAHYNIVTFCCKCDSTLRLCVQSTHVDI ->110195|E7 protein|ABL96585.1|Human papillomavirus type 16|333760 -CCKCDSTL ->110205|Protein E6|P03126.1|Human papillomavirus type 16|333760 -DKKQRFHNIRGRWTGRCMSCCRSSRTRRETQL ->110215|Protein E6|P03126.1|Human papillomavirus type 16|333760 -EKQRHLDKKQRFHNIRGRWTGRCMS ->110225|Protein E7|P06788.2|Human papillomavirus type 18|333761 -FQQLFLNTL ->110227|Protein E6|P03126.1|Human papillomavirus type 16|333760 -FRDLCIVYRDGNPYAVCDKCLKFYSKISEYRHY ->110282|Protein E6|P03126.1|Human papillomavirus type 16|333760 -HDIILECVYCKQQLLRREVYDFAFR ->110285|Protein E6|P03126.1|Human papillomavirus type 16|333760 -HNIRGRWTGR ->110306|Protein E6|P03126.1|Human papillomavirus type 16|333760 -KLPQLCTELQTTIHDIILECVYCKQQLLRREV ->110323|Protein E7|P04020.1|Human papillomavirus type 11|10580 -LLLGTLNIV ->110335|E7|AAD33253.1|Human papillomavirus type 16|333760 -MHGDTPTLHEYMLDLQPETTDLYCYEQLNDSS ->110338|Protein E6|P03126.1|Human papillomavirus type 16|333760 -MHQKRTAMFQDPQERPRKLPQLCTELQTTIHDI ->110373|Protein E6|P03126.1|Human papillomavirus type 16|333760 -PRKLPQLCTELQTTIHDIILECVYC ->110394|Protein E6|P03126.1|Human papillomavirus type 16|333760 -RCINCQKPLCPEEKQRHLDKKQRFHNIRGRWT ->110399|Protein E6|P03126.1|Human papillomavirus type 16|333760 -RGRWTGRCMSCCRSSRTRRETQL ->110401|Protein E6|P03126.1|Human papillomavirus type 16|333760 -RREVYDFAFRDLCIVYRDGNPYAVC ->110431|E7|AAD33253.1|Human papillomavirus type 16|333760 -TDLYCYEQLNDSSEEEDEIDGPAGQAEPDRAHYNIV ->110439|Replication protein E1|P03114.2|Human papillomavirus type 16|333760 -TLLQQYCLYL ->110467|Protein E6|P03126.1|Human papillomavirus type 16|333760 -YRDGNPYAVCDKCLKFYSKISEYRH ->110575|E6 protein|ACS92692.1|Human papillomavirus type 16|333760 -FAFRDLCIVY ->110624|Protein E6|P03126.1|Human papillomavirus type 16|333760 -HDIILECV ->110720|Protein E6|P03126.1|Human papillomavirus type 16|333760 -TIHDIILEC ->110744|E5 protein|AAD24036.1|Human papillomavirus type 16|333760 -YIIFVYIPL ->110829|Protein E6|P03126.1|Human papillomavirus type 16|333760 -EKQRHLDKKQRFHNI ->110846|E6 protein|CAB45108.1|Human papillomavirus type 16|333760 -EYRHYCYSL ->110917|X protein|AAP06597.1|Hepatitis B virus|10407 -KLVCSPAPC ->110940|Protein E7|P03129.1|Human papillomavirus type 16|333760 -MHGDTPTLHEYMLDL ->110982|E6 protein|CAB45108.1|Human papillomavirus type 16|333760 -QYNKPLCDLL ->111055|E6 protein|CAB45108.1|Human papillomavirus type 16|333760 -VYDFAFQDL ->111251|Protein E6|P03126.1|Human papillomavirus type 16|333760 -ELQTTIHDIILECVY ->111404|Protein E7|P03129.1|Human papillomavirus type 16|333760 -HVDIRTLEDLLMGTL ->111407|polyprotein|BAA00792.1|Hepatitis C virus|11103 -HYPCTVNYTI ->111448|polyprotein precursor|BAA02756.1|Hepatitis C virus|11103 -KGGRKPARLIVFPDL ->111479|Protein E7|P06788.2|Human papillomavirus type 18|333761 -LFLNTLSFV ->111604|L1|ABP99807.1|Human papillomavirus type 18|333761 -NVFPIFLQM ->111641|polyprotein|ABV46292.1|Hepatitis C virus|11103 -PQRKTKRNTNR ->111816|polyprotein|BAA09072.1|Hepatitis C virus|11103 -TAYSQQTRGLLG ->111860|polyprotein|BAA00792.1|Hepatitis C virus|11103 -TVNYTIFKI ->111938|Protein E6|P03126.1|Human papillomavirus type 16|333760 -VYDFAFRDLCIVYRD ->112359|Non-structural protein 2a|Q80872.1|Human coronavirus OC43|31631 -TMLDIQPED ->112503|E6 protein|ACV53993.1|Human papillomavirus type 35|10587 -FACYDLCIVY ->112504|Protein E6|P21735.2|Human papillomavirus type 45|10593 -FAFKDLCIVY ->112505|E6|CAA63882.1|Human papillomavirus type 73|51033 -FAFSDLCIVY ->112506|Protein E6|P24835.1|Human papillomavirus type 39|10588 -FAFSDLYVVY ->112519|Protein E6|P26555.1|Human papillomavirus type 58|10598 -FVFADLRIVY ->112697|Protein E6|P26554.1|Human papillomavirus type 51|10595 -VAFTEIKIVY ->113122|Protein E6|P03126.1|Human papillomavirus type 16|333760 -QERPRKLPQL ->113154|Protein E6|P03126.1|Human papillomavirus type 16|333760 -RWTGRCMSCC ->113177|Protein E6|P03126.1|Human papillomavirus type 16|333760 -SSRTRRETQL ->115656|DNA polymerase processivity factor BMRF1|SRC280248|Human gammaherpesvirus 4|10376 -TLDTKPLSV ->116123|nucleocapsid protein|ABP49342.1|Influenza A virus (A/California/10/1978(H1N1))|425557 -LPFDKSTVM ->116127|Nucleoprotein|P15682.1|Influenza A virus (A/Wilson-Smith/1933(H1N1))|381518 -LPFDRPTIM ->116136|nucleocapsid protein|ACS34671.1|Influenza A virus (A/Auckland/1/2009(H1N1))|642794 -LPFERATVM ->116781|Nucleoprotein|P05133.1|Hantaan virus 76-118|11602 -LRKKSSFYQSYLRRT ->116835|Nucleoprotein|P05133.1|Hantaan virus 76-118|11602 -SPSSIWVFAGAPDRC ->119822|110 kd polyprotein precursor|CAA28880.1|Rubella virus|11041 -EACVTSWLWSEGEGAVFYRVDLHFINLGT ->120093|unnamed protein product|CAA33016.1|Rubella virus|11041 -MDFWCVEHDRPPPATPTSLTT ->120111|Glutamate decarboxylase 1|Q99259.1|Homo sapiens|9606 -NMFTYEIAPVFVLME ->120127|unnamed protein product|CAA33016.1|Rubella virus|11041 -PFLGHDGHHGGTLRVGQHHRNASDV ->120187|E1 protein|BAA19893.1|Rubella virus|11041 -RVKFHTETRTVWQLSVAGVSC ->124973|Esat-6 like protein esxJ (Esat-6 like protein 2)|NP_215554.1|Mycobacterium tuberculosis H37Rv|83332 -AFRNIVNML ->126028|ATP-dependent helicase|NP_217813.1|Mycobacterium tuberculosis H37Rv|83332 -FMYEGDTPL ->126481|gag polyprotein p17 region|BAA83653.1|Human immunodeficiency virus 1|11676 -KSLFNTIATLY ->126482|gag protein|AAY98604.1|Human immunodeficiency virus 1|11676 -KSLFNTIAVL ->126483|gag protein|AAY98604.1|Human immunodeficiency virus 1|11676 -KSLFNTIAVLY ->126484|gag protein|AAW03034.1|Human immunodeficiency virus 1|11676 -KSLFNTVATL ->126485|gag protein|AAW03034.1|Human immunodeficiency virus 1|11676 -KSLFNTVATLY ->126486|gag protein|ADK33372.1|Human immunodeficiency virus 1|11676 -KSLFNTVAVL ->126487|gag protein|ADK33372.1|Human immunodeficiency virus 1|11676 -KSLFNTVAVLY ->126488|gag protein|AAV53168.1|Human immunodeficiency virus 1|11676 -KSLYNTIATLY ->126489|gag protein|ABI20203.1|Human immunodeficiency virus 1|11676 -KSLYNTIAVLY ->126490|Gag protein|Q1KW74|Human immunodeficiency virus 1|11676 -KSLYNTVATL ->126491|gag protein|AAV53216.1|Human immunodeficiency virus 1|11676 -KSLYNTVATLY ->126492|gag protein|BAB88077.1|Human immunodeficiency virus 1|11676 -KSLYNTVAVLY ->126993|gag polyprotein|BAB19174.1|Human immunodeficiency virus 1|11676 -RSLFNTIATLY ->126994|gag-pol polyprotein|BAC02551.1|Human immunodeficiency virus 1|11676 -RSLFNTIAVLY ->126995|gag polyprotein|BAB19171.1|Human immunodeficiency virus 1|11676 -RSLFNTVATL ->126996|Gag protein|Q9YYH6|Human immunodeficiency virus 1|11676 -RSLFNTVATLY ->126997|gag protein|BAC45024.1|Human immunodeficiency virus 1|11676 -RSLFNTVAVLY ->126999|gag polyprotein|BAB88540.1|Human immunodeficiency virus 1|11676 -RSLYNTIATLY ->127000|gag-pol fusion polyprotein precursor|CAY83124.1|Human immunodeficiency virus 1|11676 -RSLYNTIAVLY ->127001|gag polyprotein|BAA00992.1|Human immunodeficiency virus 1|11676 -RSLYNTVATL ->127002|gag protein|AAV53342.1|Human immunodeficiency virus 1|11676 -RSLYNTVATLY ->127003|gag polyprotein|BAB88551.1|Human immunodeficiency virus 1|11676 -RSLYNTVAVL ->127004|gag polyprotein|BAB88551.1|Human immunodeficiency virus 1|11676 -RSLYNTVAVLY ->127082|gag-pol polyprotein|BAC02551.1|Human immunodeficiency virus 1|11676 -SLFNTIAVLY ->127083|Gag protein|Q9YYH6|Human immunodeficiency virus 1|11676 -SLFNTVATLY ->127246|p24 protein|CAD36203.1|Human immunodeficiency virus 1|11676 -TSTLQEQIGW ->127611|6 kDa early secretory antigenic target|P0A564.2|Mycobacterium tuberculosis|1773 -AYQGVQQKW ->127792|6 kDa early secretory antigenic target|P0A564.2|Mycobacterium tuberculosis|1773 -QWNFAGIEAA ->130902|nucleocapsid protein|NP_604471.1|Andes hantavirus|46607 -IPIILKALY ->130911|G1 and G2 surface glycoprotein precursor|AAG22532.1|Andes hantavirus|46607 -IYTFTSLFSLMPDVA ->130953|G1 and G2 surface glycoprotein precursor|AAG22532.1|Andes hantavirus|46607 -LMPDVAHSL ->131070|Gag protein|Q9IN85|HIV-1 M:A|505184 -SLFNTVATL ->131096|G1 and G2 surface glycoprotein precursor|AAG22532.1|Andes hantavirus|46607 -TAHGVGEIPM ->131132|G1 and G2 surface glycoprotein precursor|AAG22532.1|Andes hantavirus|46607 -VIGQCIYTFTSLFSL ->131311|interferon-inducible peptide precursor|AAC50160.1|Homo sapiens|9606 -SLMSWSAIL ->133501|polyprotein|ABG75765.1|Dengue virus 1|11053 -AIVREAIKR ->133619|putative surface protein|AAN52495.1|Leptospira interrogans serovar Pomona|44276 -KLIVTPAAL ->133645|cell surface protein|NP_302626.1|Mycobacterium leprae|1769 -MLDHAGNMSACAGAL ->133650|cell surface protein|NP_302626.1|Mycobacterium leprae|1769 -MTQIMYNYPAMLDHA ->133702|polyprotein|ABG75765.1|Dengue virus 1|11053 -SRNSTHEMY ->133716|polyprotein|ABG75765.1|Dengue virus 1|11053 -TLYAVATTI ->134497|M protein|SRC280368|Streptococcus pyogenes|1314 -QRAAKEALDKYELENH ->135263|hemagglutinin|ACX31970.1|Influenza A virus (A/Bar-headed Goose/Qinghai/61/05(H5N1))|336238 -RLYQNPTTYI ->136348|Genome polyprotein|SRC279960|Hepatitis C virus|11103 -HAVGIFKAAV ->136349|Genome polyprotein|SRC279960|Hepatitis C virus|11103 -HAVGIFQAAV ->136350|polyprotein|BAB18806.1|Hepatitis C virus|11103 -HAVGIFRAAV ->136351|Genome polyprotein|SRC279960|Hepatitis C virus|11103 -HAVGIFRTAV ->136826|polyprotein|AFP27208.1|Dengue virus 4|11070 -CYSQVNPTTL ->136837|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 -FLLALLSCLTV ->136865|tegument protein|CAB06735.1|Human alphaherpesvirus 2|10310 -PMRARPRGEVRFLHY ->136890|polyprotein|AGO67248.1|Dengue virus 2|11060 -TPPGSRDPF ->137437|Esat-6 like protein esxJ (Esat-6 like protein 2)|NP_215554.1|Mycobacterium tuberculosis H37Rv|83332 -QTVEDEARRMW ->137609|E7 protein|ACT36476.1|Human papillomavirus type 58|10598 -ATEVRTLQQ ->137611|L1|ACX32376.1|Human papillomavirus type 58|10598 -AVPDDLYIK ->137614|E7 protein|ADP92425.1|Human papillomavirus type 58|10598 -CTIVCPSCA ->137656|E6 protein|ACT36477.1|Human papillomavirus type 58|10598 -ILIRCIICQ ->137657|E6 protein|ACT36477.1|Human papillomavirus type 58|10598 -KCLNEILIR ->137659|E6 protein|ACT36477.1|Human papillomavirus type 58|10598 -KVCLRLLSK ->137660|L1|ACL12325.1|Human papillomavirus type 58|10598 -KYTFWEVNL ->137661|E7 protein|ACT36476.1|Human papillomavirus type 58|10598 -LCINSTATE ->137685|L1|ACX32376.1|Human papillomavirus type 58|10598 -RVRLPDPNK ->137702|late protein|CAA52590.1|Human papillomavirus type 52|10618 -TSESQLFNK ->137724|L1|ACX32376.1|Human papillomavirus type 58|10598 -YTFWEVNLK ->137726|late protein|CAA52590.1|Human papillomavirus type 52|10618 -YYYAGSSRL ->139406|polyprotein|ACT37184.1|Hepatitis C virus|11103 -YLLPRPGPRL ->139746|Dense granule protein 3|B6KEU8.2|Toxoplasma gondii|5811 -FLVPFVVFL ->139747|granule antigen protein GRA6|XP_002371939.1|Toxoplasma gondii ME49|508771 -FMGVLVNSL ->139947|granule antigen protein GRA6|XP_002371939.1|Toxoplasma gondii ME49|508771 -VVFVVFMGV ->140541|hypothetical protein|NP_218210.1|Mycobacterium tuberculosis H37Rv|83332 -ALDEGLLPV ->140542|MCE-family protein MCE4B|NP_218015.1|Mycobacterium tuberculosis H37Rv|83332 -ALLGGLRPV ->140543|trehalose-6-phosphate phosphatase OtsB1|YP_177855.1|Mycobacterium tuberculosis H37Rv|83332 -AMAGSIDLL ->140544|ORF|AAA45606.1|Hepatitis C virus|11103 -ATDALMSGF ->140561|metal cation transporter P-type ATPase A CtpF|NP_216513.1|Mycobacterium tuberculosis H37Rv|83332 -GMFANRWII ->140564|esterase lipoprotein LpqC|NP_217815.1|Mycobacterium tuberculosis H37Rv|83332 -HLDDVGFLV ->140597|MCE-family protein MCE4A|YP_177977.1|Mycobacterium tuberculosis H37Rv|83332 -SLIDLLHKI ->140599|MCE-family lipoprotein LprL|NP_215107.1|Mycobacterium tuberculosis H37Rv|83332 -SLRNWIATL ->140600|glutamine synthetase GLNA1 (glutamine synthase) (GS-I)|NP_216736.1|Mycobacterium tuberculosis H37Rv|83332 -SLWKDGAPL ->140615|amino acid decarboxylase|YP_177889.1|Mycobacterium tuberculosis H37Rv|83332 -WLYPGAQNL ->140616|membrane-associated phospholipase C|NP_216866.1|Mycobacterium tuberculosis H37Rv|83332 -YLLADTFTV ->140649|ESAT-6-like protein esxH|P0A568.2|Mycobacterium tuberculosis|1773 -AMEDLVRAY ->140650|ESAT-6-like protein esxH|P0A568.2|Mycobacterium tuberculosis|1773 -AMLGHAGDM ->140651|granule antigen protein GRA6|XP_002371939.1|Toxoplasma gondii ME49|508771 -AMLTAFFLR ->140652|LOW MOLECULAR WEIGHT PROTEIN ANTIGEN 7 ESXH (10 kDa ANTIGEN) (CFP-7) (PROTEIN TB10.4)|CAA17363.1|Mycobacterium tuberculosis H37Rv|83332 -AMMARDTAE ->140654|ESAT-6-like protein esxH|P0A568.2|Mycobacterium tuberculosis|1773 -ANTMAMMAR ->140686|ESAT-6-like protein esxH|P0A568.2|Mycobacterium tuberculosis|1773 -HAMSSTHEA ->140697|major surface antigen p30|EEB01065.1|Toxoplasma gondii ME49|508771 -KSFKDILPK ->140706|LOW MOLECULAR WEIGHT PROTEIN ANTIGEN 7 ESXH (10 kDa ANTIGEN) (CFP-7) (PROTEIN TB10.4)|CAA17363.1|Mycobacterium tuberculosis H37Rv|83332 -LVRAYHAMS ->140708|LOW MOLECULAR WEIGHT PROTEIN ANTIGEN 7 ESXH (10 kDa ANTIGEN) (CFP-7) (PROTEIN TB10.4)|CAA17363.1|Mycobacterium tuberculosis H37Rv|83332 -MAMMARDTA ->140711|ESAT-6-like protein esxH|P0A568.2|Mycobacterium tuberculosis|1773 -MLGHAGDMA ->140712|LOW MOLECULAR WEIGHT PROTEIN ANTIGEN 7 ESXH (10 kDa ANTIGEN) (CFP-7) (PROTEIN TB10.4)|CAA17363.1|Mycobacterium tuberculosis H37Rv|83332 -MMARDTAEA ->140717|low molecular weight protein antigen 7|NP_214802.1|Mycobacterium tuberculosis|1773 -MYNYPAMLG ->140727|LOW MOLECULAR WEIGHT PROTEIN ANTIGEN 7 ESXH (10 kDa ANTIGEN) (CFP-7) (PROTEIN TB10.4)|CAA17363.1|Mycobacterium tuberculosis H37Rv|83332 -QAMEDLVRA ->140739|dense granule protein 7|XP_002367613.1|Toxoplasma gondii ME49|508771 -RSFKDLLKK ->140744|LOW MOLECULAR WEIGHT PROTEIN ANTIGEN 7 ESXH (10 kDa ANTIGEN) (CFP-7) (PROTEIN TB10.4)|CAA17363.1|Mycobacterium tuberculosis H37Rv|83332 -SQIMYNYPA ->140760|LOW MOLECULAR WEIGHT PROTEIN ANTIGEN 7 ESXH (10 kDa ANTIGEN) (CFP-7) (PROTEIN TB10.4)|CAA17363.1|Mycobacterium tuberculosis H37Rv|83332 -TYQAWQAQW ->140769|LOW MOLECULAR WEIGHT PROTEIN ANTIGEN 7 ESXH (10 kDa ANTIGEN) (CFP-7) (PROTEIN TB10.4)|CAA17363.1|Mycobacterium tuberculosis H37Rv|83332 -WQAQWNQAM ->141202|Uncharacterized PPE family protein PPE51|Q7D623.1|Mycobacterium tuberculosis H37Rv|83332 -AEMWAQDAA ->141206|tegument protein VP11/12|NP_044648.1|Human alphaherpesvirus 1|10298 -AILTQYWKY ->141208|tegument protein VP13/14|NP_044649.1|Human alphaherpesvirus 1|10298 -ALATVTLKY ->141211|UL29|ABI63491.1|Human alphaherpesvirus 1|10298 -ALLAKMLFY ->141212|tegument protein VP13/14|NP_044649.1|Human alphaherpesvirus 1|10298 -ALLDRDCRV ->141216|envelope glycoprotein I|NP_044669.1|Human alphaherpesvirus 1|10298 -APASVYQPA ->141217|regulatory protein ICP22|NP_044663.1|Human alphaherpesvirus 1|10298 -APRIGGRRA ->141218|regulatory protein ICP22|NP_044663.1|Human alphaherpesvirus 1|10298 -APRTWCRLL ->141221|tegument protein VP11/12|NP_044648.1|Human alphaherpesvirus 1|10298 -ATDSLNNEY ->141222|DNA packaging tegument protein UL25|NP_044626.1|Human alphaherpesvirus 1|10298 -AVLCLYLLY ->141225|tegument protein UL21|NP_044622.1|Human alphaherpesvirus 1|10298 -AYLGAFLSVL ->141226|tegument protein UL37|ADD60080.1|Human alphaherpesvirus 1|10298 -AYLPRPVEF ->141227|tegument protein UL37|ADD60080.1|Human alphaherpesvirus 1|10298 -AYSLLFPAPF ->141228|tegument protein VP11/12|NP_044648.1|Human alphaherpesvirus 1|10298 -AYVSVLYRW ->141231|envelope glycoprotein I|NP_044669.1|Human alphaherpesvirus 1|10298 -CPRRPAVAF ->141260|nuclear egress lamina protein|NP_044633.1|Human alphaherpesvirus 1|10298 -EYQRLYATF ->141262|DNA polymerase catalytic subunit|NP_044632.1|Human alphaherpesvirus 1|10298 -EYVHARWAAF ->141269|tegument protein VP13/14|NP_044649.1|Human alphaherpesvirus 1|10298 -FLADAVVRL ->141270|envelope glycoprotein B|NP_044629.1|Human alphaherpesvirus 1|10298 -FLIAYQPLL ->141271|DNA packaging tegument protein UL25|NP_044626.1|Human alphaherpesvirus 1|10298 -FLWEDQTLL ->141276|tegument protein VP13/14|NP_044649.1|Human alphaherpesvirus 1|10298 -FTAPEVGTY ->141277|transactivating tegument protein VP16|NP_044650.1|Human alphaherpesvirus 1|10298 -FTDALGIDEY ->141281|tegument protein UL21|NP_044622.1|Human alphaherpesvirus 1|10298 -FVYTPSPYVF ->141306|tegument host shutoff protein|NP_044643.1|Human alphaherpesvirus 1|10298 -HTDLHPNNTY ->141313|ribonucleotide reductase subunit 2|NP_044642.1|Human alphaherpesvirus 1|10298 -ILIEGIFFA ->141323|multifunctional expression regulator|NP_044657.1|Human alphaherpesvirus 1|10298 -KYFYCNSLF ->141324|tegument protein VP11/12|NP_044648.1|Human alphaherpesvirus 1|10298 -LASDPHYEY ->141338|envelope glycoprotein L|NP_044602.1|Human alphaherpesvirus 1|10298 -LIDGIFLRY ->141341|tegument protein VP11/12|NP_044648.1|Human alphaherpesvirus 1|10298 -LLAYVSVLY ->141354|transcriptional regulator ICP4|NP_044662.1|Human alphaherpesvirus 1|10298 -LYPDAPPLRL ->141396|ribonucleotide reductase subunit 1|NP_044641.1|Human alphaherpesvirus 1|10298 -RILGVLVHL ->141398|tegument protein VP13/14|NP_044649.1|Human alphaherpesvirus 1|10298 -RLLGFADTV ->141399|Tegument protein UL46|P10230.2|Herpes simplex virus (type 1 / strain 17)|10299 -RLNELLAYV ->141402|tegument protein VP22|NP_044651.1|Human alphaherpesvirus 1|10298 -RPTERPRAPA ->141407|tegument protein VP13/14|NP_044649.1|Human alphaherpesvirus 1|10298 -RSSLGSLLY ->141411|transactivating tegument protein VP16|NP_044650.1|Human alphaherpesvirus 1|10298 -SALPTNADLY ->141418|tegument protein VP11/12|NP_044648.1|Human alphaherpesvirus 1|10298 -SIVHHHAQY ->141422|DNA packaging tegument protein UL25|NP_044626.1|Human alphaherpesvirus 1|10298 -SSGVVFGTWY ->141423|envelope glycoprotein B|NP_044629.1|Human alphaherpesvirus 1|10298 -SVYPYDEFV ->141430|tegument serine/threonine protein kinase|NP_044614.1|Human alphaherpesvirus 1|10298 -TLLELVVSV ->141461|ubiquitin E3 ligase ICP0|NP_044601.1|Human alphaherpesvirus 1|10298 -VPGWSRRTL ->141462|tegument protein UL21|NP_044622.1|Human alphaherpesvirus 1|10298 -VPRPDDPVL ->141468|envelope glycoprotein I|NP_044669.1|Human alphaherpesvirus 1|10298 -VVRGPTVSL ->141469|envelope glycoprotein B|NP_044629.1|Human alphaherpesvirus 1|10298 -VYMSPFYGY ->141470|tegument protein UL21|NP_044622.1|Human alphaherpesvirus 1|10298 -VYTPSPYVF ->141479|single-stranded DNA-binding protein|NP_044631.1|Human alphaherpesvirus 1|10298 -YMANQILRY ->141480|ribonucleotide reductase subunit 1|NP_044641.1|Human alphaherpesvirus 1|10298 -YMESVFQMY ->141484|capsid maturation protease|NP_044627.1|Human alphaherpesvirus 1|10298 -YVAGFLALY ->142194|polyprotein|ADV57311.1|Hepatitis C virus subtype 1a|31646 -KAKKTPMGF ->142203|polyprotein|BAD73974.1|Hepatitis C virus subtype 1b|31647 -KKKKNPMGF ->142209|polyprotein|ACJ37233.1|Hepatitis C virus subtype 1a|31646 -KSKKIPMGF ->142210|polyprotein [Hepatitis C virus subtype 1a]|ABV46251.2|Hepatitis C virus subtype 1a|31646 -KSKKNPMGF ->142211|polyprotein|ACJ37204.1|Hepatitis C virus subtype 1a|31646 -KSKKTPLGF ->142212|Genome polyprotein|Q913D4.3|Hepatitis C virus subtype 1a|31646 -KSKKVPMGF ->142213|polyprotein|ABV46054.1|Hepatitis C virus subtype 1a|31646 -KSKRTPMGF ->142231|Lipoprotein lpqH precursor|P0A5J0.1|Mycobacterium tuberculosis|1773 -MKRGLTVAVAGAAILVAGLSGCSS ->142232|POSSIBLE CONSERVED TRANSMEMBRANE PROTEIN|CAB00937.1|Mycobacterium tuberculosis|1773 -MLVLLVAVLVTAVYAFVHA ->142233|ATP-dependent helicase|NP_217813.1|Mycobacterium tuberculosis|1773 -MRFAQPSALSRFSALTRDWFTSTFAAPTAAQA ->142244|polyprotein|ACJ37184.1|Hepatitis C virus subtype 1a|31646 -NSKKTPMGF ->142245|polyprotein|ACJ37204.1|Hepatitis C virus subtype 1a|31646 -NTRPPAGNW ->142246|polyprotein|BAB18810.1|Hepatitis C virus subtype 1a|31646 -NTRPPLGNW ->142247|envelope protein 2|ACY64760.1|Hepatitis C virus subtype 1a|31646 -NTRPPMGNW ->142248|polyprotein|BAB18806.1|Hepatitis C virus subtype 1a|31646 -NTRPPQGNW ->142249|polyprotein|AAY82036.1|Hepatitis C virus subtype 1a|31646 -NTRPPRGNW ->143664|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 -AISEKTIWSL ->143666|polyprotein|ACF60462.1|Hepatovirus A|12092 -ALFHEVAKL ->143680|Genome polyprotein|P06441.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 -DVSGVQAPRGSYQQQLNDPVL ->143690|Genome polyprotein|P06441.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 -GLAVDPWVE ->143705|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 -KEYTFPITL ->143726|polyprotein|CAC14074.3|Hepatovirus A|12092 -LLYNCCYHV ->143728|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 -LPWYSYLYA ->143732|polyprotein|CAC14074.3|Hepatovirus A|12092 -MMFGFHHSV ->143735|Genome polyprotein|P06441.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 -NRGKMDVSGVQAPRGSYQQQ ->143740|polyprotein|ACF60462.1|Hepatovirus A|12092 -QMMRNEFRV ->143752|Genome polyprotein|P06441.1|Hepatovirus A|12092 -SLMDLLSSL ->144207|polyprotein|CAB41951.1|Hepatitis C virus|11103 -APTLWARMVL ->144403|polyprotein|AAK08509.1|Hepatitis C virus subtype 1b|31647 -LLRHHNMVY ->144480|polyprotein|ACA50684.1|Hepatitis C virus subtype 1b|31647 -SQRQKKVTF ->144544|polyprotein precursor|BAA01728.1|Hepatitis C virus|11103 -WPAPSGARSL ->144913|Hexon protein|P04133.3|Human adenovirus 5|28285 -LLYANSAHAL ->145826|6 kDa early secretory antigenic target|P0A564.2|Mycobacterium tuberculosis|1773 -IHSLLDEGKQSLTKL ->145860|Protein E6|P04019.1|Human papillomavirus type 11|10580 -KVLIRCYLC ->145918|Protein E6|P06463.1|Human papillomavirus type 18|333761 -NLLIRCLRC ->146005|Protein E6|P04019.1|Human papillomavirus type 11|10580 -SIDQLCKTF ->146028|E6 protein|NP_040296.1|Human papillomavirus type 6b|10600 -TIDQLCKTF ->146123|polyprotein|ADV04529.1|Hepatitis C virus subtype 1b|31647 -AATLGFGSFMSRAYGI ->146124|polyprotein|AAK08509.1|Hepatitis C virus subtype 1b|31647 -AAWYIKGRL ->146182|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 -CLTHPVTK ->146188|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 -DFWESVFTGLTHIDAHFL ->146194|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 -DLQPAETTVRLRAYL ->146213|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 -EFWESVFTGLTHIDAHFL ->146219|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 -ELTPAETSVRLRAYL ->146246|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 -FLATCVNGVCWTVYHGA ->146249|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 -FLGTTVGGVMWTVYHGA ->146260|polyprotein|ADF97231.1|Hepatitis C virus subtype 3a|356426 -GAKHPALQMYTNVDQDLV ->146280|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 -GIDPNIRTGN ->146282|polyprotein|ADF97231.1|Hepatitis C virus subtype 3a|356426 -GKAIPIALLKGGRHLIF ->146283|polyprotein|AEI00313.1|Hepatitis C virus subtype 1b|31647 -GKAIPIEVIKGGRHLIF ->146284|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 -GKSTKVPAAYAAQGYKVL ->146285|polyprotein|ADF97231.1|Hepatitis C virus subtype 3a|356426 -GKSTKVPAAYVAQGYNVL ->146287|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 -GPKGPITQMYTNVDQDLV ->146288|polyprotein|ADF97231.1|Hepatitis C virus subtype 3a|356426 -GRGRLGTYRY ->146289|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 -GRGRRGIYRF ->146291|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 -GSFMSRAYGI ->146314|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 -HVAGIFRAAV ->146317|polyprotein|ADF97231.1|Hepatitis C virus subtype 3a|356426 -ICLTHPVTK ->146395|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 -KLRGMGLNAV ->146396|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 -KLRGMGLNAVAYYRGLDV ->146397|polyprotein|AEI00314.1|Hepatitis C virus subtype 1b|31647 -KLSALGLNAVAYYRGLDV ->146429|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 -LQFIPVETL ->146527|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 -RLGAVQNEV ->146528|NS3/4A protein|CAM56207.1|Hepatitis C virus|11103 -RLGPVQNEI ->146553|polyprotein precursor|BAA01761.1|Hepatitis C virus genotype 2|40271 -SMMAFSAAL ->146569|polyprotein|ADF97231.1|Hepatitis C virus subtype 3a|356426 -SWDETWKCLVRLKPTLH ->146570|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 -SWDQMWKCLIRLKPTLH ->146576|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 -TLGFGSFMSR ->146592|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 -VAPGERPSGMFDSVVL ->146595|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 -VDFVPVESM ->146617|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 -VTPGERPSGMFDSSVL ->146644|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 -YLHAPTGSGK ->147561|early protein|CAA52586.1|Human papillomavirus type 52|10618 -CYEQLGDSS ->147835|early protein|CAA52585.1|Human papillomavirus type 52|10618 -ITIRCIICQ ->147891|early protein|CAA52585.1|Human papillomavirus type 52|10618 -KTLEERVKK ->147936|dense granule protein 7|XP_002367613.1|Toxoplasma gondii ME49|508771 -LPQFATAAT ->147941|late protein|CAA52590.1|Human papillomavirus type 52|10618 -LQFIFQLCK ->147973|early protein|CAA52586.1|Human papillomavirus type 52|10618 -MRGDKATIK ->147981|late protein|CAA52590.1|Human papillomavirus type 52|10618 -MTLCAEVKK ->148117|early protein|CAA52585.1|Human papillomavirus type 52|10618 -PYGVCIMCL ->148138|early protein|CAA52586.1|Human papillomavirus type 52|10618 -QLGDSSDEE ->148160|late protein|CAA52590.1|Human papillomavirus type 52|10618 -QYRVFRIKL ->148172|late protein|CAA52590.1|Human papillomavirus type 52|10618 -RIKLPDPNK ->148177|early protein|CAA52585.1|Human papillomavirus type 52|10618 -RLQCVQCKK ->148397|Dense granule protein 3|B6KEU8.2|Toxoplasma gondii|5811 -VPFVVFLVA ->148425|early protein|CAA52585.1|Human papillomavirus type 52|10618 -VYKFLFTDL ->148619|unnamed protein product|BAA14233.1|Hepatitis C virus|11103 -GLLGCIITSLTGRDKNQVDGEVQVLSTATQSFLATCVNGVCWTVY ->149022|nonstructural protein|AAC53947.1|Hepatitis C virus genotype 1|41856 -AIAPAVQTNW ->149023|NS3 gene product|AAB02124.1|Hepatitis C virus (isolate H77)|63746 -ALGINAVAY ->149024|NS2 protein|NP_751923.1|Hepatitis C virus (isolate H77)|63746 -ALTLSPYYK ->149027|NS5 protein|BAA00702.1|Hepatitis C virus (isolate H77)|63746 -APTLWARMILMTHFFSVL ->149029|polyprotein|ABR25251.1|Hepatitis C virus (isolate H77)|63746 -CTTPCSGSW ->149031|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 -EAAGRRLAR ->149032|nonstructural 5a protein|ADH82351.1|Hepatitis C virus subtype 1a|31646 -EAARRRLAR ->149036|E2 protein|NP_751921.1|Hepatitis C virus (isolate H77)|63746 -ELSPLLLST ->149037|NS4B protein|NP_751926.1|Hepatitis C virus (isolate H77)|63746 -EVITPAVQTNW ->149038|NS3|ABN45875.1|Hepatitis C virus (isolate H77)|63746 -EVQIVSTAAQTFLAT ->149044|NS2 protein|NP_751923.1|Hepatitis C virus (isolate H77)|63746 -FLTRVEAQL ->149052|E1 protein|NP_751920.1|Hepatitis C virus (isolate H77)|63746 -GIAYFSMVGNWAKVLVVL ->149053|NS3 gene product|AAB02124.1|Hepatitis C virus|11103 -GRGKPGIYRFVAPGERPS ->149060|E2 protein|NP_751921.1|Hepatitis C virus (isolate H77)|63746 -HPEATYSRC ->149063|NS3 protease/helicase'|NP_803144.1|Hepatitis C virus (isolate H77)|63746 -KAVDFIPVENLETTMRSP ->149072|NS3 gene product|AAB02124.1|Hepatitis C virus (isolate H77)|63746 -MSKAHGVDPNIRTGVRTI ->149074|E1 protein|NP_751920.1|Hepatitis C virus (isolate H77)|63746 -NASRCWVAV ->149075|envelope glycoprotein E1|ACI88341.1|Hepatitis C virus genotype 1|41856 -NASRCWVPV ->149089|NS3|ABN45875.1|Hepatitis C virus (isolate H77)|63746 -NQVEGEVQI ->149096|polyprotein|BAB18801.1|Hepatitis C virus|11103 -RAQAPPPSW ->149097|NS5 protein|BAA00702.1|Hepatitis C virus (isolate H77)|63746 -RGGRAAICGKYLFNWAVR ->149098|E2 protein|NP_751921.1|Hepatitis C virus (isolate H77)|63746 -RSGAPTYSW ->149105|E2 protein|NP_751921.1|Hepatitis C virus (isolate H77)|63746 -SIASWAIKW ->149115|NS5 protein|BAA00702.1|Hepatitis C virus (isolate H77)|63746 -SVRARLLSR ->149117|envelope glycoprotein|AAV74049.1|Hepatitis C virus (isolate H77)|63746 -TDFDQGWGPISYANGSGP ->149126|nonstructural protein 3|AAY84762.1|Hepatitis C virus genotype 1|41856 -TVYHGAGTK ->149127|NS3|ABN45875.1|Hepatitis C virus (isolate H77)|63746 -TVYHGAGTR ->149129|NS2 protein|NP_751923.1|Hepatitis C virus (isolate H77)|63746 -VVFSRMETKLITWGADTA ->150137|Nonstructural protein NS3|NP_739587.2|Dengue virus 2|11060 -APTRVVAAEM ->150217|polyprotein|AGO67248.1|Dengue virus 2|11060 -FPQSNAPIM ->150224|polyprotein|AGO67248.1|Dengue virus 2|11060 -FTIMAAILAY ->150227|polyprotein|AGS49173.1|Dengue virus 2|11060 -FTMRHKKATY ->150252|polyprotein|AGO67248.1|Dengue virus 2|11060 -GPLKLFMAL ->150259|polyprotein|AGO67248.1|Dengue virus 2|11060 -GPWHLGKLEM ->150299|polyprotein|AGO67248.1|Dengue virus 2|11060 -ILLTAVAPSM ->150308|polyprotein|AGW21594.1|Dengue virus 1|11053 -IPMATYGWNL ->150309|polyprotein|AGO67248.1|Dengue virus 2|11060 -IPMSTYGWNL ->150341|polyprotein|AGW21594.1|Dengue virus 1|11053 -KPGTSGSPI ->150373|polyprotein|AAA42942.1|Dengue virus 2|11060 -LLILCVTQV ->150377|polyprotein|AGS49173.1|Dengue virus 2|11060 -LLLVAHYAI ->150378|polyprotein|AGW21594.1|Dengue virus 1|11053 -LLMLVTPSM ->150387|polyprotein|AGO67248.1|Dengue virus 2|11060 -LMGLGKGWPL ->150389|polyprotein|AGO67248.1|Dengue virus 2|11060 -LMMRTTWAL ->150391|polyprotein|AGS49173.1|Dengue virus 2|11060 -LMMTTIGIVL ->150399|polyprotein|AGV76873.1|Dengue virus 2|11060 -LQMENKAWLV ->150425|polyprotein|AGS49173.1|Dengue virus 2|11060 -LVISGLFPV ->150445|polyprotein|AGO67248.1|Dengue virus 2|11060 -MLLILCVTQV ->150448|polyprotein|AGO67248.1|Dengue virus 2|11060 -MMATIGIAL ->150450|polyprotein|AGO67248.1|Dengue virus 2|11060 -MPVTHSSAA ->150451|polyprotein|AGO67248.1|Dengue virus 2|11060 -MPVTHSSAAQ ->150456|polyprotein|AGO67248.1|Dengue virus 2|11060 -MSYSMCTGKF ->150461|polyprotein|AGK36298.1|Dengue virus 2|11060 -MTQKARNAL ->150474|polyprotein|AGW21594.1|Dengue virus 1|11053 -NPLTLTAAV ->150531|polyprotein|AGO67248.1|Dengue virus 2|11060 -RLRMDKLQL ->150534|polyprotein|AGO67248.1|Dengue virus 2|11060 -RPASAWTLY ->150538|polyprotein|AGW21594.1|Dengue virus 1|11053 -RPRWLDART ->150556|polyprotein|AGW21594.1|Dengue virus 1|11053 -RVIDPRRCLK ->150571|polyprotein|AGO67248.1|Dengue virus 2|11060 -SLLFKTEDGV ->150578|polyprotein|AGO67248.1|Dengue virus 2|11060 -SPCKIPFEIM ->150579|polyprotein|AGW21594.1|Dengue virus 1|11053 -SPGKFWNTTI ->150584|polyprotein|AGO67248.1|Dengue virus 2|11060 -SPILSITISE ->150612|polyprotein|AGO67248.1|Dengue virus 2|11060 -TAEAGGRAY ->150634|polyprotein|AGS49173.1|Dengue virus 2|11060 -TLMAMDLGEL ->150639|polyprotein|AGO67249.1|Dengue virus 2|11060 -TLYAVATTFV ->150643|polyprotein|AGW21594.1|Dengue virus 1|11053 -TPEGIIPALF ->150644|polyprotein|AGO67248.1|Dengue virus 2|11060 -TPEGIIPSMF ->150649|polyprotein|AGW21594.1|Dengue virus 1|11053 -TPQDNQLAYV ->150655|polyprotein|AGO67248.1|Dengue virus 2|11060 -TPRMCTREEF ->150686|polyprotein|AGO67248.1|Dengue virus 2|11060 -VLMMRTTWA ->150693|polyprotein|AGO67248.1|Dengue virus 2|11060 -VPNYNLIIM ->150698|polyprotein|AGO67248.1|Dengue virus 2|11060 -VPYLGKREDQ ->150725|polyprotein|AGO67248.1|Dengue virus 2|11060 -WLVHRQWFL ->150752|polyprotein|AGO67249.1|Dengue virus 2|11060 -YVVIAILTV ->150753|polyprotein|AGO67248.1|Dengue virus 2|11060 -YVVIAILTVV ->150974|60 kDa chaperonin|SRC280371|Yersinia enterocolitica|630 -DRGIDKAVI ->150991|60 kDa chaperonin|P48219.1|Yersinia enterocolitica|630 -GRNVVLDKS ->151001|60 kDa chaperonin|P48219.1|Yersinia enterocolitica|630 -IRAASAITA ->151003|heat shock 60kDa protein 1 (chaperonin)|AAH02676.1|Homo sapiens|9606 -IRRGVMLAV ->151012|heat shock 60kDa protein 1 (chaperonin)|AAH02676.1|Homo sapiens|9606 -KRIQEIIEQ ->151013|heat shock 60kDa protein 1 (chaperonin)|AAH02676.1|Homo sapiens|9606 -KRTLKIPAM ->154041|major capsid protein|CAB06743.1|Human alphaherpesvirus 2|10310 -AFEDRSYPAVFYLLQ ->154164|tegument protein|CAB06732.1|Human alphaherpesvirus 2|10310 -AQREAAGVYDAVRTW ->154196|tegument protein|CAB06735.1|Human alphaherpesvirus 2|10310 -ARPRRSASVAGSHGPG ->154296|UL29|CAB06754.1|Human alphaherpesvirus 2|10310 -CPLLIFDRTRKFVLA ->154346|RL2|CAB06760.1|Human alphaherpesvirus 2|10310 -DFIWTGNPRTAPRSL ->154387|RL2|CAB06760.1|Human alphaherpesvirus 2|10310 -DMETGHIGAYVVLVD ->154409|capsid associated tegument protein|CAB06749.1|Human alphaherpesvirus 2|10310 -DRLDNRLQLGMLIPG ->154448|RL2|CAB06760.1|Human alphaherpesvirus 2|10310 -EAGLMDAATPPARPPA ->154585|ribonucleotide reductase large subunit|CAB06725.1|Human alphaherpesvirus 2|10310 -FGGHYMESVFQMYTR ->154725|RL2|CAB06760.1|Human alphaherpesvirus 2|10310 -GHIGAYVVLVDQTGN ->154822|ribonucleotide reductase large subunit|CAB06725.1|Human alphaherpesvirus 2|10310 -GVLVHLRIRTREASF ->154857|tegument protein|CAB06735.1|Human alphaherpesvirus 2|10310 -HGPGPARAPPPPGGPV ->154980|tegument protein|CAB06735.1|Human alphaherpesvirus 2|10310 -KNLLQRANELVNPDA ->154996|ribonucleotide reductase large subunit|CAB06725.1|Human alphaherpesvirus 2|10310 -KTSNALCVRGARPFS ->155096|RL2|CAB06760.1|Human alphaherpesvirus 2|10310 -LHPFCIPCMKTWIPL ->155131|ribonucleotide reductase large subunit|CAB06725.1|Human alphaherpesvirus 2|10310 -LMLEYFCRCAREESK ->155139|RL2|CAB06760.1|Human alphaherpesvirus 2|10310 -LPIAGVSSVVALAPY ->155403|tegument protein|CAB06735.1|Human alphaherpesvirus 2|10310 -PKASATPATDPARGR ->155489|RL2|CAB06760.1|Human alphaherpesvirus 2|10310 -PVGNMLFDQGTLVGA ->155554|RL2|CAB06760.1|Human alphaherpesvirus 2|10310 -RAAAPAWSRRTLLPE ->155637|tegument protein|CAB06732.1|Human alphaherpesvirus 2|10310 -RLGPADRRFVALSGS ->155811|ribonucleotide reductase large subunit|CAB06725.1|Human alphaherpesvirus 2|10310 -SMSLADFHGEEFEKL ->155927|unnamed protein product|CAA30115.1|Trypanosoma cruzi|5693 -TLLTIDGGI ->155928|unnamed protein product|CAA30115.1|Trypanosoma cruzi|5693 -TLQPVERVL ->155999|RL2|CAB06760.1|Human alphaherpesvirus 2|10310 -VALAPYVNKTVTGDC ->156542|ETS translocation variant 5|NP_004445.1|Homo sapiens|9606 -ELFQDLSQL ->156550|E3 ubiquitin-protein ligase Mdm2|Q00987.1|Homo sapiens|9606 -VLFYLGQYI ->156552|U1 small nuclear ribonucleoprotein 70 kDa|NP_003080.2|Homo sapiens|9606 -YLAPENGYL ->156711|polyprotein precursor|AAG45435.1|Dengue virus 4|11070 -LAPTRVVAAEMEEAL ->156949|Protein 3a|P59632.1|SARS coronavirus|227859 -RFFTLGSITAQPVKI ->159290|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 -LLRHHNLVY ->159299|polyprotein|AAC03058.1|Hepatitis C virus subtype 3a|356426 -SQRQRKVTF ->161186|Nonstructural protein NS5|NP_739590.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 -RLLTKPWDVVPMVTQ ->161353|arsenic-transport integral membrane protein ArsA|NP_217200.1|Mycobacterium tuberculosis H37Rv|83332 -IMILLVLVSA ->161402|hypothetical protein|NP_215301.1|Mycobacterium tuberculosis H37Rv|83332 -LILATMLVA ->161641|6 kDa early secretory antigenic target|P0A564.2|Mycobacterium tuberculosis|1773 -IQGNVTSIHSLLDEG ->164233|nucleocapsid protein|AAA43837.1|Hantaan hantavirus|11599 -FVVPILLKA ->164258|nucleocapsid protein|AAA43837.1|Hantaan virus 76-118|11602 -IEPCKLLPDTAAVSL ->164264|nucleocapsid protein|AAA43837.1|Hantaan virus 76-118|11602 -ITPGRYRTAVCGLYP ->164282|nucleocapsid protein|AAA43837.1|Hantaan hantavirus|11599 -LPDTAAVSL ->164403|nucleocapsid protein|AAA43837.1|Hantaan virus 76-118|11602 -TSFVVPILLKALYML ->164417|nucleocapsid protein|AAA43837.1|Hantaan hantavirus|11599 -VPILLKALY ->164420|nucleocapsid protein|AAA43837.1|Hantaan virus 76-118|11602 -VSLLGGPATNRDYLR ->164547|envelope glycoprotein B|NP_044629.1|Herpes simplex virus (type 1 / strain 17)|10299 -RMLGDVMAV ->164551|envelope glycoprotein B|NP_044629.1|Herpes simplex virus (type 1 / strain 17)|10299 -TMLEDHEFV ->167320|possible regulatory protein|NP_302009.1|Mycobacterium leprae|1769 -LLEEGVIVL ->168240|major paraflagellar rod protein|AAA30221.1|Trypanosoma cruzi|5693 -AVPEVTDVTL ->168327|paraflagellar rod component|AAC32021.1|Trypanosoma cruzi|5693 -DIIEQMKGV ->168607|paraflagellar rod component|AAC32021.1|Trypanosoma cruzi|5693 -FVSCCGELTV ->168691|polyprotein|ABU97067.1|Hepatitis C virus subtype 1b|31647 -GLNAVAYYR ->168728|paraflagellar rod component|AAC32021.1|Trypanosoma cruzi|5693 -GVSGVINAL ->168988|major paraflagellar rod protein|AAA30221.1|Trypanosoma cruzi|5693 -KLEKIEDEL ->169050|polyprotein|ABU97067.1|Hepatitis C virus subtype 1b|31647 -KYLFNWAVK ->169658|major paraflagellar rod protein|AAA30221.1|Trypanosoma cruzi|5693 -RLYKTLGQL ->169995|polyprotein|ABU97067.1|Hepatitis C virus subtype 1b|31647 -VLYQDFDEM ->170049|polyprotein|ABU97067.1|Hepatitis C virus subtype 1b|31647 -WEYVLLLFL ->170063|polyprotein|ABU97067.1|Hepatitis C virus subtype 1b|31647 -WTRGERCNL ->177647|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 -EGAVQWMNRLIAFASR ->177701|polyprotein|ACZ60104.1|Hepatitis C virus subtype 3a|356426 -GKAKICGLYLFNWAVRTK ->177727|polyprotein|ACZ60102.1|Hepatitis C virus subtype 3a|356426 -GVMSTRCPCGASIAGHVK ->177806|polyprotein|ACZ60104.1|Hepatitis C virus subtype 3a|356426 -KLTPLPAAGQL ->177843|polyprotein|ACZ60102.1|Hepatitis C virus subtype 3a|356426 -LIHLHQNIVDVQYLYGV ->177884|polyprotein|ACZ60102.1|Hepatitis C virus genotype 1|41856 -NIVDVQYLYGVGSGMVGW ->177903|polyprotein|ACZ60102.1|Hepatitis C virus subtype 3a|356426 -PAVASLMAFTASVTSPL ->177955|polyprotein|ACZ60102.1|Hepatitis C virus subtype 3a|356426 -RPSGMFDSVVL ->177956|polyprotein|ACZ60102.1|Hepatitis C virus subtype 3a|356426 -RPSGMFDSVVLCECYDA ->178185|Protein E6|P03126.1|Human papillomavirus type 16|333760 -AFRDLCIVYRDGNPY ->178247|Protein E6|P03126.1|Human papillomavirus type 16|333760 -HLDKKQRFHNIRGRW ->178351|Protein E7|P03129.1|Human papillomavirus type 16|333760 -TPTLHEYMLDLQPET ->178829|envelope protein|BAJ51675.1|HBV genotype D|489483 -FLGPLLVLQA ->179762|cytotoxin/hemolysin|NP_301968.1|Mycobacterium leprae TN|272631 -ALDTFGIPV ->179765|cell surface protein (associated with virulence)|NP_302372.1|Mycobacterium leprae TN|272631 -APIPASVSA ->179766|cell surface protein (associated with virulence)|NP_302372.1|Mycobacterium leprae TN|272631 -APLPPSTAT ->179795|cell surface protein (associated with virulence)|NP_302372.1|Mycobacterium leprae TN|272631 -GIAGSASYY ->179799|hypothetical protein|NP_301670.1|Mycobacterium leprae TN|272631 -GPVPAVATL ->179802|cell surface protein (associated with virulence)|NP_302372.1|Mycobacterium leprae TN|272631 -HRKGLWAIL ->179823|cell surface protein (associated with virulence)|NP_302372.1|Mycobacterium leprae TN|272631 -IPASVSAPA ->179825|cytotoxin/hemolysin|NP_301968.1|Mycobacterium leprae TN|272631 -IPVAGRCCL ->179839|cytotoxin/hemolysin|NP_301968.1|Mycobacterium leprae TN|272631 -KLMGALDTF ->179840|hypothetical protein|NP_302232.1|Mycobacterium leprae TN|272631 -KVTVSSVRK ->179850|cytotoxin/hemolysin|NP_301968.1|Mycobacterium leprae TN|272631 -LPSADIVPM ->179866|cell surface protein (associated with virulence)|NP_302372.1|Mycobacterium leprae TN|272631 -NGIAGSASY ->179881|hypothetical protein|NP_302232.1|Mycobacterium leprae TN|272631 -QMLEASSSV ->179885|hypothetical protein|NP_301670.1|Mycobacterium leprae TN|272631 -RAAVVQAAL ->179891|hypothetical protein|NP_302233.1|Mycobacterium leprae TN|272631 -RPRRGSVSR ->179892|p60-family protein|NP_301879.1|Mycobacterium leprae TN|272631 -RPVPVSTAR ->179898|cell surface protein (associated with virulence)|NP_302372.1|Mycobacterium leprae TN|272631 -SASAFTMPL ->179917|cell surface protein (associated with virulence)|NP_302372.1|Mycobacterium leprae TN|272631 -VASASAFTM ->180077|PPE family protein|YP_177935.1|Mycobacterium tuberculosis H37Rv|83332 -YAEMWAQDA ->180168|gag protein|ABO14878.1|Human immunodeficiency virus 1|11676 -SLFNAVATL ->180191|gag polyprotein|BAB19174.1|Human immunodeficiency virus 1|11676 -SLFNTIATL ->180233|gag protein|ACZ34075.1|Human immunodeficiency virus 1|11676 -SLFNTVATV ->180236|gag|BAC81459.1|Human immunodeficiency virus 1|11676 -SLFNTVAVL ->180255|gag protein|AAT90688.1|Human immunodeficiency virus 1|11676 -SLFNTVVTL ->180337|pol protein|ACJ76655.1|Human immunodeficiency virus 1|11676 -LPPVVAKEI ->180360|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 -AAEGINYADRRWCFD ->180373|polyprotein|AGW21594.1|Dengue virus 1|11053 -APTRVVASEM ->180387|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 -CEALTLATGPISTLW ->180390|polyprotein|CDF77361.1|Dengue virus 3|11069 -CLMMMLPATL ->180407|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 -DNINTPEGIIPSMFE ->180408|polyprotein|AGO67248.1|Dengue virus 2|11060 -DPASIAARGY ->180411|polyprotein|AGO67248.1|Dengue virus 2|11060 -DTTPFGQQR ->180423|polyprotein|AGW21594.1|Dengue virus 1|11053 -EERDIPERSW ->180428|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 -EGEWKEGEEVQVLAL ->180433|polyprotein|AGO67248.1|Dengue virus 2|11060 -EPGQLKLNWF ->180437|polyprotein|AGO67248.1|Dengue virus 2|11060 -EPKEGTKKLM ->180440|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 -EREIPERSWNSGHEW ->180442|Chain B, Dengue Virus Rna Dependent Rna Polymerase With Residues From The Ns5 Linker Region|4C11_B|Dengue virus|12637 -ETACLGKAYA ->180443|polyprotein|AGO67248.1|Dengue virus 2|11060 -ETACLGKSYA ->180450|polyprotein|AGO67248.1|Dengue virus 2|11060 -FAGPVSQHNY ->180453|polyprotein|AGO67248.1|Dengue virus 2|11060 -FGAIYGAAF ->180460|polyprotein|AGO67248.1|Dengue virus 2|11060 -FPQSNAPIMD ->180464|polyprotein|CDF77361.1|Dengue virus 3|11069 -FTILALFLAH ->180471|polyprotein|AGO67248.1|Dengue virus 2|11060 -GEARKTFVDL ->180472|polyprotein|AGW21594.1|Dengue virus 1|11053 -GEARKTFVEL ->180483|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 -GKKKTPRMCTREEFT ->180488|polyprotein|AGO67248.1|Dengue virus 2|11060 -GPGHEEPIPM ->180496|Polyprotein|NP_056776.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 -GVFTTNIWLKLKEKQ ->180500|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 -HKKLAEAIFKLTYQN ->180503|polyprotein|AGO67248.1|Dengue virus 2|11060 -HPGAGKTKRY ->180504|polyprotein|CDF77361.1|Dengue virus 3|11069 -HPGFTILALF ->180507|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 -HTGREIVDLMCHATF ->180512|polyprotein|AGO67248.1|Dengue virus 2|11060 -IANQATVLM ->180514|polyprotein|AGO67248.1|Dengue virus 2|11060 -IAVSMANIF ->180528|polyprotein|AGO67248.1|Dengue virus 2|11060 -IPFEIMDLEK ->180529|polyprotein|AGO67248.1|Dengue virus 2|11060 -IPITAAAWY ->180531|polyprotein|AGO67248.1|Dengue virus 2|11060 -IPMTGPLVAG ->180538|Nonstructural protein NS2B|NP_739586.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 -ISGLFPVSIPITAAA ->180563|Envelope protein|NP_739583.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 -KILIGVIITWIGMNS ->180571|polyprotein|AGW21594.1|Dengue virus 1|11053 -KPRICTREEF ->180572|polyprotein|CDF77361.1|Dengue virus 3|11069 -KPRLCTREEF ->180575|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 -KRYLPAIVREAIKRG ->180579|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 -KSYAQMWSLMYFHRR ->180582|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 -KTWAYHGSYETKQTG ->180588|polyprotein|AGO67248.1|Dengue virus 2|11060 -LAYTIGTTHF ->180589|Nonstructural protein NS3|NP_739587.2|Dengue virus 2|11060 -LDARIYSDPLALKEF ->180596|polyprotein|AFP27208.1|Dengue virus 4|11070 -LETLMLVALL ->180601|polyprotein|AGO67248.1|Dengue virus 2|11060 -LILCVTQVLM ->180605|polyprotein|AGO67248.1|Dengue virus 2|11060 -LMCHATFTM ->180609|polyprotein|ABK30845.1|Dengue virus 3|11069 -LMMMLPATL ->180611|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 -LMRRGDLPVWLAYRV ->180613|envelope protein|AGT63061.1|Dengue virus 3|11069 -LPEEQDQNY ->180617|polyprotein|AGO67248.1|Dengue virus 2|11060 -LPIRYQTPAI ->180618|polyprotein|AGO67248.1|Dengue virus 2|11060 -LPLPWLPGAD ->180620|polyprotein|AGO67248.1|Dengue virus 2|11060 -LPTFMTQKAR ->180624|polyprotein|AGS49173.1|Dengue virus 2|11060 -LPVWLAYKVA ->180637|polyprotein|AGW21594.1|Dengue virus 1|11053 -MAFIAFLRF ->180640|polyprotein|AFP27208.1|Dengue virus 4|11070 -MALKDFKEF ->180641|polyprotein|AFJ91714.1|Dengue virus 1|11053 -MALSIVSLF ->180643|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 -MAMTDTTPFGQQRVF ->180646|polyprotein|AGO67248.1|Dengue virus 2|11060 -MAVGMVSIL ->180647|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 -MEEALRGLPIRYQTP ->180656|polyprotein|AGO67248.1|Dengue virus 2|11060 -MLIPTAMAF ->180657|polyprotein|CDF77361.1|Dengue virus 3|11069 -MLVTPSMTM ->180660|polyprotein|CDF77361.1|Dengue virus 3|11069 -MMLPATLAF ->180662|polyprotein|CDF77361.1|Dengue virus 3|11069 -MMMLPATLAF ->180667|polyprotein|AGO67248.1|Dengue virus 2|11060 -MPSMKRFRRE ->180668|polyprotein|AGO67248.1|Dengue virus 2|11060 -MPSVIEKMET ->180670|polyprotein|AGW21594.1|Dengue virus 1|11053 -MPVTVASAAQ ->180671|polyprotein|AGO67248.1|Dengue virus 2|11060 -MSFRDLGRVM ->180675|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 -MSTYGWNLVRLQSGV ->180681|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 -NEEYTDYMPSMKRFR ->180682|polyprotein|AGO67248.1|Dengue virus 2|11060 -NPEIEDDIF ->180684|nonstructural protein 5|AGX01519.1|Dengue virus 4|11070 -NPRLCTREEF ->180689|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 -NRAVHADMGYWIESA ->180717|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 -RDLGRVMVMVGATMT ->180718|polyprotein|AFP27208.1|Dengue virus 4|11070 -REDLWCGSL ->180723|polyprotein|AGO67248.1|Dengue virus 2|11060 -RFLEFEALGF ->180724|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 -RGEARKTFVDLMRRG ->180726|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 -RMAILGDTAWDFGSL ->180728|Nonstructural protein NS5|YP_001531176.2|Dengue virus 3|11069 -RPRLCTREEF ->180734|Nonstructural protein NS3|NP_739587.2|Dengue virus 2|11060 -RSWNSGHEW ->180735|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 -RVGTKHAILLVAVSF ->180738|polyprotein|CDF77361.1|Dengue virus 3|11069 -RYMGEDGCWY ->180750|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 -SPGTSGSPIIDKKGK ->180756|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 -STRVEMGEAAGIFMT ->180758|Nonstructural protein NS5|NP_739590.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 -SWHYDQDHPYKTWAY ->180774|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 -TLRVLNLVENWLNNN ->180778|polyprotein|AFP27208.1|Dengue virus 4|11070 -TPEGIIPTLF ->180780|polyprotein|AGW21594.1|Dengue virus 1|11053 -TPQDNQLAY ->180781|polyprotein|AGO67248.1|Dengue virus 2|11060 -TPQDNQLTY ->180789|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 -TVIDLDPIPYDPKFE ->180794|polyprotein|AGO67248.1|Dengue virus 2|11060 -VATTFVTPM ->180802|polyprotein|AGO67248.1|Dengue virus 2|11060 -VPLLAIGCY ->180803|polyprotein|AFP27208.1|Dengue virus 4|11070 -VPLLAMGCY ->180804|polyprotein|AGW21594.1|Dengue virus 1|11053 -VPNYNMIIM ->180814|polyprotein|AGO67248.1|Dengue virus 2|11060 -WAYHGSYET ->180816|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 -WGNGCGLFGKGGIVT ->180817|polyprotein|AGO67248.1|Dengue virus 2|11060 -WHYDQDHPY ->180818|Membrane glycoprotein precursor|NP_739582.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 -WILRHPGFTMMAAIL ->180828|polyprotein|AGO67248.1|Dengue virus 2|11060 -YAQMWSLMYF ->180836|polyprotein|AGT63075.1|Dengue virus 1|11053 -YGGPISQHNY ->180843|polyprotein|AFP27208.1|Dengue virus 4|11070 -YPKTKLTDWD ->180850|polyprotein|AFP27208.1|Dengue virus 4|11070 -YTPEGIIPTL ->180880|nucleocapsid protein|AAA43837.1|Hantaan hantavirus|11599 -ETKESKAIR ->181035|||| -VLSDFKVWLKKLFPGGGQICGGVYLLPRRGPRLKKSMMAFSAAL ->181036|||| -VLSDFKVWLKKSMMAFSAAL ->181152|Pol polyprotein|Q9YLQ7|Human immunodeficiency virus 1|11676 -TAFTIPSL ->181154|pol protein|ACJ76655.1|Human immunodeficiency virus 1|11676 -TAFTIPST ->181155|pol protein|AAQ76603.1|Human immunodeficiency virus 1|11676 -TAFTIPSV ->181731|Possible hydrolase|NP_215850.1|Mycobacterium tuberculosis|1773 -MLLRKGTVYVLVIRADLVNAMVAHA ->181733|Antigen 85-B|P0C5B9.1|Mycobacterium tuberculosis|1773 -MTDVSRKIRAWGRRLMIGTAAAVVLPGLVGLAGGAATAGA ->182421|polyprotein|AGO67248.1|Dengue virus 2|11060 -AAGRKSLTL ->182508|polyprotein|AFP27208.1|Dengue virus 4|11070 -AIAVASGLLW ->182554|polyprotein|ACF49259.1|Dengue virus type 1 Hawaii|10000440 -ALLATSIFK ->182599|polyprotein|AGW21594.1|Dengue virus 1|11053 -AQMWQLMYF ->182687|polyprotein|AGK36298.1|Dengue virus 2|11060 -AYRIKQRGIL ->182702|polyprotein|AGO63991.1|Dengue virus|12637 -CLMMILPAA ->182707|polyprotein|AFY10039.1|Dengue virus 4|11070 -CNLTSTWVMY ->182747|polyprotein|AGO67248.1|Dengue virus 2|11060 -CYSQVNPITL ->182836|polyprotein|ACF49259.1|Dengue virus type 1 Hawaii|10000440 -DYMTSMKRF ->182848|polyprotein|AGO67248.1|Dengue virus 2|11060 -EARKTFVDL ->182892|polyprotein|AFP27208.1|Dengue virus 4|11070 -EENMEVEIW ->182898|polyprotein|AGO67248.1|Dengue virus 2|11060 -EEREIPERSW ->182912|polyprotein|AGW21594.1|Dengue virus 1|11053 -EFFLMVLLI ->182917|polyprotein|CDF77361.1|Dengue virus 3|11069 -EFKDFAAGR ->182926|polyprotein|AFP27208.1|Dengue virus 4|11070 -EIASLPTYL ->182938|polyprotein|AGO67248.1|Dengue virus 2|11060 -EKEENLVNSL ->182939|polyprotein|CDF77361.1|Dengue virus 3|11069 -EKEENMVKSL ->182971|polyprotein|AFP27208.1|Dengue virus 4|11070 -EMCEDTVTY ->183147|polyprotein|AGW21594.1|Dengue virus 1|11053 -FCSHHFHQL ->183162|polyprotein|AGW21594.1|Dengue virus 1|11053 -FFLMVLLIPE ->183165|polyprotein|CDF77361.1|Dengue virus 3|11069 -FFMMVLLIPE ->183175|polyprotein|AGW21594.1|Dengue virus 1|11053 -FIAFLRFLA ->183223|polyprotein|AGW21594.1|Dengue virus 1|11053 -FPGKTVWFVP ->183229|polyprotein|AGW21594.1|Dengue virus 1|11053 -FPQSNAVIQD ->183231|polyprotein|AFP27208.1|Dengue virus 4|11070 -FPQSNSPIED ->183245|polyprotein|AGT63074.1|Dengue virus 1|11053 -FQSHQLWATL ->183252|polyprotein|AGT63075.1|Dengue virus 1|11053 -FSLHYAWKTM ->183275|polyprotein|AGW21594.1|Dengue virus 1|11053 -FTNMEVQLIR ->183353|polyprotein|AFP27208.1|Dengue virus 4|11070 -GESSSNPTI ->183363|gag polyprotein|BAA00992.1|Human immunodeficiency virus 1|11676 -GGKKKYKL ->183366|gag protein|ABI20203.1|Human immunodeficiency virus 1|11676 -GGKKRYKL ->183395|polyprotein|AAS49480.2|Dengue virus 3|11069 -GKKHMIAGVL ->183421|polyprotein|AGW21594.1|Dengue virus 1|11053 -GLNSRSTSL ->183437|polyprotein|AGO67248.1|Dengue virus 2|11060 -GMNSRSTSL ->183570|polyprotein|AFP27208.1|Dengue virus 4|11070 -HEMYWVSGV ->183577|polyprotein|AGK36298.1|Dengue virus 2|11060 -HFQRALIFIL ->183587|polyprotein|AGH08163.1|Dengue virus 3|11069 -HMIAGVFFTF ->183594|polyprotein|AGT63075.1|Dengue virus 1|11053 -HPASAWTLYA ->183598|polyprotein|AGW21594.1|Dengue virus 1|11053 -HPGSGKTRRY ->183619|nonstructural protein NS1|1802191G|Dengue virus|12637 -HTWTEQYKF ->183621|polyprotein|AGK36298.1|Dengue virus 2|11060 -HVQRIETWIL ->183654|polyprotein|AGW21594.1|Dengue virus 1|11053 -IAVGMVTLY ->183670|polyprotein|AGO67248.1|Dengue virus 2|11060 -IENSSVNVSL ->183672|polyprotein|AFP27208.1|Dengue virus 4|11070 -IENTSANLSL ->183708|polyprotein|AGO67248.1|Dengue virus 2|11060 -IGMNSRSTSL ->183719|polyprotein|AGO63991.1|Dengue virus|12637 -IINKRKKTSL ->183723|polyprotein|CDF77361.1|Dengue virus 3|11069 -IKLTVVVGDI ->183724|polyprotein|AGO67248.1|Dengue virus 2|11060 -IKRGLRTLIL ->183741|polyprotein|AGS49173.1|Dengue virus 2|11060 -ILCVPNAVIL ->183747|polyprotein|AGO67248.1|Dengue virus 2|11060 -ILIGVIITW ->183766|polyprotein|AGO67248.1|Dengue virus 2|11060 -ILNRRRRTA ->183779|polyprotein|AGO67248.1|Dengue virus 2|11060 -IMAVGMVSIL ->183781|polyprotein|AGO67248.1|Dengue virus 2|11060 -IMDLEKRHVL ->183793|envelope protein|AGT63061.1|Dengue virus 3|11069 -IMKIGIGVLL ->183800|polyprotein|AGT63075.1|Dengue virus 1|11053 -IMNRRKRSV ->183804|polyprotein|AGO63991.1|Dengue virus|12637 -INKRKKTSL ->183813|polyprotein|AGW21594.1|Dengue virus 1|11053 -IPEPDRQRTP ->183819|polyprotein|AGO67248.1|Dengue virus 2|11060 -IPITAAAWYL ->183825|polyprotein|AGO67248.1|Dengue virus 2|11060 -IPLALTIKGL ->183843|envelope protein|AGW23576.1|Dengue virus 3|11069 -IQNSGGTSIF ->184065|Nonstructural protein NS3|YP_001531172.2|Dengue virus 3|11069 -KLNDWDFVV ->184130|polyprotein|AFP27208.1|Dengue virus 4|11070 -KREDLWCGSL ->184131|polyprotein|AGO67248.1|Dengue virus 2|11060 -KREDQWCGSL ->184136|gag protein|ADZ56444.1|Human immunodeficiency virus 1|11676 -KRWIIMGLNK ->184212|polyprotein|AGW21594.1|Dengue virus 1|11053 -KVRKDIPQW ->184234|polyprotein|AGO67248.1|Dengue virus 2|11060 -KWKSRLNAL ->184260|polyprotein|CDF77361.1|Dengue virus 3|11069 -LAIPPTAGVL ->184264|polyprotein|CDF77361.1|Dengue virus 3|11069 -LAKRFSRGL ->184265|polyprotein|CDF77361.1|Dengue virus 3|11069 -LAKRFSRGLL ->184274|polyprotein|AGW21594.1|Dengue virus 1|11053 -LALMATFKM ->184299|envelope protein|AGT63061.1|Dengue virus 3|11069 -LATLRKLCI ->184300|envelope protein|AFN87749.1|Dengue virus 2|11060 -LATLRKYCI ->184316|polyprotein|AGW21594.1|Dengue virus 1|11053 -LEENMDVEIW ->184318|polyprotein|AFP27208.1|Dengue virus 4|11070 -LEENMEVEIW ->184337|polyprotein|AGO67248.1|Dengue virus 2|11060 -LEKRHVLGRL ->184373|polyprotein|AGO67248.1|Dengue virus 2|11060 -LGKKKTPRM ->184377|polyprotein|AGW21594.1|Dengue virus 1|11053 -LGLNSRSTSL ->184378|polyprotein|AGO67248.1|Dengue virus 2|11060 -LGMLQGRGPL ->184412|envelope protein|AGW23591.1|Dengue virus 3|11069 -LKGMSYAMCL ->184429|||| -LLFGFPVYV ->184439|polyprotein|AGO67248.1|Dengue virus 2|11060 -LLILCVTQVL ->184453|polyprotein|AFP27207.1|Dengue virus 4|11070 -LLLMRTTWAF ->184458|polyprotein|AGT17702.1|Dengue virus 1|11053 -LLMLLPTAL ->184467|polyprotein|AGO67248.1|Dengue virus 2|11060 -LLQMEDKAWL ->184512|polyprotein|AGO67248.1|Dengue virus 2|11060 -LMWKQITPEL ->184518|polyprotein|AGO67248.1|Dengue virus 2|11060 -LNRRRRTAG ->184522|polyprotein|AGW21594.1|Dengue virus 1|11053 -LPDTIETLM ->184523|polyprotein|AGW21594.1|Dengue virus 1|11053 -LPDTIETLML ->184531|polyprotein|AFP27208.1|Dengue virus 4|11070 -LPESLETLML ->184554|polyprotein|AGT63075.1|Dengue virus 1|11053 -LPQHLTQRAQ ->184571|polyprotein|AGO67248.1|Dengue virus 2|11060 -LQLKGMSYSM ->184585|NS1|AGW99229.1|Dengue virus 3|11069 -LRTTTVSGKL ->184643|polyprotein|AGW24534.1|Dengue virus 2|11060 -LTIPPTAGIL ->184658|polyprotein|CDF77361.1|Dengue virus 3|11069 -LTQKVVIFIL ->184702|non-structural protein 1|AGM49312.1|Dengue virus|12637 -LWPKTHTLW ->184713|polyprotein|AFP27208.1|Dengue virus 4|11070 -LYAVATTIL ->184736|polyprotein|AGW21594.1|Dengue virus 1|11053 -MAMVLSIVS ->184739|polyprotein|AGW21594.1|Dengue virus 1|11053 -MASSVLLWM ->184755|polyprotein|AGO67248.1|Dengue virus 2|11060 -MDLEKRHVL ->184804|non-structural protein 1|AGM49312.1|Dengue virus|12637 -MFTTNIWMKF ->184814|polyprotein|AGO67248.1|Dengue virus 2|11060 -MGLGKGWPL ->184819|polyprotein|AGH08163.1|Dengue virus 3|11069 -MIAGVFFTF ->184835|polyprotein|AGW21594.1|Dengue virus 1|11053 -MKLVMAFIAF ->184840|polyprotein|AGS49173.1|Dengue virus 2|11060 -MLINRFTMR ->184845|polyprotein|CDF77361.1|Dengue virus 3|11069 -MLKRVRNRV ->184849|nonstructural protein 5|AGX01518.1|Dengue virus 1|11053 -MLLNRFTMA ->184856|polyprotein|AGW21594.1|Dengue virus 1|11053 -MLMTGTLAVF ->184864|polyprotein|AGO67248.1|Dengue virus 2|11060 -MLRTRVGTK ->184880|polyprotein|AGT63075.1|Dengue virus 1|11053 -MNRRKRSVT ->184884|polyprotein|AGW21594.1|Dengue virus 1|11053 -MPIRYQTTAV ->184896|polyprotein|AGW21594.1|Dengue virus 1|11053 -MPVTVASAA ->184898|polyprotein|AGW21594.1|Dengue virus 1|11053 -MQRKHGGML ->184899|polyprotein|AGO67248.1|Dengue virus 2|11060 -MRGAKRMAI ->184900|polyprotein|AGO67248.1|Dengue virus 2|11060 -MRGAKRMAIL ->185050|polyprotein|AFP27208.1|Dengue virus 4|11070 -NFLEVEDYGF ->185102|polyprotein|AGT63075.1|Dengue virus 1|11053 -NRRKRSVTM ->185104|polyprotein|AGO67248.1|Dengue virus 2|11060 -NRRRRTAGV ->185124|polyprotein|AGW21594.1|Dengue virus 1|11053 -NTPEGIIPA ->185125|polyprotein|AGW21594.1|Dengue virus 1|11053 -NTPEGIIPAL ->185200|polyprotein|AGO67248.1|Dengue virus 2|11060 -PRRCMKPVIL ->185232|polyprotein|AFP27208.1|Dengue virus 4|11070 -QEEHKETWHY ->185260|polyprotein|CDF77361.1|Dengue virus 3|11069 -QLAKRFSRG ->185279|polyprotein|AGW21594.1|Dengue virus 1|11053 -QMQRKHGGML ->185327|polyprotein|ACF49259.1|Dengue virus type 1 Hawaii|10000440 -QYIYMGQPL ->185388|polyprotein|AGO67248.1|Dengue virus 2|11060 -RIKQKGILGY ->185399|polyprotein|AGO67248.1|Dengue virus 2|11060 -RKKARSTPF ->185419|envelope protein|AGW23591.1|Dengue virus 3|11069 -RLKMDKLEL ->185447|polyprotein|AGK36298.1|Dengue virus 2|11060 -RNALDNLAVL ->185465|polyprotein|AGO67248.1|Dengue virus 2|11060 -RPLKEKEENL ->185468|polyprotein|AGW21594.1|Dengue virus 1|11053 -RPMFAVGLLF ->185485|polyprotein|AGW21594.1|Dengue virus 1|11053 -RQMESEGIFL ->185491|polyprotein|AGO67248.1|Dengue virus 2|11060 -RREEEEAGVL ->185492|polyprotein|AGT63075.1|Dengue virus 1|11053 -RRKRSVTMLL ->185573|polyprotein|CDF77361.1|Dengue virus 3|11069 -RYMGEDGCW ->185651|polyprotein|ACF49259.1|Dengue virus type 1 Hawaii|10000440 -SILLSSLLK ->185685|polyprotein|CDF77361.1|Dengue virus 3|11069 -SLLFKTASG ->185710|Nonstructural protein NS5|YP_001531176.2|Dengue virus 3|11069 -SMINGVVKL ->185716|polyprotein|AAA21201.1|Dengue virus 3|11069 -SMTMRCVGI ->185734|polyprotein|CDF77361.1|Dengue virus 3|11069 -SPKRLATAI ->185741|polyprotein|AGW21594.1|Dengue virus 1|11053 -SPVRVPNYNM ->185758|polyprotein|AGO67248.1|Dengue virus 2|11060 -SRSTSLSVSL ->185817|envelope protein|AGW23590.1|Dengue virus 4|11070 -SWMIRILIGF ->185827|polyprotein|ACF49259.1|Dengue virus type 1 Hawaii|10000440 -SYKVASEGF ->185881|polyprotein|AFP27208.1|Dengue virus 4|11070 -TEIASLPTYL ->185931|polyprotein|AGO67248.1|Dengue virus 2|11060 -TKQTGSASSM ->185978|polyprotein|CDF77361.1|Dengue virus 3|11069 -TMGVLCLAIL ->186002|polyprotein|AGO67248.1|Dengue virus 2|11060 -TPMLRHSIE ->186008|polyprotein|AGI95993.1|Dengue virus 4|11070 -TPPGATDPF ->186029|envelope protein|ABV59122.1|Dengue virus 3|11069 -TPTWNRKEL ->186041|polyprotein|AGO67248.1|Dengue virus 2|11060 -TRVGTKHAIL ->186058|polyprotein|AGO67248.1|Dengue virus 2|11060 -TSKKRSWPL ->186175|polyprotein|AFY10053.1|Dengue virus 3|11069 -TWRDMAHTLI ->186192|polyprotein|AGO67248.1|Dengue virus 2|11060 -VAATMANEM ->186211|polyprotein|AGO67248.1|Dengue virus 2|11060 -VDRKGKVVGL ->186219|polyprotein|AGK36298.1|Dengue virus 2|11060 -VEDGRFWEL ->186234|polyprotein|AFY10052.1|Dengue virus 3|11069 -VEIWTKEGEK ->186242|polyprotein|AGO67248.1|Dengue virus 2|11060 -VEMGEAAGIF ->186264|polyprotein|AGO67248.1|Dengue virus 2|11060 -VGRQEKGKSL ->186301|polyprotein|AGO67248.1|Dengue virus 2|11060 -VLMHRGKRI ->186303|polyprotein|AGS14893.1|Dengue virus 4|11070 -VLMMLVAPSY ->186330|polyprotein|AFP27208.1|Dengue virus 4|11070 -VMLLVHYAI ->186354|polyprotein|AGO67248.1|Dengue virus 2|11060 -VQQLTKRFSL ->186427|polyprotein|ACF49259.1|Dengue virus type 1 Hawaii|10000440 -VVYDAKFEK ->186453|polyprotein|AFP27208.1|Dengue virus 4|11070 -WEPSKGWKNW ->186470|envelope protein|AGT63061.1|Dengue virus 3|11069 -WIMKIGIGVL ->186474|polyprotein|AGO67248.1|Dengue virus 2|11060 -WKTWGKAKML ->186524|polyprotein|AGW21594.1|Dengue virus 1|11053 -WTMKIGIGIL ->186550|polyprotein|AFY10039.1|Dengue virus 4|11070 -YDQENPYRTW ->186551|polyprotein|AGW21594.1|Dengue virus 1|11053 -YENLKYSVIV ->186559|polyprotein|AGW21594.1|Dengue virus 1|11053 -YKVASEGFQY ->186603|polyprotein|AGW21594.1|Dengue virus 1|11053 -YSDPLALREF ->186620|polyprotein|AFP27208.1|Dengue virus 4|11070 -YVILTILTI ->186640|polyprotein|AFP27207.1|Dengue virus 4|11070 -YYMATLKNV ->186641|polyprotein|AFP27207.1|Dengue virus 4|11070 -YYMATLKNVT ->186692|||| -LLFGYPVFV ->187041|polyprotein|ABG67747.1|West Nile virus|11082 -AIIEVDRSAAK ->187045|polyprotein|ABG67747.1|West Nile virus|11082 -AVVVNPSVK ->187063|polyprotein|ABG67747.1|West Nile virus|11082 -GTLTSAINR ->187069|polyprotein precursor|AAF20092.2|West Nile virus|11082 -KNMEKPGLK ->187086|polyprotein|ABG67747.1|West Nile virus|11082 -RVLSLIGLK ->187106|Vpr protein|BAA93983.1|Human immunodeficiency virus 1|11676 -AVRHFPRIW ->187154|Vif protein|CAD26959.1|Human immunodeficiency virus 1|11676 -ISKKAKGWF ->187158|Gag protein|Q1KW74|Human immunodeficiency virus 1|11676 -KAFNPEIIPMF ->187160|Protein Rev|P04616.1|Human immunodeficiency virus 1|11676 -KAVRLIKFLY ->187163|Gag polyprotein|P88150|Human immunodeficiency virus 1|11676 -KGFNPEVIPMF ->187188|PE family protein PE9|YP_177784.1|Mycobacterium tuberculosis H37Rv|83332 -RLFNANAEEYHALSA ->187189|PE-PGRS family protein PE_PGRS42|YP_177886.1|Mycobacterium tuberculosis H37Rv|83332 -SAAIAGLFG ->187197|Core protein|Q9QAC5|Hepatitis B virus|10407 -VCWGELMNL ->189204|||| -ALYNTVATL ->189275|gag protein|AAO84847.1|Human immunodeficiency virus 1|11676 -SLFNAVAVL ->189277|gag protein|AAY98604.1|Human immunodeficiency virus 1|11676 -SLFNTIAVL ->189280|||| -SLYLTVATL ->189285|gag protein|AAK30999.1|Human immunodeficiency virus 1|11676 -SLYNSVATL ->189286|||| -SLYNTAATL ->189287|gag protein|ADO94802.1|Human immunodeficiency virus 1|11676 -SLYNTIAIL ->189288|gag protein|AAV53168.1|Human immunodeficiency virus 1|11676 -SLYNTIATL ->189289|gag protein|ADO93742.1|Human immunodeficiency virus 1|11676 -SLYNTISVL ->189290|gag protein|ACO48925.1|Human immunodeficiency virus 1|11676 -SLYNTITVL ->189291|||| -SLYNTVAAL ->189292|gag protein|ABC40295.1|Human immunodeficiency virus 1|11676 -SLYNTVAIF ->189293|gag protein|BAB88077.1|Human immunodeficiency virus 1|11676 -SLYNTVAVL ->189294|Gag|O89360|Human immunodeficiency virus 1|11676 -SLYNTVSTL ->189295|gag protein|AEB70304.1|Human immunodeficiency virus 1|11676 -SLYNTVVTL ->189297|||| -SLYQTVATL ->189300|gag polyprotein|BAB88548.1|Human immunodeficiency virus 1|11676 -SVYNTVATL ->189503|hexon protein|AAD47268.1|Human adenovirus 11|10541 -TYFNLGNKF ->189546|glycosyl transferase|WP_015631503.1|Mycobacterium tuberculosis|1773 -AAPEPVARR ->189547|cyclopropane-fatty-acyl-phospholipid synthase|YP_005911842.1|Mycobacterium tuberculosis|1773 -AASAAIANR ->189566|glycosyl transferase|WP_015631503.1|Mycobacterium tuberculosis|1773 -ALADLPVTV ->189569|||| -AMLDHAGDM ->189571|Antigen 85-B|P0C5B9.1|Mycobacterium tuberculosis|1773 -ANNTRLWVY ->189575|POSSIBLE GLYCOSYL TRANSFERASE|CAB05418.1|Mycobacterium tuberculosis|1773 -ARLAGIPY ->189687|glycosyl transferase|WP_003906951.1|Mycobacterium tuberculosis|1773 -IVLVRRWPK ->189705|glycosyl transferase|WP_015631503.1|Mycobacterium tuberculosis|1773 -KYIAADRKI ->189706|cyclopropane-fatty-acyl-phospholipid synthase|WP_010924246.1|Mycobacterium tuberculosis|1773 -KYIFPGGLL ->189727|Antigen 85-B|P0C5B9.1|Mycobacterium tuberculosis|1773 -LPQWLSANR ->189740|glycosyl transferase|WP_003906951.1|Mycobacterium tuberculosis|1773 -LVYGDVIMR ->189748|||| -MLDHAGDMA ->189750|Diacylglycerol acyltransferase/mycolyltransferase Ag85B|SRC280000|Mycobacterium tuberculosis|1773 -MPVGGGSSF ->189755|||| -MYNYPTMLD ->189799|glycosyl transferase|WP_003906951.1|Mycobacterium tuberculosis|1773 -PYNLRYRVL ->189829|cyclopropane-fatty-acyl-phospholipid synthase|WP_010924246.1|Mycobacterium tuberculosis|1773 -RMWELYLAY ->189849|glycosyltransferase|WP_016721157.1|Mycobacterium tuberculosis|1773 -SIIIPTLNV ->189894|cyclopropane-fatty-acyl-phospholipid synthase|WP_010924246.1|Mycobacterium tuberculosis|1773 -VLAGSVDEL ->189905|Antigen 85-B|P0C5B9.1|Mycobacterium tuberculosis|1773 -WGAQLNAMK ->190409|polymerase|AAD16253.1|Hepatitis B virus|10407 -ESTRSASFCGSPYSW ->190443|core protein|BAF42671.1|Hepatitis B virus|10407 -HISCLTFGR ->190455|core protein|AAL31780.1|Hepatitis B virus|10407 -KEFGASVELL ->190466|large surface antigen|CAL29876.1|Hepatitis B virus|10407 -LGFFPDHQLDPAFGA ->190488|large/middle/small S proteins|AAK97183.1|Hepatitis B virus|10407 -LWEWASVRF ->190494|nucleocapsid protein|ABI96968.1|SARS coronavirus|227859 -MEVTPSGTWL ->190509|HBsAg|AAL66328.1|Hepatitis B virus|10407 -PFMPLLPIFF ->190533|nucleocapsid protein|AAP49024.1|SARS coronavirus|227859 -RRPQGLPNNIASWFT ->190556|HBsAg|AAL66328.1|Hepatitis B virus|10407 -SVIWMMWYW ->190568|polymerase|AAD16253.1|Hepatitis B virus|10407 -TYGRKLHLYSHPIILGFRKI ->190569|polymerase|ADG03431.1|Hepatitis B virus|10407 -VDKNPHNTTESRLVV ->190577|surface antigen|AAZ30211.1|Hepatitis B virus|10407 -VIWMMWYWGR ->190589|surface antigen|AAZ30211.1|Hepatitis B virus|10407 -WLSVIWMMWY ->190596|polymerase|BAD04994.1|Hepatitis B virus|10407 -YPALMPLSACIQAKR ->190821|polyprotein|AAT94261.1|Hepatitis C virus|11103 -KLLGLGINAV ->190822|polyprotein|BAB18801.1|Hepatitis C virus|11103 -KLSGLGINAI ->190826|gag polyprotein|CAB81949.1|Human immunodeficiency virus 1|11676 -KSLFNTIATL ->190827|gag protein|AAN08336.1|Human immunodeficiency virus 1|11676 -KSLYNTIATL ->190828|gag protein|ABI20203.1|Human immunodeficiency virus 1|11676 -KSLYNTIAVL ->190829|gag protein|BAB88077.1|Human immunodeficiency virus 1|11676 -KSLYNTVAVL ->190959|gag polyprotein|BAB19174.1|Human immunodeficiency virus 1|11676 -RSLFNTIATL ->190960|gag-pol polyprotein|BAC02551.1|Human immunodeficiency virus 1|11676 -RSLFNTIAVL ->190961|gag protein|BAC45024.1|Human immunodeficiency virus 1|11676 -RSLFNTVAVL ->190962|gag polyprotein|BAB88540.1|Human immunodeficiency virus 1|11676 -RSLYNTIATL ->190963|gag-pol fusion polyprotein precursor|CAY83124.1|Human immunodeficiency virus 1|11676 -RSLYNTIAVL ->190974|gag polyprotein|BAB19174.1|Human immunodeficiency virus 1|11676 -SLFNTIATLY ->190975|gag protein|BAC45024.1|Human immunodeficiency virus 1|11676 -SLFNTVAVLY ->190978|gag protein|AAV53168.1|Human immunodeficiency virus 1|11676 -SLYNTIATLY ->190979|gag protein|ABI20203.1|Human immunodeficiency virus 1|11676 -SLYNTIAVLY ->190980|gag protein|AAV53216.1|Human immunodeficiency virus 1|11676 -SLYNTVATLY ->190981|gag protein|BAB88077.1|Human immunodeficiency virus 1|11676 -SLYNTVAVLY ->191095|Capsid protein|P03146.1|Hepatitis B virus ayw/France/Tiollais/1979|490133 -YVNTNMGLK ->193060|Nef protein|Q9YYU3|Human immunodeficiency virus 1|11676 -RFPLTFGWCF ->193071|Nef protein|Q9WPU2|Human immunodeficiency virus 1|11676 -RYPLTLGWCF ->193551|Protein 3a|P59632.1|SARS coronavirus|227859 -SITAQPVKI ->193665|envelope glycoprotein B|NP_044629.1|Herpes simplex virus (type 1 / strain 17)|10299 -ALLGLTLGV ->193837|envelope glycoprotein B|NP_044629.1|Herpes simplex virus (type 1 / strain 17)|10299 -FVLATGDFV ->193840|envelope glycoprotein B|NP_044629.1|Herpes simplex virus (type 1 / strain 17)|10299 -GIFEDRAPV ->194160|BaRF1|AFJ06848.1|Human gammaherpesvirus 4|10376 -LLIEGIFFI ->194181|envelope glycoprotein B|NP_044629.1|Herpes simplex virus (type 1 / strain 17)|10299 -LLTTPKFTV ->194227|Glycoprotein B|P10211.1|Herpes simplex virus (type 1 / strain 17)|10299 -NLLTTPKFT ->194242|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis|1773 -QEAGNFERI ->194400|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis|1773 -TAGSLQGQW ->194440|envelope glycoprotein B|NP_044629.1|Herpes simplex virus (type 1 / strain 17)|10299 -TMYYKDVTV ->194442|BFRF3|YP_001129448.1|Human gammaherpesvirus 4|10376 -TPSVSSSISSL ->194449|BKRF2|AFY97944.1|Human gammaherpesvirus 4|10376 -VEDLFGANL ->194555|BNRF1|AGZ95154.1|Human gammaherpesvirus 4|10376 -WQWEHIPPA ->194567|envelope glycoprotein B|NP_044629.1|Herpes simplex virus (type 1 / strain 17)|10299 -YLANGGFLI ->194657|BNRF1|AGZ95154.1|Human gammaherpesvirus 4|10376 -YPRNPTEQGNI ->195418|6 kDa early secretory antigenic target ESXA (ESAT-6)|YP_178023.1|Mycobacterium tuberculosis H37Rv|83332 -GSGSEAYQGVQQKWD ->196087|PPE family protein PPE54|YP_177960.1|Mycobacterium tuberculosis H37Rv|83332 -TVKSMILHEIL ->226775|PreS1/PreS2/surface protein|Q2EID8|Hepatitis B virus|10407 -GYRWMCLRR ->226786|core protein|BAF42671.1|Hepatitis B virus|10407 -LVSFGVWIR ->226809|Large S protein|BAF36017.1|Hepatitis B virus|10407 -YLWEWASVR ->226853|ribonucleotide reductase subunit 2|NP_040141.1|Human alphaherpesvirus 3|10335 -ILIEGIFFV ->226871|ribonucleotide reductase subunit 2|NP_040141.1|Human alphaherpesvirus 3|10335 -MILIEGIFFV ->230028|Protein Nef|P04603.3|Human immunodeficiency virus 1|11676 -NYTPGPGIRF ->230029|Protein Nef|P03404.4|Human immunodeficiency virus 1|11676 -NYTPGPGIRY ->230030|Nef protein|BAA86664.1|Human immunodeficiency virus 1|11676 -NYTPGPGTRF ->230122|nef protein|ACR27128.1|Human immunodeficiency virus 1|11676 -FLKEKGGL ->231862|Major surface antigen p30 precursor|P13664.1|Toxoplasma gondii RH|383379 -FAGAAGSAKSAAGTASHVSI ->232152|rhoptry kinase family protein|AFO54841.1|Toxoplasma gondii type III|398031 -PPEQPFHSYGVTYTFATDA ->232153|rhoptry protein 18|CAJ27113.1|Toxoplasma gondii type I|1209525 -PPERPFQATGITYTFPTDA ->232154|rhoptry protein, putative / protein kinase domain-containing protein|XP_002367757.1|Toxoplasma gondii type II|1209523 -PPERPFQTTDITYTFTTDA ->233309|polyprotein|ACZ60102.1|Hepatitis C virus subtype 3a|356426 -VRMVMMTHF ->236085|polyprotein|ABD97104.1|Hepatitis C virus|11103 -HSKKKCDEM ->238379|polyprotein|ACE82359.1|Hepatitis C virus subtype 1a|31646 -FLVGQLFTF ->240792|Major immediate-early protein|Q9YRL8|Human betaherpesvirus 5|10359 -ELNRKMIYM ->240808|polyprotein|AAB53095.1|Tick-borne encephalitis virus|11084 -ILLDNITTL ->243835|glycosyl transferase|WP_015628558.1|Mycobacterium tuberculosis|1773 -SARLAGIPY ->244160|surface antigen 2 (CA-2)|XP_818927.1|Trypanosoma cruzi strain CL Brener|353153 -AAAGDKLSL ->244167|surface antigen 2|SRC298288|Trypanosoma cruzi|5693 -ALQVTNHRYL ->244168|surface antigen 2|SRC298288|Trypanosoma cruzi|5693 -ALRNLRVFL ->244296|surface antigen 2|SRC298288|Trypanosoma cruzi|5693 -TVFDASRSTV ->251793|transmembrane serine/threonine-protein kinase A|WP_016330371.1|Mycobacterium tuberculosis|1773 -AIIIAVLLV ->252997|transmembrane serine/threonine-protein kinase A|WP_016330371.1|Mycobacterium tuberculosis|1773 -ALAIIIAVL ->288104|nef protein|ACR27130.1|Human immunodeficiency virus 1|11676 -EVGFPVRPQVPLRPMTFK ->294287|gag protein|ABI20203.1|Human immunodeficiency virus 1|11676 -GATPQDLNTMLNTVGGH ->418940|PPE family protein PPE68|KAM81677.1|Mycobacterium tuberculosis H37Ra|419947 -AAAAGWQTL ->418942|PPE family protein PPE68|KAM81677.1|Mycobacterium tuberculosis H37Ra|419947 -ALAAATPMVV ->418943|PPE family protein PPE68|KAM81677.1|Mycobacterium tuberculosis H37Ra|419947 -ALAMEVYQA ->418944|PPE family protein PPE68|KAM81677.1|Mycobacterium tuberculosis H37Ra|419947 -ALDAQAVEL ->418945|PPE family protein PPE68|KAM81677.1|Mycobacterium tuberculosis H37Ra|419947 -ALTEMDYFI ->418947|PPE family protein PPE68|KAM81677.1|Mycobacterium tuberculosis H37Ra|419947 -AMPPELNTA ->418964|PPE family protein PPE68|KAM81677.1|Mycobacterium tuberculosis H37Ra|419947 -ELTARLNSL ->418967|PPE family protein PPE68|KAM81677.1|Mycobacterium tuberculosis H37Ra|419947 -FIRMWNQAAL ->418975|PPE family protein PPE68|KAM81677.1|Mycobacterium tuberculosis H37Ra|419947 -GINTIPIAL ->418991|polyprotein|AFY10039.1|Dengue virus 4|11070 -IPVTMALWY ->418997|PPE family protein PPE68|KAM81677.1|Mycobacterium tuberculosis H37Ra|419947 -KLEPMASIL ->419002|PPE family protein PPE68|KAM81677.1|Mycobacterium tuberculosis H37Ra|419947 -LIEKPVAPSV ->419005|polyprotein|AGW21594.1|Dengue virus 1|11053 -LLAVSGVYPM ->419006|PPE family protein PPE68|KAM81677.1|Mycobacterium tuberculosis H37Ra|419947 -LLRAESLPGA ->419017|polyprotein|AFY10034.1|Dengue virus 4|11070 -MPAMKRYSAP ->419024|polyprotein|AGW21594.1|Dengue virus 1|11053 -NMIIMDEAHF ->419031|PPE family protein PPE68|KAM81677.1|Mycobacterium tuberculosis H37Ra|419947 -QLPPAATQTL ->419037|polyprotein|AEF01538.1|Dengue virus 1|11053 -RPMFAVGILF ->419045|PPE family protein PPE68|KAM81677.1|Mycobacterium tuberculosis H37Ra|419947 -SLPEIAANHI ->419048|polyprotein|AFY10039.1|Dengue virus 4|11070 -SPRLCTREEF ->419095|polyprotein|ABR25251.1|Hepatitis C virus|11103 -AELIEANLLW ->419098|polyprotein|ABR27377.1|Hepatitis C virus|11103 -AEVIAPAVQT ->419124|polyprotein|ACF49259.1|Dengue virus type 1 Hawaii|10000440 -AVEPGKNPK ->419125|polyprotein|ACF49259.1|Dengue virus type 1 Hawaii|10000440 -AVKSEHTGR ->419128|polyprotein|ACF49259.1|Dengue virus type 1 Hawaii|10000440 -AYRHAMEEL ->419170|polyprotein|ABR25251.1|Hepatitis C virus|11103 -FAWYLKGKW ->419208|polyprotein|ACF49259.1|Dengue virus type 1 Hawaii|10000440 -GVEGEGLHK ->419229|polyprotein|ACF49259.1|Dengue virus type 1 Hawaii|10000440 -IYRILQRGL ->419298|RNA-dependent RNA polymerase|ACH97782.1|Hepatitis C virus|11103 -NSKRTPMGF ->419306|polyprotein|ACF49259.1|Dengue virus type 1 Hawaii|10000440 -PTLDIELLK ->419320|polyprotein|AGZ86443.1|Hepatitis C virus|11103 -RAEAQLHAW ->419325|Genome polyprotein|O92532.3|Hepatitis C virus|11103 -RLGPVQNEV ->419366|polyprotein|BAA00792.1|Hepatitis C virus|11103 -SVIDCNVAV ->419410|polyprotein|ABR25251.1|Hepatitis C virus|11103 -WLGNIIMFA ->419424|polyprotein|BAA00792.1|Hepatitis C virus|11103 -YLTAYQATV ->422880|External core antigen|SRC279980|Hepatitis B virus|10407 -GLKILQLL ->422981|Genome polyprotein|P26664.3|Hepatitis C virus genotype 1|41856 -AICGKYLFNW ->422983|Genome polyprotein|P27958.3|Hepatitis C virus genotype 1|41856 -ARDQLEQAL ->422984|NS5B protein|ABB72740.1|Hepatitis C virus genotype 1|41856 -ARMILLTHF ->422985|polyprotein precursor|BAA02756.1|Hepatitis C virus genotype 1|41856 -ARSVRAKLL ->422989|polyprotein|ABY67644.1|Hepatitis C virus genotype 1|41856 -FAPALPIWAR ->422990|C protein|CAB41699.1|Hepatitis B virus|10407 -FGVWIRTPPAYR ->422996|Genome polyprotein|P26664.3|Hepatitis C virus genotype 1|41856 -GAYMSKAHGI ->422997|preC/core protein|CAJ33968.1|Hepatitis B virus|10407 -GDLMNLATW ->422998|polyprotein precursor|BAA02756.1|Hepatitis C virus genotype 1|41856 -GEVPSTEDL ->422999|polyprotein|ABD97104.1|Hepatitis C virus genotype 3|356114 -GILVLFGFF ->423002|polyprotein|ABY67644.1|Hepatitis C virus genotype 1|41856 -GRAAICGRY ->423007|Genome polyprotein|P26664.3|Hepatitis C virus genotype 1|41856 -GVQEDAASLR ->423010|polyprotein|AAC03058.1|Hepatitis C virus genotype 3|356114 -IMGGELPTA ->423011|polyprotein|AER51001.1|Hepatitis C virus genotype 1|41856 -IMSGEVPSM ->423016|NS5A|ACX46481.1|Hepatitis C virus genotype 1|41856 -KFPLAMPVW ->423019|protease-helicase|AER50967.1|Hepatitis C virus genotype 1|41856 -KLVALGLNAV ->423020|polyprotein|ACE82359.1|Hepatitis C virus genotype 1|41856 -KLYISWCLW ->423022|Genome polyprotein|P27958.3|Hepatitis C virus genotype 1|41856 -KQSGENFPYL ->423031|core|CAA59522.1|Hepatitis B virus|10407 -LESPEHCSP ->423032|core protein|AJT55251.1|Hepatitis B virus|10407 -LESQDHCSP ->423033|Genome polyprotein|P26664.3|Hepatitis C virus genotype 1|41856 -LETTMRSPVF ->423036|core protein|AGS79525.1|Hepatitis B virus|10407 -LWFHISCLMF ->423044|polyprotein precursor|BAA01582.1|Hepatitis C virus genotype 1|41856 -QLEQALDCEIY ->423046|polyprotein|ACX44272.1|Hepatitis C virus genotype 1|41856 -QMAMIKLGAL ->423047|Genome polyprotein|P27958.3|Hepatitis C virus genotype 1|41856 -QRLHGLSAF ->423052|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 -RDAVILLM ->423053|core protein|AAL31859.1|Hepatitis B virus|10407 -RETVIEYLVSF ->423061|Genome polyprotein|P27958.3|Hepatitis C virus genotype 3|356114 -SQLSAPSLK ->423062|polyprotein|ACH99674.1|Hepatitis C virus genotype 1|41856 -SSVSTALAEL ->423063|pre-Core, Core|BAF49207.1|Hepatitis B virus|10407 -STLPETTVVRQ ->423068|polyprotein|ACX44241.1|Hepatitis C virus genotype 1|41856 -VLFGLMALTL ->423069|polyprotein|ACH99674.1|Hepatitis C virus genotype 1|41856 -VLTESSVSTA ->423071|polyprotein|AER51001.1|Hepatitis C virus genotype 1|41856 -VPSMEDLVNL ->423072|polyprotein|ACJ37172.1|Hepatitis C virus genotype 1|41856 -VRMILLTHF ->423073|polyprotein|ABL63011.1|Hepatitis C virus genotype 1|41856 -VRMILMTHF ->423075|polyprotein|ACX44241.1|Hepatitis C virus genotype 1|41856 -VVLFGLMAL ->423080|Genome polyprotein|P26664.3|Hepatitis C virus genotype 1|41856 -YFLTRVEAQL ->423082|Genome polyprotein|P26664.3|Hepatitis C virus genotype 1|41856 -YRFVAPGER diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/output/NeoantigenQuality.txt b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/output/NeoantigenQuality.txt deleted file mode 100755 index 89417ecf..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/output/NeoantigenQuality.txt +++ /dev/null @@ -1,5391 +0,0 @@ -NeoantigenID MT.Peptide.Form NeoantigenQuality NeoantigenAlignment IEDB_EpitopeAlignment AlignmentScore IEDB_Epitope -1 HIQDLYTVL 3.17191804867 HIQDLYTVL HAQDATTVL 28.0 6373|Genome_polyprotein|SRC279960|Hepatitis_C_virus_subtype_3a|356426 -2 GYYTLLNVF 20.9213483146 GYYTLLN GFYHILN 26.0 1516|Nucleoprotein|P03418.1|Human_respiratory_syncytial_virus_A2|11259 -3 LTLFGYYTL 0.266904846489 LTLFGYY LTLSPYY 23.0 149024|NS2_protein|NP_751923.1|Hepatitis_C_virus_(isolate_H77)|63746 -4 TLFGYYTLL 0.0 None None 0 None -5 YYTLLNVFL 0.297457866327 YTLLNVFL FTILALFL 23.0 180464|polyprotein|CDF77361.1|Dengue_virus_3|11069 -6 LAVRPSKIK 0.0 None None 0 None -7 PTYGNSTKL 0.734486359014 PTYGNS PLYGNE 25.0 75436|Polyprotein|P90247|Hepatitis_C_virus|11103 -8 TASNVEFAI 0.0 None None 0 None -9 TSSDSISHM 0.0 None None 0 None -10 RFRALNQEL 0.0 None None 0 None -11 HRNHIDRAL 0.0 None None 0 None -12 FALLFGHRF 0.733997564982 LLFGH LLFGH 28.0 37251|||| -13 HRFDYRDPV 0.0 None None 0 None -14 VADSTLLLM 0.0 None None 0 None -15 FKMGAHTEV 0.0 None None 0 None -16 FEGFPQSLL 0.217642336766 FEGFPQSLL FPGFGQSLL 32.0 23807|tax|AAG48731.1|Human_T-lymphotropic_virus_2|11909 -17 FEGFPQSLL 0.126853192431 FEGFPQSLL FPGFGQSLL 32.0 23807|tax|AAG48731.1|Human_T-lymphotropic_virus_2|11909 -18 GAQDRNSSF 0.0 None None 0 None -19 FTHLRLQEF 0.0 None None 0 None -20 LAASGPTLV 0.0 None None 0 None -21 MIVGRTYTL 0.0037423128393 IVGRTYTL ILGFVFTL 20.0 20354|M1_protein|CAA30882.1|Influenza_A_virus|11320 -22 VAAENEAVL 0.0 None None 0 None -23 IERNLINSL 1.02340662483 ERNLINSL EENLVNSL 32.0 182938|polyprotein|AGO67248.1|Dengue_virus_2|11060 -24 GEAGTIERV 0.448867741662 EAGTIERV EAGNFERI 28.0 194242|ESAT-6-like_protein_esxB|P0A566.2|Mycobacterium_tuberculosis|1773 -25 VAIFLGFYV 0.0 None None 0 None -26 YSIFQLAFV 0.0 None None 0 None -27 MALNYNRAF 0.0 None None 0 None -28 TVFGGLMAL 0.0 None None 0 None -29 LSSRLSDTL 0.0 None None 0 None -30 SRLSDTLSF 0.0 None None 0 None -31 KRTSPEELL 0.0 None None 0 None -32 HALHLRRMM 0.0 None None 0 None -33 MAGFMGMAV 0.0259001423454 MAGFMG MTGFTG 22.0 108153|polyprotein|AAF65950.1|Hepatitis_C_virus|11103 -34 RMMAGFMGM 0.795816444397 MMAGFMG LMTGFTG 24.0 108153|polyprotein|AAF65950.1|Hepatitis_C_virus|11103 -35 FVSTIIHLL 0.0 None None 0 None -36 YLVPGFSPY 0.0 None None 0 None -37 YLVPGFSPY 0.0 None None 0 None -38 KASFDHACL 0.0 None None 0 None -39 EFHDIASHV 0.0 None None 0 None -40 MCDNGSGLV 0.0 None None 0 None -41 IQNAGGSVI 0.601030334228 IQNAGGSVI IQNSGGTSI 31.0 183843|envelope_protein|AGW23576.1|Dengue_virus_3|11069 -42 TQDGALMNV 0.0 None None 0 None -43 TLGIICLLL 0.665172700533 TLGIIC TLGIVC 31.0 64818|E7|AAD33253.1|Human_papillomavirus_type_16|333760 -44 WNDKVKEAL 0.0 None None 0 None -45 QNAGGSVII 3.46504561837 QNAGGS QNAGGT 28.0 27981|IMMUNOGENIC_PROTEIN_MPT64_(ANTIGEN_MPT64/MPB64)|CAA98382.1|Mycobacterium_tuberculosis_H37Rv|83332 -46 SDYLHWEVV 0.0 None None 0 None -47 SSVPVLNML 0.0 None None 0 None -48 WALEVLLNA 0.463508918806 WALEVLL WTLVVLL 25.0 37960|membrane_protein|AAA45887.1|Human_gammaherpesvirus_4|10376 -49 YETQDGALM 0.0 None None 0 None -50 NMELPYFVL 0.50520798857 LPYFV LPYLV 22.0 13518|HCV-1|AAA45676.1|Hepatitis_C_virus_genotype_1|41856 -51 LSTPAPQVF 0.0 None None 0 None -52 VSDTEFHPL 0.0 None None 0 None -53 MVVAGQRAV 0.0 None None 0 None -54 YLHWEVVEL 0.0 None None 0 None -55 ANFPWALEV 1.23311590917 ANFPWAL TSFPWLL 28.0 34616|pol_protein|BAA32832.1|Hepatitis_B_virus|10407 -56 WYLRDVSEV 0.0 None None 0 None -57 FHDIASHVK 0.0 None None 0 None -58 FPWALEVLL 0.261558715685 WALEVLL WTLVVLL 25.0 37960|membrane_protein|AAA45887.1|Human_gammaherpesvirus_4|10376 -59 GTLGIICLL 50.3407812466 TLGIIC TLGIVC 31.0 64818|E7|AAD33253.1|Human_papillomavirus_type_16|333760 -60 YLHWEVVEL 0.0 None None 0 None -61 LQFSRMEQL 0.0 None None 0 None -62 VHLESNATV 0.0 None None 0 None -63 QMFVHLQLL 0.0 None None 0 None -64 VHLESNATV 0.0 None None 0 None -65 TQDGALMNV 0.0 None None 0 None -66 VAFCLKCNL 0.642271486634 VAFCLKCN VTFCCKCD 33.0 110184|E7|AAD33253.1|Human_papillomavirus_type_16|333760 -67 STDSLSTPA 0.0 None None 0 None -68 DILEKSSSV 0.0749249088856 LEKSSSV MEKCSSV 23.0 13456|circumsporozoite_protein|AAN87606.1|Plasmodium_falciparum|5833 -69 NMVGFSDRV 0.0 None None 0 None -70 NLGSKLQLV 0.0 None None 0 None -71 FPWALEVLL 4.41902830893 WALEVLL WTLVVLL 25.0 37960|membrane_protein|AAA45887.1|Human_gammaherpesvirus_4|10376 -72 TKDTFMMEL 0.0 None None 0 None -73 HCANFPWAL 32.1490933462 ANFPWAL TSFPWLL 28.0 34616|pol_protein|BAA32832.1|Hepatitis_B_virus|10407 -74 ESSSETSTY 0.0 None None 0 None -75 QMFVHLQLL 0.0 None None 0 None -76 QPLKYTWLL 2.79400019666 PLKYTW PYKPTW 24.0 68229|EBNA3B_(EBNA4A)_latent_protein|CAA24858.1|Human_gammaherpesvirus_4|10376 -77 SLTTLLQAL 0.0 None None 0 None -78 SLSTPAPQV 0.0 None None 0 None -79 FAINFFKEV 0.0 None None 0 None -80 YTWLLAAKV 0.0 None None 0 None -81 DLENMELPY 0.0 None None 0 None -82 EKSSSVPVL 0.0 None None 0 None -83 WLCDHPVPV 0.376517989918 WLCDHP WILRHP 25.0 180818|Membrane_glycoprotein_precursor|NP_739582.2|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -84 LLMSTLGIL 1.08239342869 LLMSTLGIL LLMGTLGIV 33.0 37573|E7_protein|ABL96585.1|Human_papillomavirus_type_16|333760 -85 IQNAGGSVI 3.24997372157 IQNAGGSVI IQNSGGTSI 31.0 183843|envelope_protein|AGW23576.1|Dengue_virus_3|11069 -86 YTWLLAAKV 0.0 None None 0 None -87 FSQEPADQM 0.0 None None 0 None -88 ILSWLVSQL 0.0 None None 0 None -89 LLLMSTLGI 172.260279525 LLMSTLGI LLMGTLGI 32.0 37573|E7_protein|ABL96585.1|Human_papillomavirus_type_16|333760 -90 FYIFNVSSI 0.0 None None 0 None -91 GLGECITQV 0.0 None None 0 None -92 LAMRRHSRI 0.0449655249052 AMRRHS AMKRYS 22.0 419017|polyprotein|AFY10034.1|Dengue_virus_4|11070 -93 LAKDSGAPV 0.0 None None 0 None -94 YLHWEVVEL 0.0 None None 0 None -95 FMMELLNRV 0.0 None None 0 None -96 WLCDHPVPV 0.403412132055 WLCDHP WILRHP 25.0 180818|Membrane_glycoprotein_precursor|NP_739582.2|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -97 FAINFFKEV 0.0 None None 0 None -98 FMMELLNRV 0.0 None None 0 None -99 TVAEKRGWK 0.0 None None 0 None -100 RLLPDTFVL 0.0 None None 0 None -101 RLLPDTFVL 0.0 None None 0 None -102 SSMAAGLEH 0.0 None None 0 None -103 MIYRLAQAK 0.0 None None 0 None -104 TPMYRTRPA 0.00472046238994 TPMYRTRP TPQVPLRP 20.0 102150|nef_protein|ACR27119.1|Human_immunodeficiency_virus_1|11676 -105 ITYYCHGGY 0.121528332848 YCHGG FCHPG 24.0 79454|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 -106 KLGSSITYY 0.0 None None 0 None -107 FPVSYGVPA 0.440869275563 VSYGVP VYYGVP 26.0 118|envelope_glycoprotein|ABS76372.1|Human_immunodeficiency_virus_1|11676 -108 IMFPVSYGV 0.0 None None 0 None -109 ISDTILKTK 0.0 None None 0 None -110 RLQTHTIYK 0.0 None None 0 None -111 ELFHVDWHV 0.224791106174 LFHVDW LVHRQW 19.0 41407|Envelope_protein|NP_739583.2|Dengue_virus_2|11060 -112 LPRQYWEAL 1.00520554562 LPRQYW LPEGYW 27.0 31997|hypothetical_protein_FTT0484|YP_169522.1|Francisella_tularensis_subsp._tularensis_SCHU_S4|177416 -113 MPHRATVYA 0.0 None None 0 None -114 KLLECSLTK 0.0 None None 0 None -115 RPQGQRPAL 43.5210604434 PQGQRPAL PRGSRPSW 27.0 36352|Polyprotein|P90247|Hepatitis_C_virus|11103 -116 SSDCIIEKK 0.000135734033585 SDCIIEKK SACQRQKK 17.0 66405|polyprotein|AAB67037.1|Hepatitis_C_virus_(isolate_H77)|63746 -117 TSSDCIIEK 0.0 None None 0 None -118 GLMGHTLHR 0.0 None None 0 None -119 LPGHAPGIL 0.097025634204 PGHAPG PGTGPG 24.0 47760|EBNA-1_protein|Q777E1|Human_gammaherpesvirus_4|10376 -120 YAYHVEWEK 0.0 None None 0 None -121 WVRWHKGCL 0.00804646235146 WVRWHKG WILRHPG 22.0 180818|Membrane_glycoprotein_precursor|NP_739582.2|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -122 SSSIRIHER 0.0 None None 0 None -123 FLSSSFSML 0.0 None None 0 None -124 FSMLKDHIK 0.0 None None 0 None -125 LSSSFSMLK 0.0 None None 0 None -126 VVGADGVGK 0.0 None None 0 None -127 AVDLSSAGM 0.0 None None 0 None -128 GMAGVLIGY 0.0543590087265 GMAGVLIG GMGPSLIG 21.0 21275|Antigen_85-B_precursor_(85B)_(Extracellular_alpha-antigen)_(Antigen_85_complex_B)_(Ag85B)_(Mycolyl_transferase_85B)_(Fibronectin-binding_protein_B)_(30_kDa_extracellular_protein)|P31952|Mycobacterium_tuberculosis|1773 -129 SSAGMAGVL 0.0 None None 0 None -130 KAAPIYKLV 0.0 None None 0 None -131 VTKAAPIYK 0.0 None None 0 None -132 FLPSWLLGI 1.88888888889 LPSWL LPQWL 26.0 13215|Antigen_85-B|P0C5B9.1|Mycobacterium_tuberculosis|1773 -133 RMAFTDHQL 38.3657688551 FTDHQL FPDHQL 28.0 190466|large_surface_antigen|CAL29876.1|Hepatitis_B_virus|10407 -134 RMAFTDHQL 20.2035463724 FTDHQL FPDHQL 28.0 190466|large_surface_antigen|CAL29876.1|Hepatitis_B_virus|10407 -135 ALQPQLGCY 0.0 None None 0 None -136 YQQALQPQL 0.0 None None 0 None -137 YQQALQPQL 0.0 None None 0 None -138 YQLKMLIKI 0.0 None None 0 None -139 ILLVVYNNV 0.0 None None 0 None -140 LLVVYNNVL 0.0 None None 0 None -141 LLVVYNNVL 0.0 None None 0 None -142 LVVYNNVLK 0.0 None None 0 None -143 LSGHSTQDL 0.0 None None 0 None -144 QALSKFKAM 0.0 None None 0 None -145 LSVDRMRKV 0.0 None None 0 None -146 LGVAARWDL 0.0 None None 0 None -147 HAVQAAVQY 0.0 None None 0 None -148 HAVQAAVQY 0.0 None None 0 None -149 KIMNSLPEM 0.0 None None 0 None -150 KIMNSLPEM 0.0 None None 0 None -151 LPEMKVQLV 0.0 None None 0 None -152 SLPEMKVQL 0.0 None None 0 None -153 LTISGECPK 0.0143889679697 ISGECP MSGEVP 22.0 423011|polyprotein|AER51001.1|Hepatitis_C_virus_genotype_1|41856 -154 AMYDVLTFA 27.3958151719 AMYDVLT ALYDVVT 29.0 3019|polyprotein|AAA45677.1|Hepatitis_C_virus_(isolate_H77)|63746 -155 ATDQAMYDV 0.00252195188532 DQAMYDV DRAHYNI 20.0 110431|E7|AAD33253.1|Human_papillomavirus_type_16|333760 -156 KIHATDQAM 0.868183841638 KIHATD KAHGTD 23.0 107925|polyprotein|AAF65964.1|Hepatitis_C_virus|11103 -157 QAMYDVLTF 24.0160297669 AMYDVLT ALYDVVT 29.0 3019|polyprotein|AAA45677.1|Hepatitis_C_virus_(isolate_H77)|63746 -158 QAMYDVLTF 184.760877861 AMYDVLT ALYDVVT 29.0 3019|polyprotein|AAA45677.1|Hepatitis_C_virus_(isolate_H77)|63746 -159 LICFLTPVK 0.0 None None 0 None -160 NLICFLTPV 0.0 None None 0 None -161 IAHIFGGAR 0.0 None None 0 None -162 LLEISKWFR 0.0 None None 0 None -163 FSDDGVLGP 0.179294280913 FSDDGVLGP YMDDVVLGA 25.0 75040|Protein_P|P03159.1|Hepatitis_B_virus|10407 -164 GSFSDDGVL 0.0 None None 0 None -165 VLGPVLTTF 0.0 None None 0 None -166 ATSIPAGSM 0.0 None None 0 None -167 IPAGSMPTV 0.289341771885 PAGSMPTV PEGIIPTL 24.0 180778|polyprotein|AFP27208.1|Dengue_virus_4|11070 -168 IMDLRNGTF 0.0 None None 0 None -169 CLSGYCSVF 1.19084512931 CLSGYC CISGVC 29.0 95281|polyprotein|ACE82433.1|Hepatitis_C_virus_genotype_1|41856 -170 CSVFAYKPM 0.0 None None 0 None -171 GYCSVFAYK 0.0 None None 0 None -172 SGYCSVFAY 0.0 None None 0 None -173 LIMALVWSL 0.0117124891175 LIMALVWSL LLMRTTWAF 21.0 184453|polyprotein|AFP27207.1|Dengue_virus_4|11070 -174 LIMALVWSL 0.0164467732015 LIMALVWSL LLMRTTWAF 21.0 184453|polyprotein|AFP27207.1|Dengue_virus_4|11070 -175 LIMALVWSL 0.00513721530405 LIMALVWSL LLMRTTWAF 21.0 184453|polyprotein|AFP27207.1|Dengue_virus_4|11070 -176 LVWSLPCGF 2.09703631178 VWSLPCGF LWHYPCTF 30.0 54820|polyprotein_precursor|BAA02756.1|Hepatitis_C_virus|11103 -177 ESDYLINEM 0.0 None None 0 None -178 YLINEMYL* 0.0 None None 0 None -179 TQMVDIWSV 0.0 None None 0 None -180 MVAFFSSHT 0.0972906201798 VAFFSSHT IAFTSEHS 24.0 25275|Glutamate_decarboxylase_2|Q05329.1|Homo_sapiens|9606 -181 VAFFSSHTY 0.636929460581 VAFFSSHTY IAFTSEHSH 26.0 25275|Glutamate_decarboxylase_2|Q05329.1|Homo_sapiens|9606 -182 VAFFSSHTY 0.477777777778 VAFFSSHTY IAFTSEHSH 26.0 25275|Glutamate_decarboxylase_2|Q05329.1|Homo_sapiens|9606 -183 VAFFSSHTY 0.357142857143 VAFFSSHTY IAFTSEHSH 26.0 25275|Glutamate_decarboxylase_2|Q05329.1|Homo_sapiens|9606 -184 VTFSTSSQL 0.0 None None 0 None -185 WVDFADSVT 0.0 None None 0 None -186 YQTFKDWGI 0.0 None None 0 None -187 ISMGQEEKK 0.0 None None 0 None -188 WISMGQEEK 0.0 None None 0 None -189 FSWQSHLLI 0.0 None None 0 None -190 QSHLLIHQR 0.0 None None 0 None -191 FYIIECIAM 0.0275788552752 YIIECIA YIMACMS 22.0 24457|polyprotein|BAA09072.1|Hepatitis_C_virus|11103 -192 TAFYIIECI 0.0 None None 0 None -193 YIIECIAMS 0.0570151100106 YIIECIA YIMACMS 22.0 24457|polyprotein|BAA09072.1|Hepatitis_C_virus|11103 -194 ASTYSQLKL 0.0 None None 0 None -195 SASTYSQLK 0.0 None None 0 None -196 VSASTYSQL 0.0 None None 0 None -197 YSQLKLWNV 0.0 None None 0 None -198 FYQHLNLMR 0.0 None None 0 None -199 YQHLNLMRV 0.0 None None 0 None -200 KPAPHPQAL 0.0 None None 0 None -201 MADSGPIYN 0.0 None None 0 None -202 GLGFYNDVV 6.41833817492 GLGFYNDV GYGFVNYV 23.0 36358|ELAV-like_protein_1|Q15717.2|Homo_sapiens|9606 -203 FCENDAEVL 0.0 None None 0 None -204 RTTQQENPR 0.0 None None 0 None -205 AMDDLDTDM 1.44491577894 AMDDLDTDM TLNDLETDV 27.0 64967|Circumsporozoite_protein_precursor|P08677.2|Plasmodium_vivax_strain_Belem|31273 -206 EECGKTFYR 0.0 None None 0 None -207 MITQFELQK 0.0 None None 0 None -208 CTAMRVAAK 0.0 None None 0 None -209 HFERLTRAL 0.0 None None 0 None -210 RLKFGNKHK 0.0108863902402 RLKFGNKHK RLRPGGKKK 22.0 54741|gag_polyprotein|BAA00992.1|Human_immunodeficiency_virus_1|11676 -211 ASQQGMAAL 0.0 None None 0 None -212 LDYASQQGM 0.0 None None 0 None -213 YASQQGMAA 0.0 None None 0 None -214 GVRAGRLQL 0.0 None None 0 None -215 VRAGRLQLF 0.0 None None 0 None -216 LFIHHIQGL 0.0 None None 0 None -217 FCSIYITLL 0.0 None None 0 None -218 HHSPSTHVM 0.0 None None 0 None -219 RSFWSHVVR 0.0 None None 0 None -220 AEVEVADKL 0.0 None None 0 None -221 KLLENLAKV 0.0 None None 0 None -222 MAEAKRMKL 0.0 None None 0 None -223 SMAEAKRMK 0.0 None None 0 None -224 SYESCDAHF 0.0 None None 0 None -225 ASFVPSMGK 0.0 None None 0 None -226 FVPSMGKNL 0.0 None None 0 None -227 IPASFVPSM 0.825781600633 IPASFVPSM LPADFFPSI 30.0 16795|precore/core_protein|AAP57273.1|Hepatitis_B_virus|10407 -228 SVSIPASFV 0.0 None None 0 None -229 HLGVPVTLR 0.0 None None 0 None -230 RVQHLGVPV 0.0 None None 0 None -231 NPNTGSVYM 0.0 None None 0 None -232 VYMNSQQSL 0.0 None None 0 None -233 VYMNSQQSL 0.0 None None 0 None -234 EMAKFKVTI 0.0 None None 0 None -235 KLFGYEMAK 0.0 None None 0 None -236 MAKFKVTIK 0.0 None None 0 None -237 HRTIPYLDL 0.0 None None 0 None -238 IVWEHRQKL 0.0 None None 0 None -239 GMVAPDVVK 0.0 None None 0 None -240 HPGVSSQFL 0.305854949793 HPGVSSQF HPTFTSQY 25.0 75718|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 -241 SPRGGPPPL 0.0 None None 0 None -242 IVHPLKPQM 0.0 None None 0 None -243 KPQMNYQTA 0.0 None None 0 None -244 AYCSYCYYF 0.0 None None 0 None -245 NAYCSYCYY 0.0 None None 0 None -246 SPAPERCMV 1.2380952381 PERCM PRRCM 26.0 56310|polyprotein|AGO67248.1|Dengue_virus_2|11060 -247 ALMDMYPHV 0.0 None None 0 None -248 IGVDDRRRL 0.0 None None 0 None -249 RRRLCILRM 0.0 None None 0 None -250 HFQWILFFV 1.9418540523 FQWILFFV LMWLSYFV 24.0 21041|Membrane_glycoprotein|Q692E0|SARS_coronavirus_TJF|284672 -251 HVPGAVPNL 0.0 None None 0 None -252 SLTGDVSPL 0.0 None None 0 None -253 HMVERIQFV 0.0123869954441 MVERIQFV MLEDHEFV 18.0 164551|envelope_glycoprotein_B|NP_044629.1|Herpes_simplex_virus_(type_1_/_strain_17)|10299 -254 HFERLTRAL 0.0 None None 0 None -255 ASQQGMAAL 0.0 None None 0 None -256 LDYASQQGM 0.0 None None 0 None -257 YASQQGMAA 0.0 None None 0 None -258 GVRAGRLQL 0.0 None None 0 None -259 VRAGRLQLF 0.0 None None 0 None -260 APAGGTASA 0.0 None None 0 None -261 HHSPSTHVM 0.0 None None 0 None -262 FGHITHPCM 0.0 None None 0 None -263 RSFWSHVVR 0.0 None None 0 None -264 AAAAAAAAT 0.0 None None 0 None -265 VSSKSQKLL 0.0 None None 0 None -266 YSLSPVSSK 0.0 None None 0 None -267 AEVEVADKL 0.0 None None 0 None -268 KLLENLAKV 0.0 None None 0 None -269 MAEAKRMKL 0.0 None None 0 None -270 SMAEAKRMK 0.0 None None 0 None -271 YRWCGFPQL 0.0 None None 0 None -272 YRWCGFPQL 0.0 None None 0 None -273 SYESCDAHF 0.0 None None 0 None -274 FLVGLWSHL 0.927664444497 FLVGLWS LLLGLWG 26.0 37498|FL-160-2_protein_-_Trypanosoma_cruzi|JH0823|Trypanosoma_cruzi|5693 -275 KPRFLVGLW 122.389953 KPRFLVGL RPMFAVGL 27.0 185468|polyprotein|AGW21594.1|Dengue_virus_1|11053 -276 LVGLWSHLL 12.7260693351 LVGLWS LLGLWG 26.0 37498|FL-160-2_protein_-_Trypanosoma_cruzi|JH0823|Trypanosoma_cruzi|5693 -277 MPPYYVGPL 0.0 None None 0 None -278 TALPTYPPY 4.49696133214 ALPTYPP SLPSYYP 24.0 28594|IMMUNOGENIC_PROTEIN_MPT64_(ANTIGEN_MPT64/MPB64)|CAA98382.1|Mycobacterium_tuberculosis_H37Rv|83332 -279 FEGFPQSPL 0.939393939394 FPQSPL FPRAPL 26.0 18390|Genome_polyprotein|P08617.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 -280 NPNTGSVYM 0.0 None None 0 None -281 VYMNSQQSL 0.0 None None 0 None -282 VYMNSQQSL 0.0 None None 0 None -283 KRQQFGSQF 0.0 None None 0 None -284 DPFALFFMA 0.0 None None 0 None -285 EYAADPFAL 0.0 None None 0 None -286 YAADPFALF 0.000123394575986 YAADPFALF YVAGFLALY 17.0 141484|capsid_maturation_protease|NP_044627.1|Human_alphaherpesvirus_1|10298 -287 HRTIPYLDL 0.0 None None 0 None -288 IVWEHRQKL 0.0 None None 0 None -289 HSVAIVSPF 0.0 None None 0 None -290 RIGFVGLFH 0.0 None None 0 None -291 HPGVSSQFL 0.305854949793 HPGVSSQF HPTFTSQY 25.0 75718|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 -292 IVHPLKPQM 0.0 None None 0 None -293 KPQMNYQTA 0.0 None None 0 None -294 AYCSYCYYF 0.0 None None 0 None -295 NAYCSYCYY 0.0 None None 0 None -296 SPAPERCMV 1.2380952381 PERCM PRRCM 26.0 56310|polyprotein|AGO67248.1|Dengue_virus_2|11060 -297 LTLAVYLSF 0.0 None None 0 None -298 ALMDMYPHV 0.0 None None 0 None -299 IGVDDRRRL 0.0 None None 0 None -300 RRRLCILRM 0.0 None None 0 None -301 DTAWDTLEL 7.29864653969 DTAWD DTAWD 32.0 180726|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -302 TAWDTLELI 0.0 None None 0 None -303 TAWDTLELI 0.0 None None 0 None -304 MSVSQKLTL 0.0 None None 0 None -305 HQRAHTGEK 0.0 None None 0 None -306 AVATITQAL 0.0 None None 0 None -307 TTVNGNTAL 0.0 None None 0 None -308 EYYSQTTGL 0.0 None None 0 None -309 YYSQTTGLC 0.0 None None 0 None -310 CPSEPNTPM 0.0 None None 0 None -311 TPMARTFDW 0.0 None None 0 None -312 GHYEVRASL 0.0 None None 0 None -313 HYEVRASLL 0.0 None None 0 None -314 MYWRRSQCC 0.0 None None 0 None -315 DYPNAYTTW 1.44061741991 DYPNAYTTW DQENPYRTW 31.0 186550|polyprotein|AFY10039.1|Dengue_virus_4|11070 -316 RYSDYPNAY 1.76428417258 SDYPN SEYPN 26.0 57703|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 -317 AADLPILTW 0.0 None None 0 None -318 WLLAADLPI 0.00994626965127 WLLAADLP WCVEHDRP 19.0 120093|unnamed_protein_product|CAA33016.1|Rubella_virus|11041 -319 IPPEANITI 0.0 None None 0 None -320 TVHNLCHIL 0.0 None None 0 None -321 FFVEKRHAF 0.599743535066 VEKRHAF LEKRHVL 24.0 183781|polyprotein|AGO67248.1|Dengue_virus_2|11060 -322 LPLTRSMSI 0.0 None None 0 None -323 AAAAATSAL 0.0 None None 0 None -324 SIYAYHVEW 0.0 None None 0 None -325 AYPQYVIEY 0.427796389876 AYPQYV GYPRYV 26.0 37254|||| -326 FSSKPSSIY 0.0 None None 0 None -327 SIYGGLVLI 0.0 None None 0 None -328 SAESGAQLL 0.0 None None 0 None -329 GIICLDYKL 0.738702286919 GIICL GVLCL 24.0 185978|polyprotein|CDF77361.1|Dengue_virus_3|11069 -330 FEDIGDEDL 0.0 None None 0 None -331 IRVEESMHL 0.142206994693 RVEESMHL RVEAQLHV 24.0 40158|polyprotein|AAA45534.1|Hepatitis_C_virus|11103 -332 AMEKLLSGK 0.0 None None 0 None -333 ARTGHLPAM 0.0 None None 0 None -334 GHLPAMEKL 0.0867552972161 GHLPAMEKL GHQAAMQML 25.0 101673|gag_protein|ABO73990.1|Human_immunodeficiency_virus_1|11676 -335 QVYHWVCEK 0.0 None None 0 None -336 HRWNRFTMI 0.0 None None 0 None -337 THRWNRFTM 0.0173518357296 THRWNRFTM THPITKFVM 21.0 103389|unnamed_protein_product_[Hepatitis_C_virus]|BAA14035.1|Hepatitis_C_virus|11103 -338 ITSGLEVIY 0.0 None None 0 None -339 ARRFWGKIM 0.0 None None 0 None -340 RFWGKIMAK 0.0 None None 0 None -341 TYEEATVYI 0.0 None None 0 None -342 EHAAALWAL 0.252958579882 HAAALWAL HPASAWTL 26.0 183594|polyprotein|AGT63075.1|Dengue_virus_1|11053 -343 LVLMNWTKK 0.418604651163 VLMNWTK MMMNWSP 26.0 42152|polyprotein|AAY82055.1|Hepatitis_C_virus_(isolate_H77)|63746 -344 FTDTAAESA 0.0 None None 0 None -345 NIEDSASFY 0.0 None None 0 None -346 SRSDAAKHL 0.0 None None 0 None -347 LRWRHCQRL 0.0 None None 0 None -348 WRHCQRLDV 0.0 None None 0 None -349 VRLGPVKSI 2.30860618466 RLGPVKS RLGPVQN 28.0 146528|NS3/4A_protein|CAM56207.1|Hepatitis_C_virus|11103 -350 SMQAHIKAL 0.0 None None 0 None -351 ESFKQTDFY 0.0 None None 0 None -352 QTDFYSMAL 0.0 None None 0 None -353 LPWMRLLLL 0.0 None None 0 None -354 MRLLLLLLV 0.0 None None 0 None -355 PRLPWMRLL 0.0 None None 0 None -356 WMRLLLLLL 0.0 None None 0 None -357 AIALHRLSL 0.0 None None 0 None -358 MRGHDWRML 0.0 None None 0 None -359 QMRGHDWRM 0.0 None None 0 None -360 HLETHNTDK 1.91662691262 ETHNTDK ECHSTDA 24.0 97111|polyprotein|ABR25251.1|Hepatitis_C_virus_(isolate_H77)|63746 -361 CSKLKHRDL 0.00687496931678 CSKLKHR CSARLHR 21.0 28508|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 -362 VVGAVGVGK 0.0 None None 0 None -363 AHPDGSWTF 5.46667302818 HPDGSWTF HPASAWTL 30.0 183594|polyprotein|AGT63075.1|Dengue_virus_1|11053 -364 WGRERGARV 0.0 None None 0 None -365 KADIPRDSY 0.0 None None 0 None -366 NVLQSSVPV 0.986093893012 NVLQSSVPV NVMLVTLPV 21.0 98308|trans-sialidase,_putative|EAN80840.1|Trypanosoma_cruzi|5693 -367 IITESGEVI 0.0 None None 0 None -368 WVYDAIITE 0.0 None None 0 None -369 FPPNILDDI 0.134347555558 PNILDDI PEIEDDI 24.0 180682|polyprotein|AGO67248.1|Dengue_virus_2|11060 -370 MASQRPLQF 0.0 None None 0 None -371 DMHVAVKIV 0.0 None None 0 None -372 FARPASPSR 0.00268626303148 PASPSR PAKPAR 24.0 53405|||| -373 IVFEVFGHH 0.0 None None 0 None -374 TTAVLTATF 0.0 None None 0 None -375 MAAAVVARL 0.0 None None 0 None -376 FSLPPSRKK 0.0 None None 0 None -377 LPMCWAMEV 0.0 None None 0 None -378 LTYSCLDNK 0.0 None None 0 None -379 LLNSGGDII 0.0 None None 0 None -380 DIYCITDFV 0.0 None None 0 None -381 FVEELADTV 0.0 None None 0 None -382 TISCTSLKK 0.0 None None 0 None -383 VTISCTSLK 0.0 None None 0 None -384 IIIKCQLPK 0.0 None None 0 None -385 RYGAGQQNL 1.47210141005 YGAGQQNL YGAGQVML 28.0 5783|Nucleoprotein|P03418.1|Human_respiratory_syncytial_virus_A2|11259 -386 TPYAACPAI 0.61364033445 TPYAAC NPYAVC 27.0 110401|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 -387 SPFNTTFPF 0.0 None None 0 None -388 QVARRVQEL 0.0 None None 0 None -389 HREARGRAL 0.0 None None 0 None -390 AIFGPSNTY 1.40284974093 AIFGP AVFGP 26.0 96123|Genome_polyprotein|P26664.3|Hepatitis_C_virus_(isolate_H77)|63746 -391 DLFQFPKAY 0.258104503658 FQFPKA FYFPRA 24.0 18390|Genome_polyprotein|P08617.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 -392 LPEDPKCEF 0.0540961051747 PEDPKCE PTDVSCE 24.0 79628|E1_protein|BAA19893.1|Rubella_virus|11041 -393 SFQPKAAVF 0.0 None None 0 None -394 PPSETGGIF 0.0 None None 0 None -395 NAGEMVIEY 0.0 None None 0 None -396 APTSSDYEF 0.0 None None 0 None -397 LFCGLPFSI 3.79000971222 FCGLPFS FCGSPYS 33.0 190409|polymerase|AAD16253.1|Hepatitis_B_virus|10407 -398 VPVASSEAS 0.0 None None 0 None -399 DPSPGIMAF 0.0 None None 0 None -400 LTYSLLTPL 0.0 None None 0 None -401 TYSLLTPLL 0.0 None None 0 None -402 CYVAICNPF 0.0 None None 0 None -403 LAAMAIDCY 0.0 None None 0 None -404 MAIDCYVAI 5.96984686185 IDCYVAI IDCNVAV 28.0 419366|polyprotein|BAA00792.1|Hepatitis_C_virus|11103 -405 YFFLGNLAF 0.0 None None 0 None -406 FPVEDRRGV 0.0 None None 0 None -407 FAQLINNKM 0.0 None None 0 None -408 RVASVVVSF 0.0 None None 0 None -409 RVASVVVSF 0.0 None None 0 None -410 FYLRYFEK* 0.0 None None 0 None -411 FFSSNLPTY 0.0 None None 0 None -412 FSSNLPTYY 12.750272737 NLPTYY SLPSYY 27.0 28594|IMMUNOGENIC_PROTEIN_MPT64_(ANTIGEN_MPT64/MPB64)|CAA98382.1|Mycobacterium_tuberculosis_H37Rv|83332 -413 NPYKAPMAE 0.00506353396253 NPYKAPM NPEVIPM 20.0 187163|Gag_polyprotein|P88150|Human_immunodeficiency_virus_1|11676 -414 AFLQKAHLI 0.0226039482404 LQKAHLI LEKRHVL 21.0 184755|polyprotein|AGO67248.1|Dengue_virus_2|11060 -415 FQGYLKDPV 0.0 None None 0 None -416 SEVLGYWAF 0.745411820705 VLGYWAF LLGLWGF 27.0 98223|trans-sialidase,_putative|EAN80725.1|Trypanosoma_cruzi|5693 -417 SEVLGYWAF 0.675840050772 VLGYWAF LLGLWGF 27.0 98223|trans-sialidase,_putative|EAN80725.1|Trypanosoma_cruzi|5693 -418 RRFGWLQTA 0.0 None None 0 None -419 GHEEKITFI 0.0 None None 0 None -420 EESIAVGTM 0.0 None None 0 None -421 EESIAVGTM 0.0 None None 0 None -422 FRYLGKCNI 0.0 None None 0 None -423 FEVGGAALF 0.0 None None 0 None -424 FEVGGAALF 0.0 None None 0 None -425 GMCVLEMAV 0.0 None None 0 None -426 VLEMAVLEI 0.0 None None 0 None -427 FLMVSRDCL 0.022042337798 FLMVSRDCL FLLALLSCL 21.0 136837|polyprotein_precursor|BAA01582.1|Hepatitis_C_virus|11103 -428 SRDCLRTVL 0.0 None None 0 None -429 VSRDCLRTV 0.0 None None 0 None -430 ALREFKFRV 0.0 None None 0 None -431 REFKFRVSA 0.0 None None 0 None -432 REFKFRVSA 0.0 None None 0 None -433 YEALREFKF 0.0 None None 0 None -434 NQMDKLAAF 0.0 None None 0 None -435 YRMSPSNQM 0.0 None None 0 None -436 KVISYPVAL 0.0 None None 0 None -437 TERTKVISY 0.0 None None 0 None -438 LHLRRKEIM 0.0 None None 0 None -439 QTSCHVFMV 0.0 None None 0 None -440 GEAGAGGTA 0.0 None None 0 None -441 EHMPNNSRL 0.0 None None 0 None -442 PRKPRSQNF 0.0 None None 0 None -443 RQWPRLSHK 0.941940860927 QWPRLSH TWPLLPH 27.0 79337|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 -444 ISLAYLVKK 0.0 None None 0 None -445 TISLAYLVK 0.0 None None 0 None -446 MFLWTVAVI 0.0 None None 0 None -447 TVAVIPILF 0.0 None None 0 None -448 KIRQLKKKK 0.0 None None 0 None -449 NEKTTPSPA 0.00746553042847 NEKTTP NSKRTP 22.0 419298|RNA-dependent_RNA_polymerase|ACH97782.1|Hepatitis_C_virus|11103 -450 NENATPSPA 0.0 None None 0 None -451 RERTANENA 0.0 None None 0 None -452 CYLQIFATR 0.0 None None 0 None -453 LPPSLQGAV 8.55128205128 PPSLQGAV PPMVEGAA 26.0 48836|EBNA-1_protein|Q777E1|Human_gammaherpesvirus_4|10376 -454 RVARSHCQR 0.0 None None 0 None -455 VPSEPSSSV 0.0 None None 0 None -456 EEWCSLWAG 0.0 None None 0 None -457 WEEWCSLWA 0.0453634499044 WEEWCSLW WPKTHTLW 22.0 184702|non-structural_protein_1|AGM49312.1|Dengue_virus|12637 -458 RLPSYMVEK 0.0 None None 0 None -459 SYMVEKREF 0.00754725742526 MVEKREF MLEDHEF 21.0 164551|envelope_glycoprotein_B|NP_044629.1|Herpes_simplex_virus_(type_1_/_strain_17)|10299 -460 GENFCTAVK 0.0 None None 0 None -461 MEGYMKAKV 0.0 None None 0 None -462 CPLPRPPPI 0.84385451991 LPRPPP LPRPGP 28.0 139406|polyprotein|ACT37184.1|Hepatitis_C_virus|11103 -463 AEEAGYPLS 0.0304382014743 EAGYPLS EVGFPVR 22.0 288104|nef_protein|ACR27130.1|Human_immunodeficiency_virus_1|11676 -464 EEAGYPLSC 0.0464643757354 EAGYPLS EVGFPVR 22.0 288104|nef_protein|ACR27130.1|Human_immunodeficiency_virus_1|11676 -465 GVYLLFALR 0.0 None None 0 None -466 VYLLFALRL 0.0 None None 0 None -467 QEASNKHAE 0.970660146699 QEASNKH QEAANKQ 26.0 3935|ESAT-6-like_protein_esxB|P0A566.2|Mycobacterium_tuberculosis|1773 -468 SEYSSSLGR 0.0 None None 0 None -469 RESGSFLST 0.0 None None 0 None -470 LYQLHNLVV 0.0 None None 0 None -471 YAAPQLHSI 0.0 None None 0 None -472 HLHDHYGPY 0.0 None None 0 None -473 FAEDGACTV 0.0 None None 0 None -474 HVIGTIGHF 0.0 None None 0 None -475 FADDEHSMV 0.0 None None 0 None -476 YANERPKSL 0.0 None None 0 None -477 FACHFTVFV 0.0 None None 0 None -478 NALDYICTV 0.0 None None 0 None -479 LAYQELPTV 0.133857018486 YQELPT YSEHPT 21.0 75718|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 -480 FVMEHSNIV 0.0 None None 0 None -481 VAFCTMNVI 0.0 None None 0 None -482 FTIRAIQVY 0.0 None None 0 None -483 MAISVVKHI 0.0395696619166 MAISVVK MALSIVS 22.0 180641|polyprotein|AFJ91714.1|Dengue_virus_1|11053 -484 RALEKLNHV 0.880797077978 ALEKLN ALEKLN 28.0 2506|M_protein,_serotype_5_precursor|P02977.2|Streptococcus_pyogenes_serotype_M5|301449 -485 FADMERHHI 1.33333333333 DMERHHI DLEKRHV 26.0 183781|polyprotein|AGO67248.1|Dengue_virus_2|11060 -486 FANRRKEEV 21.3373135759 ANRRKEEV ANKQKQEL 26.0 327|ESAT-6-like_protein_esxB|P0A566.2|Mycobacterium_tuberculosis|1773 -487 LAIDSASPV 0.0 None None 0 None -488 RALGPGHTV 0.000143960338651 ALGPGHTV AVGVYHIV 17.0 32663|small_hydrophobic_protein|AAM12943.1|Human_metapneumovirus|162145 -489 FAKVLIRTY 0.880797077978 KVLIRTY KVLIRCY 28.0 145860|Protein_E6|P04019.1|Human_papillomavirus_type_11|10580 -490 SSDDNDAFY 0.583333333333 SDDNDAFY TDNNRSFY 26.0 98603|trans-sialidase,_putative|EAN82716.1|Trypanosoma_cruzi|5693 -491 YPKGRPSHI 0.0 None None 0 None -492 WALPKTYTI 0.0 None None 0 None -493 LARHWRVHI 0.0 None None 0 None -494 FSYSASSEI 0.0 None None 0 None -495 FSFFFVNIF 0.0 None None 0 None -496 YSFDGMWKV 0.701469617998 SFDGMWKV SWDQMWKC 30.0 146570|polyprotein|ADY38595.1|Hepatitis_C_virus_subtype_1b|31647 -497 DSIHQVGMY 0.0359724199242 HQVGMY HAVGLF 22.0 23573|polyprotein|AAB67037.1|Hepatitis_C_virus_(isolate_H77)|63746 -498 MTYDLASVV 0.0 None None 0 None -499 LAFPVPLYY 0.80288104137 PVPLYY PIPIHY 28.0 47946|envelope_glycoprotein|AAC28452.1|Human_immunodeficiency_virus_1|11676 -500 YAALAMGTL 0.0 None None 0 None -501 YLFRELATI 0.0 None None 0 None -502 YMDLMGFSY 0.136231910882 YMDLMG YMSLLG 24.0 17117|matrix_protein|AAN09804.1|Measles_virus_strain_Edmonston|11235 -503 FAISHEGHM 0.0 None None 0 None -504 FSSPRLRPI 0.0 None None 0 None -505 FVYLHLNMV 0.973487792105 FVYLHLNMV LIHLHQNIV 26.0 2903|Genome_polyprotein|P27958.3|Hepatitis_C_virus_subtype_1a|31646 -506 MANNPDVMI 0.0 None None 0 None -507 AALPAAQTV 0.0 None None 0 None -508 FAWKNMDFL 0.104302556769 WKNMDFL WTSLNFL 24.0 62504|HBsAg_protein|ABF71024.1|Hepatitis_B_virus|10407 -509 FAAQGPTVF 0.0 None None 0 None -510 LALSNLPTV 0.0 None None 0 None -511 FTLEFLVCI 0.0 None None 0 None -512 FSVDFPRIY 0.208605113539 FPRIY FPRIW 24.0 187106|Vpr_protein|BAA93983.1|Human_immunodeficiency_virus_1|11676 -513 FTIFWTVYY 1.87174259914 IFWTVYY VMWTVYH 32.0 146249|polyprotein|ADE10208.1|Hepatitis_C_virus_subtype_3a|356426 -514 MADPNQCVI 1.01181629973 DPNQCV DPRRCL 24.0 150556|polyprotein|AGW21594.1|Dengue_virus_1|11053 -515 RAFWAGSVV 2.73888707955 AFWAGSVV TLWGGSVV 29.0 79351|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 -516 YHFDAIRTF 0.73105857863 FDAIRTF YDAVRTW 27.0 154164|tegument_protein|CAB06732.1|Human_alphaherpesvirus_2|10310 -517 FAKGWLLKL 0.992469783844 FAKGW FAQGW 28.0 8236|Genome_polyprotein|P27958.3|Hepatitis_C_virus_subtype_1a|31646 -518 NAQNMTITV 0.0 None None 0 None -519 RALNRVHVL 0.0 None None 0 None -520 MAPELISHL 0.0519601621127 MAPELISHL MEPTLGQHL 22.0 79308|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 -521 KAFYHPRLI 0.331355045526 FYHPR FYFPR 24.0 18390|Genome_polyprotein|P08617.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 -522 LAFVIVLLV 0.0 None None 0 None -523 CTAVVLLVY 0.0 None None 0 None -524 FTEFCDSCY 0.648148148148 FCDSCY ICDECH 26.0 107905|Genome_polyprotein|P26664.3|Hepatitis_C_virus|11103 -525 LAREPVNEL 0.0 None None 0 None -526 YTRKRTQSI 0.0 None None 0 None -527 FAPSCANSL 0.119202922022 FAPSCAN YSPSCCT 24.0 10962|envelope_glycoprotein|AAU04921.1|Human_T-lymphotropic_virus_1|11908 -528 KVYDLVHSV 0.278600815726 KVYDLVH RIYDLIE 25.0 55620|EBNA3C_latent_protein|CAD53421.1|Human_gammaherpesvirus_4|10376 -529 QAPPLMGTI 0.0 None None 0 None -530 QAFRRSISV 0.0 None None 0 None -531 FVLDHSRLV 0.12716493457 FVLDH YVLDH 25.0 25237|Transcription_activator_BRLF1|P03209.1|Human_herpesvirus_4_strain_B95-8|10377 -532 FIKRHIAPI 0.0 None None 0 None -533 YSQPFYTSY 0.0 None None 0 None -534 FAQDVDRMF 0.0 None None 0 None -535 QAPEFLQTL 0.242047279233 PEFLQTL PESLETL 25.0 184531|polyprotein|AFP27208.1|Dengue_virus_4|11070 -536 LSDISRSCY 0.0 None None 0 None -537 NAYARVLRF 0.0 None None 0 None -538 FANFFNTFL 0.0 None None 0 None -539 FIYDAVGNM 0.0 None None 0 None -540 LARECGSPL 0.0 None None 0 None -541 WHGPARPSL 0.0 None None 0 None -542 HVMFMVAFY 0.0 None None 0 None -543 MAITSMNPV 0.0 None None 0 None -544 TAVEFIMAI 0.0 None None 0 None -545 QAYGGPRYL 0.0520850061725 QAYGGP QLYRGP 22.0 38724|Genome_polyprotein|P08617.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 -546 FTIRAIQVY 0.0 None None 0 None -547 YLDYVSISY 0.0 None None 0 None -548 SAYMHHSKI 0.0 None None 0 None -549 YLMEFGQLL 0.710046526128 YLMEFG YLVSFG 24.0 69474|core_protein|BAF42671.1|Hepatitis_B_virus|10407 -550 KAEELKETV 0.0 None None 0 None -551 FALGVGTAL 0.809630010555 LGVGTAL LGIGTVL 28.0 108127|Genome_polyprotein|P26664.3|Hepatitis_C_virus|11103 -552 LVFPNSDHV 0.0 None None 0 None -553 FTLQNPSAV 0.0 None None 0 None -554 EIVDQQGHM 0.0 None None 0 None -555 FTIFWTVYY 1.15184159947 IFWTVYY VMWTVYH 32.0 146249|polyprotein|ADE10208.1|Hepatitis_C_virus_subtype_3a|356426 -556 FPNSCLSTL 0.0 None None 0 None -557 YSISDWTSI 0.0179862099621 WTSI WTSL 22.0 62504|HBsAg_protein|ABF71024.1|Hepatitis_B_virus|10407 -558 FTACYIRIV 0.0 None None 0 None -559 FEFDHIRNF 0.0205556685281 FDHIRNF FDRTRKF 22.0 154296|UL29|CAB06754.1|Human_alphaherpesvirus_2|10310 -560 YTPDELHAM 0.00621479014398 PDELHAM PDVAHSL 21.0 130953|G1_and_G2_surface_glycoprotein_precursor|AAG22532.1|Andes_hantavirus|46607 -561 FVHPATRPL 0.0 None None 0 None -562 KALRITNVY 0.0 None None 0 None -563 QARDQGSPV 0.0 None None 0 None -564 FIYDAVGNM 0.0 None None 0 None -565 EAFPEDVAV 0.0 None None 0 None -566 YATADSSSL 0.0 None None 0 None -567 RAREHSDTF 0.0 None None 0 None -568 IAIQLITHM 0.0 None None 0 None -569 MAFENNAGL 0.0 None None 0 None -570 FGHENRVSI 0.0 None None 0 None -571 NATTIVTTV 0.0 None None 0 None -572 VTFPGINLM 0.0 None None 0 None -573 DAYPRQYSL 0.0 None None 0 None -574 YIQEGFLAV 0.00185446736748 QEGFLAV QNGALAI 20.0 51685|Nuclear_antigen_EBNA-3C|Q69140.1|Human_gammaherpesvirus_4|10376 -575 FATTACHTL 0.0 None None 0 None -576 RANQCFAFV 0.0 None None 0 None -577 MTQPVWSTI 0.0 None None 0 None -578 FTEEGFCAI 0.0 None None 0 None -579 FADHPQAPF 0.0 None None 0 None -580 VAMGSAALV 0.0 None None 0 None -581 TAKDYRVYV 0.0 None None 0 None -582 EAEEWVVSY 0.0 None None 0 None -583 FTLPLMDQV 0.0 None None 0 None -584 MQMPCTIKI 0.0 None None 0 None -585 YRYFCRVPV 0.808012113223 YFCR YFCR 27.0 155131|ribonucleotide_reductase_large_subunit|CAB06725.1|Human_alphaherpesvirus_2|10310 -586 WAHAWPSPY 0.0047350399545 WAHAWPSPY WHYDEDNPY 20.0 72563|polyprotein|AAB70696.1|Dengue_virus_type_1_Hawaii|10000440 -587 IAIISVLVI 0.0 None None 0 None -588 MASCPFAKV 0.0 None None 0 None -589 NHDRFHYLL 5.22641395793 DRFHYLL DNFPYLV 22.0 9461|non_structural_protein_3|CAJ20172.1|Hepatitis_C_virus|11103 -590 FTIFWTVYY 1.73382472341 IFWTVYY VMWTVYH 32.0 146249|polyprotein|ADE10208.1|Hepatitis_C_virus_subtype_3a|356426 -591 VASQPAHVV 0.0 None None 0 None -592 EAFNCESKM 0.0 None None 0 None -593 FSSEVTVAL 0.0 None None 0 None -594 ETIKQLQEL 0.0 None None 0 None -595 YFMDPMVPL 0.0355694048832 DPMVPL DPTTPL 23.0 103392|polyprotein|BAB18806.1|Hepatitis_C_virus|11103 -596 NVYHVGMHI 0.0 None None 0 None -597 AAMEGRLPV 0.0 None None 0 None -598 NHDDDDVEI 167.634475679 NHDDDDVEI NHDSPDAEL 32.0 44133|Genome_polyprotein|P26664.3|Hepatitis_C_virus_genotype_1|41856 -599 NASVNVSHL 124.263294844 NASVNVS NSSVNVS 29.0 183670|polyprotein|AGO67248.1|Dengue_virus_2|11060 -600 EALDAGAIY 0.0 None None 0 None -601 YGRDDWEVI 0.0 None None 0 None -602 VALDKDALV 0.0 None None 0 None -603 LPFSLGKHV 0.0 None None 0 None -604 MANNPCSRY 0.0 None None 0 None -605 YEEPNTATF 0.0 None None 0 None -606 MALYHCVAI 0.0931643013308 ALYHCVAI SLYNTVAI 24.0 189292|gag_protein|ABC40295.1|Human_immunodeficiency_virus_1|11676 -607 YTLAPGVPL 0.176306491827 PGVPL PGVPF 24.0 38556|Genome_polyprotein|Q00269.3|Hepatitis_C_virus|11103 -608 KIHPFFETI 0.0 None None 0 None -609 NMDFLIAEY 0.0 None None 0 None -610 LCIPWTNPV 0.0 None None 0 None -611 SAQEHLLFV 0.0 None None 0 None -612 QSVHPVVTV 1.38374670414 QSVHPVVT KSTHPMVT 30.0 20686|UL123;_IE1|AAR31448.1|Human_betaherpesvirus_5|10359 -613 YVASDIQYM 0.0 None None 0 None -614 FHMRQVNIV 0.0 None None 0 None -615 LAKHSTSAV 0.0 None None 0 None -616 FSHQPKEKV 0.0 None None 0 None -617 YLYIPALAV 0.0 None None 0 None -618 VALFMAITI 0.0 None None 0 None -619 VAFYGLGAV 0.0 None None 0 None -620 EVDPIGNLY 0.0 None None 0 None -621 WALSIHVSV 0.0 None None 0 None -622 ITYPSQAPV 0.0 None None 0 None -623 CIALWSLAY 0.0 None None 0 None -624 FLFYVMTEV 0.0 None None 0 None -625 HAEQDSTTV 0.458333333333 QDSTTV QDATTV 26.0 6373|Genome_polyprotein|SRC279960|Hepatitis_C_virus_subtype_3a|356426 -626 DTNDNVPEF 0.0 None None 0 None -627 NSYGSRRTL 0.0 None None 0 None -628 NARCLIVHL 0.0 None None 0 None -629 FWYRNCHHV 0.0 None None 0 None -630 DADPSTPHL 1.08133686929 DPSTP DPTTP 26.0 103392|polyprotein|BAB18806.1|Hepatitis_C_virus|11103 -631 DSYIHVTYI 2.47386789457 YIHVTYI FLHVTYV 32.0 71663|Spike_glycoprotein_precursor|P59594.1|SARS_coronavirus|227859 -632 DVFDALDLM 0.0 None None 0 None -633 FSMDETGQM 0.0 None None 0 None -634 RTFNKPESV 0.0 None None 0 None -635 YSLQEMEVL 0.0 None None 0 None -636 QTVMFMATM 0.0 None None 0 None -637 VTIDGIRFI 0.0 None None 0 None -638 RALSHPQSL 0.0 None None 0 None -639 TAAGFWLMV 0.0 None None 0 None -640 FMEELGECV 0.0 None None 0 None -641 YLESNPGTI 0.0 None None 0 None -642 VPSNFVEHV 0.0 None None 0 None -643 FTEELRRTF 0.0062273472093 FTEELRR FVELMRR 20.0 39095|nonstructural_protein_3|NP_722463.1|Dengue_virus_type_1_Hawaii|10000440 -644 YGRSRGITV 0.146582464117 SRGITV DRGLTV 22.0 41269|kaposin|AAC57155.1|Human_gammaherpesvirus_8|37296 -645 FSMACNTPL 0.0 None None 0 None -646 QAADEPQLL 0.0 None None 0 None -647 YEFALQRIV 0.0 None None 0 None -648 TAAPTSASV 0.0 None None 0 None -649 LACRKAREI 0.249019834602 CRKARE CRCARE 25.0 155131|ribonucleotide_reductase_large_subunit|CAB06725.1|Human_alphaherpesvirus_2|10310 -650 FIEPLNDTI 0.0 None None 0 None -651 SALRAITRV 0.0 None None 0 None -652 RAAPKAMVL 0.0 None None 0 None -653 VADEGLNNL 0.0 None None 0 None -654 LSNDECKTI 0.0 None None 0 None -655 NAWAVMNHF 0.0 None None 0 None -656 VASNAWAVM 0.0 None None 0 None -657 LSRNLIRTI 0.830019904681 RNLIRTI QNLARTI 24.0 63010|6_kDa_early_secretory_antigenic_target|P0A564.2|Mycobacterium_tuberculosis|1773 -658 HSKEEIKVI 0.0 None None 0 None -659 DSELNFNEY 0.0 None None 0 None -660 DAAERECHL 0.0 None None 0 None -661 ISYTEVPTY 0.976082030541 ISYTEVPTY ITYTDVLRY 26.0 29186|polyprotein_precursor|NP_041724.2|West_Nile_virus|11082 -662 IASDHVVDM 0.0 None None 0 None -663 IAILICTMI 0.0 None None 0 None -664 MAKTGRFHI 0.0 None None 0 None -665 EVMEKVLPL 0.0 None None 0 None -666 FENNAGLPV 0.0 None None 0 None -667 FLHEMVAAM 0.0 None None 0 None -668 QAEPKKKPV 1.7536554713 EPKKKP EPGKNP 22.0 419124|polyprotein|ACF49259.1|Dengue_virus_type_1_Hawaii|10000440 -669 YVLHSKEEI 0.0 None None 0 None -670 FFFHNPKPL 0.430306274192 FFFHNPKPL IFFFNPGEL 25.0 43447|IMMUNOGENIC_PROTEIN_MPT64_(ANTIGEN_MPT64/MPB64)|CAA98382.1|Mycobacterium_tuberculosis_H37Rv|83332 -671 FHWNWIIVL 1.23311590917 HWNWII RWEWVV 28.0 74407|polyprotein|AAU89634.1|Hepatitis_C_virus_subtype_2a|31649 -672 YTMGIIFVL 0.0 None None 0 None -673 YVGKDIESV 0.0 None None 0 None -674 YQHYFRLLV 0.263137102792 YQHYFR YQSYLR 23.0 116781|Nucleoprotein|P05133.1|Hantaan_virus_76-118|11602 -675 MSNSMINTM 0.225806451613 NSMINTM NTMLNTV 26.0 294287|gag_protein|ABI20203.1|Human_immunodeficiency_virus_1|11676 -676 FSMLSRVLI 0.0 None None 0 None -677 FVDYPGDPV 0.0175687336762 VDYPGDPV VDFSLDPT 21.0 96156|polyprotein|ABR25251.1|Hepatitis_C_virus_(isolate_H77)|63746 -678 STAPLYSGM 3.52889315171 TAPLYS TLPVYS 23.0 98254|trans-sialidase,_putative|EAN81042.1|Trypanosoma_cruzi|5693 -679 DTVQLNVKY 0.0 None None 0 None -680 SAYMAATLL 0.0 None None 0 None -681 QAWNFLRAM 0.845286481541 QAWNF QQWNF 27.0 42797|6_kDa_early_secretory_antigenic_target|P0A564.2|Mycobacterium_tuberculosis|1773 -682 CAFGAMCAV 0.0 None None 0 None -683 IMEEEFSTI 0.0 None None 0 None -684 HAANVTQAM 0.0 None None 0 None -685 MAKQIKTKV 0.0363036459226 MAKQIKTK LAKEQKSK 21.0 8920|M_protein,_serotype_5_precursor|P02977.2|Streptococcus_pyogenes_serotype_M5|301449 -686 KAKGIYNSI 0.0 None None 0 None -687 HAPVHFLVI 0.0 None None 0 None -688 EVLQSMQRF 0.0 None None 0 None -689 YVASDIQYM 0.0 None None 0 None -690 YAAMDLSCL 0.0 None None 0 None -691 TPMTCSNTI 0.0 None None 0 None -692 EAPPGRVTF 0.0 None None 0 None -693 DTHSGAGKF 3.3511859631 HSGAGK HDGAGK 29.0 23621|Genome_polyprotein|P26664.3|Hepatitis_C_virus_(isolate_1)|11104 -694 YKYRYFCRV 0.610812498807 RYFCR EYFCR 27.0 155131|ribonucleotide_reductase_large_subunit|CAB06725.1|Human_alphaherpesvirus_2|10310 -695 LSDPHLTAV 0.0 None None 0 None -696 WAGLGGRHV 0.160072495287 GLGGRH GVGWRH 24.0 12183|EBNA3C_latent_protein|CAD53421.1|Human_gammaherpesvirus_4|10376 -697 QHTGTSVVL 0.478658436433 HTGTSVVL HIGAYVVL 23.0 154387|RL2|CAB06760.1|Human_alphaherpesvirus_2|10310 -698 STFCGTLEY 0.0 None None 0 None -699 TMYRCGPLI 0.0 None None 0 None -700 WHNQCSGHL 0.0 None None 0 None -701 FPLRNRPFY 0.40359719383 NRPFY NRSFY 23.0 98603|trans-sialidase,_putative|EAN82716.1|Trypanosoma_cruzi|5693 -702 YVGPAQLSV 0.0 None None 0 None -703 VAQHLATTY 0.0 None None 0 None -704 LVYPRFLYL 0.557903921081 YPRFLYL YPAVFYL 23.0 154041|major_capsid_protein|CAB06743.1|Human_alphaherpesvirus_2|10310 -705 FSREEMHNM 0.0 None None 0 None -706 YYPPGVVFY 0.0250303219548 YYPPGVV YTPEGII 23.0 180850|polyprotein|AFP27208.1|Dengue_virus_4|11070 -707 YLMSFFRLL 0.0 None None 0 None -708 RVFPLRGKI 0.0507541195092 RVFPLRGKI KLFPGGGQI 21.0 181035|||| -709 YPLPVANGM 0.881609743327 YPLPVANGM YPLHEQHGM 25.0 75356|EBNA3A_nuclear_protein|Q8AZJ8|Human_gammaherpesvirus_4|10376 -710 RAVCFSMEI 0.0 None None 0 None -711 QALPLDHHL 0.0 None None 0 None -712 FIEPHARFY 0.0 None None 0 None -713 FFYCIYASL 0.0 None None 0 None -714 CHDDYLVML 0.0 None None 0 None -715 KALFWTVAM 0.987412049439 KALFWTVAM KSLFNTVAV 26.0 126486|gag_protein|ADK33372.1|Human_immunodeficiency_virus_1|11676 -716 EYYEPPHRI 0.0 None None 0 None -717 PTSPMPYTY 0.196275089393 PTSPMP PTDPNP 24.0 70491|envelope_glycoprotein|AAC28452.1|Human_immunodeficiency_virus_1|11676 -718 EAVEARGAI 0.0 None None 0 None -719 NVVRLVATI 1.46700214129 NVVRLVATI NLVPMVATV 27.0 44920|tegument_protein_pp65|YP_002608275.1|Human_betaherpesvirus_5|10359 -720 YLKNSMIAV 0.0 None None 0 None -721 LQAEIVETM 0.0 None None 0 None -722 FHHKSNFLL 0.0 None None 0 None -723 KPIPAFEMV 0.0 None None 0 None -724 FLVDSNLSV 0.0 None None 0 None -725 FIDRQLTMV 0.0 None None 0 None -726 YSASSEIII 0.0 None None 0 None -727 YTPDELHAM 0.00719481474361 PDELHAM PDVAHSL 21.0 130953|G1_and_G2_surface_glycoprotein_precursor|AAG22532.1|Andes_hantavirus|46607 -728 FFYLDYVSI 0.0 None None 0 None -729 YIAPMMEKL 0.0 None None 0 None -730 EAFDRTETH 0.0 None None 0 None -731 SIVDVSIMY 0.0 None None 0 None -732 IPYTTVLHL 0.0 None None 0 None -733 EVFRHKLAM 0.0 None None 0 None -734 VMDRWNETV 1.66487546562 MDRWNE LDRWEK 25.0 19337|gag_protein|AAW57872.1|Human_immunodeficiency_virus_1|11676 -735 LLLDHGVHV 0.0 None None 0 None -736 VIFNVVRLV 0.0 None None 0 None -737 LAIKVTPSV 0.0508134355474 LAIKVTP LAISVVP 23.0 40288|kaposin|AAC57155.1|Human_gammaherpesvirus_8|37296 -738 LTDRQPLMH 0.0 None None 0 None -739 KPLPFNREV 0.0 None None 0 None -740 LNFGDITTV 0.0 None None 0 None -741 QAIDSTFYL 0.0 None None 0 None -742 LALNKGRAY 0.0 None None 0 None -743 IARQVVTAM 0.0 None None 0 None -744 GAFAFGAVF 0.0 None None 0 None -745 KSFPFQSLL 0.0 None None 0 None -746 RAGGSSVVI 0.0 None None 0 None -747 DTIPWYLRL 0.0 None None 0 None -748 MAVDGKPEY 0.0 None None 0 None -749 YLQDVVMQV 0.0 None None 0 None -750 FMVRNYEFL 0.0 None None 0 None -751 YMAGSDTTY 0.0 None None 0 None -752 VVYVLMTSV 0.0 None None 0 None -753 MPAERNGAI 0.0 None None 0 None -754 WPLQPVDHI 0.0 None None 0 None -755 MLDPHGHLI 0.0 None None 0 None -756 FISNSLNIL 0.0 None None 0 None -757 RADGDLTLI 0.0 None None 0 None -758 YQEEMIQCY 0.138922146416 YQEEMIQCY YMESVFQMY 24.0 154585|ribonucleotide_reductase_large_subunit|CAB06725.1|Human_alphaherpesvirus_2|10310 -759 FILDCHPKY 0.0 None None 0 None -760 GAYVYPLPV 1.80161146662 YVYPLPV YVYALPL 29.0 58463|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 -761 FKEAWKHTI 0.0 None None 0 None -762 LAGVKMVMI 0.0 None None 0 None -763 DAKQRIRLL 0.0 None None 0 None -764 LYYPPGVVF 0.0141268558401 YYPPGVV YTPEGII 23.0 180850|polyprotein|AFP27208.1|Dengue_virus_4|11070 -765 RASEDDRVL 0.0 None None 0 None -766 SALEYLLPL 0.982013790038 SALEYLLP SALQFLIP 30.0 22235|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 -767 AAVEPERTL 0.0 None None 0 None -768 GTDCLLLAF 0.0 None None 0 None -769 FVQLPVPII 0.0 None None 0 None -770 RIYPDRHRI 0.0 None None 0 None -771 KVDKNISHI 0.0 None None 0 None -772 RHSQWDHGL 0.0551254766838 SQWDHG TAWDFG 22.0 180726|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -773 MLYSRDHSV 0.0 None None 0 None -774 AARPLSRMV 0.0 None None 0 None -775 HAQVCSLYI 1.03982555138 HAQVCSLYI KAKICGLYL 30.0 177701|polyprotein|ACZ60104.1|Hepatitis_C_virus_subtype_3a|356426 -776 YSQPFYTSY 0.0 None None 0 None -777 MSDFQYLVV 0.0 None None 0 None -778 SANARCLIV 0.0 None None 0 None -779 SAIAIVQIL 0.0 None None 0 None -780 WMFYHFDAI 0.0 None None 0 None -781 YSKVIKCVV 0.0 None None 0 None -782 AARARGNKV 0.0 None None 0 None -783 TAYERLYLW 0.0 None None 0 None -784 TTASGVWAF 0.0 None None 0 None -785 KVREEVVTM 0.0 None None 0 None -786 MYYRVRDTM 0.0 None None 0 None -787 YVDRLLQHF 0.0 None None 0 None -788 PAIARPQAI 0.0 None None 0 None -789 YLLRAGVHL 2.34592183176 YLLRAGVHL FLLSLGIHL 30.0 16751|pol_protein|BAA32832.1|Hepatitis_B_virus|10407 -790 LVTPHMAEV 0.29585271922 LVTPHM LVTPSM 24.0 150378|polyprotein|AGW21594.1|Dengue_virus_1|11053 -791 EHVSDDDLL 0.0 None None 0 None -792 SFYHLVSTV 0.485538841086 SFYHLVST GFYHILNN 25.0 1516|Nucleoprotein|P03418.1|Human_respiratory_syncytial_virus_A2|11259 -793 FSAGNEANV 0.205224687568 SAGNEA NAGNDA 23.0 1090|Transcription_activator_BRLF1|P03209.1|Human_herpesvirus_4_strain_B95-8|10377 -794 KPGDRVVLV 0.0 None None 0 None -795 YSRGSSRCI 0.0 None None 0 None -796 YSTCVLVVL 0.0 None None 0 None -797 YSTHQTFMV 0.0 None None 0 None -798 WSLDGKYIV 1.99294213388 WSLDGKYIV WAIKWEYVV 26.0 72233|Genome_polyprotein|P27958.3|Hepatitis_C_virus_subtype_1a|31646 -799 HAWRDLSSM 0.0 None None 0 None -800 FASSLWETT 0.0 None None 0 None -801 FDYPSLFCI 0.0 None None 0 None -802 KAPPLTDVL 0.0 None None 0 None -803 DVFDALDLM 0.0 None None 0 None -804 ALYCRLATV 0.0118752492321 ALYCRLATV SLYNTIATL 20.0 190827|gag_protein|AAN08336.1|Human_immunodeficiency_virus_1|11676 -805 MVYLQIGGF 0.0 None None 0 None -806 EPFSGTASV 0.0 None None 0 None -807 ETMDELELL 0.578907805322 MDELEL MDKLEL 25.0 185419|envelope_protein|AGW23591.1|Dengue_virus_3|11069 -808 SMLNWFSPV 1.31489982056 MLNWFSPV LLIWFRPV 30.0 37507|Large_T_antigen|P03071.1|Human_polyomavirus_1|1891762 -809 NMLNLTHTY 0.0 None None 0 None -810 HSFNPEAQV 0.544692682129 HSFNPE KAFNPE 25.0 187158|Gag_protein|Q1KW74|Human_immunodeficiency_virus_1|11676 -811 SAYGSSGEL 0.0 None None 0 None -812 FSIPWAHAW 1.46617482283 FSIPWAH VSIPWTH 34.0 46480|DNA_polymerase|CAA10434.1|Hepatitis_B_virus|10407 -813 MASSAQEHL 0.0 None None 0 None -814 RHSREMALL 0.0 None None 0 None -815 WVLHHMGGM 36.5311333334 WVLHHMG WILRHPG 30.0 180818|Membrane_glycoprotein_precursor|NP_739582.2|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -816 VADSDRQLV 0.0 None None 0 None -817 IAAAWALSF 0.163128403126 AAAWAL AAAWYL 25.0 183819|polyprotein|AGO67248.1|Dengue_virus_2|11060 -818 KAESTPEIV 0.0 None None 0 None -819 LHLGHMFSL 0.107288558852 LGHMFSL LSHYFTL 22.0 59459|Trans-sialidase|SRC7915|Trypanosoma_cruzi|5693 -820 QRINLPHLL 0.0 None None 0 None -821 YALMRHRHT 0.0 None None 0 None -822 RLYPLANSL 0.0 None None 0 None -823 DHFSHASSI 0.0 None None 0 None -824 ISMEKGYNI 0.0 None None 0 None -825 FLHEMVAAM 0.0 None None 0 None -826 YVALEAQAI 0.0 None None 0 None -827 YLMTRTLPM 0.0 None None 0 None -828 QTFPQVSEL 0.0 None None 0 None -829 YPESIKAPV 0.0 None None 0 None -830 VHSKTSQLL 0.0 None None 0 None -831 TSSDRMTSV 0.0 None None 0 None -832 QMAERALYY 0.0 None None 0 None -833 LASPFATTA 0.0 None None 0 None -834 AAYTSYTPY 0.264739211661 AAYTSYTP EEYTDYMP 25.0 180681|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -835 VSCRPVVYV 0.0 None None 0 None -836 RTYHGRLAY 0.0 None None 0 None -837 LARHSAAFL 0.0 None None 0 None -838 RSEALPVSY 0.0498128500965 RSEALP RAESLP 23.0 419006|PPE_family_protein_PPE68|KAM81677.1|Mycobacterium_tuberculosis_H37Ra|419947 -839 ETKPFGLVV 0.00397696968794 KPFGLVV KPARLIV 19.0 30946|HCV-1|AAA45676.1|Hepatitis_C_virus_genotype_1|41856 -840 DVKNFWQGM 0.0 None None 0 None -841 FAELKSARM 0.0 None None 0 None -842 YMKPRLRTT 0.0 None None 0 None -843 STFCGTLEY 0.0 None None 0 None -844 HAATGPGEV 0.471180876873 HAATGPGE HAPTGSGK 28.0 146644|polyprotein|ADE10208.1|Hepatitis_C_virus_subtype_3a|356426 -845 PSQNRFLTY 10.5277024867 PSQNRF PSMKRF 22.0 180681|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -846 YISAWLDSL 0.577024181579 SAWLDS GAWMDS 27.0 30903|prM_protein|YP_001527879.1|West_Nile_virus_NY-99|10000971 -847 VPFPPKEPL 7.85759820488 VPFPPK IPYDPK 24.0 180789|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -848 KSHELVMYI 0.0 None None 0 None -849 LMLGRTNTL 0.0 None None 0 None -850 VARHTFSML 0.0 None None 0 None -851 LAIFMPPTY 0.018791562647 IFMPPTY VYMSPFY 22.0 141469|envelope_glycoprotein_B|NP_044629.1|Human_alphaherpesvirus_1|10298 -852 WAVVTMTAV 0.0 None None 0 None -853 FPRASQSLV 1.0950421762 FPRASQSLV FPGFGQSLL 23.0 23807|tax|AAG48731.1|Human_T-lymphotropic_virus_2|11909 -854 YDFLCLSLV 0.0 None None 0 None -855 NKFPGDSMV 0.0 None None 0 None -856 FSLLATVIL 0.468169410856 FSLLATV FTLVATV 25.0 98640|trans-sialidase,_putative|EAN80840.1|Trypanosoma_cruzi|5693 -857 SSSDNRNFI 0.0 None None 0 None -858 KSRNWLKSI 0.0 None None 0 None -859 QALNLQVVL 0.0 None None 0 None -860 FPVLLLDTI 4.07245586889e-05 PVLLLDT PVENLET 16.0 149063|NS3_protease/helicase'|NP_803144.1|Hepatitis_C_virus_(isolate_H77)|63746 -861 VTDFHNHSV 0.0 None None 0 None -862 LSDSMPLWM 0.0 None None 0 None -863 QSTKVNMLY 0.0 None None 0 None -864 MANHLGVGV 0.0 None None 0 None -865 HMDVEESQY 0.0 None None 0 None -866 LADPIEKEL 0.0 None None 0 None -867 MAITILVAL 0.0 None None 0 None -868 YRDNKMTRI 0.0 None None 0 None -869 FQMAERALY 0.0 None None 0 None -870 RINENTGIV 0.0 None None 0 None -871 EAGEESTSV 0.0 None None 0 None -872 RGMPPPPTV 0.746912503019 PPPPT PPPAT 25.0 120093|unnamed_protein_product|CAA33016.1|Rubella_virus|11041 -873 RLFRMFVHV 0.0 None None 0 None -874 FLTDMAKQI 0.0 None None 0 None -875 ISMQFLSSL 0.0 None None 0 None -876 HTDTNNLGI 0.0 None None 0 None -877 LALAIYTLL 0.0 None None 0 None -878 LAVCAFTVL 0.0 None None 0 None -879 AAAPNLRAL 0.0 None None 0 None -880 LVDSNLSVV 0.0 None None 0 None -881 VSSVQGITY 0.0 None None 0 None -882 HLMKQISSF 5.7878791982 HLMKQISS HLAFQLSS 23.0 24172|pX-rex-orf_I_{alternatively_spliced}|AAB23359.1|Human_T-lymphotropic_virus_1|11908 -883 EARGAIRGF 0.0 None None 0 None -884 LVSTSNHAY 0.0 None None 0 None -885 IAPRRWLLL 0.0 None None 0 None -886 RMAERRQEV 0.0 None None 0 None -887 YVVATTKLM 0.338384379032 YVVATTKL YAVATTIL 26.0 184713|polyprotein|AFP27208.1|Dengue_virus_4|11070 -888 FQDDFSPRF 0.0 None None 0 None -889 IGFNGNQIV 0.0 None None 0 None -890 KMFTCSKFV 0.0 None None 0 None -891 VAEVCPREV 0.0 None None 0 None -892 WAPLPGQML 0.0 None None 0 None -893 DAQQLATAI 0.0 None None 0 None -894 ILLNGDATV 0.000458453342916 ILLNGDAT VLLRLDGT 18.0 11214|possible_regulatory_protein|NP_302009.1|Mycobacterium_leprae|1769 -895 TIYDEDVLV 5.82753285036 TIYDEDVLV TMYYKDVTV 24.0 194440|envelope_glycoprotein_B|NP_044629.1|Herpes_simplex_virus_(type_1_/_strain_17)|10299 -896 WVKEDMGIV 0.0 None None 0 None -897 RKYGSTSSI 0.0 None None 0 None -898 MTDAQQLAT 0.0 None None 0 None -899 GFDQYRTLL 0.0 None None 0 None -900 NASGATAPL 0.0 None None 0 None -901 FFPEMGTKI 0.0 None None 0 None -902 NVHSSGKPI 0.305435862776 SSGKPI TSGSPI 22.0 22825|polyprotein|ABG75765.1|Dengue_virus_1|11053 -903 AALVGAEVV 0.0 None None 0 None -904 DHFSHASSI 0.0 None None 0 None -905 RAMGERLLL 0.0 None None 0 None -906 KIYDGKDKM 0.0 None None 0 None -907 WASGNERSL 22.1287414254 WASGNE WNSGHE 25.0 180440|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -908 LATVRSHHM 0.0 None None 0 None -909 LRDHGSFLL 0.0 None None 0 None -910 TALETSAPF 0.0 None None 0 None -911 HTFSMLSRV 0.0 None None 0 None -912 KAFHGSSGL 0.0 None None 0 None -913 LAKKPGCVF 1.69047619048 PGCVF PGCSF 26.0 44833|polyprotein|BAA03375.1|Hepatitis_C_virus_subtype_1a|31646 -914 IPNPQLGPV 4.26005083762e-05 GPV GPV 17.0 154857|tegument_protein|CAB06735.1|Human_alphaherpesvirus_2|10310 -915 QQHDGAFLI 0.0 None None 0 None -916 AAFFYLDYV 0.0 None None 0 None -917 FFPEMGTKI 0.0 None None 0 None -918 SQWDHGLSI 0.0803492524925 SQWDHG TAWDFG 22.0 180726|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -919 MSCRKIAHL 0.0 None None 0 None -920 MGFTVLTTV 0.0 None None 0 None -921 NLEVLDCRY 0.0 None None 0 None -922 LAQAVRAVL 0.0 None None 0 None -923 FMQTRYNKL 0.0 None None 0 None -924 LTHTGACPY 0.0 None None 0 None -925 KAFSDRFSL 0.0 None None 0 None -926 FLRDCSPRL 0.0 None None 0 None -927 DIFTTLKMY 0.0 None None 0 None -928 RAPPEAIAL 0.0 None None 0 None -929 STQDTPVTV 1.59510084399 STQDTPVTV ALADLPVTV 25.0 189566|glycosyl_transferase|WP_015631503.1|Mycobacterium_tuberculosis|1773 -930 QASSDWAAV 0.0 None None 0 None -931 FTRGIQTLF 0.0328747529981 RGIQTLF RGLTSLF 23.0 52652|||| -932 YRALNRVHV 0.0 None None 0 None -933 YEARLLKHM 0.0 None None 0 None -934 MELNSVNVM 0.0 None None 0 None -935 TAARLRHKV 0.0 None None 0 None -936 YAYFLDNVS 0.0 None None 0 None -937 TVLENLAVL 0.415657048035 TVLENLAVL NALDNLAVL 28.0 185447|polyprotein|AGK36298.1|Dengue_virus_2|11060 -938 HSFTHKQHL 0.0 None None 0 None -939 NMEELILAI 0.0 None None 0 None -940 IAPHRNEKL 0.0 None None 0 None -941 MMNDIVKEF 0.146493252704 MMNDIVK MINGVVK 23.0 185710|Nonstructural_protein_NS5|YP_001531176.2|Dengue_virus_3|11069 -942 FSVPLHIFL 0.133234367786 FSVPLHIFL FLVPFVVFL 25.0 139746|Dense_granule_protein_3|B6KEU8.2|Toxoplasma_gondii|5811 -943 TVMGRITTL 0.0 None None 0 None -944 FAKYWEENF 0.0 None None 0 None -945 VSDLLVLLL 0.0 None None 0 None -946 FLHVGDLVI 0.0 None None 0 None -947 EAFAHEARF 0.0 None None 0 None -948 SSLGKTQTV 0.0 None None 0 None -949 LVLIGISHV 1.0 LVLIGIS LILIGIT 26.0 59182|attachment_glycoprotein|ABQ58821.1|Human_metapneumovirus|162145 -950 FYFQVPFIY 0.0 None None 0 None -951 WSFAVAICI 0.0 None None 0 None -952 QHMIQQQAL 0.0 None None 0 None -953 FPEGYGTQV 0.38077711011 FPEGY LPEGY 25.0 31997|hypothetical_protein_FTT0484|YP_169522.1|Francisella_tularensis_subsp._tularensis_SCHU_S4|177416 -954 KPYGRNKPF 0.0 None None 0 None -955 HGFNATYHV 0.0990072203855 HGFNATY HSYGVTY 23.0 232152|rhoptry_kinase_family_protein|AFO54841.1|Toxoplasma_gondii_type_III|398031 -956 YIRTRNEFV 0.0 None None 0 None -957 YPEVFGPPL 0.511017522783 PEVFGP PEAAGP 23.0 19348|IMMUNOGENIC_PROTEIN_MPT64_(ANTIGEN_MPT64/MPB64)|CAA98382.1|Mycobacterium_tuberculosis_H37Rv|83332 -958 MVACGGTVY 0.0 None None 0 None -959 APSEHAQMV 0.0 None None 0 None -960 TRTFVEFIL 0.0 None None 0 None -961 LLSEVLLHY 0.0 None None 0 None -962 IQVGTGVTV 0.0 None None 0 None -963 LTLAFTVML 0.0 None None 0 None -964 HVGDLVIVV 0.0 None None 0 None -965 MTREELNAL 0.025913105963 MTREELNAL MTQKARNAL 23.0 150461|polyprotein|AGK36298.1|Dengue_virus_2|11060 -966 VAVQESARI 0.0 None None 0 None -967 VPSPLFSIV 0.0 None None 0 None -968 KAGGGSNEV 0.0469468239536 KAGGGSN PVGGGSS 23.0 189750|Diacylglycerol_acyltransferase/mycolyltransferase_Ag85B|SRC280000|Mycobacterium_tuberculosis|1773 -969 YMLIIVSIF 0.0 None None 0 None -970 VAPHAPVHF 0.0 None None 0 None -971 TPFHLASAV 0.0 None None 0 None -972 SARDCKDPY 0.000418357588503 SARDCKDPY SARLAGIPY 18.0 243835|glycosyl_transferase|WP_015628558.1|Mycobacterium_tuberculosis|1773 -973 FMATMPPAV 0.0 None None 0 None -974 TMVACGGTV 0.0 None None 0 None -975 NSDHVMFMV 0.0 None None 0 None -976 FMKNYFKDV 0.0 None None 0 None -977 LNVEDPVTV 0.0 None None 0 None -978 FIPINGCPI 1.34457687638 FIPINGCPI YIPLVGAPL 28.0 23365|polyprotein|BAB18806.1|Hepatitis_C_virus|11103 -979 YTSYFGYKM 1.56288713183e-05 YTSYFGYKM YTMDGEYRL 14.0 76121|polyprotein_precursor|NP_041724.2|West_Nile_virus|11082 -980 WSPHPLQIV 0.0 None None 0 None -981 YTTITPQII 0.0 None None 0 None -982 CSFYRTHTL 0.0256163049141 SFYRTHTL SFHNLHLL 22.0 79390|Protein_Tax-1|P0C213.1|Human_T-cell_lymphotropic_virus_type_1_(african_isolate)|39015 -983 NAAKNQVAM 0.0187943866999 NAAKNQVAM NASRCWVAM 21.0 21385|polyprotein|AAY82034.1|Hepatitis_C_virus_genotype_1|41856 -984 FETDGRRFL 0.0 None None 0 None -985 SVEINDIMY 0.0 None None 0 None -986 DPAPRPSLL 0.904502870813 DPAPRPSLL DPQERPRKL 24.0 110338|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 -987 QAVTEVEAV 0.138095238095 AVTEVEA AITEVEC 26.0 2102|VP1|BAF93325.1|Human_polyomavirus_1|1891762 -988 TAFQKGYGI 0.0 None None 0 None -989 ICFPVLVAL 0.27101796422 FPVLVA FPYLVA 24.0 9461|non_structural_protein_3|CAJ20172.1|Hepatitis_C_virus|11103 -990 NHVPVNHFW 0.0 None None 0 None -991 DMNDHAPEV 0.0025892563244 NDHAPEV NDFFPSV 20.0 16814|precore_protein|CAM58990.1|Hepatitis_B_virus|10407 -992 SPLPPPEQI 1.56735830397 SPLPP APLPP 26.0 179766|cell_surface_protein_(associated_with_virulence)|NP_302372.1|Mycobacterium_leprae_TN|272631 -993 LRLDGSVVI 0.915531304079 LRLDGSVV LRLDGTTL 27.0 11214|possible_regulatory_protein|NP_302009.1|Mycobacterium_leprae|1769 -994 HACSHLRQM 0.0 None None 0 None -995 FPSSQGSLY 3.38709858116 FPSSQGSL FPIVQGEL 24.0 48458|IMMUNOGENIC_PROTEIN_MPT64_(ANTIGEN_MPT64/MPB64)|CAA98382.1|Mycobacterium_tuberculosis_H37Rv|83332 -996 FNRDDCSVL 0.0 None None 0 None -997 TSFPQKVHL 0.0 None None 0 None -998 EAFAHEARF 0.0 None None 0 None -999 DAKSHELVM 0.0 None None 0 None -1000 TEYRALNRV 0.0 None None 0 None -1001 KTIWHTAEY 0.0 None None 0 None -1002 KAMLEEQLI 0.0 None None 0 None -1003 DTSDGLAVL 0.0 None None 0 None -1004 LEFGKPSTL 0.0 None None 0 None -1005 TLLEFFITL 0.0 None None 0 None -1006 FTKRQRKAM 0.0 None None 0 None -1007 FCLSTENSI 0.0 None None 0 None -1008 FQGFSVQLI 0.0 None None 0 None -1009 RVAPGYYTL 0.0 None None 0 None -1010 FYQDMMNDI 0.201754385965 YQDMMND YQQQLND 26.0 143680|Genome_polyprotein|P06441.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 -1011 CLYDSVLML 0.0 None None 0 None -1012 YTCVVSNKL 0.0 None None 0 None -1013 PAEEPTNEL 0.0 None None 0 None -1014 QVYSWLLCL 0.0 None None 0 None -1015 PANESFGHL 0.0 None None 0 None -1016 SPFAAAAAV 0.0 None None 0 None -1017 DVVHHLLSV 0.0 None None 0 None -1018 MFYPERTAL 0.0 None None 0 None -1019 VSDPACSSI 0.0 None None 0 None -1020 WAKVRTAEF 0.0 None None 0 None -1021 AALRHERAV 0.0 None None 0 None -1022 YVVATTKLM 0.22206474874 YVVATTKL YAVATTIL 26.0 184713|polyprotein|AFP27208.1|Dengue_virus_4|11070 -1023 RMLLDPNTV 0.0 None None 0 None -1024 YYDYMKPRL 0.0356673922245 YYDYM YTDYM 23.0 180681|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -1025 FPRHCVSWM 0.0 None None 0 None -1026 YLPPDPQPF 0.802965979807 LPPDPQP VPTDPNP 27.0 70491|envelope_glycoprotein|AAC28452.1|Human_immunodeficiency_virus_1|11676 -1027 HPATRPLHV 0.0 None None 0 None -1028 MVTGILLYM 0.0 None None 0 None -1029 KPISYMAII 0.222648225888 KPISYM RPVSYL 25.0 39571|polyprotein|BAD73987.1|Hepatitis_C_virus_subtype_1b|31647 -1030 DSSQRFEVI 0.0 None None 0 None -1031 STGYAISAY 0.0 None None 0 None -1032 KQLEFHIEI 0.0 None None 0 None -1033 FFCEVPVLL 0.0 None None 0 None -1034 FSMDETGQM 0.0 None None 0 None -1035 YPRQYSLKL 0.0 None None 0 None -1036 ETAYTKDGF 0.0 None None 0 None -1037 FSNHWTFWV 0.0 None None 0 None -1038 IGYANAKIY 0.0 None None 0 None -1039 DFFEDTEHY 0.0 None None 0 None -1040 DPMKVEAHV 0.0 None None 0 None -1041 GSGEHPMDY 0.0 None None 0 None -1042 SHSRGNDTL 0.0 None None 0 None -1043 FHTSSSLTV 0.0 None None 0 None -1044 VVMRICNLI 0.0 None None 0 None -1045 TALDSSLCL 0.0 None None 0 None -1046 DSDDMDLEV 0.0 None None 0 None -1047 HSYVGPAQL 0.0206560380033 HSYVGP HSVVNP 22.0 47854|Glycoprotein_I_precursor_(Glycoprotein_IV)_(GI)_(GPIV)|P09258.1|Human_alphaherpesvirus_3|10335 -1048 EMFQRYSAF 2.07487586145 EMFQRYSAF EFFTKNSAF 24.0 44214|UL123;_IE1|AAR31448.1|Human_betaherpesvirus_5|10359 -1049 MPVSIRLVV 0.0005030251957 PVSIRLVV PASRDLVV 18.0 93224|core_protein|AAL31859.1|Hepatitis_B_virus|10407 -1050 LVDGDLGKY 0.00752911114692 GDLGKY GDAGGY 22.0 3094|Antigen_85-B_precursor_(85B)_(Extracellular_alpha-antigen)_(Antigen_85_complex_B)_(Ag85B)_(Mycolyl_transferase_85B)_(Fibronectin-binding_protein_B)_(30_kDa_extracellular_protein)|P31952|Mycobacterium_tuberculosis|1773 -1051 RSLAFPVPL 0.0223084774724 LAFPVP LSFPDP 22.0 79300|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 -1052 RAFHDLRVA 0.0 None None 0 None -1053 IYDEDVLVV 0.0 None None 0 None -1054 LAMHSIWEM 0.00687735530344 HSIWE HTLWK 23.0 24943|DNA_polymerase|CAA10434.1|Hepatitis_B_virus|10407 -1055 YCRAWCQAL 0.0 None None 0 None -1056 QAVTNHSVY 0.0 None None 0 None -1057 HSQECGSFL 0.0 None None 0 None -1058 LQHTGTSVV 0.0 None None 0 None -1059 ETRAQLARH 0.0 None None 0 None -1060 RAALVGAEV 0.0 None None 0 None -1061 IPNAQNMTI 5.34979128985 PNAQNM PGAQNL 24.0 140615|amino_acid_decarboxylase|YP_177889.1|Mycobacterium_tuberculosis_H37Rv|83332 -1062 LATCCRARY 0.0 None None 0 None -1063 LMRHSMEKI 0.384767672963 RHSMEKI RHAMEEL 27.0 419128|polyprotein|ACF49259.1|Dengue_virus_type_1_Hawaii|10000440 -1064 VSARHPQHL 1.15203265572 RHPQHL RRPKHL 25.0 66195|Nucleoprotein|P41269.1|Puumala_hantavirus|11604 -1065 YKYDAGSAA 0.0 None None 0 None -1066 IIFLLGEIV 0.0406172919483 IIFLLGEIV VLFYLGQYI 24.0 156550|E3_ubiquitin-protein_ligase_Mdm2|Q00987.1|Homo_sapiens|9606 -1067 LARSQRTQV 0.0 None None 0 None -1068 NAAVETASL 0.0 None None 0 None -1069 LACSICHVY 0.0734222777342 LACSIC IVCPIC 23.0 64819|E7_protein|ABL96585.1|Human_papillomavirus_type_16|333760 -1070 DIYDVLICL 0.804762038021 YDVLIC YDIIIC 31.0 97111|polyprotein|ABR25251.1|Hepatitis_C_virus_(isolate_H77)|63746 -1071 LTMSWLTPL 0.0 None None 0 None -1072 FHNDLMPSY 0.122946002019 NDLMPS NDFFPS 23.0 16813|External_core_antigen|SRC279980|Hepatitis_B_virus|10407 -1073 VMVSPASAI 0.0 None None 0 None -1074 VFFSLLATV 25.6111406871 FSLLATV FTLVATV 25.0 98640|trans-sialidase,_putative|EAN80840.1|Trypanosoma_cruzi|5693 -1075 EASLATQIV 0.0 None None 0 None -1076 ETLVSTSTI 0.0 None None 0 None -1077 FPYQITNEH 0.0 None None 0 None -1078 RTFLPVHLL 0.0 None None 0 None -1079 LPQPGVRSL 0.548160467495 LPQPGVR LPRPGPR 28.0 139406|polyprotein|ACT37184.1|Hepatitis_C_virus|11103 -1080 VPNNCLGKV 0.268353983445 CLGKV CLGKA 24.0 180442|Chain_B,_Dengue_Virus_Rna_Dependent_Rna_Polymerase_With_Residues_From_The_Ns5_Linker_Region|4C11_B|Dengue_virus|12637 -1081 HPLEFCLLL 0.0 None None 0 None -1082 MAFVTLTDL 0.0 None None 0 None -1083 FSVQLIRKF 0.0 None None 0 None -1084 FPQMRAMSL 0.0 None None 0 None -1085 LRLNWGEPI 0.0 None None 0 None -1086 YEEDSGEYF 0.0 None None 0 None -1087 TAKGTAQLV 0.0 None None 0 None -1088 LHFHWNWII 1.5492033712 HWNWII RWEWVV 28.0 74407|polyprotein|AAU89634.1|Hepatitis_C_virus_subtype_2a|31649 -1089 DTDGQPLLL 0.0761637873905 TDGQPLL TSGSPII 22.0 22822|NS3_protein|NP_740321.1|Dengue_virus_4|11070 -1090 AHLLCTLLL 0.211842833049 AHLLCTLLL SHFLCTFTF 27.0 41622|Genome_polyprotein|P08617.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 -1091 KAPGFEKHL 0.0 None None 0 None -1092 SSYGGTIRY 0.545454545455 YGGTIR HGGTLR 26.0 120127|unnamed_protein_product|CAA33016.1|Rubella_virus|11041 -1093 YQDMMNDIV 0.240277994375 YQDMMNDIV YQQQLNDPV 27.0 143680|Genome_polyprotein|P06441.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 -1094 MQALNLQVV 0.0 None None 0 None -1095 MHYLKNSMI 0.0 None None 0 None -1096 NAKSRGWLI 0.0 None None 0 None -1097 DSNRVVCPI 0.0 None None 0 None -1098 ISNRSVLHL 0.0 None None 0 None -1099 QAELRGRVL 0.0 None None 0 None -1100 ASFDCAIEM 0.0 None None 0 None -1101 LQIGGFSSV 0.0 None None 0 None -1102 QTWRAVTTL 0.0 None None 0 None -1103 FSAQTFYVL 0.0 None None 0 None -1104 LGDDFSSAY 0.0 None None 0 None -1105 FQCAPGYAL 0.227490636034 PGYAL PGYAL 28.0 27295|polyprotein_precursor|NP_041724.2|West_Nile_virus|11082 -1106 DRETGMHLL 0.0 None None 0 None -1107 FALQRIVQK 0.0 None None 0 None -1108 DAVGNMLNL 0.0 None None 0 None -1109 FYRLHLGTY 0.0 None None 0 None -1110 FELKSPVKM 0.0 None None 0 None -1111 VLRPRWCPV 2.53947368421 RPRWCPV RPSWGPT 26.0 36352|Polyprotein|P90247|Hepatitis_C_virus|11103 -1112 HHSSFRRHL 0.0 None None 0 None -1113 FSYLTMSWL 0.0 None None 0 None -1114 WAESVEREI 0.0 None None 0 None -1115 KADVVHVTL 0.0 None None 0 None -1116 IMEENDSNI 0.0 None None 0 None -1117 LRLPHWPII 0.0 None None 0 None -1118 EAVQDPMKV 0.0 None None 0 None -1119 LIRKFAQSI 0.0 None None 0 None -1120 SHHQCGQSL 0.0 None None 0 None -1121 CTLGLGSLY 10.1824630352 CTLGLGSLY CTCGSSDLY 28.0 7116|NS3|ABN45875.1|Hepatitis_C_virus_(isolate_H77)|63746 -1122 ELAHDSYFY 0.0 None None 0 None -1123 HAANVTQAM 0.0 None None 0 None -1124 WTFWVGPFI 0.0 None None 0 None -1125 VVEHVLTTV 0.0 None None 0 None -1126 NDHDNWCII 0.0 None None 0 None -1127 IAPLLPVAV 1.72391567608 IAPLLPV FAPALPI 24.0 422989|polyprotein|ABY67644.1|Hepatitis_C_virus_genotype_1|41856 -1128 LSGPWGSPL 0.0 None None 0 None -1129 DPADPTSNL 0.0753429944852 DPADPT DPLKPT 23.0 27241|Spike_glycoprotein_precursor|P59594.1|SARS_coronavirus|227859 -1130 FPNSDHVMF 0.0 None None 0 None -1131 EVQDIQASL 0.00328204778107 VQDIQASL VQEDAASL 19.0 423007|Genome_polyprotein|P26664.3|Hepatitis_C_virus_genotype_1|41856 -1132 RPYKQGARL 0.0 None None 0 None -1133 DVAQHGARL 0.0 None None 0 None -1134 FLEKNKDAV 0.0 None None 0 None -1135 DSELAHDSY 0.0 None None 0 None -1136 MPLWMASII 0.0 None None 0 None -1137 YHFDAIRTF 5.93421006727 FDAIRTF YDAVRTW 27.0 154164|tegument_protein|CAB06732.1|Human_alphaherpesvirus_2|10310 -1138 VSTEHCLSV 0.0 None None 0 None -1139 YEAAKLLLV 0.0 None None 0 None -1140 LVQAGVDVV 0.0 None None 0 None -1141 SATASMLSV 0.0 None None 0 None -1142 DQFTKSISI 0.0 None None 0 None -1143 CALCALSNI 0.0 None None 0 None -1144 RAKPRWRVA 0.0 None None 0 None -1145 AAMDAGFLY 0.0 None None 0 None -1146 CAMTMNKYI 0.0 None None 0 None -1147 NLEPHGYVV 0.0 None None 0 None -1148 MLLSPGQNV 0.0 None None 0 None -1149 WQIHRVDIL 0.55932505738 WQIHR WLVHR 25.0 41407|Envelope_protein|NP_739583.2|Dengue_virus_2|11060 -1150 YAELGTTTK 0.0 None None 0 None -1151 YKLNRAFML 0.0 None None 0 None -1152 FAAAAAVAA 0.0 None None 0 None -1153 KMADPNQCV 1.15009746589 KMADPNQCV RVIDPRRCL 26.0 150556|polyprotein|AGW21594.1|Dengue_virus_1|11053 -1154 DPYVKAHLL 0.0 None None 0 None -1155 WPIINTPMV 0.0 None None 0 None -1156 KYYTDPSTY 1.74983759401 KYYTDPSTY KLYQNPTTY 31.0 32268|hemagglutinin|AAK38298.1|Influenza_A_virus_(A/Bar-headed_Goose/Qinghai/61/05(H5N1))|336238 -1157 RVSSYGGTI 0.0 None None 0 None -1158 EALDAGAIY 0.0 None None 0 None -1159 EFIMAITSM 0.0 None None 0 None -1160 FPWWLARVL 0.0461652934999 WLARVL WMIRIL 24.0 185817|envelope_protein|AGW23590.1|Dengue_virus_4|11070 -1161 WTLASMELV 0.0 None None 0 None -1162 IVRCLVTSV 0.0 None None 0 None -1163 MPAFHFNIL 0.00333528511973 PAFHFNI PALVFDI 19.0 24427|polyprotein|ACX44238.1|Hepatitis_C_virus_subtype_1a|31646 -1164 YRTHTLQTL 0.0 None None 0 None -1165 HASVVAAYL 0.0131278658919 HASVVAA HARFVAA 22.0 194|Hypothetical_protein_esxG_(PE_family_protein)|O53692.1|Mycobacterium_tuberculosis|1773 -1166 ISRPSSNAL 0.0281163741936 PSSNAL PQSNAV 22.0 183229|polyprotein|AGW21594.1|Dengue_virus_1|11053 -1167 RALLGCSCV 0.0 None None 0 None -1168 DAVWSRATF 0.0 None None 0 None -1169 DVVHHLLSV 0.0 None None 0 None -1170 MSFFRLLQM 0.0 None None 0 None -1171 KIIAFRKTL 0.0 None None 0 None -1172 TVSSNLSHV 0.0 None None 0 None -1173 MSVEINDIM 0.0 None None 0 None -1174 IAICRQIGI 0.0 None None 0 None -1175 ISKPSELPI 0.0 None None 0 None -1176 DPIEKELSV 0.0 None None 0 None -1177 DHSNDPTAI 0.12924811208 DHSNDPT DHQLDPA 24.0 190466|large_surface_antigen|CAL29876.1|Hepatitis_B_virus|10407 -1178 WRLAEAEML 0.0 None None 0 None -1179 RGLPWTVRV 0.0 None None 0 None -1180 KPMPTIQWI 0.407168297158 KPMPTIQW EPEPDVAW 25.0 96257|Genome_polyprotein|SRC279960|Hepatitis_C_virus|11103 -1181 RRFNLTSTF 0.0 None None 0 None -1182 RRSHTGTFL 0.338888888889 SHTGTF SHSGSF 26.0 61077|Non-capsid_protein_NS-1|P07298.1|Human_parvovirus_B19|10798 -1183 FALDENDNA 0.0 None None 0 None -1184 NPEELEQVV 0.0 None None 0 None -1185 QAMHSFGRF 0.0 None None 0 None -1186 TAIAICRQI 0.0 None None 0 None -1187 EVMEKVLPL 0.0 None None 0 None -1188 DVLPDTFTL 0.170795867243 VLPDTFT VLPCSFT 24.0 69679|polyprotein|BAD73987.1|Hepatitis_C_virus_subtype_1b|31647 -1189 RTGDRPHTF 0.0 None None 0 None -1190 QPAVFETTV 0.0911167657101 PAVFETTV PAIFQSSM 25.0 59975|pol_protein|ACJ76655.1|Human_immunodeficiency_virus_1|11676 -1191 VMDFRFGTI 0.0 None None 0 None -1192 NEDDSTFTI 0.0 None None 0 None -1193 TALGLCEEV 0.0 None None 0 None -1194 SMLSRVLII 0.0 None None 0 None -1195 DANLHKNEL 0.0 None None 0 None -1196 DHYAVESAL 0.0 None None 0 None -1197 EVKIGKMSY 0.000778543502349 EVKIGKMSY DVKKDLISY 17.0 25929|Nonstructural_protein_NS3|NP_739587.2|Dengue_virus_2_Thailand/16681/84|31634 -1198 LANGGKVPF 1.96547847148 LANGGKVPF LSNTGEIPF 32.0 108018|polyprotein|CAB41951.1|Hepatitis_C_virus|11103 -1199 IGAKHTLTI 0.0 None None 0 None -1200 EVVGGWPVV 0.0 None None 0 None -1201 VANERISMQ 0.0 None None 0 None -1202 LSLKQVISI 0.0 None None 0 None -1203 VGFPVGDSV 0.013726318129 FPVGDSV LPVADAV 22.0 75408|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 -1204 LPLDHHLAL 0.0 None None 0 None -1205 GALPLFRKY 0.0 None None 0 None -1206 VSYHPDLGI 4.0 PDLGI PDLGV 26.0 30946|HCV-1|AAA45676.1|Hepatitis_C_virus_genotype_1|41856 -1207 HLFGTSCPY 0.0 None None 0 None -1208 TATTILIMI 0.0 None None 0 None -1209 LSFMEAQSL 0.0 None None 0 None -1210 FLSLGIASL 0.0 None None 0 None -1211 RPPPTPRKV 0.0331024442478 PPPTPRKV PPATPTSL 25.0 120093|unnamed_protein_product|CAA33016.1|Rubella_virus|11041 -1212 SQLEMPETL 0.0 None None 0 None -1213 YCRLATVHM 0.0 None None 0 None -1214 VPHEDTLSL 0.0 None None 0 None -1215 KCYKQGAFI 0.0 None None 0 None -1216 LVLAFKNQV 0.0 None None 0 None -1217 TSDDFWYHA 0.0 None None 0 None -1218 RAEHFGIA* 0.0 None None 0 None -1219 QVLPWLKAF 1.81855060575 VLPWLKAF VLAWTRAF 29.0 69394|pol|AP_000202.1|Human_adenovirus_5|28285 -1220 FSIVRADGV 0.0 None None 0 None -1221 DVHDIARFL 0.0 None None 0 None -1222 SAQRPWPRV 0.0521684604953 RPWPRV RPGPRL 23.0 139406|polyprotein|ACT37184.1|Hepatitis_C_virus|11103 -1223 CAFRSQLEM 0.0 None None 0 None -1224 IIDCLVSMV 0.0 None None 0 None -1225 NPTEARVQV 0.0 None None 0 None -1226 MVLWHLPAV 7.05423432918 LWHLPAV LWHYPCT 29.0 75636|polyprotein|AAB67037.1|Hepatitis_C_virus_(isolate_H77)|63746 -1227 KVHDSVLAL 0.0 None None 0 None -1228 FVLLLTYIL 0.0 None None 0 None -1229 RSGEPMVSL 0.0 None None 0 None -1230 LPHCGHRTL 0.0 None None 0 None -1231 MTEHRGKCY 22.1797910912 MTEHRGKCY ISEYRHYCY 26.0 28484|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 -1232 RTLRISETL 0.0 None None 0 None -1233 VSAKRVSVL 0.0 None None 0 None -1234 SVYCIRKKY 0.0 None None 0 None -1235 QSMPCLMSF 0.0 None None 0 None -1236 HRYNLTQHF 1.09592266047 HRYNLTQHF KQYNVTQAF 29.0 51250|nucleocapsid_protein|ABI96968.1|SARS_coronavirus|227859 -1237 ISLMVIEKV 0.0 None None 0 None -1238 EIYSLIDNF 0.0 None None 0 None -1239 APSNHMNLV 0.0 None None 0 None -1240 FAISHEGHM 0.0 None None 0 None -1241 LTSVLTLMF 0.0 None None 0 None -1242 YAIPSKQLE 0.0 None None 0 None -1243 QALAQRNQL 0.0 None None 0 None -1244 FNCSFVLEM 0.0 None None 0 None -1245 SPRRRAASV 0.419755381749 SPRRRAASV DPRRRSRNL 24.0 9746|Genome_polyprotein|P29846.3|Hepatitis_C_virus_genotype_1|41856 -1246 AAGAPPAKI 0.0 None None 0 None -1247 DTIPWYLRL 0.0 None None 0 None -1248 FFGNNMPEF 0.0 None None 0 None -1249 NPICCDCVI 0.00546161891463 ICCDCVI ILCLCLV 21.0 49831|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 -1250 CPYSAWCVY 0.0339459746518 CPYSAWC VPYVAWL 27.0 5952|PPE_family_protein|YP_177918.1|Mycobacterium_tuberculosis_H37Rv|83332 -1251 QMCAVNSTV 0.0 None None 0 None -1252 LQMVRLCSV 0.0 None None 0 None -1253 LTRTFVEFI 0.0 None None 0 None -1254 LSATVMLTV 0.0 None None 0 None -1255 MVPREFKPI 1.21262679539 MVPREFKP IIPSMFEP 22.0 65550|Nonstructural_protein_NS3|NP_739587.2|Dengue_virus_2_Thailand/16681/84|31634 -1256 LVIQYTVKY 0.0 None None 0 None -1257 LRFPRITFF 0.0 None None 0 None -1258 TSMPVSKML 0.0 None None 0 None -1259 LMKCPCNTF 0.0 None None 0 None -1260 IHQAMFQLL 2.96146414954 HQAMFQLL HQAAMQML 27.0 101673|gag_protein|ABO73990.1|Human_immunodeficiency_virus_1|11676 -1261 VAGRRGQQL 0.0 None None 0 None -1262 HASSIIDEL 0.0 None None 0 None -1263 YARRRWPSQ 0.0 None None 0 None -1264 SSLDHHMLV 0.0 None None 0 None -1265 DLITNIEPF 0.0157884928167 ITNIEPF ISNQEPL 20.0 10650|Nucleoprotein|P05133.1|Hantaan_virus_76-118|11602 -1266 TTILIMIVF 0.0 None None 0 None -1267 LLKSNTSTL 0.0 None None 0 None -1268 LHDVYMFCI 0.0 None None 0 None -1269 STRSPNSTV 0.0 None None 0 None -1270 QELAGVKMV 0.0 None None 0 None -1271 YVPYRDNKM 0.0 None None 0 None -1272 DPADGIRLF 0.632859149645 DGIRL DGVRL 24.0 15914|Genome_polyprotein|P27958.3|Hepatitis_C_virus_subtype_1a|31646 -1273 WRCWFNGIM 0.0204388749569 WRCWFNGI WEAVFTGL 22.0 12108|polyprotein|AAP55688.1|Hepatitis_C_virus_subtype_2a|31649 -1274 CALGLHNFV 0.0 None None 0 None -1275 MEEEFSTIL 0.0 None None 0 None -1276 MLDDAPRLL 0.0 None None 0 None -1277 LGYDMFDCV 0.0 None None 0 None -1278 FVYKSGMTS 0.0 None None 0 None -1279 ESADKTAYL 0.0 None None 0 None -1280 NLQRWVTAV 0.0 None None 0 None -1281 WKLTDMSSI 0.0 None None 0 None -1282 HTLEEIYSL 0.0 None None 0 None -1283 DAFNSTERA 0.0 None None 0 None -1284 YLYPLVLMS 0.0 None None 0 None -1285 SPFKLDATY 0.0 None None 0 None -1286 FPRIYSNSL 0.0 None None 0 None -1287 YHISEEYGL 0.0 None None 0 None -1288 ASMHRFGHI 0.0 None None 0 None -1289 AIDSASPVY 0.0 None None 0 None -1290 CTFDSPARL 0.0 None None 0 None -1291 SFMEAQSLM 0.0 None None 0 None -1292 LPYELGWLF 0.0 None None 0 None -1293 NIWECNRNI 0.0 None None 0 None -1294 SPAEETVVL 0.0 None None 0 None -1295 RQIPVVGSM 0.0354353484081 IPVVGS IPLVGA 23.0 19493|polyprotein|BAA03375.1|Hepatitis_C_virus|11103 -1296 LVWALPKTY 0.753308187545 VWALPKT LWALPHA 27.0 108277|IE62|AAP32859.1|Human_alphaherpesvirus_3|10335 -1297 QARPKGKGL 0.0 None None 0 None -1298 LHLCYEFLM 0.0368205769669 LHLCYEFLM LLLCLIFLL 22.0 37466|surface_antigen|BAF44879.1|Hepatitis_B_virus|10407 -1299 HQEDGGKAL 0.0 None None 0 None -1300 RPSSNALLI 0.286396630832 PSSNALL PQSNAVI 24.0 183229|polyprotein|AGW21594.1|Dengue_virus_1|11053 -1301 QKYDGKCPL 0.0 None None 0 None -1302 YAQFRGRHR 0.0 None None 0 None -1303 VAVYSTCVL 0.0490612481147 AVYSTC ATYSRC 23.0 149060|E2_protein|NP_751921.1|Hepatitis_C_virus_(isolate_H77)|63746 -1304 FLPPARSGI 0.0 None None 0 None -1305 QHGSLSETW 0.0 None None 0 None -1306 LGLEKTTSI 0.0 None None 0 None -1307 QTVMFMATM 0.0 None None 0 None -1308 LLKPGDRVV 0.26492774281 LKPGDRVV LQPVERVL 21.0 155928|unnamed_protein_product|CAA30115.1|Trypanosoma_cruzi|5693 -1309 MPGSPRDPV 0.0 None None 0 None -1310 LTYCTTGGI 0.0 None None 0 None -1311 FQSLLSQHM 0.0 None None 0 None -1312 KEFHFNQYL 0.0 None None 0 None -1313 SSTEWVAPL 0.0 None None 0 None -1314 RSSPATHSL 8.88487276219 PATHSL PKTHTL 24.0 184702|non-structural_protein_1|AGM49312.1|Dengue_virus|12637 -1315 ELKEWAESV 0.0 None None 0 None -1316 GVVEATLSY 0.0 None None 0 None -1317 EIAELNRTI 0.0 None None 0 None -1318 GAASMIHYI 0.0 None None 0 None -1319 LVNTCIRFV 0.0 None None 0 None -1320 QAVDTDEAL 0.0 None None 0 None -1321 AATSRGQVL 0.0 None None 0 None -1322 NPLRPRESL 0.00204486978355 PLRPRES PLCPEEK 20.0 110394|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 -1323 VSSNLSHVI 0.0 None None 0 None -1324 FTFGETEVC 0.0 None None 0 None -1325 FQDDFSPRF 0.0 None None 0 None -1326 YTVKYEQKM 0.0 None None 0 None -1327 EHSDTFINL 0.0 None None 0 None -1328 YTPKLEIKV 0.0 None None 0 None -1329 ETQETMDEL 0.0 None None 0 None -1330 DLVHHTTTL 0.00705689720887 DLVHHTT DLMCHAT 21.0 180507|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -1331 LMFSGLWHL 0.0 None None 0 None -1332 VPHQIPKAV 0.0 None None 0 None -1333 MAPAAGTWV 0.0 None None 0 None -1334 FLITNALHF 0.0 None None 0 None -1335 SPKPPPQCV 0.0 None None 0 None -1336 SIADGRAWF 6.93354724607 IADGRAW VEDGRFW 28.0 186219|polyprotein|AGK36298.1|Dengue_virus_2|11060 -1337 MGYRVESEV 3.86373521516 MGYRVES MGYWIES 27.0 180689|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -1338 APAPDLVVV 0.0 None None 0 None -1339 LSANARCLI 0.0 None None 0 None -1340 DTSDGLAVL 0.0 None None 0 None -1341 EARRQGAVF 0.0 None None 0 None -1342 KVPEGDSIV 0.0 None None 0 None -1343 WRPGCLWAL 4.81834181964 GCLWAL GCVWTV 28.0 6431|Genome_polyprotein|SRC279960|Hepatitis_C_virus|11103 -1344 HGLEKVPVI 3.17241105208 HGLEKVPV HGVGEIPM 25.0 131096|G1_and_G2_surface_glycoprotein_precursor|AAG22532.1|Andes_hantavirus|46607 -1345 ITIVVISLI 0.0 None None 0 None -1346 FAMELDDLH 0.0 None None 0 None -1347 LTDKVSTPA 0.0 None None 0 None -1348 LMVSAGVFI 0.0 None None 0 None -1349 LQLEVEEAV 0.0 None None 0 None -1350 SMIHYIVLI 0.0144228035657 SMIHYIVL TTIHDIIL 20.0 110373|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 -1351 FRMFVHVYI 0.0 None None 0 None -1352 HIFLFAVLL 1.02171257151 HIFLFAVLL HLFYSAVLL 29.0 98100|trans-sialidase,_putative|EAN81657.1|Trypanosoma_cruzi|5693 -1353 QQHDGAFLI 0.0 None None 0 None -1354 VELELWGVV 0.0 None None 0 None -1355 WSLQTWRAV 0.0 None None 0 None -1356 LVQEFTRGI 0.0 None None 0 None -1357 VAAFFLSLF 0.0 None None 0 None -1358 EAEEESLAL 0.0 None None 0 None -1359 HVIVRTSRV 0.0 None None 0 None -1360 ELLEPQKTY 0.208598262901 LEPQKTY LHPNNTY 23.0 141306|tegument_host_shutoff_protein|NP_044643.1|Human_alphaherpesvirus_1|10298 -1361 AMSDGRVPV 0.0 None None 0 None -1362 RPPSPKDTV 0.0269770919451 RPPSPKDTV RPSGMFDSV 17.0 177956|polyprotein|ACZ60102.1|Hepatitis_C_virus_subtype_3a|356426 -1363 VPMCHLRLL 0.0 None None 0 None -1364 LSARSVPSI 0.0 None None 0 None -1365 QVHQRMNSL 0.0 None None 0 None -1366 EALVQMQYL 0.0 None None 0 None -1367 CAQSPWCLV 1.18395973855 CAQSPWCLV CVQGDWCPI 33.0 18941|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 -1368 LSCEAHNSM 0.0 None None 0 None -1369 QARGVKKQI 0.0 None None 0 None -1370 SHHSQCSSL 0.0 None None 0 None -1371 YGGFFVISV 0.0626169731798 GGFFVI AGFFIL 23.0 69714|Large_envelope_protein|SRC279965|Hepatitis_B_virus|10407 -1372 YVYPLPVAN 0.416751180485 YVYPLPV YVYALPL 29.0 58463|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 -1373 HSYWLLKLL 0.0 None None 0 None -1374 YRTHTLQTL 0.0 None None 0 None -1375 FTTLKMYSV 0.0 None None 0 None -1376 EHMNHTCNL 0.0 None None 0 None -1377 VAIYLYPLV 0.0 None None 0 None -1378 YEGYKYEHI 1.40213483096 YKYEHI YKLKHI 24.0 39162|gag_protein|AAV53308.1|Human_immunodeficiency_virus_1|11676 -1379 DRYVAVRHL 0.274070953293 DRYVAVR SRYWAIR 21.0 60867|nucleoprotein|CAZ65591.1|Influenza_A_virus|11320 -1380 DLIDYARYM 0.159835763185 LIDYARYM LLDFVRFM 28.0 37153|Nuclear_antigen_EBNA-3C|Q69140.1|Human_gammaherpesvirus_4|10376 -1381 NLLLWVLAI 0.0 None None 0 None -1382 HLHDHYGPY 0.0 None None 0 None -1383 NTDSTAALL 0.0 None None 0 None -1384 YVKERQTVT 0.0 None None 0 None -1385 TMECWGQKY 0.0 None None 0 None -1386 KSDDSDFLA 0.0 None None 0 None -1387 MAFVRLLHS 0.0 None None 0 None -1388 LVDNLTYTL 0.122842705901 LVDNLT LLDNIT 24.0 240808|polyprotein|AAB53095.1|Tick-borne_encephalitis_virus|11084 -1389 KHSATASML 0.0 None None 0 None -1390 FEAHEVLKL 0.0 None None 0 None -1391 LVLVGCFTI 0.0083914153634 VLVGCF VLIRCY 21.0 145860|Protein_E6|P04019.1|Human_papillomavirus_type_11|10580 -1392 TTSGIGSSM 0.0 None None 0 None -1393 KSRAPPEAI 0.0 None None 0 None -1394 AALVPTQAM 0.0 None None 0 None -1395 RQRNGVAKL 0.0 None None 0 None -1396 SSDRMTSVA 0.0 None None 0 None -1397 RPSPNRPKL 0.00679026427764 RPSPNRPKL RPDYNPPLL 22.0 103563|polyprotein|BAB18806.1|Hepatitis_C_virus|11103 -1398 SSVEVLVNY 0.0 None None 0 None -1399 YCIYASLRI 0.0 None None 0 None -1400 RLLPPVSP* 1.80198471654 RLLPPVSP RLLSPLSP 31.0 54662|pX-rex-orf_I_{alternatively_spliced}|AAB23359.1|Human_T-lymphotropic_virus_1|11908 -1401 FSLGKHVCL 0.0 None None 0 None -1402 CTDKVGTEA 0.0 None None 0 None -1403 FRRSISVRI 0.0 None None 0 None -1404 LYLHTLLTI 0.0 None None 0 None -1405 LEVPAPEAI 0.0 None None 0 None -1406 LLSEMAVAV 0.0 None None 0 None -1407 VPLVRWLKV 3.69036212386 VPLVRWL VPFVQWF 27.0 37919|envelope_protein|BAF48755.1|Hepatitis_B_virus|10407 -1408 DTLPMLGNI 0.0 None None 0 None -1409 FAFGAVFSE 0.0 None None 0 None -1410 RNYQAWNFL 1.30903243738 QAWNF QQWNF 27.0 42797|6_kDa_early_secretory_antigenic_target|P0A564.2|Mycobacterium_tuberculosis|1773 -1411 DATKNQVAM 0.0 None None 0 None -1412 QTKHNAKVY 0.0 None None 0 None -1413 IEWECTMML 0.0 None None 0 None -1414 LELEFLCPL 0.0 None None 0 None -1415 QLVNRPQSI 0.0 None None 0 None -1416 TTKKSGGHY 0.247590955559 TTKKSGGHY TTRGRDAHY 23.0 66798|glycoprotein_gp35/37|AAC59622.1|Human_gammaherpesvirus_8|37296 -1417 IVEHPAGHL 0.0 None None 0 None -1418 HRYLWKILI 0.0 None None 0 None -1419 SIFEVIWSV 0.0 None None 0 None -1420 QHDDGYLEV 0.0 None None 0 None -1421 GVAPGLQVV 0.0 None None 0 None -1422 YLAMGEEIY 0.0 None None 0 None -1423 SVVCHQLGF 0.0952288061993 VCHQLG VCARLG 22.0 73177|protein_F_[Hepatitis_C_virus_subtype_1b]|ACA50643.1|Hepatitis_C_virus_(isolate_Japanese)|11116 -1424 RTKRRVFII 0.0 None None 0 None -1425 QMAERALYY 0.0 None None 0 None -1426 LISPPQEKV 0.0 None None 0 None -1427 HLIEERDTL 0.0 None None 0 None -1428 ILKQPSQTL 0.0 None None 0 None -1429 LQVVHLNAV 0.0 None None 0 None -1430 VHDIARFLY 0.0 None None 0 None -1431 RSLPIAIEM 0.0 None None 0 None -1432 NVDEVNQIM 0.0 None None 0 None -1433 GAGVEISTV 0.0 None None 0 None -1434 VPREFKPIL 0.0992866179251 VPREFKPIL VPRPDDPVL 25.0 141462|tegument_protein_UL21|NP_044622.1|Human_alphaherpesvirus_1|10298 -1435 GAQPPMPPY 3.42634928134 PPMPPY PPQPEY 27.0 48896|Genome_polyprotein|P27958.3|Hepatitis_C_virus_subtype_1a|31646 -1436 RADLLIVVF 0.0 None None 0 None -1437 WKEDMAVHV 0.0 None None 0 None -1438 FIEPHARFY 0.0 None None 0 None -1439 DEFSGVPRV 0.0268132145174 SGVPR SGLPR 23.0 58122|pol_protein|BAA32832.1|Hepatitis_B_virus|10407 -1440 RVQPAVRAL 0.0 None None 0 None -1441 ATTIVTTVY 2.66327463302e-07 VY VY 11.0 142232|POSSIBLE_CONSERVED_TRANSMEMBRANE_PROTEIN|CAB00937.1|Mycobacterium_tuberculosis|1773 -1442 FFHNPKPLF 1.02265506822 FHNPKPLF LHGPTPLL 25.0 6591|polyprotein|AAB67037.1|Hepatitis_C_virus_(isolate_H77)|63746 -1443 VTASSGIMI 0.0 None None 0 None -1444 HKAHFQYLL 0.0 None None 0 None -1445 IGVEAGRTL 0.0 None None 0 None -1446 ETMDNGFGH 0.0 None None 0 None -1447 DFWYHAVVL 1.96158586196 DFWYHAVVL DMWEHAFYL 29.0 9415|Superoxide_dismutase|P17670.1|Mycobacterium_tuberculosis|1773 -1448 FHLASAVAL 0.0 None None 0 None -1449 LAMYLSKNY 0.0 None None 0 None -1450 HLLELPQIL 0.0 None None 0 None -1451 VSVHRAPSI 0.155290102389 VHRAPSI LHHAPSL 26.0 21000|glutamine_synthetase_GLNA1_(glutamine_synthase)_(GS-I)|NP_216736.1|Mycobacterium_tuberculosis|1773 -1452 DPAAASHPI 0.0 None None 0 None -1453 SVYLRNNKL 0.0 None None 0 None -1454 INREHIPTF 0.2996637034 EHIPTF QHLPTL 24.0 64821|Protein_Tax-1|P03409.2|Human_T-lymphotropic_virus_1|11908 -1455 AQYDDPRNL 0.0 None None 0 None -1456 RPVNAYARV 0.0 None None 0 None -1457 LARLGALLL 0.0 None None 0 None -1458 SHTGTFLLV 27.0016949153 SHTGTFLL SHSGSFQI 26.0 61077|Non-capsid_protein_NS-1|P07298.1|Human_parvovirus_B19|10798 -1459 HTVAWSNGH 26.1809399136 AWSNGH SWNSGH 28.0 180440|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -1460 TIPDSISKF 8.68426386978 IPDSISKF ITDTIDKF 25.0 12588|Glycoprotein_B_precursor_(Glycoprotein_II)|P09257.1|Human_alphaherpesvirus_3|10335 -1461 AVFEEQIKV 0.0 None None 0 None -1462 FCPLCHNPV 0.669397134211 FCPLCHN LCPHCIN 25.0 20787|Non-capsid_protein_NS-1|P07298.1|Human_parvovirus_B19|10798 -1463 RVLKCNVHL 1.08324885308 VLKCN ILKCN 27.0 47946|envelope_glycoprotein|AAC28452.1|Human_immunodeficiency_virus_1|11676 -1464 LLLPCPLLL 0.0 None None 0 None -1465 QTAEQYVFV 0.0 None None 0 None -1466 FLNSMDQQI 0.0 None None 0 None -1467 GPARGIAII 0.0 None None 0 None -1468 LASLSLKQV 0.0 None None 0 None -1469 TSVPHEDTL 0.0 None None 0 None -1470 EAEVETEAI 0.0 None None 0 None -1471 SSLSNVSQV 0.0 None None 0 None -1472 TVQNAMQIV 0.0 None None 0 None -1473 WHFIKRHIA 0.0 None None 0 None -1474 MTVAGMVLL 0.0 None None 0 None -1475 YMAGSDTTY 0.0 None None 0 None -1476 FRENFESIY 0.0 None None 0 None -1477 LATVILGAV 0.0 None None 0 None -1478 LSSGSFATM 0.0 None None 0 None -1479 DTNNLGIRI 0.0229294398523 NLGIRI DLGVRV 22.0 30946|HCV-1|AAA45676.1|Hepatitis_C_virus_genotype_1|41856 -1480 CSGCVAQVY 0.0 None None 0 None -1481 DHIRNFTTM 0.0 None None 0 None -1482 KPFISRTMM 0.0618191295436 PFISRTMM PFDKSTVM 20.0 116123|nucleocapsid_protein|ABP49342.1|Influenza_A_virus_(A/California/10/1978(H1N1))|425557 -1483 PADPAQLAV 0.0 None None 0 None -1484 YEPDTMEQY 0.0 None None 0 None -1485 EPLNDTIAI 0.0 None None 0 None -1486 QAPLAPTHM 9.89644311759 APLAPTH APVFPSH 26.0 3889|||| -1487 IHLDISSFV 0.0 None None 0 None -1488 PLMDQVSVI 0.0 None None 0 None -1489 HSLHPFPHF 0.0 None None 0 None -1490 ITFKELGAL 0.0 None None 0 None -1491 AAAREATEV 0.0 None None 0 None -1492 RTYHGRLAY 0.0 None None 0 None -1493 DADIYGKPM 0.0 None None 0 None -1494 KGYRIVVAL 0.0 None None 0 None -1495 FNMRDLSDI 0.0 None None 0 None -1496 FRKTLLNPV 0.0 None None 0 None -1497 YLAMGEEIY 0.0 None None 0 None -1498 KPFSHSCNL 0.0 None None 0 None -1499 DQATFINMY 0.0 None None 0 None -1500 ARFRIRKTI 0.0 None None 0 None -1501 RAFSFSLPC 0.081027158281 RAFSFS QAFTFS 22.0 50253|DNA_polymerase|CAA10434.1|Hepatitis_B_virus|10407 -1502 SHMCNSLLV 0.031545921554 MCNSLLV LCGMLLI 21.0 31771|Nucleoprotein|P03418.1|Human_respiratory_syncytial_virus_A2|11259 -1503 EAEEWVVSY 0.0 None None 0 None -1504 KASERFRTQ 0.0 None None 0 None -1505 QIMPHAIIF 0.226023306979 IMPHAI LLPHVI 23.0 79337|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 -1506 LLKHMPKII 0.110041217959 LKHMPKI VRHFPRI 24.0 187106|Vpr_protein|BAA93983.1|Human_immunodeficiency_virus_1|11676 -1507 ILSCNADII 0.0 None None 0 None -1508 AAQCCHKKV 0.0 None None 0 None -1509 TELDSVGPV 0.0 None None 0 None -1510 STFCGTLEY 0.0 None None 0 None -1511 GLIPPDATI 0.0516541933654 GLIPPDATI NLVPMVATV 21.0 55029|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 -1512 SAQRNAAFF 0.0 None None 0 None -1513 MDHPSGIAI 0.0 None None 0 None -1514 FTVLENLAV 0.178250809092 TVLENLAV NALDNLAV 24.0 185447|polyprotein|AGK36298.1|Dengue_virus_2|11060 -1515 KPPPQCVTL 0.502924257487 KPPPQCVTL KLTPLCVTL 28.0 32201|Gp160|Q0ED31|Human_immunodeficiency_virus_1|11676 -1516 LAIYTLLSL 0.0 None None 0 None -1517 RTVKFLMAI 0.0 None None 0 None -1518 MCLEASIPL 0.200766890345 CLEASIPL CMKTWIPL 24.0 155096|RL2|CAB06760.1|Human_alphaherpesvirus_2|10310 -1519 SAPQDSKAV 0.0 None None 0 None -1520 FIIHHRTHT 0.0 None None 0 None -1521 RKEENMESV 0.0 None None 0 None -1522 FPQVSELVL 0.0 None None 0 None -1523 YQVVAQHIY 0.0 None None 0 None -1524 DSAQRNAAF 0.0 None None 0 None -1525 KHFNNSSHF 0.0 None None 0 None -1526 EANVHGIYF 0.0 None None 0 None -1527 LSRVKAQVV 0.0 None None 0 None -1528 LENSNRSMV 0.0 None None 0 None -1529 ESKSGSPEY 10.7269076305 KSGSPEY RSGAPTY 26.0 102368|E2_protein|NP_751921.1|Hepatitis_C_virus_subtype_1a|31646 -1530 YTVKYEQKM 0.0 None None 0 None -1531 LTYGHDRQL 0.0 None None 0 None -1532 LHFHFTACY 0.0 None None 0 None -1533 DCNKTAVTI 0.0 None None 0 None -1534 QPLHSLSVL 0.547748367869 QPLHSLSV QPFHSYGV 27.0 232152|rhoptry_kinase_family_protein|AFO54841.1|Toxoplasma_gondii_type_III|398031 -1535 AACGIIQQV 0.0 None None 0 None -1536 WDQRCLHTI 0.0 None None 0 None -1537 QLQAFWKHV 0.0 None None 0 None -1538 SPHPRRRRL 0.0655592952749 PHPRRRR PEPDRQR 23.0 183813|polyprotein|AGW21594.1|Dengue_virus_1|11053 -1539 FLDKASDLL 0.0 None None 0 None -1540 SAWLFVTGI 0.0 None None 0 None -1541 FMFEMPFMQ 0.0 None None 0 None -1542 VSLQAAEEI 0.0 None None 0 None -1543 RANGNPNPT 0.0139532163774 RANGNPNP RANELVNP 21.0 154980|tegument_protein|CAB06735.1|Human_alphaherpesvirus_2|10310 -1544 ELPAFIEMM 0.0 None None 0 None -1545 CVAKCGGTV 0.0 None None 0 None -1546 LEYLAPEVL 0.0 None None 0 None -1547 TMANNPDVM 0.0 None None 0 None -1548 EAVSSASKL 0.0 None None 0 None -1549 FSLYRGWAL 0.0338147117713 FSLYRGWA FSMVGNWA 24.0 149052|E1_protein|NP_751920.1|Hepatitis_C_virus_(isolate_H77)|63746 -1550 VVIGAPYVV 0.113860246051 GAPYVV GNPYAV 22.0 110227|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 -1551 LHFHWNWII 1.13172182694 HWNWII RWEWVV 28.0 74407|polyprotein|AAU89634.1|Hepatitis_C_virus_subtype_2a|31649 -1552 MSACWSFAV 1.40795140079 SACWSF AACWGF 31.0 79506|E1_protein|BAA19893.1|Rubella_virus|11041 -1553 YIAQNDDEL 0.0 None None 0 None -1554 ETINWTLLE 0.0 None None 0 None -1555 DQYAICMKY 0.126785938088 DQYAICMK NPYAVCDK 25.0 110467|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 -1556 HAKRKTATA 0.0 None None 0 None -1557 LAAASSTAF 0.0 None None 0 None -1558 KAYGRDNTP 1.7699107108 KAYGRD KAYGTD 27.0 108230|polyprotein|AAF65953.1|Hepatitis_C_virus|11103 -1559 KHLQLYQLF 0.0 None None 0 None -1560 WAVMNHFSM 0.0 None None 0 None -1561 IERPGGSLL 0.0 None None 0 None -1562 YCFGCLSHH 0.00860509404551 YCFGCLS FCIPCMK 21.0 155096|RL2|CAB06760.1|Human_alphaherpesvirus_2|10310 -1563 QGYGGFFVI 0.00840115467717 GGFFVI AGFFIL 23.0 69714|Large_envelope_protein|SRC279965|Hepatitis_B_virus|10407 -1564 NENDLITNI 0.0 None None 0 None -1565 LPVPIIQQL 0.0 None None 0 None -1566 RLMHQLLVI 0.00726488946482 RLMHQLLVI QLFHLCLII 21.0 93431|pre-C/C_protein|ABY54138.1|Hepatitis_B_virus|10407 -1567 FHKEVFGMF 0.0 None None 0 None -1568 CTVEDGGHV 0.0 None None 0 None -1569 EVAQHLATT 0.0 None None 0 None -1570 VEHPAGHLV 3.94454377782 PAGHLV PAGHAV 28.0 23601|Genome_polyprotein|SRC279960|Hepatitis_C_virus_(isolate_H77)|63746 -1571 WKGSTECKL 0.0 None None 0 None -1572 LSDPHLTAV 0.0 None None 0 None -1573 ILTELLMVV 0.0 None None 0 None -1574 MVHLVPALV 0.00953033463174 MVHLVPAL LLHHAPSL 20.0 21000|glutamine_synthetase_GLNA1_(glutamine_synthase)_(GS-I)|NP_216736.1|Mycobacterium_tuberculosis|1773 -1575 TILENPYIM 0.0 None None 0 None -1576 DHSDSDYDF 0.0 None None 0 None -1577 NHLNIAWEL 0.76435968383 NHLNIAWEL THLYILWAV 24.0 1000|glycoprotein_gp35/37|AAC59622.1|Human_gammaherpesvirus_8|37296 -1578 FPEDVAVYT 0.0 None None 0 None -1579 YMTSSGRRF 0.0 None None 0 None -1580 SSVPLRSSV 0.0 None None 0 None -1581 LAAPPPLTE 1.95708895828 PPPLT PPPAT 25.0 120093|unnamed_protein_product|CAA33016.1|Rubella_virus|11041 -1582 VVASQPAHV 0.0 None None 0 None -1583 SMLDPHGHL 0.0 None None 0 None -1584 LVVADIHSM 0.0 None None 0 None -1585 LLYMAFVRL 0.0 None None 0 None -1586 VVTVMVTTV 0.0 None None 0 None -1587 KLIDVNHYV 0.0 None None 0 None -1588 FTQYLGLSM 0.00484909033908 FTQYLGLS FTDALGID 21.0 141277|transactivating_tegument_protein_VP16|NP_044650.1|Human_alphaherpesvirus_1|10298 -1589 FRGKHDCAL 0.0 None None 0 None -1590 EVFRHKLAM 0.0 None None 0 None -1591 RSIRLSQEI 0.0 None None 0 None -1592 HTIQKAKHM 0.0 None None 0 None -1593 PSGRPALAY 0.0 None None 0 None -1594 WQDHIRLEV 0.0 None None 0 None -1595 VLLDLRPSI 2.274058298 LLDLRP MLDLQP 24.0 110335|E7|AAD33253.1|Human_papillomavirus_type_16|333760 -1596 AVYSTCVLV 0.0927784841397 AVYSTC ATYSRC 23.0 149060|E2_protein|NP_751921.1|Hepatitis_C_virus_(isolate_H77)|63746 -1597 LALSLPACF 0.0 None None 0 None -1598 NQCPCSSDI 0.0 None None 0 None -1599 SIDPKTGVV 0.0 None None 0 None -1600 AAASHPILL 0.0 None None 0 None -1601 RLLKHMPKI 0.101153035124 LKHMPKI VRHFPRI 24.0 187106|Vpr_protein|BAA93983.1|Human_immunodeficiency_virus_1|11676 -1602 LSLTGLQVL 0.021486229198 LSLTGLQ LSLIGLK 22.0 187086|polyprotein|ABG67747.1|West_Nile_virus|11082 -1603 MSQEEKVAY 0.0 None None 0 None -1604 MIENLEHHI 0.0 None None 0 None -1605 IIATGLVTL 0.0 None None 0 None -1606 SADCGCCPM 0.0 None None 0 None -1607 CAELLSHTV 0.0 None None 0 None -1608 HISEEYGLL 0.0 None None 0 None -1609 YSFCPLCHN 0.206854960234 SFCPLCHN GLCPHCIN 25.0 20787|Non-capsid_protein_NS-1|P07298.1|Human_parvovirus_B19|10798 -1610 LPCRSLTRV 0.0 None None 0 None -1611 KVLQHGRLY 0.0 None None 0 None -1612 FLCDEEPLL 0.0 None None 0 None -1613 IPCLDDVTV 0.0 None None 0 None -1614 LASEAVSSA 0.0 None None 0 None -1615 TPTPGFSSM 0.0 None None 0 None -1616 FYLVAYAAM 0.17018469657 YLVAYA YLAAYA 26.0 74545|TcP2beta|CAA52943.1|Trypanosoma_cruzi|5693 -1617 YLKSPECFL 0.0 None None 0 None -1618 KVNTATTTM 0.0 None None 0 None -1619 LPVSTKCTV 0.0 None None 0 None -1620 SVRYAGPLY 0.297176741199 VRYAGPLY MTYAAPLF 25.0 42897|RNA_polymerase_beta-subunit|AAA21416.1|Mycobacterium_tuberculosis|1773 -1621 HTIQKAKHM 0.0 None None 0 None -1622 TFRDVAVEF 0.0366333305265 TFRDVA TWRDMA 22.0 186175|polyprotein|AFY10053.1|Dengue_virus_3|11069 -1623 DEKDLWEYI 0.0133766675551 DEKDLWEYI DQKSLENYI 25.0 28594|IMMUNOGENIC_PROTEIN_MPT64_(ANTIGEN_MPT64/MPB64)|CAA98382.1|Mycobacterium_tuberculosis_H37Rv|83332 -1624 DPADPTRDL 4.01184798055 DPADPTRDL DPAKPARLL 28.0 53405|||| -1625 EAEEWVVSY 0.0 None None 0 None -1626 CAFTVLENL 0.0 None None 0 None -1627 SWMEGQVTI 0.0 None None 0 None -1628 MTAVGYGDM 0.0 None None 0 None -1629 VSEDAKQRI 0.0 None None 0 None -1630 DVDEDGYIM 0.0 None None 0 None -1631 IVQCRVLNI 0.0 None None 0 None -1632 IASLLENIL 0.0 None None 0 None -1633 SRNWLKSIL 0.0 None None 0 None -1634 KVKPTLAMY 0.0070925003201 PTLAMY PALQMY 22.0 146260|polyprotein|ADF97231.1|Hepatitis_C_virus_subtype_3a|356426 -1635 YTMGIIFVL 0.0 None None 0 None -1636 ELKSPVKMI 0.0 None None 0 None -1637 LSLGAPSPL 0.0555525573282 LSLGAP LSLGDP 23.0 54342|UL123;_IE1|AAR31448.1|Human_betaherpesvirus_5|10359 -1638 QSIRAATEV 0.0 None None 0 None -1639 YMAATLLEF 0.0 None None 0 None -1640 CSDGSDEDA 0.319310454046 CSDGSDEDA CDDCHAQDA 21.0 6094|Genome_polyprotein|Q81495.3|Hepatitis_C_virus_(isolate_HCV-K3a/650)|356416 -1641 SYLEDVRLI 0.0 None None 0 None -1642 QVYVGDSDI 0.0 None None 0 None -1643 VIDQCLKKI 0.0 None None 0 None -1644 YPDWIRDNM 1.53360425083 YPDWI YQDWL 25.0 23288|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 -1645 RATSFGKCF 0.205486484796 SFGKCF TFGWCF 25.0 56620|Nef_protein|Q9YYU8|Human_immunodeficiency_virus_1|11676 -1646 KAGSLGIIL 0.415852219105 GSLGII GTLGIV 24.0 37573|E7_protein|ABL96585.1|Human_papillomavirus_type_16|333760 -1647 VAQQSRLVF 0.0 None None 0 None -1648 DCQSHRLTV 0.0 None None 0 None -1649 MPNVLWDLV 0.0 None None 0 None -1650 MSWLTPLMI 0.00107210420498 SWLTPLMI AWGRRLMI 18.0 181733|Antigen_85-B|P0C5B9.1|Mycobacterium_tuberculosis|1773 -1651 DANNVTCVW 0.0 None None 0 None -1652 KLLQCMSRV 0.0 None None 0 None -1653 VHLPLAVAL 0.0 None None 0 None -1654 SLYSLDATL 0.887852301761 SLYSLDATL SLYNTAATL 26.0 189286|||| -1655 FTTTQWSSL 0.276143452524 FTTTQW LSTTEW 24.0 37830|polyprotein|BAB18806.1|Hepatitis_C_virus_subtype_1b|31647 -1656 VALRDLGCL 0.0 None None 0 None -1657 MVACGGTVY 0.0 None None 0 None -1658 EMFQRYSAF 1.04802970038 EMFQRYSAF EFFTKNSAF 24.0 44214|UL123;_IE1|AAR31448.1|Human_betaherpesvirus_5|10359 -1659 DAACGIWSL 0.0 None None 0 None -1660 FTILPCTCY 0.0 None None 0 None -1661 IIYTMGIIF 0.0 None None 0 None -1662 RVYNIRGDM 0.0 None None 0 None -1663 RNDPELPTV 0.0340275143527 NDPELP NTPGLP 21.0 65497|HCV-1|AAA45676.1|Hepatitis_C_virus_genotype_1|41856 -1664 HSDSDYDFV 0.0 None None 0 None -1665 VLGEHHHHV 0.0 None None 0 None -1666 HVVDEREQM 0.0 None None 0 None -1667 GQFPYMGEV 0.000425382554656 FPYMGEV FPGGGQI 18.0 181035|||| -1668 LPPEMYVYL 0.0 None None 0 None -1669 EAYQKQLCF 0.0776136961569 YQKQLC YNKPLC 24.0 110982|E6_protein|CAB45108.1|Human_papillomavirus_type_16|333760 -1670 AATGPGEVL 0.129514787687 ATGPGEVL GTGPGNGL 25.0 47760|EBNA-1_protein|Q777E1|Human_gammaherpesvirus_4|10376 -1671 DLYATAFLV 0.0 None None 0 None -1672 GFDWKSVFI 0.0 None None 0 None -1673 FVVFSFFFV 0.0209879781055 FVVFSFF LVLFGFF 23.0 422999|polyprotein|ABD97104.1|Hepatitis_C_virus_genotype_3|356114 -1674 GRDVVHHLL 0.0 None None 0 None -1675 VTLRWYLAM 16.7007719127 TLRWYLAM TLRWFFNL 28.0 38724|Genome_polyprotein|P08617.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 -1676 LVAQYDLTV 0.0 None None 0 None -1677 RLIRGDAVV 0.0 None None 0 None -1678 FQYLVVHTE 0.0 None None 0 None -1679 KHYLMTRTL 0.0 None None 0 None -1680 FVMEHSNIV 0.0 None None 0 None -1681 HQMENNGWV 1.02571149154 QMENNGWV QMENKAWL 33.0 150399|polyprotein|AGV76873.1|Dengue_virus_2|11060 -1682 NATYSGYVY 0.0 None None 0 None -1683 KVKNSASVM 0.0 None None 0 None -1684 KQDKCFAFI 0.0 None None 0 None -1685 AQRPWPRVL 0.0843380588073 RPWPRV RPGPRL 23.0 139406|polyprotein|ACT37184.1|Hepatitis_C_virus|11103 -1686 MAATLLEFF 0.0 None None 0 None -1687 DPNTVSNSI 0.0 None None 0 None -1688 LPVSGGHVM 0.204938535034 LPVSGG MPVGGG 25.0 189750|Diacylglycerol_acyltransferase/mycolyltransferase_Ag85B|SRC280000|Mycobacterium_tuberculosis|1773 -1689 MLDDAPRLL 0.0 None None 0 None -1690 IPPDATIYF 0.0918537604584 PDATIY PDIVIY 23.0 101812|Pol_polyprotein|Q9YLQ7|Human_immunodeficiency_virus_1|11676 -1691 LHDALEVDL 0.0 None None 0 None -1692 MMEKLYPGY 0.0 None None 0 None -1693 IPFLFFTDM 0.0 None None 0 None -1694 YKLCFNTFF 0.0 None None 0 None -1695 YVTMVIDRL 0.0 None None 0 None -1696 TIYFDVVLL 0.0 None None 0 None -1697 SAWLRAISL 0.0 None None 0 None -1698 HLWPGGLSL 0.0 None None 0 None -1699 FGYMTQQRM 0.0 None None 0 None -1700 HVYILRAVF 0.0 None None 0 None -1701 LYIPALAVL 0.0 None None 0 None -1702 DPMVPLQGV 0.41651905562 DPMVPL DPTTPL 23.0 103392|polyprotein|BAB18806.1|Hepatitis_C_virus|11103 -1703 FTEEGFCAI 0.0 None None 0 None -1704 FFNDDCCEL 0.0 None None 0 None -1705 FLFHPLEFC 0.0 None None 0 None -1706 VVMWWMGIL 0.875296446467 VMWWMGIL CLWWLQYF 26.0 39591|polyprotein|AAA45677.1|Hepatitis_C_virus_(isolate_H77)|63746 -1707 KTFHHKSNF 0.0 None None 0 None -1708 QRPWPRVLL 0.245621905968 RPWPRV RPGPRL 23.0 139406|polyprotein|ACT37184.1|Hepatitis_C_virus|11103 -1709 IRVQEASTI 0.0 None None 0 None -1710 DLIDYARYM 0.484336212252 LIDYARYM LLDFVRFM 28.0 37153|Nuclear_antigen_EBNA-3C|Q69140.1|Human_gammaherpesvirus_4|10376 -1711 VTVRGFWIY 0.0 None None 0 None -1712 FMDEHAAER 0.0 None None 0 None -1713 SISDTYDPY 0.0 None None 0 None -1714 DTNDNVPEF 0.0 None None 0 None -1715 YNCTCGCSM 0.0668968271799 NCTCGCS ECTTPCS 24.0 57364|Genome_polyprotein|P26664.3|Hepatitis_C_virus|11103 -1716 LLLLASATV 0.0 None None 0 None -1717 LYMAFVRLL 0.0 None None 0 None -1718 SAEVQLSKI 0.0 None None 0 None -1719 ITACLSVLI 0.0 None None 0 None -1720 LPETKGVTL 0.440996131242 LPETKGVTL VPEVTDVTL 24.0 168240|major_paraflagellar_rod_protein|AAA30221.1|Trypanosoma_cruzi|5693 -1721 MSQEEKVAY 0.0 None None 0 None -1722 MASPQAEST 0.0 None None 0 None -1723 MSFELPYHC 0.0 None None 0 None -1724 RWNDTRATV 0.134680294585 RWNDTR RWLDAR 24.0 150538|polyprotein|AGW21594.1|Dengue_virus_1|11053 -1725 LRHERAVSM 0.0 None None 0 None -1726 LHLLVACTI 0.0 None None 0 None -1727 YGHDRQLCL 0.0 None None 0 None -1728 DATIYFDVV 0.0 None None 0 None -1729 IVCDIKEKL 0.00240549311618 IVCDIKEK IFCHSKKK 20.0 36504|polyprotein_precursor|BAA01582.1|Hepatitis_C_virus|11103 -1730 RPAQFLHEM 0.0 None None 0 None -1731 WHFVYKSGM 0.0 None None 0 None -1732 EVDPIGNLY 0.0 None None 0 None -1733 RTDGNSHEA 0.0 None None 0 None -1734 KHMPKIIHL 0.0 None None 0 None -1735 DVHDIARFL 0.0 None None 0 None -1736 PATRPLHVL 0.000259990550586 PATRPLHVL PAVGVYHIV 18.0 32663|small_hydrophobic_protein|AAM12943.1|Human_metapneumovirus|162145 -1737 LLHSNRSQI 0.0 None None 0 None -1738 PARSGIFKI 0.0 None None 0 None -1739 AALTPTEEM 0.0 None None 0 None -1740 ISAYMAATL 0.0 None None 0 None -1741 IMMSDEERI 0.0 None None 0 None -1742 KRQEGMVPV 0.581298321339 QEGMVPV DEGLLPV 25.0 140541|hypothetical_protein|NP_218210.1|Mycobacterium_tuberculosis_H37Rv|83332 -1743 LQKRATEEI 0.0136766968351 QKRATEEI QKQELDEI 20.0 327|ESAT-6-like_protein_esxB|P0A566.2|Mycobacterium_tuberculosis|1773 -1744 GKDKMTHLL 0.0 None None 0 None -1745 AQLPPWAPL 1.01158072828 AQLPPWAP AQLHVWVP 27.0 40158|polyprotein|AAA45534.1|Hepatitis_C_virus|11103 -1746 FFCEVPVLL 0.0 None None 0 None -1747 RAHKKAITT 0.0 None None 0 None -1748 FDWKSVFII 0.0 None None 0 None -1749 CLFRAARLI 0.0 None None 0 None -1750 MIEDFLRRF 0.0 None None 0 None -1751 TTTERWLRV 0.0 None None 0 None -1752 FFKDKATSK 0.0 None None 0 None -1753 HFFDAFRKF 1.97322439336 FFDAFRKF IFDRTRKF 25.0 154296|UL29|CAB06754.1|Human_alphaherpesvirus_2|10310 -1754 GALGLNRPV 0.0 None None 0 None -1755 YRTKCTLGL 0.0 None None 0 None -1756 MTVAGMVLL 0.0 None None 0 None -1757 KTLSKTAHL 0.0 None None 0 None -1758 NLYIFATCL 0.0 None None 0 None -1759 GFDTSSSSL 0.0 None None 0 None -1760 TPVLCGQPI 0.130418951884 VLCGQPI VLCLRPV 24.0 69398|X_protein|AAP06597.1|Hepatitis_B_virus|10407 -1761 WCAPGKPTL 0.0 None None 0 None -1762 ILHNQIQQV 0.629859339283 ILHNQIQQV LLHTDFEQV 25.0 37398|Non-capsid_protein_NS-1|P07298.1|Human_parvovirus_B19|10798 -1763 VVLSPEVEV 0.0 None None 0 None -1764 DSIHQVGMY 0.0155776894056 HQVGMY HAVGLF 22.0 23573|polyprotein|AAB67037.1|Hepatitis_C_virus_(isolate_H77)|63746 -1765 NHSGVGAFW 0.0 None None 0 None -1766 HNLEPHGYV 0.0 None None 0 None -1767 PSLNATTIV 0.0 None None 0 None -1768 ISGFKGDTV 0.154683020868 GFKGDTV GFPTDTV 24.0 79506|E1_protein|BAA19893.1|Rubella_virus|11041 -1769 HIASSTTSI 0.0 None None 0 None -1770 HTLHAHDPV 0.0 None None 0 None -1771 WTDYGQVFT 0.0 None None 0 None -1772 ELFRRGLRY 0.0 None None 0 None -1773 SASRTKRRV 0.0 None None 0 None -1774 NSGPSRSML 0.0 None None 0 None -1775 ESADKTAYL 0.0 None None 0 None -1776 TELEKFSKV 0.0 None None 0 None -1777 FHAQVCSLY 1.32122904181 HAQVCSLY KAKICGLY 28.0 177701|polyprotein|ACZ60104.1|Hepatitis_C_virus_subtype_3a|356426 -1778 LVVEHVLTT 0.0 None None 0 None -1779 RSYWLRLFL 0.0 None None 0 None -1780 DVDEKQLLV 0.0 None None 0 None -1781 CAIISLIFI 0.0 None None 0 None -1782 SQLEMPETL 0.0 None None 0 None -1783 NLEDVGRHL 0.0 None None 0 None -1784 HLRRIGRFI 0.0 None None 0 None -1785 KYDPDVVVM 0.0 None None 0 None -1786 KDDDCITLV 0.0 None None 0 None -1787 YDVTDSRII 0.0 None None 0 None -1788 MLLHQVAAY 0.0413203406169 MLLHQV MILHEI 24.0 196087|PPE_family_protein_PPE54|YP_177960.1|Mycobacterium_tuberculosis_H37Rv|83332 -1789 THQSGFSVI 0.0 None None 0 None -1790 DLQPVREAI 0.0 None None 0 None -1791 FAGSTQSDL 0.0 None None 0 None -1792 GSYREAQSL 0.0 None None 0 None -1793 HFMPRIQRL 0.0 None None 0 None -1794 LPLKRPGKL 0.0343305252388 LPLKRP LPFDRP 22.0 116127|Nucleoprotein|P15682.1|Influenza_A_virus_(A/Wilson-Smith/1933(H1N1))|381518 -1795 MAFPEGYGT 0.0567950827738 FPEGY LPEGY 25.0 31997|hypothetical_protein_FTT0484|YP_169522.1|Francisella_tularensis_subsp._tularensis_SCHU_S4|177416 -1796 DMQDLTEFL 0.0 None None 0 None -1797 VDFSSEVTV 0.0 None None 0 None -1798 MEVDPIGNL 0.0379279510851 MEVDPIGNL MEVTPSGTW 24.0 26273|nucleocapsid_protein|ABI96968.1|SARS_coronavirus|227859 -1799 ISRNCNSRM 0.0 None None 0 None -1800 YSLIDNFVM 0.0 None None 0 None -1801 FEMPFMQTG 0.0 None None 0 None -1802 SHELVMYIW 0.0 None None 0 None -1803 IIVSYMLII 0.0 None None 0 None -1804 AAAAAVAAL 0.0 None None 0 None -1805 LVDQKAKEV 0.0 None None 0 None -1806 FFSLLATVI 0.710550459145 FSLLATV FTLVATV 25.0 98640|trans-sialidase,_putative|EAN80840.1|Trypanosoma_cruzi|5693 -1807 IYGKPMPTI 0.0 None None 0 None -1808 YMLERLIEQ 0.0 None None 0 None -1809 CIADFLEHM 0.0 None None 0 None -1810 LPYPGSSQA 0.0 None None 0 None -1811 EAWQCQPVL 0.0 None None 0 None -1812 VATSTAQLL 0.0 None None 0 None -1813 VKYTPKLEI 0.0 None None 0 None -1814 RVSAKRVSV 0.0 None None 0 None -1815 NTWTRQMGY 0.0 None None 0 None -1816 LDFACHFTV 0.0 None None 0 None -1817 HVRIHPKLV 0.0 None None 0 None -1818 LQQNCAAYL 0.000555833253958 QQNCAAYL QDNQLAYV 19.0 150649|polyprotein|AGW21594.1|Dengue_virus_1|11053 -1819 DAVGNMLNL 0.0 None None 0 None -1820 WQAISLMVI 0.0 None None 0 None -1821 WLWKLSAVV 0.0 None None 0 None -1822 LAPTHMPEL 0.0 None None 0 None -1823 YAQTPSKTP 0.514097249368 TPSKTP TPDSTP 24.0 53041|phosphorylated_matrix_protein_(pp65)|AAA45996.1|Human_betaherpesvirus_5|10359 -1824 LLLCFLAAM 0.0771007402221 LLLCFL LLLCLI 23.0 27168|envelope_protein|BAF48755.1|Hepatitis_B_virus|10407 -1825 HMPKIIHLV 0.0 None None 0 None -1826 AQLPSYMHI 0.0 None None 0 None -1827 IKLHNPSTI 0.0 None None 0 None -1828 TLLTTHYMA 0.0 None None 0 None -1829 SYEVVIPEW 0.0 None None 0 None -1830 WVNEFGEVF 0.196334224507 WVNEFGEVF WLSDCGEAL 24.0 72790|FL-160-2_protein_-_Trypanosoma_cruzi|JH0823|Trypanosoma_cruzi|5693 -1831 LTYRHCQNF 0.0 None None 0 None -1832 LTYRHCQNF 0.0 None None 0 None -1833 RHCQNFSIL 0.0 None None 0 None -1834 YRHCQNFSI 0.0 None None 0 None -1835 YRHCQNFSI 0.0 None None 0 None -1836 FSLERIAES 0.0 None None 0 None -1837 CLHYIMGDY 0.0 None None 0 None -1838 LLACLHYIM 0.755659798581 LLACL LLACL 25.0 40262|Cytochrome_P450_2A7|P20853.1|Homo_sapiens|9606 -1839 RLLACLHYI 0.470647487397 LLACL LLACL 25.0 40262|Cytochrome_P450_2A7|P20853.1|Homo_sapiens|9606 -1840 RLLACLHYI 0.375813339906 LLACL LLACL 25.0 40262|Cytochrome_P450_2A7|P20853.1|Homo_sapiens|9606 -1841 SQSADAHSI 0.0 None None 0 None -1842 TFFSSSQSA 0.0 None None 0 None -1843 YANNHCIRT 0.0 None None 0 None -1844 FYGMTEMNY 0.197223709005 GMTEMNY ALTEMDY 25.0 418945|PPE_family_protein_PPE68|KAM81677.1|Mycobacterium_tuberculosis_H37Ra|419947 -1845 LQFYGMTEM 0.0 None None 0 None -1846 LQFYGMTEM 0.0 None None 0 None -1847 ALWMYRSLM 6.40774625238 LWMYRSLM VWLKKSMM 25.0 181036|||| -1848 ALWMYRSLM 0.855722704359 LWMYRSLM VWLKKSMM 25.0 181036|||| -1849 QALWMYRSL 0.0 None None 0 None -1850 SFRKEKRNL 0.0 None None 0 None -1851 LTSQDLAGY 0.0 None None 0 None -1852 MAGHGWGAL 0.0 None None 0 None -1853 VMSYGEQPY 0.0 None None 0 None -1854 SVSDVFHGI 0.0 None None 0 None -1855 IPNDNTLSL 0.0 None None 0 None -1856 KTIPNDNTL 0.0 None None 0 None -1857 KTIPNDNTL 0.0 None None 0 None -1858 TLSLRICTI 0.0 None None 0 None -1859 FSMRARIDV 0.0 None None 0 None -1860 RLLGQKFSM 0.0 None None 0 None -1861 IYMENERRM 0.0 None None 0 None -1862 QFLLELYSL 0.0 None None 0 None -1863 RVIRYVIGV 0.0 None None 0 None -1864 QYLSLINYY 0.0 None None 0 None -1865 STLQYLSLI 0.0 None None 0 None -1866 IAQGKPVTL 0.0 None None 0 None -1867 SVIAQGKPV 0.0 None None 0 None -1868 FAIMHAQRT 0.0922530683728 MHAQRT MHQKRT 23.0 110338|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 -1869 HTNAVFAIM 0.000248159096545 HTNAVFAIM HTTKGAALM 18.0 24986|polyprotein_precursor|NP_041724.2|West_Nile_virus|11082 -1870 NHTNAVFAI 0.0 None None 0 None -1871 HHHHHHQAW 31.6214375823 HHHHQ HHFHQ 28.0 183147|polyprotein|AGW21594.1|Dengue_virus_1|11053 -1872 QAWPPPSSA 1.66000789695 WPPPSSA WPAPSGA 32.0 144544|polyprotein_precursor|BAA01728.1|Hepatitis_C_virus|11103 -1873 AHTVARGPV 0.453229538203 HTVARGPV HPVHAGPI 24.0 24557|Gag_polyprotein|P03347.3|Human_immunodeficiency_virus_1|11676 -1874 ALQTFAHTV 0.0 None None 0 None -1875 EIYTKNHAY 0.0 None None 0 None -1876 FGYQLKEIY 0.0 None None 0 None -1877 IYTKNHAYI 0.0 None None 0 None -1878 YTKNHAYII 0.0 None None 0 None -1879 YTKNHAYII 0.0 None None 0 None -1880 HAFDRYETT 0.0 None None 0 None -1881 TTHSRPVTL 0.0 None None 0 None -1882 TTHSRPVTL 0.0 None None 0 None -1883 YETTHSRPV 0.0 None None 0 None -1884 VLFDVAGQV 5.87593218982e-05 VLFDVAGQV VIFCHPGQL 17.0 79454|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 -1885 VLFDVAGQV 9.25459319897e-05 VLFDVAGQV VIFCHPGQL 17.0 79454|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 -1886 ESKPAPAEV 0.0 None None 0 None -1887 LNVEKTEKI 0.0166822097398 VEKTEK LEKTKK 22.0 35568|Polyprotein|Q9J8D4|Dengue_virus_2|11060 -1888 MVIVFYGTL 0.0 None None 0 None -1889 MVIVFYGTL 0.0 None None 0 None -1890 SAHLTMVIV 0.0 None None 0 None -1891 YETFGAASF 0.0 None None 0 None -1892 RGVPPLRTV 0.959521069645 GVPPLRT GVPPLRA 33.0 36345|polyprotein|ABR25251.1|Hepatitis_C_virus_(isolate_H77)|63746 -1893 TAESCRSTL 0.0 None None 0 None -1894 TAESCRSTL 0.0 None None 0 None -1895 RVRAAGQRL 1.69373967722 RVRAAGQRL KIRAWGRRL 27.0 181733|Antigen_85-B|P0C5B9.1|Mycobacterium_tuberculosis|1773 -1896 DVHARESKI 0.0 None None 0 None -1897 NVPPTVQKV 0.0 None None 0 None -1898 CYYPMAGYI 0.0060192893897 YYPMAGYI YYLDRGYL 22.0 76532|outer_membrane_protein|YP_170495.1|Francisella_tularensis_subsp._tularensis_SCHU_S4|177416 -1899 CYYPMAGYI 0.0239816132828 YYPMAGYI YYLDRGYL 22.0 76532|outer_membrane_protein|YP_170495.1|Francisella_tularensis_subsp._tularensis_SCHU_S4|177416 -1900 NTRQCYYPM 0.0 None None 0 None -1901 LGYRWCLHV 0.441063931047 GYRWCL GWRWRL 25.0 37607|kaposin|AAC57155.1|Human_gammaherpesvirus_8|37296 -1902 LLLGYRWCL 5.17789244834 LLLGYRWCL LLNGWRWRL 30.0 37607|kaposin|AAC57155.1|Human_gammaherpesvirus_8|37296 -1903 TAHSSVLTL 0.0 None None 0 None -1904 TAHSSVLTL 0.0 None None 0 None -1905 FPSNHLGDL 0.0236234538092 PSNHLGD PGNGLGE 23.0 47760|EBNA-1_protein|Q777E1|Human_gammaherpesvirus_4|10376 -1906 LLLAHKKKV 0.0 None None 0 None -1907 AQILEQVEV 0.0 None None 0 None -1908 QIFKCKGTL 0.0 None None 0 None -1909 QIFKCKGTL 0.0 None None 0 None -1910 TLVGHQGPV 0.0 None None 0 None -1911 TLVGHQGPV 0.0 None None 0 None -1912 DAVELWAIV 0.0 None None 0 None -1913 VDLPLTSTI 0.00972155564068 LPLTSTI LPFHSTL 20.0 21007|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 -1914 NVVNGQMRF 0.0 None None 0 None -1915 MGAPGSEII 0.0 None None 0 None -1916 FSQFSNLKV 0.0 None None 0 None -1917 KAFSQFSNL 0.0 None None 0 None -1918 HFSVSSNLL 0.0 None None 0 None -1919 KHFSVSSNL 0.0 None None 0 None -1920 KHFSVSSNL 0.0 None None 0 None -1921 YQVLAMSTK 0.0 None None 0 None -1922 KLSSEAKTK 0.0 None None 0 None -1923 TVLRLFPFR 0.0 None None 0 None -1924 TVLRLFPFR 0.0 None None 0 None -1925 TVKDVHKAK 0.0 None None 0 None -1926 TIHNVNFSK 0.0 None None 0 None -1927 TIHNVNFSK 0.0 None None 0 None -1928 SETTFDIFV 0.0 None None 0 None -1929 GMHFSPGAR 0.0 None None 0 None -1930 FLTQPVAPK 9.05129460172 FLTQPVAP LIEKPVAP 24.0 419002|PPE_family_protein_PPE68|KAM81677.1|Mycobacterium_tuberculosis_H37Ra|419947 -1931 KAISFYMKR 0.0 None None 0 None -1932 RTVAQVTKK 0.0 None None 0 None -1933 RTVAQVTKK 0.0 None None 0 None -1934 SEDKKNTKL 0.0 None None 0 None -1935 RVAAGVQIK 0.0 None None 0 None -1936 RVAAGVQIK 0.0 None None 0 None -1937 VVGAVGVGK 0.0 None None 0 None -1938 VVGAVGVGK 0.0 None None 0 None -1939 TTTPTLKEK 0.0 None None 0 None -1940 QSLYIDRLK 0.0 None None 0 None -1941 TTIHYNYMY 0.0 None None 0 None -1942 TECIIAMSF 0.0 None None 0 None -1943 IESSYLESL 0.0 None None 0 None -1944 AEEEEEEVV 0.961625857069 AEEEEE SEEEDE 23.0 110431|E7|AAD33253.1|Human_papillomavirus_type_16|333760 -1945 TENHQPVCL 0.0 None None 0 None -1946 GQLGGLAGK 0.0 None None 0 None -1947 LSDWGPHFK 0.0 None None 0 None -1948 LSDWGPHFK 0.0 None None 0 None -1949 KPASKKEWI 0.0 None None 0 None -1950 TTKSEAIEK 0.0 None None 0 None -1951 IVRASGCEL 0.0 None None 0 None -1952 VPTELNGSM 0.0 None None 0 None -1953 VPLFPARVL 0.0 None None 0 None -1954 APAQPPMLA 32.3662874827 APAQPPM CPSQEPM 24.0 58463|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 -1955 VVGARGVGK 0.0 None None 0 None -1956 VVGARGVGK 0.0 None None 0 None -1957 KLCNSGDFR 0.0 None None 0 None -1958 HPLTENSPL 0.0 None None 0 None -1959 STVRKSPWK 0.0 None None 0 None -1960 STVRKSPWK 0.0 None None 0 None -1961 LIRMYNINK 0.0 None None 0 None -1962 LIRMYNINK 0.0 None None 0 None -1963 SPWPLSSLT 0.0 None None 0 None -1964 SLKSTRAVF 0.0 None None 0 None -1965 SVGSASSLK 0.0 None None 0 None -1966 SVGSASSLK 0.0 None None 0 None -1967 KGYGGFSRY 0.0 None None 0 None -1968 KGYGGFSRY 0.0 None None 0 None -1969 KAIGKSRPY 0.0 None None 0 None -1970 KTLRKAIGK 0.00523788333205 KTLRKAI KTILKAL 21.0 7708|gag_polyprotein|BAA00992.1|Human_immunodeficiency_virus_1|11676 -1971 KTLRKAIGK 0.00482507857332 KTLRKAI KTILKAL 21.0 7708|gag_polyprotein|BAA00992.1|Human_immunodeficiency_virus_1|11676 -1972 QALQKTLRK 0.0 None None 0 None -1973 SYQSTGDPK 0.160544975903 TGDP TGDP 24.0 2002|Large_envelope_protein|SRC279965|Hepatitis_B_virus|10407 -1974 VPEWSNNS* 0.0 None None 0 None -1975 VLETAAPGV 0.0 None None 0 None -1976 AVLDAIPLV 0.0 None None 0 None -1977 VLDAIPLVA 0.0 None None 0 None -1978 KPVVTEVRM 0.0 None None 0 None -1979 MPTNTWSGL 0.0679479043012 PTNTW PTYSW 22.0 102368|E2_protein|NP_751921.1|Hepatitis_C_virus_subtype_1a|31646 -1980 VFQGHSASI 0.0 None None 0 None -1981 SLYDFGELR 0.0 None None 0 None -1982 DSMLQTVER 0.0 None None 0 None -1983 MLQTVEREK 0.0 None None 0 None -1984 LLWKDFDQA 9.96145413497 DFDQA DFDQG 23.0 149117|envelope_glycoprotein|AAV74049.1|Hepatitis_C_virus_(isolate_H77)|63746 -1985 HVPQVADAI 0.0 None None 0 None -1986 LLEMNLMHV 0.44470519815 LLEMNLM LIEANLL 22.0 419095|polyprotein|ABR25251.1|Hepatitis_C_virus|11103 -1987 NLMHVPQVA 0.0 None None 0 None -1988 VPQVADAIL 0.0 None None 0 None -1989 FLIDGSQSV 0.0 None None 0 None -1990 FLIDGSQSV 0.0 None None 0 None -1991 SVGPEFQYV 0.0 None None 0 None -1992 LALSVTEMV 0.0 None None 0 None -1993 RLALSVTEM 0.0 None None 0 None -1994 TILQIKEEK 0.0 None None 0 None -1995 DYEAVCGHR 0.0 None None 0 None -1996 EAVCGHRAR 0.287814503571 GHRAR GHKAR 25.0 21635|gag_protein|ABO73990.1|Human_immunodeficiency_virus_1|11676 -1997 ILFQKITNR 0.0 None None 0 None -1998 KITNRGDEL 0.0 None None 0 None -1999 SPTPALGPA 0.0 None None 0 None -2000 LTPQQAQEL 0.0 None None 0 None -2001 APLGAPPPL 355.106026278 LGAPPPL LGAIPPL 29.0 73059|kaposin|AAC57155.1|Human_gammaherpesvirus_8|37296 -2002 SKTPPGAPL 1.70350167556 PPGAPL PPNAPI 27.0 93536|core_protein|AAL31859.1|Hepatitis_B_virus|10407 -2003 SKTPPGAPL 6.26781366346 PPGAPL PPNAPI 27.0 93536|core_protein|AAL31859.1|Hepatitis_B_virus|10407 -2004 MFQSLGEHI 0.0937231593112 MFQSLGEHI MEPTLGQHL 24.0 79308|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 -2005 SLGEHINTL 2.10571623096 SLGEHINTL TLGQHLPTL 30.0 79308|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 -2006 SLGEHINTL 1.0685924021 SLGEHINTL TLGQHLPTL 30.0 79308|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 -2007 AVGVGKSAL 0.0 None None 0 None -2008 YKLVVVGAV 12.5817515538 KLVVVG KLVVLG 24.0 32238|polyprotein_[Hepatitis_C_virus_subtype_1a]|ABV46251.2|Hepatitis_C_virus_(isolate_H77)|63746 -2009 AMLWALGFI 8.2714056325 MLWALGF ILWAVGL 27.0 1000|glycoprotein_gp35/37|AAC59622.1|Human_gammaherpesvirus_8|37296 -2010 FIWSVLITA 0.0 None None 0 None -2011 MLWALGFIF 3.08293386362 MLWALGF ILWAVGL 27.0 1000|glycoprotein_gp35/37|AAC59622.1|Human_gammaherpesvirus_8|37296 -2012 QTPLFIWSV 0.0 None None 0 None -2013 TPLFIWSVL 0.0 None None 0 None -2014 TQYQTPLFI 0.638287640051 QYQTP RYQTP 25.0 180617|polyprotein|AGO67248.1|Dengue_virus_2|11060 -2015 IINDGKHHV 0.0 None None 0 None -2016 GLSAEEFQL 0.0 None None 0 None -2017 SAEEFQLIR 0.0 None None 0 None -2018 APTTPKEPA 0.0115417217673 APTTPKEPA APASVYQPA 21.0 141216|envelope_glycoprotein_I|NP_044669.1|Human_alphaherpesvirus_1|10298 -2019 LLLLLLLLV 0.0 None None 0 None -2020 LLLLLLLVV 0.183789279182 LLLLLVV VLLLLVV 25.0 98540|trans-sialidase,_putative|EAN88532.1|Trypanosoma_cruzi|5693 -2021 LLLLLLVVV 0.355681484489 LLLLVVV LLLLVVM 25.0 98224|trans-sialidase,_putative|EAN82076.1|Trypanosoma_cruzi|5693 -2022 LLVVVPWGV 0.0 None None 0 None -2023 SRRHSRSPL 0.0 None None 0 None -2024 SRRHSRSPL 0.0 None None 0 None -2025 GSYSMAIPL 0.191247232974 GSYSMAIPL GLYSSTVPV 25.0 21242|polymerase|ACF94272.1|Hepatitis_B_virus|10407 -2026 MAIPLLCSY 0.0 None None 0 None -2027 NPGSYSMAI 0.0 None None 0 None -2028 RYNPGSYSM 0.0 None None 0 None -2029 RYNPGSYSM 0.0 None None 0 None -2030 SYSMAIPLL 0.0 None None 0 None -2031 CQPHAHCSL 0.0 None None 0 None -2032 HAHCSLWRR 0.0 None None 0 None -2033 IIQELTIFK 0.0 None None 0 None -2034 LPPKPVQVL 1.24074074074 PPKPVQV PPKPCGI 26.0 75376|Genome_polyprotein|P26664.3|Hepatitis_C_virus|11103 -2035 QLPPKPVQV 0.5 PPKPVQV PPKPCGI 26.0 75376|Genome_polyprotein|P26664.3|Hepatitis_C_virus|11103 -2036 GLYASLFPA 0.0 None None 0 None -2037 LFPAIIYLF 0.160615937749 FPAIIYL YPAVFYL 28.0 154041|major_capsid_protein|CAB06743.1|Human_alphaherpesvirus_2|10310 -2038 LYASLFPAI 0.0 None None 0 None -2039 PVYGLYASL 0.0 None None 0 None -2040 SLFPAIIYL 165.36965139 FPAIIYL YPAVFYL 28.0 154041|major_capsid_protein|CAB06743.1|Human_alphaherpesvirus_2|10310 -2041 SLFPAIIYL 0.19660649062 FPAIIYL YPAVFYL 28.0 154041|major_capsid_protein|CAB06743.1|Human_alphaherpesvirus_2|10310 -2042 SLFPAIIYL 0.207246371289 FPAIIYL YPAVFYL 28.0 154041|major_capsid_protein|CAB06743.1|Human_alphaherpesvirus_2|10310 -2043 VYGLYASLF 0.0 None None 0 None -2044 VYGLYASLF 0.0 None None 0 None -2045 RYNVADVSV 0.0 None None 0 None -2046 VSVAICMSL 0.0 None None 0 None -2047 YTISDDESF 0.0 None None 0 None -2048 YVQYWYYTI 0.673550706689 VQYWYY TQYWKY 28.0 141206|tegument_protein_VP11/12|NP_044648.1|Human_alphaherpesvirus_1|10298 -2049 YVQYWYYTI 0.493586768335 VQYWYY TQYWKY 28.0 141206|tegument_protein_VP11/12|NP_044648.1|Human_alphaherpesvirus_1|10298 -2050 SFYNSNRDF 0.0 None None 0 None -2051 SFYNSNRDF 0.0 None None 0 None -2052 TISFYNSNR 0.0 None None 0 None -2053 CRFELMHFK 0.0 None None 0 None -2054 ELMHFKTLY 0.00494580293464 ELMHFKTL KVLHKRTL 20.0 34101|X_protein|ACH95876.1|Hepatitis_B_virus|10407 -2055 ILGDWSNGI 0.470124959392 DWSNGI DYSNGL 26.0 51604|FL-160-2_protein_-_Trypanosoma_cruzi|JH0823|Trypanosoma_cruzi|5693 -2056 NGISALYCR 0.0 None None 0 None -2057 HIHGGTNQV 0.658346187729 HGGTN HGGTG 25.0 55336|EBNA-1|YP_401677.1|Human_gammaherpesvirus_4|10376 -2058 AFTCTSSLL 0.0 None None 0 None -2059 KAFTCTSSL 0.0 None None 0 None -2060 KAFTCTSSL 0.0 None None 0 None -2061 GDASKVWVW 0.832592284506 GDASKVWV GNASRCWV 31.0 21385|polyprotein|AAY82034.1|Hepatitis_C_virus_genotype_1|41856 -2062 STFVHGNKI 0.0 None None 0 None -2063 GEEAEASAV 0.0 None None 0 None -2064 TTSPSNTLV 0.0 None None 0 None -2065 STGLQYATK 0.0 None None 0 None -2066 SVLRCVHLL 0.0 None None 0 None -2067 GRNSFKVRV 1.9048679282 GRNSFKV GRNSFEV 32.0 37364|P53_HUMAN_Cellular_tumor_antigen_p53_(Tumor_suppressor_p53)_(Phosphoprotein_p53)_(Antigen_NY-CO-13)|P04637.2|Homo_sapiens|9606 -2068 MRTLLGDLV 0.0 None None 0 None -2069 RWDRKPMQI 0.0 None None 0 None -2070 SRSTIFMRL 0.0 None None 0 None -2071 PHLTQGNEI 0.0 None None 0 None -2072 ASTFVHGNK 0.0 None None 0 None -2073 ENAGPQNMK 0.0 None None 0 None -2074 MGQEIAALK 0.0 None None 0 None -2075 NLLGRNSFK 63.0014315849 LLGRNSFK LLGRNSFE 36.0 37364|P53_HUMAN_Cellular_tumor_antigen_p53_(Tumor_suppressor_p53)_(Phosphoprotein_p53)_(Antigen_NY-CO-13)|P04637.2|Homo_sapiens|9606 -2076 QAVCVTKPK 0.165090772535 VCVTKP ICLTHP 24.0 146317|polyprotein|ADF97231.1|Hepatitis_C_virus_subtype_3a|356426 -2077 LRCVHLLRI 0.0 None None 0 None -2078 FVHGNKIYV 0.0 None None 0 None -2079 ATKFIKKRR 0.0 None None 0 None -2080 VHLLRIFKV 0.0 None None 0 None -2081 LANAPRTLK 0.0 None None 0 None -2082 WRLTWDRHL 0.119451085397 WRLTWD WAIKWE 24.0 72233|Genome_polyprotein|P27958.3|Hepatitis_C_virus_subtype_1a|31646 -2083 CTGPPLAPR 0.0742064317743 CTGPPLAPR CGGVYLLPR 23.0 181035|||| -2084 NLTRASSKR 0.0 None None 0 None -2085 RRSGPSPTV 0.586855842399 GPSPTV GPVPAV 22.0 179799|hypothetical_protein|NP_301670.1|Mycobacterium_leprae_TN|272631 -2086 DLVAHYVHR 0.332299353923 LVAHY LVAHY 27.0 150377|polyprotein|AGS49173.1|Dengue_virus_2|11060 -2087 SSLEGFATR 0.0 None None 0 None -2088 LEDLGWANW 1.69512152692 EDLGWANW EGLGWAGW 40.0 75436|Polyprotein|P90247|Hepatitis_C_virus|11103 -2089 CVHLLRIFK 0.0 None None 0 None -2090 TIQAVCVTK 0.0 None None 0 None -2091 ITCMPGSVR 0.0886657628972 ITCMPGSV IFCHPGQL 23.0 79454|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 -2092 CSIPSICEK 0.0 None None 0 None -2093 SSRSTIFMR 0.0 None None 0 None -2094 SVTKASNLK 0.0 None None 0 None -2095 YATKFIKKR 0.0 None None 0 None -2096 FSSSDDSPR 0.0 None None 0 None -2097 VHGNKIYVL 0.0 None None 0 None -2098 WANWVLSPR 4.11764705574 WANWVLSPR WAGWLLSPR 47.0 36352|Polyprotein|P90247|Hepatitis_C_virus|11103 -2099 LSLPGGHTA 0.0 None None 0 None -2100 FRAAAEAAV 0.0 None None 0 None -2101 FRAAAEAAV 0.0 None None 0 None -2102 TSSDHSFSL 0.0 None None 0 None -2103 TSSDHSFSL 0.0 None None 0 None -2104 NHQQFYHSV 0.0 None None 0 None -2105 NHQQFYHSV 0.0 None None 0 None -2106 DYSELPHHV 0.0 None None 0 None -2107 HHVSTEQEI 0.0 None None 0 None -2108 HHVSTEQEI 0.0 None None 0 None -2109 EIISLWSPW 0.0 None None 0 None -2110 NQDPISPSL 0.243444523244 QDPISPSL EKPVAPSV 24.0 419002|PPE_family_protein_PPE68|KAM81677.1|Mycobacterium_tuberculosis_H37Ra|419947 -2111 ENASAYLTL 0.0 None None 0 None -2112 KKMENASAY 0.0 None None 0 None -2113 RRHSLPRRC 0.0 None None 0 None -2114 NMCRCLVTV 0.0 None None 0 None -2115 RLMSARLAI 0.0 None None 0 None -2116 SYSYLGLRL 0.0 None None 0 None -2117 YSYLGLRLM 0.0 None None 0 None -2118 YSYLGLRLM 0.0 None None 0 None -2119 RFSQAFFYM 0.0 None None 0 None -2120 RRFSQAFFY 0.0 None None 0 None -2121 FMMPRSSSC 0.0 None None 0 None -2122 FMMPRSSSC 0.0 None None 0 None -2123 IPAMEIFMV 0.0 None None 0 None -2124 LMAASIPAM 0.0 None None 0 None -2125 DTLQATAML 0.0 None None 0 None -2126 QATAMLDIV 0.0 None None 0 None -2127 TVTRTTATV 0.0 None None 0 None -2128 EHFPLCKTV 0.0 None None 0 None -2129 EHFPLCKTV 0.0 None None 0 None -2130 WPQCHPEEI 1.27438241384 WPQCHPEEI LPQCSPDEI 38.0 3051|UL123;_IE1|AAR31448.1|Human_betaherpesvirus_5|10359 -2131 YSYSCGHYE 0.268852568146 YSYSCGHY YPYRLWHY 24.0 10939|polyprotein|BAB18806.1|Hepatitis_C_virus_subtype_1a|31646 -2132 SHFERDYRV 0.0 None None 0 None -2133 FQTLMPDVV 0.0 None None 0 None -2134 FQTLMPDVV 0.0 None None 0 None -2135 MPDVVHQSL 2.1510778258 MPDVVHQ MPDVAHS 30.0 130953|G1_and_G2_surface_glycoprotein_precursor|AAG22532.1|Andes_hantavirus|46607 -2136 LWYTLYLMI 0.263181088307 LWYTLY LWVTVY 27.0 118|envelope_glycoprotein|ABS76372.1|Human_immunodeficiency_virus_1|11676 -2137 LYLMITTFF 0.141553469901 MITTFF MLTAFF 24.0 140651|granule_antigen_protein_GRA6|XP_002371939.1|Toxoplasma_gondii_ME49|508771 -2138 MITTFFFPL 0.390389569622 MITTFF MLTAFF 24.0 140651|granule_antigen_protein_GRA6|XP_002371939.1|Toxoplasma_gondii_ME49|508771 -2139 TLYLMITTF 1.13393265557 TLYLMITTF TLYAVATTF 31.0 150639|polyprotein|AGO67249.1|Dengue_virus_2|11060 -2140 YLMITTFFF 0.727839017994 MITTFF MLTAFF 24.0 140651|granule_antigen_protein_GRA6|XP_002371939.1|Toxoplasma_gondii_ME49|508771 -2141 YTLYLMITT 0.0 None None 0 None -2142 PTSPFQTTI 0.00448304273818 PTSPFQ PERPFQ 23.0 232154|rhoptry_protein,_putative_/_protein_kinase_domain-containing_protein|XP_002367757.1|Toxoplasma_gondii_type_II|1209523 -2143 TAERSIPTV 0.546505896162 ERSIPTV DRSYPAV 21.0 154041|major_capsid_protein|CAB06743.1|Human_alphaherpesvirus_2|10310 -2144 ERPCHREPL 2.30501930502 PCHREPL PGHEEPI 26.0 180488|polyprotein|AGO67248.1|Dengue_virus_2|11060 -2145 SSSSGPFPL 0.0 None None 0 None -2146 ELATFAKAY 0.0 None None 0 None -2147 RWDEELATF 0.0 None None 0 None -2148 ELIDLISRV 0.0 None None 0 None -2149 ELIDLISRV 0.0 None None 0 None -2150 QVNQKSSVV 0.0 None None 0 None -2151 VRLELIDLI 0.0 None None 0 None -2152 YEEYRGRLL 0.267524115073 YEEYRGRL YQDWLGRM 24.0 23288|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 -2153 YEEYRGRLL 0.0889159325107 YEEYRGRL YQDWLGRM 24.0 23288|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 -2154 CRNVHTPDL 0.0 None None 0 None -2155 YSRDQAQAL 0.0 None None 0 None -2156 YSRDQAQAL 0.0 None None 0 None -2157 FEVEGRDLL 0.0 None None 0 None -2158 FFFLCVCVF 0.0684531631414 FFFLCVCV LLILCLCL 24.0 49831|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 -2159 FFLCVCVFV 0.243568175313 FFLCVCV LILCLCL 24.0 49831|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 -2160 RRYPHKRCI 0.119202922022 YPHKRC YPPKPC 24.0 75376|Genome_polyprotein|P26664.3|Hepatitis_C_virus|11103 -2161 RRYPHKRCI 0.150450289931 YPHKRC YPPKPC 24.0 75376|Genome_polyprotein|P26664.3|Hepatitis_C_virus|11103 -2162 NMSRCCIRV 0.0 None None 0 None -2163 GLLGNGIGY 0.0 None None 0 None -2164 LLGNGIGYV 0.0 None None 0 None -2165 KILSLHLLL 0.0 None None 0 None -2166 HPAFISLAF 0.0 None None 0 None -2167 FPREKTPEV 0.911184210526 FPREKTP LPRSRTP 26.0 88849|IE62|AAP32859.1|Human_alphaherpesvirus_3|10335 -2168 WPPWLKGKY 0.578598641597 WLKGK YLKGK 22.0 419170|polyprotein|ABR25251.1|Hepatitis_C_virus|11103 -2169 IVLTGHNAY 0.0 None None 0 None -2170 IVLTGHNAY 0.0 None None 0 None -2171 VLTGHNAYL 0.0 None None 0 None -2172 QAQALGIPL 0.0 None None 0 None -2173 IVFFANNGF 0.0 None None 0 None -2174 HSESSDSEV 0.0 None None 0 None -2175 RRGSGHSEY 0.0584223726864 GSGHSE GPGHEE 24.0 180488|polyprotein|AGO67248.1|Dengue_virus_2|11060 -2176 LIMEDLVCY 0.0 None None 0 None -2177 MEDLPAACM 0.0 None None 0 None -2178 HPMASNSGG 0.00278161375312 PMASNSGG PIALLKGG 19.0 146282|polyprotein|ADF97231.1|Hepatitis_C_virus_subtype_3a|356426 -2179 DVEWRWHSY 0.0 None None 0 None -2180 DVEWRWHSY 0.0 None None 0 None -2181 ILPTCSPLV 2072.01295566 PTCSPL PACKPL 27.0 56502|polyprotein|BAD73994.1|Hepatitis_C_virus_subtype_1b|31647 -2182 LPTCSPLVF 1.81028585028 PTCSPL PACKPL 27.0 56502|polyprotein|BAD73994.1|Hepatitis_C_virus_subtype_1b|31647 -2183 VHFWPGYEY 0.0 None None 0 None -2184 SPEGDDTLY 0.0192935429649 PEGDDTLY PQGQLTAY 22.0 13701|Trans-activator_protein_BZLF1|P03206.2|Human_gammaherpesvirus_4|10376 -2185 TLVPTAPEL 0.0 None None 0 None -2186 HLIGSTTLA 2.05755395683 LIGSTTL LIGITTL 26.0 59182|attachment_glycoprotein|ABQ58821.1|Human_metapneumovirus|162145 -2187 LIGSTTLAM 0.246511627907 LIGSTTL LIGITTL 26.0 59182|attachment_glycoprotein|ABQ58821.1|Human_metapneumovirus|162145 -2188 LLMHLIGST 0.0 None None 0 None -2189 IAHQWYWTY 0.0584354508795 QWYWTY KWLWGF 23.0 62903|Genome_polyprotein|P27909.2|Dengue_virus_type_1_Hawaii|10000440 -2190 IAHQWYWTY 2.11519394372 QWYWTY KWLWGF 23.0 62903|Genome_polyprotein|P27909.2|Dengue_virus_type_1_Hawaii|10000440 -2191 LLEENGDVF 0.0 None None 0 None -2192 QRCACPHGY 0.0 None None 0 None -2193 CMYDPLGTI 0.0 None None 0 None -2194 GPHRITCMY 0.0389454916711 PHRITC PHVIFC 23.0 79337|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 -2195 NESCLSMSE 0.0 None None 0 None -2196 VANESCLSM 0.0 None None 0 None -2197 EESELYAQL 1.79691363928 EESELY EQSEFY 23.0 62355|Genome_polyprotein|P08617.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 -2198 RTAQCFLCV 0.0 None None 0 None -2199 KYSNYVWPI 10.3355467301 KYSNYVW KYTSFPW 26.0 34616|pol_protein|BAA32832.1|Hepatitis_B_virus|10407 -2200 FIFEIVGFT 0.0 None None 0 None -2201 DSSGQSNRY 1.24432386195 SSGQSNR NSGASNR 25.0 1095|glycoprotein_gp35/37|AAC59622.1|Human_gammaherpesvirus_8|37296 -2202 DSSSWSNRY 0.0 None None 0 None -2203 DSSSWSNRY 0.0 None None 0 None -2204 NRYGGGGRY 0.0 None None 0 None -2205 NRYGGGGRY 0.0 None None 0 None -2206 NEHGHRRKI 0.0 None None 0 None -2207 HTSLRGFLY 0.253521126761 HTSLRGF HLSLRGL 26.0 24302|X_protein|AAP06597.1|Hepatitis_B_virus|10407 -2208 ALNEMFCQL 0.0 None None 0 None -2209 NEMFCQLAK 0.0 None None 0 None -2210 GLYAIAVML 0.0 None None 0 None -2211 MLSFSRIAY 0.0 None None 0 None -2212 MLSFSRIAY 0.0 None None 0 None -2213 YAIAVMLSF 0.0 None None 0 None -2214 AEWDSLYVL 0.0 None None 0 None -2215 LAEWDSLYV 0.0 None None 0 None -2216 VLAEWDSLY 0.0 None None 0 None -2217 VLAEWDSLY 0.0 None None 0 None -2218 GKAFSQSAY 0.0 None None 0 None -2219 KAFSQSAYL 0.0 None None 0 None -2220 RREDLTHTL 0.0 None None 0 None -2221 RREDLTHTL 0.0 None None 0 None -2222 ERWLRQAAF 3.02094262382 RWLRQAAF RWVPGAAY 24.0 22255|polyprotein|ABR27377.1|Hepatitis_C_virus|11103 -2223 RKREEEERW 42.4491907364 KREEEE RREEEE 27.0 185491|polyprotein|AGO67248.1|Dengue_virus_2|11060 -2224 THCSPNLLF 0.0 None None 0 None -2225 HQYNIYAAL 0.351661877827 YNIYAAL YNTVAAL 23.0 189291|||| -2226 RSFTESHQY 0.0 None None 0 None -2227 ISAKIMQQW 0.0 None None 0 None -2228 YTDTISAKI 0.0 None None 0 None -2229 AAVLGMLLW 0.0 None None 0 None -2230 ISGRVVQHF 0.0 None None 0 None -2231 IAFNHGDLL 0.0 None None 0 None -2232 KYHYYGLHI 0.0 None None 0 None -2233 LSRRVTQSL 0.0 None None 0 None -2234 RRVTQSLEA 0.0 None None 0 None -2235 KTYAPLFIW 0.678885162016 TYAPLFI TYGPVFM 27.0 67349|Latent_membrane_protein_2|Q69135|Human_gammaherpesvirus_4|10376 -2236 TYAPLFIWV 1.02223796155 TYAPLFIWV TYGPVFMCL 27.0 67349|Latent_membrane_protein_2|Q69135|Human_gammaherpesvirus_4|10376 -2237 KYIAFCINI 0.587708864399 KYIAFCI RYISWCL 26.0 39591|polyprotein|AAA45677.1|Hepatitis_C_virus_(isolate_H77)|63746 -2238 YIAFCINIF 0.476894002614 YIAFCI YISWCL 24.0 423020|polyprotein|ACE82359.1|Hepatitis_C_virus_genotype_1|41856 -2239 FHYPQSIFS 0.552109387903 HYPQSIF HYMESVF 28.0 154585|ribonucleotide_reductase_large_subunit|CAB06725.1|Human_alphaherpesvirus_2|10310 -2240 MKFHYPQSI 0.0 None None 0 None -2241 NTNSNRSLI 0.0 None None 0 None -2242 FRAYQDYFL 0.0 None None 0 None -2243 FRAYQDYFL 0.0 None None 0 None -2244 LHIGKDVQL 0.0 None None 0 None -2245 QVFAAVHEW 0.000185091863979 FAAVH YAFVH 17.0 142232|POSSIBLE_CONSERVED_TRANSMEMBRANE_PROTEIN|CAB00937.1|Mycobacterium_tuberculosis|1773 -2246 RRHTDEKPY 0.465553354611 RRHTDEK QRHLDKK 25.0 110394|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 -2247 FNGNFLLSM 8.55978429414 NGNFLL NGGFLI 24.0 194567|envelope_glycoprotein_B|NP_044629.1|Herpes_simplex_virus_(type_1_/_strain_17)|10299 -2248 GSADNTVQF 0.0 None None 0 None -2249 SADNTVQFI 0.0 None None 0 None -2250 KVQREDIFY 0.0 None None 0 None -2251 YLWPSGTPA 3.65618873033 LWPSGTP LWKDGAP 27.0 140600|glutamine_synthetase_GLNA1_(glutamine_synthase)_(GS-I)|NP_216736.1|Mycobacterium_tuberculosis_H37Rv|83332 -2252 LKMVSPSPC 0.0 None None 0 None -2253 SRVARDVAM 0.0 None None 0 None -2254 QNGYSWSQF 0.0190362677864 QNGYSWS QNGACWT 26.0 6889|Agglutinin_isolectin_1_precursor|P10968.2|Triticum_aestivum|4565 -2255 SYKLSQNGY 0.355050579888 SYKLSQNG AYRIKQRG 23.0 182687|polyprotein|AGK36298.1|Dengue_virus_2|11060 -2256 WKRGKRRYF 0.438635147178 WKRGKR WTRGER 27.0 170063|polyprotein|ABU97067.1|Hepatitis_C_virus_subtype_1b|31647 -2257 CFGHCFSLY 0.36196760402 FGHCF FGWCF 25.0 56620|Nef_protein|Q9YYU8|Human_immunodeficiency_virus_1|11676 -2258 CSAIRLRNY 0.0 None None 0 None -2259 FGHCFSLYI 0.0 None None 0 None -2260 IRLRNYLCF 0.0 None None 0 None -2261 IRLRNYLCF 0.0 None None 0 None -2262 LCFGHCFSL 0.351865750194 LCFGHCF LTFGWCF 28.0 56620|Nef_protein|Q9YYU8|Human_immunodeficiency_virus_1|11676 -2263 NHLCFGHCF 643.063109635 LCFGHCF LTFGWCF 28.0 56620|Nef_protein|Q9YYU8|Human_immunodeficiency_virus_1|11676 -2264 DFVECLMWF 0.0 None None 0 None -2265 DFVECLMWF 0.0 None None 0 None -2266 NKFEPSTDL 0.0458420865757 NKFEPST NDFFPSV 19.0 16814|precore_protein|CAM58990.1|Hepatitis_B_virus|10407 -2267 AYLCCRVPL 0.256424890396 LCCRV LCCYV 24.0 11956|UL123;_IE1|AAR31448.1|Human_betaherpesvirus_5|10359 -2268 SKGTTDTPV 2.41094003631 SKGTTDTPV SPGTSGSPI 25.0 5542|Nonstructural_protein_NS3|NP_739587.2|Dengue_virus_2_Thailand/16681/84|31634 -2269 KQSNSVEPI 0.0 None None 0 None -2270 AMSAQEYYI 0.0 None None 0 None -2271 SAQEYYIDY 0.0 None None 0 None -2272 YIDYKPNHI 0.377509819097 YIDYKPN YTDYMPS 26.0 180681|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -2273 LMLLAAAIY 0.0 None None 0 None -2274 LMLLAAAIY 0.0 None None 0 None -2275 SEDDTSYFV 0.0 None None 0 None -2276 RESVKHIGY 0.0 None None 0 None -2277 YQKVVRESV 0.0 None None 0 None -2278 SSVKTPETL 0.0 None None 0 None -2279 VIHHELQVL 0.0 None None 0 None -2280 KTDATPGRL 0.0 None None 0 None -2281 IKRLTAGSL 0.0 None None 0 None -2282 KRLTAGSLF 0.0 None None 0 None -2283 KQLSHHIGA 0.0 None None 0 None -2284 FHVNWFRRY 0.0 None None 0 None -2285 FRRYEAGHF 0.0 None None 0 None -2286 RRYEAGHFL 0.0 None None 0 None -2287 RYEAGHFLW 0.0 None None 0 None -2288 VSDHTPEQH 0.00112786319425 VSDHTPEQ LSDGNPPQ 20.0 69754|Lipoprotein_lpqH_precursor|P46733.1|Mycobacterium_avium|1764 -2289 SFHMDTQNF 0.0 None None 0 None -2290 SFHMDTQNF 0.0 None None 0 None -2291 TQNFCDIGY 0.0 None None 0 None -2292 LALSVFSKL 0.0 None None 0 None -2293 TVKLALSVF 5.19636761594e-05 TVKLALSVF TVRGLTSLF 16.0 52652|||| -2294 LQFAVGQEV 0.0 None None 0 None -2295 PQVPEHLQF 0.037697488936 PQVPEH PQYSEH 23.0 38974|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 -2296 QFAVGQEVF 0.0 None None 0 None -2297 NRYGGGGRY 0.0 None None 0 None -2298 EQLKLGAIF 4.26305904452 LKLGAI IKLGAL 23.0 423046|polyprotein|ACX44272.1|Hepatitis_C_virus_genotype_1|41856 -2299 LLMPYPVIV 0.0 None None 0 None -2300 TLLMPYPVI 0.0 None None 0 None -2301 RALKPVNKI 0.0 None None 0 None -2302 KEAMENEQF 0.0 None None 0 None -2303 LTEENKEAM 0.0 None None 0 None -2304 MEVPNIASS 0.0 None None 0 None -2305 RRFASGEKV 0.0 None None 0 None -2306 TFRDVAVEF 0.0350794875147 TFRDVA TWRDMA 22.0 186175|polyprotein|AFY10053.1|Dengue_virus_3|11069 -2307 FHISLFQYM 0.0 None None 0 None -2308 LIIDEDFHI 0.0 None None 0 None -2309 VLETAAPGV 0.0 None None 0 None -2310 ESHEKGCFW 0.0 None None 0 None -2311 MADAKGYTV 2.48831775731 MADAKGY MGDAGGY 26.0 3094|Antigen_85-B_precursor_(85B)_(Extracellular_alpha-antigen)_(Antigen_85_complex_B)_(Ag85B)_(Mycolyl_transferase_85B)_(Fibronectin-binding_protein_B)_(30_kDa_extracellular_protein)|P31952|Mycobacterium_tuberculosis|1773 -2312 KQLPRILEA 0.0 None None 0 None -2313 HTCQVNGRW 0.0130808799724 TCQVNGRW SCEGLGAW 22.0 79628|E1_protein|BAA19893.1|Rubella_virus|11041 -2314 PLLPSIISL 0.0 None None 0 None -2315 AIWEAVMSA 3.99661222935 IWEAV MWEAV 25.0 37590|VP1|BAF93325.1|Human_polyomavirus_1|1891762 -2316 AVMSALPSL 0.0 None None 0 None -2317 MSALPSLNW 0.0 None None 0 None -2318 GLDGPLVHV 0.0 None None 0 None -2319 SIRVSQKGW 0.0 None None 0 None -2320 PTDPGHFLV 0.0 None None 0 None -2321 MRGEHRFHM 0.0 None None 0 None -2322 KLSHCLSKA 0.0 None None 0 None -2323 CRPQCCQSV 32.8617887736 CRPQCCQSV CRVLCCYVL 28.0 11956|UL123;_IE1|AAR31448.1|Human_betaherpesvirus_5|10359 -2324 VRNPEPSPL 0.0 None None 0 None -2325 VLVVSPWPA 0.0 None None 0 None -2326 GMLWAMMSI 0.306314234534 GMLWAM GVLWTV 23.0 95940|polyprotein|BAA32666.1|Hepatitis_C_virus_genotype_6|42182 -2327 YMGMLWAMM 0.15801288777 GMLWAM GVLWTV 23.0 95908|Genome_polyprotein|O92529.3|Hepatitis_C_virus_genotype_6|42182 -2328 SRAVTSTTI 0.0 None None 0 None -2329 KTASWAEVV 0.0 None None 0 None -2330 WTFALTSGL 0.0 None None 0 None -2331 TDFNNGSYL 0.0 None None 0 None -2332 VTDFNNGSY 0.0 None None 0 None -2333 LLDTIPWYL 0.0 None None 0 None -2334 ASSDHTTHL 0.0 None None 0 None -2335 SHSSCVWLW 0.0 None None 0 None -2336 TGSHSSCVW 0.0 None None 0 None -2337 SIGELLQVL 0.0 None None 0 None -2338 TGFVRRPLW 0.0 None None 0 None -2339 DAEPFQRGW 0.127646462332 DAEPFQR HASPFER 24.0 23566|tegument_protein_UL7|NP_044476.1|Human_alphaherpesvirus_2|10310 -2340 FIFSDTVVL 0.0547221613587 FSDTVVL FKDNVIL 23.0 50779|N_protein|AAP13445.1|SARS_coronavirus_Urbani|228330 -2341 FIFSDTVVL 0.0775477115471 FSDTVVL FKDNVIL 23.0 50779|N_protein|AAP13445.1|SARS_coronavirus_Urbani|228330 -2342 FSDTVVLLF 0.804164436493 FSDTVVLL FKDNVILL 27.0 50779|N_protein|AAP13445.1|SARS_coronavirus_Urbani|228330 -2343 MHFIFSDTV 0.0 None None 0 None -2344 TVVLLFDFW 0.0 None None 0 None -2345 YHPGAMHCV 0.0 None None 0 None -2346 CAFSGTLPW 0.0 None None 0 None -2347 FMCAFSGTL 0.0 None None 0 None -2348 STHPSLSQW 1087.72967514 STHPSLSQW NTRPPLGNW 27.0 68601|polyprotein|AAA45534.1|Hepatitis_C_virus|11103 -2349 SRKDRAPKC 0.0 None None 0 None -2350 LMGLASTTV 0.0 None None 0 None -2351 SLLAIHQWV 0.204347866324 LAIHQWV LAVDPWV 24.0 143690|Genome_polyprotein|P06441.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 -2352 SSLLAIHQW 0.0 None None 0 None -2353 AIHIVAEKK 0.0 None None 0 None -2354 ESLPPSPTW 0.0 None None 0 None -2355 WAGNVLAPY 1.87387179047 WAGNVLAP WAGWLLSP 30.0 36352|Polyprotein|P90247|Hepatitis_C_virus|11103 -2356 QIIAGHFRK 0.0 None None 0 None -2357 STSSRSHRY 0.0 None None 0 None -2358 FHQCLSIYY 1.78908850466 FHQCLSI FHLCLII 27.0 93431|pre-C/C_protein|ABY54138.1|Hepatitis_B_virus|10407 -2359 IYYWDIRYK 0.00992413375792 YYWDIRYK HTWTEQYK 20.0 183619|nonstructural_protein_NS1|1802191G|Dengue_virus|12637 -2360 LFHQCLSIY 102.125443496 LFHQCLSI LFHLCLII 31.0 93431|pre-C/C_protein|ABY54138.1|Hepatitis_B_virus|10407 -2361 SIYYWDIRY 0.0 None None 0 None -2362 SIYYWDIRY 0.0 None None 0 None -2363 SRHTIRELL 0.0 None None 0 None -2364 QINIPIGPY 0.0 None None 0 None -2365 GGMQALGLY 0.378933871481 GGMQALGLY GGSRVEGIF 20.0 61861|Nucleoprotein|P03418.1|Human_respiratory_syncytial_virus_A2|11259 -2366 FLNLSQPRK 0.0 None None 0 None -2367 RLNSHFLNL 1.98031425281 RLNSHFLNL RVDLHFINL 31.0 119822|110_kd_polyprotein_precursor|CAA28880.1|Rubella_virus|11041 -2368 ERSLQVKRV 0.0 None None 0 None -2369 LQVKRVFVK 0.0 None None 0 None -2370 RSLQVKRVF 0.0 None None 0 None -2371 RVFVKGMKK 0.0 None None 0 None -2372 CSSSIGTIW 0.0 None None 0 None -2373 WSHASASLY 0.0 None None 0 None -2374 WSHASASLY 0.0 None None 0 None -2375 KESNAGRYY 0.0 None None 0 None -2376 VKESNAGRY 0.0 None None 0 None -2377 IVSVKPNMK 0.074476186027 VSVKPN VSIAPN 23.0 19359|IMMUNOGENIC_PROTEIN_MPT64_(ANTIGEN_MPT64/MPB64)|CAA98382.1|Mycobacterium_tuberculosis_H37Rv|83332 -2378 FSYPKRPII 0.0 None None 0 None -2379 MSHPPNILK 0.0 None None 0 None -2380 GARPGLGRY 0.0 None None 0 None -2381 ITSRDATRF 0.0 None None 0 None -2382 TRFPIIASC 0.0 None None 0 None -2383 RLLSSGTAK 0.0 None None 0 None -2384 KVLELADRF 0.0 None None 0 None -2385 RVSTGSVHK 0.0 None None 0 None -2386 VVGAVGVGK 0.0 None None 0 None -2387 LSFRSSSCR 0.0 None None 0 None -2388 EMFEHLFGK 0.533333333333 EMFEHLF DMWEHAF 26.0 9415|Superoxide_dismutase|P17670.1|Mycobacterium_tuberculosis|1773 -2389 TRAHCHLPV 0.618719512219 RAHCHLPV RKHRHLPV 32.0 75408|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 -2390 ILDYMQLRK 0.0 None None 0 None -2391 KILDYMQLR 0.0 None None 0 None -2392 TTMLDRGPK 0.0 None None 0 None -2393 IHITEEEAV 0.0 None None 0 None -2394 LVSMTYDRY 0.0 None None 0 None -2395 MTYDRYVAI 0.0764884706029 YDRYVA YKRYIS 22.0 39591|polyprotein|AAA45677.1|Hepatitis_C_virus_(isolate_H77)|63746 -2396 MVLLVSMTY 0.0 None None 0 None -2397 MVLLVSMTY 0.0 None None 0 None -2398 MVLLVSMTY 0.0 None None 0 None -2399 VSMTYDRYV 0.0 None None 0 None -2400 IHMDARLHT 0.0 None None 0 None -2401 MGMALLIHM 0.0 None None 0 None -2402 FKSKVPQTW 0.0 None None 0 None -2403 VGQQQQVLW 0.0 None None 0 None -2404 DSSSWSDRY 3.70689655172 SWSDRY TWADEY 26.0 33912|FL-160-2_protein_-_Trypanosoma_cruzi|JH0823|Trypanosoma_cruzi|5693 -2405 SGGHDSSSW 0.0 None None 0 None -2406 YEEYRGHSL 0.0 None None 0 None -2407 HTSTVRESY 0.0 None None 0 None -2408 HTSTVRESY 0.0 None None 0 None -2409 SHYGQPDRQ 0.0 None None 0 None -2410 DHEVYLKHL 0.0 None None 0 None -2411 GGLFIASNW 0.0 None None 0 None -2412 KVTRLHRRK 0.0 None None 0 None -2413 LMSTSEEEF 0.0 None None 0 None -2414 LSNNCVPQM 0.0 None None 0 None -2415 STRDEIEGL 1.14900483451 RDEIEG EDEIDG 23.0 110431|E7|AAD33253.1|Human_papillomavirus_type_16|333760 -2416 RMCTVTNYF 0.0 None None 0 None -2417 VMVSLKPDK 0.0 None None 0 None -2418 CRQEQERKF 0.0 None None 0 None -2419 EQEERREQL 0.0 None None 0 None -2420 FRLEEQKVC 0.0 None None 0 None -2421 QSLCGTRFY 0.0 None None 0 None -2422 TAAAAPTPF 0.0 None None 0 None -2423 DRNTFRHSL 0.0 None None 0 None -2424 NTFRHSLVV 0.0 None None 0 None -2425 RMNSFLHIL 0.0 None None 0 None -2426 RMNSFLHIL 0.0 None None 0 None -2427 SRMNSFLHI 0.0 None None 0 None -2428 GSFPTEYIL 0.0 None None 0 None -2429 VTNCHKNYW 0.0 None None 0 None -2430 VVTNCHKNY 0.131382703091 VVTNCHK IVTFCCK 20.0 110184|E7|AAD33253.1|Human_papillomavirus_type_16|333760 -2431 DMAPTRPRW 0.172014343171 MAPTRPRW FAPALPIW 24.0 422989|polyprotein|ABY67644.1|Hepatitis_C_virus_genotype_1|41856 -2432 FRRPQESLL 0.0 None None 0 None -2433 GINNKVCFW 0.0 None None 0 None -2434 LLTDTNSWW 0.874238307242 LLTDTNSW VLTDFKTW 26.0 69797|polyprotein|BAA09073.1|Hepatitis_C_virus_subtype_1b|31647 -2435 QLLTDTNSW 0.928593037485 LLTDTNSW VLTDFKTW 26.0 69797|polyprotein|BAA09073.1|Hepatitis_C_virus_subtype_1b|31647 -2436 HQRVHSGEK 0.0 None None 0 None -2437 QRYSHQRVH 0.0 None None 0 None -2438 VKSKLIAHY 0.0 None None 0 None -2439 SVDECELHK 0.0 None None 0 None -2440 PMPPPLEPI 0.0987361416297 MPPPLEP LPDPLKP 27.0 27241|Spike_glycoprotein_precursor|P59594.1|SARS_coronavirus|227859 -2441 KEIDVIAIP 0.0 None None 0 None -2442 YKDYAAELV 0.141859211272 YKDYAA FKDFAA 25.0 182917|polyprotein|CDF77361.1|Dengue_virus_3|11069 -2443 DNLDSDNTY 0.185784734323 NLDSDNTY HYDEDNPY 24.0 72563|polyprotein|AAB70696.1|Dengue_virus_type_1_Hawaii|10000440 -2444 LAVTLGLAL 0.0 None None 0 None -2445 HNNNRPLTM 0.0 None None 0 None -2446 WAVPPLLLA 0.411375661376 AVPPLL AIPPLV 26.0 73059|kaposin|AAC57155.1|Human_gammaherpesvirus_8|37296 -2447 RCYVRGLFH 0.0 None None 0 None -2448 KITAQRLSH 0.0 None None 0 None -2449 SSLHSEPPK 0.0 None None 0 None -2450 QAQALGIPL 0.0 None None 0 None -2451 QAQALGIPL 0.0 None None 0 None -2452 IPKSPEEAI 0.0 None None 0 None -2453 PEEPTSPAA 0.206085938541 PTSPAA PTAPCA 24.0 79628|E1_protein|BAA19893.1|Rubella_virus|11041 -2454 RVQSRPIPI 0.0396216155661 SRPIPI SEPLPV 23.0 57591|Cobalamin_(vitamin_B12)_synthesis_protein/P47K_family_protein|YP_169986.1|Francisella_tularensis_subsp._tularensis_SCHU_S4|177416 -2455 HSLQQAQSV 0.0 None None 0 None -2456 PLFTTQCGK 0.0219525875844 PLFTTQ PTFTSQ 23.0 75718|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 -2457 HMEAEMAQK 0.0 None None 0 None -2458 VQLPKVSEM 0.0 None None 0 None -2459 ITAQRLSHL 0.0 None None 0 None -2460 LLLSPPVEV 0.0 None None 0 None -2461 IPILPLIYI 0.26866979834 PILPLI PFLPLL 24.0 27345|Large_envelope_protein|P03138.3|Hepatitis_B_virus_subtype_ayw|10418 -2462 AEAQTPEDS 0.0 None None 0 None -2463 LLSPPVEVK 0.0 None None 0 None -2464 TEHDVQIYV 0.0 None None 0 None -2465 FISLKFSSK 0.0 None None 0 None -2466 IPGPIPGPI 0.0153161126032 PGPIPG PGTGPG 21.0 47760|EBNA-1_protein|Q777E1|Human_gammaherpesvirus_4|10376 -2467 KTRRTSSLH 0.0 None None 0 None -2468 EEPTSPAAA 0.0642546482275 PTSPAA PTAPCA 24.0 79628|E1_protein|BAA19893.1|Rubella_virus|11041 -2469 WILSARLLK 0.0 None None 0 None -2470 QQFPSLELL 0.0 None None 0 None -2471 RPIPILPLI 0.371841950785 PILPLI PFLPLL 24.0 27345|Large_envelope_protein|P03138.3|Hepatitis_B_virus_subtype_ayw|10418 -2472 NMKEQVVIL 0.0 None None 0 None -2473 AQRLSHLNK 0.0 None None 0 None -2474 RAYRDDTDL 0.0 None None 0 None -2475 NVFWGEHFK 0.0 None None 0 None -2476 YYKDYAAEL 0.450065235762 YKDYAA FKDFAA 25.0 182917|polyprotein|CDF77361.1|Dengue_virus_3|11069 -2477 QQFPSLELL 0.0 None None 0 None -2478 SLKFSSKIK 5.34901960784 LKFSSKI LKFYSKI 26.0 110227|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 -2479 FLFGLAQNL 0.0 None None 0 None -2480 YVRGLFHSL 0.0 None None 0 None -2481 TENSETTTA 0.056544975831 TENSETT VENLETT 24.0 149063|NS3_protease/helicase'|NP_803144.1|Hepatitis_C_virus_(isolate_H77)|63746 -2482 ALGIPLTPK 0.0 None None 0 None -2483 NENTTPSPA 0.0 None None 0 None -2484 RLPEVQLPK 8.33669952536e-05 LPEVQLPK LPSDFLPS 16.0 16836|precore/core_protein_[Hepatitis_B_virus]|AAR03815.1|Hepatitis_B_virus|10407 -2485 ISLKFSSKI 1.55102040816 LKFSSKI LKFYSKI 26.0 110227|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 -2486 KEGARNVLA 0.0 None None 0 None -2487 MPNDFWARL 2.15830070732 MPNDFWARL LPNDFFPSV 28.0 16814|precore_protein|CAM58990.1|Hepatitis_B_virus|10407 -2488 FTEHDVQIY 0.0200300974578 FTEHDVQI FTNMEVQL 22.0 183275|polyprotein|AGW21594.1|Dengue_virus_1|11053 -2489 FKFHNLPPL 0.0 None None 0 None -2490 NTYRTPSVL 0.309317439303 YRTPSV YQTPAI 24.0 180617|polyprotein|AGO67248.1|Dengue_virus_2|11060 -2491 IAIPSKCLL 0.0 None None 0 None -2492 EASSAVPTV 0.0 None None 0 None -2493 MAAAVVARL 0.0 None None 0 None -2494 QEFENIKSY 16.338826617 QEFENIKS QRFHNIRG 23.0 178247|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 -2495 FQKDPPADI 0.0 None None 0 None -2496 DMYDGRFLV 0.891117731544 MYDGRFLV LYDGSFAV 29.0 93270|hypothetical_protein|NP_218356.1|Mycobacterium_tuberculosis_H37Rv|83332 -2497 PLYKVRFSK 0.0 None None 0 None -2498 VTRPFISLK 0.0 None None 0 None -2499 IILFNRLLK 0.0 None None 0 None -2500 IPYRDSVLI 0.0 None None 0 None -2501 AEASSAVPT 0.0 None None 0 None -2502 EEMPNDFWA 1.09272457194 MPNDFW LPNDFF 28.0 16814|precore_protein|CAM58990.1|Hepatitis_B_virus|10407 -2503 KMPEMHFKA 0.0221786804353 PEMHFKA PERPFQA 20.0 232153|rhoptry_protein_18|CAJ27113.1|Toxoplasma_gondii_type_I|1209525 -2504 AYSKCFISV 0.0 None None 0 None -2505 LYLKTSQDV 0.0 None None 0 None -2506 DLLTNLMYV 0.0 None None 0 None -2507 LLTNLMYVL 0.0 None None 0 None -2508 YQFPQSIDL 0.0 None None 0 None -2509 VWQRPVLNF 113.663716399 VWQRPV IWFRPV 27.0 37507|Large_T_antigen|P03071.1|Human_polyomavirus_1|1891762 -2510 VEGTFISDY 0.0 None None 0 None -2511 EELEIFMAR 0.0 None None 0 None -2512 YEMIRTFYI 0.0 None None 0 None -2513 EEFPCHKCV 0.0 None None 0 None -2514 NYMAHLVAV 0.0 None None 0 None -2515 FADFEWHFL 5.50353283986 FADFEWHF YADRKWCF 25.0 46575|polyprotein|AAG30730.1|Dengue_virus_2|11060 -2516 SFADFEWHF 10.4336370598 SFADFEWHF NYADRKWCF 26.0 46575|polyprotein|AAG30730.1|Dengue_virus_2|11060 -2517 FEQTLEELY 0.233610324193 FEQTLEE FHQTLQD 24.0 42430|Major_surface_antigen_precursor|P03141.3|Hepatitis_B_virus|10407 -2518 IYVKPLPIL 0.166416791124 IYVKPLPI IYVYALPL 25.0 58463|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 -2519 VLQIYVKPL 0.0 None None 0 None -2520 RQWRSLTTL 0.0 None None 0 None -2521 FCLGLVVTI 0.0 None None 0 None -2522 GVFCLGLVV 0.0 None None 0 None -2523 TLGVFCLGL 1.74091147886 TLGVFCLGL TMGVLCLAI 32.0 185978|polyprotein|CDF77361.1|Dengue_virus_3|11069 -2524 IVPRLIMNF 0.0 None None 0 None -2525 LIMNFTLGV 0.0 None None 0 None -2526 GEHPYQCPY 0.0 None None 0 None -2527 VLHRHMTTI 0.0 None None 0 None -2528 HEIDFYRED 0.0 None None 0 None -2529 KLDASVQHL 0.0 None None 0 None -2530 RQLKLDASV 0.0 None None 0 None -2531 FLWLWPLDF 0.00977850494065 FLWLWPLD FLYNRPLN 18.0 98040|trans-sialidase,_putative|EAN80725.1|Trypanosoma_cruzi|5693 -2532 SEDGFLWLW 0.0 None None 0 None -2533 WLWPLDFSS 0.0 None None 0 None -2534 TFRDVAVEF 0.0366333305265 TFRDVA TWRDMA 22.0 186175|polyprotein|AFY10053.1|Dengue_virus_3|11069 -2535 AFSQSAYLI 0.0 None None 0 None -2536 AYLIQHQRF 0.0 None None 0 None -2537 KAFSQSAYL 0.0 None None 0 None -2538 QEEQQQQQL 0.0 None None 0 None -2539 YLFSPQNQF 0.0 None None 0 None -2540 YLFSPQNQF 0.0 None None 0 None -2541 QARKIDHPL 0.0 None None 0 None -2542 QARKIDHPL 0.0 None None 0 None -2543 GLFVHTPCL 0.0397343073407 FVHTPC FVYTPS 24.0 141281|tegument_protein_UL21|NP_044622.1|Human_alphaherpesvirus_1|10298 -2544 RVLPAGLFV 0.0 None None 0 None -2545 VHTPCLVGL 1.29995014283 HTPCLVGL HYPCTVNF 25.0 72566|polyprotein|BAD73987.1|Hepatitis_C_virus_subtype_1b|31647 -2546 AGLDSYPEL 0.0 None None 0 None -2547 LVVSRSVSL 0.0 None None 0 None -2548 LVVSRSVSL 0.0 None None 0 None -2549 CSVDHRSVL 0.0 None None 0 None -2550 HRSVLQRIM 0.0 None None 0 None -2551 KMWEQEEKI 0.0 None None 0 None -2552 FGIISIIFV 0.0 None None 0 None -2553 GIISIIFVV 0.0 None None 0 None -2554 IFGIISIIF 0.0 None None 0 None -2555 RIFGIISII 0.0 None None 0 None -2556 STAARIFGI 0.0 None None 0 None -2557 TAARIFGII 0.0 None None 0 None -2558 LSVQLGPTV 0.0 None None 0 None -2559 CYTFNSIII 0.0 None None 0 None -2560 SIIIFGPFL 0.0 None None 0 None -2561 SIIIFGPFL 0.0 None None 0 None -2562 YTFNSIIIF 0.0 None None 0 None -2563 LEIQTPEAV 0.0 None None 0 None -2564 YLALAAQCL 186.219838246 ALAAQCL ALAAYCL 28.0 102636|Genome_polyprotein|P27958.3|Hepatitis_C_virus_subtype_1a|31646 -2565 YLALAAQCL 2537.30645606 ALAAQCL ALAAYCL 28.0 102636|Genome_polyprotein|P27958.3|Hepatitis_C_virus_subtype_1a|31646 -2566 AGCPAAQEL 0.0 None None 0 None -2567 RARPAGCPA 0.153281835099 RARPAG RARPRG 26.0 136865|tegument_protein|CAB06735.1|Human_alphaherpesvirus_2|10310 -2568 RPAGCPAAQ 0.0553403897978 RPAGCP RPQGLP 23.0 190533|nucleocapsid_protein|AAP49024.1|SARS_coronavirus|227859 -2569 AGVDHIITM 0.405289934875 DHIITM DHTITL 24.0 42455|Probable_Na(+)-translocating_NADH-quinone_reductase_subunit_A|O84639.1|Chlamydia_trachomatis|813 -2570 LSIAGVDHI 0.19293623707 LSIAGVD LSVAGVS 25.0 120187|E1_protein|BAA19893.1|Rubella_virus|11041 -2571 PPRYIGIPI 7.34699064743 YIGIPI YYGVPV 25.0 118|envelope_glycoprotein|ABS76372.1|Human_immunodeficiency_virus_1|11676 -2572 CMLVGDSAV 0.426158812917 CMLVGDSA CKLLPDTA 22.0 164258|nucleocapsid_protein|AAA43837.1|Hantaan_virus_76-118|11602 -2573 MLSSIKCML 0.0 None None 0 None -2574 MLSSIKCML 0.0 None None 0 None -2575 FGHTYVPAF 0.0 None None 0 None -2576 GQDFGHTYV 0.0 None None 0 None -2577 YSTPQGQDF 1.31803627544 STPQGQ TTPFGQ 21.0 180643|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -2578 FVGLAIGTL 0.0398377334692 GLAIGTL GLSPGTL 23.0 21638|protein_F|ABV46152.2|Hepatitis_C_virus_(isolate_Japanese)|11116 -2579 IGTLSGDAL 0.0 None None 0 None -2580 NMFEISNRL 0.0 None None 0 None -2581 VDLGSTTPL 0.0 None None 0 None -2582 IPLWGSPVT 2.31085692389 PLWGSPV PLFGYPV 27.0 48321|||| -2583 FVLSMQPVV 0.235323743699 FVLSMQP YVLDLQP 25.0 76334|Protein_E7|P17387.1|Human_papillomavirus_type_31|10585 -2584 FVLSMQPVV 0.215153137096 FVLSMQP YVLDLQP 25.0 76334|Protein_E7|P17387.1|Human_papillomavirus_type_31|10585 -2585 SMQPVVFQA 0.0 None None 0 None -2586 YYDPFVLSM 0.0 None None 0 None -2587 YYDPFVLSM 0.0 None None 0 None -2588 YSHQNGASY 0.0 None None 0 None -2589 AGVLLVLAL 0.651899369479 VLLVLAL ILLVLAL 27.0 21199|Circumsporozoite_protein_precursor|P08677.2|Plasmodium_vivax_strain_Belem|31273 -2590 RFAGVLLVL 0.452826067909 FAGVLLVL FLGPLLVL 25.0 178829|envelope_protein|BAJ51675.1|HBV_genotype_D|489483 -2591 VLALILPGT 0.0 None None 0 None -2592 VLLVLALIL 0.131262388183 VLLVLAL ILLVLAL 27.0 21199|Circumsporozoite_protein_precursor|P08677.2|Plasmodium_vivax_strain_Belem|31273 -2593 RQIPAQRDL 0.327777777778 PAQRDL PASRDL 26.0 93224|core_protein|AAL31859.1|Hepatitis_B_virus|10407 -2594 SYRKSVRQI 0.0 None None 0 None -2595 CYYELNQCL 4.36257309942 CYYELNQC CYEQLNDS 26.0 110431|E7|AAD33253.1|Human_papillomavirus_type_16|333760 -2596 CYYELNQCL 19.0060606061 CYYELNQC CYEQLNDS 26.0 110431|E7|AAD33253.1|Human_papillomavirus_type_16|333760 -2597 CPLCPFLTM 0.0 None None 0 None -2598 FMNRFQCPL 0.0 None None 0 None -2599 FMNRFQCPL 0.0 None None 0 None -2600 FQCPLCPFL 0.0 None None 0 None -2601 FQCPLCPFL 0.0 None None 0 None -2602 RFQCPLCPF 0.0 None None 0 None -2603 RFQCPLCPF 0.0 None None 0 None -2604 APEPLLLSW 0.0152696940155 PLLLS PLLLS 23.0 149036|E2_protein|NP_751921.1|Hepatitis_C_virus_(isolate_H77)|63746 -2605 ASLHHHHHR 0.0 None None 0 None -2606 RPPPSQASL 0.0 None None 0 None -2607 FPDHMACDL 0.0 None None 0 None -2608 ALLGNRTAL 0.0 None None 0 None -2609 GPVSAPGLL 0.0 None None 0 None -2610 HVYRNFLNK 0.0 None None 0 None -2611 RPRGDNGYT 0.0 None None 0 None -2612 SNSESEILK 0.0 None None 0 None -2613 AVDRYVAMR 0.0 None None 0 None -2614 RYVAMRHPL 0.0580304162483 RYVAMRHPL QYIYMGQPL 23.0 185327|polyprotein|ACF49259.1|Dengue_virus_type_1_Hawaii|10000440 -2615 YVAMRHPLR 0.0 None None 0 None -2616 RAGESVWPK 0.0 None None 0 None -2617 VWPKKINNI 11.2225440638 VWPKKI VWLKKL 24.0 181035|||| -2618 VVGADGVGK 0.0 None None 0 None -2619 KTETYDNYK 0.0 None None 0 None -2620 RQLTVESDK 0.0 None None 0 None -2621 ITLTATSQK 0.0 None None 0 None -2622 HPTASTLST 0.0 None None 0 None -2623 NPSHPTAST 0.0 None None 0 None -2624 LMLLQSGYK 0.0 None None 0 None -2625 HFPIYHLLL 0.0 None None 0 None -2626 LASSFVFLY 0.0 None None 0 None -2627 LISEGQRLK 0.0 None None 0 None -2628 KPLPLVTDL 0.0 None None 0 None -2629 LPLVTDLSL 0.0 None None 0 None -2630 APIAPTFYK 0.0 None None 0 None -2631 APTFYKPKL 0.0 None None 0 None -2632 IAPTFYKPK 0.0 None None 0 None -2633 TFYKPKLLK 0.0 None None 0 None -2634 VFQHIFDLI 0.0 None None 0 None -2635 AAATAVVAF 0.0 None None 0 None -2636 ALLRATDTI 0.0 None None 0 None -2637 APFDKHCAV 0.0 None None 0 None -2638 APFLNSVSI 0.00547938159601 APFLNSVS APIPASVS 18.0 179765|cell_surface_protein_(associated_with_virulence)|NP_302372.1|Mycobacterium_leprae_TN|272631 -2639 APHGEEAHL 0.0 None None 0 None -2640 APLLPRTHL 105.804891576 APLLPRT APLPPST 23.0 179766|cell_surface_protein_(associated_with_virulence)|NP_302372.1|Mycobacterium_leprae_TN|272631 -2641 APRRHSGRV 0.0 None None 0 None -2642 APSLPSPTA 0.528755892864 PSLPSPT PTLHGPT 22.0 6591|polyprotein|AAB67037.1|Hepatitis_C_virus_(isolate_H77)|63746 -2643 APVTLRGSY 0.0 None None 0 None -2644 ATGGHHQPL 0.687294743501 GHHQPL GHEEPI 25.0 180488|polyprotein|AGO67248.1|Dengue_virus_2|11060 -2645 AVMAFDLCV 0.0 None None 0 None -2646 AVMAFDRSV 0.0 None None 0 None -2647 AYQVSVCAF 0.565327595099 AYQVSVCA AYQATVCA 34.0 13518|HCV-1|AAA45676.1|Hepatitis_C_virus_genotype_1|41856 -2648 CTTPVTVEI 0.0 None None 0 None -2649 CYYYFLCLL 0.0 None None 0 None -2650 DTPRHRLLV 0.0 None None 0 None -2651 EAQQSSHCL 0.0 None None 0 None -2652 EPRITRSFV 0.0 None None 0 None -2653 ETGLALKYL 0.0 None None 0 None -2654 FSFQVDSPV 0.0 None None 0 None -2655 FSILSTALL 0.0453532771775 FSILSTALL FSIFLLALL 23.0 57894|polyprotein|BAD73987.1|Hepatitis_C_virus_subtype_1b|31647 -2656 GLRKTNMSL 0.0 None None 0 None -2657 GPNAMRYSL 0.0 None None 0 None -2658 GPRNCIGQA 0.127721163409 GPRNCI DPRRCL 23.0 150556|polyprotein|AGW21594.1|Dengue_virus_1|11053 -2659 HMSACHHSI 0.0 None None 0 None -2660 HPNAHSNST 0.0 None None 0 None -2661 HPWTTDMPA 0.0 None None 0 None -2662 HSNSTSFIF 0.0 None None 0 None -2663 HSNSTSFIF 0.0 None None 0 None -2664 HTWQMRNTV 0.0 None None 0 None -2665 HTWQMRNTV 0.0 None None 0 None -2666 IFSLGRHTW 0.0 None None 0 None -2667 INALIIFIF 0.0 None None 0 None -2668 IPHLLKLAC 0.0 None None 0 None -2669 ISASVCIQV 0.0 None None 0 None -2670 ITSTVMLEV 0.0 None None 0 None -2671 KAFNCSSFV 0.0 None None 0 None -2672 KAFSQSSNL 0.0 None None 0 None -2673 KLFSILSTA 0.0 None None 0 None -2674 KLWATAEAL 0.0 None None 0 None -2675 KTHRIVRRL 0.0 None None 0 None -2676 KTHRIVRRL 0.0 None None 0 None -2677 KTLRKSLPA 0.0 None None 0 None -2678 KTLRKSLPA 0.0 None None 0 None -2679 KYIFNNSII 0.987149197996 KYIFNNSII KYFYCNSLF 24.0 141323|multifunctional_expression_regulator|NP_044657.1|Human_alphaherpesvirus_1|10298 -2680 KYTSAAILV 0.0 None None 0 None -2681 LALSVTEMV 0.0 None None 0 None -2682 LHSPMYFFL 0.0 None None 0 None -2683 LHTPVYFLL 0.0 None None 0 None -2684 LLVSLTVTF 0.094208760953 LLVSLTV LLVCLTV 24.0 40264|Cytochrome_P450_2A6|P11509.3|Homo_sapiens|9606 -2685 LPGGVGRTL 0.0104130689254 LPGGVGRTL VPGWSRRTL 22.0 141461|ubiquitin_E3_ligase_ICP0|NP_044601.1|Human_alphaherpesvirus_1|10298 -2686 LPSDDRGSL 0.206878016438 DDRGSL DSRGSL 25.0 55709|Genome_polyprotein|P27958.3|Hepatitis_C_virus_subtype_1a|31646 -2687 LSVADQEKV 0.0 None None 0 None -2688 LWGKHQFIL 0.892559226889 LWGKHQFI LWGYLQYV 27.0 42094|telomer_length_regulation_protein_TEL1|EDV12172.1|Saccharomyces_cerevisiae|4932 -2689 MAFDLCVAI 0.0486655905336 FDLCV YDLCI 25.0 112503|E6_protein|ACV53993.1|Human_papillomavirus_type_35|10587 -2690 MAFDRSVAI 0.0 None None 0 None -2691 MAFDRSVAI 0.0 None None 0 None -2692 MIISASVCI 0.0 None None 0 None -2693 MIISASVCI 0.0 None None 0 None -2694 MLDLLTNTL 0.0 None None 0 None -2695 MTNGLCIWL 0.0 None None 0 None -2696 MVNATACAV 0.0 None None 0 None -2697 NAFQEARRL 0.0 None None 0 None -2698 PSAPKPSTL 6.16092555862 SAPKPST SAPLPSN 24.0 88377|IE62|AAP32859.1|Human_alphaherpesvirus_3|10335 -2699 QALRAGLAL 0.0 None None 0 None -2700 QALRAGLAL 0.0 None None 0 None -2701 QAVEFCQRV 0.0 None None 0 None -2702 QILVKICTI 0.0 None None 0 None -2703 QLHFIFHIL 0.0 None None 0 None -2704 QLWGKHQFI 9.62632414914 LWGKHQFI LWGYLQYV 27.0 42094|telomer_length_regulation_protein_TEL1|EDV12172.1|Saccharomyces_cerevisiae|4932 -2705 QPWEHVNAF 0.0 None None 0 None -2706 QQQMASRPF 0.0 None None 0 None -2707 QTSMSQSQV 0.0 None None 0 None -2708 RIIKLLVSL 0.0 None None 0 None -2709 RLALSTFEW 355.619732468 LSTFEW LSTTEW 27.0 37830|polyprotein|BAB18806.1|Hepatitis_C_virus_subtype_1b|31647 -2710 RLHSPMYFF 0.0 None None 0 None -2711 RLHSPMYFF 0.0 None None 0 None -2712 RLHTPVYFL 0.0 None None 0 None -2713 RSFTEENHM 0.0 None None 0 None -2714 RSFVPHLEI 0.0 None None 0 None -2715 RSFVPHLEI 0.0 None None 0 None -2716 RSVAICKPL 0.0 None None 0 None -2717 RVVLINNNL 0.0 None None 0 None -2718 SASSQSSSI 0.0 None None 0 None -2719 SASVCIQVV 0.0 None None 0 None -2720 SIIQDFFAW 0.0 None None 0 None -2721 SINALIIFI 0.0 None None 0 None -2722 SMSQSQVAL 0.0 None None 0 None -2723 SPAQAPIPY 0.108147812318 AQAPIP AQAPPP 24.0 149096|polyprotein|BAB18801.1|Hepatitis_C_virus|11103 -2724 SPGGWRSGW 83.0885140233 GGWRSGW GFWQEGW 32.0 75674|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 -2725 SSEQSIFVV 0.0 None None 0 None -2726 SSIPENEAI 0.0 None None 0 None -2727 STVMLEVPL 0.0 None None 0 None -2728 STVMLEVPL 0.0 None None 0 None -2729 SYSSLDEDF 0.0115200700311 YSSLDED YSRADEE 22.0 12585|ESAT-6-like_protein_esxB|P0A566.2|Mycobacterium_tuberculosis|1773 -2730 TPRHRLLVL 0.0 None None 0 None -2731 TSMYNEILI 0.0 None None 0 None -2732 TSVPVTTAV 0.0 None None 0 None -2733 VPADSTQTL 0.0 None None 0 None -2734 VSIETHLLF 0.0 None None 0 None -2735 VSIETHLLF 0.0 None None 0 None -2736 VSLTVTFVL 0.0 None None 0 None -2737 VTTAVSTFV 0.0 None None 0 None -2738 VTTGLMGAV 0.0 None None 0 None -2739 YSSLDEDFL 0.0 None None 0 None -2740 YVQKRSSQI 0.0 None None 0 None -2741 YYFLCLLL* 0.0 None None 0 None -2742 YYYFLCLLL 0.0 None None 0 None -2743 ASLDVTLRL 0.0 None None 0 None -2744 ISSHLSTLV 1.22721158737 SHLSTLV SHYFTLV 22.0 98466|Trans-sialidase|SRC7915|Trypanosoma_cruzi|5693 -2745 LSTLVDFAI 0.0 None None 0 None -2746 KTSVGSTKY 0.0 None None 0 None -2747 HPCERSDEV 0.0 None None 0 None -2748 ITVEEQHRI 0.0 None None 0 None -2749 ITVEEQHRI 0.0 None None 0 None -2750 MTAVQTLHL 0.0 None None 0 None -2751 PAMTAVQTL 0.0 None None 0 None -2752 RQLPAMTAV 0.0 None None 0 None -2753 ETVFTRSSW 0.0 None None 0 None -2754 FTRSSWDWI 0.0 None None 0 None -2755 VFTRSSWDW 0.0 None None 0 None -2756 EPPPPPSPL 0.0101907339737 PPPSPL PPCKPL 22.0 96366|polyprotein|ABR25251.1|Hepatitis_C_virus|11103 -2757 QTTQLSLNF 0.0 None None 0 None -2758 GAMDGATYI 0.0 None None 0 None -2759 MAFVKSVWL 0.0 None None 0 None -2760 CAVRRAAQV 0.0 None None 0 None -2761 QAVAQAVNW 0.0 None None 0 None -2762 NPKTWNTMV 0.0 None None 0 None -2763 QLYMNPKTW 4.12392711167 QLYMNPKTW RLYQNPTTY 31.0 135263|hemagglutinin|ACX31970.1|Influenza_A_virus_(A/Bar-headed_Goose/Qinghai/61/05(H5N1))|336238 -2764 RQVGFCVQW 0.0 None None 0 None -2765 KMLLAPGRF 1.4325134436 LLAPG LLAPG 25.0 59240|HCV-1|AAA45676.1|Hepatitis_C_virus_genotype_1|41856 -2766 MLLAPGRFI 0.588309359247 LLAPG LLAPG 25.0 59240|HCV-1|AAA45676.1|Hepatitis_C_virus_genotype_1|41856 -2767 FTMPEDEYM 0.0 None None 0 None -2768 FTMPEDEYM 0.0 None None 0 None -2769 MPEDEYMVY 0.0 None None 0 None -2770 IAWPADRTA 0.0 None None 0 None -2771 QALIRPTTF 0.514471687749 LIRPTTF LLRPTTL 28.0 13165|trans-sialidase,_putative|EAN81972.1|Trypanosoma_cruzi|5693 -2772 FPEYDGVDH 0.0 None None 0 None -2773 EIAEIEYSI 0.0 None None 0 None -2774 FVVSACNAT 0.0 None None 0 None -2775 WITPAQREY 2.29081841307 TPAQREY TPTLHEY 22.0 110940|Protein_E7|P03129.1|Human_papillomavirus_type_16|333760 -2776 EPVWGLEAI 0.0 None None 0 None -2777 RLSWQASSL 0.0 None None 0 None -2778 KIKELAAEF 0.0 None None 0 None -2779 VPILQSTPV 0.0416654367885 VPILQSTP LPIRYQTP 21.0 180647|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -2780 APRGFLTNY 0.0 None None 0 None -2781 RAAEQRRAY 0.0 None None 0 None -2782 KSASWITWI 0.34874341875 SWITW QWLTW 29.0 70634|Non-capsid_protein_NS-1|P07298.1|Human_parvovirus_B19|10798 -2783 TPWSFTGTV 0.0459224896119 PWSFTG QWNFAG 24.0 42797|6_kDa_early_secretory_antigenic_target|P0A564.2|Mycobacterium_tuberculosis|1773 -2784 GPLADATPL 0.0 None None 0 None -2785 LAGERRFAF 0.0 None None 0 None -2786 IAASAMCVF 0.0 None None 0 None -2787 SSYGRNHYI 3.39831238883 GRNHYI GRSHFL 25.0 8554|Genome_polyprotein|P08617.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 -2788 IIHTGARPY 0.0 None None 0 None -2789 DTATGNCLR 0.0 None None 0 None -2790 GPYENCSVF 0.0 None None 0 None -2791 ETYQQALGK 0.102756058551 ETYQQALGK QVYQDWLGR 23.0 23288|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 -2792 YQQALGKRF 0.0447142296507 YQQALGK YQDWLGR 21.0 23288|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 -2793 YQQALGKRF 0.165670773671 YQQALGK YQDWLGR 21.0 23288|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 -2794 FAIHKIKQF 0.0 None None 0 None -2795 GYTVNIPTI 0.0 None None 0 None -2796 HSPSVASMK 0.0 None None 0 None -2797 YTDCHASNL 0.160144923269 DCHASN DCHAQD 28.0 6094|Genome_polyprotein|Q81495.3|Hepatitis_C_virus_(isolate_HCV-K3a/650)|356416 -2798 TYSSPTPNM 0.0616536351308 TYSSPT TYTFPT 23.0 232153|rhoptry_protein_18|CAJ27113.1|Toxoplasma_gondii_type_I|1209525 -2799 DAIPFGNVP 0.0 None None 0 None -2800 IPFGNVPVL 0.0 None None 0 None -2801 NYFGVQDAI 0.0 None None 0 None -2802 ETLGRGNPM 0.0 None None 0 None -2803 MALQLFLQI 0.0 None None 0 None -2804 MALQLFLQI 0.0 None None 0 None -2805 MALQLFLQI 0.0 None None 0 None -2806 KVHSAVITI 0.0 None None 0 None -2807 QAGEYSRVV 0.0 None None 0 None -2808 RVVDCYLKV 0.0 None None 0 None -2809 WQRPTLESI 0.0 None None 0 None -2810 WQRPTLESI 0.0 None None 0 None -2811 VAQLGFQPL 0.0 None None 0 None -2812 EAINCLNVA 0.0 None None 0 None -2813 VAIDIYTDM 0.0 None None 0 None -2814 HFLHSWTNL 0.349366438751 LHSWTN LHQWIN 28.0 103322|polyprotein|BAB18806.1|Hepatitis_C_virus|11103 -2815 TFKHLVHFL 0.0 None None 0 None -2816 YTFKHLVHF 0.00127547167216 YTFKHLVHF YKFMGRSHF 19.0 8554|Genome_polyprotein|P08617.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 -2817 YTFKHLVHF 0.00173099726936 YTFKHLVHF YKFMGRSHF 19.0 8554|Genome_polyprotein|P08617.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 -2818 IIMSRNAYV 0.0 None None 0 None -2819 LRYPIIMSR 0.0 None None 0 None -2820 MSRNAYVPM 0.0 None None 0 None -2821 NAPALLTPR 0.0 None None 0 None -2822 RAGSAGGTV 0.0 None None 0 None -2823 EAFTLKATV 6.35897435897 FTLKATV FTLVATV 26.0 98640|trans-sialidase,_putative|EAN80840.1|Trypanosoma_cruzi|5693 -2824 YSVIRGEAF 0.0 None None 0 None -2825 DIYSMPEGK 0.0 None None 0 None -2826 IYSMPEGKL 0.0557903921081 YSMPEGKL YSMCTGKF 23.0 150456|polyprotein|AGO67248.1|Dengue_virus_2|11060 -2827 SMPEGKLHV 0.0224344124258 MPEGKL LPQGQL 22.0 13701|Trans-activator_protein_BZLF1|P03206.2|Human_gammaherpesvirus_4|10376 -2828 YSMPEGKLH 0.292799376299 YSMPEGKL YSMCTGKF 23.0 150456|polyprotein|AGO67248.1|Dengue_virus_2|11060 -2829 FFFLCVCVF 0.100381408019 FFFLCVCV LLILCLCL 24.0 49831|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 -2830 FFFLCVCVF 0.0684531631414 FFFLCVCV LLILCLCL 24.0 49831|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 -2831 FFLCVCVFV 0.673124000294 FFLCVCV LILCLCL 24.0 49831|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 -2832 FFLCVCVFV 0.243568175313 FFLCVCV LILCLCL 24.0 49831|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 -2833 HLLQRYNEF 0.366998782491 HLLQRYNEF NLLQRANEL 28.0 154980|tegument_protein|CAB06735.1|Human_alphaherpesvirus_2|10310 -2834 RAEERRRHL 2.38489063295 AEERRRHL PEEKQRHL 30.0 110394|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 -2835 ITTTGQKLR 0.0 None None 0 None -2836 IMALAVLII 0.0 None None 0 None -2837 TALVVVSIM 0.0 None None 0 None -2838 DVLPYDAFV 0.0894142186526 VLPYDAFV VYPYDEFV 32.0 141423|envelope_glycoprotein_B|NP_044629.1|Human_alphaherpesvirus_1|10298 -2839 LTLATFSRI 0.0 None None 0 None -2840 VLTLATFSR 0.0 None None 0 None -2841 MNQRPILTI 0.0 None None 0 None -2842 NQRPILTII 0.0 None None 0 None -2843 FNVNAPDLY 0.0 None None 0 None -2844 NVNAPDLYI 0.0 None None 0 None -2845 RFNVNAPDL 0.0 None None 0 None -2846 FHWRVNFIR 0.0 None None 0 None -2847 IFHWRVNFI 0.0 None None 0 None -2848 KIFHWRVNF 0.0 None None 0 None -2849 LHDTTTRSV 0.0 None None 0 None -2850 LHNNTTRSV 0.0 None None 0 None -2851 TTTRSVHAK 0.0 None None 0 None -2852 HFKAPKISM 0.0 None None 0 None -2853 GTSSTSCSW 0.0 None None 0 None -2854 GVRAQGCYM 0.0 None None 0 None -2855 GVRAQGCYM 0.0 None None 0 None -2856 RAQGCYMDI 0.0 None None 0 None -2857 VAEKGTSKL 0.0 None None 0 None -2858 EAFSVSPEW 0.0 None None 0 None -2859 FSVSPEWAV 0.00283478309185 FSVSPEWA FSMVGNWA 22.0 149052|E1_protein|NP_751920.1|Hepatitis_C_virus_(isolate_H77)|63746 -2860 LTRPVHGAA 3.12682962682 LTRPVHGA LKEPVHGV 28.0 27125|gag-pol_fusion_polyprotein|AAN73817.1|Human_immunodeficiency_virus_1|11676 -2861 MARTAPASG 0.0 None None 0 None -2862 AHQYFAQLL 0.0968441616774 AHQYFAQLL GHQAAMQML 19.0 101673|gag_protein|ABO73990.1|Human_immunodeficiency_virus_1|11676 -2863 AHQYFAQLL 0.100003052772 AHQYFAQLL GHQAAMQML 19.0 101673|gag_protein|ABO73990.1|Human_immunodeficiency_virus_1|11676 -2864 HQYFAQLLA 0.00076046422012 HQYFAQLL HQAAMQML 19.0 101673|gag_protein|ABO73990.1|Human_immunodeficiency_virus_1|11676 -2865 LALQRQRTY 0.0 None None 0 None -2866 LALQRQRTY 0.0 None None 0 None -2867 ATVCRDPGV 0.0 None None 0 None -2868 VCRDPGVPM 0.0 None None 0 None -2869 DAPLFNTIV 0.84762355921 PLFNTIV SLFNTVV 28.0 180255|gag_protein|AAT90688.1|Human_immunodeficiency_virus_1|11676 -2870 VDAPLFNTI 0.0 None None 0 None -2871 LSETISPLW 0.0 None None 0 None -2872 WPQRPKSQV 0.0 None None 0 None -2873 MVLPGGVDI 0.0 None None 0 None -2874 FELEWLLYT 0.0 None None 0 None -2875 HSHTTGINL 0.0 None None 0 None -2876 HSHTTGINL 0.0 None None 0 None -2877 SHTTGINLV 0.0 None None 0 None -2878 STHSHTTGI 0.0 None None 0 None -2879 STHSHTTGI 0.0 None None 0 None -2880 STHSHTTGI 0.0 None None 0 None -2881 LTLVGVVVY 0.0 None None 0 None -2882 LTLVGVVVY 0.0 None None 0 None -2883 SEYFLGLTL 0.0310160688315 SEYFLGLTL KEYTFPITL 19.0 143705|Genome_polyprotein|P08617.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 -2884 EAHSFEEEM 0.0 None None 0 None -2885 SSLQEAHSF 0.0 None None 0 None -2886 SHTTLSLDL 0.0 None None 0 None -2887 KLREFFKCA 0.0 None None 0 None -2888 VAYCPAYVV 0.546466079592 AYCPAY ANCPTY 25.0 40253|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 -2889 VAYCPAYVV 0.627529983197 AYCPAY ANCPTY 25.0 40253|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 -2890 VLIPDVVAY 0.0 None None 0 None -2891 VVAYCPAYV 0.0174448489537 AYCPAY ANCPTY 25.0 40253|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 -2892 YLVLIPDVV 0.123689109937 LVLIPDVV LVLNPSVA 20.0 46755|HCV-1|AAA45676.1|Hepatitis_C_virus_genotype_1|41856 -2893 FGIGVENFI 0.0120582173391 FGIGVENFI LGYGFVNYI 21.0 36357|ELAV-like_protein_4_(Paraneoplastic_encephalomyelitis_antigen_HuD)_(Hu-antigen_D)|P26378.1|Homo_sapiens|9606 -2894 IGVENFITL 0.0 None None 0 None -2895 ITLVVFGLI 0.207698907722 VVFGLI VLFGLL 23.0 101380|BNLF2a|YP_401721.1|Human_herpesvirus_4_type_1|36352 -2896 KVARSKPYA 0.0 None None 0 None -2897 VARSKPYAM 0.0 None None 0 None -2898 KFRCDAGLG 0.0 None None 0 None -2899 GSRESNMSR 0.0 None None 0 None -2900 MSRKKKAVK 0.0 None None 0 None -2901 RKKKAVKEK 0.0 None None 0 None -2902 QSNTWSLSK 8.97866690799 QSNTWSL QQNWWTL 25.0 74886|latent_membrane_protein_1|AAS99606.1|Human_gammaherpesvirus_4|10376 -2903 YQQSNTWSL 4.15563295911 YQQSNTWSL YLQQNWWTL 30.0 74886|latent_membrane_protein_1|AAS99606.1|Human_gammaherpesvirus_4|10376 -2904 YQQSNTWSL 2.43549839174 YQQSNTWSL YLQQNWWTL 30.0 74886|latent_membrane_protein_1|AAS99606.1|Human_gammaherpesvirus_4|10376 -2905 YKLVVVGAV 16.9067084102 KLVVVG KLVVLG 24.0 32238|polyprotein_[Hepatitis_C_virus_subtype_1a]|ABV46251.2|Hepatitis_C_virus_(isolate_H77)|63746 -2906 AVRYSRGCL 0.0 None None 0 None -2907 VRYSRGCLT 0.0 None None 0 None -2908 YSRGCLTVM 0.0 None None 0 None -2909 YSRGCLTVM 0.0 None None 0 None -2910 YSRGCLTVM 0.0 None None 0 None -2911 VQYASGNRW 0.0 None None 0 None -2912 YASGNRWTF 1.46233842452 ASGNRWTF ATGITYTF 20.0 232153|rhoptry_protein_18|CAJ27113.1|Toxoplasma_gondii_type_I|1209525 -2913 YASGNRWTF 0.0162902231496 ASGNRWTF ATGITYTF 20.0 232153|rhoptry_protein_18|CAJ27113.1|Toxoplasma_gondii_type_I|1209525 -2914 AVRNAITST 0.0 None None 0 None -2915 NAITSTSVI 0.0 None None 0 None -2916 TSIAVRNAI 0.0 None None 0 None -2917 VVLPTEAPI 0.0 None None 0 None -2918 VVLPTEAPI 0.0 None None 0 None -2919 LVATSPSPV 0.0 None None 0 None -2920 LSENAVLIL 0.0 None None 0 None -2921 LSENAVLIL 0.0 None None 0 None -2922 MALSENAVL 0.00068461137038 ALSENAVL ALSLAAVL 19.0 2884|cysteine_proteinase_cruzipain_(EC_3.4.22.-)_-_Trypanosoma_cruzi|A45629|Trypanosoma_cruzi|5693 -2923 MALSENAVL 0.00103322489989 ALSENAVL ALSLAAVL 19.0 2884|cysteine_proteinase_cruzipain_(EC_3.4.22.-)_-_Trypanosoma_cruzi|A45629|Trypanosoma_cruzi|5693 -2924 SSSGWRKSF 0.0 None None 0 None -2925 FSEASQLDF 0.0 None None 0 None -2926 FSEASQLDF 0.0 None None 0 None -2927 RTKQFSEAS 0.0 None None 0 None -2928 RGFSRQSVL 0.0 None None 0 None -2929 LTRSTLSSV 0.0 None None 0 None -2930 LTRSTLSSV 0.0 None None 0 None -2931 RADHDLGRL 0.0 None None 0 None -2932 YRADHDLGR 0.0 None None 0 None -2933 ALRVNPVLA 0.0497971668364 LRVNPV IRVSPV 23.0 56198|glycoprotein_gp35/37|AAC59622.1|Human_gammaherpesvirus_8|37296 -2934 RVNPVLAEL 0.0 None None 0 None -2935 RVNPVLAEL 0.0 None None 0 None -2936 SALRVNPVL 0.109248886427 SALRVNPV TRIRVSPV 23.0 56198|glycoprotein_gp35/37|AAC59622.1|Human_gammaherpesvirus_8|37296 -2937 SSALRVNPV 3.15088690804 SSALRVNPV TTRIRVSPV 24.0 56198|glycoprotein_gp35/37|AAC59622.1|Human_gammaherpesvirus_8|37296 -2938 LLYRRTKAF 0.0 None None 0 None -2939 LLYRRTKAF 0.0 None None 0 None -2940 LYRRTKAFI 0.0 None None 0 None -2941 RTKAFIDYE 0.0 None None 0 None -2942 ATSYELHKF 0.0 None None 0 None -2943 RTQILATSY 0.0 None None 0 None -2944 TSYELHKFY 0.0 None None 0 None -2945 TSYELHKFY 0.0 None None 0 None -2946 IQKITSPNI 0.0028984223105 IQKITSPNI IEKPVAPSV 20.0 419002|PPE_family_protein_PPE68|KAM81677.1|Mycobacterium_tuberculosis_H37Ra|419947 -2947 TSVKPSQPK 0.0 None None 0 None -2948 AIFASMAHA 0.0 None None 0 None -2949 ASMAHAMQK 0.0 None None 0 None -2950 MAHAMQKYL 0.0 None None 0 None -2951 MAHAMQKYL 0.0 None None 0 None -2952 MAHAMQKYL 0.0 None None 0 None -2953 SMAHAMQKY 0.0 None None 0 None -2954 RQRLSAPPS 0.0 None None 0 None -2955 TAHGLSPTA 1.66455725447 GLSPTA GLSPTV 26.0 21139|envelope_protein|BAF48755.1|Hepatitis_B_virus|10407 -2956 GLIEGYGGW 0.0 None None 0 None -2957 QVLGLGGHI 0.0 None None 0 None -2958 AAFNPTRDF 0.0 None None 0 None -2959 AAFNPTRDF 0.0 None None 0 None -2960 KGFVCKAHF 0.0 None None 0 None -2961 SRRACSSEL 0.0 None None 0 None -2962 SPKLKMPEM 0.0 None None 0 None -2963 SNKEKWISL 0.0 None None 0 None -2964 KRWESEHIL 0.0 None None 0 None -2965 LHNEIKTLL 0.000207822443766 LHNEIKTLL IHSMNSTIL 17.0 109332|L1_protein|ACG75893.1|Human_papillomavirus_type_16|333760 -2966 FSDKMGTLT 0.0 None None 0 None -2967 LAAERKAAL 0.0 None None 0 None -2968 TPRRSRWQL 0.0 None None 0 None -2969 MNCIRQASV 0.0 None None 0 None -2970 DQRCRLCPA 0.467544317151 RCRLC RCYLC 25.0 145860|Protein_E6|P04019.1|Human_papillomavirus_type_11|10580 -2971 HTTRSLFQY 0.0 None None 0 None -2972 PHCPQPLVY 1.64017196847 HCPQPLVY HGPTPLLY 30.0 6591|polyprotein|AAB67037.1|Hepatitis_C_virus_(isolate_H77)|63746 -2973 SLEGRIWAL 1.97995031712 EGRIWAL DGRFWEL 27.0 186219|polyprotein|AGK36298.1|Dengue_virus_2|11060 -2974 YTDFLLCAS 0.0 None None 0 None -2975 VVGARGVGK 0.0 None None 0 None -2976 RGRKNRSSV 0.0 None None 0 None -2977 FEKMHQMDL 0.0 None None 0 None -2978 QVFEKMHQM 0.0 None None 0 None -2979 ARWPFGNTM 0.0 None None 0 None -2980 GALKKALAK 0.0 None None 0 None -2981 RLIAISWPL 0.00137441037811 RLIAISW RLLTKPW 18.0 161186|Nonstructural_protein_NS5|NP_739590.2|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -2982 WPLRYVTVM 0.0 None None 0 None -2983 HILGNFLTK 0.0 None None 0 None -2984 IRCGYPTHI 0.0 None None 0 None -2985 EAGPRKGPL 2.46659552716 PRKGP PRRGP 27.0 181035|||| -2986 RLEEAGPRK 0.0 None None 0 None -2987 KLPEMKLPK 5.01765917237e-05 LPEMKLPK LPSDFLPS 16.0 16836|precore/core_protein_[Hepatitis_B_virus]|AAR03815.1|Hepatitis_B_virus|10407 -2988 MKLPKVPEM 0.0 None None 0 None -2989 DRQDQSSHY 0.0 None None 0 None -2990 SHYGQPDRQ 0.0 None None 0 None -2991 GIMPGHIQK 0.00230778161286 MPGHIQK MPSVIEK 20.0 180668|polyprotein|AGO67248.1|Dengue_virus_2|11060 -2992 IMPGHIQKK 0.0020605192972 MPGHIQK MPSVIEK 20.0 180668|polyprotein|AGO67248.1|Dengue_virus_2|11060 -2993 STMRESSPK 0.0 None None 0 None -2994 FPLFAIWPM 0.0 None None 0 None -2995 PTDPMLGLA 7.81973026172 PTDPML PDDPVL 24.0 141462|tegument_protein_UL21|NP_044622.1|Human_alphaherpesvirus_1|10298 -2996 EARSRATLA 0.0 None None 0 None -2997 FHEARSRAT 0.0 None None 0 None -2998 FSIFSTLTK 0.0 None None 0 None -2999 LPDRLTLEF 0.0 None None 0 None -3000 LPDRLTLEF 0.0 None None 0 None -3001 FSDHQSFVV 0.0794686146814 FSDHQ FPDHQ 24.0 190466|large_surface_antigen|CAL29876.1|Hepatitis_B_virus|10407 -3002 LLSQVQFPY 0.0 None None 0 None -3003 GELSVDVSF 0.0 None None 0 None -3004 LSVDVSFFF 0.0 None None 0 None -3005 LSVDVSFFF 0.0 None None 0 None -3006 SVDVSFFFK 1.57692307692 SVDVSFFFK AVDLSHFLK 26.0 5295|nef_protein|ACR27174.1|Human_immunodeficiency_virus_1|11676 -3007 VVDQGNIGK 0.0 None None 0 None -3008 MVFHKHGEK 0.0874586889695 VFHKHGEK VYHGAGSK 22.0 72039|polyprotein|CAB53095.1|Hepatitis_C_virus_subtype_1b|31647 -3009 NAYTMVFHK 0.0 None None 0 None -3010 MESNNMPFL 0.0 None None 0 None -3011 VMESNNMPF 0.0 None None 0 None -3012 IPVPVGATA 0.0 None None 0 None -3013 VPVGATASF 1.51661571138 VPVGATASF MPVGGQSSF 28.0 42342|Antigen_85-B_precursor_(85B)_(Extracellular_alpha-antigen)_(Antigen_85_complex_B)_(Ag85B)_(Mycolyl_transferase_85B)_(Fibronectin-binding_protein_B)_(30_kDa_extracellular_protein)|P31952|Mycobacterium_tuberculosis|1773 -3014 SLDLSQTNL 0.0 None None 0 None -3015 TETSSSMPG 0.0 None None 0 None -3016 HTDPHLCDF 0.0 None None 0 None -3017 SLGFKLLLR 0.884622618909 GFKLLLR NFKSLLR 22.0 52578|liver_stage_antigen-1|CAA82974.1|Plasmodium_falciparum|5833 -3018 HEQCDSSSL 0.0 None None 0 None -3019 AEKSQGPVL 0.0 None None 0 None -3020 RLLSTQAEK 0.0 None None 0 None -3021 LSDIGGLLL 0.0 None None 0 None -3022 LYLYVLSDI 0.0 None None 0 None -3023 SELSSDINL 0.0 None None 0 None -3024 MPHSQYLSA 0.0 None None 0 None -3025 EEAFVPILY 9.10107986896 AFVPILY AYVSVLY 24.0 141228|tegument_protein_VP11/12|NP_044648.1|Human_alphaherpesvirus_1|10298 -3026 QVTVSFTEM 0.0733616966506 VSFTEM VAFTEI 22.0 112697|Protein_E6|P26554.1|Human_papillomavirus_type_51|10595 -3027 TVSFTEMLK 0.0149885083017 VSFTEM VAFTEI 22.0 112697|Protein_E6|P26554.1|Human_papillomavirus_type_51|10595 -3028 VSFTEMLKK 0.0122306227742 VSFTEM VAFTEI 22.0 112697|Protein_E6|P26554.1|Human_papillomavirus_type_51|10595 -3029 LGYRCRFNK 0.0 None None 0 None -3030 LPDLFTPPL 0.625085327902 LFTPP FFTPP 25.0 10587|viral_polyprotein|AAA42941.1|Dengue_virus_2_Thailand/NGS-C/1944|11065 -3031 HTDGDTLLQ 0.00713135459058 HTDGDTLL STDSTTIL 21.0 108148|polyprotein|AAF65953.1|Hepatitis_C_virus|11103 -3032 ILAKHKSLF 0.0 None None 0 None -3033 KLTILAKHK 0.0 None None 0 None -3034 AQTHEPRQW 1.87002493797 AQTHEPRQW AVRHFPRIW 26.0 187106|Vpr_protein|BAA93983.1|Human_immunodeficiency_virus_1|11676 -3035 EAVAGHIPA 0.0 None None 0 None -3036 VAGHIPAIF 1.273 VAGHIPAI LMGYIPAV 26.0 9199|E1_protein|ABB77003.1|Hepatitis_C_virus|11103 -3037 VADLLAFTH 0.0 None None 0 None -3038 VVGAVGVGK 0.0 None None 0 None -3039 KLTSYKCKL 0.0 None None 0 None -3040 WLRVGNGAL 0.0 None None 0 None -3041 SLQLSAHRL 0.0 None None 0 None -3042 IVVISIWEI 0.0 None None 0 None -3043 SIWEIVGQA 0.228841933641 SIWEIVG STWVLVG 24.0 62004|Genome_polyprotein|P27958.3|Hepatitis_C_virus_subtype_1a|31646 -3044 YLKRGYLTL 0.0 None None 0 None -3045 MLHVDRHTL 0.0 None None 0 None -3046 VLERGQFDY 0.0 None None 0 None -3047 AALSIDHWV 0.0 None None 0 None -3048 SIDHWVAVV 0.0 None None 0 None -3049 ATAAAAAAL 0.0 None None 0 None -3050 GPATAAAAA 0.0950864586136 PATAAA PITAAA 23.0 183819|polyprotein|AGO67248.1|Dengue_virus_2|11060 -3051 LLLDTPTQL 0.0 None None 0 None -3052 HLYDTLGST 0.827970867806 HLYDTLGS RLYKTLGQ 25.0 169658|major_paraflagellar_rod_protein|AAA30221.1|Trypanosoma_cruzi|5693 -3053 LPLHLYDTL 7.53132395702 LHLYD LHLYS 23.0 190568|polymerase|AAD16253.1|Hepatitis_B_virus|10407 -3054 EEYTVWIQL 0.0 None None 0 None -3055 WEEEYTVWI 2.67996539102 WEEEYTVW WPKTHTLW 29.0 184702|non-structural_protein_1|AGM49312.1|Dengue_virus|12637 -3056 TPEDNRQPL 0.610171894935 TPEDNR TPQDNQ 27.0 150649|polyprotein|AGW21594.1|Dengue_virus_1|11053 -3057 LPEQQEGQL 0.0 None None 0 None -3058 KPMQVKTPC 0.0 None None 0 None -3059 NLQNSPLEI 0.0 None None 0 None -3060 VPNLQNSPL 0.00025151259785 VPNLQNSP VPTDPNPP 18.0 70491|envelope_glycoprotein|AAC28452.1|Human_immunodeficiency_virus_1|11676 -3061 NELYFAHVL 0.0 None None 0 None -3062 YFAHVLFSA 0.0 None None 0 None -3063 AVTRPFISL 0.0 None None 0 None -3064 FLWPLRVLS 1.97746781824 WPLRVL WMIRIL 23.0 185817|envelope_protein|AGW23590.1|Dengue_virus_4|11070 -3065 ISMKFLWPL 0.0 None None 0 None -3066 WPLRVLSQF 0.0510061316391 WPLRVLSQF WMIRILIGF 25.0 185817|envelope_protein|AGW23590.1|Dengue_virus_4|11070 -3067 REIVWEQGL 0.270327477112 VWEQG LWENG 23.0 36717|nonstructural_protein_4B|YP_001527886.1|West_Nile_virus_NY-99|10000971 -3068 TLAEKRPFM 0.000817554998277 TLAEKRPFM TLARGFPFV 22.0 64727|polyprotein_precursor|NP_041724.2|West_Nile_virus|11082 -3069 LPGHLSRAL 0.0 None None 0 None -3070 SLPGHLSRA 0.0 None None 0 None -3071 SPSSLPGHL 0.031617248785 SPSSLPGH TPDSTPCH 23.0 53041|phosphorylated_matrix_protein_(pp65)|AAA45996.1|Human_betaherpesvirus_5|10359 -3072 ALNNMFCQL 0.0 None None 0 None -3073 GPRRGSSPQ 0.0 None None 0 None -3074 SPQGAAGAA 0.0 None None 0 None -3075 KAFSQSAYL 0.0 None None 0 None -3076 FADHTVVTI 0.0 None None 0 None -3077 FADHTVVTI 0.0 None None 0 None -3078 MTAFADHTV 0.0 None None 0 None -3079 TAFADHTVV 0.0 None None 0 None -3080 GLSPRTSRH 0.140261315451 LSPRTSRH LKPGESRH 25.0 17278|Genome_polyprotein|P06441.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 -3081 LSPRTSRHI 1.36025830505 LSPRTSRH LKPGESRH 25.0 17278|Genome_polyprotein|P06441.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 -3082 RTSRHILER 0.0 None None 0 None -3083 SVQACGWRK 2.18470381235 QACGW EGCGW 28.0 75435|largest_ORF|AAB02128.1|Hepatitis_C_virus|11103 -3084 CLLSPSYYH 0.0 None None 0 None -3085 LASDRFNHI 0.0 None None 0 None -3086 QVASSPAGK 0.0 None None 0 None -3087 VASSPAGKL 0.0 None None 0 None -3088 IEYDTFGEV 0.322101512698 IEYDTF VQYDNF 24.0 32738|Liver_stage_antigen|Q25893|Plasmodium_falciparum|5833 -3089 APSSVALSL 0.0 None None 0 None -3090 NTAPSSVAL 0.0 None None 0 None -3091 EMKRHKVHI 0.0 None None 0 None -3092 ELLDYIRAV 2.20361791879 LLDYIR LLDFVR 25.0 11804|EBNA3C_latent_protein|CAD53421.1|Human_gammaherpesvirus_4|10376 -3093 PQIPPYSTF 0.0 None None 0 None -3094 ISHLHRESV 0.0 None None 0 None -3095 NLLSPDNMV 0.0 None None 0 None -3096 FASDHFLYA 0.0 None None 0 None -3097 FASDHFLYA 0.0 None None 0 None -3098 ATYVRILQR 0.0 None None 0 None -3099 FVVITATYV 0.101628132237 VITATYV VVTSTWV 24.0 14902|Genome_polyprotein|P26664.3|Hepatitis_C_virus_subtype_1a|31646 -3100 LASSSLDIV 0.0 None None 0 None -3101 FAYTILQSV 0.0 None None 0 None -3102 TILQSVPNK 0.0 None None 0 None -3103 FTLFFMAEY 0.0 None None 0 None -3104 FTLFFMAEY 0.0 None None 0 None -3105 YAAGPFTLF 0.0 None None 0 None -3106 YAAGPFTLF 0.0 None None 0 None -3107 YAAGPFTLF 0.0 None None 0 None -3108 ICSEATAAI 0.0 None None 0 None -3109 SLFNALRGK 0.437129462585 SLFNAL SLFNAV 25.0 180168|gag_protein|ABO14878.1|Human_immunodeficiency_virus_1|11676 -3110 VAIMGSTQV 0.11629553368 VAIMGST LAVMGSS 24.0 102376|Genome_polyprotein|P27958.3|Hepatitis_C_virus_subtype_1a|31646 -3111 SAYVALSNK 0.0 None None 0 None -3112 YAISARSDL 0.0 None None 0 None -3113 ATKTLRNYK 0.0 None None 0 None -3114 DVFFATKTL 0.0 None None 0 None -3115 FATKTLRNY 0.0 None None 0 None -3116 FATKTLRNY 0.0 None None 0 None -3117 FLSWCRRVV 0.0 None None 0 None -3118 LSWCRRVVL 0.0 None None 0 None -3119 RVVLELSPK 0.0 None None 0 None -3120 VVLELSPKV 0.0 None None 0 None -3121 IAIAIGAVL 0.00435035310079 IAIAIGAVL VAVAGAAIL 21.0 142231|Lipoprotein_lpqH_precursor|P0A5J0.1|Mycobacterium_tuberculosis|1773 -3122 IAIGAVLLV 0.0 None None 0 None -3123 RGMQCAICK 8.37647204165 MQCAICK LQCVQCK 27.0 148177|early_protein|CAA52585.1|Human_papillomavirus_type_52|10618 -3124 FSNADVNRL 0.0 None None 0 None -3125 MLLKPSERR 0.0 None None 0 None -3126 QLAWVPSPY 0.921133809074 AWVPS AWVPT 27.0 79628|E1_protein|BAA19893.1|Rubella_virus|11041 -3127 QLAWVPSPY 2.65839483138 AWVPS AWVPT 27.0 79628|E1_protein|BAA19893.1|Rubella_virus|11041 -3128 SSSEYMHHK 0.0 None None 0 None -3129 HIASEEPAK 0.0 None None 0 None -3130 STGFPHMLF 0.0246332875568 TGFPHML AGFYHIL 22.0 1516|Nucleoprotein|P03418.1|Human_respiratory_syncytial_virus_A2|11259 -3131 YFSTGFPHM 0.0 None None 0 None -3132 LVYMMERGK 0.0 None None 0 None -3133 VATPGRLVY 0.0 None None 0 None -3134 LLIPVAAVY 0.0 None None 0 None -3135 SAPLMELLY 0.0 None None 0 None -3136 LAMEDTGEY 0.0 None None 0 None -3137 MYLHFSDTY 0.0 None None 0 None -3138 SVSLMYLHF 1.11847247997 SLMYLH SLMYFH 28.0 180579|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -3139 RLSISQWYR 0.0 None None 0 None -3140 SQWYRVMVK 0.0 None None 0 None -3141 STWIGNKLY 0.0 None None 0 None -3142 YMYVCTPLL 0.0 None None 0 None -3143 HQRIHTGEK 0.0 None None 0 None -3144 ALGLAQGTF 0.0191045931234 GLAQGTF GLSPGTL 21.0 21638|protein_F|ABV46152.2|Hepatitis_C_virus_(isolate_Japanese)|11116 -3145 GLAQGTFVF 0.00860509404551 GLAQGTF GLSPGTL 21.0 21638|protein_F|ABV46152.2|Hepatitis_C_virus_(isolate_Japanese)|11116 -3146 GTFVFIAHF 0.0 None None 0 None -3147 KLHQVFHSI 0.149224855724 KLHQVFHSI KLHLYSHPI 23.0 190568|polymerase|AAD16253.1|Hepatitis_B_virus|10407 -3148 VTVPEKLSF 0.0 None None 0 None -3149 HPCSQPVWL 0.0 None None 0 None -3150 FPLVRSCQM 1.72844236932 LVRSCQM LIRACML 24.0 36676|polyprotein|BAA09073.1|Hepatitis_C_virus_subtype_1b|31647 -3151 MMCRDLPGF 0.631203555857 RDLPGF RELPRF 22.0 53201|Fusion_glycoprotein_F0_precursor|P03420.1|Human_respiratory_syncytial_virus_A2|11259 -3152 RVKATIVAM 0.0 None None 0 None -3153 AQGEPLGAL 0.0 None None 0 None -3154 FQVPDLHIL 0.0 None None 0 None -3155 GMQARSVEM 0.0 None None 0 None -3156 MLHLYPGPM 0.369680851064 MLHLYPGPM LFQLYRGPL 26.0 38724|Genome_polyprotein|P08617.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 -3157 SPYSEELPL 0.0 None None 0 None -3158 YAQEGFLPH 0.408477408363 QEGFLP DEGLLP 22.0 140541|hypothetical_protein|NP_218210.1|Mycobacterium_tuberculosis_H37Rv|83332 -3159 HLLFRVIPY 0.0 None None 0 None -3160 RVIPYDQSF 0.0474258731776 IPYDQS LPFDKS 23.0 116123|nucleocapsid_protein|ABP49342.1|Influenza_A_virus_(A/California/10/1978(H1N1))|425557 -3161 SIGSSATLY 0.0 None None 0 None -3162 VQKQDNSTY 0.0 None None 0 None -3163 AQVGFTLPL 0.182777813767 GFTLPL AFTMPL 24.0 179898|cell_surface_protein_(associated_with_virulence)|NP_302372.1|Mycobacterium_leprae_TN|272631 -3164 LPTPPPPPL 2.24573975693 LPTPPPPP VPTDPNPP 31.0 70491|envelope_glycoprotein|AAC28452.1|Human_immunodeficiency_virus_1|11676 -3165 YSCAGGRLF 0.0 None None 0 None -3166 FQLDVASVI 0.0 None None 0 None -3167 LDVASVIPF 0.0 None None 0 None -3168 SVIPFDICY 1.51567816772e-05 SVIPFDIC GAIPPLVC 15.0 73059|kaposin|AAC57155.1|Human_gammaherpesvirus_8|37296 -3169 RLPNLHPSF 0.0 None None 0 None -3170 LMVAVARSA 0.0 None None 0 None -3171 TQHTSFQGY 0.0 None None 0 None -3172 EQRCSLQAF 0.0 None None 0 None -3173 KSKEREHSF 0.0 None None 0 None -3174 NIDLAREAY 0.0 None None 0 None -3175 IMSFLLSSL 0.0 None None 0 None -3176 SEKEASLLY 0.0 None None 0 None -3177 YLKEHASSL 0.0 None None 0 None -3178 LVLSGSSSL 0.0 None None 0 None -3179 FWRSSCSLF 0.403383339884 FWRSSCSL LWHYPCTL 22.0 54824|polyprotein_precursor|BAA01583.1|Hepatitis_C_virus|11103 -3180 QLADQCLTM 0.0 None None 0 None -3181 LPIKDGNTL 0.0 None None 0 None -3182 LLVDRKDAM 0.0 None None 0 None -3183 TPAIRHIML 0.848547717842 TPAIRH TPMLRH 26.0 186002|polyprotein|AGO67248.1|Dengue_virus_2|11060 -3184 MQIHMGLAL 0.0 None None 0 None -3185 ALARSSDAF 0.0 None None 0 None -3186 HQGGATRVY 1.65671617909 HQGGATRVY HDGAGKRVY 29.0 23620|Genome_polyprotein|SRC279960|Hepatitis_C_virus_genotype_1|41856 -3187 FPNAGKSSF 0.0890723848157 PNAGKS PGAGKT 23.0 180503|polyprotein|AGO67248.1|Dengue_virus_2|11060 -3188 ILQEHIGAM 0.0 None None 0 None -3189 SASAGLAAM 0.0 None None 0 None -3190 HPCVPQALV 0.0 None None 0 None -3191 ATIMETLTM 0.0 None None 0 None -3192 PSDINVSSY 0.0 None None 0 None -3193 VSSYNIYWY 9.48140414761 VSSYNIYWY ISEYRHYCY 23.0 28484|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 -3194 ESSEHEGTY 0.0 None None 0 None -3195 QAWQPTASF 31.7524708941 AWQPTA AWVPTA 29.0 79628|E1_protein|BAA19893.1|Rubella_virus|11041 -3196 FLNDRLANY 0.0 None None 0 None -3197 LQIMAGRHG 0.165211067364 MAGRHG VAGSHG 24.0 154196|tegument_protein|CAB06735.1|Human_alphaherpesvirus_2|10310 -3198 WLFPTGGSV 0.427013920926 LFPTGGSV LFPGGGQI 30.0 181035|||| -3199 LMYLQKLWM 0.0 None None 0 None -3200 SIQSPFEGF 0.0 None None 0 None -3201 LALLVSTAF 0.0 None None 0 None -3202 GLIATQLLF 0.0 None None 0 None -3203 LIATQLLFY 0.0 None None 0 None -3204 LIATQLLFY 0.0 None None 0 None -3205 AVRPTFGVL 0.0 None None 0 None -3206 AMRFHFHSM 0.0102154040423 AMRFHFHSM SARLHRHAL 21.0 28508|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 -3207 MTSGLAMRF 0.0 None None 0 None -3208 FPTTTFMCL 0.0 None None 0 None -3209 ISLFPTTTF 0.0 None None 0 None -3210 SLFPTTTFM 0.0 None None 0 None -3211 SMRSSSISG 0.0 None None 0 None -3212 VQHITGPVW 0.0 None None 0 None -3213 ASDSQEALF 0.00578652736162 SDSQEALF TDNQLAVF 21.0 52496|polyprotein_precursor|NP_041724.2|West_Nile_virus|11082 -3214 FSDISEMRT 0.0 None None 0 None -3215 TLAELLGPY 0.00117570333351 TLAELLGP TIASPKGP 19.0 23883|HCV-1|AAA45676.1|Hepatitis_C_virus_subtype_1a|31646 -3216 LVNPWGEVL 1.04441668544 VNPWGE VDPWVE 25.0 143690|Genome_polyprotein|P06441.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 -3217 LPVVLQLKL 0.0 None None 0 None -3218 AQADQVDPL 0.0 None None 0 None -3219 FCDTAPVLK 0.0 None None 0 None -3220 RLHSPMYFF 0.0 None None 0 None -3221 TMCMYFRPL 0.0 None None 0 None -3222 FLVFPFTSI 0.0 None None 0 None -3223 LMADMYLLL 0.0 None None 0 None -3224 HSHLLSHSY 2.5848832505 HLLSHS HLYSHP 23.0 190568|polymerase|AAD16253.1|Hepatitis_B_virus|10407 -3225 HSHLLSHSY 0.156318463122 HLLSHS HLYSHP 23.0 190568|polymerase|AAD16253.1|Hepatitis_B_virus|10407 -3226 TQYLVFCGM 0.0 None None 0 None -3227 YLVFCGMGL 0.0 None None 0 None -3228 LIFMYLCPA 0.0 None None 0 None -3229 VAICHPLHY 0.0 None None 0 None -3230 VLVQSLMVL 0.0 None None 0 None -3231 QAQNQSITY 0.0 None None 0 None -3232 TILTFCLSY 0.00326623801259 TILTFCLSY TIMAAILAY 20.0 150224|polyprotein|AGO67248.1|Dengue_virus_2|11060 -3233 CSIQDDLPF 0.0 None None 0 None -3234 RMSRALWTL 0.0 None None 0 None -3235 KQGWCYLVY 0.0 None None 0 None -3236 YLVYVLLPL 186.049439044 YLVYVLLPL YIIFVYIPL 31.0 110744|E5_protein|AAD24036.1|Human_papillomavirus_type_16|333760 -3237 TINSAGDLF 0.0 None None 0 None -3238 FPLDEVHAK 1.3376067584 FPLDEVHA YPLHEQHG 24.0 75356|EBNA3A_nuclear_protein|Q8AZJ8|Human_gammaherpesvirus_4|10376 -3239 LTLPPLATY 0.587666896977 LTLPPLA LTIPPTA 28.0 184643|polyprotein|AGW24534.1|Dengue_virus_2|11060 -3240 PPAPPSLSL 0.0 None None 0 None -3241 MQRASRHSQ 0.0 None None 0 None -3242 QQSQSSGPG 0.0 None None 0 None -3243 MLGDPSADY 0.0 None None 0 None -3244 SADYINANY 0.0 None None 0 None -3245 GVHKGRKPF 0.0 None None 0 None -3246 ALACFARAF 0.0 None None 0 None -3247 LTGDCCFDY 0.0 None None 0 None -3248 YPKPQVSFL 0.0 None None 0 None -3249 HPLGSLQIF 0.0 None None 0 None -3250 AVGGMIASF 0.0144532044338 GMIASF GVIAAF 22.0 98085|trans-sialidase,_putative|EAN82636.1|Trypanosoma_cruzi|5693 -3251 PTEQSLTEY 0.0 None None 0 None -3252 LLMGFSLTL 0.0 None None 0 None -3253 TQGMQCSSL 0.0365911287855 TQGMQCS TRGERCN 21.0 170063|polyprotein|ABU97067.1|Hepatitis_C_virus_subtype_1b|31647 -3254 LLNLVVTSL 0.0 None None 0 None -3255 YVKIYLLPY 0.0 None None 0 None -3256 YVKIYLLPY 0.0 None None 0 None -3257 ISVFSGSEM 0.0 None None 0 None -3258 LLDEDISVF 0.0 None None 0 None -3259 STVELVPIF 0.0 None None 0 None -3260 KSADFEGLY 0.0 None None 0 None -3261 CLFSLYTAY 0.0 None None 0 None -3262 SLYTAYHVF 0.0160929247029 SLYTAYHV KLYCSYEV 22.0 32250|FL-160-2_protein_-_Trypanosoma_cruzi|JH0823|Trypanosoma_cruzi|5693 -3263 SSHLHSDHY 0.0 None None 0 None -3264 RQKHGEAPI 0.0 None None 0 None -3265 RQDVGTYTF 0.0 None None 0 None -3266 VERQDVGTY 0.0 None None 0 None -3267 HSNSTSFIF 0.0 None None 0 None -3268 NAHSNSTSF 0.0 None None 0 None -3269 ATTESDQSF 0.0 None None 0 None -3270 FPSETKVII 0.0 None None 0 None -3271 HQVASSPGH 0.0 None None 0 None -3272 SQGGPRGTF 0.0 None None 0 None -3273 GGAPHFGHF 0.0 None None 0 None -3274 GAIALIRRY 0.0 None None 0 None -3275 DTTRYVTSK 0.0 None None 0 None -3276 EPSESDTTR 0.0 None None 0 None -3277 PSESDTTRY 0.0 None None 0 None -3278 TRYVTSKIL 0.0 None None 0 None -3279 TTRYVTSKI 0.0 None None 0 None -3280 TSCSCQSSR 0.0 None None 0 None -3281 TGDSEAAPV 0.046686577341 TGDSEAAP TGNPRTAP 22.0 154346|RL2|CAB06760.1|Human_alphaherpesvirus_2|10310 -3282 LSMEETLLL 0.0 None None 0 None -3283 WWNPALWKR 10.2327872852 PALWKR PTLWAR 26.0 149027|NS5_protein|BAA00702.1|Hepatitis_C_virus_(isolate_H77)|63746 -3284 LFQDNSSQL 0.0 None None 0 None -3285 LTPPQAQEL 0.429161842612 LTPPQAQEL LTDPNPQEV 25.0 69799|envelope_glycoprotein|BAE96221.1|Human_immunodeficiency_virus_1|11676 -3286 LTPQQAQEL 0.0 None None 0 None -3287 QAQALGIPL 0.0 None None 0 None -3288 ASRPDRLSL 0.0 None None 0 None -3289 EAQGQEASR 0.0 None None 0 None -3290 WVEPQNPVL 0.000730033295762 VEPQNPVL VSPFIPLL 17.0 58740|Major_surface_antigen_precursor|P03142.4|Hepatitis_B_virus|10407 -3291 HLPHLTHTL 0.0 None None 0 None -3292 HTLATSCRR 0.0 None None 0 None -3293 ITSFDNLFR 0.0 None None 0 None -3294 SHFHKTHEV 0.0 None None 0 None -3295 YKLVVVGAV 12.5817515538 KLVVVG KLVVLG 24.0 32238|polyprotein_[Hepatitis_C_virus_subtype_1a]|ABV46251.2|Hepatitis_C_virus_(isolate_H77)|63746 -3296 FHRRLSSSL 0.0 None None 0 None -3297 FHRRLSSSL 0.0 None None 0 None -3298 FSRRSFHRR 0.0 None None 0 None -3299 RSDVWNLGI 0.0 None None 0 None -3300 VYILILPSF 0.0 None None 0 None -3301 STTIPILTL 0.0 None None 0 None -3302 TIPILTLSL 0.0 None None 0 None -3303 LSHISHLEL 0.0 None None 0 None -3304 SHLELVESL 0.0 None None 0 None -3305 SAEVRIEPM 0.108897660016 EVRIEP QVRIKP 23.0 71266|Circumsporozoite_protein_precursor|P02893.1|Plasmodium_falciparum|5833 -3306 QSHLLIHQR 0.0 None None 0 None -3307 QVITLRKSL 0.0 None None 0 None -3308 TKKQVITLR 0.0 None None 0 None -3309 MFDASKANF 0.0 None None 0 None -3310 FLDWLRTMT 0.0 None None 0 None -3311 VDWFLDWLR 11.20129968 VDWFLDWLR ISWCLWWLQ 28.0 39591|polyprotein|AAA45677.1|Hepatitis_C_virus_(isolate_H77)|63746 -3312 WFLDWLRTM 0.137841959387 WFLDWLR WCLWWLQ 25.0 39591|polyprotein|AAA45677.1|Hepatitis_C_virus_(isolate_H77)|63746 -3313 WLRTMTNVL 0.0 None None 0 None -3314 KFLQEEPQL 0.0 None None 0 None -3315 DVFRFSPYR 0.0 None None 0 None -3316 RFSPYRGLL 0.10447761194 FSPYRGLL IAPYAGLI 26.0 25388|matrix_protein|ABP96803.1|Human_metapneumovirus|162145 -3317 DSTRPPGTR 1.52773900302 PPGTR PPGSR 26.0 136890|polyprotein|AGO67248.1|Dengue_virus_2|11060 -3318 YLGVPVFYA 0.385348721615 YLGVPVF YYGVPVW 28.0 118|envelope_glycoprotein|ABS76372.1|Human_immunodeficiency_virus_1|11676 -3319 AIHIVAEKK 0.0 None None 0 None -3320 TQFELQRNK 0.0 None None 0 None -3321 VRGTDWHLK 0.0074144902417 VRGTDWH TRGRDAH 21.0 66798|glycoprotein_gp35/37|AAC59622.1|Human_gammaherpesvirus_8|37296 -3322 GFHPDPEAL 0.149003652528 GFHPD GFFPD 24.0 190466|large_surface_antigen|CAL29876.1|Hepatitis_B_virus|10407 -3323 HIRTDTYVK 0.0 None None 0 None -3324 SRWQVHGIV 0.0 None None 0 None -3325 VPACSRAHV 0.0 None None 0 None -3326 VPACSYAHV 0.0 None None 0 None -3327 MLFFRTRYI 0.0602884044705 MLFFRTRYI VLFYLGQYI 22.0 156550|E3_ubiquitin-protein_ligase_Mdm2|Q00987.1|Homo_sapiens|9606 -3328 TRYICTTVF 0.0 None None 0 None -3329 YICTTVFYT 0.0 None None 0 None -3330 AALVPTQAM 0.0 None None 0 None -3331 MPGSPRDPV 0.0 None None 0 None -3332 RRGSGHSEY 1.07898059992 GSGHSE GPGHEE 24.0 180488|polyprotein|AGO67248.1|Dengue_virus_2|11060 -3333 RICGHIFCY 2.42597295458e-05 ICGHIFC LCLIISC 15.0 93431|pre-C/C_protein|ABY54138.1|Hepatitis_B_virus|10407 -3334 GIAPLNQWV 0.842769418953 IAPLNQW LTPLRDW 24.0 36062|polyprotein|AAB67037.1|Hepatitis_C_virus_(isolate_H77)|63746 -3335 KIIATCFAV 0.0 None None 0 None -3336 KMNEPKCLK 0.0 None None 0 None -3337 SFVPWNSYV 1.65978825128 VPWNSYV LPWYSYL 29.0 143728|Genome_polyprotein|P08617.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 -3338 VPWNSYVRL 0.33737000325 VPWNSYV LPWYSYL 29.0 143728|Genome_polyprotein|P08617.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 -3339 YQLKLFACM 0.000135204617912 YQLKLFAC YRLWHYPC 17.0 75636|polyprotein|AAB67037.1|Hepatitis_C_virus_(isolate_H77)|63746 -3340 YQLKLFACM 0.000103789830269 YQLKLFAC YRLWHYPC 17.0 75636|polyprotein|AAB67037.1|Hepatitis_C_virus_(isolate_H77)|63746 -3341 RGRGGSVSI 0.0 None None 0 None -3342 IPHTAILVT 0.0 None None 0 None -3343 SIPHTAILV 0.0 None None 0 None -3344 GLSDLELRL 0.0 None None 0 None -3345 VLLRCPNKL 0.0 None None 0 None -3346 TRLAFGLFA 0.0 None None 0 None -3347 ILIACRLNK 3.55199159767 ILIACRL VLIRCYL 21.0 145860|Protein_E6|P04019.1|Human_papillomavirus_type_11|10580 -3348 LIACRLNKK 0.0 None None 0 None -3349 RLNKKKGAY 0.0 None None 0 None -3350 TLAHEASPL 0.0 None None 0 None -3351 SAWWSFGSL 0.872449058702 WSFGSL WDFGSL 31.0 180726|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -3352 NPEAMCSDL 55.4534482749 NPEAMC NPYAVC 25.0 110401|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 -3353 AMHPLFRKL 0.0 None None 0 None -3354 CRAMHPLFR 0.0 None None 0 None -3355 GPCRAMHPL 0.0 None None 0 None -3356 RAMHPLFRK 0.0 None None 0 None -3357 GYIHYVFYL 8.67210597487 GYIHYV GYLQYV 26.0 42094|telomer_length_regulation_protein_TEL1|EDV12172.1|Saccharomyces_cerevisiae|4932 -3358 GYIHYVFYL 0.750508588568 GYIHYV GYLQYV 26.0 42094|telomer_length_regulation_protein_TEL1|EDV12172.1|Saccharomyces_cerevisiae|4932 -3359 KGYIHYVFY 78.5423095416 GYIHYV GYLQYV 26.0 42094|telomer_length_regulation_protein_TEL1|EDV12172.1|Saccharomyces_cerevisiae|4932 -3360 YLGNGPNVI 0.0 None None 0 None -3361 SLSNKEVKK 0.0 None None 0 None -3362 GPRAINNFF 0.0 None None 0 None -3363 FRFSSQEAA 0.0 None None 0 None -3364 LLPPQDPHL 0.366181412717 LLPPQDPHL LLPRRGPRL 24.0 23224|polyprotein|BAB18806.1|Hepatitis_C_virus|11103 -3365 PPQDPHLPL 0.0 None None 0 None -3366 HVDPGTIGV 7.61077451306e-06 HVDPGTIG HISCLTFG 15.0 190443|core_protein|BAF42671.1|Hepatitis_B_virus|10407 -3367 GLMGAVNVA 0.0 None None 0 None -3368 LMGAVNVAK 0.0 None None 0 None -3369 PRMAIPWPR 0.0 None None 0 None -3370 WPRDVRKLV 0.0 None None 0 None -3371 KYYEALPEL 0.0 None None 0 None -3372 HYYHNVHAV 0.0 None None 0 None -3373 MVEHYYHNV 0.0 None None 0 None -3374 YHNVHAVVF 0.0 None None 0 None -3375 YYHNVHAVV 0.0 None None 0 None -3376 ARVWKFGPK 0.0 None None 0 None -3377 RVWKFGPKL 0.0 None None 0 None -3378 RVWKFGPKL 0.0 None None 0 None -3379 VLDKARVWK 0.180063784265 VLDKARVW VLDSFKTW 25.0 69435|Genome_polyprotein|SRC279960|Hepatitis_C_virus_(isolate_H77)|63746 -3380 CYEEYRGRL 0.0377885551771 CYEEYRGRL VYQDWLGRM 24.0 23288|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 -3381 GRYEEYRGH 0.0 None None 0 None -3382 APRGACYRA 0.0 None None 0 None -3383 YRADHDLGR 0.0 None None 0 None -3384 SYVCVVRNY 0.0 None None 0 None -3385 ARPFFFFLL 0.0529432793239 PFFFFLL PFVVFLV 22.0 148397|Dense_granule_protein_3|B6KEU8.2|Toxoplasma_gondii|5811 -3386 FFFFLLDKV 0.0 None None 0 None -3387 FFFLLDKVL 0.876549817799 FLLDKVL FLLTKIL 25.0 16753|Pre-S/S_protein|AAR99337.1|Hepatitis_B_virus|10407 -3388 FLLDKVLAS 2.38412935701 FLLDKVLA FLLTKILT 25.0 16753|Pre-S/S_protein|AAR99337.1|Hepatitis_B_virus|10407 -3389 HARPFFFFL 0.0 None None 0 None -3390 APSWRGLAE 0.00488637433335 APSWRGLA GPSLIGLA 20.0 21780|Antigen_85-B_precursor_(85B)_(Extracellular_alpha-antigen)_(Antigen_85_complex_B)_(Ag85B)_(Mycolyl_transferase_85B)_(Fibronectin-binding_protein_B)_(30_kDa_extracellular_protein)|P31952|Mycobacterium_tuberculosis|1773 -3391 LRLALMKKK 0.0 None None 0 None -3392 WLRLALMKK 0.0 None None 0 None -3393 VLIQQLEKV 0.0 None None 0 None -3394 YPGQVNRTA 0.441659094862 PGQVNRTA PGEINRVA 33.0 59153|Genome_polyprotein|P27958.3|Hepatitis_C_virus_subtype_1a|31646 -3395 MADVAMYGV 0.0 None None 0 None -3396 GLYYAEFGA 0.0 None None 0 None -3397 SVLAGLYYA 5.40222207826 LAGLYY LAGLFY 28.0 23270|polyprotein|AAB67036.1|Hepatitis_C_virus_(isolate_H77)|63746 -3398 TMWRREESL 0.0 None None 0 None -3399 CLWQLKAPV 0.0117840685959 CLWQLKAPV SLWKDGAPL 22.0 140600|glutamine_synthetase_GLNA1_(glutamine_synthase)_(GS-I)|NP_216736.1|Mycobacterium_tuberculosis_H37Rv|83332 -3400 RPRKAWAWC 5.41074531829 RPRKAW RPASAW 26.0 150534|polyprotein|AGO67248.1|Dengue_virus_2|11060 -3401 QRLKREEEK 2.19826332471 KREEEK RREEEE 23.0 185491|polyprotein|AGO67248.1|Dengue_virus_2|11060 -3402 VYHMSQSPL 0.0 None None 0 None -3403 FTMLLSLLA 0.0 None None 0 None -3404 GLAGFTMLL 0.186461334924 GFTML GFTMM 24.0 180818|Membrane_glycoprotein_precursor|NP_739582.2|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -3405 MLLSLLAFA 0.0 None None 0 None -3406 KVHQLAITV 0.0 None None 0 None -3407 LPKSSEKAI 0.0 None None 0 None -3408 STQEPTAYV 1.33414347629 QEPTAYV QNPTTYI 27.0 135263|hemagglutinin|ACX31970.1|Influenza_A_virus_(A/Bar-headed_Goose/Qinghai/61/05(H5N1))|336238 -3409 ARMRKHIKR 0.0 None None 0 None -3410 GPARMRKHI 0.0 None None 0 None -3411 RMRKHIKRL 0.0 None None 0 None -3412 HVGKASSSM 0.0 None None 0 None -3413 QQMEAHVGK 0.0 None None 0 None -3414 VILLPQPPK 0.0 None None 0 None -3415 YLGVPVFYA 0.385348721615 YLGVPVF YYGVPVW 28.0 118|envelope_glycoprotein|ABS76372.1|Human_immunodeficiency_virus_1|11676 -3416 AIHIVAEKK 0.0 None None 0 None -3417 IVGHTGSGK 0.972587226103 HTGSGK HPGSGK 28.0 183598|polyprotein|AGW21594.1|Dengue_virus_1|11053 -3418 LPAPPGAPP 28.8454969512 LPAPPGA WPAPPGA 35.0 72928|Genome_polyprotein|P26662.3|Hepatitis_C_virus_(isolate_Japanese)|11116 -3419 VRGTDWHLK 0.0074144902417 VRGTDWH TRGRDAH 21.0 66798|glycoprotein_gp35/37|AAC59622.1|Human_gammaherpesvirus_8|37296 -3420 RRHHSPSQR 0.689680730869 HHSPS HHAPS 28.0 21000|glutamine_synthetase_GLNA1_(glutamine_synthase)_(GS-I)|NP_216736.1|Mycobacterium_tuberculosis|1773 -3421 WLQQENHEL 0.0 None None 0 None -3422 SLQPIHHDL 0.0 None None 0 None -3423 VPACSRAHV 0.0 None None 0 None -3424 VPACSYAHV 0.0 None None 0 None -3425 LLLSPPVEV 0.0 None None 0 None -3426 LLSPPVEVK 0.0 None None 0 None -3427 RPEPPETGV 1.40283044682 PEPPET PNPPEV 26.0 70491|envelope_glycoprotein|AAC28452.1|Human_immunodeficiency_virus_1|11676 -3428 RRGSGHSEY 1.07898059992 GSGHSE GPGHEE 24.0 180488|polyprotein|AGO67248.1|Dengue_virus_2|11060 -3429 GLLQRPVHL 0.0 None None 0 None -3430 HLALGRLSR 0.0 None None 0 None -3431 KIIATCFAV 0.0 None None 0 None -3432 SFVPWNSYV 1.65978825128 VPWNSYV LPWYSYL 29.0 143728|Genome_polyprotein|P08617.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 -3433 VPWNSYVRL 0.33737000325 VPWNSYV LPWYSYL 29.0 143728|Genome_polyprotein|P08617.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 -3434 YQLKLFACM 0.000135204617912 YQLKLFAC YRLWHYPC 17.0 75636|polyprotein|AAB67037.1|Hepatitis_C_virus_(isolate_H77)|63746 -3435 YQLKLFACM 0.000103789830269 YQLKLFAC YRLWHYPC 17.0 75636|polyprotein|AAB67037.1|Hepatitis_C_virus_(isolate_H77)|63746 -3436 IPHTAILVT 0.0 None None 0 None -3437 SIPHTAILV 0.0 None None 0 None -3438 SVSSCCQPV 1.40654417103 SSCCQP SECCTP 28.0 57361|Genome_polyprotein|SRC279960|Hepatitis_C_virus_(isolate_H77)|63746 -3439 WLLEWTEAA 0.223150379312 WLLEW WAIKW 24.0 72233|Genome_polyprotein|P27958.3|Hepatitis_C_virus_subtype_1a|31646 -3440 GLSDLELRL 0.0 None None 0 None -3441 VLLRCPNKL 0.0 None None 0 None -3442 TLAHEASPL 0.0 None None 0 None -3443 ILPATILVL 0.0979841141813 ILPATI MLPATL 23.0 180662|polyprotein|CDF77361.1|Dengue_virus_3|11069 -3444 TILPATILV 0.126010530119 ILPATI MLPATL 23.0 180662|polyprotein|CDF77361.1|Dengue_virus_3|11069 -3445 SAWWSFGSL 0.872449058702 WSFGSL WDFGSL 31.0 180726|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -3446 NPEAMCSDL 55.4534482749 NPEAMC NPYAVC 25.0 110401|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 -3447 AMHPLFRKL 0.0 None None 0 None -3448 CRAMHPLFR 0.0 None None 0 None -3449 GPCRAMHPL 0.0 None None 0 None -3450 RAMHPLFRK 0.0 None None 0 None -3451 SLSNKEVKK 0.0 None None 0 None -3452 GPRAINNFF 0.0 None None 0 None -3453 LLPPQDPHL 0.366181412717 LLPPQDPHL LLPRRGPRL 24.0 23224|polyprotein|BAB18806.1|Hepatitis_C_virus|11103 -3454 PPQDPHLPL 0.0 None None 0 None -3455 GLMGAVNVA 0.0 None None 0 None -3456 LMGAVNVAK 0.0 None None 0 None -3457 KLPEVQLPK 6.62808883056e-05 LPEVQLPK LPSDFLPS 16.0 16836|precore/core_protein_[Hepatitis_B_virus]|AAR03815.1|Hepatitis_B_virus|10407 -3458 ARVWKFGPK 0.0 None None 0 None -3459 RVWKFGPKL 0.0 None None 0 None -3460 RVWKFGPKL 0.0 None None 0 None -3461 VLDKARVWK 0.180063784265 VLDKARVW VLDSFKTW 25.0 69435|Genome_polyprotein|SRC279960|Hepatitis_C_virus_(isolate_H77)|63746 -3462 APRGACYRA 0.0 None None 0 None -3463 YRADHDLGR 0.0 None None 0 None -3464 SYVCVVRNY 0.0 None None 0 None -3465 APSWRGLAE 0.00488637433335 APSWRGLA GPSLIGLA 20.0 21780|Antigen_85-B_precursor_(85B)_(Extracellular_alpha-antigen)_(Antigen_85_complex_B)_(Ag85B)_(Mycolyl_transferase_85B)_(Fibronectin-binding_protein_B)_(30_kDa_extracellular_protein)|P31952|Mycobacterium_tuberculosis|1773 -3466 VLIQQLEKV 0.0 None None 0 None -3467 GLYYAEFGA 0.0 None None 0 None -3468 SVLAGLYYA 5.40222207826 LAGLYY LAGLFY 28.0 23270|polyprotein|AAB67036.1|Hepatitis_C_virus_(isolate_H77)|63746 -3469 KPVNKILQI 0.0 None None 0 None -3470 CLWQLKAPV 0.0117840685959 CLWQLKAPV SLWKDGAPL 22.0 140600|glutamine_synthetase_GLNA1_(glutamine_synthase)_(GS-I)|NP_216736.1|Mycobacterium_tuberculosis_H37Rv|83332 -3471 RPRKAWAWC 5.41074531829 RPRKAW RPASAW 26.0 150534|polyprotein|AGO67248.1|Dengue_virus_2|11060 -3472 SLDTVAQAV 0.0 None None 0 None -3473 QRLKREEEK 2.19826332471 KREEEK RREEEE 23.0 185491|polyprotein|AGO67248.1|Dengue_virus_2|11060 -3474 RREQQLRRK 0.0 None None 0 None -3475 VYHMSQSPL 0.0 None None 0 None -3476 FTMLLSLLA 0.0 None None 0 None -3477 GLAGFTMLL 0.186461334924 GFTML GFTMM 24.0 180818|Membrane_glycoprotein_precursor|NP_739582.2|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -3478 MLLSLLAFA 0.0 None None 0 None -3479 KVHQLAITV 0.0 None None 0 None -3480 KIMHGPFMK 0.0 None None 0 None -3481 RPRWNTHGH 0.0 None None 0 None -3482 ARMRKHIKR 0.0 None None 0 None -3483 GPARMRKHI 0.0 None None 0 None -3484 RMRKHIKRL 0.0 None None 0 None -3485 VILLPQPPK 0.0 None None 0 None -3486 TPCHCTGTL 0.0 None None 0 None -3487 TPCHCTGTL 0.0 None None 0 None -3488 IPFFGQVHL 0.0 None None 0 None -3489 ILMENKSNI 0.0 None None 0 None -3490 ILMENKSNI 0.0 None None 0 None -3491 LAYLVKKMM 0.0 None None 0 None -3492 VTISLAYLV 0.0 None None 0 None -3493 LLIESKEEM 0.0 None None 0 None -3494 WVGPWHTIV 0.0 None None 0 None -3495 WWVGPWHTI 0.0 None None 0 None -3496 KTFCGDVEY 0.0 None None 0 None -3497 AVMEQINSV 0.0 None None 0 None -3498 AVMEQINSV 0.0 None None 0 None -3499 HPRINTLGS 0.0 None None 0 None -3500 FLVAFIKKI 0.0 None None 0 None -3501 FLVAFIKKI 0.0 None None 0 None -3502 GIVSWDTFL 52.5489168518 SWDTFL KWETFL 28.0 52666|Antigen_85-B|P0C5B9.1|Mycobacterium_tuberculosis|1773 -3503 IVSWDTFLV 0.838854359979 SWDTFL KWETFL 28.0 52666|Antigen_85-B|P0C5B9.1|Mycobacterium_tuberculosis|1773 -3504 SAKLTTLVV 0.0 None None 0 None -3505 KLIWHPFSI 0.0 None None 0 None -3506 YFDENIQKL 0.0 None None 0 None -3507 SPSSGQRST 0.0 None None 0 None -3508 SAQNELTEM 0.0 None None 0 None -3509 VATNSETAM 0.0 None None 0 None -3510 PLWGGIIYI 0.24231663041 PLWGGIIYI PLFGYPVYV 25.0 48321|||| -3511 YPLWGGIIY 0.0 None None 0 None -3512 AALATLHPL 0.0 None None 0 None -3513 AALATLHPL 0.0 None None 0 None -3514 LATLHPLFL 0.0 None None 0 None -3515 GLNMLITAL 0.0 None None 0 None -3516 LLTGLNMLI 0.0 None None 0 None -3517 LMWLTYTMA 0.662873031064 LMWLTY LMWLSY 32.0 21041|Membrane_glycoprotein|Q692E0|SARS_coronavirus_TJF|284672 -3518 LTYTMAFMV 0.0585597533649 YTMAFM YTSAFV 22.0 76621|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 -3519 LTYTMAFMV 0.00186523658866 YTMAFM YTSAFV 22.0 76621|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 -3520 MLITALYSL 6.89989591232e-08 LYSL VYAF 9.0 142232|POSSIBLE_CONSERVED_TRANSMEMBRANE_PROTEIN|CAB00937.1|Mycobacterium_tuberculosis|1773 -3521 NLMWLTYTM 2.28006257564 NLMWLTY GLMWLSY 32.0 21041|Membrane_glycoprotein|Q692E0|SARS_coronavirus_TJF|284672 -3522 WLTYTMAFM 0.00930680861548 YTMAFM YTSAFV 22.0 76621|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 -3523 SANTGSSVV 0.0 None None 0 None -3524 AMGSGIQPL 0.0 None None 0 None -3525 HLLEPGQAM 0.0 None None 0 None -3526 TVVGNLGII 0.0 None None 0 None -3527 HGKPTLSTV 0.0 None None 0 None -3528 LEYNTRNAY 0.0 None None 0 None -3529 LLGLTWPVV 2.39337746242 WPVV WPVL 23.0 38427|BZLF1|AAA66529.1|Human_gammaherpesvirus_4|10376 -3530 QLLGLTWPV 0.0 None None 0 None -3531 RVLFWGHIL 0.0 None None 0 None -3532 RVLFWGHIL 0.0 None None 0 None -3533 KVFNNGADL 0.0 None None 0 None -3534 LAGEWRERL 0.0 None None 0 None -3535 MNWRPILTI 0.0 None None 0 None -3536 FSDLRSSIV 0.0 None None 0 None -3537 FSDLRSSIV 0.0 None None 0 None -3538 YFSDLRSSI 0.0 None None 0 None -3539 EANFSASRV 0.0 None None 0 None -3540 TLEGFFESL 0.0 None None 0 None -3541 KILKAQEHV 0.0 None None 0 None -3542 LLQPTPPAA 0.242418891606 PTPPAA PAPPGA 25.0 72928|Genome_polyprotein|P26662.3|Hepatitis_C_virus_(isolate_Japanese)|11116 -3543 SLQVKRVFV 0.0 None None 0 None -3544 FTLEGFFES 0.0 None None 0 None -3545 PLLRDVFNV 0.0 None None 0 None -3546 AQSEIHFQV 0.0 None None 0 None -3547 LQAHSMHEV 0.0 None None 0 None -3548 LLLQPTPPA 0.0 None None 0 None -3549 SLSFSFPLL 105.166666667 LSFSFPLL LSFALPII 26.0 39339|Nucleocapsid_protein|Q89462|Sin_Nombre_hantavirus|37705 -3550 RVWDIVPTL 137.640684863 RVWDIVPTL KPWDVVPTV 37.0 32944|polyprotein|AAW51418.1|Dengue_virus_3|11069 -3551 IVMCAMCGV 0.0 None None 0 None -3552 AMCGVPFSV 1.48904088027 AMCGVPFS SFCGSPYS 28.0 190409|polymerase|AAD16253.1|Hepatitis_B_virus|10407 -3553 RQMAARECK 0.0 None None 0 None -3554 FLVYQNILK 0.0 None None 0 None -3555 FLVYQNILK 0.0 None None 0 None -3556 KVERERLEK 0.0 None None 0 None -3557 KQIEMLEYK 0.0 None None 0 None -3558 KQIEMLEYK 0.0 None None 0 None -3559 VVGAVGVGK 0.0 None None 0 None -3560 VVGAVGVGK 0.0 None None 0 None -3561 FIDTYPPVL 0.0 None None 0 None -3562 RSAFPCAHR 0.0 None None 0 None -3563 GTPRAATMK 0.0 None None 0 None -3564 TMKAKTDLK 0.0 None None 0 None -3565 TMKAKTDLK 0.0 None None 0 None -3566 GLLFAAIKR 0.0 None None 0 None -3567 LLFAAIKRR 0.0 None None 0 None -3568 YQIDRDLHK 0.0 None None 0 None -3569 QTGEKLMAK 0.0 None None 0 None -3570 QTGEKLMAK 0.0 None None 0 None -3571 SSNLIAHVR 0.0 None None 0 None -3572 GEDVDSLAL 0.280156235348 GEDVDSLAL GEEVQVLAL 27.0 180428|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -3573 AELVYILKH 0.0 None None 0 None -3574 KVAELVYIL 0.0 None None 0 None -3575 ISMKLVLRF 0.0 None None 0 None -3576 KSPGWSFQV 0.804206027719 PGWS PGWS 28.0 141461|ubiquitin_E3_ligase_ICP0|NP_044601.1|Human_alphaherpesvirus_1|10298 -3577 SWKSPGWSF 14.9348449335 PGWS PGWS 28.0 141461|ubiquitin_E3_ligase_ICP0|NP_044601.1|Human_alphaherpesvirus_1|10298 -3578 LTVDNITFL 0.00953450829996 TVDNITFL TVELLSFL 21.0 5191|core_protein|AAL31859.1|Hepatitis_B_virus|10407 -3579 DAATRVAMV 0.0 None None 0 None -3580 DSVDAATRV 0.0 None None 0 None -3581 VGAQIYHTI 0.0 None None 0 None -3582 GELSMLVTT 0.0 None None 0 None -3583 EELQLICQA 0.0 None None 0 None -3584 SEEELQLIC 0.0 None None 0 None -3585 CELHAQAAT 0.0 None None 0 None -3586 FTLRPGEVM 0.0 None None 0 None -3587 VYMPPPRLL 0.0 None None 0 None -3588 TFKKQWFYL 0.0 None None 0 None -3589 KANRESQSL 0.0 None None 0 None -3590 AAKARDREL 0.0 None None 0 None -3591 AARLRFFST 0.0 None None 0 None -3592 AFFSLSYIF 0.0 None None 0 None -3593 AHASLIPEF 0.200665922786 HASLIP HADVIP 24.0 97093|polyprotein|AAB66324.1|Hepatitis_C_virus_(isolate_H77)|63746 -3594 AHCGLGKIL 0.0811144143937 CGLGKIL CPLSKIL 24.0 6808|membrane_protein|AAA45887.1|Human_gammaherpesvirus_4|10376 -3595 AHIERRLHI 0.0 None None 0 None -3596 AHMETMAKL 0.0 None None 0 None -3597 AHMGVFTEL 0.0 None None 0 None -3598 AHQDALMLA 0.0 None None 0 None -3599 AHRPRARLA 0.0 None None 0 None -3600 AHTSAILTV 0.0 None None 0 None -3601 AIRPKSLAI 0.0 None None 0 None -3602 ALQRRRLSL 0.0 None None 0 None -3603 ALQRRVQRL 0.0 None None 0 None -3604 AMACMSSVF 0.0 None None 0 None -3605 AMCVIHFSF 1.41247187444 MCVIHFSF MCAVHPTL 25.0 7660|polyprotein|AAA45677.1|Hepatitis_C_virus_(isolate_H77)|63746 -3606 AMYLRASSL 0.0 None None 0 None -3607 APASRHLSA 0.0 None None 0 None -3608 APRLLRSPV 0.0 None None 0 None -3609 AQKEHSHLL 0.937305079721 AQKEHSHL AERKHRHL 28.0 75408|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 -3610 ARAAQVAGI 0.0 None None 0 None -3611 ARDPSPIQI 0.0 None None 0 None -3612 ARHERIHTK 0.0 None None 0 None -3613 ARINSIYGL 0.0624279351011 ARINSI ARLNSL 23.0 418964|PPE_family_protein_PPE68|KAM81677.1|Mycobacterium_tuberculosis_H37Ra|419947 -3614 ARKPRTREC 0.0 None None 0 None -3615 ARLQHCSAL 0.0 None None 0 None -3616 ARLQHCSAL 0.0 None None 0 None -3617 ARLYRGQAL 0.0 None None 0 None -3618 ARLYRGQAL 0.0 None None 0 None -3619 ARMQSYSTI 0.0 None None 0 None -3620 ARPEKLPEL 0.72119091728 RPEKLPEL RPRKLPQL 34.0 110338|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 -3621 ARQHLLQRM 0.0 None None 0 None -3622 ARRARLQHC 0.0 None None 0 None -3623 ARRKQSEMY 0.0 None None 0 None -3624 ARTRAKQNI 0.0 None None 0 None -3625 ARVQMQVTM 0.0 None None 0 None -3626 ASFSNHQRV 0.0695350378462 ASFSNH ASYSSH 24.0 53148|Transcription_activator_BRLF1|P03209.1|Human_herpesvirus_4_strain_B95-8|10377 -3627 ATDDKMTIF 0.0 None None 0 None -3628 AVDPMRAAY 0.0 None None 0 None -3629 AVMGRSWEV 0.0 None None 0 None -3630 AYATQLFFF 0.0 None None 0 None -3631 AYEDTVRQV 0.0 None None 0 None -3632 AYFTHSLSF 0.0 None None 0 None -3633 CAFSRRRPI 0.0 None None 0 None -3634 CFPLHGLQF 0.0590811205659 CFPLHGLQ SFPDPGLR 18.0 79300|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 -3635 CGDKISDRY 1.50652597592 CGDKIS AGDKLS 23.0 244160|surface_antigen_2_(CA-2)|XP_818927.1|Trypanosoma_cruzi_strain_CL_Brener|353153 -3636 CHFSCNNGF 0.0 None None 0 None -3637 CHQDHWSQL 0.0 None None 0 None -3638 CHQRCGGRV 0.0 None None 0 None -3639 CHSNSRDHL 18.4546845763 CHSNSRDHL CYDHAQTHL 25.0 7353|Early_antigen_protein_D|P03191.1|Human_herpesvirus_4_strain_B95-8|10377 -3640 CHYEKKTDL 1.15217391304 CHYEKK CHSKKK 26.0 36504|polyprotein_precursor|BAA01582.1|Hepatitis_C_virus|11103 -3641 CLKPHQGPV 0.0 None None 0 None -3642 CLLRNSACL 0.0 None None 0 None -3643 CLPSRTSSV 0.0 None None 0 None -3644 CLRDLFFPL 0.0 None None 0 None -3645 CMKQRDEEF 0.0 None None 0 None -3646 CPPNHIVSL 0.961374972059 CPPNHIVSL CPAGHAVGI 28.0 23601|Genome_polyprotein|SRC279960|Hepatitis_C_virus_(isolate_H77)|63746 -3647 CQFGTVQLV 0.0 None None 0 None -3648 CRAETRKTF 0.443490453045 AETRKTF GESRKTF 27.0 19435|polyprotein|CDF77361.1|Dengue_virus_3|11069 -3649 CRCPIRGLV 0.0 None None 0 None -3650 CREELAVHL 0.0 None None 0 None -3651 CREQHPAQL 0.0 None None 0 None -3652 CRKMFRRSA 0.0 None None 0 None -3653 CRKMGLRVM 0.0 None None 0 None -3654 CRPQCCQSV 21.594714567 CRPQCCQSV CRVLCCYVL 28.0 11956|UL123;_IE1|AAR31448.1|Human_betaherpesvirus_5|10359 -3655 CRRGLEQLL 0.545054613977 CRRGLEQLL CRAKFKQLL 25.0 54330|BZLF1|AAA66529.1|Human_gammaherpesvirus_4|10376 -3656 CRYGRFHKF 0.0 None None 0 None -3657 CSDTHTNEL 0.00915963725351 CSDTHTNE ASDSLNNE 19.0 4371|tegument_protein_VP11/12|NP_044516.1|Human_alphaherpesvirus_2|10310 -3658 CVLYKYVPI 0.0 None None 0 None -3659 CVMTKIFSL 0.835554412193 MTKIFSL LTKRFSL 23.0 186354|polyprotein|AGO67248.1|Dengue_virus_2|11060 -3660 CYLITVTPI 0.0 None None 0 None -3661 CYLVFIGCF 0.0 None None 0 None -3662 CYNSAIQAL 0.0 None None 0 None -3663 CYSRDQIYI 0.0 None None 0 None -3664 CYVAICGPL 0.0 None None 0 None -3665 CYYYFLCLL 0.0 None None 0 None -3666 DAKRHRKVL 0.0 None None 0 None -3667 DALCRLLGL 0.0 None None 0 None -3668 DFKKKKGSM 0.0 None None 0 None -3669 DHRDLGLSV 0.0 None None 0 None -3670 DILVHHLAV 0.0 None None 0 None -3671 DLGDKILAL 0.0 None None 0 None -3672 DLHTRHGSI 0.236111111111 LHTRHG LHEQHG 26.0 75356|EBNA3A_nuclear_protein|Q8AZJ8|Human_gammaherpesvirus_4|10376 -3673 DLKMGKKPV 0.0 None None 0 None -3674 DLLGHPQAL 0.00441766560472 DLLGHP DLVGWP 22.0 9316|HCV-1|AAA45676.1|Hepatitis_C_virus_subtype_1a|31646 -3675 DLPTKRPAL 3.09221511525 PTKRP PTERP 25.0 141402|tegument_protein_VP22|NP_044651.1|Human_alphaherpesvirus_1|10298 -3676 DLQQKILCM 0.0 None None 0 None -3677 DMMKEFISM 0.0 None None 0 None -3678 DPKERIKVA 0.0 None None 0 None -3679 DPRLKWVVL 0.0 None None 0 None -3680 DRGGCVAGV 0.0 None None 0 None -3681 DRMQRVISV 0.0 None None 0 None -3682 DRMQRVISV 0.0 None None 0 None -3683 DRNDFPVVL 0.104073443917 RNDFPVVL RGDLPVWL 23.0 180611|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -3684 DRQLAAQLL 0.0 None None 0 None -3685 DRSGARPHL 0.0 None None 0 None -3686 DRSHTLQRM 0.0 None None 0 None -3687 DRVERNCLL 0.0 None None 0 None -3688 DSDGEEPCY 0.0 None None 0 None -3689 DSHDYVFYL 0.0 None None 0 None -3690 DTDILSYSY 0.0421563317134 DTDILSYSY NPDIVIYQY 23.0 101813|Pol_polyprotein|Q9YLQ7|Human_immunodeficiency_virus_1|11676 -3691 DTDLYHCTA 0.0 None None 0 None -3692 DTEGILTEY 0.0 None None 0 None -3693 DYMGFTLKI 0.0 None None 0 None -3694 DYPCCIFPF 0.741073093531 DYPCCI HYPCTI 26.0 54821|E2_protein|AAM33354.1|Hepatitis_C_virus_subtype_1a|31646 -3695 DYRTVNNLI 0.0 None None 0 None -3696 EAEPYYCSL 0.0 None None 0 None -3697 EAKRQNLRL 0.0 None None 0 None -3698 EALIRHLNA 0.0370757155869 ALIRHLN SLLRHHN 23.0 96897|polyprotein|ABR25251.1|Hepatitis_C_virus_(isolate_H77)|63746 -3699 EAMNNAQKI 0.0 None None 0 None -3700 EASRRYKKV 0.0 None None 0 None -3701 EFPQKYYWW 2.66043171253 FPQKYYWW FPGKTVWF 25.0 183223|polyprotein|AGW21594.1|Dengue_virus_1|11053 -3702 EGQRRPSSV 0.0 None None 0 None -3703 EHEEDGSEI 0.0 None None 0 None -3704 EHGGKTVKV 0.0 None None 0 None -3705 EHLAAPRLV 0.0 None None 0 None -3706 EHNVTVLVV 0.0 None None 0 None -3707 EHQIGPQEI 0.0 None None 0 None -3708 EHRLHTPMY 0.0 None None 0 None -3709 EIKTIVKAI 1.03630759918 EIKTIVKAI DCKTILKAL 27.0 7708|gag_polyprotein|BAA00992.1|Human_immunodeficiency_virus_1|11676 -3710 EIMNRVVNA 0.0 None None 0 None -3711 EKRFKRKSV 0.0 None None 0 None -3712 ELACYNSAI 0.0 None None 0 None -3713 ELEHMRLRY 0.0 None None 0 None -3714 ELHARGHQV 0.0 None None 0 None -3715 ELHRQVKTL 0.0005030251957 ELHRQVKTL SLHYAWKTM 18.0 183252|polyprotein|AGT63075.1|Dengue_virus_1|11053 -3716 ELKQMCNPI 0.0 None None 0 None -3717 ELLLKVFAL 0.0 None None 0 None -3718 ELQARLAAL 0.0 None None 0 None -3719 ELRAHCETL 0.0 None None 0 None -3720 ELRRYLKSG 0.0 None None 0 None -3721 EMKCREKGF 0.0 None None 0 None -3722 EMLRRQIRL 0.0 None None 0 None -3723 EMRCQYETV 2.0101481376 MRCQYETV MNCSYENM 27.0 36306|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 -3724 EMYEKGLSV 0.0 None None 0 None -3725 EPKKKEKGM 0.0 None None 0 None -3726 EPKKRKVVP 0.0 None None 0 None -3727 EPRFRLNLF 0.0 None None 0 None -3728 ERDGLERAL 0.00214622386308 ERDGLERAL ERDIPERSW 20.0 180423|polyprotein|AGW21594.1|Dengue_virus_1|11053 -3729 ERDGLHSVV 0.0 None None 0 None -3730 ERDQLKETL 0.0 None None 0 None -3731 EREKMGVTM 0.0 None None 0 None -3732 ERFWRIILL 0.0 None None 0 None -3733 ERHVAVEGV 0.0 None None 0 None -3734 ERIDTNQKC 0.0542551505549 DTNQKC DTGQAC 24.0 22633|IMMUNOGENIC_PROTEIN_MPT64_(ANTIGEN_MPT64/MPB64)|CAA98382.1|Mycobacterium_tuberculosis_H37Rv|83332 -3735 ERKTMIKKI 0.0 None None 0 None -3736 ERLQALYMI 0.0 None None 0 None -3737 ERLQNPLRV 0.0 None None 0 None -3738 ERQCHNTAL 0.0 None None 0 None -3739 ERQCHNTAL 0.0 None None 0 None -3740 ERRDCIICC 0.0 None None 0 None -3741 ERSCWVRAI 0.0 None None 0 None -3742 ERSEQPLSV 0.0 None None 0 None -3743 ERSPQAAAV 0.0 None None 0 None -3744 ERTNQKWSV 0.0 None None 0 None -3745 ERTSATLTI 0.0 None None 0 None -3746 ERTTWVQKI 0.0 None None 0 None -3747 ERYGPVFTI 106.83056401 YGPVF YGPVF 30.0 67349|Latent_membrane_protein_2|Q69135|Human_gammaherpesvirus_4|10376 -3748 ETMLHGQVM 0.0 None None 0 None -3749 ETRPTPRLL 0.840404040404 RPTPRL RPGPRL 26.0 139406|polyprotein|ACT37184.1|Hepatitis_C_virus|11103 -3750 ETVSTTLCY 0.0 None None 0 None -3751 EYIVIPSTF 0.0 None None 0 None -3752 EYLLGSWVI 0.702063562848 LLGSWV ILGGWV 27.0 68461|polyprotein|ACZ60108.1|Hepatitis_C_virus|11103 -3753 EYNANTSVL 0.0 None None 0 None -3754 EYRPRTFCF 1.18624599551 PRTFC PRTWC 27.0 141218|regulatory_protein_ICP22|NP_044663.1|Human_alphaherpesvirus_1|10298 -3755 EYVKFLHTF 0.0 None None 0 None -3756 EYVTELPSF 0.0347332864612 EYVTELPS EYTDYMPS 22.0 180681|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -3757 FAAQHGLAV 0.0 None None 0 None -3758 FAKLRHNTQ 0.0 None None 0 None -3759 FARGQRWRL 0.121912079341 FARGQRWRL FTRGDRCNL 24.0 43937|polyprotein|AAF01178.1|Hepatitis_C_virus_subtype_2a|31649 -3760 FARGQRWRL 0.198021676537 FARGQRWRL FTRGDRCNL 24.0 43937|polyprotein|AAF01178.1|Hepatitis_C_virus_subtype_2a|31649 -3761 FCLRYGAAL 0.0 None None 0 None -3762 FCSLHCLLY 0.0 None None 0 None -3763 FCYYYFLCL 0.0 None None 0 None -3764 FEESKSYEV 0.0 None None 0 None -3765 FEFSQVLAL 0.0 None None 0 None -3766 FESHRILHL 0.0518297042583 FESHRI FQSHQL 23.0 183245|polyprotein|AGT63074.1|Dengue_virus_1|11053 -3767 FFLSYLKSL 0.0 None None 0 None -3768 FFLSYLSLV 0.0 None None 0 None -3769 FGAIRRSDA 0.0 None None 0 None -3770 FGYENSPEL 0.0 None None 0 None -3771 FHFRRPWSF 5.80280666815 HFRRPW HFPRIW 25.0 187106|Vpr_protein|BAA93983.1|Human_immunodeficiency_virus_1|11676 -3772 FHFRRPWSF 0.902255091048 HFRRPW HFPRIW 25.0 187106|Vpr_protein|BAA93983.1|Human_immunodeficiency_virus_1|11676 -3773 FHFRRPWSF 0.171144540872 HFRRPW HFPRIW 25.0 187106|Vpr_protein|BAA93983.1|Human_immunodeficiency_virus_1|11676 -3774 FHHCHPKYS 0.0 None None 0 None -3775 FHHIDSAYL 0.0124561392202 FHHIDSA FGHSDAA 21.0 79506|E1_protein|BAA19893.1|Rubella_virus|11041 -3776 FHIGSAESM 0.0 None None 0 None -3777 FHLHNAHVL 0.444444444444 LHNAHVL FHNLHLL 26.0 79390|Protein_Tax-1|P0C213.1|Human_T-cell_lymphotropic_virus_type_1_(african_isolate)|39015 -3778 FHLPYLEQK 1.18628821685 HLPYLEQ HLPYIEQ 38.0 102819|Genome_polyprotein|P27958.3|Hepatitis_C_virus_subtype_1a|31646 -3779 FHLQHWKQI 0.0 None None 0 None -3780 FHLSIHLLY 6.46174150023 SIHLLY SLHLLF 25.0 57790|Protein_Tax-1|P03409.2|Human_T-lymphotropic_virus_1|11908 -3781 FHMASGEAL 0.0 None None 0 None -3782 FHPMRTLPM 0.0 None None 0 None -3783 FHVDQATTV 0.0 None None 0 None -3784 FHYDTQLSL 0.178804383033 FHYDTQL FSYDTRC 24.0 33382|polyprotein|AAB67037.1|Hepatitis_C_virus|11103 -3785 FHYLKKQET 0.0 None None 0 None -3786 FIADKLSTL 0.0 None None 0 None -3787 FIADKLSTL 0.0 None None 0 None -3788 FICLQFWCI 0.0 None None 0 None -3789 FIMFLFVYI 0.0 None None 0 None -3790 FINNSIVYL 0.214071856287 NNSIVY NSSIVY 26.0 6817|polyprotein|AAB67037.1|Hepatitis_C_virus_(isolate_H77)|63746 -3791 FKKARWTII 0.0 None None 0 None -3792 FKNHHNRTV 0.0 None None 0 None -3793 FLARTVSTL 5.81147313029 LARTVS LARTIS 25.0 44653|6_kDa_early_secretory_antigenic_target|P0A564.2|Mycobacterium_tuberculosis|1773 -3794 FLEHGEQAY 0.0 None None 0 None -3795 FLHERKQAS 0.0 None None 0 None -3796 FLKTLWAGL 0.0 None None 0 None -3797 FLLAMLLSI 0.169887629024 LAMLLSI MAMVLSI 24.0 184736|polyprotein|AGW21594.1|Dengue_virus_1|11053 -3798 FLLEFLLPL 0.0595499389227 LEFLLP LQFLIP 25.0 22235|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 -3799 FLLFSFLFL 9.80083437792e-06 FLLFSFLFL FLVPFVVFL 15.0 139746|Dense_granule_protein_3|B6KEU8.2|Toxoplasma_gondii|5811 -3800 FLRTYKNSV 0.0 None None 0 None -3801 FLSDLTPGY 0.0 None None 0 None -3802 FLSVFYTAV 0.0 None None 0 None -3803 FLTVMLLAL 0.0 None None 0 None -3804 FLVERKTIA 0.0 None None 0 None -3805 FMAYATQLF 0.0 None None 0 None -3806 FMKYLVNFI 0.393474742824 MKYLVNF LEYLVSF 25.0 69474|core_protein|BAF42671.1|Hepatitis_B_virus|10407 -3807 FMLVMICIL 0.0 None None 0 None -3808 FMWPLHWSM 17.8722123486 FMWPLH YPWPLY 25.0 75436|Polyprotein|P90247|Hepatitis_C_virus|11103 -3809 FPAMLQAPI 0.458346535653 FPAMLQAPI FPVRPQVPL 23.0 288104|nef_protein|ACR27130.1|Human_immunodeficiency_virus_1|11676 -3810 FPIIIAWAI 0.98110662908 FPIIIAWAI FPLTFGWCF 25.0 193060|Nef_protein|Q9YYU3|Human_immunodeficiency_virus_1|11676 -3811 FPKKSLMLM 0.0 None None 0 None -3812 FPLVRSCQM 0.204347866324 LVRSCQM LIRACML 24.0 36676|polyprotein|BAA09073.1|Hepatitis_C_virus_subtype_1b|31647 -3813 FPNGRLTFL 0.0 None None 0 None -3814 FPQKYYWWF 1.4267285342 FPQKYYWW FPGKTVWF 25.0 183223|polyprotein|AGW21594.1|Dengue_virus_1|11053 -3815 FPQNRYTQE 0.0 None None 0 None -3816 FPTDCVYVM 0.0 None None 0 None -3817 FPYCRAHVL 0.0 None None 0 None -3818 FPYCRAHVL 0.0 None None 0 None -3819 FPYCRSHVF 0.0 None None 0 None -3820 FPYGSSTAL 0.0 None None 0 None -3821 FPYNSDLSL 0.0732870943231 FPYNSDL LPTNADL 22.0 141411|transactivating_tegument_protein_VP16|NP_044650.1|Human_alphaherpesvirus_1|10298 -3822 FQFGAGTQV 0.0 None None 0 None -3823 FQGRRSPSF 0.0 None None 0 None -3824 FQRKKRRKF 0.0 None None 0 None -3825 FREDPVAWV 0.0 None None 0 None -3826 FREGRPREW 0.0 None None 0 None -3827 FRGALPVQI 0.0 None None 0 None -3828 FRGDGRTCC 0.0 None None 0 None -3829 FRHSPRNLI 0.0 None None 0 None -3830 FRKELRYFL 0.0 None None 0 None -3831 FRKELRYFL 0.0 None None 0 None -3832 FRLMHNLNF 0.0 None None 0 None -3833 FRLRRVASA 0.0 None None 0 None -3834 FRLWMTTEV 0.0 None None 0 None -3835 FRNDQEETT 0.0 None None 0 None -3836 FRNGLGTGM 0.343618280556 FRNGLGTGM YLYGVGSGM 25.0 177884|polyprotein|ACZ60102.1|Hepatitis_C_virus_genotype_1|41856 -3837 FRNSRLKQC 0.0 None None 0 None -3838 FRPPAWNRL 0.0 None None 0 None -3839 FRQGHQLFH 0.0 None None 0 None -3840 FRQLEDSQV 0.0 None None 0 None -3841 FRQSRSQVV 0.0 None None 0 None -3842 FRQSRSQVV 0.0 None None 0 None -3843 FRSHVPSHL 0.0 None None 0 None -3844 FRSLQGSVF 0.0 None None 0 None -3845 FRSPEDLSL 0.0 None None 0 None -3846 FRSSASGAL 0.0 None None 0 None -3847 FRTKDGSFV 0.482142857143 FRTKDG FKTEDG 26.0 150571|polyprotein|AGO67248.1|Dengue_virus_2|11060 -3848 FRVSISQTA 0.0 None None 0 None -3849 FRYEGSLTT 3.01020070508 FRYEGS FMYEGD 23.0 126028|ATP-dependent_helicase|NP_217813.1|Mycobacterium_tuberculosis_H37Rv|83332 -3850 FSDKKTITY 0.0 None None 0 None -3851 FSFINNSIV 0.0 None None 0 None -3852 FSIPTCLMY 0.0 None None 0 None -3853 FSKAQAEYL 0.0 None None 0 None -3854 FSYPSIHRF 1.49991207554 PSIHRF PGIYRF 24.0 22046|polyprotein_precursor|BAA01582.1|Hepatitis_C_virus|11103 -3855 FTDVSRFTL 0.0953424643358 TDVSR TDVSR 24.0 181733|Antigen_85-B|P0C5B9.1|Mycobacterium_tuberculosis|1773 -3856 FTFDLYRVL 0.0 None None 0 None -3857 FTSFLLLMY 0.0 None None 0 None -3858 FVEEWTESL 0.0 None None 0 None -3859 FVQKLLFPY 0.0 None None 0 None -3860 FWCAQFTSF 1.06197345475 FWCAQFTSF FWEAVFTGL 26.0 12108|polyprotein|AAP55688.1|Hepatitis_C_virus_subtype_2a|31649 -3861 FWKKILFVI 0.0 None None 0 None -3862 FWKLFYCKF 17.0058728052 LFYCK LLYCK 25.0 25460|Fusion_glycoprotein_F0_precursor|P03420.1|Human_respiratory_syncytial_virus_A2|11259 -3863 FYADSHHCV 0.0 None None 0 None -3864 FYAIVVPML 0.114734057478 FYAIVVPM FYGKAIPL 22.0 97400|Genome_polyprotein|P26664.3|Hepatitis_C_virus|11103 -3865 FYCDDLPLL 0.0 None None 0 None -3866 FYLGTYQAV 0.681699967536 FYLGTY FYLGQY 29.0 156550|E3_ubiquitin-protein_ligase_Mdm2|Q00987.1|Homo_sapiens|9606 -3867 FYMLTCIDL 0.0 None None 0 None -3868 FYQAGSLCI 0.0 None None 0 None -3869 FYTDSSSVL 1.41214657707 TDSSSVL TDSTSIL 27.0 107894|polyprotein|CAB41951.1|Hepatitis_C_virus|11103 -3870 FYTPALFSF 0.00424010201542 FYTPALF FYCNSLF 21.0 141323|multifunctional_expression_regulator|NP_044657.1|Human_alphaherpesvirus_1|10298 -3871 GAGPRFLEL 0.0 None None 0 None -3872 GDKQHFTTL 0.0 None None 0 None -3873 GGATRVYAL 0.0 None None 0 None -3874 GHDAPRRTL 0.490665707971 HDAPRRTL HGAGTRTI 20.0 4910|polyprotein|AAB67037.1|Hepatitis_C_virus_(isolate_H77)|63746 -3875 GHKEDAGVV 0.182420233615 HKEDAGVV EEEEAGVL 23.0 185491|polyprotein|AGO67248.1|Dengue_virus_2|11060 -3876 GHKGLNQCV 0.0 None None 0 None -3877 GHLEAASCI 0.0 None None 0 None -3878 GHLQIRSLL 0.0 None None 0 None -3879 GHLSKKMTL 0.0 None None 0 None -3880 GHNSWGFGV 0.601287595144 GHNSWGFG GDTAWDFG 28.0 180726|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -3881 GHPQDGSGL 0.0 None None 0 None -3882 GHPSLSQHL 1.07017587087 HPSLSQHL EPTLGQHL 29.0 79308|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 -3883 GHTGERHRV 0.0 None None 0 None -3884 GHTPNGRHF 0.0 None None 0 None -3885 GHVAGEQML 0.431336840656 GHVAGEQML GHQAAMQML 28.0 101673|gag_protein|ABO73990.1|Human_immunodeficiency_virus_1|11676 -3886 GLHSSFMPL 0.0 None None 0 None -3887 GLSVRPHAI 0.0 None None 0 None -3888 GMFTLRMAL 0.0 None None 0 None -3889 GNYSRSSHV 0.0 None None 0 None -3890 GPCRRRFSF 0.779795817205 GPCRRRF GPADRRF 27.0 155637|tegument_protein|CAB06732.1|Human_alphaherpesvirus_2|10310 -3891 GPLPKSYAV 0.0 None None 0 None -3892 GPRTKAWFL 1.91866745733 PRTKAWFL PSTLRWFF 25.0 38724|Genome_polyprotein|P08617.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 -3893 GRAEESVVL 0.0 None None 0 None -3894 GRAPCWQRL 0.487372385753 APCWQR APAWSR 27.0 155554|RL2|CAB06760.1|Human_alphaherpesvirus_2|10310 -3895 GREAEMQEL 0.0 None None 0 None -3896 GRMHIGDEL 0.0 None None 0 None -3897 GRMMFVGTL 0.0 None None 0 None -3898 GRNGQKAAL 0.0 None None 0 None -3899 GRVEKLLDL 0.0 None None 0 None -3900 GSDSSNGAV 0.0 None None 0 None -3901 GSEDFEDTY 0.0 None None 0 None -3902 GTNIVILEY 0.0118445772921 GTNIVILE GTQAVVLK 22.0 27981|IMMUNOGENIC_PROTEIN_MPT64_(ANTIGEN_MPT64/MPB64)|CAA98382.1|Mycobacterium_tuberculosis_H37Rv|83332 -3903 GVLECPRLI 0.0 None None 0 None -3904 HAKKKPNPV 0.718544984666 KKKPNPV KKKKNPM 28.0 142203|polyprotein|BAD73974.1|Hepatitis_C_virus_subtype_1b|31647 -3905 HHIDSAYLY 0.0 None None 0 None -3906 HHKGKMKAL 0.0 None None 0 None -3907 HHKHKELQV 0.0 None None 0 None -3908 HHRFNNFML 0.0 None None 0 None -3909 HIKDKKLPL 0.0 None None 0 None -3910 HLLSHSYCL 0.109600489264 HLLSHSYCL HLYSHPIIL 24.0 190568|polymerase|AAD16253.1|Hepatitis_B_virus|10407 -3911 HLMGQLSSL 3.88330048497 HLMGQLSSL HLAFQLSSI 27.0 24172|pX-rex-orf_I_{alternatively_spliced}|AAB23359.1|Human_T-lymphotropic_virus_1|11908 -3912 HMRLRYLAA 0.0 None None 0 None -3913 HPKYSFRRL 0.0 None None 0 None -3914 HPLRYTLIM 0.0 None None 0 None -3915 HRADVYVGV 0.0 None None 0 None -3916 HREDFEARL 0.159782640157 HREDFE HGEEFE 24.0 155811|ribonucleotide_reductase_large_subunit|CAB06725.1|Human_alphaherpesvirus_2|10310 -3917 HRGTGAVYV 27.0330536607 RGTGAVYV RGTSFVYV 29.0 27285|pol_protein|BAA32832.1|Hepatitis_B_virus|10407 -3918 HRLGESQTL 0.0 None None 0 None -3919 HRLHTPMYL 0.0 None None 0 None -3920 HRQAEVHKV 0.0 None None 0 None -3921 HRQQRGQQL 0.0 None None 0 None -3922 HRSKRGSSV 0.0 None None 0 None -3923 HRTRCLSKL 0.0 None None 0 None -3924 HRYPRVMAA 0.0 None None 0 None -3925 HRYPRVMAA 0.0 None None 0 None -3926 HSHLLSHSY 2.5848832505 HLLSHS HLYSHP 23.0 190568|polymerase|AAD16253.1|Hepatitis_B_virus|10407 -3927 HSYEAGTEI 0.0 None None 0 None -3928 HTPNGRHFY 0.701274710612 TPNGRHFY TDNNRSFY 27.0 98603|trans-sialidase,_putative|EAN82716.1|Trypanosoma_cruzi|5693 -3929 HWSMWLGVF 0.372066895841 WSMWLGV WTMKIGI 25.0 186524|polyprotein|AGW21594.1|Dengue_virus_1|11053 -3930 HYATILTSL 0.0 None None 0 None -3931 HYHHRFNNF 2.27650024439 YHHRFNN YQHKFNS 30.0 23270|polyprotein|AAB67036.1|Hepatitis_C_virus_(isolate_H77)|63746 -3932 HYISIFYAL 0.00687708027962 YISIFYA YMSPFYG 22.0 141469|envelope_glycoprotein_B|NP_044629.1|Human_alphaherpesvirus_1|10298 -3933 HYLRDVLPL 0.0 None None 0 None -3934 HYQGTWYLT 0.0 None None 0 None -3935 HYRKRGAHL 0.0 None None 0 None -3936 IAHAWWAHF 0.461739437354 HAWWAHF HARWAAF 28.0 141262|DNA_polymerase_catalytic_subunit|NP_044632.1|Human_alphaherpesvirus_1|10298 -3937 IAMYFYTTL 0.0 None None 0 None -3938 IEYGSPEEL 0.0 None None 0 None -3939 IFIASIYLL 0.0 None None 0 None -3940 IFLFVIVTI 0.0 None None 0 None -3941 IFPFALIFF 0.0 None None 0 None -3942 IFPFILIFF 0.0 None None 0 None -3943 IFSEKNRLV 0.0 None None 0 None -3944 IFSFINNSI 0.0 None None 0 None -3945 IFVSSYINI 0.0 None None 0 None -3946 IGRNRSPCM 0.0 None None 0 None -3947 IHDGAVHTI 0.552631578947 HDGAVHT QEGAMHT 26.0 50596|polyprotein|ABG75765.1|Dengue_virus_1|11053 -3948 IHDRQLRSF 0.0 None None 0 None -3949 IHEDEVDDM 0.113033351011 EDEVD EDEID 25.0 110431|E7|AAD33253.1|Human_papillomavirus_type_16|333760 -3950 IHFTKKDYV 0.0 None None 0 None -3951 IHGASNHCL 0.0 None None 0 None -3952 IHIDDNKWV 0.169553246094 DDNKWV DENPWL 25.0 31802|large_delta_antigen|AAG26087.1|Hepatitis_delta_virus_TW2667|10000523 -3953 IHLLDSLRL 0.0 None None 0 None -3954 IHLLYPPSL 0.0620423197569 IHLLYPP LHVWVPP 22.0 40158|polyprotein|AAA45534.1|Hepatitis_C_virus|11103 -3955 IHPRDRSTV 0.0 None None 0 None -3956 IHTDDNKCV 0.000134201508342 IHTDDNKCV IHDIILECV 16.0 110306|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 -3957 ILAVLPSLF 0.517090203886 AVLPSLF GIIPSMF 24.0 180407|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -3958 ILKKRQQAA 0.0 None None 0 None -3959 ILKRRYQEP 0.0 None None 0 None -3960 ILLTQFHFL 0.852006511865 ILLTQF ILLTHF 23.0 422984|NS5B_protein|ABB72740.1|Hepatitis_C_virus_genotype_1|41856 -3961 ILMRQPLPA 0.0 None None 0 None -3962 ILRSKMKTV 0.0 None None 0 None -3963 ILRVYSGVL 0.0 None None 0 None -3964 ILSSRSRQL 0.0 None None 0 None -3965 ILSSRSRQL 0.0 None None 0 None -3966 INFNHDSSI 0.0 None None 0 None -3967 IQWSYWGVF 0.0967863310004 WSYWGVF WAYHGSY 24.0 180582|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -3968 IRAANRRGL 0.0 None None 0 None -3969 IRDGSTMTF 0.0 None None 0 None -3970 IREYCPYTY 0.0377782116104 IREYCPYTY ISEYRHYCY 23.0 28484|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 -3971 IRFLRQYEF 0.0 None None 0 None -3972 IRHGNVIAC 0.513115695515 GNVIAC GNMSAC 24.0 133645|cell_surface_protein|NP_302626.1|Mycobacterium_leprae|1769 -3973 IRHLNATSF 0.0 None None 0 None -3974 IRIDTIHLL 0.0 None None 0 None -3975 IRLNRQRHT 0.0 None None 0 None -3976 IRNMAPDSL 0.0 None None 0 None -3977 IRPPDSRSL 0.420410333594 PPDSRSL PPGARSM 25.0 72928|Genome_polyprotein|P26662.3|Hepatitis_C_virus_(isolate_Japanese)|11116 -3978 IRRGGKHQL 0.0 None None 0 None -3979 IRRLRPSSI 0.13780610868 RRLRPS KRLEPS 22.0 50894|Genome_polyprotein|P27909.2|Dengue_virus_type_1_Hawaii|10000440 -3980 IRRLRPSSI 0.073674283114 RRLRPS KRLEPS 22.0 50894|Genome_polyprotein|P27909.2|Dengue_virus_type_1_Hawaii|10000440 -3981 IRRRGSTSL 0.0 None None 0 None -3982 IRYLHSLQI 0.0 None None 0 None -3983 ISELLFECY 0.0271004989586 ISELLFECY ISEYRHYCY 23.0 28484|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 -3984 ISFSMSEKM 0.0 None None 0 None -3985 ISKRKVSVA 0.0 None None 0 None -3986 ISLGFFLVF 0.0249581117984 ISLGFFLV LQAGFFLL 24.0 69715|envelope_protein|BAF48755.1|Hepatitis_B_virus|10407 -3987 ISSSAGLPY 0.0 None None 0 None -3988 ITIRNPLRY 0.0 None None 0 None -3989 ITMDQKKTI 0.0 None None 0 None -3990 ITMRYIHFL 0.0 None None 0 None -3991 ITTFDRLAY 13.9529411765 TFDRL TFDRL 26.0 66405|polyprotein|AAB67037.1|Hepatitis_C_virus_(isolate_H77)|63746 -3992 IVHRQFYLF 1.36497494935 IVHRQFYL LVHRQWFL 32.0 41407|Envelope_protein|NP_739583.2|Dengue_virus_2|11060 -3993 IVMGYSSGI 0.113615285052 MGYSSGI MDYSNGL 24.0 51604|FL-160-2_protein_-_Trypanosoma_cruzi|JH0823|Trypanosoma_cruzi|5693 -3994 IWFSIPTCL 0.0 None None 0 None -3995 IYAALPYVK 0.0 None None 0 None -3996 IYAFMGTPM 0.130873138164 IYAFMGTP LRAYMNTP 24.0 65497|HCV-1|AAA45676.1|Hepatitis_C_virus_genotype_1|41856 -3997 IYCRPFTTL 0.0 None None 0 None -3998 IYCVYPDSL 0.0 None None 0 None -3999 IYGLCVVIV 6.9120502655 YGLCVV YGVCIM 27.0 148117|early_protein|CAA52585.1|Human_papillomavirus_type_52|10618 -4000 IYHDSRIHV 0.0 None None 0 None -4001 IYTIVNIKI 0.0 None None 0 None -4002 IYVDKVRHV 3.30136379321 YVDKVR YLDKVR 28.0 74605|Circumsporozoite_protein_precursor|P08677.2|Plasmodium_vivax_strain_Belem|31273 -4003 KAFKRSSYL 0.0 None None 0 None -4004 KAFKRSSYL 0.0 None None 0 None -4005 KAMERSSLM 0.0 None None 0 None -4006 KHFIHLITV 0.0 None None 0 None -4007 KHLSRSNWL 0.0 None None 0 None -4008 KHNEEIRFL 0.0 None None 0 None -4009 KHRNMHCKI 0.0 None None 0 None -4010 KHRSEISMM 0.0 None None 0 None -4011 KIHIRETAI 0.0 None None 0 None -4012 KILKKRQQA 0.0 None None 0 None -4013 KISKRKVSV 0.0 None None 0 None -4014 KKRRKFWKA 0.101871750519 KRRKFW RRRKGW 25.0 55718|Probable_membrane_glycoprotein_precursor|P03218.1|Human_herpesvirus_4_strain_B95-8|10377 -4015 KLKPKKPTL 0.0 None None 0 None -4016 KLQPYFQTL 0.0163360332358 LQPYFQ LSPYYK 22.0 149024|NS2_protein|NP_751923.1|Hepatitis_C_virus_(isolate_H77)|63746 -4017 KMFRRSAHL 0.0 None None 0 None -4018 KRCALRLLV 0.0 None None 0 None -4019 KRFKRKSVV 0.0 None None 0 None -4020 KRILMPQVM 0.0 None None 0 None -4021 KRISHKAAL 0.0 None None 0 None -4022 KRQNLRLAL 0.0 None None 0 None -4023 KRQRAMETL 0.0 None None 0 None -4024 KRSPAWNEM 2.71823855445 SPAWN APAWS 24.0 155554|RL2|CAB06760.1|Human_alphaherpesvirus_2|10310 -4025 KRYLSQREV 0.951221917101 YLSQRE YLGKRE 22.0 150698|polyprotein|AGO67248.1|Dengue_virus_2|11060 -4026 KSDGLSLAV 0.0 None None 0 None -4027 KSFSKYASF 0.0 None None 0 None -4028 KWIREGYLV 0.0 None None 0 None -4029 KYMPPCSLV 0.0 None None 0 None -4030 KYPYWYQQK 0.419548617337 KYPYW KYTFW 25.0 137660|L1|ACL12325.1|Human_papillomavirus_type_58|10598 -4031 KYSTGIGWI 0.0 None None 0 None -4032 KYSTPPYLL 0.848971252603 KYSTPPYLL KYTSFPWLL 27.0 34616|pol_protein|BAA32832.1|Hepatitis_B_virus|10407 -4033 LAGQKRCAL 0.0 None None 0 None -4034 LAKVKYTAS 0.0 None None 0 None -4035 LALLKQVSV 0.0 None None 0 None -4036 LANDPIQVV 0.0 None None 0 None -4037 LAQSFFNCL 0.0 None None 0 None -4038 LCAIYFLSI 0.0 None None 0 None -4039 LCIKHFNIL 0.0 None None 0 None -4040 LEHMRLRYL 0.0 None None 0 None -4041 LFAAVVLLI 0.0 None None 0 None -4042 LFKKARWTI 0.0 None None 0 None -4043 LFLLFSFLF 0.0 None None 0 None -4044 LFPRLPSIL 6.65851410543 FPRLP FPRAP 24.0 62355|Genome_polyprotein|P08617.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 -4045 LFSFMTHCF 0.109472071245 FSFMTHC FSYDTRC 24.0 33382|polyprotein|AAB67037.1|Hepatitis_C_virus|11103 -4046 LFSFMTHRF 0.0 None None 0 None -4047 LGRNRHFGF 0.138393893319 GRNRHF GRDAHY 22.0 66798|glycoprotein_gp35/37|AAC59622.1|Human_gammaherpesvirus_8|37296 -4048 LHAPMYNLL 0.378354025976 APMYNLL VPNYNLI 24.0 150693|polyprotein|AGO67248.1|Dengue_virus_2|11060 -4049 LHAPMYNLL 0.21694931808 APMYNLL VPNYNLI 24.0 150693|polyprotein|AGO67248.1|Dengue_virus_2|11060 -4050 LHEQLGDRL 1.76159415596 LHEQLGD CYEQLGD 28.0 147561|early_protein|CAA52586.1|Human_papillomavirus_type_52|10618 -4051 LHFDAVQIC 0.0 None None 0 None -4052 LHFMPCVYI 0.0 None None 0 None -4053 LHFVQKLLF 0.183771171451 HFVQKLLF HFQRALIF 24.0 183577|polyprotein|AGK36298.1|Dengue_virus_2|11060 -4054 LHHKHKELQ 0.000432776802688 LHHKHKELQ LHEYMLDLQ 17.0 110335|E7|AAD33253.1|Human_papillomavirus_type_16|333760 -4055 LHHTHIALL 0.0 None None 0 None -4056 LHKDSNMPV 0.0 None None 0 None -4057 LHMNLLSYF 0.0 None None 0 None -4058 LHNAHVLDV 0.5 LHNAHVL FHNLHLL 26.0 79390|Protein_Tax-1|P0C213.1|Human_T-cell_lymphotropic_virus_type_1_(african_isolate)|39015 -4059 LHQCVLRFL 0.0 None None 0 None -4060 LHQGGATRV 0.0 None None 0 None -4061 LHRASGVGV 0.0 None None 0 None -4062 LHSGLQILI 0.0 None None 0 None -4063 LHTPVYFLL 0.0 None None 0 None -4064 LHTPVYFLL 0.0 None None 0 None -4065 LHTRHGSIL 0.196978634169 LHTRHG LHEQHG 26.0 75356|EBNA3A_nuclear_protein|Q8AZJ8|Human_gammaherpesvirus_4|10376 -4066 LHVGCDEVY 0.0 None None 0 None -4067 LHYEEIPEY 0.0 None None 0 None -4068 LIATQLLFY 0.0 None None 0 None -4069 LIKHKKTHI 0.679666392493 KHKKTHI KYKLKHI 21.0 34482|gag_polyprotein|BAA00992.1|Human_immunodeficiency_virus_1|11676 -4070 LIKYRQNHA 0.0 None None 0 None -4071 LIMNKRLGL 0.0 None None 0 None -4072 LKKRQQAAL 0.0 None None 0 None -4073 LKLVKRNSL 0.0 None None 0 None -4074 LLCARAWLL 0.0 None None 0 None -4075 LLDRRPHGY 0.0 None None 0 None -4076 LLESYSASL 0.0 None None 0 None -4077 LLGHKTVTI 0.0 None None 0 None -4078 LLGKKGTSA 0.473336145345 LLGKKGTSA LLGLWGTAA 25.0 37498|FL-160-2_protein_-_Trypanosoma_cruzi|JH0823|Trypanosoma_cruzi|5693 -4079 LLHTIITPM 0.0 None None 0 None -4080 LLKKLCIKL 2.09957355011 LKKLCI LRKLCI 28.0 184299|envelope_protein|AGT63061.1|Dengue_virus_3|11069 -4081 LLKSDGLSL 0.0 None None 0 None -4082 LLKTAFHPV 0.0 None None 0 None -4083 LLLMYSYAV 0.357608766066 LLLMYSYAV LLLVAHYAI 24.0 150377|polyprotein|AGS49173.1|Dengue_virus_2|11060 -4084 LLLQALQAL 0.0 None None 0 None -4085 LLMNKPYLA 1.11933186224 NKPYL NLPYL 22.0 13518|HCV-1|AAA45676.1|Hepatitis_C_virus_genotype_1|41856 -4086 LLMYTKLVV 0.0 None None 0 None -4087 LLNVHLSKL 0.0 None None 0 None -4088 LLRDFVAPL 0.0 None None 0 None -4089 LLRGHDQSA 0.0 None None 0 None -4090 LLRLLRKAM 0.0 None None 0 None -4091 LLRNDARSL 0.0 None None 0 None -4092 LLSFKRQRA 0.0 None None 0 None -4093 LLSRKDSIF 0.0 None None 0 None -4094 LLTQRLQGL 0.228736119694 LLTQRLQGL LITGRLQSL 27.0 36724|Spike_glycoprotein_precursor|P59594.1|SARS_coronavirus|227859 -4095 LMACATQLF 0.0 None None 0 None -4096 LMGQLSSLY 0.0 None None 0 None -4097 LMKMDDPSI 0.0 None None 0 None -4098 LMKQKKSSC 0.0 None None 0 None -4099 LNKLDFYVL 0.0 None None 0 None -4100 LNRQRHTPM 18.4848484848 RHTPM RHTPV 26.0 4156|polyprotein|ABR25251.1|Hepatitis_C_virus|11103 -4101 LPALRKTGV 0.0 None None 0 None -4102 LPAVHALRL 0.0 None None 0 None -4103 LPGLHFMPG 0.0 None None 0 None -4104 LPGMRGPPG 0.212348087935 GMRGP GQRGP 24.0 48915|kaposin|AAC57155.1|Human_gammaherpesvirus_8|37296 -4105 LPKDRFFAV 0.0 None None 0 None -4106 LPKEKLAAA 0.694505649699 LPKEKL LPREKL 27.0 54706|matrix_protein_2-1|AAS22094.1|Human_metapneumovirus|162145 -4107 LPMTLLLLL 0.0 None None 0 None -4108 LPQGRESPI 0.130541001792 LPQGRE LPSGRN 22.0 54709|protein_F_[Hepatitis_C_virus_subtype_1b]|ACA50643.1|Hepatitis_C_virus_(isolate_Japanese)|11116 -4109 LPRSKDTIL 0.0 None None 0 None -4110 LPRVRGTTL 0.0 None None 0 None -4111 LPSCRLAPA 0.0 None None 0 None -4112 LPTLKFQTF 0.0 None None 0 None -4113 LPYVKKTGM 0.0 None None 0 None -4114 LQKVRQEVL 0.0 None None 0 None -4115 LQLYRFSPI 0.67159130189 QLYRFSP QLFTFSP 28.0 51346|Genome_polyprotein|P29846.3|Hepatitis_C_virus|11103 -4116 LQRRRLSLL 0.0 None None 0 None -4117 LRADTSFFL 0.0 None None 0 None -4118 LRAKYRESL 0.0 None None 0 None -4119 LRAKYRESL 0.0 None None 0 None -4120 LRAPPGPQL 10.4355383797 PGPQL PGPRL 25.0 139406|polyprotein|ACT37184.1|Hepatitis_C_virus|11103 -4121 LRCHYHHRF 0.0 None None 0 None -4122 LRETRDQPL 0.0 None None 0 None -4123 LRIMLGEIL 0.0 None None 0 None -4124 LRINEVMVY 0.0 None None 0 None -4125 LRKGPIMEV 0.0 None None 0 None -4126 LRKHQILHL 0.0 None None 0 None -4127 LRKHQITHL 0.0 None None 0 None -4128 LRKPQNSEC 0.0 None None 0 None -4129 LRKQNFQPA 0.0 None None 0 None -4130 LRLALDQYL 0.0 None None 0 None -4131 LRLEINHTI 0.0 None None 0 None -4132 LRLPGGSCM 9.609030837 LRLPGGSCM VTLPTGQCL 26.0 71409|cysteine_proteinase_cruzipain_(EC_3.4.22.-)_-_Trypanosoma_cruzi|A45629|Trypanosoma_cruzi|5693 -4133 LRLRWGQII 0.0 None None 0 None -4134 LRLSEPAEI 0.0 None None 0 None -4135 LRMSDPSHI 33.5031608636 MSDPSHI LTDPSHI 32.0 59709|polyprotein|BAD73987.1|Hepatitis_C_virus_subtype_1b|31647 -4136 LRMSRSYPT 0.0 None None 0 None -4137 LRNDARSLY 0.0 None None 0 None -4138 LRPSSIETY 0.054584495544 PSSIET PESLET 23.0 184531|polyprotein|AFP27208.1|Dengue_virus_4|11070 -4139 LRQWIVVTM 0.0 None None 0 None -4140 LRRHRDVSA 0.0863636363636 LRRHRDV LRRHIDL 26.0 51526|HCV-1|AAA45676.1|Hepatitis_C_virus|11103 -4141 LRRMNSFQV 0.0074451481212 LRRMNSF LRKKSSF 21.0 116781|Nucleoprotein|P05133.1|Hantaan_virus_76-118|11602 -4142 LRRNYRCAI 0.0 None None 0 None -4143 LRRNYRCAI 0.0 None None 0 None -4144 LRRQDYQEI 0.0 None None 0 None -4145 LRRVASALL 0.0 None None 0 None -4146 LRSDAPAQL 0.0 None None 0 None -4147 LRSEEDGLV 0.0 None None 0 None -4148 LRSERNNTM 0.0 None None 0 None -4149 LRSIRVRLL 0.169857739813 SIRVRLL SVRARLL 25.0 149115|NS5_protein|BAA00702.1|Hepatitis_C_virus_(isolate_H77)|63746 -4150 LRSQAALSL 0.0 None None 0 None -4151 LRSQFPLIL 0.0 None None 0 None -4152 LRTEQNDFI 0.0 None None 0 None -4153 LRVSDGSLL 0.0 None None 0 None -4154 LRWEYGSIL 0.714053568268 WEYGSI WDFGSV 29.0 72301|envelope_protein|YP_001527880.1|West_Nile_virus_NY-99|10000971 -4155 LRYFLKHGI 0.202505548815 LRYFLKHGI MRYVLDHLI 24.0 25237|Transcription_activator_BRLF1|P03209.1|Human_herpesvirus_4_strain_B95-8|10377 -4156 LRYGAALIY 0.0 None None 0 None -4157 LSEFPEDSY 0.0 None None 0 None -4158 LSFKRQRAM 0.0 None None 0 None -4159 LSIIRFKGL 0.0 None None 0 None -4160 LSPMNHLCY 0.0 None None 0 None -4161 LSSLWYHTY 0.0419625022834 SLWYHTY DMWEHAF 22.0 9415|Superoxide_dismutase|P17670.1|Mycobacterium_tuberculosis|1773 -4162 LSTCRKLSL 0.0 None None 0 None -4163 LTDYDTRFY 0.0314758674337 LTDYDTRFY VTDNNRSFY 22.0 98603|trans-sialidase,_putative|EAN82716.1|Trypanosoma_cruzi|5693 -4164 LTEPHLRLL 0.0 None None 0 None -4165 LTGLVWQRY 0.654105044037 LTGLVWQR VSGLAWTR 27.0 54797|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 -4166 LTIYAALPY 0.0 None None 0 None -4167 LTMCMKKSL 0.0 None None 0 None -4168 LTQKQVLNY 0.0 None None 0 None -4169 LVAQHYAAL 0.0 None None 0 None -4170 LVDTVIDAY 0.0 None None 0 None -4171 LVQNSCWLI 0.0 None None 0 None -4172 LVRDRMKEL 0.0 None None 0 None -4173 LWQSCEESF 0.0 None None 0 None -4174 LYAVMGRSW 0.0 None None 0 None -4175 LYEDTLYTV 0.015462532395 YEDTLYTV YENLKYSV 22.0 186551|polyprotein|AGW21594.1|Dengue_virus_1|11053 -4176 LYEDWCQTV 0.0 None None 0 None -4177 LYEDWCQTV 0.0 None None 0 None -4178 LYFHSFIRI 0.0 None None 0 None -4179 LYFLAGQSL 0.0 None None 0 None -4180 LYFTRPVPL 0.0 None None 0 None -4181 LYGEQGHRW 0.0 None None 0 None -4182 LYGHSTHDL 0.675789473684 LYGHSTHDL LYANSAHAL 26.0 144913|Hexon_protein|P04133.3|Human_adenovirus_5|28285 -4183 LYHRDLAKW 0.0701635842114 HRDLAKW HSDAACW 24.0 79506|E1_protein|BAA19893.1|Rubella_virus|11041 -4184 LYMINHFFC 0.0 None None 0 None -4185 LYPDINNPF 0.0201559961005 PDINNPF PDYNPPL 23.0 103563|polyprotein|BAB18806.1|Hepatitis_C_virus|11103 -4186 LYPPSLPPF 61.161244788 YPPSLP FPPALP 29.0 30815|Genome_polyprotein|P26662.3|Hepatitis_C_virus|11103 -4187 LYTAYHVFF 0.0 None None 0 None -4188 LYVWKSELV 0.0 None None 0 None -4189 MACDRYVAI 0.0 None None 0 None -4190 MAEVNITYV 0.0 None None 0 None -4191 MAFDRYVAI 0.0 None None 0 None -4192 MAFDRYVAI 0.0 None None 0 None -4193 MAHERRDQL 0.0 None None 0 None -4194 MAHERRDQL 0.0 None None 0 None -4195 MAIGHFGQL 0.0 None None 0 None -4196 MAKYWNQFL 0.0 None None 0 None -4197 MAMSSRLAL 0.0 None None 0 None -4198 MATAYIRSM 0.0 None None 0 None -4199 MAYDQFLAI 0.0 None None 0 None -4200 MAYDQFLAI 0.0 None None 0 None -4201 MAYSITCPI 2.71923629545 MAYSITCPI LAYGRTCVL 24.0 17620|Early_antigen_protein_D|P03191.1|Human_herpesvirus_4_strain_B95-8|10377 -4202 MCMKKSLRL 0.0 None None 0 None -4203 MERERKAIA 0.0 None None 0 None -4204 MEVEAEQLL 0.0 None None 0 None -4205 MFATDYTTI 0.0560253733504 ATDYTTI STDSTTI 24.0 108148|polyprotein|AAF65953.1|Hepatitis_C_virus|11103 -4206 MFTLRMALF 0.0 None None 0 None -4207 MGHLQIRSL 0.0 None None 0 None -4208 MGKSTHTSM 20.3108019723 GKSTH GKSTH 28.0 20686|UL123;_IE1|AAR31448.1|Human_betaherpesvirus_5|10359 -4209 MHEEGYNKL 0.0 None None 0 None -4210 MHEYKIQGL 0.0 None None 0 None -4211 MHFCGGSFI 0.0 None None 0 None -4212 MHHPGSRKF 0.0 None None 0 None -4213 MHKTGLLGL 0.0 None None 0 None -4214 MHNLLIHRV 0.0 None None 0 None -4215 MHPDGRFEC 0.0 None None 0 None -4216 MIFILFLVI 0.0 None None 0 None -4217 MIRVKDSLI 0.0 None None 0 None -4218 MKQKKSSCL 0.0 None None 0 None -4219 MLCFYTPAL 0.00401934350471 MLCFYTPAL LMCAVHPTL 19.0 7660|polyprotein|AAA45677.1|Hepatitis_C_virus_(isolate_H77)|63746 -4220 MLHLYPGPM 0.140845070423 MLHLYPGPM LFQLYRGPL 26.0 38724|Genome_polyprotein|P08617.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 -4221 MLKTGISTV 0.0 None None 0 None -4222 MLLMNLATA 0.284963760522 LMNLAT LMNLAT 28.0 422997|preC/core_protein|CAJ33968.1|Hepatitis_B_virus|10407 -4223 MLLSILLPL 0.00626047139659 MLLSILLP MLILGLLP 20.0 41971|putative_D-ribose-binding_protein|NP_301386.1|Mycobacterium_leprae|1769 -4224 MLLSQNASI 0.0 None None 0 None -4225 MLNKVLYRL 7.66146587433e-05 MLNKVLYRL LLNGWRWRL 16.0 37607|kaposin|AAC57155.1|Human_gammaherpesvirus_8|37296 -4226 MLRELSSAF 0.0 None None 0 None -4227 MLRRQIRLL 0.0 None None 0 None -4228 MLRRQIRLL 0.0 None None 0 None -4229 MLSLRESPM 0.0 None None 0 None -4230 MLTSKVTVL 0.0 None None 0 None -4231 MLYRTVREL 0.0 None None 0 None -4232 MLYRTVREL 0.0 None None 0 None -4233 MMQCHRLSW 0.0 None None 0 None -4234 MNKRLGLEL 0.0 None None 0 None -4235 MNYKKGRAF 0.0 None None 0 None -4236 MPILKSVLI 0.0 None None 0 None -4237 MPKKVISAL 0.0 None None 0 None -4238 MPLLKLSCS 4.68242710796 MPLLKLSC VPLLAIGC 26.0 180802|polyprotein|AGO67248.1|Dengue_virus_2|11060 -4239 MPQYLASPL 0.0 None None 0 None -4240 MQFTQALEV 0.0 None None 0 None -4241 MRAAYLDDL 0.0 None None 0 None -4242 MRCQYETVL 0.840717365425 MRCQYETV MNCSYENM 27.0 36306|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 -4243 MREQRERQL 0.0 None None 0 None -4244 MRLRGGRMI 0.0 None None 0 None -4245 MRPISGVML 0.0 None None 0 None -4246 MRQPLPASM 0.0 None None 0 None -4247 MRRRQCEEV 0.695739763979 RRQCEEV KKKCDEV 25.0 24765|polyprotein_[Hepatitis_C_virus]|ABR27360.1|Hepatitis_C_virus|11103 -4248 MRRYQSRVI 0.0 None None 0 None -4249 MRRYQSRVI 0.0 None None 0 None -4250 MRSCLRLAL 0.0 None None 0 None -4251 MRSCLRLAL 0.0 None None 0 None -4252 MSEGIVKLY 0.0 None None 0 None -4253 MSPRVFFLL 0.0 None None 0 None -4254 MSQSQVALL 0.0 None None 0 None -4255 MSRSYPTGL 0.0 None None 0 None -4256 MWPLHWSMW 0.57916563282 MWPLHWSMW LWPKTHTLW 28.0 184702|non-structural_protein_1|AGM49312.1|Dengue_virus|12637 -4257 MYCLMLQCW 0.418731580108 CLMLQC CLIISC 25.0 93431|pre-C/C_protein|ABY54138.1|Hepatitis_B_virus|10407 -4258 MYCMVFLVL 0.877192982456 MYCMVFLV LLCLIFLL 26.0 37466|surface_antigen|BAF44879.1|Hepatitis_B_virus|10407 -4259 MYGAETEKF 0.0 None None 0 None -4260 MYMSVLSLI 0.0 None None 0 None -4261 MYMSVLSLI 0.0 None None 0 None -4262 MYSVVPQMV 0.0 None None 0 None -4263 MYSVVPQMV 0.0 None None 0 None -4264 MYSYAVPPL 0.236147358092 MYSYAVP IYVYALP 25.0 58463|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 -4265 MYTKLVVGF 0.0 None None 0 None -4266 NEILRRYSV 0.0138030526412 NEILRRY NKIVRMY 23.0 34304|Gag_polyprotein|P88150|Human_immunodeficiency_virus_1|11676 -4267 NFIERFWRI 0.0 None None 0 None -4268 NFIERFWRI 0.0 None None 0 None -4269 NFSINWWPI 0.882013080391 NWWPI NWWTL 29.0 74886|latent_membrane_protein_1|AAS99606.1|Human_gammaherpesvirus_4|10376 -4270 NHHNRTVEV 0.0 None None 0 None -4271 NHKDNSRIR 0.0 None None 0 None -4272 NHPYWANTV 0.0 None None 0 None -4273 NHSDLAAEL 0.0416522757017 NHSDLAAEL NHDSPDAEL 22.0 44133|Genome_polyprotein|P26664.3|Hepatitis_C_virus_genotype_1|41856 -4274 NIDLAREAY 0.0 None None 0 None -4275 NILPHYLEL 0.0 None None 0 None -4276 NIVYHTASI 0.175337715345 NIVYHTAS NLVYSTTS 27.0 96898|Genome_polyprotein|SRC279960|Hepatitis_C_virus|11103 -4277 NIYSRIREY 1.58925032505 NIYSRIREY KFYSKISEY 28.0 30892|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 -4278 NLARKEYTI 0.0 None None 0 None -4279 NLGFRFHMA 0.0 None None 0 None -4280 NLKHRKTAA 0.0 None None 0 None -4281 NLLANFSFL 0.0 None None 0 None -4282 NLLSYFNNL 0.0 None None 0 None -4283 NLMAKNNQA 1.11457402686 NLMAKN TIMAKN 22.0 103654|polyprotein|BAB18806.1|Hepatitis_C_virus|11103 -4284 NLNYRDLYY 0.0 None None 0 None -4285 NLPSKRVSL 0.679430959251 NLPSKRVS NVPYKRIE 25.0 1356|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 -4286 NMHCKISLL 0.0 None None 0 None -4287 NPLLHMVTM 0.0 None None 0 None -4288 NPLRYLAVM 0.0 None None 0 None -4289 NPLRYTSIL 0.0 None None 0 None -4290 NQKRRSESF 0.0 None None 0 None -4291 NRDKLGLQI 0.0 None None 0 None -4292 NRFSSKLLA 0.0 None None 0 None -4293 NRGPATAEV 0.0 None None 0 None -4294 NRLDLVRFY 0.166495086687 RLDLVR RVDMVR 23.0 32998|UL123;_IE1|AAR31448.1|Human_betaherpesvirus_5|10359 -4295 NRNYCVSVY 12.7901880739 RNYCVSV RHYCYSL 26.0 110846|E6_protein|CAB45108.1|Human_papillomavirus_type_16|333760 -4296 NRPEEEEQV 0.0 None None 0 None -4297 NRQRHTPMY 1.41898148148 RHTPM RHTPV 26.0 62977|polyprotein|AAB67037.1|Hepatitis_C_virus_(isolate_H77)|63746 -4298 NRVGVSSKL 0.0 None None 0 None -4299 NSDSFTGFI 0.0 None None 0 None -4300 NSINQVKLL 0.0 None None 0 None -4301 NTHRSRLSL 0.0 None None 0 None -4302 NTMAFSTDY 0.0 None None 0 None -4303 NVKKQRAGL 0.0 None None 0 None -4304 NVNQRFLNV 0.0 None None 0 None -4305 NYLEKVRSL 0.454075512249 YLEKVRS YLDKVRA 28.0 74605|Circumsporozoite_protein_precursor|P08677.2|Plasmodium_vivax_strain_Belem|31273 -4306 NYRDLYYFL 0.0 None None 0 None -4307 NYSPRPICV 7.49382142688 NYSPRP HYAPRP 28.0 25149|polyprotein|BAD73994.1|Hepatitis_C_virus_subtype_1b|31647 -4308 PASTLSLGY 3.87509767739 PASTLSLGY PASIAARGY 25.0 11063|Nonstructural_protein_NS3|NP_739587.2|Dengue_virus_2_Thailand/16681/84|31634 -4309 PFPRWLKII 0.00831776852653 PFPRWL PFVQWF 23.0 37919|envelope_protein|BAF48755.1|Hepatitis_B_virus|10407 -4310 PHWASSIVL 0.0385912911549 WASSIV WGGSVV 22.0 79351|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 -4311 PHYDFERSC 1.37387031452 PHYDFE PEYDLE 25.0 48896|Genome_polyprotein|P27958.3|Hepatitis_C_virus_subtype_1a|31646 -4312 PIEMNPEGY 0.0 None None 0 None -4313 PRIGYSLLL 0.0214674118902 PRIGYS PRASYS 22.0 53148|Transcription_activator_BRLF1|P03209.1|Human_herpesvirus_4_strain_B95-8|10377 -4314 PRLKWVVLV 0.0 None None 0 None -4315 PRNRKPLTV 21.9346414515 PRNRKPL PRSRTPI 26.0 88849|IE62|AAP32859.1|Human_alphaherpesvirus_3|10335 -4316 PRPSRCLLL 0.584858416083 RCLLL RCLLL 26.0 23566|tegument_protein_UL7|NP_044476.1|Human_alphaherpesvirus_2|10310 -4317 PRSEEAAVL 0.0 None None 0 None -4318 PRSKDTILL 0.0 None None 0 None -4319 PRSRWRDQL 0.0 None None 0 None -4320 PRWSCQEKL 0.0 None None 0 None -4321 PSQPANSFY 0.601059658223 PSQPANSFY PSQEPMSIY 23.0 58463|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 -4322 PTALSSLWY 0.0 None None 0 None -4323 PTDVLNGAA 0.0 None None 0 None -4324 PYPETPPRW 1.35529826852 YPETPP YPDAPP 30.0 141354|transcriptional_regulator_ICP4|NP_044662.1|Human_alphaherpesvirus_1|10298 -4325 PYQGRPKLL 2.71654929577 PYQGRP PYAGEP 26.0 65810|sporozoite_surface_protein_2|NP_705260.1|Plasmodium_falciparum_3D7|36329 -4326 PYQGRPKLL 0.442771084337 PYQGRP PYAGEP 26.0 65810|sporozoite_surface_protein_2|NP_705260.1|Plasmodium_falciparum_3D7|36329 -4327 PYTSVFLSV 0.0 None None 0 None -4328 QAEARLLAL 0.0 None None 0 None -4329 QAKVKFIGV 0.468283818619 VKFIGV VRFMGV 23.0 37153|Nuclear_antigen_EBNA-3C|Q69140.1|Human_gammaherpesvirus_4|10376 -4330 QEHVRCSAI 0.0 None None 0 None -4331 QFSFDGWKF 0.00828381734168 QFSFDGWKF QYSDRRWCF 19.0 53027|nonstructural_protein_3|NP_722463.1|Dengue_virus_1_Singapore/S275/1990|33741 -4332 QGRPKLLQL 0.0 None None 0 None -4333 QHCYMSRLL 0.0 None None 0 None -4334 QHDFCGLYM 1.18519018581 QHDFCGLYM KAKICGLYL 28.0 177701|polyprotein|ACZ60104.1|Hepatitis_C_virus_subtype_3a|356426 -4335 QHLLQRMSI 0.0 None None 0 None -4336 QHMHCLQDL 0.0 None None 0 None -4337 QHPNNSKDV 0.67707530484 HPNNS HPNNT 28.0 141306|tegument_host_shutoff_protein|NP_044643.1|Human_alphaherpesvirus_1|10298 -4338 QHQRLLEVL 0.0 None None 0 None -4339 QHTESLEYM 0.0 None None 0 None -4340 QHYAALQEY 0.0199846777357 HYAALQ HQAAMQ 22.0 101673|gag_protein|ABO73990.1|Human_immunodeficiency_virus_1|11676 -4341 QILSRVAAL 1.04035259267 ILSRVAAL MLSRVAAV 27.0 98253|trans-sialidase,_putative|EAN81042.1|Trypanosoma_cruzi|5693 -4342 QLMMSLLQL 0.0 None None 0 None -4343 QLREHAATL 0.0 None None 0 None -4344 QLRRSKVSV 0.0 None None 0 None -4345 QLYPRLKML 0.0 None None 0 None -4346 QLYPRLKML 0.0 None None 0 None -4347 QMLRIFKEM 0.0 None None 0 None -4348 QMYMSVLSL 0.0 None None 0 None -4349 QPAWRKASA 0.0 None None 0 None -4350 QPLRNFISV 0.0 None None 0 None -4351 QPMCRICHE 0.449806949807 MCRICH MCDECH 26.0 107790|polyprotein|AAD56189.1|Hepatitis_C_virus|11103 -4352 QRAPVGKLL 0.0 None None 0 None -4353 QRAVSRNLM 0.0 None None 0 None -4354 QRFLFIMFL 0.0 None None 0 None -4355 QRFLNVQEL 0.0264820306828 QRFLNVQEL ERYLKDQQL 22.0 14101|envelope_glycoprotein|ABI16336.1|Human_immunodeficiency_virus_1|11676 -4356 QRGEGILDM 0.0 None None 0 None -4357 QRHGFGEEI 0.00190751343828 QRHGFGEEI QTHIFAEVL 19.0 73862|EBNA-1_protein|Q777E1|Human_gammaherpesvirus_4|10376 -4358 QRIQMYMSV 0.0 None None 0 None -4359 QRIVKPTSI 0.0 None None 0 None -4360 QRLEPVYFV 0.0 None None 0 None -4361 QRLEVPIEM 0.0 None None 0 None -4362 QRMELLITF 0.0 None None 0 None -4363 QRQARQYQL 0.0 None None 0 None -4364 QRRPSSVGL 0.0 None None 0 None -4365 QRRSIPFQM 0.0 None None 0 None -4366 QRSGKPVLM 0.0 None None 0 None -4367 QRSNSETKV 0.0 None None 0 None -4368 QRSRKGDLL 0.0 None None 0 None -4369 QSEDRSHTL 0.0 None None 0 None -4370 QSQPFSMQY 0.0 None None 0 None -4371 QSQPGNALY 0.0 None None 0 None -4372 QTCKANLCY 11.2279615819 QTCKANLCY EFCRVLCCY 23.0 11956|UL123;_IE1|AAR31448.1|Human_betaherpesvirus_5|10359 -4373 QTLACNLCY 0.0 None None 0 None -4374 QVKRKVQAL 0.0 None None 0 None -4375 QYMLTLFTA 0.0 None None 0 None -4376 RAEDTALYY 0.0 None None 0 None -4377 RAIYHSCSL 0.0 None None 0 None -4378 RAKYRESLL 0.0 None None 0 None -4379 RAPQRIPSL 0.00198664006271 PQRIPSL PSRGPKL 19.0 74800|Genome_polyprotein|SRC279960|Hepatitis_C_virus_subtype_2b|31650 -4380 RARLQHCSA 0.0 None None 0 None -4381 RARYYIQVA 0.0 None None 0 None -4382 RASQRMSSV 0.0 None None 0 None -4383 RATARFHQL 0.0 None None 0 None -4384 RFFSRFTAV 0.0 None None 0 None -4385 RFHRVIKDF 0.0 None None 0 None -4386 RFKRKSVVA 0.0 None None 0 None -4387 RFLFIMFLF 0.0 None None 0 None -4388 RFLRNFPQI 0.406366189382 LRNFPQI VRHFPRI 25.0 187106|Vpr_protein|BAA93983.1|Human_immunodeficiency_virus_1|11676 -4389 RFMKYLVNF 0.219129686223 MKYLVNF LEYLVSF 25.0 69474|core_protein|BAF42671.1|Hepatitis_B_virus|10407 -4390 RFNMLNQIF 0.0 None None 0 None -4391 RFQDHRWEL 0.0 None None 0 None -4392 RHFEEALQT 0.0 None None 0 None -4393 RHFRLMHNL 0.0 None None 0 None -4394 RHIRHGNVI 0.0 None None 0 None -4395 RHLGDQMEV 17.8416258526 RHLGDQMEV RHTSDHMSI 26.0 17278|Genome_polyprotein|P06441.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 -4396 RHRCRNRFV 0.0 None None 0 None -4397 RHSPRNLIY 0.457200416329 HSPRNLIY HGPTPLLY 25.0 6591|polyprotein|AAB67037.1|Hepatitis_C_virus_(isolate_H77)|63746 -4398 RHTPMYYFL 0.0094183334308 RHTPMYY RHHNMVY 20.0 144403|polyprotein|AAK08509.1|Hepatitis_C_virus_subtype_1b|31647 -4399 RHTPMYYFL 0.00293201762289 RHTPMYY RHHNMVY 20.0 144403|polyprotein|AAK08509.1|Hepatitis_C_virus_subtype_1b|31647 -4400 RLIVKSREL 0.0 None None 0 None -4401 RLKQEIKRL 0.0 None None 0 None -4402 RLMCGPNTI 1.71760391198 LMCGPNTI ILCVPNAV 26.0 183741|polyprotein|AGS49173.1|Dengue_virus_2|11060 -4403 RLRRVASAL 0.0 None None 0 None -4404 RMCKFLQYF 0.0 None None 0 None -4405 RMSSVGANF 0.0 None None 0 None -4406 RNFPQIYIL 0.957507082153 RNFPQIY RHFPRIW 26.0 187106|Vpr_protein|BAA93983.1|Human_immunodeficiency_virus_1|11676 -4407 RNPQELWHF 0.135340359953 NPQEL NPQEV 24.0 69799|envelope_glycoprotein|BAE96221.1|Human_immunodeficiency_virus_1|11676 -4408 RNRKRFCVP 0.0 None None 0 None -4409 RPGSRGCPM 1.15273082827 RPGSRGCPM KPGTSGSPI 28.0 150341|polyprotein|AGW21594.1|Dengue_virus_1|11053 -4410 RPKYSFHRL 0.0 None None 0 None -4411 RPRARLAAL 0.0 None None 0 None -4412 RPRARYYIQ 0.0 None None 0 None -4413 RPRQGRWWL 0.0 None None 0 None -4414 RQFPKKSLM 0.0 None None 0 None -4415 RQFYLFYNF 0.0 None None 0 None -4416 RQMISELLF 0.0 None None 0 None -4417 RQQQDYWLM 0.0241357685845 QQDYWLM QQNWWTL 25.0 74886|latent_membrane_protein_1|AAS99606.1|Human_gammaherpesvirus_4|10376 -4418 RRENSLSEI 0.0 None None 0 None -4419 RRFNMLNQI 0.0 None None 0 None -4420 RRGEAEKRL 0.0 None None 0 None -4421 RRGGSGAMV 0.0 None None 0 None -4422 RRKQSEMYI 0.0 None None 0 None -4423 RRLDYDHKL 0.0 None None 0 None -4424 RRPSRAMWL 0.0 None None 0 None -4425 RRQDYQEIL 0.0 None None 0 None -4426 RRSDAEKQL 0.111181455484 RSDAEKQ RADEEQQ 22.0 70687|ESAT-6-like_protein_esxB|P0A566.2|Mycobacterium_tuberculosis|1773 -4427 RRSKVSVEM 0.0 None None 0 None -4428 RRSPSFSRV 0.0 None None 0 None -4429 RRVASALLL 0.0 None None 0 None -4430 RRVPYRGSV 0.0 None None 0 None -4431 RRYLKSGVV 0.0 None None 0 None -4432 RSADWQRKI 0.0 None None 0 None -4433 RSELNSVEY 0.0 None None 0 None -4434 RSFPAGVEM 0.0 None None 0 None -4435 RTQDAIHEL 0.0 None None 0 None -4436 RTSSIFYSF 0.0 None None 0 None -4437 RVGQMAFVF 0.0 None None 0 None -4438 RVNDCILQV 0.0 None None 0 None -4439 RVRRRGQKL 0.000560646888862 RVRRRGQK RLRPGGKK 19.0 54741|gag_polyprotein|BAA00992.1|Human_immunodeficiency_virus_1|11676 -4440 RVSDGSLLY 0.0 None None 0 None -4441 RWQGRVRTL 0.0 None None 0 None -4442 RYAALLKCW 0.0377103973581 RYAALLKCW RYMGEDGCW 22.0 185573|polyprotein|CDF77361.1|Dengue_virus_3|11069 -4443 RYARPSRLV 36.924260273 RYARPSRL RFAQPSAL 27.0 142233|ATP-dependent_helicase|NP_217813.1|Mycobacterium_tuberculosis|1773 -4444 RYCLTTLTI 0.0 None None 0 None -4445 RYFDEPVEL 0.0 None None 0 None -4446 RYFDEPVEL 0.0 None None 0 None -4447 RYFLKHGIL 0.525137542938 RYFLKHGI RYVLDHLI 22.0 25237|Transcription_activator_BRLF1|P03209.1|Human_herpesvirus_4_strain_B95-8|10377 -4448 RYILLKRSL 0.0 None None 0 None -4449 RYLENGKEM 0.0 None None 0 None -4450 RYLKSGVVL 0.0 None None 0 None -4451 RYLPDCDYL 0.48206481189 RYLPDCDYL RYAPACKPL 25.0 56502|polyprotein|BAD73994.1|Hepatitis_C_virus_subtype_1b|31647 -4452 RYRSIISDI 0.0 None None 0 None -4453 RYVAICAPL 1.06464167115 RYVAICAPL RYAPACKPL 29.0 56502|polyprotein|BAD73994.1|Hepatitis_C_virus_subtype_1b|31647 -4454 RYVASCKPL 0.477699027983 RYVASCKPL RYAPACKPL 37.0 56502|polyprotein|BAD73994.1|Hepatitis_C_virus_subtype_1b|31647 -4455 SADYINANY 0.0 None None 0 None -4456 SAEECRTEL 0.0 None None 0 None -4457 SAKQQNQIL 0.0 None None 0 None -4458 SAKQQNQIL 0.0 None None 0 None -4459 SALGREHPA 0.0 None None 0 None -4460 SARDQPSSV 0.0 None None 0 None -4461 SARLRQRAV 0.0 None None 0 None -4462 SASNNNSEL 0.0 None None 0 None -4463 SAVRRDLTF 0.0 None None 0 None -4464 SAYDGKDYI 0.0 None None 0 None -4465 SCSSNPHLL 0.0 None None 0 None -4466 SEEERGLEL 0.0 None None 0 None -4467 SEKDRPVKV 0.0 None None 0 None -4468 SESHRTSLL 0.0 None None 0 None -4469 SEVERLDVL 0.0 None None 0 None -4470 SFFNCLWEV 0.674192438284 FFNCLWEV LLNCLWSV 34.0 37536|Spike_glycoprotein_precursor|P15423.1|Human_coronavirus_229E|11137 -4471 SFPGRVREL 0.0 None None 0 None -4472 SFQTITEQF 0.0 None None 0 None -4473 SFVDAIHTF 0.0 None None 0 None -4474 SGFEFSQVL 0.0 None None 0 None -4475 SGMARVGSL 0.484375 GMARVG GMSRIG 26.0 21347|Nucleoprotein|P59595.1|SARS_coronavirus|227859 -4476 SHKEAITAL 0.0 None None 0 None -4477 SHKKQSSVI 0.0 None None 0 None -4478 SHLQRIGTI 0.0 None None 0 None -4479 SHLTIVILF 0.0 None None 0 None -4480 SHMYVATGI 0.0 None None 0 None -4481 SHNRHVPKI 0.25312133776 RHVPKI RHFPRI 25.0 187106|Vpr_protein|BAA93983.1|Human_immunodeficiency_virus_1|11676 -4482 SHPLHYTTI 0.0 None None 0 None -4483 SHPLHYTTI 0.0 None None 0 None -4484 SHQPLPGTL 0.0 None None 0 None -4485 SHRNPLLDL 0.0 None None 0 None -4486 SHSPAGELT 0.168377764503 PAGELT PQGQLT 23.0 13701|Trans-activator_protein_BZLF1|P03206.2|Human_gammaherpesvirus_4|10376 -4487 SHSSNPHLL 0.0 None None 0 None -4488 SHTLLLTQL 0.0 None None 0 None -4489 SIFYSFLPL 0.0538659105423 SIFYSFLPL SIYVYALPL 21.0 58463|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 -4490 SKFGQGTGL 0.0 None None 0 None -4491 SKQNMPQYL 0.0 None None 0 None -4492 SLAKFDAPL 0.0 None None 0 None -4493 SLDTTTWEY 0.0 None None 0 None -4494 SLFTCVLQL 0.0 None None 0 None -4495 SLGDNSEYL 0.0 None None 0 None -4496 SLHHKHKEL 0.0 None None 0 None -4497 SLIDSSRVV 0.0 None None 0 None -4498 SLKLTQSSA 0.0 None None 0 None -4499 SLLRKHQIL 56.8225353198 SLLRKHQIL SLLRNHNLV 28.0 96898|Genome_polyprotein|SRC279960|Hepatitis_C_virus|11103 -4500 SLLRKHQIT 1.76449738892 SLLRKHQI SLLRNHNL 27.0 96898|Genome_polyprotein|SRC279960|Hepatitis_C_virus|11103 -4501 SLLVHGGPL 0.203585933289 VHGGPL VHAGPI 27.0 24557|Gag_polyprotein|P03347.3|Human_immunodeficiency_virus_1|11676 -4502 SLNHRGRVM 0.0 None None 0 None -4503 SLNHRGRVM 0.0 None None 0 None -4504 SLNPKKFSI 0.0 None None 0 None -4505 SLRAEDTAL 0.0 None None 0 None -4506 SLSETVRLV 0.0 None None 0 None -4507 SLSVRTSGL 0.0 None None 0 None -4508 SLWYHTYGL 0.584082675016 YHTYGL FHSYGV 26.0 232152|rhoptry_kinase_family_protein|AFO54841.1|Toxoplasma_gondii_type_III|398031 -4509 SLYTAYHVF 0.0168850134338 SLYTAYHV KLYCSYEV 22.0 32250|FL-160-2_protein_-_Trypanosoma_cruzi|JH0823|Trypanosoma_cruzi|5693 -4510 SLYVWKSEL 0.0 None None 0 None -4511 SMAKYWNQF 0.0 None None 0 None -4512 SMKAERPPA 0.0 None None 0 None -4513 SMKNLQRAV 0.0 None None 0 None -4514 SMKVHIKAM 0.0 None None 0 None -4515 SMMTATIVF 0.0 None None 0 None -4516 SMPANFETI 0.0 None None 0 None -4517 SMREALREL 0.0 None None 0 None -4518 SMREAVREL 0.0 None None 0 None -4519 SMRYFITSV 0.0 None None 0 None -4520 SPGPFFWMF 0.0 None None 0 None -4521 SPLFYSTCM 0.620468376578 SPLFYST SPITYST 27.0 107873|Genome_polyprotein|P26664.3|Hepatitis_C_virus|11103 -4522 SPLQLPAPL 0.0 None None 0 None -4523 SPLRYISIL 0.0 None None 0 None -4524 SPMYFFLSY 0.0 None None 0 None -4525 SPRSRPSDI 0.0 None None 0 None -4526 SPRVFFLLM 0.0 None None 0 None -4527 SPSSAYLLF 0.0 None None 0 None -4528 SQHPAQQQI 0.0 None None 0 None -4529 SQMSQLMGL 0.0776138458536 SQMSQLM AQMWQLM 22.0 182599|polyprotein|AGW21594.1|Dengue_virus_1|11053 -4530 SQPGNALYF 0.0 None None 0 None -4531 SRAMWLSLF 0.0 None None 0 None -4532 SRATADPEV 0.0 None None 0 None -4533 SRCLLLPLL 5.4232325855 RCLLL RCLLL 26.0 23566|tegument_protein_UL7|NP_044476.1|Human_alphaherpesvirus_2|10310 -4534 SREDDNRER 0.0 None None 0 None -4535 SRENRWTTV 0.132816935515 RENRWT REDQWC 23.0 53476|polyprotein|AGO67248.1|Dengue_virus_2|11060 -4536 SRFCSLHCL 0.0 None None 0 None -4537 SRFTAVREF 0.0269793149431 SRFTAVR SRYWAIR 22.0 60867|nucleoprotein|CAZ65591.1|Influenza_A_virus|11320 -4538 SRFTLRCMV 1.61952838872 SRFTLRCM GRWTGRCM 26.0 110215|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 -4539 SRFVVRPLL 0.0 None None 0 None -4540 SRGQEIKTI 0.0 None None 0 None -4541 SRHDFHVDL 0.0424328495879 SRHDFHVDL TLHEYMLDL 22.0 178351|Protein_E7|P03129.1|Human_papillomavirus_type_16|333760 -4542 SRKGDLLRI 0.0 None None 0 None -4543 SRKKRRSPP 0.0 None None 0 None -4544 SRKLRKLPT 0.0 None None 0 None -4545 SRLHTPVYF 0.0 None None 0 None -4546 SRNAYSLEI 0.0 None None 0 None -4547 SRNDFEWVY 0.02135862433 SRNDFE GRNSFE 22.0 37364|P53_HUMAN_Cellular_tumor_antigen_p53_(Tumor_suppressor_p53)_(Phosphoprotein_p53)_(Antigen_NY-CO-13)|P04637.2|Homo_sapiens|9606 -4548 SRPGALEHL 0.0 None None 0 None -4549 SRPSSKQNM 0.0 None None 0 None -4550 SRQMISELL 0.0 None None 0 None -4551 SRRARGREK 0.0 None None 0 None -4552 SRRSFWSEL 0.0 None None 0 None -4553 SRSRNAYSL 0.0 None None 0 None -4554 SRSVDVTNI 0.0 None None 0 None -4555 SRTVWEEMV 0.825050427473 SRTVWE TRTVWQ 28.0 120187|E1_protein|BAA19893.1|Rubella_virus|11041 -4556 SRWRDQLLF 0.0 None None 0 None -4557 SRYARPSRL 0.939932458239 RYARPSRL RFAQPSAL 27.0 142233|ATP-dependent_helicase|NP_217813.1|Mycobacterium_tuberculosis|1773 -4558 SSASLNSNY 0.0 None None 0 None -4559 SSDEIVQEL 0.0 None None 0 None -4560 SSKQHLKPA 0.0 None None 0 None -4561 SSLARELSL 0.0 None None 0 None -4562 SSLRRMNSF 0.00406654233374 LRRMNSF LRKKSSF 21.0 116781|Nucleoprotein|P05133.1|Hantaan_virus_76-118|11602 -4563 SSRGNGKMM 0.0 None None 0 None -4564 SSTSHIPEV 0.0 None None 0 None -4565 SSYSRVALV 0.0 None None 0 None -4566 STDDATWAA 0.0 None None 0 None -4567 STERPKMTY 0.0 None None 0 None -4568 STIYIFALF 1.09241706161 TIYIFAL SIYVYAL 26.0 58463|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 -4569 STKVHIKVL 0.0 None None 0 None -4570 STQTHPLTL 4.38726372945 TQTHPLT TLTHPIT 30.0 71412|polyprotein_[Hepatitis_C_virus_subtype_1a]|ABV46251.2|Hepatitis_C_virus_subtype_1a|31646 -4571 STSHVYHLF 0.0 None None 0 None -4572 STYNETNLI 0.0 None None 0 None -4573 STYPDQQHV 2.03088323857 STYPDQQHV SYYPDQKSL 28.0 28594|IMMUNOGENIC_PROTEIN_MPT64_(ANTIGEN_MPT64/MPB64)|CAA98382.1|Mycobacterium_tuberculosis_H37Rv|83332 -4574 SVEEKGKLL 0.0 None None 0 None -4575 SVFPTQLQL 2.29326254822 SVFPTQLQL GLFPTQIQV 32.0 20865|Nucleoprotein|P41269.1|Puumala_hantavirus|11604 -4576 SVFSEQWIF 0.0264970465526 SVFSEQWIF AVFGPLWIL 23.0 96123|Genome_polyprotein|P26664.3|Hepatitis_C_virus_(isolate_H77)|63746 -4577 SVRENCCSL 0.0 None None 0 None -4578 SWMPALECL 0.05038120655 SWMPALECL SWDETWKCL 23.0 146569|polyprotein|ADF97231.1|Hepatitis_C_virus_subtype_3a|356426 -4579 SWPLWTAIF 1.22480631271 SWPLW SWCLW 27.0 39591|polyprotein|AAA45677.1|Hepatitis_C_virus_(isolate_H77)|63746 -4580 SWVSSTLGF 0.0 None None 0 None -4581 SYAKNAQDL 0.0 None None 0 None -4582 SYARILGTV 0.0 None None 0 None -4583 SYAVICNNF 0.0 None None 0 None -4584 SYFCILRTI 0.0 None None 0 None -4585 SYFGLATVF 0.0 None None 0 None -4586 SYFLATDTI 0.0 None None 0 None -4587 SYFNNLHLW 4.77360749628 FNNLHL FHNLHL 29.0 79390|Protein_Tax-1|P0C213.1|Human_T-cell_lymphotropic_virus_type_1_(african_isolate)|39015 -4588 SYGVNLYQF 5.06976518192 YGVNLYQF YGYPVYVF 22.0 23807|tax|AAG48731.1|Human_T-lymphotropic_virus_2|11909 -4589 SYIYILITI 0.0560487592099 YILITI YVILTI 23.0 186620|polyprotein|AFP27208.1|Dengue_virus_4|11070 -4590 SYKFLAPWI 0.348021972633 YKFLAPW YRFVAPG 27.0 149053|NS3_gene_product|AAB02124.1|Hepatitis_C_virus|11103 -4591 SYPSIHRFI 0.601659125972 PSIHRFI PGIYRFV 27.0 149053|NS3_gene_product|AAB02124.1|Hepatitis_C_virus|11103 -4592 SYPSQPDGF 0.0 None None 0 None -4593 SYSLISEKL 0.0 None None 0 None -4594 SYVMDHFDI 0.965095685508 YVMDHF YVLDHL 27.0 25237|Transcription_activator_BRLF1|P03209.1|Human_herpesvirus_4_strain_B95-8|10377 -4595 SYVRIGATI 0.0 None None 0 None -4596 SYWGVFAPI 0.000607367462934 SYWGVFAPI SLWKDGAPL 19.0 140600|glutamine_synthetase_GLNA1_(glutamine_synthase)_(GS-I)|NP_216736.1|Mycobacterium_tuberculosis_H37Rv|83332 -4597 SYYKIVSSI 0.0193185218111 KIVSSI KLVSSV 22.0 95262|LAMP|AAK72632.1|Human_gammaherpesvirus_8|37296 -4598 TAAIRPKSL 0.0 None None 0 None -4599 TADVGLAGY 0.0 None None 0 None -4600 TAFDESISL 0.0 None None 0 None -4601 TAMAYDQFL 0.0 None None 0 None -4602 TDKERQRLL 0.0 None None 0 None -4603 TDYDTRFYM 0.0 None None 0 None -4604 TEFGQKQKL 0.0 None None 0 None -4605 TERDQIELL 0.0 None None 0 None -4606 TFDRLAYLW 0.0 None None 0 None -4607 TFEDNLRSL 0.0 None None 0 None -4608 TFGEVNYFF 0.243387329538 GEVNYF GEADYF 25.0 24535|EBNA-1_protein|Q777E1|Human_gammaherpesvirus_4|10376 -4609 TFITSVIRF 0.0 None None 0 None -4610 TFLIAMVFI 0.0 None None 0 None -4611 TFNDWFEII 0.755265816333 FNDWFEI FKDWEEL 27.0 6556|X_protein|AAP06597.1|Hepatitis_B_virus|10407 -4612 TFSCQLHKF 0.0 None None 0 None -4613 THAPERDLC 0.0 None None 0 None -4614 THASLSNHV 0.009151449223 HASLSNH HAMSSTH 21.0 140686|ESAT-6-like_protein_esxH|P0A568.2|Mycobacterium_tuberculosis|1773 -4615 THHGPAFSI 0.0 None None 0 None -4616 THIFGLMVI 0.0 None None 0 None -4617 THIHAAACI 0.0 None None 0 None -4618 THMERVLSL 0.0 None None 0 None -4619 THMERVLSL 0.0 None None 0 None -4620 THPIYYLKI 0.0 None None 0 None -4621 THQEALMKL 0.0 None None 0 None -4622 THREGISAI 0.561269053294 THREGI NHRQGI 25.0 34642|methionine_sulfoxide_reductase_B|YP_169878.1|Francisella_tularensis_subsp._tularensis_SCHU_S4|177416 -4623 THRSRLSLG 0.0 None None 0 None -4624 THTSYQLSA 0.0 None None 0 None -4625 THYQGTWYL 0.0 None None 0 None -4626 TIKQRPKPT 0.0 None None 0 None -4627 TKFESNLCV 0.0 None None 0 None -4628 TLDKKLEYY 1.51757846321 LDKKLE LDKKVE 26.0 27000|Heat_shock_protein_HSP_90-beta|P08238.4|Homo_sapiens|9606 -4629 TLERAALRY 0.0 None None 0 None -4630 TLGLIFLCL 0.0 None None 0 None -4631 TLMVVVWVL 0.0 None None 0 None -4632 TLTIRALPA 0.0 None None 0 None -4633 TMCMYFRPL 0.0 None None 0 None -4634 TMETSFFSF 0.0 None None 0 None -4635 TMGSWTCLF 0.475156091949 SWTCL TWKCL 24.0 146569|polyprotein|ADF97231.1|Hepatitis_C_virus_subtype_3a|356426 -4636 TMRTRHFTG 0.0 None None 0 None -4637 TMRYIHFLF 0.0 None None 0 None -4638 TMSPRVFFL 0.0 None None 0 None -4639 TPGNRTKCF 2.47406881013 GNRTKCF GNASRCW 24.0 21385|polyprotein|AAY82034.1|Hepatitis_C_virus_genotype_1|41856 -4640 TPKSMQSTL 0.0 None None 0 None -4641 TPNFRRRAI 0.0 None None 0 None -4642 TPSERSKPL 1.35857438639 SERSKP SERSQP 26.0 33856|polyprotein|BAA03375.1|Hepatitis_C_virus|11103 -4643 TPSTQTHPL 0.0722037478202 TPSTQTH TPAVQTN 24.0 149037|NS4B_protein|NP_751926.1|Hepatitis_C_virus_(isolate_H77)|63746 -4644 TRAERLTWL 0.0 None None 0 None -4645 TRALHRLIV 0.0 None None 0 None -4646 TRASDRRGI 0.0 None None 0 None -4647 TRDAPGLRV 0.0 None None 0 None -4648 TREVTVNVL 0.0 None None 0 None -4649 TRFPLKTAF 0.0 None None 0 None -4650 TRFPLPEAF 0.0 None None 0 None -4651 TRFRSFSSL 0.0 None None 0 None -4652 TRFYMYEIL 0.0 None None 0 None -4653 TRGPCRRRF 7.20424999304 GPCRRRF GPADRRF 27.0 155637|tegument_protein|CAB06732.1|Human_alphaherpesvirus_2|10310 -4654 TRGPQRQIL 0.0 None None 0 None -4655 TRGRHQKKI 0.0 None None 0 None -4656 TRHGSILAC 0.0 None None 0 None -4657 TRHRCRNRF 0.0 None None 0 None -4658 TRNCNRHLC 4.92100160943 NCNRHLC NCQKPLC 28.0 110394|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 -4659 TRPSEELEL 0.0 None None 0 None -4660 TRPTASSSV 0.0 None None 0 None -4661 TRRSQKRLQ 0.0 None None 0 None -4662 TRSAEPGYL 0.0 None None 0 None -4663 TRSSKPSDM 0.0 None None 0 None -4664 TRSWGTPQL 0.114998444797 RSWGTPQ KLWESPQ 22.0 32243|C_protein|BAB60863.1|Measles_virus|11234 -4665 TRTPHSTRC 0.683754788248 TPHSTRC TPDSTPC 27.0 53041|phosphorylated_matrix_protein_(pp65)|AAA45996.1|Human_betaherpesvirus_5|10359 -4666 TRVGSKLLI 0.638888888889 TRVGSKLLI TRVGTKHAI 26.0 186041|polyprotein|AGO67248.1|Dengue_virus_2|11060 -4667 TRYSAQADI 0.0 None None 0 None -4668 TSMWRTYVM 0.0 None None 0 None -4669 TSMWRTYVM 0.0 None None 0 None -4670 TTDGRNYIV 0.479879498782 DGRNY DGVNY 22.0 56343|structural_protein|BAA00705.1|Hepatitis_C_virus|11103 -4671 TTFDRLAYL 0.61388887253 TFDRLAYL TFDRLQVL 28.0 66405|polyprotein|AAB67037.1|Hepatitis_C_virus_(isolate_H77)|63746 -4672 TTMEDQLLF 0.0 None None 0 None -4673 TVHTRNHTA 0.0 None None 0 None -4674 TVIDAYMNF 0.0 None None 0 None -4675 TVLHRPHSA 0.0 None None 0 None -4676 TVSPQPQEV 0.980041819158 SPQPQEV DPNPQEV 28.0 69799|envelope_glycoprotein|BAE96221.1|Human_immunodeficiency_virus_1|11676 -4677 TWLQVLEAI 0.0 None None 0 None -4678 TYEEPCQAI 0.0 None None 0 None -4679 TYLADRVQI 0.0 None None 0 None -4680 TYLYPPKHW 0.0 None None 0 None -4681 TYVLYYDAL 0.0 None None 0 None -4682 TYYPLKPEI 0.443101725077 YPLKPEI FPVRPQV 25.0 288104|nef_protein|ACR27130.1|Human_immunodeficiency_virus_1|11676 -4683 TYYPLKPEI 0.232710970823 YPLKPEI FPVRPQV 25.0 288104|nef_protein|ACR27130.1|Human_immunodeficiency_virus_1|11676 -4684 VAKKKEAPA 0.0 None None 0 None -4685 VARERRKAE 0.0 None None 0 None -4686 VFERDFFKI 0.0 None None 0 None -4687 VFETGTFLI 0.0 None None 0 None -4688 VFLPMTLLL 0.0 None None 0 None -4689 VFRQGHQLF 0.0 None None 0 None -4690 VFTRVSAYI 0.0107141857233 FTRVSAY FTKNSAF 21.0 44214|UL123;_IE1|AAR31448.1|Human_betaherpesvirus_5|10359 -4691 VFYTIFTPI 0.0 None None 0 None -4692 VGKKRHDPL 0.0 None None 0 None -4693 VHALRLHLY 0.0 None None 0 None -4694 VHFDHFHPC 0.867623345477 HFDHFHP HYDQDHP 29.0 180758|Nonstructural_protein_NS5|NP_739590.2|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -4695 VHFLREVTV 0.0 None None 0 None -4696 VHHLAVSGV 1.19230769231 LAVSGV LAVSGV 26.0 419005|polyprotein|AGW21594.1|Dengue_virus_1|11053 -4697 VHIKAMQTV 0.0 None None 0 None -4698 VHIKVLQTV 0.0 None None 0 None -4699 VHKKGYNKL 0.0 None None 0 None -4700 VHKQFPITL 0.774571436042 FPITL FPITL 26.0 143705|Genome_polyprotein|P08617.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 -4701 VHKTDLERM 0.0 None None 0 None -4702 VHRGTGAVY 0.02244433038 RGTGAVY EGEGAVF 22.0 119822|110_kd_polyprotein_precursor|CAA28880.1|Rubella_virus|11041 -4703 VHSENLQNW 0.0 None None 0 None -4704 VLAIQRCPM 0.0 None None 0 None -4705 VLDEMRCQY 112.599178113 VLDEMRC VIDPRRC 24.0 150556|polyprotein|AGW21594.1|Dengue_virus_1|11053 -4706 VLKSTSCSI 0.0 None None 0 None -4707 VMKHLLSPL 0.0 None None 0 None -4708 VMSCVWFTI 0.0 None None 0 None -4709 VQMYRGHPA 0.131620119942 YRGHPA YAGEPA 23.0 65810|sporozoite_surface_protein_2|NP_705260.1|Plasmodium_falciparum_3D7|36329 -4710 VQNEDVTLL 0.0 None None 0 None -4711 VQPSQWASI 10.0381165919 PSQWA PSSWA 26.0 27878|large_surface_antigen|CAC87019.1|Hepatitis_B_virus|10407 -4712 VRDRMKELL 0.0 None None 0 None -4713 VRELRDMGI 0.0014787525281 VRELRDMG VKENFSMG 16.0 59090|nonstructural_protein_4B|YP_001527886.1|West_Nile_virus_NY-99|10000971 -4714 VRFQDESVV 0.0 None None 0 None -4715 VRFVTRYIY 0.0 None None 0 None -4716 VRFVVTITV 0.0 None None 0 None -4717 VRGTTLHLL 0.0 None None 0 None -4718 VRHQRVHQA 0.0 None None 0 None -4719 VRLKRSIQF 0.0 None None 0 None -4720 VRLSYKLTF 0.0 None None 0 None -4721 VRMEVISVT 0.0 None None 0 None -4722 VRMEVVSIT 0.0 None None 0 None -4723 VRNDHMNLR 0.0 None None 0 None -4724 VRNRCNIYI 0.0 None None 0 None -4725 VRPRARYYI 0.0 None None 0 None -4726 VRQGGVFRL 0.0 None None 0 None -4727 VRRLGPKLL 0.0 None None 0 None -4728 VRRLHCSAA 0.0 None None 0 None -4729 VRRMLTSKV 0.0 None None 0 None -4730 VRRRRRCPG 0.0 None None 0 None -4731 VRSLNLVLM 0.0 None None 0 None -4732 VRSNLEPLF 0.0 None None 0 None -4733 VRVGSDMLI 0.0 None None 0 None -4734 VRVTQKFHM 0.0 None None 0 None -4735 VSDDLVKQY 0.0 None None 0 None -4736 VSGHVSMKY 0.0 None None 0 None -4737 VSSSSSGGY 0.0 None None 0 None -4738 VTADSDPAY 0.0 None None 0 None -4739 VTAPRATTL 0.0 None None 0 None -4740 VTDVLTEPH 0.0 None None 0 None -4741 VTMDWLVRI 20.8868827501 DWLVRI SWMIRI 25.0 185817|envelope_protein|AGW23590.1|Dengue_virus_4|11070 -4742 VVAPRTLLL 0.629096369435 VVAPRTL AISPRTL 25.0 50292|gag_protein|ACR27140.1|Human_immunodeficiency_virus_1|11676 -4743 VVESLVEAY 0.0 None None 0 None -4744 VVHEVQRYL 0.0 None None 0 None -4745 VVKSKQVAL 0.0 None None 0 None -4746 VVPQMVNPF 0.0 None None 0 None -4747 VVSDVPEEL 0.0 None None 0 None -4748 VYFHMTLSF 0.0 None None 0 None -4749 VYHLFCALL 0.00735750627888 VYHLFCAL LWHYPCTL 19.0 54824|polyprotein_precursor|BAA01583.1|Hepatitis_C_virus|11103 -4750 VYISLFTCV 0.0 None None 0 None -4751 VYLRRHRDV 0.989106753813 LRRHRDV LRRHIDL 26.0 51526|HCV-1|AAA45676.1|Hepatitis_C_virus|11103 -4752 VYPRGFQEK 0.0 None None 0 None -4753 VYQVLSGGW 0.0 None None 0 None -4754 VYSEYGMDV 0.239110747927 VYSEYG TYSTYG 23.0 67471|Genome_polyprotein|Q99IB8.3|Hepatitis_C_virus_JFH-1|356411 -4755 VYSLRTRAI 0.0546114862252 VYSLRTRAI AYSQQTRGL 22.0 111816|polyprotein|BAA09072.1|Hepatitis_C_virus|11103 -4756 VYSLYWSIL 0.175675675676 VYSLYWSI LYELIWNV 26.0 108965|Prolipoprotein_diacylglyceryl_transferase|O06131.1|Mycobacterium_tuberculosis|1773 -4757 VYVVSNNNL 0.0 None None 0 None -4758 VYVVTKFLM 0.110774648364 YVVTKFLM HPITKFVM 25.0 103389|unnamed_protein_product_[Hepatitis_C_virus]|BAA14035.1|Hepatitis_C_virus|11103 -4759 VYYLLELLL 0.444897959184 YLLELL YLLEML 26.0 74774|LMP1_protein_(Epstein-Barr_virus,_putative_LYDMA_gene)|Q777A4|Human_gammaherpesvirus_4|10376 -4760 WAGSHSMRY 0.0 None None 0 None -4761 WARRKQSEM 0.0 None None 0 None -4762 WASRFSTPY 0.0 None None 0 None -4763 WFLWKQFCW 0.0 None None 0 None -4764 WGMLNSLSL 0.0 None None 0 None -4765 WHLQGPEDL 0.0 None None 0 None -4766 WHREYNFKY 0.0 None None 0 None -4767 WHSVVIQRL 0.0 None None 0 None -4768 WHVPNKPPM 0.0370999742128 WHVPNKP YHILNNP 23.0 1516|Nucleoprotein|P03418.1|Human_respiratory_syncytial_virus_A2|11259 -4769 WIEREGPEY 0.0 None None 0 None -4770 WLNENQRLV 0.0 None None 0 None -4771 WLSFRSSAS 0.0 None None 0 None -4772 WLSNFQGRY 0.0713668403123 LSNFQGRY VGNFTGLY 23.0 34027|DNA_polymerase|CAA10434.1|Hepatitis_B_virus|10407 -4773 WMEKRYLSQ 0.0 None None 0 None -4774 WMEQEGPEY 3.13980286976 QEGPEY QRGPQY 27.0 38974|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 -4775 WPLTHSQGM 39.6011817345 WPLTHSQGM WPLYGNEGM 32.0 75438|polyprotein|AAF65962.1|Hepatitis_C_virus|11103 -4776 WQRQHKLTI 3.26412079703 QRQHKLTI QRQRKVTF 26.0 159299|polyprotein|AAC03058.1|Hepatitis_C_virus_subtype_3a|356426 -4777 WRPEAVQYY 0.0 None None 0 None -4778 WSDQLSAFS 0.225160259752 WSDQLSAFS WMNRLIAFA 25.0 177647|polyprotein|ADE10208.1|Hepatitis_C_virus_subtype_3a|356426 -4779 WTDVFQIGI 0.358584414555 VFQIGI VFEVGV 24.0 59787|Hemagglutinin_glycoprotein|P08362.1|Measles_virus_strain_Edmonston|11235 -4780 WTESLAAVF 2.5146072019 WTESLAAVF WSEGEGAVF 28.0 119822|110_kd_polyprotein_precursor|CAA28880.1|Rubella_virus|11041 -4781 WVKRQKISF 0.0617858475773 VKRQKISF VKKDLISY 20.0 25929|Nonstructural_protein_NS3|NP_739587.2|Dengue_virus_2_Thailand/16681/84|31634 -4782 WVRPRRRLL 0.0 None None 0 None -4783 WVRPRRRLL 0.0 None None 0 None -4784 WYHTCGGTL 0.0 None None 0 None -4785 WYIWILLVL 0.0410194846882 WYIWIL WCLWWL 23.0 74387|Genome_polyprotein|P26664.3|Hepatitis_C_virus_(isolate_1)|11104 -4786 YAFTGLTLM 19.2063253012 FTGLT FTGLT 26.0 146213|polyprotein|ADY38595.1|Hepatitis_C_virus_subtype_1b|31647 -4787 YAMQRSWQE 2.83948962827 QRSWQ ERSWN 22.0 180440|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -4788 YARILGTVL 0.0 None None 0 None -4789 YCDDLPLLA 0.0 None None 0 None -4790 YDDARVELV 0.0 None None 0 None -4791 YEHHHSARL 0.0 None None 0 None -4792 YFGLATVFI 0.0 None None 0 None -4793 YFHSFIRIV 0.0 None None 0 None -4794 YFTSSSRYF 0.0 None None 0 None -4795 YFYNQEEYV 0.0 None None 0 None -4796 YGVTRSKAM 0.0 None None 0 None -4797 YHCTAVNAY 0.0 None None 0 None -4798 YHDACIEEA 0.0 None None 0 None -4799 YHDVSGCYI 0.0 None None 0 None -4800 YHEAGVTAL 0.815347986631 YHEAGVT FHSYGVT 24.0 232152|rhoptry_kinase_family_protein|AFO54841.1|Toxoplasma_gondii_type_III|398031 -4801 YHFSWTSDR 0.0637106609554 HFSWTS HYAWKT 23.0 183252|polyprotein|AGT63075.1|Dengue_virus_1|11053 -4802 YHHRFNNFM 1.40756158901 YHHRFNN YQHKFNS 30.0 23270|polyprotein|AAB67036.1|Hepatitis_C_virus_(isolate_H77)|63746 -4803 YHQQNVPWA 0.0 None None 0 None -4804 YICDLRRQV 0.0 None None 0 None -4805 YINNSVLPY 0.0 None None 0 None -4806 YKGSRFHRV 1.87577517247 KGSRFHRV KKQRFHNI 25.0 110829|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 -4807 YLADRVQIV 0.0 None None 0 None -4808 YLADRVQIV 0.0 None None 0 None -4809 YLENRKETL 0.0 None None 0 None -4810 YLENRKETL 0.0 None None 0 None -4811 YLEQKPCIY 0.0 None None 0 None -4812 YLFRKELRY 0.0 None None 0 None -4813 YLKEELMCL 0.0 None None 0 None -4814 YLKENFLPW 0.0 None None 0 None -4815 YLRRHRDVS 14.1396011396 LRRHRDV LRRHIDL 26.0 51526|HCV-1|AAA45676.1|Hepatitis_C_virus|11103 -4816 YLSLVEISY 0.0 None None 0 None -4817 YLTVVSLSY 0.0 None None 0 None -4818 YMDRTPGPA 0.0 None None 0 None -4819 YMKTQSKSS 0.0 None None 0 None -4820 YMLTLFTAM 0.0 None None 0 None -4821 YNFKYVDLI 0.0 None None 0 None -4822 YNVFRQLSL 0.0 None None 0 None -4823 YPMRRRQCE 0.0 None None 0 None -4824 YPRLKMLAF 0.0 None None 0 None -4825 YPSIHRFIL 3.57700862377 PSIHRFI PGIYRFV 27.0 149053|NS3_gene_product|AAB02124.1|Hepatitis_C_virus|11103 -4826 YQLHNIQVI 0.0 None None 0 None -4827 YQMQFTQAL 0.0 None None 0 None -4828 YQMQFTQAL 0.0 None None 0 None -4829 YQSEKLCSL 0.0 None None 0 None -4830 YRAGKPTLV 0.432661229328 RAGKPT RSGAPT 23.0 102368|E2_protein|NP_751921.1|Hepatitis_C_virus_subtype_1a|31646 -4831 YRASEQKLC 0.0 None None 0 None -4832 YRDNTELPY 0.0 None None 0 None -4833 YRDVHVQKV 0.0 None None 0 None -4834 YRGPLSTTI 1.76192992766 YRGPLS YRGPLD 29.0 38724|Genome_polyprotein|P08617.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 -4835 YRGSVAPIL 0.0202594406357 YRGSVAPI YAGEPAPF 21.0 65810|sporozoite_surface_protein_2|NP_705260.1|Plasmodium_falciparum_3D7|36329 -4836 YRITVVESL 0.0 None None 0 None -4837 YRLEAVHAL 0.0 None None 0 None -4838 YRLEGDTLI 0.0 None None 0 None -4839 YRQFPKKSL 0.0 None None 0 None -4840 YRRHSLRAI 0.0 None None 0 None -4841 YRTVNNLIL 0.0 None None 0 None -4842 YSFDSLCQY 0.0 None None 0 None -4843 YSRDQIYIY 0.0 None None 0 None -4844 YSRQMISEL 0.0 None None 0 None -4845 YSRQMISEL 0.0 None None 0 None -4846 YTCEQNDQL 0.0 None None 0 None -4847 YTDSSSVLN 0.372503781182 TDSSSVLN TDSTSILG 27.0 107894|polyprotein|CAB41951.1|Hepatitis_C_virus|11103 -4848 YTEDHSASL 0.0 None None 0 None -4849 YTELWFLGL 13.1651602302 YTELW YAEMW 25.0 180077|PPE_family_protein|YP_177935.1|Mycobacterium_tuberculosis_H37Rv|83332 -4850 YTLLAFSVF 0.565506111769 LLAFSVF LLATSIF 23.0 182554|polyprotein|ACF49259.1|Dengue_virus_type_1_Hawaii|10000440 -4851 YTRKCTQAI 0.0 None None 0 None -4852 YTSMWRTYV 0.0 None None 0 None -4853 YTSMWRTYV 0.0 None None 0 None -4854 YVAICSPLF 0.0 None None 0 None -4855 YVDYMMCEF 0.0 None None 0 None -4856 YVFLHQCVL 0.0 None None 0 None -4857 YVFLHQCVL 0.0 None None 0 None -4858 YVGENVRFV 0.0 None None 0 None -4859 YVGIFHFQF 0.254817840555 VGIFHF VGVYHI 24.0 32663|small_hydrophobic_protein|AAM12943.1|Human_metapneumovirus|162145 -4860 YVLTRSKAM 0.0 None None 0 None -4861 YVTVLCLTF 0.0 None None 0 None -4862 YVYSLYWSI 159.605016198 YVYSLYWSI FLYELIWNV 29.0 108965|Prolipoprotein_diacylglyceryl_transferase|O06131.1|Mycobacterium_tuberculosis|1773 -4863 YWGVFAPIW 0.0 None None 0 None -4864 YWPPQSQPF 0.0 None None 0 None -4865 YYEKIFSTL 0.0 None None 0 None -4866 YYFLCLLL* 0.0 None None 0 None -4867 YYFLRPLL* 0.0 None None 0 None -4868 YYFLRPLL* 0.0 None None 0 None -4869 YYKIVSSIL 0.0232262868802 KIVSSI KLVSSV 22.0 95262|LAMP|AAK72632.1|Human_gammaherpesvirus_8|37296 -4870 YYLVANTKF 0.0 None None 0 None -4871 YYTNFSLEL 0.0 None None 0 None -4872 YYTNFSLEL 0.0 None None 0 None -4873 YYYFLCLLL 0.0 None None 0 None -4874 YYYFLRPLL 0.00109271035499 YYYFLRPL YIYMGQPL 21.0 185327|polyprotein|ACF49259.1|Dengue_virus_type_1_Hawaii|10000440 -4875 YYYFLRPLL 0.0362833645562 YYYFLRPL YIYMGQPL 21.0 185327|polyprotein|ACF49259.1|Dengue_virus_type_1_Hawaii|10000440 -4876 LSILVDWMI 0.0 None None 0 None -4877 LVMFLSILV 0.0 None None 0 None -4878 HWPEKEWPI 1.23491252617 HWPEKEW HTPVNSW 22.0 62977|polyprotein|AAB67037.1|Hepatitis_C_virus_(isolate_H77)|63746 -4879 WLEAMQGVI 0.0 None None 0 None -4880 MNRGRRSSL 0.597274971842 MNRGRRS MNRRKRS 25.0 183800|polyprotein|AGT63075.1|Dengue_virus_1|11053 -4881 RADHAAEQV 0.0 None None 0 None -4882 TTLSPAEPT 0.0 None None 0 None -4883 CLMVLYSLI 1.07995809695 CLMVLY CLYLLY 24.0 141222|DNA_packaging_tegument_protein_UL25|NP_044626.1|Human_alphaherpesvirus_1|10298 -4884 MTPSVYGGA 0.847766230468 TPSVYGG TPRVTGG 25.0 65749|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 -4885 FCFLVVASA 0.0 None None 0 None -4886 FLVVASAYI 0.0 None None 0 None -4887 VVASAYIKL 0.0 None None 0 None -4888 NSTIIPTLI 0.0 None None 0 None -4889 SSSGVNSTI 0.0 None None 0 None -4890 STIIPTLIL 0.0 None None 0 None -4891 NLAMCFGPV 0.0 None None 0 None -4892 MVAFINEKM 0.0 None None 0 None -4893 RHSNMVAFI 1.14135041379 RHSNMV RHHNMV 27.0 144403|polyprotein|AAK08509.1|Hepatitis_C_virus_subtype_1b|31647 -4894 SILASLSTL 0.0 None None 0 None -4895 TLQQMWISK 0.0 None None 0 None -4896 RAFADTLEV 0.0 None None 0 None -4897 VLLPVSLFI 0.0179862099621 LPVSLF LPTTLF 22.0 79180|tax_protein|AAF37566.1|Human_T-lymphotropic_virus_1|11908 -4898 LLFSVTMPK 0.0192709392451 LFSVTMP LYSSTVP 22.0 21242|polymerase|ACF94272.1|Hepatitis_B_virus|10407 -4899 VPVPPAPPL 0.748451099646 VPVPPAPP VPTDPNPP 29.0 70491|envelope_glycoprotein|AAC28452.1|Human_immunodeficiency_virus_1|11676 -4900 EIFMGLPTK 2.14751919188 IFMGLP IYMGQP 23.0 185327|polyprotein|ACF49259.1|Dengue_virus_type_1_Hawaii|10000440 -4901 VYTEIFMGL 0.0 None None 0 None -4902 YYASVYTEI 0.0 None None 0 None -4903 HMWNYMQSK 0.694505649699 MWNYMQ LWGYLQ 27.0 42094|telomer_length_regulation_protein_TEL1|EDV12172.1|Saccharomyces_cerevisiae|4932 -4904 QTYQHMWNY 1.32874030798 QHMWNY KHMWNF 34.0 103020|polyprotein|ABR25251.1|Hepatitis_C_virus|11103 -4905 SRYQTYQHM 0.0 None None 0 None -4906 MIMAQMRRI 0.0 None None 0 None -4907 RRISPFSCL 0.0731052404911 RRISPFSCL RVIDPRRCL 22.0 150556|polyprotein|AGW21594.1|Dengue_virus_1|11053 -4908 ILFDEAVKL 10.417679881 LFDEAVK LFNWAVK 21.0 169050|polyprotein|ABU97067.1|Hepatitis_C_virus_subtype_1b|31647 -4909 MKYPVKSIL 0.0 None None 0 None -4910 TLIHQFQEK 0.0 None None 0 None -4911 KLGADFIGH 0.0 None None 0 None -4912 ALGPPVLLR 8.02341413363e-05 ALGPPVLL SLGLVILL 17.0 59141|Circumsporozoite_protein_precursor|P08677.2|Plasmodium_vivax_strain_Belem|31273 -4913 PPVLLRCSL 0.0266850441922 PVLLRCSL KVLIRCYL 26.0 145860|Protein_E6|P04019.1|Human_papillomavirus_type_11|10580 -4914 FTRENTLTF 0.0 None None 0 None -4915 LTFMHLSPI 0.0 None None 0 None -4916 TFMHLSPIL 0.0 None None 0 None -4917 EFVERYHVL 0.0823067794915 VERYHVL AEEYHAL 24.0 187188|PE_family_protein_PE9|YP_177784.1|Mycobacterium_tuberculosis_H37Rv|83332 -4918 RLWARGLTV 0.0 None None 0 None -4919 RLWARGLTV 0.0 None None 0 None -4920 LVWRPLREV 0.68879469979 VWRPLRE IWLKLKE 22.0 180496|Polyprotein|NP_056776.2|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -4921 SYVMLPCAL 0.0 None None 0 None -4922 VMLPCALPV 0.0284555239065 MLPCALP LLPAILP 23.0 41971|putative_D-ribose-binding_protein|NP_301386.1|Mycobacterium_leprae|1769 -4923 RLPEVQLPK 8.33669952536e-05 LPEVQLPK LPSDFLPS 16.0 16836|precore/core_protein_[Hepatitis_B_virus]|AAR03815.1|Hepatitis_B_virus|10407 -4924 APRGACYRA 0.0 None None 0 None -4925 APRGVCYGA 0.0482323961939 PRGVC PYGVC 24.0 148117|early_protein|CAA52585.1|Human_papillomavirus_type_52|10618 -4926 GLTWAVVLI 0.243238394937 TWAVVLI NWAKVLV 24.0 149052|E1_protein|NP_751920.1|Hepatitis_C_virus_(isolate_H77)|63746 -4927 QPLGLTWAV 0.0 None None 0 None -4928 YRNEDHWAW 0.109703755322 RNEDHWA KREDQWC 24.0 184131|polyprotein|AGO67248.1|Dengue_virus_2|11060 -4929 KCAEPSTRK 0.0 None None 0 None -4930 LLTDDLRSV 0.0 None None 0 None -4931 QMPTDYAEV 0.0 None None 0 None -4932 VVGARGVGK 0.0 None None 0 None -4933 ALFCGRSDY 0.000134140052187 ALFCGRSD AVFDRKSD 18.0 5316|EBNA-3B_nuclear_protein|CAD53420.1|Human_gammaherpesvirus_4|10376 -4934 SFLCHKALF 0.0 None None 0 None -4935 SFLCHKALF 0.0 None None 0 None -4936 SFLCHKALF 0.0 None None 0 None -4937 HHLLSLQYV 0.0 None None 0 None -4938 NHHLLSLQY 0.0 None None 0 None -4939 LRLLDRELL 0.0 None None 0 None -4940 QMPPMPPPL 0.0 None None 0 None -4941 SRVSGGTPL 0.0 None None 0 None -4942 IPLEVMEPF 29.4847656669 IPLEVME IPFEIMD 26.0 180528|polyprotein|AGO67248.1|Dengue_virus_2|11060 -4943 RHAACSVLV 0.0 None None 0 None -4944 TRHAACSVL 0.0 None None 0 None -4945 TRHAACSVL 0.0 None None 0 None -4946 IYLGAVNWI 0.25 GAVNWI GAVQWM 26.0 177647|polyprotein|ADE10208.1|Hepatitis_C_virus_subtype_3a|356426 -4947 YLGAVNWIY 5.08 GAVNWI GAVQWM 26.0 177647|polyprotein|ADE10208.1|Hepatitis_C_virus_subtype_3a|356426 -4948 MWALGIIAY 0.0905570014873 MWALGII LWKAGIL 23.0 24943|DNA_polymerase|CAA10434.1|Hepatitis_B_virus|10407 -4949 SPALNKMFY 0.0 None None 0 None -4950 IPGPIPGPI 0.00624824950737 PGPIPG PGTGPG 21.0 47760|EBNA-1_protein|Q777E1|Human_gammaherpesvirus_4|10376 -4951 IPGPIPGPI 0.0209180526986 PGPIPG PGTGPG 21.0 47760|EBNA-1_protein|Q777E1|Human_gammaherpesvirus_4|10376 -4952 NPGPIPGPI 7.77591539117 PGPIPGPI PGLSPGTL 22.0 21638|protein_F|ABV46152.2|Hepatitis_C_virus_(isolate_Japanese)|11116 -4953 AEYIVVARN 0.0 None None 0 None -4954 YIVVARNKY 0.0 None None 0 None -4955 IFWDLSKPM 0.0 None None 0 None -4956 IFWDLSKPM 0.0 None None 0 None -4957 IPTEKPTIL 0.654454704699 IPTEKPTIL LPFDKPTIM 32.0 38466|nucleocapsid_protein|ABF21284.1|Influenza_A_virus_(A/Iran/1/1957(H2N2))|488233 -4958 FLNRWMANT 1.07227470363 FLNRWM FANRWI 28.0 140561|metal_cation_transporter_P-type_ATPase_A_CtpF|NP_216513.1|Mycobacterium_tuberculosis_H37Rv|83332 -4959 WMANTLDAV 0.0 None None 0 None -4960 ALHTAVLLL 0.0 None None 0 None -4961 KMWDAVLYR 0.0 None None 0 None -4962 LSIESLTLV 0.0 None None 0 None -4963 TLSIESLTL 0.0 None None 0 None -4964 HRVNWVVFL 0.0 None None 0 None -4965 FLYQPNWRF 0.598090160823 YQPNWR YFPDWQ 24.0 101721|nef|AAA02639.1|Human_immunodeficiency_virus_1|11676 -4966 LRKRRSRKR 0.0 None None 0 None -4967 RQLRKRRSR 0.0 None None 0 None -4968 RRQEQPSIK 0.0 None None 0 None -4969 FQYKFTVQA 1.33795003856 QYKFTV NYKFTL 24.0 15242|trans-sialidase,_putative|EAN81560.1|Trypanosoma_cruzi|5693 -4970 ILGTPLSKV 0.0 None None 0 None -4971 VLSGAKIWL 0.098644741065 VLSGAKIWL VLSDFKVWL 32.0 181036|||| -4972 AVLIVTTTV 0.000402870290963 VLIVTTTV ILIGITTL 18.0 59182|attachment_glycoprotein|ABQ58821.1|Human_metapneumovirus|162145 -4973 LLESSNTNV 0.0 None None 0 None -4974 VVWATKYFL 82.9775661936 VVWATKYFL CLWWLQYFL 26.0 39591|polyprotein|AAA45677.1|Hepatitis_C_virus_(isolate_H77)|63746 -4975 AMCSAQEEI 0.0487567516051 AMCSAQEEI SICPSQEPM 21.0 58463|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 -4976 KLTPYMVVL 0.0 None None 0 None -4977 FRVRGAVSH 0.0 None None 0 None -4978 FRHSMVVPY 0.294968010535 RHSMVVP RHADVIP 25.0 97093|polyprotein|AAB66324.1|Hepatitis_C_virus_(isolate_H77)|63746 -4979 KRRRLWAAL 0.0 None None 0 None -4980 RRLWAALGP 0.0128120947675 WAALGP WLSQGP 22.0 59569|Genome_polyprotein|P26662.3|Hepatitis_C_virus_(isolate_Japanese)|11116 -4981 YLIISTFFL 0.0474258731776 YLIISTF YLLADTF 23.0 140616|membrane-associated_phospholipase_C|NP_216866.1|Mycobacterium_tuberculosis_H37Rv|83332 -4982 KIFNHPSTL 0.00530943111929 KIFNHPSTL SLYNTVSTL 20.0 189294|Gag|O89360|Human_immunodeficiency_virus_1|11676 -4983 RSPKKHGYM 0.155158512329 SPKKH SPEKH 25.0 60031|SAG1_protein|AAO72426.1|Toxoplasma_gondii_RH|383379 -4984 YMKMFEIPA 0.0 None None 0 None -4985 LSSIGRSPM 0.0 None None 0 None -4986 MVFCDFHGH 24.8831744361 MVFCDFHGH MSLADFHGE 29.0 155811|ribonucleotide_reductase_large_subunit|CAB06725.1|Human_alphaherpesvirus_2|10310 -4987 RSPMVFCDF 0.0 None None 0 None -4988 SIGRSPMVF 0.0 None None 0 None -4989 SSIGRSPMV 0.0 None None 0 None -4990 ATATAYLCR 0.0 None None 0 None -4991 ATAYLCRVK 0.0 None None 0 None -4992 RVKGNFQTI 0.0 None None 0 None -4993 TATAYLCRV 0.0 None None 0 None -4994 YLCRVKGNF 0.0 None None 0 None -4995 CVSCWNVSR 0.00917876698188 CVSCWNV CSSVFNV 21.0 13456|circumsporozoite_protein|AAN87606.1|Plasmodium_falciparum|5833 -4996 RLASLYKTL 0.0 None None 0 None -4997 TLPQSVDPL 0.351470470495 LPQSVDPL LPEGMDPF 27.0 38446|Glycoprotein_B_precursor_(Glycoprotein_II)|P09257.1|Human_alphaherpesvirus_3|10335 -4998 SSSYAIEKR 0.0 None None 0 None -4999 ISRSTFAEV 0.0 None None 0 None -5000 RLPISRSTF 0.271294816931 PISRSTF PITYSTY 22.0 107873|Genome_polyprotein|P26664.3|Hepatitis_C_virus|11103 -5001 STFAEVTGL 0.0341560998855 STFAEVT KTFEQVT 21.0 14198|UL123;_IE1|AAR31390.1|Human_betaherpesvirus_5|10359 -5002 STFAEVTGL 0.00982374389904 STFAEVT KTFEQVT 21.0 14198|UL123;_IE1|AAR31390.1|Human_betaherpesvirus_5|10359 -5003 FSWNGGSFV 26.3153973248 SWNGG SWNSG 27.0 180440|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -5004 FSWNGGSFV 148.274767747 SWNGG SWNSG 27.0 180440|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -5005 TINEECSEI 3.0978991727 INEECS INEDCS 30.0 103322|polyprotein|BAB18806.1|Hepatitis_C_virus|11103 -5006 ILACRWVEM 0.0 None None 0 None -5007 ESPFSSGKV 0.0 None None 0 None -5008 MLAIGCALL 0.924557240739 MLAIGC LLAIGC 29.0 180802|polyprotein|AGO67248.1|Dengue_virus_2|11060 -5009 ESIRHNVLY 0.0 None None 0 None -5010 SIRHNVLYR 0.00459874686531 SIRHNVLY GLFNNVLY 22.0 20861|Non-capsid_protein_NS-1|P07298.1|Human_parvovirus_B19|10798 -5011 LQFGPTAEG 0.0 None None 0 None -5012 QPIPSVHER 0.0 None None 0 None -5013 SVHERTDWV 0.0 None None 0 None -5014 SVHERTDWV 0.0 None None 0 None -5015 RAPSPVSFV 0.244491068542 APSPVSFV SPRPVSYL 26.0 39571|polyprotein|BAD73987.1|Hepatitis_C_virus_subtype_1b|31647 -5016 GVLVLLFTL 0.371428571429 GVLVLLFTL GILGFVFTL 26.0 20354|M1_protein|CAA30882.1|Influenza_A_virus|11320 -5017 VLAPGVLVL 0.0 None None 0 None -5018 VLAPGVLVL 0.0 None None 0 None -5019 VLVLLFTLV 0.0 None None 0 None -5020 FTFLVSLYL 0.0 None None 0 None -5021 FTFLVSLYL 0.0 None None 0 None -5022 IQAYVFTFL 0.0 None None 0 None -5023 IQAYVFTFL 0.0 None None 0 None -5024 LIQAYVFTF 0.0 None None 0 None -5025 QAYVFTFLV 0.0 None None 0 None -5026 QAYVFTFLV 0.0 None None 0 None -5027 YVFTFLVSL 0.0 None None 0 None -5028 YVFTFLVSL 0.0 None None 0 None -5029 SSSPTCSLM 0.0 None None 0 None -5030 ENWDLVTYR 0.00961312062683 ENWDLVTY QGWGPISY 20.0 8236|Genome_polyprotein|P27958.3|Hepatitis_C_virus_subtype_1a|31646 -5031 GAMENWDLV 0.0 None None 0 None -5032 LEHPGSTRF 0.758464150481 LEHPGST LRHPGFT 28.0 180818|Membrane_glycoprotein_precursor|NP_739582.2|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -5033 QTDYVLSPL 0.0 None None 0 None -5034 VLSPLTGGL 0.000641889255728 LSPLTGG FSPGTSG 18.0 17802|Nonstructural_protein_NS3|NP_739587.2|Dengue_virus_2_Thailand/16681/84|31634 -5035 ITEILDRYV 0.0654819887488 ITEILDRY ITDTIDKF 23.0 12588|Glycoprotein_B_precursor_(Glycoprotein_II)|P09257.1|Human_alphaherpesvirus_3|10335 -5036 FNKSGFKHY 0.0509955625565 FNKSGFK FSKCGFP 23.0 23864|envelope_glycoprotein(gp21,_gp46)_-_human_T-cell_lymphotropic_virus_type_1|A45714|Human_T-lymphotropic_virus_1|11908 -5037 KSGFKHYQM 0.0 None None 0 None -5038 PVFNKSGFK 0.014495615722 FNKSGF FSKCGF 23.0 23864|envelope_glycoprotein(gp21,_gp46)_-_human_T-cell_lymphotropic_virus_type_1|A45714|Human_T-lymphotropic_virus_1|11908 -5039 VLVSGIQVL 0.0 None None 0 None -5040 VLVSGIQVL 0.0 None None 0 None -5041 RSRTGEDEV 0.0 None None 0 None -5042 LGQGELSAF 0.0 None None 0 None -5043 EAQPESEGV 0.0 None None 0 None -5044 LQDFYLGTY 32.5306568234 FYLGTY FYLGQY 29.0 156550|E3_ubiquitin-protein_ligase_Mdm2|Q00987.1|Homo_sapiens|9606 -5045 VAFPLQDFY 0.0 None None 0 None -5046 ESVNILSVL 0.0 None None 0 None -5047 GLVESVNIL 0.0 None None 0 None -5048 FTVGQTEKY 0.0 None None 0 None -5049 ESFKQTYVY 0.0 None None 0 None -5050 ESFKQTYVY 0.0 None None 0 None -5051 QTYVYSMAL 0.0 None None 0 None -5052 YVYSMALVL 0.0 None None 0 None -5053 YVYSMALVL 0.0 None None 0 None -5054 YVYSMALVL 0.0 None None 0 None -5055 FSLHKDRPV 0.0 None None 0 None -5056 ATRKLIGKV 0.0 None None 0 None -5057 HLKVRTATR 0.809264845181 HLKVRT HLRIRT 27.0 154822|ribonucleotide_reductase_large_subunit|CAB06725.1|Human_alphaherpesvirus_2|10310 -5058 TATRKLIGK 0.0 None None 0 None -5059 LLPWAHSML 0.0 None None 0 None -5060 QQNAPLLPW 1.13253012048 QQNAPLL QSNAPIM 26.0 180460|polyprotein|AGO67248.1|Dengue_virus_2|11060 -5061 RIHSDEQPY 0.0 None None 0 None -5062 AVHTVPQTI 0.0 None None 0 None -5063 DPIRRHLHI 0.0 None None 0 None -5064 HILYHCYGV 0.0 None None 0 None -5065 WTRPGSEVL 0.0 None None 0 None -5066 FPYVRNFVM 0.0 None None 0 None -5067 YVRNFVMNL 0.0 None None 0 None -5068 VAHEGMRPM 1.76923076923 AHEGMRPM AHNGLRDL 26.0 65654|polyprotein_precursor|BAA01582.1|Hepatitis_C_virus|11103 -5069 RPDKMVPVV 0.0 None None 0 None -5070 ILYLLSLFT 0.0 None None 0 None -5071 LTILYLLSL 0.0 None None 0 None -5072 YLLSLFTQT 0.0 None None 0 None -5073 AAGPHVTVL 0.0 None None 0 None -5074 RASAAGPHV 0.0 None None 0 None -5075 SAAGPHVTV 0.0 None None 0 None -5076 AVADLSCML 0.0 None None 0 None -5077 CMLVLPTRL 0.0 None None 0 None -5078 LAVADLSCM 0.0 None None 0 None -5079 MLVLPTRLV 0.0 None None 0 None -5080 VAVGTEHTL 0.0 None None 0 None -5081 SVAWTTMDV 0.0 None None 0 None -5082 TMDVATPSV 0.000405605959168 MDVA MDAA 15.0 154448|RL2|CAB06760.1|Human_alphaherpesvirus_2|10310 -5083 NLYKGSVLY 0.341399031209 NLYKGSVLY TLWKAGILY 25.0 24943|DNA_polymerase|CAA10434.1|Hepatitis_B_virus|10407 -5084 DEYNFVRTY 0.0 None None 0 None -5085 RTYECFQHR 0.0 None None 0 None -5086 LPSDPRLHL 0.0 None None 0 None -5087 FLADITHLR 0.0 None None 0 None -5088 GMRYWNMMV 0.0 None None 0 None -5089 NMMVQWWLA 1.28923492085 NMMVQW DMMMNW 23.0 72322|polyprotein|AAA86907.1|Hepatitis_C_virus|11103 -5090 TPLGKGDIV 0.0 None None 0 None -5091 KVRSCIDLI 0.0 None None 0 None -5092 YEQKVRSCI 0.0 None None 0 None -5093 ALLAFATIM 0.0 None None 0 None -5094 ATIMYVPAL 0.0 None None 0 None -5095 LAFATIMYV 0.104302556769 LAFATIMY LAYVSVLY 24.0 141341|tegument_protein_VP11/12|NP_044648.1|Human_alphaherpesvirus_1|10298 -5096 LAFATIMYV 0.0894021915166 LAFATIMY LAYVSVLY 24.0 141341|tegument_protein_VP11/12|NP_044648.1|Human_alphaherpesvirus_1|10298 -5097 YALLAFATI 0.0 None None 0 None -5098 YALLAFATI 0.0 None None 0 None -5099 LLLLLLLLV 0.0 None None 0 None -5100 LLLLLLLVV 0.183789279182 LLLLLVV VLLLLVV 25.0 98540|trans-sialidase,_putative|EAN88532.1|Trypanosoma_cruzi|5693 -5101 LLLLLLVVV 0.355681484489 LLLLVVV LLLLVVM 25.0 98224|trans-sialidase,_putative|EAN82076.1|Trypanosoma_cruzi|5693 -5102 LLVVVPWGV 0.0 None None 0 None -5103 IAATPIPAM 0.195363107976 TPIPA TPLPA 25.0 177806|polyprotein|ACZ60104.1|Hepatitis_C_virus_subtype_3a|356426 -5104 HVLEIDESV 0.0 None None 0 None -5105 HVLEIDESV 0.0 None None 0 None -5106 YFNGSTNHV 0.0 None None 0 None -5107 TPLCPGELL 0.0376303451797 LCPGELL VCWGELM 23.0 187197|Core_protein|Q9QAC5|Hepatitis_B_virus|10407 -5108 LMLGLVWTI 0.0516239227798 LMLGLVWTI LMMRTTWAL 21.0 150389|polyprotein|AGO67248.1|Dengue_virus_2|11060 -5109 LMLGLVWTI 0.0094010029801 LMLGLVWTI LMMRTTWAL 21.0 150389|polyprotein|AGO67248.1|Dengue_virus_2|11060 -5110 RLMLGLVWT 0.0383304570666 LMLGLVW LMMRTTW 19.0 150686|polyprotein|AGO67248.1|Dengue_virus_2|11060 -5111 SLTADDAFV 0.0 None None 0 None -5112 PAFSLDVLM 0.0 None None 0 None -5113 YLQAEIEPV 0.0 None None 0 None -5114 YLQAEIEPV 0.0 None None 0 None -5115 LFFVDKLYK 0.0 None None 0 None -5116 ALLPLFVVL 0.0 None None 0 None -5117 ALLPLFVVL 0.0 None None 0 None -5118 KALLPLFVV 0.0 None None 0 None -5119 VVLCGNDHV 0.458740128795 VVLCGNDHV TLVCGKDGV 25.0 65118|SAG1_protein|AAO72426.1|Toxoplasma_gondii_RH|383379 -5120 TEMKRKAPF 0.0 None None 0 None -5121 AMATYHFHF 0.26894142137 ATYHFH CSHHFH 25.0 183147|polyprotein|AGW21594.1|Dengue_virus_1|11053 -5122 ATYHFHFNL 2.521436525 TYHFHFNL SEHSHFSL 25.0 25275|Glutamate_decarboxylase_2|Q05329.1|Homo_sapiens|9606 -5123 ATYHFHFNL 3.11006375559 TYHFHFNL SEHSHFSL 25.0 25275|Glutamate_decarboxylase_2|Q05329.1|Homo_sapiens|9606 -5124 KAMATYHFH 0.0 None None 0 None -5125 LKAMATYHF 0.0 None None 0 None -5126 NVFVEVVLV 0.0 None None 0 None -5127 GVKGVNSLF 0.270014098137 VKGVNSLF VRGLTSLF 27.0 52652|||| -5128 KGVNSLFKK 0.0 None None 0 None -5129 AMSTPIYQM 0.0 None None 0 None -5130 AMSTPIYQM 0.0 None None 0 None -5131 SMAMSTPIY 0.0 None None 0 None -5132 SMAMSTPIY 0.0 None None 0 None -5133 SSMAMSTPI 0.0 None None 0 None -5134 KMADEVPLK 0.0 None None 0 None -5135 FLLAFRSGA 0.0 None None 0 None -5136 LLAFRSGAL 0.0 None None 0 None -5137 RVAEVAAQV 0.0 None None 0 None -5138 KIFWFPTGL 0.0 None None 0 None -5139 AGIFLLIHF 0.0 None None 0 None -5140 FLLIHFHPL 0.557931740375 FLLIHFHPL FCSHHFHQL 25.0 183147|polyprotein|AGW21594.1|Dengue_virus_1|11053 -5141 FLLIHFHPL 0.754446387197 FLLIHFHPL FCSHHFHQL 25.0 183147|polyprotein|AGW21594.1|Dengue_virus_1|11053 -5142 GIFLLIHFH 0.0 None None 0 None -5143 LLIHFHPLA 0.831825503832 HFHPL HFHQL 25.0 183147|polyprotein|AGW21594.1|Dengue_virus_1|11053 -5144 SIVTSTFII 0.0 None None 0 None -5145 VTSTFIISL 0.0 None None 0 None -5146 LQIHGLAVE 0.0196761894216 QIHGLAV RLHGLSA 22.0 423047|Genome_polyprotein|P27958.3|Hepatitis_C_virus_genotype_1|41856 -5147 ATVLTLPHV 0.0 None None 0 None -5148 VLTLPHVTK 0.0 None None 0 None -5149 AVSNFYLPL 0.0 None None 0 None -5150 HISAVSNFY 0.0 None None 0 None -5151 HISAVSNFY 0.0 None None 0 None -5152 SVVVIIDVK 0.0 None None 0 None -5153 VVIIDVKPK 0.0 None None 0 None -5154 FQRALVQPG 4.11642215044 FQRALV FQRALI 27.0 183577|polyprotein|AGK36298.1|Dengue_virus_2|11060 -5155 ESFTATVEF 0.0 None None 0 None -5156 LAAPRGVCY 0.0886753444311 PRGVC PYGVC 24.0 148117|early_protein|CAA52585.1|Human_papillomavirus_type_52|10618 -5157 ATGATSLCF 0.0 None None 0 None -5158 GLAMCHQEL 0.0 None None 0 None -5159 LLTLAGLAM 0.0 None None 0 None -5160 TVWPSLAPL 8.65748022982 TVWPSLAPL SLWKDGAPL 23.0 140600|glutamine_synthetase_GLNA1_(glutamine_synthase)_(GS-I)|NP_216736.1|Mycobacterium_tuberculosis_H37Rv|83332 -5161 CQHKLGKRY 0.0 None None 0 None -5162 AVWRHLLLA 0.0 None None 0 None -5163 HLLLALLLL 0.0164752006047 LALLLL LALLLL 24.0 19442|nucleocapsid_protein|ABI96968.1|SARS_coronavirus|227859 -5164 LLALLLLVL 12.4294702466 LALLLL LALLLL 24.0 19442|nucleocapsid_protein|ABI96968.1|SARS_coronavirus|227859 -5165 LLALLLLVL 7.77953412607 LALLLL LALLLL 24.0 19442|nucleocapsid_protein|ABI96968.1|SARS_coronavirus|227859 -5166 LLLALLLLV 0.264895382271 LALLLL LALLLL 24.0 19442|nucleocapsid_protein|ABI96968.1|SARS_coronavirus|227859 -5167 LTRHQRTHM 6.47908572951 TRHQRTHM SRHTSDHM 24.0 17278|Genome_polyprotein|P06441.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 -5168 EAWLFLEWV 0.0 None None 0 None -5169 SEAWLFLEW 0.0 None None 0 None -5170 WILSHTVAL 0.0 None None 0 None -5171 WILSHTVAL 0.0 None None 0 None -5172 SVRKSVSTV 0.0 None None 0 None -5173 MTVTVCPPT 0.0 None None 0 None -5174 SPMVLLLAA 0.0 None None 0 None -5175 VERGSPMVL 0.0 None None 0 None -5176 VVERGSPMV 0.0 None None 0 None -5177 FEAFDHTET 0.0 None None 0 None -5178 RLFEAFDHT 0.0 None None 0 None -5179 HTCRVMGAL 0.0 None None 0 None -5180 YKIGGIGMV 0.0 None None 0 None -5181 EELTQLNEA 0.0 None None 0 None -5182 LQSRLEEEL 0.0 None None 0 None -5183 RLEEELTQL 0.0 None None 0 None -5184 FPRLGCPWF 0.0 None None 0 None -5185 RLGCPWFTL 0.0 None None 0 None -5186 RLGCPWFTL 0.0 None None 0 None -5187 DWPVFPGLF 24.1501420113 WPVFPG WPAPPG 27.0 72928|Genome_polyprotein|P26662.3|Hepatitis_C_virus_(isolate_Japanese)|11116 -5188 FNVGDDWPV 0.0 None None 0 None -5189 NYASRTQNI 0.0140565208982 NYASRTQ NWAVRTK 21.0 6308|HCV-1|AAA45676.1|Hepatitis_C_virus_genotype_1|41856 -5190 SVSSCCQPV 0.898067608919 SSCCQP SECCTP 28.0 57361|Genome_polyprotein|SRC279960|Hepatitis_C_virus_(isolate_H77)|63746 -5191 SVSSCCQPV 1.08294722702 SSCCQP SECCTP 28.0 57361|Genome_polyprotein|SRC279960|Hepatitis_C_virus_(isolate_H77)|63746 -5192 CTLGDQLSL 0.0447254880178 GDQLSL GDKLSL 25.0 244160|surface_antigen_2_(CA-2)|XP_818927.1|Trypanosoma_cruzi_strain_CL_Brener|353153 -5193 STAPQAHGV 0.0 None None 0 None -5194 STAPQAHGV 0.0 None None 0 None -5195 VSLFYSTAI 0.0 None None 0 None -5196 VSLFYSTAI 0.0 None None 0 None -5197 YSTAISVYL 0.0 None None 0 None -5198 YSTAISVYL 0.0 None None 0 None -5199 DTAPDIVEI 0.0 None None 0 None -5200 FLWDRHVRF 0.0 None None 0 None -5201 LWDRHVRFF 0.0 None None 0 None -5202 FTCLPLGSL 0.0 None None 0 None -5203 HVWLCDLPV 7.43524726743 VWLCDLPV ARLCDLPA 30.0 4172|Glycoprotein_I_precursor_(Glycoprotein_IV)_(GI)_(GPIV)|P09258.1|Human_alphaherpesvirus_3|10335 -5204 HVWLCDLPV 46.7070308887 VWLCDLPV ARLCDLPA 30.0 4172|Glycoprotein_I_precursor_(Glycoprotein_IV)_(GI)_(GPIV)|P09258.1|Human_alphaherpesvirus_3|10335 -5205 APRGVCYGA 0.0482323961939 PRGVC PYGVC 24.0 148117|early_protein|CAA52585.1|Human_papillomavirus_type_52|10618 -5206 DPEYSPGAL 0.154024773008 YSPGAL YSPGEI 25.0 59153|Genome_polyprotein|P27958.3|Hepatitis_C_virus_subtype_1a|31646 -5207 YSPGALATF 0.0 None None 0 None -5208 VLGDFLGTV 0.0 None None 0 None -5209 AVVGTVWNV 0.0 None None 0 None -5210 NVATTGLSL 0.0 None None 0 None -5211 DTTDKGALM 0.0 None None 0 None -5212 KAVSVCPEA 0.0573665433528 KAVSVCPEA QQVSIAPNA 22.0 19359|IMMUNOGENIC_PROTEIN_MPT64_(ANTIGEN_MPT64/MPB64)|CAA98382.1|Mycobacterium_tuberculosis_H37Rv|83332 -5213 SVCPEAAPA 0.0 None None 0 None -5214 VLVVGMGPV 0.0 None None 0 None -5215 IFATKPELL 0.0 None None 0 None -5216 RIFATKPEL 0.0 None None 0 None -5217 AFSQSAYLI 0.0 None None 0 None -5218 AYLIQHQRF 0.0 None None 0 None -5219 KAFSQSAYL 0.0 None None 0 None -5220 KAFSQSAYL 0.0 None None 0 None -5221 FPAPARDDF 0.0 None None 0 None -5222 SPSVMWLVH 1.99051566923 SPSVMWL SPSSIWV 26.0 116835|Nucleoprotein|P05133.1|Hantaan_virus_76-118|11602 -5223 LAVRDVFEL 0.0 None None 0 None -5224 LAVRDVFEL 0.0 None None 0 None -5225 KTLTLAKNY 0.0 None None 0 None -5226 SSGSMCNRW 0.0888800199782 SSGSMCNRW TAGSLQGQW 23.0 9920|ESAT-6-like_protein_esxB|P0A566.2|Mycobacterium_tuberculosis|1773 -5227 TTKNDIGPY 0.0 None None 0 None -5228 LGLTNNTAM 0.0 None None 0 None -5229 FTTELTAPF 0.0995002913307 FTTELTAPF FTASVTSPL 25.0 177903|polyprotein|ACZ60102.1|Hepatitis_C_virus_subtype_3a|356426 -5230 FTTELTAPF 0.139300407863 FTTELTAPF FTASVTSPL 25.0 177903|polyprotein|ACZ60102.1|Hepatitis_C_virus_subtype_3a|356426 -5231 FTTELTAPF 0.106698184746 FTTELTAPF FTASVTSPL 25.0 177903|polyprotein|ACZ60102.1|Hepatitis_C_virus_subtype_3a|356426 -5232 MPAFTTELT 0.0 None None 0 None -5233 LMALHPALF 0.0394828895203 LMALHPAL MCAVHPTL 25.0 7660|polyprotein|AAA45677.1|Hepatitis_C_virus_(isolate_H77)|63746 -5234 QCSEHDVLF 4.32142857143 CSEHD CVEHD 26.0 120093|unnamed_protein_product|CAA33016.1|Rubella_virus|11041 -5235 EPYIDNEEF 0.0 None None 0 None -5236 VVIKAIEPY 0.0 None None 0 None -5237 QVQDSNLEY 0.0 None None 0 None -5238 QVQDSNLEY 0.0 None None 0 None -5239 LASSCGCTF 3.24598726122 LASSCGCT MYPSCCCT 24.0 59786|Large_envelope_protein|P03138.3|Hepatitis_B_virus_ayw/France/Tiollais/1979|490133 -5240 LASSCGCTF 16.2484935375 LASSCGCT MYPSCCCT 24.0 59786|Large_envelope_protein|P03138.3|Hepatitis_B_virus_ayw/France/Tiollais/1979|490133 -5241 IQLLGVFVW 0.0 None None 0 None -5242 ISIQLLGVF 0.0 None None 0 None -5243 EVDFTCWKY 0.0 None None 0 None -5244 HPTAASQSR 0.0 None None 0 None -5245 IIETANVSY 0.0 None None 0 None -5246 VSYTNAWAL 0.121870305999 SYTNAWAL SYAQMWSL 26.0 180579|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -5247 FFIHSFTLM 0.0 None None 0 None -5248 MFFIHSFTL 0.0344792251349 MFFIHSFT LFYQHKFN 22.0 23270|polyprotein|AAB67036.1|Hepatitis_C_virus_(isolate_H77)|63746 -5249 MFNPIIYIF 0.0584094317908 MFNPIIY LFNNVLY 24.0 20861|Non-capsid_protein_NS-1|P07298.1|Human_parvovirus_B19|10798 -5250 LPTPVEPTV 0.987770214465 LPTPVEPT LPDPLKPT 31.0 27241|Spike_glycoprotein_precursor|P59594.1|SARS_coronavirus|227859 -5251 TPVEPTVAC 0.234271638656 TPVEPT TPYKPT 24.0 68229|EBNA3B_(EBNA4A)_latent_protein|CAA24858.1|Human_gammaherpesvirus_4|10376 -5252 HPDNVSSSY 0.0 None None 0 None -5253 LLAAARPLW 1.30039551297 LLAAARPLW ITAAAVTLW 24.0 36717|nonstructural_protein_4B|YP_001527886.1|West_Nile_virus_NY-99|10000971 -5254 SPVALQLRY 0.0 None None 0 None -5255 YQIGTDSAL 0.0 None None 0 None -5256 EAHHHFPSL 3.68937388497 HHFPSL HHAPSL 29.0 21000|glutamine_synthetase_GLNA1_(glutamine_synthase)_(GS-I)|NP_216736.1|Mycobacterium_tuberculosis|1773 -5257 EAHHHFPSL 5.17245410388 HHFPSL HHAPSL 29.0 21000|glutamine_synthetase_GLNA1_(glutamine_synthase)_(GS-I)|NP_216736.1|Mycobacterium_tuberculosis|1773 -5258 GSGEAHHHF 0.0 None None 0 None -5259 RVSSLTLHF 0.0 None None 0 None -5260 KPFSQSCEF 0.0 None None 0 None -5261 KPLLSGPWA 0.348123132681 KPLLSGP KPTLHGP 27.0 6591|polyprotein|AAB67037.1|Hepatitis_C_virus_(isolate_H77)|63746 -5262 LSMTSITSV 0.0 None None 0 None -5263 IDTDQVHTL 0.0 None None 0 None -5264 TWKDTPYYI 0.0 None None 0 None -5265 KLILTLSAI 0.0 None None 0 None -5266 SYQMSNKLI 0.0 None None 0 None -5267 YQMSNKLIL 0.0 None None 0 None -5268 YQMSNKLIL 0.0 None None 0 None -5269 LMWSVTWPK 0.418780213276 WSVTW WAIKW 25.0 149105|E2_protein|NP_751921.1|Hepatitis_C_virus_(isolate_H77)|63746 -5270 SQSETNSAV 0.0 None None 0 None -5271 SHASHLHLF 0.0 None None 0 None -5272 SHASHLHLF 0.0 None None 0 None -5273 KVLISVHLI 0.0 None None 0 None -5274 DHYLVDRTL 0.0 None None 0 None -5275 YIKPLVPPA 0.0 None None 0 None -5276 RPGQSPGQL 1.15887751873 PGQSPGQL PGLSPGTL 31.0 21638|protein_F|ABV46152.2|Hepatitis_C_virus_(isolate_Japanese)|11116 -5277 HLFESSQLV 0.0 None None 0 None -5278 HLFESSQLV 0.0 None None 0 None -5279 GVYLWEDPV 6.47717900666 LWEDP LWESP 27.0 32243|C_protein|BAB60863.1|Measles_virus|11234 -5280 YLWEDPVCG 47.588178133 LWEDP LWESP 27.0 32243|C_protein|BAB60863.1|Measles_virus|11234 -5281 RILYMADEV 0.0 None None 0 None -5282 SLLDACLIL 0.0 None None 0 None -5283 APLPMPNPL 0.226485551842 LPMPNPL IPMTGPL 24.0 180531|polyprotein|AGO67248.1|Dengue_virus_2|11060 -5284 LLLWAPLPM 0.0 None None 0 None -5285 MQLRKAPNV 0.0 None None 0 None -5286 AHACAHALL 0.0 None None 0 None -5287 GAHACAHAL 0.0 None None 0 None -5288 VLNGWLRSV 7.1854641519 VLNGW LLNGW 28.0 37607|kaposin|AAC57155.1|Human_gammaherpesvirus_8|37296 -5289 AIDDHVCMA 0.0 None None 0 None -5290 LMVPRLEYV 0.0 None None 0 None -5291 FINARGRLL 0.0 None None 0 None -5292 AIPLRGFPV 7.52036422648 IPLRGFPV LSLRGLPV 27.0 24302|X_protein|AAP06597.1|Hepatitis_B_virus|10407 -5293 FVDENNEKL 0.0 None None 0 None -5294 FVDENNEKL 0.0 None None 0 None -5295 HTARLFYFV 0.0 None None 0 None -5296 LPSTAGPEM 6.14013666685 LPSTAGP LPEAAGP 28.0 43447|IMMUNOGENIC_PROTEIN_MPT64_(ANTIGEN_MPT64/MPB64)|CAA98382.1|Mycobacterium_tuberculosis_H37Rv|83332 -5297 LPSTAGPEM 6.97269757083 LPSTAGP LPEAAGP 28.0 43447|IMMUNOGENIC_PROTEIN_MPT64_(ANTIGEN_MPT64/MPB64)|CAA98382.1|Mycobacterium_tuberculosis_H37Rv|83332 -5298 TAANGSEVM 0.0 None None 0 None -5299 TAANGSEVM 0.0 None None 0 None -5300 MADATFQSL 0.0 None None 0 None -5301 MADATFQSL 0.0 None None 0 None -5302 WFNMADATF 0.0 None None 0 None -5303 ICIWNVSKL 0.0 None None 0 None -5304 EPTITDASL 0.0 None None 0 None -5305 IFDEWLKRF 0.0 None None 0 None -5306 FTGGIVNKL 0.0472701242502 FTGGIVNKL FMGVLVNSL 24.0 139747|granule_antigen_protein_GRA6|XP_002371939.1|Toxoplasma_gondii_ME49|508771 -5307 GIVNKLCAL 0.0 None None 0 None -5308 FGSLLGTCL 0.0 None None 0 None -5309 ISGPRSPTY 0.157560426259 ISGPRSPTY INGIRRPKH 20.0 66195|Nucleoprotein|P41269.1|Puumala_hantavirus|11604 -5310 MSLNSYIKL 0.0 None None 0 None -5311 YMVIMSPRL 0.0 None None 0 None -5312 EILWTTELY 0.0 None None 0 None -5313 LEILWTTEL 0.0 None None 0 None -5314 LGTSDVRIL 0.0 None None 0 None -5315 VAFLGTSDV 0.0 None None 0 None -5316 IMIAVVDSM 0.0 None None 0 None -5317 IMIAVVDSM 0.0 None None 0 None -5318 EASVHSVPI 0.0 None None 0 None -5319 FFSSNLPTY 0.0 None None 0 None -5320 FSSNLPTYY 12.750272737 NLPTYY SLPSYY 27.0 28594|IMMUNOGENIC_PROTEIN_MPT64_(ANTIGEN_MPT64/MPB64)|CAA98382.1|Mycobacterium_tuberculosis_H37Rv|83332 -5321 VALVPESSV 0.0 None None 0 None -5322 ISRNHNSRM 0.0 None None 0 None -5323 KTFGISRNH 0.0 None None 0 None -5324 RNHNSRMNK 0.0 None None 0 None -5325 LTDLQGVIV 0.0 None None 0 None -5326 IRHEMSTFA 0.0 None None 0 None -5327 VVSDSWGSK 0.0 None None 0 None -5328 IRAANVSAL 0.0 None None 0 None -5329 IRAANVSAL 0.0 None None 0 None -5330 RAANVSALY 0.0 None None 0 None -5331 GYRERGHPY 0.0 None None 0 None -5332 VVGAVGVGK 0.0 None None 0 None -5333 LTNTLTTSK 0.0 None None 0 None -5334 AAASTSSPK 0.0 None None 0 None -5335 TSITTSTQK 0.0 None None 0 None -5336 SHPGSAEIV 0.0 None None 0 None -5337 SYYSCVAAM 0.0 None None 0 None -5338 SYYSCVAAM 0.0 None None 0 None -5339 AHTFKQRRI 0.0 None None 0 None -5340 HTFKQRRIK 0.0 None None 0 None -5341 RYEEYRGRF 0.0254287796016 YEEYRGRF YQDWLGRM 22.0 23288|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 -5342 YEEYRGRFL 0.00584663400753 YEEYRGRF YQDWLGRM 22.0 23288|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 -5343 MTTGSVFFY 0.0 None None 0 None -5344 MTTGSVFFY 0.0 None None 0 None -5345 HVLSLAETK 0.0 None None 0 None -5346 SLAETKTLY 0.0 None None 0 None -5347 KLKTVSQTK 0.0 None None 0 None -5348 ASYDQSLRV 0.0 None None 0 None -5349 FSASYDQSL 0.0 None None 0 None -5350 HLKEPLQKL 0.0 None None 0 None -5351 HLYEQGGHL 0.0 None None 0 None -5352 HQCVHTGAK 0.0 None None 0 None -5353 IAHAWWACF 0.624917866388 HAWWACF HARWAAF 30.0 141262|DNA_polymerase_catalytic_subunit|NP_044632.1|Human_alphaherpesvirus_1|10298 -5354 AMWNRCADL 0.0 None None 0 None -5355 AYTFWTYIM 0.850753683829 AYTFW KYTFW 29.0 137660|L1|ACL12325.1|Human_papillomavirus_type_58|10598 -5356 IMNARSKNV 0.0 None None 0 None -5357 YAYTFWTYI 6.89162833838 AYTFW KYTFW 29.0 137660|L1|ACL12325.1|Human_papillomavirus_type_58|10598 -5358 YAYTFWTYI 1.32063005669 AYTFW KYTFW 29.0 137660|L1|ACL12325.1|Human_papillomavirus_type_58|10598 -5359 KAARIAAKV 0.0 None None 0 None -5360 KVGQSSMWI 0.0 None None 0 None -5361 PSTSTSRPV 0.0 None None 0 None -5362 CLAAMALSI 0.0 None None 0 None -5363 WLTPVIPTL 0.234315353622 WLTPVIP WLSLLVP 24.0 62477|HBsAg_protein|ABF71024.1|Hepatitis_B_virus|10407 -5364 GLFHCTRSV 0.0 None None 0 None -5365 RNWDVCKVI 0.0 None None 0 None -5366 KIPIRLPPV 0.0 None None 0 None -5367 FMLGITPNL 0.0 None None 0 None -5368 HRHHHRCRR 0.0 None None 0 None -5369 FLAGSSLPV 0.0 None None 0 None -5370 FLAGSSLPV 0.0 None None 0 None -5371 SSFLAGSSL 0.0 None None 0 None -5372 KLPSDPDAL 0.0 None None 0 None -5373 VYAVTVVTL 0.0 None None 0 None -5374 YAVTVVTLL 0.0 None None 0 None -5375 YAVTVVTLL 0.0 None None 0 None -5376 FILICCLII 0.0653826258252 LICCLII VLCCYVL 25.0 11956|UL123;_IE1|AAR31448.1|Human_betaherpesvirus_5|10359 -5377 ILICCLIIL 0.465751713705 LICCLII VLCCYVL 25.0 11956|UL123;_IE1|AAR31448.1|Human_betaherpesvirus_5|10359 -5378 LIILENIFV 0.0 None None 0 None -5379 VFILICCLI 0.300679700821 ILICCLI ILIRCII 24.0 137656|E6_protein|ACT36477.1|Human_papillomavirus_type_58|10598 -5380 PAMKFSCSL 0.0 None None 0 None -5381 FLSLIIDAT 0.0 None None 0 None -5382 LIIDATKFI 0.0 None None 0 None -5383 LIIDATKFI 0.0 None None 0 None -5384 IMMSSEDDI 0.0 None None 0 None -5385 YLDGQPQEA 0.0825589178834 YLDGQP YRDGNP 24.0 110227|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 -5386 GLAPPQLLI 0.0 None None 0 None -5387 ARIERPHNY 0.0 None None 0 None -5388 FTSSEPSRM 0.0 None None 0 None -5389 ESEGHTIEL 0.0 None None 0 None -5390 KMQEGLLAV 0.0819874238225 QEGLLAV QNGALAI 21.0 51685|Nuclear_antigen_EBNA-3C|Q69140.1|Human_gammaherpesvirus_4|10376 diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/run.sh b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/run.sh deleted file mode 100755 index cbcf44cf..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/run.sh +++ /dev/null @@ -1,24 +0,0 @@ -############################################## -# Compute neoantigen quality -# -# Directory structure: -# -# data: -# neoantigen-data file and iebd-epitope file. -# -# alignments: -# precomputed blastp alignments for all neoantigens, split into files for each sample. -# blastp -query -db data/iedb.fasta -outfmt 5 -evalue 100000000 -gapopen 11 -gapextend 1 > -# -# src: -# source code folder -# -# output: -# source code output folder -############################################## - -# fitness model paramaters -a=26. -k=1. - -python src/main.py data/SupplementaryTable1.txt alignments $a $k > output/neontigenQuality.txt diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/src/.DS_Store b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/src/.DS_Store deleted file mode 100755 index 5008ddfcf53c02e82d7eee2e57c38e5672ef89f6..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 6148 zcmeH~Jr2S!425mzP>H1@V-^m;4Wg<&0T*E43hX&L&p$$qDprKhvt+--jT7}7np#A3 zem<@ulZcFPQ@L2!n>{z**++&mCkOWA81W14cNZlEfg7;MkzE(HCqgga^y>{tEnwC%0;vJ&^%eQ zLs35+`xjp>T0 - - NeoantigenQuality - - - - - - org.python.pydev.PyDevBuilder - - - - - - org.python.pydev.pythonNature - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/src/.pydevproject b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/src/.pydevproject deleted file mode 100755 index 037bd251..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/src/.pydevproject +++ /dev/null @@ -1,8 +0,0 @@ - - - -/${PROJECT_DIR_NAME} - -python 2.7 -Default - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/src/Aligner.py b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/src/Aligner.py deleted file mode 100755 index fbca6a36..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/src/Aligner.py +++ /dev/null @@ -1,108 +0,0 @@ -''' -Created on Jul 26, 2017 - -@author: Marta Luksza, mluksza@ias.edu -''' -from math import log, exp - -from Bio import pairwise2 -from Bio.Blast import NCBIXML -from Bio.SubsMat import MatrixInfo as matlist - - -class Aligner(object): - ''' - Class to align neoantigens with IEDB epitopes and compute TCR-recognition - probabilities. - ''' - INF = float("inf") - - @staticmethod - def align(seq1, seq2): - ''' - Smith-Waterman alignment with default parameters. - ''' - matrix = matlist.blosum62 - gap_open = -11 - gap_extend = -1 - aln = pairwise2.align.localds(seq1.upper(), seq2.upper(), matrix, gap_open, gap_extend) - return aln - - @staticmethod - def logSum(v): - ''' - compute the logarithm of a sum of exponentials - ''' - if len(v) == 0: - return -Aligner.INF - ma = max(v) - if ma == -Aligner.INF: - return -Aligner.INF - return log(sum([exp(x - ma) for x in v])) + ma - - def __init__(self): - # dictionary of computed Ri-values mapped to neoantigen identifiers - self.Ri = {} - # dictionary of IEDB epitope alignments mapped to neoantigen identifiers - self.alignments = {} - # dictionary of the highest scoring alignments mapped to neoantigen identifiers - self.maximum_alignment = {} - - def readAllBlastAlignments(self, xmlpath): - ''' - Read precomputed blastp alignments from xml files, - compute alignment scores, - find the highest scoring alignment for each neoantigen. - ''' - f = open(xmlpath) - blast_records = NCBIXML.parse(f) - maxscore = {} - try: - for brecord in blast_records: - nid = int(str(brecord.query).split("_")[1]) - for alignment in brecord.alignments: - if not nid in self.alignments: - self.alignments[nid] = {} - self.maximum_alignment[nid] = None - self.maximum_alignment[nid] = 0 - maxscore[nid] = 0 - species = " ".join((str(alignment).split())[1:-3]) - for hsp in alignment.hsps: - if not "-" in hsp.query and not "-" in hsp.sbjct: - al = Aligner.align(hsp.query, hsp.sbjct) - if len(al) > 0: - al = al[0] - self.alignments[nid][species] = al - if al[2] > maxscore[nid]: - self.maximum_alignment[nid] = species - maxscore[nid] = al[2] - except ValueError: - pass - f.close() - - def computeR(self, a=26, k=1): - ''' - Compute TCR-recognition probabilities for each neoantigen. - ''' - # iterate over all neoantigens - for i in self.alignments: - # energies of all bound states of neoantigen i - bindingEnergies = [-k * (a - el[2]) for el in list(self.alignments[i].values())] - # partition function, over all bound states and an unbound state - lZ = Aligner.logSum(bindingEnergies + [0]) - lGb = Aligner.logSum(bindingEnergies) - R = exp(lGb - lZ) - self.Ri[i] = R - - def getR(self, i): - ''' - Return precomputed R value and the highest scoring alignment - for a given neoantigen i. - ''' - emptyAlignment = [None, None, 0] - if i in self.Ri: - species = self.maximum_alignment[i] - al = self.alignments[i][species] - species = str(species).replace(" ", "_") - return [self.Ri[i], species, al] - return [0., None, emptyAlignment] diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/src/__init__.py b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/src/__init__.py deleted file mode 100755 index e69de29b..00000000 diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/src/main.py b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/src/main.py deleted file mode 100755 index 3a0b9934..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/src/main.py +++ /dev/null @@ -1,71 +0,0 @@ -''' -Created on Jul 27, 2017 - -@author: Marta Luksza, mluksza@ias.edu -''' -import sys - -from .Aligner import Aligner - - -def main(): - ''' - command line parameters: - neofile - text file with neoantigen data (supplementary data) - alignmentDirectory - folder with precomputed alignments (SI) - a - midpoint parameter of the logistic function, alignment score threshold - k - slope parameter of the logistic function - ''' - neofile = sys.argv[1] - alignmentDirectory = sys.argv[2] - - a = float(sys.argv[3]) - k = float(sys.argv[4]) - - # Compute MHC amplitudes for all neoantigens - f = open(neofile) - lines = f.readlines() - Ai = {} - data = {} - samples = set() - for line in lines[1:]: - [i, sample, _, _, _, _, mtpeptide, _, _, kdwt, kdmt] = line.strip().split() - i = int(i) - data[i] = mtpeptide.upper() - Ai[i] = float(kdwt) / float(kdmt) - samples.add(sample) - f.close() - - # Compute TCR-recognition probabilities for all neoantigens - aligner = Aligner() - for sample in samples: - xmlpath = alignmentDirectory + "/neoantigens_" + sample + "_iedb.xml" - aligner.readAllBlastAlignments(xmlpath) - aligner.computeR(a, k) - - # Compute neoantigen quality - nids = list(Ai.keys()) - nids.sort() - header = ["NeoantigenID", "MT.Peptide.Form", "NeoantigenQuality", - "NeoantigenAlignment", "IEDB_EpitopeAlignment", "AlignmentScore", "IEDB_Epitope"] - header = "\t".join(header) - print(header) - for i in nids: - A = Ai[i] - [R, species, alignment] = aligner.getR(i) - - neoAlignment = alignment[0] - epitopeAlignment = alignment[1] - score = alignment[2] - - l = [i, data[i], A * R, neoAlignment, epitopeAlignment, score, species] - l = "\t".join([str(s) for s in l]) - print(l) - - -if __name__ == '__main__': - if len(sys.argv) != 5: - print("Run as:") - print("python src/main.py ") - else: - main() From 87a61e5dfb009d738e95894afc5b75d7718fd8ab Mon Sep 17 00:00:00 2001 From: Pablo Riesgo Ferreiro Date: Wed, 3 Jun 2020 13:59:14 +0200 Subject: [PATCH 033/105] rename aligner --- input/dissimilarity_garnish/dissimilaritycalculator.py | 2 +- input/neoantigen_fitness/{Aligner_modified.py => aligner.py} | 0 input/neoantigen_fitness/neoantigen_fitness.py | 2 +- 3 files changed, 2 insertions(+), 2 deletions(-) rename input/neoantigen_fitness/{Aligner_modified.py => aligner.py} (100%) diff --git a/input/dissimilarity_garnish/dissimilaritycalculator.py b/input/dissimilarity_garnish/dissimilaritycalculator.py index 12585ed5..ea11f61c 100755 --- a/input/dissimilarity_garnish/dissimilaritycalculator.py +++ b/input/dissimilarity_garnish/dissimilaritycalculator.py @@ -4,7 +4,7 @@ import os.path from input.helpers import intermediate_files -from input.neoantigen_fitness.Aligner_modified import Aligner +from input.neoantigen_fitness.aligner import Aligner class DissimilarityCalculator(object): diff --git a/input/neoantigen_fitness/Aligner_modified.py b/input/neoantigen_fitness/aligner.py similarity index 100% rename from input/neoantigen_fitness/Aligner_modified.py rename to input/neoantigen_fitness/aligner.py diff --git a/input/neoantigen_fitness/neoantigen_fitness.py b/input/neoantigen_fitness/neoantigen_fitness.py index de212f2b..dd769869 100755 --- a/input/neoantigen_fitness/neoantigen_fitness.py +++ b/input/neoantigen_fitness/neoantigen_fitness.py @@ -5,7 +5,7 @@ from logzero import logger from input.helpers import intermediate_files -from input.neoantigen_fitness.Aligner_modified import Aligner +from input.neoantigen_fitness.aligner import Aligner class NeoantigenFitnessCalculator(object): From 5b0696c09407fe644012557c72e00fb911c2a151 Mon Sep 17 00:00:00 2001 From: Pablo Riesgo Ferreiro Date: Wed, 3 Jun 2020 22:50:05 +0200 Subject: [PATCH 034/105] remove duplicated code for MixMHCpred --- input/MixMHCpred/abstract_mixmhcpred.py | 99 +++++++++++ input/MixMHCpred/mixmhc2pred.py | 165 ++---------------- input/MixMHCpred/mixmhcpred.py | 125 +------------ input/helpers/runner.py | 5 + input/tests/__init__.py | 22 +++ .../integration_tests/test_mixmhcpred.py | 99 +++++++++++ 6 files changed, 243 insertions(+), 272 deletions(-) create mode 100755 input/MixMHCpred/abstract_mixmhcpred.py create mode 100755 input/tests/integration_tests/test_mixmhcpred.py diff --git a/input/MixMHCpred/abstract_mixmhcpred.py b/input/MixMHCpred/abstract_mixmhcpred.py new file mode 100755 index 00000000..c17ec4ba --- /dev/null +++ b/input/MixMHCpred/abstract_mixmhcpred.py @@ -0,0 +1,99 @@ +#!/usr/bin/env python + + +class AbstractMixMHCpred: + + @staticmethod + def generate_nmers(xmer_wt, xmer_mut, lengths): + """ + Generates peptides covering mutation of all lengths that are provided. Returns peptides as list + No peptide is shorter than the minimun length provided + There are no repetitions in the results + """ + length_mut = len(xmer_mut) + list_peptides = [] + pos_mut = int(AbstractMixMHCpred.mut_position_xmer_seq(xmer_mut=xmer_mut, xmer_wt=xmer_wt)) + for length in lengths: + if length <= length_mut: + start_first = pos_mut - length + starts = [start_first + s for s in range(length)] + ends = [s + length for s in starts] + for s, e in zip(starts, ends): + list_peptides.append(xmer_mut[s:e]) + return list(set([x for x in list_peptides if not x == "" and len(x) >= min(lengths)])) + + @staticmethod + def mut_position_xmer_seq(xmer_wt, xmer_mut): + """ + returns position of mutation in xmer sequence + """ + p1 = -1 + if len(xmer_wt) == len(xmer_mut): + p1 = -1 + for i, aa in enumerate(xmer_mut): + if aa != xmer_wt[i]: + p1 = i + 1 + else: + p1 = 0 + # in case sequences do not have same length + for a1, a2 in zip(xmer_wt, xmer_mut): + if a1 == a2: + p1 += 1 + return str(p1) + + def read_mixmhcpred(self, outtmp): + """ + imports output of MixMHCpred prediction + """ + counter = 0 + header = [] + dat = [] + with open(outtmp) as f: + for line in f: + line = line.rstrip().lstrip() + if line: + if line.startswith("#"): + continue + if line.startswith("Peptide"): + counter += 1 + header = line.split() + continue + line = line.split() + dat.append(line) + return header, dat + + def add_best_epitope_info(self, epitope_tuple, column_name): + """ + returns desired information of prediction of best epitope from netmhcpan output; + e.g. "%Rank": MHC I score, "HLA": HLA allele, "Icore": best epitope + """ + dat_head = epitope_tuple[0] + dat = epitope_tuple[1] + val = dat_head.index(column_name) + try: + return dat[val] + except IndexError: + return "NA" + + def extract_WT_for_best(self, xmer_wt, xmer_mut, best_mut_seq): + """ + extracts the corresponding WT epitope for best predicted mutated epitope + """ + start = xmer_mut.find(best_mut_seq) + l = len(best_mut_seq) + wt_epi = xmer_wt[start:(start + l)] + return (wt_epi) + + def extract_WT_info(self, epitope_tuple, column_name): + """ + :param epitope_tuple: + :param column_name: + :return: + """ + dat_head = epitope_tuple[0] + dat = epitope_tuple[1][0] + val = dat_head.index(column_name) + try: + return dat[val] + except IndexError: + return "NA" diff --git a/input/MixMHCpred/mixmhc2pred.py b/input/MixMHCpred/mixmhc2pred.py index 5fab203f..02133e3a 100755 --- a/input/MixMHCpred/mixmhc2pred.py +++ b/input/MixMHCpred/mixmhc2pred.py @@ -1,9 +1,9 @@ #!/usr/bin/env python +from input.MixMHCpred.abstract_mixmhcpred import AbstractMixMHCpred +from input.helpers import intermediate_files -from input.helpers import properties_manager, intermediate_files - -class MixMhc2Pred: +class MixMhc2Pred(AbstractMixMHCpred): def __init__(self, runner, configuration): """ @@ -42,45 +42,6 @@ def load_available_allelles(self): avail_alleles.append(line1) return avail_alleles - def mut_position_xmer_seq(self, xmer_wt, xmer_mut): - """ - returns position of mutation in xmer sequence - """ - p1 = -1 - if len(xmer_wt) == len(xmer_mut): - p1 = -1 - for i, aa in enumerate(xmer_mut): - if aa != xmer_wt[i]: - p1 = i + 1 - else: - p1 = 0 - # in case sequences do not have same length - for a1, a2 in zip(xmer_wt, xmer_mut): - if a1 == a2: - p1 += 1 - return str(p1) - - def generate_nmers(self, xmer_wt, xmer_mut, list_lengths): - ''' generates peptides covering mutation of all lengths that are provided. Returns peptides as list - ''' - length_mut = len(xmer_mut) - list_peptides = [] - pos_mut = int(self.mut_position_xmer_seq(xmer_mut=xmer_mut, xmer_wt=xmer_wt)) - for l in list_lengths: - l = int(l) - if l <= length_mut: - start_first = pos_mut - (l) - starts = [] - for s in range(l): - starts.append(int(start_first + s)) - ends = [] - [ends.append(int(s + (l))) for s in starts] - for s, e in zip(starts, ends): - list_peptides.append(xmer_mut[s:e]) - list_peptides_fil = [] - [list_peptides_fil.append(x) for x in list_peptides if not x == ""] - return list_peptides_fil - def prepare_dq_dp(self, list_alleles): ''' returns patient DQ/DP alleles that are relevant for prediction ''' @@ -130,25 +91,6 @@ def mixmhc2prediction(self, hla_alleles, tmpfasta, outtmp, wt=False): "-o", outtmp] self.runner.run_command(cmd) - def read_mixmhcpred(self, outtmp): - '''imports output of MixMHCpred prediction - ''' - counter = 0 - header = [] - dat = [] - with open(outtmp) as f: - for line in f: - line = line.rstrip().lstrip() - if line: - if line.startswith("#"): - continue - if line.startswith("Peptide"): - counter += 1 - header = line.split() - continue - line = line.split() - dat.append(line) - return header, dat def extract_best_per_pep(self, pred_dat): '''extract info of best allele prediction for all potential ligands per muatation @@ -193,45 +135,6 @@ def extract_best_peptide_per_mutation(self, pred_dat): head_new = ["Peptide", "%Rank", "BestAllele"] return head_new, min_pep - def add_best_epitope_info(self, epitope_tuple, column_name): - '''returns desired information of prediction of best epitope from netmhcpan output; - e.g. "%Rank": MHC I score, "HLA": HLA allele, "Icore": best epitope - ''' - dat_head = epitope_tuple[0] - dat = epitope_tuple[1] - val = dat_head.index(column_name) - try: - return dat[val] - except IndexError: - return "NA" - - def extract_WT_for_best(self, xmer_wt, xmer_mut, best_mut_seq): - '''extracts the corresponding WT epitope for best predicted mutated epitope - ''' - start = xmer_mut.find(best_mut_seq) - l = len(best_mut_seq) - wt_epi = xmer_wt[start:(start + l)] - return (wt_epi) - - def extract_WT_info(self, epitope_tuple, column_name): - ''' - ''' - dat_head = epitope_tuple[0] - dat = epitope_tuple[1][0] - val = dat_head.index(column_name) - try: - return dat[val] - except IndexError: - return "NA" - - def difference_score(self, mut_score, wt_score): - ''' calcualated difference in MixMHCpred scores between mutated and wt - ''' - try: - return str(float(wt_score) - float(mut_score)) - except ValueError: - return "NA" - def import_available_HLAII_alleles(self, path_to_HLAII_file): '''HLA II alleles for which MixMHC2pred predictions are possible ''' @@ -247,6 +150,14 @@ def import_available_HLAII_alleles(self, path_to_HLAII_file): avail_alleles.append(line1) return avail_alleles + def difference_score(self, mut_score, wt_score): + ''' calcualated difference in MixMHCpred scores between mutated and wt + ''' + try: + return str(float(wt_score) - float(mut_score)) + except ValueError: + return "NA" + def main(self, alleles, xmer_wt, xmer_mut): '''Wrapper for MHC binding prediction, extraction of best epitope and check if mutation is directed to TCR ''' @@ -254,13 +165,15 @@ def main(self, alleles, xmer_wt, xmer_mut): # prediction for peptides of length 13 to 18 based on Suppl Fig. 6 a in Racle, J., et al. # Robust prediction of HLA class II epitopes by deep motif deconvolution of immunopeptidomes. # Nat. Biotech. (2019). - seqs = self.generate_nmers(xmer_wt=xmer_wt, xmer_mut=xmer_mut, list_lengths=[13, 14, 15, 16, 17, 18]) + seqs = self.generate_nmers(xmer_wt=xmer_wt, xmer_mut=xmer_mut, lengths=[13, 14, 15, 16, 17, 18]) tmp_fasta = intermediate_files.create_temp_fasta(seqs, prefix="tmp_sequence_") # try except statement to prevent stop of input for mps shorter < 13aa + # TODO: this needs to be fixed, we could filter the list of nmers by length try: self.mixmhc2prediction(alleles, tmp_fasta, tmp_prediction) except: pass + # TODO: also all of this try-catch needs to be fixed, in general the risk here is that they hide errors try: pred = self.read_mixmhcpred(tmp_prediction) except: @@ -288,53 +201,3 @@ def main(self, alleles, xmer_wt, xmer_mut): self.best_rank_wt = self.extract_WT_info(pred_wt, "%Rank") # difference in scores between mut and wt self.difference_score_mut_wt = self.difference_score(self.best_rank_wt, self.best_rank) - - -# if __name__ == '__main__': -# -# from input import predict_all_epitopes, epitope -# -# # alleles available in MixMHC2pred -# path_to_HLAII_file = "/projects/SUMMIT/WP1.2/input/development/MixMHCpred/Alleles_list_pred2.txt" -# list_avail_hlaII = MixMhc2Pred().import_available_HLAII_alleles(path_to_HLAII_file) -# print(list_avail_hlaII) -# -# # test with ott data set -# # file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/MHC_prediction_netmhcpan4/testdat_ott.txt" -# # hla_file ="/projects/SUMMIT/WP1.2/Literature_Cohorts/data_analysis/cohorts/ott/icam_ott/alleles.csv" -# file = "/projects/SUMMIT/WP1.2/input/development/netmhcIIpan/PtCU9061.test.txt" -# hla_file = "/projects/SUMMIT/WP1.2/Literature_Cohorts/data_analysis/cohorts/rizvi/icam_rizvi/20190819_alleles_extended.csv" -# # test inest data set -# # file = "/flash/projects/WP3/AnFranziska/AnFranziska/head_seqs.txt" -# # hla_file = "/flash/projects/WP3/AnFranziska/AnFranziska/alleles.csv" -# dat = data_import.import_dat_icam(file, False) -# if "+-13_AA_(SNV)_/_-15_AA_to_STOP_(INDEL)" in dat[0]: -# dat = data_import.change_col_names(dat) -# if "patient.id" not in dat[0]: -# try: -# patient = file.split("/")[-3] -# if "Pt" not in patient: -# patient = file.split("/")[-1].split(".")[0] -# except IndexError: -# patient = file.split("/")[-1].split(".")[0] -# dat[0].append("patient.id") -# for ii, i in enumerate(dat[1]): -# dat[1][ii].append(str(patient)) -# # available MHC alleles -# set_available_mhc = predict_all_epitopes.Bunchepitopes().load_available_hla_alleles() -# # hla allele of patients -# patient_hlaI = predict_all_epitopes.Bunchepitopes().load_patient_hla_I_allels(hla_file) -# patient_hlaII = predict_all_epitopes.Bunchepitopes().load_patient_hla_II_allels(hla_file) -# -# print(patient_hlaI) -# print(patient_hlaII) -# -# for ii, i in enumerate(dat[1]): -# if ii < 10: -# print(ii) -# dict_epi = epitope.Epitope() -# dict_epi.init_properties(dat[0], dat[1][ii]) -# prediction = MixMhc2Pred() -# prediction.main(dict_epi.properties, patient_hlaII, list_avail_hlaII) -# attrs = vars(prediction) -# print(attrs) diff --git a/input/MixMHCpred/mixmhcpred.py b/input/MixMHCpred/mixmhcpred.py index 89ec156e..f40dc3c6 100755 --- a/input/MixMHCpred/mixmhcpred.py +++ b/input/MixMHCpred/mixmhcpred.py @@ -2,10 +2,11 @@ from logzero import logger -from input.helpers import properties_manager, intermediate_files +from input.MixMHCpred.abstract_mixmhcpred import AbstractMixMHCpred +from input.helpers import intermediate_files -class MixMHCpred: +class MixMHCpred(AbstractMixMHCpred): def __init__(self, runner, configuration): """ @@ -27,40 +28,6 @@ def __init__(self, runner, configuration): self.best_rank_wt = "NA" self.difference_score_mut_wt = "NA" - def mut_position_xmer_seq(self, xmer_wt, xmer_mut): - '''returns position of mutation in xmer sequence - ''' - p1 = -1 - if len(xmer_wt) == len(xmer_mut): - p1 = -1 - for i, aa in enumerate(xmer_mut): - if aa != xmer_wt[i]: - p1 = i + 1 - else: - p1 = 0 - # in case sequences do not have same length - for a1, a2 in zip(xmer_wt, xmer_mut): - if a1 == a2: - p1 += 1 - return str(p1) - - def generate_nmers(self, xmer_wt, xmer_mut, list_lengths): - ''' generates peptides covering mutation of all lengts that are provided. Returns peptides as list - ''' - list_peptides = [] - pos_mut = int(self.mut_position_xmer_seq(xmer_wt=xmer_wt, xmer_mut=xmer_mut)) - for l in list_lengths: - l = int(l) - start_first = pos_mut - (l) - starts = [] - for s in range(l): - starts.append(int(start_first + s)) - ends = [] - [ends.append(int(s + (l))) for s in starts] - for s, e in zip(starts, ends): - list_peptides.append(xmer_mut[s:e]) - return list_peptides - def mixmhcprediction(self, hla_alleles, tmpfasta, outtmp): ''' Performs MixMHCpred prediction for desired hla allele and writes result to temporary file. ''' @@ -76,26 +43,6 @@ def mixmhcprediction(self, hla_alleles, tmpfasta, outtmp): "-i", tmpfasta, "-o", outtmp]) - def read_mixmhcpred(self, outtmp): - '''imports output of MixMHCpred prediction - ''' - counter = 0 - header = [] - dat = [] - with open(outtmp) as f: - for line in f: - line = line.rstrip().lstrip() - if line: - if line.startswith("#"): - continue - if line.startswith("Peptide"): - counter += 1 - header = line.split() - continue - line = line.split() - dat.append(line) - return header, dat - def extract_best_per_pep(self, pred_dat): '''extract info of best allele prediction for all potential ligands per muatation ''' @@ -142,37 +89,6 @@ def extract_best_peptide_per_mutation(self, pred_dat): head_new = ["Peptide", "Score_bestAllele", "%Rank_bestAllele", "BestAllele"] return head_new, min_pep - def add_best_epitope_info(self, epitope_tuple, column_name): - '''returns desired information of prediction of best epitope from netmhcpan output; - e.g. "%Rank": MHC I score, "HLA": HLA allele, "Icore": best epitope - ''' - dat_head = epitope_tuple[0] - dat = epitope_tuple[1] - val = dat_head.index(column_name) - try: - return dat[val] - except IndexError: - return "NA" - - def extract_WT_for_best(self, xmer_wt, xmer_mut, best_mut_seq): - '''extracts the corresponding WT epitope for best predicted mutated epitope - ''' - start = xmer_mut.find(best_mut_seq) - l = len(best_mut_seq) - wt_epi = xmer_wt[start:(start + l)] - return (wt_epi) - - def extract_WT_info(self, epitope_tuple, column_name): - ''' - ''' - dat_head = epitope_tuple[0] - dat = epitope_tuple[1][0] - val = dat_head.index(column_name) - try: - return dat[val] - except IndexError: - return "NA" - def difference_score(self, mut_score, wt_score): ''' calcualated difference in MixMHCpred scores between mutated and wt ''' @@ -185,7 +101,7 @@ def main(self, xmer_wt, xmer_mut, alleles): '''Wrapper for MHC binding prediction, extraction of best epitope and check if mutation is directed to TCR ''' tmp_prediction = intermediate_files.create_temp_file(prefix="mixmhcpred", suffix=".txt") - seqs = self.generate_nmers(xmer_wt=xmer_wt, xmer_mut=xmer_mut, list_lengths=[8, 9, 10, 11]) + seqs = self.generate_nmers(xmer_wt=xmer_wt, xmer_mut=xmer_mut, lengths=[8, 9, 10, 11]) tmp_fasta = intermediate_files.create_temp_fasta(seqs, prefix="tmp_sequence_") self.mixmhcprediction(alleles, tmp_fasta, tmp_prediction) pred = self.read_mixmhcpred(tmp_prediction) @@ -219,36 +135,3 @@ def main(self, xmer_wt, xmer_mut, alleles): self.best_rank_wt = self.extract_WT_info(pred_wt, rank_wt_of_interest) # difference in scores between mut and wt self.difference_score_mut_wt = self.difference_score(self.best_score, self.best_score_wt) - - -# if __name__ == '__main__': -# -# from input import predict_all_epitopes, epitope -# -# # test with ott data set -# file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/MHC_prediction_netmhcpan4/testdat_ott.txt" -# hla_file = "/projects/SUMMIT/WP1.2/Literature_Cohorts/data_analysis/cohorts/ott/icam_ott/alleles.csv" -# # test inest data set -# # file = "/flash/projects/WP3/AnFranziska/AnFranziska/head_seqs.txt" -# # hla_file = "/flash/projects/WP3/AnFranziska/AnFranziska/alleles.csv" -# dat = data_import.import_dat_icam(file, False) -# if "+-13_AA_(SNV)_/_-15_AA_to_STOP_(INDEL)" in dat[0]: -# dat = data_import.change_col_names(dat) -# # available MHC alleles -# set_available_mhc = predict_all_epitopes.Bunchepitopes().load_available_hla_alleles() -# # hla allele of patients -# patient_hlaI = predict_all_epitopes.Bunchepitopes().load_patient_hla_I_allels(hla_file) -# patient_hlaII = predict_all_epitopes.Bunchepitopes().load_patient_hla_II_allels(hla_file) -# -# print(patient_hlaI) -# print(patient_hlaII) -# -# for ii, i in enumerate(dat[1]): -# if ii < 10: -# print(ii) -# dict_epi = epitope.Epitope() -# dict_epi.init_properties(dat[0], dat[1][ii]) -# prediction = MixMHCpred() -# prediction.main(dict_epi.properties, patient_hlaI) -# attrs = vars(prediction) -# print(attrs) diff --git a/input/helpers/runner.py b/input/helpers/runner.py index bfda1b02..7c558541 100755 --- a/input/helpers/runner.py +++ b/input/helpers/runner.py @@ -1,4 +1,5 @@ import subprocess +import time from logzero import logger @@ -9,14 +10,18 @@ class Runner(object): def run_command(self, cmd, **kwargs): logger.info("Starting command: {}".format(" ".join(cmd))) + start = time.time() process = subprocess.Popen(self._preprocess_command(cmd), stderr=subprocess.PIPE, stdout=subprocess.PIPE, **kwargs) output, errors = process.communicate() return_code = process.returncode + end = time.time() + logger.info("Elapsed time {} seconds".format(int(end - start))) if return_code == 0: logger.info("Finished command correctly!") logger.info(self._decode(output)) else: logger.error("Finished command with return code {}".format(return_code)) + logger.error(self._decode(output)) logger.error(self._decode(errors)) raise INPuTCommandException("Error running command '{}'".format(" ".join(cmd))) return self._decode(output), self._decode(errors) diff --git a/input/tests/__init__.py b/input/tests/__init__.py index e69de29b..25be8221 100755 --- a/input/tests/__init__.py +++ b/input/tests/__init__.py @@ -0,0 +1,22 @@ +TEST_HLAI_ALLELES = [ + 'HLA-A*24:02', 'HLA-A*02:01', 'HLA-B*15:01', 'HLA-B*44:02', 'HLA-C*07:02', 'HLA-C*05:01', + 'HLA-A*24:02', 'HLA-B*27:05', 'HLA-B*52:01', 'HLA-C*01:02', 'HLA-C*12:02', + 'HLA-A*01:01', 'HLA-B*56:01', 'HLA-B*38:01', 'HLA-C*01:02', 'HLA-C*06:02', + 'HLA-A*03:01', 'HLA-A*02:01', 'HLA-B*27:05', 'HLA-B*47:01', 'HLA-C*01:02', 'HLA-C*06:02', + 'HLA-A*02:01', 'HLA-A*25:01', 'HLA-B*27:02', 'HLA-B*18:01', 'HLA-C*02:02', 'HLA-C*12:03', + 'HLA-A*23:01', 'HLA-A*66:01', 'HLA-B*41:02', 'HLA-B*35:01', 'HLA-C*17:03', 'HLA-C*04:01', + 'HLA-A*66:01', 'HLA-A*01:01', 'HLA-B*08:01', 'HLA-C*07:01', + 'HLA-A*03:01', 'HLA-A*01:01', 'HLA-B*08:01', 'HLA-B*35:01', 'HLA-C*07:01', 'HLA-C*04:01', + 'HLA-A*24:02', 'HLA-A*68:01', 'HLA-B*35:03', 'HLA-B*13:02', 'HLA-C*06:02', 'HLA-C*04:01', + 'HLA-A*01:01', 'HLA-B*37:01', 'HLA-B*08:01', 'HLA-C*06:02', 'HLA-C*07:01'] + +TEST_HLAII_ALLELES = ['HLA-DRB1*04:01', 'HLA-DRB1*04:04', 'HLA-DQB1*03:01', 'HLA-DQB1*03:02', + 'HLA-DRB1*11:01', 'HLA-DRB1*01:01', 'HLA-DQB1*05:01', 'HLA-DQB1*03:01', + 'HLA-DRB1*11:04', 'HLA-DRB1*07:01', 'HLA-DQB1*02:02', 'HLA-DQB1*03:01', + 'HLA-DRB1*01:01', 'HLA-DRB1*07:01', 'HLA-DQB1*05:01', 'HLA-DQB1*02:02', + 'HLA-DRB1*16:01', 'HLA-DRB1*01:01', 'HLA-DQB1*05:02', 'HLA-DQB1*05:01', + 'HLA-DRB1*11:01', 'HLA-DRB1*01:01', 'HLA-DQB1*05:01', 'HLA-DQB1*03:01', + 'HLA-DRB1*03:01', 'HLA-DQB1*02:01', + 'HLA-DRB1*03:01', 'HLA-DRB1*07:01', 'HLA-DQB1*02:02', 'HLA-DQB1*02:01', + 'HLA-DRB1*15:01', 'HLA-DRB1*12:01', 'HLA-DQB1*06:02', 'HLA-DQB1*03:01', + 'HLA-DRB1*11:01', 'HLA-DRB1*03:01', 'HLA-DQB1*03:01', 'HLA-DQB1*02:01'] diff --git a/input/tests/integration_tests/test_mixmhcpred.py b/input/tests/integration_tests/test_mixmhcpred.py new file mode 100755 index 00000000..5d91e435 --- /dev/null +++ b/input/tests/integration_tests/test_mixmhcpred.py @@ -0,0 +1,99 @@ +from unittest import TestCase +from logzero import logger + +import input.tests.integration_tests.integration_test_tools as integration_test_tools +from input.MixMHCpred.abstract_mixmhcpred import AbstractMixMHCpred +from input.MixMHCpred.mixmhc2pred import MixMhc2Pred +from input.MixMHCpred.mixmhcpred import MixMHCpred +from input.helpers.runner import Runner +from input.tests import TEST_HLAI_ALLELES, TEST_HLAII_ALLELES + + +class TestMixMHCPred(TestCase): + + def setUp(self): + self.references, self.configuration = integration_test_tools.load_references() + self.runner = Runner() + + def test_mixmhcpred_epitope_iedb(self): + mixmhcpred = MixMHCpred(runner=self.runner, configuration=self.configuration) + # this is an epitope from IEDB of length 9 + mutated = 'NLVPMVATV' + wild_type = 'NLVPMVATV' + mixmhcpred.main(xmer_wt=wild_type, xmer_mut=mutated, alleles=TEST_HLAI_ALLELES[0:5]) + self.assertIsNotNone(mixmhcpred.all_peptides) + self.assertEqual("NLVPMVAT", mixmhcpred.all_peptides) + logger.debug(mixmhcpred.all_peptides) + self.assertEqual(len(mixmhcpred.all_peptides.split('|')), 1) + self.assertIsNotNone(mixmhcpred.all_scores) + logger.debug(mixmhcpred.all_scores) + self.assertEqual(len(mixmhcpred.all_scores.split('|')), 1) + self.assertEqual("-0.522931", mixmhcpred.all_scores) + self.assertIsNotNone(mixmhcpred.all_ranks) + logger.debug(mixmhcpred.all_ranks) + self.assertEqual(len(mixmhcpred.all_ranks.split('|')), 1) + self.assertEqual("77", mixmhcpred.all_ranks) + self.assertIsNotNone(mixmhcpred.all_alleles) + self.assertIsNotNone(mixmhcpred.best_peptide) + self.assertIsNotNone(mixmhcpred.best_score) + self.assertIsNotNone(mixmhcpred.best_rank) + self.assertIsNotNone(mixmhcpred.best_allele) + self.assertIsNotNone(mixmhcpred.best_peptide_wt) + self.assertIsNotNone(mixmhcpred.best_score_wt) + self.assertIsNotNone(mixmhcpred.best_rank_wt) + self.assertIsNotNone(mixmhcpred.difference_score_mut_wt) + + def test_mixmhcpred_too_small_epitope(self): + mixmhcpred = MixMHCpred(runner=self.runner, configuration=self.configuration) + mutated = 'NLVP' + wild_type = 'NLVP' + mixmhcpred.main(xmer_wt=wild_type, xmer_mut=mutated, alleles=TEST_HLAI_ALLELES) + self.assertEqual("NA", mixmhcpred.all_peptides) + + def test_mixmhcpred2_epitope_iedb(self): + mixmhcpred = MixMhc2Pred(runner=self.runner, configuration=self.configuration) + # this is an epitope from IEDB of length 15 + mutated = 'ENPVVHFFKNIVTPR' + wild_type = 'ENPVVHFFKNIVTPR' + mixmhcpred.main(xmer_wt=wild_type, xmer_mut=mutated, alleles=TEST_HLAII_ALLELES) + self.assertIsNotNone(mixmhcpred.all_peptides) + self.assertEqual(len(mixmhcpred.all_peptides.split('|')), 2) + self.assertTrue("ENPVVHFFKNIVTP" in mixmhcpred.all_peptides.split('|')) + self.assertTrue("NPVVHFFKNIVTP" in mixmhcpred.all_peptides.split('|')) + logger.debug(mixmhcpred.all_peptides) + self.assertIsNotNone(mixmhcpred.all_ranks) + self.assertEqual(len(mixmhcpred.all_ranks.split('|')), 2) + self.assertTrue("0.116547" in mixmhcpred.all_ranks.split('|')) + self.assertTrue("0.276218", mixmhcpred.all_ranks.split('|')) + logger.debug(mixmhcpred.all_ranks) + self.assertIsNotNone(mixmhcpred.all_alleles) + self.assertIsNotNone(mixmhcpred.best_peptide) + self.assertIsNotNone(mixmhcpred.best_rank) + self.assertIsNotNone(mixmhcpred.best_allele) + self.assertIsNotNone(mixmhcpred.best_peptide_wt) + self.assertIsNotNone(mixmhcpred.best_score_wt) + self.assertIsNotNone(mixmhcpred.best_rank_wt) + self.assertIsNotNone(mixmhcpred.difference_score_mut_wt) + + def test_mixmhcpred2_too_small_epitope(self): + mixmhcpred = MixMhc2Pred(runner=self.runner, configuration=self.configuration) + # this is an epitope from IEDB of length 15 + mutated = 'ENPVVHFF' + wild_type = 'ENPVVHFF' + mixmhcpred.main(xmer_wt=wild_type, xmer_mut=mutated, alleles=TEST_HLAII_ALLELES) + self.assertEqual("NA", mixmhcpred.all_peptides) + + def test_generate_nmers(self): + result = AbstractMixMHCpred.generate_nmers( + xmer_wt="DDDDDDDDD", xmer_mut="DDDDDVDDD", lengths=[8, 9, 10, 11]) + self.assertIsNotNone(result) + self.assertEqual(3, len(result)) + self.assertEqual(1, len(list(filter(lambda x: len(x) == 9, result)))) + self.assertEqual(2, len(list(filter(lambda x: len(x) == 8, result)))) + self.assertEqual(0, len(list(filter(lambda x: len(x) == 7, result)))) + self.assertEqual(0, len(list(filter(lambda x: len(x) == 6, result)))) + self.assertEqual(0, len(list(filter(lambda x: len(x) == 5, result)))) + self.assertEqual(0, len(list(filter(lambda x: len(x) == 4, result)))) + # ['DDDDDVDD', 'DDDDVDDD', 'DDDVDDD', 'DDVDDD', 'DVDDD', 'VDDD', 'DDDDDVDDD', 'DDDDVDDD', 'DDDVDDD', 'DDVDDD', + # 'DVDDD', 'VDDD'] + logger.debug(result) From c758e186b51dc2cfd26b7741b1b87308aa75dc41 Mon Sep 17 00:00:00 2001 From: Pablo Riesgo Ferreiro Date: Wed, 3 Jun 2020 23:31:52 +0200 Subject: [PATCH 035/105] remove duplicated code from BLASTP --- .../dissimilaritycalculator.py | 28 ++++----------- input/helpers/runner.py | 36 +++++++++++++++++++ input/neoantigen_fitness/aligner.py | 19 ---------- .../neoantigen_fitness/neoantigen_fitness.py | 35 ++++++------------ .../integration_tests/test_dissimilarity.py | 18 +++++++--- .../test_neoantigen_fitness.py | 1 - 6 files changed, 67 insertions(+), 70 deletions(-) diff --git a/input/dissimilarity_garnish/dissimilaritycalculator.py b/input/dissimilarity_garnish/dissimilaritycalculator.py index ea11f61c..b10203ba 100755 --- a/input/dissimilarity_garnish/dissimilaritycalculator.py +++ b/input/dissimilarity_garnish/dissimilaritycalculator.py @@ -4,41 +4,26 @@ import os.path from input.helpers import intermediate_files -from input.neoantigen_fitness.aligner import Aligner +from input.helpers.runner import BlastpRunner -class DissimilarityCalculator(object): +class DissimilarityCalculator(BlastpRunner): def __init__(self, runner, configuration): """ :type runner: input.helpers.runner.Runner :type configuration: input.references.DependenciesConfiguration """ - self.runner = runner - self.configuration = configuration + super().__init__(runner=runner, configuration=configuration) def _calc_dissimilarity(self, fasta_file, references): """ This function determines the dissimilarity to self-proteome of epitopes as described in Richman et al """ - outfile = intermediate_files.create_temp_file(prefix="tmp_prot_", suffix=".xml") - self.runner.run_command(cmd=[ - self.configuration.blastp, - "-gapopen", "11", - "-gapextend", "1", - "-outfmt", "5", - "-query", fasta_file, - "-out", outfile, - "-db", os.path.join(references.proteome_db, "homo_sapiens.mod"), - "-evalue", "100000000"]) - aligner = Aligner() - # set a to 32 for dissimilarity - aligner.readAllBlastAlignments(outfile) - aligner.computeR(a=32) - kk = 1 - similarity = aligner.Ri.get(kk, 0) # NOTE: returns 0 when not present + outfile = self.run_blastp( + fasta_file=fasta_file, database=os.path.join(references.proteome_db, "homo_sapiens.mod")) + similarity = self.parse_blastp_output(blastp_output_file=outfile, a=32) dissimilarity = 1 - similarity - os.remove(fasta_file) os.remove(outfile) return dissimilarity @@ -48,6 +33,7 @@ def calculate_dissimilarity(self, mhc_mutation, mhc_affinity, references, filter """ fastafile = intermediate_files.create_temp_fasta(sequences=[mhc_mutation], prefix="tmp_dissimilarity_", comment_prefix='M_') dissim = self._calc_dissimilarity(fastafile, references) + os.remove(fastafile) sc = dissim if filter_binder and float(mhc_affinity) >= 500: sc = 0 diff --git a/input/helpers/runner.py b/input/helpers/runner.py index 7c558541..3ca296a8 100755 --- a/input/helpers/runner.py +++ b/input/helpers/runner.py @@ -4,6 +4,8 @@ from logzero import logger from input.exceptions import INPuTCommandException +from input.helpers import intermediate_files +from input.neoantigen_fitness.aligner import Aligner class Runner(object): @@ -35,3 +37,37 @@ def _preprocess_command(cmd): def _decode(self, data): return data.decode('utf8') + + +class BlastpRunner(object): + + def __init__(self, runner, configuration): + """ + :type runner: input.helpers.runner.Runner + :type configuration: input.references.DependenciesConfiguration + """ + self.runner = runner + self.configuration = configuration + + def run_blastp(self, fasta_file, database): + ''' + This function runs BLASTP on a given database + ''' + outfile = intermediate_files.create_temp_file(prefix="tmp_blastp_", suffix=".xml") + self.runner.run_command(cmd=[ + self.configuration.blastp, + "-gapopen", "11", + "-gapextend", "1", + "-outfmt", "5", + "-query", fasta_file, + "-out", outfile, + "-db", database, + "-evalue", "100000000"]) + return outfile + + def parse_blastp_output(self, blastp_output_file, **kwargs): + aligner = Aligner() + # set a to 32 for dissimilarity + aligner.readAllBlastAlignments(blastp_output_file) + aligner.computeR(**kwargs) + return aligner.Ri.get(1, 0) # NOTE: returns 0 when not present diff --git a/input/neoantigen_fitness/aligner.py b/input/neoantigen_fitness/aligner.py index 6e596560..3c25c3e8 100755 --- a/input/neoantigen_fitness/aligner.py +++ b/input/neoantigen_fitness/aligner.py @@ -106,22 +106,3 @@ def getR(self, i): species = str(species).replace(" ", "_") return [self.Ri[i], species, al] return [0., None, emptyAlignment] - - -import sys - -if __name__ == "__main__": - a = Aligner() - a.readAllBlastAlignments(sys.argv[1]) - a.computeR() - n = [] - with open(sys.argv[2]) as f: - for line in f: - if line.startswith(">"): - nid = int(line.strip("\n").split("_")[1]) - continue - n.append((nid, line.strip("\n"))) - for nid, i in n: - x = a.getR(nid) - if x[1] != None: - print(x) diff --git a/input/neoantigen_fitness/neoantigen_fitness.py b/input/neoantigen_fitness/neoantigen_fitness.py index dd769869..ab814cd7 100755 --- a/input/neoantigen_fitness/neoantigen_fitness.py +++ b/input/neoantigen_fitness/neoantigen_fitness.py @@ -5,41 +5,27 @@ from logzero import logger from input.helpers import intermediate_files -from input.neoantigen_fitness.aligner import Aligner +from input.helpers.runner import BlastpRunner -class NeoantigenFitnessCalculator(object): +class NeoantigenFitnessCalculator(BlastpRunner): def __init__(self, runner, configuration): """ :type runner: input.helpers.runner.Runner :type configuration: input.references.DependenciesConfiguration """ - self.runner = runner - self.configuration = configuration + super().__init__(runner, configuration) def _calc_pathogen_similarity(self, fasta_file, iedb): - ''' - This function determines the PATHOGENSIMILARITY of epitopes according to Balachandran et al. using a blast search against the IEDB pathogenepitope database - ''' - outfile = intermediate_files.create_temp_file(prefix="tmp_iedb_", suffix=".xml") - self.runner.run_command(cmd=[ - self.configuration.blastp, - "-gapopen", "11", - "-gapextend", "1", - "-outfmt", "5", - "-query", fasta_file, - "-out", outfile, - "-db", os.path.join(iedb, "iedb_blast_db"), - "-evalue", "100000000"]) - a = Aligner() - a.readAllBlastAlignments(outfile) - a.computeR() - kk = 1 - x = a.Ri.get(kk, 0) # NOTE: if not present it returns 0 - os.remove(fasta_file) + """ + This function determines the PATHOGENSIMILARITY of epitopes according to Balachandran et al. using a blast + search against the IEDB pathogenepitope database + """ + outfile = self.run_blastp(fasta_file=fasta_file, database=os.path.join(iedb, "iedb_blast_db")) + similarity = self.parse_blastp_output(blastp_output_file=outfile) os.remove(outfile) - return x + return similarity def wrap_pathogen_similarity(self, mutation, iedb): fastafile = intermediate_files.create_temp_fasta(sequences=[mutation], prefix="tmpseq", comment_prefix='M_') @@ -49,6 +35,7 @@ def wrap_pathogen_similarity(self, mutation, iedb): # TODO: do we need this at all? it should not fail and if it fails we probably want to just stop execution logger.exception(ex) pathsim = 0 + os.remove(fastafile) logger.info("Peptide {} has a pathogen similarity of {}".format(mutation, pathsim)) return str(pathsim) diff --git a/input/tests/integration_tests/test_dissimilarity.py b/input/tests/integration_tests/test_dissimilarity.py index 40574643..353e7167 100755 --- a/input/tests/integration_tests/test_dissimilarity.py +++ b/input/tests/integration_tests/test_dissimilarity.py @@ -12,8 +12,16 @@ def setUp(self): self.fastafile = integration_test_tools.create_temp_aminoacid_fasta_file() self.runner = Runner() - def test_dissimilarity(self): - result = DissimilarityCalculator(runner=self.runner, configuration=self.configuration).calculate_dissimilarity( - mhc_mutation='hey', mhc_affinity='ho', - references=self.references) - self.assertEqual('0', result) + def test_dissimilar_sequences(self): + result = DissimilarityCalculator( + runner=self.runner, configuration=self.configuration)\ + .calculate_dissimilarity( + mhc_mutation='tocino', mhc_affinity='velocidad', references=self.references) + self.assertEqual(1, result) + + def test_similar_sequences(self): + result = DissimilarityCalculator( + runner=self.runner, configuration=self.configuration)\ + .calculate_dissimilarity( + mhc_mutation='DDDDDD', mhc_affinity='DDDDDD', references=self.references) + self.assertTrue(result < 0.000001) diff --git a/input/tests/integration_tests/test_neoantigen_fitness.py b/input/tests/integration_tests/test_neoantigen_fitness.py index 3418b4a1..7ae0cc15 100755 --- a/input/tests/integration_tests/test_neoantigen_fitness.py +++ b/input/tests/integration_tests/test_neoantigen_fitness.py @@ -4,7 +4,6 @@ from input.neoantigen_fitness.neoantigen_fitness import NeoantigenFitnessCalculator from input.helpers.runner import Runner import input.tests.integration_tests.integration_test_tools as integration_test_tools -from input import MHC_II, MHC_I class TestNeoantigenFitness(TestCase): From d4ede1d0c0967c6ec8bf0b6a49665e096541942c Mon Sep 17 00:00:00 2001 From: Pablo Riesgo Ferreiro Date: Thu, 4 Jun 2020 14:53:43 +0200 Subject: [PATCH 036/105] remove duplicated code from netmhcpan and netmhcIIpan --- input/MixMHCpred/abstract_mixmhcpred.py | 46 +- input/epitope.py | 9 +- input/helpers/blastp_runner.py | 36 + input/helpers/epitope_helper.py | 66 + input/helpers/runner.py | 36 - input/netmhcIIpan/__init__.py | 0 input/netmhcIIpan/netmhcIIpan_prediction.py | 276 -- input/netmhcpan4/MHC_available.csv | 4397 ----------------- .../abstract_netmhcpan_predictor.py | 17 + input/netmhcpan4/all_seqs.fasta | 16 - ...mbine_netmhcIIpan_pred_multiple_binders.py | 24 +- ...combine_netmhcpan_pred_multiple_binders.py | 22 +- input/netmhcpan4/multiple_binders.py | 180 +- input/netmhcpan4/netmhcIIpan_prediction.py | 147 + input/netmhcpan4/netmhcpan_prediction.py | 97 +- input/netmhcpan4/test.csv | 211 - input/netmhcpan4/test.txt | 11 - input/netmhcpan4/tmp.fasta | 2 - input/netmhcpan4/x.csv | 0 input/predict_all_epitopes.py | 20 +- input/references.py | 16 + .../tests/integration_tests/test_netmhcpan.py | 96 + 22 files changed, 457 insertions(+), 5268 deletions(-) create mode 100755 input/helpers/blastp_runner.py create mode 100755 input/helpers/epitope_helper.py delete mode 100755 input/netmhcIIpan/__init__.py delete mode 100755 input/netmhcIIpan/netmhcIIpan_prediction.py delete mode 100644 input/netmhcpan4/MHC_available.csv create mode 100755 input/netmhcpan4/abstract_netmhcpan_predictor.py delete mode 100644 input/netmhcpan4/all_seqs.fasta rename input/{netmhcIIpan => netmhcpan4}/combine_netmhcIIpan_pred_multiple_binders.py (91%) create mode 100755 input/netmhcpan4/netmhcIIpan_prediction.py delete mode 100644 input/netmhcpan4/test.csv delete mode 100644 input/netmhcpan4/test.txt delete mode 100644 input/netmhcpan4/tmp.fasta delete mode 100644 input/netmhcpan4/x.csv create mode 100755 input/tests/integration_tests/test_netmhcpan.py diff --git a/input/MixMHCpred/abstract_mixmhcpred.py b/input/MixMHCpred/abstract_mixmhcpred.py index c17ec4ba..987a3d90 100755 --- a/input/MixMHCpred/abstract_mixmhcpred.py +++ b/input/MixMHCpred/abstract_mixmhcpred.py @@ -1,47 +1,10 @@ -#!/usr/bin/env python +from input.helpers.epitope_helper import EpitopeHelper -class AbstractMixMHCpred: +class AbstractMixMHCpred(EpitopeHelper): @staticmethod - def generate_nmers(xmer_wt, xmer_mut, lengths): - """ - Generates peptides covering mutation of all lengths that are provided. Returns peptides as list - No peptide is shorter than the minimun length provided - There are no repetitions in the results - """ - length_mut = len(xmer_mut) - list_peptides = [] - pos_mut = int(AbstractMixMHCpred.mut_position_xmer_seq(xmer_mut=xmer_mut, xmer_wt=xmer_wt)) - for length in lengths: - if length <= length_mut: - start_first = pos_mut - length - starts = [start_first + s for s in range(length)] - ends = [s + length for s in starts] - for s, e in zip(starts, ends): - list_peptides.append(xmer_mut[s:e]) - return list(set([x for x in list_peptides if not x == "" and len(x) >= min(lengths)])) - - @staticmethod - def mut_position_xmer_seq(xmer_wt, xmer_mut): - """ - returns position of mutation in xmer sequence - """ - p1 = -1 - if len(xmer_wt) == len(xmer_mut): - p1 = -1 - for i, aa in enumerate(xmer_mut): - if aa != xmer_wt[i]: - p1 = i + 1 - else: - p1 = 0 - # in case sequences do not have same length - for a1, a2 in zip(xmer_wt, xmer_mut): - if a1 == a2: - p1 += 1 - return str(p1) - - def read_mixmhcpred(self, outtmp): + def read_mixmhcpred(outtmp): """ imports output of MixMHCpred prediction """ @@ -62,7 +25,8 @@ def read_mixmhcpred(self, outtmp): dat.append(line) return header, dat - def add_best_epitope_info(self, epitope_tuple, column_name): + @staticmethod + def add_best_epitope_info(epitope_tuple, column_name): """ returns desired information of prediction of best epitope from netmhcpan output; e.g. "%Rank": MHC I score, "HLA": HLA allele, "Icore": best epitope diff --git a/input/epitope.py b/input/epitope.py index 5fc18ced..429188aa 100755 --- a/input/epitope.py +++ b/input/epitope.py @@ -1,7 +1,5 @@ #!/usr/bin/env python -import tempfile - from logzero import logger from input import FeatureLiterature @@ -10,15 +8,14 @@ from input.MixMHCpred.mixmhc2pred import MixMhc2Pred from input.Tcell_predictor.tcellpredictor_wrapper import TcellPrediction from input.dissimilarity_garnish.dissimilaritycalculator import DissimilarityCalculator -from input.helpers import properties_manager, intermediate_files +from input.helpers import properties_manager from input.neoag.neoag_gbm_model import NeoagCalculator from input.neoantigen_fitness.neoantigen_fitness import NeoantigenFitnessCalculator -from input.netmhcIIpan.combine_netmhcIIpan_pred_multiple_binders import BestAndMultipleBinderMhcII +from input.netmhcpan4.combine_netmhcIIpan_pred_multiple_binders import BestAndMultipleBinderMhcII from input.netmhcpan4.combine_netmhcpan_pred_multiple_binders import BestAndMultipleBinder -from input.new_features import amino_acid_frequency_scores as freq_score, differential_expression, conservation_scores +from input.new_features import amino_acid_frequency_scores as freq_score, differential_expression from input.self_similarity import self_similarity from input.vaxrank import vaxrank -from input.helpers.runner import Runner class Epitope: diff --git a/input/helpers/blastp_runner.py b/input/helpers/blastp_runner.py new file mode 100755 index 00000000..200ddb81 --- /dev/null +++ b/input/helpers/blastp_runner.py @@ -0,0 +1,36 @@ +from input.helpers import intermediate_files +from input.neoantigen_fitness.aligner import Aligner + + +class BlastpRunner(object): + + def __init__(self, runner, configuration): + """ + :type runner: input.helpers.runner.Runner + :type configuration: input.references.DependenciesConfiguration + """ + self.runner = runner + self.configuration = configuration + + def run_blastp(self, fasta_file, database): + ''' + This function runs BLASTP on a given database + ''' + outfile = intermediate_files.create_temp_file(prefix="tmp_blastp_", suffix=".xml") + self.runner.run_command(cmd=[ + self.configuration.blastp, + "-gapopen", "11", + "-gapextend", "1", + "-outfmt", "5", + "-query", fasta_file, + "-out", outfile, + "-db", database, + "-evalue", "100000000"]) + return outfile + + def parse_blastp_output(self, blastp_output_file, **kwargs): + aligner = Aligner() + # set a to 32 for dissimilarity + aligner.readAllBlastAlignments(blastp_output_file) + aligner.computeR(**kwargs) + return aligner.Ri.get(1, 0) # NOTE: returns 0 when not present \ No newline at end of file diff --git a/input/helpers/epitope_helper.py b/input/helpers/epitope_helper.py new file mode 100755 index 00000000..9afc5a12 --- /dev/null +++ b/input/helpers/epitope_helper.py @@ -0,0 +1,66 @@ + + +class EpitopeHelper(object): + + @staticmethod + def generate_nmers(xmer_wt, xmer_mut, lengths): + """ + Generates peptides covering mutation of all lengths that are provided. Returns peptides as list + No peptide is shorter than the minimun length provided + There are no repetitions in the results + """ + length_mut = len(xmer_mut) + list_peptides = [] + pos_mut = int(EpitopeHelper.mut_position_xmer_seq(xmer_mut=xmer_mut, xmer_wt=xmer_wt)) + for length in lengths: + if length <= length_mut: + start_first = pos_mut - length + starts = [start_first + s for s in range(length)] + ends = [s + length for s in starts] + for s, e in zip(starts, ends): + list_peptides.append(xmer_mut[s:e]) + return list(set([x for x in list_peptides if not x == "" and len(x) >= min(lengths)])) + + @staticmethod + def mut_position_xmer_seq(xmer_wt, xmer_mut): + """ + returns position of mutation in xmer sequence + """ + p1 = -1 + if len(xmer_wt) == len(xmer_mut): + p1 = -1 + for i, aa in enumerate(xmer_mut): + if aa != xmer_wt[i]: + p1 = i + 1 + else: + p1 = 0 + # in case sequences do not have same length + for a1, a2 in zip(xmer_wt, xmer_mut): + if a1 == a2: + p1 += 1 + return str(p1) + + @staticmethod + def epitope_covers_mutation(position_mutation, position_epitope, length_epitope): + """ + checks if predicted epitope covers mutation + """ + cover = False + if position_mutation != "-1": + start = int(position_epitope) + end = start + int(length_epitope) - 1 + if int(position_mutation) >= start and int(position_mutation) <= end: + cover = True + return cover + + @staticmethod + def hamming_check_0_or_1(seq1, seq2): + '''returns number of mismatches between 2 sequences + ''' + errors = 0 + for i in range(len(seq1)): + if seq1[i] != seq2[i]: + errors += 1 + if errors >= 2: + return errors + return errors diff --git a/input/helpers/runner.py b/input/helpers/runner.py index 3ca296a8..7c558541 100755 --- a/input/helpers/runner.py +++ b/input/helpers/runner.py @@ -4,8 +4,6 @@ from logzero import logger from input.exceptions import INPuTCommandException -from input.helpers import intermediate_files -from input.neoantigen_fitness.aligner import Aligner class Runner(object): @@ -37,37 +35,3 @@ def _preprocess_command(cmd): def _decode(self, data): return data.decode('utf8') - - -class BlastpRunner(object): - - def __init__(self, runner, configuration): - """ - :type runner: input.helpers.runner.Runner - :type configuration: input.references.DependenciesConfiguration - """ - self.runner = runner - self.configuration = configuration - - def run_blastp(self, fasta_file, database): - ''' - This function runs BLASTP on a given database - ''' - outfile = intermediate_files.create_temp_file(prefix="tmp_blastp_", suffix=".xml") - self.runner.run_command(cmd=[ - self.configuration.blastp, - "-gapopen", "11", - "-gapextend", "1", - "-outfmt", "5", - "-query", fasta_file, - "-out", outfile, - "-db", database, - "-evalue", "100000000"]) - return outfile - - def parse_blastp_output(self, blastp_output_file, **kwargs): - aligner = Aligner() - # set a to 32 for dissimilarity - aligner.readAllBlastAlignments(blastp_output_file) - aligner.computeR(**kwargs) - return aligner.Ri.get(1, 0) # NOTE: returns 0 when not present diff --git a/input/netmhcIIpan/__init__.py b/input/netmhcIIpan/__init__.py deleted file mode 100755 index e69de29b..00000000 diff --git a/input/netmhcIIpan/netmhcIIpan_prediction.py b/input/netmhcIIpan/netmhcIIpan_prediction.py deleted file mode 100755 index eebe0f3c..00000000 --- a/input/netmhcIIpan/netmhcIIpan_prediction.py +++ /dev/null @@ -1,276 +0,0 @@ -#!/usr/bin/env python - -import tempfile - -from logzero import logger - -from input.helpers import data_import, properties_manager, intermediate_files - - -class NetMhcIIPanBestPrediction: - - def __init__(self, runner, configuration): - """ - :type runner: input.helpers.runner.Runner - :type configuration: input.references.DependenciesConfiguration - """ - self.runner = runner - self.configuration = configuration - self.mhcII_score = "NA" - self.epitopeII = "NA" - self.alleleII = "NA" - self.affinityII = "NA" - self.affinity_epitopeII = "NA" - self.affinity_alleleII = "NA" - - def mhc_allele_in_netmhcpan_available(self, allele, set_available_mhc): - '''checks if mhc prediction is possible for given hla allele - ''' - return allele in set_available_mhc - - def generate_mhcII_alelles_combination_list(self, hla_alleles, set_available_mhc): - ''' given list of HLA II alleles, returns list of HLA-DRB1 (2x), all possible HLA-DPA1/HLA-DPB1 (4x) and HLA-DQA1/HLA-DPQ1 (4x) - ''' - allels_for_prediction = [] - dqa_alleles = [] - dpa_alleles = [] - dqb_alleles = [] - dpb_alleles = [] - for allele in hla_alleles: - if allele.startswith("HLA-DRB1"): - allele = allele.replace("HLA-", "").replace("*", "_").replace(":", "") - if self.mhc_allele_in_netmhcpan_available(allele, set_available_mhc): - allels_for_prediction.append(allele) - else: - allele = allele.replace("*", "").replace(":", "") - if allele.startswith("HLA-DPA"): - dpa_alleles.append(allele) - elif allele.startswith("HLA-DPB"): - dpb_alleles.append(allele) - elif allele.startswith("HLA-DQA"): - dqa_alleles.append(allele) - elif allele.startswith("HLA-DQB"): - dqb_alleles.append(allele) - dp_alleles = ["-".join([x, y.replace("HLA-", "")]) for x in dpa_alleles for y in dpb_alleles] - dq_alleles = ["-".join([x, y.replace("HLA-", "")]) for x in dqa_alleles for y in dqb_alleles] - dp_dq_alleles = dp_alleles + dq_alleles - for allele in dp_dq_alleles: - if self.mhc_allele_in_netmhcpan_available(allele, set_available_mhc): - allels_for_prediction.append(allele) - return allels_for_prediction - - def mhcII_prediction(self, hla_alleles, set_available_mhc, tmpfasta, tmppred): - ''' Performs netmhcIIpan prediction for desired hla alleles and writes result to temporary file. - ''' - allels_for_prediction = self.generate_mhcII_alelles_combination_list(hla_alleles, set_available_mhc) - hla_allele = ",".join(allels_for_prediction) - tmp_folder = tempfile.mkdtemp(prefix="tmp_netmhcIIpan_") - logger.debug(tmp_folder) - lines, _ = self.runner.run_command([ - self.configuration.net_mhc2_pan, - "-a", hla_allele, - "-f", tmpfasta, - "-tdir", tmp_folder, - "-dirty"]) - logger.debug(lines) - counter = 0 - with open(tmppred, "w") as f: - for line in lines.splitlines(): - line = line.rstrip().lstrip() - if line: - if line.startswith(("#", "-", "Number", "Temporary")): - continue - if counter == 0 and line.startswith("Seq"): - counter += 1 - line = line.split() - line = line[0:-1] if len(line) > 12 else line - f.write(";".join(line) + "\n") - continue - elif counter > 0 and line.startswith("Seq"): - continue - line = line.split() - line = line[0:-2] if len(line) > 11 else line - f.write(";".join(line) + "\n") - - def mut_position_xmer_seq(self, xmer_wt, xmer_mut): - """ - returns position of mutation in xmer sequence - """ - if len(xmer_wt) == len(xmer_mut): - p1 = -1 - for i, aa in enumerate(xmer_mut): - if aa != xmer_wt[i]: - p1 = i + 1 - else: - p1 = 0 - # in case sequences do not have same length - for a1, a2 in zip(xmer_wt, xmer_mut): - if a1 == a2: - p1 += 1 - return str(p1) - - def epitope_covers_mutation(self, position_mutation, position_epitope, length_epitope): - '''checks if predicted peptide (15mer) covers mutation - ''' - cover = False - if position_mutation != "-1": - start = int(position_epitope) - 1 - end = start + int(length_epitope) - 1 - if int(position_mutation) >= start and int(position_mutation) <= end: - cover = True - return cover - - def filter_binding_predictions(self, position_xmer_sequence, tmppred): - """ - filters prediction file for predicted epitopes that cover mutations - """ - header, data = data_import.import_dat_general(tmppred) - dat_fil = [] - logger.debug(header) - pos_epi = header.index("Seq") - epi = header.index("Peptide") - for ii, i in enumerate(data): - if self.epitope_covers_mutation(position_xmer_sequence, i[pos_epi], len(i[epi])): - dat_fil.append(data[ii]) - return header, dat_fil - - def minimal_binding_score(self, prediction_tuple, rank=True): - '''reports best predicted epitope (over all alleles). indicate by rank = true if rank score should be used. if rank = False, Aff(nM) is used - ''' - dat_head = prediction_tuple[0] - dat = prediction_tuple[1] - if rank: - mhc_sc = dat_head.index("%Rank") - else: - mhc_sc = dat_head.index("Affinity(nM)") - epi = dat_head.index("Peptide") - hla_allele = dat_head.index("Allele") - max_score = float(1000000000) - allele = "NA" - epitope = "NA" - row = [] - for ii, i in enumerate(dat): - mhc_score = float(i[mhc_sc]) - if mhc_score < max_score: - max_score = mhc_score - row = i - return dat_head, row - - def add_best_epitope_info(self, epitope_tuple, column_name): - '''returns desired information of prediction of best epitope from netmhcpan output; - e.g. "%Rank": MHC I score, "HLA": HLA allele, "Icore": best epitope - ''' - dat_head = epitope_tuple[0] - dat = epitope_tuple[1] - val = dat_head.index(column_name) - try: - return dat[val] - except IndexError: - return "NA" - - def Hamming_check_0_or_1(self, seq1, seq2): - '''returns number of mismatches between 2 sequences - ''' - errors = 0 - for i in range(len(seq1)): - if seq1[i] != seq2[i]: - errors += 1 - if errors >= 2: - return errors - return errors - - def filter_for_WT_epitope_same_allele(self, prediction_tuple, mut_seq, mut_allele): - '''returns wt epitope info for given mutated sequence. here best wt for same allele as mutated sequences - ''' - dat_head = prediction_tuple[0] - dat = prediction_tuple[1] - seq_col = dat_head.index("Peptide") - allele_col = dat_head.index("Allele") - wt_epi = "NA" - for ii, i in enumerate(dat): - wt_seq = i[seq_col] - wt_allele = i[allele_col] - if (len(wt_seq) == len(mut_seq)) and wt_allele == mut_allele: - numb_mismatch = self.Hamming_check_0_or_1(mut_seq, wt_seq) - if numb_mismatch == 1: - wt_epi = i - return (dat_head, wt_epi) - - def filter_for_WT_epitope(self, prediction_tuple, mut_seq): - '''returns wt epitope info for given mutated sequence. best wt that is allowed to bind to any allele of patient - ''' - dat_head = prediction_tuple[0] - dat = prediction_tuple[1] - seq_col = dat_head.index("Peptide") - allele_col = dat_head.index("Allele") - wt_epi = [] - for ii, i in enumerate(dat): - wt_seq = i[seq_col] - wt_allele = i[allele_col] - if (len(wt_seq) == len(mut_seq)): - numb_mismatch = self.Hamming_check_0_or_1(mut_seq, wt_seq) - if numb_mismatch == 1: - wt_epi.append(i) - dt = (dat_head, wt_epi) - min = self.minimal_binding_score(dt) - return (min) - - def main(self, props_dict, set_available_mhc, dict_patient_hla): - '''Wrapper for MHC binding prediction, extraction of best epitope and check if mutation is directed to TCR - ''' - tmp_prediction = intermediate_files.create_temp_file(prefix="netmhcpanpred_", suffix=".csv") - sequence = props_dict["X..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."] - tmp_fasta = intermediate_files.create_temp_fasta([sequence], prefix="tmp_singleseq_") - alleles = properties_manager.get_hla_allele(props_dict, dict_patient_hla) - self.mhcII_prediction(alleles, set_available_mhc, tmp_fasta, tmp_prediction) - sequence_reference = props_dict["X.WT._..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."] - position_xmer_sequence = self.mut_position_xmer_seq(xmer_wt=sequence_reference, xmer_mut=sequence) - preds = self.filter_binding_predictions(position_xmer_sequence, tmp_prediction) - best_epi = self.minimal_binding_score(preds) - best_epi_affinity = self.minimal_binding_score(preds, rank=False) - - self.mhcII_score = self.add_best_epitope_info(best_epi, "%Rank") - self.epitopeII = self.add_best_epitope_info(best_epi, "Peptide") - self.alleleII = self.add_best_epitope_info(best_epi, "Allele") - self.affinityII = self.add_best_epitope_info(best_epi_affinity, "Affinity(nM)") - self.affinity_epitopeII = self.add_best_epitope_info(best_epi_affinity, "Peptide") - self.affinity_alleleII = self.add_best_epitope_info(best_epi_affinity, "Allele") - - -# if __name__ == '__main__': -# -# from input import predict_all_epitopes, epitope -# -# # file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/MHC_prediction_netmhcpan4/testdat_ott.txt" -# # hla_file ="/projects/SUMMIT/WP1.2/Literature_Cohorts/data_analysis/cohorts/ott/icam_ott/20190730_alleles.csv" -# hla_file = "/projects/SUMMIT/WP1.2/dataset_annotation/Birmingham/20190821_alleles.csv" -# file = "/projects/SUMMIT/WP1.2/dataset_annotation/Birmingham/in_files/PtBI000048T_1PEB.transcript" -# # file = "/flash/projects/WP3/AnFranziska/AnFranziska/head_seqs.txt" -# # hla_file ="/flash/projects/WP3/AnFranziska/AnFranziska/alleles.csv" -# dat = data_import.import_dat_icam(file, False) -# if "+-13_AA_(SNV)_/_-15_AA_to_STOP_(INDEL)" in dat[0]: -# dat = data_import.change_col_names(dat) -# if "patient.id" not in dat[0]: -# try: -# patient = file.split("/")[-3] -# if "Pt" not in patient: -# patient = file.split("/")[-1].split(".")[0] -# except IndexError: -# patient = file.split("/")[-1].split(".")[0] -# dat[0].append("patient.id") -# for ii, i in enumerate(dat[1]): -# dat[1][ii].append(str(patient)) -# # available MHC alleles -# set_available_mhc = predict_all_epitopes.Bunchepitopes().load_available_hla_alleles() -# set_available_mhcII = predict_all_epitopes.Bunchepitopes().load_available_hla_alleles(mhc=MHC_II) -# # hla allele of patients -# patient_hlaI = predict_all_epitopes.Bunchepitopes().load_patient_hla_I_allels(hla_file) -# patient_hlaII = predict_all_epitopes.Bunchepitopes().load_patient_hla_II_allels(hla_file) -# -# for ii, i in enumerate(dat[1]): -# if ii < 10: -# dict_epi = epitope.Epitope() -# dict_epi.init_properties(dat[0], dat[1][ii]) -# prediction = NetmhcIIpanBestPrediction() -# prediction.main(dict_epi.properties, set_available_mhcII, patient_hlaII) -# attrs = vars(prediction) diff --git a/input/netmhcpan4/MHC_available.csv b/input/netmhcpan4/MHC_available.csv deleted file mode 100644 index 24a9c50e..00000000 --- a/input/netmhcpan4/MHC_available.csv +++ /dev/null @@ -1,4397 +0,0 @@ -# [-a line] HLA-A02:01 HLA allele -HLA-A0101 -HLA-A0102 -HLA-A0103 -HLA-A0104 -HLA-A0106 -HLA-A0107 -HLA-A0108 -HLA-A0109 -HLA-A0110 -HLA-A0111 -HLA-A0112 -HLA-A0113 -HLA-A0114 -HLA-A0115 -HLA-A0117 -HLA-A0118 -HLA-A0119 -HLA-A0120 -HLA-A0121 -HLA-A0122 -HLA-A0123 -HLA-A0124 -HLA-A0125 -HLA-A0126 -HLA-A01:01 -HLA-A01:02 -HLA-A01:03 -HLA-A01:06 -HLA-A01:07 -HLA-A01:08 -HLA-A01:09 -HLA-A01:10 -HLA-A01:12 -HLA-A01:13 -HLA-A01:14 -HLA-A01:17 -HLA-A01:19 -HLA-A01:20 -HLA-A01:21 -HLA-A01:23 -HLA-A01:24 -HLA-A01:25 -HLA-A01:26 -HLA-A01:28 -HLA-A01:29 -HLA-A01:30 -HLA-A01:32 -HLA-A01:33 -HLA-A01:35 -HLA-A01:36 -HLA-A01:37 -HLA-A01:38 -HLA-A01:39 -HLA-A01:40 -HLA-A01:41 -HLA-A01:42 -HLA-A01:43 -HLA-A01:44 -HLA-A01:45 -HLA-A01:46 -HLA-A01:47 -HLA-A01:48 -HLA-A01:49 -HLA-A01:50 -HLA-A01:51 -HLA-A01:54 -HLA-A01:55 -HLA-A01:58 -HLA-A01:59 -HLA-A01:60 -HLA-A01:61 -HLA-A01:62 -HLA-A01:63 -HLA-A01:64 -HLA-A01:65 -HLA-A01:66 -HLA-A0201 -HLA-A0202 -HLA-A0203 -HLA-A0204 -HLA-A0205 -HLA-A0206 -HLA-A0207 -HLA-A0208 -HLA-A0209 -HLA-A0210 -HLA-A0211 -HLA-A0212 -HLA-A0213 -HLA-A0214 -HLA-A0215 -HLA-A0216 -HLA-A0217 -HLA-A0218 -HLA-A0219 -HLA-A0220 -HLA-A0221 -HLA-A0222 -HLA-A0224 -HLA-A0225 -HLA-A0226 -HLA-A0227 -HLA-A0228 -HLA-A0229 -HLA-A0230 -HLA-A0231 -HLA-A0233 -HLA-A0234 -HLA-A0235 -HLA-A0236 -HLA-A0237 -HLA-A0238 -HLA-A0239 -HLA-A0240 -HLA-A0241 -HLA-A0242 -HLA-A0243 -HLA-A0244 -HLA-A0245 -HLA-A0246 -HLA-A0247 -HLA-A0248 -HLA-A0249 -HLA-A0250 -HLA-A0251 -HLA-A0252 -HLA-A0254 -HLA-A0255 -HLA-A0256 -HLA-A0257 -HLA-A0258 -HLA-A0259 -HLA-A0260 -HLA-A0261 -HLA-A0262 -HLA-A0263 -HLA-A0264 -HLA-A0265 -HLA-A0266 -HLA-A0267 -HLA-A0268 -HLA-A0269 -HLA-A0270 -HLA-A0271 -HLA-A0272 -HLA-A0273 -HLA-A0274 -HLA-A0275 -HLA-A0276 -HLA-A0277 -HLA-A0278 -HLA-A0279 -HLA-A0280 -HLA-A0281 -HLA-A0283 -HLA-A0284 -HLA-A0285 -HLA-A0286 -HLA-A0287 -HLA-A0289 -HLA-A0290 -HLA-A0291 -HLA-A0292 -HLA-A0293 -HLA-A0295 -HLA-A0296 -HLA-A0297 -HLA-A0299 -HLA-A02:01 -HLA-A02:02 -HLA-A02:03 -HLA-A02:04 -HLA-A02:05 -HLA-A02:06 -HLA-A02:07 -HLA-A02:08 -HLA-A02:09 -HLA-A02:10 -HLA-A02:101 -HLA-A02:102 -HLA-A02:103 -HLA-A02:104 -HLA-A02:105 -HLA-A02:106 -HLA-A02:107 -HLA-A02:108 -HLA-A02:109 -HLA-A02:11 -HLA-A02:110 -HLA-A02:111 -HLA-A02:112 -HLA-A02:114 -HLA-A02:115 -HLA-A02:116 -HLA-A02:117 -HLA-A02:118 -HLA-A02:119 -HLA-A02:12 -HLA-A02:120 -HLA-A02:121 -HLA-A02:122 -HLA-A02:123 -HLA-A02:124 -HLA-A02:126 -HLA-A02:127 -HLA-A02:128 -HLA-A02:129 -HLA-A02:13 -HLA-A02:130 -HLA-A02:131 -HLA-A02:132 -HLA-A02:133 -HLA-A02:134 -HLA-A02:135 -HLA-A02:136 -HLA-A02:137 -HLA-A02:138 -HLA-A02:139 -HLA-A02:14 -HLA-A02:140 -HLA-A02:141 -HLA-A02:142 -HLA-A02:143 -HLA-A02:144 -HLA-A02:145 -HLA-A02:146 -HLA-A02:147 -HLA-A02:148 -HLA-A02:149 -HLA-A02:150 -HLA-A02:151 -HLA-A02:152 -HLA-A02:153 -HLA-A02:154 -HLA-A02:155 -HLA-A02:156 -HLA-A02:157 -HLA-A02:158 -HLA-A02:159 -HLA-A02:16 -HLA-A02:160 -HLA-A02:161 -HLA-A02:162 -HLA-A02:163 -HLA-A02:164 -HLA-A02:165 -HLA-A02:166 -HLA-A02:167 -HLA-A02:168 -HLA-A02:169 -HLA-A02:17 -HLA-A02:170 -HLA-A02:171 -HLA-A02:172 -HLA-A02:173 -HLA-A02:174 -HLA-A02:175 -HLA-A02:176 -HLA-A02:177 -HLA-A02:178 -HLA-A02:179 -HLA-A02:18 -HLA-A02:180 -HLA-A02:181 -HLA-A02:182 -HLA-A02:183 -HLA-A02:184 -HLA-A02:185 -HLA-A02:186 -HLA-A02:187 -HLA-A02:188 -HLA-A02:189 -HLA-A02:19 -HLA-A02:190 -HLA-A02:191 -HLA-A02:192 -HLA-A02:193 -HLA-A02:194 -HLA-A02:195 -HLA-A02:196 -HLA-A02:197 -HLA-A02:198 -HLA-A02:199 -HLA-A02:20 -HLA-A02:200 -HLA-A02:201 -HLA-A02:202 -HLA-A02:203 -HLA-A02:204 -HLA-A02:205 -HLA-A02:206 -HLA-A02:207 -HLA-A02:208 -HLA-A02:209 -HLA-A02:21 -HLA-A02:210 -HLA-A02:211 -HLA-A02:212 -HLA-A02:213 -HLA-A02:214 -HLA-A02:215 -HLA-A02:216 -HLA-A02:217 -HLA-A02:218 -HLA-A02:219 -HLA-A02:22 -HLA-A02:220 -HLA-A02:221 -HLA-A02:224 -HLA-A02:228 -HLA-A02:229 -HLA-A02:230 -HLA-A02:231 -HLA-A02:232 -HLA-A02:233 -HLA-A02:234 -HLA-A02:235 -HLA-A02:236 -HLA-A02:237 -HLA-A02:238 -HLA-A02:239 -HLA-A02:24 -HLA-A02:240 -HLA-A02:241 -HLA-A02:242 -HLA-A02:243 -HLA-A02:244 -HLA-A02:245 -HLA-A02:246 -HLA-A02:247 -HLA-A02:248 -HLA-A02:249 -HLA-A02:25 -HLA-A02:251 -HLA-A02:252 -HLA-A02:253 -HLA-A02:254 -HLA-A02:255 -HLA-A02:256 -HLA-A02:257 -HLA-A02:258 -HLA-A02:259 -HLA-A02:26 -HLA-A02:260 -HLA-A02:261 -HLA-A02:262 -HLA-A02:263 -HLA-A02:264 -HLA-A02:265 -HLA-A02:266 -HLA-A02:27 -HLA-A02:28 -HLA-A02:29 -HLA-A02:30 -HLA-A02:31 -HLA-A02:33 -HLA-A02:34 -HLA-A02:35 -HLA-A02:36 -HLA-A02:37 -HLA-A02:38 -HLA-A02:39 -HLA-A02:40 -HLA-A02:41 -HLA-A02:42 -HLA-A02:44 -HLA-A02:45 -HLA-A02:46 -HLA-A02:47 -HLA-A02:48 -HLA-A02:49 -HLA-A02:50 -HLA-A02:51 -HLA-A02:52 -HLA-A02:54 -HLA-A02:55 -HLA-A02:56 -HLA-A02:57 -HLA-A02:58 -HLA-A02:59 -HLA-A02:60 -HLA-A02:61 -HLA-A02:62 -HLA-A02:63 -HLA-A02:64 -HLA-A02:65 -HLA-A02:66 -HLA-A02:67 -HLA-A02:68 -HLA-A02:69 -HLA-A02:70 -HLA-A02:71 -HLA-A02:72 -HLA-A02:73 -HLA-A02:74 -HLA-A02:75 -HLA-A02:76 -HLA-A02:77 -HLA-A02:78 -HLA-A02:79 -HLA-A02:80 -HLA-A02:81 -HLA-A02:84 -HLA-A02:85 -HLA-A02:86 -HLA-A02:87 -HLA-A02:89 -HLA-A02:90 -HLA-A02:91 -HLA-A02:92 -HLA-A02:93 -HLA-A02:95 -HLA-A02:96 -HLA-A02:97 -HLA-A02:99 -HLA-A0301 -HLA-A0302 -HLA-A0303 -HLA-A0304 -HLA-A0305 -HLA-A0306 -HLA-A0307 -HLA-A0308 -HLA-A0309 -HLA-A0310 -HLA-A0312 -HLA-A0313 -HLA-A0314 -HLA-A0315 -HLA-A0316 -HLA-A0317 -HLA-A0318 -HLA-A0319 -HLA-A0320 -HLA-A0321 -HLA-A0322 -HLA-A0323 -HLA-A0324 -HLA-A0325 -HLA-A0326 -HLA-A0327 -HLA-A0328 -HLA-A0329 -HLA-A0330 -HLA-A03:01 -HLA-A03:02 -HLA-A03:04 -HLA-A03:05 -HLA-A03:06 -HLA-A03:07 -HLA-A03:08 -HLA-A03:09 -HLA-A03:10 -HLA-A03:12 -HLA-A03:13 -HLA-A03:14 -HLA-A03:15 -HLA-A03:16 -HLA-A03:17 -HLA-A03:18 -HLA-A03:19 -HLA-A03:20 -HLA-A03:22 -HLA-A03:23 -HLA-A03:24 -HLA-A03:25 -HLA-A03:26 -HLA-A03:27 -HLA-A03:28 -HLA-A03:29 -HLA-A03:30 -HLA-A03:31 -HLA-A03:32 -HLA-A03:33 -HLA-A03:34 -HLA-A03:35 -HLA-A03:37 -HLA-A03:38 -HLA-A03:39 -HLA-A03:40 -HLA-A03:41 -HLA-A03:42 -HLA-A03:43 -HLA-A03:44 -HLA-A03:45 -HLA-A03:46 -HLA-A03:47 -HLA-A03:48 -HLA-A03:49 -HLA-A03:50 -HLA-A03:51 -HLA-A03:52 -HLA-A03:53 -HLA-A03:54 -HLA-A03:55 -HLA-A03:56 -HLA-A03:57 -HLA-A03:58 -HLA-A03:59 -HLA-A03:60 -HLA-A03:61 -HLA-A03:62 -HLA-A03:63 -HLA-A03:64 -HLA-A03:65 -HLA-A03:66 -HLA-A03:67 -HLA-A03:70 -HLA-A03:71 -HLA-A03:72 -HLA-A03:73 -HLA-A03:74 -HLA-A03:75 -HLA-A03:76 -HLA-A03:77 -HLA-A03:78 -HLA-A03:79 -HLA-A03:80 -HLA-A03:81 -HLA-A03:82 -HLA-A1101 -HLA-A1102 -HLA-A1103 -HLA-A1104 -HLA-A1105 -HLA-A1106 -HLA-A1107 -HLA-A1108 -HLA-A1109 -HLA-A1110 -HLA-A1111 -HLA-A1112 -HLA-A1113 -HLA-A1114 -HLA-A1115 -HLA-A1116 -HLA-A1117 -HLA-A1118 -HLA-A1119 -HLA-A1120 -HLA-A1121 -HLA-A1122 -HLA-A1123 -HLA-A1124 -HLA-A1125 -HLA-A1126 -HLA-A1127 -HLA-A1128 -HLA-A1129 -HLA-A1130 -HLA-A1131 -HLA-A1132 -HLA-A11:01 -HLA-A11:02 -HLA-A11:03 -HLA-A11:04 -HLA-A11:05 -HLA-A11:06 -HLA-A11:07 -HLA-A11:08 -HLA-A11:09 -HLA-A11:10 -HLA-A11:11 -HLA-A11:12 -HLA-A11:13 -HLA-A11:14 -HLA-A11:15 -HLA-A11:16 -HLA-A11:17 -HLA-A11:18 -HLA-A11:19 -HLA-A11:20 -HLA-A11:22 -HLA-A11:23 -HLA-A11:24 -HLA-A11:25 -HLA-A11:26 -HLA-A11:27 -HLA-A11:29 -HLA-A11:30 -HLA-A11:31 -HLA-A11:32 -HLA-A11:33 -HLA-A11:34 -HLA-A11:35 -HLA-A11:36 -HLA-A11:37 -HLA-A11:38 -HLA-A11:39 -HLA-A11:40 -HLA-A11:41 -HLA-A11:42 -HLA-A11:43 -HLA-A11:44 -HLA-A11:45 -HLA-A11:46 -HLA-A11:47 -HLA-A11:48 -HLA-A11:49 -HLA-A11:51 -HLA-A11:53 -HLA-A11:54 -HLA-A11:55 -HLA-A11:56 -HLA-A11:57 -HLA-A11:58 -HLA-A11:59 -HLA-A11:60 -HLA-A11:61 -HLA-A11:62 -HLA-A11:63 -HLA-A11:64 -HLA-A2301 -HLA-A2302 -HLA-A2303 -HLA-A2304 -HLA-A2305 -HLA-A2306 -HLA-A2307 -HLA-A2309 -HLA-A2310 -HLA-A2312 -HLA-A2313 -HLA-A2314 -HLA-A2315 -HLA-A2316 -HLA-A23:01 -HLA-A23:02 -HLA-A23:03 -HLA-A23:04 -HLA-A23:05 -HLA-A23:06 -HLA-A23:09 -HLA-A23:10 -HLA-A23:12 -HLA-A23:13 -HLA-A23:14 -HLA-A23:15 -HLA-A23:16 -HLA-A23:17 -HLA-A23:18 -HLA-A23:20 -HLA-A23:21 -HLA-A23:22 -HLA-A23:23 -HLA-A23:24 -HLA-A23:25 -HLA-A23:26 -HLA-A2402 -HLA-A2403 -HLA-A2404 -HLA-A2405 -HLA-A2406 -HLA-A2407 -HLA-A2408 -HLA-A2409 -HLA-A2410 -HLA-A2411 -HLA-A2413 -HLA-A2414 -HLA-A2415 -HLA-A2417 -HLA-A2418 -HLA-A2419 -HLA-A2420 -HLA-A2421 -HLA-A2422 -HLA-A2423 -HLA-A2424 -HLA-A2425 -HLA-A2426 -HLA-A2427 -HLA-A2428 -HLA-A2429 -HLA-A2430 -HLA-A2431 -HLA-A2432 -HLA-A2433 -HLA-A2434 -HLA-A2435 -HLA-A2437 -HLA-A2438 -HLA-A2439 -HLA-A2440 -HLA-A2441 -HLA-A2442 -HLA-A2443 -HLA-A2444 -HLA-A2446 -HLA-A2447 -HLA-A2449 -HLA-A2450 -HLA-A2451 -HLA-A2452 -HLA-A2453 -HLA-A2454 -HLA-A2455 -HLA-A2456 -HLA-A2457 -HLA-A2458 -HLA-A2459 -HLA-A2461 -HLA-A2462 -HLA-A2463 -HLA-A2464 -HLA-A2465 -HLA-A2466 -HLA-A2467 -HLA-A2468 -HLA-A2469 -HLA-A2470 -HLA-A2471 -HLA-A2472 -HLA-A2473 -HLA-A2474 -HLA-A2475 -HLA-A2476 -HLA-A2477 -HLA-A2478 -HLA-A2479 -HLA-A24:02 -HLA-A24:03 -HLA-A24:04 -HLA-A24:05 -HLA-A24:06 -HLA-A24:07 -HLA-A24:08 -HLA-A24:10 -HLA-A24:100 -HLA-A24:101 -HLA-A24:102 -HLA-A24:103 -HLA-A24:104 -HLA-A24:105 -HLA-A24:106 -HLA-A24:107 -HLA-A24:108 -HLA-A24:109 -HLA-A24:110 -HLA-A24:111 -HLA-A24:112 -HLA-A24:113 -HLA-A24:114 -HLA-A24:115 -HLA-A24:116 -HLA-A24:117 -HLA-A24:118 -HLA-A24:119 -HLA-A24:120 -HLA-A24:121 -HLA-A24:122 -HLA-A24:123 -HLA-A24:124 -HLA-A24:125 -HLA-A24:126 -HLA-A24:127 -HLA-A24:128 -HLA-A24:129 -HLA-A24:13 -HLA-A24:130 -HLA-A24:131 -HLA-A24:133 -HLA-A24:134 -HLA-A24:135 -HLA-A24:136 -HLA-A24:137 -HLA-A24:138 -HLA-A24:139 -HLA-A24:14 -HLA-A24:140 -HLA-A24:141 -HLA-A24:142 -HLA-A24:143 -HLA-A24:144 -HLA-A24:15 -HLA-A24:17 -HLA-A24:18 -HLA-A24:19 -HLA-A24:20 -HLA-A24:21 -HLA-A24:22 -HLA-A24:23 -HLA-A24:24 -HLA-A24:25 -HLA-A24:26 -HLA-A24:27 -HLA-A24:28 -HLA-A24:29 -HLA-A24:30 -HLA-A24:31 -HLA-A24:32 -HLA-A24:33 -HLA-A24:34 -HLA-A24:35 -HLA-A24:37 -HLA-A24:38 -HLA-A24:39 -HLA-A24:41 -HLA-A24:42 -HLA-A24:43 -HLA-A24:44 -HLA-A24:46 -HLA-A24:47 -HLA-A24:49 -HLA-A24:50 -HLA-A24:51 -HLA-A24:52 -HLA-A24:53 -HLA-A24:54 -HLA-A24:55 -HLA-A24:56 -HLA-A24:57 -HLA-A24:58 -HLA-A24:59 -HLA-A24:61 -HLA-A24:62 -HLA-A24:63 -HLA-A24:64 -HLA-A24:66 -HLA-A24:67 -HLA-A24:68 -HLA-A24:69 -HLA-A24:70 -HLA-A24:71 -HLA-A24:72 -HLA-A24:73 -HLA-A24:74 -HLA-A24:75 -HLA-A24:76 -HLA-A24:77 -HLA-A24:78 -HLA-A24:79 -HLA-A24:80 -HLA-A24:81 -HLA-A24:82 -HLA-A24:85 -HLA-A24:87 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a/input/netmhcpan4/abstract_netmhcpan_predictor.py b/input/netmhcpan4/abstract_netmhcpan_predictor.py new file mode 100755 index 00000000..4ad613bc --- /dev/null +++ b/input/netmhcpan4/abstract_netmhcpan_predictor.py @@ -0,0 +1,17 @@ + + + +class AbstractNetMhcPanPredictor(object): + + @staticmethod + def add_best_epitope_info(epitope_tuple, column_name): + '''returns desired information of prediction of best epitope from netmhcpan output; + e.g. "%Rank": MHC I score, "HLA": HLA allele, "Icore": best epitope + ''' + dat_head = epitope_tuple[0] + dat = epitope_tuple[1] + val = dat_head.index(column_name) + try: + return dat[val] + except IndexError: + return "NA" diff --git a/input/netmhcpan4/all_seqs.fasta b/input/netmhcpan4/all_seqs.fasta deleted file mode 100644 index d83d6bc9..00000000 --- a/input/netmhcpan4/all_seqs.fasta +++ /dev/null @@ -1,16 +0,0 @@ ->0 -AMNVSHEVNQLFQLYNFELSKDMRPFF ->1 -RKPAESETGLSLENSDCYEKEAKGVES ->2 -PGFRTSDRHDVAKKACMESDWCRDSKT ->3 -KNPPLFAQKLQRETAHPTDVSISKTAL ->4 -ALASRSHQDAKRETAHPTDVSISKTAL ->5 -GLGTPSEAIEIRETAHPTDVSISKTAL ->6 -YRGSWGTVCDDSWNTNDANVVCRQLGC ->7 -HPSAEGAPEKRQDLSTHAERNGSANRN diff --git a/input/netmhcIIpan/combine_netmhcIIpan_pred_multiple_binders.py b/input/netmhcpan4/combine_netmhcIIpan_pred_multiple_binders.py similarity index 91% rename from input/netmhcIIpan/combine_netmhcIIpan_pred_multiple_binders.py rename to input/netmhcpan4/combine_netmhcIIpan_pred_multiple_binders.py index acd5fccb..359f40b6 100755 --- a/input/netmhcIIpan/combine_netmhcIIpan_pred_multiple_binders.py +++ b/input/netmhcpan4/combine_netmhcIIpan_pred_multiple_binders.py @@ -2,9 +2,9 @@ from logzero import logger -import input.netmhcIIpan.netmhcIIpan_prediction as netmhcIIpan_prediction +import input.netmhcpan4.netmhcIIpan_prediction as netmhcIIpan_prediction from input import MHC_II -from input.helpers import properties_manager, intermediate_files +from input.helpers import intermediate_files from input.netmhcpan4 import multiple_binders @@ -53,7 +53,7 @@ def MHCII_MB_score_best_per_allele(self, tuple_best_per_allele): 2 copies of DRA - DRB1 --> consider this gene 2x when averaging mhcii binding scores ''' number_alleles = len(tuple_best_per_allele) - multbind = multiple_binders.MultipleBinding(runner=self.runner, configuration=self.configuration) + multbind = multiple_binders.MultipleBinding() tuple_best_per_allele_new = list(tuple_best_per_allele) logger.debug(tuple_best_per_allele) logger.debug(len(tuple_best_per_allele)) @@ -65,7 +65,7 @@ def MHCII_MB_score_best_per_allele(self, tuple_best_per_allele): if len(tuple_best_per_allele_new) == 12: # 12 genes gene copies should be included into PHBR_II best_scores_allele = multbind.scores_to_list(tuple_best_per_allele_new) - return multbind.wrapper_mean_calculation(best_scores_allele) + return multbind.get_means(best_scores_allele) else: return ["NA", "NA", "NA"] @@ -76,8 +76,8 @@ def main(self, sequence, sequence_reference, alleles, set_available_mhc): logger.info("MUT seq MHC II: {}".format(sequence)) tmp_prediction = intermediate_files.create_temp_file(prefix="netmhcpanpred_", suffix=".csv") logger.debug(tmp_prediction) - np = netmhcIIpan_prediction.NetMhcIIPanBestPrediction(runner=self.runner, configuration=self.configuration) - mb = multiple_binders.MultipleBinding(runner=self.runner, configuration=self.configuration) + np = netmhcIIpan_prediction.NetMhcIIPanPredictor(runner=self.runner, configuration=self.configuration) + mb = multiple_binders.MultipleBinding() tmp_fasta = intermediate_files.create_temp_fasta([sequence], prefix="tmp_singleseq_") alleles_formated = np.generate_mhcII_alelles_combination_list(alleles, set_available_mhc) logger.debug(alleles_formated) @@ -95,8 +95,8 @@ def main(self, sequence, sequence_reference, alleles, set_available_mhc): all = mb.scores_to_list(list_tups) all_affinities = mb.affinities_to_list(list_tups) top10 = mb.scores_to_list(top10) - self.MHCII_score_top10 = mb.wrapper_mean_calculation(top10) - self.MHCII_score_all_epitopes = mb.wrapper_mean_calculation(all) + self.MHCII_score_top10 = mb.get_means(top10) + self.MHCII_score_all_epitopes = mb.get_means(all) self.MHCII_score_best_per_alelle = self.MHCII_MB_score_best_per_allele(best_per_alelle) self.MHCII_number_strong_binders = mb.determine_number_of_binders(all, 2) self.MHCII_number_weak_binders = mb.determine_number_of_binders(all, 10) @@ -117,8 +117,8 @@ def main(self, sequence, sequence_reference, alleles, set_available_mhc): ### PREDICTION FOR WT SEQUENCE tmp_prediction = intermediate_files.create_temp_file(prefix="netmhcpanpred_", suffix=".csv") logger.debug(tmp_prediction) - np = netmhcIIpan_prediction.NetMhcIIPanBestPrediction(runner=self.runner, configuration=self.configuration) - mb = multiple_binders.MultipleBinding(runner=self.runner, configuration=self.configuration) + np = netmhcIIpan_prediction.NetMhcIIPanPredictor(runner=self.runner, configuration=self.configuration) + mb = multiple_binders.MultipleBinding() tmp_fasta = intermediate_files.create_temp_fasta([sequence_reference], prefix="tmp_singleseq_") np.mhcII_prediction(alleles, set_available_mhc, tmp_fasta, tmp_prediction) try: @@ -134,8 +134,8 @@ def main(self, sequence, sequence_reference, alleles, set_available_mhc): all = mb.scores_to_list(list_tups) all_affinities = mb.affinities_to_list(list_tups) top10 = mb.scores_to_list(top10) - self.MHCII_score_top10_WT = mb.wrapper_mean_calculation(top10) - self.MHCII_score_all_epitopes_WT = mb.wrapper_mean_calculation(all) + self.MHCII_score_top10_WT = mb.get_means(top10) + self.MHCII_score_all_epitopes_WT = mb.get_means(all) self.MHCII_score_best_per_alelle_WT = self.MHCII_MB_score_best_per_allele(best_per_alelle) self.MHCII_number_strong_binders_WT = mb.determine_number_of_binders(all, 1) self.MHCII_number_weak_binders_WT = mb.determine_number_of_binders(all, 2) diff --git a/input/netmhcpan4/combine_netmhcpan_pred_multiple_binders.py b/input/netmhcpan4/combine_netmhcpan_pred_multiple_binders.py index 465f66e7..e9b3ff01 100755 --- a/input/netmhcpan4/combine_netmhcpan_pred_multiple_binders.py +++ b/input/netmhcpan4/combine_netmhcpan_pred_multiple_binders.py @@ -69,10 +69,10 @@ def MHC_MB_score_best_per_allele(self, tuple_best_per_allele): 2 copies of DRA - DRB1 --> consider this gene 2x when averaging mhcii binding scores ''' number_alleles = len(tuple_best_per_allele) - multbind = multiple_binders.MultipleBinding(runner=self.runner, configuration=self.configuration) + multbind = multiple_binders.MultipleBinding() tuple_best_per_allele_new = list(tuple_best_per_allele) if len(tuple_best_per_allele_new) == 6: - return multbind.wrapper_mean_calculation(tuple_best_per_allele_new) + return multbind.get_means(tuple_best_per_allele_new) else: return ["NA", "NA", "NA"] @@ -84,8 +84,8 @@ def main(self, xmer_wt, xmer_mut, alleles, set_available_mhc): logger.info("MUT seq: {}".format(xmer_mut)) tmp_prediction = intermediate_files.create_temp_file(prefix="netmhcpanpred_", suffix=".csv") logger.debug(tmp_prediction) - np = netmhcpan_prediction.NetMhcPanBestPrediction(runner=self.runner, configuration=self.configuration) - mb = multiple_binders.MultipleBinding(runner=self.runner, configuration=self.configuration) + np = netmhcpan_prediction.NetMhcPanPredictor(runner=self.runner, configuration=self.configuration) + mb = multiple_binders.MultipleBinding() tmp_fasta = intermediate_files.create_temp_fasta(sequences=[xmer_mut], prefix="tmp_singleseq_") # print alleles np.mhc_prediction(alleles, set_available_mhc, tmp_fasta, tmp_prediction) @@ -106,9 +106,9 @@ def main(self, xmer_wt, xmer_mut, alleles, set_available_mhc): all = mb.scores_to_list(list_tups) all_affinities = mb.affinities_to_list(list_tups) top10 = mb.scores_to_list(top10) - self.MHC_score_top10 = mb.wrapper_mean_calculation(top10) + self.MHC_score_top10 = mb.get_means(top10) best_per_alelle = mb.scores_to_list(best_per_alelle) - self.MHC_score_all_epitopes = mb.wrapper_mean_calculation(all) + self.MHC_score_all_epitopes = mb.get_means(all) self.MHC_score_best_per_alelle = self.MHC_MB_score_best_per_allele(best_per_alelle) self.MHC_number_strong_binders = mb.determine_number_of_binders(all, 1) self.MHC_number_weak_binders = mb.determine_number_of_binders(all, 2) @@ -140,8 +140,8 @@ def main(self, xmer_wt, xmer_mut, alleles, set_available_mhc): ### PREDICTION FOR WT SEQUENCE tmp_prediction = intermediate_files.create_temp_file(prefix="netmhcpanpred_", suffix=".csv") logger.debug(tmp_prediction) - np = netmhcpan_prediction.NetMhcPanBestPrediction(runner=self.runner, configuration=self.configuration) - mb = multiple_binders.MultipleBinding(runner=self.runner, configuration=self.configuration) + np = netmhcpan_prediction.NetMhcPanPredictor(runner=self.runner, configuration=self.configuration) + mb = multiple_binders.MultipleBinding() tmp_fasta = intermediate_files.create_temp_fasta(sequences=[xmer_wt], prefix="tmp_singleseq_") np.mhc_prediction(alleles, set_available_mhc, tmp_fasta, tmp_prediction) @@ -157,10 +157,10 @@ def main(self, xmer_wt, xmer_mut, alleles, set_available_mhc): all = mb.scores_to_list(list_tups) all_affinities = mb.affinities_to_list(list_tups) top10 = mb.scores_to_list(top10) - self.MHC_score_top10_WT = mb.wrapper_mean_calculation(top10) + self.MHC_score_top10_WT = mb.get_means(top10) best_per_alelle = mb.scores_to_list(best_per_alelle) - self.MHC_score_all_epitopes_WT = mb.wrapper_mean_calculation(all) - self.MHC_score_best_per_alelle_WT = mb.wrapper_mean_calculation(best_per_alelle) + self.MHC_score_all_epitopes_WT = mb.get_means(all) + self.MHC_score_best_per_alelle_WT = mb.get_means(best_per_alelle) self.MHC_number_strong_binders_WT = mb.determine_number_of_binders(all, 1) self.MHC_number_weak_binders_WT = mb.determine_number_of_binders(all, 2) # best prediction diff --git a/input/netmhcpan4/multiple_binders.py b/input/netmhcpan4/multiple_binders.py index c695afe2..a92ae982 100755 --- a/input/netmhcpan4/multiple_binders.py +++ b/input/netmhcpan4/multiple_binders.py @@ -1,90 +1,31 @@ -#!/usr/bin/env python - -import math +import numpy as np +import scipy.stats as stats from logzero import logger -from input.netmhcIIpan.netmhcIIpan_prediction import NetMhcIIPanBestPrediction from input import MHC_I, MHC_II -from input.netmhcpan4.netmhcpan_prediction import NetMhcPanBestPrediction class MultipleBinding: - def __init__(self, runner, configuration): - """ - :type runner: input.helpers.runner.Runner - :type configuration: input.references.DependenciesConfiguration - """ - self.runner = runner - self.configuration = configuration - self.mean_type = ["arithmetic", "harmonic", "geometric"] - self.score_all_epitopes = [] - self.score_top10 = [] - self.score_best_per_alelle = [] - self.number_strong_binders = "" - self.number_weak_binders = "" - self.epitope_seqs = "" - self.epitope_scores = "" - self.epitope_alleles = "" - self.epitope_affinities = "" - self.generator_rate = "" - - def calc_arimetric_mean(self, list_numbers): - '''Calculates the arithmetic mean from a list of numbers - ''' - sm = 0 - for num in list_numbers: - sm = sm + float(num) - try: - return str(float(sm / len(list_numbers))) - except ZeroDivisionError: - return "NA" - - def calc_harmonic_mean(self, list_numbers): - '''Calculates the harmonic mean from a list of numbers - ''' - nums = [float(num) ** -1 for num in list_numbers] - sm = 0 - for num in nums: - sm = sm + num - try: - return str(float(len(nums) / sm)) - except ZeroDivisionError: - return "NA" - - def calc_geometric_mean_inefficient(self, list_numbers): - '''Calculates the geometric mean from a list of numbers - ''' - pr = 1 - for num in list_numbers: - pr = float(num) * pr - return str(pr ** (len(list_numbers) ** -1)) - - def calc_geometric_mean(self, list_numbers): - '''Calculates the geometric mean from a list of numbers; avoids product --> suitable for larger list of number - ''' - sm = 0 - for num in list_numbers: - num_log = math.log(float(num)) - sm = float(num_log) + sm - try: - num_log_mean = sm / len(list_numbers) - num_log_mean_exp = math.exp(num_log_mean) - return str(num_log_mean_exp) - except ZeroDivisionError: - return "NA" - - def wrapper_mean_calculation(self, list_numbers): - '''returns list of arithmetic, harmonic and geometric mean from a list of numbers - ''' - return [self.calc_arimetric_mean(list_numbers), self.calc_harmonic_mean(list_numbers), - self.calc_geometric_mean(list_numbers)] + def get_means(self, list_numbers): + """ + returns list of arithmetic, harmonic and geometric mean from a list of numbers + """ + results = ["NA", "NA", "NA"] + if list_numbers is not None and len(list_numbers) > 0: + results = [ + np.mean(list_numbers), + stats.hmean(list_numbers), + stats.gmean(list_numbers) + ] + return results def generate_epi_tuple(self, prediction_out, mhc=MHC_I): - '''Takes netmhcpan4 output or netmhcpanII output as input (parsed with Netmhc[II]panBestPrediction().filter_binding_predictions) and + """ + Takes netmhcpan4 output or netmhcpanII output as input (parsed with Netmhc[II]panBestPrediction().filter_binding_predictions) and returns tuple of mhc binding rank scores, epitope and HLA allele for all predicted epitopes as list - ''' + """ pred_data = prediction_out[1] list_of_tuples = [] for ii, i in enumerate(pred_data): @@ -97,21 +38,22 @@ def generate_epi_tuple(self, prediction_out, mhc=MHC_I): return list_of_tuples def extract_top10_epis(self, tuple_epis): - '''this function sorts the predicted epitopes based on the mhc rank score and returns the top10 with lowest mhc binding score - ''' + """ + this function sorts the predicted epitopes based on the mhc rank score and returns the top10 with lowest mhc binding score + """ tuple_epis.sort(key=lambda x: float(x[0])) return tuple_epis[0:9] def check_for_homozygosity(self, patient_alleles): - """ returns alleles that occur more than one time in list of patient alleles and hence are homozygous alleles. Otherwise retunrs empty list """ - homozygos_alleles = [] - [homozygos_alleles.append(allele) for allele in patient_alleles if patient_alleles.count(allele) > 1] - return homozygos_alleles + returns alleles that occur more than one time in list of patient alleles and hence are homozygous alleles. Otherwise retunrs empty list + """ + return [allele for allele in patient_alleles if patient_alleles.count(allele) > 1] def extract_best_epi_per_alelle(self, tuple_epis, alleles): - '''this function returns the predicted epitope with the lowest binding score for each patient allele, considering homozyogosity - ''' + """ + this function returns the predicted epitope with the lowest binding score for each patient allele, considering homozyogosity + """ homo_alleles = self.check_for_homozygosity(alleles) logger.info(homo_alleles) dict_allels = {} @@ -142,71 +84,23 @@ def extract_best_epi_per_alelle(self, tuple_epis, alleles): return best_epis_per_allele def scores_to_list(self, tuple_epis): - '''Takes list of epitope tuple as input and returns a list of mhc rank scores of these tuples - ''' - list_score = [] - for epi in tuple_epis: - list_score.append(epi[0]) - return list_score + """ + Takes list of epitope tuple as input and returns a list of mhc rank scores of these tuples + """ + return [epi[0] for epi in tuple_epis] def affinities_to_list(self, tuple_epis): - '''Takes list of epitope tuple as input and returns a list of mhc rank scores of these tuples - ''' - list_score = [] - for epi in tuple_epis: - list_score.append(epi[1]) - return list_score + """ + Takes list of epitope tuple as input and returns a list of mhc rank scores of these tuples + """ + return [epi[1] for epi in tuple_epis] def determine_number_of_binders(self, list_scores, threshold=2): - '''Determines the number of HLA binders per mutation based on a threshold. Default is set to 2, which is threshold for weak binding using netmhcpan4. - ''' + """ + Determines the number of HLA binders per mutation based on a threshold. Default is set to 2, which is threshold for weak binding using netmhcpan4. + """ number_binders = 0 for score in list_scores: if float(score) < threshold: number_binders += 1 return str(number_binders) - - -# if __name__ == '__main__': -# -# from input import predict_all_epitopes, epitope -# from input.helpers import data_import -# -# file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/INPuT/nonprogramm_files/test_SD.csv" -# # file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/20170713_IS_IM_data.complete.update_Dv10.csv.annotation.csv_v2.csv" -# # file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/INPuT/nonprogramm_files/test_fulldat.txt" -# hla_file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/indels/RB_0004_labHLA_V2.csv" -# dat = data_import.import_dat_icam(file, False) -# # available MHC alleles -# set_available_mhc = predict_all_epitopes.Bunchepitopes().load_available_hla_alleles() -# -# # hla allele of patients -# patient_hlaI = predict_all_epitopes.Bunchepitopes().load_patient_hla_I_allels(hla_file) -# patient_hlaII = predict_all_epitopes.Bunchepitopes().load_patient_hla_II_allels(hla_file) -# -# Allepit = {} -# for ii, i in enumerate(dat[1]): -# # print ii -# dict_epi = epitope.Epitope() -# dict_epi.init_properties(dat[0], dat[1][ii]) -# x = MultipleBinding() -# x.main(dict_epi.properties, patient_hlaI, set_available_mhc) -# for sc, mn in zip(x.score_all_epitopes, x.mean_type): -# dict_epi.add_features(sc, "MB_score_all_epitopes_" + mn) -# for sc, mn in zip(x.score_top10, x.mean_type): -# dict_epi.add_features(sc, "MB_score_top10_" + mn) -# for sc, mn in zip(x.score_best_per_alelle, x.mean_type): -# dict_epi.add_features(sc, "MB_score_best_per_alelle_" + mn) -# dict_epi.add_features(x.epitope_scores, "MB_epitope_scores") -# dict_epi.add_features(x.epitope_seqs, "MB_epitope_sequences") -# dict_epi.add_features(x.epitope_alleles, "MB_alleles") -# dict_epi.add_features(x.number_strong_binders, "MB_number_of_strong_binders") -# dict_epi.add_features(x.number_weak_binders, "MB_number_of_weak_binders") -# z = dict_epi.properties -# for key in z: -# if key not in Allepit: -# Allepit[key] = [z[key]] -# else: -# Allepit[key].append(z[key]) -# # commented as this is test code which has to be placed elsewhere and it is the only bit using this write method -# # predict_all_epitopes.Bunchepitopes().write_to_file(Allepit) diff --git a/input/netmhcpan4/netmhcIIpan_prediction.py b/input/netmhcpan4/netmhcIIpan_prediction.py new file mode 100755 index 00000000..97711ea0 --- /dev/null +++ b/input/netmhcpan4/netmhcIIpan_prediction.py @@ -0,0 +1,147 @@ +#!/usr/bin/env python + +import tempfile + +from logzero import logger + +from input.helpers import data_import +from input.helpers.epitope_helper import EpitopeHelper +from input.netmhcpan4.abstract_netmhcpan_predictor import AbstractNetMhcPanPredictor + + +class NetMhcIIPanPredictor(EpitopeHelper, AbstractNetMhcPanPredictor): + + def __init__(self, runner, configuration): + """ + :type runner: input.helpers.runner.Runner + :type configuration: input.references.DependenciesConfiguration + """ + self.runner = runner + self.configuration = configuration + self.mhcII_score = "NA" + self.epitopeII = "NA" + self.alleleII = "NA" + self.affinityII = "NA" + self.affinity_epitopeII = "NA" + self.affinity_alleleII = "NA" + + def generate_mhcII_alelles_combination_list(self, hla_alleles, set_available_mhc): + ''' given list of HLA II alleles, returns list of HLA-DRB1 (2x), all possible HLA-DPA1/HLA-DPB1 (4x) and HLA-DQA1/HLA-DPQ1 (4x) + ''' + allels_for_prediction = [] + dqa_alleles = [] + dpa_alleles = [] + dqb_alleles = [] + dpb_alleles = [] + for allele in hla_alleles: + if allele.startswith("HLA-DRB1"): + allele = allele.replace("HLA-", "").replace("*", "_").replace(":", "") + if allele in set_available_mhc: + allels_for_prediction.append(allele) + else: + allele = allele.replace("*", "").replace(":", "") + if allele.startswith("HLA-DPA"): + dpa_alleles.append(allele) + elif allele.startswith("HLA-DPB"): + dpb_alleles.append(allele) + elif allele.startswith("HLA-DQA"): + dqa_alleles.append(allele) + elif allele.startswith("HLA-DQB"): + dqb_alleles.append(allele) + dp_alleles = ["-".join([x, y.replace("HLA-", "")]) for x in dpa_alleles for y in dpb_alleles] + dq_alleles = ["-".join([x, y.replace("HLA-", "")]) for x in dqa_alleles for y in dqb_alleles] + dp_dq_alleles = dp_alleles + dq_alleles + for allele in dp_dq_alleles: + if allele in set_available_mhc: + allels_for_prediction.append(allele) + return allels_for_prediction + + def mhcII_prediction(self, hla_alleles, set_available_mhc, tmpfasta, tmppred): + ''' Performs netmhcIIpan prediction for desired hla alleles and writes result to temporary file. + ''' + allels_for_prediction = self.generate_mhcII_alelles_combination_list(hla_alleles, set_available_mhc) + hla_allele = ",".join(allels_for_prediction) + tmp_folder = tempfile.mkdtemp(prefix="tmp_netmhcIIpan_") + logger.debug(tmp_folder) + lines, _ = self.runner.run_command([ + self.configuration.net_mhc2_pan, + "-a", hla_allele, + "-f", tmpfasta, + "-tdir", tmp_folder, + "-dirty"]) + logger.debug(lines) + counter = 0 + # TODO: avoid writing a file here, just return some data structure no need to go to the file system + with open(tmppred, "w") as f: + for line in lines.splitlines(): + line = line.rstrip().lstrip() + if line: + if line.startswith(("#", "-", "Number", "Temporary")): + continue + if counter == 0 and line.startswith("Seq"): + counter += 1 + line = line.split() + line = line[0:-1] if len(line) > 12 else line + f.write(";".join(line) + "\n") + continue + elif counter > 0 and line.startswith("Seq"): + continue + line = line.split() + line = line[0:-2] if len(line) > 11 else line + f.write(";".join(line) + "\n") + + def filter_binding_predictions(self, position_xmer_sequence, tmppred): + """ + filters prediction file for predicted epitopes that cover mutations + """ + header, data = data_import.import_dat_general(tmppred) + dat_fil = [] + logger.debug(header) + pos_epi = header.index("Seq") + epi = header.index("Peptide") + for ii, i in enumerate(data): + if self.epitope_covers_mutation(position_xmer_sequence, i[pos_epi], len(i[epi])): + dat_fil.append(data[ii]) + return header, dat_fil + + def minimal_binding_score(self, prediction_tuple, rank=True): + '''reports best predicted epitope (over all alleles). indicate by rank = true if rank score should be used. if rank = False, Aff(nM) is used + ''' + # TODO: generalize this method with netmhcpan_prediction.py + change input + dat_head = prediction_tuple[0] + dat = prediction_tuple[1] + if rank: + mhc_sc = dat_head.index("%Rank") + else: + mhc_sc = dat_head.index("Affinity(nM)") + epi = dat_head.index("Peptide") + hla_allele = dat_head.index("Allele") + max_score = float(1000000000) + allele = "NA" + epitope = "NA" + row = [] + for ii, i in enumerate(dat): + mhc_score = float(i[mhc_sc]) + if mhc_score < max_score: + max_score = mhc_score + row = i + return dat_head, row + + def filter_for_WT_epitope(self, prediction_tuple, mut_seq): + '''returns wt epitope info for given mutated sequence. best wt that is allowed to bind to any allele of patient + ''' + dat_head = prediction_tuple[0] + dat = prediction_tuple[1] + seq_col = dat_head.index("Peptide") + allele_col = dat_head.index("Allele") + wt_epi = [] + for ii, i in enumerate(dat): + wt_seq = i[seq_col] + wt_allele = i[allele_col] + if (len(wt_seq) == len(mut_seq)): + numb_mismatch = self.hamming_check_0_or_1(mut_seq, wt_seq) + if numb_mismatch == 1: + wt_epi.append(i) + dt = (dat_head, wt_epi) + min = self.minimal_binding_score(dt) + return (min) \ No newline at end of file diff --git a/input/netmhcpan4/netmhcpan_prediction.py b/input/netmhcpan4/netmhcpan_prediction.py index 9aa584a5..dc2cdc27 100755 --- a/input/netmhcpan4/netmhcpan_prediction.py +++ b/input/netmhcpan4/netmhcpan_prediction.py @@ -1,9 +1,11 @@ #!/usr/bin/env python -from input.helpers import data_import, properties_manager, intermediate_files +from input.helpers import data_import +from input.helpers.epitope_helper import EpitopeHelper +from input.netmhcpan4.abstract_netmhcpan_predictor import AbstractNetMhcPanPredictor -class NetMhcPanBestPrediction: +class NetMhcPanPredictor(EpitopeHelper, AbstractNetMhcPanPredictor): def __init__(self, runner, configuration): """ @@ -27,7 +29,7 @@ def __init__(self, runner, configuration): self.mhcI_affinity_allele_9mer = "NA" self.mhcI_affinity_epitope_9mer = "NA" - def mhc_allele_in_netmhcpan_available(self, allele, set_available_mhc): + def _mhc_allele_in_netmhcpan_available(self, allele, set_available_mhc): '''checks if mhc prediction is possible for given hla allele ''' return allele in set_available_mhc @@ -38,7 +40,7 @@ def mhc_prediction(self, hla_alleles, set_available_mhc, tmpfasta, tmppred): allels_for_prediction = [] for allele in hla_alleles: allele = allele.replace("*", "") - if self.mhc_allele_in_netmhcpan_available(allele, set_available_mhc): + if self._mhc_allele_in_netmhcpan_available(allele, set_available_mhc): allels_for_prediction.append(allele) hla_allele = ",".join(allels_for_prediction) cmd = [ @@ -48,6 +50,7 @@ def mhc_prediction(self, hla_alleles, set_available_mhc, tmpfasta, tmppred): "-BA"] lines, _ = self.runner.run_command(cmd) counter = 0 + # TODO: avoid writing a file here, just return some data structure no need to go to the file system with open(tmppred, "w") as f: for line in lines.splitlines(): line = line.rstrip().lstrip() @@ -67,33 +70,6 @@ def mhc_prediction(self, hla_alleles, set_available_mhc, tmpfasta, tmppred): line = ";".join(line) f.write(line + "\n") - def mut_position_xmer_seq(self, xmer_wt, xmer_mut): - '''returns position of mutation in xmer sequence - ''' - if len(xmer_wt) == len(xmer_mut): - p1 = -1 - for i, aa in enumerate(xmer_mut): - if aa != xmer_wt[i]: - p1 = i + 1 - else: - p1 = 0 - # in case sequences do not have same length - for a1, a2 in zip(xmer_wt, xmer_mut): - if a1 == a2: - p1 += 1 - return str(p1) - - def epitope_covers_mutation(self, position_mutation, position_epitope, length_epitope): - '''checks if predicted epitope covers mutation - ''' - cover = False - if position_mutation != "-1": - start = int(position_epitope) - end = start + int(length_epitope) - 1 - if int(position_mutation) >= start and int(position_mutation) <= end: - cover = True - return cover - def filter_binding_predictions(self, position_xmer, tmppred): '''filters prediction file for predicted epitopes that cover mutations ''' @@ -111,6 +87,7 @@ def filter_binding_predictions(self, position_xmer, tmppred): def minimal_binding_score(self, prediction_tuple, rank=True): '''reports best predicted epitope (over all alleles). indicate by rank = true if rank score should be used. if rank = False, Aff(nM) is used ''' + # TODO: generalize this method with netmhcIIpan_prediction.py + change input dat_head = prediction_tuple[0] dat = prediction_tuple[1] if rank: @@ -126,18 +103,6 @@ def minimal_binding_score(self, prediction_tuple, rank=True): row = i return dat_head, row - def add_best_epitope_info(self, epitope_tuple, column_name): - '''returns desired information of prediction of best epitope from netmhcpan output; - e.g. "%Rank": MHC I score, "HLA": HLA allele, "Peptide": best epitope - ''' - dat_head = epitope_tuple[0] - dat = epitope_tuple[1] - val = dat_head.index(column_name) - try: - return dat[val] - except IndexError: - return "NA" - def mutation_in_loop(self, position_xmer, epitope_tuple): """ returns if mutation is directed to TCR (yes or no) @@ -172,17 +137,6 @@ def filter_for_9mers(self, prediction_tuple): dat_9mers.append(i) return dat_head, dat_9mers - def Hamming_check_0_or_1(self, seq1, seq2): - '''returns number of mismatches between 2 sequences - ''' - errors = 0 - for i in range(len(seq1)): - if seq1[i] != seq2[i]: - errors += 1 - if errors >= 2: - return errors - return errors - def filter_for_WT_epitope(self, prediction_tuple, mut_seq, mut_allele): '''returns wt epitope info for given mutated sequence. best wt that is allowed to bind to any allele of patient ''' @@ -195,42 +149,9 @@ def filter_for_WT_epitope(self, prediction_tuple, mut_seq, mut_allele): wt_seq = i[seq_col] wt_allele = i[allele_col] if (len(wt_seq) == len(mut_seq)): - numb_mismatch = self.Hamming_check_0_or_1(mut_seq, wt_seq) + numb_mismatch = self.hamming_check_0_or_1(mut_seq, wt_seq) if numb_mismatch == 1: wt_epi.append(i) dt = (dat_head, wt_epi) min = self.minimal_binding_score(dt) return (min) - - -# if __name__ == '__main__': -# -# from input import predict_all_epitopes, epitope -# -# # test with ott data set -# file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/MHC_prediction_netmhcpan4/testdat_ott.txt" -# hla_file = "/projects/SUMMIT/WP1.2/Literature_Cohorts/data_analysis/cohorts/ott/icam_ott/alleles.csv" -# # test inest data set -# # file = "/flash/projects/WP3/AnFranziska/AnFranziska/head_seqs.txt" -# # hla_file = "/flash/projects/WP3/AnFranziska/AnFranziska/alleles.csv" -# dat = data_import.import_dat_icam(file, False) -# if "+-13_AA_(SNV)_/_-15_AA_to_STOP_(INDEL)" in dat[0]: -# dat = data_import.change_col_names(dat) -# # available MHC alleles -# set_available_mhc = predict_all_epitopes.Bunchepitopes().load_available_hla_alleles() -# # hla allele of patients -# patient_hlaI = predict_all_epitopes.Bunchepitopes().load_patient_hla_I_allels(hla_file) -# patient_hlaII = predict_all_epitopes.Bunchepitopes().load_patient_hla_II_allels(hla_file) -# -# print(patient_hlaI) -# print(patient_hlaII) -# -# for ii, i in enumerate(dat[1]): -# if ii < 10: -# print(ii) -# dict_epi = epitope.Epitope() -# dict_epi.init_properties(dat[0], dat[1][ii]) -# prediction = NetMhcPanBestPrediction() -# prediction.main(dict_epi.properties, set_available_mhc, patient_hlaI) -# attrs = vars(prediction) -# print(attrs) diff --git a/input/netmhcpan4/test.csv b/input/netmhcpan4/test.csv deleted file mode 100644 index 197a590c..00000000 --- a/input/netmhcpan4/test.csv +++ /dev/null @@ -1,211 +0,0 @@ -P1470L True True -V209A True True -T171I True True -A413V True True -P118L True True -V446F True True -V500F True True -P85L True True -R5S True True -P5L True True -T1326I True True -S657F True True -F59L True True -S15L True True -S15L True True -P506S True True -P490S True True -S821F True True -R391C True True -G295E True True -S547L True True -R615Q True True -S327F True True -R68W True True -Q117H True True -E763K True True -P269S True True -P526Q True True -L302F True True -G213R True True -P1054S True True -G244V True True -F317L True True -L90V True True -E37V True True -G1291E True True -H94Y True True -P255L True True -G592S True True -S200F True True -S108L True True -T344I True True -S222L True True -G564S True True -K297Q True True -A229V True True -P266S True True -G148E True True -I1080T True True -P310S True True -L308F True True -L308F True True -H219Y True True -S808F True True -R457K True True -P345L True True -P746L True True -P231L True True -P351L True True -P807S True True -S549F True True -P319S True True -P480S True True -G400E True True -E265K True True -S432F True True -K953T True True -P361S True True -P165S True True -A940V True True -A1105V True True -P182S True True -P99S True True -P173S True True -R134C True True -H31Y True True -S698L True True -S181L True True -L14F True True -S3114F True True -P1187S True True -D193N True True -S151F True True -F519I True True -G579D True True -A509T True True -G93E True True -S189L True True -P193L True True -V648A True True -P520S True True -S222F True True -L279F True True -S311F True True -P119L True True -P138L True True -L425F True True -L184F True True -P173S True True -S316F True True -R24L True True -A641V True True -P338S True True -P55L True True -A268V True True -L97F True True -H476Y True True -P346S True True -A307P True True -N147I True True -L788P True True -S479F True True -D290N True True -R893W True True -R1432Q True True -L69M True True -L214Q True True -L49V True True -R79P True True -E160K True True -S133F True True -L539F True True -R1010W True True -E1272K True True -P805S True True -A795V True True -S491F True True -P425S True True -P333S True True -P5276L True True -P578L True True -P234L True True -I21L True True -V728D True True -D178N True True -D1015N True True -N1155D True True -S1436I True True -E504K True True -D316E True True -K502T True True -D89N True True -S599F True True -Q268H True True -L786F True True -L1309F True True -L65V True True -S112L True True -R237K True True -R780Q True True -A70T True True -E242K True True -R46K True True -S61F True True -P563S True True -S530F True True -S954L True True -H82Y True True -S49F True True -P131S True True -L4518F True True -S129L True True -L218F True True -R913C True True -H284Y True True -G137S True True -S168F True True -E311K True True -L290F True True -T233I True True -G1333E True True -P86S True True -A624V True True -A235V True True -P56L True True -S259F True True -A114V True True -G1300C True True -P215S True True -S139F True True -P546S True True -F344S True True -A315V True True -P106S True True -P106S True True -L584F True True -P196T True True -P382S True True -P382L True True -S429F True True -D413N True True -R1161C True True -G460R True True -D204E True True -V93I True True -A47V True True -P152S True True -R380K True True -R129W True True -I115T True True -WT_pep_II_2 WT_pep_II_3 WT_pep_II_0 gene.x pre_existing_cell_type_update C_RPKM DQB_RPKM serex actin_binding selected_by_TSMB X WT_cons_II_1 WT_cons_II_0 WT_cons_II_3 WT_cons_II_2 mhc_II_2 mhc_II_3 mhc_II_0 mhc_II_1 any_immunogenicity gene.y next_mutation_source WT_pep_II_1 RANK_MHC RANK_EXPR Cell.Type.IM mix_id MHC_I_epitope_.best_prediction. patient_done_in_IM mutations_in_transcript MHC_I_score_.WT. MB_score_top10_arithmetic VAF_in_RNA DQA_RPKM de_novo_cell_type_update MB_score_all_epitopes_arithmetic peptide_resulting_from_this_mutation MHC_I_allele_.best_prediction. exon mut_pos_II_3 mut_pos_II_2 mut_pos_II_1 mut_pos_II_0 mut_cons_I_3 mut_cons_I_2 mut_cons_I_1 mut_cons_I_0 mRNA_for_..13_AA_.SNV._._.15_AA_to_STOP_.INDEL. MB_score_best_per_alelle_harmonic allowed_positions MHC_I_epitope_.WT. unique.keys VAF_in_normal best4_mhc_epitope chr_pos..0.based. next_mutation.potential_to_change_27mer. mutation_found_in_proteome in_cytosol coverage_normal WT_cons_I_1 WT_cons_I_0 WT_cons_I_3 WT_cons_I_2 mutation mut_pos_I_1 patient MB_score_best_per_alelle_geometric MHC_II_score_.best_prediction. in_exosome RefSeq_transcript key substitution WT_pep_I_0 WT_pep_I_1 WT_pep_I_2 WT_pep_I_3 exon_expression MHC_II_epitope_.best_prediction. MB_score_all_epitopes_harmonic peptide_count_for_this_mutation_in_this_transcript distinct_peptides_resulting_from_this_mutation keys_of_distinct_peptides_resulting_from_this_mutation IS.reactivity MHC_II_allele_.best_prediction. MHC_I_score_.best_prediction. MB_epitope_scores X..13_AA_.SNV._._.15_AA_to_STOP_.INDEL. mhc_I_0 mhc_I_1 mhc_I_2 mhc_I_3 pre_existing_update length_II_1 codon transcript_expression UCSC_transcript sample_id wt.nt Site.classification FLRT.u transcript_position max_expression_risk_.0.none.1.low.2.med.3.high. any_immunogenicity_update Clone.type B_RPKM X.WT._..13_AA_.SNV._._.15_AA_to_STOP_.INDEL. VAF_in_tumor Position_Xmer_Seq MB_number_of_weak_binders DRB_RPKM exosomal MB_score_top10_geometric MHC_II_peptide_length_.best_prediction. A_RPKM distance_to_next_mutation.AA_residues. Cx MHC_II_score_.WT. mut_pep_II_1 mut_cons_II_3 mut_cons_II_2 mut_cons_II_1 mut_cons_II_0 MB_number_of_strong_binders done_in_IM other_transcripts_with_this_peptide RNA_binding MHC_II_epitope_.WT. coverage_tumor confirmed CN.w..EC mut.ID MB_alleles MHC_I_peptide_length_.best_prediction. RANK_MHC_II mut_pep_I_2 mut_pep_I_3 mut_pep_I_0 mut_pep_I_1 MB_epitope_sequences coverage_RNA mut_pos_I_3 mut_pos_I_2 IS mut_pos_I_0 de_novo_update best4_mhc_allele mut.nt MB_score_all_epitopes_geometric IM rho best4_mhc_score MB_score_top10_harmonic length_I_3 length_I_2 length_I_1 mut_pep_II_0 MB_score_best_per_alelle_arithmetic mut_pep_II_2 mut_pep_II_3 length_II_3 length_II_2 VAF.Nx_Q30..Nx_Q30.Nz_Q30. length_II_0 directed_to_TCR -NA NA FVPQMPKLLKSLFPV KIF13B NA 84.59 9.65 FALSE FALSE FALSE NA NA 44.02 NA NA NA NA HLA-DRB1*07:01 FALSE KIF13B NA 6 53 NA RB0401_02_003-chr8_28950310 KLLKSLFLV TRUE 1 0.1 2.28144444444 0.212121212 17.72 NA 54.1728516779 2 HLA A*0201 uc003xhh.4#exon.36 NA NA NA 13 3.9 7.9 0.65 0.2 TTCGTGCCGCAAATGCCAAAGCTCCTCAAGTCTCTCTTTCTCGTCCGCGATGAGAAGAGGGGCAAGCGGCCGTCTCCCCTC 0.297988861783 SME KLLKSLFPV 57-RB0401_02_003 0 KLLKSLFLV chr8_28950310 False FALSE 465 2.95 0.2 25 3.2 chr8_28950310 4 RB0401_02_003 1.42982459317 9.58 FALSE NM_015254 57 P1470L KLLKSLFPV KSLFPVRDEK LLKSLFPV MPKLLKSLFP 3.425515898 FVPQMPKLLKSLFLV 7.23537465924 0 2 294 HLA DRB1*0701 0.1 64.0299/60.4478/64.4403/89.2683/40.7500/29.7660/63.9179/14.1155/58.2948/68.2212/42.1364/34.9062/8.2583/55.9827/91.9118/1.7824/16.7465/67.6923/7.5926/16.8009/66.9231/2.9664/5.9981/85.9756/13.2083/0.6743/16.9756/88.7805/0.5670/14.4874/27.7986/39.7870/56.7919/45.3056/15.7186/45.7639/66.0096/21.5878/4.4240/42.7500/13.1361/85.0000/58.9474/66.5000/49.5714/66.5000/45.5000/92.5000/45.6000/3.4539/3.7486/62.5000/96.6667/36.3158/20.4861/86.6667/26.0678/55.0000/59.7368/0.0876/24.0779/96.6667/78.0000/13.5979/54.0741/37.2778/52.5926/2.9722/4.2806/66.5000/96.6667/22.9057/57.3684/34.6538/92.5000/42.1875/76.1111/95.0000/93.7500/87.0000/81.6667/86.0000/72.2727/61.0000/60.0000/77.7778/70.4545/44.8462/78.3333/95.0000/41.3529/35.6000/86.0000/25.8791/41.4118/56.7241/15.7520/21.8071/92.5000/69.0000/14.8924/70.0000/37.3913/19.2600/21.1929/34.8125/77.2222/88.0000/31.7674/72.7273/60.0000/52.3077/27.7917/100.0000/100.0000/100.0000/95.0000/92.5000/95.0000/81.6667/69.1667/92.5000/5.6504/95.0000/78.3333/95.0000/95.0000/75.0000/63.3333/92.5000/51.1538/47.0000/67.5000/57.0000/45.5000/92.5000/75.0000/30.9444/37.4444/56.5000/32.9286/58.5000/80.0000/81.6667/95.0000/62.5000/69.1667/55.0000/68.3333 FVPQMPKLLKSLFLVRDEKRGKRPSPL HLA-A*02:01 HLA-A*30:01 HLA-B*15:01 HLA-B*35:08 FALSE NA 1469 6.145347743 uc003xhh.4 RB0401_02_003 G SOMATIC_HI -28.9231 4408 0 FALSE not fixed (>3 std) [u] 64.6 FVPQMPKLLKSLFPVRDEKRGKRPSPL 0.112612613 14 4 23.95 FALSE 1.45469099281 15 45.74 NA 1 44.02 NA NA NA 9.58 1 FALSE FALSE FVPQMPKLLKSLFPV 444 True 2 007-M06 HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08 9 NA LLKSLFLV MPKLLKSLFL KLLKSLFLV KSLFLVRDEK QMPKLLKSLFL/KLLKSLFLVR/KLLKSLFLVR/LLKSLFLVRDE/KSLFLVRDEK/KSLFLVRDEKR/SLFLVRDEK/LFLVRDEKRGK/FLVRDEKRGKR/LVRDEKRGK/MPKLLKSLFL/KLLKSLFLV/KLLKSLFLVR/LLKSLFLVR/KSLFLVRDE/KSLFLVRDEK/SLFLVRDEKR/LFLVRDEKR/FLVRDEKRGK/LVRDEKRGKR/PKLLKSLFL/KLLKSLFLV/LLKSLFLVR/LKSLFLVRD/KSLFLVRDE/SLFLVRDEK/LFLVRDEKR/FLVRDEKRG/LVRDEKRGK/KLLKSLFL/LLKSLFLV/LKSLFLVR/KSLFLVRD/SLFLVRDE/LFLVRDEK/FLVRDEKR/LVRDEKRG/QMPKLLKSLFL/MPKLLKSLFLV/KLLKSLFLV/KLLKSLFLV/LLKSLFLVRDE/LKSLFLVRDEK/SLFLVRDEKR/SLFLVRDEKRG/FLVRDEKRGK/FLVRDEKRGKR/LVRDEKRGKRP/MPKLLKSLFL/KLLKSLFLV/KLLKSLFLV/LLKSLFLVRD/LKSLFLVRDE/KSLFLVRDEK/SLFLVRDEKR/LFLVRDEKRG/FLVRDEKRGK/LVRDEKRGKR/PKLLKSLFL/KLLKSLFLV/LLKSLFLVR/LKSLFLVRD/KSLFLVRDE/SLFLVRDEK/LFLVRDEKR/FLVRDEKRG/LVRDEKRGK/KLLKSLFL/LLKSLFLV/LKSLFLVR/KSLFLVRD/SLFLVRDE/LFLVRDEK/FLVRDEKR/LVRDEKRG/QMPKLLKSLFL/MPKLLKSLFLV/PKLLKSLFLVR/KLLKSLFLV/LLKSLFLVRDE/LKSLFLVRDEK/SLFLVRDEKR/SLFLVRDEKRG/LFLVRDEKRGK/FLVRDEKRGKR/LVRDEKRGKRP/KLLKSLFLV/KLLKSLFLVR/LLKSLFLVRD/LKSLFLVRDE/KSLFLVRDEK/SLFLVRDEKR/LFLVRDEKRG/FLVRDEKRGK/LVRDEKRGKR/PKLLKSLFL/KLLKSLFLV/LLKSLFLVR/LKSLFLVRD/KSLFLVRDE/SLFLVRDEK/LFLVRDEKR/FLVRDEKRG/LVRDEKRGK/KLLKSLFL/LLKSLFLV/LKSLFLVR/KSLFLVRD/SLFLVRDE/LFLVRDEK/FLVRDEKR/LVRDEKRG/MPKLLKSLFLV/PKLLKSLFLVR/KLLKSLFLVRD/LLKSLFLVRDE/LKSLFLVRDEK/KSLFLVRDEKR/SLFLVRDEKRG/LFLVRDEKRGK/FLVRDEKRGKR/LVRDEKRGKRP/MPKLLKSLFL/KLLKSLFLV/KLLKSLFLVR/LLKSLFLVR/LKSLFLVRDE/KSLFLVRDEK/SLFLVRDEKR/LFLVRDEKRG/FLVRDEKRGK/LVRDEKRGKR/PKLLKSLFL/KLLKSLFLV/LLKSLFLVR/LKSLFLVRD/KSLFLVRDE/SLFLVRDEK/LFLVRDEKR/FLVRDEKRG/LVRDEKRGK/KLLKSLFL/LLKSLFLV/LKSLFLVR/KSLFLVRD/SLFLVRDE/LFLVRDEK/FLVRDEKR/LVRDEKRG 33 9 6 NA 7 NA HLA-A*02:01 A 39.2175930352 NA 0.662 0.0876 0.539351037234 10 8 10 FVPQMPKLLKSLFLV 5.29935 NA NA NA NA 0.112 15 no -NA NA LVLPMWAIALISFGV SLC20A2 NA 84.59 9.65 FALSE FALSE FALSE NA NA 6.21 NA NA NA NA HLA-DRB1*07:01 FALSE SLC20A2 NA 3 39 NA RB0401_02_003-chr8_42302267 VLGLALPM TRUE 1 0.1 2.23571111111 0.452830189 17.72 NA 36.8793894737 1 HLA A*0201 uc003xpe.3#exon.5 NA NA NA 1 0.6 3.3 7.4 1.05 TTTTCCATCATGTACACAGGAGCACCAGTGCTCGGCCTTGCTCTCCCCATGTGGGCCATAGCCCTCATTTCCTTTGGTGTC 0.832017161998 SME VLGLVLPM 332-RB0401_02_003 0 GLALPMWAI chr8_42302267 False FALSE 334 12 0.85 0.6 3.4 chr8_42302267 10 RB0401_02_003 1.88602944494 6.21 TRUE NM_006749 332 V209A VLGLVLPM MYTGAPVLGLV VLGLVLPM APVLGLVLPM 9.039554756 LALPMWAIALISFGV 10.4402476808 0 2 530 HLA DRB1*0701 0.1 31.0588/36.8500/78.2540/71.3291/87.5610/86.8293/69.8077/77.4603/72.3418/56.4162/80.1961/10.4006/24.2746/60.7090/26.2862/81.7647/32.1341/48.2951/31.0392/31.7353/29.9489/5.7492/19.8302/50.8836/42.7727/34.6750/20.8341/20.5742/11.7579/17.2162/44.3077/53.7069/90.0000/54.1810/55.3179/42.3636/42.7614/39.5833/43.0000/13.1055/67.5000/23.0330/43.7000/34.5769/9.3072/19.6923/3.7333/16.9613/16.3000/7.3751/17.3370/41.1667/13.5979/41.5000/3.7365/4.3047/2.3392/8.7870/2.4190/15.3192/11.7335/48.0000/14.2250/10.3837/21.5114/0.2643/17.9444/0.6721/38.1176/26.8814/77.0000/9.8248/46.5000/3.8371/8.7126/11.9705/75.0000/23.5648/87.0000/34.3125/45.2308/93.7500/58.2759/85.0000/30.3404/59.4828/72.7273/30.3617/14.3249/55.6897/10.9653/40.3684/48.3636/38.3182/31.0000/22.0079/23.5833/21.0214/6.8241/49.4444/18.2650/7.4200/51.4103/10.8907/27.1194/5.5886/45.7692/25.9341/91.2500/19.5050/49.0000/38.0000/53.8462/40.1053/67.5000/20.3824/54.2308/27.0417/7.3194/95.0000/92.5000/90.0000/60.8333/23.4524/65.8333/38.7143/10.8995/35.9000/1.6299/35.3000/81.6667/65.8333/75.0000/10.6516/13.7463/24.9189/6.1261/8.1687/13.9522/16.0552/50.3846/30.8333/13.8529/13.5331/49.3333/1.4900/65.0000/36.2222/26.5862/75.0000/20.4706/71.6667 FSIMYTGAPVLGLALPMWAIALISFGV HLA-A*02:01 HLA-A*30:01 HLA-B*15:01 HLA-B*35:08 FALSE NA 208 23.04052926 uc003xpe.3 RB0401_02_003 A SOMATIC_HI -30.0013 625 0 FALSE FIXED 64.6 FSIMYTGAPVLGLVLPMWAIALISFGV 0.164556962 14 4 23.95 TRUE 1.71841060798 15 45.74 NA 1 6.21 NA NA NA 6.21 1 FALSE uc010lxl.3 uc010lxm.3 FALSE LVLPMWAIALISFGV 237 True 2 007-M03 HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08 8 NA VLGLALPM APVLGLALPM VLGLALPM MYTGAPVLGLA MYTGAPVLGLA/YTGAPVLGLAL/TGAPVLGLALP/GAPVLGLALPM/APVLGLALPMW/PVLGLALPMWA/VLGLALPMWAI/LGLALPMWAIA/GLALPMWAIAL/LALPMWAIALI/ALPMWAIALIS/YTGAPVLGLA/TGAPVLGLAL/GAPVLGLALP/APVLGLALPM/PVLGLALPMW/VLGLALPMWA/LGLALPMWAI/GLALPMWAIA/LALPMWAIAL/ALPMWAIALI/TGAPVLGLA/GAPVLGLAL/APVLGLALP/PVLGLALPM/VLGLALPMW/LGLALPMWA/GLALPMWAI/LALPMWAIA/ALPMWAIAL/GAPVLGLA/APVLGLAL/PVLGLALP/VLGLALPM/LGLALPMW/GLALPMWA/LALPMWAI/ALPMWAIA/MYTGAPVLGLA/YTGAPVLGLAL/TGAPVLGLAL/GAPVLGLALPM/APVLGLALPMW/VLGLALPMWA/VLGLALPMWAI/GLALPMWAIA/GLALPMWAIAL/ALPMWAIALI/ALPMWAIALIS/YTGAPVLGLA/TGAPVLGLAL/GAPVLGLAL/APVLGLALPM/VLGLALPMW/VLGLALPMWA/GLALPMWAI/GLALPMWAIA/LALPMWAIAL/ALPMWAIALI/TGAPVLGLA/GAPVLGLAL/APVLGLALP/PVLGLALPM/VLGLALPMW/LGLALPMWA/GLALPMWAI/LALPMWAIA/ALPMWAIAL/GAPVLGLA/APVLGLAL/PVLGLALP/VLGLALPM/LGLALPMW/GLALPMWA/LALPMWAI/ALPMWAIA/MYTGAPVLGLA/YTGAPVLGLAL/TGAPVLGLAL/GAPVLGLALPM/APVLGLALPMW/PVLGLALPMW/VLGLALPMWAI/LGLALPMWAIA/GLALPMWAIAL/LALPMWAIALI/ALPMWAIALIS/YTGAPVLGLA/TGAPVLGLAL/GAPVLGLAL/APVLGLALPM/PVLGLALPMW/VLGLALPMW/LGLALPMWAI/GLALPMWAIA/LALPMWAIAL/ALPMWAIALI/TGAPVLGLA/GAPVLGLAL/APVLGLALP/PVLGLALPM/VLGLALPMW/LGLALPMWA/GLALPMWAI/LALPMWAIA/ALPMWAIAL/GAPVLGLA/APVLGLAL/PVLGLALP/VLGLALPM/LGLALPMW/GLALPMWA/LALPMWAI/ALPMWAIA/MYTGAPVLGLA/YTGAPVLGLAL/TGAPVLGLALP/APVLGLALPM/APVLGLALPMW/PVLGLALPMW/VLGLALPMWAI/LGLALPMWAIA/GLALPMWAIAL/LALPMWAIALI/LPMWAIALIS/YTGAPVLGLA/TGAPVLGLAL/GAPVLGLALP/APVLGLALPM/PVLGLALPMW/VLGLALPMW/LGLALPMWAI/GLALPMWAIA/LALPMWAIAL/ALPMWAIALI/TGAPVLGLA/GAPVLGLAL/APVLGLALP/PVLGLALPM/VLGLALPMW/LGLALPMWA/GLALPMWAI/LALPMWAIA/ALPMWAIAL/GAPVLGLA/APVLGLAL/PVLGLALP/VLGLALPM/LGLALPMW/GLALPMWA/LALPMWAI/ALPMWAIA 106 6 4 NA 4 NA HLA-A*02:01 G 25.7345053962 NA 0.991 0.2643 1.09848232032 10 8 11 LALPMWAIALISFGV 3.273025 NA NA NA NA 0.167 15 no -NA NA STAMGRSPSPKTSLS IFI16 NA 3.07 1.32 TRUE FALSE TRUE NA NA 15.19 NA NA NA NA HLA-DRB1*15:01 NA IFI16 NA 18 9 NA RB0401_02_004-chr1_158986452 SPKISLSAPP TRUE 1 0.55 0.976255555556 0.374384236 1.08 NA 48.6384324503 1 HLA B*0702 uc001ftg.3#exon.3 NA NA NA 11 0.7 0.65 7.9 8.35 GGCATGTCCACAGCCATGGGCCGTTCCCCATCTCCCAAGATCTCATTGTCAGCTCCACCCAACAGTTCTTCAACTGAGAAC 0.158691819785 S SPKTSLSAPP 46-RB0401_02_004 0 SPSPKISL chr1_158986452 False TRUE 397 20 20 14 0.5 chr1_158986452 9 RB0401_02_004 1.15378883495 11.36 FALSE NM_005531 46 T171I AMGRSPSPKT AMGRSPSPKT SPSPKTSL TAMGRSPSPKT 14.83976395 STAMGRSPSPKISLS 4.00785856668 0 1 HLA DRB1*1501 0.65 24.4416/44.5000/35.5000/47.3750/42.5000/74.3750/96.6667/96.6667/95.0000/33.2963/54.8148/5.0796/72.5000/15.6658/42.2500/26.5763/88.3333/85.0000/98.3333/32.1724/15.7681/23.1868/68.5000/13.3058/43.8000/38.2941/68.0000/98.3333/69.5000/31.8529/39.5333/82.0000/26.3559/88.3333/51.8519/98.3333/71.8750/74.3750/42.6923/57.8723/41.3214/59.1489/54.2857/90.0000/99.0000/98.0000/88.1250/28.4074/49.5333/10.9696/70.5556/15.2700/45.2857/38.0294/94.0000/93.0000/99.0000/26.8899/14.2139/22.7126/73.0556/12.4541/56.3830/42.2692/80.5000/96.0000/63.8235/20.0089/55.4255/83.0000/36.6744/90.0000/66.2500/99.0000/77.3077/56.5957/10.4247/64.2857/4.4788/15.6017/8.7256/6.9808/52.7273/23.0294/95.0000/66.0000/53.1818/9.0099/25.5556/7.7547/2.9469/0.5088/15.1949/4.1251/100.0000/63.5714/44.5000/1.9673/36.1250/0.9095/1.1125/38.7143/1.1122/92.5000/57.7778/41.2000/25.0000/28.7647/0.0424/40.3333/1.0353/39.3333/68.0000/73.3333/2.7087/67.8947/15.6238/60.4000/35.3261/36.0244/94.0000/86.4286/98.0000/94.0000/63.6000/21.5903/24.2102/30.3636/6.1072/63.8000/39.1034/100.0000/84.3750/55.5714/0.7501/65.0000/7.4053/7.5269/31.6377/14.0580/87.8571/94.0000/27.8165/21.7093/67.8947/1.3482/44.5789/8.0000/62.6000/91.0000/49.9231 GMSTAMGRSPSPKISLSAPPNSSSTEN HLA-A*02:01 HLA-A*02:64 HLA-B*07:02 HLA-B*51:53 FALSE NA 170 94.11543935 uc001ftg.3 RB0401_02_004 C SOMATIC_HI -155.311 511 0 FALSE not fixed (>4 std) [u] 5.22 GMSTAMGRSPSPKTSLSAPPNSSSTEN 0.228426396 14 9 2.08 FALSE 0.716878292177 15 14.28 NA 2 15.19 NA NA NA 11.36 1 TRUE uc010pit.2 uc001ftf.1 FALSE STAMGRSPSPKTSLS 788 True 2 010-M18 HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53 10 NA SPSPKISL TAMGRSPSPKI AMGRSPSPKI AMGRSPSPKI TAMGRSPSPKI/AMGRSPSPKI/MGRSPSPKISL/GRSPSPKISL/RSPSPKISLSA/SPSPKISLSA/PSPKISLSAPP/SPKISLSAPPN/KISLSAPPNS/KISLSAPPNSS/SLSAPPNSSS/AMGRSPSPKI/MGRSPSPKI/GRSPSPKISL/RSPSPKISLS/SPSPKISLSA/PSPKISLSAP/SPKISLSAPP/KISLSAPPN/KISLSAPPNS/ISLSAPPNSS/MGRSPSPKI/GRSPSPKIS/RSPSPKISL/SPSPKISLS/PSPKISLSA/SPKISLSAP/PKISLSAPP/KISLSAPPN/ISLSAPPNS/GRSPSPKI/RSPSPKIS/SPSPKISL/PSPKISLS/SPKISLSA/PKISLSAP/KISLSAPP/ISLSAPPN/TAMGRSPSPKI/AMGRSPSPKIS/MGRSPSPKISL/GRSPSPKISL/RSPSPKISLSA/SPSPKISLSA/PSPKISLSAPP/SPKISLSAPPN/KISLSAPPNS/KISLSAPPNSS/SLSAPPNSSS/AMGRSPSPKI/MGRSPSPKIS/GRSPSPKISL/RSPSPKISLS/SPSPKISLSA/PSPKISLSA/SPKISLSAPP/KISLSAPPN/KISLSAPPNS/ISLSAPPNSS/MGRSPSPKI/GRSPSPKIS/RSPSPKISL/SPSPKISLS/PSPKISLSA/SPKISLSAP/PKISLSAPP/KISLSAPPN/ISLSAPPNS/GRSPSPKI/RSPSPKIS/SPSPKISL/PSPKISLS/SPKISLSA/PKISLSAP/KISLSAPP/ISLSAPPN/TAMGRSPSPKI/AMGRSPSPKI/MGRSPSPKISL/GRSPSPKISLS/SPSPKISLSA/SPSPKISLSAP/SPKISLSAPP/SPKISLSAPPN/ISLSAPPNS/KISLSAPPNSS/ISLSAPPNSSS/AMGRSPSPKI/MGRSPSPKIS/GRSPSPKISL/RSPSPKISLS/SPSPKISLSA/SPKISLSAP/SPKISLSAPP/KISLSAPPN/KISLSAPPNS/ISLSAPPNSS/MGRSPSPKI/GRSPSPKIS/RSPSPKISL/SPSPKISLS/PSPKISLSA/SPKISLSAP/PKISLSAPP/KISLSAPPN/ISLSAPPNS/GRSPSPKI/RSPSPKIS/SPSPKISL/PSPKISLS/SPKISLSA/PKISLSAP/KISLSAPP/ISLSAPPN/TAMGRSPSPKI/AMGRSPSPKI/MGRSPSPKISL/GRSPSPKISLS/SPSPKISLSA/SPSPKISLSAP/SPKISLSAPP/SPKISLSAPPN/ISLSAPPNS/KISLSAPPNSS/ISLSAPPNSSS/MGRSPSPKI/GRSPSPKISL/RSPSPKISLS/SPSPKISLSA/SPKISLSAP/SPKISLSAPP/PKISLSAPPN/KISLSAPPNS/ISLSAPPNSS/MGRSPSPKI/GRSPSPKIS/RSPSPKISL/SPSPKISLS/PSPKISLSA/SPKISLSAP/PKISLSAPP/KISLSAPPN/ISLSAPPNS/GRSPSPKI/RSPSPKIS/SPSPKISL/PSPKISLS/SPKISLSA/PKISLSAP/KISLSAPP/ISLSAPPN 203 10 5 9 FALSE HLA-B*07:02 T 31.3291693532 0.767 0.0424 0.281277119204 11 8 10 STAMGRSPSPKISLS 4.210425 NA NA NA NA 0.23 15 no -NA NA KEWMQALQQAMAEQR ARAP1 NA 3.07 1.32 FALSE FALSE TRUE NA NA 26.85 NA NA NA NA HLA-DRB1*15:01 TRUE ARAP1 NA 4 26 CD4 RB0401_02_004-chr11_72421607 SDVERKEWMQV TRUE 1 4.4 6.88071111111 0.258064516 1.08 CD4+ 45.4866967105 1 HLA A*0201 uc001osu.3#exon.9 NA NA NA 5 8.4 7.5 5.1 9.05 CGGGCAGAGAGTGATGTGGAGCGGAAGGAGTGGATGCAGGTCCTGCAGCAGGCCATGGCTGAGCAGCGTGCCCGGGCCCGG 6.03172363234 SME SDVERKEWMQA 17-RB0401_02_004 0 WMQVLQQAM chr11_72421607 False TRUE 261 3.1 24 7.7 6.5 chr11_72421607 3 RB0401_02_004 6.12014898046 23.1 FALSE NM_001040118 17 A413V SDVERKEWMQA WMQALQQA WMQALQQAM WMQALQQAM 2.449545035 KEWMQVLQQAMAEQR 27.7753388709 0 1 HLA DRB1*1501 0.2 35.9545/57.3684/83.0000/82.0000/50.0000/32.3448/64.2857/75.0000/60.3571/68.5000/9.5475/35.0455/38.5294/70.6250/59.4737/21.0382/37.4444/17.9444/49.0000/47.1250/31.7647/23.8242/25.4058/80.0000/33.4444/16.9935/6.7730/9.2662/43.6000/15.3516/62.1429/53.1481/64.6429/77.0000/16.8387/37.6111/47.3750/31.4412/63.2353/65.6250/80.0000/81.5000/60.4412/28.4938/64.8529/58.7234/44.1818/60.4412/23.9145/56.5957/34.0208/76.9231/57.4468/27.5146/30.1370/25.9524/34.9375/31.3030/10.5444/23.6118/15.7500/63.9706/25.8810/10.9888/4.7442/8.5022/26.6330/4.9000/68.9583/41.7857/50.7937/74.4444/33.4808/27.2718/53.6508/31.9242/42.6000/26.3636/62.1429/70.0000/76.6667/29.6875/85.0000/90.0000/87.5000/80.0000/78.3333/22.3421/9.9520/43.7500/62.8571/37.5000/25.3704/67.0000/46.5000/50.4545/71.6667/7.3542/5.8812/49.6667/35.8889/34.6000/7.0814/31.3846/17.5976/31.3846/36.3750/17.9146/59.4444/73.3333/67.0000/17.0610/39.5000/58.3333/39.1034/19.8385/56.4286/73.5714/75.0000/45.2105/74.2857/95.0000/93.0000/91.0000/82.5000/9.5852/20.3682/53.9423/75.5000/43.8182/27.1468/71.4286/58.7143/76.0000/88.5714/7.4240/12.7159/79.5000/48.5000/16.5265/18.2896/21.4229/41.2800/70.0000/19.7205/28.9038/52.1154/55.7143/39.4138/15.2476/31.4203/75.0000 RAESDVERKEWMQVLQQAMAEQRARAR HLA-A*02:01 HLA-A*02:64 HLA-B*07:02 HLA-B*51:53 FALSE NA 412 19.04800329 uc001osu.3 RB0401_02_004 G SOMATIC_HI -13.2927 1237 0 TRUE not fixed (>3 std) [f] 5.22 RAESDVERKEWMQALQQAMAEQRARAR 0.108910891 14 0 2.08 FALSE 6.7268945984 15 14.28 NA 1 26.85 NA NA NA 23.1 0 TRUE uc001oss.3 uc010rre.2 uc001osr.3 uc001osv.3 uc009yth.3 FALSE KEWMQALQQAMAEQR 303 True 2 010-M04 HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53 11 NA WMQVLQQAM WMQVLQQAM SDVERKEWMQV WMQVLQQA SDVERKEWMQV/DVERKEWMQVL/VERKEWMQVL/ERKEWMQVLQQ/RKEWMQVLQQA/KEWMQVLQQAM/EWMQVLQQAMA/WMQVLQQAMAE/MQVLQQAMAEQ/QVLQQAMAEQR/VLQQAMAEQRA/DVERKEWMQV/VERKEWMQVL/ERKEWMQVL/RKEWMQVLQQ/KEWMQVLQQA/WMQVLQQAM/WMQVLQQAMA/MQVLQQAMAE/QVLQQAMAEQ/VLQQAMAEQR/VERKEWMQV/ERKEWMQVL/RKEWMQVLQ/KEWMQVLQQ/EWMQVLQQA/WMQVLQQAM/MQVLQQAMA/QVLQQAMAE/VLQQAMAEQ/ERKEWMQV/RKEWMQVL/KEWMQVLQ/EWMQVLQQ/WMQVLQQA/MQVLQQAM/QVLQQAMA/VLQQAMAE/SDVERKEWMQV/DVERKEWMQVL/VERKEWMQVL/ERKEWMQVLQQ/RKEWMQVLQQA/KEWMQVLQQAM/EWMQVLQQAMA/WMQVLQQAMAE/MQVLQQAMAEQ/QVLQQAMAEQR/VLQQAMAEQRA/DVERKEWMQV/VERKEWMQVL/ERKEWMQVL/RKEWMQVLQQ/KEWMQVLQQA/EWMQVLQQAM/WMQVLQQAMA/MQVLQQAMAE/QVLQQAMAEQ/VLQQAMAEQR/VERKEWMQV/ERKEWMQVL/RKEWMQVLQ/KEWMQVLQQ/EWMQVLQQA/WMQVLQQAM/MQVLQQAMA/QVLQQAMAE/VLQQAMAEQ/ERKEWMQV/RKEWMQVL/KEWMQVLQ/EWMQVLQQ/WMQVLQQA/MQVLQQAM/QVLQQAMA/VLQQAMAE/SDVERKEWMQV/DVERKEWMQVL/VERKEWMQVL/ERKEWMQVL/RKEWMQVLQQA/KEWMQVLQQAM/EWMQVLQQAM/WMQVLQQAMAE/MQVLQQAMAEQ/QVLQQAMAEQR/VLQQAMAEQRA/DVERKEWMQV/VERKEWMQVL/ERKEWMQVL/RKEWMQVLQQ/KEWMQVLQQA/EWMQVLQQAM/WMQVLQQAM/MQVLQQAMAE/QVLQQAMAEQ/VLQQAMAEQR/VERKEWMQV/ERKEWMQVL/RKEWMQVLQ/KEWMQVLQQ/EWMQVLQQA/WMQVLQQAM/MQVLQQAMA/QVLQQAMAE/VLQQAMAEQ/ERKEWMQV/RKEWMQVL/KEWMQVLQ/EWMQVLQQ/WMQVLQQA/MQVLQQAM/QVLQQAMA/VLQQAMAE/SDVERKEWMQV/DVERKEWMQVL/VERKEWMQVL/ERKEWMQVL/RKEWMQVLQQA/KEWMQVLQQAM/EWMQVLQQAMA/WMQVLQQAMAE/MQVLQQAMAEQ/QVLQQAMAEQR/VLQQAMAEQRA/DVERKEWMQV/VERKEWMQVL/ERKEWMQVL/RKEWMQVLQQ/KEWMQVLQQA/EWMQVLQQAM/MQVLQQAMA/MQVLQQAMAE/QVLQQAMAEQ/VLQQAMAEQR/VERKEWMQV/ERKEWMQVL/RKEWMQVLQ/KEWMQVLQQ/EWMQVLQQA/WMQVLQQAM/MQVLQQAMA/QVLQQAMAE/VLQQAMAEQ/ERKEWMQV/RKEWMQVL/KEWMQVLQ/EWMQVLQQ/WMQVLQQA/MQVLQQAM/QVLQQAMA/VLQQAMAE 31 3 3 10 TRUE HLA-A*02:64 A 37.3880743235 0.62 4.7442 6.56948958174 9 9 8 KEWMQVLQQAMAEQR 6.2056 NA NA NA NA 0.093 15 no -NA NA PLEDGAMPSARLRKL CAPZB NA 3.07 1.32 FALSE TRUE TRUE NA NA 21.65 NA NA NA NA HLA-DRB1*15:01 TRUE CAPZB NA 3 6 CD4 RB0401_02_004-chr1_19705096 LSARLRKL TRUE 1 2.5 1.99168888889 0.437710438 1.08 CD4+ 41.5388927632 1 HLA B*0702 uc010ocz.2#exon.3 NA NA NA 7 6.6 2.7 1.1 1.85 AGTAACAAGTATGACCCTCCCTTGGAGGATGGGGCCATGCTGTCAGCTCGGCTGAGAAAGCTGGAGGTGGAAGCCAACAAT 1.68396882471 SME PSARLRKL 92-RB0401_02_004 0 DGAMLSARL chr1_19705096 False TRUE 318 28 18 43 27 chr1_19705096 1 RB0401_02_004 1.75546241114 10.98 TRUE NM_004930 92 P118L MPSARLRKLEV MPSARLRKLEV PPLEDGAMP PSARLRKLEV 34.68628225 PLEDGAMLSARLRKL 14.4226110309 0 1 HLA DRB1*1501 0.2 19.6648/54.8148/55.5263/65.0000/34.6923/86.6667/70.0000/33.0370/38.4118/7.7804/96.6667/38.2353/46.7500/10.0292/42.0833/61.4286/63.9286/31.9706/3.6809/32.7241/47.5000/27.7593/21.8015/18.0987/77.0000/29.3750/40.8571/18.0897/2.6367/85.0000/26.2203/56.8421/57.3684/82.0000/27.3889/39.6000/37.3333/49.5714/27.3398/69.1667/72.7778/48.0000/45.7143/84.5000/47.2941/41.5714/38.2647/20.4732/97.0000/52.8571/61.4706/23.9803/47.6471/76.1538/57.9787/8.0217/5.2293/31.5909/62.3529/40.4138/27.3301/16.2857/76.1538/35.3913/18.4388/2.1164/1.9031/75.7692/37.2432/55.6383/66.6667/81.5000/32.8305/24.4514/20.2009/50.3175/1.6014/29.0000/20.1346/85.0000/20.1154/75.0000/87.5000/27.6000/85.0000/27.7500/82.5000/3.8354/25.0000/44.2500/33.6000/26.4545/65.0000/46.0000/13.8316/54.5455/15.6441/1.9281/66.0000/11.1954/26.2273/8.2056/34.4000/26.5000/3.5815/50.4545/5.3344/34.2000/46.5000/70.0000/8.7332/61.4286/55.5556/17.9146/2.1567/17.9650/34.4400/95.0000/35.7174/77.0000/66.0526/29.8409/89.2857/34.4000/87.1429/2.0813/25.4097/62.8000/60.4000/19.6615/26.7656/68.9474/33.8393/70.3571/17.3178/2.3197/75.0000/21.9207/57.7143/1.1818/44.9474/54.5192/9.1849/70.0000/5.4014/52.5962/41.3600/39.6897/5.3002/73.2143/72.1429/13.7479 SNKYDPPLEDGAMLSARLRKLEVEANN HLA-A*02:01 HLA-A*02:64 HLA-B*07:02 HLA-B*51:53 FALSE NA 117 86.19819919 uc010ocz.2 RB0401_02_004 G SOMATIC_HI -154.625 352 0 TRUE FIXED 5.22 SNKYDPPLEDGAMPSARLRKLEVEANN 0.289134438 14 4 2.08 TRUE 1.94777530156 15 14.28 NA 2 21.65 NA NA NA 10.98 0 TRUE uc021ohr.1 uc009vpk.3 uc001bce.3 FALSE PLEDGAMPSARLRKL 543 True 2 010-M03 HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53 8 NA PPLEDGAML LSARLRKLEV MLSARLRKLEV MLSARLRKLEV YDPPLEDGAML/DPPLEDGAMLS/PPLEDGAMLSA/PLEDGAMLSAR/LEDGAMLSARL/EDGAMLSARLR/DGAMLSARLRK/GAMLSARLRKL/AMLSARLRKL/MLSARLRKLEV/SARLRKLEVE/DPPLEDGAML/PPLEDGAMLS/PLEDGAMLSA/LEDGAMLSAR/EDGAMLSARL/DGAMLSARLR/GAMLSARLRK/AMLSARLRKL/MLSARLRKL/LSARLRKLEV/PPLEDGAML/PLEDGAMLS/LEDGAMLSA/EDGAMLSAR/DGAMLSARL/GAMLSARLR/AMLSARLRK/MLSARLRKL/LSARLRKLE/PLEDGAML/LEDGAMLS/EDGAMLSA/DGAMLSAR/GAMLSARL/AMLSARLR/MLSARLRK/LSARLRKL/YDPPLEDGAML/DPPLEDGAMLS/LEDGAMLSA/PLEDGAMLSAR/LEDGAMLSARL/EDGAMLSARLR/DGAMLSARLRK/GAMLSARLRKL/AMLSARLRKLE/MLSARLRKLEV/LSARLRKLEVE/DPPLEDGAML/PPLEDGAMLS/PLEDGAMLSA/LEDGAMLSAR/EDGAMLSARL/DGAMLSARLR/GAMLSARLRK/AMLSARLRKL/MLSARLRKL/LSARLRKLEV/PPLEDGAML/PLEDGAMLS/LEDGAMLSA/EDGAMLSAR/DGAMLSARL/GAMLSARLR/AMLSARLRK/MLSARLRKL/LSARLRKLE/PLEDGAML/LEDGAMLS/EDGAMLSA/DGAMLSAR/GAMLSARL/AMLSARLR/MLSARLRK/LSARLRKL/YDPPLEDGAML/DPPLEDGAML/PPLEDGAMLSA/LEDGAMLSAR/LEDGAMLSARL/EDGAMLSARLR/DGAMLSARLRK/GAMLSARLRKL/AMLSARLRKL/MLSARLRKLEV/LSARLRKLEV/DPPLEDGAML/PPLEDGAML/LEDGAMLSA/LEDGAMLSAR/EDGAMLSARL/DGAMLSARLR/GAMLSARLRK/AMLSARLRKL/MLSARLRKL/LSARLRKLEV/PPLEDGAML/PLEDGAMLS/LEDGAMLSA/EDGAMLSAR/DGAMLSARL/GAMLSARLR/AMLSARLRK/MLSARLRKL/LSARLRKLE/PLEDGAML/LEDGAMLS/EDGAMLSA/DGAMLSAR/GAMLSARL/AMLSARLR/MLSARLRK/LSARLRKL/YDPPLEDGAML/DPPLEDGAML/PPLEDGAMLSA/PLEDGAMLSAR/LEDGAMLSARL/EDGAMLSARLR/DGAMLSARL/GAMLSARLRKL/AMLSARLRKL/MLSARLRKLEV/LSARLRKLEV/DPPLEDGAML/PPLEDGAML/LEDGAMLSA/LEDGAMLSAR/EDGAMLSARL/DGAMLSARL/GAMLSARLRK/AMLSARLRKL/MLSARLRKL/LSARLRKLEV/PPLEDGAML/PLEDGAMLS/LEDGAMLSA/EDGAMLSAR/DGAMLSARL/GAMLSARLR/AMLSARLRK/MLSARLRKL/LSARLRKLE/PLEDGAML/LEDGAMLS/EDGAMLSA/DGAMLSAR/GAMLSARL/AMLSARLR/MLSARLRK/LSARLRKL 297 0 8 1 TRUE HLA-B*51:53 A 29.8486339494 0.971 1.1818 1.89804656718 10 9 11 PLEDGAMLSARLRKL 1.83075 NA NA NA NA 0.291 15 no -NA NA SVASYVYNGYSVVFV PLXNA2 NA 3.07 1.32 FALSE FALSE FALSE NA NA 6 NA NA NA NA HLA-DRB1*15:01 FALSE PLXNA2 NA 31 13 NA RB0401_02_004-chr1_208383659 NGYSVFFV TRUE 1 3.7 1.56852222222 0.19 1.08 NA 40.2155118421 2 HLA A*0201 uc001hgz.3#exon.2 NA NA NA 12 2.2 4 0.1 3.9 ACCTCTGTGGCCTCCTACGTTTACAACGGCTACAGCGTGTTTTTTGTGGGGACTAAGAGTGGCAAGCTGAAAAAGATTCGG 0.615111291441 SME NGYSVVFV 104-RB0401_02_004 0 YVYNGYSVF chr1_208383659 False FALSE 482 0.2 7 2.3 4.4 chr1_208383659 8 RB0401_02_004 0.661631922508 3.18 FALSE NM_025179 104 V446F YVYNGYSVVF YVYNGYSVVFV YVYNGYSVV YVYNGYSVV 8.62505684 SVASYVYNGYSVFFV 9.9980210742 0 2 261 HLA DRB1*1501 1.1 23.0440/28.5870/0.7789/81.0000/82.0000/68.0000/52.0370/78.0000/42.9167/37.6111/66.0000/15.5486/4.4927/17.9519/68.0000/36.8947/50.0000/27.7407/46.0000/44.3000/18.4170/3.4187/12.6583/9.0295/40.5000/29.8500/33.0370/13.3242/47.2500/32.6897/42.5833/44.3000/20.2083/79.0000/51.4815/31.0294/57.6316/81.0000/11.6218/17.5572/1.7782/81.5000/87.5000/45.8571/47.5882/76.9231/19.2344/41.4643/29.0897/6.4375/0.8550/26.6239/69.5833/48.8125/29.8077/23.8158/48.1875/17.3460/22.3391/0.3666/3.4888/18.8844/47.4706/38.7059/10.5012/8.0623/39.3143/9.2749/22.4023/26.2569/42.5385/78.8462/55.0000/16.2108/53.9683/67.9167/13.3789/30.8571/31.2308/90.0000/100.0000/82.5000/80.0000/78.3333/53.6364/43.2500/85.0000/4.5975/5.7127/50.9091/92.5000/80.0000/80.0000/41.4000/31.3846/61.4286/17.2317/1.0024/8.3360/62.1429/47.3333/80.0000/33.5000/10.7160/38.2857/36.8750/11.8664/43.0000/54.5455/90.0000/63.5714/22.4211/52.2727/68.0000/18.8934/29.7841/11.6172/63.4000/98.0000/59.7143/80.0000/64.6000/66.5789/31.2029/80.6250/7.1004/3.9301/27.7982/62.6000/39.8621/75.5000/33.1071/36.2195/62.0000/21.6388/0.6695/8.7644/17.4206/11.8974/60.8000/21.5418/16.9607/24.7070/43.1818/10.7652/20.1155/1.7586/60.0000/35.5435/24.7070/43.0909/48.0000 TSVASYVYNGYSVFFVGTKSGKLKKIR HLA-A*02:01 HLA-A*02:64 HLA-B*07:02 HLA-B*51:53 FALSE NA 445 12.56092685 uc001hgz.3 RB0401_02_004 C SOMATIC_HI -10.8231 1335 0 FALSE not fixed (>4 std) [u] 5.22 TSVASYVYNGYSVVFVGTKSGKLKKIR 0.063649222 14 7 2.08 FALSE 1.22277428082 15 14.28 NA 1 6 NA NA NA 3.18 1 FALSE FALSE SVASYVYNGYSVVFV 707 False 2 010-M31 HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53 8 NA YVYNGYSVF YVYNGYSVF YVYNGYSVFF YVYNGYSVFFV ASYVYNGYSVF/YVYNGYSVFF/YVYNGYSVFFV/VYNGYSVFFV/YNGYSVFFVGT/NGYSVFFVGTK/GYSVFFVGTKS/YSVFFVGTKSG/SVFFVGTKSGK/VFFVGTKSGKL/FFVGTKSGKLK/SYVYNGYSVF/YVYNGYSVFF/VYNGYSVFFV/YNGYSVFFVG/NGYSVFFVGT/GYSVFFVGTK/YSVFFVGTKS/SVFFVGTKSG/VFFVGTKSGK/FFVGTKSGKL/YVYNGYSVF/VYNGYSVFF/YNGYSVFFV/NGYSVFFVG/GYSVFFVGT/YSVFFVGTK/SVFFVGTKS/VFFVGTKSG/FFVGTKSGK/VYNGYSVF/YNGYSVFF/NGYSVFFV/GYSVFFVG/YSVFFVGT/SVFFVGTK/VFFVGTKS/FFVGTKSG/ASYVYNGYSVF/YVYNGYSVFF/YVYNGYSVFFV/VYNGYSVFF/YNGYSVFFVGT/NGYSVFFVGTK/GYSVFFVGTKS/YSVFFVGTKSG/SVFFVGTKSGK/VFFVGTKSGKL/FFVGTKSGKLK/SYVYNGYSVF/YVYNGYSVFF/VYNGYSVFFV/YNGYSVFFVG/NGYSVFFVGT/GYSVFFVGTK/YSVFFVGTKS/SVFFVGTKSG/VFFVGTKSGK/FFVGTKSGKL/YVYNGYSVF/VYNGYSVFF/YNGYSVFFV/NGYSVFFVG/GYSVFFVGT/YSVFFVGTK/SVFFVGTKS/VFFVGTKSG/FFVGTKSGK/VYNGYSVF/YNGYSVFF/NGYSVFFV/GYSVFFVG/YSVFFVGT/SVFFVGTK/VFFVGTKS/FFVGTKSG/ASYVYNGYSVF/SYVYNGYSVFF/YVYNGYSVFFV/VYNGYSVFF/YNGYSVFFVGT/NGYSVFFVGTK/GYSVFFVGTKS/YSVFFVGTKSG/SVFFVGTKSGK/VFFVGTKSGKL/FFVGTKSGKLK/SYVYNGYSVF/YVYNGYSVFF/VYNGYSVFF/YNGYSVFFVG/NGYSVFFVGT/GYSVFFVGTK/YSVFFVGTKS/SVFFVGTKSG/VFFVGTKSGK/FFVGTKSGKL/YVYNGYSVF/VYNGYSVFF/YNGYSVFFV/NGYSVFFVG/GYSVFFVGT/YSVFFVGTK/SVFFVGTKS/VFFVGTKSG/FFVGTKSGK/VYNGYSVF/YNGYSVFF/NGYSVFFV/GYSVFFVG/YSVFFVGT/SVFFVGTK/VFFVGTKS/FFVGTKSG/ASYVYNGYSVF/YVYNGYSVFF/YVYNGYSVFFV/VYNGYSVFF/NGYSVFFVGT/NGYSVFFVGTK/GYSVFFVGTKS/YSVFFVGTKSG/SVFFVGTKSGK/VFFVGTKSGKL/FFVGTKSGKL/SYVYNGYSVF/YVYNGYSVFF/VYNGYSVFFV/YNGYSVFFVG/NGYSVFFVGT/YSVFFVGTK/YSVFFVGTKS/SVFFVGTKSG/VFFVGTKSGK/FFVGTKSGKL/YVYNGYSVF/VYNGYSVFF/YNGYSVFFV/NGYSVFFVG/GYSVFFVGT/YSVFFVGTK/SVFFVGTKS/VFFVGTKSG/FFVGTKSGK/VYNGYSVF/YNGYSVFF/NGYSVFFV/GYSVFFVG/YSVFFVGT/SVFFVGTK/VFFVGTKS/FFVGTKSG 100 8 8 NA 8 NA HLA-A*02:64 A 27.9394651257 NA 0.419 0.3666 0.959220361657 9 9 11 SVASYVYNGYSVFFV 0.70435 NA NA NA NA 0.063 15 no -NA NA SVASYVYNGYSVVFV PLXNA2 NA 3.07 1.32 FALSE FALSE FALSE NA NA 6 NA NA NA NA HLA-DRB1*15:01 FALSE PLXNA2 NA 30 11 NA RB0401_02_004-chr1_208383659 NGYSVFFV TRUE 1 3.7 1.56852222222 0.19 1.08 NA 40.2155118421 1 HLA A*0201 uc001hha.4#exon.1 NA NA NA 12 2.2 4 0.1 3.9 ACCTCTGTGGCCTCCTACGTTTACAACGGCTACAGCGTGTTTTTTGTGGGGACTAAGAGTGGCAAGCTGAAAAAGGTAAGA 0.615111291441 SME NGYSVVFV 261-RB0401_02_004 0 YVYNGYSVF chr1_208383659 False FALSE 482 0.2 7 2.3 4.4 chr1_208383659 8 RB0401_02_004 0.661631922508 3.18 FALSE 261 V500F YVYNGYSVVF YVYNGYSVVFV YVYNGYSVV YVYNGYSVV 9.184718624 SVASYVYNGYSVFFV 9.9980210742 0 2 104 HLA DRB1*1501 1.1 23.0440/28.5870/0.7789/81.0000/82.0000/68.0000/52.0370/78.0000/42.9167/37.6111/66.0000/15.5486/4.4927/17.9519/68.0000/36.8947/50.0000/27.7407/46.0000/44.3000/18.4170/3.4187/12.6583/9.0295/40.5000/29.8500/33.0370/13.3242/47.2500/32.6897/42.5833/44.3000/20.2083/79.0000/51.4815/31.0294/57.6316/81.0000/11.6218/17.5572/1.7782/81.5000/87.5000/45.8571/47.5882/76.9231/19.2344/41.4643/29.0897/6.4375/0.8550/26.6239/69.5833/48.8125/29.8077/23.8158/48.1875/17.3460/22.3391/0.3666/3.4888/18.8844/47.4706/38.7059/10.5012/8.0623/39.3143/9.2749/22.4023/26.2569/42.5385/78.8462/55.0000/16.2108/53.9683/67.9167/13.3789/30.8571/31.2308/90.0000/100.0000/82.5000/80.0000/78.3333/53.6364/43.2500/85.0000/4.5975/5.7127/50.9091/92.5000/80.0000/80.0000/41.4000/31.3846/61.4286/17.2317/1.0024/8.3360/62.1429/47.3333/80.0000/33.5000/10.7160/38.2857/36.8750/11.8664/43.0000/54.5455/90.0000/63.5714/22.4211/52.2727/68.0000/18.8934/29.7841/11.6172/63.4000/98.0000/59.7143/80.0000/64.6000/66.5789/31.2029/80.6250/7.1004/3.9301/27.7982/62.6000/39.8621/75.5000/33.1071/36.2195/62.0000/21.6388/0.6695/8.7644/17.4206/11.8974/60.8000/21.5418/16.9607/24.7070/43.1818/10.7652/20.1155/1.7586/60.0000/35.5435/24.7070/43.0909/48.0000 TSVASYVYNGYSVFFVGTKSGKLKKVR HLA-A*02:01 HLA-A*02:64 HLA-B*07:02 HLA-B*51:53 FALSE NA 499 3.055718532 uc001hha.4 RB0401_02_004 C SOMATIC_HI -10.8231 1497 0 FALSE not fixed (>4 std) [u] 5.22 TSVASYVYNGYSVVFVGTKSGKLKKVR 0.063649222 14 7 2.08 FALSE 1.22277428082 15 14.28 NA 1 6 NA NA NA 3.18 1 FALSE FALSE SVASYVYNGYSVVFV 707 False 2 010-M30 HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53 8 NA YVYNGYSVF YVYNGYSVF YVYNGYSVFF YVYNGYSVFFV ASYVYNGYSVF/YVYNGYSVFF/YVYNGYSVFFV/VYNGYSVFFV/YNGYSVFFVGT/NGYSVFFVGTK/GYSVFFVGTKS/YSVFFVGTKSG/SVFFVGTKSGK/VFFVGTKSGKL/FFVGTKSGKLK/SYVYNGYSVF/YVYNGYSVFF/VYNGYSVFFV/YNGYSVFFVG/NGYSVFFVGT/GYSVFFVGTK/YSVFFVGTKS/SVFFVGTKSG/VFFVGTKSGK/FFVGTKSGKL/YVYNGYSVF/VYNGYSVFF/YNGYSVFFV/NGYSVFFVG/GYSVFFVGT/YSVFFVGTK/SVFFVGTKS/VFFVGTKSG/FFVGTKSGK/VYNGYSVF/YNGYSVFF/NGYSVFFV/GYSVFFVG/YSVFFVGT/SVFFVGTK/VFFVGTKS/FFVGTKSG/ASYVYNGYSVF/YVYNGYSVFF/YVYNGYSVFFV/VYNGYSVFF/YNGYSVFFVGT/NGYSVFFVGTK/GYSVFFVGTKS/YSVFFVGTKSG/SVFFVGTKSGK/VFFVGTKSGKL/FFVGTKSGKLK/SYVYNGYSVF/YVYNGYSVFF/VYNGYSVFFV/YNGYSVFFVG/NGYSVFFVGT/GYSVFFVGTK/YSVFFVGTKS/SVFFVGTKSG/VFFVGTKSGK/FFVGTKSGKL/YVYNGYSVF/VYNGYSVFF/YNGYSVFFV/NGYSVFFVG/GYSVFFVGT/YSVFFVGTK/SVFFVGTKS/VFFVGTKSG/FFVGTKSGK/VYNGYSVF/YNGYSVFF/NGYSVFFV/GYSVFFVG/YSVFFVGT/SVFFVGTK/VFFVGTKS/FFVGTKSG/ASYVYNGYSVF/SYVYNGYSVFF/YVYNGYSVFFV/VYNGYSVFF/YNGYSVFFVGT/NGYSVFFVGTK/GYSVFFVGTKS/YSVFFVGTKSG/SVFFVGTKSGK/VFFVGTKSGKL/FFVGTKSGKLK/SYVYNGYSVF/YVYNGYSVFF/VYNGYSVFF/YNGYSVFFVG/NGYSVFFVGT/GYSVFFVGTK/YSVFFVGTKS/SVFFVGTKSG/VFFVGTKSGK/FFVGTKSGKL/YVYNGYSVF/VYNGYSVFF/YNGYSVFFV/NGYSVFFVG/GYSVFFVGT/YSVFFVGTK/SVFFVGTKS/VFFVGTKSG/FFVGTKSGK/VYNGYSVF/YNGYSVFF/NGYSVFFV/GYSVFFVG/YSVFFVGT/SVFFVGTK/VFFVGTKS/FFVGTKSG/ASYVYNGYSVF/YVYNGYSVFF/YVYNGYSVFFV/VYNGYSVFF/NGYSVFFVGT/NGYSVFFVGTK/GYSVFFVGTKS/YSVFFVGTKSG/SVFFVGTKSGK/VFFVGTKSGKL/FFVGTKSGKL/SYVYNGYSVF/YVYNGYSVFF/VYNGYSVFFV/YNGYSVFFVG/NGYSVFFVGT/YSVFFVGTK/YSVFFVGTKS/SVFFVGTKSG/VFFVGTKSGK/FFVGTKSGKL/YVYNGYSVF/VYNGYSVFF/YNGYSVFFV/NGYSVFFVG/GYSVFFVGT/YSVFFVGTK/SVFFVGTKS/VFFVGTKSG/FFVGTKSGK/VYNGYSVF/YNGYSVFF/NGYSVFFV/GYSVFFVG/YSVFFVGT/SVFFVGTK/VFFVGTKS/FFVGTKSG 100 8 8 NA 8 NA HLA-A*02:64 A 27.9394651257 NA 0.419 0.3666 0.959220361657 9 9 11 SVASYVYNGYSVFFV 0.70435 NA NA NA NA 0.063 15 no -NA NA LCYWNPYWMLPSDVC GXYLT1 NA 3.07 1.32 FALSE FALSE TRUE NA NA 14.67 NA NA NA NA HLA-DRB1*15:01 TRUE GXYLT1 NA 6 51 CD4 RB0401_02_004-chr12_42523620 NLYWMLPS TRUE 1 10 6.45181111111 1 1.08 CD4+ 56.1840706667 1 HLA A*0201 uc001rms.4#exon.1 NA NA NA 5 2 19 0.8 0.8 TCGGACAGGTGTAAAGATTTCTCTCTGTGTTACTGGAATCTCTATTGGATGCTGCCCTCTGATGTTTGTGGAATGAACTGC 4.3726575571 SME NPYWMLPS 205-RB0401_02_004 0 NLYWMLPSDV chr12_42523620 False FALSE 621 0.9 11.1 1.8 26 chr12_42523620 6 RB0401_02_004 7.09428648036 4.32 FALSE NM_173601 205 P85L NPYWMLPS SLCYWNPYWML SLCYWNPYWM FSLCYWNPYW 0.214052621 LCYWNLYWMLPSDVC 30.3966534748 0 1 HLA DRB1*1501 0.2 83.0000/76.0000/81.0000/30.8333/5.1769/88.3333/85.0000/46.2500/15.5287/14.5652/81.0000/37.6111/82.0000/38.4118/5.4986/34.0385/82.0000/67.0000/53.5185/2.1187/33.8148/45.0000/51.2963/12.0951/23.5165/34.4615/61.7857/73.7500/17.6704/20.8542/29.9750/39.9333/61.4286/65.5000/29.4250/98.3333/17.8222/90.0000/86.8750/56.2766/59.4681/34.2083/7.7930/88.7500/78.8462/61.0294/41.2857/32.8136/85.6250/46.2105/58.4043/12.7621/6.3165/41.0000/81.0000/51.9841/53.8889/5.2454/42.1538/47.2941/17.6950/3.1097/31.3636/29.2692/56.0638/55.8511/16.6979/25.9365/39.5429/12.9915/47.6471/70.2778/34.0833/89.3750/23.2368/82.5000/73.3333/92.5000/87.5000/78.3333/100.0000/100.0000/100.0000/95.0000/85.0000/95.0000/59.4444/78.3333/85.0000/59.4444/80.0000/100.0000/95.0000/100.0000/51.3636/67.0000/62.1429/62.1429/57.2222/46.2500/60.7143/78.3333/90.0000/61.4286/35.8889/76.6667/76.6667/69.0000/90.0000/51.3636/100.0000/66.0000/87.5000/56.0000/48.0714/51.7308/61.4000/96.0000/99.0000/99.0000/80.6250/69.2105/85.7143/42.9565/40.8571/31.2754/53.9423/41.4000/94.0000/98.0000/98.0000/27.5138/40.7500/28.6538/22.4121/32.3934/18.9372/35.3696/58.1429/90.0000/40.1786/10.7124/22.9950/62.2000/20.7292/55.2857/26.2109/92.0000/42.4783/69.4737 SDRCKDFSLCYWNLYWMLPSDVCGMNC HLA-A*02:01 HLA-A*02:64 HLA-B*07:02 HLA-B*51:53 FALSE NA 84 3.555992537 uc001rms.4 RB0401_02_004 G SOMATIC_HI -106.598 253 0 TRUE FIXED 5.22 SDRCKDFSLCYWNPYWMLPSDVCGMNC 0.195522388 14 0 2.08 FALSE 5.69226486158 15 14.28 NA 1 14.67 NA NA NA 4.32 0 TRUE FALSE LCYWNPYWMLPSDVC 670 True 1 010-M06 HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53 8 NA SLCYWNLYWM FSLCYWNLYW NLYWMLPS SLCYWNLYWML CKDFSLCYWNL/KDFSLCYWNLY/FSLCYWNLYW/SLCYWNLYWM/SLCYWNLYWML/LCYWNLYWML/CYWNLYWMLPS/YWNLYWMLPSD/NLYWMLPSDV/NLYWMLPSDVC/LYWMLPSDVCG/KDFSLCYWNL/DFSLCYWNLY/FSLCYWNLYW/SLCYWNLYWM/LCYWNLYWML/CYWNLYWMLP/YWNLYWMLPS/WNLYWMLPSD/NLYWMLPSDV/LYWMLPSDVC/DFSLCYWNL/FSLCYWNLY/SLCYWNLYW/LCYWNLYWM/CYWNLYWML/YWNLYWMLP/WNLYWMLPS/NLYWMLPSD/LYWMLPSDV/FSLCYWNL/SLCYWNLY/LCYWNLYW/CYWNLYWM/YWNLYWML/WNLYWMLP/NLYWMLPS/LYWMLPSD/CKDFSLCYWNL/KDFSLCYWNLY/FSLCYWNLYW/FSLCYWNLYWM/SLCYWNLYWML/LCYWNLYWML/CYWNLYWMLPS/YWNLYWMLPSD/NLYWMLPSDV/NLYWMLPSDVC/LYWMLPSDVCG/KDFSLCYWNL/DFSLCYWNLY/FSLCYWNLYW/SLCYWNLYWM/LCYWNLYWML/CYWNLYWMLP/YWNLYWMLPS/WNLYWMLPSD/NLYWMLPSDV/LYWMLPSDVC/DFSLCYWNL/FSLCYWNLY/SLCYWNLYW/LCYWNLYWM/CYWNLYWML/YWNLYWMLP/WNLYWMLPS/NLYWMLPSD/LYWMLPSDV/FSLCYWNL/SLCYWNLY/LCYWNLYW/CYWNLYWM/YWNLYWML/WNLYWMLP/NLYWMLPS/LYWMLPSD/KDFSLCYWNLY/DFSLCYWNLYW/FSLCYWNLYWM/SLCYWNLYWML/LCYWNLYWML/CYWNLYWMLPS/YWNLYWMLPSD/WNLYWMLPSDV/NLYWMLPSDVC/LYWMLPSDVCG/KDFSLCYWNL/DFSLCYWNLY/FSLCYWNLYW/SLCYWNLYWM/LCYWNLYWML/CYWNLYWML/YWNLYWMLPS/WNLYWMLPSD/NLYWMLPSDV/LYWMLPSDVC/DFSLCYWNL/FSLCYWNLY/SLCYWNLYW/LCYWNLYWM/CYWNLYWML/YWNLYWMLP/WNLYWMLPS/NLYWMLPSD/LYWMLPSDV/FSLCYWNL/SLCYWNLY/LCYWNLYW/CYWNLYWM/YWNLYWML/WNLYWMLP/NLYWMLPS/LYWMLPSD/KDFSLCYWNLY/DFSLCYWNLYW/FSLCYWNLYWM/SLCYWNLYWML/LCYWNLYWML/CYWNLYWML/YWNLYWMLPSD/WNLYWMLPSDV/NLYWMLPSDVC/LYWMLPSDVCG/KDFSLCYWNL/DFSLCYWNLY/FSLCYWNLYW/SLCYWNLYWM/LCYWNLYWML/CYWNLYWML/YWNLYWMLPS/WNLYWMLPSD/NLYWMLPSDV/LYWMLPSDVC/DFSLCYWNL/FSLCYWNLY/SLCYWNLYW/LCYWNLYWM/CYWNLYWML/YWNLYWMLP/WNLYWMLPS/NLYWMLPSD/LYWMLPSDV/FSLCYWNL/SLCYWNLY/LCYWNLYW/CYWNLYWM/YWNLYWML/WNLYWMLP/NLYWMLPS/LYWMLPSD 2 7 6 1 TRUE HLA-A*02:01 A 46.1769086404 1.107 2.1187 4.93990021491 10 10 11 LCYWNLYWMLPSDVC 12.957425 NA NA NA NA 0.195 15 no -NA NA PRVWGKYLWRSPHSK C1RL NA 3.07 1.32 FALSE FALSE FALSE NA NA 17.47 NA NA NA NA HLA-DRB1*15:01 FALSE C1RL.C1RL-AS1 NA 37 36 NA RB0401_02_004-chr12_7261761 GPSVWGKYL TRUE 1 0.4 2.75427777778 0.333333333 1.08 NA 39.2620175 1 HLA B*0702 uc009zft.3#exon.0 NA NA NA 1 0.9 1.6 6.7 14.5 ATGCCTGGACCCAGTGTGTGGGGGAAATATCTCTGGAGAAGCCCTCACTCCAAAGGCTGTCCAGGCGCAATGTGGTGGCTG 0.535215763886 SME GPRVWGKYL 1-RB0401_02_004 0 GPSVWGKYL chr12_7261761 False FALSE 465 5.7 16 0.9 0.5 chr12_7261761 0 RB0401_02_004 1.91702335854 17.52 TRUE 1 R5S RVWGKYLWRS RVWGKYLWRS GPRVWGKYL MPGPRVWGKYL 1.642740292 PSVWGKYLWRSPHSK 6.26099578595 0 1 HLA DRB1*1501 1.7 37.3889/88.3333/53.3333/58.9474/42.8333/37.5000/61.0714/48.5000/55.0000/11.3014/30.9444/62.5000/26.2712/50.0000/14.3403/70.6250/85.0000/67.0000/63.2143/22.2170/50.7143/77.3077/42.6154/51.5079/51.9841/27.2621/72.2222/33.4423/41.8571/5.7095/16.7728/42.4615/35.1957/33.3462/3.2045/69.3750/80.0000/55.4255/70.2778/9.4599/0.9342/48.6667/25.3704/100.0000/80.0000/3.4245/3.7350/3.4794/90.0000/39.6667/5.8482/63.5714/0.1499/53.6364/23.3824/11.4007/61.4286/7.0358/5.6906/18.1507/3.2053/36.0488/39.8276/90.0000/77.5000/4.1679/17.2991/9.9761/68.1579/60.8000/14.6796/37.1053/2.4878/18.4863/35.5652/13.4841/77.5000/17.5888/7.5533/7.4940 MPGPSVWGKYLWRSPHSK HLA-A*02:01 HLA-A*02:64 HLA-B*07:02 HLA-B*51:53 FALSE NA 4 21.28993727 uc009zft.3 RB0401_02_004 T SOMATIC_HI -126.576 14 0 FALSE FIXED 5.22 MPGPRVWGKYLWRSPHSK 0.210893855 5 2 2.08 FALSE 2.05851975114 15 14.28 NA 1 17.47 NA NA NA 17.52 1 FALSE uc001qsn.3 uc001qso.2 FALSE PRVWGKYLWRSPHSK 716 False 1 010-M46 HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53 9 NA GPSVWGKYL MPGPSVWGKYL SVWGKYLWRS SVWGKYLWRS MPGPSVWGKYL/PGPSVWGKYLW/GPSVWGKYLWR/SVWGKYLWRS/SVWGKYLWRSP/MPGPSVWGKY/PGPSVWGKYL/GPSVWGKYLW/SVWGKYLWR/SVWGKYLWRS/MPGPSVWGK/PGPSVWGKY/GPSVWGKYL/PSVWGKYLW/SVWGKYLWR/MPGPSVWG/PGPSVWGK/GPSVWGKY/PSVWGKYL/SVWGKYLW/MPGPSVWGKYL/PGPSVWGKYLW/GPSVWGKYLWR/SVWGKYLWRS/SVWGKYLWRSP/MPGPSVWGKY/PGPSVWGKYL/GPSVWGKYLW/SVWGKYLWR/SVWGKYLWRS/MPGPSVWGK/PGPSVWGKY/GPSVWGKYL/PSVWGKYLW/SVWGKYLWR/MPGPSVWG/PGPSVWGK/GPSVWGKY/PSVWGKYL/SVWGKYLW/MPGPSVWGKYL/GPSVWGKYLW/GPSVWGKYL/SVWGKYLWRS/SVWGKYLWRSP/MPGPSVWGKY/GPSVWGKYL/GPSVWGKYL/SVWGKYLWR/SVWGKYLWRS/MPGPSVWGK/PGPSVWGKY/GPSVWGKYL/PSVWGKYLW/SVWGKYLWR/MPGPSVWG/PGPSVWGK/GPSVWGKY/PSVWGKYL/SVWGKYLW/MPGPSVWGKYL/GPSVWGKYLW/GPSVWGKYLW/PSVWGKYLW/SVWGKYLWRSP/MPGPSVWGKY/PGPSVWGKYL/GPSVWGKYLW/PSVWGKYLW/SVWGKYLWRS/MPGPSVWGK/PGPSVWGKY/GPSVWGKYL/PSVWGKYLW/SVWGKYLWR/MPGPSVWG/PGPSVWGK/GPSVWGKY/PSVWGKYL/SVWGKYLW 33 4 2 NA 0 NA HLA-B*07:02 A 25.1564253185 NA 1.201 0.1499 0.913275315926 11 9 10 PSVWGKYLWRSPHSK 4.2859 NA NA NA NA 0.212 15 no -NA NA MAVFPATARGQLGIR CARKD NA 3.07 1.32 FALSE FALSE FALSE NA NA 42.46 NA NA NA NA HLA-DRB1*15:01 FALSE CARKD NA 17 48 NA RB0401_02_004-chr13_111267905 LATARGQL TRUE 1 6.1 3.68548888889 1 1.08 NA 39.0179025 1 HLA B*0702 uc010tjl.2#exon.0 NA NA NA 4 0.8 2.3 1.7 3 ATGGCTGTGTTTCTGGCGACGGCGCGGGGGCAGCTGGGAATCCGGAATGCTGCCCGATGGCCCTGGGTCCTCGCTGTGGGG 1.83215391307 SME PATARGQL 11-RB0401_02_004 0 FLATARGQL chr13_111267905 False FALSE 609 37 19.5 16 0.2 chr13_111267905 1 RB0401_02_004 1.94891557042 19.35 FALSE NM_001242881 11 P5L FPATARGQLGI FPATARGQLGI FPATARGQL PATARGQLGI 0.439357418 MAVFLATARGQLGIR 13.7758307526 0 1 HLA DRB1*1501 0.6 85.0000/12.6946/73.1250/1.9138/79.0000/55.2632/41.1667/13.2737/16.1194/26.8644/37.4444/24.3247/62.1429/1.3494/70.0000/15.3666/32.4483/82.0000/44.4000/44.9000/83.5000/20.3705/79.2308/7.2355/78.4615/60.0000/27.1553/21.2814/22.4483/39.5714/18.2177/19.6445/42.6923/1.7880/73.8889/32.6271/21.5879/75.7692/40.2414/50.0794/78.3333/8.4685/73.3333/43.5000/64.2857/54.0909/47.3333/9.4934/26.5000/20.0962/12.5775/21.7333/67.0000/1.6457/30.0000/22.4474/25.7037/85.0000/41.0000/5.8482/75.5000/37.1053/75.0000/36.7317/56.5714/27.3119/68.4211/23.4324/40.1429/4.6679/14.9254/26.4688/71.7857/9.9875/19.0528/3.6334/32.2787/52.9808/67.3684/5.0875 MAVFLATARGQLGIRNAA HLA-A*02:01 HLA-A*02:64 HLA-B*07:02 HLA-B*51:53 FALSE NA 4 37.07048484 uc010tjl.2 RB0401_02_004 C SOMATIC_HI -168.322 13 0 FALSE FIXED 5.22 MAVFPATARGQLGIRNAA 0.24671916 5 4 2.08 FALSE 3.11664448078 15 14.28 NA 2 42.46 NA NA NA 19.35 0 FALSE FALSE MAVFPATARGQLGIR 762 True 2 010-M17 HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53 8 NA FLATARGQL LATARGQLGI FLATARGQLGI FLATARGQLGI AVFLATARGQ/AVFLATARGQL/VFLATARGQL/FLATARGQLGI/LATARGQLGIR/MAVFLATARG/AVFLATARGQ/VFLATARGQL/FLATARGQL/LATARGQLGI/MAVFLATAR/AVFLATARG/VFLATARGQ/FLATARGQL/LATARGQLG/MAVFLATA/AVFLATAR/VFLATARG/FLATARGQ/LATARGQL/AVFLATARGQ/AVFLATARGQL/VFLATARGQL/FLATARGQLGI/LATARGQLGIR/MAVFLATARG/AVFLATARGQ/VFLATARGQL/FLATARGQLG/LATARGQLGI/MAVFLATAR/AVFLATARG/VFLATARGQ/FLATARGQL/LATARGQLG/MAVFLATA/AVFLATAR/VFLATARG/FLATARGQ/LATARGQL/MAVFLATARGQ/AVFLATARGQL/VFLATARGQL/FLATARGQLGI/LATARGQLGIR/MAVFLATARG/AVFLATARGQ/VFLATARGQL/FLATARGQL/LATARGQLGI/MAVFLATAR/AVFLATARG/VFLATARGQ/FLATARGQL/LATARGQLG/MAVFLATA/AVFLATAR/VFLATARG/FLATARGQ/LATARGQL/MAVFLATARGQ/AVFLATARGQL/VFLATARGQLG/FLATARGQLGI/LATARGQLGI/MAVFLATARG/AVFLATARGQ/VFLATARGQL/FLATARGQLG/LATARGQLGI/MAVFLATAR/AVFLATARG/VFLATARGQ/FLATARGQL/LATARGQLG/MAVFLATA/AVFLATAR/VFLATARG/FLATARGQ/LATARGQL 2 0 1 NA 1 NA HLA-A*02:01 T 27.7238674133 NA 0.843 1.3494 2.62717508049 10 9 11 MAVFLATARGQLGIR 2.104125 NA NA NA NA 0.253 15 no diff --git a/input/netmhcpan4/test.txt b/input/netmhcpan4/test.txt deleted file mode 100644 index ec0a8f5a..00000000 --- a/input/netmhcpan4/test.txt +++ /dev/null @@ -1,11 +0,0 @@ -WT_pep_II_2 WT_pep_II_3 WT_pep_II_0 gene.x pre_existing_cell_type_update C_RPKM DQB_RPKM serex actin_binding selected_by_TSMB X WT_cons_II_1 WT_cons_II_0 WT_cons_II_3 WT_cons_II_2 mhc_II_2 mhc_II_3 mhc_II_0 mhc_II_1 any_immunogenicity gene.y next_mutation_source WT_pep_II_1 RANK_MHC RANK_EXPR Cell.Type.IM mix_id MHC_I_epitope_.best_prediction. patient_done_in_IM mutations_in_transcript MHC_I_score_.WT. MB_score_top10_arithmetic VAF_in_RNA DQA_RPKM de_novo_cell_type_update MB_score_all_epitopes_arithmetic peptide_resulting_from_this_mutation MHC_I_allele_.best_prediction. exon mut_pos_II_3 mut_pos_II_2 mut_pos_II_1 mut_pos_II_0 mut_cons_I_3 mut_cons_I_2 mut_cons_I_1 mut_cons_I_0 mRNA_for_..13_AA_.SNV._._.15_AA_to_STOP_.INDEL. MB_score_best_per_alelle_harmonic allowed_positions MHC_I_epitope_.WT. unique.keys VAF_in_normal best4_mhc_epitope chr_pos..0.based. next_mutation.potential_to_change_27mer. mutation_found_in_proteome in_cytosol coverage_normal WT_cons_I_1 WT_cons_I_0 WT_cons_I_3 WT_cons_I_2 mutation mut_pos_I_1 patient MB_score_best_per_alelle_geometric MHC_II_score_.best_prediction. in_exosome RefSeq_transcript key substitution WT_pep_I_0 WT_pep_I_1 WT_pep_I_2 WT_pep_I_3 exon_expression MHC_II_epitope_.best_prediction. MB_score_all_epitopes_harmonic peptide_count_for_this_mutation_in_this_transcript distinct_peptides_resulting_from_this_mutation keys_of_distinct_peptides_resulting_from_this_mutation IS.reactivity MHC_II_allele_.best_prediction. MHC_I_score_.best_prediction. MB_epitope_scores X..13_AA_.SNV._._.15_AA_to_STOP_.INDEL. mhc_I_0 mhc_I_1 mhc_I_2 mhc_I_3 pre_existing_update length_II_1 codon transcript_expression UCSC_transcript sample_id wt.nt Site.classification FLRT.u transcript_position max_expression_risk_.0.none.1.low.2.med.3.high. any_immunogenicity_update Clone.type B_RPKM X.WT._..13_AA_.SNV._._.15_AA_to_STOP_.INDEL. VAF_in_tumor Position_Xmer_Seq MB_number_of_weak_binders DRB_RPKM exosomal MB_score_top10_geometric MHC_II_peptide_length_.best_prediction. A_RPKM distance_to_next_mutation.AA_residues. Cx MHC_II_score_.WT. mut_pep_II_1 mut_cons_II_3 mut_cons_II_2 mut_cons_II_1 mut_cons_II_0 MB_number_of_strong_binders done_in_IM other_transcripts_with_this_peptide RNA_binding MHC_II_epitope_.WT. coverage_tumor confirmed CN.w..EC mut.ID MB_alleles MHC_I_peptide_length_.best_prediction. RANK_MHC_II mut_pep_I_2 mut_pep_I_3 mut_pep_I_0 mut_pep_I_1 MB_epitope_sequences coverage_RNA mut_pos_I_3 mut_pos_I_2 IS mut_pos_I_0 de_novo_update best4_mhc_allele mut.nt MB_score_all_epitopes_geometric IM rho best4_mhc_score MB_score_top10_harmonic length_I_3 length_I_2 length_I_1 mut_pep_II_0 MB_score_best_per_alelle_arithmetic mut_pep_II_2 mut_pep_II_3 length_II_3 length_II_2 VAF.Nx_Q30..Nx_Q30.Nz_Q30. length_II_0 directed_to_TCR -NA NA FVPQMPKLLKSLFPV KIF13B NA 84.59 9.65 FALSE FALSE FALSE NA NA 44.02 NA NA NA NA HLA-DRB1*07:01 FALSE KIF13B NA 6 53 NA RB0401_02_003-chr8_28950310 KLLKSLFLV TRUE 1 0.1 2.28144444444 0.212121212 17.72 NA 54.1728516779 2 HLA A*0201 uc003xhh.4#exon.36 NA NA NA 13 3.9 7.9 0.65 0.2 TTCGTGCCGCAAATGCCAAAGCTCCTCAAGTCTCTCTTTCTCGTCCGCGATGAGAAGAGGGGCAAGCGGCCGTCTCCCCTC 0.297988861783 SME KLLKSLFPV 57-RB0401_02_003 0 KLLKSLFLV chr8_28950310 False FALSE 465 2.95 0.2 25 3.2 chr8_28950310 4 RB0401_02_003 1.42982459317 9.58 FALSE NM_015254 57 P1470L KLLKSLFPV KSLFPVRDEK LLKSLFPV MPKLLKSLFP 3.425515898 FVPQMPKLLKSLFLV 7.23537465924 0 2 294 HLA DRB1*0701 0.1 64.0299/60.4478/64.4403/89.2683/40.7500/29.7660/63.9179/14.1155/58.2948/68.2212/42.1364/34.9062/8.2583/55.9827/91.9118/1.7824/16.7465/67.6923/7.5926/16.8009/66.9231/2.9664/5.9981/85.9756/13.2083/0.6743/16.9756/88.7805/0.5670/14.4874/27.7986/39.7870/56.7919/45.3056/15.7186/45.7639/66.0096/21.5878/4.4240/42.7500/13.1361/85.0000/58.9474/66.5000/49.5714/66.5000/45.5000/92.5000/45.6000/3.4539/3.7486/62.5000/96.6667/36.3158/20.4861/86.6667/26.0678/55.0000/59.7368/0.0876/24.0779/96.6667/78.0000/13.5979/54.0741/37.2778/52.5926/2.9722/4.2806/66.5000/96.6667/22.9057/57.3684/34.6538/92.5000/42.1875/76.1111/95.0000/93.7500/87.0000/81.6667/86.0000/72.2727/61.0000/60.0000/77.7778/70.4545/44.8462/78.3333/95.0000/41.3529/35.6000/86.0000/25.8791/41.4118/56.7241/15.7520/21.8071/92.5000/69.0000/14.8924/70.0000/37.3913/19.2600/21.1929/34.8125/77.2222/88.0000/31.7674/72.7273/60.0000/52.3077/27.7917/100.0000/100.0000/100.0000/95.0000/92.5000/95.0000/81.6667/69.1667/92.5000/5.6504/95.0000/78.3333/95.0000/95.0000/75.0000/63.3333/92.5000/51.1538/47.0000/67.5000/57.0000/45.5000/92.5000/75.0000/30.9444/37.4444/56.5000/32.9286/58.5000/80.0000/81.6667/95.0000/62.5000/69.1667/55.0000/68.3333 FVPQMPKLLKSLFLVRDEKRGKRPSPL HLA-A*02:01 HLA-A*30:01 HLA-B*15:01 HLA-B*35:08 FALSE NA 1469 6.145347743 uc003xhh.4 RB0401_02_003 G SOMATIC_HI -28.9231 4408 0 FALSE not fixed (>3 std) [u] 64.6 FVPQMPKLLKSLFPVRDEKRGKRPSPL 0.112612613 14 4 23.95 FALSE 1.45469099281 15 45.74 NA 1 44.02 NA NA NA 9.58 1 FALSE FALSE FVPQMPKLLKSLFPV 444 True 2 007-M06 HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08 9 NA LLKSLFLV MPKLLKSLFL KLLKSLFLV KSLFLVRDEK QMPKLLKSLFL/KLLKSLFLVR/KLLKSLFLVR/LLKSLFLVRDE/KSLFLVRDEK/KSLFLVRDEKR/SLFLVRDEK/LFLVRDEKRGK/FLVRDEKRGKR/LVRDEKRGK/MPKLLKSLFL/KLLKSLFLV/KLLKSLFLVR/LLKSLFLVR/KSLFLVRDE/KSLFLVRDEK/SLFLVRDEKR/LFLVRDEKR/FLVRDEKRGK/LVRDEKRGKR/PKLLKSLFL/KLLKSLFLV/LLKSLFLVR/LKSLFLVRD/KSLFLVRDE/SLFLVRDEK/LFLVRDEKR/FLVRDEKRG/LVRDEKRGK/KLLKSLFL/LLKSLFLV/LKSLFLVR/KSLFLVRD/SLFLVRDE/LFLVRDEK/FLVRDEKR/LVRDEKRG/QMPKLLKSLFL/MPKLLKSLFLV/KLLKSLFLV/KLLKSLFLV/LLKSLFLVRDE/LKSLFLVRDEK/SLFLVRDEKR/SLFLVRDEKRG/FLVRDEKRGK/FLVRDEKRGKR/LVRDEKRGKRP/MPKLLKSLFL/KLLKSLFLV/KLLKSLFLV/LLKSLFLVRD/LKSLFLVRDE/KSLFLVRDEK/SLFLVRDEKR/LFLVRDEKRG/FLVRDEKRGK/LVRDEKRGKR/PKLLKSLFL/KLLKSLFLV/LLKSLFLVR/LKSLFLVRD/KSLFLVRDE/SLFLVRDEK/LFLVRDEKR/FLVRDEKRG/LVRDEKRGK/KLLKSLFL/LLKSLFLV/LKSLFLVR/KSLFLVRD/SLFLVRDE/LFLVRDEK/FLVRDEKR/LVRDEKRG/QMPKLLKSLFL/MPKLLKSLFLV/PKLLKSLFLVR/KLLKSLFLV/LLKSLFLVRDE/LKSLFLVRDEK/SLFLVRDEKR/SLFLVRDEKRG/LFLVRDEKRGK/FLVRDEKRGKR/LVRDEKRGKRP/KLLKSLFLV/KLLKSLFLVR/LLKSLFLVRD/LKSLFLVRDE/KSLFLVRDEK/SLFLVRDEKR/LFLVRDEKRG/FLVRDEKRGK/LVRDEKRGKR/PKLLKSLFL/KLLKSLFLV/LLKSLFLVR/LKSLFLVRD/KSLFLVRDE/SLFLVRDEK/LFLVRDEKR/FLVRDEKRG/LVRDEKRGK/KLLKSLFL/LLKSLFLV/LKSLFLVR/KSLFLVRD/SLFLVRDE/LFLVRDEK/FLVRDEKR/LVRDEKRG/MPKLLKSLFLV/PKLLKSLFLVR/KLLKSLFLVRD/LLKSLFLVRDE/LKSLFLVRDEK/KSLFLVRDEKR/SLFLVRDEKRG/LFLVRDEKRGK/FLVRDEKRGKR/LVRDEKRGKRP/MPKLLKSLFL/KLLKSLFLV/KLLKSLFLVR/LLKSLFLVR/LKSLFLVRDE/KSLFLVRDEK/SLFLVRDEKR/LFLVRDEKRG/FLVRDEKRGK/LVRDEKRGKR/PKLLKSLFL/KLLKSLFLV/LLKSLFLVR/LKSLFLVRD/KSLFLVRDE/SLFLVRDEK/LFLVRDEKR/FLVRDEKRG/LVRDEKRGK/KLLKSLFL/LLKSLFLV/LKSLFLVR/KSLFLVRD/SLFLVRDE/LFLVRDEK/FLVRDEKR/LVRDEKRG 33 9 6 NA 7 NA HLA-A*02:01 A 39.2175930352 NA 0.662 0.0876 0.539351037234 10 8 10 FVPQMPKLLKSLFLV 5.29935 NA NA NA NA 0.112 15 no -NA NA LVLPMWAIALISFGV SLC20A2 NA 84.59 9.65 FALSE FALSE FALSE NA NA 6.21 NA NA NA NA HLA-DRB1*07:01 FALSE SLC20A2 NA 3 39 NA RB0401_02_003-chr8_42302267 VLGLALPM TRUE 1 0.1 2.23571111111 0.452830189 17.72 NA 36.8793894737 1 HLA A*0201 uc003xpe.3#exon.5 NA NA NA 1 0.6 3.3 7.4 1.05 TTTTCCATCATGTACACAGGAGCACCAGTGCTCGGCCTTGCTCTCCCCATGTGGGCCATAGCCCTCATTTCCTTTGGTGTC 0.832017161998 SME VLGLVLPM 332-RB0401_02_003 0 GLALPMWAI chr8_42302267 False FALSE 334 12 0.85 0.6 3.4 chr8_42302267 10 RB0401_02_003 1.88602944494 6.21 TRUE NM_006749 332 V209A VLGLVLPM MYTGAPVLGLV VLGLVLPM APVLGLVLPM 9.039554756 LALPMWAIALISFGV 10.4402476808 0 2 530 HLA DRB1*0701 0.1 31.0588/36.8500/78.2540/71.3291/87.5610/86.8293/69.8077/77.4603/72.3418/56.4162/80.1961/10.4006/24.2746/60.7090/26.2862/81.7647/32.1341/48.2951/31.0392/31.7353/29.9489/5.7492/19.8302/50.8836/42.7727/34.6750/20.8341/20.5742/11.7579/17.2162/44.3077/53.7069/90.0000/54.1810/55.3179/42.3636/42.7614/39.5833/43.0000/13.1055/67.5000/23.0330/43.7000/34.5769/9.3072/19.6923/3.7333/16.9613/16.3000/7.3751/17.3370/41.1667/13.5979/41.5000/3.7365/4.3047/2.3392/8.7870/2.4190/15.3192/11.7335/48.0000/14.2250/10.3837/21.5114/0.2643/17.9444/0.6721/38.1176/26.8814/77.0000/9.8248/46.5000/3.8371/8.7126/11.9705/75.0000/23.5648/87.0000/34.3125/45.2308/93.7500/58.2759/85.0000/30.3404/59.4828/72.7273/30.3617/14.3249/55.6897/10.9653/40.3684/48.3636/38.3182/31.0000/22.0079/23.5833/21.0214/6.8241/49.4444/18.2650/7.4200/51.4103/10.8907/27.1194/5.5886/45.7692/25.9341/91.2500/19.5050/49.0000/38.0000/53.8462/40.1053/67.5000/20.3824/54.2308/27.0417/7.3194/95.0000/92.5000/90.0000/60.8333/23.4524/65.8333/38.7143/10.8995/35.9000/1.6299/35.3000/81.6667/65.8333/75.0000/10.6516/13.7463/24.9189/6.1261/8.1687/13.9522/16.0552/50.3846/30.8333/13.8529/13.5331/49.3333/1.4900/65.0000/36.2222/26.5862/75.0000/20.4706/71.6667 FSIMYTGAPVLGLALPMWAIALISFGV HLA-A*02:01 HLA-A*30:01 HLA-B*15:01 HLA-B*35:08 FALSE NA 208 23.04052926 uc003xpe.3 RB0401_02_003 A SOMATIC_HI -30.0013 625 0 FALSE FIXED 64.6 FSIMYTGAPVLGLVLPMWAIALISFGV 0.164556962 14 4 23.95 TRUE 1.71841060798 15 45.74 NA 1 6.21 NA NA NA 6.21 1 FALSE uc010lxl.3 uc010lxm.3 FALSE LVLPMWAIALISFGV 237 True 2 007-M03 HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*30:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*15:01/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08/HLA-B*35:08 8 NA VLGLALPM APVLGLALPM VLGLALPM MYTGAPVLGLA MYTGAPVLGLA/YTGAPVLGLAL/TGAPVLGLALP/GAPVLGLALPM/APVLGLALPMW/PVLGLALPMWA/VLGLALPMWAI/LGLALPMWAIA/GLALPMWAIAL/LALPMWAIALI/ALPMWAIALIS/YTGAPVLGLA/TGAPVLGLAL/GAPVLGLALP/APVLGLALPM/PVLGLALPMW/VLGLALPMWA/LGLALPMWAI/GLALPMWAIA/LALPMWAIAL/ALPMWAIALI/TGAPVLGLA/GAPVLGLAL/APVLGLALP/PVLGLALPM/VLGLALPMW/LGLALPMWA/GLALPMWAI/LALPMWAIA/ALPMWAIAL/GAPVLGLA/APVLGLAL/PVLGLALP/VLGLALPM/LGLALPMW/GLALPMWA/LALPMWAI/ALPMWAIA/MYTGAPVLGLA/YTGAPVLGLAL/TGAPVLGLAL/GAPVLGLALPM/APVLGLALPMW/VLGLALPMWA/VLGLALPMWAI/GLALPMWAIA/GLALPMWAIAL/ALPMWAIALI/ALPMWAIALIS/YTGAPVLGLA/TGAPVLGLAL/GAPVLGLAL/APVLGLALPM/VLGLALPMW/VLGLALPMWA/GLALPMWAI/GLALPMWAIA/LALPMWAIAL/ALPMWAIALI/TGAPVLGLA/GAPVLGLAL/APVLGLALP/PVLGLALPM/VLGLALPMW/LGLALPMWA/GLALPMWAI/LALPMWAIA/ALPMWAIAL/GAPVLGLA/APVLGLAL/PVLGLALP/VLGLALPM/LGLALPMW/GLALPMWA/LALPMWAI/ALPMWAIA/MYTGAPVLGLA/YTGAPVLGLAL/TGAPVLGLAL/GAPVLGLALPM/APVLGLALPMW/PVLGLALPMW/VLGLALPMWAI/LGLALPMWAIA/GLALPMWAIAL/LALPMWAIALI/ALPMWAIALIS/YTGAPVLGLA/TGAPVLGLAL/GAPVLGLAL/APVLGLALPM/PVLGLALPMW/VLGLALPMW/LGLALPMWAI/GLALPMWAIA/LALPMWAIAL/ALPMWAIALI/TGAPVLGLA/GAPVLGLAL/APVLGLALP/PVLGLALPM/VLGLALPMW/LGLALPMWA/GLALPMWAI/LALPMWAIA/ALPMWAIAL/GAPVLGLA/APVLGLAL/PVLGLALP/VLGLALPM/LGLALPMW/GLALPMWA/LALPMWAI/ALPMWAIA/MYTGAPVLGLA/YTGAPVLGLAL/TGAPVLGLALP/APVLGLALPM/APVLGLALPMW/PVLGLALPMW/VLGLALPMWAI/LGLALPMWAIA/GLALPMWAIAL/LALPMWAIALI/LPMWAIALIS/YTGAPVLGLA/TGAPVLGLAL/GAPVLGLALP/APVLGLALPM/PVLGLALPMW/VLGLALPMW/LGLALPMWAI/GLALPMWAIA/LALPMWAIAL/ALPMWAIALI/TGAPVLGLA/GAPVLGLAL/APVLGLALP/PVLGLALPM/VLGLALPMW/LGLALPMWA/GLALPMWAI/LALPMWAIA/ALPMWAIAL/GAPVLGLA/APVLGLAL/PVLGLALP/VLGLALPM/LGLALPMW/GLALPMWA/LALPMWAI/ALPMWAIA 106 6 4 NA 4 NA HLA-A*02:01 G 25.7345053962 NA 0.991 0.2643 1.09848232032 10 8 11 LALPMWAIALISFGV 3.273025 NA NA NA NA 0.167 15 no -NA NA STAMGRSPSPKTSLS IFI16 NA 3.07 1.32 TRUE FALSE TRUE NA NA 15.19 NA NA NA NA HLA-DRB1*15:01 NA IFI16 NA 18 9 NA RB0401_02_004-chr1_158986452 SPKISLSAPP TRUE 1 0.55 0.976255555556 0.374384236 1.08 NA 48.6384324503 1 HLA B*0702 uc001ftg.3#exon.3 NA NA NA 11 0.7 0.65 7.9 8.35 GGCATGTCCACAGCCATGGGCCGTTCCCCATCTCCCAAGATCTCATTGTCAGCTCCACCCAACAGTTCTTCAACTGAGAAC 0.158691819785 S SPKTSLSAPP 46-RB0401_02_004 0 SPSPKISL chr1_158986452 False TRUE 397 20 20 14 0.5 chr1_158986452 9 RB0401_02_004 1.15378883495 11.36 FALSE NM_005531 46 T171I AMGRSPSPKT AMGRSPSPKT SPSPKTSL TAMGRSPSPKT 14.83976395 STAMGRSPSPKISLS 4.00785856668 0 1 HLA DRB1*1501 0.65 24.4416/44.5000/35.5000/47.3750/42.5000/74.3750/96.6667/96.6667/95.0000/33.2963/54.8148/5.0796/72.5000/15.6658/42.2500/26.5763/88.3333/85.0000/98.3333/32.1724/15.7681/23.1868/68.5000/13.3058/43.8000/38.2941/68.0000/98.3333/69.5000/31.8529/39.5333/82.0000/26.3559/88.3333/51.8519/98.3333/71.8750/74.3750/42.6923/57.8723/41.3214/59.1489/54.2857/90.0000/99.0000/98.0000/88.1250/28.4074/49.5333/10.9696/70.5556/15.2700/45.2857/38.0294/94.0000/93.0000/99.0000/26.8899/14.2139/22.7126/73.0556/12.4541/56.3830/42.2692/80.5000/96.0000/63.8235/20.0089/55.4255/83.0000/36.6744/90.0000/66.2500/99.0000/77.3077/56.5957/10.4247/64.2857/4.4788/15.6017/8.7256/6.9808/52.7273/23.0294/95.0000/66.0000/53.1818/9.0099/25.5556/7.7547/2.9469/0.5088/15.1949/4.1251/100.0000/63.5714/44.5000/1.9673/36.1250/0.9095/1.1125/38.7143/1.1122/92.5000/57.7778/41.2000/25.0000/28.7647/0.0424/40.3333/1.0353/39.3333/68.0000/73.3333/2.7087/67.8947/15.6238/60.4000/35.3261/36.0244/94.0000/86.4286/98.0000/94.0000/63.6000/21.5903/24.2102/30.3636/6.1072/63.8000/39.1034/100.0000/84.3750/55.5714/0.7501/65.0000/7.4053/7.5269/31.6377/14.0580/87.8571/94.0000/27.8165/21.7093/67.8947/1.3482/44.5789/8.0000/62.6000/91.0000/49.9231 GMSTAMGRSPSPKISLSAPPNSSSTEN HLA-A*02:01 HLA-A*02:64 HLA-B*07:02 HLA-B*51:53 FALSE NA 170 94.11543935 uc001ftg.3 RB0401_02_004 C SOMATIC_HI -155.311 511 0 FALSE not fixed (>4 std) [u] 5.22 GMSTAMGRSPSPKTSLSAPPNSSSTEN 0.228426396 14 9 2.08 FALSE 0.716878292177 15 14.28 NA 2 15.19 NA NA NA 11.36 1 TRUE uc010pit.2 uc001ftf.1 FALSE STAMGRSPSPKTSLS 788 True 2 010-M18 HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53 10 NA SPSPKISL TAMGRSPSPKI AMGRSPSPKI AMGRSPSPKI TAMGRSPSPKI/AMGRSPSPKI/MGRSPSPKISL/GRSPSPKISL/RSPSPKISLSA/SPSPKISLSA/PSPKISLSAPP/SPKISLSAPPN/KISLSAPPNS/KISLSAPPNSS/SLSAPPNSSS/AMGRSPSPKI/MGRSPSPKI/GRSPSPKISL/RSPSPKISLS/SPSPKISLSA/PSPKISLSAP/SPKISLSAPP/KISLSAPPN/KISLSAPPNS/ISLSAPPNSS/MGRSPSPKI/GRSPSPKIS/RSPSPKISL/SPSPKISLS/PSPKISLSA/SPKISLSAP/PKISLSAPP/KISLSAPPN/ISLSAPPNS/GRSPSPKI/RSPSPKIS/SPSPKISL/PSPKISLS/SPKISLSA/PKISLSAP/KISLSAPP/ISLSAPPN/TAMGRSPSPKI/AMGRSPSPKIS/MGRSPSPKISL/GRSPSPKISL/RSPSPKISLSA/SPSPKISLSA/PSPKISLSAPP/SPKISLSAPPN/KISLSAPPNS/KISLSAPPNSS/SLSAPPNSSS/AMGRSPSPKI/MGRSPSPKIS/GRSPSPKISL/RSPSPKISLS/SPSPKISLSA/PSPKISLSA/SPKISLSAPP/KISLSAPPN/KISLSAPPNS/ISLSAPPNSS/MGRSPSPKI/GRSPSPKIS/RSPSPKISL/SPSPKISLS/PSPKISLSA/SPKISLSAP/PKISLSAPP/KISLSAPPN/ISLSAPPNS/GRSPSPKI/RSPSPKIS/SPSPKISL/PSPKISLS/SPKISLSA/PKISLSAP/KISLSAPP/ISLSAPPN/TAMGRSPSPKI/AMGRSPSPKI/MGRSPSPKISL/GRSPSPKISLS/SPSPKISLSA/SPSPKISLSAP/SPKISLSAPP/SPKISLSAPPN/ISLSAPPNS/KISLSAPPNSS/ISLSAPPNSSS/AMGRSPSPKI/MGRSPSPKIS/GRSPSPKISL/RSPSPKISLS/SPSPKISLSA/SPKISLSAP/SPKISLSAPP/KISLSAPPN/KISLSAPPNS/ISLSAPPNSS/MGRSPSPKI/GRSPSPKIS/RSPSPKISL/SPSPKISLS/PSPKISLSA/SPKISLSAP/PKISLSAPP/KISLSAPPN/ISLSAPPNS/GRSPSPKI/RSPSPKIS/SPSPKISL/PSPKISLS/SPKISLSA/PKISLSAP/KISLSAPP/ISLSAPPN/TAMGRSPSPKI/AMGRSPSPKI/MGRSPSPKISL/GRSPSPKISLS/SPSPKISLSA/SPSPKISLSAP/SPKISLSAPP/SPKISLSAPPN/ISLSAPPNS/KISLSAPPNSS/ISLSAPPNSSS/MGRSPSPKI/GRSPSPKISL/RSPSPKISLS/SPSPKISLSA/SPKISLSAP/SPKISLSAPP/PKISLSAPPN/KISLSAPPNS/ISLSAPPNSS/MGRSPSPKI/GRSPSPKIS/RSPSPKISL/SPSPKISLS/PSPKISLSA/SPKISLSAP/PKISLSAPP/KISLSAPPN/ISLSAPPNS/GRSPSPKI/RSPSPKIS/SPSPKISL/PSPKISLS/SPKISLSA/PKISLSAP/KISLSAPP/ISLSAPPN 203 10 5 9 FALSE HLA-B*07:02 T 31.3291693532 0.767 0.0424 0.281277119204 11 8 10 STAMGRSPSPKISLS 4.210425 NA NA NA NA 0.23 15 no -NA NA KEWMQALQQAMAEQR ARAP1 NA 3.07 1.32 FALSE FALSE TRUE NA NA 26.85 NA NA NA NA HLA-DRB1*15:01 TRUE ARAP1 NA 4 26 CD4 RB0401_02_004-chr11_72421607 SDVERKEWMQV TRUE 1 4.4 6.88071111111 0.258064516 1.08 CD4+ 45.4866967105 1 HLA A*0201 uc001osu.3#exon.9 NA NA NA 5 8.4 7.5 5.1 9.05 CGGGCAGAGAGTGATGTGGAGCGGAAGGAGTGGATGCAGGTCCTGCAGCAGGCCATGGCTGAGCAGCGTGCCCGGGCCCGG 6.03172363234 SME SDVERKEWMQA 17-RB0401_02_004 0 WMQVLQQAM chr11_72421607 False TRUE 261 3.1 24 7.7 6.5 chr11_72421607 3 RB0401_02_004 6.12014898046 23.1 FALSE NM_001040118 17 A413V SDVERKEWMQA WMQALQQA WMQALQQAM WMQALQQAM 2.449545035 KEWMQVLQQAMAEQR 27.7753388709 0 1 HLA DRB1*1501 0.2 35.9545/57.3684/83.0000/82.0000/50.0000/32.3448/64.2857/75.0000/60.3571/68.5000/9.5475/35.0455/38.5294/70.6250/59.4737/21.0382/37.4444/17.9444/49.0000/47.1250/31.7647/23.8242/25.4058/80.0000/33.4444/16.9935/6.7730/9.2662/43.6000/15.3516/62.1429/53.1481/64.6429/77.0000/16.8387/37.6111/47.3750/31.4412/63.2353/65.6250/80.0000/81.5000/60.4412/28.4938/64.8529/58.7234/44.1818/60.4412/23.9145/56.5957/34.0208/76.9231/57.4468/27.5146/30.1370/25.9524/34.9375/31.3030/10.5444/23.6118/15.7500/63.9706/25.8810/10.9888/4.7442/8.5022/26.6330/4.9000/68.9583/41.7857/50.7937/74.4444/33.4808/27.2718/53.6508/31.9242/42.6000/26.3636/62.1429/70.0000/76.6667/29.6875/85.0000/90.0000/87.5000/80.0000/78.3333/22.3421/9.9520/43.7500/62.8571/37.5000/25.3704/67.0000/46.5000/50.4545/71.6667/7.3542/5.8812/49.6667/35.8889/34.6000/7.0814/31.3846/17.5976/31.3846/36.3750/17.9146/59.4444/73.3333/67.0000/17.0610/39.5000/58.3333/39.1034/19.8385/56.4286/73.5714/75.0000/45.2105/74.2857/95.0000/93.0000/91.0000/82.5000/9.5852/20.3682/53.9423/75.5000/43.8182/27.1468/71.4286/58.7143/76.0000/88.5714/7.4240/12.7159/79.5000/48.5000/16.5265/18.2896/21.4229/41.2800/70.0000/19.7205/28.9038/52.1154/55.7143/39.4138/15.2476/31.4203/75.0000 RAESDVERKEWMQVLQQAMAEQRARAR HLA-A*02:01 HLA-A*02:64 HLA-B*07:02 HLA-B*51:53 FALSE NA 412 19.04800329 uc001osu.3 RB0401_02_004 G SOMATIC_HI -13.2927 1237 0 TRUE not fixed (>3 std) [f] 5.22 RAESDVERKEWMQALQQAMAEQRARAR 0.108910891 14 0 2.08 FALSE 6.7268945984 15 14.28 NA 1 26.85 NA NA NA 23.1 0 TRUE uc001oss.3 uc010rre.2 uc001osr.3 uc001osv.3 uc009yth.3 FALSE KEWMQALQQAMAEQR 303 True 2 010-M04 HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53 11 NA WMQVLQQAM WMQVLQQAM SDVERKEWMQV WMQVLQQA SDVERKEWMQV/DVERKEWMQVL/VERKEWMQVL/ERKEWMQVLQQ/RKEWMQVLQQA/KEWMQVLQQAM/EWMQVLQQAMA/WMQVLQQAMAE/MQVLQQAMAEQ/QVLQQAMAEQR/VLQQAMAEQRA/DVERKEWMQV/VERKEWMQVL/ERKEWMQVL/RKEWMQVLQQ/KEWMQVLQQA/WMQVLQQAM/WMQVLQQAMA/MQVLQQAMAE/QVLQQAMAEQ/VLQQAMAEQR/VERKEWMQV/ERKEWMQVL/RKEWMQVLQ/KEWMQVLQQ/EWMQVLQQA/WMQVLQQAM/MQVLQQAMA/QVLQQAMAE/VLQQAMAEQ/ERKEWMQV/RKEWMQVL/KEWMQVLQ/EWMQVLQQ/WMQVLQQA/MQVLQQAM/QVLQQAMA/VLQQAMAE/SDVERKEWMQV/DVERKEWMQVL/VERKEWMQVL/ERKEWMQVLQQ/RKEWMQVLQQA/KEWMQVLQQAM/EWMQVLQQAMA/WMQVLQQAMAE/MQVLQQAMAEQ/QVLQQAMAEQR/VLQQAMAEQRA/DVERKEWMQV/VERKEWMQVL/ERKEWMQVL/RKEWMQVLQQ/KEWMQVLQQA/EWMQVLQQAM/WMQVLQQAMA/MQVLQQAMAE/QVLQQAMAEQ/VLQQAMAEQR/VERKEWMQV/ERKEWMQVL/RKEWMQVLQ/KEWMQVLQQ/EWMQVLQQA/WMQVLQQAM/MQVLQQAMA/QVLQQAMAE/VLQQAMAEQ/ERKEWMQV/RKEWMQVL/KEWMQVLQ/EWMQVLQQ/WMQVLQQA/MQVLQQAM/QVLQQAMA/VLQQAMAE/SDVERKEWMQV/DVERKEWMQVL/VERKEWMQVL/ERKEWMQVL/RKEWMQVLQQA/KEWMQVLQQAM/EWMQVLQQAM/WMQVLQQAMAE/MQVLQQAMAEQ/QVLQQAMAEQR/VLQQAMAEQRA/DVERKEWMQV/VERKEWMQVL/ERKEWMQVL/RKEWMQVLQQ/KEWMQVLQQA/EWMQVLQQAM/WMQVLQQAM/MQVLQQAMAE/QVLQQAMAEQ/VLQQAMAEQR/VERKEWMQV/ERKEWMQVL/RKEWMQVLQ/KEWMQVLQQ/EWMQVLQQA/WMQVLQQAM/MQVLQQAMA/QVLQQAMAE/VLQQAMAEQ/ERKEWMQV/RKEWMQVL/KEWMQVLQ/EWMQVLQQ/WMQVLQQA/MQVLQQAM/QVLQQAMA/VLQQAMAE/SDVERKEWMQV/DVERKEWMQVL/VERKEWMQVL/ERKEWMQVL/RKEWMQVLQQA/KEWMQVLQQAM/EWMQVLQQAMA/WMQVLQQAMAE/MQVLQQAMAEQ/QVLQQAMAEQR/VLQQAMAEQRA/DVERKEWMQV/VERKEWMQVL/ERKEWMQVL/RKEWMQVLQQ/KEWMQVLQQA/EWMQVLQQAM/MQVLQQAMA/MQVLQQAMAE/QVLQQAMAEQ/VLQQAMAEQR/VERKEWMQV/ERKEWMQVL/RKEWMQVLQ/KEWMQVLQQ/EWMQVLQQA/WMQVLQQAM/MQVLQQAMA/QVLQQAMAE/VLQQAMAEQ/ERKEWMQV/RKEWMQVL/KEWMQVLQ/EWMQVLQQ/WMQVLQQA/MQVLQQAM/QVLQQAMA/VLQQAMAE 31 3 3 10 TRUE HLA-A*02:64 A 37.3880743235 0.62 4.7442 6.56948958174 9 9 8 KEWMQVLQQAMAEQR 6.2056 NA NA NA NA 0.093 15 no -NA NA PLEDGAMPSARLRKL CAPZB NA 3.07 1.32 FALSE TRUE TRUE NA NA 21.65 NA NA NA NA HLA-DRB1*15:01 TRUE CAPZB NA 3 6 CD4 RB0401_02_004-chr1_19705096 LSARLRKL TRUE 1 2.5 1.99168888889 0.437710438 1.08 CD4+ 41.5388927632 1 HLA B*0702 uc010ocz.2#exon.3 NA NA NA 7 6.6 2.7 1.1 1.85 AGTAACAAGTATGACCCTCCCTTGGAGGATGGGGCCATGCTGTCAGCTCGGCTGAGAAAGCTGGAGGTGGAAGCCAACAAT 1.68396882471 SME PSARLRKL 92-RB0401_02_004 0 DGAMLSARL chr1_19705096 False TRUE 318 28 18 43 27 chr1_19705096 1 RB0401_02_004 1.75546241114 10.98 TRUE NM_004930 92 P118L MPSARLRKLEV MPSARLRKLEV PPLEDGAMP PSARLRKLEV 34.68628225 PLEDGAMLSARLRKL 14.4226110309 0 1 HLA DRB1*1501 0.2 19.6648/54.8148/55.5263/65.0000/34.6923/86.6667/70.0000/33.0370/38.4118/7.7804/96.6667/38.2353/46.7500/10.0292/42.0833/61.4286/63.9286/31.9706/3.6809/32.7241/47.5000/27.7593/21.8015/18.0987/77.0000/29.3750/40.8571/18.0897/2.6367/85.0000/26.2203/56.8421/57.3684/82.0000/27.3889/39.6000/37.3333/49.5714/27.3398/69.1667/72.7778/48.0000/45.7143/84.5000/47.2941/41.5714/38.2647/20.4732/97.0000/52.8571/61.4706/23.9803/47.6471/76.1538/57.9787/8.0217/5.2293/31.5909/62.3529/40.4138/27.3301/16.2857/76.1538/35.3913/18.4388/2.1164/1.9031/75.7692/37.2432/55.6383/66.6667/81.5000/32.8305/24.4514/20.2009/50.3175/1.6014/29.0000/20.1346/85.0000/20.1154/75.0000/87.5000/27.6000/85.0000/27.7500/82.5000/3.8354/25.0000/44.2500/33.6000/26.4545/65.0000/46.0000/13.8316/54.5455/15.6441/1.9281/66.0000/11.1954/26.2273/8.2056/34.4000/26.5000/3.5815/50.4545/5.3344/34.2000/46.5000/70.0000/8.7332/61.4286/55.5556/17.9146/2.1567/17.9650/34.4400/95.0000/35.7174/77.0000/66.0526/29.8409/89.2857/34.4000/87.1429/2.0813/25.4097/62.8000/60.4000/19.6615/26.7656/68.9474/33.8393/70.3571/17.3178/2.3197/75.0000/21.9207/57.7143/1.1818/44.9474/54.5192/9.1849/70.0000/5.4014/52.5962/41.3600/39.6897/5.3002/73.2143/72.1429/13.7479 SNKYDPPLEDGAMLSARLRKLEVEANN HLA-A*02:01 HLA-A*02:64 HLA-B*07:02 HLA-B*51:53 FALSE NA 117 86.19819919 uc010ocz.2 RB0401_02_004 G SOMATIC_HI -154.625 352 0 TRUE FIXED 5.22 SNKYDPPLEDGAMPSARLRKLEVEANN 0.289134438 14 4 2.08 TRUE 1.94777530156 15 14.28 NA 2 21.65 NA NA NA 10.98 0 TRUE uc021ohr.1 uc009vpk.3 uc001bce.3 FALSE PLEDGAMPSARLRKL 543 True 2 010-M03 HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53 8 NA PPLEDGAML LSARLRKLEV MLSARLRKLEV MLSARLRKLEV YDPPLEDGAML/DPPLEDGAMLS/PPLEDGAMLSA/PLEDGAMLSAR/LEDGAMLSARL/EDGAMLSARLR/DGAMLSARLRK/GAMLSARLRKL/AMLSARLRKL/MLSARLRKLEV/SARLRKLEVE/DPPLEDGAML/PPLEDGAMLS/PLEDGAMLSA/LEDGAMLSAR/EDGAMLSARL/DGAMLSARLR/GAMLSARLRK/AMLSARLRKL/MLSARLRKL/LSARLRKLEV/PPLEDGAML/PLEDGAMLS/LEDGAMLSA/EDGAMLSAR/DGAMLSARL/GAMLSARLR/AMLSARLRK/MLSARLRKL/LSARLRKLE/PLEDGAML/LEDGAMLS/EDGAMLSA/DGAMLSAR/GAMLSARL/AMLSARLR/MLSARLRK/LSARLRKL/YDPPLEDGAML/DPPLEDGAMLS/LEDGAMLSA/PLEDGAMLSAR/LEDGAMLSARL/EDGAMLSARLR/DGAMLSARLRK/GAMLSARLRKL/AMLSARLRKLE/MLSARLRKLEV/LSARLRKLEVE/DPPLEDGAML/PPLEDGAMLS/PLEDGAMLSA/LEDGAMLSAR/EDGAMLSARL/DGAMLSARLR/GAMLSARLRK/AMLSARLRKL/MLSARLRKL/LSARLRKLEV/PPLEDGAML/PLEDGAMLS/LEDGAMLSA/EDGAMLSAR/DGAMLSARL/GAMLSARLR/AMLSARLRK/MLSARLRKL/LSARLRKLE/PLEDGAML/LEDGAMLS/EDGAMLSA/DGAMLSAR/GAMLSARL/AMLSARLR/MLSARLRK/LSARLRKL/YDPPLEDGAML/DPPLEDGAML/PPLEDGAMLSA/LEDGAMLSAR/LEDGAMLSARL/EDGAMLSARLR/DGAMLSARLRK/GAMLSARLRKL/AMLSARLRKL/MLSARLRKLEV/LSARLRKLEV/DPPLEDGAML/PPLEDGAML/LEDGAMLSA/LEDGAMLSAR/EDGAMLSARL/DGAMLSARLR/GAMLSARLRK/AMLSARLRKL/MLSARLRKL/LSARLRKLEV/PPLEDGAML/PLEDGAMLS/LEDGAMLSA/EDGAMLSAR/DGAMLSARL/GAMLSARLR/AMLSARLRK/MLSARLRKL/LSARLRKLE/PLEDGAML/LEDGAMLS/EDGAMLSA/DGAMLSAR/GAMLSARL/AMLSARLR/MLSARLRK/LSARLRKL/YDPPLEDGAML/DPPLEDGAML/PPLEDGAMLSA/PLEDGAMLSAR/LEDGAMLSARL/EDGAMLSARLR/DGAMLSARL/GAMLSARLRKL/AMLSARLRKL/MLSARLRKLEV/LSARLRKLEV/DPPLEDGAML/PPLEDGAML/LEDGAMLSA/LEDGAMLSAR/EDGAMLSARL/DGAMLSARL/GAMLSARLRK/AMLSARLRKL/MLSARLRKL/LSARLRKLEV/PPLEDGAML/PLEDGAMLS/LEDGAMLSA/EDGAMLSAR/DGAMLSARL/GAMLSARLR/AMLSARLRK/MLSARLRKL/LSARLRKLE/PLEDGAML/LEDGAMLS/EDGAMLSA/DGAMLSAR/GAMLSARL/AMLSARLR/MLSARLRK/LSARLRKL 297 0 8 1 TRUE HLA-B*51:53 A 29.8486339494 0.971 1.1818 1.89804656718 10 9 11 PLEDGAMLSARLRKL 1.83075 NA NA NA NA 0.291 15 no -NA NA SVASYVYNGYSVVFV PLXNA2 NA 3.07 1.32 FALSE FALSE FALSE NA NA 6 NA NA NA NA HLA-DRB1*15:01 FALSE PLXNA2 NA 31 13 NA RB0401_02_004-chr1_208383659 NGYSVFFV TRUE 1 3.7 1.56852222222 0.19 1.08 NA 40.2155118421 2 HLA A*0201 uc001hgz.3#exon.2 NA NA NA 12 2.2 4 0.1 3.9 ACCTCTGTGGCCTCCTACGTTTACAACGGCTACAGCGTGTTTTTTGTGGGGACTAAGAGTGGCAAGCTGAAAAAGATTCGG 0.615111291441 SME NGYSVVFV 104-RB0401_02_004 0 YVYNGYSVF chr1_208383659 False FALSE 482 0.2 7 2.3 4.4 chr1_208383659 8 RB0401_02_004 0.661631922508 3.18 FALSE NM_025179 104 V446F YVYNGYSVVF YVYNGYSVVFV YVYNGYSVV YVYNGYSVV 8.62505684 SVASYVYNGYSVFFV 9.9980210742 0 2 261 HLA DRB1*1501 1.1 23.0440/28.5870/0.7789/81.0000/82.0000/68.0000/52.0370/78.0000/42.9167/37.6111/66.0000/15.5486/4.4927/17.9519/68.0000/36.8947/50.0000/27.7407/46.0000/44.3000/18.4170/3.4187/12.6583/9.0295/40.5000/29.8500/33.0370/13.3242/47.2500/32.6897/42.5833/44.3000/20.2083/79.0000/51.4815/31.0294/57.6316/81.0000/11.6218/17.5572/1.7782/81.5000/87.5000/45.8571/47.5882/76.9231/19.2344/41.4643/29.0897/6.4375/0.8550/26.6239/69.5833/48.8125/29.8077/23.8158/48.1875/17.3460/22.3391/0.3666/3.4888/18.8844/47.4706/38.7059/10.5012/8.0623/39.3143/9.2749/22.4023/26.2569/42.5385/78.8462/55.0000/16.2108/53.9683/67.9167/13.3789/30.8571/31.2308/90.0000/100.0000/82.5000/80.0000/78.3333/53.6364/43.2500/85.0000/4.5975/5.7127/50.9091/92.5000/80.0000/80.0000/41.4000/31.3846/61.4286/17.2317/1.0024/8.3360/62.1429/47.3333/80.0000/33.5000/10.7160/38.2857/36.8750/11.8664/43.0000/54.5455/90.0000/63.5714/22.4211/52.2727/68.0000/18.8934/29.7841/11.6172/63.4000/98.0000/59.7143/80.0000/64.6000/66.5789/31.2029/80.6250/7.1004/3.9301/27.7982/62.6000/39.8621/75.5000/33.1071/36.2195/62.0000/21.6388/0.6695/8.7644/17.4206/11.8974/60.8000/21.5418/16.9607/24.7070/43.1818/10.7652/20.1155/1.7586/60.0000/35.5435/24.7070/43.0909/48.0000 TSVASYVYNGYSVFFVGTKSGKLKKIR HLA-A*02:01 HLA-A*02:64 HLA-B*07:02 HLA-B*51:53 FALSE NA 445 12.56092685 uc001hgz.3 RB0401_02_004 C SOMATIC_HI -10.8231 1335 0 FALSE not fixed (>4 std) [u] 5.22 TSVASYVYNGYSVVFVGTKSGKLKKIR 0.063649222 14 7 2.08 FALSE 1.22277428082 15 14.28 NA 1 6 NA NA NA 3.18 1 FALSE FALSE SVASYVYNGYSVVFV 707 False 2 010-M31 HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53 8 NA YVYNGYSVF YVYNGYSVF YVYNGYSVFF YVYNGYSVFFV ASYVYNGYSVF/YVYNGYSVFF/YVYNGYSVFFV/VYNGYSVFFV/YNGYSVFFVGT/NGYSVFFVGTK/GYSVFFVGTKS/YSVFFVGTKSG/SVFFVGTKSGK/VFFVGTKSGKL/FFVGTKSGKLK/SYVYNGYSVF/YVYNGYSVFF/VYNGYSVFFV/YNGYSVFFVG/NGYSVFFVGT/GYSVFFVGTK/YSVFFVGTKS/SVFFVGTKSG/VFFVGTKSGK/FFVGTKSGKL/YVYNGYSVF/VYNGYSVFF/YNGYSVFFV/NGYSVFFVG/GYSVFFVGT/YSVFFVGTK/SVFFVGTKS/VFFVGTKSG/FFVGTKSGK/VYNGYSVF/YNGYSVFF/NGYSVFFV/GYSVFFVG/YSVFFVGT/SVFFVGTK/VFFVGTKS/FFVGTKSG/ASYVYNGYSVF/YVYNGYSVFF/YVYNGYSVFFV/VYNGYSVFF/YNGYSVFFVGT/NGYSVFFVGTK/GYSVFFVGTKS/YSVFFVGTKSG/SVFFVGTKSGK/VFFVGTKSGKL/FFVGTKSGKLK/SYVYNGYSVF/YVYNGYSVFF/VYNGYSVFFV/YNGYSVFFVG/NGYSVFFVGT/GYSVFFVGTK/YSVFFVGTKS/SVFFVGTKSG/VFFVGTKSGK/FFVGTKSGKL/YVYNGYSVF/VYNGYSVFF/YNGYSVFFV/NGYSVFFVG/GYSVFFVGT/YSVFFVGTK/SVFFVGTKS/VFFVGTKSG/FFVGTKSGK/VYNGYSVF/YNGYSVFF/NGYSVFFV/GYSVFFVG/YSVFFVGT/SVFFVGTK/VFFVGTKS/FFVGTKSG/ASYVYNGYSVF/SYVYNGYSVFF/YVYNGYSVFFV/VYNGYSVFF/YNGYSVFFVGT/NGYSVFFVGTK/GYSVFFVGTKS/YSVFFVGTKSG/SVFFVGTKSGK/VFFVGTKSGKL/FFVGTKSGKLK/SYVYNGYSVF/YVYNGYSVFF/VYNGYSVFF/YNGYSVFFVG/NGYSVFFVGT/GYSVFFVGTK/YSVFFVGTKS/SVFFVGTKSG/VFFVGTKSGK/FFVGTKSGKL/YVYNGYSVF/VYNGYSVFF/YNGYSVFFV/NGYSVFFVG/GYSVFFVGT/YSVFFVGTK/SVFFVGTKS/VFFVGTKSG/FFVGTKSGK/VYNGYSVF/YNGYSVFF/NGYSVFFV/GYSVFFVG/YSVFFVGT/SVFFVGTK/VFFVGTKS/FFVGTKSG/ASYVYNGYSVF/YVYNGYSVFF/YVYNGYSVFFV/VYNGYSVFF/NGYSVFFVGT/NGYSVFFVGTK/GYSVFFVGTKS/YSVFFVGTKSG/SVFFVGTKSGK/VFFVGTKSGKL/FFVGTKSGKL/SYVYNGYSVF/YVYNGYSVFF/VYNGYSVFFV/YNGYSVFFVG/NGYSVFFVGT/YSVFFVGTK/YSVFFVGTKS/SVFFVGTKSG/VFFVGTKSGK/FFVGTKSGKL/YVYNGYSVF/VYNGYSVFF/YNGYSVFFV/NGYSVFFVG/GYSVFFVGT/YSVFFVGTK/SVFFVGTKS/VFFVGTKSG/FFVGTKSGK/VYNGYSVF/YNGYSVFF/NGYSVFFV/GYSVFFVG/YSVFFVGT/SVFFVGTK/VFFVGTKS/FFVGTKSG 100 8 8 NA 8 NA HLA-A*02:64 A 27.9394651257 NA 0.419 0.3666 0.959220361657 9 9 11 SVASYVYNGYSVFFV 0.70435 NA NA NA NA 0.063 15 no -NA NA SVASYVYNGYSVVFV PLXNA2 NA 3.07 1.32 FALSE FALSE FALSE NA NA 6 NA NA NA NA HLA-DRB1*15:01 FALSE PLXNA2 NA 30 11 NA RB0401_02_004-chr1_208383659 NGYSVFFV TRUE 1 3.7 1.56852222222 0.19 1.08 NA 40.2155118421 1 HLA A*0201 uc001hha.4#exon.1 NA NA NA 12 2.2 4 0.1 3.9 ACCTCTGTGGCCTCCTACGTTTACAACGGCTACAGCGTGTTTTTTGTGGGGACTAAGAGTGGCAAGCTGAAAAAGGTAAGA 0.615111291441 SME NGYSVVFV 261-RB0401_02_004 0 YVYNGYSVF chr1_208383659 False FALSE 482 0.2 7 2.3 4.4 chr1_208383659 8 RB0401_02_004 0.661631922508 3.18 FALSE 261 V500F YVYNGYSVVF YVYNGYSVVFV YVYNGYSVV YVYNGYSVV 9.184718624 SVASYVYNGYSVFFV 9.9980210742 0 2 104 HLA DRB1*1501 1.1 23.0440/28.5870/0.7789/81.0000/82.0000/68.0000/52.0370/78.0000/42.9167/37.6111/66.0000/15.5486/4.4927/17.9519/68.0000/36.8947/50.0000/27.7407/46.0000/44.3000/18.4170/3.4187/12.6583/9.0295/40.5000/29.8500/33.0370/13.3242/47.2500/32.6897/42.5833/44.3000/20.2083/79.0000/51.4815/31.0294/57.6316/81.0000/11.6218/17.5572/1.7782/81.5000/87.5000/45.8571/47.5882/76.9231/19.2344/41.4643/29.0897/6.4375/0.8550/26.6239/69.5833/48.8125/29.8077/23.8158/48.1875/17.3460/22.3391/0.3666/3.4888/18.8844/47.4706/38.7059/10.5012/8.0623/39.3143/9.2749/22.4023/26.2569/42.5385/78.8462/55.0000/16.2108/53.9683/67.9167/13.3789/30.8571/31.2308/90.0000/100.0000/82.5000/80.0000/78.3333/53.6364/43.2500/85.0000/4.5975/5.7127/50.9091/92.5000/80.0000/80.0000/41.4000/31.3846/61.4286/17.2317/1.0024/8.3360/62.1429/47.3333/80.0000/33.5000/10.7160/38.2857/36.8750/11.8664/43.0000/54.5455/90.0000/63.5714/22.4211/52.2727/68.0000/18.8934/29.7841/11.6172/63.4000/98.0000/59.7143/80.0000/64.6000/66.5789/31.2029/80.6250/7.1004/3.9301/27.7982/62.6000/39.8621/75.5000/33.1071/36.2195/62.0000/21.6388/0.6695/8.7644/17.4206/11.8974/60.8000/21.5418/16.9607/24.7070/43.1818/10.7652/20.1155/1.7586/60.0000/35.5435/24.7070/43.0909/48.0000 TSVASYVYNGYSVFFVGTKSGKLKKVR HLA-A*02:01 HLA-A*02:64 HLA-B*07:02 HLA-B*51:53 FALSE NA 499 3.055718532 uc001hha.4 RB0401_02_004 C SOMATIC_HI -10.8231 1497 0 FALSE not fixed (>4 std) [u] 5.22 TSVASYVYNGYSVVFVGTKSGKLKKVR 0.063649222 14 7 2.08 FALSE 1.22277428082 15 14.28 NA 1 6 NA NA NA 3.18 1 FALSE FALSE SVASYVYNGYSVVFV 707 False 2 010-M30 HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53 8 NA YVYNGYSVF YVYNGYSVF YVYNGYSVFF YVYNGYSVFFV ASYVYNGYSVF/YVYNGYSVFF/YVYNGYSVFFV/VYNGYSVFFV/YNGYSVFFVGT/NGYSVFFVGTK/GYSVFFVGTKS/YSVFFVGTKSG/SVFFVGTKSGK/VFFVGTKSGKL/FFVGTKSGKLK/SYVYNGYSVF/YVYNGYSVFF/VYNGYSVFFV/YNGYSVFFVG/NGYSVFFVGT/GYSVFFVGTK/YSVFFVGTKS/SVFFVGTKSG/VFFVGTKSGK/FFVGTKSGKL/YVYNGYSVF/VYNGYSVFF/YNGYSVFFV/NGYSVFFVG/GYSVFFVGT/YSVFFVGTK/SVFFVGTKS/VFFVGTKSG/FFVGTKSGK/VYNGYSVF/YNGYSVFF/NGYSVFFV/GYSVFFVG/YSVFFVGT/SVFFVGTK/VFFVGTKS/FFVGTKSG/ASYVYNGYSVF/YVYNGYSVFF/YVYNGYSVFFV/VYNGYSVFF/YNGYSVFFVGT/NGYSVFFVGTK/GYSVFFVGTKS/YSVFFVGTKSG/SVFFVGTKSGK/VFFVGTKSGKL/FFVGTKSGKLK/SYVYNGYSVF/YVYNGYSVFF/VYNGYSVFFV/YNGYSVFFVG/NGYSVFFVGT/GYSVFFVGTK/YSVFFVGTKS/SVFFVGTKSG/VFFVGTKSGK/FFVGTKSGKL/YVYNGYSVF/VYNGYSVFF/YNGYSVFFV/NGYSVFFVG/GYSVFFVGT/YSVFFVGTK/SVFFVGTKS/VFFVGTKSG/FFVGTKSGK/VYNGYSVF/YNGYSVFF/NGYSVFFV/GYSVFFVG/YSVFFVGT/SVFFVGTK/VFFVGTKS/FFVGTKSG/ASYVYNGYSVF/SYVYNGYSVFF/YVYNGYSVFFV/VYNGYSVFF/YNGYSVFFVGT/NGYSVFFVGTK/GYSVFFVGTKS/YSVFFVGTKSG/SVFFVGTKSGK/VFFVGTKSGKL/FFVGTKSGKLK/SYVYNGYSVF/YVYNGYSVFF/VYNGYSVFF/YNGYSVFFVG/NGYSVFFVGT/GYSVFFVGTK/YSVFFVGTKS/SVFFVGTKSG/VFFVGTKSGK/FFVGTKSGKL/YVYNGYSVF/VYNGYSVFF/YNGYSVFFV/NGYSVFFVG/GYSVFFVGT/YSVFFVGTK/SVFFVGTKS/VFFVGTKSG/FFVGTKSGK/VYNGYSVF/YNGYSVFF/NGYSVFFV/GYSVFFVG/YSVFFVGT/SVFFVGTK/VFFVGTKS/FFVGTKSG/ASYVYNGYSVF/YVYNGYSVFF/YVYNGYSVFFV/VYNGYSVFF/NGYSVFFVGT/NGYSVFFVGTK/GYSVFFVGTKS/YSVFFVGTKSG/SVFFVGTKSGK/VFFVGTKSGKL/FFVGTKSGKL/SYVYNGYSVF/YVYNGYSVFF/VYNGYSVFFV/YNGYSVFFVG/NGYSVFFVGT/YSVFFVGTK/YSVFFVGTKS/SVFFVGTKSG/VFFVGTKSGK/FFVGTKSGKL/YVYNGYSVF/VYNGYSVFF/YNGYSVFFV/NGYSVFFVG/GYSVFFVGT/YSVFFVGTK/SVFFVGTKS/VFFVGTKSG/FFVGTKSGK/VYNGYSVF/YNGYSVFF/NGYSVFFV/GYSVFFVG/YSVFFVGT/SVFFVGTK/VFFVGTKS/FFVGTKSG 100 8 8 NA 8 NA HLA-A*02:64 A 27.9394651257 NA 0.419 0.3666 0.959220361657 9 9 11 SVASYVYNGYSVFFV 0.70435 NA NA NA NA 0.063 15 no -NA NA LCYWNPYWMLPSDVC GXYLT1 NA 3.07 1.32 FALSE FALSE TRUE NA NA 14.67 NA NA NA NA HLA-DRB1*15:01 TRUE GXYLT1 NA 6 51 CD4 RB0401_02_004-chr12_42523620 NLYWMLPS TRUE 1 10 6.45181111111 1 1.08 CD4+ 56.1840706667 1 HLA A*0201 uc001rms.4#exon.1 NA NA NA 5 2 19 0.8 0.8 TCGGACAGGTGTAAAGATTTCTCTCTGTGTTACTGGAATCTCTATTGGATGCTGCCCTCTGATGTTTGTGGAATGAACTGC 4.3726575571 SME NPYWMLPS 205-RB0401_02_004 0 NLYWMLPSDV chr12_42523620 False FALSE 621 0.9 11.1 1.8 26 chr12_42523620 6 RB0401_02_004 7.09428648036 4.32 FALSE NM_173601 205 P85L NPYWMLPS SLCYWNPYWML SLCYWNPYWM FSLCYWNPYW 0.214052621 LCYWNLYWMLPSDVC 30.3966534748 0 1 HLA DRB1*1501 0.2 83.0000/76.0000/81.0000/30.8333/5.1769/88.3333/85.0000/46.2500/15.5287/14.5652/81.0000/37.6111/82.0000/38.4118/5.4986/34.0385/82.0000/67.0000/53.5185/2.1187/33.8148/45.0000/51.2963/12.0951/23.5165/34.4615/61.7857/73.7500/17.6704/20.8542/29.9750/39.9333/61.4286/65.5000/29.4250/98.3333/17.8222/90.0000/86.8750/56.2766/59.4681/34.2083/7.7930/88.7500/78.8462/61.0294/41.2857/32.8136/85.6250/46.2105/58.4043/12.7621/6.3165/41.0000/81.0000/51.9841/53.8889/5.2454/42.1538/47.2941/17.6950/3.1097/31.3636/29.2692/56.0638/55.8511/16.6979/25.9365/39.5429/12.9915/47.6471/70.2778/34.0833/89.3750/23.2368/82.5000/73.3333/92.5000/87.5000/78.3333/100.0000/100.0000/100.0000/95.0000/85.0000/95.0000/59.4444/78.3333/85.0000/59.4444/80.0000/100.0000/95.0000/100.0000/51.3636/67.0000/62.1429/62.1429/57.2222/46.2500/60.7143/78.3333/90.0000/61.4286/35.8889/76.6667/76.6667/69.0000/90.0000/51.3636/100.0000/66.0000/87.5000/56.0000/48.0714/51.7308/61.4000/96.0000/99.0000/99.0000/80.6250/69.2105/85.7143/42.9565/40.8571/31.2754/53.9423/41.4000/94.0000/98.0000/98.0000/27.5138/40.7500/28.6538/22.4121/32.3934/18.9372/35.3696/58.1429/90.0000/40.1786/10.7124/22.9950/62.2000/20.7292/55.2857/26.2109/92.0000/42.4783/69.4737 SDRCKDFSLCYWNLYWMLPSDVCGMNC HLA-A*02:01 HLA-A*02:64 HLA-B*07:02 HLA-B*51:53 FALSE NA 84 3.555992537 uc001rms.4 RB0401_02_004 G SOMATIC_HI -106.598 253 0 TRUE FIXED 5.22 SDRCKDFSLCYWNPYWMLPSDVCGMNC 0.195522388 14 0 2.08 FALSE 5.69226486158 15 14.28 NA 1 14.67 NA NA NA 4.32 0 TRUE FALSE LCYWNPYWMLPSDVC 670 True 1 010-M06 HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53 8 NA SLCYWNLYWM FSLCYWNLYW NLYWMLPS SLCYWNLYWML CKDFSLCYWNL/KDFSLCYWNLY/FSLCYWNLYW/SLCYWNLYWM/SLCYWNLYWML/LCYWNLYWML/CYWNLYWMLPS/YWNLYWMLPSD/NLYWMLPSDV/NLYWMLPSDVC/LYWMLPSDVCG/KDFSLCYWNL/DFSLCYWNLY/FSLCYWNLYW/SLCYWNLYWM/LCYWNLYWML/CYWNLYWMLP/YWNLYWMLPS/WNLYWMLPSD/NLYWMLPSDV/LYWMLPSDVC/DFSLCYWNL/FSLCYWNLY/SLCYWNLYW/LCYWNLYWM/CYWNLYWML/YWNLYWMLP/WNLYWMLPS/NLYWMLPSD/LYWMLPSDV/FSLCYWNL/SLCYWNLY/LCYWNLYW/CYWNLYWM/YWNLYWML/WNLYWMLP/NLYWMLPS/LYWMLPSD/CKDFSLCYWNL/KDFSLCYWNLY/FSLCYWNLYW/FSLCYWNLYWM/SLCYWNLYWML/LCYWNLYWML/CYWNLYWMLPS/YWNLYWMLPSD/NLYWMLPSDV/NLYWMLPSDVC/LYWMLPSDVCG/KDFSLCYWNL/DFSLCYWNLY/FSLCYWNLYW/SLCYWNLYWM/LCYWNLYWML/CYWNLYWMLP/YWNLYWMLPS/WNLYWMLPSD/NLYWMLPSDV/LYWMLPSDVC/DFSLCYWNL/FSLCYWNLY/SLCYWNLYW/LCYWNLYWM/CYWNLYWML/YWNLYWMLP/WNLYWMLPS/NLYWMLPSD/LYWMLPSDV/FSLCYWNL/SLCYWNLY/LCYWNLYW/CYWNLYWM/YWNLYWML/WNLYWMLP/NLYWMLPS/LYWMLPSD/KDFSLCYWNLY/DFSLCYWNLYW/FSLCYWNLYWM/SLCYWNLYWML/LCYWNLYWML/CYWNLYWMLPS/YWNLYWMLPSD/WNLYWMLPSDV/NLYWMLPSDVC/LYWMLPSDVCG/KDFSLCYWNL/DFSLCYWNLY/FSLCYWNLYW/SLCYWNLYWM/LCYWNLYWML/CYWNLYWML/YWNLYWMLPS/WNLYWMLPSD/NLYWMLPSDV/LYWMLPSDVC/DFSLCYWNL/FSLCYWNLY/SLCYWNLYW/LCYWNLYWM/CYWNLYWML/YWNLYWMLP/WNLYWMLPS/NLYWMLPSD/LYWMLPSDV/FSLCYWNL/SLCYWNLY/LCYWNLYW/CYWNLYWM/YWNLYWML/WNLYWMLP/NLYWMLPS/LYWMLPSD/KDFSLCYWNLY/DFSLCYWNLYW/FSLCYWNLYWM/SLCYWNLYWML/LCYWNLYWML/CYWNLYWML/YWNLYWMLPSD/WNLYWMLPSDV/NLYWMLPSDVC/LYWMLPSDVCG/KDFSLCYWNL/DFSLCYWNLY/FSLCYWNLYW/SLCYWNLYWM/LCYWNLYWML/CYWNLYWML/YWNLYWMLPS/WNLYWMLPSD/NLYWMLPSDV/LYWMLPSDVC/DFSLCYWNL/FSLCYWNLY/SLCYWNLYW/LCYWNLYWM/CYWNLYWML/YWNLYWMLP/WNLYWMLPS/NLYWMLPSD/LYWMLPSDV/FSLCYWNL/SLCYWNLY/LCYWNLYW/CYWNLYWM/YWNLYWML/WNLYWMLP/NLYWMLPS/LYWMLPSD 2 7 6 1 TRUE HLA-A*02:01 A 46.1769086404 1.107 2.1187 4.93990021491 10 10 11 LCYWNLYWMLPSDVC 12.957425 NA NA NA NA 0.195 15 no -NA NA PRVWGKYLWRSPHSK C1RL NA 3.07 1.32 FALSE FALSE FALSE NA NA 17.47 NA NA NA NA HLA-DRB1*15:01 FALSE C1RL.C1RL-AS1 NA 37 36 NA RB0401_02_004-chr12_7261761 GPSVWGKYL TRUE 1 0.4 2.75427777778 0.333333333 1.08 NA 39.2620175 1 HLA B*0702 uc009zft.3#exon.0 NA NA NA 1 0.9 1.6 6.7 14.5 ATGCCTGGACCCAGTGTGTGGGGGAAATATCTCTGGAGAAGCCCTCACTCCAAAGGCTGTCCAGGCGCAATGTGGTGGCTG 0.535215763886 SME GPRVWGKYL 1-RB0401_02_004 0 GPSVWGKYL chr12_7261761 False FALSE 465 5.7 16 0.9 0.5 chr12_7261761 0 RB0401_02_004 1.91702335854 17.52 TRUE 1 R5S RVWGKYLWRS RVWGKYLWRS GPRVWGKYL MPGPRVWGKYL 1.642740292 PSVWGKYLWRSPHSK 6.26099578595 0 1 HLA DRB1*1501 1.7 37.3889/88.3333/53.3333/58.9474/42.8333/37.5000/61.0714/48.5000/55.0000/11.3014/30.9444/62.5000/26.2712/50.0000/14.3403/70.6250/85.0000/67.0000/63.2143/22.2170/50.7143/77.3077/42.6154/51.5079/51.9841/27.2621/72.2222/33.4423/41.8571/5.7095/16.7728/42.4615/35.1957/33.3462/3.2045/69.3750/80.0000/55.4255/70.2778/9.4599/0.9342/48.6667/25.3704/100.0000/80.0000/3.4245/3.7350/3.4794/90.0000/39.6667/5.8482/63.5714/0.1499/53.6364/23.3824/11.4007/61.4286/7.0358/5.6906/18.1507/3.2053/36.0488/39.8276/90.0000/77.5000/4.1679/17.2991/9.9761/68.1579/60.8000/14.6796/37.1053/2.4878/18.4863/35.5652/13.4841/77.5000/17.5888/7.5533/7.4940 MPGPSVWGKYLWRSPHSK HLA-A*02:01 HLA-A*02:64 HLA-B*07:02 HLA-B*51:53 FALSE NA 4 21.28993727 uc009zft.3 RB0401_02_004 T SOMATIC_HI -126.576 14 0 FALSE FIXED 5.22 MPGPRVWGKYLWRSPHSK 0.210893855 5 2 2.08 FALSE 2.05851975114 15 14.28 NA 1 17.47 NA NA NA 17.52 1 FALSE uc001qsn.3 uc001qso.2 FALSE PRVWGKYLWRSPHSK 716 False 1 010-M46 HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53 9 NA GPSVWGKYL MPGPSVWGKYL SVWGKYLWRS SVWGKYLWRS MPGPSVWGKYL/PGPSVWGKYLW/GPSVWGKYLWR/SVWGKYLWRS/SVWGKYLWRSP/MPGPSVWGKY/PGPSVWGKYL/GPSVWGKYLW/SVWGKYLWR/SVWGKYLWRS/MPGPSVWGK/PGPSVWGKY/GPSVWGKYL/PSVWGKYLW/SVWGKYLWR/MPGPSVWG/PGPSVWGK/GPSVWGKY/PSVWGKYL/SVWGKYLW/MPGPSVWGKYL/PGPSVWGKYLW/GPSVWGKYLWR/SVWGKYLWRS/SVWGKYLWRSP/MPGPSVWGKY/PGPSVWGKYL/GPSVWGKYLW/SVWGKYLWR/SVWGKYLWRS/MPGPSVWGK/PGPSVWGKY/GPSVWGKYL/PSVWGKYLW/SVWGKYLWR/MPGPSVWG/PGPSVWGK/GPSVWGKY/PSVWGKYL/SVWGKYLW/MPGPSVWGKYL/GPSVWGKYLW/GPSVWGKYL/SVWGKYLWRS/SVWGKYLWRSP/MPGPSVWGKY/GPSVWGKYL/GPSVWGKYL/SVWGKYLWR/SVWGKYLWRS/MPGPSVWGK/PGPSVWGKY/GPSVWGKYL/PSVWGKYLW/SVWGKYLWR/MPGPSVWG/PGPSVWGK/GPSVWGKY/PSVWGKYL/SVWGKYLW/MPGPSVWGKYL/GPSVWGKYLW/GPSVWGKYLW/PSVWGKYLW/SVWGKYLWRSP/MPGPSVWGKY/PGPSVWGKYL/GPSVWGKYLW/PSVWGKYLW/SVWGKYLWRS/MPGPSVWGK/PGPSVWGKY/GPSVWGKYL/PSVWGKYLW/SVWGKYLWR/MPGPSVWG/PGPSVWGK/GPSVWGKY/PSVWGKYL/SVWGKYLW 33 4 2 NA 0 NA HLA-B*07:02 A 25.1564253185 NA 1.201 0.1499 0.913275315926 11 9 10 PSVWGKYLWRSPHSK 4.2859 NA NA NA NA 0.212 15 no -NA NA MAVFPATARGQLGIR CARKD NA 3.07 1.32 FALSE FALSE FALSE NA NA 42.46 NA NA NA NA HLA-DRB1*15:01 FALSE CARKD NA 17 48 NA RB0401_02_004-chr13_111267905 LATARGQL TRUE 1 6.1 3.68548888889 1 1.08 NA 39.0179025 1 HLA B*0702 uc010tjl.2#exon.0 NA NA NA 4 0.8 2.3 1.7 3 ATGGCTGTGTTTCTGGCGACGGCGCGGGGGCAGCTGGGAATCCGGAATGCTGCCCGATGGCCCTGGGTCCTCGCTGTGGGG 1.83215391307 SME PATARGQL 11-RB0401_02_004 0 FLATARGQL chr13_111267905 False FALSE 609 37 19.5 16 0.2 chr13_111267905 1 RB0401_02_004 1.94891557042 19.35 FALSE NM_001242881 11 P5L FPATARGQLGI FPATARGQLGI FPATARGQL PATARGQLGI 0.439357418 MAVFLATARGQLGIR 13.7758307526 0 1 HLA DRB1*1501 0.6 85.0000/12.6946/73.1250/1.9138/79.0000/55.2632/41.1667/13.2737/16.1194/26.8644/37.4444/24.3247/62.1429/1.3494/70.0000/15.3666/32.4483/82.0000/44.4000/44.9000/83.5000/20.3705/79.2308/7.2355/78.4615/60.0000/27.1553/21.2814/22.4483/39.5714/18.2177/19.6445/42.6923/1.7880/73.8889/32.6271/21.5879/75.7692/40.2414/50.0794/78.3333/8.4685/73.3333/43.5000/64.2857/54.0909/47.3333/9.4934/26.5000/20.0962/12.5775/21.7333/67.0000/1.6457/30.0000/22.4474/25.7037/85.0000/41.0000/5.8482/75.5000/37.1053/75.0000/36.7317/56.5714/27.3119/68.4211/23.4324/40.1429/4.6679/14.9254/26.4688/71.7857/9.9875/19.0528/3.6334/32.2787/52.9808/67.3684/5.0875 MAVFLATARGQLGIRNAA HLA-A*02:01 HLA-A*02:64 HLA-B*07:02 HLA-B*51:53 FALSE NA 4 37.07048484 uc010tjl.2 RB0401_02_004 C SOMATIC_HI -168.322 13 0 FALSE FIXED 5.22 MAVFPATARGQLGIRNAA 0.24671916 5 4 2.08 FALSE 3.11664448078 15 14.28 NA 2 42.46 NA NA NA 19.35 0 FALSE FALSE MAVFPATARGQLGIR 762 True 2 010-M17 HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:01/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-A*02:64/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*07:02/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53/HLA-B*51:53 8 NA FLATARGQL LATARGQLGI FLATARGQLGI FLATARGQLGI AVFLATARGQ/AVFLATARGQL/VFLATARGQL/FLATARGQLGI/LATARGQLGIR/MAVFLATARG/AVFLATARGQ/VFLATARGQL/FLATARGQL/LATARGQLGI/MAVFLATAR/AVFLATARG/VFLATARGQ/FLATARGQL/LATARGQLG/MAVFLATA/AVFLATAR/VFLATARG/FLATARGQ/LATARGQL/AVFLATARGQ/AVFLATARGQL/VFLATARGQL/FLATARGQLGI/LATARGQLGIR/MAVFLATARG/AVFLATARGQ/VFLATARGQL/FLATARGQLG/LATARGQLGI/MAVFLATAR/AVFLATARG/VFLATARGQ/FLATARGQL/LATARGQLG/MAVFLATA/AVFLATAR/VFLATARG/FLATARGQ/LATARGQL/MAVFLATARGQ/AVFLATARGQL/VFLATARGQL/FLATARGQLGI/LATARGQLGIR/MAVFLATARG/AVFLATARGQ/VFLATARGQL/FLATARGQL/LATARGQLGI/MAVFLATAR/AVFLATARG/VFLATARGQ/FLATARGQL/LATARGQLG/MAVFLATA/AVFLATAR/VFLATARG/FLATARGQ/LATARGQL/MAVFLATARGQ/AVFLATARGQL/VFLATARGQLG/FLATARGQLGI/LATARGQLGI/MAVFLATARG/AVFLATARGQ/VFLATARGQL/FLATARGQLG/LATARGQLGI/MAVFLATAR/AVFLATARG/VFLATARGQ/FLATARGQL/LATARGQLG/MAVFLATA/AVFLATAR/VFLATARG/FLATARGQ/LATARGQL 2 0 1 NA 1 NA HLA-A*02:01 T 27.7238674133 NA 0.843 1.3494 2.62717508049 10 9 11 MAVFLATARGQLGIR 2.104125 NA NA NA NA 0.253 15 no diff --git a/input/netmhcpan4/tmp.fasta b/input/netmhcpan4/tmp.fasta deleted file mode 100644 index 6c07bfd5..00000000 --- a/input/netmhcpan4/tmp.fasta +++ /dev/null @@ -1,2 +0,0 @@ ->seq1 -LLKRKHRFILLRSSGNKVSDIKFQAPT diff --git a/input/netmhcpan4/x.csv b/input/netmhcpan4/x.csv deleted file mode 100644 index e69de29b..00000000 diff --git a/input/predict_all_epitopes.py b/input/predict_all_epitopes.py index 602d9b3a..29aa4d72 100755 --- a/input/predict_all_epitopes.py +++ b/input/predict_all_epitopes.py @@ -76,22 +76,6 @@ def load_nmer_frequency(frequency_file): freq_dict[w[0]] = w[1] return freq_dict - def load_available_hla_alleles(self, mhc=MHC_I): - """ - loads file with available hla alllels for netmhcpan4/netmhcIIpan prediction, returns set - :param mhc: - :return: - """ - if mhc == MHC_II: - fileMHC = self.references.available_mhc_ii - else: - fileMHC = self.references.available_mhc_i - set_available_mhc = set() - with open(fileMHC) as f: - for line in f: - set_available_mhc.add(line.strip()) - return set_available_mhc - @staticmethod def load_patient_hla_I_allels(path_to_hla_file): """ @@ -192,8 +176,8 @@ def initialise_properties(self, data, path_to_hla_file, tissue, tumour_content_f self.aa_index1_dict = aa_index.parse_aaindex1(self.references.aaindex1) self.aa_index2_dict = aa_index.parse_aaindex2(self.references.aaindex2) prov_file = self.references.prov_scores_mapped3 - self.hla_available_alleles = self.load_available_hla_alleles() - self.hlaII_available_alleles = self.load_available_hla_alleles(mhc=MHC_II) + self.hla_available_alleles = self.references.load_available_hla_alleles(mhc=MHC_I) + self.hlaII_available_alleles = self.references.load_available_hla_alleles(mhc=MHC_II) self.patient_hla_I_allels = self.load_patient_hla_I_allels(path_to_hla_file) self.patient_hla_II_allels = self.load_patient_hla_II_allels(path_to_hla_file) # tumour content diff --git a/input/references.py b/input/references.py index ab7fffbe..8d8178a9 100755 --- a/input/references.py +++ b/input/references.py @@ -89,3 +89,19 @@ def _log_configuration(self): def _get_reference_file_name(self, file_name_suffix): return os.path.join(self.reference_genome_folder, file_name_suffix) + + def load_available_hla_alleles(self, mhc=input.MHC_I): + """ + loads file with available hla alllels for netmhcpan4/netmhcIIpan prediction, returns set + :type mhc: str + :rtype list: + """ + if mhc == input.MHC_II: + fileMHC = self.available_mhc_ii + else: + fileMHC = self.available_mhc_i + set_available_mhc = set() + with open(fileMHC) as f: + for line in f: + set_available_mhc.add(line.strip()) + return set_available_mhc diff --git a/input/tests/integration_tests/test_netmhcpan.py b/input/tests/integration_tests/test_netmhcpan.py new file mode 100755 index 00000000..dfbc23be --- /dev/null +++ b/input/tests/integration_tests/test_netmhcpan.py @@ -0,0 +1,96 @@ +import os +from unittest import TestCase + +import input.tests.integration_tests.integration_test_tools as integration_test_tools +from input import MHC_I, MHC_II +from input.helpers import intermediate_files +from input.helpers.runner import Runner +from input.netmhcpan4.netmhcIIpan_prediction import NetMhcIIPanPredictor +from input.netmhcpan4.netmhcpan_prediction import NetMhcPanPredictor +from input.tests import TEST_HLAI_ALLELES, TEST_HLAII_ALLELES + + +class TestNetMhcPanPredictor(TestCase): + + def setUp(self): + self.references, self.configuration = integration_test_tools.load_references() + self.runner = Runner() + + def test_netmhcpan_epitope_iedb(self): + netmhcpan_predictor = NetMhcPanPredictor(runner=self.runner, configuration=self.configuration) + # this is an epitope from IEDB of length 9 + mutated = 'NLVPMVATV' + tmp_prediction = intermediate_files.create_temp_file(prefix="netmhcpanpred_", suffix=".csv") + tmp_fasta = intermediate_files.create_temp_fasta(sequences=[mutated], prefix="tmp_") + netmhcpan_predictor.mhc_prediction( + tmpfasta=tmp_fasta, tmppred=tmp_prediction, hla_alleles=TEST_HLAI_ALLELES, + set_available_mhc=self.references.load_available_hla_alleles(mhc=MHC_I)) + self.assertTrue(os.path.exists(tmp_prediction)) + self.assertEqual(166, len(open(tmp_prediction).readlines())) + header, rows = netmhcpan_predictor.filter_binding_predictions(4, tmp_prediction) + self.assertEqual(14, len(header)) # output has 14 columns + for r in rows: + self.assertEqual(14, len(r)) # each row has 14 columns + self.assertEqual(165, len(rows)) + + def test_netmhcpan_too_small_epitope(self): + netmhcpan_predictor = NetMhcPanPredictor(runner=self.runner, configuration=self.configuration) + mutated = 'NLVP' + tmp_prediction = intermediate_files.create_temp_file(prefix="netmhcpanpred_", suffix=".csv") + tmp_fasta = intermediate_files.create_temp_fasta(sequences=[mutated], prefix="tmp_") + netmhcpan_predictor.mhc_prediction( + tmpfasta=tmp_fasta, tmppred=tmp_prediction, hla_alleles=TEST_HLAI_ALLELES, + set_available_mhc=self.references.load_available_hla_alleles(mhc=MHC_I)) + self.assertTrue(os.path.exists(tmp_prediction)) + # TODO: this is writing ot the output file "No;peptides;derived;from;protein;ID;seq1;len;4.;Skipped" + self.assertEqual(55, len(open(tmp_prediction).readlines())) + + # TODO: it crashes here as it fails to parse the header. Fix and remove the try-except + try: + header, rows = netmhcpan_predictor.filter_binding_predictions(2, tmp_prediction) + self.assertEqual(14, len(header)) # output has 14 columns + for r in rows: + self.assertEqual(14, len(r)) # each row has 14 columns + self.assertEqual(0, len(rows)) + except: + pass + + def test_netmhc2pan_epitope_iedb(self): + netmhc2pan_predictor = NetMhcIIPanPredictor(runner=self.runner, configuration=self.configuration) + # this is an epitope from IEDB of length 15 + mutated = 'ENPVVHFFKNIVTPR' + tmp_prediction = intermediate_files.create_temp_file(prefix="netmhcpanpred_", suffix=".csv") + tmp_fasta = intermediate_files.create_temp_fasta(sequences=[mutated], prefix="tmp_") + netmhc2pan_predictor.mhcII_prediction( + tmpfasta=tmp_fasta, tmppred=tmp_prediction, hla_alleles=TEST_HLAII_ALLELES, + set_available_mhc=self.references.load_available_hla_alleles(mhc=MHC_II)) + self.assertTrue(os.path.exists(tmp_prediction)) + self.assertEqual(20, len(open(tmp_prediction).readlines())) + + header, rows = netmhc2pan_predictor.filter_binding_predictions(4, tmp_prediction) + self.assertEqual(12, len(header)) # output has 14 columns + for r in rows: + self.assertTrue(len(r) <= 12 or len(r) >= 10) # each row has 10 or 12 columns + self.assertEqual(19, len(rows)) + + def test_netmhc2pan_too_small_epitope(self): + netmhc2pan_predictor = NetMhcIIPanPredictor(runner=self.runner, configuration=self.configuration) + # this is an epitope from IEDB of length 15 + mutated = 'ENPVVH' + tmp_prediction = intermediate_files.create_temp_file(prefix="netmhcpanpred_", suffix=".csv") + tmp_fasta = intermediate_files.create_temp_fasta(sequences=[mutated], prefix="tmp_") + netmhc2pan_predictor.mhcII_prediction( + tmpfasta=tmp_fasta, tmppred=tmp_prediction, hla_alleles=TEST_HLAII_ALLELES, + set_available_mhc=self.references.load_available_hla_alleles(mhc=MHC_II)) + self.assertTrue(os.path.exists(tmp_prediction)) + self.assertEqual(1, len(open(tmp_prediction).readlines())) + + # TODO: it crashes here as it fails to parse the header. Fix and remove the try-except + try: + header, rows = netmhc2pan_predictor.filter_binding_predictions(4, tmp_prediction) + self.assertEqual(12, len(header)) # output has 14 columns + for r in rows: + self.assertTrue(len(r) <= 12 or len(r) >= 10) # each row has 10 or 12 columns + self.assertEqual(0, len(rows)) + except: + pass \ No newline at end of file From 779a8b189be8ed77a3f18a160fead9ffb2ab5904 Mon Sep 17 00:00:00 2001 From: Pablo Riesgo Ferreiro Date: Thu, 4 Jun 2020 15:10:35 +0200 Subject: [PATCH 037/105] add gitattributes --- .gitattributes | 2 ++ 1 file changed, 2 insertions(+) create mode 100755 .gitattributes diff --git a/.gitattributes b/.gitattributes new file mode 100755 index 00000000..ed6958d7 --- /dev/null +++ b/.gitattributes @@ -0,0 +1,2 @@ +* -diff +*.xml binary \ No newline at end of file From 5e2728e1d91457d9ed412930a1cb6e7429b7abc9 Mon Sep 17 00:00:00 2001 From: Pablo Riesgo Ferreiro Date: Thu, 4 Jun 2020 15:12:53 +0200 Subject: [PATCH 038/105] another try to .gitattributes --- .gitattributes | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.gitattributes b/.gitattributes index ed6958d7..ecaef752 100755 --- a/.gitattributes +++ b/.gitattributes @@ -1,2 +1,2 @@ * -diff -*.xml binary \ No newline at end of file +**/*.xml binary \ No newline at end of file From 410dcdf81a95188d2fd844a8a0a2fd441ed84734 Mon Sep 17 00:00:00 2001 From: Pablo Riesgo Ferreiro Date: Thu, 4 Jun 2020 15:22:12 +0200 Subject: [PATCH 039/105] another try to .gitattributes --- .gitattributes | 19 +++++++++++++++++-- 1 file changed, 17 insertions(+), 2 deletions(-) diff --git a/.gitattributes b/.gitattributes index ecaef752..4621b35d 100755 --- a/.gitattributes +++ b/.gitattributes @@ -1,2 +1,17 @@ -* -diff -**/*.xml binary \ No newline at end of file +# Basic .gitattributes for a python repo. + +# Source files +# ============ +*.py text diff=python +*.py3 text diff=python +*.avdl text diff +*.gitignore diff +*.gitattributes diff +MANIFEST.in diff +README.md diff + +# Binary files +# ============ +*.xml binary +*.pdf binary +*.fasta binary From 4c84db1a42833b5bd0561e7f7c1ec693f13fc29d Mon Sep 17 00:00:00 2001 From: Pablo Riesgo Ferreiro Date: Thu, 4 Jun 2020 15:23:57 +0200 Subject: [PATCH 040/105] another try to .gitattributes --- .gitattributes | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.gitattributes b/.gitattributes index 4621b35d..3efe9f22 100755 --- a/.gitattributes +++ b/.gitattributes @@ -12,6 +12,6 @@ README.md diff # Binary files # ============ -*.xml binary -*.pdf binary -*.fasta binary +**/*.xml binary +**/*.pdf binary +**/*.fasta binary From 27128ca8314de105a1c373b670f3d2c569d229a5 Mon Sep 17 00:00:00 2001 From: Pablo Riesgo Ferreiro Date: Thu, 4 Jun 2020 15:35:38 +0200 Subject: [PATCH 041/105] adding back in Balanchandran folder to have a clearer merge request. 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input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/data/iedb.fasta create mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/output/NeoantigenQuality.txt create mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/run.sh create mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/src/.DS_Store create mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/src/.project create mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/src/.pydevproject create mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/src/Aligner.py create mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/src/__init__.py create mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/src/main.py diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/.DS_Store b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/.DS_Store new file mode 100755 index 0000000000000000000000000000000000000000..29498513331c9590ed766731a6b095eb0acf43ae GIT binary patch literal 6148 zcmeHK%TB{U3>?!4RdDH%H1@V-^m;4Wg<&0T*E43hX&L&p$$qDprKhvt+--jT7}7np#A3 zem<@ulZcFPQ@L2!n>{z**++&mCkOWA81W14cNZlEfg7;MkzE(HCqgga^y>{tEnwC%0;vJ&^%eQ zLs35+`xjp>T0M_1 +HIQDLYTVL +>M_2 +GYYTLLNVF +>M_3 +LTLFGYYTL +>M_4 +TLFGYYTLL +>M_5 +YYTLLNVFL +>M_6 +LAVRPSKIK +>M_7 +PTYGNSTKL +>M_8 +TASNVEFAI +>M_9 +TSSDSISHM +>M_10 +RFRALNQEL +>M_11 +HRNHIDRAL +>M_12 +FALLFGHRF +>M_13 +HRFDYRDPV +>M_14 +VADSTLLLM +>M_15 +FKMGAHTEV +>M_16 +FEGFPQSLL +>M_17 +FEGFPQSLL +>M_18 +GAQDRNSSF +>M_19 +FTHLRLQEF +>M_20 +LAASGPTLV +>M_21 +MIVGRTYTL +>M_22 +VAAENEAVL +>M_23 +IERNLINSL +>M_24 +GEAGTIERV +>M_25 +VAIFLGFYV +>M_26 +YSIFQLAFV +>M_27 +MALNYNRAF +>M_28 +TVFGGLMAL +>M_29 +LSSRLSDTL +>M_30 +SRLSDTLSF +>M_31 +KRTSPEELL +>M_32 +HALHLRRMM +>M_33 +MAGFMGMAV +>M_34 +RMMAGFMGM +>M_35 +FVSTIIHLL +>M_36 +YLVPGFSPY +>M_37 +YLVPGFSPY +>M_38 +KASFDHACL diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_112032_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_112032_1_T_iedb.xml new file mode 100755 index 00000000..91a7ccb8 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_112032_1_T_iedb.xml @@ -0,0 +1,1246 @@ + + + + blastp + BLASTP 2.2.30+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta + Query_1 + M_1 + 9 + + + BLOSUM62 + 100000000 + 11 + 1 + F + + + + + 1 + Query_1 + M_1 + 9 + + + 1 + gnl|BL_ORD_ID|86 + 6373|Genome polyprotein|SRC279960|Hepatitis C virus subtype 3a|356426 + 86 + 10 + + + 1 + 15.3938 + 28 + 0.84849 + 1 + 9 + 2 + 10 + 0 + 0 + 6 + 6 + 0 + 9 + HIQDLYTVL + HAQDATTVL + H QD TVL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 2 + Query_2 + M_2 + 9 + + + 1 + gnl|BL_ORD_ID|23 + 1516|Nucleoprotein|P03418.1|Human respiratory syncytial virus A2|11259 + 23 + 14 + + + 1 + 13.4678 + 23 + 7.59625 + 1 + 7 + 2 + 8 + 0 + 0 + 4 + 6 + 0 + 7 + GYYTLLN + GFYHILN + G+Y +LN + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 3 + Query_3 + M_3 + 9 + + + 1 + gnl|BL_ORD_ID|1677 + 149024|NS2 protein|NP_751923.1|Hepatitis C virus (isolate H77)|63746 + 1677 + 9 + + + 1 + 12.3122 + 20 + 64.7664 + 1 + 7 + 2 + 8 + 0 + 0 + 5 + 5 + 0 + 7 + LTLFGYY + LTLSPYY + LTL YY + + + + + 2 + gnl|BL_ORD_ID|639 + 37991|polyprotein|AAY82034.1|Hepatitis C virus genotype 1|41856 + 639 + 13 + + + 1 + 11.927 + 19 + 78.6478 + 1 + 7 + 4 + 10 + 0 + 0 + 5 + 5 + 0 + 7 + LTLFGYY + LTLSPYY + LTL YY + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 4 + Query_4 + M_4 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 5 + Query_5 + M_5 + 9 + + + 1 + gnl|BL_ORD_ID|1867 + 180464|polyprotein|CDF77361.1|Dengue virus 3|11069 + 1867 + 10 + + + 1 + 12.3122 + 20 + 44.794 + 2 + 9 + 1 + 8 + 0 + 0 + 4 + 7 + 0 + 8 + YTLLNVFL + FTILALFL + +T+L +FL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 6 + Query_6 + M_6 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 7 + Query_7 + M_7 + 9 + + + 1 + gnl|BL_ORD_ID|1143 + 75436|Polyprotein|P90247|Hepatitis C virus|11103 + 1143 + 20 + + + 1 + 13.4678 + 23 + 11.6549 + 1 + 6 + 4 + 9 + 0 + 0 + 4 + 4 + 0 + 6 + PTYGNS + PLYGNE + P YGN + + + + + 2 + gnl|BL_ORD_ID|1144 + 75438|polyprotein|AAF65962.1|Hepatitis C virus|11103 + 1144 + 20 + + + 1 + 13.4678 + 23 + 11.8474 + 1 + 6 + 4 + 9 + 0 + 0 + 4 + 4 + 0 + 6 + PTYGNS + PLYGNE + P YGN + + + + + 3 + gnl|BL_ORD_ID|1142 + 75435|largest ORF|AAB02128.1|Hepatitis C virus|11103 + 1142 + 20 + + + 1 + 13.4678 + 23 + 12.0429 + 1 + 6 + 4 + 9 + 0 + 0 + 4 + 4 + 0 + 6 + PTYGNS + PLYGNE + P YGN + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 8 + Query_8 + M_8 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 9 + Query_9 + M_9 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 10 + Query_10 + M_10 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 11 + Query_11 + M_11 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 12 + Query_12 + M_12 + 9 + + + 1 + gnl|BL_ORD_ID|606 + 37251|||| + 606 + 9 + + + 1 + 13.853 + 24 + 4.4402 + 3 + 7 + 1 + 5 + 0 + 0 + 5 + 5 + 0 + 5 + LLFGH + LLFGH + LLFGH + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 13 + Query_13 + M_13 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 14 + Query_14 + M_14 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 15 + Query_15 + M_15 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 16 + Query_16 + M_16 + 9 + + + 1 + gnl|BL_ORD_ID|389 + 23807|tax|AAG48731.1|Human T-lymphotropic virus 2|11909 + 389 + 23 + + + 1 + 15.779 + 29 + 0.429649 + 1 + 9 + 2 + 10 + 0 + 0 + 7 + 7 + 0 + 9 + FEGFPQSLL + FPGFGQSLL + F GF QSLL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 17 + Query_17 + M_17 + 9 + + + 1 + gnl|BL_ORD_ID|389 + 23807|tax|AAG48731.1|Human T-lymphotropic virus 2|11909 + 389 + 23 + + + 1 + 15.779 + 29 + 0.429649 + 1 + 9 + 2 + 10 + 0 + 0 + 7 + 7 + 0 + 9 + FEGFPQSLL + FPGFGQSLL + F GF QSLL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 18 + Query_18 + M_18 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 19 + Query_19 + M_19 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 20 + Query_20 + M_20 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 21 + Query_21 + M_21 + 9 + + + 1 + gnl|BL_ORD_ID|301 + 20354|M1 protein|CAA30882.1|Influenza A virus|11320 + 301 + 9 + + + 1 + 11.927 + 19 + 70.3445 + 2 + 9 + 2 + 9 + 0 + 0 + 4 + 6 + 0 + 8 + IVGRTYTL + ILGFVFTL + I+G +TL + + + + + 2 + gnl|BL_ORD_ID|302 + 20355|Matrix protein 1|P03485.1|Influenza A virus (A/Puerto Rico/8/1934(H1N1))|211044 + 302 + 10 + + + 1 + 11.927 + 19 + 85.0569 + 2 + 9 + 2 + 9 + 0 + 0 + 4 + 6 + 0 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0.14 + + + + + 34 + Query_34 + M_34 + 9 + + + 1 + gnl|BL_ORD_ID|1357 + 108153|polyprotein|AAF65950.1|Hepatitis C virus|11103 + 1357 + 10 + + + 1 + 13.0826 + 22 + 15.0326 + 2 + 8 + 4 + 10 + 0 + 0 + 4 + 5 + 0 + 7 + MMAGFMG + LMTGFTG + +M GF G + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 35 + Query_35 + M_35 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 36 + Query_36 + M_36 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 37 + Query_37 + M_37 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 38 + Query_38 + M_38 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + + diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_113413_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_113413_1_T.fasta new file mode 100755 index 00000000..b7f441ce --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_113413_1_T.fasta @@ -0,0 +1,120 @@ +>M_39 +EFHDIASHV +>M_40 +MCDNGSGLV +>M_41 +IQNAGGSVI +>M_42 +TQDGALMNV +>M_43 +TLGIICLLL +>M_44 +WNDKVKEAL +>M_45 +QNAGGSVII +>M_46 +SDYLHWEVV +>M_47 +SSVPVLNML +>M_48 +WALEVLLNA +>M_49 +YETQDGALM +>M_50 +NMELPYFVL +>M_51 +LSTPAPQVF +>M_52 +VSDTEFHPL +>M_53 +MVVAGQRAV +>M_54 +YLHWEVVEL +>M_55 +ANFPWALEV +>M_56 +WYLRDVSEV +>M_57 +FHDIASHVK +>M_58 +FPWALEVLL +>M_59 +GTLGIICLL +>M_60 +YLHWEVVEL +>M_61 +LQFSRMEQL +>M_62 +VHLESNATV +>M_63 +QMFVHLQLL +>M_64 +VHLESNATV +>M_65 +TQDGALMNV +>M_66 +VAFCLKCNL +>M_67 +STDSLSTPA +>M_68 +DILEKSSSV +>M_69 +NMVGFSDRV +>M_70 +NLGSKLQLV +>M_71 +FPWALEVLL +>M_72 +TKDTFMMEL +>M_73 +HCANFPWAL +>M_74 +ESSSETSTY +>M_75 +QMFVHLQLL +>M_76 +QPLKYTWLL +>M_77 +SLTTLLQAL +>M_78 +SLSTPAPQV +>M_79 +FAINFFKEV +>M_80 +YTWLLAAKV +>M_81 +DLENMELPY +>M_82 +EKSSSVPVL +>M_83 +WLCDHPVPV +>M_84 +LLMSTLGIL +>M_85 +IQNAGGSVI +>M_86 +YTWLLAAKV +>M_87 +FSQEPADQM +>M_88 +ILSWLVSQL +>M_89 +LLLMSTLGI +>M_90 +FYIFNVSSI +>M_91 +GLGECITQV +>M_92 +LAMRRHSRI +>M_93 +LAKDSGAPV +>M_94 +YLHWEVVEL +>M_95 +FMMELLNRV +>M_96 +WLCDHPVPV +>M_97 +FAINFFKEV +>M_98 +FMMELLNRV diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_113413_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_113413_1_T_iedb.xml new file mode 100755 index 00000000..417ce7e1 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_113413_1_T_iedb.xml @@ -0,0 +1,2156 @@ + + + + blastp + BLASTP 2.2.30+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta + Query_1 + M_39 + 9 + + + BLOSUM62 + 100000000 + 11 + 1 + F + + + + + 1 + Query_1 + M_39 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 2 + Query_2 + M_40 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 3 + Query_3 + M_41 + 9 + + + 1 + gnl|BL_ORD_ID|2016 + 183843|envelope protein|AGW23576.1|Dengue virus 3|11069 + 2016 + 10 + + + 1 + 15.779 + 29 + 0.401267 + 1 + 9 + 1 + 9 + 0 + 0 + 6 + 8 + 0 + 9 + IQNAGGSVI + IQNSGGTSI + IQN+GG+ I + + + + + 2 + gnl|BL_ORD_ID|461 + 27981|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 + 461 + 20 + + + 1 + 15.0086 + 27 + 1.13532 + 2 + 7 + 15 + 20 + 0 + 0 + 5 + 6 + 0 + 6 + QNAGGS + QNAGGT + QNAGG+ + + + + + + + 2334 + 25004 + 0 + 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gnl|BL_ORD_ID|461 + 27981|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 + 461 + 20 + + + 1 + 15.0086 + 27 + 1.13532 + 1 + 6 + 15 + 20 + 0 + 0 + 5 + 6 + 0 + 6 + QNAGGS + QNAGGT + QNAGG+ + + + + + 2 + gnl|BL_ORD_ID|2016 + 183843|envelope protein|AGW23576.1|Dengue virus 3|11069 + 2016 + 10 + + + 1 + 14.6234 + 26 + 1.84513 + 1 + 9 + 2 + 10 + 0 + 0 + 5 + 7 + 0 + 9 + QNAGGSVII + QNSGGTSIF + QN+GG+ I + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 8 + Query_8 + M_46 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 9 + Query_9 + M_47 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 10 + Query_10 + M_48 + 9 + + + 1 + gnl|BL_ORD_ID|637 + 37960|membrane protein|AAA45887.1|Human gammaherpesvirus 4|10376 + 637 + 9 + + + 1 + 12.3122 + 20 + 60.6092 + 1 + 7 + 3 + 9 + 0 + 0 + 5 + 5 + 0 + 7 + WALEVLL + WTLVVLL + W L VLL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 11 + Query_11 + M_49 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 12 + Query_12 + M_50 + 9 + + + 1 + gnl|BL_ORD_ID|184 + 13518|HCV-1|AAA45676.1|Hepatitis C virus genotype 1|41856 + 184 + 20 + + + 1 + 12.6974 + 21 + 23.6647 + 4 + 8 + 3 + 7 + 0 + 0 + 4 + 4 + 0 + 5 + LPYFV + LPYLV + LPY V + + + + + 2 + gnl|BL_ORD_ID|183 + 13516|Genome polyprotein|P26664.3|Hepatitis C virus subtype 1a|31646 + 183 + 9 + + + 1 + 12.3122 + 20 + 47.1713 + 4 + 8 + 3 + 7 + 0 + 0 + 4 + 4 + 0 + 5 + LPYFV + LPYLV + LPY V + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 13 + Query_13 + M_51 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 14 + Query_14 + M_52 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 15 + Query_15 + M_53 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 16 + Query_16 + M_54 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 17 + Query_17 + M_55 + 9 + + + 1 + gnl|BL_ORD_ID|561 + 34616|pol protein|BAA32832.1|Hepatitis B virus|10407 + 561 + 9 + + + 1 + 14.2382 + 25 + 3.05306 + 1 + 7 + 3 + 9 + 0 + 0 + 4 + 5 + 0 + 7 + ANFPWAL + TSFPWLL + +FPW L + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 18 + Query_18 + M_56 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 19 + Query_19 + M_57 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 20 + Query_20 + M_58 + 9 + + + 1 + gnl|BL_ORD_ID|637 + 37960|membrane protein|AAA45887.1|Human gammaherpesvirus 4|10376 + 637 + 9 + + + 1 + 12.3122 + 20 + 66.9453 + 3 + 9 + 3 + 9 + 0 + 0 + 5 + 5 + 0 + 7 + WALEVLL + WTLVVLL + W L VLL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 21 + Query_21 + M_59 + 9 + + + 1 + gnl|BL_ORD_ID|979 + 64818|E7|AAD33253.1|Human papillomavirus type 16|333760 + 979 + 8 + + + 1 + 14.6234 + 26 + 1.73882 + 2 + 7 + 1 + 6 + 0 + 0 + 5 + 6 + 0 + 6 + TLGIIC + TLGIVC + TLGI+C + + + + + 2 + gnl|BL_ORD_ID|980 + 64819|E7 protein|ABL96585.1|Human papillomavirus type 16|333760 + 980 + 9 + + + 1 + 14.6234 + 26 + 2.33479 + 2 + 7 + 1 + 6 + 0 + 0 + 5 + 6 + 0 + 6 + TLGIIC + TLGIVC + TLGI+C + + + + + 3 + gnl|BL_ORD_ID|2102 + 185978|polyprotein|CDF77361.1|Dengue virus 3|11069 + 2102 + 10 + + + 1 + 14.6234 + 26 + 2.37049 + 2 + 8 + 1 + 7 + 0 + 0 + 4 + 7 + 0 + 7 + TLGIICL + TMGVLCL + T+G++CL + + + + + 4 + gnl|BL_ORD_ID|627 + 37573|E7 protein|ABL96585.1|Human papillomavirus type 16|333760 + 627 + 9 + + + 1 + 13.853 + 24 + 5.95161 + 1 + 6 + 4 + 9 + 0 + 0 + 5 + 6 + 0 + 6 + GTLGII + GTLGIV + GTLGI+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 22 + Query_22 + M_60 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 23 + Query_23 + M_61 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 24 + Query_24 + M_62 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 25 + Query_25 + M_63 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 26 + Query_26 + M_64 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 27 + Query_27 + M_65 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 28 + Query_28 + M_66 + 9 + + + 1 + gnl|BL_ORD_ID|1382 + 110184|E7|AAD33253.1|Human papillomavirus type 16|333760 + 1382 + 35 + + + 1 + 13.4678 + 23 + 9.19861 + 1 + 8 + 14 + 21 + 0 + 0 + 5 + 6 + 0 + 8 + VAFCLKCN + VTFCCKCD + V FC KC+ + + + + + 2 + gnl|BL_ORD_ID|1400 + 110467|Protein E6|P03126.1|Human papillomavirus type 16|333760 + 1400 + 25 + + + 1 + 11.5418 + 18 + 93.0417 + 2 + 7 + 8 + 13 + 0 + 0 + 4 + 4 + 0 + 6 + AFCLKC + AVCDKC + A C KC + + + + + 3 + gnl|BL_ORD_ID|1387 + 110227|Protein E6|P03126.1|Human papillomavirus type 16|333760 + 1387 + 33 + + + 1 + 11.1566 + 17 + 143.577 + 2 + 7 + 15 + 20 + 0 + 0 + 4 + 4 + 0 + 6 + AFCLKC + AVCDKC + A C KC + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 29 + Query_29 + M_67 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 30 + Query_30 + M_68 + 9 + + + 1 + gnl|BL_ORD_ID|181 + 13456|circumsporozoite protein|AAN87606.1|Plasmodium falciparum|5833 + 181 + 20 + + + 1 + 13.4678 + 23 + 9.72555 + 3 + 9 + 11 + 17 + 0 + 0 + 5 + 6 + 0 + 7 + LEKSSSV + MEKCSSV + +EK SSV + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 31 + Query_31 + M_69 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 32 + Query_32 + M_70 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 33 + Query_33 + M_71 + 9 + + + 1 + gnl|BL_ORD_ID|637 + 37960|membrane protein|AAA45887.1|Human gammaherpesvirus 4|10376 + 637 + 9 + + + 1 + 12.3122 + 20 + 66.9453 + 3 + 9 + 3 + 9 + 0 + 0 + 5 + 5 + 0 + 7 + WALEVLL + WTLVVLL + W L VLL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 34 + Query_34 + M_72 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 35 + Query_35 + M_73 + 9 + + + 1 + gnl|BL_ORD_ID|561 + 34616|pol protein|BAA32832.1|Hepatitis B virus|10407 + 561 + 9 + + + 1 + 14.2382 + 25 + 2.95178 + 3 + 9 + 3 + 9 + 0 + 0 + 4 + 5 + 0 + 7 + ANFPWAL + TSFPWLL + +FPW L + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 36 + Query_36 + M_74 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 37 + Query_37 + M_75 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 38 + Query_38 + M_76 + 9 + + + 1 + gnl|BL_ORD_ID|1020 + 68229|EBNA3B (EBNA4A) latent protein|CAA24858.1|Human gammaherpesvirus 4|10376 + 1020 + 10 + + + 1 + 11.927 + 19 + 68.8532 + 2 + 7 + 5 + 10 + 0 + 0 + 4 + 4 + 0 + 6 + PLKYTW + PYKPTW + P K TW + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 39 + Query_39 + M_77 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 40 + Query_40 + M_78 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 41 + Query_41 + M_79 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 42 + Query_42 + M_80 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 43 + Query_43 + M_81 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 44 + Query_44 + M_82 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 45 + Query_45 + M_83 + 9 + + + 1 + gnl|BL_ORD_ID|1944 + 180818|Membrane glycoprotein precursor|NP_739582.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 + 1944 + 15 + + + 1 + 13.4678 + 23 + 9.36117 + 1 + 6 + 1 + 6 + 0 + 0 + 3 + 4 + 0 + 6 + WLCDHP + WILRHP + W+ HP + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 46 + Query_46 + M_84 + 9 + + + 1 + gnl|BL_ORD_ID|627 + 37573|E7 protein|ABL96585.1|Human papillomavirus type 16|333760 + 627 + 9 + + + 1 + 15.3938 + 28 + 0.565591 + 1 + 9 + 1 + 9 + 0 + 0 + 7 + 8 + 0 + 9 + LLMSTLGIL + LLMGTLGIV + LLM TLGI+ + + + + + 2 + gnl|BL_ORD_ID|1718 + 150391|polyprotein|AGS49173.1|Dengue virus 2|11060 + 1718 + 10 + + + 1 + 14.6234 + 26 + 1.64355 + 1 + 9 + 1 + 9 + 0 + 0 + 5 + 9 + 0 + 9 + LLMSTLGIL + LMMTTIGIV + L+M+T+GI+ + + + + + 3 + gnl|BL_ORD_ID|1722 + 150448|polyprotein|AGO67248.1|Dengue virus 2|11060 + 1722 + 9 + + + 1 + 13.4678 + 23 + 8.56958 + 2 + 8 + 1 + 7 + 0 + 0 + 4 + 7 + 0 + 7 + LMSTLGI + MMATIGI + +M+T+GI + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 47 + Query_47 + M_85 + 9 + + + 1 + gnl|BL_ORD_ID|2016 + 183843|envelope protein|AGW23576.1|Dengue virus 3|11069 + 2016 + 10 + + + 1 + 15.779 + 29 + 0.401267 + 1 + 9 + 1 + 9 + 0 + 0 + 6 + 8 + 0 + 9 + IQNAGGSVI + IQNSGGTSI + IQN+GG+ I + + + + + 2 + gnl|BL_ORD_ID|461 + 27981|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 + 461 + 20 + + + 1 + 15.0086 + 27 + 1.13532 + 2 + 7 + 15 + 20 + 0 + 0 + 5 + 6 + 0 + 6 + QNAGGS + QNAGGT + QNAGG+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 48 + Query_48 + M_86 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 49 + Query_49 + M_87 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 50 + Query_50 + M_88 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 51 + Query_51 + M_89 + 9 + + + 1 + gnl|BL_ORD_ID|627 + 37573|E7 protein|ABL96585.1|Human papillomavirus type 16|333760 + 627 + 9 + + + 1 + 15.3938 + 28 + 0.690962 + 2 + 9 + 1 + 8 + 0 + 0 + 7 + 7 + 0 + 8 + LLMSTLGI + LLMGTLGI + LLM TLGI + + + + + 2 + gnl|BL_ORD_ID|1718 + 150391|polyprotein|AGS49173.1|Dengue virus 2|11060 + 1718 + 10 + + + 1 + 14.6234 + 26 + 2.17971 + 2 + 9 + 1 + 8 + 0 + 0 + 5 + 8 + 0 + 8 + LLMSTLGI + LMMTTIGI + L+M+T+GI + + + + + 3 + gnl|BL_ORD_ID|1722 + 150448|polyprotein|AGO67248.1|Dengue virus 2|11060 + 1722 + 9 + + + 1 + 13.4678 + 23 + 8.56958 + 3 + 9 + 1 + 7 + 0 + 0 + 4 + 7 + 0 + 7 + LMSTLGI + MMATIGI + +M+T+GI + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 52 + Query_52 + M_90 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 53 + Query_53 + M_91 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 54 + Query_54 + M_92 + 9 + + + 1 + gnl|BL_ORD_ID|2274 + 419017|polyprotein|AFY10034.1|Dengue virus 4|11070 + 2274 + 10 + + + 1 + 13.4678 + 23 + 10.9961 + 2 + 7 + 3 + 8 + 0 + 0 + 4 + 6 + 0 + 6 + AMRRHS + AMKRYS + AM+R+S + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 55 + Query_55 + M_93 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 56 + Query_56 + M_94 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 57 + Query_57 + M_95 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 58 + Query_58 + M_96 + 9 + + + 1 + gnl|BL_ORD_ID|1944 + 180818|Membrane glycoprotein precursor|NP_739582.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 + 1944 + 15 + + + 1 + 13.4678 + 23 + 9.36117 + 1 + 6 + 1 + 6 + 0 + 0 + 3 + 4 + 0 + 6 + WLCDHP + WILRHP + W+ HP + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 59 + Query_59 + M_97 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 60 + Query_60 + M_98 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + + diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_113520_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_113520_1_T.fasta new file mode 100755 index 00000000..5c7319a5 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_113520_1_T.fasta @@ -0,0 +1,56 @@ +>M_99 +TVAEKRGWK +>M_100 +RLLPDTFVL +>M_101 +RLLPDTFVL +>M_102 +SSMAAGLEH +>M_103 +MIYRLAQAK +>M_104 +TPMYRTRPA +>M_105 +ITYYCHGGY +>M_106 +KLGSSITYY +>M_107 +FPVSYGVPA +>M_108 +IMFPVSYGV +>M_109 +ISDTILKTK +>M_110 +RLQTHTIYK +>M_111 +ELFHVDWHV +>M_112 +LPRQYWEAL +>M_113 +MPHRATVYA +>M_114 +KLLECSLTK +>M_115 +RPQGQRPAL +>M_116 +SSDCIIEKK +>M_117 +TSSDCIIEK +>M_118 +GLMGHTLHR +>M_119 +LPGHAPGIL +>M_120 +YAYHVEWEK +>M_121 +WVRWHKGCL +>M_122 +SSSIRIHER +>M_123 +FLSSSFSML +>M_124 +FSMLKDHIK +>M_125 +LSSSFSMLK +>M_126 +VVGADGVGK diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_113520_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_113520_1_T_iedb.xml new file mode 100755 index 00000000..8f3d16ac --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_113520_1_T_iedb.xml @@ -0,0 +1,1106 @@ + + + + blastp + BLASTP 2.2.30+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta + Query_1 + M_99 + 9 + + + BLOSUM62 + 100000000 + 11 + 1 + F + + + + + 1 + Query_1 + M_99 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 2 + Query_2 + M_100 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 3 + Query_3 + M_101 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 4 + Query_4 + M_102 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 5 + Query_5 + M_103 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 6 + Query_6 + M_104 + 9 + + + 1 + gnl|BL_ORD_ID|1284 + 102150|nef protein|ACR27119.1|Human immunodeficiency virus 1|11676 + 1284 + 9 + + + 1 + 10.7714 + 16 + 449.273 + 1 + 8 + 1 + 8 + 0 + 0 + 4 + 4 + 0 + 8 + TPMYRTRP + TPQVPLRP + TP RP + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 7 + Query_7 + M_105 + 9 + + + 1 + gnl|BL_ORD_ID|1176 + 79454|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 + 1176 + 15 + + + 1 + 13.0826 + 22 + 20.7204 + 4 + 8 + 3 + 7 + 0 + 0 + 3 + 4 + 0 + 5 + YCHGG + FCHPG + +CH G + + + + + 2 + gnl|BL_ORD_ID|1160 + 76532|outer membrane protein|YP_170495.1|Francisella tularensis subsp. tularensis SCHU S4|177416 + 1160 + 10 + + + 1 + 11.5418 + 18 + 146.048 + 3 + 9 + 1 + 7 + 0 + 0 + 4 + 4 + 0 + 7 + YYCHGGY + YYLDRGY + YY GY + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 8 + Query_8 + M_106 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 9 + Query_9 + M_107 + 9 + + + 1 + gnl|BL_ORD_ID|1 + 118|envelope glycoprotein|ABS76372.1|Human immunodeficiency virus 1|11676 + 1 + 20 + + + 1 + 13.853 + 24 + 6.85717 + 3 + 8 + 9 + 14 + 0 + 0 + 5 + 5 + 0 + 6 + VSYGVP + VYYGVP + V YGVP + + + + + 2 + gnl|BL_ORD_ID|1831 + 179823|cell surface protein (associated with virulence)|NP_302372.1|Mycobacterium leprae TN|272631 + 1831 + 9 + + + 1 + 11.927 + 19 + 112.786 + 1 + 9 + 1 + 9 + 0 + 0 + 4 + 4 + 0 + 9 + FPVSYGVPA + IPASVSAPA + P S PA + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 10 + Query_10 + M_108 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 11 + Query_11 + M_109 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 12 + Query_12 + M_110 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 13 + Query_13 + M_111 + 9 + + + 1 + gnl|BL_ORD_ID|686 + 41407|Envelope protein|NP_739583.2|Dengue virus 2|11060 + 686 + 15 + + + 1 + 10.3862 + 15 + 487.414 + 2 + 7 + 7 + 12 + 0 + 0 + 3 + 3 + 0 + 6 + LFHVDW + LVHRQW + L H W + + + + + 2 + gnl|BL_ORD_ID|1746 + 150725|polyprotein|AGO67248.1|Dengue virus 2|11060 + 1746 + 9 + + + 1 + 10.001 + 14 + 843.115 + 2 + 7 + 2 + 7 + 0 + 0 + 3 + 3 + 0 + 6 + LFHVDW + LVHRQW + L H W + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 14 + Query_14 + M_112 + 9 + + + 1 + gnl|BL_ORD_ID|502 + 31997|hypothetical protein FTT0484|YP_169522.1|Francisella tularensis subsp. tularensis SCHU S4|177416 + 502 + 9 + + + 1 + 13.853 + 24 + 5.65074 + 1 + 6 + 3 + 8 + 0 + 0 + 4 + 4 + 0 + 6 + LPRQYW + LPEGYW + LP YW + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 15 + Query_15 + M_113 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 16 + Query_16 + M_114 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 17 + Query_17 + M_115 + 9 + + + 1 + gnl|BL_ORD_ID|1739 + 150643|polyprotein|AGW21594.1|Dengue virus 1|11053 + 1739 + 10 + + + 1 + 14.2382 + 25 + 3.50259 + 2 + 9 + 2 + 9 + 0 + 0 + 5 + 6 + 0 + 8 + PQGQRPAL + PEGIIPAL + P+G PAL + + + + + 2 + gnl|BL_ORD_ID|2075 + 185125|polyprotein|AGW21594.1|Dengue virus 1|11053 + 2075 + 10 + + + 1 + 14.2382 + 25 + 4.23087 + 2 + 9 + 3 + 10 + 0 + 0 + 5 + 6 + 0 + 8 + PQGQRPAL + PEGIIPAL + P+G PAL + + + + + 3 + gnl|BL_ORD_ID|577 + 36352|Polyprotein|P90247|Hepatitis C virus|11103 + 577 + 20 + + + 1 + 13.853 + 24 + 4.57317 + 2 + 9 + 10 + 17 + 0 + 0 + 4 + 6 + 0 + 8 + PQGQRPAL + PRGSRPSW + P+G RP+ + + + + + 4 + gnl|BL_ORD_ID|566 + 35237|nonstructural protein 3|NP_722463.1|Dengue virus type 1 Hawaii|10000440 + 566 + 20 + + + 1 + 13.853 + 24 + 5.14963 + 2 + 9 + 7 + 14 + 0 + 0 + 5 + 6 + 0 + 8 + PQGQRPAL + PEGIIPAL + P+G PAL + + + + + 5 + gnl|BL_ORD_ID|1107 + 72929|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 + 1107 + 15 + + + 1 + 13.0826 + 22 + 19.7105 + 2 + 6 + 4 + 8 + 0 + 0 + 4 + 4 + 0 + 5 + PQGQR + PQGSR + PQG R + + + + + 6 + gnl|BL_ORD_ID|131 + 9316|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 + 131 + 15 + + + 1 + 13.0826 + 22 + 20.0418 + 2 + 6 + 8 + 12 + 0 + 0 + 4 + 4 + 0 + 5 + PQGQR + PQGSR + PQG R + + + + + 7 + gnl|BL_ORD_ID|1933 + 180778|polyprotein|AFP27208.1|Dengue virus 4|11070 + 1933 + 10 + + + 1 + 12.6974 + 21 + 24.7764 + 2 + 9 + 2 + 9 + 0 + 0 + 4 + 5 + 0 + 8 + PQGQRPAL + PEGIIPTL + P+G P L + + + + + 8 + gnl|BL_ORD_ID|1948 + 180850|polyprotein|AFP27208.1|Dengue virus 4|11070 + 1948 + 10 + + + 1 + 12.6974 + 21 + 26.5293 + 2 + 9 + 3 + 10 + 0 + 0 + 4 + 5 + 0 + 8 + PQGQRPAL + PEGIIPTL + P+G P L + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 18 + Query_18 + M_116 + 9 + + + 1 + gnl|BL_ORD_ID|1007 + 66405|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 + 1007 + 20 + + + 1 + 10.7714 + 16 + 316.686 + 2 + 9 + 4 + 11 + 0 + 0 + 4 + 5 + 0 + 8 + SDCIIEKK + SACQRQKK + S C +KK + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 19 + Query_19 + M_117 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 20 + Query_20 + M_118 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 21 + Query_21 + M_119 + 9 + + + 1 + gnl|BL_ORD_ID|741 + 47760|EBNA-1 protein|Q777E1|Human gammaherpesvirus 4|10376 + 741 + 15 + + + 1 + 12.3122 + 20 + 43.2075 + 2 + 7 + 1 + 6 + 0 + 0 + 4 + 4 + 0 + 6 + PGHAPG + PGTGPG + PG PG + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 22 + Query_22 + M_120 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 23 + Query_23 + M_121 + 9 + + + 1 + gnl|BL_ORD_ID|1944 + 180818|Membrane glycoprotein precursor|NP_739582.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 + 1944 + 15 + + + 1 + 11.927 + 19 + 77.3377 + 1 + 7 + 1 + 7 + 0 + 0 + 3 + 4 + 0 + 7 + WVRWHKG + WILRHPG + W+ H G + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 24 + Query_24 + M_122 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 25 + Query_25 + M_123 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 26 + Query_26 + M_124 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 27 + Query_27 + M_125 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 28 + Query_28 + M_126 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + + diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114296_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114296_1_T.fasta new file mode 100755 index 00000000..2b03eb9e --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114296_1_T.fasta @@ -0,0 +1,160 @@ +>M_127 +AVDLSSAGM +>M_128 +GMAGVLIGY +>M_129 +SSAGMAGVL +>M_130 +KAAPIYKLV +>M_131 +VTKAAPIYK +>M_132 +FLPSWLLGI +>M_133 +RMAFTDHQL +>M_134 +RMAFTDHQL +>M_135 +ALQPQLGCY +>M_136 +YQQALQPQL +>M_137 +YQQALQPQL +>M_138 +YQLKMLIKI +>M_139 +ILLVVYNNV +>M_140 +LLVVYNNVL +>M_141 +LLVVYNNVL +>M_142 +LVVYNNVLK +>M_143 +LSGHSTQDL +>M_144 +QALSKFKAM +>M_145 +LSVDRMRKV +>M_146 +LGVAARWDL +>M_147 +HAVQAAVQY +>M_148 +HAVQAAVQY +>M_149 +KIMNSLPEM +>M_150 +KIMNSLPEM +>M_151 +LPEMKVQLV +>M_152 +SLPEMKVQL +>M_153 +LTISGECPK +>M_154 +AMYDVLTFA +>M_155 +ATDQAMYDV +>M_156 +KIHATDQAM +>M_157 +QAMYDVLTF +>M_158 +QAMYDVLTF +>M_159 +LICFLTPVK +>M_160 +NLICFLTPV +>M_161 +IAHIFGGAR +>M_162 +LLEISKWFR +>M_163 +FSDDGVLGP +>M_164 +GSFSDDGVL +>M_165 +VLGPVLTTF +>M_166 +ATSIPAGSM +>M_167 +IPAGSMPTV +>M_168 +IMDLRNGTF +>M_169 +CLSGYCSVF +>M_170 +CSVFAYKPM +>M_171 +GYCSVFAYK +>M_172 +SGYCSVFAY +>M_173 +LIMALVWSL +>M_174 +LIMALVWSL +>M_175 +LIMALVWSL +>M_176 +LVWSLPCGF +>M_177 +ESDYLINEM +>M_178 +YLINEMYL* +>M_179 +TQMVDIWSV +>M_180 +MVAFFSSHT +>M_181 +VAFFSSHTY +>M_182 +VAFFSSHTY +>M_183 +VAFFSSHTY +>M_184 +VTFSTSSQL +>M_185 +WVDFADSVT +>M_186 +YQTFKDWGI +>M_187 +ISMGQEEKK +>M_188 +WISMGQEEK +>M_189 +FSWQSHLLI +>M_190 +QSHLLIHQR +>M_191 +FYIIECIAM +>M_192 +TAFYIIECI +>M_193 +YIIECIAMS +>M_194 +ASTYSQLKL +>M_195 +SASTYSQLK +>M_196 +VSASTYSQL +>M_197 +YSQLKLWNV +>M_198 +FYQHLNLMR +>M_199 +YQHLNLMRV +>M_200 +KPAPHPQAL +>M_201 +MADSGPIYN +>M_202 +GLGFYNDVV +>M_203 +FCENDAEVL +>M_204 +RTTQQENPR +>M_205 +AMDDLDTDM +>M_206 +EECGKTFYR diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114296_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114296_1_T_iedb.xml new file mode 100755 index 00000000..5a71dc1f --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114296_1_T_iedb.xml @@ -0,0 +1,3362 @@ + + + + blastp + BLASTP 2.2.30+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta + Query_1 + M_127 + 9 + + + BLOSUM62 + 100000000 + 11 + 1 + F + + + + + 1 + Query_1 + M_127 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 2 + Query_2 + M_128 + 9 + + + 1 + gnl|BL_ORD_ID|339 + 21275|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 + 339 + 9 + + + 1 + 11.5418 + 18 + 157.499 + 1 + 8 + 1 + 8 + 0 + 0 + 5 + 5 + 0 + 8 + GMAGVLIG + GMGPSLIG + GM LIG + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 3 + Query_3 + M_129 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 4 + Query_4 + M_130 + 9 + + + + + 2334 + 25004 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110184|E7|AAD33253.1|Human papillomavirus type 16|333760 + 1382 + 35 + + + 1 + 11.927 + 19 + 69.4128 + 3 + 9 + 7 + 13 + 0 + 0 + 3 + 6 + 0 + 7 + DQAMYDV + DRAHYNI + D+A Y++ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 30 + Query_30 + M_156 + 9 + + + 1 + gnl|BL_ORD_ID|1339 + 107925|polyprotein|AAF65964.1|Hepatitis C virus|11103 + 1339 + 10 + + + 1 + 12.6974 + 21 + 26.9859 + 1 + 6 + 1 + 6 + 0 + 0 + 4 + 4 + 0 + 6 + KIHATD + KAHGTD + K H TD + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 31 + Query_31 + M_157 + 9 + + + 1 + gnl|BL_ORD_ID|45 + 3019|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 + 45 + 9 + + + 1 + 15.0086 + 27 + 0.989407 + 2 + 8 + 1 + 7 + 0 + 0 + 5 + 7 + 0 + 7 + AMYDVLT + ALYDVVT + A+YDV+T + + + + + 2 + gnl|BL_ORD_ID|1382 + 110184|E7|AAD33253.1|Human papillomavirus type 16|333760 + 1382 + 35 + + + 1 + 15.0086 + 27 + 1.26448 + 1 + 9 + 8 + 16 + 0 + 0 + 4 + 8 + 0 + 9 + QAMYDVLTF + RAHYNIVTF + +A Y+++TF + + + + + 3 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95281|polyprotein|ACE82433.1|Hepatitis C virus genotype 1|41856 + 1196 + 9 + + + 1 + 13.4678 + 23 + 8.87313 + 1 + 6 + 1 + 6 + 0 + 0 + 4 + 5 + 0 + 6 + CLSGYC + CISGVC + C+SG C + + + + + 2 + gnl|BL_ORD_ID|784 + 52509|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 + 784 + 15 + + + 1 + 12.6974 + 21 + 26.5542 + 1 + 6 + 7 + 12 + 0 + 0 + 3 + 5 + 0 + 6 + CLSGYC + CINGVC + C++G C + + + + + 3 + gnl|BL_ORD_ID|66 + 4910|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 + 66 + 20 + + + 1 + 12.6974 + 21 + 32.3697 + 1 + 6 + 3 + 8 + 0 + 0 + 3 + 5 + 0 + 6 + CLSGYC + CINGVC + C++G C + + + + + 4 + gnl|BL_ORD_ID|1674 + 148619|unnamed protein product|BAA14233.1|Hepatitis C virus|11103 + 1674 + 45 + + + 1 + 12.3122 + 20 + 32.7965 + 1 + 6 + 36 + 41 + 0 + 0 + 3 + 5 + 0 + 6 + CLSGYC + CVNGVC + C++G C + + + + + 5 + gnl|BL_ORD_ID|91 + 6435|polyprotein|BAB18806.1|Hepatitis C virus|11103 + 91 + 9 + + + 1 + 12.6974 + 21 + 35.3877 + 1 + 6 + 1 + 6 + 0 + 0 + 3 + 5 + 0 + 6 + CLSGYC + CINGVC + C++G C + + 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130.247 + 1 + 8 + 2 + 9 + 0 + 0 + 5 + 5 + 0 + 8 + GLGFYNDV + GYGFVNYV + G GF N V + + + + + 2 + gnl|BL_ORD_ID|578 + 36357|ELAV-like protein 4 (Paraneoplastic encephalomyelitis antigen HuD) (Hu-antigen D)|P26378.1|Homo sapiens|9606 + 578 + 9 + + + 1 + 11.1566 + 17 + 215.083 + 1 + 8 + 2 + 9 + 0 + 0 + 4 + 5 + 0 + 8 + GLGFYNDV + GYGFVNYI + G GF N + + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 77 + Query_77 + M_203 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 78 + Query_78 + M_204 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 79 + Query_79 + M_205 + 9 + + + 1 + gnl|BL_ORD_ID|984 + 64967|Circumsporozoite protein precursor|P08677.2|Plasmodium vivax strain Belem|31273 + 984 + 9 + + + 1 + 13.4678 + 23 + 9.68021 + 1 + 9 + 1 + 9 + 0 + 0 + 4 + 8 + 0 + 9 + AMDDLDTDM + TLNDLETDV + ++DL+TD+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 80 + Query_80 + M_206 + 9 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+>M_284 +DPFALFFMA +>M_285 +EYAADPFAL +>M_286 +YAADPFALF +>M_287 +HRTIPYLDL +>M_288 +IVWEHRQKL +>M_289 +HSVAIVSPF +>M_290 +RIGFVGLFH +>M_291 +HPGVSSQFL +>M_292 +IVHPLKPQM +>M_293 +KPQMNYQTA +>M_294 +AYCSYCYYF +>M_295 +NAYCSYCYY +>M_296 +SPAPERCMV +>M_297 +LTLAVYLSF +>M_298 +ALMDMYPHV +>M_299 +IGVDDRRRL +>M_300 +RRRLCILRM +>M_301 +DTAWDTLEL +>M_302 +TAWDTLELI +>M_303 +TAWDTLELI +>M_304 +MSVSQKLTL +>M_305 +HQRAHTGEK diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114432_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114432_1_T_iedb.xml new file mode 100755 index 00000000..12a5b419 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114432_1_T_iedb.xml @@ -0,0 +1,3164 @@ + + + + blastp + BLASTP 2.2.30+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta + Query_1 + M_207 + 9 + + + BLOSUM62 + 100000000 + 11 + 1 + F + + + + + 1 + Query_1 + M_207 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 2 + Query_2 + M_208 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 3 + Query_3 + M_209 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 4 + Query_4 + M_210 + 9 + + + 1 + gnl|BL_ORD_ID|829 + 54741|gag polyprotein|BAA00992.1|Human immunodeficiency virus 1|11676 + 829 + 9 + + + 1 + 12.3122 + 20 + 52.1643 + 1 + 9 + 1 + 9 + 0 + 0 + 5 + 6 + 0 + 9 + RLKFGNKHK + RLRPGGKKK + RL+ G K K + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 5 + Query_5 + M_211 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + 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found + + + 15 + Query_15 + M_221 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 16 + Query_16 + M_222 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 17 + Query_17 + M_223 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 18 + Query_18 + M_224 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 19 + Query_19 + M_225 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 20 + Query_20 + M_226 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 21 + Query_21 + M_227 + 9 + + + 1 + gnl|BL_ORD_ID|232 + 16795|precore/core protein|AAP57273.1|Hepatitis B virus|10407 + 232 + 10 + + + 1 + 15.3938 + 28 + 0.822133 + 1 + 9 + 2 + 10 + 0 + 0 + 5 + 7 + 0 + 9 + IPASFVPSM + LPADFFPSI + +PA F PS+ + + + + + 2 + gnl|BL_ORD_ID|233 + 16796|HBcAg|ABE97049.1|Hepatitis B virus|10407 + 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Query_34 + M_240 + 9 + + + 1 + gnl|BL_ORD_ID|1152 + 75718|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 + 1152 + 11 + + + 1 + 14.6234 + 26 + 2.31378 + 1 + 8 + 4 + 11 + 0 + 0 + 4 + 6 + 0 + 8 + HPGVSSQF + HPTFTSQY + HP +SQ+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 35 + Query_35 + M_241 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 36 + Query_36 + M_242 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 37 + Query_37 + M_243 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 38 + Query_38 + M_244 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 39 + Query_39 + M_245 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 40 + Query_40 + M_246 + 9 + + + 1 + gnl|BL_ORD_ID|859 + 56310|polyprotein|AGO67248.1|Dengue virus 2|11060 + 859 + 10 + + + 1 + 13.853 + 24 + 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9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 62 + Query_62 + M_268 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 63 + Query_63 + M_269 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 64 + Query_64 + M_270 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 65 + Query_65 + M_271 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 66 + Query_66 + M_272 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 67 + Query_67 + M_273 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 68 + Query_68 + M_274 + 9 + + + 1 + gnl|BL_ORD_ID|1114 + 73862|EBNA-1 protein|Q777E1|Human gammaherpesvirus 4|10376 + 1114 + 15 + + + 1 + 13.0826 + 22 + 17.2424 + 1 + 9 + 2 + 10 + 0 + 0 + 4 + 7 + 0 + 9 + FLVGLWSHL + FMVFLQTHI + F+V L +H+ + + + + + 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cruzi|JH0823|Trypanosoma cruzi|5693 + 321 + 10 + + + 1 + 7.30463 + 7 + 12470.7 + 5 + 6 + 7 + 8 + 0 + 0 + 2 + 2 + 0 + 2 + LW + LW + LW + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 69 + Query_69 + M_275 + 9 + + + 1 + gnl|BL_ORD_ID|2086 + 185468|polyprotein|AGW21594.1|Dengue virus 1|11053 + 2086 + 10 + + + 1 + 14.2382 + 25 + 3.44317 + 1 + 8 + 1 + 8 + 0 + 0 + 5 + 6 + 0 + 8 + KPRFLVGL + RPMFAVGL + +P F VGL + + + + + 2 + gnl|BL_ORD_ID|2277 + 419037|polyprotein|AEF01538.1|Dengue virus 1|11053 + 2277 + 10 + + + 1 + 13.4678 + 23 + 9.90554 + 1 + 8 + 1 + 8 + 0 + 0 + 4 + 6 + 0 + 8 + KPRFLVGL + RPMFAVGI + +P F VG+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 70 + Query_70 + M_276 + 9 + + + 1 + gnl|BL_ORD_ID|919 + 59767|polyprotein|BAB18806.1|Hepatitis C virus subtype 1a|31646 + 919 + 10 + + + 1 + 13.4678 + 23 + 9.23902 + 1 + 9 + 2 + 10 + 0 + 0 + 4 + 7 + 0 + 9 + LVGLWSHLL + MVGNWAKVL + +VG W+ +L + + + + + 2 + gnl|BL_ORD_ID|1686 + 149052|E1 protein|NP_751920.1|Hepatitis C virus (isolate H77)|63746 + 1686 + 18 + + + 1 + 13.0826 + 22 + 12.6766 + 1 + 9 + 7 + 15 + 0 + 0 + 4 + 7 + 0 + 9 + LVGLWSHLL + MVGNWAKVL + +VG W+ +L + + + + + 3 + gnl|BL_ORD_ID|623 + 37498|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 + 623 + 10 + + + 1 + 12.3122 + 20 + 39.1729 + 1 + 6 + 2 + 7 + 0 + 0 + 4 + 5 + 0 + 6 + LVGLWS + LLGLWG + L+GLW + + + + + 4 + gnl|BL_ORD_ID|615 + 37350|trans-sialidase|XP_818394.1|Trypanosoma cruzi|5693 + 615 + 10 + + + 1 + 12.3122 + 20 + 39.1729 + 1 + 6 + 1 + 6 + 0 + 0 + 4 + 5 + 0 + 6 + LVGLWS + LLGLWG + L+GLW + + + + + 5 + gnl|BL_ORD_ID|614 + 37347|Sialidase 85-1.1 precursor|P18269.2|Trypanosoma cruzi|5693 + 614 + 10 + + + 1 + 12.3122 + 20 + 39.1729 + 1 + 6 + 1 + 6 + 0 + 0 + 4 + 5 + 0 + 6 + LVGLWS + LLGLWG + L+GLW + + + + + 6 + gnl|BL_ORD_ID|616 + 37351|trans-sialidase, putative|EAN81560.1|Trypanosoma cruzi|5693 + 616 + 10 + + + 1 + 12.3122 + 20 + 39.8368 + 1 + 5 + 1 + 5 + 0 + 0 + 4 + 5 + 0 + 5 + LVGLW + LLGLW + L+GLW + + + + + 7 + gnl|BL_ORD_ID|1253 + 98223|trans-sialidase, putative|EAN80725.1|Trypanosoma cruzi|5693 + 1253 + 9 + + + 1 + 12.3122 + 20 + 41.221 + 1 + 6 + 2 + 7 + 0 + 0 + 4 + 5 + 0 + 6 + LVGLWS + LLGLWG + L+GLW + + + + + 8 + gnl|BL_ORD_ID|918 + 59766|Genome polyprotein|P27958.3|Hepatitis C virus (isolate H)|11108 + 918 + 9 + + + 1 + 12.3122 + 20 + 47.1713 + 1 + 8 + 2 + 9 + 0 + 0 + 3 + 6 + 0 + 8 + LVGLWSHL + MVGNWAKV + +VG W+ + + + + + + 9 + gnl|BL_ORD_ID|321 + 21004|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 + 321 + 10 + + + 1 + 7.68983 + 8 + 12187.2 + 4 + 5 + 7 + 8 + 0 + 0 + 2 + 2 + 0 + 2 + LW + LW + LW + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 71 + Query_71 + M_277 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 72 + Query_72 + M_278 + 9 + + + 1 + gnl|BL_ORD_ID|471 + 28594|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 + 471 + 20 + + + 1 + 12.3122 + 20 + 38.3641 + 2 + 8 + 2 + 8 + 0 + 0 + 4 + 6 + 0 + 7 + ALPTYPP + SLPSYYP + +LP+Y P + + + + + 2 + gnl|BL_ORD_ID|776 + 51643|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 + 776 + 20 + + + 1 + 12.3122 + 20 + 53.6149 + 2 + 8 + 12 + 18 + 0 + 0 + 4 + 6 + 0 + 7 + ALPTYPP + SLPSYYP + +LP+Y P + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 73 + Query_73 + M_279 + 9 + + + 1 + gnl|BL_ORD_ID|273 + 18390|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 + 273 + 20 + + + 1 + 14.2382 + 25 + 3.85699 + 4 + 9 + 3 + 8 + 0 + 0 + 4 + 6 + 0 + 6 + FPQSPL + FPRAPL + FP++PL + + + + + 2 + gnl|BL_ORD_ID|946 + 62355|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 + 946 + 20 + + + 1 + 13.853 + 24 + 4.4203 + 4 + 9 + 10 + 15 + 0 + 0 + 4 + 6 + 0 + 6 + FPQSPL + FPRAPL + FP++PL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 74 + Query_74 + M_280 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 75 + Query_75 + M_281 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 76 + Query_76 + M_282 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 77 + Query_77 + M_283 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 78 + Query_78 + M_284 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 79 + Query_79 + M_285 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 80 + Query_80 + M_286 + 9 + + + 1 + gnl|BL_ORD_ID|1587 + 141484|capsid maturation protease|NP_044627.1|Human alphaherpesvirus 1|10298 + 1587 + 9 + + + 1 + 10.3862 + 15 + 583.315 + 1 + 9 + 1 + 9 + 0 + 0 + 4 + 5 + 0 + 9 + YAADPFALF + YVAGFLALY + Y A AL+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 81 + Query_81 + M_287 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 82 + Query_82 + M_288 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 83 + Query_83 + M_289 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 84 + Query_84 + M_290 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 85 + Query_85 + M_291 + 9 + + + 1 + gnl|BL_ORD_ID|1152 + 75718|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 + 1152 + 11 + + + 1 + 14.6234 + 26 + 2.31378 + 1 + 8 + 4 + 11 + 0 + 0 + 4 + 6 + 0 + 8 + HPGVSSQF + HPTFTSQY + HP +SQ+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 86 + Query_86 + M_292 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 87 + Query_87 + M_293 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 88 + Query_88 + M_294 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 89 + Query_89 + M_295 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 90 + Query_90 + M_296 + 9 + + + 1 + gnl|BL_ORD_ID|859 + 56310|polyprotein|AGO67248.1|Dengue virus 2|11060 + 859 + 10 + + + 1 + 13.853 + 24 + 5.38895 + 4 + 8 + 5 + 9 + 0 + 0 + 4 + 4 + 0 + 5 + PERCM + PRRCM + P RCM + + + + + 2 + gnl|BL_ORD_ID|2076 + 185200|polyprotein|AGO67248.1|Dengue virus 2|11060 + 2076 + 10 + + + 1 + 13.853 + 24 + 6.19145 + 4 + 8 + 1 + 5 + 0 + 0 + 4 + 4 + 0 + 5 + PERCM + PRRCM + P RCM + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 91 + Query_91 + M_297 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 92 + Query_92 + M_298 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 93 + Query_93 + M_299 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 94 + Query_94 + M_300 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 95 + Query_95 + M_301 + 9 + + + 1 + gnl|BL_ORD_ID|1924 + 180726|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 + 1924 + 15 + + + 1 + 15.0086 + 27 + 0.917715 + 1 + 5 + 7 + 11 + 0 + 0 + 5 + 5 + 0 + 5 + DTAWD + DTAWD + DTAWD + + + + + 2 + gnl|BL_ORD_ID|439 + 27061|envelope glycoprotein|ABU89742.1|Dengue virus 2 Thailand/16681/84|31634 + 439 + 10 + + + 1 + 15.0086 + 27 + 1.37261 + 1 + 5 + 4 + 8 + 0 + 0 + 5 + 5 + 0 + 5 + DTAWD + DTAWD + DTAWD + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 96 + Query_96 + M_302 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 97 + Query_97 + M_303 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 98 + Query_98 + M_304 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 99 + Query_99 + M_305 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + + diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114445_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114445_1_T.fasta new file mode 100755 index 00000000..4d08ad1b --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114445_1_T.fasta @@ -0,0 +1,40 @@ +>M_306 +AVATITQAL +>M_307 +TTVNGNTAL +>M_308 +EYYSQTTGL +>M_309 +YYSQTTGLC +>M_310 +CPSEPNTPM +>M_311 +TPMARTFDW +>M_312 +GHYEVRASL +>M_313 +HYEVRASLL +>M_314 +MYWRRSQCC +>M_315 +DYPNAYTTW +>M_316 +RYSDYPNAY +>M_317 +AADLPILTW +>M_318 +WLLAADLPI +>M_319 +IPPEANITI +>M_320 +TVHNLCHIL +>M_321 +FFVEKRHAF +>M_322 +LPLTRSMSI +>M_323 +AAAAATSAL +>M_324 +SIYAYHVEW +>M_325 +AYPQYVIEY diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114445_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114445_1_T_iedb.xml new file mode 100755 index 00000000..59c917ba --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114445_1_T_iedb.xml @@ -0,0 +1,866 @@ + + + + blastp + BLASTP 2.2.30+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta + Query_1 + M_306 + 9 + + + BLOSUM62 + 100000000 + 11 + 1 + F + + + + + 1 + Query_1 + M_306 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 2 + Query_2 + M_307 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 3 + Query_3 + M_308 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 4 + Query_4 + M_309 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 5 + Query_5 + M_310 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 6 + Query_6 + M_311 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 7 + Query_7 + M_312 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 8 + Query_8 + M_313 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 9 + Query_9 + M_314 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 10 + Query_10 + M_315 + 9 + + + 1 + gnl|BL_ORD_ID|2124 + 186550|polyprotein|AFY10039.1|Dengue virus 4|11070 + 2124 + 10 + + + 1 + 14.2382 + 25 + 4.23087 + 1 + 9 + 2 + 10 + 0 + 0 + 5 + 5 + 0 + 9 + DYPNAYTTW + DQENPYRTW + D N Y TW + + + + + 2 + gnl|BL_ORD_ID|1174 + 79351|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 + 1174 + 17 + + + 1 + 13.4678 + 23 + 10.1282 + 3 + 9 + 1 + 7 + 0 + 0 + 4 + 4 + 0 + 7 + PNAYTTW + QNLYTLW + N YT W + + + + + 3 + gnl|BL_ORD_ID|1097 + 72563|polyprotein|AAB70696.1|Dengue virus type 1 Hawaii|10000440 + 1097 + 20 + + + 1 + 13.0826 + 22 + 14.6415 + 1 + 9 + 4 + 12 + 0 + 0 + 5 + 5 + 0 + 9 + DYPNAYTTW + DEDNPYKTW + D N Y TW + + + + + 4 + gnl|BL_ORD_ID|2189 + 190533|nucleocapsid protein|AAP49024.1|SARS coronavirus|227859 + 2189 + 15 + + + 1 + 12.3122 + 20 + 57.5015 + 3 + 9 + 7 + 13 + 0 + 0 + 3 + 4 + 0 + 7 + PNAYTTW + PNNIASW + PN +W + + + + + 5 + gnl|BL_ORD_ID|850 + 55683|nucleocapsid protein|ABI96968.1|SARS coronavirus|227859 + 850 + 15 + + + 1 + 11.5418 + 18 + 120.288 + 3 + 9 + 7 + 13 + 0 + 0 + 3 + 4 + 0 + 7 + PNAYTTW + PNNTASW + PN +W + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 11 + Query_11 + M_316 + 9 + + + 1 + gnl|BL_ORD_ID|878 + 57703|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 + 878 + 15 + + + 1 + 13.4678 + 23 + 7.23267 + 3 + 7 + 1 + 5 + 0 + 0 + 4 + 5 + 0 + 5 + SDYPN + SEYPN + S+YPN + + + + + 2 + gnl|BL_ORD_ID|559 + 34598|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 + 559 + 15 + + + 1 + 12.6974 + 21 + 22.89 + 1 + 9 + 1 + 9 + 0 + 0 + 4 + 6 + 0 + 9 + RYSDYPNAY + KYSPFRNGY + +YS + N Y + + + + + 3 + gnl|BL_ORD_ID|657 + 38974|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 + 657 + 11 + + + 1 + 12.6974 + 21 + 27.7331 + 1 + 6 + 6 + 11 + 0 + 0 + 3 + 6 + 0 + 6 + RYSDYP + QYSEHP + +YS++P + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 12 + Query_12 + M_317 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 13 + Query_13 + M_318 + 9 + + + 1 + gnl|BL_ORD_ID|1438 + 120093|unnamed protein product|CAA33016.1|Rubella virus|11041 + 1438 + 21 + + + 1 + 11.927 + 19 + 61.829 + 1 + 8 + 4 + 11 + 0 + 0 + 3 + 4 + 0 + 8 + WLLAADLP + WCVEHDRP + W + D P + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 14 + Query_14 + M_319 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 15 + Query_15 + M_320 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 16 + Query_16 + M_321 + 9 + + + 1 + gnl|BL_ORD_ID|2009 + 183781|polyprotein|AGO67248.1|Dengue virus 2|11060 + 2009 + 10 + + + 1 + 14.2382 + 25 + 4.15863 + 3 + 9 + 4 + 10 + 0 + 0 + 4 + 5 + 0 + 7 + VEKRHAF + LEKRHVL + +EKRH + + + + + 2 + gnl|BL_ORD_ID|2055 + 184755|polyprotein|AGO67248.1|Dengue virus 2|11060 + 2055 + 9 + + + 1 + 13.853 + 24 + 4.75595 + 3 + 9 + 3 + 9 + 0 + 0 + 4 + 5 + 0 + 7 + VEKRHAF + LEKRHVL + +EKRH + + + + + 3 + gnl|BL_ORD_ID|2031 + 184337|polyprotein|AGO67248.1|Dengue virus 2|11060 + 2031 + 10 + + + 1 + 13.853 + 24 + 5.38895 + 3 + 9 + 1 + 7 + 0 + 0 + 4 + 5 + 0 + 7 + VEKRHAF + LEKRHVL + +EKRH + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 17 + Query_17 + M_322 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 18 + Query_18 + M_323 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 19 + Query_19 + M_324 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 20 + Query_20 + M_325 + 9 + + + 1 + gnl|BL_ORD_ID|608 + 37254|||| + 608 + 9 + + + 1 + 13.853 + 24 + 7.58732 + 1 + 6 + 4 + 9 + 0 + 0 + 4 + 5 + 0 + 6 + AYPQYV + GYPRYV + YP+YV + + + + + 2 + gnl|BL_ORD_ID|1170 + 79294|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 + 1170 + 15 + + + 1 + 12.3122 + 20 + 46.8002 + 1 + 6 + 4 + 9 + 0 + 0 + 4 + 4 + 0 + 6 + AYPQYV + GYPVYV + YP YV + + + + + 3 + gnl|BL_ORD_ID|389 + 23807|tax|AAG48731.1|Human T-lymphotropic virus 2|11909 + 389 + 23 + + + 1 + 12.3122 + 20 + 48.9251 + 1 + 7 + 12 + 18 + 0 + 0 + 4 + 4 + 0 + 7 + AYPQYVI + GYPVYVF + YP YV + + + + + 4 + gnl|BL_ORD_ID|572 + 35845|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 + 572 + 9 + + + 1 + 12.3122 + 20 + 61.624 + 1 + 6 + 3 + 8 + 0 + 0 + 4 + 4 + 0 + 6 + AYPQYV + GYPVYV + YP YV + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + + diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114843_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114843_1_T.fasta new file mode 100755 index 00000000..da28f85e --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114843_1_T.fasta @@ -0,0 +1,10 @@ +>M_326 +FSSKPSSIY +>M_327 +SIYGGLVLI +>M_328 +SAESGAQLL +>M_329 +GIICLDYKL +>M_330 +FEDIGDEDL diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114843_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114843_1_T_iedb.xml new file mode 100755 index 00000000..0b436b58 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114843_1_T_iedb.xml @@ -0,0 +1,150 @@ + + + + blastp + BLASTP 2.2.30+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta + Query_1 + M_326 + 9 + + + BLOSUM62 + 100000000 + 11 + 1 + F + + + + + 1 + Query_1 + M_326 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 2 + Query_2 + M_327 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 3 + Query_3 + M_328 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 4 + Query_4 + M_329 + 9 + + + 1 + gnl|BL_ORD_ID|2102 + 185978|polyprotein|CDF77361.1|Dengue virus 3|11069 + 2102 + 10 + + + 1 + 12.3122 + 20 + 44.0514 + 1 + 5 + 3 + 7 + 0 + 0 + 3 + 5 + 0 + 5 + GIICL + GVLCL + G++CL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 5 + Query_5 + M_330 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + + diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116261_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116261_1_T.fasta new file mode 100755 index 00000000..8d96174b --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116261_1_T.fasta @@ -0,0 +1,64 @@ +>M_331 +IRVEESMHL +>M_332 +AMEKLLSGK +>M_333 +ARTGHLPAM +>M_334 +GHLPAMEKL +>M_335 +QVYHWVCEK +>M_336 +HRWNRFTMI +>M_337 +THRWNRFTM +>M_338 +ITSGLEVIY +>M_339 +ARRFWGKIM +>M_340 +RFWGKIMAK +>M_341 +TYEEATVYI +>M_342 +EHAAALWAL +>M_343 +LVLMNWTKK +>M_344 +FTDTAAESA +>M_345 +NIEDSASFY +>M_346 +SRSDAAKHL +>M_347 +LRWRHCQRL +>M_348 +WRHCQRLDV +>M_349 +VRLGPVKSI +>M_350 +SMQAHIKAL +>M_351 +ESFKQTDFY +>M_352 +QTDFYSMAL +>M_353 +LPWMRLLLL +>M_354 +MRLLLLLLV +>M_355 +PRLPWMRLL +>M_356 +WMRLLLLLL +>M_357 +AIALHRLSL +>M_358 +MRGHDWRML +>M_359 +QMRGHDWRM +>M_360 +HLETHNTDK +>M_361 +CSKLKHRDL +>M_362 +VVGAVGVGK diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116261_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116261_1_T_iedb.xml new file mode 100755 index 00000000..4883d2fe --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116261_1_T_iedb.xml @@ -0,0 +1,1019 @@ + + + + blastp + BLASTP 2.2.30+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta + Query_1 + M_331 + 9 + + + BLOSUM62 + 100000000 + 11 + 1 + F + + + + + 1 + Query_1 + M_331 + 9 + + + 1 + gnl|BL_ORD_ID|665 + 40158|polyprotein|AAA45534.1|Hepatitis C virus|11103 + 665 + 15 + + + 1 + 13.4678 + 23 + 7.74893 + 2 + 9 + 3 + 10 + 0 + 0 + 4 + 6 + 0 + 8 + RVEESMHL + RVEAQLHV + RVE +H+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 2 + Query_2 + M_332 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 3 + Query_3 + M_333 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 4 + Query_4 + M_334 + 9 + + + 1 + gnl|BL_ORD_ID|1271 + 101673|gag protein|ABO73990.1|Human immunodeficiency virus 1|11676 + 1271 + 9 + + + 1 + 13.853 + 24 + 6.83656 + 1 + 9 + 1 + 9 + 0 + 0 + 5 + 6 + 0 + 9 + GHLPAMEKL + GHQAAMQML + GH AM+ L + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 5 + Query_5 + M_335 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 6 + Query_6 + M_336 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 7 + Query_7 + M_337 + 9 + + + 1 + gnl|BL_ORD_ID|1297 + 103389|unnamed protein product [Hepatitis C virus]|BAA14035.1|Hepatitis C virus|11103 + 1297 + 20 + + + 1 + 14.2382 + 25 + 3.035 + 1 + 9 + 2 + 10 + 0 + 0 + 4 + 5 + 0 + 9 + THRWNRFTM + THPITKFVM + TH +F M + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 8 + Query_8 + M_338 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 9 + Query_9 + M_339 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 10 + Query_10 + M_340 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 11 + Query_11 + M_341 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 12 + Query_12 + M_342 + 9 + + + 1 + gnl|BL_ORD_ID|1994 + 183594|polyprotein|AGT63075.1|Dengue virus 1|11053 + 1994 + 10 + + + 1 + 12.6974 + 21 + 30.9217 + 2 + 9 + 1 + 8 + 0 + 0 + 4 + 5 + 0 + 8 + HAAALWAL + HPASAWTL + H A+ W L + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 13 + Query_13 + M_343 + 9 + + + 1 + gnl|BL_ORD_ID|692 + 42152|polyprotein|AAY82055.1|Hepatitis C virus (isolate H77)|63746 + 692 + 9 + + + 1 + 13.0826 + 22 + 13.4763 + 2 + 8 + 1 + 7 + 0 + 0 + 3 + 6 + 0 + 7 + VLMNWTK + MMMNWSP + ++MNW+ + + + + + 2 + gnl|BL_ORD_ID|1096 + 72322|polyprotein|AAA86907.1|Hepatitis C virus|11103 + 1096 + 15 + + + 1 + 13.0826 + 22 + 15.8531 + 2 + 8 + 3 + 9 + 0 + 0 + 3 + 6 + 0 + 7 + VLMNWTK + MMMNWSP + ++MNW+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 14 + Query_14 + M_344 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 15 + Query_15 + M_345 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 16 + Query_16 + M_346 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 17 + Query_17 + M_347 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 18 + Query_18 + M_348 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 19 + Query_19 + M_349 + 9 + + + 1 + gnl|BL_ORD_ID|1651 + 146528|NS3/4A protein|CAM56207.1|Hepatitis C virus|11103 + 1651 + 9 + + + 1 + 15.779 + 29 + 0.508093 + 2 + 8 + 1 + 7 + 0 + 0 + 5 + 7 + 0 + 7 + RLGPVKS + RLGPVQN + RLGPV++ + + + + + 2 + gnl|BL_ORD_ID|2291 + 419325|Genome polyprotein|O92532.3|Hepatitis C virus|11103 + 2291 + 9 + + + 1 + 15.779 + 29 + 0.523878 + 2 + 8 + 1 + 7 + 0 + 0 + 5 + 7 + 0 + 7 + RLGPVKS + RLGPVQN + RLGPV++ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 20 + Query_20 + M_350 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 21 + Query_21 + M_351 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 22 + Query_22 + M_352 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 23 + Query_23 + M_353 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 24 + Query_24 + M_354 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 25 + Query_25 + M_355 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 26 + Query_26 + M_356 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 27 + Query_27 + M_357 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 28 + Query_28 + M_358 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 29 + Query_29 + M_359 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 30 + Query_30 + M_360 + 9 + + + 1 + gnl|BL_ORD_ID|1224 + 97111|polyprotein|ABR25251.1|Hepatitis C virus (isolate H77)|63746 + 1224 + 18 + + + 1 + 13.4678 + 23 + 12.4678 + 3 + 9 + 8 + 14 + 0 + 0 + 4 + 5 + 0 + 7 + ETHNTDK + ECHSTDA + E H+TD + + + + + 2 + gnl|BL_ORD_ID|1337 + 107901|Genome polyprotein|P26664.3|Hepatitis C virus|11103 + 1337 + 10 + + + 1 + 13.0826 + 22 + 15.8345 + 3 + 8 + 4 + 9 + 0 + 0 + 4 + 5 + 0 + 6 + ETHNTD + ECHSTD + E H+TD + + + + + 3 + gnl|BL_ORD_ID|1320 + 107780|Genome polyprotein|P26664.3|Hepatitis C virus|11103 + 1320 + 10 + + + 1 + 12.6974 + 21 + 30.4011 + 3 + 8 + 2 + 7 + 0 + 0 + 4 + 5 + 0 + 6 + ETHNTD + ECHSTD + E H+TD + + + + + 4 + gnl|BL_ORD_ID|1321 + 107781|polyprotein|AAF65953.1|Hepatitis C virus|11103 + 1321 + 10 + + + 1 + 12.6974 + 21 + 35.4066 + 3 + 9 + 2 + 8 + 0 + 0 + 4 + 5 + 0 + 7 + ETHNTDK + ECHSTDS + E H+TD + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 31 + Query_31 + M_361 + 9 + + + 1 + gnl|BL_ORD_ID|470 + 28508|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 + 470 + 15 + + + 1 + 11.5418 + 18 + 125.819 + 1 + 7 + 6 + 12 + 0 + 0 + 4 + 4 + 0 + 7 + CSKLKHR + CSARLHR + CS HR + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 32 + Query_32 + M_362 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + + diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116397_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116397_1_T.fasta new file mode 100755 index 00000000..d653256b --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116397_1_T.fasta @@ -0,0 +1,44 @@ +>M_363 +AHPDGSWTF +>M_364 +WGRERGARV +>M_365 +KADIPRDSY +>M_366 +NVLQSSVPV +>M_367 +IITESGEVI +>M_368 +WVYDAIITE +>M_369 +FPPNILDDI +>M_370 +MASQRPLQF +>M_371 +DMHVAVKIV +>M_372 +FARPASPSR +>M_373 +IVFEVFGHH +>M_374 +TTAVLTATF +>M_375 +MAAAVVARL +>M_376 +FSLPPSRKK +>M_377 +LPMCWAMEV +>M_378 +LTYSCLDNK +>M_379 +LLNSGGDII +>M_380 +DIYCITDFV +>M_381 +FVEELADTV +>M_382 +TISCTSLKK +>M_383 +VTISCTSLK +>M_384 +IIIKCQLPK diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116397_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116397_1_T_iedb.xml new file mode 100755 index 00000000..db2f2c3b --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116397_1_T_iedb.xml @@ -0,0 +1,655 @@ + + + + blastp + BLASTP 2.2.30+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta + Query_1 + M_363 + 9 + + + BLOSUM62 + 100000000 + 11 + 1 + F + + + + + 1 + Query_1 + M_363 + 9 + + + 1 + gnl|BL_ORD_ID|1994 + 183594|polyprotein|AGT63075.1|Dengue virus 1|11053 + 1994 + 10 + + + 1 + 15.3938 + 28 + 0.809281 + 2 + 9 + 1 + 8 + 0 + 0 + 4 + 5 + 0 + 8 + HPDGSWTF + HPASAWTL + HP +WT + + + + + 2 + gnl|BL_ORD_ID|431 + 26273|nucleocapsid protein|ABI96968.1|SARS coronavirus|227859 + 431 + 15 + + + 1 + 13.4678 + 23 + 11.689 + 3 + 7 + 7 + 11 + 0 + 0 + 3 + 4 + 0 + 5 + PDGSW + PSGTW + P G+W + + + + + 3 + gnl|BL_ORD_ID|2187 + 190494|nucleocapsid protein|ABI96968.1|SARS coronavirus|227859 + 2187 + 10 + + + 1 + 13.0826 + 22 + 14.0252 + 3 + 7 + 5 + 9 + 0 + 0 + 3 + 4 + 0 + 5 + PDGSW + PSGTW + P G+W + + + + + 4 + gnl|BL_ORD_ID|1931 + 180758|Nonstructural protein NS5|NP_739590.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 + 1931 + 15 + + + 1 + 13.0826 + 22 + 16.3955 + 2 + 9 + 8 + 15 + 0 + 0 + 3 + 5 + 0 + 8 + HPDGSWTF + HPYKTWAY + HP +W + + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 2 + Query_2 + M_364 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 3 + Query_3 + M_365 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 4 + Query_4 + M_366 + 9 + + + 1 + gnl|BL_ORD_ID|1259 + 98308|trans-sialidase, putative|EAN80840.1|Trypanosoma cruzi|5693 + 1259 + 9 + + + 1 + 12.3122 + 20 + 52.1643 + 1 + 9 + 1 + 9 + 0 + 0 + 4 + 7 + 0 + 9 + NVLQSSVPV + NVMLVTLPV + NV+ ++PV + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 5 + Query_5 + M_367 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 6 + Query_6 + M_368 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 7 + Query_7 + M_369 + 9 + + + 1 + gnl|BL_ORD_ID|1917 + 180682|polyprotein|AGO67248.1|Dengue virus 2|11060 + 1917 + 9 + + + 1 + 12.6974 + 21 + 28.3449 + 3 + 9 + 2 + 8 + 0 + 0 + 5 + 5 + 0 + 7 + PNILDDI + PEIEDDI + P I DDI + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 8 + Query_8 + M_370 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 9 + Query_9 + M_371 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 10 + Query_10 + M_372 + 9 + + + 1 + gnl|BL_ORD_ID|803 + 53405|||| + 803 + 15 + + + 1 + 13.0826 + 22 + 16.6732 + 4 + 9 + 3 + 8 + 0 + 0 + 4 + 5 + 0 + 6 + PASPSR + PAKPAR + PA P+R + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 11 + Query_11 + M_373 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 12 + Query_12 + M_374 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 13 + Query_13 + M_375 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 14 + Query_14 + M_376 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 15 + Query_15 + M_377 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 16 + Query_16 + M_378 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 17 + Query_17 + M_379 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 18 + Query_18 + M_380 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 19 + Query_19 + M_381 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 20 + Query_20 + M_382 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 21 + Query_21 + M_383 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 22 + Query_22 + M_384 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + + diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116644_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116644_1_T.fasta new file mode 100755 index 00000000..ca704e0b --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116644_1_T.fasta @@ -0,0 +1,60 @@ +>M_385 +RYGAGQQNL +>M_386 +TPYAACPAI +>M_387 +SPFNTTFPF +>M_388 +QVARRVQEL +>M_389 +HREARGRAL +>M_390 +AIFGPSNTY +>M_391 +DLFQFPKAY +>M_392 +LPEDPKCEF +>M_393 +SFQPKAAVF +>M_394 +PPSETGGIF +>M_395 +NAGEMVIEY +>M_396 +APTSSDYEF +>M_397 +LFCGLPFSI +>M_398 +VPVASSEAS +>M_399 +DPSPGIMAF +>M_400 +LTYSLLTPL +>M_401 +TYSLLTPLL +>M_402 +CYVAICNPF +>M_403 +LAAMAIDCY +>M_404 +MAIDCYVAI +>M_405 +YFFLGNLAF +>M_406 +FPVEDRRGV +>M_407 +FAQLINNKM +>M_408 +RVASVVVSF +>M_409 +RVASVVVSF +>M_410 +FYLRYFEK* +>M_411 +FFSSNLPTY +>M_412 +FSSNLPTYY +>M_413 +NPYKAPMAE +>M_414 +AFLQKAHLI diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116644_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116644_1_T_iedb.xml new file mode 100755 index 00000000..d99c60f6 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116644_1_T_iedb.xml @@ -0,0 +1,1173 @@ + + + + blastp + BLASTP 2.2.30+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta + Query_1 + M_385 + 9 + + + BLOSUM62 + 100000000 + 11 + 1 + F + + + + + 1 + Query_1 + M_385 + 9 + + + 1 + gnl|BL_ORD_ID|79 + 5783|Nucleoprotein|P03418.1|Human respiratory syncytial virus A2|11259 + 79 + 14 + + + 1 + 14.6234 + 26 + 1.47122 + 2 + 9 + 2 + 9 + 0 + 0 + 6 + 6 + 0 + 8 + YGAGQQNL + YGAGQVML + YGAGQ L + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 2 + Query_2 + M_386 + 9 + + + 1 + gnl|BL_ORD_ID|1397 + 110401|Protein E6|P03126.1|Human papillomavirus type 16|333760 + 1397 + 25 + + + 1 + 13.853 + 24 + 4.88128 + 1 + 6 + 20 + 25 + 0 + 0 + 4 + 4 + 0 + 6 + TPYAAC + NPYAVC + PYA C + + + + + 2 + gnl|BL_ORD_ID|1387 + 110227|Protein E6|P03126.1|Human papillomavirus type 16|333760 + 1387 + 33 + + + 1 + 13.853 + 24 + 5.78904 + 2 + 6 + 13 + 17 + 0 + 0 + 4 + 4 + 0 + 5 + PYAAC + PYAVC + PYA C + + + + + 3 + gnl|BL_ORD_ID|1400 + 110467|Protein E6|P03126.1|Human papillomavirus type 16|333760 + 1400 + 25 + + + 1 + 13.853 + 24 + 5.83535 + 1 + 6 + 5 + 10 + 0 + 0 + 4 + 4 + 0 + 6 + TPYAAC + NPYAVC + PYA C + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 3 + Query_3 + M_387 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 4 + Query_4 + M_388 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 5 + Query_5 + M_389 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 6 + Query_6 + M_390 + 9 + + + 1 + gnl|BL_ORD_ID|1205 + 96123|Genome polyprotein|P26664.3|Hepatitis C virus (isolate H77)|63746 + 1205 + 9 + + + 1 + 14.2382 + 25 + 3.80667 + 1 + 5 + 1 + 5 + 0 + 0 + 4 + 5 + 0 + 5 + AIFGP + AVFGP + A+FGP + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 7 + Query_7 + M_391 + 9 + + + 1 + gnl|BL_ORD_ID|273 + 18390|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 + 273 + 20 + + + 1 + 13.0826 + 22 + 14.1742 + 3 + 8 + 1 + 6 + 0 + 0 + 4 + 5 + 0 + 6 + FQFPKA + FYFPRA + F FP+A + + + + + 2 + gnl|BL_ORD_ID|946 + 62355|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 + 946 + 20 + + + 1 + 13.0826 + 22 + 20.1922 + 3 + 8 + 8 + 13 + 0 + 0 + 4 + 5 + 0 + 6 + FQFPKA + FYFPRA + F FP+A + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 8 + Query_8 + M_392 + 9 + + + 1 + gnl|BL_ORD_ID|1179 + 79628|E1 protein|BAA19893.1|Rubella virus|11041 + 1179 + 21 + + + 1 + 12.6974 + 21 + 24.4562 + 2 + 8 + 1 + 7 + 0 + 0 + 4 + 4 + 0 + 7 + PEDPKCE + PTDVSCE + P D CE + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 9 + Query_9 + M_393 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 10 + Query_10 + M_394 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 11 + Query_11 + M_395 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 12 + Query_12 + M_396 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 13 + Query_13 + M_397 + 9 + + + 1 + gnl|BL_ORD_ID|2182 + 190409|polymerase|AAD16253.1|Hepatitis B virus|10407 + 2182 + 15 + + + 1 + 16.5494 + 31 + 0.211832 + 2 + 8 + 8 + 14 + 0 + 0 + 5 + 6 + 0 + 7 + FCGLPFS + FCGSPYS + FCG P+S + + + + + 2 + gnl|BL_ORD_ID|390 + 23864|envelope glycoprotein(gp21, gp46) - human T-cell lymphotropic virus type 1|A45714|Human T-lymphotropic virus 1|11908 + 390 + 9 + + + 1 + 14.2382 + 25 + 3.37936 + 3 + 7 + 5 + 9 + 0 + 0 + 4 + 4 + 0 + 5 + CGLPF + CGFPF + CG PF + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 14 + Query_14 + M_398 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 15 + Query_15 + M_399 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 16 + Query_16 + M_400 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 17 + Query_17 + M_401 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 18 + Query_18 + M_402 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 19 + Query_19 + M_403 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 20 + Query_20 + M_404 + 9 + + + 1 + gnl|BL_ORD_ID|2292 + 419366|polyprotein|BAA00792.1|Hepatitis C virus|11103 + 2292 + 9 + + + 1 + 14.2382 + 25 + 2.66858 + 3 + 9 + 3 + 9 + 0 + 0 + 5 + 6 + 0 + 7 + IDCYVAI + IDCNVAV + IDC VA+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 21 + Query_21 + M_405 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 22 + Query_22 + M_406 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 23 + Query_23 + M_407 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 24 + Query_24 + M_408 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 25 + Query_25 + M_409 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 26 + Query_26 + M_410 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 27 + Query_27 + M_411 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 28 + Query_28 + M_412 + 9 + + + 1 + gnl|BL_ORD_ID|471 + 28594|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 + 471 + 20 + + + 1 + 13.4678 + 23 + 8.80594 + 4 + 9 + 2 + 7 + 0 + 0 + 4 + 6 + 0 + 6 + NLPTYY + SLPSYY + +LP+YY + + + + + 2 + gnl|BL_ORD_ID|1971 + 182926|polyprotein|AFP27208.1|Dengue virus 4|11070 + 1971 + 9 + + + 1 + 13.4678 + 23 + 9.18751 + 3 + 8 + 3 + 8 + 0 + 0 + 4 + 6 + 0 + 6 + SNLPTY + ASLPTY + ++LPTY + + + + + 3 + gnl|BL_ORD_ID|2100 + 185881|polyprotein|AFP27208.1|Dengue virus 4|11070 + 2100 + 10 + + + 1 + 13.4678 + 23 + 9.73455 + 3 + 8 + 4 + 9 + 0 + 0 + 4 + 6 + 0 + 6 + SNLPTY + ASLPTY + ++LPTY + + + + + 4 + gnl|BL_ORD_ID|776 + 51643|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 + 776 + 20 + + + 1 + 13.4678 + 23 + 10.5613 + 5 + 9 + 13 + 17 + 0 + 0 + 4 + 5 + 0 + 5 + LPTYY + LPSYY + LP+YY + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 29 + Query_29 + M_413 + 9 + + + 1 + gnl|BL_ORD_ID|2141 + 187163|Gag polyprotein|P88150|Human immunodeficiency virus 1|11676 + 2141 + 11 + + + 1 + 11.5418 + 18 + 130.32 + 1 + 7 + 4 + 10 + 0 + 0 + 4 + 4 + 0 + 7 + NPYKAPM + NPEVIPM + NP PM + + + + + 2 + gnl|BL_ORD_ID|2139 + 187158|Gag protein|Q1KW74|Human immunodeficiency virus 1|11676 + 2139 + 11 + + + 1 + 11.5418 + 18 + 156.929 + 1 + 7 + 4 + 10 + 0 + 0 + 4 + 4 + 0 + 7 + NPYKAPM + NPEIIPM + NP PM + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 30 + Query_30 + M_414 + 9 + + + 1 + gnl|BL_ORD_ID|2055 + 184755|polyprotein|AGO67248.1|Dengue virus 2|11060 + 2055 + 9 + + + 1 + 11.927 + 19 + 104.062 + 3 + 9 + 3 + 9 + 0 + 0 + 3 + 6 + 0 + 7 + LQKAHLI + LEKRHVL + L+K H++ + + + + + 2 + gnl|BL_ORD_ID|2031 + 184337|polyprotein|AGO67248.1|Dengue virus 2|11060 + 2031 + 10 + + + 1 + 11.927 + 19 + 104.808 + 3 + 9 + 1 + 7 + 0 + 0 + 3 + 6 + 0 + 7 + LQKAHLI + LEKRHVL + L+K H++ + + + + + 3 + gnl|BL_ORD_ID|2009 + 183781|polyprotein|AGO67248.1|Dengue virus 2|11060 + 2009 + 10 + + + 1 + 11.927 + 19 + 108.205 + 3 + 9 + 4 + 10 + 0 + 0 + 3 + 6 + 0 + 7 + LQKAHLI + LEKRHVL + L+K H++ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + + diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116732_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116732_1_T.fasta new file mode 100755 index 00000000..ab50cfd0 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116732_1_T.fasta @@ -0,0 +1,56 @@ +>M_415 +FQGYLKDPV +>M_416 +SEVLGYWAF +>M_417 +SEVLGYWAF +>M_418 +RRFGWLQTA +>M_419 +GHEEKITFI +>M_420 +EESIAVGTM +>M_421 +EESIAVGTM +>M_422 +FRYLGKCNI +>M_423 +FEVGGAALF +>M_424 +FEVGGAALF +>M_425 +GMCVLEMAV +>M_426 +VLEMAVLEI +>M_427 +FLMVSRDCL +>M_428 +SRDCLRTVL +>M_429 +VSRDCLRTV +>M_430 +ALREFKFRV +>M_431 +REFKFRVSA +>M_432 +REFKFRVSA +>M_433 +YEALREFKF +>M_434 +NQMDKLAAF +>M_435 +YRMSPSNQM +>M_436 +KVISYPVAL +>M_437 +TERTKVISY +>M_438 +LHLRRKEIM +>M_439 +QTSCHVFMV +>M_440 +GEAGAGGTA +>M_441 +EHMPNNSRL +>M_442 +PRKPRSQNF diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116732_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116732_1_T_iedb.xml new file mode 100755 index 00000000..5aa795f9 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116732_1_T_iedb.xml @@ -0,0 +1,832 @@ + + + + blastp + BLASTP 2.2.30+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta + Query_1 + M_415 + 9 + + + BLOSUM62 + 100000000 + 11 + 1 + F + + + + + 1 + Query_1 + M_415 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 2 + Query_2 + M_416 + 9 + + + 1 + gnl|BL_ORD_ID|1253 + 98223|trans-sialidase, putative|EAN80725.1|Trypanosoma cruzi|5693 + 1253 + 9 + + + 1 + 13.853 + 24 + 7.58732 + 3 + 9 + 2 + 8 + 0 + 0 + 4 + 5 + 0 + 7 + VLGYWAF + LLGLWGF + +LG W F + + + + + 2 + gnl|BL_ORD_ID|616 + 37351|trans-sialidase, putative|EAN81560.1|Trypanosoma cruzi|5693 + 616 + 10 + + + 1 + 13.4678 + 23 + 7.89871 + 3 + 9 + 1 + 7 + 0 + 0 + 4 + 5 + 0 + 7 + VLGYWAF + LLGLWVF + +LG W F + + + + + 3 + gnl|BL_ORD_ID|614 + 37347|Sialidase 85-1.1 precursor|P18269.2|Trypanosoma cruzi|5693 + 614 + 10 + + + 1 + 11.927 + 19 + 77.1759 + 3 + 9 + 1 + 7 + 0 + 0 + 3 + 4 + 0 + 7 + VLGYWAF + LLGLWGL + +LG W + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 3 + Query_3 + M_417 + 9 + + + 1 + gnl|BL_ORD_ID|1253 + 98223|trans-sialidase, putative|EAN80725.1|Trypanosoma cruzi|5693 + 1253 + 9 + + + 1 + 13.853 + 24 + 7.58732 + 3 + 9 + 2 + 8 + 0 + 0 + 4 + 5 + 0 + 7 + VLGYWAF + LLGLWGF + +LG W F + + + + + 2 + gnl|BL_ORD_ID|616 + 37351|trans-sialidase, putative|EAN81560.1|Trypanosoma cruzi|5693 + 616 + 10 + + + 1 + 13.4678 + 23 + 7.89871 + 3 + 9 + 1 + 7 + 0 + 0 + 4 + 5 + 0 + 7 + VLGYWAF + LLGLWVF + +LG W F + + + + + 3 + gnl|BL_ORD_ID|614 + 37347|Sialidase 85-1.1 precursor|P18269.2|Trypanosoma cruzi|5693 + 614 + 10 + + + 1 + 11.927 + 19 + 77.1759 + 3 + 9 + 1 + 7 + 0 + 0 + 3 + 4 + 0 + 7 + VLGYWAF + LLGLWGL + +LG W + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 4 + Query_4 + M_418 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 5 + Query_5 + M_419 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 6 + Query_6 + M_420 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 7 + Query_7 + M_421 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 8 + Query_8 + M_422 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 9 + Query_9 + M_423 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 10 + Query_10 + M_424 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 11 + Query_11 + M_425 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 12 + Query_12 + M_426 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 13 + Query_13 + M_427 + 9 + + + 1 + gnl|BL_ORD_ID|1492 + 136837|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 + 1492 + 11 + + + 1 + 11.5418 + 18 + 156.929 + 1 + 9 + 1 + 9 + 0 + 0 + 4 + 5 + 0 + 9 + FLMVSRDCL + FLLALLSCL + FL+ CL + + + + + 2 + gnl|BL_ORD_ID|428 + 26111|polyprotein|BAD73987.1|Hepatitis C virus subtype 1b|31647 + 428 + 10 + + + 1 + 11.5418 + 18 + 170.632 + 1 + 9 + 2 + 10 + 0 + 0 + 4 + 5 + 0 + 9 + FLMVSRDCL + FLLALLSCL + FL+ CL + + + + + 3 + gnl|BL_ORD_ID|225 + 16706|structural protein|BAA00705.1|Hepatitis C virus|11103 + 225 + 9 + + + 1 + 11.5418 + 18 + 187.089 + 1 + 9 + 1 + 9 + 0 + 0 + 4 + 5 + 0 + 9 + FLMVSRDCL + FLLALLSCL + FL+ CL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 14 + Query_14 + M_428 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 15 + Query_15 + M_429 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 16 + Query_16 + M_430 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 17 + Query_17 + M_431 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 18 + Query_18 + M_432 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 19 + Query_19 + M_433 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 20 + Query_20 + M_434 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 21 + Query_21 + M_435 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 22 + Query_22 + M_436 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 23 + Query_23 + M_437 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 24 + Query_24 + M_438 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 25 + Query_25 + M_439 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 26 + Query_26 + M_440 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 27 + Query_27 + M_441 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 28 + Query_28 + M_442 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + + diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116846_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116846_1_T.fasta new file mode 100755 index 00000000..c4edc2b0 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116846_1_T.fasta @@ -0,0 +1,56 @@ +>M_443 +RQWPRLSHK +>M_444 +ISLAYLVKK +>M_445 +TISLAYLVK +>M_446 +MFLWTVAVI +>M_447 +TVAVIPILF +>M_448 +KIRQLKKKK +>M_449 +NEKTTPSPA +>M_450 +NENATPSPA +>M_451 +RERTANENA +>M_452 +CYLQIFATR +>M_453 +LPPSLQGAV +>M_454 +RVARSHCQR +>M_455 +VPSEPSSSV +>M_456 +EEWCSLWAG +>M_457 +WEEWCSLWA +>M_458 +RLPSYMVEK +>M_459 +SYMVEKREF +>M_460 +GENFCTAVK +>M_461 +MEGYMKAKV +>M_462 +CPLPRPPPI +>M_463 +AEEAGYPLS +>M_464 +EEAGYPLSC +>M_465 +GVYLLFALR +>M_466 +VYLLFALRL +>M_467 +QEASNKHAE +>M_468 +SEYSSSLGR +>M_469 +RESGSFLST +>M_470 +LYQLHNLVV diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116846_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116846_1_T_iedb.xml new file mode 100755 index 00000000..d3bf813a --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116846_1_T_iedb.xml @@ -0,0 +1,882 @@ + + + + blastp + BLASTP 2.2.30+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta + Query_1 + M_443 + 9 + + + BLOSUM62 + 100000000 + 11 + 1 + F + + + + + 1 + Query_1 + M_443 + 9 + + + 1 + gnl|BL_ORD_ID|1173 + 79337|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 + 1173 + 15 + + + 1 + 13.853 + 24 + 5.77703 + 2 + 8 + 4 + 10 + 0 + 0 + 4 + 4 + 0 + 7 + QWPRLSH + TWPLLPH + WP L H + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 2 + Query_2 + M_444 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 3 + Query_3 + M_445 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 4 + Query_4 + M_446 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 5 + Query_5 + M_447 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 6 + Query_6 + M_448 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 7 + Query_7 + M_449 + 9 + + + 1 + gnl|BL_ORD_ID|2288 + 419298|RNA-dependent RNA polymerase|ACH97782.1|Hepatitis C virus|11103 + 2288 + 9 + + + 1 + 11.927 + 19 + 76.3762 + 1 + 6 + 1 + 6 + 0 + 0 + 4 + 4 + 0 + 6 + NEKTTP + NSKRTP + N K TP + + + + + 2 + gnl|BL_ORD_ID|1598 + 142244|polyprotein|ACJ37184.1|Hepatitis C virus subtype 1a|31646 + 1598 + 9 + + + 1 + 11.927 + 19 + 84.261 + 1 + 6 + 1 + 6 + 0 + 0 + 4 + 4 + 0 + 6 + NEKTTP + NSKKTP + N K TP + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 8 + Query_8 + M_450 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 9 + Query_9 + M_451 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 10 + Query_10 + M_452 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 11 + Query_11 + M_453 + 9 + + + 1 + gnl|BL_ORD_ID|746 + 48836|EBNA-1 protein|Q777E1|Human gammaherpesvirus 4|10376 + 746 + 15 + + + 1 + 13.4678 + 23 + 8.59146 + 2 + 9 + 1 + 8 + 0 + 0 + 4 + 6 + 0 + 8 + PPSLQGAV + PPMVEGAA + PP ++GA + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 12 + Query_12 + M_454 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 13 + Query_13 + M_455 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 14 + Query_14 + M_456 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 15 + Query_15 + M_457 + 9 + + + 1 + gnl|BL_ORD_ID|2051 + 184702|non-structural protein 1|AGM49312.1|Dengue virus|12637 + 2051 + 9 + + + 1 + 10.7714 + 16 + 469.42 + 1 + 8 + 2 + 9 + 0 + 0 + 3 + 5 + 0 + 8 + WEEWCSLW + WPKTHTLW + W + +LW + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 16 + Query_16 + M_458 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 17 + Query_17 + M_459 + 9 + + + 1 + gnl|BL_ORD_ID|1799 + 164551|envelope glycoprotein B|NP_044629.1|Herpes simplex virus (type 1 / strain 17)|10299 + 1799 + 9 + + + 1 + 12.6974 + 21 + 23.4633 + 3 + 9 + 2 + 8 + 0 + 0 + 4 + 5 + 0 + 7 + MVEKREF + MLEDHEF + M+E EF + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 18 + Query_18 + M_460 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 19 + Query_19 + M_461 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 20 + Query_20 + M_462 + 9 + + + 1 + gnl|BL_ORD_ID|1508 + 139406|polyprotein|ACT37184.1|Hepatitis C virus|11103 + 1508 + 10 + + + 1 + 12.3122 + 20 + 39.8368 + 3 + 8 + 3 + 8 + 0 + 0 + 5 + 5 + 0 + 6 + LPRPPP + LPRPGP + LPRP P + + + + + 2 + gnl|BL_ORD_ID|1438 + 120093|unnamed protein product|CAA33016.1|Rubella virus|11041 + 1438 + 21 + + + 1 + 11.927 + 19 + 68.5496 + 5 + 8 + 10 + 13 + 0 + 0 + 4 + 4 + 0 + 4 + RPPP + RPPP + RPPP + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 21 + Query_21 + M_463 + 9 + + + 1 + gnl|BL_ORD_ID|2258 + 288104|nef protein|ACR27130.1|Human immunodeficiency virus 1|11676 + 2258 + 18 + + + 1 + 13.0826 + 22 + 13.7716 + 3 + 9 + 1 + 7 + 0 + 0 + 3 + 5 + 0 + 7 + EAGYPLS + EVGFPVR + E G+P+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 22 + Query_22 + M_464 + 9 + + + 1 + gnl|BL_ORD_ID|2258 + 288104|nef protein|ACR27130.1|Human immunodeficiency virus 1|11676 + 2258 + 18 + + + 1 + 13.0826 + 22 + 14.4713 + 2 + 8 + 1 + 7 + 0 + 0 + 3 + 5 + 0 + 7 + EAGYPLS + EVGFPVR + E G+P+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 23 + Query_23 + M_465 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 24 + Query_24 + M_466 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 25 + Query_25 + M_467 + 9 + + + 1 + gnl|BL_ORD_ID|53 + 3935|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis|1773 + 53 + 20 + + + 1 + 14.2382 + 25 + 3.6022 + 1 + 7 + 9 + 15 + 0 + 0 + 5 + 6 + 0 + 7 + QEASNKH + QEAANKQ + QEA+NK + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 26 + Query_26 + M_468 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 27 + Query_27 + M_469 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 28 + Query_28 + M_470 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + + diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_118562_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_118562_1_T.fasta new file mode 100755 index 00000000..babdc234 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_118562_1_T.fasta @@ -0,0 +1,2712 @@ +>M_471 +YAAPQLHSI +>M_472 +HLHDHYGPY +>M_473 +FAEDGACTV +>M_474 +HVIGTIGHF +>M_475 +FADDEHSMV +>M_476 +YANERPKSL +>M_477 +FACHFTVFV +>M_478 +NALDYICTV +>M_479 +LAYQELPTV +>M_480 +FVMEHSNIV +>M_481 +VAFCTMNVI +>M_482 +FTIRAIQVY +>M_483 +MAISVVKHI +>M_484 +RALEKLNHV +>M_485 +FADMERHHI +>M_486 +FANRRKEEV +>M_487 +LAIDSASPV +>M_488 +RALGPGHTV +>M_489 +FAKVLIRTY +>M_490 +SSDDNDAFY +>M_491 +YPKGRPSHI +>M_492 +WALPKTYTI +>M_493 +LARHWRVHI +>M_494 +FSYSASSEI +>M_495 +FSFFFVNIF +>M_496 +YSFDGMWKV +>M_497 +DSIHQVGMY +>M_498 +MTYDLASVV +>M_499 +LAFPVPLYY +>M_500 +YAALAMGTL +>M_501 +YLFRELATI +>M_502 +YMDLMGFSY +>M_503 +FAISHEGHM +>M_504 +FSSPRLRPI +>M_505 +FVYLHLNMV +>M_506 +MANNPDVMI +>M_507 +AALPAAQTV +>M_508 +FAWKNMDFL +>M_509 +FAAQGPTVF +>M_510 +LALSNLPTV +>M_511 +FTLEFLVCI +>M_512 +FSVDFPRIY +>M_513 +FTIFWTVYY +>M_514 +MADPNQCVI +>M_515 +RAFWAGSVV +>M_516 +YHFDAIRTF +>M_517 +FAKGWLLKL +>M_518 +NAQNMTITV +>M_519 +RALNRVHVL +>M_520 +MAPELISHL +>M_521 +KAFYHPRLI +>M_522 +LAFVIVLLV +>M_523 +CTAVVLLVY +>M_524 +FTEFCDSCY +>M_525 +LAREPVNEL +>M_526 +YTRKRTQSI +>M_527 +FAPSCANSL +>M_528 +KVYDLVHSV +>M_529 +QAPPLMGTI +>M_530 +QAFRRSISV +>M_531 +FVLDHSRLV +>M_532 +FIKRHIAPI +>M_533 +YSQPFYTSY +>M_534 +FAQDVDRMF +>M_535 +QAPEFLQTL +>M_536 +LSDISRSCY +>M_537 +NAYARVLRF +>M_538 +FANFFNTFL +>M_539 +FIYDAVGNM +>M_540 +LARECGSPL +>M_541 +WHGPARPSL +>M_542 +HVMFMVAFY +>M_543 +MAITSMNPV +>M_544 +TAVEFIMAI +>M_545 +QAYGGPRYL +>M_546 +FTIRAIQVY +>M_547 +YLDYVSISY +>M_548 +SAYMHHSKI +>M_549 +YLMEFGQLL +>M_550 +KAEELKETV +>M_551 +FALGVGTAL +>M_552 +LVFPNSDHV +>M_553 +FTLQNPSAV +>M_554 +EIVDQQGHM +>M_555 +FTIFWTVYY +>M_556 +FPNSCLSTL +>M_557 +YSISDWTSI +>M_558 +FTACYIRIV +>M_559 +FEFDHIRNF +>M_560 +YTPDELHAM +>M_561 +FVHPATRPL +>M_562 +KALRITNVY +>M_563 +QARDQGSPV +>M_564 +FIYDAVGNM +>M_565 +EAFPEDVAV +>M_566 +YATADSSSL +>M_567 +RAREHSDTF +>M_568 +IAIQLITHM +>M_569 +MAFENNAGL +>M_570 +FGHENRVSI +>M_571 +NATTIVTTV +>M_572 +VTFPGINLM +>M_573 +DAYPRQYSL +>M_574 +YIQEGFLAV +>M_575 +FATTACHTL +>M_576 +RANQCFAFV +>M_577 +MTQPVWSTI +>M_578 +FTEEGFCAI +>M_579 +FADHPQAPF +>M_580 +VAMGSAALV +>M_581 +TAKDYRVYV +>M_582 +EAEEWVVSY +>M_583 +FTLPLMDQV +>M_584 +MQMPCTIKI +>M_585 +YRYFCRVPV +>M_586 +WAHAWPSPY +>M_587 +IAIISVLVI +>M_588 +MASCPFAKV +>M_589 +NHDRFHYLL +>M_590 +FTIFWTVYY +>M_591 +VASQPAHVV +>M_592 +EAFNCESKM +>M_593 +FSSEVTVAL +>M_594 +ETIKQLQEL +>M_595 +YFMDPMVPL +>M_596 +NVYHVGMHI +>M_597 +AAMEGRLPV +>M_598 +NHDDDDVEI +>M_599 +NASVNVSHL +>M_600 +EALDAGAIY +>M_601 +YGRDDWEVI +>M_602 +VALDKDALV +>M_603 +LPFSLGKHV +>M_604 +MANNPCSRY +>M_605 +YEEPNTATF +>M_606 +MALYHCVAI +>M_607 +YTLAPGVPL +>M_608 +KIHPFFETI +>M_609 +NMDFLIAEY +>M_610 +LCIPWTNPV +>M_611 +SAQEHLLFV +>M_612 +QSVHPVVTV +>M_613 +YVASDIQYM +>M_614 +FHMRQVNIV +>M_615 +LAKHSTSAV +>M_616 +FSHQPKEKV +>M_617 +YLYIPALAV +>M_618 +VALFMAITI +>M_619 +VAFYGLGAV +>M_620 +EVDPIGNLY +>M_621 +WALSIHVSV +>M_622 +ITYPSQAPV +>M_623 +CIALWSLAY +>M_624 +FLFYVMTEV +>M_625 +HAEQDSTTV +>M_626 +DTNDNVPEF +>M_627 +NSYGSRRTL +>M_628 +NARCLIVHL +>M_629 +FWYRNCHHV +>M_630 +DADPSTPHL +>M_631 +DSYIHVTYI +>M_632 +DVFDALDLM +>M_633 +FSMDETGQM +>M_634 +RTFNKPESV +>M_635 +YSLQEMEVL +>M_636 +QTVMFMATM +>M_637 +VTIDGIRFI +>M_638 +RALSHPQSL +>M_639 +TAAGFWLMV +>M_640 +FMEELGECV +>M_641 +YLESNPGTI +>M_642 +VPSNFVEHV +>M_643 +FTEELRRTF +>M_644 +YGRSRGITV +>M_645 +FSMACNTPL +>M_646 +QAADEPQLL +>M_647 +YEFALQRIV +>M_648 +TAAPTSASV +>M_649 +LACRKAREI +>M_650 +FIEPLNDTI +>M_651 +SALRAITRV +>M_652 +RAAPKAMVL +>M_653 +VADEGLNNL +>M_654 +LSNDECKTI +>M_655 +NAWAVMNHF +>M_656 +VASNAWAVM +>M_657 +LSRNLIRTI +>M_658 +HSKEEIKVI +>M_659 +DSELNFNEY +>M_660 +DAAERECHL +>M_661 +ISYTEVPTY +>M_662 +IASDHVVDM +>M_663 +IAILICTMI +>M_664 +MAKTGRFHI +>M_665 +EVMEKVLPL +>M_666 +FENNAGLPV +>M_667 +FLHEMVAAM +>M_668 +QAEPKKKPV +>M_669 +YVLHSKEEI +>M_670 +FFFHNPKPL +>M_671 +FHWNWIIVL +>M_672 +YTMGIIFVL +>M_673 +YVGKDIESV +>M_674 +YQHYFRLLV +>M_675 +MSNSMINTM +>M_676 +FSMLSRVLI +>M_677 +FVDYPGDPV +>M_678 +STAPLYSGM +>M_679 +DTVQLNVKY +>M_680 +SAYMAATLL +>M_681 +QAWNFLRAM +>M_682 +CAFGAMCAV +>M_683 +IMEEEFSTI +>M_684 +HAANVTQAM +>M_685 +MAKQIKTKV +>M_686 +KAKGIYNSI +>M_687 +HAPVHFLVI +>M_688 +EVLQSMQRF +>M_689 +YVASDIQYM +>M_690 +YAAMDLSCL +>M_691 +TPMTCSNTI +>M_692 +EAPPGRVTF +>M_693 +DTHSGAGKF +>M_694 +YKYRYFCRV +>M_695 +LSDPHLTAV +>M_696 +WAGLGGRHV +>M_697 +QHTGTSVVL +>M_698 +STFCGTLEY +>M_699 +TMYRCGPLI +>M_700 +WHNQCSGHL +>M_701 +FPLRNRPFY +>M_702 +YVGPAQLSV +>M_703 +VAQHLATTY +>M_704 +LVYPRFLYL +>M_705 +FSREEMHNM +>M_706 +YYPPGVVFY +>M_707 +YLMSFFRLL +>M_708 +RVFPLRGKI +>M_709 +YPLPVANGM +>M_710 +RAVCFSMEI +>M_711 +QALPLDHHL +>M_712 +FIEPHARFY +>M_713 +FFYCIYASL +>M_714 +CHDDYLVML +>M_715 +KALFWTVAM +>M_716 +EYYEPPHRI +>M_717 +PTSPMPYTY +>M_718 +EAVEARGAI +>M_719 +NVVRLVATI +>M_720 +YLKNSMIAV +>M_721 +LQAEIVETM +>M_722 +FHHKSNFLL +>M_723 +KPIPAFEMV +>M_724 +FLVDSNLSV +>M_725 +FIDRQLTMV +>M_726 +YSASSEIII +>M_727 +YTPDELHAM +>M_728 +FFYLDYVSI +>M_729 +YIAPMMEKL +>M_730 +EAFDRTETH +>M_731 +SIVDVSIMY +>M_732 +IPYTTVLHL +>M_733 +EVFRHKLAM +>M_734 +VMDRWNETV +>M_735 +LLLDHGVHV +>M_736 +VIFNVVRLV +>M_737 +LAIKVTPSV +>M_738 +LTDRQPLMH +>M_739 +KPLPFNREV +>M_740 +LNFGDITTV +>M_741 +QAIDSTFYL +>M_742 +LALNKGRAY +>M_743 +IARQVVTAM +>M_744 +GAFAFGAVF +>M_745 +KSFPFQSLL +>M_746 +RAGGSSVVI +>M_747 +DTIPWYLRL +>M_748 +MAVDGKPEY +>M_749 +YLQDVVMQV +>M_750 +FMVRNYEFL +>M_751 +YMAGSDTTY +>M_752 +VVYVLMTSV +>M_753 +MPAERNGAI +>M_754 +WPLQPVDHI +>M_755 +MLDPHGHLI +>M_756 +FISNSLNIL +>M_757 +RADGDLTLI +>M_758 +YQEEMIQCY +>M_759 +FILDCHPKY +>M_760 +GAYVYPLPV +>M_761 +FKEAWKHTI +>M_762 +LAGVKMVMI +>M_763 +DAKQRIRLL +>M_764 +LYYPPGVVF +>M_765 +RASEDDRVL +>M_766 +SALEYLLPL +>M_767 +AAVEPERTL +>M_768 +GTDCLLLAF +>M_769 +FVQLPVPII +>M_770 +RIYPDRHRI +>M_771 +KVDKNISHI +>M_772 +RHSQWDHGL +>M_773 +MLYSRDHSV +>M_774 +AARPLSRMV +>M_775 +HAQVCSLYI +>M_776 +YSQPFYTSY +>M_777 +MSDFQYLVV +>M_778 +SANARCLIV +>M_779 +SAIAIVQIL +>M_780 +WMFYHFDAI +>M_781 +YSKVIKCVV +>M_782 +AARARGNKV +>M_783 +TAYERLYLW +>M_784 +TTASGVWAF +>M_785 +KVREEVVTM +>M_786 +MYYRVRDTM +>M_787 +YVDRLLQHF +>M_788 +PAIARPQAI +>M_789 +YLLRAGVHL +>M_790 +LVTPHMAEV +>M_791 +EHVSDDDLL +>M_792 +SFYHLVSTV +>M_793 +FSAGNEANV +>M_794 +KPGDRVVLV +>M_795 +YSRGSSRCI +>M_796 +YSTCVLVVL +>M_797 +YSTHQTFMV +>M_798 +WSLDGKYIV +>M_799 +HAWRDLSSM +>M_800 +FASSLWETT +>M_801 +FDYPSLFCI +>M_802 +KAPPLTDVL +>M_803 +DVFDALDLM +>M_804 +ALYCRLATV +>M_805 +MVYLQIGGF +>M_806 +EPFSGTASV +>M_807 +ETMDELELL +>M_808 +SMLNWFSPV +>M_809 +NMLNLTHTY +>M_810 +HSFNPEAQV +>M_811 +SAYGSSGEL +>M_812 +FSIPWAHAW +>M_813 +MASSAQEHL +>M_814 +RHSREMALL +>M_815 +WVLHHMGGM +>M_816 +VADSDRQLV +>M_817 +IAAAWALSF +>M_818 +KAESTPEIV +>M_819 +LHLGHMFSL +>M_820 +QRINLPHLL +>M_821 +YALMRHRHT +>M_822 +RLYPLANSL +>M_823 +DHFSHASSI +>M_824 +ISMEKGYNI +>M_825 +FLHEMVAAM +>M_826 +YVALEAQAI +>M_827 +YLMTRTLPM +>M_828 +QTFPQVSEL +>M_829 +YPESIKAPV +>M_830 +VHSKTSQLL +>M_831 +TSSDRMTSV +>M_832 +QMAERALYY +>M_833 +LASPFATTA +>M_834 +AAYTSYTPY +>M_835 +VSCRPVVYV +>M_836 +RTYHGRLAY +>M_837 +LARHSAAFL +>M_838 +RSEALPVSY +>M_839 +ETKPFGLVV +>M_840 +DVKNFWQGM +>M_841 +FAELKSARM +>M_842 +YMKPRLRTT +>M_843 +STFCGTLEY +>M_844 +HAATGPGEV +>M_845 +PSQNRFLTY +>M_846 +YISAWLDSL +>M_847 +VPFPPKEPL +>M_848 +KSHELVMYI +>M_849 +LMLGRTNTL +>M_850 +VARHTFSML +>M_851 +LAIFMPPTY +>M_852 +WAVVTMTAV +>M_853 +FPRASQSLV +>M_854 +YDFLCLSLV +>M_855 +NKFPGDSMV +>M_856 +FSLLATVIL +>M_857 +SSSDNRNFI +>M_858 +KSRNWLKSI +>M_859 +QALNLQVVL +>M_860 +FPVLLLDTI +>M_861 +VTDFHNHSV +>M_862 +LSDSMPLWM +>M_863 +QSTKVNMLY +>M_864 +MANHLGVGV +>M_865 +HMDVEESQY +>M_866 +LADPIEKEL +>M_867 +MAITILVAL +>M_868 +YRDNKMTRI +>M_869 +FQMAERALY +>M_870 +RINENTGIV +>M_871 +EAGEESTSV +>M_872 +RGMPPPPTV +>M_873 +RLFRMFVHV +>M_874 +FLTDMAKQI +>M_875 +ISMQFLSSL +>M_876 +HTDTNNLGI +>M_877 +LALAIYTLL +>M_878 +LAVCAFTVL +>M_879 +AAAPNLRAL +>M_880 +LVDSNLSVV +>M_881 +VSSVQGITY +>M_882 +HLMKQISSF +>M_883 +EARGAIRGF +>M_884 +LVSTSNHAY +>M_885 +IAPRRWLLL +>M_886 +RMAERRQEV +>M_887 +YVVATTKLM +>M_888 +FQDDFSPRF +>M_889 +IGFNGNQIV +>M_890 +KMFTCSKFV +>M_891 +VAEVCPREV +>M_892 +WAPLPGQML +>M_893 +DAQQLATAI +>M_894 +ILLNGDATV +>M_895 +TIYDEDVLV +>M_896 +WVKEDMGIV +>M_897 +RKYGSTSSI +>M_898 +MTDAQQLAT +>M_899 +GFDQYRTLL +>M_900 +NASGATAPL +>M_901 +FFPEMGTKI +>M_902 +NVHSSGKPI +>M_903 +AALVGAEVV +>M_904 +DHFSHASSI +>M_905 +RAMGERLLL +>M_906 +KIYDGKDKM +>M_907 +WASGNERSL +>M_908 +LATVRSHHM +>M_909 +LRDHGSFLL +>M_910 +TALETSAPF +>M_911 +HTFSMLSRV +>M_912 +KAFHGSSGL +>M_913 +LAKKPGCVF +>M_914 +IPNPQLGPV +>M_915 +QQHDGAFLI +>M_916 +AAFFYLDYV +>M_917 +FFPEMGTKI +>M_918 +SQWDHGLSI +>M_919 +MSCRKIAHL +>M_920 +MGFTVLTTV +>M_921 +NLEVLDCRY +>M_922 +LAQAVRAVL +>M_923 +FMQTRYNKL +>M_924 +LTHTGACPY +>M_925 +KAFSDRFSL +>M_926 +FLRDCSPRL +>M_927 +DIFTTLKMY +>M_928 +RAPPEAIAL +>M_929 +STQDTPVTV +>M_930 +QASSDWAAV +>M_931 +FTRGIQTLF +>M_932 +YRALNRVHV +>M_933 +YEARLLKHM +>M_934 +MELNSVNVM +>M_935 +TAARLRHKV +>M_936 +YAYFLDNVS +>M_937 +TVLENLAVL +>M_938 +HSFTHKQHL +>M_939 +NMEELILAI +>M_940 +IAPHRNEKL +>M_941 +MMNDIVKEF +>M_942 +FSVPLHIFL +>M_943 +TVMGRITTL +>M_944 +FAKYWEENF +>M_945 +VSDLLVLLL +>M_946 +FLHVGDLVI +>M_947 +EAFAHEARF +>M_948 +SSLGKTQTV +>M_949 +LVLIGISHV +>M_950 +FYFQVPFIY +>M_951 +WSFAVAICI +>M_952 +QHMIQQQAL +>M_953 +FPEGYGTQV +>M_954 +KPYGRNKPF +>M_955 +HGFNATYHV +>M_956 +YIRTRNEFV +>M_957 +YPEVFGPPL +>M_958 +MVACGGTVY +>M_959 +APSEHAQMV +>M_960 +TRTFVEFIL +>M_961 +LLSEVLLHY +>M_962 +IQVGTGVTV +>M_963 +LTLAFTVML +>M_964 +HVGDLVIVV +>M_965 +MTREELNAL +>M_966 +VAVQESARI +>M_967 +VPSPLFSIV +>M_968 +KAGGGSNEV +>M_969 +YMLIIVSIF +>M_970 +VAPHAPVHF +>M_971 +TPFHLASAV +>M_972 +SARDCKDPY +>M_973 +FMATMPPAV +>M_974 +TMVACGGTV +>M_975 +NSDHVMFMV +>M_976 +FMKNYFKDV +>M_977 +LNVEDPVTV +>M_978 +FIPINGCPI +>M_979 +YTSYFGYKM +>M_980 +WSPHPLQIV +>M_981 +YTTITPQII +>M_982 +CSFYRTHTL +>M_983 +NAAKNQVAM +>M_984 +FETDGRRFL +>M_985 +SVEINDIMY +>M_986 +DPAPRPSLL +>M_987 +QAVTEVEAV +>M_988 +TAFQKGYGI +>M_989 +ICFPVLVAL +>M_990 +NHVPVNHFW +>M_991 +DMNDHAPEV +>M_992 +SPLPPPEQI +>M_993 +LRLDGSVVI +>M_994 +HACSHLRQM +>M_995 +FPSSQGSLY +>M_996 +FNRDDCSVL +>M_997 +TSFPQKVHL +>M_998 +EAFAHEARF +>M_999 +DAKSHELVM +>M_1000 +TEYRALNRV +>M_1001 +KTIWHTAEY +>M_1002 +KAMLEEQLI +>M_1003 +DTSDGLAVL +>M_1004 +LEFGKPSTL +>M_1005 +TLLEFFITL +>M_1006 +FTKRQRKAM +>M_1007 +FCLSTENSI +>M_1008 +FQGFSVQLI +>M_1009 +RVAPGYYTL +>M_1010 +FYQDMMNDI +>M_1011 +CLYDSVLML +>M_1012 +YTCVVSNKL +>M_1013 +PAEEPTNEL +>M_1014 +QVYSWLLCL +>M_1015 +PANESFGHL +>M_1016 +SPFAAAAAV +>M_1017 +DVVHHLLSV +>M_1018 +MFYPERTAL +>M_1019 +VSDPACSSI +>M_1020 +WAKVRTAEF +>M_1021 +AALRHERAV +>M_1022 +YVVATTKLM +>M_1023 +RMLLDPNTV +>M_1024 +YYDYMKPRL +>M_1025 +FPRHCVSWM +>M_1026 +YLPPDPQPF +>M_1027 +HPATRPLHV +>M_1028 +MVTGILLYM +>M_1029 +KPISYMAII +>M_1030 +DSSQRFEVI +>M_1031 +STGYAISAY +>M_1032 +KQLEFHIEI +>M_1033 +FFCEVPVLL +>M_1034 +FSMDETGQM +>M_1035 +YPRQYSLKL +>M_1036 +ETAYTKDGF +>M_1037 +FSNHWTFWV +>M_1038 +IGYANAKIY +>M_1039 +DFFEDTEHY +>M_1040 +DPMKVEAHV +>M_1041 +GSGEHPMDY +>M_1042 +SHSRGNDTL +>M_1043 +FHTSSSLTV +>M_1044 +VVMRICNLI +>M_1045 +TALDSSLCL +>M_1046 +DSDDMDLEV +>M_1047 +HSYVGPAQL +>M_1048 +EMFQRYSAF +>M_1049 +MPVSIRLVV +>M_1050 +LVDGDLGKY +>M_1051 +RSLAFPVPL +>M_1052 +RAFHDLRVA +>M_1053 +IYDEDVLVV +>M_1054 +LAMHSIWEM +>M_1055 +YCRAWCQAL +>M_1056 +QAVTNHSVY +>M_1057 +HSQECGSFL +>M_1058 +LQHTGTSVV +>M_1059 +ETRAQLARH +>M_1060 +RAALVGAEV +>M_1061 +IPNAQNMTI +>M_1062 +LATCCRARY +>M_1063 +LMRHSMEKI +>M_1064 +VSARHPQHL +>M_1065 +YKYDAGSAA +>M_1066 +IIFLLGEIV +>M_1067 +LARSQRTQV +>M_1068 +NAAVETASL +>M_1069 +LACSICHVY +>M_1070 +DIYDVLICL +>M_1071 +LTMSWLTPL +>M_1072 +FHNDLMPSY +>M_1073 +VMVSPASAI +>M_1074 +VFFSLLATV +>M_1075 +EASLATQIV +>M_1076 +ETLVSTSTI +>M_1077 +FPYQITNEH +>M_1078 +RTFLPVHLL +>M_1079 +LPQPGVRSL +>M_1080 +VPNNCLGKV +>M_1081 +HPLEFCLLL +>M_1082 +MAFVTLTDL +>M_1083 +FSVQLIRKF +>M_1084 +FPQMRAMSL +>M_1085 +LRLNWGEPI +>M_1086 +YEEDSGEYF +>M_1087 +TAKGTAQLV +>M_1088 +LHFHWNWII +>M_1089 +DTDGQPLLL +>M_1090 +AHLLCTLLL +>M_1091 +KAPGFEKHL +>M_1092 +SSYGGTIRY +>M_1093 +YQDMMNDIV +>M_1094 +MQALNLQVV +>M_1095 +MHYLKNSMI +>M_1096 +NAKSRGWLI +>M_1097 +DSNRVVCPI +>M_1098 +ISNRSVLHL +>M_1099 +QAELRGRVL +>M_1100 +ASFDCAIEM +>M_1101 +LQIGGFSSV +>M_1102 +QTWRAVTTL +>M_1103 +FSAQTFYVL +>M_1104 +LGDDFSSAY +>M_1105 +FQCAPGYAL +>M_1106 +DRETGMHLL +>M_1107 +FALQRIVQK +>M_1108 +DAVGNMLNL +>M_1109 +FYRLHLGTY +>M_1110 +FELKSPVKM +>M_1111 +VLRPRWCPV +>M_1112 +HHSSFRRHL +>M_1113 +FSYLTMSWL +>M_1114 +WAESVEREI +>M_1115 +KADVVHVTL +>M_1116 +IMEENDSNI +>M_1117 +LRLPHWPII +>M_1118 +EAVQDPMKV +>M_1119 +LIRKFAQSI +>M_1120 +SHHQCGQSL +>M_1121 +CTLGLGSLY +>M_1122 +ELAHDSYFY +>M_1123 +HAANVTQAM +>M_1124 +WTFWVGPFI +>M_1125 +VVEHVLTTV +>M_1126 +NDHDNWCII +>M_1127 +IAPLLPVAV +>M_1128 +LSGPWGSPL +>M_1129 +DPADPTSNL +>M_1130 +FPNSDHVMF +>M_1131 +EVQDIQASL +>M_1132 +RPYKQGARL +>M_1133 +DVAQHGARL +>M_1134 +FLEKNKDAV +>M_1135 +DSELAHDSY +>M_1136 +MPLWMASII +>M_1137 +YHFDAIRTF +>M_1138 +VSTEHCLSV +>M_1139 +YEAAKLLLV +>M_1140 +LVQAGVDVV +>M_1141 +SATASMLSV +>M_1142 +DQFTKSISI +>M_1143 +CALCALSNI +>M_1144 +RAKPRWRVA +>M_1145 +AAMDAGFLY +>M_1146 +CAMTMNKYI +>M_1147 +NLEPHGYVV +>M_1148 +MLLSPGQNV +>M_1149 +WQIHRVDIL +>M_1150 +YAELGTTTK +>M_1151 +YKLNRAFML +>M_1152 +FAAAAAVAA +>M_1153 +KMADPNQCV +>M_1154 +DPYVKAHLL +>M_1155 +WPIINTPMV +>M_1156 +KYYTDPSTY +>M_1157 +RVSSYGGTI +>M_1158 +EALDAGAIY +>M_1159 +EFIMAITSM +>M_1160 +FPWWLARVL +>M_1161 +WTLASMELV +>M_1162 +IVRCLVTSV +>M_1163 +MPAFHFNIL +>M_1164 +YRTHTLQTL +>M_1165 +HASVVAAYL +>M_1166 +ISRPSSNAL +>M_1167 +RALLGCSCV +>M_1168 +DAVWSRATF +>M_1169 +DVVHHLLSV +>M_1170 +MSFFRLLQM +>M_1171 +KIIAFRKTL +>M_1172 +TVSSNLSHV +>M_1173 +MSVEINDIM +>M_1174 +IAICRQIGI +>M_1175 +ISKPSELPI +>M_1176 +DPIEKELSV +>M_1177 +DHSNDPTAI +>M_1178 +WRLAEAEML +>M_1179 +RGLPWTVRV +>M_1180 +KPMPTIQWI +>M_1181 +RRFNLTSTF +>M_1182 +RRSHTGTFL +>M_1183 +FALDENDNA +>M_1184 +NPEELEQVV +>M_1185 +QAMHSFGRF +>M_1186 +TAIAICRQI +>M_1187 +EVMEKVLPL +>M_1188 +DVLPDTFTL +>M_1189 +RTGDRPHTF +>M_1190 +QPAVFETTV +>M_1191 +VMDFRFGTI +>M_1192 +NEDDSTFTI +>M_1193 +TALGLCEEV +>M_1194 +SMLSRVLII +>M_1195 +DANLHKNEL +>M_1196 +DHYAVESAL +>M_1197 +EVKIGKMSY +>M_1198 +LANGGKVPF +>M_1199 +IGAKHTLTI +>M_1200 +EVVGGWPVV +>M_1201 +VANERISMQ +>M_1202 +LSLKQVISI +>M_1203 +VGFPVGDSV +>M_1204 +LPLDHHLAL +>M_1205 +GALPLFRKY +>M_1206 +VSYHPDLGI +>M_1207 +HLFGTSCPY +>M_1208 +TATTILIMI +>M_1209 +LSFMEAQSL +>M_1210 +FLSLGIASL +>M_1211 +RPPPTPRKV +>M_1212 +SQLEMPETL +>M_1213 +YCRLATVHM +>M_1214 +VPHEDTLSL +>M_1215 +KCYKQGAFI +>M_1216 +LVLAFKNQV +>M_1217 +TSDDFWYHA +>M_1218 +RAEHFGIA* +>M_1219 +QVLPWLKAF +>M_1220 +FSIVRADGV +>M_1221 +DVHDIARFL +>M_1222 +SAQRPWPRV +>M_1223 +CAFRSQLEM +>M_1224 +IIDCLVSMV +>M_1225 +NPTEARVQV +>M_1226 +MVLWHLPAV +>M_1227 +KVHDSVLAL +>M_1228 +FVLLLTYIL +>M_1229 +RSGEPMVSL +>M_1230 +LPHCGHRTL +>M_1231 +MTEHRGKCY +>M_1232 +RTLRISETL +>M_1233 +VSAKRVSVL +>M_1234 +SVYCIRKKY +>M_1235 +QSMPCLMSF +>M_1236 +HRYNLTQHF +>M_1237 +ISLMVIEKV +>M_1238 +EIYSLIDNF +>M_1239 +APSNHMNLV +>M_1240 +FAISHEGHM +>M_1241 +LTSVLTLMF +>M_1242 +YAIPSKQLE +>M_1243 +QALAQRNQL +>M_1244 +FNCSFVLEM +>M_1245 +SPRRRAASV +>M_1246 +AAGAPPAKI +>M_1247 +DTIPWYLRL +>M_1248 +FFGNNMPEF +>M_1249 +NPICCDCVI +>M_1250 +CPYSAWCVY +>M_1251 +QMCAVNSTV +>M_1252 +LQMVRLCSV +>M_1253 +LTRTFVEFI +>M_1254 +LSATVMLTV +>M_1255 +MVPREFKPI +>M_1256 +LVIQYTVKY +>M_1257 +LRFPRITFF +>M_1258 +TSMPVSKML +>M_1259 +LMKCPCNTF +>M_1260 +IHQAMFQLL +>M_1261 +VAGRRGQQL +>M_1262 +HASSIIDEL +>M_1263 +YARRRWPSQ +>M_1264 +SSLDHHMLV +>M_1265 +DLITNIEPF +>M_1266 +TTILIMIVF +>M_1267 +LLKSNTSTL +>M_1268 +LHDVYMFCI +>M_1269 +STRSPNSTV +>M_1270 +QELAGVKMV +>M_1271 +YVPYRDNKM +>M_1272 +DPADGIRLF +>M_1273 +WRCWFNGIM +>M_1274 +CALGLHNFV +>M_1275 +MEEEFSTIL +>M_1276 +MLDDAPRLL +>M_1277 +LGYDMFDCV +>M_1278 +FVYKSGMTS +>M_1279 +ESADKTAYL +>M_1280 +NLQRWVTAV +>M_1281 +WKLTDMSSI +>M_1282 +HTLEEIYSL +>M_1283 +DAFNSTERA +>M_1284 +YLYPLVLMS +>M_1285 +SPFKLDATY +>M_1286 +FPRIYSNSL +>M_1287 +YHISEEYGL +>M_1288 +ASMHRFGHI +>M_1289 +AIDSASPVY +>M_1290 +CTFDSPARL +>M_1291 +SFMEAQSLM +>M_1292 +LPYELGWLF +>M_1293 +NIWECNRNI +>M_1294 +SPAEETVVL +>M_1295 +RQIPVVGSM +>M_1296 +LVWALPKTY +>M_1297 +QARPKGKGL +>M_1298 +LHLCYEFLM +>M_1299 +HQEDGGKAL +>M_1300 +RPSSNALLI +>M_1301 +QKYDGKCPL +>M_1302 +YAQFRGRHR +>M_1303 +VAVYSTCVL +>M_1304 +FLPPARSGI +>M_1305 +QHGSLSETW +>M_1306 +LGLEKTTSI +>M_1307 +QTVMFMATM +>M_1308 +LLKPGDRVV +>M_1309 +MPGSPRDPV +>M_1310 +LTYCTTGGI +>M_1311 +FQSLLSQHM +>M_1312 +KEFHFNQYL +>M_1313 +SSTEWVAPL +>M_1314 +RSSPATHSL +>M_1315 +ELKEWAESV +>M_1316 +GVVEATLSY +>M_1317 +EIAELNRTI +>M_1318 +GAASMIHYI +>M_1319 +LVNTCIRFV +>M_1320 +QAVDTDEAL +>M_1321 +AATSRGQVL +>M_1322 +NPLRPRESL +>M_1323 +VSSNLSHVI +>M_1324 +FTFGETEVC +>M_1325 +FQDDFSPRF +>M_1326 +YTVKYEQKM +>M_1327 +EHSDTFINL +>M_1328 +YTPKLEIKV +>M_1329 +ETQETMDEL +>M_1330 +DLVHHTTTL +>M_1331 +LMFSGLWHL +>M_1332 +VPHQIPKAV +>M_1333 +MAPAAGTWV +>M_1334 +FLITNALHF +>M_1335 +SPKPPPQCV +>M_1336 +SIADGRAWF +>M_1337 +MGYRVESEV +>M_1338 +APAPDLVVV +>M_1339 +LSANARCLI +>M_1340 +DTSDGLAVL +>M_1341 +EARRQGAVF +>M_1342 +KVPEGDSIV +>M_1343 +WRPGCLWAL +>M_1344 +HGLEKVPVI +>M_1345 +ITIVVISLI +>M_1346 +FAMELDDLH +>M_1347 +LTDKVSTPA +>M_1348 +LMVSAGVFI +>M_1349 +LQLEVEEAV +>M_1350 +SMIHYIVLI +>M_1351 +FRMFVHVYI +>M_1352 +HIFLFAVLL +>M_1353 +QQHDGAFLI +>M_1354 +VELELWGVV +>M_1355 +WSLQTWRAV +>M_1356 +LVQEFTRGI +>M_1357 +VAAFFLSLF +>M_1358 +EAEEESLAL +>M_1359 +HVIVRTSRV +>M_1360 +ELLEPQKTY +>M_1361 +AMSDGRVPV +>M_1362 +RPPSPKDTV +>M_1363 +VPMCHLRLL +>M_1364 +LSARSVPSI +>M_1365 +QVHQRMNSL +>M_1366 +EALVQMQYL +>M_1367 +CAQSPWCLV +>M_1368 +LSCEAHNSM +>M_1369 +QARGVKKQI +>M_1370 +SHHSQCSSL +>M_1371 +YGGFFVISV +>M_1372 +YVYPLPVAN +>M_1373 +HSYWLLKLL +>M_1374 +YRTHTLQTL +>M_1375 +FTTLKMYSV +>M_1376 +EHMNHTCNL +>M_1377 +VAIYLYPLV +>M_1378 +YEGYKYEHI +>M_1379 +DRYVAVRHL +>M_1380 +DLIDYARYM +>M_1381 +NLLLWVLAI +>M_1382 +HLHDHYGPY +>M_1383 +NTDSTAALL +>M_1384 +YVKERQTVT +>M_1385 +TMECWGQKY +>M_1386 +KSDDSDFLA +>M_1387 +MAFVRLLHS +>M_1388 +LVDNLTYTL +>M_1389 +KHSATASML +>M_1390 +FEAHEVLKL +>M_1391 +LVLVGCFTI +>M_1392 +TTSGIGSSM +>M_1393 +KSRAPPEAI +>M_1394 +AALVPTQAM +>M_1395 +RQRNGVAKL +>M_1396 +SSDRMTSVA +>M_1397 +RPSPNRPKL +>M_1398 +SSVEVLVNY +>M_1399 +YCIYASLRI +>M_1400 +RLLPPVSP* +>M_1401 +FSLGKHVCL +>M_1402 +CTDKVGTEA +>M_1403 +FRRSISVRI +>M_1404 +LYLHTLLTI +>M_1405 +LEVPAPEAI +>M_1406 +LLSEMAVAV +>M_1407 +VPLVRWLKV +>M_1408 +DTLPMLGNI +>M_1409 +FAFGAVFSE +>M_1410 +RNYQAWNFL +>M_1411 +DATKNQVAM +>M_1412 +QTKHNAKVY +>M_1413 +IEWECTMML +>M_1414 +LELEFLCPL +>M_1415 +QLVNRPQSI +>M_1416 +TTKKSGGHY +>M_1417 +IVEHPAGHL +>M_1418 +HRYLWKILI +>M_1419 +SIFEVIWSV +>M_1420 +QHDDGYLEV +>M_1421 +GVAPGLQVV +>M_1422 +YLAMGEEIY +>M_1423 +SVVCHQLGF +>M_1424 +RTKRRVFII +>M_1425 +QMAERALYY +>M_1426 +LISPPQEKV +>M_1427 +HLIEERDTL +>M_1428 +ILKQPSQTL +>M_1429 +LQVVHLNAV +>M_1430 +VHDIARFLY +>M_1431 +RSLPIAIEM +>M_1432 +NVDEVNQIM +>M_1433 +GAGVEISTV +>M_1434 +VPREFKPIL +>M_1435 +GAQPPMPPY +>M_1436 +RADLLIVVF +>M_1437 +WKEDMAVHV +>M_1438 +FIEPHARFY +>M_1439 +DEFSGVPRV +>M_1440 +RVQPAVRAL +>M_1441 +ATTIVTTVY +>M_1442 +FFHNPKPLF +>M_1443 +VTASSGIMI +>M_1444 +HKAHFQYLL +>M_1445 +IGVEAGRTL +>M_1446 +ETMDNGFGH +>M_1447 +DFWYHAVVL +>M_1448 +FHLASAVAL +>M_1449 +LAMYLSKNY +>M_1450 +HLLELPQIL +>M_1451 +VSVHRAPSI +>M_1452 +DPAAASHPI +>M_1453 +SVYLRNNKL +>M_1454 +INREHIPTF +>M_1455 +AQYDDPRNL +>M_1456 +RPVNAYARV +>M_1457 +LARLGALLL +>M_1458 +SHTGTFLLV +>M_1459 +HTVAWSNGH +>M_1460 +TIPDSISKF +>M_1461 +AVFEEQIKV +>M_1462 +FCPLCHNPV +>M_1463 +RVLKCNVHL +>M_1464 +LLLPCPLLL +>M_1465 +QTAEQYVFV +>M_1466 +FLNSMDQQI +>M_1467 +GPARGIAII +>M_1468 +LASLSLKQV +>M_1469 +TSVPHEDTL +>M_1470 +EAEVETEAI +>M_1471 +SSLSNVSQV +>M_1472 +TVQNAMQIV +>M_1473 +WHFIKRHIA +>M_1474 +MTVAGMVLL +>M_1475 +YMAGSDTTY +>M_1476 +FRENFESIY +>M_1477 +LATVILGAV +>M_1478 +LSSGSFATM +>M_1479 +DTNNLGIRI +>M_1480 +CSGCVAQVY +>M_1481 +DHIRNFTTM +>M_1482 +KPFISRTMM +>M_1483 +PADPAQLAV +>M_1484 +YEPDTMEQY +>M_1485 +EPLNDTIAI +>M_1486 +QAPLAPTHM +>M_1487 +IHLDISSFV +>M_1488 +PLMDQVSVI +>M_1489 +HSLHPFPHF +>M_1490 +ITFKELGAL +>M_1491 +AAAREATEV +>M_1492 +RTYHGRLAY +>M_1493 +DADIYGKPM +>M_1494 +KGYRIVVAL +>M_1495 +FNMRDLSDI +>M_1496 +FRKTLLNPV +>M_1497 +YLAMGEEIY +>M_1498 +KPFSHSCNL +>M_1499 +DQATFINMY +>M_1500 +ARFRIRKTI +>M_1501 +RAFSFSLPC +>M_1502 +SHMCNSLLV +>M_1503 +EAEEWVVSY +>M_1504 +KASERFRTQ +>M_1505 +QIMPHAIIF +>M_1506 +LLKHMPKII +>M_1507 +ILSCNADII +>M_1508 +AAQCCHKKV +>M_1509 +TELDSVGPV +>M_1510 +STFCGTLEY +>M_1511 +GLIPPDATI +>M_1512 +SAQRNAAFF +>M_1513 +MDHPSGIAI +>M_1514 +FTVLENLAV +>M_1515 +KPPPQCVTL +>M_1516 +LAIYTLLSL +>M_1517 +RTVKFLMAI +>M_1518 +MCLEASIPL +>M_1519 +SAPQDSKAV +>M_1520 +FIIHHRTHT +>M_1521 +RKEENMESV +>M_1522 +FPQVSELVL +>M_1523 +YQVVAQHIY +>M_1524 +DSAQRNAAF +>M_1525 +KHFNNSSHF +>M_1526 +EANVHGIYF +>M_1527 +LSRVKAQVV +>M_1528 +LENSNRSMV +>M_1529 +ESKSGSPEY +>M_1530 +YTVKYEQKM +>M_1531 +LTYGHDRQL +>M_1532 +LHFHFTACY +>M_1533 +DCNKTAVTI +>M_1534 +QPLHSLSVL +>M_1535 +AACGIIQQV +>M_1536 +WDQRCLHTI +>M_1537 +QLQAFWKHV +>M_1538 +SPHPRRRRL +>M_1539 +FLDKASDLL +>M_1540 +SAWLFVTGI +>M_1541 +FMFEMPFMQ +>M_1542 +VSLQAAEEI +>M_1543 +RANGNPNPT +>M_1544 +ELPAFIEMM +>M_1545 +CVAKCGGTV +>M_1546 +LEYLAPEVL +>M_1547 +TMANNPDVM +>M_1548 +EAVSSASKL +>M_1549 +FSLYRGWAL +>M_1550 +VVIGAPYVV +>M_1551 +LHFHWNWII +>M_1552 +MSACWSFAV +>M_1553 +YIAQNDDEL +>M_1554 +ETINWTLLE +>M_1555 +DQYAICMKY +>M_1556 +HAKRKTATA +>M_1557 +LAAASSTAF +>M_1558 +KAYGRDNTP +>M_1559 +KHLQLYQLF +>M_1560 +WAVMNHFSM +>M_1561 +IERPGGSLL +>M_1562 +YCFGCLSHH +>M_1563 +QGYGGFFVI +>M_1564 +NENDLITNI +>M_1565 +LPVPIIQQL +>M_1566 +RLMHQLLVI +>M_1567 +FHKEVFGMF +>M_1568 +CTVEDGGHV +>M_1569 +EVAQHLATT +>M_1570 +VEHPAGHLV +>M_1571 +WKGSTECKL +>M_1572 +LSDPHLTAV +>M_1573 +ILTELLMVV +>M_1574 +MVHLVPALV +>M_1575 +TILENPYIM +>M_1576 +DHSDSDYDF +>M_1577 +NHLNIAWEL +>M_1578 +FPEDVAVYT +>M_1579 +YMTSSGRRF +>M_1580 +SSVPLRSSV +>M_1581 +LAAPPPLTE +>M_1582 +VVASQPAHV +>M_1583 +SMLDPHGHL +>M_1584 +LVVADIHSM +>M_1585 +LLYMAFVRL +>M_1586 +VVTVMVTTV +>M_1587 +KLIDVNHYV +>M_1588 +FTQYLGLSM +>M_1589 +FRGKHDCAL +>M_1590 +EVFRHKLAM +>M_1591 +RSIRLSQEI +>M_1592 +HTIQKAKHM +>M_1593 +PSGRPALAY +>M_1594 +WQDHIRLEV +>M_1595 +VLLDLRPSI +>M_1596 +AVYSTCVLV +>M_1597 +LALSLPACF +>M_1598 +NQCPCSSDI +>M_1599 +SIDPKTGVV +>M_1600 +AAASHPILL +>M_1601 +RLLKHMPKI +>M_1602 +LSLTGLQVL +>M_1603 +MSQEEKVAY +>M_1604 +MIENLEHHI +>M_1605 +IIATGLVTL +>M_1606 +SADCGCCPM +>M_1607 +CAELLSHTV +>M_1608 +HISEEYGLL +>M_1609 +YSFCPLCHN +>M_1610 +LPCRSLTRV +>M_1611 +KVLQHGRLY +>M_1612 +FLCDEEPLL +>M_1613 +IPCLDDVTV +>M_1614 +LASEAVSSA +>M_1615 +TPTPGFSSM +>M_1616 +FYLVAYAAM +>M_1617 +YLKSPECFL +>M_1618 +KVNTATTTM +>M_1619 +LPVSTKCTV +>M_1620 +SVRYAGPLY +>M_1621 +HTIQKAKHM +>M_1622 +TFRDVAVEF +>M_1623 +DEKDLWEYI +>M_1624 +DPADPTRDL +>M_1625 +EAEEWVVSY +>M_1626 +CAFTVLENL +>M_1627 +SWMEGQVTI +>M_1628 +MTAVGYGDM +>M_1629 +VSEDAKQRI +>M_1630 +DVDEDGYIM +>M_1631 +IVQCRVLNI +>M_1632 +IASLLENIL +>M_1633 +SRNWLKSIL +>M_1634 +KVKPTLAMY +>M_1635 +YTMGIIFVL +>M_1636 +ELKSPVKMI +>M_1637 +LSLGAPSPL +>M_1638 +QSIRAATEV +>M_1639 +YMAATLLEF +>M_1640 +CSDGSDEDA +>M_1641 +SYLEDVRLI +>M_1642 +QVYVGDSDI +>M_1643 +VIDQCLKKI +>M_1644 +YPDWIRDNM +>M_1645 +RATSFGKCF +>M_1646 +KAGSLGIIL +>M_1647 +VAQQSRLVF +>M_1648 +DCQSHRLTV +>M_1649 +MPNVLWDLV +>M_1650 +MSWLTPLMI +>M_1651 +DANNVTCVW +>M_1652 +KLLQCMSRV +>M_1653 +VHLPLAVAL +>M_1654 +SLYSLDATL +>M_1655 +FTTTQWSSL +>M_1656 +VALRDLGCL +>M_1657 +MVACGGTVY +>M_1658 +EMFQRYSAF +>M_1659 +DAACGIWSL +>M_1660 +FTILPCTCY +>M_1661 +IIYTMGIIF +>M_1662 +RVYNIRGDM +>M_1663 +RNDPELPTV +>M_1664 +HSDSDYDFV +>M_1665 +VLGEHHHHV +>M_1666 +HVVDEREQM +>M_1667 +GQFPYMGEV +>M_1668 +LPPEMYVYL +>M_1669 +EAYQKQLCF +>M_1670 +AATGPGEVL +>M_1671 +DLYATAFLV +>M_1672 +GFDWKSVFI +>M_1673 +FVVFSFFFV +>M_1674 +GRDVVHHLL +>M_1675 +VTLRWYLAM +>M_1676 +LVAQYDLTV +>M_1677 +RLIRGDAVV +>M_1678 +FQYLVVHTE +>M_1679 +KHYLMTRTL +>M_1680 +FVMEHSNIV +>M_1681 +HQMENNGWV +>M_1682 +NATYSGYVY +>M_1683 +KVKNSASVM +>M_1684 +KQDKCFAFI +>M_1685 +AQRPWPRVL +>M_1686 +MAATLLEFF +>M_1687 +DPNTVSNSI +>M_1688 +LPVSGGHVM +>M_1689 +MLDDAPRLL +>M_1690 +IPPDATIYF +>M_1691 +LHDALEVDL +>M_1692 +MMEKLYPGY +>M_1693 +IPFLFFTDM +>M_1694 +YKLCFNTFF +>M_1695 +YVTMVIDRL +>M_1696 +TIYFDVVLL +>M_1697 +SAWLRAISL +>M_1698 +HLWPGGLSL +>M_1699 +FGYMTQQRM +>M_1700 +HVYILRAVF +>M_1701 +LYIPALAVL +>M_1702 +DPMVPLQGV +>M_1703 +FTEEGFCAI +>M_1704 +FFNDDCCEL +>M_1705 +FLFHPLEFC +>M_1706 +VVMWWMGIL +>M_1707 +KTFHHKSNF +>M_1708 +QRPWPRVLL +>M_1709 +IRVQEASTI +>M_1710 +DLIDYARYM +>M_1711 +VTVRGFWIY +>M_1712 +FMDEHAAER +>M_1713 +SISDTYDPY +>M_1714 +DTNDNVPEF +>M_1715 +YNCTCGCSM +>M_1716 +LLLLASATV +>M_1717 +LYMAFVRLL +>M_1718 +SAEVQLSKI +>M_1719 +ITACLSVLI +>M_1720 +LPETKGVTL +>M_1721 +MSQEEKVAY +>M_1722 +MASPQAEST +>M_1723 +MSFELPYHC +>M_1724 +RWNDTRATV +>M_1725 +LRHERAVSM +>M_1726 +LHLLVACTI +>M_1727 +YGHDRQLCL +>M_1728 +DATIYFDVV +>M_1729 +IVCDIKEKL +>M_1730 +RPAQFLHEM +>M_1731 +WHFVYKSGM +>M_1732 +EVDPIGNLY +>M_1733 +RTDGNSHEA +>M_1734 +KHMPKIIHL +>M_1735 +DVHDIARFL +>M_1736 +PATRPLHVL +>M_1737 +LLHSNRSQI +>M_1738 +PARSGIFKI +>M_1739 +AALTPTEEM +>M_1740 +ISAYMAATL +>M_1741 +IMMSDEERI +>M_1742 +KRQEGMVPV +>M_1743 +LQKRATEEI +>M_1744 +GKDKMTHLL +>M_1745 +AQLPPWAPL +>M_1746 +FFCEVPVLL +>M_1747 +RAHKKAITT +>M_1748 +FDWKSVFII +>M_1749 +CLFRAARLI +>M_1750 +MIEDFLRRF +>M_1751 +TTTERWLRV +>M_1752 +FFKDKATSK +>M_1753 +HFFDAFRKF +>M_1754 +GALGLNRPV +>M_1755 +YRTKCTLGL +>M_1756 +MTVAGMVLL +>M_1757 +KTLSKTAHL +>M_1758 +NLYIFATCL +>M_1759 +GFDTSSSSL +>M_1760 +TPVLCGQPI +>M_1761 +WCAPGKPTL +>M_1762 +ILHNQIQQV +>M_1763 +VVLSPEVEV +>M_1764 +DSIHQVGMY +>M_1765 +NHSGVGAFW +>M_1766 +HNLEPHGYV +>M_1767 +PSLNATTIV +>M_1768 +ISGFKGDTV +>M_1769 +HIASSTTSI +>M_1770 +HTLHAHDPV +>M_1771 +WTDYGQVFT +>M_1772 +ELFRRGLRY +>M_1773 +SASRTKRRV +>M_1774 +NSGPSRSML +>M_1775 +ESADKTAYL +>M_1776 +TELEKFSKV +>M_1777 +FHAQVCSLY +>M_1778 +LVVEHVLTT +>M_1779 +RSYWLRLFL +>M_1780 +DVDEKQLLV +>M_1781 +CAIISLIFI +>M_1782 +SQLEMPETL +>M_1783 +NLEDVGRHL +>M_1784 +HLRRIGRFI +>M_1785 +KYDPDVVVM +>M_1786 +KDDDCITLV +>M_1787 +YDVTDSRII +>M_1788 +MLLHQVAAY +>M_1789 +THQSGFSVI +>M_1790 +DLQPVREAI +>M_1791 +FAGSTQSDL +>M_1792 +GSYREAQSL +>M_1793 +HFMPRIQRL +>M_1794 +LPLKRPGKL +>M_1795 +MAFPEGYGT +>M_1796 +DMQDLTEFL +>M_1797 +VDFSSEVTV +>M_1798 +MEVDPIGNL +>M_1799 +ISRNCNSRM +>M_1800 +YSLIDNFVM +>M_1801 +FEMPFMQTG +>M_1802 +SHELVMYIW +>M_1803 +IIVSYMLII +>M_1804 +AAAAAVAAL +>M_1805 +LVDQKAKEV +>M_1806 +FFSLLATVI +>M_1807 +IYGKPMPTI +>M_1808 +YMLERLIEQ +>M_1809 +CIADFLEHM +>M_1810 +LPYPGSSQA +>M_1811 +EAWQCQPVL +>M_1812 +VATSTAQLL +>M_1813 +VKYTPKLEI +>M_1814 +RVSAKRVSV +>M_1815 +NTWTRQMGY +>M_1816 +LDFACHFTV +>M_1817 +HVRIHPKLV +>M_1818 +LQQNCAAYL +>M_1819 +DAVGNMLNL +>M_1820 +WQAISLMVI +>M_1821 +WLWKLSAVV +>M_1822 +LAPTHMPEL +>M_1823 +YAQTPSKTP +>M_1824 +LLLCFLAAM +>M_1825 +HMPKIIHLV +>M_1826 +AQLPSYMHI diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_118562_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_118562_1_T_iedb.xml new file mode 100755 index 00000000..e5875335 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_118562_1_T_iedb.xml @@ -0,0 +1,45067 @@ + + + + blastp + BLASTP 2.2.30+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta + Query_1 + M_471 + 9 + + + BLOSUM62 + 100000000 + 11 + 1 + F + + + + + 1 + Query_1 + M_471 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 2 + Query_2 + M_472 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 3 + Query_3 + M_473 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 4 + Query_4 + M_474 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 5 + Query_5 + M_475 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 6 + Query_6 + M_476 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 7 + Query_7 + M_477 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 8 + Query_8 + M_478 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 9 + Query_9 + M_479 + 9 + + + 1 + gnl|BL_ORD_ID|1152 + 75718|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 + 1152 + 11 + + + 1 + 12.3122 + 20 + 42.1867 + 3 + 8 + 1 + 6 + 0 + 0 + 4 + 4 + 0 + 6 + YQELPT + YSEHPT + Y E PT + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 10 + Query_10 + M_480 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 11 + Query_11 + M_481 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 12 + Query_12 + M_482 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 13 + Query_13 + M_483 + 9 + + + 1 + gnl|BL_ORD_ID|1903 + 180641|polyprotein|AFJ91714.1|Dengue virus 1|11053 + 1903 + 9 + + + 1 + 12.6974 + 21 + 37.875 + 1 + 7 + 1 + 7 + 0 + 0 + 4 + 6 + 0 + 7 + MAISVVK + MALSIVS + MA+S+V + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 14 + Query_14 + M_484 + 9 + + + 1 + gnl|BL_ORD_ID|33 + 2506|M protein, serotype 5 precursor|P02977.2|Streptococcus pyogenes serotype M5|301449 + 33 + 9 + + + 1 + 14.6234 + 26 + 1.88321 + 2 + 7 + 1 + 6 + 0 + 0 + 6 + 6 + 0 + 6 + ALEKLN + ALEKLN + ALEKLN + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 15 + Query_15 + M_485 + 9 + + + 1 + gnl|BL_ORD_ID|2009 + 183781|polyprotein|AGO67248.1|Dengue virus 2|11060 + 2009 + 10 + + + 1 + 13.4678 + 23 + 8.61729 + 3 + 9 + 3 + 9 + 0 + 0 + 3 + 6 + 0 + 7 + DMERHHI + DLEKRHV + D+E+ H+ + + + + + 2 + gnl|BL_ORD_ID|2055 + 184755|polyprotein|AGO67248.1|Dengue virus 2|11060 + 2055 + 9 + + + 1 + 13.4678 + 23 + 8.87313 + 3 + 9 + 2 + 8 + 0 + 0 + 3 + 6 + 0 + 7 + DMERHHI + DLEKRHV + D+E+ H+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 16 + Query_16 + M_486 + 9 + + + 1 + gnl|BL_ORD_ID|4 + 327|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis|1773 + 4 + 20 + + + 1 + 13.853 + 24 + 4.4203 + 2 + 9 + 2 + 9 + 0 + 0 + 4 + 8 + 0 + 8 + ANRRKEEV + ANKQKQEL + AN++K+E+ + + + + + 2 + gnl|BL_ORD_ID|53 + 3935|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis|1773 + 53 + 20 + + + 1 + 13.853 + 24 + 4.97811 + 2 + 9 + 12 + 19 + 0 + 0 + 4 + 8 + 0 + 8 + ANRRKEEV + ANKQKQEL + AN++K+E+ + + + + + 3 + gnl|BL_ORD_ID|304 + 20415|circumsporozoite protein|AAN87606.1|Plasmodium falciparum|5833 + 304 + 20 + + + 1 + 13.4678 + 23 + 10.3889 + 2 + 9 + 11 + 18 + 0 + 0 + 4 + 7 + 0 + 8 + ANRRKEEV + ANKPKDEL + AN+ K+E+ + + + + + 4 + gnl|BL_ORD_ID|434 + 26870|Circumsporozoite protein precursor|P02893.1|Plasmodium falciparum|5833 + 434 + 20 + + + 1 + 13.4678 + 23 + 11.4655 + 2 + 9 + 6 + 13 + 0 + 0 + 4 + 7 + 0 + 8 + ANRRKEEV + ANKPKDEL + AN+ K+E+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 17 + Query_17 + M_487 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 18 + Query_18 + M_488 + 9 + + + 1 + gnl|BL_ORD_ID|530 + 32663|small hydrophobic protein|AAM12943.1|Human metapneumovirus|162145 + 530 + 10 + + + 1 + 10.7714 + 16 + 390.249 + 2 + 9 + 3 + 10 + 0 + 0 + 4 + 5 + 0 + 8 + ALGPGHTV + AVGVYHIV + A+G H V + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 19 + Query_19 + M_489 + 9 + + + 1 + gnl|BL_ORD_ID|1621 + 145860|Protein E6|P04019.1|Human papillomavirus type 11|10580 + 1621 + 9 + + + 1 + 15.3938 + 28 + 0.556982 + 3 + 9 + 1 + 7 + 0 + 0 + 6 + 6 + 0 + 7 + KVLIRTY + KVLIRCY + KVLIR Y + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 20 + Query_20 + M_490 + 9 + + + 1 + gnl|BL_ORD_ID|1265 + 98603|trans-sialidase, putative|EAN82716.1|Trypanosoma cruzi|5693 + 1265 + 9 + + + 1 + 14.2382 + 25 + 4.3647 + 2 + 9 + 2 + 9 + 0 + 0 + 4 + 7 + 0 + 8 + SDDNDAFY + TDNNRSFY + +D+N +FY + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 21 + Query_21 + M_491 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 22 + Query_22 + M_492 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 23 + Query_23 + M_493 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 24 + Query_24 + M_494 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 25 + Query_25 + M_495 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 26 + Query_26 + M_496 + 9 + + + 1 + gnl|BL_ORD_ID|1654 + 146570|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 + 1654 + 17 + + + 1 + 15.3938 + 28 + 0.651332 + 2 + 9 + 1 + 8 + 0 + 0 + 5 + 6 + 0 + 8 + SFDGMWKV + SWDQMWKC + S+D MWK + + + + + 2 + gnl|BL_ORD_ID|1653 + 146569|polyprotein|ADF97231.1|Hepatitis C virus subtype 3a|356426 + 1653 + 17 + + + 1 + 13.0826 + 22 + 15.9108 + 2 + 9 + 1 + 8 + 0 + 0 + 4 + 5 + 0 + 8 + SFDGMWKV + SWDETWKC + S+D WK + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 27 + Query_27 + M_497 + 9 + + + 1 + gnl|BL_ORD_ID|382 + 23573|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 + 382 + 9 + + + 1 + 13.0826 + 22 + 14.7007 + 4 + 9 + 1 + 6 + 0 + 0 + 3 + 5 + 0 + 6 + HQVGMY + HAVGLF + H VG++ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 28 + Query_28 + M_498 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 29 + Query_29 + M_499 + 9 + + + 1 + gnl|BL_ORD_ID|743 + 47946|envelope glycoprotein|AAC28452.1|Human immunodeficiency virus 1|11676 + 743 + 20 + + + 1 + 14.2382 + 25 + 4.20027 + 4 + 9 + 1 + 6 + 0 + 0 + 3 + 6 + 0 + 6 + PVPLYY + PIPIHY + P+P++Y + + + + + 2 + gnl|BL_ORD_ID|1001 + 65817|envelope glycoprotein|AAL59843.1|Human immunodeficiency virus 1|11676 + 1001 + 20 + + + 1 + 13.853 + 24 + 5.41768 + 4 + 9 + 11 + 16 + 0 + 0 + 3 + 6 + 0 + 6 + PVPLYY + PIPIHY + P+P++Y + + + + + 3 + gnl|BL_ORD_ID|1171 + 79300|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 + 1171 + 15 + + + 1 + 12.6974 + 21 + 29.7824 + 1 + 6 + 1 + 6 + 0 + 0 + 4 + 5 + 0 + 6 + LAFPVP + LSFPDP + L+FP P + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 30 + Query_30 + M_500 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 31 + Query_31 + M_501 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 32 + Query_32 + M_502 + 9 + + + 1 + gnl|BL_ORD_ID|255 + 17117|matrix protein|AAN09804.1|Measles virus strain Edmonston|11235 + 255 + 9 + + + 1 + 12.6974 + 21 + 27.8632 + 1 + 6 + 3 + 8 + 0 + 0 + 4 + 5 + 0 + 6 + YMDLMG + YMSLLG + YM L+G + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 33 + Query_33 + M_503 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 34 + Query_34 + M_504 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 35 + Query_35 + M_505 + 9 + + + 1 + gnl|BL_ORD_ID|41 + 2903|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 + 41 + 15 + + + 1 + 13.853 + 24 + 5.48445 + 1 + 9 + 6 + 14 + 0 + 0 + 4 + 7 + 0 + 9 + FVYLHLNMV + LIHLHQNIV + ++LH N+V + + + + + 2 + gnl|BL_ORD_ID|316 + 20921|polyprotein|BAA03375.1|Hepatitis C virus|11103 + 316 + 15 + + + 1 + 13.4678 + 23 + 11.2975 + 1 + 9 + 2 + 10 + 0 + 0 + 4 + 7 + 0 + 9 + FVYLHLNMV + LIHLHQNIV + ++LH N+V + + + + + 3 + gnl|BL_ORD_ID|1816 + 177843|polyprotein|ACZ60102.1|Hepatitis C virus subtype 3a|356426 + 1816 + 17 + + + 1 + 13.0826 + 22 + 17.2821 + 1 + 9 + 1 + 9 + 0 + 0 + 4 + 7 + 0 + 9 + FVYLHLNMV + LIHLHQNIV + ++LH N+V + + + + + 4 + gnl|BL_ORD_ID|1016 + 67503|Genome polyprotein|P26662.3|Hepatitis C virus|11103 + 1016 + 10 + + + 1 + 12.3122 + 20 + 47.8854 + 1 + 7 + 2 + 8 + 0 + 0 + 4 + 5 + 0 + 7 + FVYLHLN + YVYDHLT + +VY HL + + + + + 5 + gnl|BL_ORD_ID|573 + 36062|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 + 573 + 20 + + + 1 + 12.3122 + 20 + 48.9705 + 1 + 7 + 8 + 14 + 0 + 0 + 4 + 5 + 0 + 7 + FVYLHLN + YVYNHLT + +VY HL + + + + + 6 + gnl|BL_ORD_ID|279 + 18678|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 + 279 + 15 + + + 1 + 12.3122 + 20 + 55.7176 + 1 + 7 + 7 + 13 + 0 + 0 + 4 + 5 + 0 + 7 + FVYLHLN + YVYNHLT + +VY HL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 36 + Query_36 + M_506 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 37 + Query_37 + M_507 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 38 + Query_38 + M_508 + 9 + + + 1 + gnl|BL_ORD_ID|949 + 62504|HBsAg protein|ABF71024.1|Hepatitis B virus|10407 + 949 + 9 + + + 1 + 12.6974 + 21 + 31.9494 + 3 + 9 + 3 + 9 + 0 + 0 + 3 + 6 + 0 + 7 + WKNMDFL + WTSLNFL + W +++FL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 39 + Query_39 + M_509 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 40 + Query_40 + M_510 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 41 + Query_41 + M_511 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 42 + Query_42 + M_512 + 9 + + + 1 + gnl|BL_ORD_ID|2137 + 187106|Vpr protein|BAA93983.1|Human immunodeficiency virus 1|11676 + 2137 + 9 + + + 1 + 14.2382 + 25 + 4.1461 + 5 + 9 + 5 + 9 + 0 + 0 + 4 + 5 + 0 + 5 + FPRIY + FPRIW + FPRI+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 43 + Query_43 + M_513 + 9 + + + 1 + gnl|BL_ORD_ID|1633 + 146249|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 + 1633 + 17 + + + 1 + 15.0086 + 27 + 0.838218 + 3 + 9 + 9 + 15 + 0 + 0 + 4 + 6 + 0 + 7 + IFWTVYY + VMWTVYH + + WTVY+ + + + + + 2 + gnl|BL_ORD_ID|66 + 4910|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 + 66 + 20 + + + 1 + 15.0086 + 27 + 1.19565 + 3 + 9 + 7 + 13 + 0 + 0 + 4 + 6 + 0 + 7 + IFWTVYY + VCWTVYH + + WTVY+ + + + + + 3 + gnl|BL_ORD_ID|65 + 4909|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 + 65 + 15 + + + 1 + 15.0086 + 27 + 1.24275 + 3 + 9 + 7 + 13 + 0 + 0 + 4 + 6 + 0 + 7 + IFWTVYY + VCWTVYH + + WTVY+ + + + + + 4 + gnl|BL_ORD_ID|1632 + 146246|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 + 1632 + 17 + + + 1 + 14.6234 + 26 + 1.81173 + 3 + 9 + 9 + 15 + 0 + 0 + 4 + 6 + 0 + 7 + IFWTVYY + VCWTVYH + + WTVY+ + + + + + 5 + gnl|BL_ORD_ID|1674 + 148619|unnamed protein product|BAA14233.1|Hepatitis C virus|11103 + 1674 + 45 + + + 1 + 14.2382 + 25 + 3.72943 + 3 + 8 + 40 + 45 + 0 + 0 + 4 + 5 + 0 + 6 + IFWTVY + VCWTVY + + WTVY + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 44 + Query_44 + M_514 + 9 + + + 1 + gnl|BL_ORD_ID|1731 + 150556|polyprotein|AGW21594.1|Dengue virus 1|11053 + 1731 + 10 + + + 1 + 13.853 + 24 + 6.99268 + 3 + 8 + 4 + 9 + 0 + 0 + 3 + 5 + 0 + 6 + DPNQCV + DPRRCL + DP +C+ + + + + + 2 + gnl|BL_ORD_ID|859 + 56310|polyprotein|AGO67248.1|Dengue virus 2|11060 + 859 + 10 + + + 1 + 13.4678 + 23 + 9.56649 + 3 + 8 + 4 + 9 + 0 + 0 + 3 + 5 + 0 + 6 + DPNQCV + DPRRCM + DP +C+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 45 + Query_45 + M_515 + 9 + + + 1 + gnl|BL_ORD_ID|1174 + 79351|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 + 1174 + 17 + + + 1 + 15.0086 + 27 + 1.02766 + 2 + 9 + 5 + 12 + 0 + 0 + 5 + 5 + 0 + 8 + AFWAGSVV + TLWGGSVV + W GSVV + + + + + 2 + gnl|BL_ORD_ID|2018 + 184130|polyprotein|AFP27208.1|Dengue virus 4|11070 + 2018 + 10 + + + 1 + 12.6974 + 21 + 24.356 + 3 + 8 + 5 + 10 + 0 + 0 + 3 + 4 + 0 + 6 + FWAGSV + LWCGSL + W GS+ + + + + + 3 + gnl|BL_ORD_ID|1921 + 180718|polyprotein|AFP27208.1|Dengue virus 4|11070 + 1921 + 9 + + + 1 + 12.6974 + 21 + 27.8632 + 3 + 8 + 4 + 9 + 0 + 0 + 3 + 4 + 0 + 6 + FWAGSV + LWCGSL + W GS+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 46 + Query_46 + M_516 + 9 + + + 1 + gnl|BL_ORD_ID|1756 + 154164|tegument protein|CAB06732.1|Human alphaherpesvirus 2|10310 + 1756 + 15 + + + 1 + 15.779 + 29 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0 + 4 + 5 + 0 + 6 + YLMEFG + YLVSFG + YL+ FG + + + + + 2 + gnl|BL_ORD_ID|201 + 15061|core protein|BAF42671.1|Hepatitis B virus|10407 + 201 + 9 + + + 1 + 13.0826 + 22 + 16.035 + 1 + 6 + 2 + 7 + 0 + 0 + 4 + 5 + 0 + 6 + YLMEFG + YLVSFG + YL+ FG + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 80 + Query_80 + M_550 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 81 + Query_81 + M_551 + 9 + + + 1 + gnl|BL_ORD_ID|1351 + 108127|Genome polyprotein|P26664.3|Hepatitis C virus|11103 + 1351 + 10 + + + 1 + 14.2382 + 25 + 4.08767 + 3 + 9 + 3 + 9 + 0 + 0 + 5 + 6 + 0 + 7 + LGVGTAL + LGIGTVL + LG+GT L + + + + + 2 + gnl|BL_ORD_ID|1361 + 108169|Genome polyprotein|P26664.3|Hepatitis C virus|11103 + 1361 + 10 + + + 1 + 13.853 + 24 + 4.61192 + 3 + 9 + 4 + 10 + 0 + 0 + 5 + 6 + 0 + 7 + LGVGTAL + LGIGTVL + LG+GT L + + + + + 3 + gnl|BL_ORD_ID|1362 + 108171|polyprotein|AAF65953.1|Hepatitis C virus|11103 + 1362 + 10 + + + 1 + 13.853 + 24 + 4.94204 + 3 + 9 + 4 + 10 + 0 + 0 + 5 + 6 + 0 + 7 + LGVGTAL + LGIGTVL + LG+GT L + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 82 + Query_82 + M_552 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 83 + Query_83 + M_553 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 84 + Query_84 + M_554 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 85 + Query_85 + M_555 + 9 + + + 1 + gnl|BL_ORD_ID|1633 + 146249|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 + 1633 + 17 + + + 1 + 15.0086 + 27 + 0.838218 + 3 + 9 + 9 + 15 + 0 + 0 + 4 + 6 + 0 + 7 + IFWTVYY + VMWTVYH + + WTVY+ + + + + + 2 + gnl|BL_ORD_ID|66 + 4910|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 + 66 + 20 + + + 1 + 15.0086 + 27 + 1.19565 + 3 + 9 + 7 + 13 + 0 + 0 + 4 + 6 + 0 + 7 + IFWTVYY + VCWTVYH + + WTVY+ + + + + + 3 + gnl|BL_ORD_ID|65 + 4909|HCV-1|AAA45676.1|Hepatitis C virus 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Query_93 + M_563 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 94 + Query_94 + M_564 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 95 + Query_95 + M_565 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 96 + Query_96 + M_566 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 97 + Query_97 + M_567 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 98 + Query_98 + M_568 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 99 + Query_99 + M_569 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 100 + Query_100 + M_570 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 101 + Query_101 + M_571 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 102 + Query_102 + M_572 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 103 + Query_103 + M_573 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 104 + Query_104 + M_574 + 9 + + + 1 + gnl|BL_ORD_ID|777 + 51685|Nuclear antigen EBNA-3C|Q69140.1|Human gammaherpesvirus 4|10376 + 777 + 10 + + + 1 + 12.3122 + 20 + 49.5064 + 3 + 9 + 1 + 7 + 0 + 0 + 4 + 5 + 0 + 7 + QEGFLAV + QNGALAI + Q G LA+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 105 + Query_105 + M_575 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 106 + Query_106 + M_576 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 107 + Query_107 + M_577 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 108 + Query_108 + M_578 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 109 + 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kDa early secretory antigenic target|P0A564.2|Mycobacterium tuberculosis|1773 + 656 + 8 + + + 1 + 13.4678 + 23 + 11.0044 + 3 + 9 + 2 + 8 + 0 + 0 + 5 + 6 + 0 + 7 + RNLIRTI + QNLARTI + +NL RTI + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 188 + Query_188 + M_658 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 189 + Query_189 + M_659 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 190 + Query_190 + M_660 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 191 + Query_191 + M_661 + 9 + + + 1 + gnl|BL_ORD_ID|475 + 29186|polyprotein precursor|NP_041724.2|West Nile virus|11082 + 475 + 9 + + + 1 + 13.853 + 24 + 7.45662 + 1 + 9 + 1 + 9 + 0 + 0 + 5 + 7 + 0 + 9 + ISYTEVPTY + ITYTDVLRY + I+YT+V Y + + + + + 2 + gnl|BL_ORD_ID|1152 + 75718|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 + 1152 + 11 + + + 1 + 13.4678 + 23 + 11.9608 + 3 + 9 + 1 + 7 + 0 + 0 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+ 6 + EPKKKP + EPGKNP + EP K P + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 199 + Query_199 + M_669 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 200 + Query_200 + M_670 + 9 + + + 1 + gnl|BL_ORD_ID|707 + 43447|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 + 707 + 20 + + + 1 + 12.6974 + 21 + 22.9279 + 1 + 9 + 5 + 13 + 0 + 0 + 5 + 5 + 0 + 9 + FFFHNPKPL + IFFFNPGEL + FF NP L + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 201 + Query_201 + M_671 + 9 + + + 1 + gnl|BL_ORD_ID|1121 + 74407|polyprotein|AAU89634.1|Hepatitis C virus subtype 2a|31649 + 1121 + 9 + + + 1 + 12.3122 + 20 + 54.8462 + 2 + 7 + 4 + 9 + 0 + 0 + 2 + 4 + 0 + 6 + HWNWII + RWEWVV + W W++ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 202 + Query_202 + M_672 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 203 + Query_203 + M_673 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 204 + Query_204 + M_674 + 9 + + + 1 + gnl|BL_ORD_ID|1435 + 116781|Nucleoprotein|P05133.1|Hantaan virus 76-118|11602 + 1435 + 15 + + + 1 + 12.6974 + 21 + 26.9941 + 1 + 6 + 8 + 13 + 0 + 0 + 4 + 4 + 0 + 6 + YQHYFR + YQSYLR + YQ Y R + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 205 + Query_205 + M_675 + 9 + + + 1 + gnl|BL_ORD_ID|2259 + 294287|gag protein|ABI20203.1|Human immunodeficiency virus 1|11676 + 2259 + 17 + + + 1 + 13.4678 + 23 + 9.7917 + 3 + 9 + 8 + 14 + 0 + 0 + 4 + 7 + 0 + 7 + NSMINTM + NTMLNTV + N+M+NT+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 206 + Query_206 + M_676 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 207 + Query_207 + M_677 + 9 + + + 1 + gnl|BL_ORD_ID|1206 + 96156|polyprotein|ABR25251.1|Hepatitis C virus (isolate H77)|63746 + 1206 + 21 + + + 1 + 13.0826 + 22 + 17.0133 + 2 + 9 + 6 + 13 + 0 + 0 + 4 + 5 + 0 + 8 + VDYPGDPV + VDFSLDPT + VD+ DP + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 208 + Query_208 + M_678 + 9 + + + 1 + gnl|BL_ORD_ID|1258 + 98254|trans-sialidase, putative|EAN81042.1|Trypanosoma cruzi|5693 + 1258 + 9 + + + 1 + 12.6974 + 21 + 26.4654 + 2 + 7 + 4 + 9 + 0 + 0 + 4 + 5 + 0 + 6 + TAPLYS + TLPVYS + T P+YS + + + + + 2 + gnl|BL_ORD_ID|1255 + 98242|trans-sialidase, putative|EAN81042.1|Trypanosoma cruzi|5693 + 1255 + 9 + + + 1 + 12.6974 + 21 + 27.8632 + 2 + 7 + 3 + 8 + 0 + 0 + 4 + 5 + 0 + 6 + TAPLYS + TLPVYS + T P+YS + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 209 + Query_209 + M_679 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 210 + Query_210 + M_680 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 211 + Query_211 + M_681 + 9 + + + 1 + gnl|BL_ORD_ID|701 + 42797|6 kDa early secretory antigenic target|P0A564.2|Mycobacterium tuberculosis|1773 + 701 + 20 + + + 1 + 13.853 + 24 + 5.6992 + 1 + 5 + 4 + 8 + 0 + 0 + 4 + 4 + 0 + 5 + QAWNF + QQWNF + Q WNF + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 212 + Query_212 + M_682 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 213 + Query_213 + M_683 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 214 + Query_214 + M_684 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 215 + Query_215 + M_685 + 9 + + + 1 + gnl|BL_ORD_ID|126 + 8920|M protein, serotype 5 precursor|P02977.2|Streptococcus pyogenes serotype M5|301449 + 126 + 18 + + + 1 + 11.5418 + 18 + 105.162 + 1 + 8 + 3 + 10 + 0 + 0 + 4 + 7 + 0 + 8 + MAKQIKTK + LAKEQKSK + +AK+ K+K + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 216 + Query_216 + M_686 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 217 + Query_217 + M_687 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 218 + Query_218 + M_688 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 219 + Query_219 + M_689 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 220 + Query_220 + M_690 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 221 + Query_221 + M_691 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 222 + Query_222 + M_692 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 223 + Query_223 + M_693 + 9 + + + 1 + gnl|BL_ORD_ID|386 + 23621|Genome polyprotein|P26664.3|Hepatitis C virus (isolate 1)|11104 + 386 + 11 + + + 1 + 14.2382 + 25 + 3.03901 + 3 + 8 + 1 + 6 + 0 + 0 + 5 + 5 + 0 + 6 + HSGAGK + HDGAGK + H GAGK + + + + + 2 + gnl|BL_ORD_ID|1874 + 180503|polyprotein|AGO67248.1|Dengue virus 2|11060 + 1874 + 10 + + + 1 + 14.2382 + 25 + 3.21576 + 3 + 8 + 1 + 6 + 0 + 0 + 5 + 5 + 0 + 6 + HSGAGK + HPGAGK + H GAGK + + + + + 3 + gnl|BL_ORD_ID|385 + 23620|Genome polyprotein|SRC279960|Hepatitis C virus genotype 1|41856 + 385 + 10 + + + 1 + 14.2382 + 25 + 3.56308 + 3 + 8 + 1 + 6 + 0 + 0 + 5 + 5 + 0 + 6 + HSGAGK + HDGAGK + H GAGK + + + + + 4 + gnl|BL_ORD_ID|384 + 23619|Genome polyprotein|P27958.3|Hepatitis C virus (isolate H)|11108 + 384 + 9 + + + 1 + 14.2382 + 25 + 3.87216 + 3 + 8 + 1 + 6 + 0 + 0 + 5 + 5 + 0 + 6 + HSGAGK + HDGAGK + H GAGK + + + + + 5 + gnl|BL_ORD_ID|1015 + 67471|Genome polyprotein|Q99IB8.3|Hepatitis C virus JFH-1|356411 + 1015 + 9 + + + 1 + 13.853 + 24 + 5.45887 + 2 + 9 + 1 + 8 + 0 + 0 + 5 + 6 + 0 + 8 + THSGAGKF + TYSTYGKF + T+S GKF + + + + + 6 + gnl|BL_ORD_ID|474 + 29182|polyprotein|BAD73991.1|Hepatitis C virus subtype 1b|31647 + 474 + 9 + + + 1 + 13.853 + 24 + 5.45887 + 2 + 9 + 2 + 9 + 0 + 0 + 5 + 6 + 0 + 8 + THSGAGKF + TYSTYGKF + T+S GKF + + + + + 7 + gnl|BL_ORD_ID|1995 + 183598|polyprotein|AGW21594.1|Dengue virus 1|11053 + 1995 + 10 + + + 1 + 13.0826 + 22 + 15.2954 + 3 + 8 + 1 + 6 + 0 + 0 + 4 + 5 + 0 + 6 + HSGAGK + HPGSGK + H G+GK + + + + + 8 + gnl|BL_ORD_ID|847 + 55336|EBNA-1|YP_401677.1|Human gammaherpesvirus 4|10376 + 847 + 15 + + + 1 + 12.3122 + 20 + 58.4135 + 2 + 7 + 10 + 15 + 0 + 0 + 4 + 4 + 0 + 6 + THSGAG + THGGTG + TH G G + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 224 + Query_224 + M_694 + 9 + + + 1 + gnl|BL_ORD_ID|1770 + 155131|ribonucleotide reductase large subunit|CAB06725.1|Human alphaherpesvirus 2|10310 + 1770 + 15 + + + 1 + 13.4678 + 23 + 10.0248 + 4 + 8 + 4 + 8 + 0 + 0 + 4 + 4 + 0 + 5 + RYFCR + EYFCR + YFCR + + + + + 2 + gnl|BL_ORD_ID|469 + 28484|Protein E6|P03126.1|Human papillomavirus type 16|333760 + 469 + 9 + + + 1 + 13.0826 + 22 + 21.8994 + 2 + 7 + 3 + 8 + 0 + 0 + 3 + 6 + 0 + 6 + KYRYFC + EYRHYC + +YR++C + + + + + 3 + gnl|BL_ORD_ID|1406 + 110846|E6 protein|CAB45108.1|Human papillomavirus type 16|333760 + 1406 + 9 + + + 1 + 13.0826 + 22 + 22.2806 + 2 + 7 + 1 + 6 + 0 + 0 + 3 + 6 + 0 + 6 + KYRYFC + EYRHYC + +YR++C + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 225 + Query_225 + M_695 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 226 + Query_226 + M_696 + 9 + + + 1 + gnl|BL_ORD_ID|160 + 12183|EBNA3C latent protein|CAD53421.1|Human gammaherpesvirus 4|10376 + 160 + 9 + + + 1 + 11.927 + 19 + 97.5444 + 3 + 8 + 3 + 8 + 0 + 0 + 4 + 5 + 0 + 6 + GLGGRH + GVGWRH + G+G RH + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 227 + Query_227 + M_697 + 9 + + + 1 + gnl|BL_ORD_ID|1760 + 154387|RL2|CAB06760.1|Human alphaherpesvirus 2|10310 + 1760 + 15 + + + 1 + 13.0826 + 22 + 13.39 + 2 + 9 + 6 + 13 + 0 + 0 + 5 + 5 + 0 + 8 + HTGTSVVL + HIGAYVVL + H G VVL + + + + + 2 + gnl|BL_ORD_ID|1764 + 154725|RL2|CAB06760.1|Human alphaherpesvirus 2|10310 + 1764 + 15 + + + 1 + 13.0826 + 22 + 17.5339 + 2 + 9 + 2 + 9 + 0 + 0 + 5 + 5 + 0 + 8 + HTGTSVVL + HIGAYVVL + H G VVL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 228 + Query_228 + M_698 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 229 + Query_229 + M_699 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 230 + Query_230 + M_700 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 231 + Query_231 + M_701 + 9 + + + 1 + gnl|BL_ORD_ID|1265 + 98603|trans-sialidase, putative|EAN82716.1|Trypanosoma cruzi|5693 + 1265 + 9 + + + 1 + 13.0826 + 22 + 15.7589 + 5 + 9 + 5 + 9 + 0 + 0 + 4 + 4 + 0 + 5 + NRPFY + NRSFY + NR FY + + + + + 2 + gnl|BL_ORD_ID|1981 + 183231|polyprotein|AFP27208.1|Dengue virus 4|11070 + 1981 + 10 + + + 1 + 13.0826 + 22 + 18.4997 + 1 + 8 + 1 + 8 + 0 + 0 + 4 + 4 + 0 + 8 + FPLRNRPF + FPQSNSPI + FP N P + + + + + 3 + gnl|BL_ORD_ID|1866 + 180460|polyprotein|AGO67248.1|Dengue virus 2|11060 + 1866 + 10 + + + 1 + 12.6974 + 21 + 28.8893 + 1 + 8 + 1 + 8 + 0 + 0 + 4 + 4 + 0 + 8 + FPLRNRPF + FPQSNAPI + FP N P + + + + + 4 + gnl|BL_ORD_ID|1704 + 150217|polyprotein|AGO67248.1|Dengue virus 2|11060 + 1704 + 9 + + + 1 + 12.6974 + 21 + 33.6262 + 1 + 8 + 1 + 8 + 0 + 0 + 4 + 4 + 0 + 8 + FPLRNRPF + FPQSNAPI + FP N P + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 232 + Query_232 + M_702 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 233 + Query_233 + M_703 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 234 + Query_234 + M_704 + 9 + + + 1 + gnl|BL_ORD_ID|1755 + 154041|major capsid protein|CAB06743.1|Human alphaherpesvirus 2|10310 + 1755 + 15 + + + 1 + 11.927 + 19 + 87.4721 + 3 + 9 + 7 + 13 + 0 + 0 + 4 + 4 + 0 + 7 + YPRFLYL + YPAVFYL + YP YL + + + + + 2 + gnl|BL_ORD_ID|855 + 55779|fusion protein|BAB60865.1|Measles virus|11234 + 855 + 9 + + + 1 + 11.927 + 19 + 91.4136 + 3 + 9 + 3 + 9 + 0 + 0 + 4 + 5 + 0 + 7 + YPRFLYL + YPDAVYL + YP +YL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 235 + Query_235 + M_705 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 236 + Query_236 + M_706 + 9 + + + 1 + gnl|BL_ORD_ID|1948 + 180850|polyprotein|AFP27208.1|Dengue virus 4|11070 + 1948 + 10 + + + 1 + 12.3122 + 20 + 52.9061 + 1 + 7 + 1 + 7 + 0 + 0 + 3 + 5 + 0 + 7 + YYPPGVV + YTPEGII + Y P G++ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 237 + Query_237 + M_707 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 238 + Query_238 + M_708 + 9 + + + 1 + gnl|BL_ORD_ID|1950 + 181035|||| + 1950 + 44 + + + 1 + 12.6974 + 21 + 25.8912 + 1 + 9 + 11 + 19 + 0 + 0 + 4 + 7 + 0 + 9 + RVFPLRGKI + KLFPGGGQI + ++FP G+I + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 239 + Query_239 + M_709 + 9 + + + 1 + gnl|BL_ORD_ID|1139 + 75356|EBNA3A nuclear protein|Q8AZJ8|Human gammaherpesvirus 4|10376 + 1139 + 9 + + + 1 + 14.6234 + 26 + 2.22125 + 1 + 9 + 1 + 9 + 0 + 0 + 5 + 6 + 0 + 9 + YPLPVANGM + YPLHEQHGM + YPL +GM + + + + + 2 + gnl|BL_ORD_ID|1144 + 75438|polyprotein|AAF65962.1|Hepatitis C virus|11103 + 1144 + 20 + + + 1 + 10.3862 + 15 + 376.551 + 1 + 9 + 3 + 11 + 0 + 0 + 4 + 5 + 0 + 9 + YPLPVANGM + WPLYGNEGM + +PL GM + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 240 + Query_240 + M_710 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 241 + Query_241 + M_711 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 242 + Query_242 + M_712 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 243 + Query_243 + M_713 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 244 + Query_244 + M_714 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 245 + Query_245 + M_715 + 9 + + + 1 + gnl|BL_ORD_ID|1449 + 126486|gag protein|ADK33372.1|Human immunodeficiency virus 1|11676 + 1449 + 10 + + + 1 + 15.0086 + 27 + 0.933082 + 1 + 9 + 1 + 9 + 0 + 0 + 6 + 8 + 0 + 9 + KALFWTVAM + KSLFNTVAV + K+LF TVA+ + + + + + 2 + gnl|BL_ORD_ID|1450 + 126487|gag protein|ADK33372.1|Human immunodeficiency virus 1|11676 + 1450 + 11 + + + 1 + 15.0086 + 27 + 1.06128 + 1 + 9 + 1 + 9 + 0 + 0 + 6 + 8 + 0 + 9 + KALFWTVAM + KSLFNTVAV + K+LF TVA+ + + + + + 3 + gnl|BL_ORD_ID|1447 + 126484|gag protein|AAW03034.1|Human immunodeficiency virus 1|11676 + 1447 + 10 + + + 1 + 15.0086 + 27 + 1.32867 + 1 + 8 + 1 + 8 + 0 + 0 + 6 + 7 + 0 + 8 + KALFWTVA + KSLFNTVA + K+LF TVA + + + + + 4 + gnl|BL_ORD_ID|1448 + 126485|gag protein|AAW03034.1|Human immunodeficiency virus 1|11676 + 1448 + 11 + + + 1 + 14.6234 + 26 + 1.54725 + 1 + 8 + 1 + 8 + 0 + 0 + 6 + 7 + 0 + 8 + KALFWTVA + KSLFNTVA + K+LF TVA + + + + + 5 + gnl|BL_ORD_ID|1445 + 126482|gag protein|AAY98604.1|Human immunodeficiency virus 1|11676 + 1445 + 10 + + + 1 + 14.6234 + 26 + 1.7557 + 1 + 9 + 1 + 9 + 0 + 0 + 5 + 8 + 0 + 9 + KALFWTVAM + KSLFNTIAV + K+LF T+A+ + + + + + 6 + gnl|BL_ORD_ID|1446 + 126483|gag protein|AAY98604.1|Human immunodeficiency virus 1|11676 + 1446 + 11 + + + 1 + 14.6234 + 26 + 2.02142 + 1 + 9 + 1 + 9 + 0 + 0 + 5 + 8 + 0 + 9 + KALFWTVAM + KSLFNTIAV + K+LF T+A+ + + + + + 7 + gnl|BL_ORD_ID|2198 + 190826|gag polyprotein|CAB81949.1|Human immunodeficiency virus 1|11676 + 2198 + 10 + + + 1 + 14.6234 + 26 + 2.33097 + 1 + 8 + 1 + 8 + 0 + 0 + 5 + 7 + 0 + 8 + KALFWTVA + KSLFNTIA + K+LF T+A + + + + + 8 + gnl|BL_ORD_ID|2204 + 190961|gag protein|BAC45024.1|Human immunodeficiency virus 1|11676 + 2204 + 10 + + + 1 + 14.2382 + 25 + 2.75947 + 1 + 9 + 1 + 9 + 0 + 0 + 5 + 8 + 0 + 9 + KALFWTVAM + RSLFNTVAV + ++LF TVA+ + + + + + 9 + gnl|BL_ORD_ID|1444 + 126481|gag polyprotein p17 region|BAA83653.1|Human immunodeficiency virus 1|11676 + 1444 + 11 + + + 1 + 14.2382 + 25 + 2.78989 + 1 + 8 + 1 + 8 + 0 + 0 + 5 + 7 + 0 + 8 + KALFWTVA + KSLFNTIA + K+LF T+A + + + + + 10 + gnl|BL_ORD_ID|1460 + 126997|gag protein|BAC45024.1|Human immunodeficiency virus 1|11676 + 1460 + 11 + + + 1 + 14.2382 + 25 + 3.14502 + 1 + 9 + 1 + 9 + 0 + 0 + 5 + 8 + 0 + 9 + KALFWTVAM + RSLFNTVAV + ++LF TVA+ + + + + + 11 + gnl|BL_ORD_ID|1458 + 126995|gag polyprotein|BAB19171.1|Human immunodeficiency virus 1|11676 + 1458 + 10 + + + 1 + 14.2382 + 25 + 4.08767 + 1 + 8 + 1 + 8 + 0 + 0 + 5 + 7 + 0 + 8 + KALFWTVA + RSLFNTVA + ++LF TVA + + + + + 12 + gnl|BL_ORD_ID|1459 + 126996|Gag protein|Q9YYH6|Human immunodeficiency virus 1|11676 + 1459 + 11 + + + 1 + 13.853 + 24 + 4.67708 + 1 + 8 + 1 + 8 + 0 + 0 + 5 + 7 + 0 + 8 + KALFWTVA + RSLFNTVA + ++LF TVA + + + + + 13 + gnl|BL_ORD_ID|2203 + 190960|gag-pol polyprotein|BAC02551.1|Human immunodeficiency virus 1|11676 + 2203 + 10 + + + 1 + 13.853 + 24 + 5.38895 + 1 + 9 + 1 + 9 + 0 + 0 + 4 + 8 + 0 + 9 + KALFWTVAM + RSLFNTIAV + ++LF T+A+ + + + + + 14 + gnl|BL_ORD_ID|1457 + 126994|gag-pol polyprotein|BAC02551.1|Human immunodeficiency virus 1|11676 + 1457 + 11 + + + 1 + 13.853 + 24 + 6.17581 + 1 + 9 + 1 + 9 + 0 + 0 + 4 + 8 + 0 + 9 + KALFWTVAM + RSLFNTIAV + ++LF T+A+ + + + + + 15 + gnl|BL_ORD_ID|2202 + 190959|gag polyprotein|BAB19174.1|Human immunodeficiency virus 1|11676 + 2202 + 10 + + + 1 + 13.4678 + 23 + 7.49677 + 1 + 8 + 1 + 8 + 0 + 0 + 4 + 7 + 0 + 8 + KALFWTVA + RSLFNTIA + ++LF T+A + + + + + 16 + gnl|BL_ORD_ID|1456 + 126993|gag polyprotein|BAB19174.1|Human immunodeficiency virus 1|11676 + 1456 + 11 + + + 1 + 13.4678 + 23 + 8.59697 + 1 + 8 + 1 + 8 + 0 + 0 + 4 + 7 + 0 + 8 + KALFWTVA + RSLFNTIA + ++LF T+A + + + + + 17 + gnl|BL_ORD_ID|1847 + 180236|gag|BAC81459.1|Human immunodeficiency virus 1|11676 + 1847 + 9 + + + 1 + 13.0826 + 22 + 17.1877 + 2 + 9 + 1 + 8 + 0 + 0 + 5 + 7 + 0 + 8 + ALFWTVAM + SLFNTVAV + +LF TVA+ + + + + + 18 + gnl|BL_ORD_ID|2208 + 190975|gag protein|BAC45024.1|Human immunodeficiency virus 1|11676 + 2208 + 10 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21242|polymerase|ACF94272.1|Hepatitis B virus|10407 + 338 + 9 + + + 1 + 11.1566 + 17 + 287.485 + 1 + 9 + 1 + 9 + 0 + 0 + 4 + 5 + 0 + 9 + GAYVYPLPV + GLYSSTVPV + G Y +PV + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 291 + Query_291 + M_761 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 292 + Query_292 + M_762 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 293 + Query_293 + M_763 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 294 + Query_294 + M_764 + 9 + + + 1 + gnl|BL_ORD_ID|1948 + 180850|polyprotein|AFP27208.1|Dengue virus 4|11070 + 1948 + 10 + + + 1 + 12.3122 + 20 + 49.5064 + 2 + 8 + 1 + 7 + 0 + 0 + 3 + 5 + 0 + 7 + YYPPGVV + YTPEGII + Y P G++ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 295 + Query_295 + M_765 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 296 + 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25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 335 + Query_335 + M_805 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 336 + Query_336 + M_806 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 337 + Query_337 + M_807 + 9 + + + 1 + gnl|BL_ORD_ID|2083 + 185419|envelope protein|AGW23591.1|Dengue virus 3|11069 + 2083 + 9 + + + 1 + 13.4678 + 23 + 10.9354 + 3 + 8 + 4 + 9 + 0 + 0 + 5 + 6 + 0 + 6 + MDELEL + MDKLEL + MD+LEL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 338 + Query_338 + M_808 + 9 + + + 1 + gnl|BL_ORD_ID|624 + 37507|Large T antigen|P03071.1|Human polyomavirus 1|1891762 + 624 + 9 + + + 1 + 15.3938 + 28 + 0.690962 + 2 + 9 + 2 + 9 + 0 + 0 + 5 + 6 + 0 + 8 + MLNWFSPV + LLIWFRPV + +L WF PV + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 339 + Query_339 + M_809 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 340 + Query_340 + M_810 + 9 + + + 1 + gnl|BL_ORD_ID|2139 + 187158|Gag protein|Q1KW74|Human immunodeficiency virus 1|11676 + 2139 + 11 + + + 1 + 13.853 + 24 + 5.66142 + 1 + 6 + 1 + 6 + 0 + 0 + 4 + 5 + 0 + 6 + HSFNPE + KAFNPE + +FNPE + + + + + 2 + gnl|BL_ORD_ID|2141 + 187163|Gag polyprotein|P88150|Human immunodeficiency virus 1|11676 + 2141 + 11 + + + 1 + 13.4678 + 23 + 8.0187 + 1 + 7 + 1 + 7 + 0 + 0 + 4 + 4 + 0 + 7 + HSFNPEA + KGFNPEV + FNPE + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 341 + Query_341 + M_811 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 342 + Query_342 + M_812 + 9 + + + 1 + gnl|BL_ORD_ID|730 + 46480|DNA polymerase|CAA10434.1|Hepatitis B virus|10407 + 730 + 9 + + + 1 + 15.779 + 29 + 0.439716 + 1 + 7 + 2 + 8 + 0 + 0 + 5 + 5 + 0 + 7 + FSIPWAH + VSIPWTH + SIPW H + + + + + 2 + gnl|BL_ORD_ID|879 + 57723|polyprotein|CAB53095.1|Hepatitis C virus|11103 + 879 + 10 + + + 1 + 12.3122 + 20 + 44.0514 + 1 + 8 + 2 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0.267 + 0.14 + + + No hits found + + + 347 + Query_347 + M_817 + 9 + + + 1 + gnl|BL_ORD_ID|2014 + 183819|polyprotein|AGO67248.1|Dengue virus 2|11060 + 2014 + 10 + + + 1 + 12.3122 + 20 + 52.9061 + 2 + 7 + 5 + 10 + 0 + 0 + 5 + 5 + 0 + 6 + AAAWAL + AAAWYL + AAAW L + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 348 + Query_348 + M_818 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 349 + Query_349 + M_819 + 9 + + + 1 + gnl|BL_ORD_ID|904 + 59459|Trans-sialidase|SRC7915|Trypanosoma cruzi|5693 + 904 + 9 + + + 1 + 12.3122 + 20 + 53.0441 + 3 + 9 + 2 + 8 + 0 + 0 + 4 + 5 + 0 + 7 + LGHMFSL + LSHYFTL + L H F+L + + + + + 2 + gnl|BL_ORD_ID|1262 + 98466|Trans-sialidase|SRC7915|Trypanosoma cruzi|5693 + 1262 + 10 + + + 1 + 12.3122 + 20 + 56.5271 + 3 + 9 + 2 + 8 + 0 + 0 + 4 + 5 + 0 + 7 + LGHMFSL + LSHYFTL + L H F+L + + + + + 3 + gnl|BL_ORD_ID|247 + 16890|trans-sialidase|XP_810777.1|Trypanosoma cruzi|5693 + 247 + 9 + + + 1 + 11.927 + 19 + 102.395 + 3 + 9 + 2 + 8 + 0 + 0 + 4 + 5 + 0 + 7 + LGHMFSL + LSHNFTL + L H F+L + + + + + 4 + gnl|BL_ORD_ID|1242 + 98039|Trans-sialidase|SRC7915|Trypanosoma cruzi|5693 + 1242 + 10 + + + 1 + 11.5418 + 18 + 117.155 + 3 + 9 + 2 + 8 + 0 + 0 + 4 + 5 + 0 + 7 + LGHMFSL + LSHNFTL + L H F+L + + + + + 5 + gnl|BL_ORD_ID|246 + 16889|trans-sialidase, putative|EAN82636.1|Trypanosoma cruzi|5693 + 246 + 9 + + + 1 + 11.5418 + 18 + 143.267 + 3 + 9 + 2 + 8 + 0 + 0 + 4 + 5 + 0 + 7 + LGHMFSL + LSHDFTL + L H F+L + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 350 + Query_350 + M_820 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 351 + Query_351 + M_821 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 352 + Query_352 + M_822 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 353 + Query_353 + M_823 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 354 + Query_354 + M_824 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 355 + Query_355 + M_825 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 356 + Query_356 + M_826 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 357 + Query_357 + M_827 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 358 + Query_358 + M_828 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 359 + Query_359 + M_829 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 360 + Query_360 + M_830 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 361 + Query_361 + M_831 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 362 + Query_362 + M_832 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 363 + Query_363 + M_833 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 364 + Query_364 + M_834 + 9 + + + 1 + gnl|BL_ORD_ID|1916 + 180681|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 + 1916 + 15 + + + 1 + 13.0826 + 22 + 14.8197 + 1 + 8 + 2 + 9 + 0 + 0 + 4 + 4 + 0 + 8 + AAYTSYTP + EEYTDYMP + YT Y P + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 365 + Query_365 + M_835 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 366 + Query_366 + M_836 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 367 + Query_367 + M_837 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 368 + Query_368 + M_838 + 9 + + + 1 + gnl|BL_ORD_ID|2273 + 419006|PPE family protein PPE68|KAM81677.1|Mycobacterium tuberculosis H37Ra|419947 + 2273 + 10 + + + 1 + 13.4678 + 23 + 10.0795 + 1 + 6 + 3 + 8 + 0 + 0 + 4 + 6 + 0 + 6 + RSEALP + RAESLP + R+E+LP + + + + + 2 + gnl|BL_ORD_ID|328 + 21078|Antigen 85-B precursor|P21160.1|Mycobacterium kansasii|1768 + 328 + 9 + + + 1 + 13.0826 + 22 + 18.7436 + 4 + 9 + 1 + 6 + 0 + 0 + 4 + 4 + 0 + 6 + ALPVSY + GLPVEY + LPV Y + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 369 + Query_369 + M_839 + 9 + + + 1 + gnl|BL_ORD_ID|490 + 30946|HCV-1|AAA45676.1|Hepatitis C virus genotype 1|41856 + 490 + 20 + + + 1 + 11.1566 + 17 + 183.47 + 3 + 9 + 5 + 11 + 0 + 0 + 4 + 5 + 0 + 7 + KPFGLVV + KPARLIV + KP L+V + + + + + 2 + gnl|BL_ORD_ID|1414 + 111448|polyprotein precursor|BAA02756.1|Hepatitis C virus|11103 + 1414 + 15 + + + 1 + 11.1566 + 17 + 190.157 + 3 + 9 + 5 + 11 + 0 + 0 + 4 + 5 + 0 + 7 + KPFGLVV + KPARLIV + KP L+V + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 370 + Query_370 + M_840 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 371 + Query_371 + M_841 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 372 + Query_372 + M_842 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 373 + Query_373 + M_843 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 374 + Query_374 + M_844 + 9 + + + 1 + gnl|BL_ORD_ID|1659 + 146644|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 + 1659 + 10 + + + 1 + 13.853 + 24 + 6.29996 + 1 + 8 + 3 + 10 + 0 + 0 + 5 + 6 + 0 + 8 + HAATGPGE + HAPTGSGK + HA TG G+ + + + + + 2 + gnl|BL_ORD_ID|394 + 24219|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 + 394 + 15 + + + 1 + 13.4678 + 23 + 7.61659 + 1 + 8 + 3 + 10 + 0 + 0 + 5 + 6 + 0 + 8 + HAATGPGE + HAPTGSGK + HA TG G+ + + + + + 3 + gnl|BL_ORD_ID|393 + 24218|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 + 393 + 10 + + + 1 + 13.4678 + 23 + 8.92274 + 1 + 8 + 3 + 10 + 0 + 0 + 5 + 6 + 0 + 8 + HAATGPGE + HAPTGSGK + HA TG G+ + + + + + 4 + gnl|BL_ORD_ID|741 + 47760|EBNA-1 protein|Q777E1|Human gammaherpesvirus 4|10376 + 741 + 15 + + + 1 + 12.3122 + 20 + 51.4826 + 3 + 8 + 2 + 7 + 0 + 0 + 4 + 4 + 0 + 6 + ATGPGE + GTGPGN + TGPG + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 375 + Query_375 + M_845 + 9 + + + 1 + gnl|BL_ORD_ID|1916 + 180681|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 + 1916 + 15 + + + 1 + 13.0826 + 22 + 20.0418 + 1 + 6 + 9 + 14 + 0 + 0 + 4 + 4 + 0 + 6 + PSQNRF + PSMKRF + PS RF + + + + + 2 + gnl|BL_ORD_ID|1911 + 180667|polyprotein|AGO67248.1|Dengue virus 2|11060 + 1911 + 10 + + + 1 + 13.0826 + 22 + 21.2326 + 1 + 6 + 2 + 7 + 0 + 0 + 4 + 4 + 0 + 6 + PSQNRF + PSMKRF + PS RF + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 376 + Query_376 + M_846 + 9 + + + 1 + gnl|BL_ORD_ID|488 + 30903|prM protein|YP_001527879.1|West Nile virus NY-99|10000971 + 488 + 16 + + + 1 + 14.2382 + 25 + 3.11811 + 3 + 8 + 2 + 7 + 0 + 0 + 4 + 5 + 0 + 6 + SAWLDS + GAWMDS + AW+DS + + + + + 2 + gnl|BL_ORD_ID|484 + 30266|Transcriptional regulator IE63 homolog|Q04360.1|Human herpesvirus 4 strain B95-8|10377 + 484 + 9 + + + 1 + 11.927 + 19 + 95.9763 + 4 + 8 + 3 + 7 + 0 + 0 + 3 + 4 + 0 + 5 + AWLDS + TWLDA + WLD+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 377 + Query_377 + M_847 + 9 + + + 1 + gnl|BL_ORD_ID|1936 + 180789|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 + 1936 + 15 + + + 1 + 11.927 + 19 + 61.2314 + 1 + 6 + 8 + 13 + 0 + 0 + 3 + 5 + 0 + 6 + VPFPPK + IPYDPK + +P+ PK + + + + + 2 + gnl|BL_ORD_ID|1211 + 96366|polyprotein|ABR25251.1|Hepatitis C virus|11103 + 1211 + 12 + + + 1 + 11.1566 + 17 + 174.36 + 4 + 9 + 5 + 10 + 0 + 0 + 4 + 5 + 0 + 6 + PPKEPL + PPCKPL + PP +PL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 378 + Query_378 + M_848 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 379 + Query_379 + 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gnl|BL_ORD_ID|1640 + 146287|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 + 1640 + 18 + + + 1 + 11.1566 + 17 + 184.539 + 2 + 9 + 2 + 9 + 0 + 0 + 4 + 6 + 0 + 8 + PEGYGTQV + PKGPITQM + P+G TQ+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 484 + Query_484 + M_954 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 485 + Query_485 + M_955 + 9 + + + 1 + gnl|BL_ORD_ID|1408 + 110940|Protein E7|P03129.1|Human papillomavirus type 16|333760 + 1408 + 15 + + + 1 + 11.927 + 19 + 60.2782 + 1 + 8 + 2 + 9 + 0 + 0 + 4 + 4 + 0 + 8 + HGFNATYH + HGDTPTLH + HG T H + + + + + 2 + gnl|BL_ORD_ID|1392 + 110335|E7|AAD33253.1|Human papillomavirus type 16|333760 + 1392 + 32 + + + 1 + 11.5418 + 18 + 87.5281 + 1 + 8 + 2 + 9 + 0 + 0 + 4 + 4 + 0 + 8 + HGFNATYH + HGDTPTLH + HG T H + + + + + 3 + gnl|BL_ORD_ID|2243 + 232152|rhoptry kinase family protein|AFO54841.1|Toxoplasma gondii type III|398031 + 2243 + 19 + + + 1 + 11.5418 + 18 + 130.88 + 1 + 7 + 7 + 13 + 0 + 0 + 3 + 4 + 0 + 7 + HGFNATY + HSYGVTY + H + TY + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 486 + Query_486 + M_956 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 487 + Query_487 + M_957 + 9 + + + 1 + gnl|BL_ORD_ID|285 + 19348|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 + 285 + 20 + + + 1 + 12.6974 + 21 + 33.3894 + 2 + 7 + 5 + 10 + 0 + 0 + 4 + 4 + 0 + 6 + PEVFGP + PEAAGP + PE GP + + + + + 2 + gnl|BL_ORD_ID|866 + 56620|Nef protein|Q9YYU8|Human immunodeficiency virus 1|11676 + 866 + 10 + + + 1 + 12.6974 + 21 + 38.5196 + 1 + 6 + 2 + 7 + 0 + 0 + 4 + 4 + 0 + 6 + YPEVFG + YPLTFG + YP FG + + + + + 3 + gnl|BL_ORD_ID|1281 + 102046|nef protein|ACQ72180.1|Human immunodeficiency virus 1|11676 + 1281 + 8 + + + 1 + 12.6974 + 21 + 38.9267 + 1 + 6 + 2 + 7 + 0 + 0 + 4 + 4 + 0 + 6 + YPEVFG + YPLTFG + YP FG + + + + + 4 + gnl|BL_ORD_ID|1288 + 102254|nef protein|ACQ72180.1|Human immunodeficiency virus 1|11676 + 1288 + 9 + + + 1 + 12.3122 + 20 + 43.3628 + 1 + 6 + 1 + 6 + 0 + 0 + 4 + 4 + 0 + 6 + YPEVFG + YPLTFG + YP FG + + + + + 5 + gnl|BL_ORD_ID|707 + 43447|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 + 707 + 20 + + + 1 + 11.927 + 19 + 78.9367 + 2 + 7 + 15 + 20 + 0 + 0 + 4 + 4 + 0 + 6 + PEVFGP + PEAAGP + PE GP + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 488 + Query_488 + M_958 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 489 + Query_489 + M_959 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 490 + Query_490 + M_960 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 491 + Query_491 + M_961 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 492 + Query_492 + M_962 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 493 + Query_493 + M_963 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 494 + Query_494 + M_964 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 495 + Query_495 + M_965 + 9 + + + 1 + gnl|BL_ORD_ID|1726 + 150461|polyprotein|AGK36298.1|Dengue virus 2|11060 + 1726 + 9 + + + 1 + 13.0826 + 22 + 14.4474 + 1 + 9 + 1 + 9 + 0 + 0 + 5 + 7 + 0 + 9 + MTREELNAL + MTQKARNAL + MT++ NAL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 496 + Query_496 + M_966 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 497 + Query_497 + M_967 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 498 + Query_498 + M_968 + 9 + + + 1 + gnl|BL_ORD_ID|2175 + 189750|Diacylglycerol acyltransferase/mycolyltransferase Ag85B|SRC280000|Mycobacterium tuberculosis|1773 + 2175 + 9 + + + 1 + 11.5418 + 18 + 147.871 + 1 + 7 + 2 + 8 + 0 + 0 + 4 + 5 + 0 + 7 + KAGGGSN + PVGGGSS + GGGS+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 499 + Query_499 + M_969 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 500 + Query_500 + M_970 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 501 + Query_501 + M_971 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 502 + Query_502 + M_972 + 9 + + + 1 + gnl|BL_ORD_ID|2251 + 243835|glycosyl transferase|WP_015628558.1|Mycobacterium tuberculosis|1773 + 2251 + 9 + + + 1 + 13.0826 + 22 + 18.4218 + 1 + 9 + 1 + 9 + 0 + 0 + 5 + 5 + 0 + 9 + SARDCKDPY + SARLAGIPY + SAR PY + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 503 + Query_503 + M_973 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 504 + Query_504 + M_974 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 505 + Query_505 + M_975 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 506 + Query_506 + M_976 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 507 + Query_507 + M_977 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 508 + Query_508 + M_978 + 9 + + + 1 + gnl|BL_ORD_ID|378 + 23365|polyprotein|BAB18806.1|Hepatitis C virus|11103 + 378 + 10 + + + 1 + 14.6234 + 26 + 2.00506 + 1 + 9 + 2 + 10 + 0 + 0 + 4 + 7 + 0 + 9 + FIPINGCPI + YIPLVGAPL + +IP+ G P+ + + + + + 2 + gnl|BL_ORD_ID|296 + 19493|polyprotein|BAA03375.1|Hepatitis C virus|11103 + 296 + 15 + + + 1 + 13.853 + 24 + 4.45371 + 1 + 8 + 8 + 15 + 0 + 0 + 4 + 6 + 0 + 8 + FIPINGCP + YIPLVGAP + +IP+ G P + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 509 + Query_509 + M_979 + 9 + + + 1 + gnl|BL_ORD_ID|1153 + 76121|polyprotein precursor|NP_041724.2|West Nile virus|11082 + 1153 + 9 + + + 1 + 8.46023 + 10 + 5101.61 + 1 + 9 + 1 + 9 + 0 + 0 + 3 + 5 + 0 + 9 + YTSYFGYKM + YTMDGEYRL + YT Y++ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 510 + Query_510 + M_980 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 511 + Query_511 + M_981 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 512 + Query_512 + M_982 + 9 + + + 1 + gnl|BL_ORD_ID|1175 + 79390|Protein Tax-1|P0C213.1|Human T-cell lymphotropic virus type 1 (african isolate)|39015 + 1175 + 15 + + + 1 + 11.927 + 19 + 69.3823 + 2 + 9 + 1 + 8 + 0 + 0 + 4 + 5 + 0 + 8 + SFYRTHTL + SFHNLHLL + SF+ H L + + + + + 2 + gnl|BL_ORD_ID|880 + 57790|Protein Tax-1|P03409.2|Human T-lymphotropic virus 1|11908 + 880 + 9 + + + 1 + 11.5418 + 18 + 122.194 + 2 + 9 + 1 + 8 + 0 + 0 + 4 + 5 + 0 + 8 + SFYRTHTL + SFHSLHLL + SF+ H L + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 513 + Query_513 + M_983 + 9 + + + 1 + gnl|BL_ORD_ID|341 + 21385|polyprotein|AAY82034.1|Hepatitis C virus genotype 1|41856 + 341 + 10 + + + 1 + 13.853 + 24 + 7.36741 + 1 + 9 + 2 + 10 + 0 + 0 + 5 + 7 + 0 + 9 + NAAKNQVAM + NASRCWVAM + NA++ VAM + + + + + 2 + gnl|BL_ORD_ID|706 + 43310|polyprotein|AAW78019.1|Hepatitis C virus (isolate H77)|63746 + 706 + 9 + + + 1 + 13.4678 + 23 + 7.85574 + 1 + 9 + 1 + 9 + 0 + 0 + 5 + 7 + 0 + 9 + NAAKNQVAM + NASRCWVAM + NA++ VAM + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 514 + Query_514 + M_984 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 515 + Query_515 + M_985 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 516 + Query_516 + M_986 + 9 + + + 1 + gnl|BL_ORD_ID|1171 + 79300|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 + 1171 + 15 + + + 1 + 12.3122 + 20 + 43.2075 + 1 + 9 + 5 + 13 + 0 + 0 + 5 + 5 + 0 + 9 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523 + Query_523 + M_993 + 9 + + + 1 + gnl|BL_ORD_ID|152 + 11214|possible regulatory protein|NP_302009.1|Mycobacterium leprae|1769 + 152 + 15 + + + 1 + 15.0086 + 27 + 0.94895 + 1 + 8 + 5 + 12 + 0 + 0 + 5 + 7 + 0 + 8 + LRLDGSVV + LRLDGTTL + LRLDG+ + + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 524 + Query_524 + M_994 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 525 + Query_525 + M_995 + 9 + + + 1 + gnl|BL_ORD_ID|745 + 48458|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 + 745 + 20 + + + 1 + 13.853 + 24 + 4.81213 + 1 + 8 + 6 + 13 + 0 + 0 + 5 + 5 + 0 + 8 + FPSSQGSL + FPIVQGEL + FP QG L + + + + + 2 + gnl|BL_ORD_ID|1994 + 183594|polyprotein|AGT63075.1|Dengue virus 1|11053 + 1994 + 10 + + + 1 + 13.0826 + 22 + 16.9691 + 2 + 9 + 2 + 9 + 0 + 0 + 4 + 6 + 0 + 8 + PSSQGSLY + PASAWTLY + P+S +LY + + + + + 3 + gnl|BL_ORD_ID|1729 + 150534|polyprotein|AGO67248.1|Dengue virus 2|11060 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2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 574 + Query_574 + M_1044 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 575 + Query_575 + M_1045 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 576 + Query_576 + M_1046 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 577 + Query_577 + M_1047 + 9 + + + 1 + gnl|BL_ORD_ID|742 + 47854|Glycoprotein I precursor (Glycoprotein IV) (GI) (GPIV)|P09258.1|Human alphaherpesvirus 3|10335 + 742 + 10 + + + 1 + 12.6974 + 21 + 37.2442 + 1 + 6 + 2 + 7 + 0 + 0 + 4 + 4 + 0 + 6 + HSYVGP + HSVVNP + HS V P + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 578 + Query_578 + M_1048 + 9 + + + 1 + gnl|BL_ORD_ID|716 + 44214|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 + 716 + 11 + + + 1 + 13.4678 + 23 + 7.61059 + 1 + 9 + 3 + 11 + 0 + 0 + 5 + 6 + 0 + 9 + EMFQRYSAF + EFFTKNSAF + E F + SAF + 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hits found + + + 593 + Query_593 + M_1063 + 9 + + + 1 + gnl|BL_ORD_ID|2284 + 419128|polyprotein|ACF49259.1|Dengue virus type 1 Hawaii|10000440 + 2284 + 9 + + + 1 + 14.6234 + 26 + 1.91441 + 3 + 9 + 3 + 9 + 0 + 0 + 4 + 7 + 0 + 7 + RHSMEKI + RHAMEEL + RH+ME++ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 594 + Query_594 + M_1064 + 9 + + + 1 + gnl|BL_ORD_ID|1006 + 66195|Nucleoprotein|P41269.1|Puumala hantavirus|11604 + 1006 + 15 + + + 1 + 13.853 + 24 + 5.02902 + 4 + 9 + 10 + 15 + 0 + 0 + 4 + 5 + 0 + 6 + RHPQHL + RRPKHL + R P+HL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 595 + Query_595 + M_1065 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 596 + Query_596 + M_1066 + 9 + + + 1 + gnl|BL_ORD_ID|1781 + 156550|E3 ubiquitin-protein ligase Mdm2|Q00987.1|Homo sapiens|9606 + 1781 + 9 + + + 1 + 12.6974 + 21 + 26.9236 + 1 + 9 + 1 + 9 + 0 + 0 + 3 + 7 + 0 + 9 + IIFLLGEIV + VLFYLGQYI + ++F LG+ + + + + + + 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4 + 6 + 0 + 6 + YDVLIC + YDIIIC + YD++IC + + + + + 3 + gnl|BL_ORD_ID|1317 + 107760|polyprotein|AAD56189.1|Hepatitis C virus|11103 + 1317 + 10 + + + 1 + 13.4678 + 23 + 12.2057 + 3 + 8 + 2 + 7 + 0 + 0 + 3 + 6 + 0 + 6 + YDVLIC + YDIIMC + YD+++C + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 601 + Query_601 + M_1071 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 602 + Query_602 + M_1072 + 9 + + + 1 + gnl|BL_ORD_ID|234 + 16813|External core antigen|SRC279980|Hepatitis B virus|10407 + 234 + 10 + + + 1 + 13.0826 + 22 + 18.1832 + 3 + 8 + 4 + 9 + 0 + 0 + 4 + 4 + 0 + 6 + NDLMPS + NDFFPS + ND PS + + + + + 2 + gnl|BL_ORD_ID|235 + 16814|precore protein|CAM58990.1|Hepatitis B virus|10407 + 235 + 10 + + + 1 + 13.0826 + 22 + 19.1489 + 3 + 8 + 4 + 9 + 0 + 0 + 4 + 4 + 0 + 6 + NDLMPS + NDFFPS + ND PS + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 603 + Query_603 + M_1073 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 604 + Query_604 + M_1074 + 9 + + + 1 + gnl|BL_ORD_ID|1266 + 98640|trans-sialidase, putative|EAN80840.1|Trypanosoma cruzi|5693 + 1266 + 9 + + + 1 + 13.4678 + 23 + 9.02895 + 3 + 9 + 3 + 9 + 0 + 0 + 5 + 7 + 0 + 7 + FSLLATV + FTLVATV + F+L+ATV + + + + + 2 + gnl|BL_ORD_ID|1245 + 98044|trans-sialidase, putative|EAN80840.1|Trypanosoma cruzi|5693 + 1245 + 9 + + + 1 + 13.4678 + 23 + 10.561 + 3 + 9 + 1 + 7 + 0 + 0 + 5 + 7 + 0 + 7 + FSLLATV + FTLVATV + F+L+ATV + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 605 + Query_605 + M_1075 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 606 + Query_606 + M_1076 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 607 + Query_607 + M_1077 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 608 + Query_608 + M_1078 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 609 + Query_609 + M_1079 + 9 + + + 1 + gnl|BL_ORD_ID|1171 + 79300|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 + 1171 + 15 + + + 1 + 14.2382 + 25 + 3.03951 + 1 + 7 + 3 + 9 + 0 + 0 + 4 + 5 + 0 + 7 + LPQPGVR + FPDPGLR + P PG+R + + + + + 2 + gnl|BL_ORD_ID|2238 + 230028|Protein Nef|P04603.3|Human immunodeficiency virus 1|11676 + 2238 + 10 + + + 1 + 13.853 + 24 + 5.02829 + 2 + 7 + 4 + 9 + 0 + 0 + 4 + 5 + 0 + 6 + PQPGVR + PGPGIR + P PG+R + + + + + 3 + gnl|BL_ORD_ID|2239 + 230029|Protein Nef|P03404.4|Human immunodeficiency virus 1|11676 + 2239 + 10 + + + 1 + 13.853 + 24 + 5.11607 + 2 + 7 + 4 + 9 + 0 + 0 + 4 + 5 + 0 + 6 + PQPGVR + PGPGIR + P PG+R + + + + + 4 + gnl|BL_ORD_ID|1508 + 139406|polyprotein|ACT37184.1|Hepatitis C virus|11103 + 1508 + 10 + + + 1 + 13.853 + 24 + 5.67669 + 1 + 7 + 3 + 9 + 0 + 0 + 5 + 6 + 0 + 7 + LPQPGVR + LPRPGPR + LP+PG R + + + + + 5 + gnl|BL_ORD_ID|1106 + 72928|Genome polyprotein|P26662.3|Hepatitis C virus (isolate Japanese)|11116 + 1106 + 10 + + + 1 + 13.853 + 24 + 7.36741 + 4 + 9 + 5 + 10 + 0 + 0 + 4 + 5 + 0 + 6 + PGVRSL + PGARSM + PG RS+ + + + + + 6 + gnl|BL_ORD_ID|2240 + 230030|Nef protein|BAA86664.1|Human immunodeficiency virus 1|11676 + 2240 + 10 + + + 1 + 13.0826 + 22 + 16.9691 + 2 + 7 + 4 + 9 + 0 + 0 + 4 + 4 + 0 + 6 + PQPGVR + PGPGTR + P PG R + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 610 + Query_610 + M_1080 + 9 + + + 1 + gnl|BL_ORD_ID|1862 + 180442|Chain B, Dengue Virus Rna Dependent Rna Polymerase With Residues From The Ns5 Linker Region|4C11_B|Dengue virus|12637 + 1862 + 10 + + + 1 + 13.4678 + 23 + 12.4198 + 5 + 9 + 4 + 8 + 0 + 0 + 4 + 4 + 0 + 5 + CLGKV + CLGKA + CLGK + + + + + 2 + gnl|BL_ORD_ID|193 + 14324|Chain B, Dengue Virus Rna Dependent Rna Polymerase With Residues From The Ns5 Linker Region|4C11_B|Dengue virus|12637 + 193 + 9 + + + 1 + 13.0826 + 22 + 14.1983 + 5 + 9 + 4 + 8 + 0 + 0 + 4 + 4 + 0 + 5 + CLGKV + CLGKA + CLGK + + + + + 3 + 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C virus (isolate H77)|63746 + 1149 + 10 + + + 1 + 15.0086 + 27 + 1.44144 + 3 + 9 + 3 + 9 + 0 + 0 + 4 + 4 + 0 + 7 + LWHLPAV + LWHYPCT + LWH P + + + + + 2 + gnl|BL_ORD_ID|832 + 54820|polyprotein precursor|BAA02756.1|Hepatitis C virus|11103 + 832 + 9 + + + 1 + 14.6234 + 26 + 1.52328 + 3 + 9 + 2 + 8 + 0 + 0 + 4 + 4 + 0 + 7 + LWHLPAV + LWHYPCT + LWH P + + + + + 3 + gnl|BL_ORD_ID|831 + 54819|JK3|CAA43789.1|Hepatitis C virus|11103 + 831 + 9 + + + 1 + 14.6234 + 26 + 1.6522 + 3 + 9 + 2 + 8 + 0 + 0 + 4 + 4 + 0 + 7 + LWHLPAV + LWHYPCT + LWH P + + + + + 4 + gnl|BL_ORD_ID|833 + 54821|E2 protein|AAM33354.1|Hepatitis C virus subtype 1a|31646 + 833 + 9 + + + 1 + 14.6234 + 26 + 1.67935 + 3 + 9 + 2 + 8 + 0 + 0 + 4 + 4 + 0 + 7 + LWHLPAV + LWHYPCT + LWH P + + + + + 5 + gnl|BL_ORD_ID|835 + 54825|polyprotein|BAA03375.1|Hepatitis C virus|11103 + 835 + 9 + + + 1 + 14.6234 + 26 + 1.73509 + 3 + 9 + 2 + 8 + 0 + 0 + 4 + 4 + 0 + 7 + LWHLPAV + LWHYPCT + LWH P + + + + + 6 + gnl|BL_ORD_ID|834 + 54824|polyprotein precursor|BAA01583.1|Hepatitis C virus|11103 + 834 + 9 + + + 1 + 14.6234 + 26 + 1.88321 + 3 + 9 + 2 + 8 + 0 + 0 + 4 + 4 + 0 + 7 + LWHLPAV + LWHYPCT + LWH P + + + + + 7 + gnl|BL_ORD_ID|1010 + 67210|NS3 protein|NP_739587.1|Dengue virus 2 Thailand/NGS-C/1944|11065 + 1010 + 9 + + + 1 + 12.6974 + 21 + 39.1808 + 3 + 9 + 2 + 8 + 0 + 0 + 2 + 6 + 0 + 7 + LWHLPAV + VWFVPSI + +W +P++ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 757 + Query_757 + M_1227 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 758 + Query_758 + M_1228 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 759 + Query_759 + M_1229 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 760 + Query_760 + M_1230 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 761 + Query_761 + M_1231 + 9 + + + 1 + gnl|BL_ORD_ID|469 + 28484|Protein E6|P03126.1|Human papillomavirus type 16|333760 + 469 + 9 + + + 1 + 14.2382 + 25 + 4.3647 + 1 + 9 + 1 + 9 + 0 + 0 + 4 + 7 + 0 + 9 + MTEHRGKCY + ISEYRHYCY + ++E+R CY + + + + + 2 + gnl|BL_ORD_ID|1406 + 110846|E6 protein|CAB45108.1|Human papillomavirus type 16|333760 + 1406 + 9 + + + 1 + 12.6974 + 21 + 30.8766 + 3 + 9 + 1 + 7 + 0 + 0 + 4 + 5 + 0 + 7 + EHRGKCY + EYRHYCY + E+R CY + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 762 + Query_762 + M_1232 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 763 + Query_763 + M_1233 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 764 + Query_764 + M_1234 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 765 + Query_765 + M_1235 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 766 + Query_766 + M_1236 + 9 + + + 1 + gnl|BL_ORD_ID|764 + 51250|nucleocapsid protein|ABI96968.1|SARS coronavirus|227859 + 764 + 15 + + + 1 + 15.779 + 29 + 0.411155 + 1 + 9 + 7 + 15 + 0 + 0 + 5 + 7 + 0 + 9 + HRYNLTQHF + KQYNVTQAF + +YN+TQ F + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 767 + Query_767 + M_1237 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 768 + Query_768 + M_1238 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 769 + Query_769 + M_1239 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 770 + Query_770 + M_1240 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 771 + Query_771 + M_1241 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 772 + Query_772 + M_1242 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 773 + Query_773 + M_1243 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits 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Query_949 + M_1419 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 950 + Query_950 + M_1420 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 951 + Query_951 + M_1421 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 952 + Query_952 + M_1422 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 953 + Query_953 + M_1423 + 9 + + + 1 + gnl|BL_ORD_ID|1111 + 73177|protein F [Hepatitis C virus subtype 1b]|ACA50643.1|Hepatitis C virus (isolate Japanese)|11116 + 1111 + 9 + + + 1 + 13.0826 + 22 + 20.7937 + 3 + 8 + 2 + 7 + 0 + 0 + 4 + 5 + 0 + 6 + VCHQLG + VCARLG + VC +LG + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 954 + Query_954 + M_1424 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 955 + Query_955 + M_1425 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + 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141462|tegument protein UL21|NP_044622.1|Human alphaherpesvirus 1|10298 + 1581 + 9 + + + 1 + 13.4678 + 23 + 8.42175 + 1 + 9 + 1 + 9 + 0 + 0 + 5 + 6 + 0 + 9 + VPREFKPIL + VPRPDDPVL + VPR P+L + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 965 + Query_965 + M_1435 + 9 + + + 1 + gnl|BL_ORD_ID|747 + 48896|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 + 747 + 15 + + + 1 + 12.3122 + 20 + 53.9857 + 4 + 9 + 1 + 6 + 0 + 0 + 4 + 4 + 0 + 6 + PPMPPY + PPQPEY + PP P Y + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 966 + Query_966 + M_1436 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 967 + Query_967 + M_1437 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 968 + Query_968 + M_1438 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 969 + Query_969 + M_1439 + 9 + + + 1 + gnl|BL_ORD_ID|886 + 58122|pol protein|BAA32832.1|Hepatitis B virus|10407 + 886 + 10 + + + 1 + 13.4678 + 23 + 9.73455 + 4 + 8 + 1 + 5 + 0 + 0 + 4 + 5 + 0 + 5 + SGVPR + SGLPR + SG+PR + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 970 + Query_970 + M_1440 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 971 + Query_971 + M_1441 + 9 + + + 1 + gnl|BL_ORD_ID|1596 + 142232|POSSIBLE CONSERVED TRANSMEMBRANE PROTEIN|CAB00937.1|Mycobacterium tuberculosis|1773 + 1596 + 19 + + + 1 + 6.53423 + 5 + 16334.9 + 8 + 9 + 13 + 14 + 0 + 0 + 2 + 2 + 0 + 2 + VY + VY + VY + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 972 + Query_972 + M_1442 + 9 + + + 1 + gnl|BL_ORD_ID|96 + 6591|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 + 96 + 18 + + + 1 + 14.2382 + 25 + 3.03664 + 2 + 9 + 9 + 16 + 0 + 0 + 4 + 4 + 0 + 8 + FHNPKPLF + LHGPTPLL + H P PL + + + + + 2 + gnl|BL_ORD_ID|707 + 43447|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 + 707 + 20 + + + 1 + 13.0826 + 22 + 19.8728 + 1 + 9 + 6 + 14 + 0 + 0 + 5 + 5 + 0 + 9 + FFHNPKPLF + FFFNPGELL + FF NP L + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 973 + Query_973 + M_1443 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 974 + Query_974 + M_1444 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 975 + Query_975 + M_1445 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 976 + Query_976 + M_1446 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 977 + Query_977 + M_1447 + 9 + + + 1 + gnl|BL_ORD_ID|133 + 9415|Superoxide dismutase|P17670.1|Mycobacterium tuberculosis|1773 + 133 + 10 + + + 1 + 13.853 + 24 + 4.3044 + 1 + 9 + 1 + 9 + 0 + 0 + 5 + 5 + 0 + 9 + DFWYHAVVL + DMWEHAFYL + D W HA L + + + + + 2 + gnl|BL_ORD_ID|132 + 9414|Superoxide dismutase|P17670.1|Mycobacterium tuberculosis|1773 + 132 + 9 + + + 1 + 13.853 + 24 + 5.45887 + 1 + 9 + 1 + 9 + 0 + 0 + 5 + 5 + 0 + 9 + DFWYHAVVL + DMWEHAFYL + D W HA L + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 978 + Query_978 + M_1448 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 979 + Query_979 + M_1449 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 980 + Query_980 + M_1450 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 981 + Query_981 + M_1451 + 9 + + + 1 + gnl|BL_ORD_ID|320 + 21000|glutamine synthetase GLNA1 (glutamine synthase) (GS-I)|NP_216736.1|Mycobacterium tuberculosis|1773 + 320 + 9 + + + 1 + 14.2382 + 25 + 4.07578 + 3 + 9 + 3 + 9 + 0 + 0 + 4 + 6 + 0 + 7 + VHRAPSI + LHHAPSL + +H APS+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 982 + Query_982 + M_1452 + 9 + + + + + 2334 + 25004 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225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 988 + Query_988 + M_1458 + 9 + + + 1 + gnl|BL_ORD_ID|931 + 61077|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 + 931 + 9 + + + 1 + 14.6234 + 26 + 2.07889 + 1 + 8 + 2 + 9 + 0 + 0 + 4 + 7 + 0 + 8 + SHTGTFLL + SHSGSFQI + SH+G+F + + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 989 + Query_989 + M_1459 + 9 + + + 1 + gnl|BL_ORD_ID|1861 + 180440|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 + 1861 + 15 + + + 1 + 12.6974 + 21 + 22.514 + 4 + 9 + 8 + 13 + 0 + 0 + 3 + 6 + 0 + 6 + AWSNGH + SWNSGH + +W++GH + + + + + 2 + gnl|BL_ORD_ID|1926 + 180734|Nonstructural protein NS3|NP_739587.2|Dengue virus 2|11060 + 1926 + 9 + + + 1 + 12.3122 + 20 + 40.5299 + 4 + 9 + 2 + 7 + 0 + 0 + 3 + 6 + 0 + 6 + AWSNGH + SWNSGH + +W++GH + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 990 + Query_990 + M_1460 + 9 + + + 1 + gnl|BL_ORD_ID|163 + 12588|Glycoprotein B precursor (Glycoprotein II)|P09257.1|Human alphaherpesvirus 3|10335 + 163 + 11 + + + 1 + 14.2382 + 25 + 3.80034 + 2 + 9 + 2 + 9 + 0 + 0 + 5 + 6 + 0 + 8 + IPDSISKF + ITDTIDKF + I D+I KF + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 991 + Query_991 + M_1461 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 992 + Query_992 + M_1462 + 9 + + + 1 + gnl|BL_ORD_ID|1036 + 69398|X protein|AAP06597.1|Hepatitis B virus|10407 + 1036 + 9 + + + 1 + 11.927 + 19 + 87.0561 + 4 + 9 + 2 + 7 + 0 + 0 + 4 + 4 + 0 + 6 + LCHNPV + LCLRPV + LC PV + + + + + 2 + gnl|BL_ORD_ID|310 + 20787|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 + 310 + 10 + + + 1 + 11.927 + 19 + 93.6922 + 1 + 7 + 2 + 8 + 0 + 0 + 4 + 4 + 0 + 7 + FCPLCHN + LCPHCIN + CP C N + + + + + 3 + gnl|BL_ORD_ID|309 + 20786|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 + 309 + 9 + + + 1 + 11.927 + 19 + 102.395 + 1 + 7 + 2 + 8 + 0 + 0 + 4 + 4 + 0 + 7 + FCPLCHN + LCPHCIN + CP C N + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 993 + Query_993 + M_1463 + 9 + + + 1 + gnl|BL_ORD_ID|743 + 47946|envelope glycoprotein|AAC28452.1|Human immunodeficiency virus 1|11676 + 743 + 20 + + + 1 + 13.853 + 24 + 5.6992 + 2 + 6 + 14 + 18 + 0 + 0 + 4 + 5 + 0 + 5 + VLKCN + ILKCN + +LKCN + + + + + 2 + gnl|BL_ORD_ID|1570 + 141396|ribonucleotide reductase subunit 1|NP_044641.1|Human alphaherpesvirus 1|10298 + 1570 + 9 + + + 1 + 13.0826 + 22 + 22.6682 + 1 + 9 + 1 + 9 + 0 + 0 + 5 + 6 + 0 + 9 + RVLKCNVHL + RILGVLVHL + R+L VHL + + + + + 3 + gnl|BL_ORD_ID|156 + 11956|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 + 156 + 11 + + + 1 + 11.927 + 19 + 69.0218 + 1 + 7 + 4 + 10 + 0 + 0 + 5 + 5 + 0 + 7 + RVLKCNV + RVLCCYV + RVL C V + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 994 + Query_994 + M_1464 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 995 + Query_995 + M_1465 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 996 + Query_996 + M_1466 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 997 + Query_997 + M_1467 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 998 + Query_998 + M_1468 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 999 + Query_999 + M_1469 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1000 + Query_1000 + M_1470 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1001 + Query_1001 + M_1471 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1002 + Query_1002 + M_1472 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1003 + Query_1003 + M_1473 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1004 + Query_1004 + M_1474 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1005 + Query_1005 + M_1475 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1006 + Query_1006 + M_1476 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1007 + Query_1007 + M_1477 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1008 + Query_1008 + M_1478 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1009 + Query_1009 + M_1479 + 9 + + + 1 + gnl|BL_ORD_ID|490 + 30946|HCV-1|AAA45676.1|Hepatitis C virus genotype 1|41856 + 490 + 20 + + + 1 + 12.6974 + 21 + 22.5677 + 4 + 9 + 14 + 19 + 0 + 0 + 3 + 6 + 0 + 6 + NLGIRI + DLGVRV + +LG+R+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 1010 + Query_1010 + M_1480 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1011 + Query_1011 + M_1481 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1012 + Query_1012 + M_1482 + 9 + + + 1 + gnl|BL_ORD_ID|1432 + 116123|nucleocapsid protein|ABP49342.1|Influenza A virus (A/California/10/1978(H1N1))|425557 + 1432 + 9 + + + 1 + 11.927 + 19 + 82.8955 + 2 + 9 + 2 + 9 + 0 + 0 + 4 + 5 + 0 + 8 + PFISRTMM + PFDKSTVM + PF T+M + + + + + 2 + gnl|BL_ORD_ID|1232 + 97467|nucleocapsid protein|ACP44251.1|Influenza A virus (A/Fujian/411/2002(H3N2))|293090 + 1232 + 9 + + + 1 + 11.927 + 19 + 94.432 + 2 + 9 + 2 + 9 + 0 + 0 + 4 + 5 + 0 + 8 + PFISRTMM + PFEKSTIM + PF T+M + + + + + 3 + gnl|BL_ORD_ID|649 + 38471|nucleocapsid protein|ABC46569.1|Influenza A virus (A/Memphis/4/1980(H3N2))|383578 + 649 + 9 + + + 1 + 11.927 + 19 + 99.1366 + 2 + 9 + 2 + 9 + 0 + 0 + 4 + 5 + 0 + 8 + PFISRTMM + PFEKSTVM + PF T+M + + + + + 4 + gnl|BL_ORD_ID|647 + 38466|nucleocapsid protein|ABF21284.1|Influenza A virus (A/Iran/1/1957(H2N2))|488233 + 647 + 9 + + + 1 + 11.5418 + 18 + 165.102 + 2 + 9 + 2 + 9 + 0 + 0 + 4 + 5 + 0 + 8 + PFISRTMM + PFDKPTIM + PF T+M + + + + + 5 + gnl|BL_ORD_ID|648 + 38468|nucleoprotein|CAA24268.1|Influenza A virus (A/Puerto Rico/8/1934(H1N1))|211044 + 648 + 9 + + + 1 + 11.5418 + 18 + 181.349 + 2 + 9 + 2 + 9 + 0 + 0 + 4 + 5 + 0 + 8 + PFISRTMM + PFDRTTIM + PF T+M + + + + + 6 + gnl|BL_ORD_ID|650 + 38472|nucleoprotein|AAV48837.1|Influenza A virus (A/Brevig Mission/1/1918(H1N1))|88776 + 650 + 9 + + + 1 + 11.5418 + 18 + 187.089 + 2 + 9 + 2 + 9 + 0 + 0 + 4 + 5 + 0 + 8 + PFISRTMM + PFERATIM + PF T+M + + + + + 7 + gnl|BL_ORD_ID|1434 + 116136|nucleocapsid protein|ACS34671.1|Influenza A virus (A/Auckland/1/2009(H1N1))|642794 + 1434 + 9 + + + 1 + 11.1566 + 17 + 199.082 + 2 + 9 + 2 + 9 + 0 + 0 + 4 + 5 + 0 + 8 + PFISRTMM + PFERATVM + PF T+M + + + + + 8 + gnl|BL_ORD_ID|1433 + 116127|Nucleoprotein|P15682.1|Influenza A virus (A/Wilson-Smith/1933(H1N1))|381518 + 1433 + 9 + + + 1 + 11.1566 + 17 + 291.863 + 2 + 9 + 2 + 9 + 0 + 0 + 4 + 5 + 0 + 8 + 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gnl|BL_ORD_ID|1339 + 107925|polyprotein|AAF65964.1|Hepatitis C virus|11103 + 1339 + 10 + + + 1 + 12.6974 + 21 + 32.5356 + 1 + 6 + 1 + 6 + 0 + 0 + 4 + 5 + 0 + 6 + KAYGRD + KAHGTD + KA+G D + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 1089 + Query_1089 + M_1559 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1090 + Query_1090 + M_1560 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1091 + Query_1091 + M_1561 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1092 + Query_1092 + M_1562 + 9 + + + 1 + gnl|BL_ORD_ID|1769 + 155096|RL2|CAB06760.1|Human alphaherpesvirus 2|10310 + 1769 + 15 + + + 1 + 11.927 + 19 + 86.1406 + 1 + 7 + 4 + 10 + 0 + 0 + 2 + 4 + 0 + 7 + YCFGCLS + FCIPCMK + +C C+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 1093 + Query_1093 + M_1563 + 9 + + + 1 + gnl|BL_ORD_ID|1050 + 69714|Large envelope protein|SRC279965|Hepatitis B virus|10407 + 1050 + 9 + + + 1 + 12.3122 + 20 + 53.938 + 4 + 9 + 4 + 9 + 0 + 0 + 3 + 5 + 0 + 6 + GGFFVI + AGFFIL + GFF++ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 1094 + Query_1094 + M_1564 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1095 + Query_1095 + M_1565 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1096 + Query_1096 + M_1566 + 9 + + + 1 + gnl|BL_ORD_ID|1186 + 93431|pre-C/C protein|ABY54138.1|Hepatitis B virus|10407 + 1186 + 20 + + + 1 + 11.5418 + 18 + 98.2529 + 1 + 9 + 2 + 10 + 0 + 0 + 4 + 6 + 0 + 9 + RLMHQLLVI + QLFHLCLII + +L H L+I + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 1097 + Query_1097 + M_1567 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1098 + Query_1098 + M_1568 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1099 + Query_1099 + M_1569 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1100 + Query_1100 + M_1570 + 9 + + + 1 + gnl|BL_ORD_ID|383 + 23601|Genome polyprotein|SRC279960|Hepatitis C virus (isolate H77)|63746 + 383 + 21 + + + 1 + 14.2382 + 25 + 3.66708 + 4 + 9 + 3 + 8 + 0 + 0 + 5 + 5 + 0 + 6 + PAGHLV + PAGHAV + PAGH V + + + + + 2 + gnl|BL_ORD_ID|597 + 37127|polyprotein|AAY82030.1|Hepatitis C virus genotype 1|41856 + 597 + 9 + + + 1 + 13.853 + 24 + 5.00793 + 4 + 9 + 4 + 9 + 0 + 0 + 5 + 5 + 0 + 6 + PAGHLV + PAGHAV + PAGH V + + + + + 3 + gnl|BL_ORD_ID|598 + 37136|Genome polyprotein|P27958.3|Hepatitis C virus|11103 + 598 + 9 + + + 1 + 12.6974 + 21 + 38.5226 + 4 + 9 + 4 + 9 + 0 + 0 + 4 + 4 + 0 + 6 + PAGHLV + PTGHAV + P GH V + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 1101 + Query_1101 + M_1571 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1102 + Query_1102 + M_1572 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1103 + Query_1103 + M_1573 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1104 + Query_1104 + M_1574 + 9 + + + 1 + gnl|BL_ORD_ID|320 + 21000|glutamine synthetase GLNA1 (glutamine synthase) (GS-I)|NP_216736.1|Mycobacterium tuberculosis|1773 + 320 + 9 + + + 1 + 11.5418 + 18 + 150.225 + 1 + 8 + 2 + 9 + 0 + 0 + 3 + 6 + 0 + 8 + MVHLVPAL + LLHHAPSL + ++H P+L + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 1105 + Query_1105 + M_1575 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1106 + Query_1106 + M_1576 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1107 + Query_1107 + M_1577 + 9 + + + 1 + gnl|BL_ORD_ID|10 + 1000|glycoprotein gp35/37|AAC59622.1|Human gammaherpesvirus 8|37296 + 10 + 15 + + + 1 + 13.0826 + 22 + 21.0678 + 1 + 9 + 5 + 13 + 0 + 0 + 4 + 5 + 0 + 9 + NHLNIAWEL 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Query_1114 + M_1584 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1115 + Query_1115 + M_1585 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1116 + Query_1116 + M_1586 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1117 + Query_1117 + M_1587 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1118 + Query_1118 + M_1588 + 9 + + + 1 + gnl|BL_ORD_ID|1561 + 141277|transactivating tegument protein VP16|NP_044650.1|Human alphaherpesvirus 1|10298 + 1561 + 10 + + + 1 + 12.6974 + 21 + 26.0802 + 1 + 8 + 1 + 8 + 0 + 0 + 4 + 5 + 0 + 8 + FTQYLGLS + FTDALGID + FT LG+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 1119 + Query_1119 + M_1589 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1120 + Query_1120 + M_1590 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1121 + Query_1121 + M_1591 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1122 + Query_1122 + M_1592 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1123 + Query_1123 + M_1593 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1124 + Query_1124 + M_1594 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1125 + Query_1125 + M_1595 + 9 + + + 1 + gnl|BL_ORD_ID|1392 + 110335|E7|AAD33253.1|Human papillomavirus type 16|333760 + 1392 + 32 + + + 1 + 14.2382 + 25 + 4.6455 + 2 + 7 + 12 + 17 + 0 + 0 + 4 + 6 + 0 + 6 + LLDLRP + MLDLQP + +LDL+P + + + + + 2 + gnl|BL_ORD_ID|1138 + 75075|E7 protein|ABL96585.1|Human papillomavirus type 16|333760 + 1138 + 10 + + + 1 + 13.853 + 24 + 6.08483 + 2 + 8 + 2 + 8 + 0 + 0 + 4 + 6 + 0 + 7 + LLDLRPS + MLDLQPE + +LDL+P + + + + + 3 + gnl|BL_ORD_ID|1823 + 178351|Protein E7|P03129.1|Human papillomavirus type 16|333760 + 1823 + 15 + + + 1 + 13.853 + 24 + 6.40908 + 2 + 8 + 8 + 14 + 0 + 0 + 4 + 6 + 0 + 7 + LLDLRPS + MLDLQPE + +LDL+P + + + + + 4 + gnl|BL_ORD_ID|1137 + 75074|Protein E7|P03129.1|Human papillomavirus type 16|333760 + 1137 + 9 + + + 1 + 13.853 + 24 + 6.83656 + 2 + 8 + 2 + 8 + 0 + 0 + 4 + 6 + 0 + 7 + LLDLRPS + MLDLQPE + +LDL+P + + + + + 5 + gnl|BL_ORD_ID|1117 + 74288|Protein E7|P36831.1|Human papillomavirus type 52|10618 + 1117 + 10 + + + 1 + 13.4678 + 23 + 9.07951 + 2 + 8 + 2 + 8 + 0 + 0 + 4 + 6 + 0 + 7 + LLDLRPS + ILDLQPE + +LDL+P + + + + + 6 + gnl|BL_ORD_ID|1157 + 76334|Protein E7|P17387.1|Human papillomavirus type 31|10585 + 1157 + 10 + + + 1 + 13.4678 + 23 + 12.2057 + 2 + 8 + 2 + 8 + 0 + 0 + 4 + 6 + 0 + 7 + LLDLRPS + VLDLQPE + +LDL+P + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 1126 + Query_1126 + M_1596 + 9 + + + 1 + gnl|BL_ORD_ID|1688 + 149060|E2 protein|NP_751921.1|Hepatitis C virus (isolate H77)|63746 + 1688 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25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1138 + Query_1138 + M_1608 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1139 + Query_1139 + M_1609 + 9 + + + 1 + gnl|BL_ORD_ID|310 + 20787|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 + 310 + 10 + + + 1 + 12.3122 + 20 + 42.6014 + 2 + 9 + 1 + 8 + 0 + 0 + 4 + 4 + 0 + 8 + SFCPLCHN + GLCPHCIN + CP C N + + + + + 2 + gnl|BL_ORD_ID|309 + 20786|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 + 309 + 9 + + + 1 + 12.3122 + 20 + 51.2985 + 2 + 9 + 1 + 8 + 0 + 0 + 4 + 4 + 0 + 8 + SFCPLCHN + GLCPHCIN + CP C N + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 1140 + Query_1140 + M_1610 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1141 + Query_1141 + M_1611 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1142 + Query_1142 + M_1612 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1143 + Query_1143 + M_1613 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1144 + Query_1144 + M_1614 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1145 + Query_1145 + M_1615 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1146 + Query_1146 + M_1616 + 9 + + + 1 + gnl|BL_ORD_ID|1122 + 74545|TcP2beta|CAA52943.1|Trypanosoma cruzi|5693 + 1122 + 10 + + + 1 + 12.6974 + 21 + 37.8768 + 2 + 7 + 1 + 6 + 0 + 0 + 5 + 5 + 0 + 6 + YLVAYA + YLAAYA + YL AYA + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 1147 + Query_1147 + M_1617 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1148 + Query_1148 + M_1618 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1149 + Query_1149 + M_1619 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1150 + Query_1150 + M_1620 + 9 + + + 1 + gnl|BL_ORD_ID|703 + 42897|RNA polymerase beta-subunit|AAA21416.1|Mycobacterium tuberculosis|1773 + 703 + 9 + + + 1 + 14.2382 + 25 + 4.1461 + 2 + 9 + 1 + 8 + 0 + 0 + 4 + 6 + 0 + 8 + VRYAGPLY + MTYAAPLF + + YA PL+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 1151 + Query_1151 + M_1621 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1152 + Query_1152 + M_1622 + 9 + + + 1 + gnl|BL_ORD_ID|2108 + 186175|polyprotein|AFY10053.1|Dengue virus 3|11069 + 2108 + 10 + + + 1 + 13.853 + 24 + 6.08483 + 1 + 6 + 1 + 6 + 0 + 0 + 4 + 6 + 0 + 6 + TFRDVA + TWRDMA + T+RD+A + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 1153 + Query_1153 + M_1623 + 9 + + + 1 + gnl|BL_ORD_ID|471 + 28594|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 + 471 + 20 + + + 1 + 13.853 + 24 + 4.57317 + 1 + 9 + 9 + 17 + 0 + 0 + 5 + 6 + 0 + 9 + DEKDLWEYI + DQKSLENYI + D+K L YI + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 1154 + Query_1154 + M_1624 + 9 + + + 1 + gnl|BL_ORD_ID|803 + 53405|||| + 803 + 15 + + + 1 + 15.3938 + 28 + 0.751673 + 1 + 9 + 2 + 10 + 0 + 0 + 6 + 6 + 0 + 9 + DPADPTRDL + DPAKPARLL + DPA P R L + + + + + 2 + gnl|BL_ORD_ID|694 + 42295|Circumsporozoite protein precursor|P02893.1|Plasmodium falciparum|5833 + 694 + 9 + + + 1 + 13.853 + 24 + 4.6749 + 2 + 9 + 2 + 9 + 0 + 0 + 4 + 6 + 0 + 8 + PADPTRDL + PNDPNRNV + P DP R++ + + + + + 3 + gnl|BL_ORD_ID|765 + 51311|X protein|ABR68906.1|Hepatitis B virus|10407 + 765 + 9 + + + 1 + 13.0826 + 22 + 17.1877 + 4 + 9 + 3 + 8 + 0 + 0 + 4 + 5 + 0 + 6 + DPTRDL + DPARDV + DP RD+ + + + + + 4 + gnl|BL_ORD_ID|448 + 27241|Spike glycoprotein precursor|P59594.1|SARS coronavirus|227859 + 448 + 9 + + + 1 + 11.927 + 19 + 82.8955 + 1 + 6 + 4 + 9 + 0 + 0 + 4 + 4 + 0 + 6 + DPADPT + DPLKPT + DP PT + + + + + + + 2334 + 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2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1303 + Query_1303 + M_1773 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1304 + Query_1304 + M_1774 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1305 + Query_1305 + M_1775 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1306 + Query_1306 + M_1776 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1307 + Query_1307 + M_1777 + 9 + + + 1 + gnl|BL_ORD_ID|1813 + 177701|polyprotein|ACZ60104.1|Hepatitis C virus subtype 3a|356426 + 1813 + 18 + + + 1 + 15.3938 + 28 + 0.594437 + 2 + 9 + 2 + 9 + 0 + 0 + 4 + 6 + 0 + 8 + HAQVCSLY + KAKICGLY + A++C LY + + + + + 2 + gnl|BL_ORD_ID|1793 + 164264|nucleocapsid protein|AAA43837.1|Hantaan virus 76-118|11602 + 1793 + 15 + + + 1 + 14.6234 + 26 + 2.07692 + 1 + 9 + 6 + 14 + 0 + 0 + 4 + 5 + 0 + 9 + FHAQVCSLY + YRTAVCGLY + + 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M_1816 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1347 + Query_1347 + M_1817 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1348 + Query_1348 + M_1818 + 9 + + + 1 + gnl|BL_ORD_ID|1741 + 150649|polyprotein|AGW21594.1|Dengue virus 1|11053 + 1741 + 10 + + + 1 + 11.1566 + 17 + 228.313 + 2 + 9 + 3 + 10 + 0 + 0 + 4 + 5 + 0 + 8 + QQNCAAYL + QDNQLAYV + Q N AY+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 1349 + Query_1349 + M_1819 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1350 + Query_1350 + M_1820 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1351 + Query_1351 + M_1821 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1352 + Query_1352 + M_1822 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1353 + Query_1353 + M_1823 + 9 + + + 1 + gnl|BL_ORD_ID|910 + 59585|polymerase|AAD16253.1|Hepatitis B virus|10407 + 910 + 9 + + + 1 + 13.0826 + 22 + 18.4218 + 1 + 6 + 3 + 8 + 0 + 0 + 4 + 5 + 0 + 6 + YAQTPS + YADSPS + YA +PS + + + + + 2 + gnl|BL_ORD_ID|793 + 53041|phosphorylated matrix protein (pp65)|AAA45996.1|Human betaherpesvirus 5|10359 + 793 + 11 + + + 1 + 12.3122 + 20 + 59.6252 + 4 + 9 + 3 + 8 + 0 + 0 + 4 + 4 + 0 + 6 + TPSKTP + TPDSTP + TP TP + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 1354 + Query_1354 + M_1824 + 9 + + + 1 + gnl|BL_ORD_ID|442 + 27168|envelope protein|BAF48755.1|Hepatitis B virus|10407 + 442 + 9 + + + 1 + 10.7714 + 16 + 411.363 + 1 + 6 + 2 + 7 + 0 + 0 + 4 + 5 + 0 + 6 + LLLCFL + LLLCLI + LLLC + + + + + + 2 + gnl|BL_ORD_ID|621 + 37466|surface antigen|BAF44879.1|Hepatitis B virus|10407 + 621 + 9 + + + 1 + 10.7714 + 16 + 497.585 + 1 + 6 + 1 + 6 + 0 + 0 + 4 + 5 + 0 + 6 + LLLCFL + LLLCLI + LLLC + + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + 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+TFFSSSQSA +>M_1843 +YANNHCIRT +>M_1844 +FYGMTEMNY +>M_1845 +LQFYGMTEM +>M_1846 +LQFYGMTEM +>M_1847 +ALWMYRSLM +>M_1848 +ALWMYRSLM +>M_1849 +QALWMYRSL +>M_1850 +SFRKEKRNL +>M_1851 +LTSQDLAGY +>M_1852 +MAGHGWGAL +>M_1853 +VMSYGEQPY +>M_1854 +SVSDVFHGI +>M_1855 +IPNDNTLSL +>M_1856 +KTIPNDNTL +>M_1857 +KTIPNDNTL +>M_1858 +TLSLRICTI +>M_1859 +FSMRARIDV +>M_1860 +RLLGQKFSM +>M_1861 +IYMENERRM +>M_1862 +QFLLELYSL +>M_1863 +RVIRYVIGV +>M_1864 +QYLSLINYY +>M_1865 +STLQYLSLI +>M_1866 +IAQGKPVTL +>M_1867 +SVIAQGKPV +>M_1868 +FAIMHAQRT +>M_1869 +HTNAVFAIM +>M_1870 +NHTNAVFAI +>M_1871 +HHHHHHQAW +>M_1872 +QAWPPPSSA +>M_1873 +AHTVARGPV +>M_1874 +ALQTFAHTV +>M_1875 +EIYTKNHAY +>M_1876 +FGYQLKEIY +>M_1877 +IYTKNHAYI +>M_1878 +YTKNHAYII +>M_1879 +YTKNHAYII +>M_1880 +HAFDRYETT +>M_1881 +TTHSRPVTL +>M_1882 +TTHSRPVTL +>M_1883 +YETTHSRPV +>M_1884 +VLFDVAGQV +>M_1885 +VLFDVAGQV +>M_1886 +ESKPAPAEV +>M_1887 +LNVEKTEKI +>M_1888 +MVIVFYGTL +>M_1889 +MVIVFYGTL +>M_1890 +SAHLTMVIV +>M_1891 +YETFGAASF +>M_1892 +RGVPPLRTV +>M_1893 +TAESCRSTL +>M_1894 +TAESCRSTL +>M_1895 +RVRAAGQRL +>M_1896 +DVHARESKI +>M_1897 +NVPPTVQKV +>M_1898 +CYYPMAGYI +>M_1899 +CYYPMAGYI +>M_1900 +NTRQCYYPM +>M_1901 +LGYRWCLHV +>M_1902 +LLLGYRWCL +>M_1903 +TAHSSVLTL +>M_1904 +TAHSSVLTL +>M_1905 +FPSNHLGDL +>M_1906 +LLLAHKKKV +>M_1907 +AQILEQVEV +>M_1908 +QIFKCKGTL +>M_1909 +QIFKCKGTL +>M_1910 +TLVGHQGPV +>M_1911 +TLVGHQGPV +>M_1912 +DAVELWAIV +>M_1913 +VDLPLTSTI +>M_1914 +NVVNGQMRF +>M_1915 +MGAPGSEII +>M_1916 +FSQFSNLKV +>M_1917 +KAFSQFSNL +>M_1918 +HFSVSSNLL +>M_1919 +KHFSVSSNL +>M_1920 +KHFSVSSNL diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_118813_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_118813_1_T_iedb.xml new file mode 100755 index 00000000..0c91beb3 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_118813_1_T_iedb.xml @@ -0,0 +1,2608 @@ + + + + blastp + BLASTP 2.2.30+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta + Query_1 + M_1827 + 9 + + + BLOSUM62 + 100000000 + 11 + 1 + F + + + + + 1 + Query_1 + M_1827 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 2 + Query_2 + M_1828 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 3 + Query_3 + M_1829 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 4 + Query_4 + M_1830 + 9 + + + 1 + gnl|BL_ORD_ID|1103 + 72790|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 + 1103 + 9 + + + 1 + 13.853 + 24 + 5.65074 + 1 + 9 + 1 + 9 + 0 + 0 + 3 + 6 + 0 + 9 + WVNEFGEVF + WLSDCGEAL + W+++ GE + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 5 + Query_5 + M_1831 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 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2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 61 + Query_61 + M_1887 + 9 + + + 1 + gnl|BL_ORD_ID|569 + 35568|Polyprotein|Q9J8D4|Dengue virus 2|11060 + 569 + 8 + + + 1 + 11.5418 + 18 + 135.128 + 3 + 8 + 1 + 6 + 0 + 0 + 4 + 6 + 0 + 6 + VEKTEK + LEKTKK + +EKT+K + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 62 + Query_62 + M_1888 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 63 + Query_63 + M_1889 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 64 + Query_64 + M_1890 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 65 + Query_65 + M_1891 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 66 + Query_66 + M_1892 + 9 + + + 1 + gnl|BL_ORD_ID|576 + 36345|polyprotein|ABR25251.1|Hepatitis C virus (isolate H77)|63746 + 576 + 10 + + + 1 + 16.1642 + 30 + 0.338287 + 2 + 8 + 2 + 8 + 0 + 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tularensis subsp. tularensis SCHU S4|177416 + 1160 + 10 + + + 1 + 11.1566 + 17 + 190.083 + 2 + 9 + 1 + 8 + 0 + 0 + 4 + 5 + 0 + 8 + YYPMAGYI + YYLDRGYL + YY GY+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 73 + Query_73 + M_1899 + 9 + + + 1 + gnl|BL_ORD_ID|1160 + 76532|outer membrane protein|YP_170495.1|Francisella tularensis subsp. tularensis SCHU S4|177416 + 1160 + 10 + + + 1 + 11.1566 + 17 + 190.083 + 2 + 9 + 1 + 8 + 0 + 0 + 4 + 5 + 0 + 8 + YYPMAGYI + YYLDRGYL + YY GY+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 74 + Query_74 + M_1900 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 75 + Query_75 + M_1901 + 9 + + + 1 + gnl|BL_ORD_ID|629 + 37607|kaposin|AAC57155.1|Human gammaherpesvirus 8|37296 + 629 + 9 + + + 1 + 12.6974 + 21 + 23.4633 + 2 + 7 + 4 + 9 + 0 + 0 + 4 + 5 + 0 + 6 + GYRWCL + GWRWRL + G+RW L + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 76 + Query_76 + M_1902 + 9 + + + 1 + gnl|BL_ORD_ID|629 + 37607|kaposin|AAC57155.1|Human gammaherpesvirus 8|37296 + 629 + 9 + + + 1 + 14.2382 + 25 + 3.87216 + 1 + 9 + 1 + 9 + 0 + 0 + 6 + 7 + 0 + 9 + LLLGYRWCL + LLNGWRWRL + LL G+RW L + + + + + 2 + gnl|BL_ORD_ID|626 + 37536|Spike glycoprotein precursor|P15423.1|Human coronavirus 229E|11137 + 626 + 9 + + + 1 + 9.61583 + 13 + 1239.7 + 1 + 7 + 1 + 7 + 0 + 0 + 4 + 4 + 0 + 7 + LLLGYRW + LLLNCLW + LLL W + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 77 + Query_77 + M_1903 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 78 + Query_78 + M_1904 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 79 + Query_79 + M_1905 + 9 + + + 1 + gnl|BL_ORD_ID|741 + 47760|EBNA-1 protein|Q777E1|Human gammaherpesvirus 4|10376 + 741 + 15 + + + 1 + 13.0826 + 22 + 16.6732 + 2 + 8 + 5 + 11 + 0 + 0 + 4 + 5 + 0 + 7 + PSNHLGD + PGNGLGE + P N LG+ + + + + + + + 2334 + 25004 + 0 + 225036 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a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_119118_2_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_119118_2_T.fasta new file mode 100755 index 00000000..a2c43fcd --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_119118_2_T.fasta @@ -0,0 +1,50 @@ +>M_1921 +YQVLAMSTK +>M_1922 +KLSSEAKTK +>M_1923 +TVLRLFPFR +>M_1924 +TVLRLFPFR +>M_1925 +TVKDVHKAK +>M_1926 +TIHNVNFSK +>M_1927 +TIHNVNFSK +>M_1928 +SETTFDIFV +>M_1929 +GMHFSPGAR +>M_1930 +FLTQPVAPK +>M_1931 +KAISFYMKR +>M_1932 +RTVAQVTKK +>M_1933 +RTVAQVTKK +>M_1934 +SEDKKNTKL +>M_1935 +RVAAGVQIK +>M_1936 +RVAAGVQIK +>M_1937 +VVGAVGVGK +>M_1938 +VVGAVGVGK +>M_1939 +TTTPTLKEK +>M_1940 +QSLYIDRLK +>M_1941 +TTIHYNYMY +>M_1942 +TECIIAMSF +>M_1943 +IESSYLESL +>M_1944 +AEEEEEEVV +>M_1945 +TENHQPVCL diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_119118_2_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_119118_2_T_iedb.xml new file mode 100755 index 00000000..6c7a7c78 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_119118_2_T_iedb.xml @@ -0,0 +1,577 @@ + + + + blastp + BLASTP 2.2.30+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta + Query_1 + M_1921 + 9 + + + BLOSUM62 + 100000000 + 11 + 1 + F + + + + + 1 + Query_1 + M_1921 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 2 + Query_2 + M_1922 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 3 + Query_3 + M_1923 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 4 + Query_4 + M_1924 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 5 + Query_5 + M_1925 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 6 + Query_6 + M_1926 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 7 + Query_7 + M_1927 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 8 + Query_8 + M_1928 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 9 + Query_9 + M_1929 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 10 + Query_10 + M_1930 + 9 + + + 1 + gnl|BL_ORD_ID|2271 + 419002|PPE family protein PPE68|KAM81677.1|Mycobacterium tuberculosis H37Ra|419947 + 2271 + 10 + + + 1 + 13.4678 + 23 + 7.76238 + 1 + 8 + 1 + 8 + 0 + 0 + 4 + 6 + 0 + 8 + FLTQPVAP + LIEKPVAP + + +PVAP + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 11 + Query_11 + M_1931 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 12 + Query_12 + M_1932 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 13 + Query_13 + M_1933 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 14 + Query_14 + M_1934 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 15 + Query_15 + M_1935 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 16 + Query_16 + M_1936 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 17 + Query_17 + M_1937 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 18 + Query_18 + M_1938 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 19 + Query_19 + M_1939 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 20 + Query_20 + M_1940 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 21 + Query_21 + M_1941 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 22 + Query_22 + M_1942 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 23 + Query_23 + M_1943 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 24 + Query_24 + M_1944 + 9 + + + 1 + gnl|BL_ORD_ID|1398 + 110431|E7|AAD33253.1|Human papillomavirus type 16|333760 + 1398 + 36 + + + 1 + 10.7714 + 16 + 242.357 + 1 + 6 + 13 + 18 + 0 + 0 + 4 + 6 + 0 + 6 + AEEEEE + SEEEDE + +EEE+E + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 25 + Query_25 + M_1945 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + + diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_119914_2_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_119914_2_T.fasta new file mode 100755 index 00000000..34547d25 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_119914_2_T.fasta @@ -0,0 +1,58 @@ +>M_1946 +GQLGGLAGK +>M_1947 +LSDWGPHFK +>M_1948 +LSDWGPHFK +>M_1949 +KPASKKEWI +>M_1950 +TTKSEAIEK +>M_1951 +IVRASGCEL +>M_1952 +VPTELNGSM +>M_1953 +VPLFPARVL +>M_1954 +APAQPPMLA +>M_1955 +VVGARGVGK +>M_1956 +VVGARGVGK +>M_1957 +KLCNSGDFR +>M_1958 +HPLTENSPL +>M_1959 +STVRKSPWK +>M_1960 +STVRKSPWK +>M_1961 +LIRMYNINK +>M_1962 +LIRMYNINK +>M_1963 +SPWPLSSLT +>M_1964 +SLKSTRAVF +>M_1965 +SVGSASSLK +>M_1966 +SVGSASSLK +>M_1967 +KGYGGFSRY +>M_1968 +KGYGGFSRY +>M_1969 +KAIGKSRPY +>M_1970 +KTLRKAIGK +>M_1971 +KTLRKAIGK +>M_1972 +QALQKTLRK +>M_1973 +SYQSTGDPK +>M_1974 +VPEWSNNS* diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_119914_2_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_119914_2_T_iedb.xml new file mode 100755 index 00000000..6278990d --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_119914_2_T_iedb.xml @@ -0,0 +1,739 @@ + + + + blastp + BLASTP 2.2.30+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta + Query_1 + M_1946 + 9 + + + BLOSUM62 + 100000000 + 11 + 1 + F + + + + + 1 + Query_1 + M_1946 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 2 + Query_2 + M_1947 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 3 + Query_3 + M_1948 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 4 + Query_4 + M_1949 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 5 + Query_5 + M_1950 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 6 + Query_6 + M_1951 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 7 + Query_7 + M_1952 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 8 + Query_8 + M_1953 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 9 + Query_9 + M_1954 + 9 + + + 1 + gnl|BL_ORD_ID|889 + 58463|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 + 889 + 20 + + + 1 + 13.0826 + 22 + 16.1327 + 1 + 7 + 3 + 9 + 0 + 0 + 4 + 5 + 0 + 7 + APAQPPM + CPSQEPM + P+Q PM + + + + + 2 + gnl|BL_ORD_ID|749 + 49485|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 + 749 + 11 + + + 1 + 13.0826 + 22 + 16.8999 + 2 + 7 + 1 + 6 + 0 + 0 + 4 + 5 + 0 + 6 + PAQPPM + PSQEPM + P+Q PM + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 10 + Query_10 + M_1955 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 11 + Query_11 + M_1956 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 12 + Query_12 + M_1957 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 13 + Query_13 + M_1958 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 14 + Query_14 + M_1959 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 15 + Query_15 + M_1960 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 16 + Query_16 + M_1961 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 17 + Query_17 + M_1962 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 18 + Query_18 + M_1963 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 19 + Query_19 + M_1964 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 20 + Query_20 + M_1965 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 21 + Query_21 + M_1966 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 22 + Query_22 + M_1967 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 23 + Query_23 + M_1968 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 24 + Query_24 + M_1969 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 25 + Query_25 + M_1970 + 9 + + + 1 + gnl|BL_ORD_ID|115 + 7708|gag polyprotein|BAA00992.1|Human immunodeficiency virus 1|11676 + 115 + 9 + + + 1 + 11.5418 + 18 + 165.102 + 1 + 7 + 3 + 9 + 0 + 0 + 4 + 6 + 0 + 7 + KTLRKAI + KTILKAL + KT+ KA+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 26 + Query_26 + M_1971 + 9 + + + 1 + gnl|BL_ORD_ID|115 + 7708|gag polyprotein|BAA00992.1|Human immunodeficiency virus 1|11676 + 115 + 9 + + + 1 + 11.5418 + 18 + 165.102 + 1 + 7 + 3 + 9 + 0 + 0 + 4 + 6 + 0 + 7 + KTLRKAI + KTILKAL + KT+ KA+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 27 + Query_27 + M_1972 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 28 + Query_28 + M_1973 + 9 + + + 1 + gnl|BL_ORD_ID|26 + 2002|Large envelope protein|SRC279965|Hepatitis B virus|10407 + 26 + 10 + + + 1 + 13.4678 + 23 + 10.0795 + 5 + 8 + 6 + 9 + 0 + 0 + 4 + 4 + 0 + 4 + TGDP + TGDP + TGDP + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 29 + Query_29 + M_1974 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + + diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_119995_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_119995_1_T.fasta new file mode 100755 index 00000000..f889c16c --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_119995_1_T.fasta @@ -0,0 +1,172 @@ +>M_1975 +VLETAAPGV +>M_1976 +AVLDAIPLV +>M_1977 +VLDAIPLVA +>M_1978 +KPVVTEVRM +>M_1979 +MPTNTWSGL +>M_1980 +VFQGHSASI +>M_1981 +SLYDFGELR +>M_1982 +DSMLQTVER +>M_1983 +MLQTVEREK +>M_1984 +LLWKDFDQA +>M_1985 +HVPQVADAI +>M_1986 +LLEMNLMHV +>M_1987 +NLMHVPQVA +>M_1988 +VPQVADAIL +>M_1989 +FLIDGSQSV +>M_1990 +FLIDGSQSV +>M_1991 +SVGPEFQYV +>M_1992 +LALSVTEMV +>M_1993 +RLALSVTEM +>M_1994 +TILQIKEEK +>M_1995 +DYEAVCGHR +>M_1996 +EAVCGHRAR +>M_1997 +ILFQKITNR +>M_1998 +KITNRGDEL +>M_1999 +SPTPALGPA +>M_2000 +LTPQQAQEL +>M_2001 +APLGAPPPL +>M_2002 +SKTPPGAPL +>M_2003 +SKTPPGAPL +>M_2004 +MFQSLGEHI +>M_2005 +SLGEHINTL +>M_2006 +SLGEHINTL +>M_2007 +AVGVGKSAL +>M_2008 +YKLVVVGAV +>M_2009 +AMLWALGFI +>M_2010 +FIWSVLITA +>M_2011 +MLWALGFIF +>M_2012 +QTPLFIWSV +>M_2013 +TPLFIWSVL +>M_2014 +TQYQTPLFI +>M_2015 +IINDGKHHV +>M_2016 +GLSAEEFQL +>M_2017 +SAEEFQLIR +>M_2018 +APTTPKEPA +>M_2019 +LLLLLLLLV +>M_2020 +LLLLLLLVV +>M_2021 +LLLLLLVVV +>M_2022 +LLVVVPWGV +>M_2023 +SRRHSRSPL +>M_2024 +SRRHSRSPL +>M_2025 +GSYSMAIPL +>M_2026 +MAIPLLCSY +>M_2027 +NPGSYSMAI +>M_2028 +RYNPGSYSM +>M_2029 +RYNPGSYSM +>M_2030 +SYSMAIPLL +>M_2031 +CQPHAHCSL +>M_2032 +HAHCSLWRR +>M_2033 +IIQELTIFK +>M_2034 +LPPKPVQVL +>M_2035 +QLPPKPVQV +>M_2036 +GLYASLFPA +>M_2037 +LFPAIIYLF +>M_2038 +LYASLFPAI +>M_2039 +PVYGLYASL +>M_2040 +SLFPAIIYL +>M_2041 +SLFPAIIYL +>M_2042 +SLFPAIIYL +>M_2043 +VYGLYASLF +>M_2044 +VYGLYASLF +>M_2045 +RYNVADVSV +>M_2046 +VSVAICMSL +>M_2047 +YTISDDESF +>M_2048 +YVQYWYYTI +>M_2049 +YVQYWYYTI +>M_2050 +SFYNSNRDF +>M_2051 +SFYNSNRDF +>M_2052 +TISFYNSNR +>M_2053 +CRFELMHFK +>M_2054 +ELMHFKTLY +>M_2055 +ILGDWSNGI +>M_2056 +NGISALYCR +>M_2057 +HIHGGTNQV +>M_2058 +AFTCTSSLL +>M_2059 +KAFTCTSSL +>M_2060 +KAFTCTSSL diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_119995_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_119995_1_T_iedb.xml new file mode 100755 index 00000000..2c8c8541 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_119995_1_T_iedb.xml @@ -0,0 +1,3002 @@ + + + + blastp + BLASTP 2.2.30+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta + Query_1 + M_1975 + 9 + + + BLOSUM62 + 100000000 + 11 + 1 + F + + + + + 1 + Query_1 + M_1975 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 2 + Query_2 + M_1976 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 3 + Query_3 + M_1977 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 4 + Query_4 + M_1978 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 5 + Query_5 + M_1979 + 9 + + + 1 + gnl|BL_ORD_ID|1289 + 102368|E2 protein|NP_751921.1|Hepatitis C virus subtype 1a|31646 + 1289 + 15 + + + 1 + 11.5418 + 18 + 98.8375 + 2 + 6 + 6 + 10 + 0 + 0 + 3 + 4 + 0 + 5 + PTNTW + PTYSW + PT +W + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 6 + Query_6 + M_1980 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 7 + Query_7 + M_1981 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 8 + Query_8 + M_1982 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 9 + Query_9 + M_1983 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 10 + Query_10 + M_1984 + 9 + + + 1 + gnl|BL_ORD_ID|1699 + 149117|envelope glycoprotein|AAV74049.1|Hepatitis C virus (isolate H77)|63746 + 1699 + 18 + + + 1 + 13.4678 + 23 + 11.4723 + 5 + 9 + 2 + 6 + 0 + 0 + 4 + 4 + 0 + 5 + DFDQA + DFDQG + DFDQ + + + + + 2 + gnl|BL_ORD_ID|103 + 6936|Genome polyprotein|P26664.3|Hepatitis C virus (isolate 1)|11104 + 103 + 11 + + + 1 + 13.0826 + 22 + 18.7359 + 5 + 9 + 6 + 10 + 0 + 0 + 4 + 4 + 0 + 5 + DFDQA + DFDQG + DFDQ + + + + + 3 + gnl|BL_ORD_ID|841 + 55226|HCV-1|AAA45676.1|Hepatitis C virus|11103 + 841 + 10 + + + 1 + 13.0826 + 22 + 19.8203 + 5 + 9 + 5 + 9 + 0 + 0 + 4 + 4 + 0 + 5 + DFDQA + DFDQG + DFDQ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 11 + Query_11 + M_1985 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 12 + Query_12 + M_1986 + 9 + + + 1 + gnl|BL_ORD_ID|2280 + 419095|polyprotein|ABR25251.1|Hepatitis C virus|11103 + 2280 + 10 + + + 1 + 11.927 + 19 + 66.6359 + 1 + 7 + 3 + 9 + 0 + 0 + 4 + 6 + 0 + 7 + LLEMNLM + LIEANLL + L+E NL+ + + + + + 2 + gnl|BL_ORD_ID|168 + 13091|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 + 168 + 9 + + + 1 + 11.927 + 19 + 82.8955 + 1 + 7 + 2 + 8 + 0 + 0 + 4 + 6 + 0 + 7 + LLEMNLM + LIEANLL + L+E NL+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 13 + Query_13 + M_1987 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 14 + Query_14 + M_1988 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 15 + Query_15 + M_1989 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 16 + Query_16 + M_1990 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 17 + Query_17 + M_1991 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 18 + Query_18 + M_1992 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 19 + Query_19 + M_1993 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 20 + Query_20 + M_1994 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 21 + Query_21 + M_1995 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 22 + Query_22 + M_1996 + 9 + + + 1 + gnl|BL_ORD_ID|343 + 21635|gag protein|ABO73990.1|Human immunodeficiency virus 1|11676 + 343 + 9 + + + 1 + 13.4678 + 23 + 10.3786 + 5 + 9 + 3 + 7 + 0 + 0 + 4 + 5 + 0 + 5 + GHRAR + GHKAR + GH+AR + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 23 + Query_23 + M_1997 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 24 + Query_24 + M_1998 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 25 + Query_25 + M_1999 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 26 + Query_26 + M_2000 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 27 + Query_27 + M_2001 + 9 + + + 1 + gnl|BL_ORD_ID|1110 + 73059|kaposin|AAC57155.1|Human gammaherpesvirus 8|37296 + 1110 + 15 + + + 1 + 14.2382 + 25 + 2.93584 + 3 + 9 + 5 + 11 + 0 + 0 + 6 + 6 + 0 + 7 + LGAPPPL + LGAIPPL + LGA PPL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 28 + Query_28 + M_2002 + 9 + + + 1 + gnl|BL_ORD_ID|1187 + 93536|core protein|AAL31859.1|Hepatitis B virus|10407 + 1187 + 11 + + + 1 + 12.6974 + 21 + 26.8092 + 4 + 9 + 5 + 10 + 0 + 0 + 4 + 5 + 0 + 6 + PPGAPL + PPNAPI + PP AP+ + + + + + 2 + gnl|BL_ORD_ID|1316 + 107754|Genome polyprotein|P26664.3|Hepatitis C virus|11103 + 1316 + 10 + + + 1 + 12.6974 + 21 + 30.9217 + 3 + 7 + 2 + 6 + 0 + 0 + 4 + 5 + 0 + 5 + TPPGA + TPPGS + TPPG+ + + + + + 3 + gnl|BL_ORD_ID|1766 + 154857|tegument protein|CAB06735.1|Human alphaherpesvirus 2|10310 + 1766 + 16 + + + 1 + 4.99343 + 1 + 101281 + 8 + 9 + 15 + 16 + 0 + 0 + 1 + 2 + 0 + 2 + PL + PV + P+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 29 + Query_29 + M_2003 + 9 + + + 1 + gnl|BL_ORD_ID|1187 + 93536|core protein|AAL31859.1|Hepatitis B virus|10407 + 1187 + 11 + + + 1 + 12.6974 + 21 + 26.8092 + 4 + 9 + 5 + 10 + 0 + 0 + 4 + 5 + 0 + 6 + PPGAPL + PPNAPI + PP AP+ + + + + + 2 + gnl|BL_ORD_ID|1316 + 107754|Genome polyprotein|P26664.3|Hepatitis C virus|11103 + 1316 + 10 + + + 1 + 12.6974 + 21 + 30.9217 + 3 + 7 + 2 + 6 + 0 + 0 + 4 + 5 + 0 + 5 + TPPGA + TPPGS + TPPG+ + + + + + 3 + gnl|BL_ORD_ID|1766 + 154857|tegument protein|CAB06735.1|Human alphaherpesvirus 2|10310 + 1766 + 16 + + + 1 + 4.99343 + 1 + 101281 + 8 + 9 + 15 + 16 + 0 + 0 + 1 + 2 + 0 + 2 + PL + PV + P+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 30 + Query_30 + M_2004 + 9 + + + 1 + gnl|BL_ORD_ID|1172 + 79308|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 + 1172 + 16 + + + 1 + 13.853 + 24 + 7.02995 + 1 + 9 + 1 + 9 + 0 + 0 + 4 + 7 + 0 + 9 + MFQSLGEHI + MEPTLGQHL + M +LG+H+ + + + + + 2 + gnl|BL_ORD_ID|981 + 64821|Protein Tax-1|P03409.2|Human T-lymphotropic virus 1|11908 + 981 + 9 + + + 1 + 13.0826 + 22 + 20.0871 + 4 + 9 + 1 + 6 + 0 + 0 + 3 + 6 + 0 + 6 + SLGEHI + TLGQHL + +LG+H+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 31 + Query_31 + M_2005 + 9 + + + 1 + gnl|BL_ORD_ID|1172 + 79308|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 + 1172 + 16 + + + 1 + 16.1642 + 30 + 0.328782 + 1 + 9 + 4 + 12 + 0 + 0 + 5 + 8 + 0 + 9 + SLGEHINTL + TLGQHLPTL + +LG+H+ TL + + + + + 2 + gnl|BL_ORD_ID|981 + 64821|Protein Tax-1|P03409.2|Human T-lymphotropic virus 1|11908 + 981 + 9 + + + 1 + 15.779 + 29 + 0.48278 + 1 + 9 + 1 + 9 + 0 + 0 + 5 + 8 + 0 + 9 + SLGEHINTL + TLGQHLPTL + +LG+H+ TL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 32 + Query_32 + M_2006 + 9 + + + 1 + gnl|BL_ORD_ID|1172 + 79308|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 + 1172 + 16 + + + 1 + 16.1642 + 30 + 0.328782 + 1 + 9 + 4 + 12 + 0 + 0 + 5 + 8 + 0 + 9 + SLGEHINTL + TLGQHLPTL + +LG+H+ TL + + + + + 2 + gnl|BL_ORD_ID|981 + 64821|Protein Tax-1|P03409.2|Human T-lymphotropic virus 1|11908 + 981 + 9 + + + 1 + 15.779 + 29 + 0.48278 + 1 + 9 + 1 + 9 + 0 + 0 + 5 + 8 + 0 + 9 + SLGEHINTL + TLGQHLPTL + +LG+H+ TL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 33 + Query_33 + M_2007 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 34 + Query_34 + M_2008 + 9 + + + 1 + gnl|BL_ORD_ID|524 + 32238|polyprotein [Hepatitis C virus subtype 1a]|ABV46251.2|Hepatitis C virus (isolate H77)|63746 + 524 + 10 + + + 1 + 12.6974 + 21 + 30.9217 + 2 + 7 + 1 + 6 + 0 + 0 + 5 + 6 + 0 + 6 + KLVVVG + KLVVLG + KLVV+G + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 35 + Query_35 + M_2009 + 9 + + + 1 + gnl|BL_ORD_ID|10 + 1000|glycoprotein gp35/37|AAC59622.1|Human gammaherpesvirus 8|37296 + 10 + 15 + + + 1 + 13.853 + 24 + 5.67783 + 2 + 8 + 9 + 15 + 0 + 0 + 4 + 6 + 0 + 7 + MLWALGF + ILWAVGL + +LWA+G + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 36 + Query_36 + M_2010 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 37 + Query_37 + M_2011 + 9 + + + 1 + gnl|BL_ORD_ID|10 + 1000|glycoprotein gp35/37|AAC59622.1|Human gammaherpesvirus 8|37296 + 10 + 15 + + + 1 + 13.853 + 24 + 4.94253 + 1 + 7 + 9 + 15 + 0 + 0 + 4 + 6 + 0 + 7 + MLWALGF + ILWAVGL + +LWA+G + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 38 + Query_38 + M_2012 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 39 + Query_39 + M_2013 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 40 + Query_40 + M_2014 + 9 + + + 1 + gnl|BL_ORD_ID|1897 + 180617|polyprotein|AGO67248.1|Dengue virus 2|11060 + 1897 + 10 + + + 1 + 13.4678 + 23 + 9.40133 + 2 + 6 + 4 + 8 + 0 + 0 + 4 + 5 + 0 + 5 + QYQTP + RYQTP + +YQTP + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 41 + Query_41 + M_2015 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 42 + Query_42 + M_2016 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 43 + Query_43 + M_2017 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 44 + Query_44 + M_2018 + 9 + + + 1 + gnl|BL_ORD_ID|305 + 20417|HCV-1|AAA45676.1|Hepatitis C virus genotype 1|41856 + 305 + 20 + + + 1 + 11.927 + 19 + 61.3622 + 3 + 9 + 10 + 16 + 0 + 0 + 4 + 4 + 0 + 7 + TTPKEPA + TLPGNPA + T P PA + + + + + 2 + gnl|BL_ORD_ID|1545 + 141216|envelope glycoprotein I|NP_044669.1|Human alphaherpesvirus 1|10298 + 1545 + 9 + + + 1 + 11.5418 + 18 + 134.458 + 1 + 9 + 1 + 9 + 0 + 0 + 4 + 6 + 0 + 9 + APTTPKEPA + APASVYQPA + AP + +PA + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 45 + Query_45 + M_2019 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 46 + Query_46 + M_2020 + 9 + + + 1 + gnl|BL_ORD_ID|1263 + 98540|trans-sialidase, putative|EAN88532.1|Trypanosoma cruzi|5693 + 1263 + 10 + + + 1 + 11.1566 + 17 + 242.571 + 3 + 9 + 4 + 10 + 0 + 0 + 6 + 7 + 0 + 7 + LLLLLVV + VLLLLVV + +LLLLVV + + + + + 2 + gnl|BL_ORD_ID|1254 + 98224|trans-sialidase, putative|EAN82076.1|Trypanosoma cruzi|5693 + 1254 + 10 + + + 1 + 11.1566 + 17 + 286.165 + 4 + 9 + 1 + 6 + 0 + 0 + 6 + 6 + 0 + 6 + LLLLVV + LLLLVV + LLLLVV + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 47 + Query_47 + M_2021 + 9 + + + 1 + gnl|BL_ORD_ID|1263 + 98540|trans-sialidase, putative|EAN88532.1|Trypanosoma cruzi|5693 + 1263 + 10 + + + 1 + 11.1566 + 17 + 231.802 + 3 + 8 + 5 + 10 + 0 + 0 + 6 + 6 + 0 + 6 + LLLLVV + LLLLVV + LLLLVV + + + + + 2 + gnl|BL_ORD_ID|1254 + 98224|trans-sialidase, putative|EAN82076.1|Trypanosoma cruzi|5693 + 1254 + 10 + + + 1 + 11.1566 + 17 + 250.006 + 3 + 9 + 1 + 7 + 0 + 0 + 6 + 7 + 0 + 7 + LLLLVVV + LLLLVVM + LLLLVV+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 48 + Query_48 + M_2022 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 49 + Query_49 + M_2023 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 50 + Query_50 + M_2024 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 51 + Query_51 + M_2025 + 9 + + + 1 + gnl|BL_ORD_ID|338 + 21242|polymerase|ACF94272.1|Hepatitis B virus|10407 + 338 + 9 + + + 1 + 13.0826 + 22 + 19.071 + 1 + 9 + 1 + 9 + 0 + 0 + 4 + 6 + 0 + 9 + GSYSMAIPL + GLYSSTVPV + G YS +P+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 52 + Query_52 + M_2026 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 53 + Query_53 + M_2027 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 54 + Query_54 + M_2028 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 55 + Query_55 + M_2029 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 56 + Query_56 + M_2030 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 57 + Query_57 + M_2031 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 58 + Query_58 + M_2032 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 59 + Query_59 + M_2033 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 60 + Query_60 + M_2034 + 9 + + + 1 + gnl|BL_ORD_ID|1140 + 75376|Genome polyprotein|P26664.3|Hepatitis C virus|11103 + 1140 + 8 + + + 1 + 13.0826 + 22 + 15.3199 + 2 + 8 + 2 + 8 + 0 + 0 + 4 + 5 + 0 + 7 + PPKPVQV + PPKPCGI + PPKP + + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 61 + Query_61 + M_2035 + 9 + + + 1 + gnl|BL_ORD_ID|1140 + 75376|Genome polyprotein|P26664.3|Hepatitis C virus|11103 + 1140 + 8 + + + 1 + 13.0826 + 22 + 14.7957 + 3 + 9 + 2 + 8 + 0 + 0 + 4 + 5 + 0 + 7 + PPKPVQV + PPKPCGI + PPKP + + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 62 + Query_62 + M_2036 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 63 + Query_63 + M_2037 + 9 + + + 1 + gnl|BL_ORD_ID|1755 + 154041|major capsid protein|CAB06743.1|Human alphaherpesvirus 2|10310 + 1755 + 15 + + + 1 + 14.2382 + 25 + 3.03951 + 2 + 8 + 7 + 13 + 0 + 0 + 4 + 6 + 0 + 7 + FPAIIYL + YPAVFYL + +PA+ YL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 64 + Query_64 + M_2038 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 65 + Query_65 + M_2039 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 66 + Query_66 + M_2040 + 9 + + + 1 + gnl|BL_ORD_ID|1755 + 154041|major capsid protein|CAB06743.1|Human alphaherpesvirus 2|10310 + 1755 + 15 + + + 1 + 14.6234 + 26 + 2.04141 + 3 + 9 + 7 + 13 + 0 + 0 + 4 + 6 + 0 + 7 + FPAIIYL + YPAVFYL + +PA+ YL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 67 + Query_67 + M_2041 + 9 + + + 1 + gnl|BL_ORD_ID|1755 + 154041|major capsid protein|CAB06743.1|Human alphaherpesvirus 2|10310 + 1755 + 15 + + + 1 + 14.6234 + 26 + 2.04141 + 3 + 9 + 7 + 13 + 0 + 0 + 4 + 6 + 0 + 7 + FPAIIYL + YPAVFYL + +PA+ YL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 68 + Query_68 + M_2042 + 9 + + + 1 + gnl|BL_ORD_ID|1755 + 154041|major capsid protein|CAB06743.1|Human alphaherpesvirus 2|10310 + 1755 + 15 + + + 1 + 14.6234 + 26 + 2.04141 + 3 + 9 + 7 + 13 + 0 + 0 + 4 + 6 + 0 + 7 + FPAIIYL + YPAVFYL + +PA+ YL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 69 + Query_69 + M_2043 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 70 + Query_70 + M_2044 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 71 + Query_71 + M_2045 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 72 + Query_72 + M_2046 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 73 + Query_73 + M_2047 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 74 + Query_74 + M_2048 + 9 + + + 1 + gnl|BL_ORD_ID|1541 + 141206|tegument protein VP11/12|NP_044648.1|Human alphaherpesvirus 1|10298 + 1541 + 9 + + + 1 + 12.6974 + 21 + 31.9494 + 2 + 7 + 4 + 9 + 0 + 0 + 4 + 4 + 0 + 6 + VQYWYY + TQYWKY + QYW Y + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 75 + Query_75 + M_2049 + 9 + + + 1 + gnl|BL_ORD_ID|1541 + 141206|tegument protein VP11/12|NP_044648.1|Human alphaherpesvirus 1|10298 + 1541 + 9 + + + 1 + 12.6974 + 21 + 31.9494 + 2 + 7 + 4 + 9 + 0 + 0 + 4 + 4 + 0 + 6 + VQYWYY + TQYWKY + QYW Y + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 76 + Query_76 + M_2050 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 77 + Query_77 + M_2051 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 78 + Query_78 + M_2052 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 79 + Query_79 + M_2053 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 80 + Query_80 + M_2054 + 9 + + + 1 + gnl|BL_ORD_ID|555 + 34101|X protein|ACH95876.1|Hepatitis B virus|10407 + 555 + 10 + + + 1 + 11.5418 + 18 + 115.311 + 1 + 8 + 1 + 8 + 0 + 0 + 3 + 7 + 0 + 8 + ELMHFKTL + KVLHKRTL + +++H +TL + + + + + 2 + gnl|BL_ORD_ID|1042 + 69524|X protein|ACH95876.1|Hepatitis B virus|10407 + 1042 + 9 + + + 1 + 11.1566 + 17 + 221.814 + 2 + 8 + 1 + 7 + 0 + 0 + 3 + 6 + 0 + 7 + LMHFKTL + VLHKRTL + ++H +TL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 81 + Query_81 + M_2055 + 9 + + + 1 + gnl|BL_ORD_ID|775 + 51604|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 + 775 + 10 + + + 1 + 14.6234 + 26 + 1.78499 + 4 + 9 + 3 + 8 + 0 + 0 + 4 + 6 + 0 + 6 + DWSNGI + DYSNGL + D+SNG+ + + + + + 2 + gnl|BL_ORD_ID|623 + 37498|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 + 623 + 10 + + + 1 + 10.7714 + 16 + 303.747 + 1 + 8 + 2 + 9 + 0 + 0 + 3 + 4 + 0 + 8 + ILGDWSNG + LLGLWGTA + +LG W + + + + + 3 + gnl|BL_ORD_ID|615 + 37350|trans-sialidase|XP_818394.1|Trypanosoma cruzi|5693 + 615 + 10 + + + 1 + 10.7714 + 16 + 303.747 + 1 + 8 + 1 + 8 + 0 + 0 + 3 + 4 + 0 + 8 + ILGDWSNG + LLGLWGTA + +LG W + + + + + 4 + gnl|BL_ORD_ID|321 + 21004|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 + 321 + 10 + + + 1 + 7.30463 + 7 + 14472.4 + 4 + 5 + 7 + 8 + 0 + 0 + 1 + 1 + 0 + 2 + DW + LW + W + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 82 + Query_82 + M_2056 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 83 + Query_83 + M_2057 + 9 + + + 1 + gnl|BL_ORD_ID|847 + 55336|EBNA-1|YP_401677.1|Human gammaherpesvirus 4|10376 + 847 + 15 + + + 1 + 12.3122 + 20 + 58.4135 + 3 + 7 + 11 + 15 + 0 + 0 + 4 + 4 + 0 + 5 + HGGTN + HGGTG + HGGT + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 84 + Query_84 + M_2058 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 85 + Query_85 + M_2059 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 86 + Query_86 + M_2060 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + + diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_120070_2_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_120070_2_T.fasta new file mode 100755 index 00000000..415651ea --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_120070_2_T.fasta @@ -0,0 +1,76 @@ +>M_2061 +GDASKVWVW +>M_2062 +STFVHGNKI +>M_2063 +GEEAEASAV +>M_2064 +TTSPSNTLV +>M_2065 +STGLQYATK +>M_2066 +SVLRCVHLL +>M_2067 +GRNSFKVRV +>M_2068 +MRTLLGDLV +>M_2069 +RWDRKPMQI +>M_2070 +SRSTIFMRL +>M_2071 +PHLTQGNEI +>M_2072 +ASTFVHGNK +>M_2073 +ENAGPQNMK +>M_2074 +MGQEIAALK +>M_2075 +NLLGRNSFK +>M_2076 +QAVCVTKPK +>M_2077 +LRCVHLLRI +>M_2078 +FVHGNKIYV +>M_2079 +ATKFIKKRR +>M_2080 +VHLLRIFKV +>M_2081 +LANAPRTLK +>M_2082 +WRLTWDRHL +>M_2083 +CTGPPLAPR +>M_2084 +NLTRASSKR +>M_2085 +RRSGPSPTV +>M_2086 +DLVAHYVHR +>M_2087 +SSLEGFATR +>M_2088 +LEDLGWANW +>M_2089 +CVHLLRIFK +>M_2090 +TIQAVCVTK +>M_2091 +ITCMPGSVR +>M_2092 +CSIPSICEK +>M_2093 +SSRSTIFMR +>M_2094 +SVTKASNLK +>M_2095 +YATKFIKKR +>M_2096 +FSSSDDSPR +>M_2097 +VHGNKIYVL +>M_2098 +WANWVLSPR diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_120070_2_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_120070_2_T_iedb.xml new file mode 100755 index 00000000..22e96f0f --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_120070_2_T_iedb.xml @@ -0,0 +1,1584 @@ + + + + blastp + BLASTP 2.2.30+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta + Query_1 + M_2061 + 9 + + + BLOSUM62 + 100000000 + 11 + 1 + F + + + + + 1 + Query_1 + M_2061 + 9 + + + 1 + gnl|BL_ORD_ID|341 + 21385|polyprotein|AAY82034.1|Hepatitis C virus genotype 1|41856 + 341 + 10 + + + 1 + 15.779 + 29 + 0.401267 + 1 + 8 + 1 + 8 + 0 + 0 + 5 + 7 + 0 + 8 + GDASKVWV + GNASRCWV + G+AS+ WV + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 2 + Query_2 + M_2062 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 3 + Query_3 + M_2063 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 4 + Query_4 + M_2064 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 5 + Query_5 + M_2065 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 6 + Query_6 + M_2066 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 7 + Query_7 + M_2067 + 9 + + + 1 + gnl|BL_ORD_ID|617 + 37364|P53_HUMAN Cellular tumor antigen p53 (Tumor suppressor p53) (Phosphoprotein p53) (Antigen NY-CO-13)|P04637.2|Homo sapiens|9606 + 617 + 9 + + + 1 + 16.5494 + 31 + 0.265948 + 1 + 7 + 3 + 9 + 0 + 0 + 6 + 7 + 0 + 7 + GRNSFKV + GRNSFEV + GRNSF+V + + + + + 2 + gnl|BL_ORD_ID|1613 + 143740|polyprotein|ACF60462.1|Hepatovirus A|12092 + 1613 + 9 + + + 1 + 13.0826 + 22 + 14.4474 + 2 + 7 + 4 + 9 + 0 + 0 + 4 + 5 + 0 + 6 + RNSFKV + RNEFRV + RN F+V + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 8 + Query_8 + M_2068 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 9 + Query_9 + M_2069 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 10 + Query_10 + M_2070 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 11 + Query_11 + M_2071 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 12 + Query_12 + M_2072 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 13 + Query_13 + M_2073 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 14 + Query_14 + M_2074 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 15 + Query_15 + M_2075 + 9 + + + 1 + gnl|BL_ORD_ID|617 + 37364|P53_HUMAN Cellular tumor antigen p53 (Tumor suppressor p53) (Phosphoprotein p53) (Antigen NY-CO-13)|P04637.2|Homo sapiens|9606 + 617 + 9 + + + 1 + 18.0902 + 35 + 0.111589 + 2 + 9 + 1 + 8 + 0 + 0 + 7 + 8 + 0 + 8 + LLGRNSFK + LLGRNSFE + LLGRNSF+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 16 + Query_16 + M_2076 + 9 + + + 1 + gnl|BL_ORD_ID|1645 + 146317|polyprotein|ADF97231.1|Hepatitis C virus subtype 3a|356426 + 1645 + 9 + + + 1 + 13.0826 + 22 + 13.7128 + 3 + 8 + 1 + 6 + 0 + 0 + 3 + 5 + 0 + 6 + VCVTKP + ICLTHP + +C+T P + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 17 + Query_17 + M_2077 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 18 + Query_18 + M_2078 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 19 + Query_19 + M_2079 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 20 + Query_20 + M_2080 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 21 + Query_21 + M_2081 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 22 + Query_22 + M_2082 + 9 + + + 1 + gnl|BL_ORD_ID|1539 + 140769|LOW MOLECULAR WEIGHT PROTEIN ANTIGEN 7 ESXH (10 kDa ANTIGEN) (CFP-7) (PROTEIN TB10.4)|CAA17363.1|Mycobacterium tuberculosis H37Rv|83332 + 1539 + 9 + + + 1 + 12.3122 + 20 + 59.6102 + 1 + 9 + 1 + 9 + 0 + 0 + 2 + 6 + 0 + 9 + WRLTWDRHL + WQAQWNQAM + W+ W++ + + + + + + 2 + gnl|BL_ORD_ID|1092 + 72233|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 + 1092 + 15 + + + 1 + 11.1566 + 17 + 190.157 + 1 + 6 + 1 + 6 + 0 + 0 + 2 + 4 + 0 + 6 + WRLTWD + WAIKWE + W + W+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 23 + Query_23 + M_2083 + 9 + + + 1 + gnl|BL_ORD_ID|1950 + 181035|||| + 1950 + 44 + + + 1 + 13.4678 + 23 + 10.2905 + 1 + 9 + 20 + 28 + 0 + 0 + 5 + 5 + 0 + 9 + CTGPPLAPR + CGGVYLLPR + C G L PR + + + + + 2 + gnl|BL_ORD_ID|344 + 21638|protein F|ABV46152.2|Hepatitis C virus (isolate Japanese)|11116 + 344 + 9 + + + 1 + 11.927 + 19 + 95.9763 + 3 + 8 + 1 + 6 + 0 + 0 + 4 + 5 + 0 + 6 + GPPLAP + GPGLSP + GP L+P + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 24 + Query_24 + M_2084 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 25 + Query_25 + M_2085 + 9 + + + 1 + gnl|BL_ORD_ID|1829 + 179799|hypothetical protein|NP_301670.1|Mycobacterium leprae TN|272631 + 1829 + 9 + + + 1 + 12.3122 + 20 + 53.938 + 4 + 9 + 1 + 6 + 0 + 0 + 4 + 4 + 0 + 6 + GPSPTV + GPVPAV + GP P V + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 26 + Query_26 + M_2086 + 9 + + + 1 + gnl|BL_ORD_ID|1714 + 150377|polyprotein|AGS49173.1|Dengue virus 2|11060 + 1714 + 9 + + + 1 + 13.853 + 24 + 7.45662 + 2 + 6 + 3 + 7 + 0 + 0 + 5 + 5 + 0 + 5 + LVAHY + LVAHY + LVAHY + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 27 + Query_27 + M_2087 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 28 + Query_28 + M_2088 + 9 + + + 1 + gnl|BL_ORD_ID|1143 + 75436|Polyprotein|P90247|Hepatitis C virus|11103 + 1143 + 20 + + + 1 + 16.5494 + 31 + 0.231862 + 2 + 9 + 9 + 16 + 0 + 0 + 6 + 6 + 0 + 8 + EDLGWANW + EGLGWAGW + E LGWA W + + + + + 2 + gnl|BL_ORD_ID|1144 + 75438|polyprotein|AAF65962.1|Hepatitis C virus|11103 + 1144 + 20 + + + 1 + 16.1642 + 30 + 0.347768 + 2 + 9 + 9 + 16 + 0 + 0 + 5 + 6 + 0 + 8 + EDLGWANW + EGMGWAGW + E +GWA W + + + + + 3 + gnl|BL_ORD_ID|710 + 43624|Genome polyprotein|P26660.3|Hepatitis C virus isolate HC-J6|11113 + 710 + 9 + + + 1 + 16.1642 + 30 + 0.349175 + 2 + 9 + 2 + 9 + 0 + 0 + 6 + 6 + 0 + 8 + EDLGWANW + EGLGWAGW + E LGWA W + + + + + 4 + gnl|BL_ORD_ID|116 + 7999|core protein|BAA82580.1|Hepatitis C virus|11103 + 116 + 9 + + + 1 + 16.1642 + 30 + 0.356759 + 2 + 9 + 2 + 9 + 0 + 0 + 6 + 6 + 0 + 8 + EDLGWANW + EGLGWAGW + E LGWA W + + + + + 5 + gnl|BL_ORD_ID|712 + 43628|polyprotein|BAA03375.1|Hepatitis C virus subtype 1b|31647 + 712 + 9 + + + 1 + 15.779 + 29 + 0.457844 + 2 + 9 + 2 + 9 + 0 + 0 + 5 + 6 + 0 + 8 + EDLGWANW + EGMGWAGW + E +GWA W + + + + + 6 + gnl|BL_ORD_ID|713 + 43756|Genome polyprotein|SRC279960|Hepatitis C virus subtype 2a|31649 + 713 + 9 + + + 1 + 15.0086 + 27 + 1.05395 + 2 + 9 + 2 + 9 + 0 + 0 + 5 + 5 + 0 + 8 + EDLGWANW + ETCGWAGW + E GWA W + + + + + 7 + gnl|BL_ORD_ID|577 + 36352|Polyprotein|P90247|Hepatitis C virus|11103 + 577 + 20 + + + 1 + 15.0086 + 27 + 1.17519 + 4 + 9 + 1 + 6 + 0 + 0 + 5 + 5 + 0 + 6 + LGWANW + LGWAGW + LGWA W + + + + + 8 + gnl|BL_ORD_ID|708 + 43619|Genome polyprotein|P26664.3|Hepatitis C virus|11103 + 708 + 9 + + + 1 + 15.0086 + 27 + 1.21609 + 2 + 9 + 2 + 9 + 0 + 0 + 5 + 5 + 0 + 8 + EDLGWANW + EGCGWAGW + E GWA W + + + + + 9 + gnl|BL_ORD_ID|711 + 43627|core protein|AAX68853.1|Hepatitis C virus subtype 1b|31647 + 711 + 9 + + + 1 + 15.0086 + 27 + 1.2556 + 2 + 9 + 2 + 9 + 0 + 0 + 5 + 5 + 0 + 8 + EDLGWANW + EGLGWTGW + E LGW W + + + + + 10 + gnl|BL_ORD_ID|2120 + 186453|polyprotein|AFP27208.1|Dengue virus 4|11070 + 2120 + 10 + + + 1 + 13.4678 + 23 + 7.76238 + 5 + 9 + 6 + 10 + 0 + 0 + 4 + 4 + 0 + 5 + GWANW + GWKNW + GW NW + + + + + 11 + gnl|BL_ORD_ID|315 + 20894|polyprotein [Hepatitis C virus]|BAF91806.1|Hepatitis C virus|11103 + 315 + 9 + + + 1 + 13.4678 + 23 + 10.0233 + 4 + 9 + 2 + 7 + 0 + 0 + 4 + 4 + 0 + 6 + LGWANW + LGWVGW + LGW W + + + + + 12 + gnl|BL_ORD_ID|160 + 12183|EBNA3C latent protein|CAD53421.1|Human gammaherpesvirus 4|10376 + 160 + 9 + + + 1 + 12.6974 + 21 + 32.4991 + 4 + 9 + 4 + 9 + 0 + 0 + 3 + 5 + 0 + 6 + LGWANW + VGWRHW + +GW +W + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 29 + Query_29 + M_2089 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 30 + Query_30 + M_2090 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 31 + Query_31 + M_2091 + 9 + + + 1 + gnl|BL_ORD_ID|1176 + 79454|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 + 1176 + 15 + + + 1 + 13.853 + 24 + 7.10896 + 1 + 8 + 2 + 9 + 0 + 0 + 4 + 5 + 0 + 8 + ITCMPGSV + IFCHPGQL + I C PG + + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 32 + Query_32 + M_2092 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 33 + Query_33 + M_2093 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 34 + Query_34 + M_2094 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 35 + Query_35 + M_2095 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 36 + Query_36 + M_2096 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 37 + Query_37 + M_2097 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 38 + Query_38 + M_2098 + 9 + + + 1 + gnl|BL_ORD_ID|577 + 36352|Polyprotein|P90247|Hepatitis C virus|11103 + 577 + 20 + + + 1 + 19.631 + 39 + 0.0260695 + 1 + 9 + 3 + 11 + 0 + 0 + 7 + 8 + 0 + 9 + WANWVLSPR + WAGWLLSPR + WA W+LSPR + + + + + 2 + gnl|BL_ORD_ID|1144 + 75438|polyprotein|AAF65962.1|Hepatitis C virus|11103 + 1144 + 20 + + + 1 + 17.3198 + 33 + 0.118837 + 1 + 8 + 13 + 20 + 0 + 0 + 6 + 7 + 0 + 8 + WANWVLSP + WAGWLLSP + WA W+LSP + + + + + 3 + gnl|BL_ORD_ID|1143 + 75436|Polyprotein|P90247|Hepatitis C virus|11103 + 1143 + 20 + + + 1 + 17.3198 + 33 + 0.120923 + 1 + 8 + 13 + 20 + 0 + 0 + 6 + 7 + 0 + 8 + WANWVLSP + WAGWLLSP + WA W+LSP + + + + + 4 + gnl|BL_ORD_ID|1142 + 75435|largest ORF|AAB02128.1|Hepatitis C virus|11103 + 1142 + 20 + + + 1 + 15.779 + 29 + 0.412688 + 1 + 8 + 13 + 20 + 0 + 0 + 5 + 6 + 0 + 8 + WANWVLSP + WMGWLLSP + W W+LSP + + + + + 5 + gnl|BL_ORD_ID|315 + 20894|polyprotein [Hepatitis C virus]|BAF91806.1|Hepatitis C virus|11103 + 315 + 9 + + + 1 + 12.3122 + 20 + 65.8473 + 1 + 6 + 4 + 9 + 0 + 0 + 3 + 4 + 0 + 6 + WANWVL + WVGWLL + W W+L + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + + diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_120920_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_120920_1_T.fasta new file mode 100755 index 00000000..bb5924de --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_120920_1_T.fasta @@ -0,0 +1,126 @@ +>M_2099 +LSLPGGHTA +>M_2100 +FRAAAEAAV +>M_2101 +FRAAAEAAV +>M_2102 +TSSDHSFSL +>M_2103 +TSSDHSFSL +>M_2104 +NHQQFYHSV +>M_2105 +NHQQFYHSV +>M_2106 +DYSELPHHV +>M_2107 +HHVSTEQEI +>M_2108 +HHVSTEQEI +>M_2109 +EIISLWSPW +>M_2110 +NQDPISPSL +>M_2111 +ENASAYLTL +>M_2112 +KKMENASAY +>M_2113 +RRHSLPRRC +>M_2114 +NMCRCLVTV +>M_2115 +RLMSARLAI +>M_2116 +SYSYLGLRL +>M_2117 +YSYLGLRLM +>M_2118 +YSYLGLRLM +>M_2119 +RFSQAFFYM +>M_2120 +RRFSQAFFY +>M_2121 +FMMPRSSSC +>M_2122 +FMMPRSSSC +>M_2123 +IPAMEIFMV +>M_2124 +LMAASIPAM +>M_2125 +DTLQATAML +>M_2126 +QATAMLDIV +>M_2127 +TVTRTTATV +>M_2128 +EHFPLCKTV +>M_2129 +EHFPLCKTV +>M_2130 +WPQCHPEEI +>M_2131 +YSYSCGHYE +>M_2132 +SHFERDYRV +>M_2133 +FQTLMPDVV +>M_2134 +FQTLMPDVV +>M_2135 +MPDVVHQSL +>M_2136 +LWYTLYLMI +>M_2137 +LYLMITTFF +>M_2138 +MITTFFFPL +>M_2139 +TLYLMITTF +>M_2140 +YLMITTFFF +>M_2141 +YTLYLMITT +>M_2142 +PTSPFQTTI +>M_2143 +TAERSIPTV +>M_2144 +ERPCHREPL +>M_2145 +SSSSGPFPL +>M_2146 +ELATFAKAY +>M_2147 +RWDEELATF +>M_2148 +ELIDLISRV +>M_2149 +ELIDLISRV +>M_2150 +QVNQKSSVV +>M_2151 +VRLELIDLI +>M_2152 +YEEYRGRLL +>M_2153 +YEEYRGRLL +>M_2154 +CRNVHTPDL +>M_2155 +YSRDQAQAL +>M_2156 +YSRDQAQAL +>M_2157 +FEVEGRDLL +>M_2158 +FFFLCVCVF +>M_2159 +FFLCVCVFV +>M_2160 +RRYPHKRCI +>M_2161 +RRYPHKRCI diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_120920_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_120920_1_T_iedb.xml new file mode 100755 index 00000000..ae438936 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_120920_1_T_iedb.xml @@ -0,0 +1,1853 @@ + + + + blastp + BLASTP 2.2.30+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta + Query_1 + M_2099 + 9 + + + BLOSUM62 + 100000000 + 11 + 1 + F + + + + + 1 + Query_1 + M_2099 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 2 + Query_2 + M_2100 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 3 + Query_3 + M_2101 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 4 + Query_4 + M_2102 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 5 + Query_5 + M_2103 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 6 + Query_6 + M_2104 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 7 + Query_7 + M_2105 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 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gnl|BL_ORD_ID|1140 + 75376|Genome polyprotein|P26664.3|Hepatitis C virus|11103 + 1140 + 8 + + + 1 + 12.6974 + 21 + 24.9053 + 3 + 8 + 1 + 6 + 0 + 0 + 4 + 4 + 0 + 6 + YPHKRC + YPPKPC + YP K C + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 63 + Query_63 + M_2161 + 9 + + + 1 + gnl|BL_ORD_ID|1140 + 75376|Genome polyprotein|P26664.3|Hepatitis C virus|11103 + 1140 + 8 + + + 1 + 12.6974 + 21 + 24.9053 + 3 + 8 + 1 + 6 + 0 + 0 + 4 + 4 + 0 + 6 + YPHKRC + YPPKPC + YP K C + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + + diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_121511_2_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_121511_2_T.fasta new file mode 100755 index 00000000..ac5e8004 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_121511_2_T.fasta @@ -0,0 +1,116 @@ +>M_2162 +NMSRCCIRV +>M_2163 +GLLGNGIGY +>M_2164 +LLGNGIGYV +>M_2165 +KILSLHLLL +>M_2166 +HPAFISLAF +>M_2167 +FPREKTPEV +>M_2168 +WPPWLKGKY +>M_2169 +IVLTGHNAY +>M_2170 +IVLTGHNAY +>M_2171 +VLTGHNAYL +>M_2172 +QAQALGIPL +>M_2173 +IVFFANNGF +>M_2174 +HSESSDSEV +>M_2175 +RRGSGHSEY +>M_2176 +LIMEDLVCY +>M_2177 +MEDLPAACM +>M_2178 +HPMASNSGG +>M_2179 +DVEWRWHSY +>M_2180 +DVEWRWHSY +>M_2181 +ILPTCSPLV +>M_2182 +LPTCSPLVF +>M_2183 +VHFWPGYEY +>M_2184 +SPEGDDTLY +>M_2185 +TLVPTAPEL +>M_2186 +HLIGSTTLA +>M_2187 +LIGSTTLAM +>M_2188 +LLMHLIGST +>M_2189 +IAHQWYWTY +>M_2190 +IAHQWYWTY +>M_2191 +LLEENGDVF +>M_2192 +QRCACPHGY +>M_2193 +CMYDPLGTI +>M_2194 +GPHRITCMY +>M_2195 +NESCLSMSE +>M_2196 +VANESCLSM +>M_2197 +EESELYAQL +>M_2198 +RTAQCFLCV +>M_2199 +KYSNYVWPI +>M_2200 +FIFEIVGFT +>M_2201 +DSSGQSNRY +>M_2202 +DSSSWSNRY +>M_2203 +DSSSWSNRY +>M_2204 +NRYGGGGRY +>M_2205 +NRYGGGGRY +>M_2206 +NEHGHRRKI +>M_2207 +HTSLRGFLY +>M_2208 +ALNEMFCQL +>M_2209 +NEMFCQLAK +>M_2210 +GLYAIAVML +>M_2211 +MLSFSRIAY +>M_2212 +MLSFSRIAY +>M_2213 +YAIAVMLSF +>M_2214 +AEWDSLYVL +>M_2215 +LAEWDSLYV +>M_2216 +VLAEWDSLY +>M_2217 +VLAEWDSLY +>M_2218 +GKAFSQSAY +>M_2219 +KAFSQSAYL diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_121511_2_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_121511_2_T_iedb.xml new file mode 100755 index 00000000..bbcebff2 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_121511_2_T_iedb.xml @@ -0,0 +1,1923 @@ + + + + blastp + BLASTP 2.2.30+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta + Query_1 + M_2162 + 9 + + + BLOSUM62 + 100000000 + 11 + 1 + F + + + + + 1 + Query_1 + M_2162 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 2 + Query_2 + M_2163 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 3 + Query_3 + M_2164 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 4 + Query_4 + M_2165 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 5 + Query_5 + M_2166 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 6 + Query_6 + M_2167 + 9 + + + 1 + gnl|BL_ORD_ID|1181 + 88849|IE62|AAP32859.1|Human alphaherpesvirus 3|10335 + 1181 + 9 + + + 1 + 14.2382 + 25 + 2.85402 + 1 + 7 + 2 + 8 + 0 + 0 + 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Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta + Query_1 + M_2220 + 9 + + + BLOSUM62 + 100000000 + 11 + 1 + F + + + + + 1 + Query_1 + M_2220 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 2 + Query_2 + M_2221 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 3 + Query_3 + M_2222 + 9 + + + 1 + gnl|BL_ORD_ID|357 + 22255|polyprotein|ABR27377.1|Hepatitis C virus|11103 + 357 + 9 + + + 1 + 13.853 + 24 + 5.95161 + 2 + 9 + 2 + 9 + 0 + 0 + 4 + 6 + 0 + 8 + RWLRQAAF + RWVPGAAY + RW+ AA+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 4 + Query_4 + M_2223 + 9 + + + 1 + gnl|BL_ORD_ID|2088 + 185491|polyprotein|AGO67248.1|Dengue virus 2|11060 + 2088 + 10 + + + 1 + 12.3122 + 20 + 62.4024 + 2 + 7 + 1 + 6 + 0 + 0 + 5 + 6 + 0 + 6 + KREEEE + RREEEE + 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14.6234 + 26 + 1.85254 + 2 + 8 + 1 + 7 + 0 + 0 + 4 + 6 + 0 + 7 + TYAPLFI + TYGPVFM + TY P+F+ + + + + + 2 + gnl|BL_ORD_ID|2312 + 423020|polyprotein|ACE82359.1|Hepatitis C virus genotype 1|41856 + 2312 + 9 + + + 1 + 10.001 + 14 + 866.983 + 1 + 9 + 1 + 9 + 0 + 0 + 3 + 4 + 0 + 9 + KTYAPLFIW + KLYISWCLW + K Y +W + + + + + 3 + gnl|BL_ORD_ID|664 + 39591|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 + 664 + 20 + + + 1 + 9.61583 + 13 + 985.051 + 1 + 9 + 6 + 14 + 0 + 0 + 3 + 4 + 0 + 9 + KTYAPLFIW + KRYISWCLW + K Y +W + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 17 + Query_17 + M_2236 + 9 + + + 1 + gnl|BL_ORD_ID|1011 + 67349|Latent membrane protein 2|Q69135|Human gammaherpesvirus 4|10376 + 1011 + 9 + + + 1 + 14.6234 + 26 + 1.62552 + 1 + 9 + 1 + 9 + 0 + 0 + 4 + 7 + 0 + 9 + TYAPLFIWV + TYGPVFMCL + TY P+F+ + + + + + + 2 + gnl|BL_ORD_ID|82 + 5952|PPE family protein|YP_177918.1|Mycobacterium tuberculosis H37Rv|83332 + 82 + 9 + + + 1 + 11.1566 + 17 + 211.79 + 1 + 9 + 1 + 9 + 0 + 0 + 3 + 4 + 0 + 9 + TYAPLFIWV + AYVPYVAWL + Y P W+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 18 + Query_18 + M_2237 + 9 + + + 1 + gnl|BL_ORD_ID|664 + 39591|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 + 664 + 20 + + + 1 + 14.2382 + 25 + 3.035 + 1 + 7 + 7 + 13 + 0 + 0 + 3 + 7 + 0 + 7 + KYIAFCI + RYISWCL + +YI++C+ + + + + + 2 + gnl|BL_ORD_ID|2312 + 423020|polyprotein|ACE82359.1|Hepatitis C virus genotype 1|41856 + 2312 + 9 + + + 1 + 13.4678 + 23 + 10.7466 + 2 + 7 + 3 + 8 + 0 + 0 + 3 + 6 + 0 + 6 + YIAFCI + YISWCL + YI++C+ + + + + + 3 + gnl|BL_ORD_ID|1120 + 74387|Genome polyprotein|P26664.3|Hepatitis C virus (isolate 1)|11104 + 1120 + 9 + + + 1 + 13.4678 + 23 + 11.5219 + 2 + 7 + 1 + 6 + 0 + 0 + 3 + 6 + 0 + 6 + YIAFCI + YISWCL + YI++C+ + + + + + 4 + gnl|BL_ORD_ID|1119 + 74386|HCV-1|AAA45676.1|Hepatitis C virus|11103 + 1119 + 8 + + + 1 + 13.4678 + 23 + 12.8716 + 2 + 7 + 1 + 6 + 0 + 0 + 3 + 6 + 0 + 6 + YIAFCI + YISWCL + YI++C+ + + + + + 5 + gnl|BL_ORD_ID|399 + 24457|polyprotein|BAA09072.1|Hepatitis C virus|11103 + 399 + 15 + + + 1 + 13.0826 + 22 + 13.39 + 1 + 8 + 5 + 12 + 0 + 0 + 4 + 6 + 0 + 8 + KYIAFCIN + KYIMACMS + KYI C++ + + + + + 6 + gnl|BL_ORD_ID|1297 + 103389|unnamed protein product [Hepatitis C virus]|BAA14035.1|Hepatitis C virus|11103 + 1297 + 20 + + + 1 + 11.5418 + 18 + 116.798 + 1 + 8 + 7 + 14 + 0 + 0 + 2 + 6 + 0 + 8 + KYIAFCIN + KFVMACMS + K++ C++ + + + + + 7 + gnl|BL_ORD_ID|1502 + 137660|L1|ACL12325.1|Human papillomavirus type 58|10598 + 1502 + 9 + + + 1 + 11.5418 + 18 + 150.225 + 1 + 9 + 1 + 9 + 0 + 0 + 3 + 6 + 0 + 9 + KYIAFCINI + KYTFWEVNL + KY + +N+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 19 + Query_19 + M_2238 + 9 + + + 1 + gnl|BL_ORD_ID|2312 + 423020|polyprotein|ACE82359.1|Hepatitis C virus genotype 1|41856 + 2312 + 9 + + + 1 + 13.4678 + 23 + 11.5219 + 1 + 6 + 3 + 8 + 0 + 0 + 3 + 6 + 0 + 6 + YIAFCI + YISWCL + YI++C+ + + + + + 2 + gnl|BL_ORD_ID|1120 + 74387|Genome polyprotein|P26664.3|Hepatitis C virus (isolate 1)|11104 + 1120 + 9 + + + 1 + 13.4678 + 23 + 13.0154 + 1 + 6 + 1 + 6 + 0 + 0 + 3 + 6 + 0 + 6 + YIAFCI + YISWCL + YI++C+ + + + + + 3 + gnl|BL_ORD_ID|664 + 39591|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 + 664 + 20 + + + 1 + 13.0826 + 22 + 13.0672 + 1 + 6 + 8 + 13 + 0 + 0 + 3 + 6 + 0 + 6 + YIAFCI + YISWCL + YI++C+ + + + + + 4 + gnl|BL_ORD_ID|1119 + 74386|HCV-1|AAA45676.1|Hepatitis C virus|11103 + 1119 + 8 + + + 1 + 13.4678 + 23 + 13.8002 + 1 + 6 + 1 + 6 + 0 + 0 + 3 + 6 + 0 + 6 + YIAFCI + YISWCL + YI++C+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 20 + Query_20 + M_2239 + 9 + + + 1 + gnl|BL_ORD_ID|1763 + 154585|ribonucleotide reductase large subunit|CAB06725.1|Human alphaherpesvirus 2|10310 + 1763 + 15 + + + 1 + 14.2382 + 25 + 2.38473 + 2 + 8 + 4 + 10 + 0 + 0 + 4 + 6 + 0 + 7 + HYPQSIF + HYMESVF + HY +S+F + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 21 + Query_21 + M_2240 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 22 + Query_22 + M_2241 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 23 + Query_23 + M_2242 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 24 + Query_24 + M_2243 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 25 + Query_25 + M_2244 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 26 + Query_26 + M_2245 + 9 + + + 1 + gnl|BL_ORD_ID|1596 + 142232|POSSIBLE CONSERVED TRANSMEMBRANE PROTEIN|CAB00937.1|Mycobacterium tuberculosis|1773 + 1596 + 19 + + + 1 + 10.001 + 14 + 683.554 + 3 + 7 + 14 + 18 + 0 + 0 + 3 + 4 + 0 + 5 + FAAVH + YAFVH + +A VH + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 27 + Query_27 + M_2246 + 9 + + + 1 + gnl|BL_ORD_ID|1395 + 110394|Protein E6|P03126.1|Human papillomavirus type 16|333760 + 1395 + 32 + + + 1 + 12.6974 + 21 + 25.5546 + 1 + 7 + 15 + 21 + 0 + 0 + 4 + 6 + 0 + 7 + RRHTDEK + QRHLDKK + +RH D+K + + + + + 2 + gnl|BL_ORD_ID|1405 + 110829|Protein E6|P03126.1|Human papillomavirus type 16|333760 + 1405 + 15 + + + 1 + 12.6974 + 21 + 26.1211 + 1 + 7 + 3 + 9 + 0 + 0 + 4 + 6 + 0 + 7 + RRHTDEK + QRHLDKK + +RH D+K + + + + + 3 + gnl|BL_ORD_ID|1385 + 110215|Protein E6|P03126.1|Human papillomavirus type 16|333760 + 1385 + 25 + + + 1 + 12.6974 + 21 + 28.4868 + 2 + 8 + 4 + 10 + 0 + 0 + 4 + 5 + 0 + 7 + RHTDEKP + RHLDKKQ + RH D+K + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + + diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_123126_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_123126_1_T.fasta new file mode 100755 index 00000000..eda51dc1 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_123126_1_T.fasta @@ -0,0 +1,120 @@ +>M_2247 +FNGNFLLSM +>M_2248 +GSADNTVQF +>M_2249 +SADNTVQFI +>M_2250 +KVQREDIFY +>M_2251 +YLWPSGTPA +>M_2252 +LKMVSPSPC +>M_2253 +SRVARDVAM +>M_2254 +QNGYSWSQF +>M_2255 +SYKLSQNGY +>M_2256 +WKRGKRRYF +>M_2257 +CFGHCFSLY +>M_2258 +CSAIRLRNY +>M_2259 +FGHCFSLYI +>M_2260 +IRLRNYLCF +>M_2261 +IRLRNYLCF +>M_2262 +LCFGHCFSL +>M_2263 +NHLCFGHCF +>M_2264 +DFVECLMWF +>M_2265 +DFVECLMWF +>M_2266 +NKFEPSTDL +>M_2267 +AYLCCRVPL +>M_2268 +SKGTTDTPV +>M_2269 +KQSNSVEPI +>M_2270 +AMSAQEYYI +>M_2271 +SAQEYYIDY +>M_2272 +YIDYKPNHI +>M_2273 +LMLLAAAIY +>M_2274 +LMLLAAAIY +>M_2275 +SEDDTSYFV +>M_2276 +RESVKHIGY +>M_2277 +YQKVVRESV +>M_2278 +SSVKTPETL +>M_2279 +VIHHELQVL +>M_2280 +KTDATPGRL +>M_2281 +IKRLTAGSL +>M_2282 +KRLTAGSLF +>M_2283 +KQLSHHIGA +>M_2284 +FHVNWFRRY +>M_2285 +FRRYEAGHF +>M_2286 +RRYEAGHFL +>M_2287 +RYEAGHFLW +>M_2288 +VSDHTPEQH +>M_2289 +SFHMDTQNF +>M_2290 +SFHMDTQNF +>M_2291 +TQNFCDIGY +>M_2292 +LALSVFSKL +>M_2293 +TVKLALSVF +>M_2294 +LQFAVGQEV +>M_2295 +PQVPEHLQF +>M_2296 +QFAVGQEVF +>M_2297 +NRYGGGGRY +>M_2298 +EQLKLGAIF +>M_2299 +LLMPYPVIV +>M_2300 +TLLMPYPVI +>M_2301 +RALKPVNKI +>M_2302 +KEAMENEQF +>M_2303 +LTEENKEAM +>M_2304 +MEVPNIASS +>M_2305 +RRFASGEKV +>M_2306 +TFRDVAVEF diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_123126_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_123126_1_T_iedb.xml new file mode 100755 index 00000000..6f4861f5 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_123126_1_T_iedb.xml @@ -0,0 +1,2774 @@ + + + + blastp + BLASTP 2.2.30+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta + Query_1 + M_2247 + 9 + + + BLOSUM62 + 100000000 + 11 + 1 + F + + + + + 1 + Query_1 + M_2247 + 9 + + + 1 + gnl|BL_ORD_ID|2229 + 194567|envelope glycoprotein B|NP_044629.1|Herpes simplex virus (type 1 / strain 17)|10299 + 2229 + 9 + + + 1 + 12.6974 + 21 + 35.9943 + 2 + 7 + 4 + 9 + 0 + 0 + 4 + 5 + 0 + 6 + NGNFLL + NGGFLI + NG FL+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 2 + Query_2 + M_2248 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 3 + Query_3 + M_2249 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 4 + Query_4 + M_2250 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 5 + Query_5 + M_2251 + 9 + + + 1 + gnl|BL_ORD_ID|1520 + 140600|glutamine synthetase GLNA1 (glutamine synthase) (GS-I)|NP_216736.1|Mycobacterium tuberculosis H37Rv|83332 + 1520 + 9 + + + 1 + 13.853 + 24 + 6.48995 + 2 + 8 + 2 + 8 + 0 + 0 + 4 + 4 + 0 + 7 + LWPSGTP + LWKDGAP + LW G P + + + + + 2 + gnl|BL_ORD_ID|2041 + 184512|polyprotein|AGO67248.1|Dengue virus 2|11060 + 2041 + 10 + + + 1 + 11.927 + 19 + 90.726 + 2 + 8 + 2 + 8 + 0 + 0 + 3 + 4 + 0 + 7 + LWPSGTP + MWKQITP + +W TP + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 6 + Query_6 + M_2252 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 7 + Query_7 + M_2253 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 8 + Query_8 + M_2254 + 9 + + + 1 + gnl|BL_ORD_ID|101 + 6889|Agglutinin isolectin 1 precursor|P10968.2|Triticum aestivum|4565 + 101 + 9 + + + 1 + 14.2382 + 25 + 3.49608 + 1 + 7 + 2 + 8 + 0 + 0 + 4 + 5 + 0 + 7 + QNGYSWS + QNGACWT + QNG W+ + + + + + 2 + gnl|BL_ORD_ID|1194 + 95279|polyprotein|BAG31965.1|Hepatitis C virus|11103 + 1194 + 9 + + + 1 + 13.853 + 24 + 6.48995 + 2 + 7 + 3 + 8 + 0 + 0 + 4 + 4 + 0 + 6 + NGYSWS + NGVCWS + NG WS + + + + + 3 + gnl|BL_ORD_ID|1193 + 95278|polyprotein|BAC67110.1|Hepatitis C virus|11103 + 1193 + 9 + + + 1 + 13.853 + 24 + 6.48995 + 2 + 7 + 3 + 8 + 0 + 0 + 4 + 4 + 0 + 6 + NGYSWS + NGVCWS + NG WS + + + + + 4 + gnl|BL_ORD_ID|66 + 4910|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 + 66 + 20 + + + 1 + 13.4678 + 23 + 8.23977 + 2 + 9 + 5 + 12 + 0 + 0 + 3 + 5 + 0 + 8 + NGYSWSQF + NGVCWTVY + NG W+ + + + + + + 5 + gnl|BL_ORD_ID|65 + 4909|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 + 65 + 15 + + + 1 + 13.4678 + 23 + 9.20205 + 2 + 9 + 5 + 12 + 0 + 0 + 3 + 5 + 0 + 8 + NGYSWSQF + NGVCWTVY + NG W+ + + + + + + 6 + gnl|BL_ORD_ID|1632 + 146246|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 + 1632 + 17 + + + 1 + 13.4678 + 23 + 10.4757 + 2 + 9 + 7 + 14 + 0 + 0 + 3 + 5 + 0 + 8 + NGYSWSQF + NGVCWTVY + NG W+ + + + + + + 7 + gnl|BL_ORD_ID|784 + 52509|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 + 784 + 15 + + + 1 + 13.4678 + 23 + 12.0936 + 2 + 7 + 9 + 14 + 0 + 0 + 3 + 4 + 0 + 6 + NGYSWS + NGVCWT + NG W+ + + + + + 8 + gnl|BL_ORD_ID|107 + 7292|polyprotein|AAA75355.1|Hepatitis C virus subtype 1b|31647 + 107 + 9 + + + 1 + 13.0826 + 22 + 16.035 + 2 + 7 + 3 + 8 + 0 + 0 + 3 + 4 + 0 + 6 + NGYSWS + NGVCWT + NG W+ + + + + + 9 + gnl|BL_ORD_ID|89 + 6432|polyprotein [Hepatitis C virus]|CAL46125.1|Hepatitis C virus (isolate H77)|63746 + 89 + 9 + + + 1 + 13.0826 + 22 + 16.035 + 2 + 7 + 3 + 8 + 0 + 0 + 3 + 4 + 0 + 6 + NGYSWS + NGLCWT + NG W+ + + + + + 10 + gnl|BL_ORD_ID|1674 + 148619|unnamed protein product|BAA14233.1|Hepatitis C virus|11103 + 1674 + 45 + + + 1 + 13.0826 + 22 + 16.0472 + 2 + 9 + 38 + 45 + 0 + 0 + 3 + 5 + 0 + 8 + NGYSWSQF + NGVCWTVY + NG W+ + + + + + + 11 + gnl|BL_ORD_ID|91 + 6435|polyprotein|BAB18806.1|Hepatitis C virus|11103 + 91 + 9 + + + 1 + 13.0826 + 22 + 16.6015 + 2 + 7 + 3 + 8 + 0 + 0 + 3 + 4 + 0 + 6 + NGYSWS + NGVCWT + NG W+ + + + + + 12 + gnl|BL_ORD_ID|1197 + 95297|polyprotein|BAA09072.1|Hepatitis C virus genotype 1|41856 + 1197 + 9 + + + 1 + 13.0826 + 22 + 18.4218 + 2 + 7 + 3 + 8 + 0 + 0 + 3 + 4 + 0 + 6 + NGYSWS + NGVCWT + NG W+ + + + + + 13 + gnl|BL_ORD_ID|90 + 6433|Genome polyprotein|SRC279960|Hepatitis C virus subtype 1a|31646 + 90 + 9 + + + 1 + 13.0826 + 22 + 19.404 + 2 + 7 + 3 + 8 + 0 + 0 + 3 + 4 + 0 + 6 + NGYSWS + NGVCWT + NG W+ + + + + + 14 + gnl|BL_ORD_ID|1195 + 95280|Genome polyprotein|O39928.3|Hepatitis C virus genotype 5|33746 + 1195 + 9 + + + 1 + 12.6974 + 21 + 38.5226 + 2 + 7 + 3 + 8 + 0 + 0 + 3 + 4 + 0 + 6 + NGYSWS + NGVMWT + NG W+ + + + + + 15 + gnl|BL_ORD_ID|1192 + 95265|polyprotein|ABL63009.1|Hepatitis C virus genotype 4|33745 + 1192 + 9 + + + 1 + 12.3122 + 20 + 40.5299 + 2 + 7 + 3 + 8 + 0 + 0 + 3 + 4 + 0 + 6 + NGYSWS + NGVMWT + NG W+ + + + + + 16 + gnl|BL_ORD_ID|27 + 2033|polyprotein|BAA32665.1|Hepatitis C virus genotype 6|42182 + 27 + 9 + + + 1 + 12.3122 + 20 + 40.5299 + 2 + 7 + 3 + 8 + 0 + 0 + 3 + 4 + 0 + 6 + NGYSWS + NGVMWT + NG W+ + + + + + 17 + gnl|BL_ORD_ID|1199 + 95854|Genome polyprotein|O39927.3|Hepatitis C virus genotype 6|42182 + 1199 + 9 + + + 1 + 12.3122 + 20 + 49.6079 + 2 + 7 + 3 + 8 + 0 + 0 + 3 + 4 + 0 + 6 + NGYSWS + NGVMWT + NG W+ + + + + + 18 + gnl|BL_ORD_ID|1200 + 95890|polyprotein|ABE98152.1|Hepatitis C virus genotype 6|42182 + 1200 + 9 + + + 1 + 12.3122 + 20 + 51.2985 + 2 + 7 + 3 + 8 + 0 + 0 + 3 + 4 + 0 + 6 + NGYSWS + NGVMWT + NG W+ + + + + + 19 + gnl|BL_ORD_ID|397 + 24390|Major capsid protein L1|P50816.2|Human papillomavirus type 44|10592 + 397 + 9 + + + 1 + 11.927 + 19 + 102.395 + 1 + 8 + 2 + 9 + 0 + 0 + 3 + 3 + 0 + 8 + QNGYSWSQ + NNGICWGN + NG W + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 9 + Query_9 + M_2255 + 9 + + + 1 + gnl|BL_ORD_ID|1961 + 182687|polyprotein|AGK36298.1|Dengue virus 2|11060 + 1961 + 10 + + + 1 + 13.4678 + 23 + 9.40133 + 1 + 8 + 1 + 8 + 0 + 0 + 3 + 6 + 0 + 8 + SYKLSQNG + AYRIKQRG + +Y++ Q G + + + + + 2 + gnl|BL_ORD_ID|1888 + 180582|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 + 1888 + 15 + + + 1 + 12.3122 + 20 + 41.1784 + 1 + 8 + 8 + 15 + 0 + 0 + 4 + 5 + 0 + 8 + SYKLSQNG + SYETKQTG + SY+ Q G + + + + + 3 + gnl|BL_ORD_ID|2287 + 419229|polyprotein|ACF49259.1|Dengue virus type 1 Hawaii|10000440 + 2287 + 9 + + + 1 + 12.3122 + 20 + 61.624 + 2 + 8 + 2 + 8 + 0 + 0 + 3 + 5 + 0 + 7 + YKLSQNG + YRILQRG + Y++ Q G + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 10 + Query_10 + M_2256 + 9 + + + 1 + gnl|BL_ORD_ID|1811 + 170063|polyprotein|ABU97067.1|Hepatitis C virus subtype 1b|31647 + 1811 + 9 + + + 1 + 13.853 + 24 + 7.07804 + 1 + 6 + 1 + 6 + 0 + 0 + 4 + 5 + 0 + 6 + WKRGKR + WTRGER + W RG+R + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 11 + Query_11 + M_2257 + 9 + + + 1 + gnl|BL_ORD_ID|866 + 56620|Nef protein|Q9YYU8|Human immunodeficiency virus 1|11676 + 866 + 10 + + + 1 + 12.6974 + 21 + 25.6384 + 2 + 6 + 6 + 10 + 0 + 0 + 4 + 4 + 0 + 5 + FGHCF + FGWCF + FG CF + + + + + 2 + gnl|BL_ORD_ID|2214 + 193060|Nef protein|Q9YYU3|Human immunodeficiency virus 1|11676 + 2214 + 10 + + + 1 + 12.6974 + 21 + 30.4011 + 2 + 6 + 6 + 10 + 0 + 0 + 4 + 4 + 0 + 5 + FGHCF + FGWCF + FG CF + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 12 + Query_12 + M_2258 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 13 + Query_13 + M_2259 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 14 + Query_14 + M_2260 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 15 + Query_15 + M_2261 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 16 + Query_16 + M_2262 + 9 + + + 1 + gnl|BL_ORD_ID|866 + 56620|Nef protein|Q9YYU8|Human immunodeficiency virus 1|11676 + 866 + 10 + + + 1 + 14.2382 + 25 + 3.50259 + 1 + 7 + 4 + 10 + 0 + 0 + 5 + 5 + 0 + 7 + LCFGHCF + LTFGWCF + L FG CF + + + + + 2 + gnl|BL_ORD_ID|2214 + 193060|Nef protein|Q9YYU3|Human immunodeficiency virus 1|11676 + 2214 + 10 + + + 1 + 14.2382 + 25 + 4.15863 + 1 + 7 + 4 + 10 + 0 + 0 + 5 + 5 + 0 + 7 + LCFGHCF + LTFGWCF + L FG CF + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 17 + Query_17 + M_2263 + 9 + + + 1 + gnl|BL_ORD_ID|866 + 56620|Nef protein|Q9YYU8|Human immunodeficiency virus 1|11676 + 866 + 10 + + + 1 + 14.2382 + 25 + 2.66759 + 3 + 9 + 4 + 10 + 0 + 0 + 5 + 5 + 0 + 7 + LCFGHCF + LTFGWCF + L FG CF + + + + + 2 + gnl|BL_ORD_ID|2214 + 193060|Nef protein|Q9YYU3|Human immunodeficiency virus 1|11676 + 2214 + 10 + + + 1 + 14.2382 + 25 + 3.16139 + 3 + 9 + 4 + 10 + 0 + 0 + 5 + 5 + 0 + 7 + LCFGHCF + LTFGWCF + L FG CF + + + + + 3 + gnl|BL_ORD_ID|1332 + 107872|Genome polyprotein|P26664.3|Hepatitis C virus|11103 + 1332 + 10 + + + 1 + 10.7714 + 16 + 373.491 + 1 + 7 + 2 + 8 + 0 + 0 + 4 + 4 + 0 + 7 + NHLCFGH + RHLIFCH + HL F H + + + + 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Query_25 + M_2271 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 26 + Query_26 + M_2272 + 9 + + + 1 + gnl|BL_ORD_ID|1916 + 180681|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 + 1916 + 15 + + + 1 + 13.4678 + 23 + 9.20205 + 1 + 7 + 4 + 10 + 0 + 0 + 4 + 5 + 0 + 7 + YIDYKPN + YTDYMPS + Y DY P+ + + + + + 2 + gnl|BL_ORD_ID|558 + 34482|gag polyprotein|BAA00992.1|Human immunodeficiency virus 1|11676 + 558 + 9 + + + 1 + 11.927 + 19 + 84.261 + 3 + 9 + 1 + 7 + 0 + 0 + 4 + 4 + 0 + 7 + DYKPNHI + KYKLKHI + YK HI + + + + + 3 + gnl|BL_ORD_ID|659 + 39162|gag protein|AAV53308.1|Human immunodeficiency virus 1|11676 + 659 + 15 + + + 1 + 11.5418 + 18 + 108.251 + 3 + 9 + 8 + 14 + 0 + 0 + 4 + 4 + 0 + 7 + DYKPNHI + KYKLKHI + YK HI + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 27 + Query_27 + M_2273 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 28 + Query_28 + M_2274 + 9 + + + 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2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 45 + Query_45 + M_2291 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 46 + Query_46 + M_2292 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 47 + Query_47 + M_2293 + 9 + + + 1 + gnl|BL_ORD_ID|786 + 52652|||| + 786 + 27 + + + 1 + 10.3862 + 15 + 322.823 + 1 + 9 + 12 + 20 + 0 + 0 + 4 + 6 + 0 + 9 + TVKLALSVF + TVRGLTSLF + TV+ S+F + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 48 + Query_48 + M_2294 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 49 + Query_49 + M_2295 + 9 + + + 1 + gnl|BL_ORD_ID|657 + 38974|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 + 657 + 11 + + + 1 + 12.3122 + 20 + 51.4474 + 1 + 6 + 5 + 10 + 0 + 0 + 4 + 4 + 0 + 6 + PQVPEH + PQYSEH + PQ EH + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 50 + Query_50 + M_2296 + 9 + + + 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0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 58 + Query_58 + M_2304 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 59 + Query_59 + M_2305 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 60 + Query_60 + M_2306 + 9 + + + 1 + gnl|BL_ORD_ID|2108 + 186175|polyprotein|AFY10053.1|Dengue virus 3|11069 + 2108 + 10 + + + 1 + 13.853 + 24 + 6.08483 + 1 + 6 + 1 + 6 + 0 + 0 + 4 + 6 + 0 + 6 + TFRDVA + TWRDMA + T+RD+A + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + + diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_124242_3_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_124242_3_T.fasta new file mode 100755 index 00000000..bd231bd7 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_124242_3_T.fasta @@ -0,0 +1,92 @@ +>M_2307 +FHISLFQYM +>M_2308 +LIIDEDFHI +>M_2309 +VLETAAPGV +>M_2310 +ESHEKGCFW +>M_2311 +MADAKGYTV +>M_2312 +KQLPRILEA +>M_2313 +HTCQVNGRW +>M_2314 +PLLPSIISL +>M_2315 +AIWEAVMSA +>M_2316 +AVMSALPSL +>M_2317 +MSALPSLNW +>M_2318 +GLDGPLVHV +>M_2319 +SIRVSQKGW +>M_2320 +PTDPGHFLV +>M_2321 +MRGEHRFHM +>M_2322 +KLSHCLSKA +>M_2323 +CRPQCCQSV +>M_2324 +VRNPEPSPL +>M_2325 +VLVVSPWPA +>M_2326 +GMLWAMMSI +>M_2327 +YMGMLWAMM +>M_2328 +SRAVTSTTI +>M_2329 +KTASWAEVV +>M_2330 +WTFALTSGL +>M_2331 +TDFNNGSYL +>M_2332 +VTDFNNGSY +>M_2333 +LLDTIPWYL +>M_2334 +ASSDHTTHL +>M_2335 +SHSSCVWLW +>M_2336 +TGSHSSCVW +>M_2337 +SIGELLQVL +>M_2338 +TGFVRRPLW +>M_2339 +DAEPFQRGW +>M_2340 +FIFSDTVVL +>M_2341 +FIFSDTVVL +>M_2342 +FSDTVVLLF +>M_2343 +MHFIFSDTV +>M_2344 +TVVLLFDFW +>M_2345 +YHPGAMHCV +>M_2346 +CAFSGTLPW +>M_2347 +FMCAFSGTL +>M_2348 +STHPSLSQW +>M_2349 +SRKDRAPKC +>M_2350 +LMGLASTTV +>M_2351 +SLLAIHQWV +>M_2352 +SSLLAIHQW diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_124242_3_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_124242_3_T_iedb.xml new file mode 100755 index 00000000..1e232a20 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_124242_3_T_iedb.xml @@ -0,0 +1,1631 @@ + + + + blastp + BLASTP 2.2.30+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta + Query_1 + M_2307 + 9 + + + BLOSUM62 + 100000000 + 11 + 1 + F + + + + + 1 + Query_1 + M_2307 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 2 + Query_2 + M_2308 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 3 + Query_3 + M_2309 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 4 + Query_4 + M_2310 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 5 + Query_5 + M_2311 + 9 + + + 1 + gnl|BL_ORD_ID|50 + 3094|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 + 50 + 9 + + 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1 + 14.2382 + 25 + 3.10506 + 1 + 9 + 1 + 9 + 0 + 0 + 4 + 5 + 0 + 9 + STHPSLSQW + NTRPPLGNW + +T P L W + + + + + 4 + gnl|BL_ORD_ID|1601 + 142247|envelope protein 2|ACY64760.1|Hepatitis C virus subtype 1a|31646 + 1601 + 9 + + + 1 + 13.4678 + 23 + 7.72035 + 1 + 9 + 1 + 9 + 0 + 0 + 3 + 5 + 0 + 9 + STHPSLSQW + NTRPPMGNW + +T P + W + + + + + 5 + gnl|BL_ORD_ID|1599 + 142245|polyprotein|ACJ37204.1|Hepatitis C virus subtype 1a|31646 + 1599 + 9 + + + 1 + 12.3122 + 20 + 56.7066 + 1 + 9 + 1 + 9 + 0 + 0 + 3 + 4 + 0 + 9 + STHPSLSQW + NTRPPAGNW + +T P W + + + + + 6 + gnl|BL_ORD_ID|1603 + 142249|polyprotein|AAY82036.1|Hepatitis C virus subtype 1a|31646 + 1603 + 9 + + + 1 + 12.3122 + 20 + 60.6092 + 1 + 9 + 1 + 9 + 0 + 0 + 3 + 4 + 0 + 9 + STHPSLSQW + NTRPPRGNW + +T P W + + + + + 7 + gnl|BL_ORD_ID|1602 + 142248|polyprotein|BAB18806.1|Hepatitis C virus subtype 1a|31646 + 1602 + 9 + + + 1 + 11.927 + 19 + 110.987 + 1 + 9 + 1 + 9 + 0 + 0 + 3 + 4 + 0 + 9 + STHPSLSQW + NTRPPQGNW + +T P W + + + + + + + 2334 + 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00000000..90bf1be6 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_124756_1_T.fasta @@ -0,0 +1,174 @@ +>M_2353 +AIHIVAEKK +>M_2354 +ESLPPSPTW +>M_2355 +WAGNVLAPY +>M_2356 +QIIAGHFRK +>M_2357 +STSSRSHRY +>M_2358 +FHQCLSIYY +>M_2359 +IYYWDIRYK +>M_2360 +LFHQCLSIY +>M_2361 +SIYYWDIRY +>M_2362 +SIYYWDIRY +>M_2363 +SRHTIRELL +>M_2364 +QINIPIGPY +>M_2365 +GGMQALGLY +>M_2366 +FLNLSQPRK +>M_2367 +RLNSHFLNL +>M_2368 +ERSLQVKRV +>M_2369 +LQVKRVFVK +>M_2370 +RSLQVKRVF +>M_2371 +RVFVKGMKK +>M_2372 +CSSSIGTIW +>M_2373 +WSHASASLY +>M_2374 +WSHASASLY +>M_2375 +KESNAGRYY +>M_2376 +VKESNAGRY +>M_2377 +IVSVKPNMK +>M_2378 +FSYPKRPII +>M_2379 +MSHPPNILK +>M_2380 +GARPGLGRY +>M_2381 +ITSRDATRF +>M_2382 +TRFPIIASC +>M_2383 +RLLSSGTAK +>M_2384 +KVLELADRF +>M_2385 +RVSTGSVHK +>M_2386 +VVGAVGVGK +>M_2387 +LSFRSSSCR +>M_2388 +EMFEHLFGK +>M_2389 +TRAHCHLPV +>M_2390 +ILDYMQLRK +>M_2391 +KILDYMQLR +>M_2392 +TTMLDRGPK +>M_2393 +IHITEEEAV +>M_2394 +LVSMTYDRY +>M_2395 +MTYDRYVAI +>M_2396 +MVLLVSMTY +>M_2397 +MVLLVSMTY +>M_2398 +MVLLVSMTY +>M_2399 +VSMTYDRYV +>M_2400 +IHMDARLHT +>M_2401 +MGMALLIHM +>M_2402 +FKSKVPQTW +>M_2403 +VGQQQQVLW +>M_2404 +DSSSWSDRY +>M_2405 +SGGHDSSSW +>M_2406 +YEEYRGHSL +>M_2407 +HTSTVRESY +>M_2408 +HTSTVRESY +>M_2409 +SHYGQPDRQ +>M_2410 +DHEVYLKHL +>M_2411 +GGLFIASNW +>M_2412 +KVTRLHRRK +>M_2413 +LMSTSEEEF +>M_2414 +LSNNCVPQM +>M_2415 +STRDEIEGL +>M_2416 +RMCTVTNYF +>M_2417 +VMVSLKPDK +>M_2418 +CRQEQERKF +>M_2419 +EQEERREQL +>M_2420 +FRLEEQKVC +>M_2421 +QSLCGTRFY +>M_2422 +TAAAAPTPF +>M_2423 +DRNTFRHSL +>M_2424 +NTFRHSLVV +>M_2425 +RMNSFLHIL +>M_2426 +RMNSFLHIL +>M_2427 +SRMNSFLHI +>M_2428 +GSFPTEYIL +>M_2429 +VTNCHKNYW +>M_2430 +VVTNCHKNY +>M_2431 +DMAPTRPRW +>M_2432 +FRRPQESLL +>M_2433 +GINNKVCFW +>M_2434 +LLTDTNSWW +>M_2435 +QLLTDTNSW +>M_2436 +HQRVHSGEK +>M_2437 +QRYSHQRVH +>M_2438 +VKSKLIAHY +>M_2439 +SVDECELHK diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_124756_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_124756_1_T_iedb.xml new file mode 100755 index 00000000..2842ee1f --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_124756_1_T_iedb.xml @@ -0,0 +1,2615 @@ + + + + blastp + BLASTP 2.2.30+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta + Query_1 + M_2353 + 9 + + + BLOSUM62 + 100000000 + 11 + 1 + F + + + + + 1 + Query_1 + M_2353 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 2 + Query_2 + M_2354 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 3 + Query_3 + M_2355 + 9 + + + 1 + gnl|BL_ORD_ID|577 + 36352|Polyprotein|P90247|Hepatitis C virus|11103 + 577 + 20 + + + 1 + 14.2382 + 25 + 2.6 + 1 + 8 + 3 + 10 + 0 + 0 + 5 + 7 + 0 + 8 + WAGNVLAP + WAGWLLSP + WAG +L+P + + + + + 2 + gnl|BL_ORD_ID|1144 + 75438|polyprotein|AAF65962.1|Hepatitis C virus|11103 + 1144 + 20 + + + 1 + 14.2382 + 25 + 2.64513 + 1 + 8 + 13 + 20 + 0 + 0 + 5 + 7 + 0 + 8 + WAGNVLAP + WAGWLLSP + WAG +L+P + + + + + 3 + gnl|BL_ORD_ID|1143 + 75436|Polyprotein|P90247|Hepatitis C virus|11103 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0.14 + + + No hits found + + + 6 + Query_6 + M_2358 + 9 + + + 1 + gnl|BL_ORD_ID|1186 + 93431|pre-C/C protein|ABY54138.1|Hepatitis B virus|10407 + 1186 + 20 + + + 1 + 13.4678 + 23 + 12.4431 + 1 + 7 + 4 + 10 + 0 + 0 + 5 + 5 + 0 + 7 + FHQCLSI + FHLCLII + FH CL I + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 7 + Query_7 + M_2359 + 9 + + + 1 + gnl|BL_ORD_ID|1996 + 183619|nonstructural protein NS1|1802191G|Dengue virus|12637 + 1996 + 9 + + + 1 + 11.1566 + 17 + 266.5 + 2 + 9 + 1 + 8 + 0 + 0 + 3 + 5 + 0 + 8 + YYWDIRYK + HTWTEQYK + + W +YK + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 8 + Query_8 + M_2360 + 9 + + + 1 + gnl|BL_ORD_ID|1186 + 93431|pre-C/C protein|ABY54138.1|Hepatitis B virus|10407 + 1186 + 20 + + + 1 + 14.6234 + 26 + 2.38548 + 1 + 8 + 3 + 10 + 0 + 0 + 6 + 6 + 0 + 8 + LFHQCLSI + LFHLCLII + LFH CL I + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 9 + Query_9 + M_2361 + 9 + + + + + 2334 + 25004 + 0 + 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found + + + 85 + Query_85 + M_2437 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 86 + Query_86 + M_2438 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 87 + Query_87 + M_2439 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + + diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_125196_3_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_125196_3_T.fasta new file mode 100755 index 00000000..67783270 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_125196_3_T.fasta @@ -0,0 +1,126 @@ +>M_2440 +PMPPPLEPI +>M_2441 +KEIDVIAIP +>M_2442 +YKDYAAELV +>M_2443 +DNLDSDNTY +>M_2444 +LAVTLGLAL +>M_2445 +HNNNRPLTM +>M_2446 +WAVPPLLLA +>M_2447 +RCYVRGLFH +>M_2448 +KITAQRLSH +>M_2449 +SSLHSEPPK +>M_2450 +QAQALGIPL +>M_2451 +QAQALGIPL +>M_2452 +IPKSPEEAI +>M_2453 +PEEPTSPAA +>M_2454 +RVQSRPIPI +>M_2455 +HSLQQAQSV +>M_2456 +PLFTTQCGK +>M_2457 +HMEAEMAQK +>M_2458 +VQLPKVSEM +>M_2459 +ITAQRLSHL +>M_2460 +LLLSPPVEV +>M_2461 +IPILPLIYI +>M_2462 +AEAQTPEDS +>M_2463 +LLSPPVEVK +>M_2464 +TEHDVQIYV +>M_2465 +FISLKFSSK +>M_2466 +IPGPIPGPI +>M_2467 +KTRRTSSLH +>M_2468 +EEPTSPAAA +>M_2469 +WILSARLLK +>M_2470 +QQFPSLELL +>M_2471 +RPIPILPLI +>M_2472 +NMKEQVVIL +>M_2473 +AQRLSHLNK +>M_2474 +RAYRDDTDL +>M_2475 +NVFWGEHFK +>M_2476 +YYKDYAAEL +>M_2477 +QQFPSLELL +>M_2478 +SLKFSSKIK +>M_2479 +FLFGLAQNL +>M_2480 +YVRGLFHSL +>M_2481 +TENSETTTA +>M_2482 +ALGIPLTPK +>M_2483 +NENTTPSPA +>M_2484 +RLPEVQLPK +>M_2485 +ISLKFSSKI +>M_2486 +KEGARNVLA +>M_2487 +MPNDFWARL +>M_2488 +FTEHDVQIY +>M_2489 +FKFHNLPPL +>M_2490 +NTYRTPSVL +>M_2491 +IAIPSKCLL +>M_2492 +EASSAVPTV +>M_2493 +MAAAVVARL +>M_2494 +QEFENIKSY +>M_2495 +FQKDPPADI +>M_2496 +DMYDGRFLV +>M_2497 +PLYKVRFSK +>M_2498 +VTRPFISLK +>M_2499 +IILFNRLLK +>M_2500 +IPYRDSVLI +>M_2501 +AEASSAVPT +>M_2502 +EEMPNDFWA diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_125196_3_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_125196_3_T_iedb.xml new file mode 100755 index 00000000..0ae81462 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_125196_3_T_iedb.xml @@ -0,0 +1,2325 @@ + + + + blastp + BLASTP 2.2.30+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta + Query_1 + M_2440 + 9 + + + BLOSUM62 + 100000000 + 11 + 1 + F + + + + + 1 + Query_1 + M_2440 + 9 + + + 1 + gnl|BL_ORD_ID|448 + 27241|Spike glycoprotein precursor|P59594.1|SARS coronavirus|227859 + 448 + 9 + + + 1 + 11.927 + 19 + 77.6399 + 2 + 8 + 2 + 8 + 0 + 0 + 4 + 6 + 0 + 7 + MPPPLEP + LPDPLKP + +P PL+P + + + + + 2 + gnl|BL_ORD_ID|1581 + 141462|tegument protein UL21|NP_044622.1|Human alphaherpesvirus 1|10298 + 1581 + 9 + + + 1 + 10.3862 + 15 + 702.182 + 2 + 9 + 1 + 8 + 0 + 0 + 3 + 6 + 0 + 8 + MPPPLEPI + VPRPDDPV + +P P +P+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 2 + Query_2 + M_2441 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 3 + Query_3 + M_2442 + 9 + + + 1 + gnl|BL_ORD_ID|1970 + 182917|polyprotein|CDF77361.1|Dengue virus 3|11069 + 1970 + 9 + + + 1 + 14.2382 + 25 + 4.1461 + 1 + 6 + 2 + 7 + 0 + 0 + 4 + 6 + 0 + 6 + YKDYAA + FKDFAA + +KD+AA + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 4 + Query_4 + M_2443 + 9 + + + 1 + gnl|BL_ORD_ID|1097 + 72563|polyprotein|AAB70696.1|Dengue virus type 1 Hawaii|10000440 + 1097 + 20 + + + 1 + 12.6974 + 21 + 29.0269 + 2 + 9 + 2 + 9 + 0 + 0 + 4 + 5 + 0 + 8 + NLDSDNTY + HYDEDNPY + + D DN Y + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 5 + Query_5 + M_2444 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 6 + Query_6 + M_2445 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 7 + Query_7 + M_2446 + 9 + + + 1 + gnl|BL_ORD_ID|1110 + 73059|kaposin|AAC57155.1|Human gammaherpesvirus 8|37296 + 1110 + 15 + + + 1 + 13.0826 + 22 + 17.5339 + 2 + 7 + 7 + 12 + 0 + 0 + 4 + 6 + 0 + 6 + AVPPLL + AIPPLV + A+PPL+ + + + + + 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141402|tegument protein VP22|NP_044651.1|Human alphaherpesvirus 1|10298 + 1573 + 10 + + + 1 + 11.927 + 19 + 68.8532 + 2 + 8 + 4 + 10 + 0 + 0 + 4 + 5 + 0 + 7 + EEPTSPA + ERPRAPA + E P +PA + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 15 + Query_15 + M_2454 + 9 + + + 1 + gnl|BL_ORD_ID|876 + 57591|Cobalamin (vitamin B12) synthesis protein/P47K family protein|YP_169986.1|Francisella tularensis subsp. tularensis SCHU S4|177416 + 876 + 10 + + + 1 + 12.6974 + 21 + 25.2038 + 4 + 9 + 1 + 6 + 0 + 0 + 3 + 5 + 0 + 6 + SRPIPI + SEPLPV + S P+P+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 16 + Query_16 + M_2455 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 17 + Query_17 + M_2456 + 9 + + + 1 + gnl|BL_ORD_ID|1152 + 75718|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 + 1152 + 11 + + + 1 + 13.0826 + 22 + 16.3278 + 1 + 6 + 5 + 10 + 0 + 0 + 4 + 5 + 0 + 6 + PLFTTQ + PTFTSQ + P FT+Q + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 18 + Query_18 + M_2457 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 19 + Query_19 + M_2458 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 20 + Query_20 + M_2459 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 21 + Query_21 + M_2460 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 22 + Query_22 + M_2461 + 9 + + + 1 + gnl|BL_ORD_ID|452 + 27345|Large envelope protein|P03138.3|Hepatitis B virus subtype ayw|10418 + 452 + 9 + + + 1 + 11.927 + 19 + 82.8955 + 2 + 7 + 4 + 9 + 0 + 0 + 4 + 5 + 0 + 6 + PILPLI + PFLPLL + P LPL+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 23 + Query_23 + M_2462 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 24 + Query_24 + M_2463 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 25 + Query_25 + M_2464 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 26 + Query_26 + M_2465 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 27 + Query_27 + M_2466 + 9 + + + 1 + gnl|BL_ORD_ID|741 + 47760|EBNA-1 protein|Q777E1|Human gammaherpesvirus 4|10376 + 741 + 15 + + + 1 + 10.3862 + 15 + 419.458 + 2 + 7 + 1 + 6 + 0 + 0 + 4 + 4 + 0 + 6 + PGPIPG + PGTGPG + PG PG + + + + + 2 + gnl|BL_ORD_ID|75 + 5542|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 + 75 + 15 + + + 1 + 10.001 + 14 + 709.084 + 2 + 9 + 8 + 15 + 0 + 0 + 4 + 4 + 0 + 8 + PGPIPGPI + PGTSGSPI + PG PI + + + + + 3 + gnl|BL_ORD_ID|1929 + 180750|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 + 1929 + 15 + + + 1 + 10.001 + 14 + 819.307 + 2 + 9 + 2 + 9 + 0 + 0 + 4 + 4 + 0 + 8 + PGPIPGPI + PGTSGSPI + PG PI + + + + + 4 + gnl|BL_ORD_ID|260 + 17802|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 + 260 + 15 + + + 1 + 10.001 + 14 + 830.077 + 2 + 9 + 3 + 10 + 0 + 0 + 4 + 4 + 0 + 8 + PGPIPGPI + PGTSGSPI + PG PI + + + + + 5 + gnl|BL_ORD_ID|1712 + 150341|polyprotein|AGW21594.1|Dengue virus 1|11053 + 1712 + 9 + + + 1 + 9.61583 + 13 + 1362.74 + 2 + 9 + 2 + 9 + 0 + 0 + 4 + 4 + 0 + 8 + PGPIPGPI + PGTSGSPI + PG PI + + + + + 6 + gnl|BL_ORD_ID|1766 + 154857|tegument protein|CAB06735.1|Human alphaherpesvirus 2|10310 + 1766 + 16 + + + 1 + 4.99343 + 1 + 89081.4 + 7 + 9 + 14 + 16 + 0 + 0 + 2 + 3 + 0 + 3 + GPI + GPV + GP+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 28 + Query_28 + M_2467 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 29 + Query_29 + M_2468 + 9 + + + 1 + gnl|BL_ORD_ID|1179 + 79628|E1 protein|BAA19893.1|Rubella virus|11041 + 1179 + 21 + + + 1 + 12.6974 + 21 + 30.3943 + 3 + 8 + 14 + 19 + 0 + 0 + 4 + 5 + 0 + 6 + PTSPAA + PTAPCA + PT+P A + + + + + 2 + gnl|BL_ORD_ID|1573 + 141402|tegument protein VP22|NP_044651.1|Human alphaherpesvirus 1|10298 + 1573 + 10 + + + 1 + 12.3122 + 20 + 62.4024 + 1 + 7 + 4 + 10 + 0 + 0 + 4 + 5 + 0 + 7 + EEPTSPA + ERPRAPA + E P +PA + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 30 + Query_30 + M_2469 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 31 + Query_31 + M_2470 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 32 + Query_32 + M_2471 + 9 + + + 1 + gnl|BL_ORD_ID|452 + 27345|Large envelope protein|P03138.3|Hepatitis B virus subtype ayw|10418 + 452 + 9 + + + 1 + 11.927 + 19 + 105.754 + 4 + 9 + 4 + 9 + 0 + 0 + 4 + 5 + 0 + 6 + PILPLI + PFLPLL + P LPL+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 33 + Query_33 + M_2472 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 34 + Query_34 + M_2473 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 35 + Query_35 + M_2474 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 36 + Query_36 + M_2475 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 37 + Query_37 + M_2476 + 9 + + + 1 + gnl|BL_ORD_ID|1970 + 182917|polyprotein|CDF77361.1|Dengue virus 3|11069 + 1970 + 9 + + + 1 + 13.853 + 24 + 4.59527 + 2 + 7 + 2 + 7 + 0 + 0 + 4 + 6 + 0 + 6 + YKDYAA + FKDFAA + +KD+AA + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 38 + Query_38 + M_2477 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 39 + Query_39 + M_2478 + 9 + + + 1 + gnl|BL_ORD_ID|1387 + 110227|Protein E6|P03126.1|Human papillomavirus type 16|333760 + 1387 + 33 + + + 1 + 14.6234 + 26 + 2.38904 + 2 + 8 + 21 + 27 + 0 + 0 + 6 + 6 + 0 + 7 + LKFSSKI + LKFYSKI + LKF SKI + + + + + 2 + gnl|BL_ORD_ID|1400 + 110467|Protein E6|P03126.1|Human papillomavirus type 16|333760 + 1400 + 25 + + + 1 + 14.6234 + 26 + 2.651 + 1 + 8 + 13 + 20 + 0 + 0 + 6 + 6 + 0 + 8 + SLKFSSKI + CLKFYSKI + LKF SKI + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 40 + Query_40 + M_2479 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 41 + Query_41 + M_2480 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 42 + Query_42 + M_2481 + 9 + + + 1 + gnl|BL_ORD_ID|1689 + 149063|NS3 protease/helicase'|NP_803144.1|Hepatitis C virus (isolate H77)|63746 + 1689 + 18 + + + 1 + 12.6974 + 21 + 27.7051 + 1 + 7 + 8 + 14 + 0 + 0 + 5 + 5 + 0 + 7 + TENSETT + VENLETT + EN ETT + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 43 + Query_43 + M_2482 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 44 + Query_44 + M_2483 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 45 + Query_45 + M_2484 + 9 + + + 1 + gnl|BL_ORD_ID|241 + 16836|precore/core protein [Hepatitis B virus]|AAR03815.1|Hepatitis B virus|10407 + 241 + 10 + + + 1 + 10.3862 + 15 + 499.131 + 2 + 9 + 2 + 9 + 0 + 0 + 4 + 4 + 0 + 8 + LPEVQLPK + LPSDFLPS + LP LP + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 46 + Query_46 + M_2485 + 9 + + + 1 + gnl|BL_ORD_ID|1387 + 110227|Protein E6|P03126.1|Human papillomavirus type 16|333760 + 1387 + 33 + + + 1 + 15.0086 + 27 + 1.24899 + 3 + 9 + 21 + 27 + 0 + 0 + 6 + 6 + 0 + 7 + LKFSSKI + LKFYSKI + LKF SKI + + + + + 2 + gnl|BL_ORD_ID|1400 + 110467|Protein E6|P03126.1|Human papillomavirus type 16|333760 + 1400 + 25 + + + 1 + 14.2382 + 25 + 2.9789 + 3 + 9 + 14 + 20 + 0 + 0 + 6 + 6 + 0 + 7 + LKFSSKI + LKFYSKI + LKF SKI + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 47 + Query_47 + M_2486 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 48 + Query_48 + M_2487 + 9 + + + 1 + gnl|BL_ORD_ID|235 + 16814|precore protein|CAM58990.1|Hepatitis B virus|10407 + 235 + 10 + + + 1 + 15.3938 + 28 + 0.822133 + 1 + 9 + 2 + 10 + 0 + 0 + 4 + 7 + 0 + 9 + MPNDFWARL + LPNDFFPSV + +PNDF+ + + + + + + 2 + gnl|BL_ORD_ID|234 + 16813|External core antigen|SRC279980|Hepatitis B virus|10407 + 234 + 10 + + + 1 + 15.0086 + 27 + 1.18631 + 1 + 6 + 2 + 7 + 0 + 0 + 4 + 6 + 0 + 6 + MPNDFW + LPNDFF + +PNDF+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 49 + Query_49 + M_2488 + 9 + + + 1 + gnl|BL_ORD_ID|1984 + 183275|polyprotein|AGW21594.1|Dengue virus 1|11053 + 1984 + 10 + + + 1 + 13.0826 + 22 + 16.111 + 1 + 8 + 1 + 8 + 0 + 0 + 4 + 6 + 0 + 8 + FTEHDVQI + FTNMEVQL + FT +VQ+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 50 + Query_50 + M_2489 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 51 + Query_51 + M_2490 + 9 + + + 1 + gnl|BL_ORD_ID|1897 + 180617|polyprotein|AGO67248.1|Dengue virus 2|11060 + 1897 + 10 + + + 1 + 13.4678 + 23 + 12.2057 + 3 + 8 + 5 + 10 + 0 + 0 + 3 + 6 + 0 + 6 + YRTPSV + YQTPAI + Y+TP++ + + + + + 2 + gnl|BL_ORD_ID|2153 + 189289|gag protein|ADO93742.1|Human immunodeficiency virus 1|11676 + 2153 + 9 + + + 1 + 12.3122 + 20 + 44.8495 + 3 + 9 + 3 + 9 + 0 + 0 + 5 + 5 + 0 + 7 + YRTPSVL + YNTISVL + Y T SVL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 52 + Query_52 + M_2491 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 53 + Query_53 + M_2492 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 54 + Query_54 + M_2493 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 55 + Query_55 + M_2494 + 9 + + + 1 + gnl|BL_ORD_ID|1822 + 178247|Protein E6|P03126.1|Human papillomavirus type 16|333760 + 1822 + 15 + + + 1 + 14.2382 + 25 + 3.43226 + 1 + 8 + 6 + 13 + 0 + 0 + 4 + 5 + 0 + 8 + QEFENIKS + QRFHNIRG + Q F NI+ + + + + + 2 + gnl|BL_ORD_ID|1384 + 110205|Protein E6|P03126.1|Human papillomavirus type 16|333760 + 1384 + 32 + + + 1 + 14.2382 + 25 + 4.11038 + 1 + 7 + 4 + 10 + 0 + 0 + 4 + 5 + 0 + 7 + QEFENIK + QRFHNIR + Q F NI+ + + + + + 3 + gnl|BL_ORD_ID|1385 + 110215|Protein E6|P03126.1|Human papillomavirus type 16|333760 + 1385 + 25 + + + 1 + 14.2382 + 25 + 4.57287 + 1 + 8 + 10 + 17 + 0 + 0 + 4 + 5 + 0 + 8 + QEFENIKS + QRFHNIRG + Q F NI+ + + + + + 4 + gnl|BL_ORD_ID|1395 + 110394|Protein E6|P03126.1|Human papillomavirus type 16|333760 + 1395 + 32 + + + 1 + 13.0826 + 22 + 18.1365 + 1 + 7 + 22 + 28 + 0 + 0 + 4 + 5 + 0 + 7 + QEFENIK + QRFHNIR + Q F NI+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 56 + Query_56 + M_2495 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 57 + Query_57 + M_2496 + 9 + + + 1 + gnl|BL_ORD_ID|1185 + 93270|hypothetical protein|NP_218356.1|Mycobacterium tuberculosis H37Rv|83332 + 1185 + 9 + + + 1 + 15.0086 + 27 + 0.92904 + 2 + 9 + 2 + 9 + 0 + 0 + 5 + 6 + 0 + 8 + MYDGRFLV + LYDGSFAV + +YDG F V + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 58 + Query_58 + M_2497 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 59 + Query_59 + M_2498 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 60 + Query_60 + M_2499 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 61 + Query_61 + M_2500 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 62 + Query_62 + M_2501 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 63 + Query_63 + M_2502 + 9 + + + 1 + gnl|BL_ORD_ID|235 + 16814|precore protein|CAM58990.1|Hepatitis B virus|10407 + 235 + 10 + + + 1 + 15.0086 + 27 + 0.948031 + 3 + 8 + 2 + 7 + 0 + 0 + 4 + 6 + 0 + 6 + MPNDFW + LPNDFF + +PNDF+ + + + + + 2 + gnl|BL_ORD_ID|234 + 16813|External core antigen|SRC279980|Hepatitis B virus|10407 + 234 + 10 + + + 1 + 15.0086 + 27 + 0.978697 + 3 + 8 + 2 + 7 + 0 + 0 + 4 + 6 + 0 + 6 + MPNDFW + LPNDFF + +PNDF+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + + diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_126613_2_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_126613_2_T.fasta new file mode 100755 index 00000000..73fb9895 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_126613_2_T.fasta @@ -0,0 +1,70 @@ +>M_2503 +KMPEMHFKA +>M_2504 +AYSKCFISV +>M_2505 +LYLKTSQDV +>M_2506 +DLLTNLMYV +>M_2507 +LLTNLMYVL +>M_2508 +YQFPQSIDL +>M_2509 +VWQRPVLNF +>M_2510 +VEGTFISDY +>M_2511 +EELEIFMAR +>M_2512 +YEMIRTFYI +>M_2513 +EEFPCHKCV +>M_2514 +NYMAHLVAV +>M_2515 +FADFEWHFL +>M_2516 +SFADFEWHF +>M_2517 +FEQTLEELY +>M_2518 +IYVKPLPIL +>M_2519 +VLQIYVKPL +>M_2520 +RQWRSLTTL +>M_2521 +FCLGLVVTI +>M_2522 +GVFCLGLVV +>M_2523 +TLGVFCLGL +>M_2524 +IVPRLIMNF +>M_2525 +LIMNFTLGV +>M_2526 +GEHPYQCPY +>M_2527 +VLHRHMTTI +>M_2528 +HEIDFYRED +>M_2529 +KLDASVQHL +>M_2530 +RQLKLDASV +>M_2531 +FLWLWPLDF +>M_2532 +SEDGFLWLW +>M_2533 +WLWPLDFSS +>M_2534 +TFRDVAVEF +>M_2535 +AFSQSAYLI +>M_2536 +AYLIQHQRF +>M_2537 +KAFSQSAYL diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_126613_2_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_126613_2_T_iedb.xml new file mode 100755 index 00000000..2a4695b8 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_126613_2_T_iedb.xml @@ -0,0 +1,1190 @@ + + + + blastp + BLASTP 2.2.30+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta + Query_1 + M_2503 + 9 + + + BLOSUM62 + 100000000 + 11 + 1 + F + + + + + 1 + Query_1 + M_2503 + 9 + + + 1 + gnl|BL_ORD_ID|2244 + 232153|rhoptry protein 18|CAJ27113.1|Toxoplasma gondii type I|1209525 + 2244 + 19 + + + 1 + 12.3122 + 20 + 38.4826 + 3 + 9 + 2 + 8 + 0 + 0 + 4 + 5 + 0 + 7 + PEMHFKA + PERPFQA + PE F+A + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 2 + Query_2 + M_2504 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 3 + Query_3 + M_2505 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 4 + Query_4 + M_2506 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 5 + Query_5 + M_2507 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + 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00000000..d1c98dee --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_126796_3_T.fasta @@ -0,0 +1,132 @@ +>M_2538 +QEEQQQQQL +>M_2539 +YLFSPQNQF +>M_2540 +YLFSPQNQF +>M_2541 +QARKIDHPL +>M_2542 +QARKIDHPL +>M_2543 +GLFVHTPCL +>M_2544 +RVLPAGLFV +>M_2545 +VHTPCLVGL +>M_2546 +AGLDSYPEL +>M_2547 +LVVSRSVSL +>M_2548 +LVVSRSVSL +>M_2549 +CSVDHRSVL +>M_2550 +HRSVLQRIM +>M_2551 +KMWEQEEKI +>M_2552 +FGIISIIFV +>M_2553 +GIISIIFVV +>M_2554 +IFGIISIIF +>M_2555 +RIFGIISII +>M_2556 +STAARIFGI +>M_2557 +TAARIFGII +>M_2558 +LSVQLGPTV +>M_2559 +CYTFNSIII +>M_2560 +SIIIFGPFL +>M_2561 +SIIIFGPFL +>M_2562 +YTFNSIIIF +>M_2563 +LEIQTPEAV +>M_2564 +YLALAAQCL +>M_2565 +YLALAAQCL +>M_2566 +AGCPAAQEL +>M_2567 +RARPAGCPA +>M_2568 +RPAGCPAAQ +>M_2569 +AGVDHIITM +>M_2570 +LSIAGVDHI +>M_2571 +PPRYIGIPI +>M_2572 +CMLVGDSAV +>M_2573 +MLSSIKCML +>M_2574 +MLSSIKCML +>M_2575 +FGHTYVPAF +>M_2576 +GQDFGHTYV +>M_2577 +YSTPQGQDF +>M_2578 +FVGLAIGTL +>M_2579 +IGTLSGDAL +>M_2580 +NMFEISNRL +>M_2581 +VDLGSTTPL +>M_2582 +IPLWGSPVT +>M_2583 +FVLSMQPVV +>M_2584 +FVLSMQPVV +>M_2585 +SMQPVVFQA +>M_2586 +YYDPFVLSM +>M_2587 +YYDPFVLSM +>M_2588 +YSHQNGASY +>M_2589 +AGVLLVLAL +>M_2590 +RFAGVLLVL +>M_2591 +VLALILPGT +>M_2592 +VLLVLALIL +>M_2593 +RQIPAQRDL +>M_2594 +SYRKSVRQI +>M_2595 +CYYELNQCL +>M_2596 +CYYELNQCL +>M_2597 +CPLCPFLTM +>M_2598 +FMNRFQCPL +>M_2599 +FMNRFQCPL +>M_2600 +FQCPLCPFL +>M_2601 +FQCPLCPFL +>M_2602 +RFQCPLCPF +>M_2603 +RFQCPLCPF diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_126796_3_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_126796_3_T_iedb.xml new file mode 100755 index 00000000..fed7e106 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_126796_3_T_iedb.xml @@ -0,0 +1,2526 @@ + + + + blastp + BLASTP 2.2.30+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta + Query_1 + M_2538 + 9 + + + BLOSUM62 + 100000000 + 11 + 1 + F + + + + + 1 + Query_1 + M_2538 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 2 + Query_2 + M_2539 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 3 + Query_3 + M_2540 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 4 + Query_4 + M_2541 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 5 + Query_5 + M_2542 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 6 + Query_6 + M_2543 + 9 + + + 1 + gnl|BL_ORD_ID|1562 + 141281|tegument protein UL21|NP_044622.1|Human alphaherpesvirus 1|10298 + 1562 + 10 + + + 1 + 13.4678 + 23 + 10.6199 + 3 + 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hits found + + + 13 + Query_13 + M_2550 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 14 + Query_14 + M_2551 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 15 + Query_15 + M_2552 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 16 + Query_16 + M_2553 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 17 + Query_17 + M_2554 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 18 + Query_18 + M_2555 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 19 + Query_19 + M_2556 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 20 + Query_20 + M_2557 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 21 + Query_21 + M_2558 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + 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gnl|BL_ORD_ID|1856 + 180411|polyprotein|AGO67248.1|Dengue virus 2|11060 + 1856 + 9 + + + 1 + 11.5418 + 18 + 138.797 + 2 + 7 + 2 + 7 + 0 + 0 + 4 + 5 + 0 + 6 + STPQGQ + TTPFGQ + +TP GQ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 41 + Query_41 + M_2578 + 9 + + + 1 + gnl|BL_ORD_ID|344 + 21638|protein F|ABV46152.2|Hepatitis C virus (isolate Japanese)|11116 + 344 + 9 + + + 1 + 13.0826 + 22 + 18.7436 + 3 + 9 + 3 + 9 + 0 + 0 + 5 + 6 + 0 + 7 + GLAIGTL + GLSPGTL + GL+ GTL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 42 + Query_42 + M_2579 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 43 + Query_43 + M_2580 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 44 + Query_44 + M_2581 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 45 + Query_45 + M_2582 + 9 + + + 1 + gnl|BL_ORD_ID|744 + 48321|||| + 744 + 9 + + + 1 + 15.0086 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subtype 1a|31646 + 833 + 9 + + + 1 + 13.0826 + 22 + 18.4218 + 3 + 9 + 2 + 8 + 0 + 0 + 4 + 4 + 0 + 7 + LWGSPVT + LWHYPCT + LW P T + + + + + 7 + gnl|BL_ORD_ID|831 + 54819|JK3|CAA43789.1|Hepatitis C virus|11103 + 831 + 9 + + + 1 + 13.0826 + 22 + 18.4218 + 3 + 9 + 2 + 8 + 0 + 0 + 4 + 4 + 0 + 7 + LWGSPVT + LWHYPCT + LW P T + + + + + 8 + gnl|BL_ORD_ID|834 + 54824|polyprotein precursor|BAA01583.1|Hepatitis C virus|11103 + 834 + 9 + + + 1 + 13.0826 + 22 + 18.7436 + 3 + 9 + 2 + 8 + 0 + 0 + 4 + 4 + 0 + 7 + LWGSPVT + LWHYPCT + LW P T + + + + + 9 + gnl|BL_ORD_ID|835 + 54825|polyprotein|BAA03375.1|Hepatitis C virus|11103 + 835 + 9 + + + 1 + 13.0826 + 22 + 19.7427 + 3 + 9 + 2 + 8 + 0 + 0 + 4 + 4 + 0 + 7 + LWGSPVT + LWHYPCT + LW P T + + + + + 10 + gnl|BL_ORD_ID|609 + 37255|||| + 609 + 9 + + + 1 + 12.6974 + 21 + 26.0147 + 3 + 9 + 2 + 8 + 0 + 0 + 4 + 5 + 0 + 7 + LWGSPVT + LFGYPVA + L+G PV + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 46 + Query_46 + M_2583 + 9 + + + 1 + gnl|BL_ORD_ID|1157 + 76334|Protein E7|P17387.1|Human papillomavirus type 31|10585 + 1157 + 10 + + + 1 + 14.6234 + 26 + 1.81479 + 1 + 7 + 1 + 7 + 0 + 0 + 4 + 6 + 0 + 7 + FVLSMQP + YVLDLQP + +VL +QP + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 47 + Query_47 + M_2584 + 9 + + + 1 + gnl|BL_ORD_ID|1157 + 76334|Protein E7|P17387.1|Human papillomavirus type 31|10585 + 1157 + 10 + + + 1 + 14.6234 + 26 + 1.81479 + 1 + 7 + 1 + 7 + 0 + 0 + 4 + 6 + 0 + 7 + FVLSMQP + YVLDLQP + +VL +QP + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 48 + Query_48 + M_2585 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 49 + Query_49 + M_2586 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 50 + Query_50 + M_2587 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 51 + Query_51 + M_2588 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 52 + Query_52 + M_2589 + 9 + + + 1 + gnl|BL_ORD_ID|336 + 21199|Circumsporozoite protein precursor|P08677.2|Plasmodium vivax strain Belem|31273 + 336 + 10 + + + 1 + 12.6974 + 21 + 30.4011 + 3 + 9 + 4 + 10 + 0 + 0 + 6 + 7 + 0 + 7 + VLLVLAL + ILLVLAL + +LLVLAL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 53 + Query_53 + M_2590 + 9 + + + 1 + gnl|BL_ORD_ID|1824 + 178829|envelope protein|BAJ51675.1|HBV genotype D|489483 + 1824 + 10 + + + 1 + 12.6974 + 21 + 25.6384 + 2 + 9 + 1 + 8 + 0 + 0 + 6 + 6 + 0 + 8 + FAGVLLVL + FLGPLLVL + F G LLVL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 54 + Query_54 + M_2591 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 55 + Query_55 + M_2592 + 9 + + + 1 + gnl|BL_ORD_ID|336 + 21199|Circumsporozoite protein precursor|P08677.2|Plasmodium vivax strain Belem|31273 + 336 + 10 + + + 1 + 12.3122 + 20 + 46.3152 + 1 + 7 + 4 + 10 + 0 + 0 + 6 + 7 + 0 + 7 + VLLVLAL + ILLVLAL + +LLVLAL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 56 + Query_56 + M_2593 + 9 + + + 1 + gnl|BL_ORD_ID|1184 + 93224|core protein|AAL31859.1|Hepatitis B virus|10407 + 1184 + 14 + + + 1 + 15.0086 + 27 + 1.285 + 4 + 9 + 4 + 9 + 0 + 0 + 5 + 5 + 0 + 6 + PAQRDL + PASRDL + PA RDL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 57 + Query_57 + M_2594 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 58 + Query_58 + M_2595 + 9 + + + 1 + gnl|BL_ORD_ID|1398 + 110431|E7|AAD33253.1|Human papillomavirus type 16|333760 + 1398 + 36 + + + 1 + 13.0826 + 22 + 14.7121 + 1 + 8 + 5 + 12 + 0 + 0 + 4 + 5 + 0 + 8 + CYYELNQC + CYEQLNDS + CY +LN + + + + + 2 + gnl|BL_ORD_ID|1392 + 110335|E7|AAD33253.1|Human papillomavirus type 16|333760 + 1392 + 32 + + + 1 + 13.0826 + 22 + 19.4872 + 1 + 8 + 24 + 31 + 0 + 0 + 4 + 5 + 0 + 8 + CYYELNQC + CYEQLNDS + CY +LN + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 59 + Query_59 + M_2596 + 9 + + + 1 + gnl|BL_ORD_ID|1398 + 110431|E7|AAD33253.1|Human papillomavirus type 16|333760 + 1398 + 36 + + + 1 + 13.0826 + 22 + 14.7121 + 1 + 8 + 5 + 12 + 0 + 0 + 4 + 5 + 0 + 8 + CYYELNQC + CYEQLNDS + CY +LN + + + + + 2 + gnl|BL_ORD_ID|1392 + 110335|E7|AAD33253.1|Human papillomavirus type 16|333760 + 1392 + 32 + + + 1 + 13.0826 + 22 + 19.4872 + 1 + 8 + 24 + 31 + 0 + 0 + 4 + 5 + 0 + 8 + CYYELNQC + CYEQLNDS + CY +LN + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 60 + Query_60 + M_2597 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 61 + Query_61 + M_2598 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 62 + Query_62 + M_2599 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 63 + Query_63 + M_2600 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 64 + Query_64 + M_2601 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 65 + Query_65 + M_2602 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 66 + Query_66 + M_2603 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + + diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_127486_2_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_127486_2_T.fasta new file mode 100755 index 00000000..86c0b387 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_127486_2_T.fasta @@ -0,0 +1,62 @@ +>M_2604 +APEPLLLSW +>M_2605 +ASLHHHHHR +>M_2606 +RPPPSQASL +>M_2607 +FPDHMACDL +>M_2608 +ALLGNRTAL +>M_2609 +GPVSAPGLL +>M_2610 +HVYRNFLNK +>M_2611 +RPRGDNGYT +>M_2612 +SNSESEILK +>M_2613 +AVDRYVAMR +>M_2614 +RYVAMRHPL +>M_2615 +YVAMRHPLR +>M_2616 +RAGESVWPK +>M_2617 +VWPKKINNI +>M_2618 +VVGADGVGK +>M_2619 +KTETYDNYK +>M_2620 +RQLTVESDK +>M_2621 +ITLTATSQK +>M_2622 +HPTASTLST +>M_2623 +NPSHPTAST +>M_2624 +LMLLQSGYK +>M_2625 +HFPIYHLLL +>M_2626 +LASSFVFLY +>M_2627 +LISEGQRLK +>M_2628 +KPLPLVTDL +>M_2629 +LPLVTDLSL +>M_2630 +APIAPTFYK +>M_2631 +APTFYKPKL +>M_2632 +IAPTFYKPK +>M_2633 +TFYKPKLLK +>M_2634 +VFQHIFDLI diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_127486_2_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_127486_2_T_iedb.xml new file mode 100755 index 00000000..cb107982 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_127486_2_T_iedb.xml @@ -0,0 +1,724 @@ + + + + blastp + BLASTP 2.2.30+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta + Query_1 + M_2604 + 9 + + + BLOSUM62 + 100000000 + 11 + 1 + F + + + + + 1 + Query_1 + M_2604 + 9 + + + 1 + gnl|BL_ORD_ID|1682 + 149036|E2 protein|NP_751921.1|Hepatitis C virus (isolate H77)|63746 + 1682 + 9 + + + 1 + 12.3122 + 20 + 55.769 + 4 + 8 + 4 + 8 + 0 + 0 + 5 + 5 + 0 + 5 + PLLLS + PLLLS + PLLLS + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 2 + Query_2 + M_2605 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 3 + Query_3 + M_2606 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 4 + Query_4 + M_2607 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 5 + Query_5 + M_2608 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 6 + Query_6 + M_2609 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 7 + Query_7 + M_2610 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 8 + Query_8 + M_2611 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 9 + Query_9 + M_2612 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 10 + Query_10 + M_2613 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 11 + Query_11 + M_2614 + 9 + + + 1 + gnl|BL_ORD_ID|2080 + 185327|polyprotein|ACF49259.1|Dengue virus type 1 Hawaii|10000440 + 2080 + 9 + + + 1 + 13.853 + 24 + 5.18352 + 1 + 9 + 1 + 9 + 0 + 0 + 4 + 6 + 0 + 9 + RYVAMRHPL + QYIYMGQPL + +Y+ M PL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 12 + Query_12 + M_2615 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 13 + 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a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_128984_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_128984_1_T_iedb.xml new file mode 100755 index 00000000..ef42d15d --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_128984_1_T_iedb.xml @@ -0,0 +1,3116 @@ + + + + blastp + BLASTP 2.2.30+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta + Query_1 + M_2635 + 9 + + + BLOSUM62 + 100000000 + 11 + 1 + F + + + + + 1 + Query_1 + M_2635 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 2 + Query_2 + M_2636 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 3 + Query_3 + M_2637 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 4 + Query_4 + M_2638 + 9 + + + 1 + gnl|BL_ORD_ID|1826 + 179765|cell surface protein (associated with virulence)|NP_302372.1|Mycobacterium leprae TN|272631 + 1826 + 9 + + + 1 + 11.1566 + 17 + 202.191 + 1 + 8 + 1 + 8 + 0 + 0 + 5 + 5 + 0 + 8 + APFLNSVS + APIPASVS + AP SVS + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 5 + Query_5 + M_2639 + 9 + + + + + 2334 + 25004 + 0 + 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0.14 + + + No hits found + + + 43 + Query_43 + M_2677 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 44 + Query_44 + M_2678 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 45 + Query_45 + M_2679 + 9 + + + 1 + gnl|BL_ORD_ID|1565 + 141323|multifunctional expression regulator|NP_044657.1|Human alphaherpesvirus 1|10298 + 1565 + 9 + + + 1 + 13.0826 + 22 + 15.7589 + 1 + 9 + 1 + 9 + 0 + 0 + 4 + 6 + 0 + 9 + KYIFNNSII + KYFYCNSLF + KY + NS+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 46 + Query_46 + M_2680 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 47 + Query_47 + M_2681 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 48 + Query_48 + M_2682 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 49 + Query_49 + M_2683 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 50 + Query_50 + M_2684 + 9 + + + 1 + gnl|BL_ORD_ID|670 + 40264|Cytochrome P450 2A6|P11509.3|Homo sapiens|9606 + 670 + 10 + + + 1 + 12.6974 + 21 + 34.8136 + 1 + 7 + 4 + 10 + 0 + 0 + 6 + 6 + 0 + 7 + LLVSLTV + LLVCLTV + LLV LTV + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 51 + Query_51 + M_2685 + 9 + + + 1 + gnl|BL_ORD_ID|1580 + 141461|ubiquitin E3 ligase ICP0|NP_044601.1|Human alphaherpesvirus 1|10298 + 1580 + 9 + + + 1 + 13.0826 + 22 + 14.4474 + 1 + 9 + 1 + 9 + 0 + 0 + 5 + 6 + 0 + 9 + LPGGVGRTL + VPGWSRRTL + +PG RTL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 52 + Query_52 + M_2686 + 9 + + + 1 + gnl|BL_ORD_ID|851 + 55709|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 + 851 + 15 + + + 1 + 13.0826 + 22 + 12.5116 + 4 + 9 + 5 + 10 + 0 + 0 + 5 + 5 + 0 + 6 + DDRGSL + DSRGSL + D RGSL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 53 + Query_53 + M_2687 + 9 + 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Query_60 + M_2694 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 61 + Query_61 + M_2695 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 62 + Query_62 + M_2696 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 63 + Query_63 + M_2697 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 64 + Query_64 + M_2698 + 9 + + + 1 + gnl|BL_ORD_ID|1180 + 88377|IE62|AAP32859.1|Human alphaherpesvirus 3|10335 + 1180 + 9 + + + 1 + 12.3122 + 20 + 55.769 + 2 + 8 + 1 + 7 + 0 + 0 + 5 + 5 + 0 + 7 + SAPKPST + SAPLPSN + SAP PS + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 65 + Query_65 + M_2699 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 66 + Query_66 + M_2700 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 67 + Query_67 + M_2701 + 9 + + + + + 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2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 89 + Query_89 + M_2723 + 9 + + + 1 + gnl|BL_ORD_ID|1694 + 149096|polyprotein|BAB18801.1|Hepatitis C virus|11103 + 1694 + 9 + + + 1 + 11.927 + 19 + 95.9763 + 3 + 8 + 2 + 7 + 0 + 0 + 5 + 5 + 0 + 6 + AQAPIP + AQAPPP + AQAP P + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 90 + Query_90 + M_2724 + 9 + + + 1 + gnl|BL_ORD_ID|1151 + 75674|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 + 1151 + 15 + + + 1 + 13.0826 + 22 + 16.1221 + 3 + 9 + 6 + 12 + 0 + 0 + 4 + 5 + 0 + 7 + GGWRSGW + GFWQEGW + G W+ GW + + + + + 2 + gnl|BL_ORD_ID|800 + 53246|polyprotein precursor|AAF20092.2|West Nile virus|11082 + 800 + 9 + + + 1 + 10.7714 + 16 + 393.541 + 4 + 9 + 2 + 7 + 0 + 0 + 3 + 4 + 0 + 6 + GWRSGW + AWNSGY + W SG+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 91 + Query_91 + M_2725 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 92 + Query_92 + M_2726 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 93 + Query_93 + M_2727 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 94 + Query_94 + M_2728 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 95 + Query_95 + M_2729 + 9 + + + 1 + gnl|BL_ORD_ID|162 + 12585|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis|1773 + 162 + 20 + + + 1 + 12.6974 + 21 + 34.4393 + 2 + 8 + 13 + 19 + 0 + 0 + 4 + 5 + 0 + 7 + YSSLDED + YSRADEE + YS DE+ + + + + + 2 + gnl|BL_ORD_ID|1071 + 70687|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis|1773 + 1071 + 20 + + + 1 + 12.3122 + 20 + 42.7067 + 2 + 8 + 3 + 9 + 0 + 0 + 4 + 5 + 0 + 7 + YSSLDED + YSRADEE + YS DE+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 96 + Query_96 + M_2730 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 97 + Query_97 + M_2731 + 9 + 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Query_106 + M_2740 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 107 + Query_107 + M_2741 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 108 + Query_108 + M_2742 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + + diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_129049_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_129049_1_T.fasta new file mode 100755 index 00000000..29de5645 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_129049_1_T.fasta @@ -0,0 +1,54 @@ +>M_2743 +ASLDVTLRL +>M_2744 +ISSHLSTLV +>M_2745 +LSTLVDFAI +>M_2746 +KTSVGSTKY +>M_2747 +HPCERSDEV +>M_2748 +ITVEEQHRI +>M_2749 +ITVEEQHRI +>M_2750 +MTAVQTLHL +>M_2751 +PAMTAVQTL +>M_2752 +RQLPAMTAV +>M_2753 +ETVFTRSSW +>M_2754 +FTRSSWDWI +>M_2755 +VFTRSSWDW +>M_2756 +EPPPPPSPL +>M_2757 +QTTQLSLNF +>M_2758 +GAMDGATYI +>M_2759 +MAFVKSVWL +>M_2760 +CAVRRAAQV +>M_2761 +QAVAQAVNW +>M_2762 +NPKTWNTMV +>M_2763 +QLYMNPKTW +>M_2764 +RQVGFCVQW +>M_2765 +KMLLAPGRF +>M_2766 +MLLAPGRFI +>M_2767 +FTMPEDEYM +>M_2768 +FTMPEDEYM +>M_2769 +MPEDEYMVY diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_129049_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_129049_1_T_iedb.xml new file mode 100755 index 00000000..30ba0cad --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_129049_1_T_iedb.xml @@ -0,0 +1,754 @@ + + + + blastp + BLASTP 2.2.30+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta + Query_1 + M_2743 + 9 + + + BLOSUM62 + 100000000 + 11 + 1 + F + + + + + 1 + Query_1 + M_2743 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 2 + Query_2 + M_2744 + 9 + + + 1 + gnl|BL_ORD_ID|1262 + 98466|Trans-sialidase|SRC7915|Trypanosoma cruzi|5693 + 1262 + 10 + + + 1 + 12.3122 + 20 + 49.5064 + 3 + 9 + 3 + 9 + 0 + 0 + 5 + 5 + 0 + 7 + SHLSTLV + SHYFTLV + SH TLV + + + + + 2 + gnl|BL_ORD_ID|904 + 59459|Trans-sialidase|SRC7915|Trypanosoma cruzi|5693 + 904 + 9 + + + 1 + 12.3122 + 20 + 63.7024 + 3 + 9 + 3 + 9 + 0 + 0 + 5 + 5 + 0 + 7 + SHLSTLV + SHYFTLV + SH TLV + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 3 + Query_3 + M_2745 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 4 + Query_4 + M_2746 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 5 + Query_5 + M_2747 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 6 + Query_6 + M_2748 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 7 + Query_7 + M_2749 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 8 + Query_8 + M_2750 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 9 + Query_9 + M_2751 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 10 + Query_10 + M_2752 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 11 + Query_11 + M_2753 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 12 + Query_12 + M_2754 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 13 + Query_13 + M_2755 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 14 + Query_14 + M_2756 + 9 + + + 1 + gnl|BL_ORD_ID|1211 + 96366|polyprotein|ABR25251.1|Hepatitis C virus|11103 + 1211 + 12 + + + 1 + 10.3862 + 15 + 463.357 + 4 + 9 + 5 + 10 + 0 + 0 + 4 + 4 + 0 + 6 + PPPSPL + PPCKPL + PP PL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 15 + Query_15 + M_2757 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 16 + Query_16 + M_2758 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 17 + Query_17 + M_2759 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 18 + Query_18 + M_2760 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 19 + Query_19 + M_2761 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 20 + Query_20 + M_2762 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 21 + Query_21 + M_2763 + 9 + + + 1 + gnl|BL_ORD_ID|1486 + 135263|hemagglutinin|ACX31970.1|Influenza A virus (A/Bar-headed Goose/Qinghai/61/05(H5N1))|336238 + 1486 + 10 + + + 1 + 16.1642 + 30 + 0.390189 + 1 + 9 + 1 + 9 + 0 + 0 + 5 + 7 + 0 + 9 + QLYMNPKTW + RLYQNPTTY + +LY NP T+ + + + + + 2 + gnl|BL_ORD_ID|527 + 32268|hemagglutinin|AAK38298.1|Influenza A virus (A/Bar-headed Goose/Qinghai/61/05(H5N1))|336238 + 527 + 10 + + + 1 + 15.779 + 29 + 0.412579 + 1 + 9 + 1 + 9 + 0 + 0 + 5 + 7 + 0 + 9 + QLYMNPKTW + KLYQNPTTY + +LY NP T+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 22 + Query_22 + M_2764 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 23 + Query_23 + M_2765 + 9 + + + 1 + gnl|BL_ORD_ID|902 + 59240|HCV-1|AAA45676.1|Hepatitis C virus genotype 1|41856 + 902 + 11 + + + 1 + 13.853 + 24 + 5.19029 + 3 + 7 + 2 + 6 + 0 + 0 + 5 + 5 + 0 + 5 + LLAPG + LLAPG + LLAPG + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 24 + Query_24 + M_2766 + 9 + + + 1 + gnl|BL_ORD_ID|902 + 59240|HCV-1|AAA45676.1|Hepatitis C virus genotype 1|41856 + 902 + 11 + + + 1 + 13.853 + 24 + 5.28123 + 2 + 6 + 2 + 6 + 0 + 0 + 5 + 5 + 0 + 5 + LLAPG + LLAPG + LLAPG + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 25 + Query_25 + M_2767 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 26 + Query_26 + M_2768 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 27 + Query_27 + M_2769 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + + diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_129675_2_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_129675_2_T.fasta new file mode 100755 index 00000000..708278e5 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_129675_2_T.fasta @@ -0,0 +1,38 @@ +>M_2770 +IAWPADRTA +>M_2771 +QALIRPTTF +>M_2772 +FPEYDGVDH +>M_2773 +EIAEIEYSI +>M_2774 +FVVSACNAT +>M_2775 +WITPAQREY +>M_2776 +EPVWGLEAI +>M_2777 +RLSWQASSL +>M_2778 +KIKELAAEF +>M_2779 +VPILQSTPV +>M_2780 +APRGFLTNY +>M_2781 +RAAEQRRAY +>M_2782 +KSASWITWI +>M_2783 +TPWSFTGTV +>M_2784 +GPLADATPL +>M_2785 +LAGERRFAF +>M_2786 +IAASAMCVF +>M_2787 +SSYGRNHYI +>M_2788 +IIHTGARPY diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_129675_2_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_129675_2_T_iedb.xml new file mode 100755 index 00000000..c4cadf10 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_129675_2_T_iedb.xml @@ -0,0 +1,845 @@ + + + + blastp + BLASTP 2.2.30+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta + Query_1 + M_2770 + 9 + + + BLOSUM62 + 100000000 + 11 + 1 + F + + + + + 1 + Query_1 + M_2770 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 2 + Query_2 + M_2771 + 9 + + + 1 + gnl|BL_ORD_ID|172 + 13165|trans-sialidase, putative|EAN81972.1|Trypanosoma cruzi|5693 + 172 + 9 + + + 1 + 15.0086 + 27 + 1.19683 + 3 + 9 + 2 + 8 + 0 + 0 + 5 + 6 + 0 + 7 + LIRPTTF + LLRPTTL + L+RPTT + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 3 + Query_3 + M_2772 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 4 + Query_4 + M_2773 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 5 + Query_5 + M_2774 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 6 + Query_6 + M_2775 + 9 + + + 1 + gnl|BL_ORD_ID|1408 + 110940|Protein E7|P03129.1|Human papillomavirus type 16|333760 + 1408 + 15 + + + 1 + 13.0826 + 22 + 13.39 + 3 + 9 + 5 + 11 + 0 + 0 + 4 + 4 + 0 + 7 + TPAQREY + TPTLHEY + TP EY + + + + + 2 + gnl|BL_ORD_ID|1392 + 110335|E7|AAD33253.1|Human papillomavirus type 16|333760 + 1392 + 32 + + + 1 + 13.0826 + 22 + 19.7687 + 3 + 9 + 5 + 11 + 0 + 0 + 4 + 4 + 0 + 7 + TPAQREY + TPTLHEY + TP EY + + + + + 3 + gnl|BL_ORD_ID|1823 + 178351|Protein E7|P03129.1|Human papillomavirus type 16|333760 + 1823 + 15 + + + 1 + 12.6974 + 21 + 31.7906 + 3 + 9 + 1 + 7 + 0 + 0 + 4 + 4 + 0 + 7 + TPAQREY + TPTLHEY + TP EY + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 7 + Query_7 + M_2776 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 8 + Query_8 + M_2777 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 9 + Query_9 + M_2778 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 10 + Query_10 + M_2779 + 9 + + + 1 + gnl|BL_ORD_ID|1906 + 180647|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 + 1906 + 15 + + + 1 + 11.927 + 19 + 77.3377 + 1 + 8 + 8 + 15 + 0 + 0 + 4 + 5 + 0 + 8 + VPILQSTP + LPIRYQTP + +PI TP + + + + + 2 + gnl|BL_ORD_ID|1897 + 180617|polyprotein|AGO67248.1|Dengue virus 2|11060 + 1897 + 10 + + + 1 + 11.5418 + 18 + 128.811 + 1 + 9 + 1 + 9 + 0 + 0 + 4 + 5 + 0 + 9 + VPILQSTPV + LPIRYQTPA + +PI TP + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 11 + Query_11 + M_2780 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 12 + Query_12 + M_2781 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 13 + Query_13 + M_2782 + 9 + + + 1 + gnl|BL_ORD_ID|1142 + 75435|largest ORF|AAB02128.1|Hepatitis C virus|11103 + 1142 + 20 + + + 1 + 12.6974 + 21 + 27.6963 + 1 + 9 + 9 + 17 + 0 + 0 + 2 + 5 + 0 + 9 + KSASWITWI + EGCGWMGWL + + W+ W+ + + + + + 2 + gnl|BL_ORD_ID|1070 + 70634|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 + 1070 + 9 + + + 1 + 12.6974 + 21 + 35.3877 + 4 + 8 + 3 + 7 + 0 + 0 + 3 + 4 + 0 + 5 + SWITW + QWLTW + W+TW + + + + + 3 + gnl|BL_ORD_ID|315 + 20894|polyprotein [Hepatitis C virus]|BAF91806.1|Hepatitis C virus|11103 + 315 + 9 + + + 1 + 11.927 + 19 + 82.8955 + 4 + 9 + 3 + 8 + 0 + 0 + 2 + 4 + 0 + 6 + SWITWI + GWVGWL + W+ W+ + + + + + 4 + gnl|BL_ORD_ID|1277 + 101967|pol protein|ACJ76655.1|Human immunodeficiency virus 1|11676 + 1277 + 10 + + + 1 + 11.927 + 19 + 108.205 + 1 + 8 + 3 + 10 + 0 + 0 + 3 + 5 + 0 + 8 + KSASWITW + QKETWETW + + +W TW + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 14 + Query_14 + M_2783 + 9 + + + 1 + gnl|BL_ORD_ID|701 + 42797|6 kDa early secretory antigenic target|P0A564.2|Mycobacterium tuberculosis|1773 + 701 + 20 + + + 1 + 13.0826 + 22 + 15.1234 + 2 + 7 + 5 + 10 + 0 + 0 + 3 + 4 + 0 + 6 + PWSFTG + QWNFAG + W+F G + + + + + 2 + gnl|BL_ORD_ID|1471 + 127792|6 kDa early secretory antigenic target|P0A564.2|Mycobacterium tuberculosis|1773 + 1471 + 10 + + + 1 + 13.0826 + 22 + 21.2326 + 3 + 7 + 2 + 6 + 0 + 0 + 3 + 4 + 0 + 5 + WSFTG + WNFAG + W+F G + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 15 + Query_15 + M_2784 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 16 + Query_16 + M_2785 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 17 + Query_17 + M_2786 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 18 + Query_18 + M_2787 + 9 + + + 1 + gnl|BL_ORD_ID|123 + 8554|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 + 123 + 20 + + + 1 + 13.853 + 24 + 5.06317 + 4 + 9 + 10 + 15 + 0 + 0 + 3 + 6 + 0 + 6 + GRNHYI + GRSHFL + GR+H++ + + + + + 2 + gnl|BL_ORD_ID|688 + 41622|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 + 688 + 20 + + + 1 + 13.853 + 24 + 6.41204 + 4 + 9 + 2 + 7 + 0 + 0 + 3 + 6 + 0 + 6 + GRNHYI + GRSHFL + GR+H++ + + + + + 3 + gnl|BL_ORD_ID|578 + 36357|ELAV-like protein 4 (Paraneoplastic encephalomyelitis antigen HuD) (Hu-antigen D)|P26378.1|Homo sapiens|9606 + 578 + 9 + + + 1 + 10.7714 + 16 + 324.284 + 2 + 9 + 2 + 9 + 0 + 0 + 4 + 5 + 0 + 8 + SYGRNHYI + GYGFVNYI + YG +YI + + + + + 4 + gnl|BL_ORD_ID|579 + 36358|ELAV-like protein 1|Q15717.2|Homo sapiens|9606 + 579 + 9 + + + 1 + 10.3862 + 15 + 617.74 + 2 + 9 + 2 + 9 + 0 + 0 + 3 + 5 + 0 + 8 + SYGRNHYI + GYGFVNYV + YG +Y+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 19 + Query_19 + M_2788 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + + diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_131144_2_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_131144_2_T.fasta new file mode 100755 index 00000000..3e7a8fb1 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_131144_2_T.fasta @@ -0,0 +1,120 @@ +>M_2789 +DTATGNCLR +>M_2790 +GPYENCSVF +>M_2791 +ETYQQALGK +>M_2792 +YQQALGKRF +>M_2793 +YQQALGKRF +>M_2794 +FAIHKIKQF +>M_2795 +GYTVNIPTI +>M_2796 +HSPSVASMK +>M_2797 +YTDCHASNL +>M_2798 +TYSSPTPNM +>M_2799 +DAIPFGNVP +>M_2800 +IPFGNVPVL +>M_2801 +NYFGVQDAI +>M_2802 +ETLGRGNPM +>M_2803 +MALQLFLQI +>M_2804 +MALQLFLQI +>M_2805 +MALQLFLQI +>M_2806 +KVHSAVITI +>M_2807 +QAGEYSRVV +>M_2808 +RVVDCYLKV +>M_2809 +WQRPTLESI +>M_2810 +WQRPTLESI +>M_2811 +VAQLGFQPL +>M_2812 +EAINCLNVA +>M_2813 +VAIDIYTDM +>M_2814 +HFLHSWTNL +>M_2815 +TFKHLVHFL +>M_2816 +YTFKHLVHF +>M_2817 +YTFKHLVHF +>M_2818 +IIMSRNAYV +>M_2819 +LRYPIIMSR +>M_2820 +MSRNAYVPM +>M_2821 +NAPALLTPR +>M_2822 +RAGSAGGTV +>M_2823 +EAFTLKATV +>M_2824 +YSVIRGEAF +>M_2825 +DIYSMPEGK +>M_2826 +IYSMPEGKL +>M_2827 +SMPEGKLHV +>M_2828 +YSMPEGKLH +>M_2829 +FFFLCVCVF +>M_2830 +FFFLCVCVF +>M_2831 +FFLCVCVFV +>M_2832 +FFLCVCVFV +>M_2833 +HLLQRYNEF +>M_2834 +RAEERRRHL +>M_2835 +ITTTGQKLR +>M_2836 +IMALAVLII +>M_2837 +TALVVVSIM +>M_2838 +DVLPYDAFV +>M_2839 +LTLATFSRI +>M_2840 +VLTLATFSR +>M_2841 +MNQRPILTI +>M_2842 +NQRPILTII +>M_2843 +FNVNAPDLY +>M_2844 +NVNAPDLYI +>M_2845 +RFNVNAPDL +>M_2846 +FHWRVNFIR +>M_2847 +IFHWRVNFI +>M_2848 +KIFHWRVNF diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_131144_2_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_131144_2_T_iedb.xml new file mode 100755 index 00000000..7034a12b --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_131144_2_T_iedb.xml @@ -0,0 +1,1820 @@ + + + + blastp + BLASTP 2.2.30+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta + Query_1 + M_2789 + 9 + + + BLOSUM62 + 100000000 + 11 + 1 + F + + + + + 1 + Query_1 + M_2789 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 2 + Query_2 + M_2790 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 3 + Query_3 + M_2791 + 9 + + + 1 + gnl|BL_ORD_ID|376 + 23288|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 + 376 + 15 + + + 1 + 13.853 + 24 + 5.58032 + 1 + 9 + 5 + 13 + 0 + 0 + 4 + 6 + 0 + 9 + ETYQQALGK + QVYQDWLGR + + YQ LG+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 4 + Query_4 + M_2792 + 9 + + + 1 + gnl|BL_ORD_ID|376 + 23288|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 + 376 + 15 + + + 1 + 12.6974 + 21 + 26.9941 + 1 + 7 + 7 + 13 + 0 + 0 + 4 + 5 + 0 + 7 + YQQALGK + YQDWLGR + YQ LG+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 5 + Query_5 + M_2793 + 9 + + + 1 + gnl|BL_ORD_ID|376 + 23288|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 + 376 + 15 + + + 1 + 12.6974 + 21 + 26.9941 + 1 + 7 + 7 + 13 + 0 + 0 + 4 + 5 + 0 + 7 + YQQALGK + YQDWLGR + YQ LG+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 6 + Query_6 + M_2794 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 7 + Query_7 + M_2795 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 8 + Query_8 + M_2796 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 9 + Query_9 + M_2797 + 9 + + + 1 + gnl|BL_ORD_ID|83 + 6094|Genome polyprotein|Q81495.3|Hepatitis C virus (isolate HCV-K3a/650)|356416 + 83 + 15 + + + 1 + 14.2382 + 25 + 3.49239 + 3 + 8 + 3 + 8 + 0 + 0 + 4 + 5 + 0 + 6 + DCHASN + DCHAQD + DCHA + + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 10 + Query_10 + M_2798 + 9 + + + 1 + gnl|BL_ORD_ID|2244 + 232153|rhoptry protein 18|CAJ27113.1|Toxoplasma gondii type I|1209525 + 2244 + 19 + + + 1 + 11.927 + 19 + 88.393 + 1 + 6 + 12 + 17 + 0 + 0 + 4 + 5 + 0 + 6 + TYSSPT + TYTFPT + TY+ PT + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 11 + Query_11 + M_2799 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 12 + Query_12 + M_2800 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 13 + Query_13 + M_2801 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 14 + Query_14 + M_2802 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 15 + Query_15 + M_2803 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 16 + Query_16 + M_2804 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 17 + Query_17 + M_2805 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 18 + Query_18 + M_2806 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 19 + Query_19 + M_2807 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 20 + Query_20 + M_2808 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 21 + Query_21 + M_2809 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 22 + Query_22 + M_2810 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 23 + Query_23 + M_2811 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 24 + Query_24 + M_2812 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 25 + Query_25 + M_2813 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 26 + Query_26 + M_2814 + 9 + + + 1 + gnl|BL_ORD_ID|1296 + 103322|polyprotein|BAB18806.1|Hepatitis C virus|11103 + 1296 + 20 + + + 1 + 13.4678 + 23 + 11.4655 + 3 + 8 + 3 + 8 + 0 + 0 + 4 + 4 + 0 + 6 + LHSWTN + LHQWIN + LH W N + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 27 + Query_27 + M_2815 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 28 + Query_28 + M_2816 + 9 + + + 1 + gnl|BL_ORD_ID|123 + 8554|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 + 123 + 20 + + + 1 + 10.001 + 14 + 536.103 + 1 + 9 + 6 + 14 + 0 + 0 + 4 + 4 + 0 + 9 + YTFKHLVHF + YKFMGRSHF + Y F HF + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 29 + Query_29 + M_2817 + 9 + + + 1 + gnl|BL_ORD_ID|123 + 8554|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 + 123 + 20 + + + 1 + 10.001 + 14 + 536.103 + 1 + 9 + 6 + 14 + 0 + 0 + 4 + 4 + 0 + 9 + YTFKHLVHF + YKFMGRSHF + Y F HF + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 30 + Query_30 + M_2818 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 31 + Query_31 + M_2819 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 32 + Query_32 + M_2820 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 33 + Query_33 + M_2821 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 34 + Query_34 + M_2822 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 35 + Query_35 + M_2823 + 9 + + + 1 + gnl|BL_ORD_ID|1266 + 98640|trans-sialidase, putative|EAN80840.1|Trypanosoma cruzi|5693 + 1266 + 9 + + + 1 + 13.853 + 24 + 5.65074 + 3 + 9 + 3 + 9 + 0 + 0 + 6 + 6 + 0 + 7 + FTLKATV + FTLVATV + FTL ATV + + + + + 2 + gnl|BL_ORD_ID|1245 + 98044|trans-sialidase, putative|EAN80840.1|Trypanosoma cruzi|5693 + 1245 + 9 + + + 1 + 13.853 + 24 + 5.65074 + 3 + 9 + 1 + 7 + 0 + 0 + 6 + 6 + 0 + 7 + FTLKATV + FTLVATV + FTL ATV + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 36 + Query_36 + M_2824 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 37 + Query_37 + M_2825 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 38 + Query_38 + M_2826 + 9 + + + 1 + gnl|BL_ORD_ID|1725 + 150456|polyprotein|AGO67248.1|Dengue virus 2|11060 + 1725 + 10 + + + 1 + 14.2382 + 25 + 2.71312 + 2 + 9 + 3 + 10 + 0 + 0 + 5 + 5 + 0 + 8 + YSMPEGKL + YSMCTGKF + YSM GK + + + + + 2 + gnl|BL_ORD_ID|186 + 13701|Trans-activator protein BZLF1|P03206.2|Human gammaherpesvirus 4|10376 + 186 + 11 + + + 1 + 13.0826 + 22 + 18.1034 + 4 + 9 + 3 + 8 + 0 + 0 + 3 + 6 + 0 + 6 + MPEGKL + LPQGQL + +P+G+L + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 39 + Query_39 + M_2827 + 9 + + + 1 + gnl|BL_ORD_ID|186 + 13701|Trans-activator protein BZLF1|P03206.2|Human gammaherpesvirus 4|10376 + 186 + 11 + + + 1 + 13.0826 + 22 + 16.6114 + 2 + 7 + 3 + 8 + 0 + 0 + 3 + 6 + 0 + 6 + MPEGKL + LPQGQL + +P+G+L + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 40 + Query_40 + M_2828 + 9 + + + 1 + gnl|BL_ORD_ID|1725 + 150456|polyprotein|AGO67248.1|Dengue virus 2|11060 + 1725 + 10 + + + 1 + 14.2382 + 25 + 2.75947 + 1 + 8 + 3 + 10 + 0 + 0 + 5 + 5 + 0 + 8 + YSMPEGKL + YSMCTGKF + YSM GK + + + + + 2 + gnl|BL_ORD_ID|186 + 13701|Trans-activator protein BZLF1|P03206.2|Human gammaherpesvirus 4|10376 + 186 + 11 + + + 1 + 13.0826 + 22 + 17.4916 + 3 + 8 + 3 + 8 + 0 + 0 + 3 + 6 + 0 + 6 + MPEGKL + LPQGQL + +P+G+L + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 41 + Query_41 + M_2829 + 9 + + + 1 + gnl|BL_ORD_ID|750 + 49831|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 + 750 + 15 + + + 1 + 11.927 + 19 + 74.9817 + 1 + 8 + 4 + 11 + 0 + 0 + 3 + 5 + 0 + 8 + FFFLCVCV + LLILCLCL + LC+C+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 42 + Query_42 + M_2830 + 9 + + + 1 + gnl|BL_ORD_ID|750 + 49831|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 + 750 + 15 + + + 1 + 11.927 + 19 + 74.9817 + 1 + 8 + 4 + 11 + 0 + 0 + 3 + 5 + 0 + 8 + FFFLCVCV + LLILCLCL + LC+C+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 43 + Query_43 + M_2831 + 9 + + + 1 + gnl|BL_ORD_ID|750 + 49831|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 + 750 + 15 + + + 1 + 11.5418 + 18 + 131.587 + 1 + 7 + 5 + 11 + 0 + 0 + 3 + 5 + 0 + 7 + FFLCVCV + LILCLCL + LC+C+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 44 + Query_44 + M_2832 + 9 + + + 1 + gnl|BL_ORD_ID|750 + 49831|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 + 750 + 15 + + + 1 + 11.5418 + 18 + 131.587 + 1 + 7 + 5 + 11 + 0 + 0 + 3 + 5 + 0 + 7 + FFLCVCV + LILCLCL + LC+C+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 45 + Query_45 + M_2833 + 9 + + + 1 + gnl|BL_ORD_ID|1767 + 154980|tegument protein|CAB06735.1|Human alphaherpesvirus 2|10310 + 1767 + 15 + + + 1 + 16.1642 + 30 + 0.279828 + 1 + 9 + 2 + 10 + 0 + 0 + 6 + 7 + 0 + 9 + HLLQRYNEF + NLLQRANEL + +LLQR NE + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 46 + Query_46 + M_2834 + 9 + + + 1 + gnl|BL_ORD_ID|1395 + 110394|Protein E6|P03126.1|Human papillomavirus type 16|333760 + 1395 + 32 + + + 1 + 15.0086 + 27 + 1.766 + 2 + 9 + 11 + 18 + 0 + 0 + 5 + 7 + 0 + 8 + AEERRRHL + PEEKQRHL + EE++RHL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 47 + Query_47 + M_2835 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 48 + Query_48 + M_2836 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 49 + Query_49 + M_2837 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 50 + Query_50 + M_2838 + 9 + + + 1 + gnl|BL_ORD_ID|1578 + 141423|envelope glycoprotein B|NP_044629.1|Human alphaherpesvirus 1|10298 + 1578 + 9 + + + 1 + 15.779 + 29 + 0.442703 + 2 + 9 + 2 + 9 + 0 + 0 + 6 + 6 + 0 + 8 + VLPYDAFV + VYPYDEFV + V PYD FV + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 51 + Query_51 + M_2839 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 52 + Query_52 + M_2840 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 53 + Query_53 + M_2841 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 54 + Query_54 + M_2842 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 55 + Query_55 + M_2843 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 56 + Query_56 + M_2844 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 57 + Query_57 + M_2845 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 58 + Query_58 + M_2846 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 59 + Query_59 + M_2847 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 60 + Query_60 + M_2848 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + + diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_131327_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_131327_1_T.fasta new file mode 100755 index 00000000..ec8b2bf3 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_131327_1_T.fasta @@ -0,0 +1,224 @@ +>M_2849 +LHDTTTRSV +>M_2850 +LHNNTTRSV +>M_2851 +TTTRSVHAK +>M_2852 +HFKAPKISM +>M_2853 +GTSSTSCSW +>M_2854 +GVRAQGCYM +>M_2855 +GVRAQGCYM +>M_2856 +RAQGCYMDI +>M_2857 +VAEKGTSKL +>M_2858 +EAFSVSPEW +>M_2859 +FSVSPEWAV +>M_2860 +LTRPVHGAA +>M_2861 +MARTAPASG +>M_2862 +AHQYFAQLL +>M_2863 +AHQYFAQLL +>M_2864 +HQYFAQLLA +>M_2865 +LALQRQRTY +>M_2866 +LALQRQRTY +>M_2867 +ATVCRDPGV +>M_2868 +VCRDPGVPM +>M_2869 +DAPLFNTIV +>M_2870 +VDAPLFNTI +>M_2871 +LSETISPLW +>M_2872 +WPQRPKSQV +>M_2873 +MVLPGGVDI +>M_2874 +FELEWLLYT +>M_2875 +HSHTTGINL +>M_2876 +HSHTTGINL +>M_2877 +SHTTGINLV +>M_2878 +STHSHTTGI +>M_2879 +STHSHTTGI +>M_2880 +STHSHTTGI +>M_2881 +LTLVGVVVY +>M_2882 +LTLVGVVVY +>M_2883 +SEYFLGLTL +>M_2884 +EAHSFEEEM +>M_2885 +SSLQEAHSF +>M_2886 +SHTTLSLDL +>M_2887 +KLREFFKCA +>M_2888 +VAYCPAYVV +>M_2889 +VAYCPAYVV +>M_2890 +VLIPDVVAY +>M_2891 +VVAYCPAYV +>M_2892 +YLVLIPDVV +>M_2893 +FGIGVENFI +>M_2894 +IGVENFITL +>M_2895 +ITLVVFGLI +>M_2896 +KVARSKPYA +>M_2897 +VARSKPYAM +>M_2898 +KFRCDAGLG +>M_2899 +GSRESNMSR +>M_2900 +MSRKKKAVK +>M_2901 +RKKKAVKEK +>M_2902 +QSNTWSLSK +>M_2903 +YQQSNTWSL +>M_2904 +YQQSNTWSL +>M_2905 +YKLVVVGAV +>M_2906 +AVRYSRGCL +>M_2907 +VRYSRGCLT +>M_2908 +YSRGCLTVM +>M_2909 +YSRGCLTVM +>M_2910 +YSRGCLTVM +>M_2911 +VQYASGNRW +>M_2912 +YASGNRWTF +>M_2913 +YASGNRWTF +>M_2914 +AVRNAITST +>M_2915 +NAITSTSVI +>M_2916 +TSIAVRNAI +>M_2917 +VVLPTEAPI +>M_2918 +VVLPTEAPI +>M_2919 +LVATSPSPV +>M_2920 +LSENAVLIL +>M_2921 +LSENAVLIL +>M_2922 +MALSENAVL +>M_2923 +MALSENAVL +>M_2924 +SSSGWRKSF +>M_2925 +FSEASQLDF +>M_2926 +FSEASQLDF +>M_2927 +RTKQFSEAS +>M_2928 +RGFSRQSVL +>M_2929 +LTRSTLSSV +>M_2930 +LTRSTLSSV +>M_2931 +RADHDLGRL +>M_2932 +YRADHDLGR +>M_2933 +ALRVNPVLA +>M_2934 +RVNPVLAEL +>M_2935 +RVNPVLAEL +>M_2936 +SALRVNPVL +>M_2937 +SSALRVNPV +>M_2938 +LLYRRTKAF +>M_2939 +LLYRRTKAF +>M_2940 +LYRRTKAFI +>M_2941 +RTKAFIDYE +>M_2942 +ATSYELHKF +>M_2943 +RTQILATSY +>M_2944 +TSYELHKFY +>M_2945 +TSYELHKFY +>M_2946 +IQKITSPNI +>M_2947 +TSVKPSQPK +>M_2948 +AIFASMAHA +>M_2949 +ASMAHAMQK +>M_2950 +MAHAMQKYL +>M_2951 +MAHAMQKYL +>M_2952 +MAHAMQKYL +>M_2953 +SMAHAMQKY +>M_2954 +RQRLSAPPS +>M_2955 +TAHGLSPTA +>M_2956 +GLIEGYGGW +>M_2957 +QVLGLGGHI +>M_2958 +AAFNPTRDF +>M_2959 +AAFNPTRDF +>M_2960 +KGFVCKAHF diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_131327_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_131327_1_T_iedb.xml new file mode 100755 index 00000000..651f706c --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_131327_1_T_iedb.xml @@ -0,0 +1,3217 @@ + + + + blastp + BLASTP 2.2.30+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta + Query_1 + M_2849 + 9 + + + BLOSUM62 + 100000000 + 11 + 1 + F + + + + + 1 + Query_1 + M_2849 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 2 + Query_2 + M_2850 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 3 + Query_3 + M_2851 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 4 + Query_4 + M_2852 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 5 + Query_5 + M_2853 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 6 + Query_6 + M_2854 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 7 + Query_7 + M_2855 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 8 + Query_8 + M_2856 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 9 + Query_9 + M_2857 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 10 + Query_10 + M_2858 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 11 + Query_11 + M_2859 + 9 + + + 1 + gnl|BL_ORD_ID|1686 + 149052|E1 protein|NP_751920.1|Hepatitis C virus (isolate H77)|63746 + 1686 + 18 + + + 1 + 13.0826 + 22 + 17.338 + 1 + 8 + 5 + 12 + 0 + 0 + 4 + 5 + 0 + 8 + FSVSPEWA + FSMVGNWA + FS+ WA + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 12 + Query_12 + M_2860 + 9 + + + 1 + gnl|BL_ORD_ID|441 + 27125|gag-pol fusion polyprotein|AAN73817.1|Human immunodeficiency virus 1|11676 + 441 + 9 + + + 1 + 15.3938 + 28 + 0.845687 + 1 + 8 + 2 + 9 + 0 + 0 + 5 + 5 + 0 + 8 + LTRPVHGA + LKEPVHGV + L PVHG + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 13 + Query_13 + M_2861 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 14 + Query_14 + M_2862 + 9 + + + 1 + gnl|BL_ORD_ID|1271 + 101673|gag protein|ABO73990.1|Human immunodeficiency virus 1|11676 + 1271 + 9 + + + 1 + 11.5418 + 18 + 152.614 + 1 + 9 + 1 + 9 + 0 + 0 + 4 + 5 + 0 + 9 + AHQYFAQLL + GHQAAMQML + HQ Q+L + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 15 + Query_15 + M_2863 + 9 + + + 1 + gnl|BL_ORD_ID|1271 + 101673|gag protein|ABO73990.1|Human immunodeficiency virus 1|11676 + 1271 + 9 + + + 1 + 11.5418 + 18 + 152.614 + 1 + 9 + 1 + 9 + 0 + 0 + 4 + 5 + 0 + 9 + AHQYFAQLL + GHQAAMQML + HQ Q+L + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 16 + Query_16 + M_2864 + 9 + + + 1 + gnl|BL_ORD_ID|1271 + 101673|gag protein|ABO73990.1|Human immunodeficiency virus 1|11676 + 1271 + 9 + + + 1 + 11.1566 + 17 + 199.082 + 1 + 8 + 2 + 9 + 0 + 0 + 4 + 5 + 0 + 8 + HQYFAQLL + HQAAMQML + HQ Q+L + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 17 + Query_17 + M_2865 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 18 + Query_18 + M_2866 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 19 + Query_19 + M_2867 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 20 + Query_20 + M_2868 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 21 + Query_21 + M_2869 + 9 + + + 1 + gnl|BL_ORD_ID|1848 + 180255|gag protein|AAT90688.1|Human immunodeficiency virus 1|11676 + 1848 + 9 + + + 1 + 14.6234 + 26 + 1.85254 + 3 + 9 + 1 + 7 + 0 + 0 + 5 + 6 + 0 + 7 + PLFNTIV + SLFNTVV + LFNT+V + + + + + 2 + gnl|BL_ORD_ID|2159 + 189295|gag protein|AEB70304.1|Human immunodeficiency virus 1|11676 + 2159 + 9 + + + 1 + 13.853 + 24 + 6.16125 + 3 + 9 + 1 + 7 + 0 + 0 + 4 + 6 + 0 + 7 + PLFNTIV + SLYNTVV + L+NT+V + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 22 + Query_22 + M_2870 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 23 + Query_23 + M_2871 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 24 + Query_24 + M_2872 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 25 + Query_25 + M_2873 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 26 + Query_26 + M_2874 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 27 + Query_27 + M_2875 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 28 + Query_28 + M_2876 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 29 + Query_29 + M_2877 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 30 + Query_30 + M_2878 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 31 + Query_31 + M_2879 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 32 + Query_32 + M_2880 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 33 + Query_33 + M_2881 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 34 + Query_34 + M_2882 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 35 + Query_35 + M_2883 + 9 + + + 1 + gnl|BL_ORD_ID|1608 + 143705|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 + 1608 + 9 + + + 1 + 11.5418 + 18 + 132.337 + 1 + 9 + 1 + 9 + 0 + 0 + 4 + 5 + 0 + 9 + SEYFLGLTL + KEYTFPITL + EY +TL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 36 + Query_36 + M_2884 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 37 + Query_37 + M_2885 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 38 + Query_38 + M_2886 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 39 + Query_39 + M_2887 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 40 + Query_40 + M_2888 + 9 + + + 1 + gnl|BL_ORD_ID|668 + 40253|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 + 668 + 15 + + + 1 + 13.0826 + 22 + 15.3281 + 2 + 7 + 6 + 11 + 0 + 0 + 4 + 4 + 0 + 6 + AYCPAY + ANCPTY + A CP Y + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 41 + Query_41 + M_2889 + 9 + + + 1 + gnl|BL_ORD_ID|668 + 40253|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 + 668 + 15 + + + 1 + 13.0826 + 22 + 15.3281 + 2 + 7 + 6 + 11 + 0 + 0 + 4 + 4 + 0 + 6 + AYCPAY + ANCPTY + A CP Y + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 42 + Query_42 + M_2890 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 43 + Query_43 + M_2891 + 9 + + + 1 + gnl|BL_ORD_ID|668 + 40253|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 + 668 + 15 + + + 1 + 13.0826 + 22 + 15.3281 + 3 + 8 + 6 + 11 + 0 + 0 + 4 + 4 + 0 + 6 + AYCPAY + ANCPTY + A CP Y + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 44 + Query_44 + M_2892 + 9 + + + 1 + gnl|BL_ORD_ID|737 + 46755|HCV-1|AAA45676.1|Hepatitis C virus genotype 1|41856 + 737 + 20 + + + 1 + 12.3122 + 20 + 47.5082 + 2 + 9 + 12 + 19 + 0 + 0 + 5 + 5 + 0 + 8 + LVLIPDVV + LVLNPSVA + LVL P V + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 45 + Query_45 + M_2893 + 9 + + + 1 + gnl|BL_ORD_ID|578 + 36357|ELAV-like protein 4 (Paraneoplastic encephalomyelitis antigen HuD) (Hu-antigen D)|P26378.1|Homo sapiens|9606 + 578 + 9 + + + 1 + 11.5418 + 18 + 187.089 + 1 + 9 + 1 + 9 + 0 + 0 + 4 + 5 + 0 + 9 + FGIGVENFI + LGYGFVNYI + G G N+I + + + + + 2 + gnl|BL_ORD_ID|579 + 36358|ELAV-like protein 1|Q15717.2|Homo sapiens|9606 + 579 + 9 + + + 1 + 10.7714 + 16 + 339.179 + 1 + 9 + 1 + 9 + 0 + 0 + 3 + 5 + 0 + 9 + FGIGVENFI + LGYGFVNYV + G G N++ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 46 + Query_46 + M_2894 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 47 + Query_47 + M_2895 + 9 + + + 1 + gnl|BL_ORD_ID|2326 + 423068|polyprotein|ACX44241.1|Hepatitis C virus genotype 1|41856 + 2326 + 10 + + + 1 + 12.3122 + 20 + 51.1794 + 4 + 9 + 1 + 6 + 0 + 0 + 4 + 6 + 0 + 6 + VVFGLI + VLFGLM + V+FGL+ + + + + + 2 + gnl|BL_ORD_ID|1269 + 101380|BNLF2a|YP_401721.1|Human herpesvirus 4 type 1|36352 + 1269 + 9 + + + 1 + 12.3122 + 20 + 58.627 + 4 + 9 + 1 + 6 + 0 + 0 + 4 + 6 + 0 + 6 + VVFGLI + VLFGLL + V+FGL+ + + + + + 3 + gnl|BL_ORD_ID|2331 + 423075|polyprotein|ACX44241.1|Hepatitis C virus genotype 1|41856 + 2331 + 9 + + + 1 + 12.3122 + 20 + 68.0606 + 4 + 9 + 2 + 7 + 0 + 0 + 4 + 6 + 0 + 6 + VVFGLI + VLFGLM + V+FGL+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 48 + Query_48 + M_2896 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 49 + Query_49 + M_2897 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 50 + Query_50 + M_2898 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 51 + Query_51 + M_2899 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 52 + Query_52 + M_2900 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 53 + Query_53 + M_2901 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 54 + Query_54 + M_2902 + 9 + + + 1 + gnl|BL_ORD_ID|1132 + 74886|latent membrane protein 1|AAS99606.1|Human gammaherpesvirus 4|10376 + 1132 + 9 + + + 1 + 12.6974 + 21 + 33.058 + 1 + 7 + 3 + 9 + 0 + 0 + 4 + 5 + 0 + 7 + QSNTWSL + QQNWWTL + Q N W+L + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 55 + Query_55 + M_2903 + 9 + + + 1 + gnl|BL_ORD_ID|1132 + 74886|latent membrane protein 1|AAS99606.1|Human gammaherpesvirus 4|10376 + 1132 + 9 + + + 1 + 13.853 + 24 + 7.20201 + 1 + 9 + 1 + 9 + 0 + 0 + 5 + 6 + 0 + 9 + YQQSNTWSL + YLQQNWWTL + Y Q N W+L + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 56 + Query_56 + M_2904 + 9 + + + 1 + gnl|BL_ORD_ID|1132 + 74886|latent membrane protein 1|AAS99606.1|Human gammaherpesvirus 4|10376 + 1132 + 9 + + + 1 + 13.853 + 24 + 7.20201 + 1 + 9 + 1 + 9 + 0 + 0 + 5 + 6 + 0 + 9 + YQQSNTWSL + YLQQNWWTL + Y Q N W+L + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 57 + Query_57 + M_2905 + 9 + + + 1 + gnl|BL_ORD_ID|524 + 32238|polyprotein [Hepatitis C virus subtype 1a]|ABV46251.2|Hepatitis C virus (isolate H77)|63746 + 524 + 10 + + + 1 + 12.6974 + 21 + 30.9217 + 2 + 7 + 1 + 6 + 0 + 0 + 5 + 6 + 0 + 6 + KLVVVG + KLVVLG + KLVV+G + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 58 + Query_58 + M_2906 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 59 + Query_59 + M_2907 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 60 + Query_60 + M_2908 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 61 + Query_61 + M_2909 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 62 + Query_62 + M_2910 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 63 + Query_63 + M_2911 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 64 + Query_64 + M_2912 + 9 + + + 1 + gnl|BL_ORD_ID|2244 + 232153|rhoptry protein 18|CAJ27113.1|Toxoplasma gondii type I|1209525 + 2244 + 19 + + + 1 + 12.3122 + 20 + 39.084 + 2 + 9 + 8 + 15 + 0 + 0 + 4 + 6 + 0 + 8 + ASGNRWTF + ATGITYTF + A+G +TF + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 65 + Query_65 + M_2913 + 9 + + + 1 + gnl|BL_ORD_ID|2244 + 232153|rhoptry protein 18|CAJ27113.1|Toxoplasma gondii type I|1209525 + 2244 + 19 + + + 1 + 12.3122 + 20 + 39.084 + 2 + 9 + 8 + 15 + 0 + 0 + 4 + 6 + 0 + 8 + ASGNRWTF + ATGITYTF + A+G +TF + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 66 + Query_66 + M_2914 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 67 + Query_67 + M_2915 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 68 + Query_68 + M_2916 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 69 + Query_69 + M_2917 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 70 + Query_70 + M_2918 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 71 + Query_71 + M_2919 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 72 + Query_72 + M_2920 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 73 + Query_73 + M_2921 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 74 + Query_74 + M_2922 + 9 + + + 1 + gnl|BL_ORD_ID|40 + 2884|cysteine proteinase cruzipain (EC 3.4.22.-) - Trypanosoma cruzi|A45629|Trypanosoma cruzi|5693 + 40 + 10 + + + 1 + 11.5418 + 18 + 139.346 + 2 + 9 + 1 + 8 + 0 + 0 + 6 + 6 + 0 + 8 + ALSENAVL + ALSLAAVL + ALS AVL + + + + + 2 + gnl|BL_ORD_ID|39 + 2883|cysteine proteinase cruzipain (EC 3.4.22.-) - Trypanosoma cruzi|A45629|Trypanosoma cruzi|5693 + 39 + 9 + + + 1 + 11.5418 + 18 + 157.499 + 2 + 9 + 1 + 8 + 0 + 0 + 6 + 6 + 0 + 8 + ALSENAVL + ALSLAAVL + ALS AVL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 75 + Query_75 + M_2923 + 9 + + + 1 + gnl|BL_ORD_ID|40 + 2884|cysteine proteinase cruzipain (EC 3.4.22.-) - Trypanosoma cruzi|A45629|Trypanosoma cruzi|5693 + 40 + 10 + + + 1 + 11.5418 + 18 + 139.346 + 2 + 9 + 1 + 8 + 0 + 0 + 6 + 6 + 0 + 8 + ALSENAVL + ALSLAAVL + ALS AVL + + + + + 2 + gnl|BL_ORD_ID|39 + 2883|cysteine proteinase cruzipain (EC 3.4.22.-) - Trypanosoma cruzi|A45629|Trypanosoma cruzi|5693 + 39 + 9 + + + 1 + 11.5418 + 18 + 157.499 + 2 + 9 + 1 + 8 + 0 + 0 + 6 + 6 + 0 + 8 + ALSENAVL + ALSLAAVL + ALS AVL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 76 + Query_76 + M_2924 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 77 + Query_77 + M_2925 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 78 + Query_78 + M_2926 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 79 + Query_79 + M_2927 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 80 + Query_80 + M_2928 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 81 + Query_81 + M_2929 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 82 + Query_82 + M_2930 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 83 + Query_83 + M_2931 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 84 + Query_84 + M_2932 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 85 + Query_85 + M_2933 + 9 + + + 1 + gnl|BL_ORD_ID|857 + 56198|glycoprotein gp35/37|AAC59622.1|Human gammaherpesvirus 8|37296 + 857 + 15 + + + 1 + 13.0826 + 22 + 17.2424 + 2 + 7 + 5 + 10 + 0 + 0 + 4 + 6 + 0 + 6 + LRVNPV + IRVSPV + +RV+PV + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 86 + Query_86 + M_2934 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 87 + Query_87 + M_2935 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 88 + Query_88 + M_2936 + 9 + + + 1 + gnl|BL_ORD_ID|857 + 56198|glycoprotein gp35/37|AAC59622.1|Human gammaherpesvirus 8|37296 + 857 + 15 + + + 1 + 13.0826 + 22 + 17.2424 + 1 + 8 + 3 + 10 + 0 + 0 + 4 + 7 + 0 + 8 + SALRVNPV + TRIRVSPV + + +RV+PV + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 89 + Query_89 + M_2937 + 9 + + + 1 + gnl|BL_ORD_ID|857 + 56198|glycoprotein gp35/37|AAC59622.1|Human gammaherpesvirus 8|37296 + 857 + 15 + + + 1 + 13.4678 + 23 + 8.0204 + 1 + 9 + 2 + 10 + 0 + 0 + 4 + 8 + 0 + 9 + SSALRVNPV + TTRIRVSPV + ++ +RV+PV + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 90 + Query_90 + M_2938 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 91 + Query_91 + M_2939 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 92 + Query_92 + M_2940 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 93 + Query_93 + M_2941 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 94 + Query_94 + M_2942 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 95 + Query_95 + M_2943 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 96 + Query_96 + M_2944 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 97 + Query_97 + M_2945 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 98 + Query_98 + M_2946 + 9 + + + 1 + gnl|BL_ORD_ID|2271 + 419002|PPE family protein PPE68|KAM81677.1|Mycobacterium tuberculosis H37Ra|419947 + 2271 + 10 + + + 1 + 11.927 + 19 + 81.0261 + 1 + 9 + 2 + 10 + 0 + 0 + 3 + 7 + 0 + 9 + IQKITSPNI + IEKPVAPSV + I+K +P++ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 99 + Query_99 + M_2947 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 100 + Query_100 + M_2948 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 101 + Query_101 + M_2949 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 102 + Query_102 + M_2950 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 103 + Query_103 + M_2951 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 104 + Query_104 + M_2952 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 105 + Query_105 + M_2953 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 106 + Query_106 + M_2954 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 107 + Query_107 + M_2955 + 9 + + + 1 + gnl|BL_ORD_ID|332 + 21139|envelope protein|BAF48755.1|Hepatitis B virus|10407 + 332 + 10 + + + 1 + 14.2382 + 25 + 3.10797 + 4 + 9 + 1 + 6 + 0 + 0 + 5 + 5 + 0 + 6 + GLSPTA + GLSPTV + GLSPT + + + + + 2 + gnl|BL_ORD_ID|331 + 21137|Major surface antigen precursor|P03142.4|Hepatitis B virus subtype adw|106821 + 331 + 10 + + + 1 + 14.2382 + 25 + 3.68732 + 4 + 9 + 1 + 6 + 0 + 0 + 5 + 5 + 0 + 6 + GLSPTA + GLSPTV + GLSPT + + + + + 3 + gnl|BL_ORD_ID|1392 + 110335|E7|AAD33253.1|Human papillomavirus type 16|333760 + 1392 + 32 + + + 1 + 13.0826 + 22 + 19.2096 + 3 + 8 + 2 + 7 + 0 + 0 + 4 + 5 + 0 + 6 + HGLSPT + HGDTPT + HG +PT + + + + + 4 + gnl|BL_ORD_ID|1408 + 110940|Protein E7|P03129.1|Human papillomavirus type 16|333760 + 1408 + 15 + + + 1 + 12.6974 + 21 + 27.8948 + 3 + 8 + 2 + 7 + 0 + 0 + 4 + 5 + 0 + 6 + HGLSPT + HGDTPT + HG +PT + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 108 + Query_108 + M_2956 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 109 + Query_109 + M_2957 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 110 + Query_110 + M_2958 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 111 + Query_111 + M_2959 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 112 + Query_112 + M_2960 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + + diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_131909_2_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_131909_2_T.fasta new file mode 100755 index 00000000..c4488424 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_131909_2_T.fasta @@ -0,0 +1,76 @@ +>M_2961 +SRRACSSEL +>M_2962 +SPKLKMPEM +>M_2963 +SNKEKWISL +>M_2964 +KRWESEHIL +>M_2965 +LHNEIKTLL +>M_2966 +FSDKMGTLT +>M_2967 +LAAERKAAL +>M_2968 +TPRRSRWQL +>M_2969 +MNCIRQASV +>M_2970 +DQRCRLCPA +>M_2971 +HTTRSLFQY +>M_2972 +PHCPQPLVY +>M_2973 +SLEGRIWAL +>M_2974 +YTDFLLCAS +>M_2975 +VVGARGVGK +>M_2976 +RGRKNRSSV +>M_2977 +FEKMHQMDL +>M_2978 +QVFEKMHQM +>M_2979 +ARWPFGNTM +>M_2980 +GALKKALAK +>M_2981 +RLIAISWPL +>M_2982 +WPLRYVTVM +>M_2983 +HILGNFLTK +>M_2984 +IRCGYPTHI +>M_2985 +EAGPRKGPL +>M_2986 +RLEEAGPRK +>M_2987 +KLPEMKLPK +>M_2988 +MKLPKVPEM +>M_2989 +DRQDQSSHY +>M_2990 +SHYGQPDRQ +>M_2991 +GIMPGHIQK +>M_2992 +IMPGHIQKK +>M_2993 +STMRESSPK +>M_2994 +FPLFAIWPM +>M_2995 +PTDPMLGLA +>M_2996 +EARSRATLA +>M_2997 +FHEARSRAT +>M_2998 +FSIFSTLTK diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_131909_2_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_131909_2_T_iedb.xml new file mode 100755 index 00000000..40c7799e --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_131909_2_T_iedb.xml @@ -0,0 +1,1221 @@ + + + + blastp + BLASTP 2.2.30+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta + Query_1 + M_2961 + 9 + + + BLOSUM62 + 100000000 + 11 + 1 + F + + + + + 1 + Query_1 + M_2961 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 2 + Query_2 + M_2962 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 3 + Query_3 + M_2963 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 4 + Query_4 + M_2964 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 5 + Query_5 + M_2965 + 9 + + + 1 + gnl|BL_ORD_ID|1378 + 109332|L1 protein|ACG75893.1|Human papillomavirus type 16|333760 + 1378 + 9 + + + 1 + 9.61583 + 13 + 1457.43 + 1 + 9 + 1 + 9 + 0 + 0 + 3 + 6 + 0 + 9 + LHNEIKTLL + IHSMNSTIL + +H+ T+L + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 6 + Query_6 + M_2966 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 7 + Query_7 + M_2967 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 8 + Query_8 + M_2968 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 9 + Query_9 + M_2969 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 10 + Query_10 + M_2970 + 9 + + + 1 + gnl|BL_ORD_ID|1621 + 145860|Protein E6|P04019.1|Human papillomavirus type 11|10580 + 1621 + 9 + + + 1 + 12.6974 + 21 + 39.1808 + 3 + 7 + 5 + 9 + 0 + 0 + 4 + 4 + 0 + 5 + RCRLC + RCYLC + RC LC + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 11 + Query_11 + M_2971 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 12 + Query_12 + M_2972 + 9 + + + 1 + gnl|BL_ORD_ID|96 + 6591|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 + 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gnl|BL_ORD_ID|1912 + 180668|polyprotein|AGO67248.1|Dengue virus 2|11060 + 1912 + 10 + + + 1 + 12.6974 + 21 + 26.0802 + 3 + 9 + 1 + 7 + 0 + 0 + 4 + 5 + 0 + 7 + MPGHIQK + MPSVIEK + MP I+K + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 32 + Query_32 + M_2992 + 9 + + + 1 + gnl|BL_ORD_ID|1912 + 180668|polyprotein|AGO67248.1|Dengue virus 2|11060 + 1912 + 10 + + + 1 + 12.6974 + 21 + 35.4066 + 2 + 8 + 1 + 7 + 0 + 0 + 4 + 5 + 0 + 7 + MPGHIQK + MPSVIEK + MP I+K + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 33 + Query_33 + M_2993 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 34 + Query_34 + M_2994 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 35 + Query_35 + M_2995 + 9 + + + 1 + gnl|BL_ORD_ID|242 + 16839|External core antigen|SRC279980|Hepatitis B virus|10407 + 242 + 10 + + + 1 + 12.6974 + 21 + 26.0802 + 1 + 8 + 3 + 10 + 0 + 0 + 4 + 6 + 0 + 8 + PTDPMLGL + PSDTNMGL + P+D +GL + + + + + 2 + gnl|BL_ORD_ID|1581 + 141462|tegument protein UL21|NP_044622.1|Human alphaherpesvirus 1|10298 + 1581 + 9 + + + 1 + 12.3122 + 20 + 40.5299 + 1 + 6 + 4 + 9 + 0 + 0 + 4 + 5 + 0 + 6 + PTDPML + PDDPVL + P DP+L + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 36 + Query_36 + M_2996 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 37 + Query_37 + M_2997 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 38 + Query_38 + M_2998 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + + diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132080_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132080_1_T.fasta new file mode 100755 index 00000000..7703bccd --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132080_1_T.fasta @@ -0,0 +1,80 @@ +>M_2999 +LPDRLTLEF +>M_3000 +LPDRLTLEF +>M_3001 +FSDHQSFVV +>M_3002 +LLSQVQFPY +>M_3003 +GELSVDVSF +>M_3004 +LSVDVSFFF +>M_3005 +LSVDVSFFF +>M_3006 +SVDVSFFFK +>M_3007 +VVDQGNIGK +>M_3008 +MVFHKHGEK +>M_3009 +NAYTMVFHK +>M_3010 +MESNNMPFL +>M_3011 +VMESNNMPF +>M_3012 +IPVPVGATA +>M_3013 +VPVGATASF +>M_3014 +SLDLSQTNL +>M_3015 +TETSSSMPG +>M_3016 +HTDPHLCDF +>M_3017 +SLGFKLLLR +>M_3018 +HEQCDSSSL +>M_3019 +AEKSQGPVL +>M_3020 +RLLSTQAEK +>M_3021 +LSDIGGLLL +>M_3022 +LYLYVLSDI +>M_3023 +SELSSDINL +>M_3024 +MPHSQYLSA +>M_3025 +EEAFVPILY +>M_3026 +QVTVSFTEM +>M_3027 +TVSFTEMLK +>M_3028 +VSFTEMLKK +>M_3029 +LGYRCRFNK +>M_3030 +LPDLFTPPL +>M_3031 +HTDGDTLLQ +>M_3032 +ILAKHKSLF +>M_3033 +KLTILAKHK +>M_3034 +AQTHEPRQW +>M_3035 +EAVAGHIPA +>M_3036 +VAGHIPAIF +>M_3037 +VADLLAFTH +>M_3038 +VVGAVGVGK diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132080_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132080_1_T_iedb.xml new file mode 100755 index 00000000..5a5e9535 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132080_1_T_iedb.xml @@ -0,0 +1,1566 @@ + + + + blastp + BLASTP 2.2.30+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta + Query_1 + M_2999 + 9 + + + BLOSUM62 + 100000000 + 11 + 1 + F + + + + + 1 + Query_1 + M_2999 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 2 + Query_2 + M_3000 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 3 + Query_3 + M_3001 + 9 + + + 1 + gnl|BL_ORD_ID|2185 + 190466|large surface antigen|CAL29876.1|Hepatitis B virus|10407 + 2185 + 15 + + + 1 + 13.4678 + 23 + 7.48645 + 1 + 5 + 4 + 8 + 0 + 0 + 4 + 4 + 0 + 5 + FSDHQ + FPDHQ + F DHQ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 4 + Query_4 + M_3002 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 5 + Query_5 + M_3003 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 6 + Query_6 + M_3004 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 7 + Query_7 + M_3005 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 8 + Query_8 + M_3006 + 9 + + + 1 + gnl|BL_ORD_ID|72 + 5295|nef protein|ACR27174.1|Human immunodeficiency virus 1|11676 + 72 + 9 + + + 1 + 14.6234 + 26 + 1.88321 + 1 + 9 + 1 + 9 + 0 + 0 + 5 + 7 + 0 + 9 + SVDVSFFFK + AVDLSHFLK + +VD+S F K + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 9 + Query_9 + M_3007 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 10 + Query_10 + M_3008 + 9 + + + 1 + gnl|BL_ORD_ID|1090 + 72039|polyprotein|CAB53095.1|Hepatitis C virus subtype 1b|31647 + 1090 + 10 + + + 1 + 12.6974 + 21 + 23.5358 + 2 + 9 + 1 + 8 + 0 + 0 + 4 + 5 + 0 + 8 + VFHKHGEK + VYHGAGSK + V+H G K + + + + + 2 + gnl|BL_ORD_ID|1089 + 72038|Polyprotein|Q9IZA3|Hepatitis C virus subtype 2a|31649 + 1089 + 10 + 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+ MPVGGQSSF + +PVG +SF + + + + + 2 + gnl|BL_ORD_ID|2175 + 189750|Diacylglycerol acyltransferase/mycolyltransferase Ag85B|SRC280000|Mycobacterium tuberculosis|1773 + 2175 + 9 + + + 1 + 15.0086 + 27 + 1.15928 + 1 + 9 + 1 + 9 + 0 + 0 + 5 + 7 + 0 + 9 + VPVGATASF + MPVGGGSSF + +PVG +SF + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 16 + Query_16 + M_3014 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 17 + Query_17 + M_3015 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 18 + Query_18 + M_3016 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 19 + Query_19 + M_3017 + 9 + + + 1 + gnl|BL_ORD_ID|785 + 52578|liver stage antigen-1|CAA82974.1|Plasmodium falciparum|5833 + 785 + 9 + + + 1 + 12.6974 + 21 + 30.8766 + 3 + 9 + 3 + 9 + 0 + 0 + 5 + 5 + 0 + 7 + GFKLLLR + NFKSLLR + FK LLR + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 20 + Query_20 + M_3018 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 21 + Query_21 + M_3019 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 22 + Query_22 + M_3020 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 23 + Query_23 + M_3021 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 24 + Query_24 + M_3022 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 25 + Query_25 + M_3023 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 26 + Query_26 + M_3024 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 27 + Query_27 + M_3025 + 9 + + + 1 + gnl|BL_ORD_ID|1553 + 141228|tegument protein VP11/12|NP_044648.1|Human alphaherpesvirus 1|10298 + 1553 + 9 + + + 1 + 13.4678 + 23 + 8.56958 + 3 + 9 + 1 + 7 + 0 + 0 + 4 + 6 + 0 + 7 + AFVPILY + AYVSVLY + A+V +LY + + + + + 2 + gnl|BL_ORD_ID|1568 + 141341|tegument protein VP11/12|NP_044648.1|Human alphaherpesvirus 1|10298 + 1568 + 9 + + + 1 + 13.4678 + 23 + 11.9303 + 3 + 9 + 3 + 9 + 0 + 0 + 4 + 6 + 0 + 7 + AFVPILY + AYVSVLY + A+V +LY + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 28 + Query_28 + M_3026 + 9 + + + 1 + gnl|BL_ORD_ID|1427 + 112697|Protein E6|P26554.1|Human papillomavirus type 51|10595 + 1427 + 10 + + + 1 + 13.0826 + 22 + 16.6782 + 4 + 9 + 1 + 6 + 0 + 0 + 4 + 6 + 0 + 6 + VSFTEM + VAFTEI + V+FTE+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 29 + Query_29 + M_3027 + 9 + + + 1 + gnl|BL_ORD_ID|1427 + 112697|Protein E6|P26554.1|Human papillomavirus type 51|10595 + 1427 + 10 + + + 1 + 13.0826 + 22 + 14.2707 + 2 + 7 + 1 + 6 + 0 + 0 + 4 + 6 + 0 + 6 + VSFTEM + VAFTEI + V+FTE+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 30 + Query_30 + M_3028 + 9 + + + 1 + gnl|BL_ORD_ID|1427 + 112697|Protein E6|P26554.1|Human papillomavirus type 51|10595 + 1427 + 10 + + + 1 + 13.4678 + 23 + 11.9953 + 1 + 6 + 1 + 6 + 0 + 0 + 4 + 6 + 0 + 6 + VSFTEM + VAFTEI + V+FTE+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 31 + Query_31 + M_3029 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 32 + Query_32 + M_3030 + 9 + + + 1 + gnl|BL_ORD_ID|141 + 10587|viral polyprotein|AAA42941.1|Dengue virus 2 Thailand/NGS-C/1944|11065 + 141 + 9 + + + 1 + 13.0826 + 22 + 23.0624 + 4 + 8 + 3 + 7 + 0 + 0 + 4 + 4 + 0 + 5 + LFTPP + FFTPP + FTPP + + + + + 2 + gnl|BL_ORD_ID|235 + 16814|precore protein|CAM58990.1|Hepatitis B virus|10407 + 235 + 10 + + + 1 + 10.7714 + 16 + 347.035 + 1 + 9 + 2 + 10 + 0 + 0 + 4 + 6 + 0 + 9 + LPDLFTPPL + LPNDFFPSV + LP+ F P + + + + + + 3 + gnl|BL_ORD_ID|234 + 16813|External core antigen|SRC279980|Hepatitis B virus|10407 + 234 + 10 + + + 1 + 10.7714 + 16 + 384.587 + 1 + 7 + 2 + 8 + 0 + 0 + 4 + 5 + 0 + 7 + LPDLFTP + LPNDFFP + LP+ F P + + + + + 4 + gnl|BL_ORD_ID|239 + 16832|core protein|BAF42671.1|Hepatitis B virus|10407 + 239 + 10 + + + 1 + 10.3862 + 15 + 626.674 + 1 + 9 + 2 + 10 + 0 + 0 + 4 + 5 + 0 + 9 + LPDLFTPPL + LPSDFFPSI + LP F P + + + + + + 5 + gnl|BL_ORD_ID|69 + 5191|core protein|AAL31859.1|Hepatitis B virus|10407 + 69 + 17 + + + 1 + 10.001 + 14 + 641.761 + 1 + 9 + 9 + 17 + 0 + 0 + 4 + 5 + 0 + 9 + LPDLFTPPL + LPSDFFPSV + LP F P + + + + + + 6 + gnl|BL_ORD_ID|241 + 16836|precore/core protein [Hepatitis B virus]|AAR03815.1|Hepatitis B virus|10407 + 241 + 10 + + + 1 + 10.3862 + 15 + 731.165 + 1 + 9 + 2 + 10 + 0 + 0 + 4 + 5 + 0 + 9 + LPDLFTPPL + LPSDFLPSV + LP F P + + + + + + 7 + gnl|BL_ORD_ID|240 + 16833|core protein|CAL29866.1|Hepatitis B virus|10407 + 240 + 10 + + + 1 + 10.001 + 14 + 817.025 + 1 + 9 + 2 + 10 + 0 + 0 + 4 + 5 + 0 + 9 + LPDLFTPPL + LPSDFFPSV + LP F P + + + + + + 8 + gnl|BL_ORD_ID|653 + 38701|core protein|AAL31859.1|Hepatitis B virus|10407 + 653 + 9 + + + 1 + 10.001 + 14 + 831.41 + 1 + 9 + 1 + 9 + 0 + 0 + 4 + 5 + 0 + 9 + LPDLFTPPL + LPSDFFPSV + LP F P + + + + + + 9 + gnl|BL_ORD_ID|238 + 16831|External core antigen|SRC279980|Hepatitis B virus|10407 + 238 + 10 + + + 1 + 10.001 + 14 + 887.43 + 1 + 7 + 2 + 8 + 0 + 0 + 4 + 4 + 0 + 7 + LPDLFTP + LPSDFFP + LP F P + + + + + 10 + gnl|BL_ORD_ID|237 + 16827|External core antigen|SRC279980|Hepatitis B virus|10407 + 237 + 10 + + + 1 + 10.001 + 14 + 887.43 + 1 + 7 + 2 + 8 + 0 + 0 + 4 + 4 + 0 + 7 + LPDLFTP + LPSDFFP + LP F P + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 33 + Query_33 + M_3031 + 9 + + + 1 + gnl|BL_ORD_ID|1355 + 108148|polyprotein|AAF65953.1|Hepatitis C virus|11103 + 1355 + 10 + + + 1 + 11.5418 + 18 + 175.991 + 1 + 8 + 1 + 8 + 0 + 0 + 4 + 5 + 0 + 8 + HTDGDTLL + STDSTTIL + TD T+L + + + + + 2 + gnl|BL_ORD_ID|1359 + 108158|polyprotein|AAF65953.1|Hepatitis C virus|11103 + 1359 + 10 + + + 1 + 11.1566 + 17 + 253.803 + 2 + 8 + 1 + 7 + 0 + 0 + 4 + 5 + 0 + 7 + TDGDTLL + TDSTTIL + TD T+L + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 34 + Query_34 + M_3032 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 35 + Query_35 + M_3033 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 36 + Query_36 + M_3034 + 9 + + + 1 + gnl|BL_ORD_ID|2137 + 187106|Vpr protein|BAA93983.1|Human immunodeficiency virus 1|11676 + 2137 + 9 + + + 1 + 14.2382 + 25 + 3.55601 + 1 + 9 + 1 + 9 + 0 + 0 + 5 + 5 + 0 + 9 + AQTHEPRQW + AVRHFPRIW + A H PR W + + + + + 2 + gnl|BL_ORD_ID|1931 + 180758|Nonstructural protein NS5|NP_739590.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 + 1931 + 15 + + + 1 + 10.7714 + 16 + 365.404 + 2 + 9 + 6 + 13 + 0 + 0 + 3 + 4 + 0 + 8 + QTHEPRQW + QDHPYKTW + Q H + W + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 37 + Query_37 + M_3035 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 38 + Query_38 + M_3036 + 9 + + + 1 + gnl|BL_ORD_ID|128 + 9199|E1 protein|ABB77003.1|Hepatitis C virus|11103 + 128 + 9 + + + 1 + 14.2382 + 25 + 3.32254 + 1 + 8 + 2 + 9 + 0 + 0 + 4 + 7 + 0 + 8 + VAGHIPAI + LMGYIPAV + + G+IPA+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 39 + Query_39 + M_3037 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 40 + Query_40 + M_3038 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + + diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132221_2_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132221_2_T.fasta new file mode 100755 index 00000000..04e045d2 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132221_2_T.fasta @@ -0,0 +1,74 @@ +>M_3039 +KLTSYKCKL +>M_3040 +WLRVGNGAL +>M_3041 +SLQLSAHRL +>M_3042 +IVVISIWEI +>M_3043 +SIWEIVGQA +>M_3044 +YLKRGYLTL +>M_3045 +MLHVDRHTL +>M_3046 +VLERGQFDY +>M_3047 +AALSIDHWV +>M_3048 +SIDHWVAVV +>M_3049 +ATAAAAAAL +>M_3050 +GPATAAAAA +>M_3051 +LLLDTPTQL +>M_3052 +HLYDTLGST +>M_3053 +LPLHLYDTL +>M_3054 +EEYTVWIQL +>M_3055 +WEEEYTVWI +>M_3056 +TPEDNRQPL +>M_3057 +LPEQQEGQL +>M_3058 +KPMQVKTPC +>M_3059 +NLQNSPLEI +>M_3060 +VPNLQNSPL +>M_3061 +NELYFAHVL +>M_3062 +YFAHVLFSA +>M_3063 +AVTRPFISL +>M_3064 +FLWPLRVLS +>M_3065 +ISMKFLWPL +>M_3066 +WPLRVLSQF +>M_3067 +REIVWEQGL +>M_3068 +TLAEKRPFM +>M_3069 +LPGHLSRAL +>M_3070 +SLPGHLSRA +>M_3071 +SPSSLPGHL +>M_3072 +ALNNMFCQL +>M_3073 +GPRRGSSPQ +>M_3074 +SPQGAAGAA +>M_3075 +KAFSQSAYL diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132221_2_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132221_2_T_iedb.xml new file mode 100755 index 00000000..1c80711c --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132221_2_T_iedb.xml @@ -0,0 +1,1367 @@ + + + + blastp + BLASTP 2.2.30+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta + Query_1 + M_3039 + 9 + + + BLOSUM62 + 100000000 + 11 + 1 + F + + + + + 1 + Query_1 + M_3039 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 2 + Query_2 + M_3040 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 3 + Query_3 + M_3041 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 4 + Query_4 + M_3042 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 5 + Query_5 + M_3043 + 9 + + + 1 + gnl|BL_ORD_ID|939 + 62004|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 + 939 + 15 + + + 1 + 12.6974 + 21 + 27.8948 + 1 + 7 + 1 + 7 + 0 + 0 + 4 + 5 + 0 + 7 + SIWEIVG + STWVLVG + S W +VG + + + + + 2 + gnl|BL_ORD_ID|2122 + 186474|polyprotein|AGO67248.1|Dengue virus 2|11060 + 2122 + 10 + + + 1 + 11.5418 + 18 + 155.455 + 3 + 9 + 1 + 7 + 0 + 0 + 3 + 5 + 0 + 7 + WEIVGQA + WKTWGKA + W+ G+A + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 6 + Query_6 + M_3044 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 7 + Query_7 + M_3045 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 8 + Query_8 + M_3046 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 9 + Query_9 + M_3047 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 10 + Query_10 + M_3048 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 11 + Query_11 + M_3049 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 12 + Query_12 + M_3050 + 9 + + + 1 + gnl|BL_ORD_ID|2014 + 183819|polyprotein|AGO67248.1|Dengue virus 2|11060 + 2014 + 10 + + + 1 + 11.927 + 19 + 68.8532 + 2 + 7 + 2 + 7 + 0 + 0 + 5 + 5 + 0 + 6 + PATAAA + PITAAA + P TAAA + + + + + 2 + gnl|BL_ORD_ID|1882 + 180538|Nonstructural protein NS2B|NP_739586.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 + 1882 + 15 + + + 1 + 11.927 + 19 + 73.829 + 2 + 7 + 10 + 15 + 0 + 0 + 5 + 5 + 0 + 6 + PATAAA + PITAAA + P TAAA + + + + + 3 + gnl|BL_ORD_ID|1880 + 180529|polyprotein|AGO67248.1|Dengue virus 2|11060 + 1880 + 9 + + + 1 + 11.927 + 19 + 82.8955 + 2 + 7 + 2 + 7 + 0 + 0 + 5 + 5 + 0 + 6 + PATAAA + PITAAA + P TAAA + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 13 + Query_13 + M_3051 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 14 + Query_14 + M_3052 + 9 + + + 1 + gnl|BL_ORD_ID|1808 + 169658|major paraflagellar rod protein|AAA30221.1|Trypanosoma cruzi|5693 + 1808 + 9 + + + 1 + 14.2382 + 25 + 3.05306 + 1 + 8 + 1 + 8 + 0 + 0 + 5 + 5 + 0 + 8 + HLYDTLGS + RLYKTLGQ + LY TLG + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 15 + Query_15 + M_3053 + 9 + + + 1 + gnl|BL_ORD_ID|2191 + 190568|polymerase|AAD16253.1|Hepatitis B virus|10407 + 2191 + 20 + + + 1 + 12.3122 + 20 + 44.0299 + 3 + 7 + 6 + 10 + 0 + 0 + 4 + 4 + 0 + 5 + LHLYD + LHLYS + LHLY + + + + + 2 + gnl|BL_ORD_ID|498 + 31898|P protein|P17100.1|Hepatitis B virus|10407 + 498 + 9 + + + 1 + 11.927 + 19 + 75.1319 + 3 + 7 + 2 + 6 + 0 + 0 + 4 + 4 + 0 + 5 + LHLYD + LHLYS + LHLY + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 16 + Query_16 + M_3054 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 17 + Query_17 + M_3055 + 9 + + + 1 + gnl|BL_ORD_ID|2051 + 184702|non-structural protein 1|AGM49312.1|Dengue virus|12637 + 2051 + 9 + + + 1 + 13.4678 + 23 + 9.85027 + 1 + 8 + 2 + 9 + 0 + 0 + 3 + 6 + 0 + 8 + WEEEYTVW + WPKTHTLW + W + +T+W + + + + + 2 + gnl|BL_ORD_ID|552 + 33912|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 + 552 + 10 + + + 1 + 11.927 + 19 + 81.0261 + 1 + 5 + 3 + 7 + 0 + 0 + 3 + 4 + 0 + 5 + WEEEY + WADEY + W +EY + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 18 + Query_18 + M_3056 + 9 + + + 1 + gnl|BL_ORD_ID|1741 + 150649|polyprotein|AGW21594.1|Dengue virus 1|11053 + 1741 + 10 + + + 1 + 14.2382 + 25 + 3.44317 + 1 + 6 + 1 + 6 + 0 + 0 + 4 + 6 + 0 + 6 + TPEDNR + TPQDNQ + TP+DN+ + + + + + 2 + gnl|BL_ORD_ID|1934 + 180780|polyprotein|AGW21594.1|Dengue virus 1|11053 + 1934 + 9 + + + 1 + 14.2382 + 25 + 4.0067 + 1 + 6 + 1 + 6 + 0 + 0 + 4 + 6 + 0 + 6 + TPEDNR + TPQDNQ + TP+DN+ + + + + + 3 + gnl|BL_ORD_ID|1935 + 180781|polyprotein|AGO67248.1|Dengue virus 2|11060 + 1935 + 9 + + + 1 + 13.853 + 24 + 4.75595 + 1 + 6 + 1 + 6 + 0 + 0 + 4 + 6 + 0 + 6 + TPEDNR + TPQDNQ + TP+DN+ + + + + + 4 + gnl|BL_ORD_ID|2105 + 186029|envelope protein|ABV59122.1|Dengue virus 3|11069 + 2105 + 9 + + + 1 + 13.0826 + 22 + 13.9535 + 1 + 9 + 1 + 9 + 0 + 0 + 5 + 6 + 0 + 9 + TPEDNRQPL + TPTWNRKEL + TP NR+ L + + + + + 5 + gnl|BL_ORD_ID|1494 + 136890|polyprotein|AGO67248.1|Dengue virus 2|11060 + 1494 + 9 + + + 1 + 12.6974 + 21 + 30.3534 + 1 + 9 + 1 + 9 + 0 + 0 + 4 + 5 + 0 + 9 + TPEDNRQPL + TPPGSRDPF + TP +R P + + + + + 6 + gnl|BL_ORD_ID|2013 + 183813|polyprotein|AGW21594.1|Dengue virus 1|11053 + 2013 + 10 + + + 1 + 11.927 + 19 + 75.9314 + 2 + 7 + 2 + 7 + 0 + 0 + 4 + 5 + 0 + 6 + PEDNRQ + PEPDRQ + PE +RQ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 19 + Query_19 + M_3057 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 20 + Query_20 + M_3058 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 21 + Query_21 + M_3059 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 22 + Query_22 + M_3060 + 9 + + + 1 + gnl|BL_ORD_ID|1068 + 70491|envelope glycoprotein|AAC28452.1|Human immunodeficiency virus 1|11676 + 1068 + 10 + + + 1 + 10.3862 + 15 + 691.436 + 1 + 8 + 1 + 8 + 0 + 0 + 4 + 4 + 0 + 8 + VPNLQNSP + VPTDPNPP + VP N P + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 23 + Query_23 + M_3061 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 24 + Query_24 + M_3062 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 25 + Query_25 + M_3063 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 26 + Query_26 + M_3064 + 9 + + + 1 + gnl|BL_ORD_ID|2098 + 185817|envelope protein|AGW23590.1|Dengue virus 4|11070 + 2098 + 10 + + + 1 + 12.3122 + 20 + 52.9061 + 3 + 8 + 2 + 7 + 0 + 0 + 3 + 5 + 0 + 6 + WPLRVL + WMIRIL + W +R+L + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 27 + Query_27 + M_3065 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 28 + Query_28 + M_3066 + 9 + + + 1 + gnl|BL_ORD_ID|2098 + 185817|envelope protein|AGW23590.1|Dengue virus 4|11070 + 2098 + 10 + + + 1 + 13.4678 + 23 + 7.62841 + 1 + 9 + 2 + 10 + 0 + 0 + 4 + 6 + 0 + 9 + WPLRVLSQF + WMIRILIGF + W +R+L F + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 29 + Query_29 + M_3067 + 9 + + + 1 + gnl|BL_ORD_ID|588 + 36717|nonstructural protein 4B|YP_001527886.1|West Nile virus NY-99|10000971 + 588 + 18 + + + 1 + 12.3122 + 20 + 41.1077 + 4 + 8 + 9 + 13 + 0 + 0 + 3 + 4 + 0 + 5 + VWEQG + LWENG + +WE G + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 30 + Query_30 + M_3068 + 9 + + + 1 + gnl|BL_ORD_ID|974 + 64727|polyprotein precursor|NP_041724.2|West Nile virus|11082 + 974 + 9 + + + 1 + 13.4678 + 23 + 10.7466 + 1 + 9 + 1 + 9 + 0 + 0 + 5 + 6 + 0 + 9 + TLAEKRPFM + TLARGFPFV + TLA PF+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 31 + Query_31 + M_3069 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 32 + Query_32 + M_3070 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 33 + Query_33 + M_3071 + 9 + + + 1 + gnl|BL_ORD_ID|793 + 53041|phosphorylated matrix protein (pp65)|AAA45996.1|Human betaherpesvirus 5|10359 + 793 + 11 + + + 1 + 13.0826 + 22 + 14.7222 + 1 + 8 + 3 + 10 + 0 + 0 + 4 + 5 + 0 + 8 + SPSSLPGH + TPDSTPCH + +P S P H + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 34 + Query_34 + M_3072 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 35 + Query_35 + M_3073 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 36 + Query_36 + M_3074 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 37 + Query_37 + M_3075 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + + diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132607_2_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132607_2_T.fasta new file mode 100755 index 00000000..517f5990 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132607_2_T.fasta @@ -0,0 +1,98 @@ +>M_3076 +FADHTVVTI +>M_3077 +FADHTVVTI +>M_3078 +MTAFADHTV +>M_3079 +TAFADHTVV +>M_3080 +GLSPRTSRH +>M_3081 +LSPRTSRHI +>M_3082 +RTSRHILER +>M_3083 +SVQACGWRK +>M_3084 +CLLSPSYYH +>M_3085 +LASDRFNHI +>M_3086 +QVASSPAGK +>M_3087 +VASSPAGKL +>M_3088 +IEYDTFGEV +>M_3089 +APSSVALSL +>M_3090 +NTAPSSVAL +>M_3091 +EMKRHKVHI +>M_3092 +ELLDYIRAV +>M_3093 +PQIPPYSTF +>M_3094 +ISHLHRESV +>M_3095 +NLLSPDNMV +>M_3096 +FASDHFLYA +>M_3097 +FASDHFLYA +>M_3098 +ATYVRILQR +>M_3099 +FVVITATYV +>M_3100 +LASSSLDIV +>M_3101 +FAYTILQSV +>M_3102 +TILQSVPNK +>M_3103 +FTLFFMAEY +>M_3104 +FTLFFMAEY +>M_3105 +YAAGPFTLF +>M_3106 +YAAGPFTLF +>M_3107 +YAAGPFTLF +>M_3108 +ICSEATAAI +>M_3109 +SLFNALRGK +>M_3110 +VAIMGSTQV +>M_3111 +SAYVALSNK +>M_3112 +YAISARSDL +>M_3113 +ATKTLRNYK +>M_3114 +DVFFATKTL +>M_3115 +FATKTLRNY +>M_3116 +FATKTLRNY +>M_3117 +FLSWCRRVV +>M_3118 +LSWCRRVVL +>M_3119 +RVVLELSPK +>M_3120 +VVLELSPKV +>M_3121 +IAIAIGAVL +>M_3122 +IAIGAVLLV +>M_3123 +RGMQCAICK +>M_3124 +FSNADVNRL diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132607_2_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132607_2_T_iedb.xml new file mode 100755 index 00000000..29c73261 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132607_2_T_iedb.xml @@ -0,0 +1,1665 @@ + + + + blastp + BLASTP 2.2.30+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta + Query_1 + M_3076 + 9 + + + BLOSUM62 + 100000000 + 11 + 1 + F + + + + + 1 + Query_1 + M_3076 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 2 + Query_2 + M_3077 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 3 + Query_3 + M_3078 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 4 + Query_4 + M_3079 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 5 + Query_5 + M_3080 + 9 + + + 1 + gnl|BL_ORD_ID|256 + 17278|Genome polyprotein|P06441.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 + 256 + 20 + + + 1 + 13.4678 + 23 + 10.9145 + 2 + 9 + 4 + 11 + 0 + 0 + 5 + 5 + 0 + 8 + LSPRTSRH + LKPGESRH + L P SRH + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 6 + Query_6 + M_3081 + 9 + + + 1 + gnl|BL_ORD_ID|664 + 39591|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 + 664 + 20 + + + 1 + 15.0086 + 27 + 1.23765 + 1 + 9 + 1 + 9 + 0 + 0 + 5 + 6 + 0 + 9 + LSPRTSRHI + LSPYYKRYI + LSP R+I + + + + + 2 + gnl|BL_ORD_ID|663 + 39590|polyprotein|AAY82030.1|Hepatitis C virus|11103 + 663 + 11 + + + 1 + 14.2382 + 25 + 2.83796 + 1 + 9 + 1 + 9 + 0 + 0 + 5 + 6 + 0 + 9 + LSPRTSRHI + LSPYYKRYI + LSP R+I + + + + + 3 + gnl|BL_ORD_ID|662 + 39589|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 + 662 + 10 + + + 1 + 14.2382 + 25 + 3.68732 + 1 + 9 + 1 + 9 + 0 + 0 + 5 + 6 + 0 + 9 + LSPRTSRHI + LSPYYKRYI + LSP R+I + + + + + 4 + gnl|BL_ORD_ID|256 + 17278|Genome polyprotein|P06441.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 + 256 + 20 + + + 1 + 13.853 + 24 + 6.63101 + 1 + 8 + 4 + 11 + 0 + 0 + 5 + 5 + 0 + 8 + LSPRTSRH + LKPGESRH + L P SRH + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 7 + Query_7 + M_3082 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 8 + Query_8 + M_3083 + 9 + + + 1 + gnl|BL_ORD_ID|1142 + 75435|largest ORF|AAB02128.1|Hepatitis C virus|11103 + 1142 + 20 + + + 1 + 13.4678 + 23 + 8.80594 + 3 + 7 + 9 + 13 + 0 + 0 + 3 + 4 + 0 + 5 + QACGW + EGCGW + + CGW + + + + + 2 + gnl|BL_ORD_ID|709 + 43621|largest ORF|AAB02128.1|Hepatitis C virus (isolate H77)|63746 + 709 + 9 + + + 1 + 13.4678 + 23 + 12.1399 + 3 + 7 + 2 + 6 + 0 + 0 + 3 + 4 + 0 + 5 + QACGW + EGCGW + + CGW + + + + + 3 + gnl|BL_ORD_ID|708 + 43619|Genome polyprotein|P26664.3|Hepatitis C virus|11103 + 708 + 9 + + + 1 + 13.0826 + 22 + 14.1983 + 3 + 7 + 2 + 6 + 0 + 0 + 3 + 4 + 0 + 5 + QACGW + EGCGW + + CGW + + + + + 4 + gnl|BL_ORD_ID|713 + 43756|Genome polyprotein|SRC279960|Hepatitis C virus subtype 2a|31649 + 713 + 9 + + + 1 + 13.0826 + 22 + 14.7007 + 3 + 7 + 2 + 6 + 0 + 0 + 3 + 4 + 0 + 5 + QACGW + ETCGW + + CGW + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 9 + Query_9 + M_3084 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 10 + Query_10 + M_3085 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 11 + Query_11 + M_3086 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 12 + Query_12 + M_3087 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 13 + Query_13 + M_3088 + 9 + + + 1 + gnl|BL_ORD_ID|531 + 32738|Liver stage antigen|Q25893|Plasmodium falciparum|5833 + 531 + 9 + + + 1 + 13.4678 + 23 + 10.7466 + 1 + 6 + 4 + 9 + 0 + 0 + 3 + 5 + 0 + 6 + IEYDTF + VQYDNF + ++YD F + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 14 + Query_14 + M_3089 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 15 + Query_15 + M_3090 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 16 + Query_16 + M_3091 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 17 + Query_17 + M_3092 + 9 + + + 1 + gnl|BL_ORD_ID|155 + 11804|EBNA3C latent protein|CAD53421.1|Human gammaherpesvirus 4|10376 + 155 + 10 + + + 1 + 14.2382 + 25 + 3.88217 + 2 + 7 + 4 + 9 + 0 + 0 + 4 + 6 + 0 + 6 + LLDYIR + LLDFVR + LLD++R + + + + + 2 + gnl|BL_ORD_ID|601 + 37153|Nuclear antigen EBNA-3C|Q69140.1|Human gammaherpesvirus 4|10376 + 601 + 10 + + + 1 + 14.2382 + 25 + 4.01795 + 2 + 7 + 1 + 6 + 0 + 0 + 4 + 6 + 0 + 6 + LLDYIR + LLDFVR + LLD++R + + + + + 3 + gnl|BL_ORD_ID|1127 + 74768|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 + 1127 + 9 + + + 1 + 12.6974 + 21 + 26.0147 + 2 + 8 + 2 + 8 + 0 + 0 + 5 + 6 + 0 + 7 + LLDYIRA + LLDGLRA + LLD +RA + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 18 + Query_18 + M_3093 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 19 + Query_19 + M_3094 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 20 + Query_20 + M_3095 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 21 + Query_21 + M_3096 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 22 + Query_22 + M_3097 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 23 + Query_23 + M_3098 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 24 + Query_24 + M_3099 + 9 + + + 1 + gnl|BL_ORD_ID|200 + 14902|Genome polyprotein|P26664.3|Hepatitis C virus subtype 1a|31646 + 200 + 9 + + + 1 + 13.0826 + 22 + 16.6015 + 3 + 9 + 2 + 8 + 0 + 0 + 4 + 7 + 0 + 7 + VITATYV + VVTSTWV + V+T+T+V + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 25 + Query_25 + M_3100 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 26 + Query_26 + M_3101 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 27 + Query_27 + M_3102 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 28 + Query_28 + M_3103 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 29 + Query_29 + M_3104 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 30 + Query_30 + M_3105 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 31 + Query_31 + M_3106 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 32 + Query_32 + M_3107 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 33 + Query_33 + M_3108 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 34 + Query_34 + M_3109 + 9 + + + 1 + gnl|BL_ORD_ID|1844 + 180168|gag protein|ABO14878.1|Human immunodeficiency virus 1|11676 + 1844 + 9 + + + 1 + 13.853 + 24 + 5.36545 + 1 + 6 + 1 + 6 + 0 + 0 + 5 + 6 + 0 + 6 + SLFNAL + SLFNAV + SLFNA+ + + + + + 2 + gnl|BL_ORD_ID|2146 + 189275|gag protein|AAO84847.1|Human immunodeficiency virus 1|11676 + 2146 + 9 + + + 1 + 13.853 + 24 + 5.45887 + 1 + 6 + 1 + 6 + 0 + 0 + 5 + 6 + 0 + 6 + SLFNAL + SLFNAV + SLFNA+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 35 + Query_35 + M_3110 + 9 + + + 1 + gnl|BL_ORD_ID|1290 + 102376|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 + 1290 + 15 + + + 1 + 13.853 + 24 + 5.77703 + 1 + 7 + 8 + 14 + 0 + 0 + 4 + 7 + 0 + 7 + VAIMGST + LAVMGSS + +A+MGS+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 36 + Query_36 + M_3111 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 37 + Query_37 + M_3112 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 38 + Query_38 + M_3113 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 39 + Query_39 + M_3114 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 40 + Query_40 + M_3115 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 41 + Query_41 + M_3116 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 42 + Query_42 + M_3117 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 43 + Query_43 + M_3118 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 44 + Query_44 + M_3119 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 45 + Query_45 + M_3120 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 46 + Query_46 + M_3121 + 9 + + + 1 + gnl|BL_ORD_ID|1595 + 142231|Lipoprotein lpqH precursor|P0A5J0.1|Mycobacterium tuberculosis|1773 + 1595 + 24 + + + 1 + 10.3862 + 15 + 335.171 + 1 + 9 + 7 + 15 + 0 + 0 + 4 + 7 + 0 + 9 + IAIAIGAVL + VAVAGAAIL + +A+A A+L + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 47 + Query_47 + M_3122 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 48 + Query_48 + M_3123 + 9 + + + 1 + gnl|BL_ORD_ID|2035 + 184412|envelope protein|AGW23591.1|Dengue virus 3|11069 + 2035 + 10 + + + 1 + 13.4678 + 23 + 8.32231 + 1 + 8 + 2 + 9 + 0 + 0 + 4 + 6 + 0 + 8 + RGMQCAIC + KGMSYAMC + +GM A+C + + + + + 2 + gnl|BL_ORD_ID|1388 + 110282|Protein E6|P03126.1|Human papillomavirus type 16|333760 + 1388 + 25 + + + 1 + 13.0826 + 22 + 15.2941 + 3 + 9 + 5 + 11 + 0 + 0 + 3 + 5 + 0 + 7 + MQCAICK + LECVYCK + ++C CK + + + + + 3 + gnl|BL_ORD_ID|1671 + 148177|early protein|CAA52585.1|Human papillomavirus type 52|10618 + 1671 + 9 + + + 1 + 12.6974 + 21 + 24.707 + 3 + 9 + 2 + 8 + 0 + 0 + 4 + 5 + 0 + 7 + MQCAICK + LQCVQCK + +QC CK + + + + + 4 + gnl|BL_ORD_ID|1661 + 147835|early protein|CAA52585.1|Human papillomavirus type 52|10618 + 1661 + 9 + + + 1 + 11.927 + 19 + 85.6478 + 3 + 9 + 3 + 9 + 0 + 0 + 3 + 6 + 0 + 7 + MQCAICK + IRCIICQ + ++C IC+ + + + + + 5 + gnl|BL_ORD_ID|1499 + 137656|E6 protein|ACT36477.1|Human papillomavirus type 58|10598 + 1499 + 9 + + + 1 + 11.927 + 19 + 87.0561 + 3 + 9 + 3 + 9 + 0 + 0 + 3 + 6 + 0 + 7 + MQCAICK + IRCIICQ + ++C IC+ + + + + + 6 + gnl|BL_ORD_ID|1390 + 110306|Protein E6|P03126.1|Human papillomavirus type 16|333760 + 1390 + 32 + + + 1 + 11.5418 + 18 + 120.694 + 3 + 9 + 18 + 24 + 0 + 0 + 3 + 5 + 0 + 7 + MQCAICK + LECVYCK + ++C CK + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 49 + Query_49 + M_3124 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + + diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132916_2_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132916_2_T.fasta new file mode 100755 index 00000000..797c1d82 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132916_2_T.fasta @@ -0,0 +1,38 @@ +>M_3125 +MLLKPSERR +>M_3126 +QLAWVPSPY +>M_3127 +QLAWVPSPY +>M_3128 +SSSEYMHHK +>M_3129 +HIASEEPAK +>M_3130 +STGFPHMLF +>M_3131 +YFSTGFPHM +>M_3132 +LVYMMERGK +>M_3133 +VATPGRLVY +>M_3134 +LLIPVAAVY +>M_3135 +SAPLMELLY +>M_3136 +LAMEDTGEY +>M_3137 +MYLHFSDTY +>M_3138 +SVSLMYLHF +>M_3139 +RLSISQWYR +>M_3140 +SQWYRVMVK +>M_3141 +STWIGNKLY +>M_3142 +YMYVCTPLL +>M_3143 +HQRIHTGEK diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132916_2_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132916_2_T_iedb.xml new file mode 100755 index 00000000..fc0cf64a --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132916_2_T_iedb.xml @@ -0,0 +1,511 @@ + + + + blastp + BLASTP 2.2.30+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta + Query_1 + M_3125 + 9 + + + BLOSUM62 + 100000000 + 11 + 1 + F + + + + + 1 + Query_1 + M_3125 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 2 + Query_2 + M_3126 + 9 + + + 1 + gnl|BL_ORD_ID|1179 + 79628|E1 protein|BAA19893.1|Rubella virus|11041 + 1179 + 21 + + + 1 + 13.853 + 24 + 6.94735 + 3 + 7 + 11 + 15 + 0 + 0 + 4 + 5 + 0 + 5 + AWVPS + AWVPT + AWVP+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 3 + Query_3 + M_3127 + 9 + + + 1 + gnl|BL_ORD_ID|1179 + 79628|E1 protein|BAA19893.1|Rubella virus|11041 + 1179 + 21 + + + 1 + 13.853 + 24 + 6.94735 + 3 + 7 + 11 + 15 + 0 + 0 + 4 + 5 + 0 + 5 + AWVPS + AWVPT + AWVP+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 4 + Query_4 + M_3128 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 5 + Query_5 + M_3129 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 6 + Query_6 + M_3130 + 9 + + + 1 + gnl|BL_ORD_ID|23 + 1516|Nucleoprotein|P03418.1|Human respiratory syncytial virus A2|11259 + 23 + 14 + + + 1 + 12.6974 + 21 + 30.4718 + 2 + 8 + 1 + 7 + 0 + 0 + 4 + 5 + 0 + 7 + TGFPHML + AGFYHIL + GF H+L + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 7 + Query_7 + M_3131 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 8 + Query_8 + M_3132 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 9 + Query_9 + M_3133 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 10 + Query_10 + M_3134 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 11 + Query_11 + M_3135 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 12 + Query_12 + M_3136 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 13 + Query_13 + M_3137 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 14 + Query_14 + M_3138 + 9 + + + 1 + gnl|BL_ORD_ID|1887 + 180579|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 + 1887 + 15 + + + 1 + 14.6234 + 26 + 2.26419 + 3 + 8 + 8 + 13 + 0 + 0 + 5 + 5 + 0 + 6 + SLMYLH + SLMYFH + SLMY H + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 15 + Query_15 + M_3139 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 16 + Query_16 + M_3140 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 17 + Query_17 + M_3141 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 18 + Query_18 + M_3142 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 19 + Query_19 + M_3143 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + + diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132940_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132940_1_T.fasta new file mode 100755 index 00000000..4ee0029b --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132940_1_T.fasta @@ -0,0 +1,262 @@ +>M_3144 +ALGLAQGTF +>M_3145 +GLAQGTFVF +>M_3146 +GTFVFIAHF +>M_3147 +KLHQVFHSI +>M_3148 +VTVPEKLSF +>M_3149 +HPCSQPVWL +>M_3150 +FPLVRSCQM +>M_3151 +MMCRDLPGF +>M_3152 +RVKATIVAM +>M_3153 +AQGEPLGAL +>M_3154 +FQVPDLHIL +>M_3155 +GMQARSVEM +>M_3156 +MLHLYPGPM +>M_3157 +SPYSEELPL +>M_3158 +YAQEGFLPH +>M_3159 +HLLFRVIPY +>M_3160 +RVIPYDQSF +>M_3161 +SIGSSATLY +>M_3162 +VQKQDNSTY +>M_3163 +AQVGFTLPL +>M_3164 +LPTPPPPPL +>M_3165 +YSCAGGRLF +>M_3166 +FQLDVASVI +>M_3167 +LDVASVIPF +>M_3168 +SVIPFDICY +>M_3169 +RLPNLHPSF +>M_3170 +LMVAVARSA +>M_3171 +TQHTSFQGY +>M_3172 +EQRCSLQAF +>M_3173 +KSKEREHSF +>M_3174 +NIDLAREAY +>M_3175 +IMSFLLSSL +>M_3176 +SEKEASLLY +>M_3177 +YLKEHASSL +>M_3178 +LVLSGSSSL +>M_3179 +FWRSSCSLF +>M_3180 +QLADQCLTM +>M_3181 +LPIKDGNTL +>M_3182 +LLVDRKDAM +>M_3183 +TPAIRHIML +>M_3184 +MQIHMGLAL +>M_3185 +ALARSSDAF +>M_3186 +HQGGATRVY +>M_3187 +FPNAGKSSF +>M_3188 +ILQEHIGAM +>M_3189 +SASAGLAAM +>M_3190 +HPCVPQALV +>M_3191 +ATIMETLTM +>M_3192 +PSDINVSSY +>M_3193 +VSSYNIYWY +>M_3194 +ESSEHEGTY +>M_3195 +QAWQPTASF +>M_3196 +FLNDRLANY +>M_3197 +LQIMAGRHG +>M_3198 +WLFPTGGSV +>M_3199 +LMYLQKLWM +>M_3200 +SIQSPFEGF +>M_3201 +LALLVSTAF +>M_3202 +GLIATQLLF +>M_3203 +LIATQLLFY +>M_3204 +LIATQLLFY +>M_3205 +AVRPTFGVL +>M_3206 +AMRFHFHSM +>M_3207 +MTSGLAMRF +>M_3208 +FPTTTFMCL +>M_3209 +ISLFPTTTF +>M_3210 +SLFPTTTFM +>M_3211 +SMRSSSISG +>M_3212 +VQHITGPVW +>M_3213 +ASDSQEALF +>M_3214 +FSDISEMRT +>M_3215 +TLAELLGPY +>M_3216 +LVNPWGEVL +>M_3217 +LPVVLQLKL +>M_3218 +AQADQVDPL +>M_3219 +FCDTAPVLK +>M_3220 +RLHSPMYFF +>M_3221 +TMCMYFRPL +>M_3222 +FLVFPFTSI +>M_3223 +LMADMYLLL +>M_3224 +HSHLLSHSY +>M_3225 +HSHLLSHSY +>M_3226 +TQYLVFCGM +>M_3227 +YLVFCGMGL +>M_3228 +LIFMYLCPA +>M_3229 +VAICHPLHY +>M_3230 +VLVQSLMVL +>M_3231 +QAQNQSITY +>M_3232 +TILTFCLSY +>M_3233 +CSIQDDLPF +>M_3234 +RMSRALWTL +>M_3235 +KQGWCYLVY +>M_3236 +YLVYVLLPL +>M_3237 +TINSAGDLF +>M_3238 +FPLDEVHAK +>M_3239 +LTLPPLATY +>M_3240 +PPAPPSLSL +>M_3241 +MQRASRHSQ +>M_3242 +QQSQSSGPG +>M_3243 +MLGDPSADY +>M_3244 +SADYINANY +>M_3245 +GVHKGRKPF +>M_3246 +ALACFARAF +>M_3247 +LTGDCCFDY +>M_3248 +YPKPQVSFL +>M_3249 +HPLGSLQIF +>M_3250 +AVGGMIASF +>M_3251 +PTEQSLTEY +>M_3252 +LLMGFSLTL +>M_3253 +TQGMQCSSL +>M_3254 +LLNLVVTSL +>M_3255 +YVKIYLLPY +>M_3256 +YVKIYLLPY +>M_3257 +ISVFSGSEM +>M_3258 +LLDEDISVF +>M_3259 +STVELVPIF +>M_3260 +KSADFEGLY +>M_3261 +CLFSLYTAY +>M_3262 +SLYTAYHVF +>M_3263 +SSHLHSDHY +>M_3264 +RQKHGEAPI +>M_3265 +RQDVGTYTF +>M_3266 +VERQDVGTY +>M_3267 +HSNSTSFIF +>M_3268 +NAHSNSTSF +>M_3269 +ATTESDQSF +>M_3270 +FPSETKVII +>M_3271 +HQVASSPGH +>M_3272 +SQGGPRGTF +>M_3273 +GGAPHFGHF +>M_3274 +GAIALIRRY diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132940_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132940_1_T_iedb.xml new file mode 100755 index 00000000..ca2e9615 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132940_1_T_iedb.xml @@ -0,0 +1,4011 @@ + + + + blastp + BLASTP 2.2.30+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta + Query_1 + M_3144 + 9 + + + BLOSUM62 + 100000000 + 11 + 1 + F + + + + + 1 + Query_1 + M_3144 + 9 + + + 1 + gnl|BL_ORD_ID|344 + 21638|protein F|ABV46152.2|Hepatitis C virus (isolate Japanese)|11116 + 344 + 9 + + + 1 + 12.3122 + 20 + 49.6079 + 3 + 9 + 3 + 9 + 0 + 0 + 4 + 5 + 0 + 7 + GLAQGTF + GLSPGTL + GL+ GT + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 2 + Query_2 + M_3145 + 9 + + + 1 + gnl|BL_ORD_ID|344 + 21638|protein F|ABV46152.2|Hepatitis C virus (isolate Japanese)|11116 + 344 + 9 + + + 1 + 12.6974 + 21 + 37.2378 + 1 + 7 + 3 + 9 + 0 + 0 + 4 + 5 + 0 + 7 + GLAQGTF + GLSPGTL + GL+ GT + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 3 + Query_3 + M_3146 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 4 + Query_4 + M_3147 + 9 + + + 1 + gnl|BL_ORD_ID|2191 + 190568|polymerase|AAD16253.1|Hepatitis B virus|10407 + 2191 + 20 + + + 1 + 11.927 + 19 + 77.7846 + 1 + 9 + 5 + 13 + 0 + 0 + 5 + 5 + 0 + 9 + KLHQVFHSI + KLHLYSHPI + KLH H I + + + + + 2 + gnl|BL_ORD_ID|498 + 31898|P protein|P17100.1|Hepatitis B virus|10407 + 498 + 9 + + + 1 + 11.927 + 19 + 92.9112 + 1 + 9 + 1 + 9 + 0 + 0 + 5 + 5 + 0 + 9 + KLHQVFHSI + KLHLYSHPI + KLH H I + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 5 + Query_5 + M_3148 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 6 + Query_6 + M_3149 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 7 + Query_7 + M_3150 + 9 + + + 1 + gnl|BL_ORD_ID|586 + 36676|polyprotein|BAA09073.1|Hepatitis C virus subtype 1b|31647 + 586 + 9 + + + 1 + 13.0826 + 22 + 18.1053 + 3 + 9 + 1 + 7 + 0 + 0 + 3 + 6 + 0 + 7 + LVRSCQM + LIRACML + L+R+C + + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 8 + Query_8 + M_3151 + 9 + + + 1 + gnl|BL_ORD_ID|799 + 53201|Fusion glycoprotein F0 precursor|P03420.1|Human respiratory syncytial virus A2|11259 + 799 + 9 + + + 1 + 13.0826 + 22 + 14.1983 + 4 + 9 + 4 + 9 + 0 + 0 + 4 + 5 + 0 + 6 + RDLPGF + RELPRF + R+LP F + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 9 + Query_9 + M_3152 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 10 + Query_10 + M_3153 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 11 + Query_11 + M_3154 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 12 + Query_12 + M_3155 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 13 + Query_13 + M_3156 + 9 + + + 1 + gnl|BL_ORD_ID|654 + 38724|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 + 654 + 20 + + + 1 + 14.2382 + 25 + 2.55563 + 1 + 9 + 11 + 19 + 0 + 0 + 4 + 6 + 0 + 9 + MLHLYPGPM + LFQLYRGPL + + LY GP+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 14 + Query_14 + M_3157 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 15 + Query_15 + M_3158 + 9 + + + 1 + gnl|BL_ORD_ID|1512 + 140541|hypothetical protein|NP_218210.1|Mycobacterium tuberculosis H37Rv|83332 + 1512 + 9 + + + 1 + 13.4678 + 23 + 11.1275 + 3 + 8 + 3 + 8 + 0 + 0 + 4 + 4 + 0 + 6 + QEGFLP + DEGLLP + EG LP + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 16 + Query_16 + M_3159 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 17 + Query_17 + M_3160 + 9 + + + 1 + gnl|BL_ORD_ID|1432 + 116123|nucleocapsid protein|ABP49342.1|Influenza A virus (A/California/10/1978(H1N1))|425557 + 1432 + 9 + + + 1 + 13.4678 + 23 + 7.72035 + 3 + 8 + 1 + 6 + 0 + 0 + 3 + 6 + 0 + 6 + IPYDQS + LPFDKS + +P+D+S + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 18 + Query_18 + M_3161 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 19 + Query_19 + M_3162 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 20 + Query_20 + M_3163 + 9 + + + 1 + gnl|BL_ORD_ID|1841 + 179898|cell surface protein (associated with virulence)|NP_302372.1|Mycobacterium leprae TN|272631 + 1841 + 9 + + + 1 + 13.853 + 24 + 5.18352 + 4 + 9 + 4 + 9 + 0 + 0 + 4 + 5 + 0 + 6 + GFTLPL + AFTMPL + FT+PL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 21 + Query_21 + M_3164 + 9 + + + 1 + gnl|BL_ORD_ID|1068 + 70491|envelope glycoprotein|AAC28452.1|Human immunodeficiency virus 1|11676 + 1068 + 10 + + + 1 + 11.927 + 19 + 95.2093 + 1 + 8 + 1 + 8 + 0 + 0 + 5 + 6 + 0 + 8 + LPTPPPPP + VPTDPNPP + +PT P PP + + + + + 2 + gnl|BL_ORD_ID|1276 + 101821|vif protein|ACC96167.1|Human immunodeficiency virus 1|11676 + 1276 + 11 + + + 1 + 9.61583 + 13 + 1292.96 + 3 + 8 + 2 + 7 + 0 + 0 + 4 + 4 + 0 + 6 + TPPPPP + TKPPLP + T PP P + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 22 + Query_22 + M_3165 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 23 + Query_23 + M_3166 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 24 + Query_24 + M_3167 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 25 + Query_25 + M_3168 + 9 + + + 1 + gnl|BL_ORD_ID|1110 + 73059|kaposin|AAC57155.1|Human gammaherpesvirus 8|37296 + 1110 + 15 + + + 1 + 10.3862 + 15 + 500.815 + 1 + 8 + 6 + 13 + 0 + 0 + 3 + 4 + 0 + 8 + SVIPFDIC + GAIPPLVC + IP +C + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 26 + Query_26 + M_3169 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 27 + Query_27 + M_3170 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 28 + Query_28 + M_3171 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 29 + Query_29 + M_3172 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 30 + Query_30 + M_3173 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 31 + Query_31 + M_3174 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 32 + Query_32 + M_3175 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 33 + Query_33 + M_3176 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 34 + Query_34 + M_3177 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 35 + Query_35 + M_3178 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 36 + Query_36 + M_3179 + 9 + + + 1 + gnl|BL_ORD_ID|834 + 54824|polyprotein precursor|BAA01583.1|Hepatitis C virus|11103 + 834 + 9 + + + 1 + 12.6974 + 21 + 25.1356 + 1 + 8 + 2 + 9 + 0 + 0 + 3 + 4 + 0 + 8 + FWRSSCSL + LWHYPCTL + W C+L + + + + + 2 + gnl|BL_ORD_ID|1149 + 75636|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 + 1149 + 10 + + + 1 + 11.927 + 19 + 66.6359 + 1 + 8 + 3 + 10 + 0 + 0 + 2 + 4 + 0 + 8 + FWRSSCSL + LWHYPCTI + W C++ + + + + + 3 + gnl|BL_ORD_ID|833 + 54821|E2 protein|AAM33354.1|Hepatitis C virus subtype 1a|31646 + 833 + 9 + + + 1 + 11.927 + 19 + 73.9069 + 1 + 8 + 2 + 9 + 0 + 0 + 2 + 4 + 0 + 8 + FWRSSCSL + LWHYPCTI + W C++ + + + + + 4 + gnl|BL_ORD_ID|835 + 54825|polyprotein|BAA03375.1|Hepatitis C virus|11103 + 835 + 9 + + + 1 + 11.927 + 19 + 110.987 + 1 + 8 + 2 + 9 + 0 + 0 + 2 + 4 + 0 + 8 + FWRSSCSL + LWHYPCTV + W C++ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 37 + Query_37 + M_3180 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 38 + Query_38 + M_3181 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 39 + Query_39 + M_3182 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 40 + Query_40 + M_3183 + 9 + + + 1 + gnl|BL_ORD_ID|2103 + 186002|polyprotein|AGO67248.1|Dengue virus 2|11060 + 2103 + 9 + + + 1 + 13.853 + 24 + 5.74926 + 1 + 6 + 1 + 6 + 0 + 0 + 4 + 5 + 0 + 6 + TPAIRH + TPMLRH + TP +RH + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 41 + Query_41 + M_3184 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 42 + Query_42 + M_3185 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 43 + Query_43 + M_3186 + 9 + + + 1 + gnl|BL_ORD_ID|385 + 23620|Genome polyprotein|SRC279960|Hepatitis C virus genotype 1|41856 + 385 + 10 + + + 1 + 15.0086 + 27 + 1.14868 + 1 + 9 + 1 + 9 + 0 + 0 + 5 + 5 + 0 + 9 + HQGGATRVY + HDGAGKRVY + H G RVY + + + + + 2 + gnl|BL_ORD_ID|386 + 23621|Genome polyprotein|P26664.3|Hepatitis C virus (isolate 1)|11104 + 386 + 11 + + + 1 + 15.0086 + 27 + 1.29055 + 1 + 9 + 1 + 9 + 0 + 0 + 5 + 5 + 0 + 9 + HQGGATRVY + HDGAGKRVY + H G RVY + + + + + 3 + gnl|BL_ORD_ID|384 + 23619|Genome polyprotein|P27958.3|Hepatitis C virus (isolate H)|11108 + 384 + 9 + + + 1 + 15.0086 + 27 + 1.33879 + 1 + 9 + 1 + 9 + 0 + 0 + 5 + 5 + 0 + 9 + HQGGATRVY + HDGAGKRVY + H G RVY + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 44 + Query_44 + M_3187 + 9 + + + 1 + gnl|BL_ORD_ID|1874 + 180503|polyprotein|AGO67248.1|Dengue virus 2|11060 + 1874 + 10 + + + 1 + 13.0826 + 22 + 18.1832 + 2 + 7 + 2 + 7 + 0 + 0 + 4 + 5 + 0 + 6 + PNAGKS + PGAGKT + P AGK+ + + + + + 2 + gnl|BL_ORD_ID|389 + 23807|tax|AAG48731.1|Human T-lymphotropic virus 2|11909 + 389 + 23 + + + 1 + 12.6974 + 21 + 26.0558 + 1 + 7 + 2 + 8 + 0 + 0 + 4 + 5 + 0 + 7 + FPNAGKS + FPGFGQS + FP G+S + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 45 + Query_45 + M_3188 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 46 + Query_46 + M_3189 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 47 + Query_47 + M_3190 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 48 + Query_48 + M_3191 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 49 + Query_49 + M_3192 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 50 + Query_50 + M_3193 + 9 + + + 1 + gnl|BL_ORD_ID|469 + 28484|Protein E6|P03126.1|Human papillomavirus type 16|333760 + 469 + 9 + + + 1 + 11.5418 + 18 + 150.225 + 1 + 9 + 1 + 9 + 0 + 0 + 4 + 5 + 0 + 9 + VSSYNIYWY + ISEYRHYCY + +S Y Y Y + + + + + 2 + gnl|BL_ORD_ID|353 + 21960|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 + 353 + 10 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0.14 + + + No hits found + + + 113 + Query_113 + M_3256 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 114 + Query_114 + M_3257 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 115 + Query_115 + M_3258 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 116 + Query_116 + M_3259 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 117 + Query_117 + M_3260 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 118 + Query_118 + M_3261 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 119 + Query_119 + M_3262 + 9 + + + 1 + gnl|BL_ORD_ID|526 + 32250|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 + 526 + 9 + + + 1 + 12.6974 + 21 + 33.058 + 1 + 8 + 1 + 8 + 0 + 0 + 4 + 5 + 0 + 8 + SLYTAYHV + KLYCSYEV + LY +Y V + + + + + + + 2334 + 25004 + 0 + 225036 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+LSMEETLLL +>M_3283 +WWNPALWKR +>M_3284 +LFQDNSSQL +>M_3285 +LTPPQAQEL +>M_3286 +LTPQQAQEL +>M_3287 +QAQALGIPL +>M_3288 +ASRPDRLSL +>M_3289 +EAQGQEASR +>M_3290 +WVEPQNPVL +>M_3291 +HLPHLTHTL +>M_3292 +HTLATSCRR +>M_3293 +ITSFDNLFR +>M_3294 +SHFHKTHEV +>M_3295 +YKLVVVGAV +>M_3296 +FHRRLSSSL +>M_3297 +FHRRLSSSL +>M_3298 +FSRRSFHRR +>M_3299 +RSDVWNLGI +>M_3300 +VYILILPSF +>M_3301 +STTIPILTL +>M_3302 +TIPILTLSL +>M_3303 +LSHISHLEL +>M_3304 +SHLELVESL +>M_3305 +SAEVRIEPM +>M_3306 +QSHLLIHQR +>M_3307 +QVITLRKSL +>M_3308 +TKKQVITLR +>M_3309 +MFDASKANF +>M_3310 +FLDWLRTMT +>M_3311 +VDWFLDWLR +>M_3312 +WFLDWLRTM +>M_3313 +WLRTMTNVL +>M_3314 +KFLQEEPQL +>M_3315 +DVFRFSPYR +>M_3316 +RFSPYRGLL +>M_3317 +DSTRPPGTR diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_133761_2_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_133761_2_T_iedb.xml new file mode 100755 index 00000000..6e8c146f --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_133761_2_T_iedb.xml @@ -0,0 +1,1517 @@ + + + + blastp + BLASTP 2.2.30+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta + Query_1 + M_3275 + 9 + + + BLOSUM62 + 100000000 + 11 + 1 + F + + + + + 1 + Query_1 + M_3275 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 2 + Query_2 + M_3276 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 3 + Query_3 + M_3277 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 4 + Query_4 + M_3278 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 5 + Query_5 + M_3279 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 6 + Query_6 + M_3280 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 7 + Query_7 + M_3281 + 9 + + + 1 + gnl|BL_ORD_ID|1759 + 154346|RL2|CAB06760.1|Human alphaherpesvirus 2|10310 + 1759 + 15 + + + 1 + 13.0826 + 22 + 18.437 + 1 + 8 + 5 + 12 + 0 + 0 + 4 + 5 + 0 + 8 + TGDSEAAP + TGNPRTAP + TG+ AP + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 8 + Query_8 + M_3282 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 9 + Query_9 + M_3283 + 9 + + + 1 + gnl|BL_ORD_ID|549 + 33681|||| + 549 + 10 + + + 1 + 15.0086 + 27 + 0.933082 + 3 + 9 + 4 + 10 + 0 + 0 + 4 + 6 + 0 + 7 + NPALWKR + GPAIYKR + PA++KR + + + + + 2 + gnl|BL_ORD_ID|1678 + 149027|NS5 protein|BAA00702.1|Hepatitis C virus (isolate H77)|63746 + 1678 + 18 + + + 1 + 13.4678 + 23 + 8.48241 + 4 + 9 + 2 + 7 + 0 + 0 + 4 + 4 + 0 + 6 + PALWKR + PTLWAR + P LW R + + + + + 3 + gnl|BL_ORD_ID|1615 + 144207|polyprotein|CAB41951.1|Hepatitis C virus|11103 + 1615 + 10 + + + 1 + 13.0826 + 22 + 14.7743 + 4 + 9 + 2 + 7 + 0 + 0 + 4 + 4 + 0 + 6 + PALWKR + PTLWAR + P LW R + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 10 + Query_10 + M_3284 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 11 + Query_11 + M_3285 + 9 + + + 1 + gnl|BL_ORD_ID|1060 + 69799|envelope glycoprotein|BAE96221.1|Human immunodeficiency virus 1|11676 + 1060 + 10 + + + 1 + 13.0826 + 22 + 16.6782 + 1 + 9 + 2 + 10 + 0 + 0 + 5 + 6 + 0 + 9 + LTPPQAQEL + LTDPNPQEV + LT P QE+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 12 + Query_12 + M_3286 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 13 + Query_13 + M_3287 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 14 + Query_14 + M_3288 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 15 + Query_15 + M_3289 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 16 + Query_16 + M_3290 + 9 + + + 1 + gnl|BL_ORD_ID|891 + 58740|Major surface antigen precursor|P03142.4|Hepatitis B virus|10407 + 891 + 10 + + + 1 + 10.7714 + 16 + 368.054 + 2 + 9 + 3 + 10 + 0 + 0 + 4 + 5 + 0 + 8 + VEPQNPVL + VSPFIPLL + V P P+L + + + + + 2 + gnl|BL_ORD_ID|478 + 29455|Major surface antigen precursor|P03141.3|Hepatitis B virus subtype adw2|10408 + 478 + 9 + + + 1 + 10.7714 + 16 + 393.541 + 2 + 9 + 2 + 9 + 0 + 0 + 4 + 5 + 0 + 8 + VEPQNPVL + VSPFIPLL + V P P+L + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 17 + Query_17 + M_3291 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 18 + Query_18 + M_3292 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 19 + Query_19 + M_3293 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 20 + Query_20 + M_3294 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 21 + Query_21 + M_3295 + 9 + + + 1 + gnl|BL_ORD_ID|524 + 32238|polyprotein [Hepatitis C virus subtype 1a]|ABV46251.2|Hepatitis C virus (isolate H77)|63746 + 524 + 10 + + + 1 + 12.6974 + 21 + 30.9217 + 2 + 7 + 1 + 6 + 0 + 0 + 5 + 6 + 0 + 6 + KLVVVG + KLVVLG + KLVV+G + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 22 + Query_22 + M_3296 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 23 + Query_23 + M_3297 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 24 + Query_24 + M_3298 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 25 + Query_25 + M_3299 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 26 + Query_26 + M_3300 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 27 + Query_27 + M_3301 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 28 + Query_28 + M_3302 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 29 + Query_29 + M_3303 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 30 + Query_30 + M_3304 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 31 + Query_31 + M_3305 + 9 + + + 1 + gnl|BL_ORD_ID|1075 + 71266|Circumsporozoite protein precursor|P02893.1|Plasmodium falciparum|5833 + 1075 + 20 + + + 1 + 13.853 + 24 + 4.4203 + 3 + 8 + 8 + 13 + 0 + 0 + 4 + 6 + 0 + 6 + EVRIEP + QVRIKP + +VRI+P + + + + + 2 + gnl|BL_ORD_ID|304 + 20415|circumsporozoite protein|AAN87606.1|Plasmodium falciparum|5833 + 304 + 20 + + + 1 + 13.853 + 24 + 7.45549 + 3 + 8 + 3 + 8 + 0 + 0 + 4 + 6 + 0 + 6 + EVRIEP + QVRIKP + +VRI+P + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 32 + Query_32 + M_3306 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 33 + Query_33 + M_3307 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 34 + Query_34 + M_3308 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 35 + Query_35 + M_3309 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 36 + Query_36 + M_3310 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 37 + Query_37 + M_3311 + 9 + + + 1 + gnl|BL_ORD_ID|664 + 39591|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 + 664 + 20 + + + 1 + 12.3122 + 20 + 56.0891 + 1 + 9 + 9 + 17 + 0 + 0 + 4 + 6 + 0 + 9 + VDWFLDWLR + ISWCLWWLQ + + W L WL+ + + + + + 2 + gnl|BL_ORD_ID|1120 + 74387|Genome polyprotein|P26664.3|Hepatitis C virus (isolate 1)|11104 + 1120 + 9 + + + 1 + 11.5418 + 18 + 138.797 + 1 + 8 + 2 + 9 + 0 + 0 + 4 + 5 + 0 + 8 + VDWFLDWL + ISWCLWWL + + W L WL + + + + + 3 + gnl|BL_ORD_ID|1697 + 149105|E2 protein|NP_751921.1|Hepatitis C virus (isolate H77)|63746 + 1697 + 9 + + + 1 + 10.7714 + 16 + 365.422 + 1 + 7 + 3 + 9 + 0 + 0 + 2 + 3 + 0 + 7 + VDWFLDW + ASWAIKW + W + W + + + + + 4 + gnl|BL_ORD_ID|1119 + 74386|HCV-1|AAA45676.1|Hepatitis C virus|11103 + 1119 + 8 + + + 1 + 10.3862 + 15 + 795.381 + 1 + 7 + 2 + 8 + 0 + 0 + 3 + 4 + 0 + 7 + VDWFLDW + ISWCLWW + + W L W + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 38 + Query_38 + M_3312 + 9 + + + 1 + gnl|BL_ORD_ID|664 + 39591|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 + 664 + 20 + + + 1 + 10.3862 + 15 + 413.002 + 1 + 7 + 11 + 17 + 0 + 0 + 4 + 5 + 0 + 7 + WFLDWLR + WCLWWLQ + W L WL+ + + + + + 2 + gnl|BL_ORD_ID|1120 + 74387|Genome polyprotein|P26664.3|Hepatitis C virus (isolate 1)|11104 + 1120 + 9 + + + 1 + 10.001 + 14 + 968.836 + 1 + 6 + 4 + 9 + 0 + 0 + 4 + 4 + 0 + 6 + WFLDWL + WCLWWL + W L WL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 39 + Query_39 + M_3313 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 40 + Query_40 + M_3314 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 41 + Query_41 + M_3315 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 42 + Query_42 + M_3316 + 9 + + + 1 + gnl|BL_ORD_ID|421 + 25388|matrix protein|ABP96803.1|Human metapneumovirus|162145 + 421 + 10 + + + 1 + 14.6234 + 26 + 1.59035 + 2 + 9 + 1 + 8 + 0 + 0 + 4 + 6 + 0 + 8 + FSPYRGLL + IAPYAGLI + +PY GL+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 43 + Query_43 + M_3317 + 9 + + + 1 + gnl|BL_ORD_ID|1494 + 136890|polyprotein|AGO67248.1|Dengue virus 2|11060 + 1494 + 9 + + + 1 + 13.0826 + 22 + 13.4763 + 5 + 9 + 2 + 6 + 0 + 0 + 4 + 5 + 0 + 5 + PPGTR + PPGSR + PPG+R + + + + + 2 + gnl|BL_ORD_ID|1106 + 72928|Genome polyprotein|P26662.3|Hepatitis C virus (isolate Japanese)|11116 + 1106 + 10 + + + 1 + 13.0826 + 22 + 15.8345 + 5 + 9 + 4 + 8 + 0 + 0 + 4 + 4 + 0 + 5 + PPGTR + PPGAR + PPG R + + + + + 3 + gnl|BL_ORD_ID|1599 + 142245|polyprotein|ACJ37204.1|Hepatitis C virus subtype 1a|31646 + 1599 + 9 + + + 1 + 13.0826 + 22 + 18.1053 + 2 + 7 + 1 + 6 + 0 + 0 + 4 + 5 + 0 + 6 + STRPPG + NTRPPA + +TRPP + + + + + 4 + gnl|BL_ORD_ID|1601 + 142247|envelope protein 2|ACY64760.1|Hepatitis C virus subtype 1a|31646 + 1601 + 9 + + + 1 + 13.0826 + 22 + 19.071 + 2 + 6 + 1 + 5 + 0 + 0 + 4 + 5 + 0 + 5 + STRPP + NTRPP + +TRPP + + + + + 5 + gnl|BL_ORD_ID|1602 + 142248|polyprotein|BAB18806.1|Hepatitis C virus subtype 1a|31646 + 1602 + 9 + + + 1 + 13.0826 + 22 + 19.404 + 2 + 6 + 1 + 5 + 0 + 0 + 4 + 5 + 0 + 5 + STRPP + NTRPP + +TRPP + + + + + 6 + gnl|BL_ORD_ID|1603 + 142249|polyprotein|AAY82036.1|Hepatitis C virus subtype 1a|31646 + 1603 + 9 + + + 1 + 13.0826 + 22 + 23.0624 + 2 + 6 + 1 + 5 + 0 + 0 + 4 + 5 + 0 + 5 + STRPP + NTRPP + +TRPP + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + + diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_133954_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_133954_1_T.fasta new file mode 100755 index 00000000..43cd5767 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_133954_1_T.fasta @@ -0,0 +1,336 @@ +>M_3318 +YLGVPVFYA +>M_3319 +AIHIVAEKK +>M_3320 +TQFELQRNK +>M_3321 +VRGTDWHLK +>M_3322 +GFHPDPEAL +>M_3323 +HIRTDTYVK +>M_3324 +SRWQVHGIV +>M_3325 +VPACSRAHV +>M_3326 +VPACSYAHV +>M_3327 +MLFFRTRYI +>M_3328 +TRYICTTVF +>M_3329 +YICTTVFYT +>M_3330 +AALVPTQAM +>M_3331 +MPGSPRDPV +>M_3332 +RRGSGHSEY +>M_3333 +RICGHIFCY +>M_3334 +GIAPLNQWV +>M_3335 +KIIATCFAV +>M_3336 +KMNEPKCLK +>M_3337 +SFVPWNSYV +>M_3338 +VPWNSYVRL +>M_3339 +YQLKLFACM +>M_3340 +YQLKLFACM +>M_3341 +RGRGGSVSI +>M_3342 +IPHTAILVT +>M_3343 +SIPHTAILV +>M_3344 +GLSDLELRL +>M_3345 +VLLRCPNKL +>M_3346 +TRLAFGLFA +>M_3347 +ILIACRLNK +>M_3348 +LIACRLNKK +>M_3349 +RLNKKKGAY +>M_3350 +TLAHEASPL +>M_3351 +SAWWSFGSL +>M_3352 +NPEAMCSDL +>M_3353 +AMHPLFRKL +>M_3354 +CRAMHPLFR +>M_3355 +GPCRAMHPL +>M_3356 +RAMHPLFRK +>M_3357 +GYIHYVFYL +>M_3358 +GYIHYVFYL +>M_3359 +KGYIHYVFY +>M_3360 +YLGNGPNVI +>M_3361 +SLSNKEVKK +>M_3362 +GPRAINNFF +>M_3363 +FRFSSQEAA +>M_3364 +LLPPQDPHL +>M_3365 +PPQDPHLPL +>M_3366 +HVDPGTIGV +>M_3367 +GLMGAVNVA +>M_3368 +LMGAVNVAK +>M_3369 +PRMAIPWPR +>M_3370 +WPRDVRKLV +>M_3371 +KYYEALPEL +>M_3372 +HYYHNVHAV +>M_3373 +MVEHYYHNV +>M_3374 +YHNVHAVVF +>M_3375 +YYHNVHAVV +>M_3376 +ARVWKFGPK +>M_3377 +RVWKFGPKL +>M_3378 +RVWKFGPKL +>M_3379 +VLDKARVWK +>M_3380 +CYEEYRGRL +>M_3381 +GRYEEYRGH +>M_3382 +APRGACYRA +>M_3383 +YRADHDLGR +>M_3384 +SYVCVVRNY +>M_3385 +ARPFFFFLL +>M_3386 +FFFFLLDKV +>M_3387 +FFFLLDKVL +>M_3388 +FLLDKVLAS +>M_3389 +HARPFFFFL +>M_3390 +APSWRGLAE +>M_3391 +LRLALMKKK +>M_3392 +WLRLALMKK +>M_3393 +VLIQQLEKV +>M_3394 +YPGQVNRTA +>M_3395 +MADVAMYGV +>M_3396 +GLYYAEFGA +>M_3397 +SVLAGLYYA +>M_3398 +TMWRREESL +>M_3399 +CLWQLKAPV +>M_3400 +RPRKAWAWC +>M_3401 +QRLKREEEK +>M_3402 +VYHMSQSPL +>M_3403 +FTMLLSLLA +>M_3404 +GLAGFTMLL +>M_3405 +MLLSLLAFA +>M_3406 +KVHQLAITV +>M_3407 +LPKSSEKAI +>M_3408 +STQEPTAYV +>M_3409 +ARMRKHIKR +>M_3410 +GPARMRKHI +>M_3411 +RMRKHIKRL +>M_3412 +HVGKASSSM +>M_3413 +QQMEAHVGK +>M_3414 +VILLPQPPK +>M_3415 +YLGVPVFYA +>M_3416 +AIHIVAEKK +>M_3417 +IVGHTGSGK +>M_3418 +LPAPPGAPP +>M_3419 +VRGTDWHLK +>M_3420 +RRHHSPSQR +>M_3421 +WLQQENHEL +>M_3422 +SLQPIHHDL +>M_3423 +VPACSRAHV +>M_3424 +VPACSYAHV +>M_3425 +LLLSPPVEV +>M_3426 +LLSPPVEVK +>M_3427 +RPEPPETGV +>M_3428 +RRGSGHSEY +>M_3429 +GLLQRPVHL +>M_3430 +HLALGRLSR +>M_3431 +KIIATCFAV +>M_3432 +SFVPWNSYV +>M_3433 +VPWNSYVRL +>M_3434 +YQLKLFACM +>M_3435 +YQLKLFACM +>M_3436 +IPHTAILVT +>M_3437 +SIPHTAILV +>M_3438 +SVSSCCQPV +>M_3439 +WLLEWTEAA +>M_3440 +GLSDLELRL +>M_3441 +VLLRCPNKL +>M_3442 +TLAHEASPL +>M_3443 +ILPATILVL +>M_3444 +TILPATILV +>M_3445 +SAWWSFGSL +>M_3446 +NPEAMCSDL +>M_3447 +AMHPLFRKL +>M_3448 +CRAMHPLFR +>M_3449 +GPCRAMHPL +>M_3450 +RAMHPLFRK +>M_3451 +SLSNKEVKK +>M_3452 +GPRAINNFF +>M_3453 +LLPPQDPHL +>M_3454 +PPQDPHLPL +>M_3455 +GLMGAVNVA +>M_3456 +LMGAVNVAK +>M_3457 +KLPEVQLPK +>M_3458 +ARVWKFGPK +>M_3459 +RVWKFGPKL +>M_3460 +RVWKFGPKL +>M_3461 +VLDKARVWK +>M_3462 +APRGACYRA +>M_3463 +YRADHDLGR +>M_3464 +SYVCVVRNY +>M_3465 +APSWRGLAE +>M_3466 +VLIQQLEKV +>M_3467 +GLYYAEFGA +>M_3468 +SVLAGLYYA +>M_3469 +KPVNKILQI +>M_3470 +CLWQLKAPV +>M_3471 +RPRKAWAWC +>M_3472 +SLDTVAQAV +>M_3473 +QRLKREEEK +>M_3474 +RREQQLRRK +>M_3475 +VYHMSQSPL +>M_3476 +FTMLLSLLA +>M_3477 +GLAGFTMLL +>M_3478 +MLLSLLAFA +>M_3479 +KVHQLAITV +>M_3480 +KIMHGPFMK +>M_3481 +RPRWNTHGH +>M_3482 +ARMRKHIKR +>M_3483 +GPARMRKHI +>M_3484 +RMRKHIKRL +>M_3485 +VILLPQPPK diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_133954_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_133954_1_T_iedb.xml new file mode 100755 index 00000000..23b6434e --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_133954_1_T_iedb.xml @@ -0,0 +1,6405 @@ + + + + blastp + BLASTP 2.2.30+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta + Query_1 + M_3318 + 9 + + + BLOSUM62 + 100000000 + 11 + 1 + F + + + + + 1 + Query_1 + M_3318 + 9 + + + 1 + gnl|BL_ORD_ID|1 + 118|envelope glycoprotein|ABS76372.1|Human immunodeficiency virus 1|11676 + 1 + 20 + + + 1 + 14.6234 + 26 + 1.57628 + 1 + 7 + 10 + 16 + 0 + 0 + 5 + 6 + 0 + 7 + YLGVPVF + YYGVPVW + Y GVPV+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 2 + Query_2 + M_3319 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 3 + Query_3 + M_3320 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 4 + Query_4 + M_3321 + 9 + + + 1 + gnl|BL_ORD_ID|1008 + 66798|glycoprotein gp35/37|AAC59622.1|Human gammaherpesvirus 8|37296 + 1008 + 15 + + + 1 + 12.6974 + 21 + 22.1438 + 1 + 7 + 2 + 8 + 0 + 0 + 4 + 4 + 0 + 7 + VRGTDWH + TRGRDAH + RG D H + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 5 + Query_5 + M_3322 + 9 + + + 1 + gnl|BL_ORD_ID|2185 + 190466|large surface antigen|CAL29876.1|Hepatitis B virus|10407 + 2185 + 15 + + + 1 + 12.6974 + 21 + 30.2729 + 1 + 5 + 2 + 6 + 0 + 0 + 4 + 4 + 0 + 5 + GFHPD + GFFPD + GF PD + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 6 + Query_6 + M_3323 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 7 + Query_7 + M_3324 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 8 + Query_8 + M_3325 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 9 + Query_9 + M_3326 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 10 + Query_10 + M_3327 + 9 + + + 1 + gnl|BL_ORD_ID|1781 + 156550|E3 ubiquitin-protein ligase Mdm2|Q00987.1|Homo sapiens|9606 + 1781 + 9 + + + 1 + 12.6974 + 21 + 30.3534 + 1 + 9 + 1 + 9 + 0 + 0 + 4 + 7 + 0 + 9 + MLFFRTRYI + VLFYLGQYI + +LF+ +YI + + + + + 2 + gnl|BL_ORD_ID|608 + 37254|||| + 608 + 9 + + + 1 + 12.3122 + 20 + 62.655 + 1 + 9 + 1 + 9 + 0 + 0 + 4 + 6 + 0 + 9 + MLFFRTRYI + LLFGYPRYV + +LF RY+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 11 + Query_11 + M_3328 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 12 + Query_12 + M_3329 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 13 + Query_13 + M_3330 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 14 + Query_14 + M_3331 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 15 + Query_15 + M_3332 + 9 + + + 1 + gnl|BL_ORD_ID|1871 + 180488|polyprotein|AGO67248.1|Dengue virus 2|11060 + 1871 + 10 + + + 1 + 13.0826 + 22 + 16.3922 + 3 + 8 + 1 + 6 + 0 + 0 + 4 + 4 + 0 + 6 + GSGHSE + GPGHEE + G GH E + + + + + 2 + gnl|BL_ORD_ID|657 + 38974|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 + 657 + 11 + + + 1 + 12.3122 + 20 + 38.8163 + 1 + 9 + 2 + 10 + 0 + 0 + 4 + 7 + 0 + 9 + RRGSGHSEY + QRGPQYSEH + +RG +SE+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 16 + Query_16 + M_3333 + 9 + + + 1 + gnl|BL_ORD_ID|1186 + 93431|pre-C/C protein|ABY54138.1|Hepatitis B virus|10407 + 1186 + 20 + + + 1 + 8.84543 + 11 + 2528.11 + 2 + 8 + 6 + 12 + 0 + 0 + 3 + 4 + 0 + 7 + ICGHIFC + LCLIISC + +C I C + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 17 + Query_17 + M_3334 + 9 + + + 1 + gnl|BL_ORD_ID|573 + 36062|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 + 573 + 20 + + + 1 + 13.0826 + 22 + 15.1234 + 2 + 8 + 13 + 19 + 0 + 0 + 3 + 4 + 0 + 7 + IAPLNQW + LTPLRDW + + PL W + + + + + 2 + gnl|BL_ORD_ID|996 + 65654|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 + 996 + 15 + + + 1 + 12.3122 + 20 + 41.8446 + 3 + 9 + 1 + 7 + 0 + 0 + 3 + 3 + 0 + 7 + APLNQWV + TPLRDWA + PL W + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 18 + Query_18 + M_3335 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 19 + Query_19 + M_3336 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 20 + Query_20 + M_3337 + 9 + + + 1 + gnl|BL_ORD_ID|1610 + 143728|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 + 1610 + 9 + + + 1 + 14.2382 + 25 + 3.00197 + 3 + 9 + 1 + 7 + 0 + 0 + 4 + 6 + 0 + 7 + VPWNSYV + LPWYSYL + +PW SY+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 21 + Query_21 + M_3338 + 9 + + + 1 + gnl|BL_ORD_ID|1610 + 143728|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 + 1610 + 9 + + + 1 + 14.2382 + 25 + 3.05306 + 1 + 7 + 1 + 7 + 0 + 0 + 4 + 6 + 0 + 7 + VPWNSYV + LPWYSYL + +PW SY+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + 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+ + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 28 + Query_28 + M_3345 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 29 + Query_29 + M_3346 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 30 + Query_30 + M_3347 + 9 + + + 1 + gnl|BL_ORD_ID|1621 + 145860|Protein E6|P04019.1|Human papillomavirus type 11|10580 + 1621 + 9 + + + 1 + 11.1566 + 17 + 208.544 + 1 + 7 + 2 + 8 + 0 + 0 + 4 + 5 + 0 + 7 + ILIACRL + VLIRCYL + +LI C L + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 31 + Query_31 + M_3348 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 32 + Query_32 + M_3349 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 33 + Query_33 + M_3350 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 34 + Query_34 + M_3351 + 9 + + + 1 + gnl|BL_ORD_ID|1924 + 180726|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 + 1924 + 15 + + + 1 + 15.0086 + 27 + 1.14188 + 4 + 9 + 10 + 15 + 0 + 0 + 5 + 5 + 0 + 6 + WSFGSL + WDFGSL + W FGSL + + + + + 2 + gnl|BL_ORD_ID|1095 + 72301|envelope protein|YP_001527880.1|West Nile virus NY-99|10000971 + 1095 + 18 + + + 1 + 13.4678 + 23 + 7.53558 + 4 + 9 + 1 + 6 + 0 + 0 + 4 + 5 + 0 + 6 + WSFGSL + WDFGSV + W FGS+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 35 + Query_35 + M_3352 + 9 + + + 1 + gnl|BL_ORD_ID|1397 + 110401|Protein E6|P03126.1|Human papillomavirus type 16|333760 + 1397 + 25 + + + 1 + 14.2382 + 25 + 3.81797 + 1 + 6 + 20 + 25 + 0 + 0 + 4 + 5 + 0 + 6 + NPEAMC + NPYAVC + NP A+C + + + + + 2 + gnl|BL_ORD_ID|1400 + 110467|Protein E6|P03126.1|Human papillomavirus type 16|333760 + 1400 + 25 + + + 1 + 14.2382 + 25 + 3.88133 + 1 + 6 + 5 + 10 + 0 + 0 + 4 + 5 + 0 + 6 + NPEAMC + NPYAVC + NP A+C + + + + + 3 + gnl|BL_ORD_ID|1387 + 110227|Protein E6|P03126.1|Human papillomavirus type 16|333760 + 1387 + 33 + + + 1 + 14.2382 + 25 + 4.76191 + 1 + 6 + 12 + 17 + 0 + 0 + 4 + 5 + 0 + 6 + NPEAMC + NPYAVC + NP A+C + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 36 + Query_36 + M_3353 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 37 + Query_37 + M_3354 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 38 + Query_38 + M_3355 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 39 + Query_39 + M_3356 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 40 + Query_40 + M_3357 + 9 + + + 1 + gnl|BL_ORD_ID|691 + 42094|telomer length regulation protein TEL1|EDV12172.1|Saccharomyces cerevisiae|4932 + 691 + 9 + + + 1 + 13.0826 + 22 + 15.4875 + 1 + 6 + 4 + 9 + 0 + 0 + 4 + 5 + 0 + 6 + GYIHYV + GYLQYV + GY+ YV + + + + + 2 + gnl|BL_ORD_ID|579 + 36358|ELAV-like protein 1|Q15717.2|Homo sapiens|9606 + 579 + 9 + + + 1 + 12.3122 + 20 + 53.0441 + 1 + 6 + 4 + 9 + 0 + 0 + 3 + 6 + 0 + 6 + GYIHYV + GFVNYV + G+++YV + + + + + 3 + gnl|BL_ORD_ID|578 + 36357|ELAV-like protein 4 (Paraneoplastic encephalomyelitis antigen HuD) (Hu-antigen D)|P26378.1|Homo sapiens|9606 + 578 + 9 + + + 1 + 11.927 + 19 + 109.216 + 1 + 6 + 4 + 9 + 0 + 0 + 2 + 6 + 0 + 6 + GYIHYV + GFVNYI + G+++Y+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 41 + Query_41 + M_3358 + 9 + + + 1 + gnl|BL_ORD_ID|691 + 42094|telomer length regulation protein TEL1|EDV12172.1|Saccharomyces cerevisiae|4932 + 691 + 9 + + + 1 + 13.0826 + 22 + 15.4875 + 1 + 6 + 4 + 9 + 0 + 0 + 4 + 5 + 0 + 6 + GYIHYV + GYLQYV + GY+ YV + + + + + 2 + gnl|BL_ORD_ID|579 + 36358|ELAV-like protein 1|Q15717.2|Homo sapiens|9606 + 579 + 9 + + + 1 + 12.3122 + 20 + 53.0441 + 1 + 6 + 4 + 9 + 0 + 0 + 3 + 6 + 0 + 6 + GYIHYV + GFVNYV + G+++YV + + + + + 3 + gnl|BL_ORD_ID|578 + 36357|ELAV-like protein 4 (Paraneoplastic encephalomyelitis antigen HuD) (Hu-antigen D)|P26378.1|Homo sapiens|9606 + 578 + 9 + + + 1 + 11.927 + 19 + 109.216 + 1 + 6 + 4 + 9 + 0 + 0 + 2 + 6 + 0 + 6 + GYIHYV + GFVNYI + G+++Y+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 42 + Query_42 + M_3359 + 9 + + + 1 + gnl|BL_ORD_ID|691 + 42094|telomer length regulation protein TEL1|EDV12172.1|Saccharomyces cerevisiae|4932 + 691 + 9 + + + 1 + 13.0826 + 22 + 14.7007 + 2 + 7 + 4 + 9 + 0 + 0 + 4 + 5 + 0 + 6 + GYIHYV + GYLQYV + GY+ YV + + + + + 2 + gnl|BL_ORD_ID|579 + 36358|ELAV-like protein 1|Q15717.2|Homo sapiens|9606 + 579 + 9 + + + 1 + 12.3122 + 20 + 51.2985 + 2 + 7 + 4 + 9 + 0 + 0 + 3 + 6 + 0 + 6 + GYIHYV + GFVNYV + G+++YV + + + + + 3 + gnl|BL_ORD_ID|389 + 23807|tax|AAG48731.1|Human T-lymphotropic virus 2|11909 + 389 + 23 + + + 1 + 11.927 + 19 + 72.4855 + 2 + 8 + 12 + 18 + 0 + 0 + 5 + 5 + 0 + 7 + GYIHYVF + GYPVYVF + GY YVF + + + + + 4 + gnl|BL_ORD_ID|578 + 36357|ELAV-like protein 4 (Paraneoplastic encephalomyelitis antigen HuD) (Hu-antigen D)|P26378.1|Homo sapiens|9606 + 578 + 9 + + + 1 + 11.927 + 19 + 104.062 + 2 + 7 + 4 + 9 + 0 + 0 + 2 + 6 + 0 + 6 + GYIHYV + GFVNYI + G+++Y+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 43 + Query_43 + M_3360 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 44 + Query_44 + M_3361 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 45 + Query_45 + M_3362 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 46 + Query_46 + M_3363 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 47 + Query_47 + M_3364 + 9 + + + 1 + gnl|BL_ORD_ID|374 + 23224|polyprotein|BAB18806.1|Hepatitis C virus|11103 + 374 + 15 + + + 1 + 13.853 + 24 + 6.75013 + 1 + 9 + 4 + 12 + 0 + 0 + 5 + 6 + 0 + 9 + LLPPQDPHL + LLPRRGPRL + LLP + P L + + + + + 2 + gnl|BL_ORD_ID|1950 + 181035|||| + 1950 + 44 + + + 1 + 13.4678 + 23 + 10.7201 + 1 + 9 + 25 + 33 + 0 + 0 + 5 + 6 + 0 + 9 + LLPPQDPHL + LLPRRGPRL + LLP + P L + + + + + 3 + gnl|BL_ORD_ID|1130 + 74798|polyprotein|BAA03375.1|Hepatitis C virus|11103 + 1130 + 10 + + + 1 + 13.0826 + 22 + 16.3922 + 1 + 9 + 2 + 10 + 0 + 0 + 5 + 6 + 0 + 9 + LLPPQDPHL + LLPRRGPRL + LLP + P L + + + + + 4 + gnl|BL_ORD_ID|630 + 37685|polyprotein|BAA03375.1|Hepatitis C virus|11103 + 630 + 9 + + + 1 + 13.0826 + 22 + 18.1053 + 1 + 9 + 1 + 9 + 0 + 0 + 5 + 6 + 0 + 9 + LLPPQDPHL + LLPRRGPRL + LLP + P L + + + + + 5 + gnl|BL_ORD_ID|1508 + 139406|polyprotein|ACT37184.1|Hepatitis C virus|11103 + 1508 + 10 + + + 1 + 10.7714 + 16 + 299.259 + 1 + 9 + 2 + 10 + 0 + 0 + 5 + 5 + 0 + 9 + LLPPQDPHL + LLPRPGPRL + LLP P L + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 48 + Query_48 + M_3365 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 49 + Query_49 + M_3366 + 9 + + + 1 + gnl|BL_ORD_ID|2183 + 190443|core protein|BAF42671.1|Hepatitis B virus|10407 + 2183 + 9 + + + 1 + 10.7714 + 16 + 370.892 + 1 + 8 + 1 + 8 + 0 + 0 + 3 + 4 + 0 + 8 + HVDPGTIG + HISCLTFG + H+ T G + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 50 + Query_50 + M_3367 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 51 + Query_51 + M_3368 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 52 + Query_52 + M_3369 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 53 + Query_53 + M_3370 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 54 + Query_54 + M_3371 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 55 + Query_55 + M_3372 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 56 + Query_56 + M_3373 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 57 + Query_57 + M_3374 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 58 + Query_58 + M_3375 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 59 + Query_59 + M_3376 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 60 + Query_60 + M_3377 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 61 + Query_61 + M_3378 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 62 + Query_62 + M_3379 + 9 + + + 1 + gnl|BL_ORD_ID|1038 + 69435|Genome polyprotein|SRC279960|Hepatitis C virus (isolate H77)|63746 + 1038 + 9 + + + 1 + 13.4678 + 23 + 11.5219 + 1 + 8 + 1 + 8 + 0 + 0 + 4 + 5 + 0 + 8 + VLDKARVW + VLDSFKTW + VLD + W + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 63 + Query_63 + M_3380 + 9 + + + 1 + gnl|BL_ORD_ID|376 + 23288|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 + 376 + 15 + + + 1 + 14.2382 + 25 + 3.37317 + 1 + 9 + 6 + 14 + 0 + 0 + 3 + 7 + 0 + 9 + CYEEYRGRL + VYQDWLGRM + Y+++ GR+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 64 + Query_64 + M_3381 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 65 + Query_65 + M_3382 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 66 + Query_66 + M_3383 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 67 + Query_67 + M_3384 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 68 + Query_68 + M_3385 + 9 + + + 1 + gnl|BL_ORD_ID|1672 + 148397|Dense granule protein 3|B6KEU8.2|Toxoplasma gondii|5811 + 1672 + 9 + + + 1 + 11.927 + 19 + 76.3762 + 3 + 9 + 2 + 8 + 0 + 0 + 4 + 5 + 0 + 7 + PFFFFLL + PFVVFLV + PF FL+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 69 + Query_69 + M_3386 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 70 + Query_70 + M_3387 + 9 + + + 1 + gnl|BL_ORD_ID|228 + 16753|Pre-S/S protein|AAR99337.1|Hepatitis B virus|10407 + 228 + 9 + + + 1 + 13.0826 + 22 + 18.4218 + 3 + 9 + 1 + 7 + 0 + 0 + 5 + 6 + 0 + 7 + FLLDKVL + FLLTKIL + FLL K+L + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 71 + Query_71 + M_3388 + 9 + + + 1 + gnl|BL_ORD_ID|228 + 16753|Pre-S/S protein|AAR99337.1|Hepatitis B virus|10407 + 228 + 9 + + + 1 + 13.853 + 24 + 7.07804 + 1 + 8 + 1 + 8 + 0 + 0 + 5 + 6 + 0 + 8 + FLLDKVLA + FLLTKILT + FLL K+L + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 72 + Query_72 + M_3389 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 73 + Query_73 + M_3390 + 9 + + + 1 + gnl|BL_ORD_ID|350 + 21780|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 + 350 + 9 + + + 1 + 13.0826 + 22 + 17.4884 + 1 + 8 + 1 + 8 + 0 + 0 + 5 + 5 + 0 + 8 + APSWRGLA + GPSLIGLA + PS GLA + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 74 + Query_74 + M_3391 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 75 + Query_75 + M_3392 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 76 + Query_76 + M_3393 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 77 + Query_77 + M_3394 + 9 + + + 1 + gnl|BL_ORD_ID|899 + 59153|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 + 899 + 15 + + + 1 + 17.705 + 34 + 0.120504 + 2 + 9 + 7 + 14 + 0 + 0 + 5 + 7 + 0 + 8 + PGQVNRTA + PGEINRVA + PG++NR A + + + + + 2 + gnl|BL_ORD_ID|925 + 60059|Genome polyprotein|P27958.3|Hepatitis C virus genotype 1|41856 + 925 + 10 + + + 1 + 17.3198 + 33 + 0.174505 + 2 + 9 + 2 + 9 + 0 + 0 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gnl|BL_ORD_ID|472 + 28657|gag protein|CAB00235.1|Human immunodeficiency virus 1|11676 + 472 + 9 + + + 1 + 11.927 + 19 + 107.472 + 2 + 8 + 3 + 9 + 0 + 0 + 4 + 4 + 0 + 7 + PRKAWAW + PRTLNAW + PR AW + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 84 + Query_84 + M_3401 + 9 + + + 1 + gnl|BL_ORD_ID|2088 + 185491|polyprotein|AGO67248.1|Dengue virus 2|11060 + 2088 + 10 + + + 1 + 11.1566 + 17 + 205.223 + 4 + 9 + 1 + 6 + 0 + 0 + 4 + 6 + 0 + 6 + KREEEK + RREEEE + +REEE+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 85 + Query_85 + M_3402 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 86 + Query_86 + M_3403 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 87 + Query_87 + M_3404 + 9 + + + 1 + gnl|BL_ORD_ID|1944 + 180818|Membrane glycoprotein precursor|NP_739582.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 + 1944 + 15 + + + 1 + 13.0826 + 22 + 12.5116 + 4 + 8 + 7 + 11 + 0 + 0 + 4 + 5 + 0 + 5 + GFTML + GFTMM + GFTM+ + + + + + 2 + gnl|BL_ORD_ID|1686 + 149052|E1 protein|NP_751920.1|Hepatitis C virus (isolate H77)|63746 + 1686 + 18 + + + 1 + 13.0826 + 22 + 15.2048 + 1 + 8 + 1 + 8 + 0 + 0 + 4 + 7 + 0 + 8 + GLAGFTML + GIAYFSMV + G+A F+M+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 88 + Query_88 + M_3405 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 89 + Query_89 + M_3406 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 90 + Query_90 + M_3407 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 91 + Query_91 + M_3408 + 9 + + + 1 + gnl|BL_ORD_ID|1486 + 135263|hemagglutinin|ACX31970.1|Influenza A virus (A/Bar-headed Goose/Qinghai/61/05(H5N1))|336238 + 1486 + 10 + + + 1 + 14.2382 + 25 + 2.71312 + 3 + 9 + 4 + 10 + 0 + 0 + 4 + 5 + 0 + 7 + QEPTAYV + QNPTTYI + Q PT Y+ + + + + + 2 + gnl|BL_ORD_ID|527 + 32268|hemagglutinin|AAK38298.1|Influenza A virus (A/Bar-headed Goose/Qinghai/61/05(H5N1))|336238 + 527 + 10 + + + 1 + 14.2382 + 25 + 2.71312 + 3 + 9 + 4 + 10 + 0 + 0 + 4 + 5 + 0 + 7 + QEPTAYV + QNPTTYI + Q PT Y+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 92 + Query_92 + M_3409 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 93 + Query_93 + M_3410 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 94 + Query_94 + M_3411 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 95 + Query_95 + M_3412 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 96 + Query_96 + M_3413 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 97 + Query_97 + M_3414 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 98 + Query_98 + M_3415 + 9 + + + 1 + gnl|BL_ORD_ID|1 + 118|envelope glycoprotein|ABS76372.1|Human immunodeficiency virus 1|11676 + 1 + 20 + + + 1 + 14.6234 + 26 + 1.57628 + 1 + 7 + 10 + 16 + 0 + 0 + 5 + 6 + 0 + 7 + YLGVPVF + YYGVPVW + Y GVPV+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 99 + Query_99 + M_3416 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 100 + Query_100 + M_3417 + 9 + + + 1 + gnl|BL_ORD_ID|1995 + 183598|polyprotein|AGW21594.1|Dengue virus 1|11053 + 1995 + 10 + + + 1 + 13.853 + 24 + 5.02829 + 4 + 9 + 1 + 6 + 0 + 0 + 5 + 5 + 0 + 6 + HTGSGK + HPGSGK + H GSGK + + + + + 2 + gnl|BL_ORD_ID|386 + 23621|Genome polyprotein|P26664.3|Hepatitis C virus (isolate 1)|11104 + 386 + 11 + + + 1 + 13.0826 + 22 + 16.0488 + 4 + 9 + 1 + 6 + 0 + 0 + 4 + 5 + 0 + 6 + HTGSGK + HDGAGK + H G+GK + + + + + 3 + gnl|BL_ORD_ID|385 + 23620|Genome polyprotein|SRC279960|Hepatitis C virus genotype 1|41856 + 385 + 10 + + + 1 + 13.0826 + 22 + 17.5659 + 4 + 9 + 1 + 6 + 0 + 0 + 4 + 5 + 0 + 6 + HTGSGK + HDGAGK + H G+GK + + + + + 4 + gnl|BL_ORD_ID|384 + 23619|Genome polyprotein|P27958.3|Hepatitis C virus (isolate H)|11108 + 384 + 9 + + + 1 + 13.0826 + 22 + 20.4374 + 4 + 9 + 1 + 6 + 0 + 0 + 4 + 5 + 0 + 6 + HTGSGK + HDGAGK + H G+GK + + + + + 5 + gnl|BL_ORD_ID|1874 + 180503|polyprotein|AGO67248.1|Dengue virus 2|11060 + 1874 + 10 + + + 1 + 12.6974 + 21 + 23.1358 + 4 + 9 + 1 + 6 + 0 + 0 + 4 + 5 + 0 + 6 + HTGSGK + HPGAGK + H G+GK + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 101 + Query_101 + M_3418 + 9 + + + 1 + gnl|BL_ORD_ID|1106 + 72928|Genome polyprotein|P26662.3|Hepatitis C virus (isolate Japanese)|11116 + 1106 + 10 + + + 1 + 14.6234 + 26 + 1.61671 + 1 + 7 + 1 + 7 + 0 + 0 + 6 + 6 + 0 + 7 + LPAPPGA + WPAPPGA + PAPPGA + + + + + 2 + gnl|BL_ORD_ID|1187 + 93536|core protein|AAL31859.1|Hepatitis B virus|10407 + 1187 + 11 + + + 1 + 11.1566 + 17 + 185.696 + 4 + 8 + 5 + 9 + 0 + 0 + 4 + 4 + 0 + 5 + PPGAP + PPNAP + PP AP + + + + + 3 + gnl|BL_ORD_ID|1831 + 179823|cell surface protein (associated with virulence)|NP_302372.1|Mycobacterium leprae TN|272631 + 1831 + 9 + + + 1 + 10.7714 + 16 + 339.179 + 1 + 8 + 1 + 8 + 0 + 0 + 4 + 5 + 0 + 8 + LPAPPGAP + IPASVSAP + +PA AP + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 102 + Query_102 + M_3419 + 9 + + + 1 + gnl|BL_ORD_ID|1008 + 66798|glycoprotein gp35/37|AAC59622.1|Human gammaherpesvirus 8|37296 + 1008 + 15 + + + 1 + 12.6974 + 21 + 22.1438 + 1 + 7 + 2 + 8 + 0 + 0 + 4 + 4 + 0 + 7 + VRGTDWH + TRGRDAH + RG D H + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 103 + Query_103 + M_3420 + 9 + + + 1 + gnl|BL_ORD_ID|320 + 21000|glutamine synthetase GLNA1 (glutamine synthase) (GS-I)|NP_216736.1|Mycobacterium tuberculosis|1773 + 320 + 9 + + + 1 + 13.853 + 24 + 6.71897 + 3 + 7 + 4 + 8 + 0 + 0 + 4 + 5 + 0 + 5 + HHSPS + HHAPS + HH+PS + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 104 + Query_104 + M_3421 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 105 + Query_105 + M_3422 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 106 + Query_106 + M_3423 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 107 + Query_107 + M_3424 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 108 + Query_108 + M_3425 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 109 + Query_109 + M_3426 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 110 + Query_110 + M_3427 + 9 + + + 1 + gnl|BL_ORD_ID|1827 + 179766|cell surface protein (associated with virulence)|NP_302372.1|Mycobacterium leprae TN|272631 + 1827 + 9 + + + 1 + 11.927 + 19 + 82.8955 + 2 + 9 + 2 + 9 + 0 + 0 + 4 + 4 + 0 + 8 + PEPPETGV + PLPPSTAT + P PP T + + + + + 2 + gnl|BL_ORD_ID|1068 + 70491|envelope glycoprotein|AAC28452.1|Human immunodeficiency virus 1|11676 + 1068 + 10 + + + 1 + 11.927 + 19 + 85.0569 + 2 + 7 + 5 + 10 + 0 + 0 + 4 + 4 + 0 + 6 + PEPPET + PNPPEV + P PPE + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 111 + Query_111 + M_3428 + 9 + + + 1 + gnl|BL_ORD_ID|1871 + 180488|polyprotein|AGO67248.1|Dengue virus 2|11060 + 1871 + 10 + + + 1 + 13.0826 + 22 + 16.3922 + 3 + 8 + 1 + 6 + 0 + 0 + 4 + 4 + 0 + 6 + GSGHSE + GPGHEE + G GH E + + + + + 2 + gnl|BL_ORD_ID|657 + 38974|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 + 657 + 11 + + + 1 + 12.3122 + 20 + 38.8163 + 1 + 9 + 2 + 10 + 0 + 0 + 4 + 7 + 0 + 9 + RRGSGHSEY + QRGPQYSEH + +RG +SE+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 112 + Query_112 + M_3429 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 113 + Query_113 + M_3430 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 114 + Query_114 + M_3431 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 115 + Query_115 + M_3432 + 9 + + + 1 + gnl|BL_ORD_ID|1610 + 143728|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 + 1610 + 9 + + + 1 + 14.2382 + 25 + 3.00197 + 3 + 9 + 1 + 7 + 0 + 0 + 4 + 6 + 0 + 7 + VPWNSYV + LPWYSYL + +PW SY+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 116 + Query_116 + M_3433 + 9 + + + 1 + gnl|BL_ORD_ID|1610 + 143728|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 + 1610 + 9 + + + 1 + 14.2382 + 25 + 3.05306 + 1 + 7 + 1 + 7 + 0 + 0 + 4 + 6 + 0 + 7 + VPWNSYV + LPWYSYL + +PW SY+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 117 + Query_117 + M_3434 + 9 + + + 1 + gnl|BL_ORD_ID|1149 + 75636|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 + 1149 + 10 + + + 1 + 11.5418 + 18 + 153.051 + 1 + 8 + 1 + 8 + 0 + 0 + 3 + 5 + 0 + 8 + YQLKLFAC + YRLWHYPC + Y+L + C + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 118 + Query_118 + M_3435 + 9 + + + 1 + gnl|BL_ORD_ID|1149 + 75636|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 + 1149 + 10 + + + 1 + 11.5418 + 18 + 153.051 + 1 + 8 + 1 + 8 + 0 + 0 + 3 + 5 + 0 + 8 + YQLKLFAC + YRLWHYPC + Y+L + C + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 119 + Query_119 + M_3436 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 120 + Query_120 + M_3437 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 121 + Query_121 + M_3438 + 9 + + + 1 + gnl|BL_ORD_ID|872 + 57361|Genome polyprotein|SRC279960|Hepatitis C virus (isolate H77)|63746 + 872 + 11 + + + 1 + 12.6974 + 21 + 28.2065 + 3 + 8 + 1 + 6 + 0 + 0 + 4 + 4 + 0 + 6 + SSCCQP + SECCTP + S CC P + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 122 + Query_122 + M_3439 + 9 + + + 1 + gnl|BL_ORD_ID|664 + 39591|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 + 664 + 20 + + + 1 + 10.3862 + 15 + 495.983 + 1 + 7 + 11 + 17 + 0 + 0 + 3 + 4 + 0 + 7 + WLLEWTE + WCLWWLQ + W L W + + + + + + 2 + gnl|BL_ORD_ID|1092 + 72233|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 + 1092 + 15 + + + 1 + 10.001 + 14 + 852.012 + 1 + 5 + 1 + 5 + 0 + 0 + 2 + 4 + 0 + 5 + WLLEW + WAIKW + W ++W + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 123 + Query_123 + M_3440 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 124 + Query_124 + M_3441 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 125 + Query_125 + M_3442 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 126 + Query_126 + M_3443 + 9 + + + 1 + gnl|BL_ORD_ID|1910 + 180662|polyprotein|CDF77361.1|Dengue virus 3|11069 + 1910 + 10 + + + 1 + 13.0826 + 22 + 22.3554 + 1 + 6 + 3 + 8 + 0 + 0 + 4 + 6 + 0 + 6 + ILPATI + MLPATL + +LPAT+ + + + + + 2 + gnl|BL_ORD_ID|1853 + 180390|polyprotein|CDF77361.1|Dengue virus 3|11069 + 1853 + 10 + + + 1 + 12.6974 + 21 + 22.7423 + 1 + 6 + 5 + 10 + 0 + 0 + 4 + 6 + 0 + 6 + ILPATI + MLPATL + +LPAT+ + + + + + 3 + gnl|BL_ORD_ID|1894 + 180609|polyprotein|ABK30845.1|Dengue virus 3|11069 + 1894 + 9 + + + 1 + 12.6974 + 21 + 24.2855 + 1 + 6 + 4 + 9 + 0 + 0 + 4 + 6 + 0 + 6 + ILPATI + MLPATL + +LPAT+ + + + + + 4 + gnl|BL_ORD_ID|1909 + 180660|polyprotein|CDF77361.1|Dengue virus 3|11069 + 1909 + 9 + + + 1 + 12.6974 + 21 + 24.707 + 1 + 6 + 2 + 7 + 0 + 0 + 4 + 6 + 0 + 6 + ILPATI + MLPATL + +LPAT+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 127 + Query_127 + M_3444 + 9 + + + 1 + gnl|BL_ORD_ID|1910 + 180662|polyprotein|CDF77361.1|Dengue virus 3|11069 + 1910 + 10 + + + 1 + 13.0826 + 22 + 20.1646 + 2 + 7 + 3 + 8 + 0 + 0 + 4 + 6 + 0 + 6 + ILPATI + MLPATL + +LPAT+ + + + + + 2 + gnl|BL_ORD_ID|1853 + 180390|polyprotein|CDF77361.1|Dengue virus 3|11069 + 1853 + 10 + + + 1 + 13.0826 + 22 + 21.6006 + 2 + 7 + 5 + 10 + 0 + 0 + 4 + 6 + 0 + 6 + ILPATI + MLPATL + +LPAT+ + + + + + 3 + gnl|BL_ORD_ID|1909 + 180660|polyprotein|CDF77361.1|Dengue virus 3|11069 + 1909 + 9 + + + 1 + 13.0826 + 22 + 21.8994 + 2 + 7 + 2 + 7 + 0 + 0 + 4 + 6 + 0 + 6 + ILPATI + MLPATL + +LPAT+ + + + + + 4 + gnl|BL_ORD_ID|1894 + 180609|polyprotein|ABK30845.1|Dengue virus 3|11069 + 1894 + 9 + + + 1 + 13.0826 + 22 + 22.2806 + 2 + 7 + 4 + 9 + 0 + 0 + 4 + 6 + 0 + 6 + ILPATI + MLPATL + +LPAT+ + + + + + 5 + gnl|BL_ORD_ID|983 + 64948|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 + 983 + 9 + + + 1 + 11.927 + 19 + 104.062 + 1 + 9 + 1 + 9 + 0 + 0 + 5 + 7 + 0 + 9 + TILPATILV + TLLYATVEV + T+L AT+ V + + + + + 6 + gnl|BL_ORD_ID|6 + 449|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 + 6 + 10 + + + 1 + 11.5418 + 18 + 157.893 + 1 + 7 + 4 + 10 + 0 + 0 + 4 + 6 + 0 + 7 + TILPATI + TLLYATV + T+L AT+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 128 + Query_128 + M_3445 + 9 + + + 1 + gnl|BL_ORD_ID|1924 + 180726|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 + 1924 + 15 + + + 1 + 15.0086 + 27 + 1.14188 + 4 + 9 + 10 + 15 + 0 + 0 + 5 + 5 + 0 + 6 + WSFGSL + WDFGSL + W FGSL + + + + + 2 + gnl|BL_ORD_ID|1095 + 72301|envelope protein|YP_001527880.1|West Nile virus NY-99|10000971 + 1095 + 18 + + + 1 + 13.4678 + 23 + 7.53558 + 4 + 9 + 1 + 6 + 0 + 0 + 4 + 5 + 0 + 6 + WSFGSL + WDFGSV + W FGS+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 129 + Query_129 + M_3446 + 9 + + + 1 + gnl|BL_ORD_ID|1397 + 110401|Protein E6|P03126.1|Human papillomavirus type 16|333760 + 1397 + 25 + + + 1 + 14.2382 + 25 + 3.81797 + 1 + 6 + 20 + 25 + 0 + 0 + 4 + 5 + 0 + 6 + NPEAMC + NPYAVC + NP A+C + + + + + 2 + gnl|BL_ORD_ID|1400 + 110467|Protein E6|P03126.1|Human papillomavirus type 16|333760 + 1400 + 25 + + + 1 + 14.2382 + 25 + 3.88133 + 1 + 6 + 5 + 10 + 0 + 0 + 4 + 5 + 0 + 6 + NPEAMC + NPYAVC + NP A+C + + + + + 3 + gnl|BL_ORD_ID|1387 + 110227|Protein E6|P03126.1|Human papillomavirus type 16|333760 + 1387 + 33 + + + 1 + 14.2382 + 25 + 4.76191 + 1 + 6 + 12 + 17 + 0 + 0 + 4 + 5 + 0 + 6 + NPEAMC + NPYAVC + NP A+C + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 130 + Query_130 + M_3447 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 131 + Query_131 + M_3448 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 132 + Query_132 + M_3449 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 133 + Query_133 + M_3450 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 134 + Query_134 + M_3451 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 135 + Query_135 + M_3452 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 136 + Query_136 + M_3453 + 9 + + + 1 + gnl|BL_ORD_ID|374 + 23224|polyprotein|BAB18806.1|Hepatitis C virus|11103 + 374 + 15 + + + 1 + 13.853 + 24 + 6.75013 + 1 + 9 + 4 + 12 + 0 + 0 + 5 + 6 + 0 + 9 + LLPPQDPHL + LLPRRGPRL + LLP + P L + + + + + 2 + gnl|BL_ORD_ID|1950 + 181035|||| + 1950 + 44 + + + 1 + 13.4678 + 23 + 10.7201 + 1 + 9 + 25 + 33 + 0 + 0 + 5 + 6 + 0 + 9 + LLPPQDPHL + LLPRRGPRL + LLP + P L + + + + + 3 + gnl|BL_ORD_ID|1130 + 74798|polyprotein|BAA03375.1|Hepatitis C virus|11103 + 1130 + 10 + + + 1 + 13.0826 + 22 + 16.3922 + 1 + 9 + 2 + 10 + 0 + 0 + 5 + 6 + 0 + 9 + LLPPQDPHL + LLPRRGPRL + LLP + P L + + + + + 4 + gnl|BL_ORD_ID|630 + 37685|polyprotein|BAA03375.1|Hepatitis C virus|11103 + 630 + 9 + + + 1 + 13.0826 + 22 + 18.1053 + 1 + 9 + 1 + 9 + 0 + 0 + 5 + 6 + 0 + 9 + LLPPQDPHL + LLPRRGPRL + LLP + P L + + + + + 5 + gnl|BL_ORD_ID|1508 + 139406|polyprotein|ACT37184.1|Hepatitis C virus|11103 + 1508 + 10 + + + 1 + 10.7714 + 16 + 299.259 + 1 + 9 + 2 + 10 + 0 + 0 + 5 + 5 + 0 + 9 + LLPPQDPHL + LLPRPGPRL + LLP P L + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 137 + Query_137 + M_3454 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 138 + Query_138 + M_3455 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 139 + Query_139 + M_3456 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 140 + Query_140 + M_3457 + 9 + + + 1 + gnl|BL_ORD_ID|241 + 16836|precore/core protein [Hepatitis B virus]|AAR03815.1|Hepatitis B virus|10407 + 241 + 10 + + + 1 + 10.3862 + 15 + 506.338 + 2 + 9 + 2 + 9 + 0 + 0 + 4 + 4 + 0 + 8 + LPEVQLPK + LPSDFLPS + LP LP + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 141 + Query_141 + M_3458 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 142 + Query_142 + M_3459 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 143 + Query_143 + M_3460 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 144 + Query_144 + M_3461 + 9 + + + 1 + gnl|BL_ORD_ID|1038 + 69435|Genome polyprotein|SRC279960|Hepatitis C virus (isolate H77)|63746 + 1038 + 9 + + + 1 + 13.4678 + 23 + 11.5219 + 1 + 8 + 1 + 8 + 0 + 0 + 4 + 5 + 0 + 8 + VLDKARVW + VLDSFKTW + VLD + W + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 145 + Query_145 + M_3462 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 146 + Query_146 + M_3463 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 147 + Query_147 + M_3464 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 148 + Query_148 + M_3465 + 9 + + + 1 + gnl|BL_ORD_ID|350 + 21780|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 + 350 + 9 + + + 1 + 13.0826 + 22 + 17.4884 + 1 + 8 + 1 + 8 + 0 + 0 + 5 + 5 + 0 + 8 + APSWRGLA + GPSLIGLA + PS GLA + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 149 + Query_149 + M_3466 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 150 + Query_150 + M_3467 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 151 + Query_151 + M_3468 + 9 + + + 1 + gnl|BL_ORD_ID|375 + 23270|polyprotein|AAB67036.1|Hepatitis C virus (isolate H77)|63746 + 375 + 15 + + + 1 + 14.6234 + 26 + 2.2254 + 3 + 8 + 3 + 8 + 0 + 0 + 5 + 6 + 0 + 6 + LAGLYY + LAGLFY + LAGL+Y + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 152 + Query_152 + M_3469 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 153 + Query_153 + M_3470 + 9 + + + 1 + gnl|BL_ORD_ID|1520 + 140600|glutamine synthetase GLNA1 (glutamine synthase) (GS-I)|NP_216736.1|Mycobacterium tuberculosis H37Rv|83332 + 1520 + 9 + + + 1 + 13.0826 + 22 + 18.1053 + 1 + 9 + 1 + 9 + 0 + 0 + 4 + 6 + 0 + 9 + CLWQLKAPV + SLWKDGAPL + LW+ AP+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 154 + Query_154 + M_3471 + 9 + + + 1 + gnl|BL_ORD_ID|1729 + 150534|polyprotein|AGO67248.1|Dengue virus 2|11060 + 1729 + 9 + + + 1 + 12.6974 + 21 + 24.707 + 1 + 6 + 1 + 6 + 0 + 0 + 4 + 4 + 0 + 6 + RPRKAW + RPASAW + RP AW + + + + + 2 + gnl|BL_ORD_ID|928 + 60238|Gag polyprotein|P03347.3|Human immunodeficiency virus 1|11676 + 928 + 9 + + + 1 + 11.927 + 19 + 80.227 + 2 + 9 + 2 + 9 + 0 + 0 + 4 + 4 + 0 + 8 + PRKAWAWC + PRTLNAWV + PR AW + + + + + 3 + gnl|BL_ORD_ID|756 + 50292|gag protein|ACR27140.1|Human immunodeficiency virus 1|11676 + 756 + 11 + + + 1 + 11.927 + 19 + 106.287 + 2 + 8 + 5 + 11 + 0 + 0 + 4 + 4 + 0 + 7 + PRKAWAW + PRTLNAW + PR AW + + + + + 4 + gnl|BL_ORD_ID|472 + 28657|gag protein|CAB00235.1|Human immunodeficiency virus 1|11676 + 472 + 9 + + + 1 + 11.927 + 19 + 107.472 + 2 + 8 + 3 + 9 + 0 + 0 + 4 + 4 + 0 + 7 + PRKAWAW + PRTLNAW + PR AW + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 155 + Query_155 + M_3472 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 156 + Query_156 + M_3473 + 9 + + + 1 + gnl|BL_ORD_ID|2088 + 185491|polyprotein|AGO67248.1|Dengue virus 2|11060 + 2088 + 10 + + + 1 + 11.1566 + 17 + 205.223 + 4 + 9 + 1 + 6 + 0 + 0 + 4 + 6 + 0 + 6 + KREEEK + RREEEE + +REEE+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 157 + Query_157 + M_3474 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 158 + Query_158 + M_3475 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 159 + Query_159 + M_3476 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 160 + Query_160 + M_3477 + 9 + + + 1 + gnl|BL_ORD_ID|1944 + 180818|Membrane glycoprotein precursor|NP_739582.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 + 1944 + 15 + + + 1 + 13.0826 + 22 + 12.5116 + 4 + 8 + 7 + 11 + 0 + 0 + 4 + 5 + 0 + 5 + GFTML + GFTMM + GFTM+ + + + + + 2 + gnl|BL_ORD_ID|1686 + 149052|E1 protein|NP_751920.1|Hepatitis C virus (isolate H77)|63746 + 1686 + 18 + + + 1 + 13.0826 + 22 + 15.2048 + 1 + 8 + 1 + 8 + 0 + 0 + 4 + 7 + 0 + 8 + GLAGFTML + GIAYFSMV + G+A F+M+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 161 + Query_161 + M_3478 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 162 + Query_162 + M_3479 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 163 + Query_163 + M_3480 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 164 + Query_164 + M_3481 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 165 + Query_165 + M_3482 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 166 + Query_166 + M_3483 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 167 + Query_167 + M_3484 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 168 + Query_168 + M_3485 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + + diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134127_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134127_1_T.fasta new file mode 100755 index 00000000..b2113c0f --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134127_1_T.fasta @@ -0,0 +1,108 @@ +>M_3486 +TPCHCTGTL +>M_3487 +TPCHCTGTL +>M_3488 +IPFFGQVHL +>M_3489 +ILMENKSNI +>M_3490 +ILMENKSNI +>M_3491 +LAYLVKKMM +>M_3492 +VTISLAYLV +>M_3493 +LLIESKEEM +>M_3494 +WVGPWHTIV +>M_3495 +WWVGPWHTI +>M_3496 +KTFCGDVEY +>M_3497 +AVMEQINSV +>M_3498 +AVMEQINSV +>M_3499 +HPRINTLGS +>M_3500 +FLVAFIKKI +>M_3501 +FLVAFIKKI +>M_3502 +GIVSWDTFL +>M_3503 +IVSWDTFLV +>M_3504 +SAKLTTLVV +>M_3505 +KLIWHPFSI +>M_3506 +YFDENIQKL +>M_3507 +SPSSGQRST +>M_3508 +SAQNELTEM +>M_3509 +VATNSETAM +>M_3510 +PLWGGIIYI +>M_3511 +YPLWGGIIY +>M_3512 +AALATLHPL +>M_3513 +AALATLHPL +>M_3514 +LATLHPLFL +>M_3515 +GLNMLITAL +>M_3516 +LLTGLNMLI +>M_3517 +LMWLTYTMA +>M_3518 +LTYTMAFMV +>M_3519 +LTYTMAFMV +>M_3520 +MLITALYSL +>M_3521 +NLMWLTYTM +>M_3522 +WLTYTMAFM +>M_3523 +SANTGSSVV +>M_3524 +AMGSGIQPL +>M_3525 +HLLEPGQAM +>M_3526 +TVVGNLGII +>M_3527 +HGKPTLSTV +>M_3528 +LEYNTRNAY +>M_3529 +LLGLTWPVV +>M_3530 +QLLGLTWPV +>M_3531 +RVLFWGHIL +>M_3532 +RVLFWGHIL +>M_3533 +KVFNNGADL +>M_3534 +LAGEWRERL +>M_3535 +MNWRPILTI +>M_3536 +FSDLRSSIV +>M_3537 +FSDLRSSIV +>M_3538 +YFSDLRSSI +>M_3539 +EANFSASRV diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134127_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134127_1_T_iedb.xml new file mode 100755 index 00000000..70b4f12a --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134127_1_T_iedb.xml @@ -0,0 +1,1681 @@ + + + + blastp + BLASTP 2.2.30+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta + Query_1 + M_3486 + 9 + + + BLOSUM62 + 100000000 + 11 + 1 + F + + + + + 1 + Query_1 + M_3486 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 2 + Query_2 + M_3487 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 3 + Query_3 + M_3488 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 4 + Query_4 + M_3489 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 5 + Query_5 + M_3490 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 6 + Query_6 + M_3491 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 7 + Query_7 + M_3492 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 8 + Query_8 + M_3493 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 9 + Query_9 + M_3494 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 10 + Query_10 + M_3495 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 11 + Query_11 + M_3496 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 12 + Query_12 + M_3497 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 13 + Query_13 + M_3498 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 14 + Query_14 + M_3499 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 15 + Query_15 + M_3500 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 16 + Query_16 + M_3501 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 17 + Query_17 + M_3502 + 9 + + + 1 + gnl|BL_ORD_ID|787 + 52666|Antigen 85-B|P0C5B9.1|Mycobacterium tuberculosis|1773 + 787 + 9 + + + 1 + 14.2382 + 25 + 3.10506 + 4 + 9 + 4 + 9 + 0 + 0 + 4 + 5 + 0 + 6 + SWDTFL + KWETFL + W+TFL + + + + + 2 + gnl|BL_ORD_ID|317 + 20929|Circumsporozoite protein precursor|P02893.1|Plasmodium falciparum|5833 + 317 + 9 + + + 1 + 10.3862 + 15 + 712.196 + 1 + 9 + 1 + 9 + 0 + 0 + 3 + 6 + 0 + 9 + GIVSWDTFL + GLIMVLSFL + G++ +FL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 18 + Query_18 + M_3503 + 9 + + + 1 + gnl|BL_ORD_ID|787 + 52666|Antigen 85-B|P0C5B9.1|Mycobacterium tuberculosis|1773 + 787 + 9 + + + 1 + 14.2382 + 25 + 3.05306 + 3 + 8 + 4 + 9 + 0 + 0 + 4 + 5 + 0 + 6 + SWDTFL + KWETFL + W+TFL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 19 + Query_19 + M_3504 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 20 + Query_20 + M_3505 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 21 + Query_21 + M_3506 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 22 + Query_22 + M_3507 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 23 + Query_23 + M_3508 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 24 + Query_24 + M_3509 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 25 + Query_25 + M_3510 + 9 + + + 1 + gnl|BL_ORD_ID|744 + 48321|||| + 744 + 9 + + + 1 + 13.4678 + 23 + 12.57 + 1 + 9 + 1 + 9 + 0 + 0 + 4 + 7 + 0 + 9 + PLWGGIIYI + PLFGYPVYV + PL+G +Y+ + + + + + 2 + gnl|BL_ORD_ID|606 + 37251|||| + 606 + 9 + + + 1 + 11.5418 + 18 + 165.102 + 2 + 9 + 2 + 9 + 0 + 0 + 3 + 6 + 0 + 8 + LWGGIIYI + LFGHPVYV + L+G +Y+ + + + + + 3 + gnl|BL_ORD_ID|607 + 37253|||| + 607 + 9 + + + 1 + 11.1566 + 17 + 202.191 + 2 + 9 + 2 + 9 + 0 + 0 + 3 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16 + 497.585 + 2 + 9 + 1 + 8 + 0 + 0 + 3 + 6 + 0 + 8 + LWGGIIYI + LFGYPVYV + L+G +Y+ + + + + + 9 + gnl|BL_ORD_ID|571 + 35844|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 + 571 + 8 + + + 1 + 10.7714 + 16 + 522.979 + 2 + 9 + 1 + 8 + 0 + 0 + 3 + 6 + 0 + 8 + LWGGIIYI + LFGYPVYV + L+G +Y+ + + + + + 10 + gnl|BL_ORD_ID|610 + 37257|Protein Tax-1|P03409.2|Human T-lymphotropic virus 1|11908 + 610 + 9 + + + 1 + 10.3862 + 15 + 534.993 + 2 + 9 + 2 + 9 + 0 + 0 + 3 + 6 + 0 + 8 + LWGGIIYI + LFGYPVYV + L+G +Y+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 26 + Query_26 + M_3511 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 27 + Query_27 + M_3512 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 28 + Query_28 + M_3513 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 29 + Query_29 + M_3514 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 30 + Query_30 + M_3515 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 31 + Query_31 + M_3516 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 32 + Query_32 + M_3517 + 9 + + + 1 + gnl|BL_ORD_ID|325 + 21041|Membrane glycoprotein|Q692E0|SARS coronavirus TJF|284672 + 325 + 9 + + + 1 + 15.3938 + 28 + 0.807007 + 1 + 6 + 2 + 7 + 0 + 0 + 5 + 6 + 0 + 6 + LMWLTY + LMWLSY + LMWL+Y + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 33 + Query_33 + M_3518 + 9 + + + 1 + gnl|BL_ORD_ID|1162 + 76621|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 + 1162 + 11 + + + 1 + 11.927 + 19 + 70.1482 + 3 + 8 + 2 + 7 + 0 + 0 + 4 + 5 + 0 + 6 + YTMAFM + YTSAFV + YT AF+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 34 + Query_34 + M_3519 + 9 + + + 1 + gnl|BL_ORD_ID|1162 + 76621|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 + 1162 + 11 + + + 1 + 11.927 + 19 + 70.1482 + 3 + 8 + 2 + 7 + 0 + 0 + 4 + 5 + 0 + 6 + YTMAFM + YTSAFV + YT AF+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 35 + Query_35 + M_3520 + 9 + + + 1 + gnl|BL_ORD_ID|1596 + 142232|POSSIBLE CONSERVED TRANSMEMBRANE PROTEIN|CAB00937.1|Mycobacterium tuberculosis|1773 + 1596 + 19 + + + 1 + 7.68983 + 8 + 7255.43 + 6 + 9 + 13 + 16 + 0 + 0 + 1 + 3 + 0 + 4 + LYSL + VYAF + +Y+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 36 + Query_36 + M_3521 + 9 + + + 1 + gnl|BL_ORD_ID|325 + 21041|Membrane glycoprotein|Q692E0|SARS coronavirus TJF|284672 + 325 + 9 + + + 1 + 15.779 + 29 + 0.548509 + 1 + 7 + 1 + 7 + 0 + 0 + 5 + 6 + 0 + 7 + NLMWLTY + GLMWLSY + LMWL+Y + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 37 + Query_37 + M_3522 + 9 + + + 1 + gnl|BL_ORD_ID|1812 + 177647|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 + 1812 + 16 + + + 1 + 12.3122 + 20 + 47.9018 + 1 + 8 + 6 + 13 + 0 + 0 + 3 + 5 + 0 + 8 + WLTYTMAF + WMNRLIAF + W+ +AF + + + + + 2 + gnl|BL_ORD_ID|1162 + 76621|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 + 1162 + 11 + + + 1 + 11.927 + 19 + 65.7443 + 4 + 9 + 2 + 7 + 0 + 0 + 4 + 5 + 0 + 6 + YTMAFM + YTSAFV + YT AF+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 38 + Query_38 + M_3523 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 39 + Query_39 + M_3524 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 40 + Query_40 + M_3525 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 41 + Query_41 + M_3526 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 42 + Query_42 + M_3527 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 43 + Query_43 + M_3528 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 44 + Query_44 + M_3529 + 9 + + + 1 + gnl|BL_ORD_ID|645 + 38427|BZLF1|AAA66529.1|Human gammaherpesvirus 4|10376 + 645 + 9 + + + 1 + 11.5418 + 18 + 132.337 + 6 + 9 + 6 + 9 + 0 + 0 + 3 + 4 + 0 + 4 + WPVV + WPVL + WPV+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 45 + Query_45 + M_3530 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 46 + Query_46 + M_3531 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 47 + Query_47 + M_3532 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 48 + Query_48 + M_3533 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 49 + Query_49 + M_3534 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 50 + Query_50 + M_3535 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 51 + Query_51 + M_3536 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 52 + Query_52 + M_3537 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 53 + Query_53 + M_3538 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 54 + Query_54 + M_3539 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + + diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134510_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134510_1_T.fasta new file mode 100755 index 00000000..9d7ce536 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134510_1_T.fasta @@ -0,0 +1,26 @@ +>M_3540 +TLEGFFESL +>M_3541 +KILKAQEHV +>M_3542 +LLQPTPPAA +>M_3543 +SLQVKRVFV +>M_3544 +FTLEGFFES +>M_3545 +PLLRDVFNV +>M_3546 +AQSEIHFQV +>M_3547 +LQAHSMHEV +>M_3548 +LLLQPTPPA +>M_3549 +SLSFSFPLL +>M_3550 +RVWDIVPTL +>M_3551 +IVMCAMCGV +>M_3552 +AMCGVPFSV diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134510_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134510_1_T_iedb.xml new file mode 100755 index 00000000..32faa078 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134510_1_T_iedb.xml @@ -0,0 +1,615 @@ + + + + blastp + BLASTP 2.2.30+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta + Query_1 + M_3540 + 9 + + + BLOSUM62 + 100000000 + 11 + 1 + F + + + + + 1 + Query_1 + M_3540 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 2 + Query_2 + M_3541 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 3 + Query_3 + M_3542 + 9 + + + 1 + gnl|BL_ORD_ID|1106 + 72928|Genome polyprotein|P26662.3|Hepatitis C virus (isolate Japanese)|11116 + 1106 + 10 + + + 1 + 12.3122 + 20 + 62.4024 + 4 + 9 + 2 + 7 + 0 + 0 + 4 + 4 + 0 + 6 + PTPPAA + PAPPGA + P PP A + + + + + 2 + gnl|BL_ORD_ID|1179 + 79628|E1 protein|BAA19893.1|Rubella virus|11041 + 1179 + 21 + + + 1 + 11.5418 + 18 + 116.985 + 4 + 9 + 14 + 19 + 0 + 0 + 4 + 4 + 0 + 6 + PTPPAA + PTAPCA + PT P A + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 4 + Query_4 + M_3543 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 5 + Query_5 + M_3544 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 6 + Query_6 + M_3545 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 7 + Query_7 + M_3546 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 8 + Query_8 + M_3547 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 9 + Query_9 + M_3548 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 10 + Query_10 + M_3549 + 9 + + + 1 + gnl|BL_ORD_ID|660 + 39339|Nucleocapsid protein|Q89462|Sin Nombre hantavirus|37705 + 660 + 15 + + + 1 + 13.853 + 24 + 7.10896 + 2 + 9 + 1 + 8 + 0 + 0 + 4 + 7 + 0 + 8 + LSFSFPLL + LSFALPII + LSF+ P++ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 11 + Query_11 + M_3550 + 9 + + + 1 + gnl|BL_ORD_ID|538 + 32944|polyprotein|AAW51418.1|Dengue virus 3|11069 + 538 + 9 + + + 1 + 16.9346 + 32 + 0.261971 + 1 + 9 + 1 + 9 + 0 + 0 + 5 + 8 + 0 + 9 + RVWDIVPTL + KPWDVVPTV + + WD+VPT+ + + + + + 2 + gnl|BL_ORD_ID|536 + 32942|Polyprotein|Q9J8D4|Dengue virus 2|11060 + 536 + 9 + + + 1 + 15.779 + 29 + 0.485957 + 1 + 9 + 1 + 9 + 0 + 0 + 4 + 8 + 0 + 9 + RVWDIVPTL + KPWDVLPTV + + WD++PT+ + + + + + 3 + gnl|BL_ORD_ID|1787 + 161186|Nonstructural protein NS5|NP_739590.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 + 1787 + 15 + + + 1 + 15.0086 + 27 + 1.12275 + 3 + 7 + 7 + 11 + 0 + 0 + 4 + 5 + 0 + 5 + WDIVP + WDVVP + WD+VP + + + + + 4 + gnl|BL_ORD_ID|533 + 32939|polyprotein|AAK67712.1|Dengue virus 2|11060 + 533 + 9 + + + 1 + 15.0086 + 27 + 1.17789 + 1 + 9 + 1 + 9 + 0 + 0 + 4 + 7 + 0 + 9 + RVWDIVPTL + KPWDIIPMV + + WDI+P + + + + + + 5 + gnl|BL_ORD_ID|537 + 32943|polyprotein|AAL96681.1|Dengue virus 2|11060 + 537 + 9 + + + 1 + 15.0086 + 27 + 1.45111 + 1 + 9 + 1 + 9 + 0 + 0 + 4 + 7 + 0 + 9 + RVWDIVPTL + KPWDVVPMV + + WD+VP + + + + + + 6 + gnl|BL_ORD_ID|534 + 32940|polyprotein|ABG75765.1|Dengue virus type 1 Hawaii|10000440 + 534 + 9 + + + 1 + 14.2382 + 25 + 2.71372 + 1 + 9 + 1 + 9 + 0 + 0 + 3 + 7 + 0 + 9 + RVWDIVPTL + KPWDVIPMV + + WD++P + + + + + + 7 + gnl|BL_ORD_ID|535 + 32941|DEN polyprotein|AAC40835.1|Dengue virus 2|11060 + 535 + 9 + + + 1 + 13.853 + 24 + 5.95161 + 1 + 9 + 1 + 9 + 0 + 0 + 3 + 7 + 0 + 9 + RVWDIVPTL + KPWDVLPMV + + WD++P + + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 12 + Query_12 + M_3551 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 13 + Query_13 + M_3552 + 9 + + + 1 + gnl|BL_ORD_ID|2182 + 190409|polymerase|AAD16253.1|Hepatitis B virus|10407 + 2182 + 15 + + + 1 + 15.3938 + 28 + 0.658828 + 1 + 8 + 7 + 14 + 0 + 0 + 4 + 6 + 0 + 8 + AMCGVPFS + SFCGSPYS + + CG P+S + + + + + 2 + gnl|BL_ORD_ID|390 + 23864|envelope glycoprotein(gp21, gp46) - human T-cell lymphotropic virus type 1|A45714|Human T-lymphotropic virus 1|11908 + 390 + 9 + + + 1 + 14.6234 + 26 + 2.45448 + 1 + 7 + 3 + 9 + 0 + 0 + 4 + 5 + 0 + 7 + AMCGVPF + SKCGFPF + + CG PF + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + + diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134611_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134611_1_T.fasta new file mode 100755 index 00000000..9830ebcb --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134611_1_T.fasta @@ -0,0 +1,38 @@ +>M_3553 +RQMAARECK +>M_3554 +FLVYQNILK +>M_3555 +FLVYQNILK +>M_3556 +KVERERLEK +>M_3557 +KQIEMLEYK +>M_3558 +KQIEMLEYK +>M_3559 +VVGAVGVGK +>M_3560 +VVGAVGVGK +>M_3561 +FIDTYPPVL +>M_3562 +RSAFPCAHR +>M_3563 +GTPRAATMK +>M_3564 +TMKAKTDLK +>M_3565 +TMKAKTDLK +>M_3566 +GLLFAAIKR +>M_3567 +LLFAAIKRR +>M_3568 +YQIDRDLHK +>M_3569 +QTGEKLMAK +>M_3570 +QTGEKLMAK +>M_3571 +SSNLIAHVR diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134611_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134611_1_T_iedb.xml new file mode 100755 index 00000000..155a1ef3 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134611_1_T_iedb.xml @@ -0,0 +1,403 @@ + + + + blastp + BLASTP 2.2.30+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta + Query_1 + M_3553 + 9 + + + BLOSUM62 + 100000000 + 11 + 1 + F + + + + + 1 + Query_1 + M_3553 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 2 + Query_2 + M_3554 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 3 + Query_3 + M_3555 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 4 + Query_4 + M_3556 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 5 + Query_5 + M_3557 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 6 + Query_6 + M_3558 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 7 + Query_7 + M_3559 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 8 + Query_8 + M_3560 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 9 + Query_9 + M_3561 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 10 + Query_10 + M_3562 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 11 + Query_11 + M_3563 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 12 + Query_12 + M_3564 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 13 + Query_13 + M_3565 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 14 + Query_14 + M_3566 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 15 + Query_15 + M_3567 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 16 + Query_16 + M_3568 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 17 + Query_17 + M_3569 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 18 + Query_18 + M_3570 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 19 + Query_19 + M_3571 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + + diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134702_2_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134702_2_T.fasta new file mode 100755 index 00000000..d6a788c6 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134702_2_T.fasta @@ -0,0 +1,36 @@ +>M_3572 +GEDVDSLAL +>M_3573 +AELVYILKH +>M_3574 +KVAELVYIL +>M_3575 +ISMKLVLRF +>M_3576 +KSPGWSFQV +>M_3577 +SWKSPGWSF +>M_3578 +LTVDNITFL +>M_3579 +DAATRVAMV +>M_3580 +DSVDAATRV +>M_3581 +VGAQIYHTI +>M_3582 +GELSMLVTT +>M_3583 +EELQLICQA +>M_3584 +SEEELQLIC +>M_3585 +CELHAQAAT +>M_3586 +FTLRPGEVM +>M_3587 +VYMPPPRLL +>M_3588 +TFKKQWFYL +>M_3589 +KANRESQSL diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134702_2_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134702_2_T_iedb.xml new file mode 100755 index 00000000..da61382f --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134702_2_T_iedb.xml @@ -0,0 +1,519 @@ + + + + blastp + BLASTP 2.2.30+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta + Query_1 + M_3572 + 9 + + + BLOSUM62 + 100000000 + 11 + 1 + F + + + + + 1 + Query_1 + M_3572 + 9 + + + 1 + gnl|BL_ORD_ID|1858 + 180428|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 + 1858 + 15 + + + 1 + 15.0086 + 27 + 1.35294 + 1 + 9 + 7 + 15 + 0 + 0 + 6 + 7 + 0 + 9 + GEDVDSLAL + GEEVQVLAL + GE+V LAL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 2 + Query_2 + M_3573 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 3 + Query_3 + M_3574 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 4 + Query_4 + M_3575 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 5 + Query_5 + M_3576 + 9 + + + 1 + gnl|BL_ORD_ID|1580 + 141461|ubiquitin E3 ligase ICP0|NP_044601.1|Human alphaherpesvirus 1|10298 + 1580 + 9 + + + 1 + 13.853 + 24 + 4.51705 + 3 + 6 + 2 + 5 + 0 + 0 + 4 + 4 + 0 + 4 + PGWS + PGWS + PGWS + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 6 + Query_6 + M_3577 + 9 + + + 1 + gnl|BL_ORD_ID|1580 + 141461|ubiquitin E3 ligase ICP0|NP_044601.1|Human alphaherpesvirus 1|10298 + 1580 + 9 + + + 1 + 13.4678 + 23 + 9.18751 + 5 + 8 + 2 + 5 + 0 + 0 + 4 + 4 + 0 + 4 + PGWS + PGWS + PGWS + + + + + 2 + gnl|BL_ORD_ID|951 + 62616|Chain A, Dengue Virus 4 Ns3 Helicase In Complex With Ssrna|2JLU_A|Dengue virus 4 Thailand/0348/1991|408688 + 951 + 9 + + + 1 + 13.0826 + 22 + 22.6682 + 1 + 9 + 1 + 9 + 0 + 0 + 4 + 5 + 0 + 9 + SWKSPGWSF + SYKDREWCF + S+K W F + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 7 + Query_7 + M_3578 + 9 + + + 1 + gnl|BL_ORD_ID|69 + 5191|core protein|AAL31859.1|Hepatitis B virus|10407 + 69 + 17 + + + 1 + 11.927 + 19 + 75.4827 + 2 + 9 + 2 + 9 + 0 + 0 + 4 + 7 + 0 + 8 + TVDNITFL + TVELLSFL + TV+ ++FL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 8 + Query_8 + M_3579 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 9 + Query_9 + M_3580 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 10 + Query_10 + M_3581 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 11 + Query_11 + M_3582 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 12 + Query_12 + M_3583 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 13 + Query_13 + M_3584 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 14 + Query_14 + M_3585 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 15 + Query_15 + M_3586 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 16 + Query_16 + M_3587 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 17 + Query_17 + M_3588 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 18 + Query_18 + M_3589 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + + diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_135773_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_135773_1_T.fasta new file mode 100755 index 00000000..c0cf645e --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_135773_1_T.fasta @@ -0,0 +1,2572 @@ +>M_3590 +AAKARDREL +>M_3591 +AARLRFFST +>M_3592 +AFFSLSYIF +>M_3593 +AHASLIPEF +>M_3594 +AHCGLGKIL +>M_3595 +AHIERRLHI +>M_3596 +AHMETMAKL +>M_3597 +AHMGVFTEL +>M_3598 +AHQDALMLA +>M_3599 +AHRPRARLA +>M_3600 +AHTSAILTV +>M_3601 +AIRPKSLAI +>M_3602 +ALQRRRLSL +>M_3603 +ALQRRVQRL +>M_3604 +AMACMSSVF +>M_3605 +AMCVIHFSF +>M_3606 +AMYLRASSL +>M_3607 +APASRHLSA +>M_3608 +APRLLRSPV +>M_3609 +AQKEHSHLL +>M_3610 +ARAAQVAGI +>M_3611 +ARDPSPIQI +>M_3612 +ARHERIHTK +>M_3613 +ARINSIYGL +>M_3614 +ARKPRTREC +>M_3615 +ARLQHCSAL +>M_3616 +ARLQHCSAL +>M_3617 +ARLYRGQAL +>M_3618 +ARLYRGQAL +>M_3619 +ARMQSYSTI +>M_3620 +ARPEKLPEL +>M_3621 +ARQHLLQRM +>M_3622 +ARRARLQHC +>M_3623 +ARRKQSEMY +>M_3624 +ARTRAKQNI +>M_3625 +ARVQMQVTM +>M_3626 +ASFSNHQRV +>M_3627 +ATDDKMTIF +>M_3628 +AVDPMRAAY +>M_3629 +AVMGRSWEV +>M_3630 +AYATQLFFF +>M_3631 +AYEDTVRQV +>M_3632 +AYFTHSLSF +>M_3633 +CAFSRRRPI +>M_3634 +CFPLHGLQF +>M_3635 +CGDKISDRY +>M_3636 +CHFSCNNGF +>M_3637 +CHQDHWSQL +>M_3638 +CHQRCGGRV +>M_3639 +CHSNSRDHL +>M_3640 +CHYEKKTDL +>M_3641 +CLKPHQGPV +>M_3642 +CLLRNSACL +>M_3643 +CLPSRTSSV +>M_3644 +CLRDLFFPL +>M_3645 +CMKQRDEEF +>M_3646 +CPPNHIVSL +>M_3647 +CQFGTVQLV +>M_3648 +CRAETRKTF +>M_3649 +CRCPIRGLV +>M_3650 +CREELAVHL +>M_3651 +CREQHPAQL +>M_3652 +CRKMFRRSA +>M_3653 +CRKMGLRVM +>M_3654 +CRPQCCQSV +>M_3655 +CRRGLEQLL +>M_3656 +CRYGRFHKF +>M_3657 +CSDTHTNEL +>M_3658 +CVLYKYVPI +>M_3659 +CVMTKIFSL +>M_3660 +CYLITVTPI +>M_3661 +CYLVFIGCF +>M_3662 +CYNSAIQAL +>M_3663 +CYSRDQIYI +>M_3664 +CYVAICGPL +>M_3665 +CYYYFLCLL +>M_3666 +DAKRHRKVL +>M_3667 +DALCRLLGL +>M_3668 +DFKKKKGSM +>M_3669 +DHRDLGLSV +>M_3670 +DILVHHLAV +>M_3671 +DLGDKILAL +>M_3672 +DLHTRHGSI +>M_3673 +DLKMGKKPV +>M_3674 +DLLGHPQAL +>M_3675 +DLPTKRPAL +>M_3676 +DLQQKILCM +>M_3677 +DMMKEFISM +>M_3678 +DPKERIKVA +>M_3679 +DPRLKWVVL +>M_3680 +DRGGCVAGV +>M_3681 +DRMQRVISV +>M_3682 +DRMQRVISV +>M_3683 +DRNDFPVVL +>M_3684 +DRQLAAQLL +>M_3685 +DRSGARPHL +>M_3686 +DRSHTLQRM +>M_3687 +DRVERNCLL +>M_3688 +DSDGEEPCY +>M_3689 +DSHDYVFYL +>M_3690 +DTDILSYSY +>M_3691 +DTDLYHCTA +>M_3692 +DTEGILTEY +>M_3693 +DYMGFTLKI +>M_3694 +DYPCCIFPF +>M_3695 +DYRTVNNLI +>M_3696 +EAEPYYCSL +>M_3697 +EAKRQNLRL +>M_3698 +EALIRHLNA +>M_3699 +EAMNNAQKI +>M_3700 +EASRRYKKV +>M_3701 +EFPQKYYWW +>M_3702 +EGQRRPSSV +>M_3703 +EHEEDGSEI +>M_3704 +EHGGKTVKV +>M_3705 +EHLAAPRLV +>M_3706 +EHNVTVLVV +>M_3707 +EHQIGPQEI +>M_3708 +EHRLHTPMY +>M_3709 +EIKTIVKAI +>M_3710 +EIMNRVVNA +>M_3711 +EKRFKRKSV +>M_3712 +ELACYNSAI +>M_3713 +ELEHMRLRY +>M_3714 +ELHARGHQV +>M_3715 +ELHRQVKTL +>M_3716 +ELKQMCNPI +>M_3717 +ELLLKVFAL +>M_3718 +ELQARLAAL +>M_3719 +ELRAHCETL +>M_3720 +ELRRYLKSG +>M_3721 +EMKCREKGF +>M_3722 +EMLRRQIRL +>M_3723 +EMRCQYETV +>M_3724 +EMYEKGLSV +>M_3725 +EPKKKEKGM +>M_3726 +EPKKRKVVP +>M_3727 +EPRFRLNLF +>M_3728 +ERDGLERAL +>M_3729 +ERDGLHSVV +>M_3730 +ERDQLKETL +>M_3731 +EREKMGVTM +>M_3732 +ERFWRIILL +>M_3733 +ERHVAVEGV +>M_3734 +ERIDTNQKC +>M_3735 +ERKTMIKKI +>M_3736 +ERLQALYMI +>M_3737 +ERLQNPLRV +>M_3738 +ERQCHNTAL +>M_3739 +ERQCHNTAL +>M_3740 +ERRDCIICC +>M_3741 +ERSCWVRAI +>M_3742 +ERSEQPLSV +>M_3743 +ERSPQAAAV +>M_3744 +ERTNQKWSV +>M_3745 +ERTSATLTI +>M_3746 +ERTTWVQKI +>M_3747 +ERYGPVFTI +>M_3748 +ETMLHGQVM +>M_3749 +ETRPTPRLL +>M_3750 +ETVSTTLCY +>M_3751 +EYIVIPSTF +>M_3752 +EYLLGSWVI +>M_3753 +EYNANTSVL +>M_3754 +EYRPRTFCF +>M_3755 +EYVKFLHTF +>M_3756 +EYVTELPSF +>M_3757 +FAAQHGLAV +>M_3758 +FAKLRHNTQ +>M_3759 +FARGQRWRL +>M_3760 +FARGQRWRL +>M_3761 +FCLRYGAAL +>M_3762 +FCSLHCLLY +>M_3763 +FCYYYFLCL +>M_3764 +FEESKSYEV +>M_3765 +FEFSQVLAL +>M_3766 +FESHRILHL +>M_3767 +FFLSYLKSL +>M_3768 +FFLSYLSLV +>M_3769 +FGAIRRSDA +>M_3770 +FGYENSPEL +>M_3771 +FHFRRPWSF +>M_3772 +FHFRRPWSF +>M_3773 +FHFRRPWSF +>M_3774 +FHHCHPKYS +>M_3775 +FHHIDSAYL +>M_3776 +FHIGSAESM +>M_3777 +FHLHNAHVL +>M_3778 +FHLPYLEQK +>M_3779 +FHLQHWKQI +>M_3780 +FHLSIHLLY +>M_3781 +FHMASGEAL +>M_3782 +FHPMRTLPM +>M_3783 +FHVDQATTV +>M_3784 +FHYDTQLSL +>M_3785 +FHYLKKQET +>M_3786 +FIADKLSTL +>M_3787 +FIADKLSTL +>M_3788 +FICLQFWCI +>M_3789 +FIMFLFVYI +>M_3790 +FINNSIVYL +>M_3791 +FKKARWTII +>M_3792 +FKNHHNRTV +>M_3793 +FLARTVSTL +>M_3794 +FLEHGEQAY +>M_3795 +FLHERKQAS +>M_3796 +FLKTLWAGL +>M_3797 +FLLAMLLSI +>M_3798 +FLLEFLLPL +>M_3799 +FLLFSFLFL +>M_3800 +FLRTYKNSV +>M_3801 +FLSDLTPGY +>M_3802 +FLSVFYTAV +>M_3803 +FLTVMLLAL +>M_3804 +FLVERKTIA +>M_3805 +FMAYATQLF +>M_3806 +FMKYLVNFI +>M_3807 +FMLVMICIL +>M_3808 +FMWPLHWSM +>M_3809 +FPAMLQAPI +>M_3810 +FPIIIAWAI +>M_3811 +FPKKSLMLM +>M_3812 +FPLVRSCQM +>M_3813 +FPNGRLTFL +>M_3814 +FPQKYYWWF +>M_3815 +FPQNRYTQE +>M_3816 +FPTDCVYVM +>M_3817 +FPYCRAHVL +>M_3818 +FPYCRAHVL +>M_3819 +FPYCRSHVF +>M_3820 +FPYGSSTAL +>M_3821 +FPYNSDLSL +>M_3822 +FQFGAGTQV +>M_3823 +FQGRRSPSF +>M_3824 +FQRKKRRKF +>M_3825 +FREDPVAWV +>M_3826 +FREGRPREW +>M_3827 +FRGALPVQI +>M_3828 +FRGDGRTCC +>M_3829 +FRHSPRNLI +>M_3830 +FRKELRYFL +>M_3831 +FRKELRYFL +>M_3832 +FRLMHNLNF +>M_3833 +FRLRRVASA +>M_3834 +FRLWMTTEV +>M_3835 +FRNDQEETT +>M_3836 +FRNGLGTGM +>M_3837 +FRNSRLKQC +>M_3838 +FRPPAWNRL +>M_3839 +FRQGHQLFH +>M_3840 +FRQLEDSQV +>M_3841 +FRQSRSQVV +>M_3842 +FRQSRSQVV +>M_3843 +FRSHVPSHL +>M_3844 +FRSLQGSVF +>M_3845 +FRSPEDLSL +>M_3846 +FRSSASGAL +>M_3847 +FRTKDGSFV +>M_3848 +FRVSISQTA +>M_3849 +FRYEGSLTT +>M_3850 +FSDKKTITY +>M_3851 +FSFINNSIV +>M_3852 +FSIPTCLMY +>M_3853 +FSKAQAEYL +>M_3854 +FSYPSIHRF +>M_3855 +FTDVSRFTL +>M_3856 +FTFDLYRVL +>M_3857 +FTSFLLLMY +>M_3858 +FVEEWTESL +>M_3859 +FVQKLLFPY +>M_3860 +FWCAQFTSF +>M_3861 +FWKKILFVI +>M_3862 +FWKLFYCKF +>M_3863 +FYADSHHCV +>M_3864 +FYAIVVPML +>M_3865 +FYCDDLPLL +>M_3866 +FYLGTYQAV +>M_3867 +FYMLTCIDL +>M_3868 +FYQAGSLCI +>M_3869 +FYTDSSSVL +>M_3870 +FYTPALFSF +>M_3871 +GAGPRFLEL +>M_3872 +GDKQHFTTL +>M_3873 +GGATRVYAL +>M_3874 +GHDAPRRTL +>M_3875 +GHKEDAGVV +>M_3876 +GHKGLNQCV +>M_3877 +GHLEAASCI +>M_3878 +GHLQIRSLL +>M_3879 +GHLSKKMTL +>M_3880 +GHNSWGFGV +>M_3881 +GHPQDGSGL +>M_3882 +GHPSLSQHL +>M_3883 +GHTGERHRV +>M_3884 +GHTPNGRHF +>M_3885 +GHVAGEQML +>M_3886 +GLHSSFMPL +>M_3887 +GLSVRPHAI +>M_3888 +GMFTLRMAL +>M_3889 +GNYSRSSHV +>M_3890 +GPCRRRFSF +>M_3891 +GPLPKSYAV +>M_3892 +GPRTKAWFL +>M_3893 +GRAEESVVL +>M_3894 +GRAPCWQRL +>M_3895 +GREAEMQEL +>M_3896 +GRMHIGDEL +>M_3897 +GRMMFVGTL +>M_3898 +GRNGQKAAL +>M_3899 +GRVEKLLDL +>M_3900 +GSDSSNGAV +>M_3901 +GSEDFEDTY +>M_3902 +GTNIVILEY +>M_3903 +GVLECPRLI +>M_3904 +HAKKKPNPV +>M_3905 +HHIDSAYLY +>M_3906 +HHKGKMKAL +>M_3907 +HHKHKELQV +>M_3908 +HHRFNNFML +>M_3909 +HIKDKKLPL +>M_3910 +HLLSHSYCL +>M_3911 +HLMGQLSSL +>M_3912 +HMRLRYLAA +>M_3913 +HPKYSFRRL +>M_3914 +HPLRYTLIM +>M_3915 +HRADVYVGV +>M_3916 +HREDFEARL +>M_3917 +HRGTGAVYV +>M_3918 +HRLGESQTL +>M_3919 +HRLHTPMYL +>M_3920 +HRQAEVHKV +>M_3921 +HRQQRGQQL +>M_3922 +HRSKRGSSV +>M_3923 +HRTRCLSKL +>M_3924 +HRYPRVMAA +>M_3925 +HRYPRVMAA +>M_3926 +HSHLLSHSY +>M_3927 +HSYEAGTEI +>M_3928 +HTPNGRHFY +>M_3929 +HWSMWLGVF +>M_3930 +HYATILTSL +>M_3931 +HYHHRFNNF +>M_3932 +HYISIFYAL +>M_3933 +HYLRDVLPL +>M_3934 +HYQGTWYLT +>M_3935 +HYRKRGAHL +>M_3936 +IAHAWWAHF +>M_3937 +IAMYFYTTL +>M_3938 +IEYGSPEEL +>M_3939 +IFIASIYLL +>M_3940 +IFLFVIVTI +>M_3941 +IFPFALIFF +>M_3942 +IFPFILIFF +>M_3943 +IFSEKNRLV +>M_3944 +IFSFINNSI +>M_3945 +IFVSSYINI +>M_3946 +IGRNRSPCM +>M_3947 +IHDGAVHTI +>M_3948 +IHDRQLRSF +>M_3949 +IHEDEVDDM +>M_3950 +IHFTKKDYV +>M_3951 +IHGASNHCL +>M_3952 +IHIDDNKWV +>M_3953 +IHLLDSLRL +>M_3954 +IHLLYPPSL +>M_3955 +IHPRDRSTV +>M_3956 +IHTDDNKCV +>M_3957 +ILAVLPSLF +>M_3958 +ILKKRQQAA +>M_3959 +ILKRRYQEP +>M_3960 +ILLTQFHFL +>M_3961 +ILMRQPLPA +>M_3962 +ILRSKMKTV +>M_3963 +ILRVYSGVL +>M_3964 +ILSSRSRQL +>M_3965 +ILSSRSRQL +>M_3966 +INFNHDSSI +>M_3967 +IQWSYWGVF +>M_3968 +IRAANRRGL +>M_3969 +IRDGSTMTF +>M_3970 +IREYCPYTY +>M_3971 +IRFLRQYEF +>M_3972 +IRHGNVIAC +>M_3973 +IRHLNATSF +>M_3974 +IRIDTIHLL +>M_3975 +IRLNRQRHT +>M_3976 +IRNMAPDSL +>M_3977 +IRPPDSRSL +>M_3978 +IRRGGKHQL +>M_3979 +IRRLRPSSI +>M_3980 +IRRLRPSSI +>M_3981 +IRRRGSTSL +>M_3982 +IRYLHSLQI +>M_3983 +ISELLFECY +>M_3984 +ISFSMSEKM +>M_3985 +ISKRKVSVA +>M_3986 +ISLGFFLVF +>M_3987 +ISSSAGLPY +>M_3988 +ITIRNPLRY +>M_3989 +ITMDQKKTI +>M_3990 +ITMRYIHFL +>M_3991 +ITTFDRLAY +>M_3992 +IVHRQFYLF +>M_3993 +IVMGYSSGI +>M_3994 +IWFSIPTCL +>M_3995 +IYAALPYVK +>M_3996 +IYAFMGTPM +>M_3997 +IYCRPFTTL +>M_3998 +IYCVYPDSL +>M_3999 +IYGLCVVIV +>M_4000 +IYHDSRIHV +>M_4001 +IYTIVNIKI +>M_4002 +IYVDKVRHV +>M_4003 +KAFKRSSYL +>M_4004 +KAFKRSSYL +>M_4005 +KAMERSSLM +>M_4006 +KHFIHLITV +>M_4007 +KHLSRSNWL +>M_4008 +KHNEEIRFL +>M_4009 +KHRNMHCKI +>M_4010 +KHRSEISMM +>M_4011 +KIHIRETAI +>M_4012 +KILKKRQQA +>M_4013 +KISKRKVSV +>M_4014 +KKRRKFWKA +>M_4015 +KLKPKKPTL +>M_4016 +KLQPYFQTL +>M_4017 +KMFRRSAHL +>M_4018 +KRCALRLLV +>M_4019 +KRFKRKSVV +>M_4020 +KRILMPQVM +>M_4021 +KRISHKAAL +>M_4022 +KRQNLRLAL +>M_4023 +KRQRAMETL +>M_4024 +KRSPAWNEM +>M_4025 +KRYLSQREV +>M_4026 +KSDGLSLAV +>M_4027 +KSFSKYASF +>M_4028 +KWIREGYLV +>M_4029 +KYMPPCSLV +>M_4030 +KYPYWYQQK +>M_4031 +KYSTGIGWI +>M_4032 +KYSTPPYLL +>M_4033 +LAGQKRCAL +>M_4034 +LAKVKYTAS +>M_4035 +LALLKQVSV +>M_4036 +LANDPIQVV +>M_4037 +LAQSFFNCL +>M_4038 +LCAIYFLSI +>M_4039 +LCIKHFNIL +>M_4040 +LEHMRLRYL +>M_4041 +LFAAVVLLI +>M_4042 +LFKKARWTI +>M_4043 +LFLLFSFLF +>M_4044 +LFPRLPSIL +>M_4045 +LFSFMTHCF +>M_4046 +LFSFMTHRF +>M_4047 +LGRNRHFGF +>M_4048 +LHAPMYNLL +>M_4049 +LHAPMYNLL +>M_4050 +LHEQLGDRL +>M_4051 +LHFDAVQIC +>M_4052 +LHFMPCVYI +>M_4053 +LHFVQKLLF +>M_4054 +LHHKHKELQ +>M_4055 +LHHTHIALL +>M_4056 +LHKDSNMPV +>M_4057 +LHMNLLSYF +>M_4058 +LHNAHVLDV +>M_4059 +LHQCVLRFL +>M_4060 +LHQGGATRV +>M_4061 +LHRASGVGV +>M_4062 +LHSGLQILI +>M_4063 +LHTPVYFLL +>M_4064 +LHTPVYFLL +>M_4065 +LHTRHGSIL +>M_4066 +LHVGCDEVY +>M_4067 +LHYEEIPEY +>M_4068 +LIATQLLFY +>M_4069 +LIKHKKTHI +>M_4070 +LIKYRQNHA +>M_4071 +LIMNKRLGL +>M_4072 +LKKRQQAAL +>M_4073 +LKLVKRNSL +>M_4074 +LLCARAWLL +>M_4075 +LLDRRPHGY +>M_4076 +LLESYSASL +>M_4077 +LLGHKTVTI +>M_4078 +LLGKKGTSA +>M_4079 +LLHTIITPM +>M_4080 +LLKKLCIKL +>M_4081 +LLKSDGLSL +>M_4082 +LLKTAFHPV +>M_4083 +LLLMYSYAV +>M_4084 +LLLQALQAL +>M_4085 +LLMNKPYLA +>M_4086 +LLMYTKLVV +>M_4087 +LLNVHLSKL +>M_4088 +LLRDFVAPL +>M_4089 +LLRGHDQSA +>M_4090 +LLRLLRKAM +>M_4091 +LLRNDARSL +>M_4092 +LLSFKRQRA +>M_4093 +LLSRKDSIF +>M_4094 +LLTQRLQGL +>M_4095 +LMACATQLF +>M_4096 +LMGQLSSLY +>M_4097 +LMKMDDPSI +>M_4098 +LMKQKKSSC +>M_4099 +LNKLDFYVL +>M_4100 +LNRQRHTPM +>M_4101 +LPALRKTGV +>M_4102 +LPAVHALRL +>M_4103 +LPGLHFMPG +>M_4104 +LPGMRGPPG +>M_4105 +LPKDRFFAV +>M_4106 +LPKEKLAAA +>M_4107 +LPMTLLLLL +>M_4108 +LPQGRESPI +>M_4109 +LPRSKDTIL +>M_4110 +LPRVRGTTL +>M_4111 +LPSCRLAPA +>M_4112 +LPTLKFQTF +>M_4113 +LPYVKKTGM +>M_4114 +LQKVRQEVL +>M_4115 +LQLYRFSPI +>M_4116 +LQRRRLSLL +>M_4117 +LRADTSFFL +>M_4118 +LRAKYRESL +>M_4119 +LRAKYRESL +>M_4120 +LRAPPGPQL +>M_4121 +LRCHYHHRF +>M_4122 +LRETRDQPL +>M_4123 +LRIMLGEIL +>M_4124 +LRINEVMVY +>M_4125 +LRKGPIMEV +>M_4126 +LRKHQILHL +>M_4127 +LRKHQITHL +>M_4128 +LRKPQNSEC +>M_4129 +LRKQNFQPA +>M_4130 +LRLALDQYL +>M_4131 +LRLEINHTI +>M_4132 +LRLPGGSCM +>M_4133 +LRLRWGQII +>M_4134 +LRLSEPAEI +>M_4135 +LRMSDPSHI +>M_4136 +LRMSRSYPT +>M_4137 +LRNDARSLY +>M_4138 +LRPSSIETY +>M_4139 +LRQWIVVTM +>M_4140 +LRRHRDVSA +>M_4141 +LRRMNSFQV +>M_4142 +LRRNYRCAI +>M_4143 +LRRNYRCAI +>M_4144 +LRRQDYQEI +>M_4145 +LRRVASALL +>M_4146 +LRSDAPAQL +>M_4147 +LRSEEDGLV +>M_4148 +LRSERNNTM +>M_4149 +LRSIRVRLL +>M_4150 +LRSQAALSL +>M_4151 +LRSQFPLIL +>M_4152 +LRTEQNDFI +>M_4153 +LRVSDGSLL +>M_4154 +LRWEYGSIL +>M_4155 +LRYFLKHGI +>M_4156 +LRYGAALIY +>M_4157 +LSEFPEDSY +>M_4158 +LSFKRQRAM +>M_4159 +LSIIRFKGL +>M_4160 +LSPMNHLCY +>M_4161 +LSSLWYHTY +>M_4162 +LSTCRKLSL +>M_4163 +LTDYDTRFY +>M_4164 +LTEPHLRLL +>M_4165 +LTGLVWQRY +>M_4166 +LTIYAALPY +>M_4167 +LTMCMKKSL +>M_4168 +LTQKQVLNY +>M_4169 +LVAQHYAAL +>M_4170 +LVDTVIDAY +>M_4171 +LVQNSCWLI +>M_4172 +LVRDRMKEL +>M_4173 +LWQSCEESF +>M_4174 +LYAVMGRSW +>M_4175 +LYEDTLYTV +>M_4176 +LYEDWCQTV +>M_4177 +LYEDWCQTV +>M_4178 +LYFHSFIRI +>M_4179 +LYFLAGQSL +>M_4180 +LYFTRPVPL +>M_4181 +LYGEQGHRW +>M_4182 +LYGHSTHDL +>M_4183 +LYHRDLAKW +>M_4184 +LYMINHFFC +>M_4185 +LYPDINNPF +>M_4186 +LYPPSLPPF +>M_4187 +LYTAYHVFF +>M_4188 +LYVWKSELV +>M_4189 +MACDRYVAI +>M_4190 +MAEVNITYV +>M_4191 +MAFDRYVAI +>M_4192 +MAFDRYVAI +>M_4193 +MAHERRDQL +>M_4194 +MAHERRDQL +>M_4195 +MAIGHFGQL +>M_4196 +MAKYWNQFL +>M_4197 +MAMSSRLAL +>M_4198 +MATAYIRSM +>M_4199 +MAYDQFLAI +>M_4200 +MAYDQFLAI +>M_4201 +MAYSITCPI +>M_4202 +MCMKKSLRL +>M_4203 +MERERKAIA +>M_4204 +MEVEAEQLL +>M_4205 +MFATDYTTI +>M_4206 +MFTLRMALF +>M_4207 +MGHLQIRSL +>M_4208 +MGKSTHTSM +>M_4209 +MHEEGYNKL +>M_4210 +MHEYKIQGL +>M_4211 +MHFCGGSFI +>M_4212 +MHHPGSRKF +>M_4213 +MHKTGLLGL +>M_4214 +MHNLLIHRV +>M_4215 +MHPDGRFEC +>M_4216 +MIFILFLVI +>M_4217 +MIRVKDSLI +>M_4218 +MKQKKSSCL +>M_4219 +MLCFYTPAL +>M_4220 +MLHLYPGPM +>M_4221 +MLKTGISTV +>M_4222 +MLLMNLATA +>M_4223 +MLLSILLPL +>M_4224 +MLLSQNASI +>M_4225 +MLNKVLYRL +>M_4226 +MLRELSSAF +>M_4227 +MLRRQIRLL +>M_4228 +MLRRQIRLL +>M_4229 +MLSLRESPM +>M_4230 +MLTSKVTVL +>M_4231 +MLYRTVREL +>M_4232 +MLYRTVREL +>M_4233 +MMQCHRLSW +>M_4234 +MNKRLGLEL +>M_4235 +MNYKKGRAF +>M_4236 +MPILKSVLI +>M_4237 +MPKKVISAL +>M_4238 +MPLLKLSCS +>M_4239 +MPQYLASPL +>M_4240 +MQFTQALEV +>M_4241 +MRAAYLDDL +>M_4242 +MRCQYETVL +>M_4243 +MREQRERQL +>M_4244 +MRLRGGRMI +>M_4245 +MRPISGVML +>M_4246 +MRQPLPASM +>M_4247 +MRRRQCEEV +>M_4248 +MRRYQSRVI +>M_4249 +MRRYQSRVI +>M_4250 +MRSCLRLAL +>M_4251 +MRSCLRLAL +>M_4252 +MSEGIVKLY +>M_4253 +MSPRVFFLL +>M_4254 +MSQSQVALL +>M_4255 +MSRSYPTGL +>M_4256 +MWPLHWSMW +>M_4257 +MYCLMLQCW +>M_4258 +MYCMVFLVL +>M_4259 +MYGAETEKF +>M_4260 +MYMSVLSLI +>M_4261 +MYMSVLSLI +>M_4262 +MYSVVPQMV +>M_4263 +MYSVVPQMV +>M_4264 +MYSYAVPPL +>M_4265 +MYTKLVVGF +>M_4266 +NEILRRYSV +>M_4267 +NFIERFWRI +>M_4268 +NFIERFWRI +>M_4269 +NFSINWWPI +>M_4270 +NHHNRTVEV +>M_4271 +NHKDNSRIR +>M_4272 +NHPYWANTV +>M_4273 +NHSDLAAEL +>M_4274 +NIDLAREAY +>M_4275 +NILPHYLEL +>M_4276 +NIVYHTASI +>M_4277 +NIYSRIREY +>M_4278 +NLARKEYTI +>M_4279 +NLGFRFHMA +>M_4280 +NLKHRKTAA +>M_4281 +NLLANFSFL +>M_4282 +NLLSYFNNL +>M_4283 +NLMAKNNQA +>M_4284 +NLNYRDLYY +>M_4285 +NLPSKRVSL +>M_4286 +NMHCKISLL +>M_4287 +NPLLHMVTM +>M_4288 +NPLRYLAVM +>M_4289 +NPLRYTSIL +>M_4290 +NQKRRSESF +>M_4291 +NRDKLGLQI +>M_4292 +NRFSSKLLA +>M_4293 +NRGPATAEV +>M_4294 +NRLDLVRFY +>M_4295 +NRNYCVSVY +>M_4296 +NRPEEEEQV +>M_4297 +NRQRHTPMY +>M_4298 +NRVGVSSKL +>M_4299 +NSDSFTGFI +>M_4300 +NSINQVKLL +>M_4301 +NTHRSRLSL +>M_4302 +NTMAFSTDY +>M_4303 +NVKKQRAGL +>M_4304 +NVNQRFLNV +>M_4305 +NYLEKVRSL +>M_4306 +NYRDLYYFL +>M_4307 +NYSPRPICV +>M_4308 +PASTLSLGY +>M_4309 +PFPRWLKII +>M_4310 +PHWASSIVL +>M_4311 +PHYDFERSC +>M_4312 +PIEMNPEGY +>M_4313 +PRIGYSLLL +>M_4314 +PRLKWVVLV +>M_4315 +PRNRKPLTV +>M_4316 +PRPSRCLLL +>M_4317 +PRSEEAAVL +>M_4318 +PRSKDTILL +>M_4319 +PRSRWRDQL +>M_4320 +PRWSCQEKL +>M_4321 +PSQPANSFY +>M_4322 +PTALSSLWY +>M_4323 +PTDVLNGAA +>M_4324 +PYPETPPRW +>M_4325 +PYQGRPKLL +>M_4326 +PYQGRPKLL +>M_4327 +PYTSVFLSV +>M_4328 +QAEARLLAL +>M_4329 +QAKVKFIGV +>M_4330 +QEHVRCSAI +>M_4331 +QFSFDGWKF +>M_4332 +QGRPKLLQL +>M_4333 +QHCYMSRLL +>M_4334 +QHDFCGLYM +>M_4335 +QHLLQRMSI +>M_4336 +QHMHCLQDL +>M_4337 +QHPNNSKDV +>M_4338 +QHQRLLEVL +>M_4339 +QHTESLEYM +>M_4340 +QHYAALQEY +>M_4341 +QILSRVAAL +>M_4342 +QLMMSLLQL +>M_4343 +QLREHAATL +>M_4344 +QLRRSKVSV +>M_4345 +QLYPRLKML +>M_4346 +QLYPRLKML +>M_4347 +QMLRIFKEM +>M_4348 +QMYMSVLSL +>M_4349 +QPAWRKASA +>M_4350 +QPLRNFISV +>M_4351 +QPMCRICHE +>M_4352 +QRAPVGKLL +>M_4353 +QRAVSRNLM +>M_4354 +QRFLFIMFL +>M_4355 +QRFLNVQEL +>M_4356 +QRGEGILDM +>M_4357 +QRHGFGEEI +>M_4358 +QRIQMYMSV +>M_4359 +QRIVKPTSI +>M_4360 +QRLEPVYFV +>M_4361 +QRLEVPIEM +>M_4362 +QRMELLITF +>M_4363 +QRQARQYQL +>M_4364 +QRRPSSVGL +>M_4365 +QRRSIPFQM +>M_4366 +QRSGKPVLM +>M_4367 +QRSNSETKV +>M_4368 +QRSRKGDLL +>M_4369 +QSEDRSHTL +>M_4370 +QSQPFSMQY +>M_4371 +QSQPGNALY +>M_4372 +QTCKANLCY +>M_4373 +QTLACNLCY +>M_4374 +QVKRKVQAL +>M_4375 +QYMLTLFTA +>M_4376 +RAEDTALYY +>M_4377 +RAIYHSCSL +>M_4378 +RAKYRESLL +>M_4379 +RAPQRIPSL +>M_4380 +RARLQHCSA +>M_4381 +RARYYIQVA +>M_4382 +RASQRMSSV +>M_4383 +RATARFHQL +>M_4384 +RFFSRFTAV +>M_4385 +RFHRVIKDF +>M_4386 +RFKRKSVVA +>M_4387 +RFLFIMFLF +>M_4388 +RFLRNFPQI +>M_4389 +RFMKYLVNF +>M_4390 +RFNMLNQIF +>M_4391 +RFQDHRWEL +>M_4392 +RHFEEALQT +>M_4393 +RHFRLMHNL +>M_4394 +RHIRHGNVI +>M_4395 +RHLGDQMEV +>M_4396 +RHRCRNRFV +>M_4397 +RHSPRNLIY +>M_4398 +RHTPMYYFL +>M_4399 +RHTPMYYFL +>M_4400 +RLIVKSREL +>M_4401 +RLKQEIKRL +>M_4402 +RLMCGPNTI +>M_4403 +RLRRVASAL +>M_4404 +RMCKFLQYF +>M_4405 +RMSSVGANF +>M_4406 +RNFPQIYIL +>M_4407 +RNPQELWHF +>M_4408 +RNRKRFCVP +>M_4409 +RPGSRGCPM +>M_4410 +RPKYSFHRL +>M_4411 +RPRARLAAL +>M_4412 +RPRARYYIQ +>M_4413 +RPRQGRWWL +>M_4414 +RQFPKKSLM +>M_4415 +RQFYLFYNF +>M_4416 +RQMISELLF +>M_4417 +RQQQDYWLM +>M_4418 +RRENSLSEI +>M_4419 +RRFNMLNQI +>M_4420 +RRGEAEKRL +>M_4421 +RRGGSGAMV +>M_4422 +RRKQSEMYI +>M_4423 +RRLDYDHKL +>M_4424 +RRPSRAMWL +>M_4425 +RRQDYQEIL +>M_4426 +RRSDAEKQL +>M_4427 +RRSKVSVEM +>M_4428 +RRSPSFSRV +>M_4429 +RRVASALLL +>M_4430 +RRVPYRGSV +>M_4431 +RRYLKSGVV +>M_4432 +RSADWQRKI +>M_4433 +RSELNSVEY +>M_4434 +RSFPAGVEM +>M_4435 +RTQDAIHEL +>M_4436 +RTSSIFYSF +>M_4437 +RVGQMAFVF +>M_4438 +RVNDCILQV +>M_4439 +RVRRRGQKL +>M_4440 +RVSDGSLLY +>M_4441 +RWQGRVRTL +>M_4442 +RYAALLKCW +>M_4443 +RYARPSRLV +>M_4444 +RYCLTTLTI +>M_4445 +RYFDEPVEL +>M_4446 +RYFDEPVEL +>M_4447 +RYFLKHGIL +>M_4448 +RYILLKRSL +>M_4449 +RYLENGKEM +>M_4450 +RYLKSGVVL +>M_4451 +RYLPDCDYL +>M_4452 +RYRSIISDI +>M_4453 +RYVAICAPL +>M_4454 +RYVASCKPL +>M_4455 +SADYINANY +>M_4456 +SAEECRTEL +>M_4457 +SAKQQNQIL +>M_4458 +SAKQQNQIL +>M_4459 +SALGREHPA +>M_4460 +SARDQPSSV +>M_4461 +SARLRQRAV +>M_4462 +SASNNNSEL +>M_4463 +SAVRRDLTF +>M_4464 +SAYDGKDYI +>M_4465 +SCSSNPHLL +>M_4466 +SEEERGLEL +>M_4467 +SEKDRPVKV +>M_4468 +SESHRTSLL +>M_4469 +SEVERLDVL +>M_4470 +SFFNCLWEV +>M_4471 +SFPGRVREL +>M_4472 +SFQTITEQF +>M_4473 +SFVDAIHTF +>M_4474 +SGFEFSQVL +>M_4475 +SGMARVGSL +>M_4476 +SHKEAITAL +>M_4477 +SHKKQSSVI +>M_4478 +SHLQRIGTI +>M_4479 +SHLTIVILF +>M_4480 +SHMYVATGI +>M_4481 +SHNRHVPKI +>M_4482 +SHPLHYTTI +>M_4483 +SHPLHYTTI +>M_4484 +SHQPLPGTL +>M_4485 +SHRNPLLDL +>M_4486 +SHSPAGELT +>M_4487 +SHSSNPHLL +>M_4488 +SHTLLLTQL +>M_4489 +SIFYSFLPL +>M_4490 +SKFGQGTGL +>M_4491 +SKQNMPQYL +>M_4492 +SLAKFDAPL +>M_4493 +SLDTTTWEY +>M_4494 +SLFTCVLQL +>M_4495 +SLGDNSEYL +>M_4496 +SLHHKHKEL +>M_4497 +SLIDSSRVV +>M_4498 +SLKLTQSSA +>M_4499 +SLLRKHQIL +>M_4500 +SLLRKHQIT +>M_4501 +SLLVHGGPL +>M_4502 +SLNHRGRVM +>M_4503 +SLNHRGRVM +>M_4504 +SLNPKKFSI +>M_4505 +SLRAEDTAL +>M_4506 +SLSETVRLV +>M_4507 +SLSVRTSGL +>M_4508 +SLWYHTYGL +>M_4509 +SLYTAYHVF +>M_4510 +SLYVWKSEL +>M_4511 +SMAKYWNQF +>M_4512 +SMKAERPPA +>M_4513 +SMKNLQRAV +>M_4514 +SMKVHIKAM +>M_4515 +SMMTATIVF +>M_4516 +SMPANFETI +>M_4517 +SMREALREL +>M_4518 +SMREAVREL +>M_4519 +SMRYFITSV +>M_4520 +SPGPFFWMF +>M_4521 +SPLFYSTCM +>M_4522 +SPLQLPAPL +>M_4523 +SPLRYISIL +>M_4524 +SPMYFFLSY +>M_4525 +SPRSRPSDI +>M_4526 +SPRVFFLLM +>M_4527 +SPSSAYLLF +>M_4528 +SQHPAQQQI +>M_4529 +SQMSQLMGL +>M_4530 +SQPGNALYF +>M_4531 +SRAMWLSLF +>M_4532 +SRATADPEV +>M_4533 +SRCLLLPLL +>M_4534 +SREDDNRER +>M_4535 +SRENRWTTV +>M_4536 +SRFCSLHCL +>M_4537 +SRFTAVREF +>M_4538 +SRFTLRCMV +>M_4539 +SRFVVRPLL +>M_4540 +SRGQEIKTI +>M_4541 +SRHDFHVDL +>M_4542 +SRKGDLLRI +>M_4543 +SRKKRRSPP +>M_4544 +SRKLRKLPT +>M_4545 +SRLHTPVYF +>M_4546 +SRNAYSLEI +>M_4547 +SRNDFEWVY +>M_4548 +SRPGALEHL +>M_4549 +SRPSSKQNM +>M_4550 +SRQMISELL +>M_4551 +SRRARGREK +>M_4552 +SRRSFWSEL +>M_4553 +SRSRNAYSL +>M_4554 +SRSVDVTNI +>M_4555 +SRTVWEEMV +>M_4556 +SRWRDQLLF +>M_4557 +SRYARPSRL +>M_4558 +SSASLNSNY +>M_4559 +SSDEIVQEL +>M_4560 +SSKQHLKPA +>M_4561 +SSLARELSL +>M_4562 +SSLRRMNSF +>M_4563 +SSRGNGKMM +>M_4564 +SSTSHIPEV +>M_4565 +SSYSRVALV +>M_4566 +STDDATWAA +>M_4567 +STERPKMTY +>M_4568 +STIYIFALF +>M_4569 +STKVHIKVL +>M_4570 +STQTHPLTL +>M_4571 +STSHVYHLF +>M_4572 +STYNETNLI +>M_4573 +STYPDQQHV +>M_4574 +SVEEKGKLL +>M_4575 +SVFPTQLQL +>M_4576 +SVFSEQWIF +>M_4577 +SVRENCCSL +>M_4578 +SWMPALECL +>M_4579 +SWPLWTAIF +>M_4580 +SWVSSTLGF +>M_4581 +SYAKNAQDL +>M_4582 +SYARILGTV +>M_4583 +SYAVICNNF +>M_4584 +SYFCILRTI +>M_4585 +SYFGLATVF +>M_4586 +SYFLATDTI +>M_4587 +SYFNNLHLW +>M_4588 +SYGVNLYQF +>M_4589 +SYIYILITI +>M_4590 +SYKFLAPWI +>M_4591 +SYPSIHRFI +>M_4592 +SYPSQPDGF +>M_4593 +SYSLISEKL +>M_4594 +SYVMDHFDI +>M_4595 +SYVRIGATI +>M_4596 +SYWGVFAPI +>M_4597 +SYYKIVSSI +>M_4598 +TAAIRPKSL +>M_4599 +TADVGLAGY +>M_4600 +TAFDESISL +>M_4601 +TAMAYDQFL +>M_4602 +TDKERQRLL +>M_4603 +TDYDTRFYM +>M_4604 +TEFGQKQKL +>M_4605 +TERDQIELL +>M_4606 +TFDRLAYLW +>M_4607 +TFEDNLRSL +>M_4608 +TFGEVNYFF +>M_4609 +TFITSVIRF +>M_4610 +TFLIAMVFI +>M_4611 +TFNDWFEII +>M_4612 +TFSCQLHKF +>M_4613 +THAPERDLC +>M_4614 +THASLSNHV +>M_4615 +THHGPAFSI +>M_4616 +THIFGLMVI +>M_4617 +THIHAAACI +>M_4618 +THMERVLSL +>M_4619 +THMERVLSL +>M_4620 +THPIYYLKI +>M_4621 +THQEALMKL +>M_4622 +THREGISAI +>M_4623 +THRSRLSLG +>M_4624 +THTSYQLSA +>M_4625 +THYQGTWYL +>M_4626 +TIKQRPKPT +>M_4627 +TKFESNLCV +>M_4628 +TLDKKLEYY +>M_4629 +TLERAALRY +>M_4630 +TLGLIFLCL +>M_4631 +TLMVVVWVL +>M_4632 +TLTIRALPA +>M_4633 +TMCMYFRPL +>M_4634 +TMETSFFSF +>M_4635 +TMGSWTCLF +>M_4636 +TMRTRHFTG +>M_4637 +TMRYIHFLF +>M_4638 +TMSPRVFFL +>M_4639 +TPGNRTKCF +>M_4640 +TPKSMQSTL +>M_4641 +TPNFRRRAI +>M_4642 +TPSERSKPL +>M_4643 +TPSTQTHPL +>M_4644 +TRAERLTWL +>M_4645 +TRALHRLIV +>M_4646 +TRASDRRGI +>M_4647 +TRDAPGLRV +>M_4648 +TREVTVNVL +>M_4649 +TRFPLKTAF +>M_4650 +TRFPLPEAF +>M_4651 +TRFRSFSSL +>M_4652 +TRFYMYEIL +>M_4653 +TRGPCRRRF +>M_4654 +TRGPQRQIL +>M_4655 +TRGRHQKKI +>M_4656 +TRHGSILAC +>M_4657 +TRHRCRNRF +>M_4658 +TRNCNRHLC +>M_4659 +TRPSEELEL +>M_4660 +TRPTASSSV +>M_4661 +TRRSQKRLQ +>M_4662 +TRSAEPGYL +>M_4663 +TRSSKPSDM +>M_4664 +TRSWGTPQL +>M_4665 +TRTPHSTRC +>M_4666 +TRVGSKLLI +>M_4667 +TRYSAQADI +>M_4668 +TSMWRTYVM +>M_4669 +TSMWRTYVM +>M_4670 +TTDGRNYIV +>M_4671 +TTFDRLAYL +>M_4672 +TTMEDQLLF +>M_4673 +TVHTRNHTA +>M_4674 +TVIDAYMNF +>M_4675 +TVLHRPHSA +>M_4676 +TVSPQPQEV +>M_4677 +TWLQVLEAI +>M_4678 +TYEEPCQAI +>M_4679 +TYLADRVQI +>M_4680 +TYLYPPKHW +>M_4681 +TYVLYYDAL +>M_4682 +TYYPLKPEI +>M_4683 +TYYPLKPEI +>M_4684 +VAKKKEAPA +>M_4685 +VARERRKAE +>M_4686 +VFERDFFKI +>M_4687 +VFETGTFLI +>M_4688 +VFLPMTLLL +>M_4689 +VFRQGHQLF +>M_4690 +VFTRVSAYI +>M_4691 +VFYTIFTPI +>M_4692 +VGKKRHDPL +>M_4693 +VHALRLHLY +>M_4694 +VHFDHFHPC +>M_4695 +VHFLREVTV +>M_4696 +VHHLAVSGV +>M_4697 +VHIKAMQTV +>M_4698 +VHIKVLQTV +>M_4699 +VHKKGYNKL +>M_4700 +VHKQFPITL +>M_4701 +VHKTDLERM +>M_4702 +VHRGTGAVY +>M_4703 +VHSENLQNW +>M_4704 +VLAIQRCPM +>M_4705 +VLDEMRCQY +>M_4706 +VLKSTSCSI +>M_4707 +VMKHLLSPL +>M_4708 +VMSCVWFTI +>M_4709 +VQMYRGHPA +>M_4710 +VQNEDVTLL +>M_4711 +VQPSQWASI +>M_4712 +VRDRMKELL +>M_4713 +VRELRDMGI +>M_4714 +VRFQDESVV +>M_4715 +VRFVTRYIY +>M_4716 +VRFVVTITV +>M_4717 +VRGTTLHLL +>M_4718 +VRHQRVHQA +>M_4719 +VRLKRSIQF +>M_4720 +VRLSYKLTF +>M_4721 +VRMEVISVT +>M_4722 +VRMEVVSIT +>M_4723 +VRNDHMNLR +>M_4724 +VRNRCNIYI +>M_4725 +VRPRARYYI +>M_4726 +VRQGGVFRL +>M_4727 +VRRLGPKLL +>M_4728 +VRRLHCSAA +>M_4729 +VRRMLTSKV +>M_4730 +VRRRRRCPG +>M_4731 +VRSLNLVLM +>M_4732 +VRSNLEPLF +>M_4733 +VRVGSDMLI +>M_4734 +VRVTQKFHM +>M_4735 +VSDDLVKQY +>M_4736 +VSGHVSMKY +>M_4737 +VSSSSSGGY +>M_4738 +VTADSDPAY +>M_4739 +VTAPRATTL +>M_4740 +VTDVLTEPH +>M_4741 +VTMDWLVRI +>M_4742 +VVAPRTLLL +>M_4743 +VVESLVEAY +>M_4744 +VVHEVQRYL +>M_4745 +VVKSKQVAL +>M_4746 +VVPQMVNPF +>M_4747 +VVSDVPEEL +>M_4748 +VYFHMTLSF +>M_4749 +VYHLFCALL +>M_4750 +VYISLFTCV +>M_4751 +VYLRRHRDV +>M_4752 +VYPRGFQEK +>M_4753 +VYQVLSGGW +>M_4754 +VYSEYGMDV +>M_4755 +VYSLRTRAI +>M_4756 +VYSLYWSIL +>M_4757 +VYVVSNNNL +>M_4758 +VYVVTKFLM +>M_4759 +VYYLLELLL +>M_4760 +WAGSHSMRY +>M_4761 +WARRKQSEM +>M_4762 +WASRFSTPY +>M_4763 +WFLWKQFCW +>M_4764 +WGMLNSLSL +>M_4765 +WHLQGPEDL +>M_4766 +WHREYNFKY +>M_4767 +WHSVVIQRL +>M_4768 +WHVPNKPPM +>M_4769 +WIEREGPEY +>M_4770 +WLNENQRLV +>M_4771 +WLSFRSSAS +>M_4772 +WLSNFQGRY +>M_4773 +WMEKRYLSQ +>M_4774 +WMEQEGPEY +>M_4775 +WPLTHSQGM +>M_4776 +WQRQHKLTI +>M_4777 +WRPEAVQYY +>M_4778 +WSDQLSAFS +>M_4779 +WTDVFQIGI +>M_4780 +WTESLAAVF +>M_4781 +WVKRQKISF +>M_4782 +WVRPRRRLL +>M_4783 +WVRPRRRLL +>M_4784 +WYHTCGGTL +>M_4785 +WYIWILLVL +>M_4786 +YAFTGLTLM +>M_4787 +YAMQRSWQE +>M_4788 +YARILGTVL +>M_4789 +YCDDLPLLA +>M_4790 +YDDARVELV +>M_4791 +YEHHHSARL +>M_4792 +YFGLATVFI +>M_4793 +YFHSFIRIV +>M_4794 +YFTSSSRYF +>M_4795 +YFYNQEEYV +>M_4796 +YGVTRSKAM +>M_4797 +YHCTAVNAY +>M_4798 +YHDACIEEA +>M_4799 +YHDVSGCYI +>M_4800 +YHEAGVTAL +>M_4801 +YHFSWTSDR +>M_4802 +YHHRFNNFM +>M_4803 +YHQQNVPWA +>M_4804 +YICDLRRQV +>M_4805 +YINNSVLPY +>M_4806 +YKGSRFHRV +>M_4807 +YLADRVQIV +>M_4808 +YLADRVQIV +>M_4809 +YLENRKETL +>M_4810 +YLENRKETL +>M_4811 +YLEQKPCIY +>M_4812 +YLFRKELRY +>M_4813 +YLKEELMCL +>M_4814 +YLKENFLPW +>M_4815 +YLRRHRDVS +>M_4816 +YLSLVEISY +>M_4817 +YLTVVSLSY +>M_4818 +YMDRTPGPA +>M_4819 +YMKTQSKSS +>M_4820 +YMLTLFTAM +>M_4821 +YNFKYVDLI +>M_4822 +YNVFRQLSL +>M_4823 +YPMRRRQCE +>M_4824 +YPRLKMLAF +>M_4825 +YPSIHRFIL +>M_4826 +YQLHNIQVI +>M_4827 +YQMQFTQAL +>M_4828 +YQMQFTQAL +>M_4829 +YQSEKLCSL +>M_4830 +YRAGKPTLV +>M_4831 +YRASEQKLC +>M_4832 +YRDNTELPY +>M_4833 +YRDVHVQKV +>M_4834 +YRGPLSTTI +>M_4835 +YRGSVAPIL +>M_4836 +YRITVVESL +>M_4837 +YRLEAVHAL +>M_4838 +YRLEGDTLI +>M_4839 +YRQFPKKSL +>M_4840 +YRRHSLRAI +>M_4841 +YRTVNNLIL +>M_4842 +YSFDSLCQY +>M_4843 +YSRDQIYIY +>M_4844 +YSRQMISEL +>M_4845 +YSRQMISEL +>M_4846 +YTCEQNDQL +>M_4847 +YTDSSSVLN +>M_4848 +YTEDHSASL +>M_4849 +YTELWFLGL +>M_4850 +YTLLAFSVF +>M_4851 +YTRKCTQAI +>M_4852 +YTSMWRTYV +>M_4853 +YTSMWRTYV +>M_4854 +YVAICSPLF +>M_4855 +YVDYMMCEF +>M_4856 +YVFLHQCVL +>M_4857 +YVFLHQCVL +>M_4858 +YVGENVRFV +>M_4859 +YVGIFHFQF +>M_4860 +YVLTRSKAM +>M_4861 +YVTVLCLTF +>M_4862 +YVYSLYWSI +>M_4863 +YWGVFAPIW +>M_4864 +YWPPQSQPF +>M_4865 +YYEKIFSTL +>M_4866 +YYFLCLLL* +>M_4867 +YYFLRPLL* +>M_4868 +YYFLRPLL* +>M_4869 +YYKIVSSIL +>M_4870 +YYLVANTKF +>M_4871 +YYTNFSLEL +>M_4872 +YYTNFSLEL +>M_4873 +YYYFLCLLL +>M_4874 +YYYFLRPLL +>M_4875 +YYYFLRPLL diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_135773_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_135773_1_T_iedb.xml new file mode 100755 index 00000000..c0028a47 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_135773_1_T_iedb.xml @@ -0,0 +1,41743 @@ + + + + blastp + BLASTP 2.2.30+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta + Query_1 + M_3590 + 9 + + + BLOSUM62 + 100000000 + 11 + 1 + F + + + + + 1 + Query_1 + M_3590 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 2 + Query_2 + M_3591 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 3 + Query_3 + M_3592 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 4 + Query_4 + M_3593 + 9 + + + 1 + gnl|BL_ORD_ID|1223 + 97093|polyprotein|AAB66324.1|Hepatitis C virus (isolate H77)|63746 + 1223 + 10 + + + 1 + 13.4678 + 23 + 8.17864 + 2 + 7 + 4 + 9 + 0 + 0 + 4 + 5 + 0 + 6 + HASLIP + HADVIP + HA +IP + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 5 + Query_5 + M_3594 + 9 + + + 1 + gnl|BL_ORD_ID|99 + 6808|membrane protein|AAA45887.1|Human gammaherpesvirus 4|10376 + 99 + 8 + + + 1 + 13.853 + 24 + 7.77379 + 3 + 9 + 1 + 7 + 0 + 0 + 5 + 5 + 0 + 7 + CGLGKIL + CPLSKIL + C L KIL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 6 + Query_6 + M_3595 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 7 + Query_7 + M_3596 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 8 + Query_8 + M_3597 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 9 + Query_9 + M_3598 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 10 + Query_10 + M_3599 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 11 + Query_11 + M_3600 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 12 + Query_12 + M_3601 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 13 + Query_13 + M_3602 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 14 + Query_14 + M_3603 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 15 + Query_15 + M_3604 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 16 + Query_16 + M_3605 + 9 + + + 1 + gnl|BL_ORD_ID|114 + 7660|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 + 114 + 20 + + + 1 + 13.0826 + 22 + 16.9313 + 2 + 9 + 7 + 14 + 0 + 0 + 3 + 5 + 0 + 8 + MCVIHFSF + MCAVHPTL + MC +H + + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 17 + Query_17 + M_3606 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 18 + Query_18 + M_3607 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 19 + Query_19 + M_3608 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 20 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13.4678 + 23 + 10.0233 + 1 + 6 + 4 + 9 + 0 + 0 + 4 + 6 + 0 + 6 + ARINSI + ARLNSL + AR+NS+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 25 + Query_25 + M_3614 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 26 + Query_26 + M_3615 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 27 + Query_27 + M_3616 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 28 + Query_28 + M_3617 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 29 + Query_29 + M_3618 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 30 + Query_30 + M_3619 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 31 + Query_31 + M_3620 + 9 + + + 1 + gnl|BL_ORD_ID|1393 + 110338|Protein E6|P03126.1|Human papillomavirus type 16|333760 + 1393 + 33 + + + 1 + 16.5494 + 31 + 0.25572 + 2 + 9 + 15 + 22 + 0 + 0 + 6 + 7 + 0 + 8 + RPEKLPEL + RPRKLPQL + RP KLP+L + + + + + 2 + gnl|BL_ORD_ID|1428 + 113122|Protein E6|P03126.1|Human papillomavirus type 16|333760 + 1428 + 10 + + + 1 + 16.1642 + 30 + 0.350719 + 2 + 9 + 3 + 10 + 0 + 0 + 6 + 7 + 0 + 8 + RPEKLPEL + RPRKLPQL + RP KLP+L + + + + + 3 + gnl|BL_ORD_ID|1394 + 110373|Protein E6|P03126.1|Human papillomavirus type 16|333760 + 1394 + 25 + + + 1 + 14.6234 + 26 + 1.89486 + 3 + 9 + 1 + 7 + 0 + 0 + 5 + 6 + 0 + 7 + PEKLPEL + PRKLPQL + P KLP+L + + + + + 4 + gnl|BL_ORD_ID|2189 + 190533|nucleocapsid protein|AAP49024.1|SARS coronavirus|227859 + 2189 + 15 + + + 1 + 13.853 + 24 + 6.19118 + 2 + 8 + 2 + 8 + 0 + 0 + 4 + 5 + 0 + 7 + RPEKLPE + RPQGLPN + RP+ LP + + + + + 5 + gnl|BL_ORD_ID|850 + 55683|nucleocapsid protein|ABI96968.1|SARS coronavirus|227859 + 850 + 15 + + + 1 + 13.853 + 24 + 6.40908 + 2 + 8 + 2 + 8 + 0 + 0 + 4 + 5 + 0 + 7 + RPEKLPE + RPQGLPN + RP+ LP + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 32 + Query_32 + M_3621 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 33 + Query_33 + M_3622 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 34 + Query_34 + M_3623 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 35 + Query_35 + M_3624 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 36 + Query_36 + M_3625 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 37 + Query_37 + M_3626 + 9 + + + 1 + gnl|BL_ORD_ID|798 + 53148|Transcription activator BRLF1|P03209.1|Human herpesvirus 4 strain B95-8|10377 + 798 + 15 + + + 1 + 13.4678 + 23 + 12.0936 + 1 + 6 + 10 + 15 + 0 + 0 + 4 + 6 + 0 + 6 + ASFSNH + ASYSSH + AS+S+H + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 38 + Query_38 + M_3627 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 39 + Query_39 + M_3628 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 40 + Query_40 + M_3629 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 41 + Query_41 + M_3630 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 42 + Query_42 + M_3631 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 43 + Query_43 + M_3632 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 44 + Query_44 + M_3633 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 45 + Query_45 + M_3634 + 9 + + + 1 + gnl|BL_ORD_ID|1171 + 79300|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 + 1171 + 15 + + + 1 + 11.927 + 19 + 83.5344 + 1 + 8 + 2 + 9 + 0 + 0 + 4 + 5 + 0 + 8 + CFPLHGLQ + SFPDPGLR + FP GL+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 46 + Query_46 + M_3635 + 9 + + + 1 + gnl|BL_ORD_ID|2252 + 244160|surface antigen 2 (CA-2)|XP_818927.1|Trypanosoma cruzi strain CL Brener|353153 + 2252 + 9 + + + 1 + 13.0826 + 22 + 13.4763 + 1 + 6 + 3 + 8 + 0 + 0 + 4 + 5 + 0 + 6 + CGDKIS + AGDKLS + GDK+S + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 47 + Query_47 + M_3636 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 48 + Query_48 + M_3637 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 49 + Query_49 + M_3638 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 50 + Query_50 + M_3639 + 9 + + + 1 + gnl|BL_ORD_ID|109 + 7353|Early antigen protein D|P03191.1|Human herpesvirus 4 strain B95-8|10377 + 109 + 9 + + + 1 + 12.3122 + 20 + 45.611 + 1 + 9 + 1 + 9 + 0 + 0 + 3 + 7 + 0 + 9 + CHSNSRDHL + CYDHAQTHL + C+ +++ HL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 51 + Query_51 + M_3640 + 9 + + + 1 + gnl|BL_ORD_ID|582 + 36504|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 + 582 + 9 + + + 1 + 12.6974 + 21 + 26.0147 + 1 + 6 + 4 + 9 + 0 + 0 + 4 + 5 + 0 + 6 + CHYEKK + CHSKKK + CH +KK + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 52 + Query_52 + M_3641 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 53 + Query_53 + M_3642 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 54 + Query_54 + M_3643 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 55 + Query_55 + M_3644 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 56 + Query_56 + M_3645 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 57 + Query_57 + M_3646 + 9 + + + 1 + gnl|BL_ORD_ID|383 + 23601|Genome polyprotein|SRC279960|Hepatitis C virus (isolate H77)|63746 + 383 + 21 + + + 1 + 15.0086 + 27 + 1.18025 + 1 + 9 + 2 + 10 + 0 + 0 + 4 + 5 + 0 + 9 + CPPNHIVSL + CPAGHAVGI + CP H V + + + + + + 2 + gnl|BL_ORD_ID|597 + 37127|polyprotein|AAY82030.1|Hepatitis C virus genotype 1|41856 + 597 + 9 + + + 1 + 13.853 + 24 + 7.07804 + 1 + 7 + 3 + 9 + 0 + 0 + 4 + 4 + 0 + 7 + CPPNHIV + CPAGHAV + CP H V + + + + + 3 + gnl|BL_ORD_ID|598 + 37136|Genome polyprotein|P27958.3|Hepatitis C virus|11103 + 598 + 9 + + + 1 + 13.4678 + 23 + 9.5131 + 1 + 7 + 3 + 9 + 0 + 0 + 4 + 4 + 0 + 7 + CPPNHIV + CPTGHAV + CP H V + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 58 + Query_58 + M_3647 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 59 + Query_59 + M_3648 + 9 + + + 1 + gnl|BL_ORD_ID|291 + 19435|polyprotein|CDF77361.1|Dengue virus 3|11069 + 291 + 10 + + + 1 + 15.0086 + 27 + 1.14868 + 3 + 9 + 1 + 7 + 0 + 0 + 5 + 6 + 0 + 7 + AETRKTF + GESRKTF + E+RKTF + + + + + 2 + gnl|BL_ORD_ID|290 + 19434|Genome polyprotein|P27915.1|Dengue virus 3|11069 + 290 + 9 + + + 1 + 15.0086 + 27 + 1.29649 + 3 + 9 + 1 + 7 + 0 + 0 + 5 + 6 + 0 + 7 + AETRKTF + GESRKTF + E+RKTF + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 60 + Query_60 + M_3649 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 61 + Query_61 + M_3650 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 62 + Query_62 + M_3651 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 63 + Query_63 + M_3652 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 64 + Query_64 + M_3653 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 65 + Query_65 + M_3654 + 9 + + + 1 + gnl|BL_ORD_ID|156 + 11956|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 + 156 + 11 + + + 1 + 12.3122 + 20 + 38.8163 + 1 + 9 + 3 + 11 + 0 + 0 + 4 + 5 + 0 + 9 + CRPQCCQSV + CRVLCCYVL + CR CC + + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 66 + Query_66 + M_3655 + 9 + + + 1 + gnl|BL_ORD_ID|810 + 54330|BZLF1|AAA66529.1|Human gammaherpesvirus 4|10376 + 810 + 13 + + + 1 + 13.853 + 24 + 5.6596 + 1 + 9 + 3 + 11 + 0 + 0 + 5 + 6 + 0 + 9 + CRRGLEQLL + CRAKFKQLL + CR +QLL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 67 + Query_67 + M_3656 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 68 + Query_68 + M_3657 + 9 + + + 1 + gnl|BL_ORD_ID|61 + 4371|tegument protein VP11/12|NP_044516.1|Human alphaherpesvirus 2|10310 + 61 + 9 + + + 1 + 11.927 + 19 + 112.786 + 1 + 8 + 1 + 8 + 0 + 0 + 4 + 5 + 0 + 8 + CSDTHTNE + ASDSLNNE + SD+ NE + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 69 + Query_69 + M_3658 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 70 + Query_70 + M_3659 + 9 + + + 1 + gnl|BL_ORD_ID|2118 + 186354|polyprotein|AGO67248.1|Dengue virus 2|11060 + 2118 + 10 + + + 1 + 13.4678 + 23 + 10.9961 + 3 + 9 + 4 + 10 + 0 + 0 + 5 + 6 + 0 + 7 + MTKIFSL + LTKRFSL + +TK FSL + + + + + 2 + gnl|BL_ORD_ID|445 + 27216|polyprotein|BAD73987.1|Hepatitis C virus subtype 1b|31647 + 445 + 9 + + + 1 + 12.6974 + 21 + 31.4086 + 2 + 9 + 2 + 9 + 0 + 0 + 4 + 6 + 0 + 8 + VMTKIFSL + LMTHFFSI + +MT FS+ + + + + + 3 + gnl|BL_ORD_ID|1678 + 149027|NS5 protein|BAA00702.1|Hepatitis C virus (isolate H77)|63746 + 1678 + 18 + + + 1 + 12.3122 + 20 + 40.471 + 2 + 9 + 10 + 17 + 0 + 0 + 4 + 6 + 0 + 8 + VMTKIFSL + LMTHFFSV + +MT FS+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 71 + Query_71 + M_3660 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 72 + Query_72 + M_3661 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 73 + Query_73 + M_3662 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 74 + Query_74 + M_3663 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 75 + Query_75 + M_3664 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 76 + Query_76 + M_3665 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 77 + Query_77 + M_3666 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 78 + Query_78 + M_3667 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 79 + Query_79 + M_3668 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 80 + Query_80 + M_3669 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 81 + Query_81 + M_3670 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 82 + Query_82 + M_3671 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 83 + Query_83 + M_3672 + 9 + + + 1 + gnl|BL_ORD_ID|1139 + 75356|EBNA3A nuclear protein|Q8AZJ8|Human gammaherpesvirus 4|10376 + 1139 + 9 + + + 1 + 13.4678 + 23 + 12.7908 + 2 + 7 + 3 + 8 + 0 + 0 + 4 + 5 + 0 + 6 + LHTRHG + LHEQHG + LH +HG + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 84 + Query_84 + M_3673 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 85 + Query_85 + M_3674 + 9 + + + 1 + gnl|BL_ORD_ID|131 + 9316|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 + 131 + 15 + + + 1 + 13.4678 + 23 + 11.8896 + 1 + 6 + 1 + 6 + 0 + 0 + 4 + 5 + 0 + 6 + DLLGHP + DLVGWP + DL+G P + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 86 + Query_86 + M_3675 + 9 + + + 1 + gnl|BL_ORD_ID|1573 + 141402|tegument protein VP22|NP_044651.1|Human alphaherpesvirus 1|10298 + 1573 + 10 + + + 1 + 12.6974 + 21 + 27.4501 + 3 + 7 + 2 + 6 + 0 + 0 + 4 + 5 + 0 + 5 + PTKRP + PTERP + PT+RP + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + 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146213|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 + 1630 + 18 + + + 1 + 12.3122 + 20 + 38.0157 + 1 + 9 + 2 + 10 + 0 + 0 + 4 + 5 + 0 + 9 + FWCAQFTSF + FWESVFTGL + FW + FT + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 272 + Query_272 + M_3861 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 273 + Query_273 + M_3862 + 9 + + + 1 + gnl|BL_ORD_ID|422 + 25460|Fusion glycoprotein F0 precursor|P03420.1|Human respiratory syncytial virus A2|11259 + 422 + 11 + + + 1 + 13.4678 + 23 + 10.7778 + 4 + 8 + 6 + 10 + 0 + 0 + 4 + 4 + 0 + 5 + LFYCK + LLYCK + L YCK + + + + + 2 + gnl|BL_ORD_ID|1960 + 182599|polyprotein|AGW21594.1|Dengue virus 1|11053 + 1960 + 9 + + + 1 + 12.3122 + 20 + 45.611 + 1 + 6 + 3 + 8 + 0 + 0 + 3 + 4 + 0 + 6 + FWKLFY + MWQLMY + W+L Y + + + + + 3 + gnl|BL_ORD_ID|1887 + 180579|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 + 1887 + 15 + + + 1 + 11.5418 + 18 + 98.8375 + 1 + 6 + 6 + 11 + 0 + 0 + 3 + 3 + 0 + 6 + FWKLFY + MWSLMY + W L Y + + + + + 4 + gnl|BL_ORD_ID|1945 + 180828|polyprotein|AGO67248.1|Dengue virus 2|11060 + 1945 + 10 + + + 1 + 11.5418 + 18 + 137.176 + 1 + 6 + 4 + 9 + 0 + 0 + 3 + 3 + 0 + 6 + FWKLFY + MWSLMY + W L Y + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 274 + Query_274 + M_3863 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 275 + Query_275 + M_3864 + 9 + + + 1 + gnl|BL_ORD_ID|1231 + 97400|Genome polyprotein|P26664.3|Hepatitis C virus|11103 + 1231 + 10 + + + 1 + 12.6974 + 21 + 25.2038 + 1 + 8 + 3 + 10 + 0 + 0 + 3 + 5 + 0 + 8 + FYAIVVPM + FYGKAIPL + FY +P+ + + + + + 2 + gnl|BL_ORD_ID|274 + 18397|Genome polyprotein|P26662.3|Hepatitis C virus|11103 + 274 + 11 + + + 1 + 12.6974 + 21 + 35.1103 + 1 + 8 + 1 + 8 + 0 + 0 + 3 + 5 + 0 + 8 + FYAIVVPM + FYGKAIPI + FY +P+ + + + + + 3 + gnl|BL_ORD_ID|1230 + 97399|polyprotein|ACZ60108.1|Hepatitis C virus subtype 3a|356426 + 1230 + 10 + + + 1 + 12.3122 + 20 + 51.1794 + 1 + 8 + 3 + 10 + 0 + 0 + 3 + 5 + 0 + 8 + FYAIVVPM + FYGKAIPI + FY +P+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 276 + Query_276 + M_3865 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 277 + Query_277 + M_3866 + 9 + + + 1 + gnl|BL_ORD_ID|1781 + 156550|E3 ubiquitin-protein ligase Mdm2|Q00987.1|Homo sapiens|9606 + 1781 + 9 + + + 1 + 14.2382 + 25 + 3.55601 + 1 + 6 + 3 + 8 + 0 + 0 + 5 + 5 + 0 + 6 + FYLGTY + FYLGQY + FYLG Y + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 278 + Query_278 + M_3867 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 279 + Query_279 + M_3868 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 280 + Query_280 + M_3869 + 9 + + + 1 + gnl|BL_ORD_ID|1336 + 107894|polyprotein|CAB41951.1|Hepatitis C virus|11103 + 1336 + 10 + + + 1 + 14.2382 + 25 + 4.23087 + 3 + 9 + 3 + 9 + 0 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27.2657 + 2 + 9 + 13 + 20 + 0 + 0 + 4 + 5 + 0 + 8 + HDAPRRTL + HGAGTRTI + H A RT+ + + + + + 2 + gnl|BL_ORD_ID|1089 + 72038|Polyprotein|Q9IZA3|Hepatitis C virus subtype 2a|31649 + 1089 + 10 + + + 1 + 12.6974 + 21 + 35.4066 + 2 + 9 + 3 + 10 + 0 + 0 + 4 + 5 + 0 + 8 + HDAPRRTL + HGAGNKTL + H A +TL + + + + + 3 + gnl|BL_ORD_ID|1090 + 72039|polyprotein|CAB53095.1|Hepatitis C virus subtype 1b|31647 + 1090 + 10 + + + 1 + 12.3122 + 20 + 41.8935 + 2 + 9 + 3 + 10 + 0 + 0 + 4 + 5 + 0 + 8 + HDAPRRTL + HGAGSKTL + H A +TL + + + + + 4 + gnl|BL_ORD_ID|391 + 23883|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 + 391 + 15 + + + 1 + 11.5418 + 18 + 100.351 + 2 + 9 + 1 + 8 + 0 + 0 + 4 + 5 + 0 + 8 + HDAPRRTL + HGAGTRTI + H A RT+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 286 + Query_286 + M_3875 + 9 + + + 1 + gnl|BL_ORD_ID|2088 + 185491|polyprotein|AGO67248.1|Dengue virus 2|11060 + 2088 + 10 + + + 1 + 13.0826 + 22 + 19.8203 + 2 + 9 + 3 + 10 + 0 + 0 + 4 + 7 + 0 + 8 + HKEDAGVV 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GHVAGEQML + GHQAAMQML + GH A QML + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 297 + Query_297 + M_3886 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 298 + Query_298 + M_3887 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 299 + Query_299 + M_3888 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 300 + Query_300 + M_3889 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 301 + Query_301 + M_3890 + 9 + + + 1 + gnl|BL_ORD_ID|1775 + 155637|tegument protein|CAB06732.1|Human alphaherpesvirus 2|10310 + 1775 + 15 + + + 1 + 14.6234 + 26 + 1.37617 + 1 + 7 + 3 + 9 + 0 + 0 + 5 + 5 + 0 + 7 + GPCRRRF + GPADRRF + GP RRF + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 302 + Query_302 + M_3891 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 303 + Query_303 + M_3892 + 9 + + + 1 + gnl|BL_ORD_ID|654 + 38724|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 + 654 + 20 + + + 1 + 13.0826 + 22 + 20.5164 + 2 + 9 + 2 + 9 + 0 + 0 + 4 + 4 + 0 + 8 + PRTKAWFL + PSTLRWFF + P T WF + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 304 + Query_304 + M_3893 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 305 + Query_305 + M_3894 + 9 + + + 1 + gnl|BL_ORD_ID|1774 + 155554|RL2|CAB06760.1|Human alphaherpesvirus 2|10310 + 1774 + 15 + + + 1 + 13.853 + 24 + 4.61107 + 3 + 8 + 4 + 9 + 0 + 0 + 4 + 4 + 0 + 6 + APCWQR + APAWSR + AP W R + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 306 + Query_306 + M_3895 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 307 + Query_307 + M_3896 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 308 + Query_308 + M_3897 + 9 + + 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180689|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 + 1919 + 15 + + + 1 + 12.6974 + 21 + 22.89 + 1 + 9 + 4 + 12 + 0 + 0 + 3 + 5 + 0 + 9 + IHIDDNKWV + VHADMGYWI + +H D W+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 364 + Query_364 + M_3953 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 365 + Query_365 + M_3954 + 9 + + + 1 + gnl|BL_ORD_ID|665 + 40158|polyprotein|AAA45534.1|Hepatitis C virus|11103 + 665 + 15 + + + 1 + 12.3122 + 20 + 57.5015 + 1 + 7 + 8 + 14 + 0 + 0 + 3 + 5 + 0 + 7 + IHLLYPP + LHVWVPP + +H+ PP + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 366 + Query_366 + M_3955 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 367 + Query_367 + M_3956 + 9 + + + 1 + gnl|BL_ORD_ID|1390 + 110306|Protein E6|P03126.1|Human papillomavirus type 16|333760 + 1390 + 32 + + + 1 + 10.001 + 14 + 635.848 + 1 + 9 + 13 + 21 + 0 + 0 + 4 + 5 + 0 + 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Query_381 + M_3970 + 9 + + + 1 + gnl|BL_ORD_ID|469 + 28484|Protein E6|P03126.1|Human papillomavirus type 16|333760 + 469 + 9 + + + 1 + 10.7714 + 16 + 354.707 + 1 + 9 + 1 + 9 + 0 + 0 + 5 + 5 + 0 + 9 + IREYCPYTY + ISEYRHYCY + I EY Y Y + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 382 + Query_382 + M_3971 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 383 + Query_383 + M_3972 + 9 + + + 1 + gnl|BL_ORD_ID|1481 + 133645|cell surface protein|NP_302626.1|Mycobacterium leprae|1769 + 1481 + 15 + + + 1 + 13.0826 + 22 + 17.8301 + 4 + 9 + 6 + 11 + 0 + 0 + 4 + 5 + 0 + 6 + GNVIAC + GNMSAC + GN+ AC + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 384 + Query_384 + M_3973 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 385 + Query_385 + M_3974 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 386 + Query_386 + M_3975 + 9 + + + + + 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20 + + + 1 + 13.4678 + 23 + 11.8474 + 2 + 7 + 3 + 8 + 0 + 0 + 4 + 5 + 0 + 6 + RRLRPS + KRLEPS + +RL PS + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 391 + Query_391 + M_3980 + 9 + + + 1 + gnl|BL_ORD_ID|761 + 50894|Genome polyprotein|P27909.2|Dengue virus type 1 Hawaii|10000440 + 761 + 20 + + + 1 + 13.4678 + 23 + 11.8474 + 2 + 7 + 3 + 8 + 0 + 0 + 4 + 5 + 0 + 6 + RRLRPS + KRLEPS + +RL PS + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 392 + Query_392 + M_3981 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 393 + Query_393 + M_3982 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 394 + Query_394 + M_3983 + 9 + + + 1 + gnl|BL_ORD_ID|469 + 28484|Protein E6|P03126.1|Human papillomavirus type 16|333760 + 469 + 9 + + + 1 + 12.6974 + 21 + 31.4086 + 1 + 9 + 1 + 9 + 0 + 0 + 5 + 5 + 0 + 9 + ISELLFECY + ISEYRHYCY + ISE CY + + + + + + + 2334 + 25004 + 0 + 225036 + 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M_4034 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 446 + Query_446 + M_4035 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 447 + Query_447 + M_4036 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 448 + Query_448 + M_4037 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 449 + Query_449 + M_4038 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 450 + Query_450 + M_4039 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 451 + Query_451 + M_4040 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 452 + Query_452 + M_4041 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 453 + Query_453 + M_4042 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits 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Query_552 + M_4141 + 9 + + + 1 + gnl|BL_ORD_ID|1435 + 116781|Nucleoprotein|P05133.1|Hantaan virus 76-118|11602 + 1435 + 15 + + + 1 + 12.3122 + 20 + 41.1784 + 1 + 7 + 1 + 7 + 0 + 0 + 4 + 6 + 0 + 7 + LRRMNSF + LRKKSSF + LR+ +SF + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 553 + Query_553 + M_4142 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 554 + Query_554 + M_4143 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 555 + Query_555 + M_4144 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 556 + Query_556 + M_4145 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 557 + Query_557 + M_4146 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 558 + Query_558 + M_4147 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 559 + Query_559 + M_4148 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 560 + Query_560 + M_4149 + 9 + + + 1 + gnl|BL_ORD_ID|1698 + 149115|NS5 protein|BAA00702.1|Hepatitis C virus (isolate H77)|63746 + 1698 + 9 + + + 1 + 13.4678 + 23 + 11.9303 + 3 + 9 + 1 + 7 + 0 + 0 + 5 + 6 + 0 + 7 + SIRVRLL + SVRARLL + S+R RLL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 561 + Query_561 + M_4150 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 562 + Query_562 + M_4151 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 563 + Query_563 + M_4152 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 564 + Query_564 + M_4153 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 565 + Query_565 + M_4154 + 9 + + + 1 + gnl|BL_ORD_ID|1095 + 72301|envelope protein|YP_001527880.1|West Nile virus NY-99|10000971 + 1095 + 18 + + + 1 + 15.0086 + 27 + 1.37027 + 3 + 8 + 1 + 6 + 0 + 0 + 3 + 6 + 0 + 6 + WEYGSI + WDFGSV + W++GS+ + + + + + 2 + gnl|BL_ORD_ID|1924 + 180726|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 + 1924 + 15 + + + 1 + 14.6234 + 26 + 2.14985 + 3 + 8 + 10 + 15 + 0 + 0 + 3 + 6 + 0 + 6 + WEYGSI + WDFGSL + W++GS+ + + + + + 3 + gnl|BL_ORD_ID|1110 + 73059|kaposin|AAC57155.1|Human gammaherpesvirus 8|37296 + 1110 + 15 + + + 1 + 13.853 + 24 + 4.45371 + 2 + 8 + 2 + 8 + 0 + 0 + 4 + 5 + 0 + 7 + RWEYGSI + RWRLGAI + RW G+I + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 566 + Query_566 + M_4155 + 9 + + + 1 + gnl|BL_ORD_ID|418 + 25237|Transcription activator BRLF1|P03209.1|Human herpesvirus 4 strain B95-8|10377 + 418 + 15 + + + 1 + 14.2382 + 25 + 2.88535 + 1 + 9 + 7 + 15 + 0 + 0 + 5 + 6 + 0 + 9 + LRYFLKHGI + MRYVLDHLI + +RY L H I + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 567 + Query_567 + M_4156 + 9 + + + + + 2334 + 25004 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+ + 578 + Query_578 + M_4167 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 579 + Query_579 + M_4168 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 580 + Query_580 + M_4169 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 581 + Query_581 + M_4170 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 582 + Query_582 + M_4171 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 583 + Query_583 + M_4172 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 584 + Query_584 + M_4173 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 585 + Query_585 + M_4174 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 586 + Query_586 + M_4175 + 9 + + + 1 + gnl|BL_ORD_ID|2125 + 186551|polyprotein|AGW21594.1|Dengue virus 1|11053 + 2125 + 10 + + + 1 + 12.3122 + 20 + 48.6895 + 2 + 9 + 1 + 8 + 0 + 0 + 4 + 6 + 0 + 8 + YEDTLYTV + YENLKYSV + YE+ Y+V + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 587 + Query_587 + M_4176 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 588 + Query_588 + M_4177 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 589 + Query_589 + M_4178 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 590 + Query_590 + M_4179 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 591 + Query_591 + M_4180 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 592 + Query_592 + M_4181 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 593 + Query_593 + M_4182 + 9 + + + 1 + gnl|BL_ORD_ID|1619 + 144913|Hexon protein|P04133.3|Human adenovirus 5|28285 + 1619 + 10 + + + 1 + 14.2382 + 25 + 3.62465 + 1 + 9 + 2 + 10 + 0 + 0 + 5 + 6 + 0 + 9 + LYGHSTHDL + LYANSAHAL + LY +S H L + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 594 + Query_594 + M_4183 + 9 + + + 1 + gnl|BL_ORD_ID|1177 + 79506|E1 protein|BAA19893.1|Rubella virus|11041 + 1177 + 20 + + + 1 + 13.4678 + 23 + 8.37795 + 3 + 9 + 4 + 10 + 0 + 0 + 4 + 4 + 0 + 7 + HRDLAKW + HSDAACW + H D A W + + + + + 2 + gnl|BL_ORD_ID|1384 + 110205|Protein E6|P03126.1|Human papillomavirus type 16|333760 + 1384 + 32 + + + 1 + 10.7714 + 16 + 223.475 + 2 + 9 + 6 + 13 + 0 + 0 + 2 + 4 + 0 + 8 + YHRDLAKW + FHNIRGRW + +H +W + + + + + 3 + gnl|BL_ORD_ID|1395 + 110394|Protein E6|P03126.1|Human papillomavirus type 16|333760 + 1395 + 32 + + + 1 + 10.7714 + 16 + 260.809 + 2 + 9 + 24 + 31 + 0 + 0 + 2 + 4 + 0 + 8 + YHRDLAKW + FHNIRGRW + +H +W + + + + + 4 + gnl|BL_ORD_ID|1385 + 110215|Protein E6|P03126.1|Human papillomavirus type 16|333760 + 1385 + 25 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0.14 + + + No hits found + + + 604 + Query_604 + M_4193 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 605 + Query_605 + M_4194 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 606 + Query_606 + M_4195 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 607 + Query_607 + M_4196 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 608 + Query_608 + M_4197 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 609 + Query_609 + M_4198 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 610 + Query_610 + M_4199 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 611 + Query_611 + M_4200 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 612 + Query_612 + M_4201 + 9 + + + 1 + gnl|BL_ORD_ID|259 + 17620|Early antigen protein D|P03191.1|Human herpesvirus 4 strain B95-8|10377 + 259 + 15 + + + 1 + 13.853 + 24 + 5.11701 + 1 + 9 + 4 + 12 + 0 + 0 + 4 + 6 + 0 + 9 + MAYSITCPI + LAYGRTCVL + +AY TC + + + + + + 2 + gnl|BL_ORD_ID|258 + 17619|Early antigen protein D|P03191.1|Human herpesvirus 4 strain B95-8|10377 + 258 + 14 + + + 1 + 13.853 + 24 + 5.3697 + 1 + 9 + 4 + 12 + 0 + 0 + 4 + 6 + 0 + 9 + MAYSITCPI + LAYGRTCVL + +AY TC + + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 613 + Query_613 + M_4202 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 614 + Query_614 + M_4203 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 615 + Query_615 + M_4204 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 616 + Query_616 + M_4205 + 9 + + + 1 + gnl|BL_ORD_ID|1355 + 108148|polyprotein|AAF65953.1|Hepatitis C virus|11103 + 1355 + 10 + + + 1 + 13.0826 + 22 + 20.8706 + 3 + 9 + 1 + 7 + 0 + 0 + 5 + 6 + 0 + 7 + ATDYTTI + STDSTTI + +TD TTI + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 617 + Query_617 + M_4206 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 618 + Query_618 + M_4207 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 619 + Query_619 + M_4208 + 9 + + + 1 + gnl|BL_ORD_ID|306 + 20686|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 + 306 + 11 + + + 1 + 14.2382 + 25 + 3.14502 + 2 + 6 + 1 + 5 + 0 + 0 + 5 + 5 + 0 + 5 + GKSTH + GKSTH + GKSTH + + + + + 2 + gnl|BL_ORD_ID|256 + 17278|Genome polyprotein|P06441.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 + 256 + 20 + + + 1 + 13.853 + 24 + 5.14963 + 2 + 8 + 7 + 13 + 0 + 0 + 5 + 6 + 0 + 7 + GKSTHTS + GESRHTS + G+S HTS + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 620 + Query_620 + M_4209 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 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225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 630 + Query_630 + M_4219 + 9 + + + 1 + gnl|BL_ORD_ID|114 + 7660|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 + 114 + 20 + + + 1 + 11.1566 + 17 + 164.091 + 1 + 9 + 6 + 14 + 0 + 0 + 3 + 5 + 0 + 9 + MLCFYTPAL + LMCAVHPTL + ++C P L + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 631 + Query_631 + M_4220 + 9 + + + 1 + gnl|BL_ORD_ID|654 + 38724|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 + 654 + 20 + + + 1 + 14.2382 + 25 + 2.55563 + 1 + 9 + 11 + 19 + 0 + 0 + 4 + 6 + 0 + 9 + MLHLYPGPM + LFQLYRGPL + + LY GP+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 632 + Query_632 + M_4221 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 633 + Query_633 + M_4222 + 9 + + + 1 + gnl|BL_ORD_ID|2303 + 422997|preC/core protein|CAJ33968.1|Hepatitis B virus|10407 + 2303 + 9 + + + 1 + 14.6234 + 26 + 2.11355 + 3 + 8 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Query_638 + M_4227 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 639 + Query_639 + M_4228 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 640 + Query_640 + M_4229 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 641 + Query_641 + M_4230 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 642 + Query_642 + M_4231 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 643 + Query_643 + M_4232 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 644 + Query_644 + M_4233 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 645 + Query_645 + M_4234 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 646 + Query_646 + M_4235 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + 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M_4241 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 653 + Query_653 + M_4242 + 9 + + + 1 + gnl|BL_ORD_ID|575 + 36306|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 + 575 + 15 + + + 1 + 14.6234 + 26 + 2.07692 + 1 + 8 + 4 + 11 + 0 + 0 + 4 + 5 + 0 + 8 + MRCQYETV + MNCSYENM + M C YE + + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 654 + Query_654 + M_4243 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 655 + Query_655 + M_4244 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 656 + Query_656 + M_4245 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 657 + Query_657 + M_4246 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 658 + Query_658 + M_4247 + 9 + + + 1 + gnl|BL_ORD_ID|409 + 24765|polyprotein [Hepatitis C virus]|ABR27360.1|Hepatitis C virus|11103 + 409 + 9 + + 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74387|Genome polyprotein|P26664.3|Hepatitis C virus (isolate 1)|11104 + 1120 + 9 + + + 1 + 10.3862 + 15 + 504.867 + 4 + 9 + 2 + 7 + 0 + 0 + 2 + 4 + 0 + 6 + LHWSMW + ISWCLW + + W +W + + + + + 6 + gnl|BL_ORD_ID|1119 + 74386|HCV-1|AAA45676.1|Hepatitis C virus|11103 + 1119 + 8 + + + 1 + 10.7714 + 16 + 530.711 + 4 + 9 + 2 + 7 + 0 + 0 + 2 + 4 + 0 + 6 + LHWSMW + ISWCLW + + W +W + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 668 + Query_668 + M_4257 + 9 + + + 1 + gnl|BL_ORD_ID|1186 + 93431|pre-C/C protein|ABY54138.1|Hepatitis B virus|10407 + 1186 + 20 + + + 1 + 11.927 + 19 + 74.4218 + 3 + 8 + 7 + 12 + 0 + 0 + 3 + 5 + 0 + 6 + CLMLQC + CLIISC + CL++ C + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 669 + Query_669 + M_4258 + 9 + + + 1 + gnl|BL_ORD_ID|621 + 37466|surface antigen|BAF44879.1|Hepatitis B virus|10407 + 621 + 9 + + + 1 + 12.6974 + 21 + 28.8346 + 1 + 8 + 2 + 9 + 0 + 0 + 3 + 7 + 0 + 8 + MYCMVFLV + LLCLIFLL + + C++FL+ + + + + + 2 + gnl|BL_ORD_ID|596 + 37120|Major surface antigen precursor|P17399.3|Hepatitis B virus|10407 + 596 + 9 + + + 1 + 12.6974 + 21 + 33.6262 + 1 + 8 + 1 + 8 + 0 + 0 + 3 + 7 + 0 + 8 + MYCMVFLV + LLCLIFLL + + C++FL+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 670 + Query_670 + M_4259 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 671 + Query_671 + M_4260 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 672 + Query_672 + M_4261 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 673 + Query_673 + M_4262 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 674 + Query_674 + M_4263 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 675 + Query_675 + M_4264 + 9 + + + 1 + gnl|BL_ORD_ID|889 + 58463|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 + 889 + 20 + + + 1 + 12.6974 + 21 + 25.6057 + 1 + 7 + 11 + 17 + 0 + 0 + 4 + 6 + 0 + 7 + MYSYAVP + IYVYALP + +Y YA+P + + + + + 2 + gnl|BL_ORD_ID|338 + 21242|polymerase|ACF94272.1|Hepatitis B virus|10407 + 338 + 9 + + + 1 + 12.3122 + 20 + 45.611 + 1 + 7 + 2 + 8 + 0 + 0 + 4 + 5 + 0 + 7 + MYSYAVP + LYSSTVP + +YS VP + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 676 + Query_676 + M_4265 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 677 + Query_677 + M_4266 + 9 + + + 1 + gnl|BL_ORD_ID|557 + 34304|Gag polyprotein|P88150|Human immunodeficiency virus 1|11676 + 557 + 14 + + + 1 + 13.0826 + 22 + 17.8721 + 1 + 7 + 8 + 14 + 0 + 0 + 4 + 6 + 0 + 7 + NEILRRY + NKIVRMY + N+I+R Y + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 678 + Query_678 + M_4267 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 679 + Query_679 + M_4268 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 680 + Query_680 + M_4269 + 9 + + + 1 + gnl|BL_ORD_ID|1132 + 74886|latent membrane protein 1|AAS99606.1|Human gammaherpesvirus 4|10376 + 1132 + 9 + + + 1 + 12.6974 + 21 + 31.9494 + 5 + 9 + 5 + 9 + 0 + 0 + 3 + 4 + 0 + 5 + NWWPI + NWWTL + NWW + + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 681 + Query_681 + M_4270 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 682 + Query_682 + M_4271 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 683 + Query_683 + M_4272 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 684 + Query_684 + M_4273 + 9 + + + 1 + gnl|BL_ORD_ID|715 + 44133|Genome polyprotein|P26664.3|Hepatitis C virus genotype 1|41856 + 715 + 9 + + + 1 + 11.927 + 19 + 69.1936 + 1 + 9 + 1 + 9 + 0 + 0 + 5 + 5 + 0 + 9 + NHSDLAAEL + NHDSPDAEL + NH AEL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 685 + Query_685 + M_4274 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 686 + Query_686 + M_4275 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 687 + Query_687 + M_4276 + 9 + + + 1 + gnl|BL_ORD_ID|1219 + 96898|Genome polyprotein|SRC279960|Hepatitis C virus|11103 + 1219 + 17 + + + 1 + 13.853 + 24 + 4.23286 + 1 + 8 + 7 + 14 + 0 + 0 + 5 + 6 + 0 + 8 + NIVYHTAS + NLVYSTTS + N+VY T S + + + + + 2 + gnl|BL_ORD_ID|1218 + 96897|polyprotein|ABR25251.1|Hepatitis C virus (isolate H77)|63746 + 1218 + 17 + + + 1 + 13.853 + 24 + 5.7721 + 1 + 8 + 7 + 14 + 0 + 0 + 5 + 6 + 0 + 8 + NIVYHTAS + NLVYSTTS + N+VY T S + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 688 + Query_688 + M_4277 + 9 + + + 1 + gnl|BL_ORD_ID|487 + 30892|Protein E6|P03126.1|Human papillomavirus type 16|333760 + 487 + 9 + + + 1 + 14.6234 + 26 + 1.76369 + 1 + 9 + 1 + 9 + 0 + 0 + 5 + 6 + 0 + 9 + NIYSRIREY + KFYSKISEY + YS+I EY + + + + + 2 + gnl|BL_ORD_ID|1400 + 110467|Protein E6|P03126.1|Human papillomavirus type 16|333760 + 1400 + 25 + + + 1 + 14.6234 + 26 + 2.69562 + 2 + 9 + 16 + 23 + 0 + 0 + 5 + 6 + 0 + 8 + IYSRIREY + FYSKISEY + YS+I EY + + + + + 3 + gnl|BL_ORD_ID|1387 + 110227|Protein E6|P03126.1|Human papillomavirus type 16|333760 + 1387 + 33 + + + 1 + 14.2382 + 25 + 3.62324 + 1 + 9 + 22 + 30 + 0 + 0 + 5 + 6 + 0 + 9 + NIYSRIREY + KFYSKISEY + YS+I EY + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 689 + Query_689 + M_4278 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 690 + Query_690 + M_4279 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 691 + Query_691 + M_4280 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 692 + Query_692 + M_4281 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 693 + Query_693 + M_4282 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 694 + Query_694 + M_4283 + 9 + + + 1 + gnl|BL_ORD_ID|1300 + 103654|polyprotein|BAB18806.1|Hepatitis C virus|11103 + 1300 + 9 + + + 1 + 12.6974 + 21 + 26.0147 + 1 + 6 + 1 + 6 + 0 + 0 + 4 + 5 + 0 + 6 + NLMAKN + TIMAKN + +MAKN + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 695 + Query_695 + M_4284 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 696 + Query_696 + M_4285 + 9 + + + 1 + gnl|BL_ORD_ID|21 + 1356|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 + 21 + 15 + + + 1 + 14.6234 + 26 + 1.63256 + 1 + 8 + 5 + 12 + 0 + 0 + 4 + 6 + 0 + 8 + NLPSKRVS + NVPYKRIE + N+P KR+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 697 + Query_697 + M_4286 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 698 + Query_698 + M_4287 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 699 + Query_699 + M_4288 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 700 + Query_700 + M_4289 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 701 + Query_701 + M_4290 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 702 + Query_702 + M_4291 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 703 + Query_703 + M_4292 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 704 + Query_704 + M_4293 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 705 + Query_705 + M_4294 + 9 + + + 1 + gnl|BL_ORD_ID|540 + 32998|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 + 540 + 11 + + + 1 + 13.4678 + 23 + 12.17 + 2 + 7 + 6 + 11 + 0 + 0 + 4 + 6 + 0 + 6 + RLDLVR + RVDMVR + R+D+VR + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 706 + Query_706 + M_4295 + 9 + + + 1 + gnl|BL_ORD_ID|1406 + 110846|E6 protein|CAB45108.1|Human papillomavirus type 16|333760 + 1406 + 9 + + + 1 + 13.853 + 24 + 6.71897 + 2 + 8 + 3 + 9 + 0 + 0 + 4 + 6 + 0 + 7 + RNYCVSV + RHYCYSL + R+YC S+ + + + + + 2 + gnl|BL_ORD_ID|855 + 55779|fusion protein|BAB60865.1|Measles virus|11234 + 855 + 9 + + + 1 + 11.5418 + 18 + 175.774 + 2 + 9 + 1 + 8 + 0 + 0 + 4 + 5 + 0 + 8 + RNYCVSVY + RRYPDAVY + R Y +VY + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 707 + Query_707 + M_4296 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 708 + Query_708 + M_4297 + 9 + + + 1 + gnl|BL_ORD_ID|958 + 62977|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 + 958 + 10 + + + 1 + 13.853 + 24 + 4.37925 + 4 + 8 + 3 + 7 + 0 + 0 + 4 + 5 + 0 + 5 + RHTPM + RHTPV + RHTP+ + + + + + 2 + gnl|BL_ORD_ID|55 + 4156|polyprotein|ABR25251.1|Hepatitis C virus|11103 + 55 + 9 + + + 1 + 13.853 + 24 + 4.51705 + 4 + 8 + 2 + 6 + 0 + 0 + 4 + 5 + 0 + 5 + RHTPM + RHTPV + RHTP+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 709 + Query_709 + M_4298 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 710 + Query_710 + M_4299 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 711 + Query_711 + M_4300 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 712 + Query_712 + M_4301 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 713 + Query_713 + M_4302 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 714 + Query_714 + M_4303 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 715 + Query_715 + M_4304 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 716 + Query_716 + M_4305 + 9 + + + 1 + gnl|BL_ORD_ID|1125 + 74605|Circumsporozoite protein precursor|P08677.2|Plasmodium vivax strain Belem|31273 + 1125 + 9 + + + 1 + 15.3938 + 28 + 0.735125 + 2 + 8 + 1 + 7 + 0 + 0 + 5 + 7 + 0 + 7 + YLEKVRS + YLDKVRA + YL+KVR+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 717 + Query_717 + M_4306 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 718 + Query_718 + M_4307 + 9 + + + 1 + gnl|BL_ORD_ID|416 + 25149|polyprotein|BAD73994.1|Hepatitis C virus subtype 1b|31647 + 416 + 9 + + + 1 + 14.6234 + 26 + 2.07889 + 1 + 6 + 1 + 6 + 0 + 0 + 4 + 6 + 0 + 6 + NYSPRP + HYAPRP + +Y+PRP + + + + + 2 + gnl|BL_ORD_ID|1551 + 141226|tegument protein UL37|ADD60080.1|Human alphaherpesvirus 1|10298 + 1551 + 9 + + + 1 + 13.853 + 24 + 5.84954 + 2 + 7 + 2 + 7 + 0 + 0 + 4 + 5 + 0 + 6 + YSPRPI + YLPRPV + Y PRP+ + + + + + 3 + gnl|BL_ORD_ID|2240 + 230030|Nef protein|BAA86664.1|Human immunodeficiency virus 1|11676 + 2240 + 10 + + + 1 + 13.4678 + 23 + 7.76238 + 1 + 6 + 1 + 6 + 0 + 0 + 4 + 5 + 0 + 6 + NYSPRP + NYTPGP + NY+P P + + + + + 4 + gnl|BL_ORD_ID|2238 + 230028|Protein Nef|P04603.3|Human immunodeficiency virus 1|11676 + 2238 + 10 + + + 1 + 13.4678 + 23 + 7.89871 + 1 + 6 + 1 + 6 + 0 + 0 + 4 + 5 + 0 + 6 + NYSPRP + NYTPGP + NY+P P + + + + + 5 + gnl|BL_ORD_ID|2239 + 230029|Protein Nef|P03404.4|Human immunodeficiency virus 1|11676 + 2239 + 10 + + + 1 + 13.4678 + 23 + 9.73455 + 1 + 6 + 1 + 6 + 0 + 0 + 4 + 5 + 0 + 6 + NYSPRP + NYTPGP + NY+P P + + + + + 6 + gnl|BL_ORD_ID|1011 + 67349|Latent membrane protein 2|Q69135|Human gammaherpesvirus 4|10376 + 1011 + 9 + + + 1 + 11.927 + 19 + 92.9112 + 1 + 9 + 1 + 9 + 0 + 0 + 3 + 5 + 0 + 9 + NYSPRPICV + TYGPVFMCL + Y P +C+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 719 + Query_719 + M_4308 + 9 + + + 1 + gnl|BL_ORD_ID|150 + 11063|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 + 150 + 15 + + + 1 + 14.2382 + 25 + 4.08331 + 1 + 9 + 7 + 15 + 0 + 0 + 5 + 6 + 0 + 9 + PASTLSLGY + PASIAARGY + PAS + GY + + + + + 2 + gnl|BL_ORD_ID|1855 + 180408|polyprotein|AGO67248.1|Dengue virus 2|11060 + 1855 + 10 + + + 1 + 13.853 + 24 + 4.61192 + 1 + 9 + 2 + 10 + 0 + 0 + 5 + 6 + 0 + 9 + PASTLSLGY + PASIAARGY + PAS + GY + + + + + 3 + gnl|BL_ORD_ID|1639 + 146285|polyprotein|ADF97231.1|Hepatitis C virus subtype 3a|356426 + 1639 + 18 + + + 1 + 13.4678 + 23 + 11.4723 + 1 + 9 + 7 + 15 + 0 + 0 + 4 + 7 + 0 + 9 + PASTLSLGY + PAAYVAQGY + PA+ ++ GY + + + + + 4 + gnl|BL_ORD_ID|1638 + 146284|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 + 1638 + 18 + + + 1 + 12.3122 + 20 + 44.435 + 1 + 9 + 7 + 15 + 0 + 0 + 4 + 6 + 0 + 9 + PASTLSLGY + PAAYAAQGY + PA+ + GY + + + + + 5 + gnl|BL_ORD_ID|737 + 46755|HCV-1|AAA45676.1|Hepatitis C virus genotype 1|41856 + 737 + 20 + + + 1 + 11.927 + 19 + 58.6701 + 1 + 9 + 1 + 9 + 0 + 0 + 4 + 6 + 0 + 9 + PASTLSLGY + PAAYAAQGY + PA+ + GY + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 720 + Query_720 + M_4309 + 9 + + + 1 + gnl|BL_ORD_ID|636 + 37919|envelope protein|BAF48755.1|Hepatitis B virus|10407 + 636 + 10 + + + 1 + 12.3122 + 20 + 47.0941 + 1 + 6 + 4 + 9 + 0 + 0 + 3 + 4 + 0 + 6 + PFPRWL + PFVQWF + PF +W + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 721 + Query_721 + M_4310 + 9 + + + 1 + gnl|BL_ORD_ID|1174 + 79351|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 + 1174 + 17 + + + 1 + 12.6974 + 21 + 34.1537 + 3 + 8 + 7 + 12 + 0 + 0 + 3 + 4 + 0 + 6 + WASSIV + WGGSVV + W S+V + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 722 + Query_722 + M_4311 + 9 + + + 1 + gnl|BL_ORD_ID|747 + 48896|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 + 747 + 15 + + + 1 + 13.853 + 24 + 4.22764 + 1 + 6 + 4 + 9 + 0 + 0 + 4 + 4 + 0 + 6 + PHYDFE + PEYDLE + P YD E + + + + + 2 + gnl|BL_ORD_ID|619 + 37398|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 + 619 + 10 + + + 1 + 13.853 + 24 + 7.36741 + 2 + 7 + 3 + 8 + 0 + 0 + 4 + 5 + 0 + 6 + HYDFER + HTDFEQ + H DFE+ + + + + + 3 + gnl|BL_ORD_ID|581 + 36432|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 + 581 + 9 + + + 1 + 13.4678 + 23 + 8.56958 + 2 + 7 + 2 + 7 + 0 + 0 + 4 + 5 + 0 + 6 + HYDFER + HTDFEQ + H DFE+ + + + + + 4 + gnl|BL_ORD_ID|618 + 37397|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 + 618 + 9 + + + 1 + 13.4678 + 23 + 8.72003 + 2 + 7 + 3 + 8 + 0 + 0 + 4 + 5 + 0 + 6 + HYDFER + HTDFEQ + H DFE+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 723 + Query_723 + M_4312 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 724 + Query_724 + M_4313 + 9 + + + 1 + gnl|BL_ORD_ID|798 + 53148|Transcription activator BRLF1|P03209.1|Human herpesvirus 4 strain B95-8|10377 + 798 + 15 + + + 1 + 13.4678 + 23 + 12.0936 + 1 + 6 + 8 + 13 + 0 + 0 + 4 + 4 + 0 + 6 + PRIGYS + PRASYS + PR YS + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 725 + Query_725 + M_4314 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 726 + Query_726 + M_4315 + 9 + + + 1 + gnl|BL_ORD_ID|854 + 55744|polyprotein precursor|NP_041724.2|West Nile virus|11082 + 854 + 9 + + + 1 + 14.2382 + 25 + 3.74233 + 2 + 9 + 2 + 9 + 0 + 0 + 5 + 7 + 0 + 8 + RNRKPLTV + RSRRSLTV + R+R+ LTV + + + + + 2 + gnl|BL_ORD_ID|1181 + 88849|IE62|AAP32859.1|Human alphaherpesvirus 3|10335 + 1181 + 9 + + + 1 + 13.853 + 24 + 7.20201 + 1 + 7 + 3 + 9 + 0 + 0 + 4 + 6 + 0 + 7 + PRNRKPL + PRSRTPI + PR+R P+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 727 + Query_727 + M_4316 + 9 + + + 1 + gnl|BL_ORD_ID|381 + 23566|tegument protein UL7|NP_044476.1|Human alphaherpesvirus 2|10310 + 381 + 13 + + + 1 + 13.4678 + 23 + 10.7509 + 5 + 9 + 9 + 13 + 0 + 0 + 5 + 5 + 0 + 5 + RCLLL + RCLLL + RCLLL + + + + + 2 + gnl|BL_ORD_ID|1731 + 150556|polyprotein|AGW21594.1|Dengue virus 1|11053 + 1731 + 10 + + + 1 + 12.6974 + 21 + 26.5293 + 3 + 7 + 5 + 9 + 0 + 0 + 4 + 4 + 0 + 5 + PSRCL + PRRCL + P RCL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 728 + Query_728 + M_4317 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 729 + Query_729 + M_4318 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 730 + Query_730 + M_4319 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 731 + Query_731 + M_4320 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 732 + Query_732 + M_4321 + 9 + + + 1 + gnl|BL_ORD_ID|889 + 58463|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 + 889 + 20 + + + 1 + 12.6974 + 21 + 33.9105 + 1 + 9 + 4 + 12 + 0 + 0 + 5 + 5 + 0 + 9 + PSQPANSFY + PSQEPMSIY + PSQ S Y + + + + + 2 + gnl|BL_ORD_ID|749 + 49485|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 + 749 + 11 + + + 1 + 12.3122 + 20 + 50.6074 + 1 + 9 + 1 + 9 + 0 + 0 + 5 + 5 + 0 + 9 + PSQPANSFY + PSQEPMSIY + PSQ S Y + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 733 + Query_733 + M_4322 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 734 + Query_734 + M_4323 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 735 + Query_735 + M_4324 + 9 + + + 1 + gnl|BL_ORD_ID|1569 + 141354|transcriptional regulator ICP4|NP_044662.1|Human alphaherpesvirus 1|10298 + 1569 + 10 + + + 1 + 13.4678 + 23 + 8.46851 + 2 + 7 + 2 + 7 + 0 + 0 + 4 + 5 + 0 + 6 + YPETPP + YPDAPP + YP+ PP + + + + + 2 + gnl|BL_ORD_ID|1759 + 154346|RL2|CAB06760.1|Human alphaherpesvirus 2|10310 + 1759 + 15 + + + 1 + 12.3122 + 20 + 59.339 + 3 + 8 + 8 + 13 + 0 + 0 + 4 + 4 + 0 + 6 + PETPPR + PRTAPR + P T PR + + + + + 3 + gnl|BL_ORD_ID|1438 + 120093|unnamed protein product|CAA33016.1|Rubella virus|11041 + 1438 + 21 + + + 1 + 10.001 + 14 + 777.216 + 1 + 6 + 11 + 16 + 0 + 0 + 4 + 4 + 0 + 6 + PYPETP + PPPATP + P P TP + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 736 + Query_736 + M_4325 + 9 + + + 1 + gnl|BL_ORD_ID|1000 + 65810|sporozoite surface protein 2|NP_705260.1|Plasmodium falciparum 3D7|36329 + 1000 + 10 + + + 1 + 13.4678 + 23 + 8.61729 + 1 + 6 + 2 + 7 + 0 + 0 + 4 + 4 + 0 + 6 + PYQGRP + PYAGEP + PY G P + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 737 + Query_737 + M_4326 + 9 + + + 1 + gnl|BL_ORD_ID|1000 + 65810|sporozoite surface protein 2|NP_705260.1|Plasmodium falciparum 3D7|36329 + 1000 + 10 + + + 1 + 13.4678 + 23 + 8.61729 + 1 + 6 + 2 + 7 + 0 + 0 + 4 + 4 + 0 + 6 + PYQGRP + PYAGEP + PY G P + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 738 + Query_738 + M_4327 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 739 + Query_739 + M_4328 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 740 + Query_740 + M_4329 + 9 + + + 1 + gnl|BL_ORD_ID|601 + 37153|Nuclear antigen EBNA-3C|Q69140.1|Human gammaherpesvirus 4|10376 + 601 + 10 + + + 1 + 13.0826 + 22 + 14.2707 + 4 + 9 + 5 + 10 + 0 + 0 + 4 + 6 + 0 + 6 + VKFIGV + VRFMGV + V+F+GV + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 741 + Query_741 + M_4330 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 742 + Query_742 + M_4331 + 9 + + + 1 + gnl|BL_ORD_ID|792 + 53027|nonstructural protein 3|NP_722463.1|Dengue virus 1 Singapore/S275/1990|33741 + 792 + 9 + + + 1 + 11.1566 + 17 + 254.603 + 1 + 9 + 1 + 9 + 0 + 0 + 4 + 5 + 0 + 9 + QFSFDGWKF + QYSDRRWCF + Q+S W F + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 743 + Query_743 + M_4332 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 744 + Query_744 + M_4333 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 745 + Query_745 + M_4334 + 9 + + + 1 + gnl|BL_ORD_ID|1813 + 177701|polyprotein|ACZ60104.1|Hepatitis C virus subtype 3a|356426 + 1813 + 18 + + + 1 + 15.3938 + 28 + 0.691719 + 1 + 9 + 2 + 10 + 0 + 0 + 4 + 6 + 0 + 9 + QHDFCGLYM + KAKICGLYL + + CGLY+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 746 + Query_746 + M_4335 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 747 + Query_747 + M_4336 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 748 + Query_748 + M_4337 + 9 + + + 1 + gnl|BL_ORD_ID|1563 + 141306|tegument host shutoff protein|NP_044643.1|Human alphaherpesvirus 1|10298 + 1563 + 10 + + + 1 + 13.853 + 24 + 5.48318 + 2 + 6 + 5 + 9 + 0 + 0 + 4 + 5 + 0 + 5 + HPNNS + HPNNT + HPNN+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 749 + Query_749 + M_4338 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 750 + Query_750 + M_4339 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 751 + Query_751 + M_4340 + 9 + + + 1 + gnl|BL_ORD_ID|1271 + 101673|gag protein|ABO73990.1|Human immunodeficiency virus 1|11676 + 1271 + 9 + + + 1 + 11.927 + 19 + 71.5135 + 2 + 7 + 2 + 7 + 0 + 0 + 4 + 5 + 0 + 6 + HYAALQ + HQAAMQ + H AA+Q + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 752 + Query_752 + M_4341 + 9 + + + 1 + gnl|BL_ORD_ID|1257 + 98253|trans-sialidase, putative|EAN81042.1|Trypanosoma cruzi|5693 + 1257 + 9 + + + 1 + 14.6234 + 26 + 1.57352 + 2 + 9 + 1 + 8 + 0 + 0 + 6 + 8 + 0 + 8 + ILSRVAAL + MLSRVAAV + +LSRVAA+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 753 + Query_753 + M_4342 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 754 + Query_754 + M_4343 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 755 + Query_755 + M_4344 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 756 + Query_756 + M_4345 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 757 + Query_757 + M_4346 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 758 + Query_758 + M_4347 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 759 + Query_759 + M_4348 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 760 + Query_760 + M_4349 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 761 + Query_761 + M_4350 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 762 + Query_762 + M_4351 + 9 + + + 1 + gnl|BL_ORD_ID|1323 + 107790|polyprotein|AAD56189.1|Hepatitis C virus|11103 + 1323 + 10 + + + 1 + 12.6974 + 21 + 37.8768 + 3 + 8 + 4 + 9 + 0 + 0 + 4 + 4 + 0 + 6 + MCRICH + MCDECH + MC CH + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 763 + Query_763 + M_4352 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 764 + Query_764 + M_4353 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 765 + Query_765 + M_4354 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 766 + Query_766 + M_4355 + 9 + + + 1 + gnl|BL_ORD_ID|191 + 14101|envelope glycoprotein|ABI16336.1|Human immunodeficiency virus 1|11676 + 191 + 9 + + + 1 + 12.6974 + 21 + 30.8766 + 1 + 9 + 1 + 9 + 0 + 0 + 4 + 7 + 0 + 9 + QRFLNVQEL + ERYLKDQQL + +R+L Q+L + + + + + 2 + gnl|BL_ORD_ID|864 + 56574|envelope glycoprotein|ABI16336.1|Human immunodeficiency virus 1|11676 + 864 + 9 + + + 1 + 11.927 + 19 + 69.1936 + 2 + 9 + 1 + 8 + 0 + 0 + 4 + 6 + 0 + 8 + RFLNVQEL + RYLKDQQL + R+L Q+L + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 767 + Query_767 + M_4356 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 768 + Query_768 + M_4357 + 9 + + + 1 + gnl|BL_ORD_ID|1114 + 73862|EBNA-1 protein|Q777E1|Human gammaherpesvirus 4|10376 + 1114 + 15 + + + 1 + 13.0826 + 22 + 16.3955 + 1 + 9 + 7 + 15 + 0 + 0 + 4 + 5 + 0 + 9 + QRHGFGEEI + QTHIFAEVL + Q H F E + + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 769 + Query_769 + M_4358 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 770 + Query_770 + M_4359 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 771 + Query_771 + M_4360 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 772 + Query_772 + M_4361 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 773 + Query_773 + M_4362 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 774 + Query_774 + M_4363 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 775 + Query_775 + M_4364 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 776 + Query_776 + M_4365 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 777 + Query_777 + M_4366 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 778 + Query_778 + M_4367 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 779 + Query_779 + M_4368 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 780 + Query_780 + M_4369 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 781 + Query_781 + M_4370 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 782 + Query_782 + M_4371 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 783 + Query_783 + M_4372 + 9 + + + 1 + gnl|BL_ORD_ID|1674 + 148619|unnamed protein product|BAA14233.1|Hepatitis C virus|11103 + 1674 + 45 + + + 1 + 11.927 + 19 + 52.3928 + 2 + 9 + 35 + 42 + 0 + 0 + 3 + 5 + 0 + 8 + TCKANLCY + TCVNGVCW + TC +C+ + + + + + 2 + gnl|BL_ORD_ID|1632 + 146246|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 + 1632 + 17 + + + 1 + 11.927 + 19 + 83.9093 + 2 + 9 + 4 + 11 + 0 + 0 + 3 + 5 + 0 + 8 + TCKANLCY + TCVNGVCW + TC +C+ + + + + + 3 + gnl|BL_ORD_ID|66 + 4910|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 + 66 + 20 + + + 1 + 11.927 + 19 + 86.1921 + 2 + 9 + 2 + 9 + 0 + 0 + 3 + 5 + 0 + 8 + TCKANLCY + TCINGVCW + TC +C+ + + + + + 4 + gnl|BL_ORD_ID|784 + 52509|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 + 784 + 15 + + + 1 + 11.927 + 19 + 94.4229 + 2 + 9 + 6 + 13 + 0 + 0 + 3 + 5 + 0 + 8 + TCKANLCY + TCINGVCW + TC +C+ + + + + + 5 + gnl|BL_ORD_ID|65 + 4909|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 + 65 + 15 + + + 1 + 11.5418 + 18 + 101.887 + 2 + 9 + 2 + 9 + 0 + 0 + 3 + 5 + 0 + 8 + TCKANLCY + TCINGVCW + TC +C+ + 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147835|early protein|CAA52585.1|Human papillomavirus type 52|10618 + 1661 + 9 + + + 1 + 13.4678 + 23 + 11.9303 + 3 + 9 + 1 + 7 + 0 + 0 + 3 + 6 + 0 + 7 + FTLRCMV + ITIRCII + T+RC++ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 950 + Query_950 + M_4539 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 951 + Query_951 + M_4540 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 952 + Query_952 + M_4541 + 9 + + + 1 + gnl|BL_ORD_ID|1823 + 178351|Protein E7|P03129.1|Human papillomavirus type 16|333760 + 1823 + 15 + + + 1 + 12.6974 + 21 + 26.5542 + 1 + 9 + 3 + 11 + 0 + 0 + 3 + 7 + 0 + 9 + SRHDFHVDL + TLHEYMLDL + + H++ +DL + + + + + 2 + gnl|BL_ORD_ID|982 + 64830|E7 protein|ABL96585.1|Human papillomavirus type 16|333760 + 982 + 9 + + + 1 + 12.3122 + 20 + 40.5299 + 1 + 9 + 1 + 9 + 0 + 0 + 3 + 7 + 0 + 9 + SRHDFHVDL + TLHEYMLDL + + H++ +DL + + + + + 3 + gnl|BL_ORD_ID|1408 + 110940|Protein E7|P03129.1|Human papillomavirus type 16|333760 + 1408 + 15 + + + 1 + 12.3122 + 20 + 54.8452 + 1 + 9 + 7 + 15 + 0 + 0 + 3 + 7 + 0 + 9 + SRHDFHVDL + TLHEYMLDL + + H++ +DL + + + + + 4 + gnl|BL_ORD_ID|1392 + 110335|E7|AAD33253.1|Human papillomavirus type 16|333760 + 1392 + 32 + + + 1 + 11.1566 + 17 + 167.857 + 3 + 9 + 9 + 15 + 0 + 0 + 3 + 6 + 0 + 7 + HDFHVDL + HEYMLDL + H++ +DL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 953 + Query_953 + M_4542 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 954 + Query_954 + M_4543 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 955 + Query_955 + M_4544 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 956 + Query_956 + M_4545 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 957 + Query_957 + M_4546 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 958 + Query_958 + M_4547 + 9 + + + 1 + gnl|BL_ORD_ID|617 + 37364|P53_HUMAN Cellular tumor antigen p53 (Tumor suppressor p53) (Phosphoprotein p53) (Antigen NY-CO-13)|P04637.2|Homo sapiens|9606 + 617 + 9 + + + 1 + 13.0826 + 22 + 17.1877 + 1 + 6 + 3 + 8 + 0 + 0 + 4 + 4 + 0 + 6 + SRNDFE + GRNSFE + RN FE + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 959 + Query_959 + M_4548 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 960 + Query_960 + M_4549 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 961 + Query_961 + M_4550 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 962 + Query_962 + M_4551 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 963 + Query_963 + M_4552 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 964 + Query_964 + M_4553 + 9 + + + + 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product [Hepatitis C virus]|BAA14035.1|Hepatitis C virus|11103 + 1297 + 20 + + + 1 + 13.853 + 24 + 4.73116 + 4 + 8 + 2 + 6 + 0 + 0 + 4 + 5 + 0 + 5 + THPLT + THPIT + THP+T + + + + + 3 + gnl|BL_ORD_ID|985 + 65090|polyprotein|BAB18810.1|Hepatitis C virus (isolate H77)|63746 + 985 + 8 + + + 1 + 13.853 + 24 + 5.69712 + 2 + 8 + 1 + 7 + 0 + 0 + 5 + 6 + 0 + 7 + TQTHPLT + TLTHPIT + T THP+T + + + + + 4 + gnl|BL_ORD_ID|986 + 65092|Genome polyprotein|P26664.3|Hepatitis C virus genotype 1|41856 + 986 + 8 + + + 1 + 13.4678 + 23 + 8.77767 + 2 + 8 + 1 + 7 + 0 + 0 + 5 + 6 + 0 + 7 + TQTHPLT + TLTHPVT + T THP+T + + + + + 5 + gnl|BL_ORD_ID|1645 + 146317|polyprotein|ADF97231.1|Hepatitis C virus subtype 3a|356426 + 1645 + 9 + + + 1 + 13.0826 + 22 + 13.9535 + 4 + 8 + 4 + 8 + 0 + 0 + 4 + 5 + 0 + 5 + THPLT + THPVT + THP+T + + + + + 6 + gnl|BL_ORD_ID|1627 + 146182|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 + 1627 + 8 + + + 1 + 13.0826 + 22 + 15.0555 + 4 + 8 + 3 + 7 + 0 + 0 + 4 + 5 + 0 + 5 + THPLT + THPVT + THP+T + + + + + 7 + gnl|BL_ORD_ID|1608 + 143705|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 + 1608 + 9 + + + 1 + 12.3122 + 20 + 44.8495 + 4 + 9 + 4 + 9 + 0 + 0 + 4 + 5 + 0 + 6 + THPLTL + TFPITL + T P+TL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 982 + Query_982 + M_4571 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 983 + Query_983 + M_4572 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 984 + Query_984 + M_4573 + 9 + + + 1 + gnl|BL_ORD_ID|471 + 28594|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 + 471 + 20 + + + 1 + 15.0086 + 27 + 1.02375 + 1 + 9 + 5 + 13 + 0 + 0 + 5 + 7 + 0 + 9 + STYPDQQHV + SYYPDQKSL + S YPDQ+ + + + + + + 2 + gnl|BL_ORD_ID|1173 + 79337|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 + 1173 + 15 + + + 1 + 12.6974 + 21 + 28.3557 + 2 + 9 + 4 + 11 + 0 + 0 + 4 + 5 + 0 + 8 + TYPDQQHV + TWPLLPHV + T+P HV + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 985 + Query_985 + M_4574 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 986 + Query_986 + M_4575 + 9 + + + 1 + gnl|BL_ORD_ID|313 + 20865|Nucleoprotein|P41269.1|Puumala hantavirus|11604 + 313 + 9 + + + 1 + 16.1642 + 30 + 0.361887 + 1 + 9 + 1 + 9 + 0 + 0 + 5 + 8 + 0 + 9 + SVFPTQLQL + GLFPTQIQV + +FPTQ+Q+ + + + + + 2 + gnl|BL_ORD_ID|1416 + 111604|L1|ABP99807.1|Human papillomavirus type 18|333761 + 1416 + 9 + + + 1 + 14.2382 + 25 + 3.93883 + 1 + 9 + 1 + 9 + 0 + 0 + 5 + 7 + 0 + 9 + SVFPTQLQL + NVFPIFLQM + +VFP LQ+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 987 + Query_987 + M_4576 + 9 + + + 1 + gnl|BL_ORD_ID|1205 + 96123|Genome polyprotein|P26664.3|Hepatitis C virus (isolate H77)|63746 + 1205 + 9 + + + 1 + 13.4678 + 23 + 7.85574 + 1 + 9 + 1 + 9 + 0 + 0 + 4 + 5 + 0 + 9 + SVFSEQWIF + AVFGPLWIL + +VF WI + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 988 + Query_988 + M_4577 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 989 + Query_989 + M_4578 + 9 + + + 1 + gnl|BL_ORD_ID|1653 + 146569|polyprotein|ADF97231.1|Hepatitis C virus subtype 3a|356426 + 1653 + 17 + + + 1 + 12.3122 + 20 + 57.3063 + 1 + 9 + 1 + 9 + 0 + 0 + 4 + 5 + 0 + 9 + SWMPALECL + SWDETWKCL + SW +CL + + + + + 2 + gnl|BL_ORD_ID|1654 + 146570|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 + 1654 + 17 + + + 1 + 11.5418 + 18 + 129.081 + 1 + 9 + 1 + 9 + 0 + 0 + 4 + 5 + 0 + 9 + SWMPALECL + SWDQMWKCL + SW +CL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 990 + Query_990 + M_4579 + 9 + + + 1 + gnl|BL_ORD_ID|664 + 39591|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 + 664 + 20 + + + 1 + 11.927 + 19 + 59.5549 + 1 + 5 + 10 + 14 + 0 + 0 + 4 + 4 + 0 + 5 + SWPLW + SWCLW + SW LW + + + + + 2 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8 + YGVNLYQF + YGYPVYVF + YG +Y F + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 1000 + Query_1000 + M_4589 + 9 + + + 1 + gnl|BL_ORD_ID|2128 + 186620|polyprotein|AFP27208.1|Dengue virus 4|11070 + 2128 + 9 + + + 1 + 11.1566 + 17 + 291.863 + 4 + 9 + 1 + 6 + 0 + 0 + 3 + 6 + 0 + 6 + YILITI + YVILTI + Y+++TI + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 1001 + Query_1001 + M_4590 + 9 + + + 1 + gnl|BL_ORD_ID|1687 + 149053|NS3 gene product|AAB02124.1|Hepatitis C virus|11103 + 1687 + 18 + + + 1 + 15.0086 + 27 + 1.25718 + 2 + 8 + 8 + 14 + 0 + 0 + 4 + 6 + 0 + 7 + YKFLAPW + YRFVAPG + Y+F+AP + + + + + 2 + gnl|BL_ORD_ID|2333 + 423082|Genome polyprotein|P26664.3|Hepatitis C virus genotype 1|41856 + 2333 + 9 + + + 1 + 15.0086 + 27 + 1.49881 + 2 + 7 + 1 + 6 + 0 + 0 + 4 + 6 + 0 + 6 + YKFLAP + YRFVAP + Y+F+AP + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 1002 + Query_1002 + M_4591 + 9 + + + 1 + gnl|BL_ORD_ID|1687 + 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0.14 + + + No hits found + + + 1041 + Query_1041 + M_4630 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1042 + Query_1042 + M_4631 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1043 + Query_1043 + M_4632 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1044 + Query_1044 + M_4633 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1045 + Query_1045 + M_4634 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1046 + Query_1046 + M_4635 + 9 + + + 1 + gnl|BL_ORD_ID|1653 + 146569|polyprotein|ADF97231.1|Hepatitis C virus subtype 3a|356426 + 1653 + 17 + + + 1 + 12.3122 + 20 + 41.9577 + 4 + 8 + 5 + 9 + 0 + 0 + 3 + 4 + 0 + 5 + SWTCL + TWKCL + +W CL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 1047 + Query_1047 + M_4636 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1048 + Query_1048 + M_4637 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1049 + Query_1049 + M_4638 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1050 + Query_1050 + M_4639 + 9 + + + 1 + gnl|BL_ORD_ID|341 + 21385|polyprotein|AAY82034.1|Hepatitis C virus genotype 1|41856 + 341 + 10 + + + 1 + 13.853 + 24 + 5.29638 + 3 + 9 + 1 + 7 + 0 + 0 + 3 + 6 + 0 + 7 + GNRTKCF + GNASRCW + GN ++C+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 1051 + Query_1051 + M_4640 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1052 + Query_1052 + M_4641 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1053 + Query_1053 + M_4642 + 9 + + + 1 + gnl|BL_ORD_ID|551 + 33856|polyprotein|BAA03375.1|Hepatitis C virus|11103 + 551 + 9 + + + 1 + 13.853 + 24 + 5.55396 + 3 + 8 + 3 + 8 + 0 + 0 + 5 + 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alphaherpesvirus 2|10310 + 1775 + 15 + + + 1 + 15.0086 + 27 + 1.24275 + 3 + 9 + 3 + 9 + 0 + 0 + 5 + 5 + 0 + 7 + GPCRRRF + GPADRRF + GP RRF + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 1065 + Query_1065 + M_4654 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1066 + Query_1066 + M_4655 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1067 + Query_1067 + M_4656 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1068 + Query_1068 + M_4657 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1069 + Query_1069 + M_4658 + 9 + + + 1 + gnl|BL_ORD_ID|1395 + 110394|Protein E6|P03126.1|Human papillomavirus type 16|333760 + 1395 + 32 + + + 1 + 13.4678 + 23 + 12.8091 + 3 + 9 + 4 + 10 + 0 + 0 + 4 + 5 + 0 + 7 + NCNRHLC + NCQKPLC + NC + LC + + + + + 2 + gnl|BL_ORD_ID|957 + 62903|Genome polyprotein|P27909.2|Dengue virus 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1092 + 15 + + + 1 + 12.6974 + 21 + 31.7906 + 2 + 9 + 7 + 14 + 0 + 0 + 5 + 6 + 0 + 8 + YVVTKFLM + YVVLLFLL + YVV FL+ + + + + + 3 + gnl|BL_ORD_ID|203 + 15110|Genome polyprotein|P26663.3|Hepatitis C virus|11103 + 203 + 9 + + + 1 + 11.5418 + 18 + 152.614 + 2 + 9 + 2 + 9 + 0 + 0 + 4 + 6 + 0 + 8 + YVVTKFLM + YVLLLFLL + YV+ FL+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 1170 + Query_1170 + M_4759 + 9 + + + 1 + gnl|BL_ORD_ID|1128 + 74774|LMP1 protein (Epstein-Barr virus, putative LYDMA gene)|Q777A4|Human gammaherpesvirus 4|10376 + 1128 + 9 + + + 1 + 12.6974 + 21 + 35.9943 + 3 + 8 + 1 + 6 + 0 + 0 + 5 + 6 + 0 + 6 + YLLELL + YLLEML + YLLE+L + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 1171 + Query_1171 + M_4760 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1172 + Query_1172 + M_4761 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1173 + Query_1173 + M_4762 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8|37296 + 1110 + 15 + + + 1 + 12.3122 + 20 + 58.4135 + 1 + 9 + 3 + 11 + 0 + 0 + 3 + 5 + 0 + 9 + WHVPNKPPM + WRLGAIPPL + W + PP+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 1180 + Query_1180 + M_4769 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1181 + Query_1181 + M_4770 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1182 + Query_1182 + M_4771 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1183 + Query_1183 + M_4772 + 9 + + + 1 + gnl|BL_ORD_ID|554 + 34027|DNA polymerase|CAA10434.1|Hepatitis B virus|10407 + 554 + 9 + + + 1 + 13.0826 + 22 + 20.0871 + 2 + 9 + 2 + 9 + 0 + 0 + 4 + 5 + 0 + 8 + LSNFQGRY + VGNFTGLY + + NF G Y + + + + + 2 + gnl|BL_ORD_ID|1630 + 146213|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 + 1630 + 18 + + + 1 + 11.927 + 19 + 86.7645 + 1 + 7 + 3 + 9 + 0 + 0 + 4 + 4 + 0 + 7 + WLSNFQG + WESVFTG + W S F G + + 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150450|polyprotein|AGO67248.1|Dengue virus 2|11060 + 1723 + 9 + + + 1 + 14.2382 + 25 + 4.3647 + 2 + 8 + 2 + 8 + 0 + 0 + 4 + 5 + 0 + 7 + PLTHSQG + PVTHSSA + P+THS + + + + + 3 + gnl|BL_ORD_ID|1724 + 150451|polyprotein|AGO67248.1|Dengue virus 2|11060 + 1724 + 10 + + + 1 + 13.853 + 24 + 4.8573 + 2 + 8 + 2 + 8 + 0 + 0 + 4 + 5 + 0 + 7 + PLTHSQG + PVTHSSA + P+THS + + + + + 4 + gnl|BL_ORD_ID|2051 + 184702|non-structural protein 1|AGM49312.1|Dengue virus|12637 + 2051 + 9 + + + 1 + 13.853 + 24 + 5.65074 + 1 + 6 + 2 + 7 + 0 + 0 + 4 + 5 + 0 + 6 + WPLTHS + WPKTHT + WP TH+ + + + + + 5 + gnl|BL_ORD_ID|1139 + 75356|EBNA3A nuclear protein|Q8AZJ8|Human gammaherpesvirus 4|10376 + 1139 + 9 + + + 1 + 13.4678 + 23 + 13.0154 + 1 + 9 + 1 + 9 + 0 + 0 + 4 + 5 + 0 + 9 + WPLTHSQGM + YPLHEQHGM + +PL GM + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 1187 + Query_1187 + M_4776 + 9 + + + 1 + gnl|BL_ORD_ID|1786 + 159299|polyprotein|AAC03058.1|Hepatitis C virus subtype 3a|356426 + 1786 + 9 + + + 1 + 14.2382 + 25 + 4.21767 + 2 + 9 + 2 + 9 + 0 + 0 + 5 + 6 + 0 + 8 + QRQHKLTI + QRQRKVTF + QRQ K+T + + + + + 2 + gnl|BL_ORD_ID|1007 + 66405|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 + 1007 + 20 + + + 1 + 13.853 + 24 + 4.65152 + 1 + 9 + 6 + 14 + 0 + 0 + 5 + 6 + 0 + 9 + WQRQHKLTI + CQRQKKVTF + QRQ K+T + + + + + 3 + gnl|BL_ORD_ID|1617 + 144480|polyprotein|ACA50684.1|Hepatitis C virus subtype 1b|31647 + 1617 + 9 + + + 1 + 13.853 + 24 + 5.00793 + 2 + 9 + 2 + 9 + 0 + 0 + 5 + 6 + 0 + 8 + QRQHKLTI + QRQKKVTF + QRQ K+T + + + + + 4 + gnl|BL_ORD_ID|2051 + 184702|non-structural protein 1|AGM49312.1|Dengue virus|12637 + 2051 + 9 + + + 1 + 11.927 + 19 + 75.1319 + 1 + 7 + 2 + 8 + 0 + 0 + 3 + 4 + 0 + 7 + WQRQHKL + WPKTHTL + W + H L + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 1188 + Query_1188 + M_4777 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1189 + Query_1189 + M_4778 + 9 + + + 1 + gnl|BL_ORD_ID|1812 + 177647|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 + 1812 + 16 + + + 1 + 13.853 + 24 + 4.97938 + 1 + 9 + 6 + 14 + 0 + 0 + 4 + 7 + 0 + 9 + WSDQLSAFS + WMNRLIAFA + W ++L AF+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 1190 + Query_1190 + M_4779 + 9 + + + 1 + gnl|BL_ORD_ID|921 + 59787|Hemagglutinin glycoprotein|P08362.1|Measles virus strain Edmonston|11235 + 921 + 10 + + + 1 + 13.0826 + 22 + 13.3135 + 4 + 9 + 5 + 10 + 0 + 0 + 3 + 6 + 0 + 6 + VFQIGI + VFEVGV + VF++G+ + + + + + 2 + gnl|BL_ORD_ID|2123 + 186524|polyprotein|AGW21594.1|Dengue virus 1|11053 + 2123 + 10 + + + 1 + 12.3122 + 20 + 61.3845 + 1 + 9 + 1 + 9 + 0 + 0 + 5 + 5 + 0 + 9 + WTDVFQIGI + WTMKIGIGI + WT IGI + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 1191 + Query_1191 + M_4780 + 9 + + + 1 + gnl|BL_ORD_ID|1437 + 119822|110 kd polyprotein precursor|CAA28880.1|Rubella virus|11041 + 1437 + 29 + + + 1 + 14.6234 + 26 + 2.01102 + 1 + 9 + 9 + 17 + 0 + 0 + 5 + 6 + 0 + 9 + WTESLAAVF + WSEGEGAVF + W+E AVF + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 1192 + Query_1192 + M_4781 + 9 + + + 1 + gnl|BL_ORD_ID|427 + 25929|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 + 427 + 15 + + + 1 + 12.3122 + 20 + 50.6727 + 2 + 9 + 8 + 15 + 0 + 0 + 4 + 6 + 0 + 8 + VKRQKISF + VKKDLISY + VK+ IS+ + + + + + 2 + gnl|BL_ORD_ID|9 + 790|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 + 9 + 15 + + + 1 + 12.3122 + 20 + 51.4826 + 2 + 9 + 3 + 10 + 0 + 0 + 4 + 6 + 0 + 8 + VKRQKISF + VKKDLISY + VK+ IS+ + + + + + 3 + gnl|BL_ORD_ID|943 + 62184|nonstructural protein 3|NP_722463.1|Dengue virus type 1 Hawaii|10000440 + 943 + 15 + + + 1 + 11.927 + 19 + 74.9817 + 2 + 9 + 2 + 9 + 0 + 0 + 4 + 6 + 0 + 8 + VKRQKISF + VKKDLISY + VK+ IS+ + + + + + 4 + gnl|BL_ORD_ID|761 + 50894|Genome polyprotein|P27909.2|Dengue virus type 1 Hawaii|10000440 + 761 + 20 + + + 1 + 11.927 + 19 + 76.6481 + 2 + 9 + 12 + 19 + 0 + 0 + 4 + 6 + 0 + 8 + VKRQKISF + VKKDLISY + VK+ IS+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 1193 + Query_1193 + M_4782 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1194 + Query_1194 + M_4783 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1195 + Query_1195 + M_4784 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1196 + Query_1196 + M_4785 + 9 + + + 1 + gnl|BL_ORD_ID|885 + 57987|envelope protein|YP_001527880.1|West Nile virus NY-99|10000971 + 885 + 18 + + + 1 + 11.5418 + 18 + 116.517 + 4 + 9 + 5 + 10 + 0 + 0 + 4 + 5 + 0 + 6 + WILLVL + WVDLVL + W+ LVL + + + + + 2 + gnl|BL_ORD_ID|801 + 53341|envelope protein|YP_001527880.1|West Nile virus NY-99|10000971 + 801 + 17 + + + 1 + 11.5418 + 18 + 136.848 + 4 + 9 + 12 + 17 + 0 + 0 + 4 + 5 + 0 + 6 + WILLVL + WVDLVL + W+ LVL + + + + + 3 + gnl|BL_ORD_ID|637 + 37960|membrane protein|AAA45887.1|Human gammaherpesvirus 4|10376 + 637 + 9 + + + 1 + 9.61583 + 13 + 1779.2 + 1 + 7 + 3 + 9 + 0 + 0 + 3 + 5 + 0 + 7 + WYIWILL + WTLVVLL + W + +LL + + + + + 4 + gnl|BL_ORD_ID|664 + 39591|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 + 664 + 20 + + + 1 + 8.84543 + 11 + 1791.35 + 1 + 4 + 11 + 14 + 0 + 0 + 2 + 3 + 0 + 4 + WYIW + WCLW + W +W + + + + + 5 + gnl|BL_ORD_ID|1120 + 74387|Genome polyprotein|P26664.3|Hepatitis C virus (isolate 1)|11104 + 1120 + 9 + + + 1 + 9.23063 + 12 + 2628.29 + 1 + 6 + 4 + 9 + 0 + 0 + 3 + 4 + 0 + 6 + WYIWIL + WCLWWL + W +W L + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 1197 + Query_1197 + M_4786 + 9 + + + 1 + gnl|BL_ORD_ID|1630 + 146213|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 + 1630 + 18 + + + 1 + 13.853 + 24 + 6.14503 + 3 + 7 + 7 + 11 + 0 + 0 + 5 + 5 + 0 + 5 + FTGLT + FTGLT + FTGLT + + + + + 2 + gnl|BL_ORD_ID|1027 + 68581|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 + 1027 + 20 + + + 1 + 13.853 + 24 + 6.30518 + 3 + 7 + 2 + 6 + 0 + 0 + 5 + 5 + 0 + 5 + FTGLT + FTGLT + FTGLT + + + + + 3 + gnl|BL_ORD_ID|1628 + 146188|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 + 1628 + 18 + + + 1 + 13.853 + 24 + 6.46733 + 3 + 7 + 7 + 11 + 0 + 0 + 5 + 5 + 0 + 5 + FTGLT + FTGLT + FTGLT + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 1198 + Query_1198 + M_4787 + 9 + + + 1 + gnl|BL_ORD_ID|1861 + 180440|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 + 1861 + 15 + + + 1 + 11.927 + 19 + 82.259 + 4 + 8 + 6 + 10 + 0 + 0 + 3 + 4 + 0 + 5 + QRSWQ + ERSWN + +RSW + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 1199 + Query_1199 + M_4788 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1200 + Query_1200 + M_4789 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1201 + Query_1201 + M_4790 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1202 + Query_1202 + M_4791 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1203 + Query_1203 + M_4792 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1204 + Query_1204 + M_4793 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1205 + Query_1205 + M_4794 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1206 + Query_1206 + M_4795 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1207 + Query_1207 + M_4796 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1208 + Query_1208 + M_4797 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1209 + Query_1209 + M_4798 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1210 + Query_1210 + M_4799 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1211 + Query_1211 + M_4800 + 9 + + + 1 + gnl|BL_ORD_ID|2243 + 232152|rhoptry kinase family protein|AFO54841.1|Toxoplasma gondii type III|398031 + 2243 + 19 + + + 1 + 13.0826 + 22 + 17.6919 + 1 + 7 + 6 + 12 + 0 + 0 + 4 + 5 + 0 + 7 + YHEAGVT + FHSYGVT + +H GVT + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 1212 + Query_1212 + M_4801 + 9 + + + 1 + gnl|BL_ORD_ID|1983 + 183252|polyprotein|AGT63075.1|Dengue virus 1|11053 + 1983 + 10 + + + 1 + 11.927 + 19 + 78.4397 + 2 + 7 + 4 + 9 + 0 + 0 + 2 + 5 + 0 + 6 + HFSWTS + HYAWKT + H++W + + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 1213 + Query_1213 + M_4802 + 9 + + + 1 + gnl|BL_ORD_ID|375 + 23270|polyprotein|AAB67036.1|Hepatitis C virus (isolate H77)|63746 + 375 + 15 + + + 1 + 15.0086 + 27 + 1.20133 + 1 + 7 + 8 + 14 + 0 + 0 + 4 + 6 + 0 + 7 + YHHRFNN + YQHKFNS + Y H+FN+ + + + + + 2 + gnl|BL_ORD_ID|23 + 1516|Nucleoprotein|P03418.1|Human respiratory syncytial virus A2|11259 + 23 + 14 + + + 1 + 11.1566 + 17 + 165.457 + 1 + 7 + 3 + 9 + 0 + 0 + 3 + 5 + 0 + 7 + YHHRFNN + FYHILNN + ++H NN + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 1214 + Query_1214 + M_4803 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1215 + Query_1215 + M_4804 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1216 + Query_1216 + M_4805 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 1217 + Query_1217 + M_4806 + 9 + + + 1 + gnl|BL_ORD_ID|1405 + 110829|Protein E6|P03126.1|Human papillomavirus type 16|333760 + 1405 + 15 + + + 1 + 13.4678 + 23 + 7.74893 + 2 + 9 + 8 + 15 + 0 + 0 + 4 + 5 + 0 + 8 + KGSRFHRV + KKQRFHNI + K RFH + + + + + + 2 + gnl|BL_ORD_ID|1822 + 178247|Protein E6|P03126.1|Human papillomavirus type 16|333760 + 1822 + 15 + + + 1 + 13.0826 + 22 + 14.0874 + 2 + 9 + 4 + 11 + 0 + 0 + 4 + 5 + 0 + 8 + KGSRFHRV + KKQRFHNI + K RFH + + + + + + 3 + gnl|BL_ORD_ID|1385 + 110215|Protein E6|P03126.1|Human papillomavirus type 16|333760 + 1385 + 25 + + + 1 + 13.0826 + 22 + 16.7731 + 2 + 9 + 8 + 15 + 0 + 0 + 4 + 5 + 0 + 8 + KGSRFHRV + KKQRFHNI + K RFH + + + + + + 4 + gnl|BL_ORD_ID|1384 + 110205|Protein E6|P03126.1|Human papillomavirus type 16|333760 + 1384 + 32 + + + 1 + 13.0826 + 22 + 17.6218 + 2 + 9 + 2 + 9 + 0 + 0 + 4 + 5 + 0 + 8 + KGSRFHRV + KKQRFHNI + K RFH + + + + + + 5 + gnl|BL_ORD_ID|1395 + 110394|Protein E6|P03126.1|Human papillomavirus type 16|333760 + 1395 + 32 + + + 1 + 12.3122 + 20 + 36.3427 + 2 + 9 + 20 + 27 + 0 + 0 + 4 + 5 + 0 + 8 + KGSRFHRV + KKQRFHNI + K RFH + + + + + + 6 + gnl|BL_ORD_ID|786 + 52652|||| + 786 + 27 + + + 1 + 12.3122 + 20 + 45.1033 + 3 + 9 + 7 + 13 + 0 + 0 + 4 + 5 + 0 + 7 + GSRFHRV + GSQSHTV + GS+ H V + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 1218 + Query_1218 + M_4807 + 9 + + + + + 2334 + 25004 + 0 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+WLEAMQGVI +>M_4880 +MNRGRRSSL +>M_4881 +RADHAAEQV +>M_4882 +TTLSPAEPT +>M_4883 +CLMVLYSLI +>M_4884 +MTPSVYGGA +>M_4885 +FCFLVVASA +>M_4886 +FLVVASAYI +>M_4887 +VVASAYIKL +>M_4888 +NSTIIPTLI +>M_4889 +SSSGVNSTI +>M_4890 +STIIPTLIL +>M_4891 +NLAMCFGPV +>M_4892 +MVAFINEKM +>M_4893 +RHSNMVAFI diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_136103_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_136103_1_T_iedb.xml new file mode 100755 index 00000000..8d9d2dc7 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_136103_1_T_iedb.xml @@ -0,0 +1,742 @@ + + + + blastp + BLASTP 2.2.30+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta + Query_1 + M_4876 + 9 + + + BLOSUM62 + 100000000 + 11 + 1 + F + + + + + 1 + Query_1 + M_4876 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 2 + Query_2 + M_4877 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 3 + Query_3 + M_4878 + 9 + + + 1 + gnl|BL_ORD_ID|958 + 62977|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 + 958 + 10 + + + 1 + 11.5418 + 18 + 153.051 + 1 + 7 + 4 + 10 + 0 + 0 + 3 + 3 + 0 + 7 + HWPEKEW + HTPVNSW + H P W + + + + + 2 + gnl|BL_ORD_ID|55 + 4156|polyprotein|ABR25251.1|Hepatitis C virus|11103 + 55 + 9 + + + 1 + 11.5418 + 18 + 184.198 + 1 + 7 + 3 + 9 + 0 + 0 + 3 + 3 + 0 + 7 + HWPEKEW + HTPVNSW + H P W + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 4 + 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virus 2|11060 + 2042 + 9 + + + 1 + 12.3122 + 20 + 56.7066 + 1 + 8 + 1 + 8 + 0 + 0 + 4 + 7 + 0 + 8 + MNRGRRSS + LNRRRRTA + +NR RR++ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 6 + Query_6 + M_4881 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 7 + Query_7 + M_4882 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 8 + Query_8 + M_4883 + 9 + + + 1 + gnl|BL_ORD_ID|1549 + 141222|DNA packaging tegument protein UL25|NP_044626.1|Human alphaherpesvirus 1|10298 + 1549 + 9 + + + 1 + 11.5418 + 18 + 118.346 + 1 + 6 + 4 + 9 + 0 + 0 + 4 + 5 + 0 + 6 + CLMVLY + CLYLLY + CL +LY + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 9 + Query_9 + M_4884 + 9 + + + 1 + gnl|BL_ORD_ID|999 + 65749|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 + 999 + 11 + + + 1 + 13.4678 + 23 + 7.47922 + 2 + 8 + 1 + 7 + 0 + 0 + 5 + 5 + 0 + 7 + TPSVYGG + TPRVTGG + TP V GG + + + + + 2 + gnl|BL_ORD_ID|998 + 65748|pp65|AAA45994.1|Human betaherpesvirus 5|10359 + 998 + 10 + + + 1 + 13.4678 + 23 + 8.46851 + 2 + 8 + 1 + 7 + 0 + 0 + 5 + 5 + 0 + 7 + TPSVYGG + TPRVTGG + TP V GG + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 10 + Query_10 + M_4885 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 11 + Query_11 + M_4886 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 12 + Query_12 + M_4887 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 13 + Query_13 + M_4888 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 14 + Query_14 + M_4889 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 15 + Query_15 + M_4890 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 16 + Query_16 + M_4891 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 17 + Query_17 + M_4892 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 18 + Query_18 + M_4893 + 9 + + + 1 + gnl|BL_ORD_ID|1616 + 144403|polyprotein|AAK08509.1|Hepatitis C virus subtype 1b|31647 + 1616 + 9 + + + 1 + 14.6234 + 26 + 2.53786 + 1 + 6 + 3 + 8 + 0 + 0 + 5 + 5 + 0 + 6 + RHSNMV + RHHNMV + RH NMV + + + + + 2 + gnl|BL_ORD_ID|1785 + 159290|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 + 1785 + 9 + + + 1 + 13.4678 + 23 + 11.7244 + 1 + 6 + 3 + 8 + 0 + 0 + 4 + 5 + 0 + 6 + RHSNMV + RHHNLV + RH N+V + + + + + 3 + gnl|BL_ORD_ID|1218 + 96897|polyprotein|ABR25251.1|Hepatitis C virus (isolate H77)|63746 + 1218 + 17 + + + 1 + 13.0826 + 22 + 13.7 + 1 + 6 + 4 + 9 + 0 + 0 + 4 + 5 + 0 + 6 + RHSNMV + RHHNLV + RH N+V + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + + diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_136546_2_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_136546_2_T.fasta new file mode 100755 index 00000000..f6e6c44a --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_136546_2_T.fasta @@ -0,0 +1,78 @@ +>M_4894 +SILASLSTL +>M_4895 +TLQQMWISK +>M_4896 +RAFADTLEV +>M_4897 +VLLPVSLFI +>M_4898 +LLFSVTMPK +>M_4899 +VPVPPAPPL +>M_4900 +EIFMGLPTK +>M_4901 +VYTEIFMGL +>M_4902 +YYASVYTEI +>M_4903 +HMWNYMQSK +>M_4904 +QTYQHMWNY +>M_4905 +SRYQTYQHM +>M_4906 +MIMAQMRRI +>M_4907 +RRISPFSCL +>M_4908 +ILFDEAVKL +>M_4909 +MKYPVKSIL +>M_4910 +TLIHQFQEK +>M_4911 +KLGADFIGH +>M_4912 +ALGPPVLLR +>M_4913 +PPVLLRCSL +>M_4914 +FTRENTLTF +>M_4915 +LTFMHLSPI +>M_4916 +TFMHLSPIL +>M_4917 +EFVERYHVL +>M_4918 +RLWARGLTV +>M_4919 +RLWARGLTV +>M_4920 +LVWRPLREV +>M_4921 +SYVMLPCAL +>M_4922 +VMLPCALPV +>M_4923 +RLPEVQLPK +>M_4924 +APRGACYRA +>M_4925 +APRGVCYGA +>M_4926 +GLTWAVVLI +>M_4927 +QPLGLTWAV +>M_4928 +YRNEDHWAW +>M_4929 +KCAEPSTRK +>M_4930 +LLTDDLRSV +>M_4931 +QMPTDYAEV +>M_4932 +VVGARGVGK diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_136546_2_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_136546_2_T_iedb.xml new file mode 100755 index 00000000..b982e37c --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_136546_2_T_iedb.xml @@ -0,0 +1,1402 @@ + + + + blastp + BLASTP 2.2.30+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta + Query_1 + M_4894 + 9 + + + BLOSUM62 + 100000000 + 11 + 1 + F + + + + + 1 + Query_1 + M_4894 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 2 + Query_2 + M_4895 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 3 + Query_3 + M_4896 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 4 + Query_4 + M_4897 + 9 + + + 1 + gnl|BL_ORD_ID|1168 + 79180|tax protein|AAF37566.1|Human T-lymphotropic virus 1|11908 + 1168 + 15 + + + 1 + 12.6974 + 21 + 24.4548 + 3 + 8 + 3 + 8 + 0 + 0 + 4 + 5 + 0 + 6 + LPVSLF + LPTTLF + LP +LF + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 5 + Query_5 + M_4898 + 9 + + + 1 + gnl|BL_ORD_ID|338 + 21242|polymerase|ACF94272.1|Hepatitis B virus|10407 + 338 + 9 + + + 1 + 13.0826 + 22 + 19.7427 + 2 + 8 + 2 + 8 + 0 + 0 + 4 + 6 + 0 + 7 + LFSVTMP + LYSSTVP + L+S T+P + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 6 + Query_6 + M_4899 + 9 + + + 1 + gnl|BL_ORD_ID|1068 + 70491|envelope glycoprotein|AAC28452.1|Human immunodeficiency virus 1|11676 + 1068 + 10 + + + 1 + 11.927 + 19 + 86.442 + 1 + 8 + 1 + 8 + 0 + 0 + 5 + 5 + 0 + 8 + VPVPPAPP + VPTDPNPP + VP P PP + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 7 + Query_7 + M_4900 + 9 + + + 1 + gnl|BL_ORD_ID|2080 + 185327|polyprotein|ACF49259.1|Dengue virus type 1 Hawaii|10000440 + 2080 + 9 + + + 1 + 13.4678 + 23 + 8.87313 + 2 + 7 + 3 + 8 + 0 + 0 + 4 + 5 + 0 + 6 + IFMGLP + IYMGQP + I+MG P + + + + + 2 + gnl|BL_ORD_ID|141 + 10587|viral polyprotein|AAA42941.1|Dengue virus 2 Thailand/NGS-C/1944|11065 + 141 + 9 + + + 1 + 11.1566 + 17 + 232.278 + 1 + 9 + 1 + 9 + 0 + 0 + 3 + 5 + 0 + 9 + EIFMGLPTK + DVFFTPPEK + ++F P K + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 8 + Query_8 + M_4901 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 9 + Query_9 + M_4902 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 10 + Query_10 + M_4903 + 9 + + + 1 + gnl|BL_ORD_ID|691 + 42094|telomer length regulation protein TEL1|EDV12172.1|Saccharomyces cerevisiae|4932 + 691 + 9 + + + 1 + 13.853 + 24 + 6.60345 + 2 + 7 + 2 + 7 + 0 + 0 + 3 + 5 + 0 + 6 + MWNYMQ + LWGYLQ + +W Y+Q + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 11 + Query_11 + M_4904 + 9 + + + 1 + gnl|BL_ORD_ID|1295 + 103020|polyprotein|ABR25251.1|Hepatitis C virus|11103 + 1295 + 10 + + + 1 + 16.1642 + 30 + 0.390189 + 4 + 9 + 5 + 10 + 0 + 0 + 4 + 6 + 0 + 6 + QHMWNY + KHMWNF + +HMWN+ + + + + + 2 + gnl|BL_ORD_ID|1029 + 68605|Genome polyprotein|P26662.3|Hepatitis C virus|11103 + 1029 + 10 + + + 1 + 16.1642 + 30 + 0.392937 + 4 + 9 + 5 + 10 + 0 + 0 + 4 + 6 + 0 + 6 + QHMWNY + KHMWNF + +HMWN+ + + + + + 3 + gnl|BL_ORD_ID|272 + 18337|polyprotein|BAD73987.1|Hepatitis C virus subtype 1b|31647 + 272 + 9 + + + 1 + 15.779 + 29 + 0.436744 + 4 + 9 + 4 + 9 + 0 + 0 + 4 + 6 + 0 + 6 + QHMWNY + KHMWNF + +HMWN+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 12 + Query_12 + M_4905 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 13 + Query_13 + M_4906 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 14 + Query_14 + M_4907 + 9 + + + 1 + gnl|BL_ORD_ID|1731 + 150556|polyprotein|AGW21594.1|Dengue virus 1|11053 + 1731 + 10 + + + 1 + 12.6974 + 21 + 26.0802 + 1 + 9 + 1 + 9 + 0 + 0 + 5 + 5 + 0 + 9 + RRISPFSCL + RVIDPRRCL + R I P CL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 15 + Query_15 + M_4908 + 9 + + + 1 + gnl|BL_ORD_ID|1807 + 169050|polyprotein|ABU97067.1|Hepatitis C virus subtype 1b|31647 + 1807 + 9 + + + 1 + 13.4678 + 23 + 8.13377 + 2 + 8 + 3 + 9 + 0 + 0 + 5 + 6 + 0 + 7 + LFDEAVK + LFNWAVK + LF+ AVK + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 16 + Query_16 + M_4909 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 17 + Query_17 + M_4910 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 18 + Query_18 + M_4911 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 19 + Query_19 + M_4912 + 9 + + + 1 + gnl|BL_ORD_ID|898 + 59141|Circumsporozoite protein precursor|P08677.2|Plasmodium vivax strain Belem|31273 + 898 + 10 + + + 1 + 10.7714 + 16 + 303.747 + 1 + 8 + 1 + 8 + 0 + 0 + 4 + 6 + 0 + 8 + ALGPPVLL + SLGLVILL + +LG +LL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 20 + Query_20 + M_4913 + 9 + + + 1 + gnl|BL_ORD_ID|1621 + 145860|Protein E6|P04019.1|Human papillomavirus type 11|10580 + 1621 + 9 + + + 1 + 13.853 + 24 + 5.84954 + 2 + 9 + 1 + 8 + 0 + 0 + 5 + 6 + 0 + 8 + PVLLRCSL + KVLIRCYL + VL+RC L + + + + + 2 + gnl|BL_ORD_ID|114 + 7660|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 + 114 + 20 + + + 1 + 11.927 + 19 + 83.707 + 3 + 9 + 4 + 10 + 0 + 0 + 3 + 6 + 0 + 7 + VLLRCSL + ILLMCAV + +LL C++ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 21 + Query_21 + M_4914 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 22 + Query_22 + M_4915 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 23 + Query_23 + M_4916 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 24 + Query_24 + M_4917 + 9 + + + 1 + gnl|BL_ORD_ID|2142 + 187188|PE family protein PE9|YP_177784.1|Mycobacterium tuberculosis H37Rv|83332 + 2142 + 15 + + + 1 + 13.4678 + 23 + 10.3735 + 3 + 9 + 7 + 13 + 0 + 0 + 4 + 4 + 0 + 7 + VERYHVL + AEEYHAL + E YH L + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 25 + Query_25 + M_4918 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 26 + Query_26 + M_4919 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 27 + Query_27 + M_4920 + 9 + + + 1 + gnl|BL_ORD_ID|1872 + 180496|Polyprotein|NP_056776.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 + 1872 + 15 + + + 1 + 12.3122 + 20 + 36.7879 + 2 + 8 + 7 + 13 + 0 + 0 + 3 + 5 + 0 + 7 + VWRPLRE + IWLKLKE + +W L+E + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 28 + Query_28 + M_4921 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 29 + Query_29 + M_4922 + 9 + + + 1 + gnl|BL_ORD_ID|690 + 41971|putative D-ribose-binding protein|NP_301386.1|Mycobacterium leprae|1769 + 690 + 15 + + + 1 + 11.5418 + 18 + 154.909 + 2 + 8 + 6 + 12 + 0 + 0 + 4 + 5 + 0 + 7 + MLPCALP + LLPAILP + +LP LP + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 30 + Query_30 + M_4923 + 9 + + + 1 + gnl|BL_ORD_ID|241 + 16836|precore/core protein [Hepatitis B virus]|AAR03815.1|Hepatitis B virus|10407 + 241 + 10 + + + 1 + 10.3862 + 15 + 499.131 + 2 + 9 + 2 + 9 + 0 + 0 + 4 + 4 + 0 + 8 + LPEVQLPK + LPSDFLPS + LP LP + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 31 + Query_31 + M_4924 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 32 + Query_32 + M_4925 + 9 + + + 1 + gnl|BL_ORD_ID|1667 + 148117|early protein|CAA52585.1|Human papillomavirus type 52|10618 + 1667 + 9 + + + 1 + 12.6974 + 21 + 26.9236 + 2 + 6 + 1 + 5 + 0 + 0 + 4 + 4 + 0 + 5 + PRGVC + PYGVC + P GVC + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 33 + Query_33 + M_4926 + 9 + + + 1 + gnl|BL_ORD_ID|1686 + 149052|E1 protein|NP_751920.1|Hepatitis C virus (isolate H77)|63746 + 1686 + 18 + + + 1 + 12.3122 + 20 + 44.435 + 3 + 9 + 10 + 16 + 0 + 0 + 4 + 5 + 0 + 7 + TWAVVLI + NWAKVLV + WA VL+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 34 + Query_34 + M_4927 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 35 + Query_35 + M_4928 + 9 + + + 1 + gnl|BL_ORD_ID|2019 + 184131|polyprotein|AGO67248.1|Dengue virus 2|11060 + 2019 + 10 + + + 1 + 12.6974 + 21 + 23.5358 + 2 + 8 + 1 + 7 + 0 + 0 + 3 + 4 + 0 + 7 + RNEDHWA + KREDQWC + + ED W + + + + + 2 + gnl|BL_ORD_ID|805 + 53476|polyprotein|AGO67248.1|Dengue virus 2|11060 + 805 + 9 + + + 1 + 12.3122 + 20 + 65.8473 + 4 + 8 + 2 + 6 + 0 + 0 + 3 + 3 + 0 + 5 + EDHWA + EDQWC + ED W + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 36 + Query_36 + M_4929 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 37 + Query_37 + M_4930 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 38 + Query_38 + M_4931 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 39 + Query_39 + M_4932 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + + diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_136587_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_136587_1_T.fasta new file mode 100755 index 00000000..13a39e09 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_136587_1_T.fasta @@ -0,0 +1,50 @@ +>M_4933 +ALFCGRSDY +>M_4934 +SFLCHKALF +>M_4935 +SFLCHKALF +>M_4936 +SFLCHKALF +>M_4937 +HHLLSLQYV +>M_4938 +NHHLLSLQY +>M_4939 +LRLLDRELL +>M_4940 +QMPPMPPPL +>M_4941 +SRVSGGTPL +>M_4942 +IPLEVMEPF +>M_4943 +RHAACSVLV +>M_4944 +TRHAACSVL +>M_4945 +TRHAACSVL +>M_4946 +IYLGAVNWI +>M_4947 +YLGAVNWIY +>M_4948 +MWALGIIAY +>M_4949 +SPALNKMFY +>M_4950 +IPGPIPGPI +>M_4951 +IPGPIPGPI +>M_4952 +NPGPIPGPI +>M_4953 +AEYIVVARN +>M_4954 +YIVVARNKY +>M_4955 +IFWDLSKPM +>M_4956 +IFWDLSKPM +>M_4957 +IPTEKPTIL diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_136587_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_136587_1_T_iedb.xml new file mode 100755 index 00000000..4479cd1c --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_136587_1_T_iedb.xml @@ -0,0 +1,1298 @@ + + + + blastp + BLASTP 2.2.30+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta + Query_1 + M_4933 + 9 + + + BLOSUM62 + 100000000 + 11 + 1 + F + + + + + 1 + Query_1 + M_4933 + 9 + + + 1 + gnl|BL_ORD_ID|73 + 5316|EBNA-3B nuclear protein|CAD53420.1|Human gammaherpesvirus 4|10376 + 73 + 10 + + + 1 + 11.927 + 19 + 106.494 + 1 + 8 + 1 + 8 + 0 + 0 + 4 + 6 + 0 + 8 + ALFCGRSD + AVFDRKSD + A+F +SD + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 2 + Query_2 + M_4934 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 3 + Query_3 + M_4935 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 4 + Query_4 + M_4936 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 5 + Query_5 + M_4937 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 6 + Query_6 + M_4938 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 7 + Query_7 + M_4939 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 8 + Query_8 + M_4940 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 9 + Query_9 + M_4941 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 10 + Query_10 + M_4942 + 9 + + + 1 + gnl|BL_ORD_ID|1879 + 180528|polyprotein|AGO67248.1|Dengue virus 2|11060 + 1879 + 10 + + + 1 + 13.853 + 24 + 6.41039 + 1 + 7 + 1 + 7 + 0 + 0 + 4 + 6 + 0 + 7 + IPLEVME + IPFEIMD + IP E+M+ + + + + + 2 + gnl|BL_ORD_ID|1733 + 150578|polyprotein|AGO67248.1|Dengue virus 2|11060 + 1733 + 10 + + + 1 + 13.0826 + 22 + 15.2954 + 1 + 6 + 5 + 10 + 0 + 0 + 4 + 5 + 0 + 6 + IPLEVM + IPFEIM + IP E+M + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 11 + Query_11 + M_4943 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 12 + Query_12 + M_4944 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 13 + Query_13 + M_4945 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 14 + Query_14 + M_4946 + 9 + + + 1 + gnl|BL_ORD_ID|1812 + 177647|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 + 1812 + 16 + + + 1 + 13.853 + 24 + 5.42889 + 4 + 9 + 2 + 7 + 0 + 0 + 4 + 5 + 0 + 6 + GAVNWI + GAVQWM + GAV W+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 15 + Query_15 + M_4947 + 9 + + + 1 + gnl|BL_ORD_ID|1812 + 177647|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 + 1812 + 16 + + + 1 + 13.853 + 24 + 5.3359 + 3 + 8 + 2 + 7 + 0 + 0 + 4 + 5 + 0 + 6 + GAVNWI + GAVQWM + GAV W+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 16 + Query_16 + M_4948 + 9 + + + 1 + gnl|BL_ORD_ID|413 + 24943|DNA polymerase|CAA10434.1|Hepatitis B virus|10407 + 413 + 11 + + + 1 + 12.3122 + 20 + 60.6062 + 1 + 7 + 3 + 9 + 0 + 0 + 3 + 5 + 0 + 7 + MWALGII + LWKAGIL + +W GI+ + + + + + 2 + gnl|BL_ORD_ID|988 + 65148|DNA polymerase|CAA10434.1|Hepatitis B virus|10407 + 988 + 10 + + + 1 + 11.927 + 19 + 69.9879 + 1 + 7 + 2 + 8 + 0 + 0 + 3 + 5 + 0 + 7 + MWALGII + LWKAGIL + +W GI+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 17 + Query_17 + M_4949 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 18 + Query_18 + M_4950 + 9 + + + 1 + gnl|BL_ORD_ID|741 + 47760|EBNA-1 protein|Q777E1|Human gammaherpesvirus 4|10376 + 741 + 15 + + + 1 + 10.3862 + 15 + 419.458 + 2 + 7 + 1 + 6 + 0 + 0 + 4 + 4 + 0 + 6 + PGPIPG + PGTGPG + PG PG + + + + + 2 + gnl|BL_ORD_ID|75 + 5542|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 + 75 + 15 + + + 1 + 10.001 + 14 + 709.084 + 2 + 9 + 8 + 15 + 0 + 0 + 4 + 4 + 0 + 8 + PGPIPGPI + PGTSGSPI + PG PI + + + + + 3 + gnl|BL_ORD_ID|1929 + 180750|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 + 1929 + 15 + + + 1 + 10.001 + 14 + 819.307 + 2 + 9 + 2 + 9 + 0 + 0 + 4 + 4 + 0 + 8 + PGPIPGPI + PGTSGSPI + PG PI + + + + + 4 + gnl|BL_ORD_ID|260 + 17802|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 + 260 + 15 + + + 1 + 10.001 + 14 + 830.077 + 2 + 9 + 3 + 10 + 0 + 0 + 4 + 4 + 0 + 8 + PGPIPGPI + PGTSGSPI + PG PI + + + + + 5 + gnl|BL_ORD_ID|1712 + 150341|polyprotein|AGW21594.1|Dengue virus 1|11053 + 1712 + 9 + + + 1 + 9.61583 + 13 + 1362.74 + 2 + 9 + 2 + 9 + 0 + 0 + 4 + 4 + 0 + 8 + PGPIPGPI + PGTSGSPI + PG PI + + + + + 6 + gnl|BL_ORD_ID|1766 + 154857|tegument protein|CAB06735.1|Human alphaherpesvirus 2|10310 + 1766 + 16 + + + 1 + 4.99343 + 1 + 89081.4 + 7 + 9 + 14 + 16 + 0 + 0 + 2 + 3 + 0 + 3 + GPI + GPV + GP+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 19 + Query_19 + M_4951 + 9 + + + 1 + gnl|BL_ORD_ID|741 + 47760|EBNA-1 protein|Q777E1|Human gammaherpesvirus 4|10376 + 741 + 15 + + + 1 + 10.3862 + 15 + 419.458 + 2 + 7 + 1 + 6 + 0 + 0 + 4 + 4 + 0 + 6 + PGPIPG + PGTGPG + PG PG + + + + + 2 + gnl|BL_ORD_ID|75 + 5542|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 + 75 + 15 + + + 1 + 10.001 + 14 + 709.084 + 2 + 9 + 8 + 15 + 0 + 0 + 4 + 4 + 0 + 8 + PGPIPGPI + PGTSGSPI + PG PI + + + + + 3 + gnl|BL_ORD_ID|1929 + 180750|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 + 1929 + 15 + + + 1 + 10.001 + 14 + 819.307 + 2 + 9 + 2 + 9 + 0 + 0 + 4 + 4 + 0 + 8 + PGPIPGPI + PGTSGSPI + PG PI + + + + + 4 + gnl|BL_ORD_ID|260 + 17802|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 + 260 + 15 + + + 1 + 10.001 + 14 + 830.077 + 2 + 9 + 3 + 10 + 0 + 0 + 4 + 4 + 0 + 8 + PGPIPGPI + PGTSGSPI + PG PI + + + + + 5 + gnl|BL_ORD_ID|1712 + 150341|polyprotein|AGW21594.1|Dengue virus 1|11053 + 1712 + 9 + + + 1 + 9.61583 + 13 + 1362.74 + 2 + 9 + 2 + 9 + 0 + 0 + 4 + 4 + 0 + 8 + PGPIPGPI + PGTSGSPI + PG PI + + + + + 6 + gnl|BL_ORD_ID|1766 + 154857|tegument protein|CAB06735.1|Human alphaherpesvirus 2|10310 + 1766 + 16 + + + 1 + 4.99343 + 1 + 89081.4 + 7 + 9 + 14 + 16 + 0 + 0 + 2 + 3 + 0 + 3 + GPI + GPV + GP+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 20 + Query_20 + M_4952 + 9 + + + 1 + gnl|BL_ORD_ID|344 + 21638|protein F|ABV46152.2|Hepatitis C virus (isolate Japanese)|11116 + 344 + 9 + + + 1 + 10.7714 + 16 + 376.438 + 2 + 9 + 2 + 9 + 0 + 0 + 4 + 5 + 0 + 8 + PGPIPGPI + PGLSPGTL + PG PG + + + + + + 2 + gnl|BL_ORD_ID|741 + 47760|EBNA-1 protein|Q777E1|Human gammaherpesvirus 4|10376 + 741 + 15 + + + 1 + 10.3862 + 15 + 449.179 + 2 + 7 + 1 + 6 + 0 + 0 + 4 + 4 + 0 + 6 + PGPIPG + PGTGPG + PG PG + + + + + 3 + gnl|BL_ORD_ID|75 + 5542|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 + 75 + 15 + + + 1 + 10.3862 + 15 + 461.604 + 1 + 9 + 7 + 15 + 0 + 0 + 4 + 5 + 0 + 9 + NPGPIPGPI + SPGTSGSPI + +PG PI + + + + + 4 + gnl|BL_ORD_ID|260 + 17802|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 + 260 + 15 + + + 1 + 10.3862 + 15 + 550.452 + 1 + 9 + 2 + 10 + 0 + 0 + 4 + 5 + 0 + 9 + NPGPIPGPI + SPGTSGSPI + +PG PI + + + + + 5 + gnl|BL_ORD_ID|1929 + 180750|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 + 1929 + 15 + + + 1 + 10.3862 + 15 + 557.903 + 1 + 9 + 1 + 9 + 0 + 0 + 4 + 5 + 0 + 9 + NPGPIPGPI + SPGTSGSPI + +PG PI + + + + + 6 + gnl|BL_ORD_ID|1712 + 150341|polyprotein|AGW21594.1|Dengue virus 1|11053 + 1712 + 9 + + + 1 + 10.001 + 14 + 1206.48 + 1 + 9 + 1 + 9 + 0 + 0 + 4 + 4 + 0 + 9 + NPGPIPGPI + KPGTSGSPI + PG PI + + + + + 7 + gnl|BL_ORD_ID|1766 + 154857|tegument protein|CAB06735.1|Human alphaherpesvirus 2|10310 + 1766 + 16 + + + 1 + 4.99343 + 1 + 83537.4 + 7 + 9 + 14 + 16 + 0 + 0 + 2 + 3 + 0 + 3 + GPI + GPV + GP+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 21 + Query_21 + M_4953 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 22 + Query_22 + M_4954 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 23 + Query_23 + M_4955 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 24 + Query_24 + M_4956 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 25 + Query_25 + M_4957 + 9 + + + 1 + gnl|BL_ORD_ID|647 + 38466|nucleocapsid protein|ABF21284.1|Influenza A virus (A/Iran/1/1957(H2N2))|488233 + 647 + 9 + + + 1 + 15.779 + 29 + 0.476466 + 1 + 9 + 1 + 9 + 0 + 0 + 5 + 8 + 0 + 9 + IPTEKPTIL + LPFDKPTIM + +P +KPTI+ + + + + + 2 + gnl|BL_ORD_ID|1433 + 116127|Nucleoprotein|P15682.1|Influenza A virus (A/Wilson-Smith/1933(H1N1))|381518 + 1433 + 9 + + + 1 + 15.0086 + 27 + 1.10528 + 1 + 9 + 1 + 9 + 0 + 0 + 4 + 8 + 0 + 9 + IPTEKPTIL + LPFDRPTIM + +P ++PTI+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + + diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_137814_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_137814_1_T.fasta new file mode 100755 index 00000000..452ea838 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_137814_1_T.fasta @@ -0,0 +1,50 @@ +>M_4958 +FLNRWMANT +>M_4959 +WMANTLDAV +>M_4960 +ALHTAVLLL +>M_4961 +KMWDAVLYR +>M_4962 +LSIESLTLV +>M_4963 +TLSIESLTL +>M_4964 +HRVNWVVFL +>M_4965 +FLYQPNWRF +>M_4966 +LRKRRSRKR +>M_4967 +RQLRKRRSR +>M_4968 +RRQEQPSIK +>M_4969 +FQYKFTVQA +>M_4970 +ILGTPLSKV +>M_4971 +VLSGAKIWL +>M_4972 +AVLIVTTTV +>M_4973 +LLESSNTNV +>M_4974 +VVWATKYFL +>M_4975 +AMCSAQEEI +>M_4976 +KLTPYMVVL +>M_4977 +FRVRGAVSH +>M_4978 +FRHSMVVPY +>M_4979 +KRRRLWAAL +>M_4980 +RRLWAALGP +>M_4981 +YLIISTFFL +>M_4982 +KIFNHPSTL diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_137814_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_137814_1_T_iedb.xml new file mode 100755 index 00000000..d612c630 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_137814_1_T_iedb.xml @@ -0,0 +1,1072 @@ + + + + blastp + BLASTP 2.2.30+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta + Query_1 + M_4958 + 9 + + + BLOSUM62 + 100000000 + 11 + 1 + F + + + + + 1 + Query_1 + M_4958 + 9 + + + 1 + gnl|BL_ORD_ID|1516 + 140561|metal cation transporter P-type ATPase A CtpF|NP_216513.1|Mycobacterium tuberculosis H37Rv|83332 + 1516 + 9 + + + 1 + 13.853 + 24 + 4.4402 + 1 + 6 + 3 + 8 + 0 + 0 + 4 + 5 + 0 + 6 + FLNRWM + FANRWI + F NRW+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 2 + Query_2 + M_4959 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 3 + Query_3 + M_4960 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 4 + Query_4 + M_4961 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 5 + Query_5 + M_4962 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 6 + Query_6 + M_4963 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 7 + Query_7 + M_4964 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 8 + Query_8 + M_4965 + 9 + + + 1 + gnl|BL_ORD_ID|1272 + 101721|nef|AAA02639.1|Human immunodeficiency virus 1|11676 + 1272 + 10 + + + 1 + 11.927 + 19 + 78.4397 + 3 + 8 + 5 + 10 + 0 + 0 + 3 + 5 + 0 + 6 + YQPNWR + YFPDWQ + Y P+W+ + + + + + 2 + gnl|BL_ORD_ID|1287 + 102235|nef protein|ACR27119.1|Human immunodeficiency virus 1|11676 + 1287 + 9 + + + 1 + 11.927 + 19 + 91.4136 + 3 + 8 + 1 + 6 + 0 + 0 + 3 + 5 + 0 + 6 + YQPNWR + YFPDWQ + Y P+W+ + + + + + 3 + gnl|BL_ORD_ID|1285 + 102151|nef protein|ACR27128.1|Human immunodeficiency virus 1|11676 + 1285 + 11 + + + 1 + 11.927 + 19 + 98.2033 + 3 + 8 + 4 + 9 + 0 + 0 + 3 + 5 + 0 + 6 + YQPNWR + YFPDWQ + Y P+W+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 9 + Query_9 + M_4966 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 10 + Query_10 + M_4967 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 11 + Query_11 + M_4968 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 12 + Query_12 + M_4969 + 9 + + + 1 + gnl|BL_ORD_ID|210 + 15242|trans-sialidase, putative|EAN81560.1|Trypanosoma cruzi|5693 + 210 + 9 + + + 1 + 13.0826 + 22 + 15.4875 + 2 + 7 + 3 + 8 + 0 + 0 + 4 + 5 + 0 + 6 + QYKFTV + NYKFTL + YKFT+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 13 + Query_13 + M_4970 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 14 + Query_14 + M_4971 + 9 + + + 1 + gnl|BL_ORD_ID|1951 + 181036|||| + 1951 + 20 + + + 1 + 15.779 + 29 + 0.402259 + 1 + 9 + 1 + 9 + 0 + 0 + 6 + 7 + 0 + 9 + VLSGAKIWL + VLSDFKVWL + VLS K+WL + + + + + 2 + gnl|BL_ORD_ID|1950 + 181035|||| + 1950 + 44 + + + 1 + 15.3938 + 28 + 1.34675 + 1 + 9 + 1 + 9 + 0 + 0 + 6 + 7 + 0 + 9 + VLSGAKIWL + VLSDFKVWL + VLS K+WL + + + + + 3 + gnl|BL_ORD_ID|1055 + 69751|polyprotein|BAB18806.1|Hepatitis C virus genotype 1|41856 + 1055 + 9 + + + 1 + 14.6234 + 26 + 1.82241 + 1 + 9 + 1 + 9 + 0 + 0 + 6 + 6 + 0 + 9 + VLSGAKIWL + VLSDFKTWL + VLS K WL + + + + + 4 + gnl|BL_ORD_ID|1056 + 69753|polyprotein|AAK49500.1|Hepatitis C virus genotype 3|356114 + 1056 + 9 + + + 1 + 13.853 + 24 + 5.09494 + 1 + 9 + 1 + 9 + 0 + 0 + 5 + 6 + 0 + 9 + VLSGAKIWL + VLSDFRTWL + VLS + WL + + + + + 5 + gnl|BL_ORD_ID|1054 + 69750|polyprotein|AAC03058.1|Hepatitis C virus genotype 3|356114 + 1054 + 9 + + + 1 + 13.853 + 24 + 5.74926 + 1 + 9 + 1 + 9 + 0 + 0 + 6 + 6 + 0 + 9 + VLSGAKIWL + VLSDFKSWL + VLS K WL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 15 + Query_15 + M_4972 + 9 + + + 1 + gnl|BL_ORD_ID|901 + 59182|attachment glycoprotein|ABQ58821.1|Human metapneumovirus|162145 + 901 + 10 + + + 1 + 9.61583 + 13 + 1296.37 + 2 + 9 + 3 + 10 + 0 + 0 + 4 + 6 + 0 + 8 + VLIVTTTV + ILIGITTL + +LI TT+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 16 + Query_16 + M_4973 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 17 + Query_17 + M_4974 + 9 + + + 1 + gnl|BL_ORD_ID|664 + 39591|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 + 664 + 20 + + + 1 + 13.0826 + 22 + 15.6203 + 1 + 9 + 12 + 20 + 0 + 0 + 4 + 6 + 0 + 9 + VVWATKYFL + CLWWLQYFL + +W +YFL + + + + + 2 + gnl|BL_ORD_ID|1945 + 180828|polyprotein|AGO67248.1|Dengue virus 2|11060 + 1945 + 10 + + + 1 + 12.3122 + 20 + 52.036 + 2 + 8 + 4 + 10 + 0 + 0 + 3 + 5 + 0 + 7 + VWATKYF + MWSLMYF + +W+ YF + + + + + 3 + gnl|BL_ORD_ID|1887 + 180579|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 + 1887 + 15 + + + 1 + 12.3122 + 20 + 53.1389 + 2 + 8 + 6 + 12 + 0 + 0 + 3 + 5 + 0 + 7 + VWATKYF + MWSLMYF + +W+ YF + + + + + 4 + gnl|BL_ORD_ID|1960 + 182599|polyprotein|AGW21594.1|Dengue virus 1|11053 + 1960 + 9 + + + 1 + 11.927 + 19 + 110.987 + 2 + 8 + 3 + 9 + 0 + 0 + 3 + 4 + 0 + 7 + VWATKYF + MWQLMYF + +W YF + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 18 + Query_18 + M_4975 + 9 + + + 1 + gnl|BL_ORD_ID|889 + 58463|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 + 889 + 20 + + + 1 + 13.0826 + 22 + 16.661 + 1 + 9 + 1 + 9 + 0 + 0 + 3 + 7 + 0 + 9 + AMCSAQEEI + SICPSQEPM + ++C +QE + + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 19 + Query_19 + M_4976 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 20 + Query_20 + M_4977 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 21 + Query_21 + M_4978 + 9 + + + 1 + gnl|BL_ORD_ID|1223 + 97093|polyprotein|AAB66324.1|Hepatitis C virus (isolate H77)|63746 + 1223 + 10 + + + 1 + 13.853 + 24 + 5.20543 + 2 + 8 + 3 + 9 + 0 + 0 + 4 + 6 + 0 + 7 + RHSMVVP + RHADVIP + RH+ V+P + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 22 + Query_22 + M_4979 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 23 + Query_23 + M_4980 + 9 + + + 1 + gnl|BL_ORD_ID|909 + 59569|Genome polyprotein|P26662.3|Hepatitis C virus (isolate Japanese)|11116 + 909 + 10 + + + 1 + 11.927 + 19 + 99.9004 + 4 + 9 + 5 + 10 + 0 + 0 + 3 + 4 + 0 + 6 + WAALGP + WLSQGP + W + GP + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 24 + Query_24 + M_4981 + 9 + + + 1 + gnl|BL_ORD_ID|1522 + 140616|membrane-associated phospholipase C|NP_216866.1|Mycobacterium tuberculosis H37Rv|83332 + 1522 + 9 + + + 1 + 12.3122 + 20 + 48.7826 + 1 + 7 + 1 + 7 + 0 + 0 + 4 + 5 + 0 + 7 + YLIISTF + YLLADTF + YL+ TF + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 25 + Query_25 + M_4982 + 9 + + + 1 + gnl|BL_ORD_ID|2158 + 189294|Gag|O89360|Human immunodeficiency virus 1|11676 + 2158 + 9 + + + 1 + 12.3122 + 20 + 52.1643 + 1 + 9 + 1 + 9 + 0 + 0 + 4 + 6 + 0 + 9 + KIFNHPSTL + SLYNTVSTL + ++N STL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + + diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_137854_2_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_137854_2_T.fasta new file mode 100755 index 00000000..3d9bfe8d --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_137854_2_T.fasta @@ -0,0 +1,160 @@ +>M_4983 +RSPKKHGYM +>M_4984 +YMKMFEIPA +>M_4985 +LSSIGRSPM +>M_4986 +MVFCDFHGH +>M_4987 +RSPMVFCDF +>M_4988 +SIGRSPMVF +>M_4989 +SSIGRSPMV +>M_4990 +ATATAYLCR +>M_4991 +ATAYLCRVK +>M_4992 +RVKGNFQTI +>M_4993 +TATAYLCRV +>M_4994 +YLCRVKGNF +>M_4995 +CVSCWNVSR +>M_4996 +RLASLYKTL +>M_4997 +TLPQSVDPL +>M_4998 +SSSYAIEKR +>M_4999 +ISRSTFAEV +>M_5000 +RLPISRSTF +>M_5001 +STFAEVTGL +>M_5002 +STFAEVTGL +>M_5003 +FSWNGGSFV +>M_5004 +FSWNGGSFV +>M_5005 +TINEECSEI +>M_5006 +ILACRWVEM +>M_5007 +ESPFSSGKV +>M_5008 +MLAIGCALL +>M_5009 +ESIRHNVLY +>M_5010 +SIRHNVLYR +>M_5011 +LQFGPTAEG +>M_5012 +QPIPSVHER +>M_5013 +SVHERTDWV +>M_5014 +SVHERTDWV +>M_5015 +RAPSPVSFV +>M_5016 +GVLVLLFTL +>M_5017 +VLAPGVLVL +>M_5018 +VLAPGVLVL +>M_5019 +VLVLLFTLV +>M_5020 +FTFLVSLYL +>M_5021 +FTFLVSLYL +>M_5022 +IQAYVFTFL +>M_5023 +IQAYVFTFL +>M_5024 +LIQAYVFTF +>M_5025 +QAYVFTFLV +>M_5026 +QAYVFTFLV +>M_5027 +YVFTFLVSL +>M_5028 +YVFTFLVSL +>M_5029 +SSSPTCSLM +>M_5030 +ENWDLVTYR +>M_5031 +GAMENWDLV +>M_5032 +LEHPGSTRF +>M_5033 +QTDYVLSPL +>M_5034 +VLSPLTGGL +>M_5035 +ITEILDRYV +>M_5036 +FNKSGFKHY +>M_5037 +KSGFKHYQM +>M_5038 +PVFNKSGFK +>M_5039 +VLVSGIQVL +>M_5040 +VLVSGIQVL +>M_5041 +RSRTGEDEV +>M_5042 +LGQGELSAF +>M_5043 +EAQPESEGV +>M_5044 +LQDFYLGTY +>M_5045 +VAFPLQDFY +>M_5046 +ESVNILSVL +>M_5047 +GLVESVNIL +>M_5048 +FTVGQTEKY +>M_5049 +ESFKQTYVY +>M_5050 +ESFKQTYVY +>M_5051 +QTYVYSMAL +>M_5052 +YVYSMALVL +>M_5053 +YVYSMALVL +>M_5054 +YVYSMALVL +>M_5055 +FSLHKDRPV +>M_5056 +ATRKLIGKV +>M_5057 +HLKVRTATR +>M_5058 +TATRKLIGK +>M_5059 +LLPWAHSML +>M_5060 +QQNAPLLPW +>M_5061 +RIHSDEQPY +>M_5062 +AVHTVPQTI diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_137854_2_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_137854_2_T_iedb.xml new file mode 100755 index 00000000..77954074 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_137854_2_T_iedb.xml @@ -0,0 +1,2720 @@ + + + + blastp + BLASTP 2.2.30+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta + Query_1 + M_4983 + 9 + + + BLOSUM62 + 100000000 + 11 + 1 + F + + + + + 1 + Query_1 + M_4983 + 9 + + + 1 + gnl|BL_ORD_ID|924 + 60031|SAG1 protein|AAO72426.1|Toxoplasma gondii RH|383379 + 924 + 9 + + + 1 + 13.0826 + 22 + 16.035 + 2 + 6 + 1 + 5 + 0 + 0 + 4 + 5 + 0 + 5 + SPKKH + SPEKH + SP+KH + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 2 + Query_2 + M_4984 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 3 + Query_3 + M_4985 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 4 + Query_4 + M_4986 + 9 + + + 1 + gnl|BL_ORD_ID|1776 + 155811|ribonucleotide reductase large subunit|CAB06725.1|Human alphaherpesvirus 2|10310 + 1776 + 15 + + + 1 + 16.1642 + 30 + 0.342581 + 1 + 9 + 2 + 10 + 0 + 0 + 5 + 5 + 0 + 9 + MVFCDFHGH + MSLADFHGE + M DFHG + + + + + 2 + gnl|BL_ORD_ID|1975 + 183147|polyprotein|AGW21594.1|Dengue virus 1|11053 + 1975 + 9 + + + 1 + 11.5418 + 18 + 116.464 + 3 + 9 + 1 + 7 + 0 + 0 + 4 + 4 + 0 + 7 + FCDFHGH + FCSHHFH + FC H H + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 5 + Query_5 + M_4987 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 6 + Query_6 + M_4988 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 7 + Query_7 + M_4989 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 8 + Query_8 + M_4990 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 9 + Query_9 + M_4991 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 10 + Query_10 + M_4992 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 11 + Query_11 + M_4993 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 12 + Query_12 + M_4994 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 13 + Query_13 + M_4995 + 9 + + + 1 + gnl|BL_ORD_ID|181 + 13456|circumsporozoite protein|AAN87606.1|Plasmodium falciparum|5833 + 181 + 20 + + + 1 + 11.927 + 19 + 62.285 + 1 + 7 + 14 + 20 + 0 + 0 + 4 + 5 + 0 + 7 + CVSCWNV + CSSVFNV + C S +NV + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 14 + Query_14 + M_4996 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 15 + Query_15 + M_4997 + 9 + + + 1 + gnl|BL_ORD_ID|646 + 38446|Glycoprotein B precursor (Glycoprotein II)|P09257.1|Human alphaherpesvirus 3|10335 + 646 + 11 + + + 1 + 15.0086 + 27 + 1.31191 + 2 + 9 + 1 + 8 + 0 + 0 + 4 + 6 + 0 + 8 + LPQSVDPL + LPEGMDPF + LP+ +DP + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 16 + Query_16 + M_4998 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 17 + Query_17 + M_4999 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 18 + Query_18 + M_5000 + 9 + + + 1 + gnl|BL_ORD_ID|1333 + 107873|Genome polyprotein|P26664.3|Hepatitis C virus|11103 + 1333 + 10 + + + 1 + 13.4678 + 23 + 10.2566 + 3 + 9 + 3 + 9 + 0 + 0 + 4 + 6 + 0 + 7 + PISRSTF + PITYSTY + PI+ ST+ + + + + + 2 + gnl|BL_ORD_ID|965 + 63963|HCV-1|AAA45676.1|Hepatitis C virus|11103 + 965 + 10 + + + 1 + 13.4678 + 23 + 11.3855 + 3 + 9 + 4 + 10 + 0 + 0 + 4 + 6 + 0 + 7 + PISRSTF + PITYSTY + PI+ ST+ + + + + + 3 + gnl|BL_ORD_ID|1434 + 116136|nucleocapsid protein|ACS34671.1|Influenza A virus (A/Auckland/1/2009(H1N1))|642794 + 1434 + 9 + + + 1 + 13.0826 + 22 + 16.6015 + 2 + 8 + 1 + 7 + 0 + 0 + 4 + 5 + 0 + 7 + LPISRST + LPFERAT + LP R+T + + + + + 4 + gnl|BL_ORD_ID|650 + 38472|nucleoprotein|AAV48837.1|Influenza A virus (A/Brevig Mission/1/1918(H1N1))|88776 + 650 + 9 + + + 1 + 13.0826 + 22 + 18.1053 + 2 + 8 + 1 + 7 + 0 + 0 + 4 + 5 + 0 + 7 + LPISRST + LPFERAT + LP R+T + + + + + 5 + gnl|BL_ORD_ID|964 + 63784|Genome polyprotein|P26663.3|Hepatitis C virus|11103 + 964 + 10 + + + 1 + 13.0826 + 22 + 18.1832 + 3 + 9 + 4 + 10 + 0 + 0 + 3 + 6 + 0 + 7 + PISRSTF + PVTYSTY + P++ ST+ + + + + + 6 + gnl|BL_ORD_ID|1432 + 116123|nucleocapsid protein|ABP49342.1|Influenza A virus (A/California/10/1978(H1N1))|425557 + 1432 + 9 + + + 1 + 13.0826 + 22 + 20.0871 + 2 + 8 + 1 + 7 + 0 + 0 + 4 + 5 + 0 + 7 + LPISRST + LPFDKST + LP +ST + + + + + 7 + gnl|BL_ORD_ID|649 + 38471|nucleocapsid protein|ABC46569.1|Influenza A virus (A/Memphis/4/1980(H3N2))|383578 + 649 + 9 + + + 1 + 13.0826 + 22 + 21.1561 + 2 + 8 + 1 + 7 + 0 + 0 + 4 + 5 + 0 + 7 + LPISRST + LPFEKST + LP +ST + + + + + 8 + gnl|BL_ORD_ID|648 + 38468|nucleoprotein|CAA24268.1|Influenza A virus (A/Puerto Rico/8/1934(H1N1))|211044 + 648 + 9 + + + 1 + 13.0826 + 22 + 21.5246 + 2 + 8 + 1 + 7 + 0 + 0 + 4 + 5 + 0 + 7 + LPISRST + LPFDRTT + LP R+T + + + + + 9 + gnl|BL_ORD_ID|1232 + 97467|nucleocapsid protein|ACP44251.1|Influenza A virus (A/Fujian/411/2002(H3N2))|293090 + 1232 + 9 + + + 1 + 13.0826 + 22 + 22.6682 + 2 + 8 + 1 + 7 + 0 + 0 + 4 + 5 + 0 + 7 + LPISRST + LPFEKST + LP +ST + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 19 + Query_19 + M_5001 + 9 + + + 1 + gnl|BL_ORD_ID|192 + 14198|UL123; IE1|AAR31390.1|Human betaherpesvirus 5|10359 + 192 + 11 + + + 1 + 11.927 + 19 + 64.6849 + 1 + 7 + 4 + 10 + 0 + 0 + 4 + 5 + 0 + 7 + STFAEVT + KTFEQVT + TF +VT + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 20 + Query_20 + M_5002 + 9 + + + 1 + gnl|BL_ORD_ID|192 + 14198|UL123; IE1|AAR31390.1|Human betaherpesvirus 5|10359 + 192 + 11 + + + 1 + 11.927 + 19 + 64.6849 + 1 + 7 + 4 + 10 + 0 + 0 + 4 + 5 + 0 + 7 + STFAEVT + KTFEQVT + TF +VT + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 21 + Query_21 + M_5003 + 9 + + + 1 + gnl|BL_ORD_ID|1861 + 180440|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 + 1861 + 15 + + + 1 + 13.0826 + 22 + 16.1221 + 2 + 6 + 8 + 12 + 0 + 0 + 4 + 4 + 0 + 5 + SWNGG + SWNSG + SWN G + + + + + 2 + gnl|BL_ORD_ID|1926 + 180734|Nonstructural protein NS3|NP_739587.2|Dengue virus 2|11060 + 1926 + 9 + + + 1 + 12.6974 + 21 + 33.058 + 2 + 6 + 2 + 6 + 0 + 0 + 4 + 4 + 0 + 5 + SWNGG + SWNSG + SWN G + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 22 + Query_22 + M_5004 + 9 + + + 1 + gnl|BL_ORD_ID|1861 + 180440|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 + 1861 + 15 + + + 1 + 13.0826 + 22 + 16.1221 + 2 + 6 + 8 + 12 + 0 + 0 + 4 + 4 + 0 + 5 + SWNGG + SWNSG + SWN G + + + + + 2 + gnl|BL_ORD_ID|1926 + 180734|Nonstructural protein NS3|NP_739587.2|Dengue virus 2|11060 + 1926 + 9 + + + 1 + 12.6974 + 21 + 33.058 + 2 + 6 + 2 + 6 + 0 + 0 + 4 + 4 + 0 + 5 + SWNGG + SWNSG + SWN G + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 23 + Query_23 + M_5005 + 9 + + + 1 + gnl|BL_ORD_ID|1296 + 103322|polyprotein|BAB18806.1|Hepatitis C virus|11103 + 1296 + 20 + + + 1 + 15.0086 + 27 + 1.00627 + 2 + 7 + 7 + 12 + 0 + 0 + 5 + 6 + 0 + 6 + INEECS + INEDCS + INE+CS + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 24 + Query_24 + M_5006 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 25 + Query_25 + M_5007 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 26 + Query_26 + M_5008 + 9 + + + 1 + gnl|BL_ORD_ID|1938 + 180802|polyprotein|AGO67248.1|Dengue virus 2|11060 + 1938 + 9 + + + 1 + 14.6234 + 26 + 2.22125 + 1 + 6 + 3 + 8 + 0 + 0 + 5 + 6 + 0 + 6 + MLAIGC + LLAIGC + +LAIGC + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 27 + Query_27 + M_5009 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 28 + Query_28 + M_5010 + 9 + + + 1 + gnl|BL_ORD_ID|312 + 20861|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 + 312 + 9 + + + 1 + 11.927 + 19 + 75.1319 + 1 + 8 + 1 + 8 + 0 + 0 + 4 + 6 + 0 + 8 + SIRHNVLY + GLFNNVLY + + +NVLY + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 29 + Query_29 + M_5011 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 30 + Query_30 + M_5012 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 31 + Query_31 + M_5013 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 32 + Query_32 + M_5014 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 33 + Query_33 + M_5015 + 9 + + + 1 + gnl|BL_ORD_ID|661 + 39571|polyprotein|BAD73987.1|Hepatitis C virus subtype 1b|31647 + 661 + 10 + + + 1 + 13.853 + 24 + 4.77406 + 2 + 9 + 2 + 9 + 0 + 0 + 4 + 7 + 0 + 8 + APSPVSFV + SPRPVSYL + +P PVS++ + + + + + 2 + gnl|BL_ORD_ID|2163 + 189546|glycosyl transferase|WP_015631503.1|Mycobacterium tuberculosis|1773 + 2163 + 9 + + + 1 + 12.6974 + 21 + 37.875 + 2 + 7 + 2 + 7 + 0 + 0 + 4 + 5 + 0 + 6 + APSPVS + APEPVA + AP PV+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 34 + Query_34 + M_5016 + 9 + + + 1 + gnl|BL_ORD_ID|301 + 20354|M1 protein|CAA30882.1|Influenza A virus|11320 + 301 + 9 + + + 1 + 13.0826 + 22 + 20.7937 + 1 + 9 + 1 + 9 + 0 + 0 + 5 + 7 + 0 + 9 + GVLVLLFTL + GILGFVFTL + G+L +FTL + + + + + 2 + gnl|BL_ORD_ID|302 + 20355|Matrix protein 1|P03485.1|Influenza A virus (A/Puerto Rico/8/1934(H1N1))|211044 + 302 + 10 + + + 1 + 13.0826 + 22 + 21.2326 + 1 + 9 + 1 + 9 + 0 + 0 + 5 + 7 + 0 + 9 + GVLVLLFTL + GILGFVFTL + G+L +FTL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 35 + Query_35 + M_5017 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 36 + Query_36 + M_5018 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 37 + Query_37 + M_5019 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 38 + Query_38 + M_5020 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 39 + Query_39 + M_5021 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 40 + Query_40 + M_5022 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 41 + Query_41 + M_5023 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 42 + Query_42 + M_5024 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 43 + Query_43 + M_5025 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 44 + Query_44 + M_5026 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 45 + Query_45 + M_5027 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 46 + Query_46 + M_5028 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 47 + Query_47 + M_5029 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 48 + Query_48 + M_5030 + 9 + + + 1 + gnl|BL_ORD_ID|120 + 8236|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 + 120 + 15 + + + 1 + 12.6974 + 21 + 29.2994 + 1 + 8 + 4 + 11 + 0 + 0 + 2 + 5 + 0 + 8 + ENWDLVTY + QGWGPISY + + W ++Y + + + + + 2 + gnl|BL_ORD_ID|1699 + 149117|envelope glycoprotein|AAV74049.1|Hepatitis C virus (isolate H77)|63746 + 1699 + 18 + + + 1 + 12.6974 + 21 + 29.5284 + 1 + 8 + 5 + 12 + 0 + 0 + 2 + 5 + 0 + 8 + ENWDLVTY + QGWGPISY + + W ++Y + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 49 + Query_49 + M_5031 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 50 + Query_50 + M_5032 + 9 + + + 1 + gnl|BL_ORD_ID|1944 + 180818|Membrane glycoprotein precursor|NP_739582.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 + 1944 + 15 + + + 1 + 15.0086 + 27 + 1.30769 + 1 + 7 + 3 + 9 + 0 + 0 + 5 + 5 + 0 + 7 + LEHPGST + LRHPGFT + L HPG T + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 51 + Query_51 + M_5033 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 52 + Query_52 + M_5034 + 9 + + + 1 + gnl|BL_ORD_ID|260 + 17802|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 + 260 + 15 + + + 1 + 11.1566 + 17 + 219.749 + 2 + 8 + 1 + 7 + 0 + 0 + 4 + 4 + 0 + 7 + LSPLTGG + FSPGTSG + SP T G + + + + + 2 + gnl|BL_ORD_ID|75 + 5542|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 + 75 + 15 + + + 1 + 11.1566 + 17 + 246.442 + 2 + 8 + 6 + 12 + 0 + 0 + 4 + 4 + 0 + 7 + LSPLTGG + FSPGTSG + SP T G + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 53 + Query_53 + M_5035 + 9 + + + 1 + gnl|BL_ORD_ID|163 + 12588|Glycoprotein B precursor (Glycoprotein II)|P09257.1|Human alphaherpesvirus 3|10335 + 163 + 11 + + + 1 + 13.0826 + 22 + 14.9787 + 1 + 8 + 2 + 9 + 0 + 0 + 3 + 7 + 0 + 8 + ITEILDRY + ITDTIDKF + IT+ +D++ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 54 + Query_54 + M_5036 + 9 + + + 1 + gnl|BL_ORD_ID|390 + 23864|envelope glycoprotein(gp21, gp46) - human T-cell lymphotropic virus type 1|A45714|Human T-lymphotropic virus 1|11908 + 390 + 9 + + + 1 + 12.6974 + 21 + 37.875 + 1 + 7 + 2 + 8 + 0 + 0 + 4 + 5 + 0 + 7 + FNKSGFK + FSKCGFP + F+K GF + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 55 + Query_55 + M_5037 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 56 + Query_56 + M_5038 + 9 + + + 1 + gnl|BL_ORD_ID|390 + 23864|envelope glycoprotein(gp21, gp46) - human T-cell lymphotropic virus type 1|A45714|Human T-lymphotropic virus 1|11908 + 390 + 9 + + + 1 + 12.6974 + 21 + 37.875 + 3 + 8 + 2 + 7 + 0 + 0 + 4 + 5 + 0 + 6 + FNKSGF + FSKCGF + F+K GF + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 57 + Query_57 + M_5039 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 58 + Query_58 + M_5040 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 59 + Query_59 + M_5041 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 60 + Query_60 + M_5042 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 61 + Query_61 + M_5043 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 62 + Query_62 + M_5044 + 9 + + + 1 + gnl|BL_ORD_ID|1412 + 111404|Protein E7|P03129.1|Human papillomavirus type 16|333760 + 1412 + 15 + + + 1 + 14.2382 + 25 + 3.74365 + 1 + 8 + 7 + 14 + 0 + 0 + 4 + 6 + 0 + 8 + LQDFYLGT + LEDLLMGT + L+D +GT + + + + + 2 + gnl|BL_ORD_ID|1781 + 156550|E3 ubiquitin-protein ligase Mdm2|Q00987.1|Homo sapiens|9606 + 1781 + 9 + + + 1 + 14.2382 + 25 + 4.29054 + 4 + 9 + 3 + 8 + 0 + 0 + 5 + 5 + 0 + 6 + FYLGTY + FYLGQY + FYLG Y + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 63 + Query_63 + M_5045 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 64 + Query_64 + M_5046 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 65 + Query_65 + M_5047 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 66 + Query_66 + M_5048 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 67 + Query_67 + M_5049 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 68 + Query_68 + M_5050 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 69 + Query_69 + M_5051 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 70 + Query_70 + M_5052 + 9 + + + + 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b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_138385_2_T.fasta new file mode 100755 index 00000000..89206968 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_138385_2_T.fasta @@ -0,0 +1,104 @@ +>M_5063 +DPIRRHLHI +>M_5064 +HILYHCYGV +>M_5065 +WTRPGSEVL +>M_5066 +FPYVRNFVM +>M_5067 +YVRNFVMNL +>M_5068 +VAHEGMRPM +>M_5069 +RPDKMVPVV +>M_5070 +ILYLLSLFT +>M_5071 +LTILYLLSL +>M_5072 +YLLSLFTQT +>M_5073 +AAGPHVTVL +>M_5074 +RASAAGPHV +>M_5075 +SAAGPHVTV +>M_5076 +AVADLSCML +>M_5077 +CMLVLPTRL +>M_5078 +LAVADLSCM +>M_5079 +MLVLPTRLV +>M_5080 +VAVGTEHTL +>M_5081 +SVAWTTMDV +>M_5082 +TMDVATPSV +>M_5083 +NLYKGSVLY +>M_5084 +DEYNFVRTY +>M_5085 +RTYECFQHR +>M_5086 +LPSDPRLHL +>M_5087 +FLADITHLR +>M_5088 +GMRYWNMMV +>M_5089 +NMMVQWWLA +>M_5090 +TPLGKGDIV +>M_5091 +KVRSCIDLI +>M_5092 +YEQKVRSCI +>M_5093 +ALLAFATIM +>M_5094 +ATIMYVPAL +>M_5095 +LAFATIMYV +>M_5096 +LAFATIMYV +>M_5097 +YALLAFATI +>M_5098 +YALLAFATI +>M_5099 +LLLLLLLLV +>M_5100 +LLLLLLLVV +>M_5101 +LLLLLLVVV +>M_5102 +LLVVVPWGV +>M_5103 +IAATPIPAM +>M_5104 +HVLEIDESV +>M_5105 +HVLEIDESV +>M_5106 +YFNGSTNHV +>M_5107 +TPLCPGELL +>M_5108 +LMLGLVWTI +>M_5109 +LMLGLVWTI +>M_5110 +RLMLGLVWT +>M_5111 +SLTADDAFV +>M_5112 +PAFSLDVLM +>M_5113 +YLQAEIEPV +>M_5114 +YLQAEIEPV diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_138385_2_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_138385_2_T_iedb.xml new file mode 100755 index 00000000..385d1a53 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_138385_2_T_iedb.xml @@ -0,0 +1,1610 @@ + + + + blastp + BLASTP 2.2.30+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta + Query_1 + M_5063 + 9 + + + BLOSUM62 + 100000000 + 11 + 1 + F + + + + + 1 + Query_1 + M_5063 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 2 + Query_2 + M_5064 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 3 + Query_3 + M_5065 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 4 + Query_4 + M_5066 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 5 + Query_5 + M_5067 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 6 + Query_6 + M_5068 + 9 + + + 1 + gnl|BL_ORD_ID|996 + 65654|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 + 996 + 15 + + + 1 + 14.6234 + 26 + 1.57759 + 2 + 9 + 7 + 14 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No hits found + + + 15 + Query_15 + M_5077 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 16 + Query_16 + M_5078 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 17 + Query_17 + M_5079 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 18 + Query_18 + M_5080 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 19 + Query_19 + M_5081 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 20 + Query_20 + M_5082 + 9 + + + 1 + gnl|BL_ORD_ID|1762 + 154448|RL2|CAB06760.1|Human alphaherpesvirus 2|10310 + 1762 + 16 + + + 1 + 8.46023 + 10 + 4206.81 + 2 + 5 + 5 + 8 + 0 + 0 + 3 + 3 + 0 + 4 + MDVA + MDAA + MD A + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 21 + Query_21 + M_5083 + 9 + + + 1 + gnl|BL_ORD_ID|413 + 24943|DNA polymerase|CAA10434.1|Hepatitis B virus|10407 + 413 + 11 + + + 1 + 13.853 + 24 + 4.51774 + 1 + 9 + 2 + 10 + 0 + 0 + 4 + 6 + 0 + 9 + NLYKGSVLY + TLWKAGILY + L+K +LY + + + + + 2 + gnl|BL_ORD_ID|988 + 65148|DNA polymerase|CAA10434.1|Hepatitis B virus|10407 + 988 + 10 + + + 1 + 13.853 + 24 + 4.53299 + 1 + 9 + 1 + 9 + 0 + 0 + 4 + 6 + 0 + 9 + NLYKGSVLY + TLWKAGILY + L+K +LY + + + + + 3 + gnl|BL_ORD_ID|683 + 41093|polyprotein|AGO67248.1|Dengue virus 2|11060 + 683 + 9 + + + 1 + 13.4678 + 23 + 11.1275 + 1 + 6 + 3 + 8 + 0 + 0 + 3 + 6 + 0 + 6 + NLYKGS + NIFRGS + N+++GS + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 22 + Query_22 + M_5084 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 23 + Query_23 + M_5085 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 24 + Query_24 + M_5086 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 25 + Query_25 + M_5087 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + 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Query_33 + M_5095 + 9 + + + 1 + gnl|BL_ORD_ID|1568 + 141341|tegument protein VP11/12|NP_044648.1|Human alphaherpesvirus 1|10298 + 1568 + 9 + + + 1 + 13.0826 + 22 + 18.4218 + 1 + 8 + 2 + 9 + 0 + 0 + 3 + 7 + 0 + 8 + LAFATIMY + LAYVSVLY + LA+ +++Y + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 34 + Query_34 + M_5096 + 9 + + + 1 + gnl|BL_ORD_ID|1568 + 141341|tegument protein VP11/12|NP_044648.1|Human alphaherpesvirus 1|10298 + 1568 + 9 + + + 1 + 13.0826 + 22 + 18.4218 + 1 + 8 + 2 + 9 + 0 + 0 + 3 + 7 + 0 + 8 + LAFATIMY + LAYVSVLY + LA+ +++Y + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 35 + Query_35 + M_5097 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 36 + Query_36 + M_5098 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 37 + Query_37 + M_5099 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 38 + Query_38 + M_5100 + 9 + + + 1 + gnl|BL_ORD_ID|1263 + 98540|trans-sialidase, putative|EAN88532.1|Trypanosoma cruzi|5693 + 1263 + 10 + + + 1 + 11.1566 + 17 + 242.571 + 3 + 9 + 4 + 10 + 0 + 0 + 6 + 7 + 0 + 7 + LLLLLVV + VLLLLVV + +LLLLVV + + + + + 2 + gnl|BL_ORD_ID|1254 + 98224|trans-sialidase, putative|EAN82076.1|Trypanosoma cruzi|5693 + 1254 + 10 + + + 1 + 11.1566 + 17 + 286.165 + 4 + 9 + 1 + 6 + 0 + 0 + 6 + 6 + 0 + 6 + LLLLVV + LLLLVV + LLLLVV + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 39 + Query_39 + M_5101 + 9 + + + 1 + gnl|BL_ORD_ID|1263 + 98540|trans-sialidase, putative|EAN88532.1|Trypanosoma cruzi|5693 + 1263 + 10 + + + 1 + 11.1566 + 17 + 231.802 + 3 + 8 + 5 + 10 + 0 + 0 + 6 + 6 + 0 + 6 + LLLLVV + LLLLVV + LLLLVV + + + + + 2 + gnl|BL_ORD_ID|1254 + 98224|trans-sialidase, putative|EAN82076.1|Trypanosoma cruzi|5693 + 1254 + 10 + + + 1 + 11.1566 + 17 + 250.006 + 3 + 9 + 1 + 7 + 0 + 0 + 6 + 7 + 0 + 7 + LLLLVVV + LLLLVVM + LLLLVV+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 40 + Query_40 + M_5102 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 41 + Query_41 + M_5103 + 9 + + + 1 + gnl|BL_ORD_ID|1815 + 177806|polyprotein|ACZ60104.1|Hepatitis C virus subtype 3a|356426 + 1815 + 11 + + + 1 + 13.0826 + 22 + 14.9787 + 4 + 8 + 3 + 7 + 0 + 0 + 4 + 5 + 0 + 5 + TPIPA + TPLPA + TP+PA + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 42 + Query_42 + M_5104 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 43 + Query_43 + M_5105 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 44 + Query_44 + M_5106 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 45 + Query_45 + M_5107 + 9 + + + 1 + gnl|BL_ORD_ID|2144 + 187197|Core protein|Q9QAC5|Hepatitis B virus|10407 + 2144 + 9 + + + 1 + 13.4678 + 23 + 8.42175 + 3 + 9 + 1 + 7 + 0 + 0 + 4 + 6 + 0 + 7 + LCPGELL + VCWGELM + +C GEL+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 46 + Query_46 + M_5108 + 9 + + + 1 + gnl|BL_ORD_ID|1717 + 150389|polyprotein|AGO67248.1|Dengue virus 2|11060 + 1717 + 9 + + + 1 + 10.7714 + 16 + 354.707 + 1 + 9 + 1 + 9 + 0 + 0 + 3 + 5 + 0 + 9 + LMLGLVWTI + LMMRTTWAL + LM+ W + + + + + + 2 + gnl|BL_ORD_ID|1743 + 150686|polyprotein|AGO67248.1|Dengue virus 2|11060 + 1743 + 9 + + + 1 + 10.7714 + 16 + 442.738 + 1 + 7 + 2 + 8 + 0 + 0 + 3 + 4 + 0 + 7 + LMLGLVW + LMMRTTW + LM+ W + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 47 + Query_47 + M_5109 + 9 + + + 1 + gnl|BL_ORD_ID|1717 + 150389|polyprotein|AGO67248.1|Dengue virus 2|11060 + 1717 + 9 + + + 1 + 10.7714 + 16 + 354.707 + 1 + 9 + 1 + 9 + 0 + 0 + 3 + 5 + 0 + 9 + LMLGLVWTI + LMMRTTWAL + LM+ W + + + + + + 2 + gnl|BL_ORD_ID|1743 + 150686|polyprotein|AGO67248.1|Dengue virus 2|11060 + 1743 + 9 + + + 1 + 10.7714 + 16 + 442.738 + 1 + 7 + 2 + 8 + 0 + 0 + 3 + 4 + 0 + 7 + LMLGLVW + LMMRTTW + LM+ W + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 48 + Query_48 + M_5110 + 9 + + + 1 + gnl|BL_ORD_ID|1743 + 150686|polyprotein|AGO67248.1|Dengue virus 2|11060 + 1743 + 9 + + + 1 + 10.3862 + 15 + 654.037 + 2 + 8 + 2 + 8 + 0 + 0 + 3 + 4 + 0 + 7 + LMLGLVW + LMMRTTW + LM+ W + + + + + 2 + gnl|BL_ORD_ID|1717 + 150389|polyprotein|AGO67248.1|Dengue virus 2|11060 + 1717 + 9 + + + 1 + 10.3862 + 15 + 732.621 + 2 + 8 + 1 + 7 + 0 + 0 + 3 + 4 + 0 + 7 + LMLGLVW + LMMRTTW + LM+ W + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 49 + Query_49 + M_5111 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 50 + Query_50 + M_5112 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 51 + Query_51 + M_5113 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 52 + Query_52 + M_5114 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + + diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_138625_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_138625_1_T.fasta new file mode 100755 index 00000000..764f3386 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_138625_1_T.fasta @@ -0,0 +1,106 @@ +>M_5115 +LFFVDKLYK +>M_5116 +ALLPLFVVL +>M_5117 +ALLPLFVVL +>M_5118 +KALLPLFVV +>M_5119 +VVLCGNDHV +>M_5120 +TEMKRKAPF +>M_5121 +AMATYHFHF +>M_5122 +ATYHFHFNL +>M_5123 +ATYHFHFNL +>M_5124 +KAMATYHFH +>M_5125 +LKAMATYHF +>M_5126 +NVFVEVVLV +>M_5127 +GVKGVNSLF +>M_5128 +KGVNSLFKK +>M_5129 +AMSTPIYQM +>M_5130 +AMSTPIYQM +>M_5131 +SMAMSTPIY +>M_5132 +SMAMSTPIY +>M_5133 +SSMAMSTPI +>M_5134 +KMADEVPLK +>M_5135 +FLLAFRSGA +>M_5136 +LLAFRSGAL +>M_5137 +RVAEVAAQV +>M_5138 +KIFWFPTGL +>M_5139 +AGIFLLIHF +>M_5140 +FLLIHFHPL +>M_5141 +FLLIHFHPL +>M_5142 +GIFLLIHFH +>M_5143 +LLIHFHPLA +>M_5144 +SIVTSTFII +>M_5145 +VTSTFIISL +>M_5146 +LQIHGLAVE +>M_5147 +ATVLTLPHV +>M_5148 +VLTLPHVTK +>M_5149 +AVSNFYLPL +>M_5150 +HISAVSNFY +>M_5151 +HISAVSNFY +>M_5152 +SVVVIIDVK +>M_5153 +VVIIDVKPK +>M_5154 +FQRALVQPG +>M_5155 +ESFTATVEF +>M_5156 +LAAPRGVCY +>M_5157 +ATGATSLCF +>M_5158 +GLAMCHQEL +>M_5159 +LLTLAGLAM +>M_5160 +TVWPSLAPL +>M_5161 +CQHKLGKRY +>M_5162 +AVWRHLLLA +>M_5163 +HLLLALLLL +>M_5164 +LLALLLLVL +>M_5165 +LLALLLLVL +>M_5166 +LLLALLLLV +>M_5167 +LTRHQRTHM diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_138625_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_138625_1_T_iedb.xml new file mode 100755 index 00000000..24e9475d --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_138625_1_T_iedb.xml @@ -0,0 +1,1766 @@ + + + + blastp + BLASTP 2.2.30+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta + Query_1 + M_5115 + 9 + + + BLOSUM62 + 100000000 + 11 + 1 + F + + + + + 1 + Query_1 + M_5115 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 2 + Query_2 + M_5116 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 3 + Query_3 + M_5117 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 4 + Query_4 + M_5118 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 5 + Query_5 + M_5119 + 9 + + + 1 + gnl|BL_ORD_ID|987 + 65118|SAG1 protein|AAO72426.1|Toxoplasma gondii RH|383379 + 987 + 9 + + + 1 + 13.4678 + 23 + 13.0154 + 1 + 9 + 1 + 9 + 0 + 0 + 4 + 6 + 0 + 9 + VVLCGNDHV + TLVCGKDGV + ++CG D V + + + + + 2 + gnl|BL_ORD_ID|671 + 40286|SAG1 protein|AAO72426.1|Toxoplasma gondii RH|383379 + 671 + 9 + + + 1 + 13.4678 + 23 + 13.0154 + 2 + 9 + 1 + 8 + 0 + 0 + 4 + 6 + 0 + 8 + VLCGNDHV + LVCGKDGV + ++CG D V + + + + + 3 + gnl|BL_ORD_ID|1075 + 71266|Circumsporozoite protein precursor|P02893.1|Plasmodium falciparum|5833 + 1075 + 20 + + + 1 + 13.0826 + 22 + 16.3948 + 2 + 6 + 1 + 5 + 0 + 0 + 4 + 4 + 0 + 5 + VLCGN + VTCGN + V CGN + + + + + 4 + gnl|BL_ORD_ID|1074 + 71265|Circumsporozoite protein precursor|P02893.1|Plasmodium falciparum|5833 + 1074 + 10 + + + 1 + 12.6974 + 21 + 28.4017 + 2 + 6 + 1 + 5 + 0 + 0 + 4 + 4 + 0 + 5 + VLCGN + VTCGN + V CGN + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 6 + Query_6 + M_5120 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 7 + Query_7 + M_5121 + 9 + + + 1 + gnl|BL_ORD_ID|1975 + 183147|polyprotein|AGW21594.1|Dengue virus 1|11053 + 1975 + 9 + + + 1 + 11.927 + 19 + 69.1936 + 3 + 8 + 2 + 7 + 0 + 0 + 3 + 5 + 0 + 6 + ATYHFH + CSHHFH + ++HFH + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 8 + Query_8 + M_5122 + 9 + + + 1 + gnl|BL_ORD_ID|419 + 25275|Glutamate decarboxylase 2|Q05329.1|Homo sapiens|9606 + 419 + 13 + + + 1 + 12.3122 + 20 + 42.7536 + 2 + 9 + 5 + 12 + 0 + 0 + 4 + 6 + 0 + 8 + TYHFHFNL + SEHSHFSL + + H HF+L + + + + + 2 + gnl|BL_ORD_ID|1975 + 183147|polyprotein|AGW21594.1|Dengue virus 1|11053 + 1975 + 9 + + + 1 + 11.927 + 19 + 76.3762 + 1 + 6 + 2 + 7 + 0 + 0 + 3 + 5 + 0 + 6 + ATYHFH + CSHHFH + ++HFH + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 9 + Query_9 + M_5123 + 9 + + + 1 + gnl|BL_ORD_ID|419 + 25275|Glutamate decarboxylase 2|Q05329.1|Homo sapiens|9606 + 419 + 13 + + + 1 + 12.3122 + 20 + 42.7536 + 2 + 9 + 5 + 12 + 0 + 0 + 4 + 6 + 0 + 8 + TYHFHFNL + SEHSHFSL + + H HF+L + + + + + 2 + gnl|BL_ORD_ID|1975 + 183147|polyprotein|AGW21594.1|Dengue virus 1|11053 + 1975 + 9 + + + 1 + 11.927 + 19 + 76.3762 + 1 + 6 + 2 + 7 + 0 + 0 + 3 + 5 + 0 + 6 + ATYHFH + CSHHFH + ++HFH + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 10 + Query_10 + M_5124 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 11 + Query_11 + M_5125 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 12 + Query_12 + M_5126 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 13 + Query_13 + M_5127 + 9 + + + 1 + gnl|BL_ORD_ID|786 + 52652|||| + 786 + 27 + + + 1 + 15.0086 + 27 + 1.22232 + 2 + 9 + 13 + 20 + 0 + 0 + 5 + 7 + 0 + 8 + VKGVNSLF + VRGLTSLF + V+G+ SLF + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 14 + Query_14 + M_5128 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 15 + Query_15 + M_5129 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 16 + Query_16 + M_5130 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 17 + Query_17 + M_5131 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 18 + Query_18 + M_5132 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 19 + Query_19 + M_5133 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 20 + Query_20 + M_5134 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 21 + Query_21 + M_5135 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 22 + Query_22 + M_5136 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 23 + Query_23 + M_5137 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 24 + Query_24 + M_5138 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 25 + Query_25 + M_5139 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 26 + Query_26 + M_5140 + 9 + + + 1 + gnl|BL_ORD_ID|624 + 37507|Large T antigen|P03071.1|Human polyomavirus 1|1891762 + 624 + 9 + + + 1 + 13.853 + 24 + 6.71897 + 2 + 9 + 2 + 9 + 0 + 0 + 5 + 6 + 0 + 8 + LLIHFHPL + LLIWFRPV + LLI F P+ + + + + + 2 + gnl|BL_ORD_ID|1975 + 183147|polyprotein|AGW21594.1|Dengue virus 1|11053 + 1975 + 9 + + + 1 + 12.3122 + 20 + 61.624 + 1 + 9 + 1 + 9 + 0 + 0 + 5 + 5 + 0 + 9 + FLLIHFHPL + FCSHHFHQL + F HFH L + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 27 + Query_27 + M_5141 + 9 + + + 1 + gnl|BL_ORD_ID|624 + 37507|Large T antigen|P03071.1|Human polyomavirus 1|1891762 + 624 + 9 + + + 1 + 13.853 + 24 + 6.71897 + 2 + 9 + 2 + 9 + 0 + 0 + 5 + 6 + 0 + 8 + LLIHFHPL + LLIWFRPV + LLI F P+ + + + + + 2 + gnl|BL_ORD_ID|1975 + 183147|polyprotein|AGW21594.1|Dengue virus 1|11053 + 1975 + 9 + + + 1 + 12.3122 + 20 + 61.624 + 1 + 9 + 1 + 9 + 0 + 0 + 5 + 5 + 0 + 9 + FLLIHFHPL + FCSHHFHQL + F HFH L + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 28 + Query_28 + M_5142 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 29 + Query_29 + M_5143 + 9 + + + 1 + gnl|BL_ORD_ID|624 + 37507|Large T antigen|P03071.1|Human polyomavirus 1|1891762 + 624 + 9 + + + 1 + 13.853 + 24 + 4.83846 + 1 + 8 + 2 + 9 + 0 + 0 + 5 + 6 + 0 + 8 + LLIHFHPL + LLIWFRPV + LLI F P+ + + + + + 2 + gnl|BL_ORD_ID|1975 + 183147|polyprotein|AGW21594.1|Dengue virus 1|11053 + 1975 + 9 + + + 1 + 12.3122 + 20 + 59.6102 + 4 + 8 + 5 + 9 + 0 + 0 + 4 + 4 + 0 + 5 + HFHPL + HFHQL + HFH L + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 30 + Query_30 + M_5144 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 31 + Query_31 + M_5145 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 32 + Query_32 + M_5146 + 9 + + + 1 + gnl|BL_ORD_ID|2320 + 423047|Genome polyprotein|P27958.3|Hepatitis C virus genotype 1|41856 + 2320 + 9 + + + 1 + 12.6974 + 21 + 35.9943 + 2 + 8 + 2 + 8 + 0 + 0 + 3 + 6 + 0 + 7 + QIHGLAV + RLHGLSA + ++HGL+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 33 + Query_33 + M_5147 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 34 + Query_34 + M_5148 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 35 + Query_35 + M_5149 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 36 + Query_36 + M_5150 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 37 + Query_37 + M_5151 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 38 + Query_38 + M_5152 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 39 + Query_39 + M_5153 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 40 + Query_40 + M_5154 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+ + No hits found + + + 46 + Query_46 + M_5160 + 9 + + + 1 + gnl|BL_ORD_ID|1520 + 140600|glutamine synthetase GLNA1 (glutamine synthase) (GS-I)|NP_216736.1|Mycobacterium tuberculosis H37Rv|83332 + 1520 + 9 + + + 1 + 13.0826 + 22 + 21.1561 + 1 + 9 + 1 + 9 + 0 + 0 + 4 + 6 + 0 + 9 + TVWPSLAPL + SLWKDGAPL + ++W APL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 47 + Query_47 + M_5161 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 48 + Query_48 + M_5162 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 49 + Query_49 + M_5163 + 9 + + + 1 + gnl|BL_ORD_ID|292 + 19442|nucleocapsid protein|ABI96968.1|SARS coronavirus|227859 + 292 + 10 + + + 1 + 11.1566 + 17 + 246.263 + 4 + 9 + 5 + 10 + 0 + 0 + 6 + 6 + 0 + 6 + LALLLL + LALLLL + LALLLL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 50 + Query_50 + M_5164 + 9 + + + 1 + gnl|BL_ORD_ID|292 + 19442|nucleocapsid 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+RLGCPWFTL +>M_5187 +DWPVFPGLF +>M_5188 +FNVGDDWPV +>M_5189 +NYASRTQNI +>M_5190 +SVSSCCQPV +>M_5191 +SVSSCCQPV +>M_5192 +CTLGDQLSL +>M_5193 +STAPQAHGV +>M_5194 +STAPQAHGV +>M_5195 +VSLFYSTAI +>M_5196 +VSLFYSTAI +>M_5197 +YSTAISVYL +>M_5198 +YSTAISVYL +>M_5199 +DTAPDIVEI +>M_5200 +FLWDRHVRF +>M_5201 +LWDRHVRFF +>M_5202 +FTCLPLGSL +>M_5203 +HVWLCDLPV +>M_5204 +HVWLCDLPV +>M_5205 +APRGVCYGA +>M_5206 +DPEYSPGAL +>M_5207 +YSPGALATF +>M_5208 +VLGDFLGTV +>M_5209 +AVVGTVWNV +>M_5210 +NVATTGLSL +>M_5211 +DTTDKGALM +>M_5212 +KAVSVCPEA +>M_5213 +SVCPEAAPA +>M_5214 +VLVVGMGPV +>M_5215 +IFATKPELL +>M_5216 +RIFATKPEL +>M_5217 +AFSQSAYLI +>M_5218 +AYLIQHQRF +>M_5219 +KAFSQSAYL +>M_5220 +KAFSQSAYL +>M_5221 +FPAPARDDF diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_138926_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_138926_1_T_iedb.xml new file mode 100755 index 00000000..4e49d0f8 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_138926_1_T_iedb.xml @@ -0,0 +1,1429 @@ + + + + blastp + BLASTP 2.2.30+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta + Query_1 + M_5168 + 9 + + + BLOSUM62 + 100000000 + 11 + 1 + F + + + + + 1 + Query_1 + M_5168 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 2 + Query_2 + M_5169 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 3 + Query_3 + M_5170 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 4 + Query_4 + M_5171 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 5 + Query_5 + M_5172 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 6 + Query_6 + M_5173 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 7 + Query_7 + M_5174 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 8 + Query_8 + M_5175 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 9 + Query_9 + M_5176 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 10 + Query_10 + M_5177 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 11 + Query_11 + M_5178 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 12 + Query_12 + M_5179 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 13 + Query_13 + M_5180 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 14 + Query_14 + M_5181 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 15 + Query_15 + M_5182 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 16 + Query_16 + M_5183 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 17 + Query_17 + M_5184 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 18 + Query_18 + M_5185 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 19 + Query_19 + M_5186 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 20 + Query_20 + M_5187 + 9 + + + 1 + gnl|BL_ORD_ID|1106 + 72928|Genome polyprotein|P26662.3|Hepatitis C virus (isolate Japanese)|11116 + 1106 + 10 + + + 1 + 13.4678 + 23 + 12.4198 + 2 + 7 + 1 + 6 + 0 + 0 + 4 + 4 + 0 + 6 + WPVFPG + WPAPPG + WP PG + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 21 + Query_21 + M_5188 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 22 + Query_22 + M_5189 + 9 + + + 1 + gnl|BL_ORD_ID|84 + 6308|HCV-1|AAA45676.1|Hepatitis C virus genotype 1|41856 + 84 + 20 + + + 1 + 13.853 + 24 + 7.21037 + 1 + 7 + 7 + 13 + 0 + 0 + 4 + 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gnl|BL_ORD_ID|2252 + 244160|surface antigen 2 (CA-2)|XP_818927.1|Trypanosoma cruzi strain CL Brener|353153 + 2252 + 9 + + + 1 + 14.2382 + 25 + 4.0067 + 4 + 9 + 4 + 9 + 0 + 0 + 5 + 6 + 0 + 6 + GDQLSL + GDKLSL + GD+LSL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 26 + Query_26 + M_5193 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 27 + Query_27 + M_5194 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 28 + Query_28 + M_5195 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 29 + Query_29 + M_5196 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 30 + Query_30 + M_5197 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 31 + Query_31 + M_5198 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 32 + Query_32 + M_5199 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 33 + Query_33 + M_5200 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 34 + Query_34 + M_5201 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 35 + Query_35 + M_5202 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 36 + Query_36 + M_5203 + 9 + + + 1 + gnl|BL_ORD_ID|57 + 4172|Glycoprotein I precursor (Glycoprotein IV) (GI) (GPIV)|P09258.1|Human alphaherpesvirus 3|10335 + 57 + 11 + + + 1 + 15.3938 + 28 + 0.668034 + 2 + 9 + 1 + 8 + 0 + 0 + 5 + 5 + 0 + 8 + VWLCDLPV + ARLCDLPA + LCDLP + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 37 + Query_37 + M_5204 + 9 + + + 1 + gnl|BL_ORD_ID|57 + 4172|Glycoprotein I precursor (Glycoprotein IV) (GI) (GPIV)|P09258.1|Human alphaherpesvirus 3|10335 + 57 + 11 + + + 1 + 15.3938 + 28 + 0.668034 + 2 + 9 + 1 + 8 + 0 + 0 + 5 + 5 + 0 + 8 + VWLCDLPV + ARLCDLPA + LCDLP + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 38 + Query_38 + M_5205 + 9 + + + 1 + gnl|BL_ORD_ID|1667 + 148117|early protein|CAA52585.1|Human papillomavirus type 52|10618 + 1667 + 9 + + + 1 + 12.6974 + 21 + 26.9236 + 2 + 6 + 1 + 5 + 0 + 0 + 4 + 4 + 0 + 5 + PRGVC + PYGVC + P GVC + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 39 + Query_39 + M_5206 + 9 + + + 1 + gnl|BL_ORD_ID|899 + 59153|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 + 899 + 15 + + + 1 + 13.4678 + 23 + 10.0248 + 4 + 9 + 5 + 10 + 0 + 0 + 4 + 5 + 0 + 6 + YSPGAL + YSPGEI + YSPG + + + + + + 2 + gnl|BL_ORD_ID|256 + 17278|Genome polyprotein|P06441.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 + 256 + 20 + + + 1 + 12.6974 + 21 + 21.519 + 2 + 7 + 2 + 7 + 0 + 0 + 4 + 4 + 0 + 6 + PEYSPG + PELKPG + PE PG + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 40 + Query_40 + M_5207 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 41 + Query_41 + M_5208 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 42 + Query_42 + M_5209 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 43 + Query_43 + M_5210 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 44 + Query_44 + M_5211 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 45 + Query_45 + M_5212 + 9 + + + 1 + gnl|BL_ORD_ID|287 + 19359|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 + 287 + 20 + + + 1 + 13.4678 + 23 + 8.9532 + 1 + 9 + 9 + 17 + 0 + 0 + 4 + 6 + 0 + 9 + KAVSVCPEA + QQVSIAPNA + + VS+ P A + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 46 + Query_46 + M_5213 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 47 + Query_47 + M_5214 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 48 + Query_48 + M_5215 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 49 + Query_49 + M_5216 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 50 + Query_50 + M_5217 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 51 + Query_51 + M_5218 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 52 + Query_52 + M_5219 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 53 + Query_53 + M_5220 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 54 + Query_54 + M_5221 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + + diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_139381_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_139381_1_T.fasta new file mode 100755 index 00000000..a16d5f0c --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_139381_1_T.fasta @@ -0,0 +1,78 @@ +>M_5222 +SPSVMWLVH +>M_5223 +LAVRDVFEL +>M_5224 +LAVRDVFEL +>M_5225 +KTLTLAKNY +>M_5226 +SSGSMCNRW +>M_5227 +TTKNDIGPY +>M_5228 +LGLTNNTAM +>M_5229 +FTTELTAPF +>M_5230 +FTTELTAPF +>M_5231 +FTTELTAPF +>M_5232 +MPAFTTELT +>M_5233 +LMALHPALF +>M_5234 +QCSEHDVLF +>M_5235 +EPYIDNEEF +>M_5236 +VVIKAIEPY +>M_5237 +QVQDSNLEY +>M_5238 +QVQDSNLEY +>M_5239 +LASSCGCTF +>M_5240 +LASSCGCTF +>M_5241 +IQLLGVFVW +>M_5242 +ISIQLLGVF +>M_5243 +EVDFTCWKY +>M_5244 +HPTAASQSR +>M_5245 +IIETANVSY +>M_5246 +VSYTNAWAL +>M_5247 +FFIHSFTLM +>M_5248 +MFFIHSFTL +>M_5249 +MFNPIIYIF +>M_5250 +LPTPVEPTV +>M_5251 +TPVEPTVAC +>M_5252 +HPDNVSSSY +>M_5253 +LLAAARPLW +>M_5254 +SPVALQLRY +>M_5255 +YQIGTDSAL +>M_5256 +EAHHHFPSL +>M_5257 +EAHHHFPSL +>M_5258 +GSGEAHHHF +>M_5259 +RVSSLTLHF +>M_5260 +KPFSQSCEF diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_139381_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_139381_1_T_iedb.xml new file mode 100755 index 00000000..fcd36868 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_139381_1_T_iedb.xml @@ -0,0 +1,1822 @@ + + + + blastp + BLASTP 2.2.30+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta + Query_1 + M_5222 + 9 + + + BLOSUM62 + 100000000 + 11 + 1 + F + + + + + 1 + Query_1 + M_5222 + 9 + + + 1 + gnl|BL_ORD_ID|431 + 26273|nucleocapsid protein|ABI96968.1|SARS coronavirus|227859 + 431 + 15 + + + 1 + 13.853 + 24 + 5.29758 + 1 + 9 + 6 + 14 + 0 + 0 + 4 + 6 + 0 + 9 + SPSVMWLVH + TPSGTWLTY + +PS WL + + + + + + 2 + gnl|BL_ORD_ID|1436 + 116835|Nucleoprotein|P05133.1|Hantaan virus 76-118|11602 + 1436 + 15 + + + 1 + 13.4678 + 23 + 9.36117 + 1 + 7 + 1 + 7 + 0 + 0 + 4 + 6 + 0 + 7 + SPSVMWL + SPSSIWV + SPS +W+ + + + + + 3 + gnl|BL_ORD_ID|2187 + 190494|nucleocapsid protein|ABI96968.1|SARS coronavirus|227859 + 2187 + 10 + + + 1 + 12.6974 + 21 + 24.356 + 1 + 7 + 4 + 10 + 0 + 0 + 4 + 5 + 0 + 7 + SPSVMWL + TPSGTWL + +PS WL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 2 + Query_2 + M_5223 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 3 + Query_3 + M_5224 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 4 + Query_4 + M_5225 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 5 + Query_5 + M_5226 + 9 + + + 1 + gnl|BL_ORD_ID|136 + 9920|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis|1773 + 136 + 18 + + + 1 + 13.0826 + 22 + 15.4571 + 1 + 9 + 6 + 14 + 0 + 0 + 3 + 7 + 0 + 9 + SSGSMCNRW + TAGSLQGQW + ++GS+ +W + + + + + 2 + gnl|BL_ORD_ID|2224 + 194400|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis|1773 + 2224 + 9 + + + 1 + 13.0826 + 22 + 18.4218 + 1 + 9 + 1 + 9 + 0 + 0 + 3 + 7 + 0 + 9 + SSGSMCNRW + TAGSLQGQW + ++GS+ +W + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 6 + Query_6 + M_5227 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 7 + Query_7 + M_5228 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 8 + Query_8 + M_5229 + 9 + + + 1 + gnl|BL_ORD_ID|1818 + 177903|polyprotein|ACZ60102.1|Hepatitis C virus subtype 3a|356426 + 1818 + 17 + + + 1 + 13.4678 + 23 + 9.62753 + 1 + 9 + 9 + 17 + 0 + 0 + 4 + 6 + 0 + 9 + FTTELTAPF + FTASVTSPL + FT +T+P + + + + + 2 + gnl|BL_ORD_ID|1597 + 142233|ATP-dependent helicase|NP_217813.1|Mycobacterium tuberculosis|1773 + 1597 + 32 + + + 1 + 11.927 + 19 + 52.8651 + 1 + 8 + 20 + 27 + 0 + 0 + 4 + 5 + 0 + 8 + FTTELTAP + FTSTFAAP + FT+ AP + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 9 + Query_9 + M_5230 + 9 + + + 1 + gnl|BL_ORD_ID|1818 + 177903|polyprotein|ACZ60102.1|Hepatitis C virus subtype 3a|356426 + 1818 + 17 + + + 1 + 13.4678 + 23 + 9.62753 + 1 + 9 + 9 + 17 + 0 + 0 + 4 + 6 + 0 + 9 + FTTELTAPF + FTASVTSPL + FT +T+P + + + + + 2 + gnl|BL_ORD_ID|1597 + 142233|ATP-dependent helicase|NP_217813.1|Mycobacterium tuberculosis|1773 + 1597 + 32 + + + 1 + 11.927 + 19 + 52.8651 + 1 + 8 + 20 + 27 + 0 + 0 + 4 + 5 + 0 + 8 + FTTELTAP + FTSTFAAP + FT+ AP + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 10 + Query_10 + M_5231 + 9 + + + 1 + gnl|BL_ORD_ID|1818 + 177903|polyprotein|ACZ60102.1|Hepatitis C virus subtype 3a|356426 + 1818 + 17 + + + 1 + 13.4678 + 23 + 9.62753 + 1 + 9 + 9 + 17 + 0 + 0 + 4 + 6 + 0 + 9 + FTTELTAPF + FTASVTSPL + FT +T+P + + + + + 2 + gnl|BL_ORD_ID|1597 + 142233|ATP-dependent helicase|NP_217813.1|Mycobacterium tuberculosis|1773 + 1597 + 32 + + + 1 + 11.927 + 19 + 52.8651 + 1 + 8 + 20 + 27 + 0 + 0 + 4 + 5 + 0 + 8 + FTTELTAP + FTSTFAAP + FT+ AP + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 11 + Query_11 + M_5232 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 12 + Query_12 + M_5233 + 9 + + + 1 + gnl|BL_ORD_ID|114 + 7660|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 + 114 + 20 + + + 1 + 13.4678 + 23 + 8.10378 + 1 + 8 + 7 + 14 + 0 + 0 + 4 + 6 + 0 + 8 + LMALHPAL + MCAVHPTL + + A+HP L + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 13 + Query_13 + M_5234 + 9 + + + 1 + gnl|BL_ORD_ID|1438 + 120093|unnamed protein product|CAA33016.1|Rubella virus|11041 + 1438 + 21 + + + 1 + 13.853 + 24 + 6.7201 + 2 + 6 + 5 + 9 + 0 + 0 + 4 + 4 + 0 + 5 + CSEHD + CVEHD + C EHD + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 14 + Query_14 + M_5235 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 15 + Query_15 + M_5236 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 16 + Query_16 + M_5237 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 17 + Query_17 + M_5238 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 18 + Query_18 + M_5239 + 9 + + + 1 + gnl|BL_ORD_ID|920 + 59786|Large envelope protein|P03138.3|Hepatitis B virus ayw/France/Tiollais/1979|490133 + 920 + 10 + + + 1 + 11.5418 + 18 + 148.349 + 1 + 8 + 2 + 9 + 0 + 0 + 4 + 5 + 0 + 8 + LASSCGCT + MYPSCCCT + + SC CT + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 19 + Query_19 + M_5240 + 9 + + + 1 + gnl|BL_ORD_ID|920 + 59786|Large envelope protein|P03138.3|Hepatitis B virus ayw/France/Tiollais/1979|490133 + 920 + 10 + + + 1 + 11.5418 + 18 + 148.349 + 1 + 8 + 2 + 9 + 0 + 0 + 4 + 5 + 0 + 8 + LASSCGCT + MYPSCCCT + + SC CT + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 20 + Query_20 + M_5241 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 21 + Query_21 + M_5242 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 22 + Query_22 + M_5243 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 23 + Query_23 + M_5244 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 24 + Query_24 + M_5245 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 25 + Query_25 + M_5246 + 9 + + + 1 + gnl|BL_ORD_ID|1887 + 180579|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 + 1887 + 15 + + + 1 + 13.4678 + 23 + 7.35849 + 2 + 9 + 2 + 9 + 0 + 0 + 4 + 5 + 0 + 8 + SYTNAWAL + SYAQMWSL + SY W+L + + + + + 2 + gnl|BL_ORD_ID|943 + 62184|nonstructural protein 3|NP_722463.1|Dengue virus type 1 Hawaii|10000440 + 943 + 15 + + + 1 + 13.4678 + 23 + 9.36117 + 1 + 9 + 7 + 15 + 0 + 0 + 3 + 4 + 0 + 9 + VSYTNAWAL + ISYGGGWRF + +SY W + + + + + 3 + gnl|BL_ORD_ID|9 + 790|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 + 9 + 15 + + + 1 + 13.4678 + 23 + 9.36117 + 1 + 7 + 8 + 14 + 0 + 0 + 3 + 4 + 0 + 7 + VSYTNAW + ISYGGGW + +SY W + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 26 + Query_26 + M_5247 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 27 + Query_27 + M_5248 + 9 + + + 1 + gnl|BL_ORD_ID|375 + 23270|polyprotein|AAB67036.1|Hepatitis C virus (isolate H77)|63746 + 375 + 15 + + + 1 + 12.3122 + 20 + 38.6124 + 1 + 8 + 6 + 13 + 0 + 0 + 3 + 5 + 0 + 8 + MFFIHSFT + LFYQHKFN + +F+ H F + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 28 + Query_28 + M_5249 + 9 + + + 1 + gnl|BL_ORD_ID|312 + 20861|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 + 312 + 9 + + + 1 + 13.0826 + 22 + 18.4218 + 1 + 7 + 2 + 8 + 0 + 0 + 3 + 6 + 0 + 7 + MFNPIIY + LFNNVLY + +FN ++Y + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 29 + Query_29 + M_5250 + 9 + + + 1 + gnl|BL_ORD_ID|448 + 27241|Spike glycoprotein precursor|P59594.1|SARS coronavirus|227859 + 448 + 9 + + + 1 + 14.2382 + 25 + 2.90246 + 1 + 8 + 2 + 9 + 0 + 0 + 5 + 7 + 0 + 8 + LPTPVEPT + LPDPLKPT + LP P++PT + + + + + 2 + gnl|BL_ORD_ID|1020 + 68229|EBNA3B (EBNA4A) latent protein|CAA24858.1|Human gammaherpesvirus 4|10376 + 1020 + 10 + + + 1 + 12.3122 + 20 + 63.4362 + 3 + 8 + 4 + 9 + 0 + 0 + 4 + 5 + 0 + 6 + TPVEPT + TPYKPT + TP +PT + + + + + 3 + gnl|BL_ORD_ID|240 + 16833|core protein|CAL29866.1|Hepatitis B virus|10407 + 240 + 10 + + + 1 + 11.927 + 19 + 78.4397 + 1 + 9 + 2 + 10 + 0 + 0 + 4 + 6 + 0 + 9 + LPTPVEPTV + LPSDFFPSV + LP+ P+V + + + + + 4 + gnl|BL_ORD_ID|69 + 5191|core protein|AAL31859.1|Hepatitis B virus|10407 + 69 + 17 + + + 1 + 11.927 + 19 + 93.2086 + 1 + 9 + 9 + 17 + 0 + 0 + 4 + 6 + 0 + 9 + LPTPVEPTV + LPSDFFPSV + LP+ P+V + + + + + 5 + gnl|BL_ORD_ID|653 + 38701|core protein|AAL31859.1|Hepatitis B virus|10407 + 653 + 9 + + + 1 + 11.927 + 19 + 107.472 + 1 + 9 + 1 + 9 + 0 + 0 + 4 + 6 + 0 + 9 + LPTPVEPTV + LPSDFFPSV + LP+ P+V + + + + + 6 + gnl|BL_ORD_ID|239 + 16832|core protein|BAF42671.1|Hepatitis B virus|10407 + 239 + 10 + + + 1 + 11.5418 + 18 + 119.026 + 1 + 9 + 2 + 10 + 0 + 0 + 3 + 6 + 0 + 9 + LPTPVEPTV + LPSDFFPSI + LP+ P++ + + + + + 7 + gnl|BL_ORD_ID|241 + 16836|precore/core protein [Hepatitis B virus]|AAR03815.1|Hepatitis B virus|10407 + 241 + 10 + + + 1 + 11.5418 + 18 + 124.81 + 1 + 9 + 2 + 10 + 0 + 0 + 4 + 6 + 0 + 9 + LPTPVEPTV + LPSDFLPSV + LP+ P+V + + + + + 8 + gnl|BL_ORD_ID|235 + 16814|precore protein|CAM58990.1|Hepatitis B virus|10407 + 235 + 10 + + + 1 + 11.5418 + 18 + 128.811 + 1 + 9 + 2 + 10 + 0 + 0 + 4 + 5 + 0 + 9 + LPTPVEPTV + LPNDFFPSV + LP P+V + + + + + 9 + gnl|BL_ORD_ID|233 + 16796|HBcAg|ABE97049.1|Hepatitis B virus|10407 + 233 + 10 + + + 1 + 11.5418 + 18 + 162.878 + 1 + 9 + 2 + 10 + 0 + 0 + 4 + 5 + 0 + 9 + LPTPVEPTV + LPADFFPSV + LP P+V + + + + + 10 + gnl|BL_ORD_ID|244 + 16857|pre-c/core|CAA59565.1|Hepatitis B virus|10407 + 244 + 10 + + + 1 + 11.1566 + 17 + 224.873 + 1 + 9 + 2 + 10 + 0 + 0 + 4 + 5 + 0 + 9 + LPTPVEPTV + LPVDFFPSV + LP P+V + + + + + 11 + gnl|BL_ORD_ID|232 + 16795|precore/core protein|AAP57273.1|Hepatitis B virus|10407 + 232 + 10 + + + 1 + 11.1566 + 17 + 235.341 + 1 + 9 + 2 + 10 + 0 + 0 + 3 + 5 + 0 + 9 + LPTPVEPTV + LPADFFPSI + LP P++ + + + + + 12 + gnl|BL_ORD_ID|1438 + 120093|unnamed protein product|CAA33016.1|Rubella virus|11041 + 1438 + 21 + + + 1 + 10.7714 + 16 + 331.885 + 2 + 8 + 11 + 17 + 0 + 0 + 4 + 4 + 0 + 7 + PTPVEPT + PPPATPT + P P PT + + + + + 13 + gnl|BL_ORD_ID|243 + 16856|||| + 243 + 10 + + + 1 + 10.7714 + 16 + 336.948 + 1 + 9 + 2 + 10 + 0 + 0 + 3 + 5 + 0 + 9 + LPTPVEPTV + LPVDFFPSI + LP P++ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 30 + Query_30 + M_5251 + 9 + + + 1 + gnl|BL_ORD_ID|1020 + 68229|EBNA3B (EBNA4A) latent protein|CAA24858.1|Human gammaherpesvirus 4|10376 + 1020 + 10 + + + 1 + 12.3122 + 20 + 40.5114 + 1 + 6 + 4 + 9 + 0 + 0 + 4 + 5 + 0 + 6 + TPVEPT + TPYKPT + TP +PT + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 31 + Query_31 + M_5252 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 32 + Query_32 + M_5253 + 9 + + + 1 + gnl|BL_ORD_ID|588 + 36717|nonstructural protein 4B|YP_001527886.1|West Nile virus NY-99|10000971 + 588 + 18 + + + 1 + 12.6974 + 21 + 25.1685 + 1 + 9 + 2 + 10 + 0 + 0 + 5 + 6 + 0 + 9 + LLAAARPLW + ITAAAVTLW + + AAA LW + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 33 + Query_33 + M_5254 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 34 + Query_34 + M_5255 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 35 + Query_35 + M_5256 + 9 + + + 1 + gnl|BL_ORD_ID|320 + 21000|glutamine synthetase GLNA1 (glutamine synthase) (GS-I)|NP_216736.1|Mycobacterium tuberculosis|1773 + 320 + 9 + + + 1 + 13.4678 + 23 + 8.13377 + 4 + 9 + 4 + 9 + 0 + 0 + 5 + 5 + 0 + 6 + HHFPSL + HHAPSL + HH PSL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 36 + Query_36 + M_5257 + 9 + + + 1 + gnl|BL_ORD_ID|320 + 21000|glutamine synthetase GLNA1 (glutamine synthase) (GS-I)|NP_216736.1|Mycobacterium tuberculosis|1773 + 320 + 9 + + + 1 + 13.4678 + 23 + 8.13377 + 4 + 9 + 4 + 9 + 0 + 0 + 5 + 5 + 0 + 6 + HHFPSL + HHAPSL + HH PSL + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 37 + Query_37 + M_5258 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 38 + Query_38 + M_5259 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 39 + Query_39 + M_5260 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + + diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_139936_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_139936_1_T.fasta new file mode 100755 index 00000000..837993b7 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_139936_1_T.fasta @@ -0,0 +1,70 @@ +>M_5261 +KPLLSGPWA +>M_5262 +LSMTSITSV +>M_5263 +IDTDQVHTL +>M_5264 +TWKDTPYYI +>M_5265 +KLILTLSAI +>M_5266 +SYQMSNKLI +>M_5267 +YQMSNKLIL +>M_5268 +YQMSNKLIL +>M_5269 +LMWSVTWPK +>M_5270 +SQSETNSAV +>M_5271 +SHASHLHLF +>M_5272 +SHASHLHLF +>M_5273 +KVLISVHLI +>M_5274 +DHYLVDRTL +>M_5275 +YIKPLVPPA +>M_5276 +RPGQSPGQL +>M_5277 +HLFESSQLV +>M_5278 +HLFESSQLV +>M_5279 +GVYLWEDPV +>M_5280 +YLWEDPVCG +>M_5281 +RILYMADEV +>M_5282 +SLLDACLIL +>M_5283 +APLPMPNPL +>M_5284 +LLLWAPLPM +>M_5285 +MQLRKAPNV +>M_5286 +AHACAHALL +>M_5287 +GAHACAHAL +>M_5288 +VLNGWLRSV +>M_5289 +AIDDHVCMA +>M_5290 +LMVPRLEYV +>M_5291 +FINARGRLL +>M_5292 +AIPLRGFPV +>M_5293 +FVDENNEKL +>M_5294 +FVDENNEKL +>M_5295 +HTARLFYFV diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_139936_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_139936_1_T_iedb.xml new file mode 100755 index 00000000..e696aaad --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_139936_1_T_iedb.xml @@ -0,0 +1,1051 @@ + + + + blastp + BLASTP 2.2.30+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta + Query_1 + M_5261 + 9 + + + BLOSUM62 + 100000000 + 11 + 1 + F + + + + + 1 + Query_1 + M_5261 + 9 + + + 1 + gnl|BL_ORD_ID|96 + 6591|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 + 96 + 18 + + + 1 + 13.853 + 24 + 5.73946 + 1 + 7 + 6 + 12 + 0 + 0 + 5 + 5 + 0 + 7 + KPLLSGP + KPTLHGP + KP L GP + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 2 + Query_2 + M_5262 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 3 + Query_3 + M_5263 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 4 + Query_4 + M_5264 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 5 + Query_5 + M_5265 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 6 + Query_6 + M_5266 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 7 + Query_7 + M_5267 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 8 + Query_8 + M_5268 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 9 + Query_9 + M_5269 + 9 + + + 1 + gnl|BL_ORD_ID|1697 + 149105|E2 protein|NP_751921.1|Hepatitis C virus (isolate H77)|63746 + 1697 + 9 + + + 1 + 11.1566 + 17 + 225.252 + 3 + 7 + 5 + 9 + 0 + 0 + 2 + 4 + 0 + 5 + WSVTW + WAIKW + W++ W + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 10 + Query_10 + M_5270 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 11 + Query_11 + M_5271 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 12 + Query_12 + M_5272 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 13 + Query_13 + M_5273 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 14 + Query_14 + M_5274 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 15 + Query_15 + M_5275 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 16 + Query_16 + M_5276 + 9 + + + 1 + gnl|BL_ORD_ID|344 + 21638|protein F|ABV46152.2|Hepatitis C virus (isolate Japanese)|11116 + 344 + 9 + + + 1 + 15.0086 + 27 + 0.92904 + 2 + 9 + 2 + 9 + 0 + 0 + 6 + 6 + 0 + 8 + PGQSPGQL + PGLSPGTL + PG SPG L + + + + + 2 + gnl|BL_ORD_ID|741 + 47760|EBNA-1 protein|Q777E1|Human gammaherpesvirus 4|10376 + 741 + 15 + + + 1 + 12.6974 + 21 + 27.4409 + 2 + 8 + 1 + 7 + 0 + 0 + 4 + 4 + 0 + 7 + PGQSPGQ + PGTGPGN + PG PG + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 17 + Query_17 + M_5277 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 18 + Query_18 + M_5278 + 9 + + + + + 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Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta + Query_1 + M_5296 + 9 + + + BLOSUM62 + 100000000 + 11 + 1 + F + + + + + 1 + Query_1 + M_5296 + 9 + + + 1 + gnl|BL_ORD_ID|707 + 43447|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 + 707 + 20 + + + 1 + 14.2382 + 25 + 2.73772 + 1 + 7 + 14 + 20 + 0 + 0 + 5 + 5 + 0 + 7 + LPSTAGP + LPEAAGP + LP AGP + + + + + 2 + gnl|BL_ORD_ID|285 + 19348|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 + 285 + 20 + + + 1 + 14.2382 + 25 + 3.42196 + 1 + 7 + 4 + 10 + 0 + 0 + 5 + 5 + 0 + 7 + LPSTAGP + LPEAAGP + LP AGP + + + + + 3 + gnl|BL_ORD_ID|993 + 65550|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 + 993 + 15 + + + 1 + 11.5418 + 18 + 141.75 + 1 + 8 + 6 + 13 + 0 + 0 + 4 + 5 + 0 + 8 + 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a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_141002_2_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_141002_2_T.fasta new file mode 100755 index 00000000..77f5f7f7 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_141002_2_T.fasta @@ -0,0 +1,62 @@ +>M_5322 +ISRNHNSRM +>M_5323 +KTFGISRNH +>M_5324 +RNHNSRMNK +>M_5325 +LTDLQGVIV +>M_5326 +IRHEMSTFA +>M_5327 +VVSDSWGSK +>M_5328 +IRAANVSAL +>M_5329 +IRAANVSAL +>M_5330 +RAANVSALY +>M_5331 +GYRERGHPY +>M_5332 +VVGAVGVGK +>M_5333 +LTNTLTTSK +>M_5334 +AAASTSSPK +>M_5335 +TSITTSTQK +>M_5336 +SHPGSAEIV +>M_5337 +SYYSCVAAM +>M_5338 +SYYSCVAAM +>M_5339 +AHTFKQRRI +>M_5340 +HTFKQRRIK +>M_5341 +RYEEYRGRF +>M_5342 +YEEYRGRFL +>M_5343 +MTTGSVFFY +>M_5344 +MTTGSVFFY +>M_5345 +HVLSLAETK +>M_5346 +SLAETKTLY +>M_5347 +KLKTVSQTK +>M_5348 +ASYDQSLRV +>M_5349 +FSASYDQSL +>M_5350 +HLKEPLQKL +>M_5351 +HLYEQGGHL +>M_5352 +HQCVHTGAK diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_141002_2_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_141002_2_T_iedb.xml new file mode 100755 index 00000000..41672e73 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_141002_2_T_iedb.xml @@ -0,0 +1,697 @@ + + + + blastp + BLASTP 2.2.30+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta + Query_1 + M_5322 + 9 + + + BLOSUM62 + 100000000 + 11 + 1 + F + + + + + 1 + Query_1 + M_5322 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 2 + Query_2 + M_5323 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 3 + Query_3 + M_5324 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 4 + Query_4 + M_5325 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 5 + Query_5 + M_5326 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 6 + Query_6 + M_5327 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 7 + Query_7 + M_5328 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 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Query_31 + M_5352 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + + diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_141146_2_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_141146_2_T.fasta new file mode 100755 index 00000000..93f95ae9 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_141146_2_T.fasta @@ -0,0 +1,76 @@ +>M_5353 +IAHAWWACF +>M_5354 +AMWNRCADL +>M_5355 +AYTFWTYIM +>M_5356 +IMNARSKNV +>M_5357 +YAYTFWTYI +>M_5358 +YAYTFWTYI +>M_5359 +KAARIAAKV +>M_5360 +KVGQSSMWI +>M_5361 +PSTSTSRPV +>M_5362 +CLAAMALSI +>M_5363 +WLTPVIPTL +>M_5364 +GLFHCTRSV +>M_5365 +RNWDVCKVI +>M_5366 +KIPIRLPPV +>M_5367 +FMLGITPNL +>M_5368 +HRHHHRCRR +>M_5369 +FLAGSSLPV +>M_5370 +FLAGSSLPV +>M_5371 +SSFLAGSSL +>M_5372 +KLPSDPDAL +>M_5373 +VYAVTVVTL +>M_5374 +YAVTVVTLL +>M_5375 +YAVTVVTLL +>M_5376 +FILICCLII +>M_5377 +ILICCLIIL +>M_5378 +LIILENIFV +>M_5379 +VFILICCLI +>M_5380 +PAMKFSCSL +>M_5381 +FLSLIIDAT +>M_5382 +LIIDATKFI +>M_5383 +LIIDATKFI +>M_5384 +IMMSSEDDI +>M_5385 +YLDGQPQEA +>M_5386 +GLAPPQLLI +>M_5387 +ARIERPHNY +>M_5388 +FTSSEPSRM +>M_5389 +ESEGHTIEL +>M_5390 +KMQEGLLAV diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_141146_2_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_141146_2_T_iedb.xml new file mode 100755 index 00000000..0bb39458 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_141146_2_T_iedb.xml @@ -0,0 +1,1557 @@ + + + + blastp + BLASTP 2.2.30+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta + Query_1 + M_5353 + 9 + + + BLOSUM62 + 100000000 + 11 + 1 + F + + + + + 1 + Query_1 + M_5353 + 9 + + + 1 + gnl|BL_ORD_ID|1556 + 141262|DNA polymerase catalytic subunit|NP_044632.1|Human alphaherpesvirus 1|10298 + 1556 + 10 + + + 1 + 13.853 + 24 + 4.45544 + 3 + 9 + 4 + 10 + 0 + 0 + 5 + 5 + 0 + 7 + HAWWACF + HARWAAF + HA WA F + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 2 + Query_2 + M_5354 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 3 + Query_3 + M_5355 + 9 + + + 1 + gnl|BL_ORD_ID|1502 + 137660|L1|ACL12325.1|Human papillomavirus type 58|10598 + 1502 + 9 + + + 1 + 13.853 + 24 + 7.07804 + 1 + 5 + 1 + 5 + 0 + 0 + 4 + 4 + 0 + 5 + AYTFW + KYTFW + YTFW + + + + + 2 + gnl|BL_ORD_ID|81 + 5938|EBNA3A nuclear protein|Q8AZJ8|Human gammaherpesvirus 4|10376 + 81 + 9 + + + 1 + 12.6974 + 21 + 39.8499 + 1 + 7 + 1 + 7 + 0 + 0 + 4 + 5 + 0 + 7 + AYTFWTY + AYSSWMY + AY+ W Y + + + + + 3 + gnl|BL_ORD_ID|578 + 36357|ELAV-like protein 4 (Paraneoplastic encephalomyelitis antigen HuD) (Hu-antigen D)|P26378.1|Homo sapiens|9606 + 578 + 9 + + + 1 + 12.3122 + 20 + 57.6592 + 1 + 8 + 2 + 9 + 0 + 0 + 4 + 4 + 0 + 8 + AYTFWTYI + GYGFVNYI + Y F YI + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 4 + Query_4 + M_5356 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 5 + Query_5 + M_5357 + 9 + + + 1 + gnl|BL_ORD_ID|1502 + 137660|L1|ACL12325.1|Human papillomavirus type 58|10598 + 1502 + 9 + + + 1 + 13.4678 + 23 + 10.0233 + 2 + 6 + 1 + 5 + 0 + 0 + 4 + 4 + 0 + 5 + AYTFW + KYTFW + YTFW + + + + + 2 + gnl|BL_ORD_ID|147 + 10939|polyprotein|BAB18806.1|Hepatitis C virus subtype 1a|31646 + 147 + 9 + + + 1 + 13.0826 + 22 + 18.7436 + 1 + 8 + 2 + 9 + 0 + 0 + 4 + 4 + 0 + 8 + YAYTFWTY + YPYRLWHY + Y Y W Y + + + + + 3 + gnl|BL_ORD_ID|1145 + 75448|polyprotein|BAB18806.1|Hepatitis C virus|11103 + 1145 + 8 + + + 1 + 13.0826 + 22 + 22.4497 + 1 + 8 + 1 + 8 + 0 + 0 + 4 + 4 + 0 + 8 + YAYTFWTY + YPYRLWHY + Y Y W Y + + + + + 4 + gnl|BL_ORD_ID|81 + 5938|EBNA3A nuclear protein|Q8AZJ8|Human gammaherpesvirus 4|10376 + 81 + 9 + + + 1 + 12.6974 + 21 + 36.611 + 2 + 8 + 1 + 7 + 0 + 0 + 4 + 5 + 0 + 7 + AYTFWTY + AYSSWMY + AY+ W Y + + + + + 5 + gnl|BL_ORD_ID|578 + 36357|ELAV-like protein 4 (Paraneoplastic encephalomyelitis antigen HuD) (Hu-antigen D)|P26378.1|Homo sapiens|9606 + 578 + 9 + + + 1 + 11.927 + 19 + 78.9234 + 2 + 9 + 2 + 9 + 0 + 0 + 4 + 4 + 0 + 8 + AYTFWTYI + GYGFVNYI + Y F YI + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 6 + Query_6 + M_5358 + 9 + + + 1 + gnl|BL_ORD_ID|1502 + 137660|L1|ACL12325.1|Human papillomavirus type 58|10598 + 1502 + 9 + + + 1 + 13.4678 + 23 + 10.0233 + 2 + 6 + 1 + 5 + 0 + 0 + 4 + 4 + 0 + 5 + AYTFW + KYTFW + YTFW + + + + + 2 + gnl|BL_ORD_ID|147 + 10939|polyprotein|BAB18806.1|Hepatitis C virus subtype 1a|31646 + 147 + 9 + + + 1 + 13.0826 + 22 + 18.7436 + 1 + 8 + 2 + 9 + 0 + 0 + 4 + 4 + 0 + 8 + YAYTFWTY + YPYRLWHY + Y Y W Y + + + + + 3 + gnl|BL_ORD_ID|1145 + 75448|polyprotein|BAB18806.1|Hepatitis C virus|11103 + 1145 + 8 + + + 1 + 13.0826 + 22 + 22.4497 + 1 + 8 + 1 + 8 + 0 + 0 + 4 + 4 + 0 + 8 + YAYTFWTY + YPYRLWHY + Y Y W Y + + + + + 4 + gnl|BL_ORD_ID|81 + 5938|EBNA3A nuclear protein|Q8AZJ8|Human gammaherpesvirus 4|10376 + 81 + 9 + + + 1 + 12.6974 + 21 + 36.611 + 2 + 8 + 1 + 7 + 0 + 0 + 4 + 5 + 0 + 7 + AYTFWTY + AYSSWMY + AY+ W Y + + + + + 5 + gnl|BL_ORD_ID|578 + 36357|ELAV-like protein 4 (Paraneoplastic encephalomyelitis antigen HuD) (Hu-antigen D)|P26378.1|Homo sapiens|9606 + 578 + 9 + + + 1 + 11.927 + 19 + 78.9234 + 2 + 9 + 2 + 9 + 0 + 0 + 4 + 4 + 0 + 8 + AYTFWTYI + GYGFVNYI + Y F YI + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 7 + Query_7 + M_5359 + 9 + + + + + 2334 + 25004 + 0 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found + + + 13 + Query_13 + M_5365 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 14 + Query_14 + M_5366 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 15 + Query_15 + M_5367 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 16 + Query_16 + M_5368 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 17 + Query_17 + M_5369 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 18 + Query_18 + M_5370 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 19 + Query_19 + M_5371 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 20 + Query_20 + M_5372 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 21 + Query_21 + M_5373 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 22 + Query_22 + M_5374 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 23 + Query_23 + M_5375 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 24 + Query_24 + M_5376 + 9 + + + 1 + gnl|BL_ORD_ID|156 + 11956|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 + 156 + 11 + + + 1 + 10.7714 + 16 + 322.541 + 3 + 9 + 5 + 11 + 0 + 0 + 2 + 6 + 0 + 7 + LICCLII + VLCCYVL + ++CC ++ + + + + + 2 + gnl|BL_ORD_ID|1499 + 137656|E6 protein|ACT36477.1|Human papillomavirus type 58|10598 + 1499 + 9 + + + 1 + 10.3862 + 15 + 519.728 + 2 + 8 + 1 + 7 + 0 + 0 + 5 + 6 + 0 + 7 + ILICCLI + ILIRCII + ILI C+I + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 25 + Query_25 + M_5377 + 9 + + + 1 + gnl|BL_ORD_ID|156 + 11956|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 + 156 + 11 + + + 1 + 10.7714 + 16 + 341.939 + 2 + 8 + 5 + 11 + 0 + 0 + 2 + 6 + 0 + 7 + LICCLII + VLCCYVL + ++CC ++ + + + + + 2 + gnl|BL_ORD_ID|1499 + 137656|E6 protein|ACT36477.1|Human papillomavirus type 58|10598 + 1499 + 9 + + + 1 + 10.3862 + 15 + 600.299 + 1 + 7 + 1 + 7 + 0 + 0 + 5 + 6 + 0 + 7 + ILICCLI + ILIRCII + ILI C+I + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 26 + Query_26 + M_5378 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 27 + Query_27 + M_5379 + 9 + + + 1 + gnl|BL_ORD_ID|1499 + 137656|E6 protein|ACT36477.1|Human papillomavirus type 58|10598 + 1499 + 9 + + + 1 + 10.7714 + 16 + 462.613 + 3 + 9 + 1 + 7 + 0 + 0 + 5 + 6 + 0 + 7 + ILICCLI + ILIRCII + ILI C+I + + + + + 2 + gnl|BL_ORD_ID|156 + 11956|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 + 156 + 11 + + + 1 + 10.3862 + 15 + 596.566 + 4 + 9 + 5 + 10 + 0 + 0 + 2 + 5 + 0 + 6 + LICCLI + VLCCYV + ++CC + + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 28 + Query_28 + M_5380 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 29 + Query_29 + M_5381 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 30 + Query_30 + M_5382 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 31 + Query_31 + M_5383 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 32 + Query_32 + M_5384 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 33 + Query_33 + M_5385 + 9 + + + 1 + gnl|BL_ORD_ID|1387 + 110227|Protein E6|P03126.1|Human papillomavirus type 16|333760 + 1387 + 33 + + + 1 + 14.2382 + 25 + 3.73557 + 1 + 6 + 8 + 13 + 0 + 0 + 4 + 4 + 0 + 6 + YLDGQP + YRDGNP + Y DG P + + + + + 2 + gnl|BL_ORD_ID|1400 + 110467|Protein E6|P03126.1|Human papillomavirus type 16|333760 + 1400 + 25 + + + 1 + 13.853 + 24 + 7.91622 + 1 + 6 + 1 + 6 + 0 + 0 + 4 + 4 + 0 + 6 + YLDGQP + YRDGNP + Y DG P + + + + + 3 + gnl|BL_ORD_ID|1397 + 110401|Protein E6|P03126.1|Human papillomavirus type 16|333760 + 1397 + 25 + + + 1 + 13.4678 + 23 + 8.70865 + 1 + 6 + 16 + 21 + 0 + 0 + 4 + 4 + 0 + 6 + YLDGQP + YRDGNP + Y DG P + + + + + 4 + gnl|BL_ORD_ID|1821 + 178185|Protein E6|P03126.1|Human papillomavirus type 16|333760 + 1821 + 15 + + + 1 + 13.4678 + 23 + 10.5523 + 1 + 6 + 9 + 14 + 0 + 0 + 4 + 4 + 0 + 6 + YLDGQP + YRDGNP + Y DG P + + + + + 5 + gnl|BL_ORD_ID|1059 + 69798|Lipoprotein lpqH precursor|P0A5J0.1|Mycobacterium tuberculosis|1773 + 1059 + 10 + + + 1 + 13.4678 + 23 + 12.6375 + 3 + 9 + 4 + 10 + 0 + 0 + 4 + 4 + 0 + 7 + DGQPQEA + DGNPPEV + DG P E + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + 34 + Query_34 + M_5386 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 35 + Query_35 + M_5387 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 36 + Query_36 + M_5388 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 37 + Query_37 + M_5389 + 9 + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 38 + Query_38 + M_5390 + 9 + + + 1 + gnl|BL_ORD_ID|777 + 51685|Nuclear antigen EBNA-3C|Q69140.1|Human gammaherpesvirus 4|10376 + 777 + 10 + + + 1 + 12.6974 + 21 + 30.4011 + 3 + 9 + 1 + 7 + 0 + 0 + 4 + 5 + 0 + 7 + QEGLLAV + QNGALAI + Q G LA+ + + + + + + + 2334 + 25004 + 0 + 225036 + 0.041 + 0.267 + 0.14 + + + + + + diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/data/.DS_Store b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/data/.DS_Store new file mode 100755 index 0000000000000000000000000000000000000000..5008ddfcf53c02e82d7eee2e57c38e5672ef89f6 GIT binary patch literal 6148 zcmeH~Jr2S!425mzP>H1@V-^m;4Wg<&0T*E43hX&L&p$$qDprKhvt+--jT7}7np#A3 zem<@ulZcFPQ@L2!n>{z**++&mCkOWA81W14cNZlEfg7;MkzE(HCqgga^y>{tEnwC%0;vJ&^%eQ zLs35+`xjp>T046|hypothetical protein ML1057|NP_301777.1|Mycobacterium leprae|1769 +AAALEQLLGQTADVA +>118|envelope glycoprotein|ABS76372.1|Human immunodeficiency virus 1|11676 +AAEQLWVTVYYGVPVWKEAT +>140|Accessory protein p30II|SRC276210|Human T-lymphotropic virus 1|11908 +AAFSSARFL +>194|Hypothetical protein esxG (PE family protein)|O53692.1|Mycobacterium tuberculosis|1773 +AAHARFVAA +>327|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis|1773 +AANKQKQELDEISTNIRQAG +>420|Genome polyprotein|P26664.3|Hepatitis C virus genotype 1|41856 +AARVTAIL +>449|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 +AASTLLYATV +>465|polyprotein|BAA09072.1|Hepatitis C virus|11103 +AATLGFGAYMSKAHG +>716|polyprotein|BAB18806.1|Hepatitis C virus subtype 1a|31646 +ADLMGYIPLV +>790|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 +ADVKKDLISYGGGWK +>1000|glycoprotein gp35/37|AAC59622.1|Human gammaherpesvirus 8|37296 +AEIRTHLYILWAVGL +>1078|10 kda culture filtrate antigen esxB (cfp10)|ZP_04982462.1|Mycobacterium tuberculosis|1773 +AEMKTDAA +>1079|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis H37Rv|83332 +AEMKTDAATL +>1080|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis H37Rv|83332 +AEMKTDAATLA +>1090|Transcription activator BRLF1|P03209.1|Human herpesvirus 4 strain B95-8|10377 +AENAGNDAC +>1095|glycoprotein gp35/37|AAC59622.1|Human gammaherpesvirus 8|37296 +AENGRNSGASNRVPF +>1129|gag protein|AAV53342.1|Human immunodeficiency virus 1|11676 +AEQASQDVKNW +>1154|RL2|NP_044469.1|Human herpesvirus 2 strain HG52|10315 +AERQGSPTPA +>1211|polyprotein precursor|NP_041724.2|West Nile virus|11082 +AEVEEHRTV +>1226|Polyprotein|Q9IZA3|Hepatitis C virus|11103 +AEVTQHGSY +>1230|gag protein|AAW03034.1|Human immunodeficiency virus 1|11676 +AEWDRVHPV +>1356|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 +AFLTNVPYKRIEELL +>1421|polyprotein|BAD73991.1|Hepatitis C virus subtype 1b|31647 +AFYGVWPLL +>1516|Nucleoprotein|P03418.1|Human respiratory syncytial virus A2|11259 +AGFYHILNNPKASL +>1658|Nucleoprotein|P03418.1|Human respiratory syncytial virus A2|11259 +AGQVMLRWGVLAKS +>1994|structural protein|BAA00705.1|Hepatitis C virus subtype 1a|31646 +AILHTPGCV +>2002|Large envelope protein|SRC279965|Hepatitis B virus|10407 +AILSKTGDPV +>2033|polyprotein|BAA32665.1|Hepatitis C virus genotype 6|42182 +AINGVMWTV +>2058|6 kDa early secretory antigenic target|P0A564.2|Mycobacterium tuberculosis|1773 +AIQGNVTSI +>2102|VP1|BAF93325.1|Human polyomavirus 1|1891762 +AITEVECFL +>2154|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 +AKARAKKDELR +>2244|polyprotein|NP_671491.1|Hepatitis C virus|11103 +AKLVALGINAVAYYR +>2387|Genome polyprotein|O39929.3|Hepatitis C virus|11103 +ALAHGVRAL +>2506|M protein, serotype 5 precursor|P02977.2|Streptococcus pyogenes serotype M5|301449 +ALEKLNKEL +>2527|Circumsporozoite protein-related antigen precursor|P04923.2|Plasmodium falciparum|5833 +ALFFIIFNK +>2556|PE_PGRS 33|AAU10330.1|Mycobacterium tuberculosis|1773 +ALGGGATGV +>2758|pol protein|BAA32832.1|Hepatitis B virus|10407 +ALMPLYACI +>2860|polyprotein|AAU89634.1|Hepatitis C virus|11103 +ALRGMGLNA +>2861|Genome polyprotein|P26661.3|Hepatitis C virus isolate HC-J8|11115 +ALRGMGVNAV +>2883|cysteine proteinase cruzipain (EC 3.4.22.-) - Trypanosoma cruzi|A45629|Trypanosoma cruzi|5693 +ALSLAAVLV +>2884|cysteine proteinase cruzipain (EC 3.4.22.-) - Trypanosoma cruzi|A45629|Trypanosoma cruzi|5693 +ALSLAAVLVV +>2903|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 +ALSTGLIHLHQNIVD +>2957|||| +ALVFPSHHH +>3017|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 +ALYDVVSKL +>3018|polyprotein|BAA25076.1|Hepatitis C virus (isolate H77)|63746 +ALYDVVSTL +>3019|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 +ALYDVVTKL +>3024|precursor protein|AAB02126.1|Hepatitis C virus (isolate H77)|63746 +ALYEVVSKL +>3026|polyprotein|CAB53095.1|Hepatitis C virus subtype 1b|31647 +ALYGVWPLL +>3051|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 +AMAALQNLPQCSPDEIMAYA +>3064|6 kDa early secretory antigenic target|P0A564.2|Mycobacterium tuberculosis|1773 +AMASTEGNV +>3094|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 +AMGDAGGYK +>3587|protein F [Hepatitis C virus subtype 1b]|ACA50643.1|Hepatitis C virus (isolate Japanese)|11116 +APGWVCARL +>3889|||| +APVFPSHHP +>3935|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis|1773 +AQAAVVRFQEAANKQKQELD +>4002|PPE family protein|YP_177918.1|Mycobacterium tuberculosis H37Rv|83332 +AQLLTEFAI +>4156|polyprotein|ABR25251.1|Hepatitis C virus|11103 +ARHTPVNSW +>4169|PqqC-like protein|O84616.1|Chlamydia trachomatis|813 +ARKLLLDNL +>4172|Glycoprotein I precursor (Glycoprotein IV) (GI) (GPIV)|P09258.1|Human alphaherpesvirus 3|10335 +ARLCDLPATPK +>4197|polyprotein|ACB87119.1|Hepatitis C virus subtype 1a|31646 +ARMILMTHF +>4236|polyprotein|BAA03375.1|Hepatitis C virus|11103 +ARRGREILL +>4289|Major DNA-binding protein|P03227.1|Human herpesvirus 4 strain B95-8|10377 +ARYAYYLQF +>4371|tegument protein VP11/12|NP_044516.1|Human alphaherpesvirus 2|10310 +ASDSLNNEY +>4668|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 +ASPKGPVIQMYTNVD +>4682|LOW MOLECULAR WEIGHT T-CELL ANTIGEN TB8.4 (Hypothetical protein)|O50430|Mycobacterium tuberculosis H37Rv|83332 +ASPVAQSYL +>4735|polyprotein|AAY82034.1|Hepatitis C virus|11103 +ASRCWVAM +>4909|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 +ATCINGVCWTVYHGA +>4910|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 +ATCINGVCWTVYHGAGTRTI +>4916|NS3|AAU44857.1|Hepatitis C virus|11103 +ATDALMTGF +>4917|Genome polyprotein|P26664.3|Hepatitis C virus genotype 1|41856 +ATDALMTGY +>5191|core protein|AAL31859.1|Hepatitis B virus|10407 +ATVELLSFLPSDFFPSV +>5196|60 kDa chaperonin 2|P0A520.2|Mycobacterium tuberculosis|1773 +ATVLAQALVREGLRN +>5213|nonstructural protein 5|YP_001527887.1|West Nile virus NY-99|10000971 +ATWAENIQV +>5295|nef protein|ACR27174.1|Human immunodeficiency virus 1|11676 +AVDLSHFLK +>5316|EBNA-3B nuclear protein|CAD53420.1|Human gammaherpesvirus 4|10376 +AVFDRKSDAK +>5381|LOW MOLECULAR WEIGHT T-CELL ANTIGEN TB8.4 (Hypothetical protein)|O50430|Mycobacterium tuberculosis|1773 +AVINTTCNYGQ +>5542|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 +AVSLDFSPGTSGSPI +>5623|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 +AVYLLDGLR +>5714|Genome polyprotein|P26662.3|Hepatitis C virus|11103 +AYAAQGYKVL +>5727|Polyprotein|Q9IZA3|Hepatitis C virus subtype 2a|31649 +AYAMRVPEVI +>5783|Nucleoprotein|P03418.1|Human respiratory syncytial virus A2|11259 +AYGAGQVMLRWGVL +>5934|polyprotein|CAB53095.1|Hepatitis C virus subtype 1b|31647 +AYSQQTRGL +>5938|EBNA3A nuclear protein|Q8AZJ8|Human gammaherpesvirus 4|10376 +AYSSWMYSY +>5952|PPE family protein|YP_177918.1|Mycobacterium tuberculosis H37Rv|83332 +AYVPYVAWL +>6094|Genome polyprotein|Q81495.3|Hepatitis C virus (isolate HCV-K3a/650)|356416 +CDDCHAQDATSILGI +>6308|HCV-1|AAA45676.1|Hepatitis C virus genotype 1|41856 +CGKYLFNWAVRTKLKLTPIA +>6372|Genome polyprotein|SRC279960|Hepatitis C virus|11103 +CHAQDATSVL +>6373|Genome polyprotein|SRC279960|Hepatitis C virus subtype 3a|356426 +CHAQDATTVL +>6430|polyprotein|BAB18810.1|Hepatitis C virus genotype 1|41856 +CINGACWTV +>6431|Genome polyprotein|SRC279960|Hepatitis C virus|11103 +CINGCVWTV +>6432|polyprotein [Hepatitis C virus]|CAL46125.1|Hepatitis C virus (isolate H77)|63746 +CINGLCWTV +>6433|Genome polyprotein|SRC279960|Hepatitis C virus subtype 1a|31646 +CINGVCWTA +>6435|polyprotein|BAB18806.1|Hepatitis C virus|11103 +CINGVCWTV +>6437|Genome polyprotein|SRC279960|Hepatitis C virus|11103 +CINGVWCTV +>6511|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 +CKPLLREEVSFRVGL +>6556|X protein|AAP06597.1|Hepatitis B virus|10407 +CLFKDWEEL +>6568|latent membrane protein 2|AAB59844.1|Human gammaherpesvirus 4|10376 +CLGGLLTMV +>6591|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 +CLIRLKPTLHGPTPLLYR +>6631|core protein|AAL31859.1|Hepatitis B virus|10407 +CLTFGRETV +>6636|polyprotein|ABU97067.1|Hepatitis C virus subtype 1b|31647 +CLVDYPYRL +>6808|membrane protein|AAA45887.1|Human gammaherpesvirus 4|10376 +CPLSKILL +>6817|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 +CPNSSIVY +>6889|Agglutinin isolectin 1 precursor|P10968.2|Triticum aestivum|4565 +CQNGACWTS +>6901|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 +CQTYKWETF +>6936|Genome polyprotein|P26664.3|Hepatitis C virus (isolate 1)|11104 +CRPLTDFDQGW +>7116|NS3|ABN45875.1|Hepatitis C virus (isolate H77)|63746 +CTCGSSDLY +>7270|Genome polyprotein|P26664.3|Hepatitis C virus|11103 +CVIGGAGNNT +>7291|neuramindase|AAT73327.1|Influenza A virus (A/Puerto Rico/8/1934(H1N1))|211044 +CVNGSCFTV +>7292|polyprotein|AAA75355.1|Hepatitis C virus subtype 1b|31647 +CVNGVCWTV +>7338|nonstructural protein 4A|YP_001527885.1|West Nile virus NY-99|10000971 +CWMAEVPGTKIAGMLLL +>7353|Early antigen protein D|P03191.1|Human herpesvirus 4 strain B95-8|10377 +CYDHAQTHL +>7436|Genome polyprotein|P26663.3|Hepatitis C virus|11103 +CYSIEPLDL +>7447|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 +CYVLEETSVML +>7481|Major outer membrane porin, serovar E precursor|P17451.1|Chlamydia trachomatis|813 +DADKYAVTV +>7538|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 +DAIDESGSGEEERPV +>7660|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 +DAVILLMCAVHPTLVFDITK +>7708|gag polyprotein|BAA00992.1|Human immunodeficiency virus 1|11676 +DCKTILKAL +>7999|core protein|BAA82580.1|Hepatitis C virus|11103 +DEGLGWAGW +>8052|polyprotein|NP_671491.1|Hepatitis C virus|11103 +DELAAKLVALGINAV +>8064|circumsporozoite protein|AAN87606.1|Plasmodium falciparum|5833 +DELDYENDIEKKICKMEKCS +>8191|Transcriptional regulator IE63 homolog|Q04360.1|Human herpesvirus 4 strain B95-8|10377 +DEVEFLGHY +>8236|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 +DFAQGWGPISYANGS +>8285|Genome polyprotein|P26662.3|Hepatitis C virus|11103 +DFKTWLQSKL +>8293|Polyprotein|Q9IZA3|Hepatitis C virus subtype 2a|31649 +DFNASTDLL +>8554|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 +DHMSIYKFMGRSHFLCTFTF +>8685|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 +DIKVQFQSG +>8910|Polyprotein|Q9J8D4|Dengue virus 2|11060 +DKKGKVVGL +>8920|M protein, serotype 5 precursor|P02977.2|Streptococcus pyogenes serotype M5|301449 +DKLAKEQKSKQNIGALKQ +>9114|Genome polyprotein|SRC279960|Hepatitis C virus subtype 1a|31646 +DLIAQPIRLL +>9199|E1 protein|ABB77003.1|Hepatitis C virus|11103 +DLMGYIPAV +>9203|polyprotein|BAA03375.1|Hepatitis C virus|11103 +DLMGYIPLV +>9209|polyprotein|CAB53095.1|Hepatitis C virus|11103 +DLMGYLPLV +>9316|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 +DLVGWPAPQGSRSLT +>9414|Superoxide dismutase|P17670.1|Mycobacterium tuberculosis|1773 +DMWEHAFYL +>9415|Superoxide dismutase|P17670.1|Mycobacterium tuberculosis|1773 +DMWEHAFYLQ +>9461|non structural protein 3|CAJ20172.1|Hepatitis C virus|11103 +DNFPYLVAY +>9746|Genome polyprotein|P29846.3|Hepatitis C virus genotype 1|41856 +DPRRRSRNL +>9920|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis|1773 +DQVESTAGSLQGQWRGAA +>9974|gag polyprotein|BAA00992.1|Human immunodeficiency virus 1|11676 +DRFYKTLRA +>9995|Exodeoxyribonuclease V, Gamma|NP_220158.1|Chlamydia trachomatis|813 +DRLALLANL +>9999|DNA packaging tegument protein UL25|NP_044494.1|Human alphaherpesvirus 2|10310 +DRLDNRLQL +>10448|nuclear protein EBNA2|AAA45903.1|Human gammaherpesvirus 4|10376 +DTPLIPLTIF +>10587|viral polyprotein|AAA42941.1|Dengue virus 2 Thailand/NGS-C/1944|11065 +DVFFTPPEK +>10650|Nucleoprotein|P05133.1|Hantaan virus 76-118|11602 +DVKVKEISNQEPLKL +>10681|nucleocapsid protein|AAA43837.1|Hantaan hantavirus|11599 +DVNGIRKPK +>10736|trans-sialidase|XP_814755.1|Trypanosoma cruzi|5693 +DVSRPTAVV +>10763|polyprotein|ABV46054.1|Hepatitis C virus subtype 1a|31646 +DVVCCSMSY +>10790|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 +DVVVVATDALMTGYT +>10939|polyprotein|BAB18806.1|Hepatitis C virus subtype 1a|31646 +DYPYRLWHY +>10962|envelope glycoprotein|AAU04921.1|Human T-lymphotropic virus 1|11908 +DYSPSCCTL +>11014|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 +EADVQQWLT +>11063|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 +EAHFTDPASIAARGY +>11125|NS3 protein|NP_739587.1|Dengue virus 2 Thailand/NGS-C/1944|11065 +EALRGLPIR +>11214|possible regulatory protein|NP_302009.1|Mycobacterium leprae|1769 +EAVLLRLDGTTLEVE +>11258|Nucleoprotein|P41269.1|Puumala hantavirus|11604 +ECPFIKPEV +>11455|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 +EDTSASGSGEDAIDE +>11804|EBNA3C latent protein|CAD53421.1|Human gammaherpesvirus 4|10376 +EENLLDFVRF +>11956|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 +EFCRVLCCYVL +>12060|Myosin heavy chain, skeletal muscle, adult 2 (Myosin heavy chain IIa) (MyHC-IIa)|Q9UKX2.1|Homo sapiens|9606 +EFQKMRRDL +>12062|hypothetical glycine-rich protein Rv3812 - Mycobacterium tuberculosis (strain H37RV)|H70520|Mycobacterium tuberculosis|1773 +EFQTVSNQL +>12108|polyprotein|AAP55688.1|Hepatitis C virus subtype 2a|31649 +EFWEAVFTGL +>12183|EBNA3C latent protein|CAD53421.1|Human gammaherpesvirus 4|10376 +EGGVGWRHW +>12583|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis H37Rv|83332 +EISTNIRQA +>12585|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis|1773 +EISTNIRQAGVQYSRADEEQ +>12588|Glycoprotein B precursor (Glycoprotein II)|P09257.1|Human alphaherpesvirus 3|10335 +EITDTIDKFGK +>12616|gag protein|AAV53308.1|Human immunodeficiency virus 1|11676 +EIYKRWII +>12926|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 +ELAAKLVAL +>12928|Genome polyprotein|Q81754.3|Hepatitis C virus|11103 +ELAAKLVGL +>12941|||| +ELAGIGILTV +>13091|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 +ELIEANLLW +>13119|envelope protein|AGW23591.1|Dengue virus 3|11069 +ELKGMSYAM +>13133|UL123; IE1|AAR31419.1|Human herpesvirus 5 TB40|10000408 +ELKRKMIYM +>13135|UL123; IE1|AAR31504.1|Human betaherpesvirus 5|10359 +ELKRKMMYM +>13165|trans-sialidase, putative|EAN81972.1|Trypanosoma cruzi|5693 +ELLRPTTLV +>13195|6 kDa early secretory antigenic target|P0A564.2|Mycobacterium tuberculosis|1773 +ELNNALQNL +>13215|Antigen 85-B|P0C5B9.1|Mycobacterium tuberculosis|1773 +ELPQWLSANR +>13257|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 +ELRRKMMYM +>13262|gag polyprotein|BAA00992.1|Human immunodeficiency virus 1|11676 +ELRSLYNTV +>13283|glycoprotein gp35/37|AAC59622.1|Human gammaherpesvirus 8|37296 +ELTDALISAFSGSYS +>13346|nonstructural protein 3|NP_722463.1|Dengue virus 1|11053 +EMAEALKGMPIRYQT +>13358|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 +EMEEALRGLPIRYQT +>13386|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis|1773 +EMKTDAATL +>13456|circumsporozoite protein|AAN87606.1|Plasmodium falciparum|5833 +ENDIEKKICKMEKCSSVFNV +>13473|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 +ENFVRSSNL +>13516|Genome polyprotein|P26664.3|Hepatitis C virus subtype 1a|31646 +ENLPYLVAY +>13518|HCV-1|AAA45676.1|Hepatitis C virus genotype 1|41856 +ENLPYLVAYQATVCARAQAP +>13638|polyprotein|BAB18810.1|Hepatitis C virus (isolate H77)|63746 +EPEPDVAVL +>13701|Trans-activator protein BZLF1|P03206.2|Human gammaherpesvirus 4|10376 +EPLPQGQLTAY +>13946|UL123; IE1|AAR31390.1|Human betaherpesvirus 5|10359 +EQVTEDCNENP +>13983|ATP-dependent zinc protease|NP_220362.1|Chlamydia trachomatis|813 +EREQTLNQL +>13991|hypothetical protein CT850|NP_220372.1|Chlamydia trachomatis|813 +ERFLAQEQL +>14001|Nucleocapsid protein|Q89462|Sin Nombre hantavirus|37705 +ERIDDFLAA +>14101|envelope glycoprotein|ABI16336.1|Human immunodeficiency virus 1|11676 +ERYLKDQQL +>14198|UL123; IE1|AAR31390.1|Human betaherpesvirus 5|10359 +ESLKTFEQVTE +>14324|Chain B, Dengue Virus Rna Dependent Rna Polymerase With Residues From The Ns5 Linker Region|4C11_B|Dengue virus|12637 +ETACLGKAY +>14325|polyprotein|AGO67248.1|Dengue virus 2|11060 +ETACLGKSY +>14381|polyprotein|BAA25076.1|Hepatitis C virus|11103 +ETFWAKHMW +>14427|polyprotein|BAD73974.1|Hepatitis C virus subtype 1b|31647 +ETIKGGRHL +>14720|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 +EVIAPAVQTNW +>14727|polyprotein|AAB67036.1|Hepatitis C virus subtype 1a|31646 +EVIKGGRHL +>14731|gag protein|ACD85912.1|Human immunodeficiency virus 1|11676 +EVIPMFSAL +>14902|Genome polyprotein|P26664.3|Hepatitis C virus subtype 1a|31646 +EVVTSTWVL +>15061|core protein|BAF42671.1|Hepatitis B virus|10407 +EYLVSFGVW +>15100|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 +EYTNIPISL +>15110|Genome polyprotein|P26663.3|Hepatitis C virus|11103 +EYVLLLFLL +>15226|trans-sialidase|XP_810383.1|Trypanosoma cruzi|5693 +FANCNFTLV +>15230|Trans-sialidase|SRC7915|Trypanosoma cruzi|5693 +FANHDFTLV +>15231|trans-sialidase|XP_817875.1|Trypanosoma cruzi|5693 +FANHKFTLV +>15232|trans-sialidase, putative|EAN82291.1|Trypanosoma cruzi|5693 +FANHNFTLV +>15233|trans-sialidase, putative|EAN81456.1|Trypanosoma cruzi|5693 +FANNEFTLV +>15234|trans-sialidase|XP_815749.1|Trypanosoma cruzi|5693 +FANNKFTLV +>15242|trans-sialidase, putative|EAN81560.1|Trypanosoma cruzi|5693 +FANYKFTLV +>15244|trans-sialidase|XP_818893.1|Trypanosoma cruzi|5693 +FANYNFTLV +>15787|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 +FFCFAWYLKGRWVPG +>15879|Core antigen|P69708.1|Hepatitis B virus|10407 +FFPSIRDLL +>15885|envelope|BAK20487.1|Human T-lymphotropic virus 1|11908 +FFQFCPLIF +>15914|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 +FFTELDGVRLHRFAP +>16156|Spike glycoprotein precursor|P59594.1|SARS coronavirus|227859 +FIAGLIAIV +>16250|liver stage antigen-1|CAA82974.1|Plasmodium falciparum|5833 +FILVNLLIFH +>16332|secreted antigen Ag85B|AAO62005.1|Mycobacterium tuberculosis|1773 +FIYAGSLSA +>16333|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 +FIYAGSLSAL +>16521|polyprotein|ABU97067.1|Hepatitis C virus subtype 1b|31647 +FLARLIWWL +>16548|Glycoprotein GP110 precursor|P03188.1|Human herpesvirus 4 strain B95-8|10377 +FLDKGTYTL +>16617|Large envelope protein|SRC279965|Hepatitis B virus|10407 +FLGGTRVCL +>16623|gag protein|AAV53308.1|Human immunodeficiency virus 1|11676 +FLGKIWPSYK +>16685|Gag-Pol polyprotein|SRC279958|Human immunodeficiency virus 1|11676 +FLKEKKGL +>16706|structural protein|BAA00705.1|Hepatitis C virus|11103 +FLLALLSCL +>16725|Genome polyprotein|P26664.3|Hepatitis C virus subtype 1a|31646 +FLLLADARV +>16751|pol protein|BAA32832.1|Hepatitis B virus|10407 +FLLSLGIHL +>16753|Pre-S/S protein|AAR99337.1|Hepatitis B virus|10407 +FLLTKILTI +>16755|envelope protein|BAF48755.1|Hepatitis B virus|10407 +FLLTRILTI +>16756|Large envelope protein|SRC279965|Hepatitis B virus|10407 +FLLTRILTL +>16772|Type IV pili glycosylation protein|YP_169902.1|Francisella tularensis subsp. tularensis SCHU S4|177416 +FLMPFMHYIV +>16795|precore/core protein|AAP57273.1|Hepatitis B virus|10407 +FLPADFFPSI +>16796|HBcAg|ABE97049.1|Hepatitis B virus|10407 +FLPADFFPSV +>16813|External core antigen|SRC279980|Hepatitis B virus|10407 +FLPNDFFPSA +>16814|precore protein|CAM58990.1|Hepatitis B virus|10407 +FLPNDFFPSV +>16815|core protein [Hepatitis B virus]|AAR19324.1|Hepatitis B virus|10407 +FLPPDFFPSV +>16827|External core antigen|SRC279980|Hepatitis B virus|10407 +FLPSDFFPGV +>16831|External core antigen|SRC279980|Hepatitis B virus|10407 +FLPSDFFPSA +>16832|core protein|BAF42671.1|Hepatitis B virus|10407 +FLPSDFFPSI +>16833|core protein|CAL29866.1|Hepatitis B virus|10407 +FLPSDFFPSV +>16836|precore/core protein [Hepatitis B virus]|AAR03815.1|Hepatitis B virus|10407 +FLPSDFLPSV +>16839|External core antigen|SRC279980|Hepatitis B virus|10407 +FLPSDTNMGL +>16856|||| +FLPVDFFPSI +>16857|pre-c/core|CAA59565.1|Hepatitis B virus|10407 +FLPVDFFPSV +>16878|EBNA-3A|AFY97830.1|Human gammaherpesvirus 4|10376 +FLRGRAYGL +>16889|trans-sialidase, putative|EAN82636.1|Trypanosoma cruzi|5693 +FLSHDFTLV +>16890|trans-sialidase|XP_810777.1|Trypanosoma cruzi|5693 +FLSHNFTLV +>16924|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 +FLTSELPQW +>16936|tegument protein VP13/14|NP_044517.1|Human alphaherpesvirus 2|10310 +FLVDAIVRV +>16937|tegument protein VP13/14|NP_044517.1|Human alphaherpesvirus 2|10310 +FLVDAIVRVA +>16966|polyprotein|BAA03375.1|Hepatitis C virus|11103 +FLVSQLFTF +>16979|Latent membrane protein 2|Q69135|Human gammaherpesvirus 4|10376 +FLYALALLL +>17079|hypothetical protein FTT1095c|YP_170074.1|Francisella tularensis subsp. tularensis SCHU S4|177416 +FMPKVNFEV +>17110|EBNA-1 protein|Q777E1|Human gammaherpesvirus 4|10376 +FMVFLQTHI +>17117|matrix protein|AAN09804.1|Measles virus strain Edmonston|11235 +FMYMSLLGV +>17278|Genome polyprotein|P06441.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 +FPELKPGESRHTSDHMSIYK +>17321|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 +FPKTTNGCSQA +>17619|Early antigen protein D|P03191.1|Human herpesvirus 4 strain B95-8|10377 +FRNLAYGRTCVLGK +>17620|Early antigen protein D|P03191.1|Human herpesvirus 4 strain B95-8|10377 +FRNLAYGRTCVLGKE +>17802|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 +FSPGTSGSPIIDKKG +>18011|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 +FTLVAPVSI +>18062|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 +FTSAVLLLV +>18142|polyprotein precursor|NP_041724.2|West Nile virus|11082 +FVDVGVSAL +>18144|trans-sialidase|XP_804884.1|Trypanosoma cruzi|5693 +FVDYNFSLV +>18145|trypomastigote surface glycoprotein|AAA30259.1|Trypanosoma cruzi|5693 +FVDYNFTIV +>18242|trans-sialidase, putative|EAN80731.1|Trypanosoma cruzi|5693 +FVNHRFTLV +>18250|Trans-sialidase|SRC7915|Trypanosoma cruzi|5693 +FVNYDFALV +>18251|trans-sialidase|XP_820181.1|Trypanosoma cruzi|5693 +FVNYDFTIV +>18252|trans-sialidase|XP_814186.1|Trypanosoma cruzi|5693 +FVNYNFTLV +>18276|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 +FVRSSNLKF +>18284|Trans-sialidase|SRC7915|Trypanosoma cruzi|5693 +FVSCDFTIV +>18337|polyprotein|BAD73987.1|Hepatitis C virus subtype 1b|31647 +FWAKHMWNF +>18390|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 +FYFPRAPLNSNAMLSTESMM +>18397|Genome polyprotein|P26662.3|Hepatitis C virus|11103 +FYGKAIPIEAI +>18400|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 +FYGMWPLL +>18401|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 +FYGMWPLLL +>18474|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 +FYTPLADQF +>18507|10 kDa culture filtrate antigen EsxB|NP_218391.1|Mycobacterium tuberculosis H37Rv|83332 +GAAGTAAQAAVVRFQ +>18678|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 +GALTGTYVYNHLTPL +>18847|polyprotein|AEH28241.1|Hepatitis C virus subtype 1b|31647 +GAYMSKAHGV +>18941|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 +GDCVQGDWCPISGGL +>19225|polyprotein|AGO67248.1|Dengue virus 2|11060 +GEDGCWYGM +>19305|Genome polyprotein|P26664.3|Hepatitis C virus|11103 +GEIPFYGKAI +>19337|gag protein|AAW57872.1|Human immunodeficiency virus 1|11676 +GELDRWEKI +>19348|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 +GELLPEAAGPTQVLVPRSAI +>19351|core protein|AAL31859.1|Hepatitis B virus|10407 +GELMTLATW +>19359|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 +GELSKQTGQQVSIAPNAGLD +>19366|Hepatitis C virus core, matrix, envelope and non-structural protein RNA.|AAA72945.1|Hepatitis C virus|11103 +GEMPSTEDL +>19370|Genome polyprotein|P26664.3|Hepatitis C virus genotype 6|42182 +GENDTDVFVL +>19434|Genome polyprotein|P27915.1|Dengue virus 3|11069 +GESRKTFVE +>19435|polyprotein|CDF77361.1|Dengue virus 3|11069 +GESRKTFVEL +>19442|nucleocapsid protein|ABI96968.1|SARS coronavirus|227859 +GETALALLLL +>19463|Carbamoyl-phosphate synthase large chain|YP_170571.1|Francisella tularensis subsp. tularensis SCHU S4|177416 +GEVLGVIVQF +>19490|Genome polyprotein|P26663.3|Hepatitis C virus (isolate BK)|11105 +GFADLMGYI +>19492|Genome polyprotein|P29846.3|Hepatitis C virus|11103 +GFADLMGYIPL +>19493|polyprotein|BAA03375.1|Hepatitis C virus|11103 +GFADLMGYIPLVGAP +>19575|glycoprotein B precursor|AAB72100.1|Human alphaherpesvirus 2|10310 +GFLIAYQPLL +>19628|Genome polyprotein|P26662.3|Hepatitis C virus|11103 +GFTGDFDSV +>19898|gag protein|AAV53308.1|Human immunodeficiency virus 1|11676 +GGKKKYKLK +>20023|EBNA-1|YP_401677.1|Human gammaherpesvirus 4|10376 +GGSKTSLYNLRRGTA +>20354|M1 protein|CAA30882.1|Influenza A virus|11320 +GILGFVFTL +>20355|Matrix protein 1|P03485.1|Influenza A virus (A/Puerto Rico/8/1934(H1N1))|211044 +GILGFVFTLT +>20369|HEAT SHOCK PROTEIN HSPX (ALPHA-CRSTALLIN HOMOLOG) (14 kDa ANTIGEN) (HSP16.3)|NP_216547.1|Mycobacterium tuberculosis H37Rv|83332 +GILTVSVAV +>20415|circumsporozoite protein|AAN87606.1|Plasmodium falciparum|5833 +GIQVRIKPGSANKPKDELDY +>20417|HCV-1|AAA45676.1|Hepatitis C virus genotype 1|41856 +GIQYLAGLSTLPGNPAIASL +>20686|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 +GKSTHPMVTRS +>20752|tegument protein VP13/14|NP_044517.1|Human alphaherpesvirus 2|10310 +GLADTVVAC +>20772|Genome polyprotein|SRC279960|Hepatitis C virus|11103 +GLASLFTQGA +>20786|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 +GLCPHCINV +>20787|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 +GLCPHCINVG +>20788|BMLF1 protein|CAD53409.1|Human gammaherpesvirus 4|10376 +GLCTLVAML +>20861|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 +GLFNNVLYH +>20865|Nucleoprotein|P41269.1|Puumala hantavirus|11604 +GLFPTQIQV +>20892|latent membrane protein 2|AAB59844.1|Human gammaherpesvirus 4|10376 +GLGTLGAAL +>20894|polyprotein [Hepatitis C virus]|BAF91806.1|Hepatitis C virus|11103 +GLGWVGWLL +>20921|polyprotein|BAA03375.1|Hepatitis C virus|11103 +GLIHLHQNIVDVQYL +>20929|Circumsporozoite protein precursor|P02893.1|Plasmodium falciparum|5833 +GLIMVLSFL +>20988|Genome polyprotein|P26662.3|Hepatitis C virus (isolate Japanese)|11116 +GLLGCIITSL +>20994|Circumsporozoite-related antigen|SRC280086|Plasmodium falciparum|5833 +GLLGNVSTV +>21000|glutamine synthetase GLNA1 (glutamine synthase) (GS-I)|NP_216736.1|Mycobacterium tuberculosis|1773 +GLLHHAPSL +>21004|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 +GLLLLGLWGT +>21007|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 +GLLPFHSTL +>21013|trans-sialidase, putative|EAN80935.1|Trypanosoma cruzi|5693 +GLLPSLLLLL +>21038|cysteine proteinase cruzipain (EC 3.4.22.-) - Trypanosoma cruzi|A45629|Trypanosoma cruzi|5693 +GLMNNAFEWI +>21041|Membrane glycoprotein|Q692E0|SARS coronavirus TJF|284672 +GLMWLSYFV +>21070|polymerase|CAA53358.1|Hepatitis B virus subtype AYR|10000437 +GLPRYVARL +>21071|Protein P|SRC279982|Hepatitis B virus subtype adr|106820 +GLPRYVVCL +>21078|Antigen 85-B precursor|P21160.1|Mycobacterium kansasii|1768 +GLPVEYLQV +>21079|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 +GLQDCTMLV +>21116|X protein|BAG70907.1|Hepatitis B virus|10407 +GLSAMSTTDL +>21137|Major surface antigen precursor|P03142.4|Hepatitis B virus subtype adw|106821 +GLSPTVWLSA +>21139|envelope protein|BAF48755.1|Hepatitis B virus|10407 +GLSPTVWLSV +>21145|DNA polymerase|CAA10434.1|Hepatitis B virus|10407 +GLSRYVARL +>21146|polymerase|AAD16253.1|Hepatitis B virus|10407 +GLSRYVARLS +>21190|Genome polyprotein|P27958.3|Hepatitis C virus (isolate H)|11108 +GLVGLLTPGA +>21199|Circumsporozoite protein precursor|P08677.2|Plasmodium vivax strain Belem|31273 +GLVILLVLAL +>21230|polyprotein precursor|AAP22088.1|West Nile virus|11082 +GLYKSAPRR +>21242|polymerase|ACF94272.1|Hepatitis B virus|10407 +GLYSSTVPV +>21275|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 +GMGPSLIGL +>21347|Nucleoprotein|P59595.1|SARS coronavirus|227859 +GMSRIGMEV +>21385|polyprotein|AAY82034.1|Hepatitis C virus genotype 1|41856 +GNASRCWVAM +>21576|nucleocapsid protein|AAA43837.1|Hantaan virus 76-118|11602 +GPATNRDYL +>21635|gag protein|ABO73990.1|Human immunodeficiency virus 1|11676 +GPGHKARVL +>21638|protein F|ABV46152.2|Hepatitis C virus (isolate Japanese)|11116 +GPGLSPGTL +>21656|protease|CAB06750.1|Human alphaherpesvirus 2|10310 +GPHETITAL +>21663|polyprotein precursor|NP_041724.2|West Nile virus|11082 +GPIRFVLAL +>21754|Genome polyprotein|SRC279960|Hepatitis C virus genotype 1|41856 +GPRLGFRAT +>21757|polyprotein|BAA09072.1|Hepatitis C virus|11103 +GPRLGVRAT +>21762|Genome polyprotein|Q99IB8.3|Hepatitis C virus|11103 +GPRLGVRTT +>21780|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 +GPSLIGLAM +>21894|Polyprotein|P90247|Hepatitis C virus|11103 +GQIVGGVYL +>21895|core protein|AAS15195.1|Hepatitis C virus (isolate H77)|63746 +GQIVGGVYLL +>21960|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 +GQSSFYSDWY +>21982|HCV-1|AAA45676.1|Hepatitis C virus|11103 +GRAAICGKY +>22046|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 +GRGKPGIYRF +>22235|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 +GRVIGSALQFLIPRL +>22255|polyprotein|ABR27377.1|Hepatitis C virus|11103 +GRWVPGAAY +>22633|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 +GTDTGQACQIQMSDPAYNIN +>22801|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 +GTRLAAGSPSSEYPN +>22817|polyprotein|AAK49562.1|Dengue virus 2|11060 +GTSGSPIADKK +>22818|Nonstructural protein NS3|NP_739587.2|Dengue virus 2|11060 +GTSGSPIIDK +>22819|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 +GTSGSPIIDKK +>22820|Nonstructural protein NS3|YP_001531172.2|Dengue virus 3|11069 +GTSGSPIINR +>22822|NS3 protein|NP_740321.1|Dengue virus 4|11070 +GTSGSPIINRK +>22823|NS3 protein|NP_739587.1|Dengue virus 2|11060 +GTSGSPIVDK +>22824|polyprotein|AAG30730.1|Dengue virus 2|11060 +GTSGSPIVDR +>22825|polyprotein|ABG75765.1|Dengue virus 1|11053 +GTSGSPIVNR +>22910|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 +GVAGALVAFK +>22919|Genome polyprotein|SRC279960|Hepatitis C virus|11103 +GVASFFTPGA +>22976|nuclear antigen EBNA-1|AAA67277.1|Human gammaherpesvirus 4|10376 +GVFVYGGSKTSLYNL +>23129|polyprotein|BAB18806.1|Hepatitis C virus subtype 1a|31646 +GVRVLEDGV +>23137|liver stage antigen-1|CAA82974.1|Plasmodium falciparum|5833 +GVSENIFLK +>23151|polymerase ORF|CAA46356.1|Hepatitis B virus subtype ayw|10418 +GVSRYVARL +>23224|polyprotein|BAB18806.1|Hepatitis C virus|11103 +GVYLLPRRGPRLGVR +>23270|polyprotein|AAB67036.1|Hepatitis C virus (isolate H77)|63746 +GWLAGLFYQHKFNSS +>23288|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 +GWSGQVYQDWLGRMN +>23306|LOW MOLECULAR WEIGHT PROTEIN ANTIGEN 7 ESXH (10 kDa ANTIGEN) (CFP-7) (PROTEIN TB10.4)|CAA17363.1|Mycobacterium tuberculosis H37Rv|83332 +GYAGTLQSL +>23365|polyprotein|BAB18806.1|Hepatitis C virus|11103 +GYIPLVGAPL +>23474|polyprotein|AAP55688.1|Hepatitis C virus subtype 2a|31649 +GYTGDFDSVI +>23542|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 +HAKALKERMV +>23566|tegument protein UL7|NP_044476.1|Human alphaherpesvirus 2|10310 +HASPFERVRCLLL +>23573|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 +HAVGLFRAA +>23601|Genome polyprotein|SRC279960|Hepatitis C virus (isolate H77)|63746 +HCPAGHAVGIFRAAVCTRGVA +>23619|Genome polyprotein|P27958.3|Hepatitis C virus (isolate H)|11108 +HDGAGKRVY +>23620|Genome polyprotein|SRC279960|Hepatitis C virus genotype 1|41856 +HDGAGKRVYL +>23621|Genome polyprotein|P26664.3|Hepatitis C virus (isolate 1)|11104 +HDGAGKRVYYL +>23754|Genome polyprotein|P26664.3|Hepatitis C virus genotype 1|41856 +HEYPVGSQL +>23797|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 +HFLCTFTFNSNNKEYTFPIT +>23807|tax|AAG48731.1|Human T-lymphotropic virus 2|11909 +HFPGFGQSLLYGYPVYVFGDCVQ +>23864|envelope glycoprotein(gp21, gp46) - human T-cell lymphotropic virus type 1|A45714|Human T-lymphotropic virus 1|11908 +HFSKCGFPF +>23883|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 +HGAGTRTIASPKGPV +>24172|pX-rex-orf I {alternatively spliced}|AAB23359.1|Human T-lymphotropic virus 1|11908 +HLAFQLSSI +>24218|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 +HLHAPTGSGK +>24219|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 +HLHAPTGSGKSTKVP +>24299|X protein|BAF81690.1|Hepatitis B virus|10407 +HLSLRGLFV +>24302|X protein|AAP06597.1|Hepatitis B virus|10407 +HLSLRGLPV +>24390|Major capsid protein L1|P50816.2|Human papillomavirus type 44|10592 +HNNGICWGN +>24427|polyprotein|ACX44238.1|Hepatitis C virus subtype 1a|31646 +HPALVFDIT +>24457|polyprotein|BAA09072.1|Hepatitis C virus|11103 +HPITKYIMACMSADL +>24479|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 +HPNIEEVAL +>24535|EBNA-1 protein|Q777E1|Human gammaherpesvirus 4|10376 +HPVGEADYF +>24536|EBNA-1|YP_401677.1|Human gammaherpesvirus 4|10376 +HPVGEADYFEY +>24557|Gag polyprotein|P03347.3|Human immunodeficiency virus 1|11676 +HPVHAGPIA +>24759|polyprotein|AAY82031.1|Hepatitis C virus|11103 +HSKKKCDDL +>24760|polyprotein|ACP19428.1|Hepatitis C virus subtype 1b|31647 +HSKKKCDEF +>24761|polyprotein|ACZ60102.1|Hepatitis C virus subtype 3a|356426 +HSKKKCDEI +>24762|NS3|ABW71987.1|Hepatitis C virus subtype 1b|31647 +HSKKKCDEL +>24764|polyprotein [Hepatitis C virus subtype 1b]|ABV46195.2|Hepatitis C virus|11103 +HSKKKCDELT +>24765|polyprotein [Hepatitis C virus]|ABR27360.1|Hepatitis C virus|11103 +HSKKKCDEV +>24768|NS3 [Hepatitis C virus]|AAU44886.1|Hepatitis C virus subtype 1b|31647 +HSKRKCDEF +>24769|polyprotein|AAY82032.1|Hepatitis C virus subtype 1b|31647 +HSKRKCDEL +>24818|polyprotein|ABL63011.1|Hepatitis C virus|11103 +HSNIEEVAL +>24943|DNA polymerase|CAA10434.1|Hepatitis B virus|10407 +HTLWKAGILYK +>24986|polyprotein precursor|NP_041724.2|West Nile virus|11082 +HTTKGAALM +>25133|Envelope glycoprotein precursor|P27312.1|Puumala hantavirus|11604 +HWMDATFNL +>25149|polyprotein|BAD73994.1|Hepatitis C virus subtype 1b|31647 +HYAPRPCGI +>25186|polyprotein|AAK32686.1|Hepatitis C virus|11103 +HYPCTVNFTI +>25237|Transcription activator BRLF1|P03209.1|Human herpesvirus 4 strain B95-8|10377 +IACPIVMRYVLDHLI +>25275|Glutamate decarboxylase 2|Q05329.1|Homo sapiens|9606 +IAFTSEHSHFSLK +>25370|Trans-sialidase|SRC7915|Trypanosoma cruzi|5693 +IANYNFTLV +>25388|matrix protein|ABP96803.1|Human metapneumovirus|162145 +IAPYAGLIMI +>25460|Fusion glycoprotein F0 precursor|P03420.1|Human respiratory syncytial virus A2|11259 +IAVGLLLYCKA +>25677|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 +IDTCISATFR +>25756|membrane protein|AAA45887.1|Human gammaherpesvirus 4|10376 +IEDPPFNSL +>25782|pol protein|ACJ76655.1|Human immunodeficiency virus 1|11676 +IEELRQHLL +>25839|gag protein|ACN42927.1|Human immunodeficiency virus 1|11676 +IEIKDTKEAL +>25929|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 +IEPSWADVKKDLISY +>26111|polyprotein|BAD73987.1|Hepatitis C virus subtype 1b|31647 +IFLLALLSCL +>26174|Genome polyprotein|Q9WMX2.3|Hepatitis C virus|11103 +IFTITKILL +>26186|UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-me so-diaminopimelate ligase|YP_169478.1|Francisella tularensis subsp. tularensis SCHU S4|177416 +IFWQFHQLL +>26273|nucleocapsid protein|ABI96968.1|SARS coronavirus|227859 +IGMEVTPSGTWLTYH +>26579|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 +IILNGSLLTL +>26666|Receptor tyrosine-protein kinase erbB-2 precursor|P04626.1|Homo sapiens|9606 +IISAVVGIL +>26870|Circumsporozoite protein precursor|P02893.1|Plasmodium falciparum|5833 +IKPGSANKPKDELDYENDIE +>26954|HCV-1|AAA45676.1|Hepatitis C virus genotype 1|41856 +ILAGYGAGV +>26965|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 +ILAPTRVVAAEMEEA +>27000|Heat shock protein HSP 90-beta|P08238.4|Homo sapiens|9606 +ILDKKVEKV +>27011|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 +ILDSFDPLV +>27061|envelope glycoprotein|ABU89742.1|Dengue virus 2 Thailand/16681/84|31634 +ILGDTAWDFG +>27096|HCV-1|AAA45676.1|Hepatitis C virus (isolate H)|11108 +ILHTPGCV +>27125|gag-pol fusion polyprotein|AAN73817.1|Human immunodeficiency virus 1|11676 +ILKEPVHGV +>27168|envelope protein|BAF48755.1|Hepatitis B virus|10407 +ILLLCLIFL +>27169|envelope protein|BAF48755.1|Hepatitis B virus|10407 +ILLLCLIFLL +>27195|polyprotein|ABG67747.1|West Nile virus|11082 +ILLWEIPDV +>27216|polyprotein|BAD73987.1|Hepatitis C virus subtype 1b|31647 +ILMTHFFSI +>27217|VP1|AAL37677.1|JC polyomavirus|10632 +ILMWEAVTL +>27239|polyprotein|BAB18806.1|Hepatitis C virus subtype 1b|31647 +ILPCSFTTL +>27241|Spike glycoprotein precursor|P59594.1|SARS coronavirus|227859 +ILPDPLKPT +>27245|Hemagglutinin glycoprotein|P08362.1|Measles virus strain Edmonston|11235 +ILPGQDLQYV +>27285|pol protein|BAA32832.1|Hepatitis B virus|10407 +ILRGTSFVYV +>27295|polyprotein precursor|NP_041724.2|West Nile virus|11082 +ILRNPGYAL +>27345|Large envelope protein|P03138.3|Hepatitis B virus subtype ayw|10418 +ILSPFLPLL +>27365|precore/core protein|BAE97616.1|Hepatitis B virus|10407 +ILSTLPETTV +>27564|organic solvent tolerance protein|YP_169505.1|Francisella tularensis subsp. tularensis SCHU S4|177416 +IMSSFEFQV +>27586|ESAT-6-like protein esxH|P0A568.2|Mycobacterium tuberculosis|1773 +IMYNYPAML +>27770|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 +INYADRRWCF +>27811|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 +IPDREVLY +>27847|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 +IPFYGKAI +>27878|large surface antigen|CAC87019.1|Hepatitis B virus|10407 +IPIPSSWAF +>27901|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 +IPKLVANNT +>27981|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 +IPPRGTQAVVLKVYQNAGGT +>27983|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 +IPPSFLQAMRKYSPF +>28126|matrix protein|ABP96803.1|Human metapneumovirus|162145 +IPYTAAVQV +>28222|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 +IQSALKLAIYKAT +>28282|Nucleoprotein|P41269.1|Puumala hantavirus|11604 +IREFMEKECPFIKPE +>28338|hypothetical protein CT339|NP_219846.1|Chlamydia trachomatis|813 +IRMFKILPL +>28364|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis H37Rv|83332 +IRQAGVQYSR +>28403|Invasin repeat family phosphatase|NP_220117.1|Chlamydia trachomatis|813 +IRSSVQNKL +>28484|Protein E6|P03126.1|Human papillomavirus type 16|333760 +ISEYRHYCY +>28508|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 +ISGGLCSARLHRHAL +>28594|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 +ISLPSYYPDQKSLENYIAQT +>28657|gag protein|CAB00235.1|Human immunodeficiency virus 1|11676 +ISPRTLNAW +>29181|unnamed protein product|BAA14233.1|Hepatitis C virus subtype 1b|31647 +ITYSTYCKF +>29182|polyprotein|BAD73991.1|Hepatitis C virus subtype 1b|31647 +ITYSTYGKF +>29186|polyprotein precursor|NP_041724.2|West Nile virus|11082 +ITYTDVLRY +>29287|polyprotein|BAA09073.1|Hepatitis C virus subtype 1b|31647 +IVGGVYLLPR +>29352|pol protein|AAS38336.1|Human immunodeficiency virus 1|11676 +IVLPEKDSW +>29455|Major surface antigen precursor|P03141.3|Hepatitis B virus subtype adw2|10408 +IVSPFIPLL +>29466|Epstein-Barr nuclear antigen 4|P03203.3|Human herpesvirus 4 strain B95-8|10377 +IVTDFSVIK +>29558|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 +IYAGSLSAL +>29655|pol protein|ACJ76655.1|Human immunodeficiency virus 1|11676 +IYQEPFKNLK +>29804|p24|AAB82828.1|Human immunodeficiency virus 1|11676 +KAFSPEVIPMF +>30138|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 +KDELRRKMMYM +>30266|Transcriptional regulator IE63 homolog|Q04360.1|Human herpesvirus 4 strain B95-8|10377 +KDTWLDARM +>30464|nef protein|ACR27130.1|Human immunodeficiency virus 1|11676 +KEKGGLEGL +>30815|Genome polyprotein|P26662.3|Hepatitis C virus|11103 +KFPPALPIW +>30892|Protein E6|P03126.1|Human papillomavirus type 16|333760 +KFYSKISEY +>30903|prM protein|YP_001527879.1|West Nile virus NY-99|10000971 +KGAWMDSTKATRYLVK +>30913|polyprotein precursor|NP_041724.2|West Nile virus|11082 +KGDTTTGVY +>30946|HCV-1|AAA45676.1|Hepatitis C virus genotype 1|41856 +KGGRKPARLIVFPDLGVRVC +>31004|M protein, serotype 5 precursor|P02977.2|Streptococcus pyogenes serotype M5|301449 +KGLRRDLDA +>31747|polyprotein|AGO67248.1|Dengue virus 2|11060 +KLAEAIFKL +>31756|matrix protein 2-1|AAS22094.1|Human metapneumovirus|162145 +KLAKLIIDL +>31771|Nucleoprotein|P03418.1|Human respiratory syncytial virus A2|11259 +KLCGMLLITEDANH +>31802|large delta antigen|AAG26087.1|Hepatitis delta virus TW2667|10000523 +KLEDENPWL +>31803|large delta antigen|AAG26087.1|Hepatitis delta virus TW2667|10000523 +KLEDLERDL +>31884|HAD superfamily protein|YP_169641.1|Francisella tularensis subsp. tularensis SCHU S4|177416 +KLGGYVSFV +>31898|P protein|P17100.1|Hepatitis B virus|10407 +KLHLYSHPI +>31902|Secreted antigen Ag85A|Q847N5|Mycobacterium tuberculosis|1773 +KLIANNTRV +>31974|short chain dehydrogenase|YP_169584.1|Francisella tularensis subsp. tularensis SCHU S4|177416 +KLLGQINLV +>31996|nucleocapsid protein|AAA43837.1|Hantaan virus 76-118|11602 +KLLPDTAAV +>31997|hypothetical protein FTT0484|YP_169522.1|Francisella tularensis subsp. tularensis SCHU S4|177416 +KLLPEGYWV +>32047|M protein, serotype 5 precursor|P02977.2|Streptococcus pyogenes serotype M5|301449 +KLNKELEES +>32069|Spike glycoprotein precursor|P59594.1|SARS coronavirus BJ01|228407 +KLPDDFMGCV +>32073|Protein E6|P06463.1|Human papillomavirus type 18|333761 +KLPDLCTEL +>32085|Protein E6|P03126.1|Human papillomavirus type 16|333760 +KLPQLCTEL +>32103|60 kDa chaperonin 2|P0A520.2|Mycobacterium tuberculosis|1773 +KLQERLAKL +>32147|nonstructural protein 3|NP_722463.1|Dengue virus type 1 Hawaii|10000440 +KLRTLVLAPTRVVAS +>32150|polyprotein|AAF65953.1|Hepatitis C virus|11103 +KLSALGLNAV +>32165|Hepatitis C virus core, matrix, envelope and non-structural protein RNA.|AAA72945.1|Hepatitis C virus (isolate BK)|11105 +KLSGLGINAV +>32166|Genome polyprotein|SRC279960|Hepatitis C virus (isolate H77)|63746 +KLSGLGLNAI +>32167|polyprotein|BAB18806.1|Hepatitis C virus|11103 +KLSGLGLNAV +>32174|non structural protein 3|CAJ20172.1|Hepatitis C virus|11103 +KLSNLGLNAV +>32179|polyprotein|ABU97067.1|Hepatitis C virus (isolate H77)|63746 +KLSSLGLNAV +>32187|polyprotein [Hepatitis C virus subtype 1a]|ACA50630.1|Hepatitis C virus (isolate H77)|63746 +KLTALGVNAV +>32201|Gp160|Q0ED31|Human immunodeficiency virus 1|11676 +KLTPLCVTL +>32208|Genome polyprotein|P26664.3|Hepatitis C virus subtype 1a|31646 +KLVALGINAV +>32209|polyprotein precursor|BAA01582.1|Hepatitis C virus (isolate H77)|63746 +KLVALGVNAV +>32210|polyprotein|AAY82027.1|Hepatitis C virus|11103 +KLVAMGINAV +>32212|polyprotein [Hepatitis C virus subtype 1a]|ACA50667.1|Hepatitis C virus (isolate H77)|63746 +KLVAMGVNAV +>32213|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 +KLVANNTRL +>32223|polyprotein [Hepatitis C virus subtype 1a]|ABW86969.1|Hepatitis C virus (isolate H77)|63746 +KLVGLGLNAV +>32237|polyprotein|ABV46286.2|Hepatitis C virus subtype 1b|31647 +KLVSLGVNAV +>32238|polyprotein [Hepatitis C virus subtype 1a]|ABV46251.2|Hepatitis C virus (isolate H77)|63746 +KLVVLGINAV +>32243|C protein|BAB60863.1|Measles virus|11234 +KLWESPQEI +>32250|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 +KLYCSYEVA +>32268|hemagglutinin|AAK38298.1|Influenza A virus (A/Bar-headed Goose/Qinghai/61/05(H5N1))|336238 +KLYQNPTTYI +>32393|Myosin heavy chain, skeletal muscle, adult 2 (Myosin heavy chain IIa) (MyHC-IIa)|Q9UKX2.1|Homo sapiens|9606 +KMRRDLEEA +>32605|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 +KNSAFPKTTNG +>32663|small hydrophobic protein|AAM12943.1|Human metapneumovirus|162145 +KPAVGVYHIV +>32738|Liver stage antigen|Q25893|Plasmodium falciparum|5833 +KPIVQYDNF +>32741|circumsporozoite protein|ABF83988.1|Plasmodium falciparum|5833 +KPKDELDY +>32939|polyprotein|AAK67712.1|Dengue virus 2|11060 +KPWDIIPMV +>32940|polyprotein|ABG75765.1|Dengue virus type 1 Hawaii|10000440 +KPWDVIPMV +>32941|DEN polyprotein|AAC40835.1|Dengue virus 2|11060 +KPWDVLPMV +>32942|Polyprotein|Q9J8D4|Dengue virus 2|11060 +KPWDVLPTV +>32943|polyprotein|AAL96681.1|Dengue virus 2|11060 +KPWDVVPMV +>32944|polyprotein|AAW51418.1|Dengue virus 3|11069 +KPWDVVPTV +>32955|P protein|P31870.1|Hepatitis B virus|10407 +KQAFTFSPTYKAFLC +>32998|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 +KQIKVRVDMVR +>33245|60 kDa chaperonin|P48219.1|Yersinia enterocolitica|630 +KRVVINKDT +>33250|gag protein|ABO73990.1|Human immunodeficiency virus 1|11676 +KRWIILGLNK +>33362|Circumsporozoite protein|Q27325|Plasmodium falciparum|5833 +KSKDELDY +>33381|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 +KSKKTPMGF +>33382|polyprotein|AAB67037.1|Hepatitis C virus|11103 +KSKKTPMGFSYDTRC +>33502|envelope glycoprotein E|NP_044538.1|Human alphaherpesvirus 2|10310 +KSRRPLTTF +>33576|polyprotein|ABG67747.1|West Nile virus|11082 +KSYETEYPK +>33618|pol protein|ACJ76655.1|Human immunodeficiency virus 1|11676 +KTAVQMAVF +>33681|||| +KTGGPAIYKR +>33749|nonstructural protein 4B|YP_001527886.1|West Nile virus NY-99|10000971 +KTKSDISSLFGQRIEVK +>33856|polyprotein|BAA03375.1|Hepatitis C virus|11103 +KTSERSQPR +>33912|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 +KTWADEYLCV +>33979|fusion protein|ABQ58820.1|Human metapneumovirus|162145 +KVEGEQHVIK +>34027|DNA polymerase|CAA10434.1|Hepatitis B virus|10407 +KVGNFTGLY +>34101|X protein|ACH95876.1|Hepatitis B virus|10407 +KVLHKRTLGL +>34251|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 +KVVSLVILA +>34304|Gag polyprotein|P88150|Human immunodeficiency virus 1|11676 +KWIILGLNKIVRMY +>34482|gag polyprotein|BAA00992.1|Human immunodeficiency virus 1|11676 +KYKLKHIVW +>34598|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 +KYSPFRNGYMEPTLG +>34605|NS3 protein|Q3LXL6|Dengue virus 3|11069 +KYTDRKWCF +>34616|pol protein|BAA32832.1|Hepatitis B virus|10407 +KYTSFPWLL +>34637|Polyprotein|Q9IZA3|Hepatitis C virus subtype 2a|31649 +KYVQMALLAL +>34642|methionine sulfoxide reductase B|YP_169878.1|Francisella tularensis subsp. tularensis SCHU S4|177416 +KYWNNHRQGI +>34671|polyprotein|NP_671491.1|Hepatitis C virus|11103 +LAAKLVALGINAVAY +>34918|polyprotein precursor|AAG45435.1|Dengue virus 4|11070 +LAPTRVVAAEME +>35237|nonstructural protein 3|NP_722463.1|Dengue virus type 1 Hawaii|10000440 +LDNINTPEGIIPALFEPERE +>35238|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 +LDNINTPEGIIPSMF +>35407|polyprotein|ACE82359.1|Hepatitis C virus subtype 1a|31646 +LEDRDRSEL +>35568|Polyprotein|Q9J8D4|Dengue virus 2|11060 +LEKTKKDL +>35785|14 kDa antigen|P0A5B7.2|Mycobacterium tuberculosis|1773 +LFAAFPSFA +>35844|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 +LFGYPVYV +>35845|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 +LFGYPVYVF +>36062|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 +LGALTGTYVYNHLTPLRDWA +>36102|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 +LGFGAYMSK +>36306|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 +LGRMNCSYENMTALE +>36345|polyprotein|ABR25251.1|Hepatitis C virus (isolate H77)|63746 +LGVPPLRAWR +>36352|Polyprotein|P90247|Hepatitis C virus|11103 +LGWAGWLLSPRGSRPSWGPT +>36357|ELAV-like protein 4 (Paraneoplastic encephalomyelitis antigen HuD) (Hu-antigen D)|P26378.1|Homo sapiens|9606 +LGYGFVNYI +>36358|ELAV-like protein 1|Q15717.2|Homo sapiens|9606 +LGYGFVNYV +>36402|P protein|Q05486.1|Hepatitis B virus|10407 +LHLYSHPIILGFRKI +>36432|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 +LHTDFEQVM +>36504|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 +LIFCHSKKK +>36563|Accessory protein p30II|P0C214.1|Human T-lymphotropic virus 1|11908 +LIISPLPRV +>36599|putative D-ribose-binding protein|NP_301386.1|Mycobacterium leprae|1769 +LILGLLPAI +>36621|glycoprotein gp35/37|AAC59622.1|Human gammaherpesvirus 8|37296 +LILYLCVPRCRRKKP +>36676|polyprotein|BAA09073.1|Hepatitis C virus subtype 1b|31647 +LIRACMLVR +>36688|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 +LIRLKPTL +>36717|nonstructural protein 4B|YP_001527886.1|West Nile virus NY-99|10000971 +LITAAAVTLWENGASSVW +>36723|Spike glycoprotein precursor|P15423.1|Human coronavirus 229E|11137 +LITGRLAAL +>36724|Spike glycoprotein precursor|P59594.1|SARS coronavirus|227859 +LITGRLQSL +>37073|sporozoite surface protein 2|NP_705260.1|Plasmodium falciparum 3D7|36329 +LLACAGLAY +>37074|sporozoite surface protein 2|NP_705260.1|Plasmodium falciparum 3D7|36329 +LLACAGLAYK +>37079|Genome polyprotein|P26664.3|Hepatitis C virus|11103 +LLADARVCSC +>37097|polyprotein|AAY82030.1|Hepatitis C virus genotype 1|41856 +LLALLSCLTV +>37115|Circumsporozoite|SRC280011|Plasmodium falciparum|5833 +LLAVSSILLL +>37120|Major surface antigen precursor|P17399.3|Hepatitis B virus|10407 +LLCLIFLLV +>37127|polyprotein|AAY82030.1|Hepatitis C virus genotype 1|41856 +LLCPAGHAV +>37136|Genome polyprotein|P27958.3|Hepatitis C virus|11103 +LLCPTGHAV +>37140|Hypothetical protein esxG (PE family protein)|O53692.1|Mycobacterium tuberculosis|1773 +LLDAHIPQL +>37146|6 kDa early secretory antigenic target|P0A564.2|Mycobacterium tuberculosis|1773 +LLDEGKQSL +>37153|Nuclear antigen EBNA-3C|Q69140.1|Human gammaherpesvirus 4|10376 +LLDFVRFMGV +>37170|Major surface antigen precursor|P12934.3|Hepatitis B virus|10407 +LLDPRVRGL +>37181|core|CAA59522.1|Hepatitis B virus|10407 +LLDTASALY +>37187|surface antigen|BAF44879.1|Hepatitis B virus|10407 +LLDYQGMLPV +>37246|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 +LLFEEYTNI +>37251|||| +LLFGHPVYV +>37253|||| +LLFGYAVYV +>37254|||| +LLFGYPRYV +>37255|||| +LLFGYPVAV +>37257|Protein Tax-1|P03409.2|Human T-lymphotropic virus 1|11908 +LLFGYPVYV +>37273|Genome polyprotein|P26664.3|Hepatitis C virus (isolate 1)|11104 +LLFLLLADA +>37286|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 +LLFNILGGWV +>37317|Genome polyprotein|P26662.3|Hepatitis C virus (isolate Japanese)|11116 +LLGCIITSL +>37347|Sialidase 85-1.1 precursor|P18269.2|Trypanosoma cruzi|5693 +LLGLWGLATA +>37350|trans-sialidase|XP_818394.1|Trypanosoma cruzi|5693 +LLGLWGTAAL +>37351|trans-sialidase, putative|EAN81560.1|Trypanosoma cruzi|5693 +LLGLWVFAAL +>37364|P53_HUMAN Cellular tumor antigen p53 (Tumor suppressor p53) (Phosphoprotein p53) (Antigen NY-CO-13)|P04637.2|Homo sapiens|9606 +LLGRNSFEV +>37397|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 +LLHTDFEQV +>37398|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 +LLHTDFEQVM +>37453|polyprotein|BAD73987.1|Hepatitis C virus subtype 1b|31647 +LLKRLHQWI +>37466|surface antigen|BAF44879.1|Hepatitis B virus|10407 +LLLCLIFLL +>37473|Nucleoprotein|P59595.1|SARS coronavirus|227859 +LLLDRLNQL +>37498|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 +LLLGLWGTAA +>37507|Large T antigen|P03071.1|Human polyomavirus 1|1891762 +LLLIWFRPV +>37511|||| +LLLKATLCI +>37536|Spike glycoprotein precursor|P15423.1|Human coronavirus 229E|11137 +LLLNCLWSV +>37573|E7 protein|ABL96585.1|Human papillomavirus type 16|333760 +LLMGTLGIV +>37590|VP1|BAF93325.1|Human polyomavirus 1|1891762 +LLMWEAVTV +>37607|kaposin|AAC57155.1|Human gammaherpesvirus 8|37296 +LLNGWRWRL +>37685|polyprotein|BAA03375.1|Hepatitis C virus|11103 +LLPRRGPRL +>37700|vimentin|NP_003371.1|Homo sapiens|9606 +LLQDSVDFSL +>37738|polyprotein|AAA45534.1|Hepatitis C virus (isolate Taiwan)|31645 +LLREEVSFRV +>37769|Latent membrane protein 2|Q69135|Human gammaherpesvirus 4|10376 +LLSAWILTA +>37830|polyprotein|BAB18806.1|Hepatitis C virus subtype 1b|31647 +LLSTTEWQI +>37877|cysteine proteinase cruzipain (EC 3.4.22.-) - Trypanosoma cruzi|A45629|Trypanosoma cruzi|5693 +LLTTSGVSA +>37919|envelope protein|BAF48755.1|Hepatitis B virus|10407 +LLVPFVQWFV +>37960|membrane protein|AAA45887.1|Human gammaherpesvirus 4|10376 +LLWTLVVLL +>37970|tax|AAG48731.1|Human T-lymphotropic virus 2|11909 +LLYGYPVYV +>37991|polyprotein|AAY82034.1|Hepatitis C virus genotype 1|41856 +LMALTLSPYYKRY +>38052|Glycoprotein GP85 precursor|P03231.1|Human gammaherpesvirus 4|10376 +LMIIPLINV +>38082|cysteine proteinase cruzipain (EC 3.4.22.-) - Trypanosoma cruzi|A45629|Trypanosoma cruzi|5693 +LMNNAFEWI +>38083|cysteine proteinase cruzipain (EC 3.4.22.-) - Trypanosoma cruzi|A45629|Trypanosoma cruzi|5693 +LMNNAFEWIV +>38152|L-aspartate oxidase|YP_170403.1|Francisella tularensis subsp. tularensis SCHU S4|177416 +LMWDNVGLV +>38400|polyprotein|ABG75765.1|Dengue virus 1|11053 +LPAIVREAI +>38427|BZLF1|AAA66529.1|Human gammaherpesvirus 4|10376 +LPCVLWPVL +>38446|Glycoprotein B precursor (Glycoprotein II)|P09257.1|Human alphaherpesvirus 3|10335 +LPEGMDPFAEK +>38466|nucleocapsid protein|ABF21284.1|Influenza A virus (A/Iran/1/1957(H2N2))|488233 +LPFDKPTIM +>38468|nucleoprotein|CAA24268.1|Influenza A virus (A/Puerto Rico/8/1934(H1N1))|211044 +LPFDRTTIM +>38471|nucleocapsid protein|ABC46569.1|Influenza A virus (A/Memphis/4/1980(H3N2))|383578 +LPFEKSTVM +>38472|nucleoprotein|AAV48837.1|Influenza A virus (A/Brevig Mission/1/1918(H1N1))|88776 +LPFERATIM +>38494|polyprotein|BAA03375.1|Hepatitis C virus|11103 +LPGCSFSIF +>38556|Genome polyprotein|Q00269.3|Hepatitis C virus|11103 +LPKLPGVPF +>38701|core protein|AAL31859.1|Hepatitis B virus|10407 +LPSDFFPSV +>38724|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 +LPSTLRWFFNLFQLYRGPLD +>38851|Trans-activator protein BZLF1|P03206.2|Human herpesvirus 4 strain B95-8|10377 +LQHYREVAA +>38922|6 kDa early secretory antigenic target|P0A564.2|Mycobacterium tuberculosis|1773 +LQNLARTI +>38974|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 +LQRGPQYSEHP +>39095|nonstructural protein 3|NP_722463.1|Dengue virus type 1 Hawaii|10000440 +LRGEARKTFVELMRR +>39162|gag protein|AAV53308.1|Human immunodeficiency virus 1|11676 +LRPGGKKKYKLKHIV +>39339|Nucleocapsid protein|Q89462|Sin Nombre hantavirus|37705 +LSFALPIILKALYML +>39571|polyprotein|BAD73987.1|Hepatitis C virus subtype 1b|31647 +LSPRPVSYLK +>39589|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 +LSPYYKRYIS +>39590|polyprotein|AAY82030.1|Hepatitis C virus|11103 +LSPYYKRYISW +>39591|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 +LSPYYKRYISWCLWWLQYFL +>40158|polyprotein|AAA45534.1|Hepatitis C virus|11103 +LTRVEAQLHVWVPPL +>40210|polyprotein|ABR25251.1|Hepatitis C virus (isolate H77)|63746 +LTTSQTLLF +>40247|polyprotein precursor|NP_041724.2|West Nile virus|11082 +LTYRHKVVK +>40253|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 +LVACHANCPTYRSHL +>40262|Cytochrome P450 2A7|P20853.1|Homo sapiens|9606 +LVALLACLTV +>40264|Cytochrome P450 2A6|P11509.3|Homo sapiens|9606 +LVALLVCLTV +>40286|SAG1 protein|AAO72426.1|Toxoplasma gondii RH|383379 +LVCGKDGVK +>40288|kaposin|AAC57155.1|Human gammaherpesvirus 8|37296 +LVCLLAISVVPPSGQ +>40447|Major surface antigen precursor|P12934.3|Hepatitis B virus|10407 +LVLLDYQGML +>40468|structural protein|BAA00705.1|Hepatitis C virus subtype 1a|31646 +LVMAQLLRI +>40470|Genome polyprotein|SRC279960|Hepatitis C virus|11103 +LVMAQLLRT +>40559|polyprotein|ADF97231.1|Hepatitis C virus subtype 3a|356426 +LVRLKPTL +>40624|DNA polymerase|CAA10434.1|Hepatitis B virus|10407 +LVVDFSQFSR +>40637|polyprotein|BAA03375.1|Hepatitis C virus|11103 +LVVSQLLRI +>40664|core|CAA59522.1|Hepatitis B virus|10407 +LWFHISCLTF +>40784|Genome polyprotein|P26662.3|Hepatitis C virus|11103 +LYGVWPLLL +>41082|Genome polyprotein|P26664.3|Hepatitis C virus (isolate 1)|11104 +MALTLSPY +>41085|polyprotein|ABR25251.1|Hepatitis C virus|11103 +MALYDVVSKLPLAVM +>41093|polyprotein|AGO67248.1|Dengue virus 2|11060 +MANIFRGSY +>41174|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 +MAYAQKIFKIL +>41269|kaposin|AAC57155.1|Human gammaherpesvirus 8|37296 +MDRGLTVFVAVHVPD +>41407|Envelope protein|NP_739583.2|Dengue virus 2|11060 +MENKAWLVHRQWFLD +>41482|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 +MFDSSVLCECYDAGC +>41622|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 +MGRSHFLCTFTFNSNNKEYT +>41898|polyprotein|AAF01178.1|Hepatitis C virus subtype 2a|31649 +MLAAQMFIV +>41971|putative D-ribose-binding protein|NP_301386.1|Mycobacterium leprae|1769 +MLILGLLPAILPACG +>42094|telomer length regulation protein TEL1|EDV12172.1|Saccharomyces cerevisiae|4932 +MLWGYLQYV +>42152|polyprotein|AAY82055.1|Hepatitis C virus (isolate H77)|63746 +MMMNWSPTT +>42290|protein antigen|AAA29733.1|Plasmodium falciparum|5833 +MPLETQLAI +>42295|Circumsporozoite protein precursor|P02893.1|Plasmodium falciparum|5833 +MPNDPNRNV +>42299|nonstructural protein 3|YP_001527884.1|West Nile virus|11082 +MPNGLIAQF +>42342|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 +MPVGGQSSF +>42430|Major surface antigen precursor|P03141.3|Hepatitis B virus|10407 +MQWNSTAFHQTLQDP +>42455|Probable Na(+)-translocating NADH-quinone reductase subunit A|O84639.1|Chlamydia trachomatis|813 +MRDHTITLL +>42672|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 +MSSTQIRTEIPVALL +>42737|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 +MTALEAVSLNGTRLA +>42797|6 kDa early secretory antigenic target|P0A564.2|Mycobacterium tuberculosis|1773 +MTEQQWNFAGIEAAASAIQG +>42819|polyprotein precursor|NP_041724.2|West Nile virus|11082 +MTKEEFTRY +>42897|RNA polymerase beta-subunit|AAA21416.1|Mycobacterium tuberculosis|1773 +MTYAAPLFV +>43089|Polyprotein|Q9IZA3|Hepatitis C virus subtype 2a|31649 +MYSSAEGDL +>43108|Major outer membrane porin, serovar E precursor|P17451.1|Chlamydia trachomatis|813 +NAACMALNI +>43310|polyprotein|AAW78019.1|Hepatitis C virus (isolate H77)|63746 +NASRCWVAM +>43447|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 +NDGVIFFFNPGELLPEAAGP +>43619|Genome polyprotein|P26664.3|Hepatitis C virus|11103 +NEGCGWAGW +>43621|largest ORF|AAB02128.1|Hepatitis C virus (isolate H77)|63746 +NEGCGWMGW +>43624|Genome polyprotein|P26660.3|Hepatitis C virus isolate HC-J6|11113 +NEGLGWAGW +>43627|core protein|AAX68853.1|Hepatitis C virus subtype 1b|31647 +NEGLGWTGW +>43628|polyprotein|BAA03375.1|Hepatitis C virus subtype 1b|31647 +NEGMGWAGW +>43756|Genome polyprotein|SRC279960|Hepatitis C virus subtype 2a|31649 +NETCGWAGW +>43937|polyprotein|AAF01178.1|Hepatitis C virus subtype 2a|31649 +NFTRGDRCNL +>44133|Genome polyprotein|P26664.3|Hepatitis C virus genotype 1|41856 +NHDSPDAEL +>44214|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 +NIEFFTKNSAF +>44327|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis H37Rv|83332 +NIRQAGVQY +>44649|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 +NLAMAIAKSVPVYGM +>44653|6 kDa early secretory antigenic target|P0A564.2|Mycobacterium tuberculosis|1773 +NLARTISEAGQAMASTEGNV +>44802|PE-PGRS family protein|ZP_02552202.1|Mycobacterium tuberculosis|1773 +NLLVTGFDT +>44833|polyprotein|BAA03375.1|Hepatitis C virus subtype 1a|31646 +NLPGCSFSI +>44920|tegument protein pp65|YP_002608275.1|Human betaherpesvirus 5|10359 +NLVPMVATV +>44976|Major outer membrane porin, serovar A precursor|P23732.1|Chlamydia trachomatis|813 +NMFTPYIGV +>45374|nucleocapsid protein|AEQ63625.1|Respiratory syncytial virus|12814 +NPKASLLSL +>45652|Probable ATP-dependent Clp protease ATP-binding subunit|O84288.1|Chlamydia trachomatis|813 +NRAKQVIKL +>45672|hypothetical protein CT847|NP_220368.1|Chlamydia trachomatis|813 +NRELIQQEL +>45677|Probable outer membrane protein pmpC precursor|O84419.1|Chlamydia trachomatis|813 +NRFSVAYML +>45749|glycoprotein gp35/37|AAC59622.1|Human gammaherpesvirus 8|37296 +NRVPFSATTTTTRGR +>46243|E2 protein|NP_751921.1|Hepatitis C virus (isolate H77)|63746 +NTRPPLGNWF +>46480|DNA polymerase|CAA10434.1|Hepatitis B virus|10407 +NVSIPWTHK +>46499|6 kDa early secretory antigenic target|P0A564.2|Mycobacterium tuberculosis|1773 +NVTSIHSLL +>46575|polyprotein|AAG30730.1|Dengue virus 2|11060 +NYADRKWCF +>46576|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 +NYADRRWCF +>46625|hypothetical glycine-rich protein Rv3812 - Mycobacterium tuberculosis (strain H37RV)|H70520|Mycobacterium tuberculosis|1773 +NYIPQQLAL +>46672|Periplasmic L-asparaginase II precursor|YP_169502.1|Francisella tularensis subsp. tularensis SCHU S4|177416 +NYNNLDDKF +>46713|Polyprotein|Q9IZA3|Hepatitis C virus subtype 2a|31649 +NYTIFKIRM +>46755|HCV-1|AAA45676.1|Hepatitis C virus genotype 1|41856 +PAAYAAQGYKVLVLNPSVAA +>46931|||| +PARLLLKATLCIPHV +>47005|RL2|CAB06705.1|Human alphaherpesvirus 2|10310 +PAWSRRTLL +>47017|Genome polyprotein|P26664.3|Hepatitis C virus genotype 1|41856 +PCEPEPDVAVL +>47760|EBNA-1 protein|Q777E1|Human gammaherpesvirus 4|10376 +PGTGPGNGLGEKGDT +>47854|Glycoprotein I precursor (Glycoprotein IV) (GI) (GPIV)|P09258.1|Human alphaherpesvirus 3|10335 +PHSVVNPFVK +>47946|envelope glycoprotein|AAC28452.1|Human immunodeficiency virus 1|11676 +PIPIHYCAPAGFAILKCNNK +>48321|||| +PLFGYPVYV +>48458|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 +PLPVVFPIVQGELSKQTGQQ +>48836|EBNA-1 protein|Q777E1|Human gammaherpesvirus 4|10376 +PPMVEGAAAEGDDGD +>48896|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 +PPQPEYDLELITSCS +>48915|kaposin|AAC57155.1|Human gammaherpesvirus 8|37296 +PPSGQRGPVAFRTRV +>49485|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 +PSQEPMSIYVY +>49831|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 +PVALLILCLCLVACH +>50089|Genome polyprotein|P26662.3|Hepatitis C virus|11103 +PYFVRAQGLI +>50104|polyprotein|BAA25076.1|Hepatitis C virus|11103 +PYIEQGMQL +>50124|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 +PYKRIEELL +>50130|membrane protein|AAA45887.1|Human gammaherpesvirus 4|10376 +PYLFWLAAIA +>50253|DNA polymerase|CAA10434.1|Hepatitis B virus|10407 +QAFTFSPTYK +>50292|gag protein|ACR27140.1|Human immunodeficiency virus 1|11676 +QAISPRTLNAW +>50298|EBNA3A nuclear protein|Q8AZJ8|Human gammaherpesvirus 4|10376 +QAKWRLQTL +>50586|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 +QEFFWDANDIY +>50596|polyprotein|ABG75765.1|Dengue virus 1|11053 +QEGAMHTAL +>50779|N protein|AAP13445.1|SARS coronavirus Urbani|228330 +QFKDNVILL +>50894|Genome polyprotein|P27909.2|Dengue virus type 1 Hawaii|10000440 +QGKRLEPSWASVKKDLISYG +>51089|UL123; IE1|AAR31390.1|Human betaherpesvirus 5|10359 +QIKVRVDMV +>51104|LOW MOLECULAR WEIGHT PROTEIN ANTIGEN 7 ESXH (10 kDa ANTIGEN) (CFP-7) (PROTEIN TB10.4)|CAA17363.1|Mycobacterium tuberculosis H37Rv|83332 +QIMYNYPAM +>51250|nucleocapsid protein|ABI96968.1|SARS coronavirus|227859 +QKRTATKQYNVTQAF +>51311|X protein|ABR68906.1|Hepatitis B virus|10407 +QLDPARDVL +>51342|myosin-9|NP_002464.1|Homo sapiens|9606 +QLFNHTMFI +>51346|Genome polyprotein|P29846.3|Hepatitis C virus|11103 +QLFTFSPRR +>51351|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 +QLGAFLTNV +>51388|polyprotein|AGO67248.1|Dengue virus 2|11060 +QLKGMSYSM +>51410|hypothetical protein ML1057|NP_301777.1|Mycobacterium leprae|1769 +QLLGQTADV +>51526|HCV-1|AAA45676.1|Hepatitis C virus|11103 +QLRRHIDLLV +>51528|Genome polyprotein|SRC279960|Hepatitis C virus genotype 1|41856 +QLRRIDLLV +>51532|polyprotein|AAA45534.1|Hepatitis C virus|11103 +QLSAPSLKATCTANH +>51562|polyprotein|AGO67248.1|Dengue virus 2|11060 +QLTYVVIAIL +>51604|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 +QMDYSNGLFV +>51643|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 +QMSDPAYNINISLPSYYPDQ +>51685|Nuclear antigen EBNA-3C|Q69140.1|Human gammaherpesvirus 4|10376 +QNGALAINTF +>51805|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 +QPEKGGRKPA +>51946|EBNA3C latent protein|CAD53421.1|Human gammaherpesvirus 4|10376 +QPRAPIRPI +>51947|EBNA3C latent protein|CAD53421.1|Human gammaherpesvirus 4|10376 +QPRAPIRPIPT +>52287|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 +QSALKLAIYK +>52431|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 +QSSFYSDWY +>52496|polyprotein precursor|NP_041724.2|West Nile virus|11082 +QTDNQLAVF +>52509|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 +QTFLATCINGVCWTV +>52578|liver stage antigen-1|CAA82974.1|Plasmodium falciparum|5833 +QTNFKSLLR +>52652|||| +QTTVVGGSQSHTVRGLTSLFSPGASQN +>52666|Antigen 85-B|P0C5B9.1|Mycobacterium tuberculosis|1773 +QTYKWETFL +>52746|Nucleoprotein|P03418.1|Human respiratory syncytial virus A2|11259 +QVMLRWGVL +>52760|nef protein|ACR27174.1|Human immunodeficiency virus 1|11676 +QVPLRPMTYK +>52886|pp65|AAA45994.1|Human betaherpesvirus 5|10359 +QYDPVAALF +>52888|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 +QYDPVAALFFF +>53027|nonstructural protein 3|NP_722463.1|Dengue virus 1 Singapore/S275/1990|33741 +QYSDRRWCF +>53041|phosphorylated matrix protein (pp65)|AAA45996.1|Human betaherpesvirus 5|10359 +QYTPDSTPCHR +>53077|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis|1773 +RADEEQQQAL +>53114|envelope glycoprotein|ABI16336.1|Human immunodeficiency virus 1|11676 +RAIEAQQHL +>53128|BZLF1|AAA66529.1|Human gammaherpesvirus 4|10376 +RAKFKQLL +>53129|BZLF1|AAA66529.1|Human gammaherpesvirus 4|10376 +RAKFKQLLQ +>53148|Transcription activator BRLF1|P03209.1|Human herpesvirus 4 strain B95-8|10377 +RALIKTLPRASYSSH +>53201|Fusion glycoprotein F0 precursor|P03420.1|Human respiratory syncytial virus A2|11259 +RARRELPRF +>53246|polyprotein precursor|AAF20092.2|West Nile virus|11082 +RAWNSGYEW +>53341|envelope protein|YP_001527880.1|West Nile virus NY-99|10000971 +RDFLEGVSGATWVDLVL +>53370|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 +RDKFLSAATSSTPREAPYEL +>53405|||| +RDPAKPARLLLKATL +>53437|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 +RDWAHNGL +>53476|polyprotein|AGO67248.1|Dengue virus 2|11060 +REDQWCGSL +>53541|Genome polyprotein|P26664.3|Hepatitis C virus (isolate 1)|11104 +REISVPAEIL +>53953|kaposin|AAC57155.1|Human gammaherpesvirus 8|37296 +RGPVAFRTRVATGAH +>54175|envelope glycoprotein|ACR43875.1|Human immunodeficiency virus 1|11676 +RIKQIINMW +>54176|Polyprotein|Q9J8D4|Dengue virus 2|11060 +RIKQKGIL +>54330|BZLF1|AAA66529.1|Human gammaherpesvirus 4|10376 +RKCRAKFKQLLQH +>54342|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 +RKEVNSQLSLGDPLFPELAE +>54501|nonstructural protein 2B|YP_001527883.1|West Nile virus NY-99|10000971 +RLDDDGNFQL +>54504|possible regulatory protein|NP_302009.1|Mycobacterium leprae|1769 +RLDGTTLEV +>54568|polyprotein|BAA03375.1|Hepatitis C virus|11103 +RLGVRATRK +>54587|monooxygenase family protein|YP_170175.1|Francisella tularensis subsp. tularensis SCHU S4|177416 +RLIGHISTL +>54605|HCV-1|AAA45676.1|Hepatitis C virus|11103 +RLIVFPDLGV +>54650|polyprotein|AAU89634.1|Hepatitis C virus subtype 2a|31649 +RLLLLGLLLL +>54654|trans-sialidase|XP_816729.1|Trypanosoma cruzi|5693 +RLLPSLLLLL +>54662|pX-rex-orf I {alternatively spliced}|AAB23359.1|Human T-lymphotropic virus 1|11908 +RLLSPLSPL +>54664|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 +RLLSPTTIV +>54680|Spike glycoprotein precursor|P59594.1|SARS coronavirus|227859 +RLNEVAKNL +>54686|Major outer membrane porin, serovar E precursor|P17451.1|Chlamydia trachomatis|813 +RLNMFTPYI +>54690|Nucleoprotein|P59595.1|SARS coronavirus|227859 +RLNQLESKV +>54704|hydrolase|WP_015628351.1|Mycobacterium tuberculosis|1773 +RLPLVLPAV +>54706|matrix protein 2-1|AAS22094.1|Human metapneumovirus|162145 +RLPREKLKK +>54709|protein F [Hepatitis C virus subtype 1b]|ACA50643.1|Hepatitis C virus (isolate Japanese)|11116 +RLPSGRNLV +>54728|EBNA3A nuclear protein|Q8AZJ8|Human gammaherpesvirus 4|10376 +RLRAEAQVK +>54730|envelope glycoprotein|AAB06256.1|Human immunodeficiency virus 1|11676 +RLRDLLLIVTR +>54741|gag polyprotein|BAA00992.1|Human immunodeficiency virus 1|11676 +RLRPGGKKK +>54797|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 +RLTVSGLAWTR +>54819|JK3|CAA43789.1|Hepatitis C virus|11103 +RLWHYPCTA +>54820|polyprotein precursor|BAA02756.1|Hepatitis C virus|11103 +RLWHYPCTF +>54821|E2 protein|AAM33354.1|Hepatitis C virus subtype 1a|31646 +RLWHYPCTI +>54824|polyprotein precursor|BAA01583.1|Hepatitis C virus|11103 +RLWHYPCTL +>54825|polyprotein|BAA03375.1|Hepatitis C virus|11103 +RLWHYPCTV +>54903|Genome polyprotein|P26663.3|Hepatitis C virus|11103 +RMILMTHFF +>54965|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 +RMYVGGVEHR +>55029|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 +RNLVPMVATVQ +>55102|polyprotein precursor|NP_041724.2|West Nile virus|11082 +RPAADGKTV +>55184|Nucleoprotein|P41269.1|Puumala hantavirus|11604 +RPKHLYVSM +>55226|HCV-1|AAA45676.1|Hepatitis C virus|11103 +RPLTDFDQGW +>55251|Epstein-Barr nuclear antigen 3|SRC279942|Human gammaherpesvirus 4|10376 +RPPIFIRLL +>55252|EBNA3A nuclear protein|Q8AZJ8|Human gammaherpesvirus 4|10376 +RPPIFIRRL +>55253|EBNA3A nuclear protein|Q8AZJ8|Human gammaherpesvirus 4|10376 +RPPIFIRRLH +>55295|Early antigen protein D|P03191.1|Human herpesvirus 4 strain B95-8|10377 +RPQGGSRPEFVKL +>55320|tegument protein VP22|NP_044519.1|Human alphaherpesvirus 2|10310 +RPRGEVRFL +>55336|EBNA-1|YP_401677.1|Human gammaherpesvirus 4|10376 +RPSCIGCKGTHGGTG +>55526|glycoprotein D|AAB60552.1|Human alphaherpesvirus 2|10310 +RRAQMAPKR +>55620|EBNA3C latent protein|CAD53421.1|Human gammaherpesvirus 4|10376 +RRIYDLIEL +>55683|nucleocapsid protein|ABI96968.1|SARS coronavirus|227859 +RRPQGLPNNTASWFT +>55709|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 +RRRGDSRGSLLSPRP +>55718|Probable membrane glycoprotein precursor|P03218.1|Human herpesvirus 4 strain B95-8|10377 +RRRKGWIPL +>55734|membrane protein|AAA45887.1|Human gammaherpesvirus 4|10376 +RRRWRRLTV +>55744|polyprotein precursor|NP_041724.2|West Nile virus|11082 +RRSRRSLTV +>55779|fusion protein|BAB60865.1|Measles virus|11234 +RRYPDAVYL +>55881|polyprotein precursor|NP_041724.2|West Nile virus|11082 +RSLFGGMSW +>56198|glycoprotein gp35/37|AAC59622.1|Human gammaherpesvirus 8|37296 +RTTRIRVSPVAENGR +>56247|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 +RVCEKMALY +>56310|polyprotein|AGO67248.1|Dengue virus 2|11060 +RVIDPRRCMK +>56343|structural protein|BAA00705.1|Hepatitis C virus|11103 +RVLEDGVNYA +>56344|polyprotein precursor|NP_041724.2|West Nile virus|11082 +RVLEMVEDW +>56390|Transcription activator BRLF1|P03209.1|Human herpesvirus 4 strain B95-8|10377 +RVRAYTYSK +>56502|polyprotein|BAD73994.1|Hepatitis C virus subtype 1b|31647 +RYAPACKPL +>56574|envelope glycoprotein|ABI16336.1|Human immunodeficiency virus 1|11676 +RYLKDQQLL +>56589|polyprotein precursor|NP_041724.2|West Nile virus|11082 +RYLVKTESW +>56620|Nef protein|Q9YYU8|Human immunodeficiency virus 1|11676 +RYPLTFGWCF +>56646|nucleocapsid protein|AAA43837.1|Hantaan virus 76-118|11602 +RYRTAVCGL +>56650|EBNA3A nuclear protein|Q8AZJ8|Human gammaherpesvirus 4|10376 +RYSIFFDY +>56814|DNA polymerase|CAA10434.1|Hepatitis B virus|10407 +SAICSVVRR +>56861|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 +SALKLAIYKA +>57313|Polyprotein|Q9IZA3|Hepatitis C virus|11103 +SDWAANGL +>57361|Genome polyprotein|SRC279960|Hepatitis C virus (isolate H77)|63746 +SECCTPCSGSW +>57364|Genome polyprotein|P26664.3|Hepatitis C virus|11103 +SECTTPCSGSW +>57438|gag protein|ABO73990.1|Human immunodeficiency virus 1|11676 +SEGATPQDL +>57560|BZLF1|AAA66529.1|Human gammaherpesvirus 4|10376 +SENDRLRLL +>57591|Cobalamin (vitamin B12) synthesis protein/P47K family protein|YP_169986.1|Francisella tularensis subsp. tularensis SCHU S4|177416 +SEPLPVATTF +>57628|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 +SESSFFNLI +>57703|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 +SEYPNVSVSVEDTSA +>57723|polyprotein|CAB53095.1|Hepatitis C virus|11103 +SFAIKWEYVL +>57790|Protein Tax-1|P03409.2|Human T-lymphotropic virus 1|11908 +SFHSLHLLF +>57828|Protein Tax-1|P03409.2|Human T-lymphotropic virus 1|11908 +SFLLSHGLI +>57893|polyprotein|BAA03375.1|Hepatitis C virus|11103 +SFSIFLLAL +>57894|polyprotein|BAD73987.1|Hepatitis C virus subtype 1b|31647 +SFSIFLLALL +>57986|envelope glycoprotein|AAK62756.1|West Nile virus|11082 +SGATWVDLV +>57987|envelope protein|YP_001527880.1|West Nile virus NY-99|10000971 +SGATWVDLVLEGDSCVTI +>58122|pol protein|BAA32832.1|Hepatitis B virus|10407 +SGLPRYVARL +>58249|glycoprotein gp35/37|AAC59622.1|Human gammaherpesvirus 8|37296 +SGSYSSGEPSRTTRI +>58446|pX-rex-orf I|SRC240587|Human T-lymphotropic virus 1|11908 +SIAINPQLL +>58463|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 +SICPSQEPMSIYVYALPLKM +>58721|VP1|BAB68863.1|JC polyomavirus|10632 +SITEVECFL +>58740|Major surface antigen precursor|P03142.4|Hepatitis B virus|10407 +SIVSPFIPLL +>59020|Genome polyprotein|P29846.3|Hepatitis C virus (isolate Taiwan)|31645 +SLASLFTQGA +>59021|polyprotein|AAN40570.2|Hepatitis C virus|11103 +SLASLFTSGA +>59044|Major outer membrane porin, serovar E precursor|P17451.1|Chlamydia trachomatis|813 +SLDQSVVEL +>59088|polyprotein precursor|NP_041724.2|West Nile virus|11082 +SLFGGMSWI +>59089|nonstructural protein 4B|YP_001527886.1|West Nile virus NY-99|10000971 +SLFGQRIEV +>59090|nonstructural protein 4B|YP_001527886.1|West Nile virus NY-99|10000971 +SLFGQRIEVKENFSMGEF +>59141|Circumsporozoite protein precursor|P08677.2|Plasmodium vivax strain Belem|31273 +SLGLVILLVL +>59153|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 +SLHSYSPGEINRVAA +>59154|polyprotein|AAP55688.1|Hepatitis C virus subtype 2a|31649 +SLHTGFLASL +>59182|attachment glycoprotein|ABQ58821.1|Human metapneumovirus|162145 +SLILIGITTL +>59240|HCV-1|AAA45676.1|Hepatitis C virus genotype 1|41856 +SLLAPGAKQNV +>59336|polyprotein|AAA45534.1|Hepatitis C virus genotype 1|41856 +SLMAFTAAV +>59459|Trans-sialidase|SRC7915|Trypanosoma cruzi|5693 +SLSHYFTLV +>59521|polyprotein|ACB87121.1|Hepatitis C virus subtype 1a|31646 +SLTPPHSAK +>59524|nonstructural protein 4B|YP_001527886.1|West Nile virus NY-99|10000971 +SLTSINVQA +>59551|Glycoprotein GP85 precursor|P03231.1|Human gammaherpesvirus 4|10376 +SLVIVTTFV +>59561|polyprotein precursor|NP_041724.2|West Nile virus|11082 +SLVNGVVRL +>59569|Genome polyprotein|P26662.3|Hepatitis C virus (isolate Japanese)|11116 +SLVSWLSQGP +>59585|polymerase|AAD16253.1|Hepatitis B virus|10407 +SLYADSPSV +>59594|Phosphate transport system permease protein PstA 1|SRC280197|Mycobacterium tuberculosis|1773 +SLYFGGICV +>59612|gag protein|ABI20203.1|Human immunodeficiency virus 1|11676 +SLYNTIAVL +>59613|Gag polyprotein|P03347.3|Human immunodeficiency virus 1|11676 +SLYNTVATL +>59627|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 +SMAGSSAMI +>59709|polyprotein|BAD73987.1|Hepatitis C virus subtype 1b|31647 +SMLTDPSHI +>59722|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 +SMNATLVQA +>59765|Genome polyprotein|SRC279960|Hepatitis C virus|11103 +SMVGNMAKV +>59766|Genome polyprotein|P27958.3|Hepatitis C virus (isolate H)|11108 +SMVGNWAKV +>59767|polyprotein|BAB18806.1|Hepatitis C virus subtype 1a|31646 +SMVGNWAKVL +>59786|Large envelope protein|P03138.3|Hepatitis B virus ayw/France/Tiollais/1979|490133 +SMYPSCCCTK +>59787|Hemagglutinin glycoprotein|P08362.1|Measles virus strain Edmonston|11235 +SMYRVFEVGV +>59975|pol protein|ACJ76655.1|Human immunodeficiency virus 1|11676 +SPAIFQSSM +>60009|Genome polyprotein|P26664.3|Hepatitis C virus genotype 1|41856 +SPDAELIEANL +>60031|SAG1 protein|AAO72426.1|Toxoplasma gondii RH|383379 +SPEKHHCTV +>60059|Genome polyprotein|P27958.3|Hepatitis C virus genotype 1|41856 +SPGEINRVAA +>60092|nucleocapsid protein|ABK96997.1|Human metapneumovirus|162145 +SPKAGLLSL +>60104|polyprotein|AGW21594.1|Dengue virus 1|11053 +SPKRLSAAI +>60238|Gag polyprotein|P03347.3|Human immunodeficiency virus 1|11676 +SPRTLNAWV +>60867|nucleoprotein|CAZ65591.1|Influenza A virus|11320 +SRYWAIRTR +>60931|latent membrane protein 2|AAB59844.1|Human gammaherpesvirus 4|10376 +SSCSSCPLSKI +>61077|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 +SSHSGSFQI +>61622|polyprotein|BAA03375.1|Hepatitis C virus|11103 +STGLIHLHQ +>61741|Core protein|Q9QAC5|Hepatitis B virus|10407 +STLPETTVV +>61745|C protein|CAB41699.1|Hepatitis B virus|10407 +STLPETTVVRR +>61787|HCV-1|AAA45676.1|Hepatitis C virus|11103 +STNPKPQK +>61788|HCV-1|AAA45676.1|Hepatitis C virus|11103 +STNPKPQKK +>61790|polyprotein|BAB18806.1|Hepatitis C virus|11103 +STNPKPQRK +>61861|Nucleoprotein|P03418.1|Human respiratory syncytial virus A2|11259 +STRGGSRVEGIFAG +>62004|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 +STWVLVGGVLAALAA +>62052|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 +SVASSSASQLSA +>62127|cysteine proteinase cruzipain (EC 3.4.22.-) - Trypanosoma cruzi|A45629|Trypanosoma cruzi|5693 +SVFRENLFL +>62139|envelope glycoprotein|AAK62756.1|West Nile virus|11082 +SVGGVFTSV +>62184|nonstructural protein 3|NP_722463.1|Dengue virus type 1 Hawaii|10000440 +SVKKDLISYGGGWRF +>62244|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 +SVMKRRIEEIC +>62305|EBNA3A nuclear protein|Q8AZJ8|Human gammaherpesvirus 4|10376 +SVRDRLARL +>62355|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 +SVTEQSEFYFPRAPLNSNAM +>62367|Genome polyprotein|SRC279960|Hepatitis C virus|11103 +SVTSFFTQGA +>62477|HBsAg protein|ABF71024.1|Hepatitis B virus|10407 +SWLSLLVPF +>62504|HBsAg protein|ABF71024.1|Hepatitis B virus|10407 +SWWTSLNFL +>62564|polyprotein precursor|AAF20092.2|West Nile virus|11082 +SYHDRRWCF +>62616|Chain A, Dengue Virus 4 Ns3 Helicase In Complex With Ssrna|2JLU_A|Dengue virus 4 Thailand/0348/1991|408688 +SYKDREWCF +>62713|polyprotein|AAP55688.1|Hepatitis C virus subtype 2a|31649 +SYSWTGALI +>62731|polyprotein|BAD73987.1|Hepatitis C virus subtype 1b|31647 +SYTWTGALI +>62797|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis|1773 +TAAQAAVVRF +>62799|10 kDa culture filtrate antigen EsxB|NP_218391.1|Mycobacterium tuberculosis H37Rv|83332 +TAAQAAVVRFQEAAN +>62900|viral protein 2|CAG70336.1|Human parvovirus B19|10798 +TAKSRVHPL +>62903|Genome polyprotein|P27909.2|Dengue virus type 1 Hawaii|10000440 +TAKWLWGFLSRNKKPRICTR +>62977|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 +TARHTPVNSW +>63010|6 kDa early secretory antigenic target|P0A564.2|Mycobacterium tuberculosis|1773 +TATELNNALQNLARTISEAG +>63285|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 +TEADVQQWL +>63286|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 +TEADVQQWLTW +>63508|gag protein|AAN03145.1|Human immunodeficiency virus 1|11676 +TERQANFL +>63582|polyprotein precursor|NP_041724.2|West Nile virus|11082 +TEVMTAVGL +>63784|Genome polyprotein|P26663.3|Hepatitis C virus|11103 +TGAPVTYSTY +>63963|HCV-1|AAA45676.1|Hepatitis C virus|11103 +TGSPITYSTY +>64286|polyprotein|AAB70696.1|Dengue virus type 1 Hawaii|10000440 +TIENTTANISLTAIA +>64312|M protein, serotype 5 precursor|P02977.2|Streptococcus pyogenes serotype M5|301449 +TIGTLKKILDETVKDKIA +>64320|Protein E6|P03126.1|Human papillomavirus type 16|333760 +TIHDIILECV +>64404|Genome polyprotein|P26664.3|Hepatitis C virus genotype 1|41856 +TINYTIFK +>64405|polyprotein|ACB87121.1|Hepatitis C virus|11103 +TINYTIFKI +>64412|PE_PGRS 33|AAU10330.1|Mycobacterium tuberculosis|1773 +TIPEALAAV +>64489|polyprotein|BAA03375.1|Hepatitis C virus|11103 +TITTGSPITYS +>64710|Membrane glycoprotein|Q692E0|SARS coronavirus TJF|284672 +TLACFVLAAV +>64727|polyprotein precursor|NP_041724.2|West Nile virus|11082 +TLARGFPFV +>64763|Early antigen protein D|P03191.1|Human herpesvirus 4 strain B95-8|10377 +TLDYKPLSV +>64769|kinetoplastid membrane protein KMP-11|EAN87014.1|Trypanosoma cruzi|5693 +TLEEFSAKL +>64794|Glycoprotein GP85 precursor|P03231.1|Human gammaherpesvirus 4|10376 +TLFIGSHVV +>64810|polyprotein|BAB18806.1|Hepatitis C virus|11103 +TLGFGAYMSK +>64818|E7|AAD33253.1|Human papillomavirus type 16|333760 +TLGIVCPI +>64819|E7 protein|ABL96585.1|Human papillomavirus type 16|333760 +TLGIVCPIC +>64821|Protein Tax-1|P03409.2|Human T-lymphotropic virus 1|11908 +TLGQHLPTL +>64830|E7 protein|ABL96585.1|Human papillomavirus type 16|333760 +TLHEYMLDL +>64948|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 +TLLYATVEV +>64967|Circumsporozoite protein precursor|P08677.2|Plasmodium vivax strain Belem|31273 +TLNDLETDV +>65090|polyprotein|BAB18810.1|Hepatitis C virus (isolate H77)|63746 +TLTHPITK +>65092|Genome polyprotein|P26664.3|Hepatitis C virus genotype 1|41856 +TLTHPVTK +>65118|SAG1 protein|AAO72426.1|Toxoplasma gondii RH|383379 +TLVCGKDGV +>65148|DNA polymerase|CAA10434.1|Hepatitis B virus|10407 +TLWKAGILYK +>65494|polyprotein|AAY82030.1|Hepatitis C virus|11103 +TPAETTVRL +>65497|HCV-1|AAA45676.1|Hepatitis C virus genotype 1|41856 +TPAETTVRLRAYMNTPGLPV +>65509|DNA polymerase|CAA10434.1|Hepatitis B virus|10407 +TPARVTGGVF +>65549|polyprotein|AGO67248.1|Dengue virus 2|11060 +TPEGIIPSM +>65550|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 +TPEGIIPSMFEPERE +>65567|polyprotein|AJE59927.1|Japanese encephalitis virus|11072 +TPFGQQRVF +>65589|nucleocapsid protein|AAA43837.1|Hantaan virus 76-118|11602 +TPGRYRTAV +>65654|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 +TPLRDWAHNGLRDLA +>65703|gag protein|CAB00235.1|Human immunodeficiency virus 1|11676 +TPQDLNTM +>65748|pp65|AAA45994.1|Human betaherpesvirus 5|10359 +TPRVTGGGAM +>65749|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 +TPRVTGGGAMA +>65810|sporozoite surface protein 2|NP_705260.1|Plasmodium falciparum 3D7|36329 +TPYAGEPAPF +>65817|envelope glycoprotein|AAL59843.1|Human immunodeficiency virus 1|11676 +TQACPKVSFEPIPIHYCAPA +>65929|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 +TQRTSKTLKVLTPPIT +>65965|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 +TQVLVPRSAIDSMLA +>66084|M protein, serotype 5 precursor|P02977.2|Streptococcus pyogenes serotype M5|301449 +TRQELANKQQESKENEKAL +>66106|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 +TRTIASPKGPVIQMY +>66195|Nucleoprotein|P41269.1|Puumala hantavirus|11604 +TSFEDINGIRRPKHL +>66405|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 +TSRSACQRQKKVTFDRLQVL +>66798|glycoprotein gp35/37|AAC59622.1|Human gammaherpesvirus 8|37296 +TTRGRDAHYNAEIRT +>67087|polyprotein|AAK32686.1|Hepatitis C virus|11103 +TVNFTIFKV +>67210|NS3 protein|NP_739587.1|Dengue virus 2 Thailand/NGS-C/1944|11065 +TVWFVPSIK +>67349|Latent membrane protein 2|Q69135|Human gammaherpesvirus 4|10376 +TYGPVFMCL +>67362|polyprotein|AGW21594.1|Dengue virus 1|11053 +TYGWNLVKL +>67382|Type IV pili associated protein|YP_170126.1|Francisella tularensis subsp. tularensis SCHU S4|177416 +TYLGIDLGF +>67385|HER2 receptor|AAA75493.1|Homo sapiens|9606 +TYLPTNASL +>67471|Genome polyprotein|Q99IB8.3|Hepatitis C virus JFH-1|356411 +TYSTYGKFL +>67503|Genome polyprotein|P26662.3|Hepatitis C virus|11103 +TYVYDHLTPL +>67596|Genome polyprotein|P26664.3|Hepatitis C virus (isolate 1)|11104 +VAGALVAFK +>67764|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 +VATDALMTGYTGDFD +>68194|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 +VEGEVQIVSTAAQTF +>68229|EBNA3B (EBNA4A) latent protein|CAA24858.1|Human gammaherpesvirus 4|10376 +VEITPYKPTW +>68443|polyprotein|AAF01178.1|Hepatitis C virus subtype 2a|31649 +VFDITKWLL +>68461|polyprotein|ACZ60108.1|Hepatitis C virus|11103 +VFFNILGGWV +>68521|Genome polyprotein|P26662.3|Hepatitis C virus|11103 +VFLVSQLFTF +>68549|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 +VFPTKDVALRH +>68562|unnamed protein product|BAA14233.1|Hepatitis C virus subtype 1b|31647 +VFSDMETKL +>68563|polyprotein|CAB53095.1|Hepatitis C virus subtype 1b|31647 +VFSDMETKV +>68581|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 +VFTGLTHIDAHFLSQTKQSG +>68601|polyprotein|AAA45534.1|Hepatitis C virus|11103 +VFVLNNTRPPLGNWF +>68605|Genome polyprotein|P26662.3|Hepatitis C virus|11103 +VFWAKHMWNF +>68694|Genome polyprotein|P26664.3|Hepatitis C virus (isolate 1)|11104 +VGIYLLPNR +>68908|nonstructural protein|AAC53959.1|Hepatitis C virus (isolate H77)|63746 +VIAPAVQTNW +>69076|Genome polyprotein|P26664.3|Hepatitis C virus|11103 +VIPTSGDVVV +>69349|Genome polyprotein|P29846.3|Hepatitis C virus (isolate Taiwan)|31645 +VLAALAAYCL +>69387|fusion protein|ABQ58820.1|Human metapneumovirus|162145 +VLATAVREL +>69394|pol|AP_000202.1|Human adenovirus 5|28285 +VLAWTRAFV +>69398|X protein|AAP06597.1|Hepatitis B virus|10407 +VLCLRPVGA +>69404|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 +VLCPKNMIIKP +>69435|Genome polyprotein|SRC279960|Hepatitis C virus (isolate H77)|63746 +VLDSFKTWL +>69452|UL123; IE1|AAR31666.1|Human betaherpesvirus 5|10359 +VLEETSVML +>69474|core protein|BAF42671.1|Hepatitis B virus|10407 +VLEYLVSFGV +>69500|X protein|BAG70907.1|Hepatitis B virus|10407 +VLGGCRHKL +>69524|X protein|ACH95876.1|Hepatitis B virus|10407 +VLHKRTLGL +>69558|EBNA-1 protein|Q777E1|Human gammaherpesvirus 4|10376 +VLKDAIKDL +>69581|Major surface antigen precursor|P12934.3|Hepatitis B virus|10407 +VLLDYQGML +>69646|Alanine dehydrogenase|P30234.2|Mycobacterium tuberculosis|1773 +VLMGGVPGVE +>69649|myosin-9|NP_002464.1|Homo sapiens|9606 +VLMIKALEL +>69661|polyprotein precursor|NP_041724.2|West Nile virus|11082 +VLNETTNWL +>69671|polyprotein|AGO67248.1|Dengue virus 2|11060 +VLNPYMPSV +>69679|polyprotein|BAD73987.1|Hepatitis C virus subtype 1b|31647 +VLPCSFTTL +>69714|Large envelope protein|SRC279965|Hepatitis B virus|10407 +VLQAGFFIL +>69715|envelope protein|BAF48755.1|Hepatitis B virus|10407 +VLQAGFFLL +>69719|proteinase 3|AAH96184.1|Homo sapiens|9606 +VLQELNVTV +>69731|Major outer envelope glycoprotein gp350|Q66537|Human gammaherpesvirus 4|10376 +VLQWASLAV +>69750|polyprotein|AAC03058.1|Hepatitis C virus genotype 3|356114 +VLSDFKSWL +>69751|polyprotein|BAB18806.1|Hepatitis C virus genotype 1|41856 +VLSDFKTWL +>69753|polyprotein|AAK49500.1|Hepatitis C virus genotype 3|356114 +VLSDFRTWL +>69754|Lipoprotein lpqH precursor|P46733.1|Mycobacterium avium|1764 +VLSDGNPPQV +>69797|polyprotein|BAA09073.1|Hepatitis C virus subtype 1b|31647 +VLTDFKTWL +>69798|Lipoprotein lpqH precursor|P0A5J0.1|Mycobacterium tuberculosis|1773 +VLTDGNPPEV +>69799|envelope glycoprotein|BAE96221.1|Human immunodeficiency virus 1|11676 +VLTDPNPQEV +>69907|envelope|BAK20487.1|Human T-lymphotropic virus 1|11908 +VLYSPNVSV +>69913|cysteine proteinase cruzipain (EC 3.4.22.-) - Trypanosoma cruzi|A45629|Trypanosoma cruzi|5693 +VMACLVPAA +>69980|polyprotein|AAF01178.1|Hepatitis C virus subtype 2a|31649 +VMLAAQMFIV +>69991|Nucleoprotein|P03418.1|Human respiratory syncytial virus A2|11259 +VMLRWGVLAKSVKN +>69996|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 +VMMSCSSEA +>70017|membrane protein|AAA45887.1|Human gammaherpesvirus 4|10376 +VMSNTLLSAW +>70365|Truncated Nef protein|P04601.4|Human immunodeficiency virus 1|11676 +VPLRPMTYK +>70491|envelope glycoprotein|AAC28452.1|Human immunodeficiency virus 1|11676 +VPTDPNPPEV +>70516|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 +VPYKRIEEL +>70634|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 +VQQWLTWCN +>70687|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis|1773 +VQYSRADEEQQQALSSQMGF +>70789|Nucleoprotein|P41269.1|Puumala hantavirus|11604 +VRNIMSPVM +>70932|EBNA-3B nuclear protein|CAD53420.1|Human gammaherpesvirus 4|10376 +VSFIEFVGW +>71265|Circumsporozoite protein precursor|P02893.1|Plasmodium falciparum|5833 +VTCGNGIQVR +>71266|Circumsporozoite protein precursor|P02893.1|Plasmodium falciparum|5833 +VTCGNGIQVRIKPGSANKPK +>71290|DNA processivity factor|AAO73452.1|Human betaherpesvirus 5|10359 +VTEHDTLLY +>71409|cysteine proteinase cruzipain (EC 3.4.22.-) - Trypanosoma cruzi|A45629|Trypanosoma cruzi|5693 +VTLPTGQCL +>71412|polyprotein [Hepatitis C virus subtype 1a]|ABV46251.2|Hepatitis C virus subtype 1a|31646 +VTLTHPITK +>71616|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 +VVCMYLYQLSPPITW +>71631|polymerase|ACT90735.1|Hepatitis B virus|10407 +VVDFSQFSR +>71650|polyprotein precursor|AAP22088.1|West Nile virus|11082 +VVEKQSGLY +>71657|polyprotein|AAF01178.1|Hepatitis C virus subtype 2a|31649 +VVFDITKWLL +>71663|Spike glycoprotein precursor|P59594.1|SARS coronavirus|227859 +VVFLHVTYV +>71734|polyprotein|AAF01178.1|Hepatitis C virus subtype 2a|31649 +VVLDSLDPMV +>71756|cysteine proteinase cruzipain (EC 3.4.22.-) - Trypanosoma cruzi|A45629|Trypanosoma cruzi|5693 +VVMACLVPAA +>71847|core protein|AAL31859.1|Hepatitis B virus|10407 +VVSYVNTNMGLKFRQL +>71988|Protein E6|P03126.1|Human papillomavirus type 16|333760 +VYDFAFRDL +>72006|polyprotein|BAD73994.1|Hepatitis C virus subtype 1b|31647 +VYEAADMIM +>72038|Polyprotein|Q9IZA3|Hepatitis C virus subtype 2a|31649 +VYHGAGNKTL +>72039|polyprotein|CAB53095.1|Hepatitis C virus subtype 1b|31647 +VYHGAGSKTL +>72165|Genome polyprotein|P26662.3|Hepatitis C virus|11103 +VYSTTSRSASL +>72233|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 +WAIKWEYVVLLFLLL +>72261|Gag polyprotein|P03347.3|Human immunodeficiency virus 1|11676 +WASRELERF +>72269|glycoprotein gp35/37|AAC59622.1|Human gammaherpesvirus 8|37296 +WAVGLLLGLVLILYL +>72301|envelope protein|YP_001527880.1|West Nile virus NY-99|10000971 +WDFGSVGGVFTSVGKAVH +>72322|polyprotein|AAA86907.1|Hepatitis C virus|11103 +WDMMMNWSPTAALVV +>72563|polyprotein|AAB70696.1|Dengue virus type 1 Hawaii|10000440 +WHYDEDNPYKTWAYHGSYEV +>72564|JK3|CAA43789.1|Hepatitis C virus subtype 1b|31647 +WHYPCTANF +>72566|polyprotein|BAD73987.1|Hepatitis C virus subtype 1b|31647 +WHYPCTVNF +>72621|cysteine proteinase cruzipain (EC 3.4.22.-) - Trypanosoma cruzi|A45629|Trypanosoma cruzi|5693 +WIIKNSWTA +>72721|hypothetical protein FTT0869|YP_169869.1|Francisella tularensis subsp. tularensis SCHU S4|177416 +WLGNHGFEV +>72722|polyprotein|AAF01178.1|Hepatitis C virus subtype 2a|31649 +WLGNIIQYA +>72790|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 +WLSDCGEAL +>72794|Large envelope protein|P03138.3|Hepatitis B virus|10407 +WLSLLVPFV +>72842|polyprotein|ABG67747.1|West Nile virus|11082 +WMDSTKATRY +>72928|Genome polyprotein|P26662.3|Hepatitis C virus (isolate Japanese)|11116 +WPAPPGARSM +>72929|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 +WPAPQGSRSLTPCTC +>72979|Major outer membrane porin, serovar A precursor|P23732.1|Chlamydia trachomatis|813 +WQASLALSY +>72985|LOW MOLECULAR WEIGHT PROTEIN ANTIGEN 7 ESXH (10 kDa ANTIGEN) (CFP-7) (PROTEIN TB10.4)|CAA17363.1|Mycobacterium tuberculosis H37Rv|83332 +WQGDTGITY +>73059|kaposin|AAC57155.1|Human gammaherpesvirus 8|37296 +WRWRLGAIPPLVCLL +>73177|protein F [Hepatitis C virus subtype 1b]|ACA50643.1|Hepatitis C virus (isolate Japanese)|11116 +WVCARLGRL +>73296|hemK protein homolog|YP_169235.1|Francisella tularensis subsp. tularensis SCHU S4|177416 +WYTNLDTDKF +>73306|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 +WYYQSGLSI +>73862|EBNA-1 protein|Q777E1|Human gammaherpesvirus 4|10376 +YFMVFLQTHIFAEVL +>74020|Genome polyprotein|P26664.3|Hepatitis C virus|11103 +YGKAIPLEVI +>74180|reverse transcriptase|CAJ26826.1|Hepatitis B virus|10407 +YIDDVVLGA +>74288|Protein E7|P36831.1|Human papillomavirus type 52|10618 +YILDLQPETT +>74305|Nonstructural protein NS5|NP_739590.2|Dengue virus 2 Thailand/NGS-C/1944|11065 +YILRDVSKK +>74386|HCV-1|AAA45676.1|Hepatitis C virus|11103 +YISWCLWW +>74387|Genome polyprotein|P26664.3|Hepatitis C virus (isolate 1)|11104 +YISWCLWWL +>74407|polyprotein|AAU89634.1|Hepatitis C virus subtype 2a|31649 +YIVRWEWVV +>74545|TcP2beta|CAA52943.1|Trypanosoma cruzi|5693 +YLAAYALVGL +>74558|polyprotein|AGW21594.1|Dengue virus 1|11053 +YLAGAGLAF +>74590|glycoprotein gp35/37|AAC59622.1|Human gammaherpesvirus 8|37296 +YLCVPRCRRKKPYIV +>74605|Circumsporozoite protein precursor|P08677.2|Plasmodium vivax strain Belem|31273 +YLDKVRATV +>74635|matrix protein|AEQ63649.1|Respiratory syncytial virus|12814 +YLEKESIYY +>74768|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 +YLLDGLRAQ +>74774|LMP1 protein (Epstein-Barr virus, putative LYDMA gene)|Q777A4|Human gammaherpesvirus 4|10376 +YLLEMLWRL +>74797|polyprotein|BAA09073.1|Hepatitis C virus subtype 1b|31647 +YLLPRRGPR +>74798|polyprotein|BAA03375.1|Hepatitis C virus|11103 +YLLPRRGPRL +>74800|Genome polyprotein|SRC279960|Hepatitis C virus subtype 2b|31650 +YLLPSRGPKL +>74886|latent membrane protein 1|AAS99606.1|Human gammaherpesvirus 4|10376 +YLQQNWWTL +>74961|polyprotein|ABU97067.1|Hepatitis C virus subtype 1b|31647 +YLVAYQATV +>74988|polyprotein|BAB18806.1|Hepatitis C virus|11103 +YLVTRHADV +>75024|Protein Tax-1|P03409.2|Human T-lymphotropic virus 1|11908 +YLYQLSPPI +>75040|Protein P|P03159.1|Hepatitis B virus|10407 +YMDDVVLGA +>75074|Protein E7|P03129.1|Human papillomavirus type 16|333760 +YMLDLQPET +>75075|E7 protein|ABL96585.1|Human papillomavirus type 16|333760 +YMLDLQPETT +>75356|EBNA3A nuclear protein|Q8AZJ8|Human gammaherpesvirus 4|10376 +YPLHEQHGM +>75376|Genome polyprotein|P26664.3|Hepatitis C virus|11103 +YPPKPCGI +>75408|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 +YPSAAERKHRHLPVADAVIH +>75435|largest ORF|AAB02128.1|Hepatitis C virus|11103 +YPWPLYGNEGCGWMGWLLSP +>75436|Polyprotein|P90247|Hepatitis C virus|11103 +YPWPLYGNEGLGWAGWLLSP +>75438|polyprotein|AAF65962.1|Hepatitis C virus|11103 +YPWPLYGNEGMGWAGWLLSP +>75448|polyprotein|BAB18806.1|Hepatitis C virus|11103 +YPYRLWHY +>75495|6 kDa early secretory antigenic target|P0A564.2|Mycobacterium tuberculosis|1773 +YQGVQQKWDATATELNNALQ +>75614|polyprotein precursor|NP_041724.2|West Nile virus|11082 +YRHKVVKVM +>75632|predicted Efflux Protein|NP_220159.1|Chlamydia trachomatis|813 +YRLLLTRVL +>75636|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 +YRLWHYPCTI +>75673|Early antigen protein D|P03191.1|Human herpesvirus 4 strain B95-8|10377 +YRSGIIAVV +>75674|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 +YRSHLGFWQEGWSGQ +>75718|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 +YSEHPTFTSQY +>76121|polyprotein precursor|NP_041724.2|West Nile virus|11082 +YTMDGEYRL +>76245|reverse transcriptase|CAJ26474.1|Hepatitis B virus|10407 +YVDDVVLGA +>76277|Genome polyprotein|SRC279960|Hepatitis C virus|11103 +YVGDLCGCV +>76333|BRLF1|ABB89247.1|Human gammaherpesvirus 4|10376 +YVLDHLIVV +>76334|Protein E7|P17387.1|Human papillomavirus type 31|10585 +YVLDLQPEAT +>76370|core protein|BAF42671.1|Hepatitis B virus|10407 +YVNVNMGLK +>76529|polyprotein|ABU97067.1|Hepatitis C virus subtype 1b|31647 +YYKVFLARL +>76532|outer membrane protein|YP_170495.1|Francisella tularensis subsp. tularensis SCHU S4|177416 +YYLDRGYLDF +>76591|Genome polyprotein|P26664.3|Hepatitis C virus|11103 +YYRGLDVSVI +>76621|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 +YYTSAFVFPTK +>78346|BARF1 protein|CAD53469.1|Human gammaherpesvirus 4|10376 +AFLGERVTL +>78382|BARF1 protein|CAD53469.1|Human gammaherpesvirus 4|10376 +FLGERVTLT +>78432|BARF1 protein|CAD53469.1|Human gammaherpesvirus 4|10376 +KLGPGEEQV +>78501|BARF1 protein|CAD53469.1|Human gammaherpesvirus 4|10376 +RFIAQLLLL +>78534|BARF1 protein|CAD53469.1|Human gammaherpesvirus 4|10376 +TLTSYWRRV +>79180|tax protein|AAF37566.1|Human T-lymphotropic virus 1|11908 +DCLPTTLFQPVRAPV +>79208|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 +EYTNIPISLLFNEKEA +>79294|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 +LLFGYPVYVFGDCVQ +>79300|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 +LSFPDPGLRPQNLYT +>79308|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 +MEPTLGQHLPTLSFPD +>79337|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 +PPITWPLLPHVIFCH +>79351|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 +QNLYTLWGGSVVCMYLY +>79390|Protein Tax-1|P0C213.1|Human T-cell lymphotropic virus type 1 (african isolate)|39015 +SFHNLHLLFEEYTNI +>79454|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 +VIFCHPGQLGAFLTN +>79506|E1 protein|BAA19893.1|Rubella virus|11041 +AFGHSDAACWGFPTDTVMSV +>79601|envelope protein|BAF48755.1|Hepatitis B virus|10407 +LLCLIFLLVL +>79628|E1 protein|BAA19893.1|Rubella virus|11041 +PTDVSCEGLGAWVPTAPCARI +>88377|IE62|AAP32859.1|Human alphaherpesvirus 3|10335 +SAPLPSNRV +>88849|IE62|AAP32859.1|Human alphaherpesvirus 3|10335 +SLPRSRTPI +>92301|ATP-dependent Clp protease proteolytic subunit|NP_216976.1|Mycobacterium tuberculosis H37Rv|83332 +AIYDTMQYV +>92817|secreted antigen 85-B fbpB (85B) (antigen 85 complex B) (Mycolyl transferase 85B) (fibronectin-binding protein B) (extracellular alpha-antigen)|NP_216402.1|Mycobacterium tuberculosis H37Rv|83332 +GLAGGAATA +>93224|core protein|AAL31859.1|Hepatitis B virus|10407 +LEDPASRDLVVSYV +>93270|hypothetical protein|NP_218356.1|Mycobacterium tuberculosis H37Rv|83332 +LLYDGSFAV +>93431|pre-C/C protein|ABY54138.1|Hepatitis B virus|10407 +MQLFHLCLIISCTCPTVQAS +>93536|core protein|AAL31859.1|Hepatitis B virus|10407 +PAYRPPNAPIL +>95234|latent membrane protein 1|AAS99606.1|Human gammaherpesvirus 4|10376 +ALLVLYSFA +>95261|LAMP|AAK72632.1|Human gammaherpesvirus 8|37296 +ATVKTGNIKL +>95262|LAMP|AAK72632.1|Human gammaherpesvirus 8|37296 +ATVKTGNIKLVSSVS +>95264|Genome polyprotein|O92532.3|Hepatitis C virus genotype 6|42182 +AVNGVLWTV +>95265|polyprotein|ABL63009.1|Hepatitis C virus genotype 4|33745 +AVNGVMWTV +>95278|polyprotein|BAC67110.1|Hepatitis C virus|11103 +CINGVCWSI +>95279|polyprotein|BAG31965.1|Hepatitis C virus|11103 +CINGVCWSV +>95280|Genome polyprotein|O39928.3|Hepatitis C virus genotype 5|33746 +CINGVMWTL +>95281|polyprotein|ACE82433.1|Hepatitis C virus genotype 1|41856 +CISGVCWTV +>95297|polyprotein|BAA09072.1|Hepatitis C virus genotype 1|41856 +CTNGVCWTV +>95298|Genome polyprotein|Q913V3.1|Hepatitis C virus (isolate 1)|11104 +CVNGACWTV +>95854|Genome polyprotein|O39927.3|Hepatitis C virus genotype 6|42182 +SINGVMWTV +>95890|polyprotein|ABE98152.1|Hepatitis C virus genotype 6|42182 +SVNGVMWTV +>95908|Genome polyprotein|O92529.3|Hepatitis C virus genotype 6|42182 +TINGVLWTV +>95937|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 +TVGGVMWTV +>95940|polyprotein|BAA32666.1|Hepatitis C virus genotype 6|42182 +TVNGVLWTV +>96120|polyprotein|BAB18806.1|Hepatitis C virus (isolate H77)|63746 +ATLGFGAYMSKA +>96123|Genome polyprotein|P26664.3|Hepatitis C virus (isolate H77)|63746 +AVFGPLWIL +>96156|polyprotein|ABR25251.1|Hepatitis C virus (isolate H77)|63746 +CVTQTVDFSLDPTFTIETTTL +>96257|Genome polyprotein|SRC279960|Hepatitis C virus|11103 +EPEPDVAW +>96346|Genome polyprotein|SRC279960|Hepatitis C virus (isolate H77)|63746 +GVDPNVRTGVRT +>96358|polyprotein|BAB18806.1|Hepatitis C virus (isolate H77)|63746 +HAVGIFRAA +>96365|polyprotein|AAB66324.1|Hepatitis C virus (isolate H77)|63746 +HPTLVFDITKL +>96366|polyprotein|ABR25251.1|Hepatitis C virus|11103 +HRFAPPCKPLLR +>96369|polyprotein|BAB18810.1|Hepatitis C virus|11103 +HVVGIFRAA +>96547|Genome polyprotein|Q913D4.3|Hepatitis C virus (isolate H77)|63746 +LFFNILGGWV +>96601|polyprotein|ABR25251.1|Hepatitis C virus (isolate H77)|63746 +LPYIEQGMML +>96633|polyprotein|ABR25251.1|Hepatitis C virus (isolate H77)|63746 +LYGMWPLLL +>96827|Genome polyprotein|SRC279960|Hepatitis C virus (isolate H77)|63746 +RLADFAQGW +>96836|polyprotein|ABR25251.1|Hepatitis C virus (isolate H77)|63746 +RQVGDFHYV +>96897|polyprotein|ABR25251.1|Hepatitis C virus (isolate H77)|63746 +SLLRHHNLVYSTTSRSA +>96898|Genome polyprotein|SRC279960|Hepatitis C virus|11103 +SLLRNHNLVYSTTSRSA +>96957|polyprotein|ABR25251.1|Hepatitis C virus (isolate H77)|63746 +THFFSVLIARDQ +>96958|Genome polyprotein|SRC279960|Hepatitis C virus|11103 +THLFSVLMARDQ +>97044|Genome polyprotein|SRC279960|Hepatitis C virus (isolate H77)|63746 +VITPVVQTNW +>97093|polyprotein|AAB66324.1|Hepatitis C virus (isolate H77)|63746 +VTRHADVIPV +>97111|polyprotein|ABR25251.1|Hepatitis C virus (isolate H77)|63746 +YDIIICDECHSTDATSIL +>97226|Genome polyprotein|P26664.3|Hepatitis C virus|11103 +CHSTDATSIL +>97227|polyprotein|CAB41951.1|Hepatitis C virus|11103 +CHSTDSTSIL +>97338|Genome polyprotein|P26664.3|Hepatitis C virus|11103 +GIDPNIRTGV +>97365|polyprotein|CAA03854.1|Hepatitis C virus|11103 +GTDPNIRTGV +>97373|polyprotein|ACE82359.1|Hepatitis C virus subtype 1a|31646 +GVDPNIRTGV +>97399|polyprotein|ACZ60108.1|Hepatitis C virus subtype 3a|356426 +IPFYGKAIPI +>97400|Genome polyprotein|P26664.3|Hepatitis C virus|11103 +IPFYGKAIPL +>97467|nucleocapsid protein|ACP44251.1|Influenza A virus (A/Fujian/411/2002(H3N2))|293090 +LPFEKSTIM +>97558|Genome polyprotein|SRC279960|Hepatitis C virus|11103 +PPHPNIEEVA +>97630|polyprotein|AAF65953.1|Hepatitis C virus|11103 +SALGLNAVAY +>97641|polyprotein|CAA03854.1|Hepatitis C virus|11103 +SGLGLNAVAY +>97719|Genome polyprotein|P26664.3|Hepatitis C virus|11103 +VALGINAVAY +>97720|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 +VALGVNAVAY +>97750|Genome polyprotein|P26664.3|Hepatitis C virus|11103 +VPHPNIEEVA +>97876|trans-sialidase, putative|EAN81705.1|Trypanosoma cruzi|5693 +ALSSSLGNV +>97905|trans-sialidase, putative|EAN88532.1|Trypanosoma cruzi|5693 +AVAEAQCKK +>97961|trans-sialidase, putative|EAN81042.1|Trypanosoma cruzi|5693 +DVAASSLLY +>98039|Trans-sialidase|SRC7915|Trypanosoma cruzi|5693 +FLSHNFTLVF +>98040|trans-sialidase, putative|EAN80725.1|Trypanosoma cruzi|5693 +FLYNRPLNS +>98042|trans-sialidase, putative|EAN80840.1|Trypanosoma cruzi|5693 +FQGAWAEWPV +>98044|trans-sialidase, putative|EAN80840.1|Trypanosoma cruzi|5693 +FTLVATVSI +>98046|trans-sialidase, putative|EAN82835.1|Trypanosoma cruzi|5693 +FTSAVLLLL +>98051|trans-sialidase, putative|EAN82716.1|Trypanosoma cruzi|5693 +FVSPSLVSA +>98085|trans-sialidase, putative|EAN82636.1|Trypanosoma cruzi|5693 +GVIAAFAEGH +>98100|trans-sialidase, putative|EAN81657.1|Trypanosoma cruzi|5693 +HLFYSAVLL +>98101|trans-sialidase, putative|EAN80725.1|Trypanosoma cruzi|5693 +HNFTLVASV +>98126|trans-sialidase, putative|EAN81650.1|Trypanosoma cruzi|5693 +ITATIEGRK +>98138|trans-sialidase, putative|EAN81657.1|Trypanosoma cruzi|5693 +IYMLVGKYS +>98223|trans-sialidase, putative|EAN80725.1|Trypanosoma cruzi|5693 +LLLGLWGFA +>98224|trans-sialidase, putative|EAN82076.1|Trypanosoma cruzi|5693 +LLLLVVMMCC +>98242|trans-sialidase, putative|EAN81042.1|Trypanosoma cruzi|5693 +LVTLPVYSK +>98244|trans-sialidase, putative|EAN80840.1|Trypanosoma cruzi|5693 +LWLTDNTHI +>98253|trans-sialidase, putative|EAN81042.1|Trypanosoma cruzi|5693 +MLSRVAAVK +>98254|trans-sialidase, putative|EAN81042.1|Trypanosoma cruzi|5693 +MLVTLPVYS +>98308|trans-sialidase, putative|EAN80840.1|Trypanosoma cruzi|5693 +NVMLVTLPV +>98431|trans-sialidase, putative|EAN82235.1|Trypanosoma cruzi|5693 +RVLLLLLLGL +>98459|trans-sialidase, putative|EAN80725.1|Trypanosoma cruzi|5693 +SIPTAGLVAV +>98466|Trans-sialidase|SRC7915|Trypanosoma cruzi|5693 +SLSHYFTLVF +>98540|trans-sialidase, putative|EAN88532.1|Trypanosoma cruzi|5693 +TSAVLLLLVV +>98560|trans-sialidase, putative|EAN80918.1|Trypanosoma cruzi|5693 +VALMLQGNK +>98603|trans-sialidase, putative|EAN82716.1|Trypanosoma cruzi|5693 +VTDNNRSFY +>98640|trans-sialidase, putative|EAN80840.1|Trypanosoma cruzi|5693 +YNFTLVATV +>98757|G1 and G2 surface glycoprotein precursor|AAG22532.1|Andes hantavirus|46607 +ELGLISIEAASDIKL +>100124|polyprotein|BAD73977.1|Hepatitis C virus subtype 1b|31647 +HSRKKCDEL +>101380|BNLF2a|YP_401721.1|Human herpesvirus 4 type 1|36352 +VLFGLLCLL +>101645|Protein Vpr|P69728.1|Human immunodeficiency virus 1|11676 +FPRIWLHGL +>101673|gag protein|ABO73990.1|Human immunodeficiency virus 1|11676 +GHQAAMQML +>101721|nef|AAA02639.1|Human immunodeficiency virus 1|11676 +HTQGYFPDWQ +>101766|nef protein|ACQ77160.1|Human immunodeficiency virus 1|11676 +KAAVDLSHFL +>101812|Pol polyprotein|Q9YLQ7|Human immunodeficiency virus 1|11676 +KQNPDIVIY +>101813|Pol polyprotein|Q9YLQ7|Human immunodeficiency virus 1|11676 +KQNPDIVIYQY +>101821|vif protein|ACC96167.1|Human immunodeficiency virus 1|11676 +KTKPPLPSVKK +>101967|pol protein|ACJ76655.1|Human immunodeficiency virus 1|11676 +PIQKETWETW +>101990|gag polyprotein|BAH60623.1|Human immunodeficiency virus 1|11676 +QASQEVKNW +>102032|nef protein|AAA87476.1|Human immunodeficiency virus 1|11676 +RPMTYKAAV +>102037|Gag polyprotein|P15832.3|Human immunodeficiency virus 2|11709 +RRWIQLGLQK +>102046|nef protein|ACQ72180.1|Human immunodeficiency virus 1|11676 +RYPLTFGW +>102104|Gag-Pol polyprotein|P03366.3|Human immunodeficiency virus 1|11676 +TAFTIPSI +>102149|Gag polyprotein|P03347.3|Human immunodeficiency virus 1|11676 +TPQDLNTML +>102150|nef protein|ACR27119.1|Human immunodeficiency virus 1|11676 +TPQVPLRPM +>102151|nef protein|ACR27128.1|Human immunodeficiency virus 1|11676 +TQGYFPDWQNY +>102205|envelope glycoprotein|ACR43875.1|Human immunodeficiency virus 1|11676 +VPVWKEATTTL +>102235|nef protein|ACR27119.1|Human immunodeficiency virus 1|11676 +YFPDWQNYT +>102254|nef protein|ACQ72180.1|Human immunodeficiency virus 1|11676 +YPLTFGWCY +>102368|E2 protein|NP_751921.1|Hepatitis C virus subtype 1a|31646 +DRSGAPTYSWGANDT +>102376|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 +DVVSKLPLAVMGSSY +>102611|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 +LHQNIVDVQYLYGVG +>102636|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 +LVGGVLAALAAYCLS +>102819|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 +SQHLPYIEQGMMLAE +>102922|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 +VTVSHPNIEEVALST +>103020|polyprotein|ABR25251.1|Hepatitis C virus|11103 +AFWAKHMWNF +>103322|polyprotein|BAB18806.1|Hepatitis C virus|11103 +KRLHQWINEDCSTPCSGSWL +>103389|unnamed protein product [Hepatitis C virus]|BAA14035.1|Hepatitis C virus|11103 +LTHPITKFVMACMSADLEVV +>103392|polyprotein|BAB18806.1|Hepatitis C virus|11103 +LTRDPTTPL +>103563|polyprotein|BAB18806.1|Hepatitis C virus|11103 +RPDYNPPLL +>103654|polyprotein|BAB18806.1|Hepatitis C virus|11103 +TIMAKNEVF +>104114|Glutamate decarboxylase 2|Q05329.1|Homo sapiens|9606 +MIARFKMFPEVKEKG +>104419|polyprotein|BAA00792.1|Hepatitis C virus|11103 +ALYDITQKL +>105333|Latent membrane protein 2|P0C729.1|Human gammaherpesvirus 4|10376 +MGSLEMVPM +>107720|polyprotein|AAF65953.1|Hepatitis C virus|11103 +AAKLSALGLN +>107721|polyprotein|AAD56189.1|Hepatitis C virus|11103 +AAKLSALGVN +>107722|Genome polyprotein|P26664.3|Hepatitis C virus|11103 +AAKLVALGIN +>107727|Genome polyprotein|P26664.3|Hepatitis C virus|11103 +AETAGARLVV +>107732|polyprotein|AAF65964.1|Hepatitis C virus|11103 +AHGTDPNIRT +>107733|Genome polyprotein|P26664.3|Hepatitis C virus|11103 +ALGINAVAYY +>107734|polyprotein|AAF65953.1|Hepatitis C virus|11103 +ALGLNAVAYY +>107735|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 +ALGVNAVAYY +>107738|polyprotein|CAB41951.1|Hepatitis C virus|11103 +ALSNTGEIPF +>107748|polyprotein|AAF65950.1|Hepatitis C virus|11103 +ATDALMTGFT +>107749|Genome polyprotein|P26664.3|Hepatitis C virus|11103 +ATDALMTGYT +>107752|Genome polyprotein|P26664.3|Hepatitis C virus|11103 +ATLGFGAYMS +>107754|Genome polyprotein|P26664.3|Hepatitis C virus|11103 +ATPPGSVTVP +>107760|polyprotein|AAD56189.1|Hepatitis C virus|11103 +AYDIIMCDEC +>107762|Genome polyprotein|P26664.3|Hepatitis C virus|11103 +AYYRGLDVSV +>107777|Genome polyprotein|P26664.3|Hepatitis C virus|11103 +DATSILGIGT +>107780|Genome polyprotein|P26664.3|Hepatitis C virus|11103 +DECHSTDATS +>107781|polyprotein|AAF65953.1|Hepatitis C virus|11103 +DECHSTDSTT +>107782|Genome polyprotein|SRC279960|Hepatitis C virus|11103 +DELAAKLSLG +>107790|polyprotein|AAD56189.1|Hepatitis C virus|11103 +DIIMCDECHS +>107801|polyprotein|AAF65953.1|Hepatitis C virus|11103 +DSTTILGIGT +>107802|Genome polyprotein|P26664.3|Hepatitis C virus|11103 +DVSVIPTSGD +>107818|Genome polyprotein|P26664.3|Hepatitis C virus|11103 +EIPFYGKAIP +>107821|polyprotein|AAF65953.1|Hepatitis C virus|11103 +ELAAKLSALG +>107822|Genome polyprotein|P26664.3|Hepatitis C virus|11103 +ELAAKLVALG +>107840|polyprotein|AAF65950.1|Hepatitis C virus|11103 +FTGDFDSVID +>107862|polyprotein|AAA86907.1|Hepatitis C virus|11103 +GLGINAVAYY +>107863|polyprotein|AAF65950.1|Hepatitis C virus|11103 +GLGLNAVAYY +>107872|Genome polyprotein|P26664.3|Hepatitis C virus|11103 +GRHLIFCHSK +>107873|Genome polyprotein|P26664.3|Hepatitis C virus|11103 +GSPITYSTYG +>107877|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 +GVNAVAYYRG +>107888|Genome polyprotein|P26664.3|Hepatitis C virus|11103 +HPNIEEVALS +>107894|polyprotein|CAB41951.1|Hepatitis C virus|11103 +HSTDSTSILG +>107901|Genome polyprotein|P26664.3|Hepatitis C virus|11103 +ICDECHSTDA +>107905|Genome polyprotein|P26664.3|Hepatitis C virus|11103 +IIICDECHST +>107925|polyprotein|AAF65964.1|Hepatitis C virus|11103 +KAHGTDPNIR +>107945|polyprotein|BAA09073.1|Hepatitis C virus|11103 +KLSALGVNAV +>107984|polyprotein|AAF65953.1|Hepatitis C virus|11103 +LAAKLSALGL +>107985|Genome polyprotein|P26664.3|Hepatitis C virus|11103 +LADGGCSGGA +>108001|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 +LGVNAVAYYR +>108016|polyprotein|AAF65953.1|Hepatitis C virus|11103 +LSALGLNAVA +>108017|polyprotein|BAA09073.1|Hepatitis C virus|11103 +LSALGVNAVA +>108018|polyprotein|CAB41951.1|Hepatitis C virus|11103 +LSNTGEIPFY +>108020|Genome polyprotein|P26664.3|Hepatitis C virus|11103 +LSTTGEIPFY +>108067|Genome polyprotein|P26664.3|Hepatitis C virus|11103 +PHPNIEEVAL +>108079|Genome polyprotein|P26664.3|Hepatitis C virus|11103 +QAETAGARLV +>108100|Genome polyprotein|P26664.3|Hepatitis C virus|11103 +RLVVLATATP +>108127|Genome polyprotein|P26664.3|Hepatitis C virus|11103 +SILGIGTVLD +>108130|Genome polyprotein|P26664.3|Hepatitis C virus|11103 +SKAHGIDPNI +>108139|polyprotein|CAB41951.1|Hepatitis C virus|11103 +SNTGEIPFYG +>108147|Genome polyprotein|P26664.3|Hepatitis C virus|11103 +STDATSILGI +>108148|polyprotein|AAF65953.1|Hepatitis C virus|11103 +STDSTTILGI +>108149|Genome polyprotein|P26664.3|Hepatitis C virus|11103 +STTGEIPFYG +>108153|polyprotein|AAF65950.1|Hepatitis C virus|11103 +TDALMTGFTG +>108154|Genome polyprotein|P26664.3|Hepatitis C virus|11103 +TDALMTGYTG +>108158|polyprotein|AAF65953.1|Hepatitis C virus|11103 +TDSTTILGIG +>108163|polyprotein|CAB41951.1|Hepatitis C virus|11103 +TLSFGAYMSK +>108169|Genome polyprotein|P26664.3|Hepatitis C virus|11103 +TSILGIGTVL +>108171|polyprotein|AAF65953.1|Hepatitis C virus|11103 +TTILGIGTVL +>108175|Genome polyprotein|P26664.3|Hepatitis C virus|11103 +TYGKFLADGG +>108180|polyprotein|AAF65950.1|Hepatitis C virus|11103 +VATDALMTGF +>108181|Genome polyprotein|P26664.3|Hepatitis C virus|11103 +VATDALMTGY +>108218|Genome polyprotein|P26664.3|Hepatitis C virus|11103 +YDIIICDECH +>108225|polyprotein|ABR25251.1|Hepatitis C virus|11103 +YGKAIPLEAI +>108226|polyprotein|AAF65953.1|Hepatitis C virus|11103 +YGTDPNIRTG +>108229|Genome polyprotein|P26664.3|Hepatitis C virus|11103 +YMSKAHGIDP +>108230|polyprotein|AAF65953.1|Hepatitis C virus|11103 +YMSKAYGTDP +>108232|Genome polyprotein|P26664.3|Hepatitis C virus|11103 +YSTYGKFLAD +>108277|IE62|AAP32859.1|Human alphaherpesvirus 3|10335 +ALWALPHAA +>108687|Genome polyprotein|Q81495.3|Hepatitis C virus|11103 +VVSDFKTWL +>108770|E2 protein|ACS92695.1|Human papillomavirus type 16|333760 +ALQAIELQL +>108957|hypothetical protein|NP_216006.1|Mycobacterium tuberculosis|1773 +FLLGLLFFV +>108965|Prolipoprotein diacylglyceryl transferase|O06131.1|Mycobacterium tuberculosis|1773 +FLYELIWNV +>109331|L1|ABP99807.1|Human papillomavirus type 18|333761 +IHSMNSSIL +>109332|L1 protein|ACG75893.1|Human papillomavirus type 16|333760 +IHSMNSTIL +>109984|E2 protein|ACS92695.1|Human papillomavirus type 16|333760 +TLQDVSLEV +>110018|polyprotein|AGO67248.1|Dengue virus 2|11060 +VAFLRFLTI +>110125|E2 protein|ACS92695.1|Human papillomavirus type 16|333760 +YICEEASVTV +>110184|E7|AAD33253.1|Human papillomavirus type 16|333760 +AGQAEPDRAHYNIVTFCCKCDSTLRLCVQSTHVDI +>110195|E7 protein|ABL96585.1|Human papillomavirus type 16|333760 +CCKCDSTL +>110205|Protein E6|P03126.1|Human papillomavirus type 16|333760 +DKKQRFHNIRGRWTGRCMSCCRSSRTRRETQL +>110215|Protein E6|P03126.1|Human papillomavirus type 16|333760 +EKQRHLDKKQRFHNIRGRWTGRCMS +>110225|Protein E7|P06788.2|Human papillomavirus type 18|333761 +FQQLFLNTL +>110227|Protein E6|P03126.1|Human papillomavirus type 16|333760 +FRDLCIVYRDGNPYAVCDKCLKFYSKISEYRHY +>110282|Protein E6|P03126.1|Human papillomavirus type 16|333760 +HDIILECVYCKQQLLRREVYDFAFR +>110285|Protein E6|P03126.1|Human papillomavirus type 16|333760 +HNIRGRWTGR +>110306|Protein E6|P03126.1|Human papillomavirus type 16|333760 +KLPQLCTELQTTIHDIILECVYCKQQLLRREV +>110323|Protein E7|P04020.1|Human papillomavirus type 11|10580 +LLLGTLNIV +>110335|E7|AAD33253.1|Human papillomavirus type 16|333760 +MHGDTPTLHEYMLDLQPETTDLYCYEQLNDSS +>110338|Protein E6|P03126.1|Human papillomavirus type 16|333760 +MHQKRTAMFQDPQERPRKLPQLCTELQTTIHDI +>110373|Protein E6|P03126.1|Human papillomavirus type 16|333760 +PRKLPQLCTELQTTIHDIILECVYC +>110394|Protein E6|P03126.1|Human papillomavirus type 16|333760 +RCINCQKPLCPEEKQRHLDKKQRFHNIRGRWT +>110399|Protein E6|P03126.1|Human papillomavirus type 16|333760 +RGRWTGRCMSCCRSSRTRRETQL +>110401|Protein E6|P03126.1|Human papillomavirus type 16|333760 +RREVYDFAFRDLCIVYRDGNPYAVC +>110431|E7|AAD33253.1|Human papillomavirus type 16|333760 +TDLYCYEQLNDSSEEEDEIDGPAGQAEPDRAHYNIV +>110439|Replication protein E1|P03114.2|Human papillomavirus type 16|333760 +TLLQQYCLYL +>110467|Protein E6|P03126.1|Human papillomavirus type 16|333760 +YRDGNPYAVCDKCLKFYSKISEYRH +>110575|E6 protein|ACS92692.1|Human papillomavirus type 16|333760 +FAFRDLCIVY +>110624|Protein E6|P03126.1|Human papillomavirus type 16|333760 +HDIILECV +>110720|Protein E6|P03126.1|Human papillomavirus type 16|333760 +TIHDIILEC +>110744|E5 protein|AAD24036.1|Human papillomavirus type 16|333760 +YIIFVYIPL +>110829|Protein E6|P03126.1|Human papillomavirus type 16|333760 +EKQRHLDKKQRFHNI +>110846|E6 protein|CAB45108.1|Human papillomavirus type 16|333760 +EYRHYCYSL +>110917|X protein|AAP06597.1|Hepatitis B virus|10407 +KLVCSPAPC +>110940|Protein E7|P03129.1|Human papillomavirus type 16|333760 +MHGDTPTLHEYMLDL +>110982|E6 protein|CAB45108.1|Human papillomavirus type 16|333760 +QYNKPLCDLL +>111055|E6 protein|CAB45108.1|Human papillomavirus type 16|333760 +VYDFAFQDL +>111251|Protein E6|P03126.1|Human papillomavirus type 16|333760 +ELQTTIHDIILECVY +>111404|Protein E7|P03129.1|Human papillomavirus type 16|333760 +HVDIRTLEDLLMGTL +>111407|polyprotein|BAA00792.1|Hepatitis C virus|11103 +HYPCTVNYTI +>111448|polyprotein precursor|BAA02756.1|Hepatitis C virus|11103 +KGGRKPARLIVFPDL +>111479|Protein E7|P06788.2|Human papillomavirus type 18|333761 +LFLNTLSFV +>111604|L1|ABP99807.1|Human papillomavirus type 18|333761 +NVFPIFLQM +>111641|polyprotein|ABV46292.1|Hepatitis C virus|11103 +PQRKTKRNTNR +>111816|polyprotein|BAA09072.1|Hepatitis C virus|11103 +TAYSQQTRGLLG +>111860|polyprotein|BAA00792.1|Hepatitis C virus|11103 +TVNYTIFKI +>111938|Protein E6|P03126.1|Human papillomavirus type 16|333760 +VYDFAFRDLCIVYRD +>112359|Non-structural protein 2a|Q80872.1|Human coronavirus OC43|31631 +TMLDIQPED +>112503|E6 protein|ACV53993.1|Human papillomavirus type 35|10587 +FACYDLCIVY +>112504|Protein E6|P21735.2|Human papillomavirus type 45|10593 +FAFKDLCIVY +>112505|E6|CAA63882.1|Human papillomavirus type 73|51033 +FAFSDLCIVY +>112506|Protein E6|P24835.1|Human papillomavirus type 39|10588 +FAFSDLYVVY +>112519|Protein E6|P26555.1|Human papillomavirus type 58|10598 +FVFADLRIVY +>112697|Protein E6|P26554.1|Human papillomavirus type 51|10595 +VAFTEIKIVY +>113122|Protein E6|P03126.1|Human papillomavirus type 16|333760 +QERPRKLPQL +>113154|Protein E6|P03126.1|Human papillomavirus type 16|333760 +RWTGRCMSCC +>113177|Protein E6|P03126.1|Human papillomavirus type 16|333760 +SSRTRRETQL +>115656|DNA polymerase processivity factor BMRF1|SRC280248|Human gammaherpesvirus 4|10376 +TLDTKPLSV +>116123|nucleocapsid protein|ABP49342.1|Influenza A virus (A/California/10/1978(H1N1))|425557 +LPFDKSTVM +>116127|Nucleoprotein|P15682.1|Influenza A virus (A/Wilson-Smith/1933(H1N1))|381518 +LPFDRPTIM +>116136|nucleocapsid protein|ACS34671.1|Influenza A virus (A/Auckland/1/2009(H1N1))|642794 +LPFERATVM +>116781|Nucleoprotein|P05133.1|Hantaan virus 76-118|11602 +LRKKSSFYQSYLRRT +>116835|Nucleoprotein|P05133.1|Hantaan virus 76-118|11602 +SPSSIWVFAGAPDRC +>119822|110 kd polyprotein precursor|CAA28880.1|Rubella virus|11041 +EACVTSWLWSEGEGAVFYRVDLHFINLGT +>120093|unnamed protein product|CAA33016.1|Rubella virus|11041 +MDFWCVEHDRPPPATPTSLTT +>120111|Glutamate decarboxylase 1|Q99259.1|Homo sapiens|9606 +NMFTYEIAPVFVLME +>120127|unnamed protein product|CAA33016.1|Rubella virus|11041 +PFLGHDGHHGGTLRVGQHHRNASDV +>120187|E1 protein|BAA19893.1|Rubella virus|11041 +RVKFHTETRTVWQLSVAGVSC +>124973|Esat-6 like protein esxJ (Esat-6 like protein 2)|NP_215554.1|Mycobacterium tuberculosis H37Rv|83332 +AFRNIVNML +>126028|ATP-dependent helicase|NP_217813.1|Mycobacterium tuberculosis H37Rv|83332 +FMYEGDTPL +>126481|gag polyprotein p17 region|BAA83653.1|Human immunodeficiency virus 1|11676 +KSLFNTIATLY +>126482|gag protein|AAY98604.1|Human immunodeficiency virus 1|11676 +KSLFNTIAVL +>126483|gag protein|AAY98604.1|Human immunodeficiency virus 1|11676 +KSLFNTIAVLY +>126484|gag protein|AAW03034.1|Human immunodeficiency virus 1|11676 +KSLFNTVATL +>126485|gag protein|AAW03034.1|Human immunodeficiency virus 1|11676 +KSLFNTVATLY +>126486|gag protein|ADK33372.1|Human immunodeficiency virus 1|11676 +KSLFNTVAVL +>126487|gag protein|ADK33372.1|Human immunodeficiency virus 1|11676 +KSLFNTVAVLY +>126488|gag protein|AAV53168.1|Human immunodeficiency virus 1|11676 +KSLYNTIATLY +>126489|gag protein|ABI20203.1|Human immunodeficiency virus 1|11676 +KSLYNTIAVLY +>126490|Gag protein|Q1KW74|Human immunodeficiency virus 1|11676 +KSLYNTVATL +>126491|gag protein|AAV53216.1|Human immunodeficiency virus 1|11676 +KSLYNTVATLY +>126492|gag protein|BAB88077.1|Human immunodeficiency virus 1|11676 +KSLYNTVAVLY +>126993|gag polyprotein|BAB19174.1|Human immunodeficiency virus 1|11676 +RSLFNTIATLY +>126994|gag-pol polyprotein|BAC02551.1|Human immunodeficiency virus 1|11676 +RSLFNTIAVLY +>126995|gag polyprotein|BAB19171.1|Human immunodeficiency virus 1|11676 +RSLFNTVATL +>126996|Gag protein|Q9YYH6|Human immunodeficiency virus 1|11676 +RSLFNTVATLY +>126997|gag protein|BAC45024.1|Human immunodeficiency virus 1|11676 +RSLFNTVAVLY +>126999|gag polyprotein|BAB88540.1|Human immunodeficiency virus 1|11676 +RSLYNTIATLY +>127000|gag-pol fusion polyprotein precursor|CAY83124.1|Human immunodeficiency virus 1|11676 +RSLYNTIAVLY +>127001|gag polyprotein|BAA00992.1|Human immunodeficiency virus 1|11676 +RSLYNTVATL +>127002|gag protein|AAV53342.1|Human immunodeficiency virus 1|11676 +RSLYNTVATLY +>127003|gag polyprotein|BAB88551.1|Human immunodeficiency virus 1|11676 +RSLYNTVAVL +>127004|gag polyprotein|BAB88551.1|Human immunodeficiency virus 1|11676 +RSLYNTVAVLY +>127082|gag-pol polyprotein|BAC02551.1|Human immunodeficiency virus 1|11676 +SLFNTIAVLY +>127083|Gag protein|Q9YYH6|Human immunodeficiency virus 1|11676 +SLFNTVATLY +>127246|p24 protein|CAD36203.1|Human immunodeficiency virus 1|11676 +TSTLQEQIGW +>127611|6 kDa early secretory antigenic target|P0A564.2|Mycobacterium tuberculosis|1773 +AYQGVQQKW +>127792|6 kDa early secretory antigenic target|P0A564.2|Mycobacterium tuberculosis|1773 +QWNFAGIEAA +>130902|nucleocapsid protein|NP_604471.1|Andes hantavirus|46607 +IPIILKALY +>130911|G1 and G2 surface glycoprotein precursor|AAG22532.1|Andes hantavirus|46607 +IYTFTSLFSLMPDVA +>130953|G1 and G2 surface glycoprotein precursor|AAG22532.1|Andes hantavirus|46607 +LMPDVAHSL +>131070|Gag protein|Q9IN85|HIV-1 M:A|505184 +SLFNTVATL +>131096|G1 and G2 surface glycoprotein precursor|AAG22532.1|Andes hantavirus|46607 +TAHGVGEIPM +>131132|G1 and G2 surface glycoprotein precursor|AAG22532.1|Andes hantavirus|46607 +VIGQCIYTFTSLFSL +>131311|interferon-inducible peptide precursor|AAC50160.1|Homo sapiens|9606 +SLMSWSAIL +>133501|polyprotein|ABG75765.1|Dengue virus 1|11053 +AIVREAIKR +>133619|putative surface protein|AAN52495.1|Leptospira interrogans serovar Pomona|44276 +KLIVTPAAL +>133645|cell surface protein|NP_302626.1|Mycobacterium leprae|1769 +MLDHAGNMSACAGAL +>133650|cell surface protein|NP_302626.1|Mycobacterium leprae|1769 +MTQIMYNYPAMLDHA +>133702|polyprotein|ABG75765.1|Dengue virus 1|11053 +SRNSTHEMY +>133716|polyprotein|ABG75765.1|Dengue virus 1|11053 +TLYAVATTI +>134497|M protein|SRC280368|Streptococcus pyogenes|1314 +QRAAKEALDKYELENH +>135263|hemagglutinin|ACX31970.1|Influenza A virus (A/Bar-headed Goose/Qinghai/61/05(H5N1))|336238 +RLYQNPTTYI +>136348|Genome polyprotein|SRC279960|Hepatitis C virus|11103 +HAVGIFKAAV +>136349|Genome polyprotein|SRC279960|Hepatitis C virus|11103 +HAVGIFQAAV +>136350|polyprotein|BAB18806.1|Hepatitis C virus|11103 +HAVGIFRAAV +>136351|Genome polyprotein|SRC279960|Hepatitis C virus|11103 +HAVGIFRTAV +>136826|polyprotein|AFP27208.1|Dengue virus 4|11070 +CYSQVNPTTL +>136837|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 +FLLALLSCLTV +>136865|tegument protein|CAB06735.1|Human alphaherpesvirus 2|10310 +PMRARPRGEVRFLHY +>136890|polyprotein|AGO67248.1|Dengue virus 2|11060 +TPPGSRDPF +>137437|Esat-6 like protein esxJ (Esat-6 like protein 2)|NP_215554.1|Mycobacterium tuberculosis H37Rv|83332 +QTVEDEARRMW +>137609|E7 protein|ACT36476.1|Human papillomavirus type 58|10598 +ATEVRTLQQ +>137611|L1|ACX32376.1|Human papillomavirus type 58|10598 +AVPDDLYIK +>137614|E7 protein|ADP92425.1|Human papillomavirus type 58|10598 +CTIVCPSCA +>137656|E6 protein|ACT36477.1|Human papillomavirus type 58|10598 +ILIRCIICQ +>137657|E6 protein|ACT36477.1|Human papillomavirus type 58|10598 +KCLNEILIR +>137659|E6 protein|ACT36477.1|Human papillomavirus type 58|10598 +KVCLRLLSK +>137660|L1|ACL12325.1|Human papillomavirus type 58|10598 +KYTFWEVNL +>137661|E7 protein|ACT36476.1|Human papillomavirus type 58|10598 +LCINSTATE +>137685|L1|ACX32376.1|Human papillomavirus type 58|10598 +RVRLPDPNK +>137702|late protein|CAA52590.1|Human papillomavirus type 52|10618 +TSESQLFNK +>137724|L1|ACX32376.1|Human papillomavirus type 58|10598 +YTFWEVNLK +>137726|late protein|CAA52590.1|Human papillomavirus type 52|10618 +YYYAGSSRL +>139406|polyprotein|ACT37184.1|Hepatitis C virus|11103 +YLLPRPGPRL +>139746|Dense granule protein 3|B6KEU8.2|Toxoplasma gondii|5811 +FLVPFVVFL +>139747|granule antigen protein GRA6|XP_002371939.1|Toxoplasma gondii ME49|508771 +FMGVLVNSL +>139947|granule antigen protein GRA6|XP_002371939.1|Toxoplasma gondii ME49|508771 +VVFVVFMGV +>140541|hypothetical protein|NP_218210.1|Mycobacterium tuberculosis H37Rv|83332 +ALDEGLLPV +>140542|MCE-family protein MCE4B|NP_218015.1|Mycobacterium tuberculosis H37Rv|83332 +ALLGGLRPV +>140543|trehalose-6-phosphate phosphatase OtsB1|YP_177855.1|Mycobacterium tuberculosis H37Rv|83332 +AMAGSIDLL +>140544|ORF|AAA45606.1|Hepatitis C virus|11103 +ATDALMSGF +>140561|metal cation transporter P-type ATPase A CtpF|NP_216513.1|Mycobacterium tuberculosis H37Rv|83332 +GMFANRWII +>140564|esterase lipoprotein LpqC|NP_217815.1|Mycobacterium tuberculosis H37Rv|83332 +HLDDVGFLV +>140597|MCE-family protein MCE4A|YP_177977.1|Mycobacterium tuberculosis H37Rv|83332 +SLIDLLHKI +>140599|MCE-family lipoprotein LprL|NP_215107.1|Mycobacterium tuberculosis H37Rv|83332 +SLRNWIATL +>140600|glutamine synthetase GLNA1 (glutamine synthase) (GS-I)|NP_216736.1|Mycobacterium tuberculosis H37Rv|83332 +SLWKDGAPL +>140615|amino acid decarboxylase|YP_177889.1|Mycobacterium tuberculosis H37Rv|83332 +WLYPGAQNL +>140616|membrane-associated phospholipase C|NP_216866.1|Mycobacterium tuberculosis H37Rv|83332 +YLLADTFTV +>140649|ESAT-6-like protein esxH|P0A568.2|Mycobacterium tuberculosis|1773 +AMEDLVRAY +>140650|ESAT-6-like protein esxH|P0A568.2|Mycobacterium tuberculosis|1773 +AMLGHAGDM +>140651|granule antigen protein GRA6|XP_002371939.1|Toxoplasma gondii ME49|508771 +AMLTAFFLR +>140652|LOW MOLECULAR WEIGHT PROTEIN ANTIGEN 7 ESXH (10 kDa ANTIGEN) (CFP-7) (PROTEIN TB10.4)|CAA17363.1|Mycobacterium tuberculosis H37Rv|83332 +AMMARDTAE +>140654|ESAT-6-like protein esxH|P0A568.2|Mycobacterium tuberculosis|1773 +ANTMAMMAR +>140686|ESAT-6-like protein esxH|P0A568.2|Mycobacterium tuberculosis|1773 +HAMSSTHEA +>140697|major surface antigen p30|EEB01065.1|Toxoplasma gondii ME49|508771 +KSFKDILPK +>140706|LOW MOLECULAR WEIGHT PROTEIN ANTIGEN 7 ESXH (10 kDa ANTIGEN) (CFP-7) (PROTEIN TB10.4)|CAA17363.1|Mycobacterium tuberculosis H37Rv|83332 +LVRAYHAMS +>140708|LOW MOLECULAR WEIGHT PROTEIN ANTIGEN 7 ESXH (10 kDa ANTIGEN) (CFP-7) (PROTEIN TB10.4)|CAA17363.1|Mycobacterium tuberculosis H37Rv|83332 +MAMMARDTA +>140711|ESAT-6-like protein esxH|P0A568.2|Mycobacterium tuberculosis|1773 +MLGHAGDMA +>140712|LOW MOLECULAR WEIGHT PROTEIN ANTIGEN 7 ESXH (10 kDa ANTIGEN) (CFP-7) (PROTEIN TB10.4)|CAA17363.1|Mycobacterium tuberculosis H37Rv|83332 +MMARDTAEA +>140717|low molecular weight protein antigen 7|NP_214802.1|Mycobacterium tuberculosis|1773 +MYNYPAMLG +>140727|LOW MOLECULAR WEIGHT PROTEIN ANTIGEN 7 ESXH (10 kDa ANTIGEN) (CFP-7) (PROTEIN TB10.4)|CAA17363.1|Mycobacterium tuberculosis H37Rv|83332 +QAMEDLVRA +>140739|dense granule protein 7|XP_002367613.1|Toxoplasma gondii ME49|508771 +RSFKDLLKK +>140744|LOW MOLECULAR WEIGHT PROTEIN ANTIGEN 7 ESXH (10 kDa ANTIGEN) (CFP-7) (PROTEIN TB10.4)|CAA17363.1|Mycobacterium tuberculosis H37Rv|83332 +SQIMYNYPA +>140760|LOW MOLECULAR WEIGHT PROTEIN ANTIGEN 7 ESXH (10 kDa ANTIGEN) (CFP-7) (PROTEIN TB10.4)|CAA17363.1|Mycobacterium tuberculosis H37Rv|83332 +TYQAWQAQW +>140769|LOW MOLECULAR WEIGHT PROTEIN ANTIGEN 7 ESXH (10 kDa ANTIGEN) (CFP-7) (PROTEIN TB10.4)|CAA17363.1|Mycobacterium tuberculosis H37Rv|83332 +WQAQWNQAM +>141202|Uncharacterized PPE family protein PPE51|Q7D623.1|Mycobacterium tuberculosis H37Rv|83332 +AEMWAQDAA +>141206|tegument protein VP11/12|NP_044648.1|Human alphaherpesvirus 1|10298 +AILTQYWKY +>141208|tegument protein VP13/14|NP_044649.1|Human alphaherpesvirus 1|10298 +ALATVTLKY +>141211|UL29|ABI63491.1|Human alphaherpesvirus 1|10298 +ALLAKMLFY +>141212|tegument protein VP13/14|NP_044649.1|Human alphaherpesvirus 1|10298 +ALLDRDCRV +>141216|envelope glycoprotein I|NP_044669.1|Human alphaherpesvirus 1|10298 +APASVYQPA +>141217|regulatory protein ICP22|NP_044663.1|Human alphaherpesvirus 1|10298 +APRIGGRRA +>141218|regulatory protein ICP22|NP_044663.1|Human alphaherpesvirus 1|10298 +APRTWCRLL +>141221|tegument protein VP11/12|NP_044648.1|Human alphaherpesvirus 1|10298 +ATDSLNNEY +>141222|DNA packaging tegument protein UL25|NP_044626.1|Human alphaherpesvirus 1|10298 +AVLCLYLLY +>141225|tegument protein UL21|NP_044622.1|Human alphaherpesvirus 1|10298 +AYLGAFLSVL +>141226|tegument protein UL37|ADD60080.1|Human alphaherpesvirus 1|10298 +AYLPRPVEF +>141227|tegument protein UL37|ADD60080.1|Human alphaherpesvirus 1|10298 +AYSLLFPAPF +>141228|tegument protein VP11/12|NP_044648.1|Human alphaherpesvirus 1|10298 +AYVSVLYRW +>141231|envelope glycoprotein I|NP_044669.1|Human alphaherpesvirus 1|10298 +CPRRPAVAF +>141260|nuclear egress lamina protein|NP_044633.1|Human alphaherpesvirus 1|10298 +EYQRLYATF +>141262|DNA polymerase catalytic subunit|NP_044632.1|Human alphaherpesvirus 1|10298 +EYVHARWAAF +>141269|tegument protein VP13/14|NP_044649.1|Human alphaherpesvirus 1|10298 +FLADAVVRL +>141270|envelope glycoprotein B|NP_044629.1|Human alphaherpesvirus 1|10298 +FLIAYQPLL +>141271|DNA packaging tegument protein UL25|NP_044626.1|Human alphaherpesvirus 1|10298 +FLWEDQTLL +>141276|tegument protein VP13/14|NP_044649.1|Human alphaherpesvirus 1|10298 +FTAPEVGTY +>141277|transactivating tegument protein VP16|NP_044650.1|Human alphaherpesvirus 1|10298 +FTDALGIDEY +>141281|tegument protein UL21|NP_044622.1|Human alphaherpesvirus 1|10298 +FVYTPSPYVF +>141306|tegument host shutoff protein|NP_044643.1|Human alphaherpesvirus 1|10298 +HTDLHPNNTY +>141313|ribonucleotide reductase subunit 2|NP_044642.1|Human alphaherpesvirus 1|10298 +ILIEGIFFA +>141323|multifunctional expression regulator|NP_044657.1|Human alphaherpesvirus 1|10298 +KYFYCNSLF +>141324|tegument protein VP11/12|NP_044648.1|Human alphaherpesvirus 1|10298 +LASDPHYEY +>141338|envelope glycoprotein L|NP_044602.1|Human alphaherpesvirus 1|10298 +LIDGIFLRY +>141341|tegument protein VP11/12|NP_044648.1|Human alphaherpesvirus 1|10298 +LLAYVSVLY +>141354|transcriptional regulator ICP4|NP_044662.1|Human alphaherpesvirus 1|10298 +LYPDAPPLRL +>141396|ribonucleotide reductase subunit 1|NP_044641.1|Human alphaherpesvirus 1|10298 +RILGVLVHL +>141398|tegument protein VP13/14|NP_044649.1|Human alphaherpesvirus 1|10298 +RLLGFADTV +>141399|Tegument protein UL46|P10230.2|Herpes simplex virus (type 1 / strain 17)|10299 +RLNELLAYV +>141402|tegument protein VP22|NP_044651.1|Human alphaherpesvirus 1|10298 +RPTERPRAPA +>141407|tegument protein VP13/14|NP_044649.1|Human alphaherpesvirus 1|10298 +RSSLGSLLY +>141411|transactivating tegument protein VP16|NP_044650.1|Human alphaherpesvirus 1|10298 +SALPTNADLY +>141418|tegument protein VP11/12|NP_044648.1|Human alphaherpesvirus 1|10298 +SIVHHHAQY +>141422|DNA packaging tegument protein UL25|NP_044626.1|Human alphaherpesvirus 1|10298 +SSGVVFGTWY +>141423|envelope glycoprotein B|NP_044629.1|Human alphaherpesvirus 1|10298 +SVYPYDEFV +>141430|tegument serine/threonine protein kinase|NP_044614.1|Human alphaherpesvirus 1|10298 +TLLELVVSV +>141461|ubiquitin E3 ligase ICP0|NP_044601.1|Human alphaherpesvirus 1|10298 +VPGWSRRTL +>141462|tegument protein UL21|NP_044622.1|Human alphaherpesvirus 1|10298 +VPRPDDPVL +>141468|envelope glycoprotein I|NP_044669.1|Human alphaherpesvirus 1|10298 +VVRGPTVSL +>141469|envelope glycoprotein B|NP_044629.1|Human alphaherpesvirus 1|10298 +VYMSPFYGY +>141470|tegument protein UL21|NP_044622.1|Human alphaherpesvirus 1|10298 +VYTPSPYVF +>141479|single-stranded DNA-binding protein|NP_044631.1|Human alphaherpesvirus 1|10298 +YMANQILRY +>141480|ribonucleotide reductase subunit 1|NP_044641.1|Human alphaherpesvirus 1|10298 +YMESVFQMY +>141484|capsid maturation protease|NP_044627.1|Human alphaherpesvirus 1|10298 +YVAGFLALY +>142194|polyprotein|ADV57311.1|Hepatitis C virus subtype 1a|31646 +KAKKTPMGF +>142203|polyprotein|BAD73974.1|Hepatitis C virus subtype 1b|31647 +KKKKNPMGF +>142209|polyprotein|ACJ37233.1|Hepatitis C virus subtype 1a|31646 +KSKKIPMGF +>142210|polyprotein [Hepatitis C virus subtype 1a]|ABV46251.2|Hepatitis C virus subtype 1a|31646 +KSKKNPMGF +>142211|polyprotein|ACJ37204.1|Hepatitis C virus subtype 1a|31646 +KSKKTPLGF +>142212|Genome polyprotein|Q913D4.3|Hepatitis C virus subtype 1a|31646 +KSKKVPMGF +>142213|polyprotein|ABV46054.1|Hepatitis C virus subtype 1a|31646 +KSKRTPMGF +>142231|Lipoprotein lpqH precursor|P0A5J0.1|Mycobacterium tuberculosis|1773 +MKRGLTVAVAGAAILVAGLSGCSS +>142232|POSSIBLE CONSERVED TRANSMEMBRANE PROTEIN|CAB00937.1|Mycobacterium tuberculosis|1773 +MLVLLVAVLVTAVYAFVHA +>142233|ATP-dependent helicase|NP_217813.1|Mycobacterium tuberculosis|1773 +MRFAQPSALSRFSALTRDWFTSTFAAPTAAQA +>142244|polyprotein|ACJ37184.1|Hepatitis C virus subtype 1a|31646 +NSKKTPMGF +>142245|polyprotein|ACJ37204.1|Hepatitis C virus subtype 1a|31646 +NTRPPAGNW +>142246|polyprotein|BAB18810.1|Hepatitis C virus subtype 1a|31646 +NTRPPLGNW +>142247|envelope protein 2|ACY64760.1|Hepatitis C virus subtype 1a|31646 +NTRPPMGNW +>142248|polyprotein|BAB18806.1|Hepatitis C virus subtype 1a|31646 +NTRPPQGNW +>142249|polyprotein|AAY82036.1|Hepatitis C virus subtype 1a|31646 +NTRPPRGNW +>143664|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 +AISEKTIWSL +>143666|polyprotein|ACF60462.1|Hepatovirus A|12092 +ALFHEVAKL +>143680|Genome polyprotein|P06441.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 +DVSGVQAPRGSYQQQLNDPVL +>143690|Genome polyprotein|P06441.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 +GLAVDPWVE +>143705|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 +KEYTFPITL +>143726|polyprotein|CAC14074.3|Hepatovirus A|12092 +LLYNCCYHV +>143728|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 +LPWYSYLYA +>143732|polyprotein|CAC14074.3|Hepatovirus A|12092 +MMFGFHHSV +>143735|Genome polyprotein|P06441.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 +NRGKMDVSGVQAPRGSYQQQ +>143740|polyprotein|ACF60462.1|Hepatovirus A|12092 +QMMRNEFRV +>143752|Genome polyprotein|P06441.1|Hepatovirus A|12092 +SLMDLLSSL +>144207|polyprotein|CAB41951.1|Hepatitis C virus|11103 +APTLWARMVL +>144403|polyprotein|AAK08509.1|Hepatitis C virus subtype 1b|31647 +LLRHHNMVY +>144480|polyprotein|ACA50684.1|Hepatitis C virus subtype 1b|31647 +SQRQKKVTF +>144544|polyprotein precursor|BAA01728.1|Hepatitis C virus|11103 +WPAPSGARSL +>144913|Hexon protein|P04133.3|Human adenovirus 5|28285 +LLYANSAHAL +>145826|6 kDa early secretory antigenic target|P0A564.2|Mycobacterium tuberculosis|1773 +IHSLLDEGKQSLTKL +>145860|Protein E6|P04019.1|Human papillomavirus type 11|10580 +KVLIRCYLC +>145918|Protein E6|P06463.1|Human papillomavirus type 18|333761 +NLLIRCLRC +>146005|Protein E6|P04019.1|Human papillomavirus type 11|10580 +SIDQLCKTF +>146028|E6 protein|NP_040296.1|Human papillomavirus type 6b|10600 +TIDQLCKTF +>146123|polyprotein|ADV04529.1|Hepatitis C virus subtype 1b|31647 +AATLGFGSFMSRAYGI +>146124|polyprotein|AAK08509.1|Hepatitis C virus subtype 1b|31647 +AAWYIKGRL +>146182|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 +CLTHPVTK +>146188|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 +DFWESVFTGLTHIDAHFL +>146194|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 +DLQPAETTVRLRAYL +>146213|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 +EFWESVFTGLTHIDAHFL +>146219|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 +ELTPAETSVRLRAYL +>146246|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 +FLATCVNGVCWTVYHGA +>146249|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 +FLGTTVGGVMWTVYHGA +>146260|polyprotein|ADF97231.1|Hepatitis C virus subtype 3a|356426 +GAKHPALQMYTNVDQDLV +>146280|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 +GIDPNIRTGN +>146282|polyprotein|ADF97231.1|Hepatitis C virus subtype 3a|356426 +GKAIPIALLKGGRHLIF +>146283|polyprotein|AEI00313.1|Hepatitis C virus subtype 1b|31647 +GKAIPIEVIKGGRHLIF +>146284|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 +GKSTKVPAAYAAQGYKVL +>146285|polyprotein|ADF97231.1|Hepatitis C virus subtype 3a|356426 +GKSTKVPAAYVAQGYNVL +>146287|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 +GPKGPITQMYTNVDQDLV +>146288|polyprotein|ADF97231.1|Hepatitis C virus subtype 3a|356426 +GRGRLGTYRY +>146289|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 +GRGRRGIYRF +>146291|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 +GSFMSRAYGI +>146314|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 +HVAGIFRAAV +>146317|polyprotein|ADF97231.1|Hepatitis C virus subtype 3a|356426 +ICLTHPVTK +>146395|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 +KLRGMGLNAV +>146396|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 +KLRGMGLNAVAYYRGLDV +>146397|polyprotein|AEI00314.1|Hepatitis C virus subtype 1b|31647 +KLSALGLNAVAYYRGLDV +>146429|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 +LQFIPVETL +>146527|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 +RLGAVQNEV +>146528|NS3/4A protein|CAM56207.1|Hepatitis C virus|11103 +RLGPVQNEI +>146553|polyprotein precursor|BAA01761.1|Hepatitis C virus genotype 2|40271 +SMMAFSAAL +>146569|polyprotein|ADF97231.1|Hepatitis C virus subtype 3a|356426 +SWDETWKCLVRLKPTLH +>146570|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 +SWDQMWKCLIRLKPTLH +>146576|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 +TLGFGSFMSR +>146592|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 +VAPGERPSGMFDSVVL +>146595|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 +VDFVPVESM +>146617|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 +VTPGERPSGMFDSSVL +>146644|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 +YLHAPTGSGK +>147561|early protein|CAA52586.1|Human papillomavirus type 52|10618 +CYEQLGDSS +>147835|early protein|CAA52585.1|Human papillomavirus type 52|10618 +ITIRCIICQ +>147891|early protein|CAA52585.1|Human papillomavirus type 52|10618 +KTLEERVKK +>147936|dense granule protein 7|XP_002367613.1|Toxoplasma gondii ME49|508771 +LPQFATAAT +>147941|late protein|CAA52590.1|Human papillomavirus type 52|10618 +LQFIFQLCK +>147973|early protein|CAA52586.1|Human papillomavirus type 52|10618 +MRGDKATIK +>147981|late protein|CAA52590.1|Human papillomavirus type 52|10618 +MTLCAEVKK +>148117|early protein|CAA52585.1|Human papillomavirus type 52|10618 +PYGVCIMCL +>148138|early protein|CAA52586.1|Human papillomavirus type 52|10618 +QLGDSSDEE +>148160|late protein|CAA52590.1|Human papillomavirus type 52|10618 +QYRVFRIKL +>148172|late protein|CAA52590.1|Human papillomavirus type 52|10618 +RIKLPDPNK +>148177|early protein|CAA52585.1|Human papillomavirus type 52|10618 +RLQCVQCKK +>148397|Dense granule protein 3|B6KEU8.2|Toxoplasma gondii|5811 +VPFVVFLVA +>148425|early protein|CAA52585.1|Human papillomavirus type 52|10618 +VYKFLFTDL +>148619|unnamed protein product|BAA14233.1|Hepatitis C virus|11103 +GLLGCIITSLTGRDKNQVDGEVQVLSTATQSFLATCVNGVCWTVY +>149022|nonstructural protein|AAC53947.1|Hepatitis C virus genotype 1|41856 +AIAPAVQTNW +>149023|NS3 gene product|AAB02124.1|Hepatitis C virus (isolate H77)|63746 +ALGINAVAY +>149024|NS2 protein|NP_751923.1|Hepatitis C virus (isolate H77)|63746 +ALTLSPYYK +>149027|NS5 protein|BAA00702.1|Hepatitis C virus (isolate H77)|63746 +APTLWARMILMTHFFSVL +>149029|polyprotein|ABR25251.1|Hepatitis C virus (isolate H77)|63746 +CTTPCSGSW +>149031|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 +EAAGRRLAR +>149032|nonstructural 5a protein|ADH82351.1|Hepatitis C virus subtype 1a|31646 +EAARRRLAR +>149036|E2 protein|NP_751921.1|Hepatitis C virus (isolate H77)|63746 +ELSPLLLST +>149037|NS4B protein|NP_751926.1|Hepatitis C virus (isolate H77)|63746 +EVITPAVQTNW +>149038|NS3|ABN45875.1|Hepatitis C virus (isolate H77)|63746 +EVQIVSTAAQTFLAT +>149044|NS2 protein|NP_751923.1|Hepatitis C virus (isolate H77)|63746 +FLTRVEAQL +>149052|E1 protein|NP_751920.1|Hepatitis C virus (isolate H77)|63746 +GIAYFSMVGNWAKVLVVL +>149053|NS3 gene product|AAB02124.1|Hepatitis C virus|11103 +GRGKPGIYRFVAPGERPS +>149060|E2 protein|NP_751921.1|Hepatitis C virus (isolate H77)|63746 +HPEATYSRC +>149063|NS3 protease/helicase'|NP_803144.1|Hepatitis C virus (isolate H77)|63746 +KAVDFIPVENLETTMRSP +>149072|NS3 gene product|AAB02124.1|Hepatitis C virus (isolate H77)|63746 +MSKAHGVDPNIRTGVRTI +>149074|E1 protein|NP_751920.1|Hepatitis C virus (isolate H77)|63746 +NASRCWVAV +>149075|envelope glycoprotein E1|ACI88341.1|Hepatitis C virus genotype 1|41856 +NASRCWVPV +>149089|NS3|ABN45875.1|Hepatitis C virus (isolate H77)|63746 +NQVEGEVQI +>149096|polyprotein|BAB18801.1|Hepatitis C virus|11103 +RAQAPPPSW +>149097|NS5 protein|BAA00702.1|Hepatitis C virus (isolate H77)|63746 +RGGRAAICGKYLFNWAVR +>149098|E2 protein|NP_751921.1|Hepatitis C virus (isolate H77)|63746 +RSGAPTYSW +>149105|E2 protein|NP_751921.1|Hepatitis C virus (isolate H77)|63746 +SIASWAIKW +>149115|NS5 protein|BAA00702.1|Hepatitis C virus (isolate H77)|63746 +SVRARLLSR +>149117|envelope glycoprotein|AAV74049.1|Hepatitis C virus (isolate H77)|63746 +TDFDQGWGPISYANGSGP +>149126|nonstructural protein 3|AAY84762.1|Hepatitis C virus genotype 1|41856 +TVYHGAGTK +>149127|NS3|ABN45875.1|Hepatitis C virus (isolate H77)|63746 +TVYHGAGTR +>149129|NS2 protein|NP_751923.1|Hepatitis C virus (isolate H77)|63746 +VVFSRMETKLITWGADTA +>150137|Nonstructural protein NS3|NP_739587.2|Dengue virus 2|11060 +APTRVVAAEM +>150217|polyprotein|AGO67248.1|Dengue virus 2|11060 +FPQSNAPIM +>150224|polyprotein|AGO67248.1|Dengue virus 2|11060 +FTIMAAILAY +>150227|polyprotein|AGS49173.1|Dengue virus 2|11060 +FTMRHKKATY +>150252|polyprotein|AGO67248.1|Dengue virus 2|11060 +GPLKLFMAL +>150259|polyprotein|AGO67248.1|Dengue virus 2|11060 +GPWHLGKLEM +>150299|polyprotein|AGO67248.1|Dengue virus 2|11060 +ILLTAVAPSM +>150308|polyprotein|AGW21594.1|Dengue virus 1|11053 +IPMATYGWNL +>150309|polyprotein|AGO67248.1|Dengue virus 2|11060 +IPMSTYGWNL +>150341|polyprotein|AGW21594.1|Dengue virus 1|11053 +KPGTSGSPI +>150373|polyprotein|AAA42942.1|Dengue virus 2|11060 +LLILCVTQV +>150377|polyprotein|AGS49173.1|Dengue virus 2|11060 +LLLVAHYAI +>150378|polyprotein|AGW21594.1|Dengue virus 1|11053 +LLMLVTPSM +>150387|polyprotein|AGO67248.1|Dengue virus 2|11060 +LMGLGKGWPL +>150389|polyprotein|AGO67248.1|Dengue virus 2|11060 +LMMRTTWAL +>150391|polyprotein|AGS49173.1|Dengue virus 2|11060 +LMMTTIGIVL +>150399|polyprotein|AGV76873.1|Dengue virus 2|11060 +LQMENKAWLV +>150425|polyprotein|AGS49173.1|Dengue virus 2|11060 +LVISGLFPV +>150445|polyprotein|AGO67248.1|Dengue virus 2|11060 +MLLILCVTQV +>150448|polyprotein|AGO67248.1|Dengue virus 2|11060 +MMATIGIAL +>150450|polyprotein|AGO67248.1|Dengue virus 2|11060 +MPVTHSSAA +>150451|polyprotein|AGO67248.1|Dengue virus 2|11060 +MPVTHSSAAQ +>150456|polyprotein|AGO67248.1|Dengue virus 2|11060 +MSYSMCTGKF +>150461|polyprotein|AGK36298.1|Dengue virus 2|11060 +MTQKARNAL +>150474|polyprotein|AGW21594.1|Dengue virus 1|11053 +NPLTLTAAV +>150531|polyprotein|AGO67248.1|Dengue virus 2|11060 +RLRMDKLQL +>150534|polyprotein|AGO67248.1|Dengue virus 2|11060 +RPASAWTLY +>150538|polyprotein|AGW21594.1|Dengue virus 1|11053 +RPRWLDART +>150556|polyprotein|AGW21594.1|Dengue virus 1|11053 +RVIDPRRCLK +>150571|polyprotein|AGO67248.1|Dengue virus 2|11060 +SLLFKTEDGV +>150578|polyprotein|AGO67248.1|Dengue virus 2|11060 +SPCKIPFEIM +>150579|polyprotein|AGW21594.1|Dengue virus 1|11053 +SPGKFWNTTI +>150584|polyprotein|AGO67248.1|Dengue virus 2|11060 +SPILSITISE +>150612|polyprotein|AGO67248.1|Dengue virus 2|11060 +TAEAGGRAY +>150634|polyprotein|AGS49173.1|Dengue virus 2|11060 +TLMAMDLGEL +>150639|polyprotein|AGO67249.1|Dengue virus 2|11060 +TLYAVATTFV +>150643|polyprotein|AGW21594.1|Dengue virus 1|11053 +TPEGIIPALF +>150644|polyprotein|AGO67248.1|Dengue virus 2|11060 +TPEGIIPSMF +>150649|polyprotein|AGW21594.1|Dengue virus 1|11053 +TPQDNQLAYV +>150655|polyprotein|AGO67248.1|Dengue virus 2|11060 +TPRMCTREEF +>150686|polyprotein|AGO67248.1|Dengue virus 2|11060 +VLMMRTTWA +>150693|polyprotein|AGO67248.1|Dengue virus 2|11060 +VPNYNLIIM +>150698|polyprotein|AGO67248.1|Dengue virus 2|11060 +VPYLGKREDQ +>150725|polyprotein|AGO67248.1|Dengue virus 2|11060 +WLVHRQWFL +>150752|polyprotein|AGO67249.1|Dengue virus 2|11060 +YVVIAILTV +>150753|polyprotein|AGO67248.1|Dengue virus 2|11060 +YVVIAILTVV +>150974|60 kDa chaperonin|SRC280371|Yersinia enterocolitica|630 +DRGIDKAVI +>150991|60 kDa chaperonin|P48219.1|Yersinia enterocolitica|630 +GRNVVLDKS +>151001|60 kDa chaperonin|P48219.1|Yersinia enterocolitica|630 +IRAASAITA +>151003|heat shock 60kDa protein 1 (chaperonin)|AAH02676.1|Homo sapiens|9606 +IRRGVMLAV +>151012|heat shock 60kDa protein 1 (chaperonin)|AAH02676.1|Homo sapiens|9606 +KRIQEIIEQ +>151013|heat shock 60kDa protein 1 (chaperonin)|AAH02676.1|Homo sapiens|9606 +KRTLKIPAM +>154041|major capsid protein|CAB06743.1|Human alphaherpesvirus 2|10310 +AFEDRSYPAVFYLLQ +>154164|tegument protein|CAB06732.1|Human alphaherpesvirus 2|10310 +AQREAAGVYDAVRTW +>154196|tegument protein|CAB06735.1|Human alphaherpesvirus 2|10310 +ARPRRSASVAGSHGPG +>154296|UL29|CAB06754.1|Human alphaherpesvirus 2|10310 +CPLLIFDRTRKFVLA +>154346|RL2|CAB06760.1|Human alphaherpesvirus 2|10310 +DFIWTGNPRTAPRSL +>154387|RL2|CAB06760.1|Human alphaherpesvirus 2|10310 +DMETGHIGAYVVLVD +>154409|capsid associated tegument protein|CAB06749.1|Human alphaherpesvirus 2|10310 +DRLDNRLQLGMLIPG +>154448|RL2|CAB06760.1|Human alphaherpesvirus 2|10310 +EAGLMDAATPPARPPA +>154585|ribonucleotide reductase large subunit|CAB06725.1|Human alphaherpesvirus 2|10310 +FGGHYMESVFQMYTR +>154725|RL2|CAB06760.1|Human alphaherpesvirus 2|10310 +GHIGAYVVLVDQTGN +>154822|ribonucleotide reductase large subunit|CAB06725.1|Human alphaherpesvirus 2|10310 +GVLVHLRIRTREASF +>154857|tegument protein|CAB06735.1|Human alphaherpesvirus 2|10310 +HGPGPARAPPPPGGPV +>154980|tegument protein|CAB06735.1|Human alphaherpesvirus 2|10310 +KNLLQRANELVNPDA +>154996|ribonucleotide reductase large subunit|CAB06725.1|Human alphaherpesvirus 2|10310 +KTSNALCVRGARPFS +>155096|RL2|CAB06760.1|Human alphaherpesvirus 2|10310 +LHPFCIPCMKTWIPL +>155131|ribonucleotide reductase large subunit|CAB06725.1|Human alphaherpesvirus 2|10310 +LMLEYFCRCAREESK +>155139|RL2|CAB06760.1|Human alphaherpesvirus 2|10310 +LPIAGVSSVVALAPY +>155403|tegument protein|CAB06735.1|Human alphaherpesvirus 2|10310 +PKASATPATDPARGR +>155489|RL2|CAB06760.1|Human alphaherpesvirus 2|10310 +PVGNMLFDQGTLVGA +>155554|RL2|CAB06760.1|Human alphaherpesvirus 2|10310 +RAAAPAWSRRTLLPE +>155637|tegument protein|CAB06732.1|Human alphaherpesvirus 2|10310 +RLGPADRRFVALSGS +>155811|ribonucleotide reductase large subunit|CAB06725.1|Human alphaherpesvirus 2|10310 +SMSLADFHGEEFEKL +>155927|unnamed protein product|CAA30115.1|Trypanosoma cruzi|5693 +TLLTIDGGI +>155928|unnamed protein product|CAA30115.1|Trypanosoma cruzi|5693 +TLQPVERVL +>155999|RL2|CAB06760.1|Human alphaherpesvirus 2|10310 +VALAPYVNKTVTGDC +>156542|ETS translocation variant 5|NP_004445.1|Homo sapiens|9606 +ELFQDLSQL +>156550|E3 ubiquitin-protein ligase Mdm2|Q00987.1|Homo sapiens|9606 +VLFYLGQYI +>156552|U1 small nuclear ribonucleoprotein 70 kDa|NP_003080.2|Homo sapiens|9606 +YLAPENGYL +>156711|polyprotein precursor|AAG45435.1|Dengue virus 4|11070 +LAPTRVVAAEMEEAL +>156949|Protein 3a|P59632.1|SARS coronavirus|227859 +RFFTLGSITAQPVKI +>159290|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 +LLRHHNLVY +>159299|polyprotein|AAC03058.1|Hepatitis C virus subtype 3a|356426 +SQRQRKVTF +>161186|Nonstructural protein NS5|NP_739590.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 +RLLTKPWDVVPMVTQ +>161353|arsenic-transport integral membrane protein ArsA|NP_217200.1|Mycobacterium tuberculosis H37Rv|83332 +IMILLVLVSA +>161402|hypothetical protein|NP_215301.1|Mycobacterium tuberculosis H37Rv|83332 +LILATMLVA +>161641|6 kDa early secretory antigenic target|P0A564.2|Mycobacterium tuberculosis|1773 +IQGNVTSIHSLLDEG +>164233|nucleocapsid protein|AAA43837.1|Hantaan hantavirus|11599 +FVVPILLKA +>164258|nucleocapsid protein|AAA43837.1|Hantaan virus 76-118|11602 +IEPCKLLPDTAAVSL +>164264|nucleocapsid protein|AAA43837.1|Hantaan virus 76-118|11602 +ITPGRYRTAVCGLYP +>164282|nucleocapsid protein|AAA43837.1|Hantaan hantavirus|11599 +LPDTAAVSL +>164403|nucleocapsid protein|AAA43837.1|Hantaan virus 76-118|11602 +TSFVVPILLKALYML +>164417|nucleocapsid protein|AAA43837.1|Hantaan hantavirus|11599 +VPILLKALY +>164420|nucleocapsid protein|AAA43837.1|Hantaan virus 76-118|11602 +VSLLGGPATNRDYLR +>164547|envelope glycoprotein B|NP_044629.1|Herpes simplex virus (type 1 / strain 17)|10299 +RMLGDVMAV +>164551|envelope glycoprotein B|NP_044629.1|Herpes simplex virus (type 1 / strain 17)|10299 +TMLEDHEFV +>167320|possible regulatory protein|NP_302009.1|Mycobacterium leprae|1769 +LLEEGVIVL +>168240|major paraflagellar rod protein|AAA30221.1|Trypanosoma cruzi|5693 +AVPEVTDVTL +>168327|paraflagellar rod component|AAC32021.1|Trypanosoma cruzi|5693 +DIIEQMKGV +>168607|paraflagellar rod component|AAC32021.1|Trypanosoma cruzi|5693 +FVSCCGELTV +>168691|polyprotein|ABU97067.1|Hepatitis C virus subtype 1b|31647 +GLNAVAYYR +>168728|paraflagellar rod component|AAC32021.1|Trypanosoma cruzi|5693 +GVSGVINAL +>168988|major paraflagellar rod protein|AAA30221.1|Trypanosoma cruzi|5693 +KLEKIEDEL +>169050|polyprotein|ABU97067.1|Hepatitis C virus subtype 1b|31647 +KYLFNWAVK +>169658|major paraflagellar rod protein|AAA30221.1|Trypanosoma cruzi|5693 +RLYKTLGQL +>169995|polyprotein|ABU97067.1|Hepatitis C virus subtype 1b|31647 +VLYQDFDEM +>170049|polyprotein|ABU97067.1|Hepatitis C virus subtype 1b|31647 +WEYVLLLFL +>170063|polyprotein|ABU97067.1|Hepatitis C virus subtype 1b|31647 +WTRGERCNL +>177647|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 +EGAVQWMNRLIAFASR +>177701|polyprotein|ACZ60104.1|Hepatitis C virus subtype 3a|356426 +GKAKICGLYLFNWAVRTK +>177727|polyprotein|ACZ60102.1|Hepatitis C virus subtype 3a|356426 +GVMSTRCPCGASIAGHVK +>177806|polyprotein|ACZ60104.1|Hepatitis C virus subtype 3a|356426 +KLTPLPAAGQL +>177843|polyprotein|ACZ60102.1|Hepatitis C virus subtype 3a|356426 +LIHLHQNIVDVQYLYGV +>177884|polyprotein|ACZ60102.1|Hepatitis C virus genotype 1|41856 +NIVDVQYLYGVGSGMVGW +>177903|polyprotein|ACZ60102.1|Hepatitis C virus subtype 3a|356426 +PAVASLMAFTASVTSPL +>177955|polyprotein|ACZ60102.1|Hepatitis C virus subtype 3a|356426 +RPSGMFDSVVL +>177956|polyprotein|ACZ60102.1|Hepatitis C virus subtype 3a|356426 +RPSGMFDSVVLCECYDA +>178185|Protein E6|P03126.1|Human papillomavirus type 16|333760 +AFRDLCIVYRDGNPY +>178247|Protein E6|P03126.1|Human papillomavirus type 16|333760 +HLDKKQRFHNIRGRW +>178351|Protein E7|P03129.1|Human papillomavirus type 16|333760 +TPTLHEYMLDLQPET +>178829|envelope protein|BAJ51675.1|HBV genotype D|489483 +FLGPLLVLQA +>179762|cytotoxin/hemolysin|NP_301968.1|Mycobacterium leprae TN|272631 +ALDTFGIPV +>179765|cell surface protein (associated with virulence)|NP_302372.1|Mycobacterium leprae TN|272631 +APIPASVSA +>179766|cell surface protein (associated with virulence)|NP_302372.1|Mycobacterium leprae TN|272631 +APLPPSTAT +>179795|cell surface protein (associated with virulence)|NP_302372.1|Mycobacterium leprae TN|272631 +GIAGSASYY +>179799|hypothetical protein|NP_301670.1|Mycobacterium leprae TN|272631 +GPVPAVATL +>179802|cell surface protein (associated with virulence)|NP_302372.1|Mycobacterium leprae TN|272631 +HRKGLWAIL +>179823|cell surface protein (associated with virulence)|NP_302372.1|Mycobacterium leprae TN|272631 +IPASVSAPA +>179825|cytotoxin/hemolysin|NP_301968.1|Mycobacterium leprae TN|272631 +IPVAGRCCL +>179839|cytotoxin/hemolysin|NP_301968.1|Mycobacterium leprae TN|272631 +KLMGALDTF +>179840|hypothetical protein|NP_302232.1|Mycobacterium leprae TN|272631 +KVTVSSVRK +>179850|cytotoxin/hemolysin|NP_301968.1|Mycobacterium leprae TN|272631 +LPSADIVPM +>179866|cell surface protein (associated with virulence)|NP_302372.1|Mycobacterium leprae TN|272631 +NGIAGSASY +>179881|hypothetical protein|NP_302232.1|Mycobacterium leprae TN|272631 +QMLEASSSV +>179885|hypothetical protein|NP_301670.1|Mycobacterium leprae TN|272631 +RAAVVQAAL +>179891|hypothetical protein|NP_302233.1|Mycobacterium leprae TN|272631 +RPRRGSVSR +>179892|p60-family protein|NP_301879.1|Mycobacterium leprae TN|272631 +RPVPVSTAR +>179898|cell surface protein (associated with virulence)|NP_302372.1|Mycobacterium leprae TN|272631 +SASAFTMPL +>179917|cell surface protein (associated with virulence)|NP_302372.1|Mycobacterium leprae TN|272631 +VASASAFTM +>180077|PPE family protein|YP_177935.1|Mycobacterium tuberculosis H37Rv|83332 +YAEMWAQDA +>180168|gag protein|ABO14878.1|Human immunodeficiency virus 1|11676 +SLFNAVATL +>180191|gag polyprotein|BAB19174.1|Human immunodeficiency virus 1|11676 +SLFNTIATL +>180233|gag protein|ACZ34075.1|Human immunodeficiency virus 1|11676 +SLFNTVATV +>180236|gag|BAC81459.1|Human immunodeficiency virus 1|11676 +SLFNTVAVL +>180255|gag protein|AAT90688.1|Human immunodeficiency virus 1|11676 +SLFNTVVTL +>180337|pol protein|ACJ76655.1|Human immunodeficiency virus 1|11676 +LPPVVAKEI +>180360|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 +AAEGINYADRRWCFD +>180373|polyprotein|AGW21594.1|Dengue virus 1|11053 +APTRVVASEM +>180387|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 +CEALTLATGPISTLW +>180390|polyprotein|CDF77361.1|Dengue virus 3|11069 +CLMMMLPATL +>180407|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 +DNINTPEGIIPSMFE +>180408|polyprotein|AGO67248.1|Dengue virus 2|11060 +DPASIAARGY +>180411|polyprotein|AGO67248.1|Dengue virus 2|11060 +DTTPFGQQR +>180423|polyprotein|AGW21594.1|Dengue virus 1|11053 +EERDIPERSW +>180428|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 +EGEWKEGEEVQVLAL +>180433|polyprotein|AGO67248.1|Dengue virus 2|11060 +EPGQLKLNWF +>180437|polyprotein|AGO67248.1|Dengue virus 2|11060 +EPKEGTKKLM +>180440|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 +EREIPERSWNSGHEW +>180442|Chain B, Dengue Virus Rna Dependent Rna Polymerase With Residues From The Ns5 Linker Region|4C11_B|Dengue virus|12637 +ETACLGKAYA +>180443|polyprotein|AGO67248.1|Dengue virus 2|11060 +ETACLGKSYA +>180450|polyprotein|AGO67248.1|Dengue virus 2|11060 +FAGPVSQHNY +>180453|polyprotein|AGO67248.1|Dengue virus 2|11060 +FGAIYGAAF +>180460|polyprotein|AGO67248.1|Dengue virus 2|11060 +FPQSNAPIMD +>180464|polyprotein|CDF77361.1|Dengue virus 3|11069 +FTILALFLAH +>180471|polyprotein|AGO67248.1|Dengue virus 2|11060 +GEARKTFVDL +>180472|polyprotein|AGW21594.1|Dengue virus 1|11053 +GEARKTFVEL +>180483|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 +GKKKTPRMCTREEFT +>180488|polyprotein|AGO67248.1|Dengue virus 2|11060 +GPGHEEPIPM +>180496|Polyprotein|NP_056776.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 +GVFTTNIWLKLKEKQ +>180500|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 +HKKLAEAIFKLTYQN +>180503|polyprotein|AGO67248.1|Dengue virus 2|11060 +HPGAGKTKRY +>180504|polyprotein|CDF77361.1|Dengue virus 3|11069 +HPGFTILALF +>180507|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 +HTGREIVDLMCHATF +>180512|polyprotein|AGO67248.1|Dengue virus 2|11060 +IANQATVLM +>180514|polyprotein|AGO67248.1|Dengue virus 2|11060 +IAVSMANIF +>180528|polyprotein|AGO67248.1|Dengue virus 2|11060 +IPFEIMDLEK +>180529|polyprotein|AGO67248.1|Dengue virus 2|11060 +IPITAAAWY +>180531|polyprotein|AGO67248.1|Dengue virus 2|11060 +IPMTGPLVAG +>180538|Nonstructural protein NS2B|NP_739586.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 +ISGLFPVSIPITAAA +>180563|Envelope protein|NP_739583.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 +KILIGVIITWIGMNS +>180571|polyprotein|AGW21594.1|Dengue virus 1|11053 +KPRICTREEF +>180572|polyprotein|CDF77361.1|Dengue virus 3|11069 +KPRLCTREEF +>180575|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 +KRYLPAIVREAIKRG +>180579|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 +KSYAQMWSLMYFHRR +>180582|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 +KTWAYHGSYETKQTG +>180588|polyprotein|AGO67248.1|Dengue virus 2|11060 +LAYTIGTTHF +>180589|Nonstructural protein NS3|NP_739587.2|Dengue virus 2|11060 +LDARIYSDPLALKEF +>180596|polyprotein|AFP27208.1|Dengue virus 4|11070 +LETLMLVALL +>180601|polyprotein|AGO67248.1|Dengue virus 2|11060 +LILCVTQVLM +>180605|polyprotein|AGO67248.1|Dengue virus 2|11060 +LMCHATFTM +>180609|polyprotein|ABK30845.1|Dengue virus 3|11069 +LMMMLPATL +>180611|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 +LMRRGDLPVWLAYRV +>180613|envelope protein|AGT63061.1|Dengue virus 3|11069 +LPEEQDQNY +>180617|polyprotein|AGO67248.1|Dengue virus 2|11060 +LPIRYQTPAI +>180618|polyprotein|AGO67248.1|Dengue virus 2|11060 +LPLPWLPGAD +>180620|polyprotein|AGO67248.1|Dengue virus 2|11060 +LPTFMTQKAR +>180624|polyprotein|AGS49173.1|Dengue virus 2|11060 +LPVWLAYKVA +>180637|polyprotein|AGW21594.1|Dengue virus 1|11053 +MAFIAFLRF +>180640|polyprotein|AFP27208.1|Dengue virus 4|11070 +MALKDFKEF +>180641|polyprotein|AFJ91714.1|Dengue virus 1|11053 +MALSIVSLF +>180643|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 +MAMTDTTPFGQQRVF +>180646|polyprotein|AGO67248.1|Dengue virus 2|11060 +MAVGMVSIL +>180647|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 +MEEALRGLPIRYQTP +>180656|polyprotein|AGO67248.1|Dengue virus 2|11060 +MLIPTAMAF +>180657|polyprotein|CDF77361.1|Dengue virus 3|11069 +MLVTPSMTM +>180660|polyprotein|CDF77361.1|Dengue virus 3|11069 +MMLPATLAF +>180662|polyprotein|CDF77361.1|Dengue virus 3|11069 +MMMLPATLAF +>180667|polyprotein|AGO67248.1|Dengue virus 2|11060 +MPSMKRFRRE +>180668|polyprotein|AGO67248.1|Dengue virus 2|11060 +MPSVIEKMET +>180670|polyprotein|AGW21594.1|Dengue virus 1|11053 +MPVTVASAAQ +>180671|polyprotein|AGO67248.1|Dengue virus 2|11060 +MSFRDLGRVM +>180675|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 +MSTYGWNLVRLQSGV +>180681|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 +NEEYTDYMPSMKRFR +>180682|polyprotein|AGO67248.1|Dengue virus 2|11060 +NPEIEDDIF +>180684|nonstructural protein 5|AGX01519.1|Dengue virus 4|11070 +NPRLCTREEF +>180689|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 +NRAVHADMGYWIESA +>180717|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 +RDLGRVMVMVGATMT +>180718|polyprotein|AFP27208.1|Dengue virus 4|11070 +REDLWCGSL +>180723|polyprotein|AGO67248.1|Dengue virus 2|11060 +RFLEFEALGF +>180724|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 +RGEARKTFVDLMRRG +>180726|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 +RMAILGDTAWDFGSL +>180728|Nonstructural protein NS5|YP_001531176.2|Dengue virus 3|11069 +RPRLCTREEF +>180734|Nonstructural protein NS3|NP_739587.2|Dengue virus 2|11060 +RSWNSGHEW +>180735|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 +RVGTKHAILLVAVSF +>180738|polyprotein|CDF77361.1|Dengue virus 3|11069 +RYMGEDGCWY +>180750|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 +SPGTSGSPIIDKKGK +>180756|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 +STRVEMGEAAGIFMT +>180758|Nonstructural protein NS5|NP_739590.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 +SWHYDQDHPYKTWAY +>180774|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 +TLRVLNLVENWLNNN +>180778|polyprotein|AFP27208.1|Dengue virus 4|11070 +TPEGIIPTLF +>180780|polyprotein|AGW21594.1|Dengue virus 1|11053 +TPQDNQLAY +>180781|polyprotein|AGO67248.1|Dengue virus 2|11060 +TPQDNQLTY +>180789|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 +TVIDLDPIPYDPKFE +>180794|polyprotein|AGO67248.1|Dengue virus 2|11060 +VATTFVTPM +>180802|polyprotein|AGO67248.1|Dengue virus 2|11060 +VPLLAIGCY +>180803|polyprotein|AFP27208.1|Dengue virus 4|11070 +VPLLAMGCY +>180804|polyprotein|AGW21594.1|Dengue virus 1|11053 +VPNYNMIIM +>180814|polyprotein|AGO67248.1|Dengue virus 2|11060 +WAYHGSYET +>180816|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 +WGNGCGLFGKGGIVT +>180817|polyprotein|AGO67248.1|Dengue virus 2|11060 +WHYDQDHPY +>180818|Membrane glycoprotein precursor|NP_739582.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 +WILRHPGFTMMAAIL +>180828|polyprotein|AGO67248.1|Dengue virus 2|11060 +YAQMWSLMYF +>180836|polyprotein|AGT63075.1|Dengue virus 1|11053 +YGGPISQHNY +>180843|polyprotein|AFP27208.1|Dengue virus 4|11070 +YPKTKLTDWD +>180850|polyprotein|AFP27208.1|Dengue virus 4|11070 +YTPEGIIPTL +>180880|nucleocapsid protein|AAA43837.1|Hantaan hantavirus|11599 +ETKESKAIR +>181035|||| +VLSDFKVWLKKLFPGGGQICGGVYLLPRRGPRLKKSMMAFSAAL +>181036|||| +VLSDFKVWLKKSMMAFSAAL +>181152|Pol polyprotein|Q9YLQ7|Human immunodeficiency virus 1|11676 +TAFTIPSL +>181154|pol protein|ACJ76655.1|Human immunodeficiency virus 1|11676 +TAFTIPST +>181155|pol protein|AAQ76603.1|Human immunodeficiency virus 1|11676 +TAFTIPSV +>181731|Possible hydrolase|NP_215850.1|Mycobacterium tuberculosis|1773 +MLLRKGTVYVLVIRADLVNAMVAHA +>181733|Antigen 85-B|P0C5B9.1|Mycobacterium tuberculosis|1773 +MTDVSRKIRAWGRRLMIGTAAAVVLPGLVGLAGGAATAGA +>182421|polyprotein|AGO67248.1|Dengue virus 2|11060 +AAGRKSLTL +>182508|polyprotein|AFP27208.1|Dengue virus 4|11070 +AIAVASGLLW +>182554|polyprotein|ACF49259.1|Dengue virus type 1 Hawaii|10000440 +ALLATSIFK +>182599|polyprotein|AGW21594.1|Dengue virus 1|11053 +AQMWQLMYF +>182687|polyprotein|AGK36298.1|Dengue virus 2|11060 +AYRIKQRGIL +>182702|polyprotein|AGO63991.1|Dengue virus|12637 +CLMMILPAA +>182707|polyprotein|AFY10039.1|Dengue virus 4|11070 +CNLTSTWVMY +>182747|polyprotein|AGO67248.1|Dengue virus 2|11060 +CYSQVNPITL +>182836|polyprotein|ACF49259.1|Dengue virus type 1 Hawaii|10000440 +DYMTSMKRF +>182848|polyprotein|AGO67248.1|Dengue virus 2|11060 +EARKTFVDL +>182892|polyprotein|AFP27208.1|Dengue virus 4|11070 +EENMEVEIW +>182898|polyprotein|AGO67248.1|Dengue virus 2|11060 +EEREIPERSW +>182912|polyprotein|AGW21594.1|Dengue virus 1|11053 +EFFLMVLLI +>182917|polyprotein|CDF77361.1|Dengue virus 3|11069 +EFKDFAAGR +>182926|polyprotein|AFP27208.1|Dengue virus 4|11070 +EIASLPTYL +>182938|polyprotein|AGO67248.1|Dengue virus 2|11060 +EKEENLVNSL +>182939|polyprotein|CDF77361.1|Dengue virus 3|11069 +EKEENMVKSL +>182971|polyprotein|AFP27208.1|Dengue virus 4|11070 +EMCEDTVTY +>183147|polyprotein|AGW21594.1|Dengue virus 1|11053 +FCSHHFHQL +>183162|polyprotein|AGW21594.1|Dengue virus 1|11053 +FFLMVLLIPE +>183165|polyprotein|CDF77361.1|Dengue virus 3|11069 +FFMMVLLIPE +>183175|polyprotein|AGW21594.1|Dengue virus 1|11053 +FIAFLRFLA +>183223|polyprotein|AGW21594.1|Dengue virus 1|11053 +FPGKTVWFVP +>183229|polyprotein|AGW21594.1|Dengue virus 1|11053 +FPQSNAVIQD +>183231|polyprotein|AFP27208.1|Dengue virus 4|11070 +FPQSNSPIED +>183245|polyprotein|AGT63074.1|Dengue virus 1|11053 +FQSHQLWATL +>183252|polyprotein|AGT63075.1|Dengue virus 1|11053 +FSLHYAWKTM +>183275|polyprotein|AGW21594.1|Dengue virus 1|11053 +FTNMEVQLIR +>183353|polyprotein|AFP27208.1|Dengue virus 4|11070 +GESSSNPTI +>183363|gag polyprotein|BAA00992.1|Human immunodeficiency virus 1|11676 +GGKKKYKL +>183366|gag protein|ABI20203.1|Human immunodeficiency virus 1|11676 +GGKKRYKL +>183395|polyprotein|AAS49480.2|Dengue virus 3|11069 +GKKHMIAGVL +>183421|polyprotein|AGW21594.1|Dengue virus 1|11053 +GLNSRSTSL +>183437|polyprotein|AGO67248.1|Dengue virus 2|11060 +GMNSRSTSL +>183570|polyprotein|AFP27208.1|Dengue virus 4|11070 +HEMYWVSGV +>183577|polyprotein|AGK36298.1|Dengue virus 2|11060 +HFQRALIFIL +>183587|polyprotein|AGH08163.1|Dengue virus 3|11069 +HMIAGVFFTF +>183594|polyprotein|AGT63075.1|Dengue virus 1|11053 +HPASAWTLYA +>183598|polyprotein|AGW21594.1|Dengue virus 1|11053 +HPGSGKTRRY +>183619|nonstructural protein NS1|1802191G|Dengue virus|12637 +HTWTEQYKF +>183621|polyprotein|AGK36298.1|Dengue virus 2|11060 +HVQRIETWIL +>183654|polyprotein|AGW21594.1|Dengue virus 1|11053 +IAVGMVTLY +>183670|polyprotein|AGO67248.1|Dengue virus 2|11060 +IENSSVNVSL +>183672|polyprotein|AFP27208.1|Dengue virus 4|11070 +IENTSANLSL +>183708|polyprotein|AGO67248.1|Dengue virus 2|11060 +IGMNSRSTSL +>183719|polyprotein|AGO63991.1|Dengue virus|12637 +IINKRKKTSL +>183723|polyprotein|CDF77361.1|Dengue virus 3|11069 +IKLTVVVGDI +>183724|polyprotein|AGO67248.1|Dengue virus 2|11060 +IKRGLRTLIL +>183741|polyprotein|AGS49173.1|Dengue virus 2|11060 +ILCVPNAVIL +>183747|polyprotein|AGO67248.1|Dengue virus 2|11060 +ILIGVIITW +>183766|polyprotein|AGO67248.1|Dengue virus 2|11060 +ILNRRRRTA +>183779|polyprotein|AGO67248.1|Dengue virus 2|11060 +IMAVGMVSIL +>183781|polyprotein|AGO67248.1|Dengue virus 2|11060 +IMDLEKRHVL +>183793|envelope protein|AGT63061.1|Dengue virus 3|11069 +IMKIGIGVLL +>183800|polyprotein|AGT63075.1|Dengue virus 1|11053 +IMNRRKRSV +>183804|polyprotein|AGO63991.1|Dengue virus|12637 +INKRKKTSL +>183813|polyprotein|AGW21594.1|Dengue virus 1|11053 +IPEPDRQRTP +>183819|polyprotein|AGO67248.1|Dengue virus 2|11060 +IPITAAAWYL +>183825|polyprotein|AGO67248.1|Dengue virus 2|11060 +IPLALTIKGL +>183843|envelope protein|AGW23576.1|Dengue virus 3|11069 +IQNSGGTSIF +>184065|Nonstructural protein NS3|YP_001531172.2|Dengue virus 3|11069 +KLNDWDFVV +>184130|polyprotein|AFP27208.1|Dengue virus 4|11070 +KREDLWCGSL +>184131|polyprotein|AGO67248.1|Dengue virus 2|11060 +KREDQWCGSL +>184136|gag protein|ADZ56444.1|Human immunodeficiency virus 1|11676 +KRWIIMGLNK +>184212|polyprotein|AGW21594.1|Dengue virus 1|11053 +KVRKDIPQW +>184234|polyprotein|AGO67248.1|Dengue virus 2|11060 +KWKSRLNAL +>184260|polyprotein|CDF77361.1|Dengue virus 3|11069 +LAIPPTAGVL +>184264|polyprotein|CDF77361.1|Dengue virus 3|11069 +LAKRFSRGL +>184265|polyprotein|CDF77361.1|Dengue virus 3|11069 +LAKRFSRGLL +>184274|polyprotein|AGW21594.1|Dengue virus 1|11053 +LALMATFKM +>184299|envelope protein|AGT63061.1|Dengue virus 3|11069 +LATLRKLCI +>184300|envelope protein|AFN87749.1|Dengue virus 2|11060 +LATLRKYCI +>184316|polyprotein|AGW21594.1|Dengue virus 1|11053 +LEENMDVEIW +>184318|polyprotein|AFP27208.1|Dengue virus 4|11070 +LEENMEVEIW +>184337|polyprotein|AGO67248.1|Dengue virus 2|11060 +LEKRHVLGRL +>184373|polyprotein|AGO67248.1|Dengue virus 2|11060 +LGKKKTPRM +>184377|polyprotein|AGW21594.1|Dengue virus 1|11053 +LGLNSRSTSL +>184378|polyprotein|AGO67248.1|Dengue virus 2|11060 +LGMLQGRGPL +>184412|envelope protein|AGW23591.1|Dengue virus 3|11069 +LKGMSYAMCL +>184429|||| +LLFGFPVYV +>184439|polyprotein|AGO67248.1|Dengue virus 2|11060 +LLILCVTQVL +>184453|polyprotein|AFP27207.1|Dengue virus 4|11070 +LLLMRTTWAF +>184458|polyprotein|AGT17702.1|Dengue virus 1|11053 +LLMLLPTAL +>184467|polyprotein|AGO67248.1|Dengue virus 2|11060 +LLQMEDKAWL +>184512|polyprotein|AGO67248.1|Dengue virus 2|11060 +LMWKQITPEL +>184518|polyprotein|AGO67248.1|Dengue virus 2|11060 +LNRRRRTAG +>184522|polyprotein|AGW21594.1|Dengue virus 1|11053 +LPDTIETLM +>184523|polyprotein|AGW21594.1|Dengue virus 1|11053 +LPDTIETLML +>184531|polyprotein|AFP27208.1|Dengue virus 4|11070 +LPESLETLML +>184554|polyprotein|AGT63075.1|Dengue virus 1|11053 +LPQHLTQRAQ +>184571|polyprotein|AGO67248.1|Dengue virus 2|11060 +LQLKGMSYSM +>184585|NS1|AGW99229.1|Dengue virus 3|11069 +LRTTTVSGKL +>184643|polyprotein|AGW24534.1|Dengue virus 2|11060 +LTIPPTAGIL +>184658|polyprotein|CDF77361.1|Dengue virus 3|11069 +LTQKVVIFIL +>184702|non-structural protein 1|AGM49312.1|Dengue virus|12637 +LWPKTHTLW +>184713|polyprotein|AFP27208.1|Dengue virus 4|11070 +LYAVATTIL +>184736|polyprotein|AGW21594.1|Dengue virus 1|11053 +MAMVLSIVS +>184739|polyprotein|AGW21594.1|Dengue virus 1|11053 +MASSVLLWM +>184755|polyprotein|AGO67248.1|Dengue virus 2|11060 +MDLEKRHVL +>184804|non-structural protein 1|AGM49312.1|Dengue virus|12637 +MFTTNIWMKF +>184814|polyprotein|AGO67248.1|Dengue virus 2|11060 +MGLGKGWPL +>184819|polyprotein|AGH08163.1|Dengue virus 3|11069 +MIAGVFFTF +>184835|polyprotein|AGW21594.1|Dengue virus 1|11053 +MKLVMAFIAF +>184840|polyprotein|AGS49173.1|Dengue virus 2|11060 +MLINRFTMR +>184845|polyprotein|CDF77361.1|Dengue virus 3|11069 +MLKRVRNRV +>184849|nonstructural protein 5|AGX01518.1|Dengue virus 1|11053 +MLLNRFTMA +>184856|polyprotein|AGW21594.1|Dengue virus 1|11053 +MLMTGTLAVF +>184864|polyprotein|AGO67248.1|Dengue virus 2|11060 +MLRTRVGTK +>184880|polyprotein|AGT63075.1|Dengue virus 1|11053 +MNRRKRSVT +>184884|polyprotein|AGW21594.1|Dengue virus 1|11053 +MPIRYQTTAV +>184896|polyprotein|AGW21594.1|Dengue virus 1|11053 +MPVTVASAA +>184898|polyprotein|AGW21594.1|Dengue virus 1|11053 +MQRKHGGML +>184899|polyprotein|AGO67248.1|Dengue virus 2|11060 +MRGAKRMAI +>184900|polyprotein|AGO67248.1|Dengue virus 2|11060 +MRGAKRMAIL +>185050|polyprotein|AFP27208.1|Dengue virus 4|11070 +NFLEVEDYGF +>185102|polyprotein|AGT63075.1|Dengue virus 1|11053 +NRRKRSVTM +>185104|polyprotein|AGO67248.1|Dengue virus 2|11060 +NRRRRTAGV +>185124|polyprotein|AGW21594.1|Dengue virus 1|11053 +NTPEGIIPA +>185125|polyprotein|AGW21594.1|Dengue virus 1|11053 +NTPEGIIPAL +>185200|polyprotein|AGO67248.1|Dengue virus 2|11060 +PRRCMKPVIL +>185232|polyprotein|AFP27208.1|Dengue virus 4|11070 +QEEHKETWHY +>185260|polyprotein|CDF77361.1|Dengue virus 3|11069 +QLAKRFSRG +>185279|polyprotein|AGW21594.1|Dengue virus 1|11053 +QMQRKHGGML +>185327|polyprotein|ACF49259.1|Dengue virus type 1 Hawaii|10000440 +QYIYMGQPL +>185388|polyprotein|AGO67248.1|Dengue virus 2|11060 +RIKQKGILGY +>185399|polyprotein|AGO67248.1|Dengue virus 2|11060 +RKKARSTPF +>185419|envelope protein|AGW23591.1|Dengue virus 3|11069 +RLKMDKLEL +>185447|polyprotein|AGK36298.1|Dengue virus 2|11060 +RNALDNLAVL +>185465|polyprotein|AGO67248.1|Dengue virus 2|11060 +RPLKEKEENL +>185468|polyprotein|AGW21594.1|Dengue virus 1|11053 +RPMFAVGLLF +>185485|polyprotein|AGW21594.1|Dengue virus 1|11053 +RQMESEGIFL +>185491|polyprotein|AGO67248.1|Dengue virus 2|11060 +RREEEEAGVL +>185492|polyprotein|AGT63075.1|Dengue virus 1|11053 +RRKRSVTMLL +>185573|polyprotein|CDF77361.1|Dengue virus 3|11069 +RYMGEDGCW +>185651|polyprotein|ACF49259.1|Dengue virus type 1 Hawaii|10000440 +SILLSSLLK +>185685|polyprotein|CDF77361.1|Dengue virus 3|11069 +SLLFKTASG +>185710|Nonstructural protein NS5|YP_001531176.2|Dengue virus 3|11069 +SMINGVVKL +>185716|polyprotein|AAA21201.1|Dengue virus 3|11069 +SMTMRCVGI +>185734|polyprotein|CDF77361.1|Dengue virus 3|11069 +SPKRLATAI +>185741|polyprotein|AGW21594.1|Dengue virus 1|11053 +SPVRVPNYNM +>185758|polyprotein|AGO67248.1|Dengue virus 2|11060 +SRSTSLSVSL +>185817|envelope protein|AGW23590.1|Dengue virus 4|11070 +SWMIRILIGF +>185827|polyprotein|ACF49259.1|Dengue virus type 1 Hawaii|10000440 +SYKVASEGF +>185881|polyprotein|AFP27208.1|Dengue virus 4|11070 +TEIASLPTYL +>185931|polyprotein|AGO67248.1|Dengue virus 2|11060 +TKQTGSASSM +>185978|polyprotein|CDF77361.1|Dengue virus 3|11069 +TMGVLCLAIL +>186002|polyprotein|AGO67248.1|Dengue virus 2|11060 +TPMLRHSIE +>186008|polyprotein|AGI95993.1|Dengue virus 4|11070 +TPPGATDPF +>186029|envelope protein|ABV59122.1|Dengue virus 3|11069 +TPTWNRKEL +>186041|polyprotein|AGO67248.1|Dengue virus 2|11060 +TRVGTKHAIL +>186058|polyprotein|AGO67248.1|Dengue virus 2|11060 +TSKKRSWPL +>186175|polyprotein|AFY10053.1|Dengue virus 3|11069 +TWRDMAHTLI +>186192|polyprotein|AGO67248.1|Dengue virus 2|11060 +VAATMANEM +>186211|polyprotein|AGO67248.1|Dengue virus 2|11060 +VDRKGKVVGL +>186219|polyprotein|AGK36298.1|Dengue virus 2|11060 +VEDGRFWEL +>186234|polyprotein|AFY10052.1|Dengue virus 3|11069 +VEIWTKEGEK +>186242|polyprotein|AGO67248.1|Dengue virus 2|11060 +VEMGEAAGIF +>186264|polyprotein|AGO67248.1|Dengue virus 2|11060 +VGRQEKGKSL +>186301|polyprotein|AGO67248.1|Dengue virus 2|11060 +VLMHRGKRI +>186303|polyprotein|AGS14893.1|Dengue virus 4|11070 +VLMMLVAPSY +>186330|polyprotein|AFP27208.1|Dengue virus 4|11070 +VMLLVHYAI +>186354|polyprotein|AGO67248.1|Dengue virus 2|11060 +VQQLTKRFSL +>186427|polyprotein|ACF49259.1|Dengue virus type 1 Hawaii|10000440 +VVYDAKFEK +>186453|polyprotein|AFP27208.1|Dengue virus 4|11070 +WEPSKGWKNW +>186470|envelope protein|AGT63061.1|Dengue virus 3|11069 +WIMKIGIGVL +>186474|polyprotein|AGO67248.1|Dengue virus 2|11060 +WKTWGKAKML +>186524|polyprotein|AGW21594.1|Dengue virus 1|11053 +WTMKIGIGIL +>186550|polyprotein|AFY10039.1|Dengue virus 4|11070 +YDQENPYRTW +>186551|polyprotein|AGW21594.1|Dengue virus 1|11053 +YENLKYSVIV +>186559|polyprotein|AGW21594.1|Dengue virus 1|11053 +YKVASEGFQY +>186603|polyprotein|AGW21594.1|Dengue virus 1|11053 +YSDPLALREF +>186620|polyprotein|AFP27208.1|Dengue virus 4|11070 +YVILTILTI +>186640|polyprotein|AFP27207.1|Dengue virus 4|11070 +YYMATLKNV +>186641|polyprotein|AFP27207.1|Dengue virus 4|11070 +YYMATLKNVT +>186692|||| +LLFGYPVFV +>187041|polyprotein|ABG67747.1|West Nile virus|11082 +AIIEVDRSAAK +>187045|polyprotein|ABG67747.1|West Nile virus|11082 +AVVVNPSVK +>187063|polyprotein|ABG67747.1|West Nile virus|11082 +GTLTSAINR +>187069|polyprotein precursor|AAF20092.2|West Nile virus|11082 +KNMEKPGLK +>187086|polyprotein|ABG67747.1|West Nile virus|11082 +RVLSLIGLK +>187106|Vpr protein|BAA93983.1|Human immunodeficiency virus 1|11676 +AVRHFPRIW +>187154|Vif protein|CAD26959.1|Human immunodeficiency virus 1|11676 +ISKKAKGWF +>187158|Gag protein|Q1KW74|Human immunodeficiency virus 1|11676 +KAFNPEIIPMF +>187160|Protein Rev|P04616.1|Human immunodeficiency virus 1|11676 +KAVRLIKFLY +>187163|Gag polyprotein|P88150|Human immunodeficiency virus 1|11676 +KGFNPEVIPMF +>187188|PE family protein PE9|YP_177784.1|Mycobacterium tuberculosis H37Rv|83332 +RLFNANAEEYHALSA +>187189|PE-PGRS family protein PE_PGRS42|YP_177886.1|Mycobacterium tuberculosis H37Rv|83332 +SAAIAGLFG +>187197|Core protein|Q9QAC5|Hepatitis B virus|10407 +VCWGELMNL +>189204|||| +ALYNTVATL +>189275|gag protein|AAO84847.1|Human immunodeficiency virus 1|11676 +SLFNAVAVL +>189277|gag protein|AAY98604.1|Human immunodeficiency virus 1|11676 +SLFNTIAVL +>189280|||| +SLYLTVATL +>189285|gag protein|AAK30999.1|Human immunodeficiency virus 1|11676 +SLYNSVATL +>189286|||| +SLYNTAATL +>189287|gag protein|ADO94802.1|Human immunodeficiency virus 1|11676 +SLYNTIAIL +>189288|gag protein|AAV53168.1|Human immunodeficiency virus 1|11676 +SLYNTIATL +>189289|gag protein|ADO93742.1|Human immunodeficiency virus 1|11676 +SLYNTISVL +>189290|gag protein|ACO48925.1|Human immunodeficiency virus 1|11676 +SLYNTITVL +>189291|||| +SLYNTVAAL +>189292|gag protein|ABC40295.1|Human immunodeficiency virus 1|11676 +SLYNTVAIF +>189293|gag protein|BAB88077.1|Human immunodeficiency virus 1|11676 +SLYNTVAVL +>189294|Gag|O89360|Human immunodeficiency virus 1|11676 +SLYNTVSTL +>189295|gag protein|AEB70304.1|Human immunodeficiency virus 1|11676 +SLYNTVVTL +>189297|||| +SLYQTVATL +>189300|gag polyprotein|BAB88548.1|Human immunodeficiency virus 1|11676 +SVYNTVATL +>189503|hexon protein|AAD47268.1|Human adenovirus 11|10541 +TYFNLGNKF +>189546|glycosyl transferase|WP_015631503.1|Mycobacterium tuberculosis|1773 +AAPEPVARR +>189547|cyclopropane-fatty-acyl-phospholipid synthase|YP_005911842.1|Mycobacterium tuberculosis|1773 +AASAAIANR +>189566|glycosyl transferase|WP_015631503.1|Mycobacterium tuberculosis|1773 +ALADLPVTV +>189569|||| +AMLDHAGDM +>189571|Antigen 85-B|P0C5B9.1|Mycobacterium tuberculosis|1773 +ANNTRLWVY +>189575|POSSIBLE GLYCOSYL TRANSFERASE|CAB05418.1|Mycobacterium tuberculosis|1773 +ARLAGIPY +>189687|glycosyl transferase|WP_003906951.1|Mycobacterium tuberculosis|1773 +IVLVRRWPK +>189705|glycosyl transferase|WP_015631503.1|Mycobacterium tuberculosis|1773 +KYIAADRKI +>189706|cyclopropane-fatty-acyl-phospholipid synthase|WP_010924246.1|Mycobacterium tuberculosis|1773 +KYIFPGGLL +>189727|Antigen 85-B|P0C5B9.1|Mycobacterium tuberculosis|1773 +LPQWLSANR +>189740|glycosyl transferase|WP_003906951.1|Mycobacterium tuberculosis|1773 +LVYGDVIMR +>189748|||| +MLDHAGDMA +>189750|Diacylglycerol acyltransferase/mycolyltransferase Ag85B|SRC280000|Mycobacterium tuberculosis|1773 +MPVGGGSSF +>189755|||| +MYNYPTMLD +>189799|glycosyl transferase|WP_003906951.1|Mycobacterium tuberculosis|1773 +PYNLRYRVL +>189829|cyclopropane-fatty-acyl-phospholipid synthase|WP_010924246.1|Mycobacterium tuberculosis|1773 +RMWELYLAY +>189849|glycosyltransferase|WP_016721157.1|Mycobacterium tuberculosis|1773 +SIIIPTLNV +>189894|cyclopropane-fatty-acyl-phospholipid synthase|WP_010924246.1|Mycobacterium tuberculosis|1773 +VLAGSVDEL +>189905|Antigen 85-B|P0C5B9.1|Mycobacterium tuberculosis|1773 +WGAQLNAMK +>190409|polymerase|AAD16253.1|Hepatitis B virus|10407 +ESTRSASFCGSPYSW +>190443|core protein|BAF42671.1|Hepatitis B virus|10407 +HISCLTFGR +>190455|core protein|AAL31780.1|Hepatitis B virus|10407 +KEFGASVELL +>190466|large surface antigen|CAL29876.1|Hepatitis B virus|10407 +LGFFPDHQLDPAFGA +>190488|large/middle/small S proteins|AAK97183.1|Hepatitis B virus|10407 +LWEWASVRF +>190494|nucleocapsid protein|ABI96968.1|SARS coronavirus|227859 +MEVTPSGTWL +>190509|HBsAg|AAL66328.1|Hepatitis B virus|10407 +PFMPLLPIFF +>190533|nucleocapsid protein|AAP49024.1|SARS coronavirus|227859 +RRPQGLPNNIASWFT +>190556|HBsAg|AAL66328.1|Hepatitis B virus|10407 +SVIWMMWYW +>190568|polymerase|AAD16253.1|Hepatitis B virus|10407 +TYGRKLHLYSHPIILGFRKI +>190569|polymerase|ADG03431.1|Hepatitis B virus|10407 +VDKNPHNTTESRLVV +>190577|surface antigen|AAZ30211.1|Hepatitis B virus|10407 +VIWMMWYWGR +>190589|surface antigen|AAZ30211.1|Hepatitis B virus|10407 +WLSVIWMMWY +>190596|polymerase|BAD04994.1|Hepatitis B virus|10407 +YPALMPLSACIQAKR +>190821|polyprotein|AAT94261.1|Hepatitis C virus|11103 +KLLGLGINAV +>190822|polyprotein|BAB18801.1|Hepatitis C virus|11103 +KLSGLGINAI +>190826|gag polyprotein|CAB81949.1|Human immunodeficiency virus 1|11676 +KSLFNTIATL +>190827|gag protein|AAN08336.1|Human immunodeficiency virus 1|11676 +KSLYNTIATL +>190828|gag protein|ABI20203.1|Human immunodeficiency virus 1|11676 +KSLYNTIAVL +>190829|gag protein|BAB88077.1|Human immunodeficiency virus 1|11676 +KSLYNTVAVL +>190959|gag polyprotein|BAB19174.1|Human immunodeficiency virus 1|11676 +RSLFNTIATL +>190960|gag-pol polyprotein|BAC02551.1|Human immunodeficiency virus 1|11676 +RSLFNTIAVL +>190961|gag protein|BAC45024.1|Human immunodeficiency virus 1|11676 +RSLFNTVAVL +>190962|gag polyprotein|BAB88540.1|Human immunodeficiency virus 1|11676 +RSLYNTIATL +>190963|gag-pol fusion polyprotein precursor|CAY83124.1|Human immunodeficiency virus 1|11676 +RSLYNTIAVL +>190974|gag polyprotein|BAB19174.1|Human immunodeficiency virus 1|11676 +SLFNTIATLY +>190975|gag protein|BAC45024.1|Human immunodeficiency virus 1|11676 +SLFNTVAVLY +>190978|gag protein|AAV53168.1|Human immunodeficiency virus 1|11676 +SLYNTIATLY +>190979|gag protein|ABI20203.1|Human immunodeficiency virus 1|11676 +SLYNTIAVLY +>190980|gag protein|AAV53216.1|Human immunodeficiency virus 1|11676 +SLYNTVATLY +>190981|gag protein|BAB88077.1|Human immunodeficiency virus 1|11676 +SLYNTVAVLY +>191095|Capsid protein|P03146.1|Hepatitis B virus ayw/France/Tiollais/1979|490133 +YVNTNMGLK +>193060|Nef protein|Q9YYU3|Human immunodeficiency virus 1|11676 +RFPLTFGWCF +>193071|Nef protein|Q9WPU2|Human immunodeficiency virus 1|11676 +RYPLTLGWCF +>193551|Protein 3a|P59632.1|SARS coronavirus|227859 +SITAQPVKI +>193665|envelope glycoprotein B|NP_044629.1|Herpes simplex virus (type 1 / strain 17)|10299 +ALLGLTLGV +>193837|envelope glycoprotein B|NP_044629.1|Herpes simplex virus (type 1 / strain 17)|10299 +FVLATGDFV +>193840|envelope glycoprotein B|NP_044629.1|Herpes simplex virus (type 1 / strain 17)|10299 +GIFEDRAPV +>194160|BaRF1|AFJ06848.1|Human gammaherpesvirus 4|10376 +LLIEGIFFI +>194181|envelope glycoprotein B|NP_044629.1|Herpes simplex virus (type 1 / strain 17)|10299 +LLTTPKFTV +>194227|Glycoprotein B|P10211.1|Herpes simplex virus (type 1 / strain 17)|10299 +NLLTTPKFT +>194242|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis|1773 +QEAGNFERI +>194400|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis|1773 +TAGSLQGQW +>194440|envelope glycoprotein B|NP_044629.1|Herpes simplex virus (type 1 / strain 17)|10299 +TMYYKDVTV +>194442|BFRF3|YP_001129448.1|Human gammaherpesvirus 4|10376 +TPSVSSSISSL +>194449|BKRF2|AFY97944.1|Human gammaherpesvirus 4|10376 +VEDLFGANL +>194555|BNRF1|AGZ95154.1|Human gammaherpesvirus 4|10376 +WQWEHIPPA +>194567|envelope glycoprotein B|NP_044629.1|Herpes simplex virus (type 1 / strain 17)|10299 +YLANGGFLI +>194657|BNRF1|AGZ95154.1|Human gammaherpesvirus 4|10376 +YPRNPTEQGNI +>195418|6 kDa early secretory antigenic target ESXA (ESAT-6)|YP_178023.1|Mycobacterium tuberculosis H37Rv|83332 +GSGSEAYQGVQQKWD +>196087|PPE family protein PPE54|YP_177960.1|Mycobacterium tuberculosis H37Rv|83332 +TVKSMILHEIL +>226775|PreS1/PreS2/surface protein|Q2EID8|Hepatitis B virus|10407 +GYRWMCLRR +>226786|core protein|BAF42671.1|Hepatitis B virus|10407 +LVSFGVWIR +>226809|Large S protein|BAF36017.1|Hepatitis B virus|10407 +YLWEWASVR +>226853|ribonucleotide reductase subunit 2|NP_040141.1|Human alphaherpesvirus 3|10335 +ILIEGIFFV +>226871|ribonucleotide reductase subunit 2|NP_040141.1|Human alphaherpesvirus 3|10335 +MILIEGIFFV +>230028|Protein Nef|P04603.3|Human immunodeficiency virus 1|11676 +NYTPGPGIRF +>230029|Protein Nef|P03404.4|Human immunodeficiency virus 1|11676 +NYTPGPGIRY +>230030|Nef protein|BAA86664.1|Human immunodeficiency virus 1|11676 +NYTPGPGTRF +>230122|nef protein|ACR27128.1|Human immunodeficiency virus 1|11676 +FLKEKGGL +>231862|Major surface antigen p30 precursor|P13664.1|Toxoplasma gondii RH|383379 +FAGAAGSAKSAAGTASHVSI +>232152|rhoptry kinase family protein|AFO54841.1|Toxoplasma gondii type III|398031 +PPEQPFHSYGVTYTFATDA +>232153|rhoptry protein 18|CAJ27113.1|Toxoplasma gondii type I|1209525 +PPERPFQATGITYTFPTDA +>232154|rhoptry protein, putative / protein kinase domain-containing protein|XP_002367757.1|Toxoplasma gondii type II|1209523 +PPERPFQTTDITYTFTTDA +>233309|polyprotein|ACZ60102.1|Hepatitis C virus subtype 3a|356426 +VRMVMMTHF +>236085|polyprotein|ABD97104.1|Hepatitis C virus|11103 +HSKKKCDEM +>238379|polyprotein|ACE82359.1|Hepatitis C virus subtype 1a|31646 +FLVGQLFTF +>240792|Major immediate-early protein|Q9YRL8|Human betaherpesvirus 5|10359 +ELNRKMIYM +>240808|polyprotein|AAB53095.1|Tick-borne encephalitis virus|11084 +ILLDNITTL +>243835|glycosyl transferase|WP_015628558.1|Mycobacterium tuberculosis|1773 +SARLAGIPY +>244160|surface antigen 2 (CA-2)|XP_818927.1|Trypanosoma cruzi strain CL Brener|353153 +AAAGDKLSL +>244167|surface antigen 2|SRC298288|Trypanosoma cruzi|5693 +ALQVTNHRYL +>244168|surface antigen 2|SRC298288|Trypanosoma cruzi|5693 +ALRNLRVFL +>244296|surface antigen 2|SRC298288|Trypanosoma cruzi|5693 +TVFDASRSTV +>251793|transmembrane serine/threonine-protein kinase A|WP_016330371.1|Mycobacterium tuberculosis|1773 +AIIIAVLLV +>252997|transmembrane serine/threonine-protein kinase A|WP_016330371.1|Mycobacterium tuberculosis|1773 +ALAIIIAVL +>288104|nef protein|ACR27130.1|Human immunodeficiency virus 1|11676 +EVGFPVRPQVPLRPMTFK +>294287|gag protein|ABI20203.1|Human immunodeficiency virus 1|11676 +GATPQDLNTMLNTVGGH +>418940|PPE family protein PPE68|KAM81677.1|Mycobacterium tuberculosis H37Ra|419947 +AAAAGWQTL +>418942|PPE family protein PPE68|KAM81677.1|Mycobacterium tuberculosis H37Ra|419947 +ALAAATPMVV +>418943|PPE family protein PPE68|KAM81677.1|Mycobacterium tuberculosis H37Ra|419947 +ALAMEVYQA +>418944|PPE family protein PPE68|KAM81677.1|Mycobacterium tuberculosis H37Ra|419947 +ALDAQAVEL +>418945|PPE family protein PPE68|KAM81677.1|Mycobacterium tuberculosis H37Ra|419947 +ALTEMDYFI +>418947|PPE family protein PPE68|KAM81677.1|Mycobacterium tuberculosis H37Ra|419947 +AMPPELNTA +>418964|PPE family protein PPE68|KAM81677.1|Mycobacterium tuberculosis H37Ra|419947 +ELTARLNSL +>418967|PPE family protein PPE68|KAM81677.1|Mycobacterium tuberculosis H37Ra|419947 +FIRMWNQAAL +>418975|PPE family protein PPE68|KAM81677.1|Mycobacterium tuberculosis H37Ra|419947 +GINTIPIAL +>418991|polyprotein|AFY10039.1|Dengue virus 4|11070 +IPVTMALWY +>418997|PPE family protein PPE68|KAM81677.1|Mycobacterium tuberculosis H37Ra|419947 +KLEPMASIL +>419002|PPE family protein PPE68|KAM81677.1|Mycobacterium tuberculosis H37Ra|419947 +LIEKPVAPSV +>419005|polyprotein|AGW21594.1|Dengue virus 1|11053 +LLAVSGVYPM +>419006|PPE family protein PPE68|KAM81677.1|Mycobacterium tuberculosis H37Ra|419947 +LLRAESLPGA +>419017|polyprotein|AFY10034.1|Dengue virus 4|11070 +MPAMKRYSAP +>419024|polyprotein|AGW21594.1|Dengue virus 1|11053 +NMIIMDEAHF +>419031|PPE family protein PPE68|KAM81677.1|Mycobacterium tuberculosis H37Ra|419947 +QLPPAATQTL +>419037|polyprotein|AEF01538.1|Dengue virus 1|11053 +RPMFAVGILF +>419045|PPE family protein PPE68|KAM81677.1|Mycobacterium tuberculosis H37Ra|419947 +SLPEIAANHI +>419048|polyprotein|AFY10039.1|Dengue virus 4|11070 +SPRLCTREEF +>419095|polyprotein|ABR25251.1|Hepatitis C virus|11103 +AELIEANLLW +>419098|polyprotein|ABR27377.1|Hepatitis C virus|11103 +AEVIAPAVQT +>419124|polyprotein|ACF49259.1|Dengue virus type 1 Hawaii|10000440 +AVEPGKNPK +>419125|polyprotein|ACF49259.1|Dengue virus type 1 Hawaii|10000440 +AVKSEHTGR +>419128|polyprotein|ACF49259.1|Dengue virus type 1 Hawaii|10000440 +AYRHAMEEL +>419170|polyprotein|ABR25251.1|Hepatitis C virus|11103 +FAWYLKGKW +>419208|polyprotein|ACF49259.1|Dengue virus type 1 Hawaii|10000440 +GVEGEGLHK +>419229|polyprotein|ACF49259.1|Dengue virus type 1 Hawaii|10000440 +IYRILQRGL +>419298|RNA-dependent RNA polymerase|ACH97782.1|Hepatitis C virus|11103 +NSKRTPMGF +>419306|polyprotein|ACF49259.1|Dengue virus type 1 Hawaii|10000440 +PTLDIELLK +>419320|polyprotein|AGZ86443.1|Hepatitis C virus|11103 +RAEAQLHAW +>419325|Genome polyprotein|O92532.3|Hepatitis C virus|11103 +RLGPVQNEV +>419366|polyprotein|BAA00792.1|Hepatitis C virus|11103 +SVIDCNVAV +>419410|polyprotein|ABR25251.1|Hepatitis C virus|11103 +WLGNIIMFA +>419424|polyprotein|BAA00792.1|Hepatitis C virus|11103 +YLTAYQATV +>422880|External core antigen|SRC279980|Hepatitis B virus|10407 +GLKILQLL +>422981|Genome polyprotein|P26664.3|Hepatitis C virus genotype 1|41856 +AICGKYLFNW +>422983|Genome polyprotein|P27958.3|Hepatitis C virus genotype 1|41856 +ARDQLEQAL +>422984|NS5B protein|ABB72740.1|Hepatitis C virus genotype 1|41856 +ARMILLTHF +>422985|polyprotein precursor|BAA02756.1|Hepatitis C virus genotype 1|41856 +ARSVRAKLL +>422989|polyprotein|ABY67644.1|Hepatitis C virus genotype 1|41856 +FAPALPIWAR +>422990|C protein|CAB41699.1|Hepatitis B virus|10407 +FGVWIRTPPAYR +>422996|Genome polyprotein|P26664.3|Hepatitis C virus genotype 1|41856 +GAYMSKAHGI +>422997|preC/core protein|CAJ33968.1|Hepatitis B virus|10407 +GDLMNLATW +>422998|polyprotein precursor|BAA02756.1|Hepatitis C virus genotype 1|41856 +GEVPSTEDL +>422999|polyprotein|ABD97104.1|Hepatitis C virus genotype 3|356114 +GILVLFGFF +>423002|polyprotein|ABY67644.1|Hepatitis C virus genotype 1|41856 +GRAAICGRY +>423007|Genome polyprotein|P26664.3|Hepatitis C virus genotype 1|41856 +GVQEDAASLR +>423010|polyprotein|AAC03058.1|Hepatitis C virus genotype 3|356114 +IMGGELPTA +>423011|polyprotein|AER51001.1|Hepatitis C virus genotype 1|41856 +IMSGEVPSM +>423016|NS5A|ACX46481.1|Hepatitis C virus genotype 1|41856 +KFPLAMPVW +>423019|protease-helicase|AER50967.1|Hepatitis C virus genotype 1|41856 +KLVALGLNAV +>423020|polyprotein|ACE82359.1|Hepatitis C virus genotype 1|41856 +KLYISWCLW +>423022|Genome polyprotein|P27958.3|Hepatitis C virus genotype 1|41856 +KQSGENFPYL +>423031|core|CAA59522.1|Hepatitis B virus|10407 +LESPEHCSP +>423032|core protein|AJT55251.1|Hepatitis B virus|10407 +LESQDHCSP +>423033|Genome polyprotein|P26664.3|Hepatitis C virus genotype 1|41856 +LETTMRSPVF +>423036|core protein|AGS79525.1|Hepatitis B virus|10407 +LWFHISCLMF +>423044|polyprotein precursor|BAA01582.1|Hepatitis C virus genotype 1|41856 +QLEQALDCEIY +>423046|polyprotein|ACX44272.1|Hepatitis C virus genotype 1|41856 +QMAMIKLGAL +>423047|Genome polyprotein|P27958.3|Hepatitis C virus genotype 1|41856 +QRLHGLSAF +>423052|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 +RDAVILLM +>423053|core protein|AAL31859.1|Hepatitis B virus|10407 +RETVIEYLVSF +>423061|Genome polyprotein|P27958.3|Hepatitis C virus genotype 3|356114 +SQLSAPSLK +>423062|polyprotein|ACH99674.1|Hepatitis C virus genotype 1|41856 +SSVSTALAEL +>423063|pre-Core, Core|BAF49207.1|Hepatitis B virus|10407 +STLPETTVVRQ +>423068|polyprotein|ACX44241.1|Hepatitis C virus genotype 1|41856 +VLFGLMALTL +>423069|polyprotein|ACH99674.1|Hepatitis C virus genotype 1|41856 +VLTESSVSTA +>423071|polyprotein|AER51001.1|Hepatitis C virus genotype 1|41856 +VPSMEDLVNL +>423072|polyprotein|ACJ37172.1|Hepatitis C virus genotype 1|41856 +VRMILLTHF +>423073|polyprotein|ABL63011.1|Hepatitis C virus genotype 1|41856 +VRMILMTHF +>423075|polyprotein|ACX44241.1|Hepatitis C virus genotype 1|41856 +VVLFGLMAL +>423080|Genome polyprotein|P26664.3|Hepatitis C virus genotype 1|41856 +YFLTRVEAQL +>423082|Genome polyprotein|P26664.3|Hepatitis C virus genotype 1|41856 +YRFVAPGER diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/output/NeoantigenQuality.txt b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/output/NeoantigenQuality.txt new file mode 100755 index 00000000..89417ecf --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/output/NeoantigenQuality.txt @@ -0,0 +1,5391 @@ +NeoantigenID MT.Peptide.Form NeoantigenQuality NeoantigenAlignment IEDB_EpitopeAlignment AlignmentScore IEDB_Epitope +1 HIQDLYTVL 3.17191804867 HIQDLYTVL HAQDATTVL 28.0 6373|Genome_polyprotein|SRC279960|Hepatitis_C_virus_subtype_3a|356426 +2 GYYTLLNVF 20.9213483146 GYYTLLN GFYHILN 26.0 1516|Nucleoprotein|P03418.1|Human_respiratory_syncytial_virus_A2|11259 +3 LTLFGYYTL 0.266904846489 LTLFGYY LTLSPYY 23.0 149024|NS2_protein|NP_751923.1|Hepatitis_C_virus_(isolate_H77)|63746 +4 TLFGYYTLL 0.0 None None 0 None +5 YYTLLNVFL 0.297457866327 YTLLNVFL FTILALFL 23.0 180464|polyprotein|CDF77361.1|Dengue_virus_3|11069 +6 LAVRPSKIK 0.0 None None 0 None +7 PTYGNSTKL 0.734486359014 PTYGNS PLYGNE 25.0 75436|Polyprotein|P90247|Hepatitis_C_virus|11103 +8 TASNVEFAI 0.0 None None 0 None +9 TSSDSISHM 0.0 None None 0 None +10 RFRALNQEL 0.0 None None 0 None +11 HRNHIDRAL 0.0 None None 0 None +12 FALLFGHRF 0.733997564982 LLFGH LLFGH 28.0 37251|||| +13 HRFDYRDPV 0.0 None None 0 None +14 VADSTLLLM 0.0 None None 0 None +15 FKMGAHTEV 0.0 None None 0 None +16 FEGFPQSLL 0.217642336766 FEGFPQSLL FPGFGQSLL 32.0 23807|tax|AAG48731.1|Human_T-lymphotropic_virus_2|11909 +17 FEGFPQSLL 0.126853192431 FEGFPQSLL FPGFGQSLL 32.0 23807|tax|AAG48731.1|Human_T-lymphotropic_virus_2|11909 +18 GAQDRNSSF 0.0 None None 0 None +19 FTHLRLQEF 0.0 None None 0 None +20 LAASGPTLV 0.0 None None 0 None +21 MIVGRTYTL 0.0037423128393 IVGRTYTL ILGFVFTL 20.0 20354|M1_protein|CAA30882.1|Influenza_A_virus|11320 +22 VAAENEAVL 0.0 None None 0 None +23 IERNLINSL 1.02340662483 ERNLINSL EENLVNSL 32.0 182938|polyprotein|AGO67248.1|Dengue_virus_2|11060 +24 GEAGTIERV 0.448867741662 EAGTIERV EAGNFERI 28.0 194242|ESAT-6-like_protein_esxB|P0A566.2|Mycobacterium_tuberculosis|1773 +25 VAIFLGFYV 0.0 None None 0 None +26 YSIFQLAFV 0.0 None None 0 None +27 MALNYNRAF 0.0 None None 0 None +28 TVFGGLMAL 0.0 None None 0 None +29 LSSRLSDTL 0.0 None None 0 None +30 SRLSDTLSF 0.0 None None 0 None +31 KRTSPEELL 0.0 None None 0 None +32 HALHLRRMM 0.0 None None 0 None +33 MAGFMGMAV 0.0259001423454 MAGFMG MTGFTG 22.0 108153|polyprotein|AAF65950.1|Hepatitis_C_virus|11103 +34 RMMAGFMGM 0.795816444397 MMAGFMG LMTGFTG 24.0 108153|polyprotein|AAF65950.1|Hepatitis_C_virus|11103 +35 FVSTIIHLL 0.0 None None 0 None +36 YLVPGFSPY 0.0 None None 0 None +37 YLVPGFSPY 0.0 None None 0 None +38 KASFDHACL 0.0 None None 0 None +39 EFHDIASHV 0.0 None None 0 None +40 MCDNGSGLV 0.0 None None 0 None +41 IQNAGGSVI 0.601030334228 IQNAGGSVI IQNSGGTSI 31.0 183843|envelope_protein|AGW23576.1|Dengue_virus_3|11069 +42 TQDGALMNV 0.0 None None 0 None +43 TLGIICLLL 0.665172700533 TLGIIC TLGIVC 31.0 64818|E7|AAD33253.1|Human_papillomavirus_type_16|333760 +44 WNDKVKEAL 0.0 None None 0 None +45 QNAGGSVII 3.46504561837 QNAGGS QNAGGT 28.0 27981|IMMUNOGENIC_PROTEIN_MPT64_(ANTIGEN_MPT64/MPB64)|CAA98382.1|Mycobacterium_tuberculosis_H37Rv|83332 +46 SDYLHWEVV 0.0 None None 0 None +47 SSVPVLNML 0.0 None None 0 None +48 WALEVLLNA 0.463508918806 WALEVLL WTLVVLL 25.0 37960|membrane_protein|AAA45887.1|Human_gammaherpesvirus_4|10376 +49 YETQDGALM 0.0 None None 0 None +50 NMELPYFVL 0.50520798857 LPYFV LPYLV 22.0 13518|HCV-1|AAA45676.1|Hepatitis_C_virus_genotype_1|41856 +51 LSTPAPQVF 0.0 None None 0 None +52 VSDTEFHPL 0.0 None None 0 None +53 MVVAGQRAV 0.0 None None 0 None +54 YLHWEVVEL 0.0 None None 0 None +55 ANFPWALEV 1.23311590917 ANFPWAL TSFPWLL 28.0 34616|pol_protein|BAA32832.1|Hepatitis_B_virus|10407 +56 WYLRDVSEV 0.0 None None 0 None +57 FHDIASHVK 0.0 None None 0 None +58 FPWALEVLL 0.261558715685 WALEVLL WTLVVLL 25.0 37960|membrane_protein|AAA45887.1|Human_gammaherpesvirus_4|10376 +59 GTLGIICLL 50.3407812466 TLGIIC TLGIVC 31.0 64818|E7|AAD33253.1|Human_papillomavirus_type_16|333760 +60 YLHWEVVEL 0.0 None None 0 None +61 LQFSRMEQL 0.0 None None 0 None +62 VHLESNATV 0.0 None None 0 None +63 QMFVHLQLL 0.0 None None 0 None +64 VHLESNATV 0.0 None None 0 None +65 TQDGALMNV 0.0 None None 0 None +66 VAFCLKCNL 0.642271486634 VAFCLKCN VTFCCKCD 33.0 110184|E7|AAD33253.1|Human_papillomavirus_type_16|333760 +67 STDSLSTPA 0.0 None None 0 None +68 DILEKSSSV 0.0749249088856 LEKSSSV MEKCSSV 23.0 13456|circumsporozoite_protein|AAN87606.1|Plasmodium_falciparum|5833 +69 NMVGFSDRV 0.0 None None 0 None +70 NLGSKLQLV 0.0 None None 0 None +71 FPWALEVLL 4.41902830893 WALEVLL WTLVVLL 25.0 37960|membrane_protein|AAA45887.1|Human_gammaherpesvirus_4|10376 +72 TKDTFMMEL 0.0 None None 0 None +73 HCANFPWAL 32.1490933462 ANFPWAL TSFPWLL 28.0 34616|pol_protein|BAA32832.1|Hepatitis_B_virus|10407 +74 ESSSETSTY 0.0 None None 0 None +75 QMFVHLQLL 0.0 None None 0 None +76 QPLKYTWLL 2.79400019666 PLKYTW PYKPTW 24.0 68229|EBNA3B_(EBNA4A)_latent_protein|CAA24858.1|Human_gammaherpesvirus_4|10376 +77 SLTTLLQAL 0.0 None None 0 None +78 SLSTPAPQV 0.0 None None 0 None +79 FAINFFKEV 0.0 None None 0 None +80 YTWLLAAKV 0.0 None None 0 None +81 DLENMELPY 0.0 None None 0 None +82 EKSSSVPVL 0.0 None None 0 None +83 WLCDHPVPV 0.376517989918 WLCDHP WILRHP 25.0 180818|Membrane_glycoprotein_precursor|NP_739582.2|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 +84 LLMSTLGIL 1.08239342869 LLMSTLGIL LLMGTLGIV 33.0 37573|E7_protein|ABL96585.1|Human_papillomavirus_type_16|333760 +85 IQNAGGSVI 3.24997372157 IQNAGGSVI IQNSGGTSI 31.0 183843|envelope_protein|AGW23576.1|Dengue_virus_3|11069 +86 YTWLLAAKV 0.0 None None 0 None +87 FSQEPADQM 0.0 None None 0 None +88 ILSWLVSQL 0.0 None None 0 None +89 LLLMSTLGI 172.260279525 LLMSTLGI LLMGTLGI 32.0 37573|E7_protein|ABL96585.1|Human_papillomavirus_type_16|333760 +90 FYIFNVSSI 0.0 None None 0 None +91 GLGECITQV 0.0 None None 0 None +92 LAMRRHSRI 0.0449655249052 AMRRHS AMKRYS 22.0 419017|polyprotein|AFY10034.1|Dengue_virus_4|11070 +93 LAKDSGAPV 0.0 None None 0 None +94 YLHWEVVEL 0.0 None None 0 None +95 FMMELLNRV 0.0 None None 0 None +96 WLCDHPVPV 0.403412132055 WLCDHP WILRHP 25.0 180818|Membrane_glycoprotein_precursor|NP_739582.2|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 +97 FAINFFKEV 0.0 None None 0 None +98 FMMELLNRV 0.0 None None 0 None +99 TVAEKRGWK 0.0 None None 0 None +100 RLLPDTFVL 0.0 None None 0 None +101 RLLPDTFVL 0.0 None None 0 None +102 SSMAAGLEH 0.0 None None 0 None +103 MIYRLAQAK 0.0 None None 0 None +104 TPMYRTRPA 0.00472046238994 TPMYRTRP TPQVPLRP 20.0 102150|nef_protein|ACR27119.1|Human_immunodeficiency_virus_1|11676 +105 ITYYCHGGY 0.121528332848 YCHGG FCHPG 24.0 79454|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 +106 KLGSSITYY 0.0 None None 0 None +107 FPVSYGVPA 0.440869275563 VSYGVP VYYGVP 26.0 118|envelope_glycoprotein|ABS76372.1|Human_immunodeficiency_virus_1|11676 +108 IMFPVSYGV 0.0 None None 0 None +109 ISDTILKTK 0.0 None None 0 None +110 RLQTHTIYK 0.0 None None 0 None +111 ELFHVDWHV 0.224791106174 LFHVDW LVHRQW 19.0 41407|Envelope_protein|NP_739583.2|Dengue_virus_2|11060 +112 LPRQYWEAL 1.00520554562 LPRQYW LPEGYW 27.0 31997|hypothetical_protein_FTT0484|YP_169522.1|Francisella_tularensis_subsp._tularensis_SCHU_S4|177416 +113 MPHRATVYA 0.0 None None 0 None +114 KLLECSLTK 0.0 None None 0 None +115 RPQGQRPAL 43.5210604434 PQGQRPAL PRGSRPSW 27.0 36352|Polyprotein|P90247|Hepatitis_C_virus|11103 +116 SSDCIIEKK 0.000135734033585 SDCIIEKK SACQRQKK 17.0 66405|polyprotein|AAB67037.1|Hepatitis_C_virus_(isolate_H77)|63746 +117 TSSDCIIEK 0.0 None None 0 None +118 GLMGHTLHR 0.0 None None 0 None +119 LPGHAPGIL 0.097025634204 PGHAPG PGTGPG 24.0 47760|EBNA-1_protein|Q777E1|Human_gammaherpesvirus_4|10376 +120 YAYHVEWEK 0.0 None None 0 None +121 WVRWHKGCL 0.00804646235146 WVRWHKG WILRHPG 22.0 180818|Membrane_glycoprotein_precursor|NP_739582.2|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 +122 SSSIRIHER 0.0 None None 0 None +123 FLSSSFSML 0.0 None None 0 None +124 FSMLKDHIK 0.0 None None 0 None +125 LSSSFSMLK 0.0 None None 0 None +126 VVGADGVGK 0.0 None None 0 None +127 AVDLSSAGM 0.0 None None 0 None +128 GMAGVLIGY 0.0543590087265 GMAGVLIG GMGPSLIG 21.0 21275|Antigen_85-B_precursor_(85B)_(Extracellular_alpha-antigen)_(Antigen_85_complex_B)_(Ag85B)_(Mycolyl_transferase_85B)_(Fibronectin-binding_protein_B)_(30_kDa_extracellular_protein)|P31952|Mycobacterium_tuberculosis|1773 +129 SSAGMAGVL 0.0 None None 0 None +130 KAAPIYKLV 0.0 None None 0 None +131 VTKAAPIYK 0.0 None None 0 None +132 FLPSWLLGI 1.88888888889 LPSWL LPQWL 26.0 13215|Antigen_85-B|P0C5B9.1|Mycobacterium_tuberculosis|1773 +133 RMAFTDHQL 38.3657688551 FTDHQL FPDHQL 28.0 190466|large_surface_antigen|CAL29876.1|Hepatitis_B_virus|10407 +134 RMAFTDHQL 20.2035463724 FTDHQL FPDHQL 28.0 190466|large_surface_antigen|CAL29876.1|Hepatitis_B_virus|10407 +135 ALQPQLGCY 0.0 None None 0 None +136 YQQALQPQL 0.0 None None 0 None +137 YQQALQPQL 0.0 None None 0 None +138 YQLKMLIKI 0.0 None None 0 None +139 ILLVVYNNV 0.0 None None 0 None +140 LLVVYNNVL 0.0 None None 0 None +141 LLVVYNNVL 0.0 None None 0 None +142 LVVYNNVLK 0.0 None None 0 None +143 LSGHSTQDL 0.0 None None 0 None +144 QALSKFKAM 0.0 None None 0 None +145 LSVDRMRKV 0.0 None None 0 None +146 LGVAARWDL 0.0 None None 0 None +147 HAVQAAVQY 0.0 None None 0 None +148 HAVQAAVQY 0.0 None None 0 None +149 KIMNSLPEM 0.0 None None 0 None +150 KIMNSLPEM 0.0 None None 0 None +151 LPEMKVQLV 0.0 None None 0 None +152 SLPEMKVQL 0.0 None None 0 None +153 LTISGECPK 0.0143889679697 ISGECP MSGEVP 22.0 423011|polyprotein|AER51001.1|Hepatitis_C_virus_genotype_1|41856 +154 AMYDVLTFA 27.3958151719 AMYDVLT ALYDVVT 29.0 3019|polyprotein|AAA45677.1|Hepatitis_C_virus_(isolate_H77)|63746 +155 ATDQAMYDV 0.00252195188532 DQAMYDV DRAHYNI 20.0 110431|E7|AAD33253.1|Human_papillomavirus_type_16|333760 +156 KIHATDQAM 0.868183841638 KIHATD KAHGTD 23.0 107925|polyprotein|AAF65964.1|Hepatitis_C_virus|11103 +157 QAMYDVLTF 24.0160297669 AMYDVLT ALYDVVT 29.0 3019|polyprotein|AAA45677.1|Hepatitis_C_virus_(isolate_H77)|63746 +158 QAMYDVLTF 184.760877861 AMYDVLT ALYDVVT 29.0 3019|polyprotein|AAA45677.1|Hepatitis_C_virus_(isolate_H77)|63746 +159 LICFLTPVK 0.0 None None 0 None +160 NLICFLTPV 0.0 None None 0 None +161 IAHIFGGAR 0.0 None None 0 None +162 LLEISKWFR 0.0 None None 0 None +163 FSDDGVLGP 0.179294280913 FSDDGVLGP YMDDVVLGA 25.0 75040|Protein_P|P03159.1|Hepatitis_B_virus|10407 +164 GSFSDDGVL 0.0 None None 0 None +165 VLGPVLTTF 0.0 None None 0 None +166 ATSIPAGSM 0.0 None None 0 None +167 IPAGSMPTV 0.289341771885 PAGSMPTV PEGIIPTL 24.0 180778|polyprotein|AFP27208.1|Dengue_virus_4|11070 +168 IMDLRNGTF 0.0 None None 0 None +169 CLSGYCSVF 1.19084512931 CLSGYC CISGVC 29.0 95281|polyprotein|ACE82433.1|Hepatitis_C_virus_genotype_1|41856 +170 CSVFAYKPM 0.0 None None 0 None +171 GYCSVFAYK 0.0 None None 0 None +172 SGYCSVFAY 0.0 None None 0 None +173 LIMALVWSL 0.0117124891175 LIMALVWSL LLMRTTWAF 21.0 184453|polyprotein|AFP27207.1|Dengue_virus_4|11070 +174 LIMALVWSL 0.0164467732015 LIMALVWSL LLMRTTWAF 21.0 184453|polyprotein|AFP27207.1|Dengue_virus_4|11070 +175 LIMALVWSL 0.00513721530405 LIMALVWSL LLMRTTWAF 21.0 184453|polyprotein|AFP27207.1|Dengue_virus_4|11070 +176 LVWSLPCGF 2.09703631178 VWSLPCGF LWHYPCTF 30.0 54820|polyprotein_precursor|BAA02756.1|Hepatitis_C_virus|11103 +177 ESDYLINEM 0.0 None None 0 None +178 YLINEMYL* 0.0 None None 0 None +179 TQMVDIWSV 0.0 None None 0 None +180 MVAFFSSHT 0.0972906201798 VAFFSSHT IAFTSEHS 24.0 25275|Glutamate_decarboxylase_2|Q05329.1|Homo_sapiens|9606 +181 VAFFSSHTY 0.636929460581 VAFFSSHTY IAFTSEHSH 26.0 25275|Glutamate_decarboxylase_2|Q05329.1|Homo_sapiens|9606 +182 VAFFSSHTY 0.477777777778 VAFFSSHTY IAFTSEHSH 26.0 25275|Glutamate_decarboxylase_2|Q05329.1|Homo_sapiens|9606 +183 VAFFSSHTY 0.357142857143 VAFFSSHTY IAFTSEHSH 26.0 25275|Glutamate_decarboxylase_2|Q05329.1|Homo_sapiens|9606 +184 VTFSTSSQL 0.0 None None 0 None +185 WVDFADSVT 0.0 None None 0 None +186 YQTFKDWGI 0.0 None None 0 None +187 ISMGQEEKK 0.0 None None 0 None +188 WISMGQEEK 0.0 None None 0 None +189 FSWQSHLLI 0.0 None None 0 None +190 QSHLLIHQR 0.0 None None 0 None +191 FYIIECIAM 0.0275788552752 YIIECIA YIMACMS 22.0 24457|polyprotein|BAA09072.1|Hepatitis_C_virus|11103 +192 TAFYIIECI 0.0 None None 0 None +193 YIIECIAMS 0.0570151100106 YIIECIA YIMACMS 22.0 24457|polyprotein|BAA09072.1|Hepatitis_C_virus|11103 +194 ASTYSQLKL 0.0 None None 0 None +195 SASTYSQLK 0.0 None None 0 None +196 VSASTYSQL 0.0 None None 0 None +197 YSQLKLWNV 0.0 None None 0 None +198 FYQHLNLMR 0.0 None None 0 None +199 YQHLNLMRV 0.0 None None 0 None +200 KPAPHPQAL 0.0 None None 0 None +201 MADSGPIYN 0.0 None None 0 None +202 GLGFYNDVV 6.41833817492 GLGFYNDV GYGFVNYV 23.0 36358|ELAV-like_protein_1|Q15717.2|Homo_sapiens|9606 +203 FCENDAEVL 0.0 None None 0 None +204 RTTQQENPR 0.0 None None 0 None +205 AMDDLDTDM 1.44491577894 AMDDLDTDM TLNDLETDV 27.0 64967|Circumsporozoite_protein_precursor|P08677.2|Plasmodium_vivax_strain_Belem|31273 +206 EECGKTFYR 0.0 None None 0 None +207 MITQFELQK 0.0 None None 0 None +208 CTAMRVAAK 0.0 None None 0 None +209 HFERLTRAL 0.0 None None 0 None +210 RLKFGNKHK 0.0108863902402 RLKFGNKHK RLRPGGKKK 22.0 54741|gag_polyprotein|BAA00992.1|Human_immunodeficiency_virus_1|11676 +211 ASQQGMAAL 0.0 None None 0 None +212 LDYASQQGM 0.0 None None 0 None +213 YASQQGMAA 0.0 None None 0 None +214 GVRAGRLQL 0.0 None None 0 None +215 VRAGRLQLF 0.0 None None 0 None +216 LFIHHIQGL 0.0 None None 0 None +217 FCSIYITLL 0.0 None None 0 None +218 HHSPSTHVM 0.0 None None 0 None +219 RSFWSHVVR 0.0 None None 0 None +220 AEVEVADKL 0.0 None None 0 None +221 KLLENLAKV 0.0 None None 0 None +222 MAEAKRMKL 0.0 None None 0 None +223 SMAEAKRMK 0.0 None None 0 None +224 SYESCDAHF 0.0 None None 0 None +225 ASFVPSMGK 0.0 None None 0 None +226 FVPSMGKNL 0.0 None None 0 None +227 IPASFVPSM 0.825781600633 IPASFVPSM LPADFFPSI 30.0 16795|precore/core_protein|AAP57273.1|Hepatitis_B_virus|10407 +228 SVSIPASFV 0.0 None None 0 None +229 HLGVPVTLR 0.0 None None 0 None +230 RVQHLGVPV 0.0 None None 0 None +231 NPNTGSVYM 0.0 None None 0 None +232 VYMNSQQSL 0.0 None None 0 None +233 VYMNSQQSL 0.0 None None 0 None +234 EMAKFKVTI 0.0 None None 0 None +235 KLFGYEMAK 0.0 None None 0 None +236 MAKFKVTIK 0.0 None None 0 None +237 HRTIPYLDL 0.0 None None 0 None +238 IVWEHRQKL 0.0 None None 0 None +239 GMVAPDVVK 0.0 None None 0 None +240 HPGVSSQFL 0.305854949793 HPGVSSQF HPTFTSQY 25.0 75718|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 +241 SPRGGPPPL 0.0 None None 0 None +242 IVHPLKPQM 0.0 None None 0 None +243 KPQMNYQTA 0.0 None None 0 None +244 AYCSYCYYF 0.0 None None 0 None +245 NAYCSYCYY 0.0 None None 0 None +246 SPAPERCMV 1.2380952381 PERCM PRRCM 26.0 56310|polyprotein|AGO67248.1|Dengue_virus_2|11060 +247 ALMDMYPHV 0.0 None None 0 None +248 IGVDDRRRL 0.0 None None 0 None +249 RRRLCILRM 0.0 None None 0 None +250 HFQWILFFV 1.9418540523 FQWILFFV LMWLSYFV 24.0 21041|Membrane_glycoprotein|Q692E0|SARS_coronavirus_TJF|284672 +251 HVPGAVPNL 0.0 None None 0 None +252 SLTGDVSPL 0.0 None None 0 None +253 HMVERIQFV 0.0123869954441 MVERIQFV MLEDHEFV 18.0 164551|envelope_glycoprotein_B|NP_044629.1|Herpes_simplex_virus_(type_1_/_strain_17)|10299 +254 HFERLTRAL 0.0 None None 0 None +255 ASQQGMAAL 0.0 None None 0 None +256 LDYASQQGM 0.0 None None 0 None +257 YASQQGMAA 0.0 None None 0 None +258 GVRAGRLQL 0.0 None None 0 None +259 VRAGRLQLF 0.0 None None 0 None +260 APAGGTASA 0.0 None None 0 None +261 HHSPSTHVM 0.0 None None 0 None +262 FGHITHPCM 0.0 None None 0 None +263 RSFWSHVVR 0.0 None None 0 None +264 AAAAAAAAT 0.0 None None 0 None +265 VSSKSQKLL 0.0 None None 0 None +266 YSLSPVSSK 0.0 None None 0 None +267 AEVEVADKL 0.0 None None 0 None +268 KLLENLAKV 0.0 None None 0 None +269 MAEAKRMKL 0.0 None None 0 None +270 SMAEAKRMK 0.0 None None 0 None +271 YRWCGFPQL 0.0 None None 0 None +272 YRWCGFPQL 0.0 None None 0 None +273 SYESCDAHF 0.0 None None 0 None +274 FLVGLWSHL 0.927664444497 FLVGLWS LLLGLWG 26.0 37498|FL-160-2_protein_-_Trypanosoma_cruzi|JH0823|Trypanosoma_cruzi|5693 +275 KPRFLVGLW 122.389953 KPRFLVGL RPMFAVGL 27.0 185468|polyprotein|AGW21594.1|Dengue_virus_1|11053 +276 LVGLWSHLL 12.7260693351 LVGLWS LLGLWG 26.0 37498|FL-160-2_protein_-_Trypanosoma_cruzi|JH0823|Trypanosoma_cruzi|5693 +277 MPPYYVGPL 0.0 None None 0 None +278 TALPTYPPY 4.49696133214 ALPTYPP SLPSYYP 24.0 28594|IMMUNOGENIC_PROTEIN_MPT64_(ANTIGEN_MPT64/MPB64)|CAA98382.1|Mycobacterium_tuberculosis_H37Rv|83332 +279 FEGFPQSPL 0.939393939394 FPQSPL FPRAPL 26.0 18390|Genome_polyprotein|P08617.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 +280 NPNTGSVYM 0.0 None None 0 None +281 VYMNSQQSL 0.0 None None 0 None +282 VYMNSQQSL 0.0 None None 0 None +283 KRQQFGSQF 0.0 None None 0 None +284 DPFALFFMA 0.0 None None 0 None +285 EYAADPFAL 0.0 None None 0 None +286 YAADPFALF 0.000123394575986 YAADPFALF YVAGFLALY 17.0 141484|capsid_maturation_protease|NP_044627.1|Human_alphaherpesvirus_1|10298 +287 HRTIPYLDL 0.0 None None 0 None +288 IVWEHRQKL 0.0 None None 0 None +289 HSVAIVSPF 0.0 None None 0 None +290 RIGFVGLFH 0.0 None None 0 None +291 HPGVSSQFL 0.305854949793 HPGVSSQF HPTFTSQY 25.0 75718|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 +292 IVHPLKPQM 0.0 None None 0 None +293 KPQMNYQTA 0.0 None None 0 None +294 AYCSYCYYF 0.0 None None 0 None +295 NAYCSYCYY 0.0 None None 0 None +296 SPAPERCMV 1.2380952381 PERCM PRRCM 26.0 56310|polyprotein|AGO67248.1|Dengue_virus_2|11060 +297 LTLAVYLSF 0.0 None None 0 None +298 ALMDMYPHV 0.0 None None 0 None +299 IGVDDRRRL 0.0 None None 0 None +300 RRRLCILRM 0.0 None None 0 None +301 DTAWDTLEL 7.29864653969 DTAWD DTAWD 32.0 180726|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 +302 TAWDTLELI 0.0 None None 0 None +303 TAWDTLELI 0.0 None None 0 None +304 MSVSQKLTL 0.0 None None 0 None +305 HQRAHTGEK 0.0 None None 0 None +306 AVATITQAL 0.0 None None 0 None +307 TTVNGNTAL 0.0 None None 0 None +308 EYYSQTTGL 0.0 None None 0 None +309 YYSQTTGLC 0.0 None None 0 None +310 CPSEPNTPM 0.0 None None 0 None +311 TPMARTFDW 0.0 None None 0 None +312 GHYEVRASL 0.0 None None 0 None +313 HYEVRASLL 0.0 None None 0 None +314 MYWRRSQCC 0.0 None None 0 None +315 DYPNAYTTW 1.44061741991 DYPNAYTTW DQENPYRTW 31.0 186550|polyprotein|AFY10039.1|Dengue_virus_4|11070 +316 RYSDYPNAY 1.76428417258 SDYPN SEYPN 26.0 57703|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 +317 AADLPILTW 0.0 None None 0 None +318 WLLAADLPI 0.00994626965127 WLLAADLP WCVEHDRP 19.0 120093|unnamed_protein_product|CAA33016.1|Rubella_virus|11041 +319 IPPEANITI 0.0 None None 0 None +320 TVHNLCHIL 0.0 None None 0 None +321 FFVEKRHAF 0.599743535066 VEKRHAF LEKRHVL 24.0 183781|polyprotein|AGO67248.1|Dengue_virus_2|11060 +322 LPLTRSMSI 0.0 None None 0 None +323 AAAAATSAL 0.0 None None 0 None +324 SIYAYHVEW 0.0 None None 0 None +325 AYPQYVIEY 0.427796389876 AYPQYV GYPRYV 26.0 37254|||| +326 FSSKPSSIY 0.0 None None 0 None +327 SIYGGLVLI 0.0 None None 0 None +328 SAESGAQLL 0.0 None None 0 None +329 GIICLDYKL 0.738702286919 GIICL GVLCL 24.0 185978|polyprotein|CDF77361.1|Dengue_virus_3|11069 +330 FEDIGDEDL 0.0 None None 0 None +331 IRVEESMHL 0.142206994693 RVEESMHL RVEAQLHV 24.0 40158|polyprotein|AAA45534.1|Hepatitis_C_virus|11103 +332 AMEKLLSGK 0.0 None None 0 None +333 ARTGHLPAM 0.0 None None 0 None +334 GHLPAMEKL 0.0867552972161 GHLPAMEKL GHQAAMQML 25.0 101673|gag_protein|ABO73990.1|Human_immunodeficiency_virus_1|11676 +335 QVYHWVCEK 0.0 None None 0 None +336 HRWNRFTMI 0.0 None None 0 None +337 THRWNRFTM 0.0173518357296 THRWNRFTM THPITKFVM 21.0 103389|unnamed_protein_product_[Hepatitis_C_virus]|BAA14035.1|Hepatitis_C_virus|11103 +338 ITSGLEVIY 0.0 None None 0 None +339 ARRFWGKIM 0.0 None None 0 None +340 RFWGKIMAK 0.0 None None 0 None +341 TYEEATVYI 0.0 None None 0 None +342 EHAAALWAL 0.252958579882 HAAALWAL HPASAWTL 26.0 183594|polyprotein|AGT63075.1|Dengue_virus_1|11053 +343 LVLMNWTKK 0.418604651163 VLMNWTK MMMNWSP 26.0 42152|polyprotein|AAY82055.1|Hepatitis_C_virus_(isolate_H77)|63746 +344 FTDTAAESA 0.0 None None 0 None +345 NIEDSASFY 0.0 None None 0 None +346 SRSDAAKHL 0.0 None None 0 None +347 LRWRHCQRL 0.0 None None 0 None +348 WRHCQRLDV 0.0 None None 0 None +349 VRLGPVKSI 2.30860618466 RLGPVKS RLGPVQN 28.0 146528|NS3/4A_protein|CAM56207.1|Hepatitis_C_virus|11103 +350 SMQAHIKAL 0.0 None None 0 None +351 ESFKQTDFY 0.0 None None 0 None +352 QTDFYSMAL 0.0 None None 0 None +353 LPWMRLLLL 0.0 None None 0 None +354 MRLLLLLLV 0.0 None None 0 None +355 PRLPWMRLL 0.0 None None 0 None +356 WMRLLLLLL 0.0 None None 0 None +357 AIALHRLSL 0.0 None None 0 None +358 MRGHDWRML 0.0 None None 0 None +359 QMRGHDWRM 0.0 None None 0 None +360 HLETHNTDK 1.91662691262 ETHNTDK ECHSTDA 24.0 97111|polyprotein|ABR25251.1|Hepatitis_C_virus_(isolate_H77)|63746 +361 CSKLKHRDL 0.00687496931678 CSKLKHR CSARLHR 21.0 28508|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 +362 VVGAVGVGK 0.0 None None 0 None +363 AHPDGSWTF 5.46667302818 HPDGSWTF HPASAWTL 30.0 183594|polyprotein|AGT63075.1|Dengue_virus_1|11053 +364 WGRERGARV 0.0 None None 0 None +365 KADIPRDSY 0.0 None None 0 None +366 NVLQSSVPV 0.986093893012 NVLQSSVPV NVMLVTLPV 21.0 98308|trans-sialidase,_putative|EAN80840.1|Trypanosoma_cruzi|5693 +367 IITESGEVI 0.0 None None 0 None +368 WVYDAIITE 0.0 None None 0 None +369 FPPNILDDI 0.134347555558 PNILDDI PEIEDDI 24.0 180682|polyprotein|AGO67248.1|Dengue_virus_2|11060 +370 MASQRPLQF 0.0 None None 0 None +371 DMHVAVKIV 0.0 None None 0 None +372 FARPASPSR 0.00268626303148 PASPSR PAKPAR 24.0 53405|||| +373 IVFEVFGHH 0.0 None None 0 None +374 TTAVLTATF 0.0 None None 0 None +375 MAAAVVARL 0.0 None None 0 None +376 FSLPPSRKK 0.0 None None 0 None +377 LPMCWAMEV 0.0 None None 0 None +378 LTYSCLDNK 0.0 None None 0 None +379 LLNSGGDII 0.0 None None 0 None +380 DIYCITDFV 0.0 None None 0 None +381 FVEELADTV 0.0 None None 0 None +382 TISCTSLKK 0.0 None None 0 None +383 VTISCTSLK 0.0 None None 0 None +384 IIIKCQLPK 0.0 None None 0 None +385 RYGAGQQNL 1.47210141005 YGAGQQNL YGAGQVML 28.0 5783|Nucleoprotein|P03418.1|Human_respiratory_syncytial_virus_A2|11259 +386 TPYAACPAI 0.61364033445 TPYAAC NPYAVC 27.0 110401|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 +387 SPFNTTFPF 0.0 None None 0 None +388 QVARRVQEL 0.0 None None 0 None +389 HREARGRAL 0.0 None None 0 None +390 AIFGPSNTY 1.40284974093 AIFGP AVFGP 26.0 96123|Genome_polyprotein|P26664.3|Hepatitis_C_virus_(isolate_H77)|63746 +391 DLFQFPKAY 0.258104503658 FQFPKA FYFPRA 24.0 18390|Genome_polyprotein|P08617.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 +392 LPEDPKCEF 0.0540961051747 PEDPKCE PTDVSCE 24.0 79628|E1_protein|BAA19893.1|Rubella_virus|11041 +393 SFQPKAAVF 0.0 None None 0 None +394 PPSETGGIF 0.0 None None 0 None +395 NAGEMVIEY 0.0 None None 0 None +396 APTSSDYEF 0.0 None None 0 None +397 LFCGLPFSI 3.79000971222 FCGLPFS FCGSPYS 33.0 190409|polymerase|AAD16253.1|Hepatitis_B_virus|10407 +398 VPVASSEAS 0.0 None None 0 None +399 DPSPGIMAF 0.0 None None 0 None +400 LTYSLLTPL 0.0 None None 0 None +401 TYSLLTPLL 0.0 None None 0 None +402 CYVAICNPF 0.0 None None 0 None +403 LAAMAIDCY 0.0 None None 0 None +404 MAIDCYVAI 5.96984686185 IDCYVAI IDCNVAV 28.0 419366|polyprotein|BAA00792.1|Hepatitis_C_virus|11103 +405 YFFLGNLAF 0.0 None None 0 None +406 FPVEDRRGV 0.0 None None 0 None +407 FAQLINNKM 0.0 None None 0 None +408 RVASVVVSF 0.0 None None 0 None +409 RVASVVVSF 0.0 None None 0 None +410 FYLRYFEK* 0.0 None None 0 None +411 FFSSNLPTY 0.0 None None 0 None +412 FSSNLPTYY 12.750272737 NLPTYY SLPSYY 27.0 28594|IMMUNOGENIC_PROTEIN_MPT64_(ANTIGEN_MPT64/MPB64)|CAA98382.1|Mycobacterium_tuberculosis_H37Rv|83332 +413 NPYKAPMAE 0.00506353396253 NPYKAPM NPEVIPM 20.0 187163|Gag_polyprotein|P88150|Human_immunodeficiency_virus_1|11676 +414 AFLQKAHLI 0.0226039482404 LQKAHLI LEKRHVL 21.0 184755|polyprotein|AGO67248.1|Dengue_virus_2|11060 +415 FQGYLKDPV 0.0 None None 0 None +416 SEVLGYWAF 0.745411820705 VLGYWAF LLGLWGF 27.0 98223|trans-sialidase,_putative|EAN80725.1|Trypanosoma_cruzi|5693 +417 SEVLGYWAF 0.675840050772 VLGYWAF LLGLWGF 27.0 98223|trans-sialidase,_putative|EAN80725.1|Trypanosoma_cruzi|5693 +418 RRFGWLQTA 0.0 None None 0 None +419 GHEEKITFI 0.0 None None 0 None +420 EESIAVGTM 0.0 None None 0 None +421 EESIAVGTM 0.0 None None 0 None +422 FRYLGKCNI 0.0 None None 0 None +423 FEVGGAALF 0.0 None None 0 None +424 FEVGGAALF 0.0 None None 0 None +425 GMCVLEMAV 0.0 None None 0 None +426 VLEMAVLEI 0.0 None None 0 None +427 FLMVSRDCL 0.022042337798 FLMVSRDCL FLLALLSCL 21.0 136837|polyprotein_precursor|BAA01582.1|Hepatitis_C_virus|11103 +428 SRDCLRTVL 0.0 None None 0 None +429 VSRDCLRTV 0.0 None None 0 None +430 ALREFKFRV 0.0 None None 0 None +431 REFKFRVSA 0.0 None None 0 None +432 REFKFRVSA 0.0 None None 0 None +433 YEALREFKF 0.0 None None 0 None +434 NQMDKLAAF 0.0 None None 0 None +435 YRMSPSNQM 0.0 None None 0 None +436 KVISYPVAL 0.0 None None 0 None +437 TERTKVISY 0.0 None None 0 None +438 LHLRRKEIM 0.0 None None 0 None +439 QTSCHVFMV 0.0 None None 0 None +440 GEAGAGGTA 0.0 None None 0 None +441 EHMPNNSRL 0.0 None None 0 None +442 PRKPRSQNF 0.0 None None 0 None +443 RQWPRLSHK 0.941940860927 QWPRLSH TWPLLPH 27.0 79337|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 +444 ISLAYLVKK 0.0 None None 0 None +445 TISLAYLVK 0.0 None None 0 None +446 MFLWTVAVI 0.0 None None 0 None +447 TVAVIPILF 0.0 None None 0 None +448 KIRQLKKKK 0.0 None None 0 None +449 NEKTTPSPA 0.00746553042847 NEKTTP NSKRTP 22.0 419298|RNA-dependent_RNA_polymerase|ACH97782.1|Hepatitis_C_virus|11103 +450 NENATPSPA 0.0 None None 0 None +451 RERTANENA 0.0 None None 0 None +452 CYLQIFATR 0.0 None None 0 None +453 LPPSLQGAV 8.55128205128 PPSLQGAV PPMVEGAA 26.0 48836|EBNA-1_protein|Q777E1|Human_gammaherpesvirus_4|10376 +454 RVARSHCQR 0.0 None None 0 None +455 VPSEPSSSV 0.0 None None 0 None +456 EEWCSLWAG 0.0 None None 0 None +457 WEEWCSLWA 0.0453634499044 WEEWCSLW WPKTHTLW 22.0 184702|non-structural_protein_1|AGM49312.1|Dengue_virus|12637 +458 RLPSYMVEK 0.0 None None 0 None +459 SYMVEKREF 0.00754725742526 MVEKREF MLEDHEF 21.0 164551|envelope_glycoprotein_B|NP_044629.1|Herpes_simplex_virus_(type_1_/_strain_17)|10299 +460 GENFCTAVK 0.0 None None 0 None +461 MEGYMKAKV 0.0 None None 0 None +462 CPLPRPPPI 0.84385451991 LPRPPP LPRPGP 28.0 139406|polyprotein|ACT37184.1|Hepatitis_C_virus|11103 +463 AEEAGYPLS 0.0304382014743 EAGYPLS EVGFPVR 22.0 288104|nef_protein|ACR27130.1|Human_immunodeficiency_virus_1|11676 +464 EEAGYPLSC 0.0464643757354 EAGYPLS EVGFPVR 22.0 288104|nef_protein|ACR27130.1|Human_immunodeficiency_virus_1|11676 +465 GVYLLFALR 0.0 None None 0 None +466 VYLLFALRL 0.0 None None 0 None +467 QEASNKHAE 0.970660146699 QEASNKH QEAANKQ 26.0 3935|ESAT-6-like_protein_esxB|P0A566.2|Mycobacterium_tuberculosis|1773 +468 SEYSSSLGR 0.0 None None 0 None +469 RESGSFLST 0.0 None None 0 None +470 LYQLHNLVV 0.0 None None 0 None +471 YAAPQLHSI 0.0 None None 0 None +472 HLHDHYGPY 0.0 None None 0 None +473 FAEDGACTV 0.0 None None 0 None +474 HVIGTIGHF 0.0 None None 0 None +475 FADDEHSMV 0.0 None None 0 None +476 YANERPKSL 0.0 None None 0 None +477 FACHFTVFV 0.0 None None 0 None +478 NALDYICTV 0.0 None None 0 None +479 LAYQELPTV 0.133857018486 YQELPT YSEHPT 21.0 75718|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 +480 FVMEHSNIV 0.0 None None 0 None +481 VAFCTMNVI 0.0 None None 0 None +482 FTIRAIQVY 0.0 None None 0 None +483 MAISVVKHI 0.0395696619166 MAISVVK MALSIVS 22.0 180641|polyprotein|AFJ91714.1|Dengue_virus_1|11053 +484 RALEKLNHV 0.880797077978 ALEKLN ALEKLN 28.0 2506|M_protein,_serotype_5_precursor|P02977.2|Streptococcus_pyogenes_serotype_M5|301449 +485 FADMERHHI 1.33333333333 DMERHHI DLEKRHV 26.0 183781|polyprotein|AGO67248.1|Dengue_virus_2|11060 +486 FANRRKEEV 21.3373135759 ANRRKEEV ANKQKQEL 26.0 327|ESAT-6-like_protein_esxB|P0A566.2|Mycobacterium_tuberculosis|1773 +487 LAIDSASPV 0.0 None None 0 None +488 RALGPGHTV 0.000143960338651 ALGPGHTV AVGVYHIV 17.0 32663|small_hydrophobic_protein|AAM12943.1|Human_metapneumovirus|162145 +489 FAKVLIRTY 0.880797077978 KVLIRTY KVLIRCY 28.0 145860|Protein_E6|P04019.1|Human_papillomavirus_type_11|10580 +490 SSDDNDAFY 0.583333333333 SDDNDAFY TDNNRSFY 26.0 98603|trans-sialidase,_putative|EAN82716.1|Trypanosoma_cruzi|5693 +491 YPKGRPSHI 0.0 None None 0 None +492 WALPKTYTI 0.0 None None 0 None +493 LARHWRVHI 0.0 None None 0 None +494 FSYSASSEI 0.0 None None 0 None +495 FSFFFVNIF 0.0 None None 0 None +496 YSFDGMWKV 0.701469617998 SFDGMWKV SWDQMWKC 30.0 146570|polyprotein|ADY38595.1|Hepatitis_C_virus_subtype_1b|31647 +497 DSIHQVGMY 0.0359724199242 HQVGMY HAVGLF 22.0 23573|polyprotein|AAB67037.1|Hepatitis_C_virus_(isolate_H77)|63746 +498 MTYDLASVV 0.0 None None 0 None +499 LAFPVPLYY 0.80288104137 PVPLYY PIPIHY 28.0 47946|envelope_glycoprotein|AAC28452.1|Human_immunodeficiency_virus_1|11676 +500 YAALAMGTL 0.0 None None 0 None +501 YLFRELATI 0.0 None None 0 None +502 YMDLMGFSY 0.136231910882 YMDLMG YMSLLG 24.0 17117|matrix_protein|AAN09804.1|Measles_virus_strain_Edmonston|11235 +503 FAISHEGHM 0.0 None None 0 None +504 FSSPRLRPI 0.0 None None 0 None +505 FVYLHLNMV 0.973487792105 FVYLHLNMV LIHLHQNIV 26.0 2903|Genome_polyprotein|P27958.3|Hepatitis_C_virus_subtype_1a|31646 +506 MANNPDVMI 0.0 None None 0 None +507 AALPAAQTV 0.0 None None 0 None +508 FAWKNMDFL 0.104302556769 WKNMDFL WTSLNFL 24.0 62504|HBsAg_protein|ABF71024.1|Hepatitis_B_virus|10407 +509 FAAQGPTVF 0.0 None None 0 None +510 LALSNLPTV 0.0 None None 0 None +511 FTLEFLVCI 0.0 None None 0 None +512 FSVDFPRIY 0.208605113539 FPRIY FPRIW 24.0 187106|Vpr_protein|BAA93983.1|Human_immunodeficiency_virus_1|11676 +513 FTIFWTVYY 1.87174259914 IFWTVYY VMWTVYH 32.0 146249|polyprotein|ADE10208.1|Hepatitis_C_virus_subtype_3a|356426 +514 MADPNQCVI 1.01181629973 DPNQCV DPRRCL 24.0 150556|polyprotein|AGW21594.1|Dengue_virus_1|11053 +515 RAFWAGSVV 2.73888707955 AFWAGSVV TLWGGSVV 29.0 79351|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 +516 YHFDAIRTF 0.73105857863 FDAIRTF YDAVRTW 27.0 154164|tegument_protein|CAB06732.1|Human_alphaherpesvirus_2|10310 +517 FAKGWLLKL 0.992469783844 FAKGW FAQGW 28.0 8236|Genome_polyprotein|P27958.3|Hepatitis_C_virus_subtype_1a|31646 +518 NAQNMTITV 0.0 None None 0 None +519 RALNRVHVL 0.0 None None 0 None +520 MAPELISHL 0.0519601621127 MAPELISHL MEPTLGQHL 22.0 79308|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 +521 KAFYHPRLI 0.331355045526 FYHPR FYFPR 24.0 18390|Genome_polyprotein|P08617.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 +522 LAFVIVLLV 0.0 None None 0 None +523 CTAVVLLVY 0.0 None None 0 None +524 FTEFCDSCY 0.648148148148 FCDSCY ICDECH 26.0 107905|Genome_polyprotein|P26664.3|Hepatitis_C_virus|11103 +525 LAREPVNEL 0.0 None None 0 None +526 YTRKRTQSI 0.0 None None 0 None +527 FAPSCANSL 0.119202922022 FAPSCAN YSPSCCT 24.0 10962|envelope_glycoprotein|AAU04921.1|Human_T-lymphotropic_virus_1|11908 +528 KVYDLVHSV 0.278600815726 KVYDLVH RIYDLIE 25.0 55620|EBNA3C_latent_protein|CAD53421.1|Human_gammaherpesvirus_4|10376 +529 QAPPLMGTI 0.0 None None 0 None +530 QAFRRSISV 0.0 None None 0 None +531 FVLDHSRLV 0.12716493457 FVLDH YVLDH 25.0 25237|Transcription_activator_BRLF1|P03209.1|Human_herpesvirus_4_strain_B95-8|10377 +532 FIKRHIAPI 0.0 None None 0 None +533 YSQPFYTSY 0.0 None None 0 None +534 FAQDVDRMF 0.0 None None 0 None +535 QAPEFLQTL 0.242047279233 PEFLQTL PESLETL 25.0 184531|polyprotein|AFP27208.1|Dengue_virus_4|11070 +536 LSDISRSCY 0.0 None None 0 None +537 NAYARVLRF 0.0 None None 0 None +538 FANFFNTFL 0.0 None None 0 None +539 FIYDAVGNM 0.0 None None 0 None +540 LARECGSPL 0.0 None None 0 None +541 WHGPARPSL 0.0 None None 0 None +542 HVMFMVAFY 0.0 None None 0 None +543 MAITSMNPV 0.0 None None 0 None +544 TAVEFIMAI 0.0 None None 0 None +545 QAYGGPRYL 0.0520850061725 QAYGGP QLYRGP 22.0 38724|Genome_polyprotein|P08617.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 +546 FTIRAIQVY 0.0 None None 0 None +547 YLDYVSISY 0.0 None None 0 None +548 SAYMHHSKI 0.0 None None 0 None +549 YLMEFGQLL 0.710046526128 YLMEFG YLVSFG 24.0 69474|core_protein|BAF42671.1|Hepatitis_B_virus|10407 +550 KAEELKETV 0.0 None None 0 None +551 FALGVGTAL 0.809630010555 LGVGTAL LGIGTVL 28.0 108127|Genome_polyprotein|P26664.3|Hepatitis_C_virus|11103 +552 LVFPNSDHV 0.0 None None 0 None +553 FTLQNPSAV 0.0 None None 0 None +554 EIVDQQGHM 0.0 None None 0 None +555 FTIFWTVYY 1.15184159947 IFWTVYY VMWTVYH 32.0 146249|polyprotein|ADE10208.1|Hepatitis_C_virus_subtype_3a|356426 +556 FPNSCLSTL 0.0 None None 0 None +557 YSISDWTSI 0.0179862099621 WTSI WTSL 22.0 62504|HBsAg_protein|ABF71024.1|Hepatitis_B_virus|10407 +558 FTACYIRIV 0.0 None None 0 None +559 FEFDHIRNF 0.0205556685281 FDHIRNF FDRTRKF 22.0 154296|UL29|CAB06754.1|Human_alphaherpesvirus_2|10310 +560 YTPDELHAM 0.00621479014398 PDELHAM PDVAHSL 21.0 130953|G1_and_G2_surface_glycoprotein_precursor|AAG22532.1|Andes_hantavirus|46607 +561 FVHPATRPL 0.0 None None 0 None +562 KALRITNVY 0.0 None None 0 None +563 QARDQGSPV 0.0 None None 0 None +564 FIYDAVGNM 0.0 None None 0 None +565 EAFPEDVAV 0.0 None None 0 None +566 YATADSSSL 0.0 None None 0 None +567 RAREHSDTF 0.0 None None 0 None +568 IAIQLITHM 0.0 None None 0 None +569 MAFENNAGL 0.0 None None 0 None +570 FGHENRVSI 0.0 None None 0 None +571 NATTIVTTV 0.0 None None 0 None +572 VTFPGINLM 0.0 None None 0 None +573 DAYPRQYSL 0.0 None None 0 None +574 YIQEGFLAV 0.00185446736748 QEGFLAV QNGALAI 20.0 51685|Nuclear_antigen_EBNA-3C|Q69140.1|Human_gammaherpesvirus_4|10376 +575 FATTACHTL 0.0 None None 0 None +576 RANQCFAFV 0.0 None None 0 None +577 MTQPVWSTI 0.0 None None 0 None +578 FTEEGFCAI 0.0 None None 0 None +579 FADHPQAPF 0.0 None None 0 None +580 VAMGSAALV 0.0 None None 0 None +581 TAKDYRVYV 0.0 None None 0 None +582 EAEEWVVSY 0.0 None None 0 None +583 FTLPLMDQV 0.0 None None 0 None +584 MQMPCTIKI 0.0 None None 0 None +585 YRYFCRVPV 0.808012113223 YFCR YFCR 27.0 155131|ribonucleotide_reductase_large_subunit|CAB06725.1|Human_alphaherpesvirus_2|10310 +586 WAHAWPSPY 0.0047350399545 WAHAWPSPY WHYDEDNPY 20.0 72563|polyprotein|AAB70696.1|Dengue_virus_type_1_Hawaii|10000440 +587 IAIISVLVI 0.0 None None 0 None +588 MASCPFAKV 0.0 None None 0 None +589 NHDRFHYLL 5.22641395793 DRFHYLL DNFPYLV 22.0 9461|non_structural_protein_3|CAJ20172.1|Hepatitis_C_virus|11103 +590 FTIFWTVYY 1.73382472341 IFWTVYY VMWTVYH 32.0 146249|polyprotein|ADE10208.1|Hepatitis_C_virus_subtype_3a|356426 +591 VASQPAHVV 0.0 None None 0 None +592 EAFNCESKM 0.0 None None 0 None +593 FSSEVTVAL 0.0 None None 0 None +594 ETIKQLQEL 0.0 None None 0 None +595 YFMDPMVPL 0.0355694048832 DPMVPL DPTTPL 23.0 103392|polyprotein|BAB18806.1|Hepatitis_C_virus|11103 +596 NVYHVGMHI 0.0 None None 0 None +597 AAMEGRLPV 0.0 None None 0 None +598 NHDDDDVEI 167.634475679 NHDDDDVEI NHDSPDAEL 32.0 44133|Genome_polyprotein|P26664.3|Hepatitis_C_virus_genotype_1|41856 +599 NASVNVSHL 124.263294844 NASVNVS NSSVNVS 29.0 183670|polyprotein|AGO67248.1|Dengue_virus_2|11060 +600 EALDAGAIY 0.0 None None 0 None +601 YGRDDWEVI 0.0 None None 0 None +602 VALDKDALV 0.0 None None 0 None +603 LPFSLGKHV 0.0 None None 0 None +604 MANNPCSRY 0.0 None None 0 None +605 YEEPNTATF 0.0 None None 0 None +606 MALYHCVAI 0.0931643013308 ALYHCVAI SLYNTVAI 24.0 189292|gag_protein|ABC40295.1|Human_immunodeficiency_virus_1|11676 +607 YTLAPGVPL 0.176306491827 PGVPL PGVPF 24.0 38556|Genome_polyprotein|Q00269.3|Hepatitis_C_virus|11103 +608 KIHPFFETI 0.0 None None 0 None +609 NMDFLIAEY 0.0 None None 0 None +610 LCIPWTNPV 0.0 None None 0 None +611 SAQEHLLFV 0.0 None None 0 None +612 QSVHPVVTV 1.38374670414 QSVHPVVT KSTHPMVT 30.0 20686|UL123;_IE1|AAR31448.1|Human_betaherpesvirus_5|10359 +613 YVASDIQYM 0.0 None None 0 None +614 FHMRQVNIV 0.0 None None 0 None +615 LAKHSTSAV 0.0 None None 0 None +616 FSHQPKEKV 0.0 None None 0 None +617 YLYIPALAV 0.0 None None 0 None +618 VALFMAITI 0.0 None None 0 None +619 VAFYGLGAV 0.0 None None 0 None +620 EVDPIGNLY 0.0 None None 0 None +621 WALSIHVSV 0.0 None None 0 None +622 ITYPSQAPV 0.0 None None 0 None +623 CIALWSLAY 0.0 None None 0 None +624 FLFYVMTEV 0.0 None None 0 None +625 HAEQDSTTV 0.458333333333 QDSTTV QDATTV 26.0 6373|Genome_polyprotein|SRC279960|Hepatitis_C_virus_subtype_3a|356426 +626 DTNDNVPEF 0.0 None None 0 None +627 NSYGSRRTL 0.0 None None 0 None +628 NARCLIVHL 0.0 None None 0 None +629 FWYRNCHHV 0.0 None None 0 None +630 DADPSTPHL 1.08133686929 DPSTP DPTTP 26.0 103392|polyprotein|BAB18806.1|Hepatitis_C_virus|11103 +631 DSYIHVTYI 2.47386789457 YIHVTYI FLHVTYV 32.0 71663|Spike_glycoprotein_precursor|P59594.1|SARS_coronavirus|227859 +632 DVFDALDLM 0.0 None None 0 None +633 FSMDETGQM 0.0 None None 0 None +634 RTFNKPESV 0.0 None None 0 None +635 YSLQEMEVL 0.0 None None 0 None +636 QTVMFMATM 0.0 None None 0 None +637 VTIDGIRFI 0.0 None None 0 None +638 RALSHPQSL 0.0 None None 0 None +639 TAAGFWLMV 0.0 None None 0 None +640 FMEELGECV 0.0 None None 0 None +641 YLESNPGTI 0.0 None None 0 None +642 VPSNFVEHV 0.0 None None 0 None +643 FTEELRRTF 0.0062273472093 FTEELRR FVELMRR 20.0 39095|nonstructural_protein_3|NP_722463.1|Dengue_virus_type_1_Hawaii|10000440 +644 YGRSRGITV 0.146582464117 SRGITV DRGLTV 22.0 41269|kaposin|AAC57155.1|Human_gammaherpesvirus_8|37296 +645 FSMACNTPL 0.0 None None 0 None +646 QAADEPQLL 0.0 None None 0 None +647 YEFALQRIV 0.0 None None 0 None +648 TAAPTSASV 0.0 None None 0 None +649 LACRKAREI 0.249019834602 CRKARE CRCARE 25.0 155131|ribonucleotide_reductase_large_subunit|CAB06725.1|Human_alphaherpesvirus_2|10310 +650 FIEPLNDTI 0.0 None None 0 None +651 SALRAITRV 0.0 None None 0 None +652 RAAPKAMVL 0.0 None None 0 None +653 VADEGLNNL 0.0 None None 0 None +654 LSNDECKTI 0.0 None None 0 None +655 NAWAVMNHF 0.0 None None 0 None +656 VASNAWAVM 0.0 None None 0 None +657 LSRNLIRTI 0.830019904681 RNLIRTI QNLARTI 24.0 63010|6_kDa_early_secretory_antigenic_target|P0A564.2|Mycobacterium_tuberculosis|1773 +658 HSKEEIKVI 0.0 None None 0 None +659 DSELNFNEY 0.0 None None 0 None +660 DAAERECHL 0.0 None None 0 None +661 ISYTEVPTY 0.976082030541 ISYTEVPTY ITYTDVLRY 26.0 29186|polyprotein_precursor|NP_041724.2|West_Nile_virus|11082 +662 IASDHVVDM 0.0 None None 0 None +663 IAILICTMI 0.0 None None 0 None +664 MAKTGRFHI 0.0 None None 0 None +665 EVMEKVLPL 0.0 None None 0 None +666 FENNAGLPV 0.0 None None 0 None +667 FLHEMVAAM 0.0 None None 0 None +668 QAEPKKKPV 1.7536554713 EPKKKP EPGKNP 22.0 419124|polyprotein|ACF49259.1|Dengue_virus_type_1_Hawaii|10000440 +669 YVLHSKEEI 0.0 None None 0 None +670 FFFHNPKPL 0.430306274192 FFFHNPKPL IFFFNPGEL 25.0 43447|IMMUNOGENIC_PROTEIN_MPT64_(ANTIGEN_MPT64/MPB64)|CAA98382.1|Mycobacterium_tuberculosis_H37Rv|83332 +671 FHWNWIIVL 1.23311590917 HWNWII RWEWVV 28.0 74407|polyprotein|AAU89634.1|Hepatitis_C_virus_subtype_2a|31649 +672 YTMGIIFVL 0.0 None None 0 None +673 YVGKDIESV 0.0 None None 0 None +674 YQHYFRLLV 0.263137102792 YQHYFR YQSYLR 23.0 116781|Nucleoprotein|P05133.1|Hantaan_virus_76-118|11602 +675 MSNSMINTM 0.225806451613 NSMINTM NTMLNTV 26.0 294287|gag_protein|ABI20203.1|Human_immunodeficiency_virus_1|11676 +676 FSMLSRVLI 0.0 None None 0 None +677 FVDYPGDPV 0.0175687336762 VDYPGDPV VDFSLDPT 21.0 96156|polyprotein|ABR25251.1|Hepatitis_C_virus_(isolate_H77)|63746 +678 STAPLYSGM 3.52889315171 TAPLYS TLPVYS 23.0 98254|trans-sialidase,_putative|EAN81042.1|Trypanosoma_cruzi|5693 +679 DTVQLNVKY 0.0 None None 0 None +680 SAYMAATLL 0.0 None None 0 None +681 QAWNFLRAM 0.845286481541 QAWNF QQWNF 27.0 42797|6_kDa_early_secretory_antigenic_target|P0A564.2|Mycobacterium_tuberculosis|1773 +682 CAFGAMCAV 0.0 None None 0 None +683 IMEEEFSTI 0.0 None None 0 None +684 HAANVTQAM 0.0 None None 0 None +685 MAKQIKTKV 0.0363036459226 MAKQIKTK LAKEQKSK 21.0 8920|M_protein,_serotype_5_precursor|P02977.2|Streptococcus_pyogenes_serotype_M5|301449 +686 KAKGIYNSI 0.0 None None 0 None +687 HAPVHFLVI 0.0 None None 0 None +688 EVLQSMQRF 0.0 None None 0 None +689 YVASDIQYM 0.0 None None 0 None +690 YAAMDLSCL 0.0 None None 0 None +691 TPMTCSNTI 0.0 None None 0 None +692 EAPPGRVTF 0.0 None None 0 None +693 DTHSGAGKF 3.3511859631 HSGAGK HDGAGK 29.0 23621|Genome_polyprotein|P26664.3|Hepatitis_C_virus_(isolate_1)|11104 +694 YKYRYFCRV 0.610812498807 RYFCR EYFCR 27.0 155131|ribonucleotide_reductase_large_subunit|CAB06725.1|Human_alphaherpesvirus_2|10310 +695 LSDPHLTAV 0.0 None None 0 None +696 WAGLGGRHV 0.160072495287 GLGGRH GVGWRH 24.0 12183|EBNA3C_latent_protein|CAD53421.1|Human_gammaherpesvirus_4|10376 +697 QHTGTSVVL 0.478658436433 HTGTSVVL HIGAYVVL 23.0 154387|RL2|CAB06760.1|Human_alphaherpesvirus_2|10310 +698 STFCGTLEY 0.0 None None 0 None +699 TMYRCGPLI 0.0 None None 0 None +700 WHNQCSGHL 0.0 None None 0 None +701 FPLRNRPFY 0.40359719383 NRPFY NRSFY 23.0 98603|trans-sialidase,_putative|EAN82716.1|Trypanosoma_cruzi|5693 +702 YVGPAQLSV 0.0 None None 0 None +703 VAQHLATTY 0.0 None None 0 None +704 LVYPRFLYL 0.557903921081 YPRFLYL YPAVFYL 23.0 154041|major_capsid_protein|CAB06743.1|Human_alphaherpesvirus_2|10310 +705 FSREEMHNM 0.0 None None 0 None +706 YYPPGVVFY 0.0250303219548 YYPPGVV YTPEGII 23.0 180850|polyprotein|AFP27208.1|Dengue_virus_4|11070 +707 YLMSFFRLL 0.0 None None 0 None +708 RVFPLRGKI 0.0507541195092 RVFPLRGKI KLFPGGGQI 21.0 181035|||| +709 YPLPVANGM 0.881609743327 YPLPVANGM YPLHEQHGM 25.0 75356|EBNA3A_nuclear_protein|Q8AZJ8|Human_gammaherpesvirus_4|10376 +710 RAVCFSMEI 0.0 None None 0 None +711 QALPLDHHL 0.0 None None 0 None +712 FIEPHARFY 0.0 None None 0 None +713 FFYCIYASL 0.0 None None 0 None +714 CHDDYLVML 0.0 None None 0 None +715 KALFWTVAM 0.987412049439 KALFWTVAM KSLFNTVAV 26.0 126486|gag_protein|ADK33372.1|Human_immunodeficiency_virus_1|11676 +716 EYYEPPHRI 0.0 None None 0 None +717 PTSPMPYTY 0.196275089393 PTSPMP PTDPNP 24.0 70491|envelope_glycoprotein|AAC28452.1|Human_immunodeficiency_virus_1|11676 +718 EAVEARGAI 0.0 None None 0 None +719 NVVRLVATI 1.46700214129 NVVRLVATI NLVPMVATV 27.0 44920|tegument_protein_pp65|YP_002608275.1|Human_betaherpesvirus_5|10359 +720 YLKNSMIAV 0.0 None None 0 None +721 LQAEIVETM 0.0 None None 0 None +722 FHHKSNFLL 0.0 None None 0 None +723 KPIPAFEMV 0.0 None None 0 None +724 FLVDSNLSV 0.0 None None 0 None +725 FIDRQLTMV 0.0 None None 0 None +726 YSASSEIII 0.0 None None 0 None +727 YTPDELHAM 0.00719481474361 PDELHAM PDVAHSL 21.0 130953|G1_and_G2_surface_glycoprotein_precursor|AAG22532.1|Andes_hantavirus|46607 +728 FFYLDYVSI 0.0 None None 0 None +729 YIAPMMEKL 0.0 None None 0 None +730 EAFDRTETH 0.0 None None 0 None +731 SIVDVSIMY 0.0 None None 0 None +732 IPYTTVLHL 0.0 None None 0 None +733 EVFRHKLAM 0.0 None None 0 None +734 VMDRWNETV 1.66487546562 MDRWNE LDRWEK 25.0 19337|gag_protein|AAW57872.1|Human_immunodeficiency_virus_1|11676 +735 LLLDHGVHV 0.0 None None 0 None +736 VIFNVVRLV 0.0 None None 0 None +737 LAIKVTPSV 0.0508134355474 LAIKVTP LAISVVP 23.0 40288|kaposin|AAC57155.1|Human_gammaherpesvirus_8|37296 +738 LTDRQPLMH 0.0 None None 0 None +739 KPLPFNREV 0.0 None None 0 None +740 LNFGDITTV 0.0 None None 0 None +741 QAIDSTFYL 0.0 None None 0 None +742 LALNKGRAY 0.0 None None 0 None +743 IARQVVTAM 0.0 None None 0 None +744 GAFAFGAVF 0.0 None None 0 None +745 KSFPFQSLL 0.0 None None 0 None +746 RAGGSSVVI 0.0 None None 0 None +747 DTIPWYLRL 0.0 None None 0 None +748 MAVDGKPEY 0.0 None None 0 None +749 YLQDVVMQV 0.0 None None 0 None +750 FMVRNYEFL 0.0 None None 0 None +751 YMAGSDTTY 0.0 None None 0 None +752 VVYVLMTSV 0.0 None None 0 None +753 MPAERNGAI 0.0 None None 0 None +754 WPLQPVDHI 0.0 None None 0 None +755 MLDPHGHLI 0.0 None None 0 None +756 FISNSLNIL 0.0 None None 0 None +757 RADGDLTLI 0.0 None None 0 None +758 YQEEMIQCY 0.138922146416 YQEEMIQCY YMESVFQMY 24.0 154585|ribonucleotide_reductase_large_subunit|CAB06725.1|Human_alphaherpesvirus_2|10310 +759 FILDCHPKY 0.0 None None 0 None +760 GAYVYPLPV 1.80161146662 YVYPLPV YVYALPL 29.0 58463|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 +761 FKEAWKHTI 0.0 None None 0 None +762 LAGVKMVMI 0.0 None None 0 None +763 DAKQRIRLL 0.0 None None 0 None +764 LYYPPGVVF 0.0141268558401 YYPPGVV YTPEGII 23.0 180850|polyprotein|AFP27208.1|Dengue_virus_4|11070 +765 RASEDDRVL 0.0 None None 0 None +766 SALEYLLPL 0.982013790038 SALEYLLP SALQFLIP 30.0 22235|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 +767 AAVEPERTL 0.0 None None 0 None +768 GTDCLLLAF 0.0 None None 0 None +769 FVQLPVPII 0.0 None None 0 None +770 RIYPDRHRI 0.0 None None 0 None +771 KVDKNISHI 0.0 None None 0 None +772 RHSQWDHGL 0.0551254766838 SQWDHG TAWDFG 22.0 180726|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 +773 MLYSRDHSV 0.0 None None 0 None +774 AARPLSRMV 0.0 None None 0 None +775 HAQVCSLYI 1.03982555138 HAQVCSLYI KAKICGLYL 30.0 177701|polyprotein|ACZ60104.1|Hepatitis_C_virus_subtype_3a|356426 +776 YSQPFYTSY 0.0 None None 0 None +777 MSDFQYLVV 0.0 None None 0 None +778 SANARCLIV 0.0 None None 0 None +779 SAIAIVQIL 0.0 None None 0 None +780 WMFYHFDAI 0.0 None None 0 None +781 YSKVIKCVV 0.0 None None 0 None +782 AARARGNKV 0.0 None None 0 None +783 TAYERLYLW 0.0 None None 0 None +784 TTASGVWAF 0.0 None None 0 None +785 KVREEVVTM 0.0 None None 0 None +786 MYYRVRDTM 0.0 None None 0 None +787 YVDRLLQHF 0.0 None None 0 None +788 PAIARPQAI 0.0 None None 0 None +789 YLLRAGVHL 2.34592183176 YLLRAGVHL FLLSLGIHL 30.0 16751|pol_protein|BAA32832.1|Hepatitis_B_virus|10407 +790 LVTPHMAEV 0.29585271922 LVTPHM LVTPSM 24.0 150378|polyprotein|AGW21594.1|Dengue_virus_1|11053 +791 EHVSDDDLL 0.0 None None 0 None +792 SFYHLVSTV 0.485538841086 SFYHLVST GFYHILNN 25.0 1516|Nucleoprotein|P03418.1|Human_respiratory_syncytial_virus_A2|11259 +793 FSAGNEANV 0.205224687568 SAGNEA NAGNDA 23.0 1090|Transcription_activator_BRLF1|P03209.1|Human_herpesvirus_4_strain_B95-8|10377 +794 KPGDRVVLV 0.0 None None 0 None +795 YSRGSSRCI 0.0 None None 0 None +796 YSTCVLVVL 0.0 None None 0 None +797 YSTHQTFMV 0.0 None None 0 None +798 WSLDGKYIV 1.99294213388 WSLDGKYIV WAIKWEYVV 26.0 72233|Genome_polyprotein|P27958.3|Hepatitis_C_virus_subtype_1a|31646 +799 HAWRDLSSM 0.0 None None 0 None +800 FASSLWETT 0.0 None None 0 None +801 FDYPSLFCI 0.0 None None 0 None +802 KAPPLTDVL 0.0 None None 0 None +803 DVFDALDLM 0.0 None None 0 None +804 ALYCRLATV 0.0118752492321 ALYCRLATV SLYNTIATL 20.0 190827|gag_protein|AAN08336.1|Human_immunodeficiency_virus_1|11676 +805 MVYLQIGGF 0.0 None None 0 None +806 EPFSGTASV 0.0 None None 0 None +807 ETMDELELL 0.578907805322 MDELEL MDKLEL 25.0 185419|envelope_protein|AGW23591.1|Dengue_virus_3|11069 +808 SMLNWFSPV 1.31489982056 MLNWFSPV LLIWFRPV 30.0 37507|Large_T_antigen|P03071.1|Human_polyomavirus_1|1891762 +809 NMLNLTHTY 0.0 None None 0 None +810 HSFNPEAQV 0.544692682129 HSFNPE KAFNPE 25.0 187158|Gag_protein|Q1KW74|Human_immunodeficiency_virus_1|11676 +811 SAYGSSGEL 0.0 None None 0 None +812 FSIPWAHAW 1.46617482283 FSIPWAH VSIPWTH 34.0 46480|DNA_polymerase|CAA10434.1|Hepatitis_B_virus|10407 +813 MASSAQEHL 0.0 None None 0 None +814 RHSREMALL 0.0 None None 0 None +815 WVLHHMGGM 36.5311333334 WVLHHMG WILRHPG 30.0 180818|Membrane_glycoprotein_precursor|NP_739582.2|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 +816 VADSDRQLV 0.0 None None 0 None +817 IAAAWALSF 0.163128403126 AAAWAL AAAWYL 25.0 183819|polyprotein|AGO67248.1|Dengue_virus_2|11060 +818 KAESTPEIV 0.0 None None 0 None +819 LHLGHMFSL 0.107288558852 LGHMFSL LSHYFTL 22.0 59459|Trans-sialidase|SRC7915|Trypanosoma_cruzi|5693 +820 QRINLPHLL 0.0 None None 0 None +821 YALMRHRHT 0.0 None None 0 None +822 RLYPLANSL 0.0 None None 0 None +823 DHFSHASSI 0.0 None None 0 None +824 ISMEKGYNI 0.0 None None 0 None +825 FLHEMVAAM 0.0 None None 0 None +826 YVALEAQAI 0.0 None None 0 None +827 YLMTRTLPM 0.0 None None 0 None +828 QTFPQVSEL 0.0 None None 0 None +829 YPESIKAPV 0.0 None None 0 None +830 VHSKTSQLL 0.0 None None 0 None +831 TSSDRMTSV 0.0 None None 0 None +832 QMAERALYY 0.0 None None 0 None +833 LASPFATTA 0.0 None None 0 None +834 AAYTSYTPY 0.264739211661 AAYTSYTP EEYTDYMP 25.0 180681|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 +835 VSCRPVVYV 0.0 None None 0 None +836 RTYHGRLAY 0.0 None None 0 None +837 LARHSAAFL 0.0 None None 0 None +838 RSEALPVSY 0.0498128500965 RSEALP RAESLP 23.0 419006|PPE_family_protein_PPE68|KAM81677.1|Mycobacterium_tuberculosis_H37Ra|419947 +839 ETKPFGLVV 0.00397696968794 KPFGLVV KPARLIV 19.0 30946|HCV-1|AAA45676.1|Hepatitis_C_virus_genotype_1|41856 +840 DVKNFWQGM 0.0 None None 0 None +841 FAELKSARM 0.0 None None 0 None +842 YMKPRLRTT 0.0 None None 0 None +843 STFCGTLEY 0.0 None None 0 None +844 HAATGPGEV 0.471180876873 HAATGPGE HAPTGSGK 28.0 146644|polyprotein|ADE10208.1|Hepatitis_C_virus_subtype_3a|356426 +845 PSQNRFLTY 10.5277024867 PSQNRF PSMKRF 22.0 180681|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 +846 YISAWLDSL 0.577024181579 SAWLDS GAWMDS 27.0 30903|prM_protein|YP_001527879.1|West_Nile_virus_NY-99|10000971 +847 VPFPPKEPL 7.85759820488 VPFPPK IPYDPK 24.0 180789|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 +848 KSHELVMYI 0.0 None None 0 None +849 LMLGRTNTL 0.0 None None 0 None +850 VARHTFSML 0.0 None None 0 None +851 LAIFMPPTY 0.018791562647 IFMPPTY VYMSPFY 22.0 141469|envelope_glycoprotein_B|NP_044629.1|Human_alphaherpesvirus_1|10298 +852 WAVVTMTAV 0.0 None None 0 None +853 FPRASQSLV 1.0950421762 FPRASQSLV FPGFGQSLL 23.0 23807|tax|AAG48731.1|Human_T-lymphotropic_virus_2|11909 +854 YDFLCLSLV 0.0 None None 0 None +855 NKFPGDSMV 0.0 None None 0 None +856 FSLLATVIL 0.468169410856 FSLLATV FTLVATV 25.0 98640|trans-sialidase,_putative|EAN80840.1|Trypanosoma_cruzi|5693 +857 SSSDNRNFI 0.0 None None 0 None +858 KSRNWLKSI 0.0 None None 0 None +859 QALNLQVVL 0.0 None None 0 None +860 FPVLLLDTI 4.07245586889e-05 PVLLLDT PVENLET 16.0 149063|NS3_protease/helicase'|NP_803144.1|Hepatitis_C_virus_(isolate_H77)|63746 +861 VTDFHNHSV 0.0 None None 0 None +862 LSDSMPLWM 0.0 None None 0 None +863 QSTKVNMLY 0.0 None None 0 None +864 MANHLGVGV 0.0 None None 0 None +865 HMDVEESQY 0.0 None None 0 None +866 LADPIEKEL 0.0 None None 0 None +867 MAITILVAL 0.0 None None 0 None +868 YRDNKMTRI 0.0 None None 0 None +869 FQMAERALY 0.0 None None 0 None +870 RINENTGIV 0.0 None None 0 None +871 EAGEESTSV 0.0 None None 0 None +872 RGMPPPPTV 0.746912503019 PPPPT PPPAT 25.0 120093|unnamed_protein_product|CAA33016.1|Rubella_virus|11041 +873 RLFRMFVHV 0.0 None None 0 None +874 FLTDMAKQI 0.0 None None 0 None +875 ISMQFLSSL 0.0 None None 0 None +876 HTDTNNLGI 0.0 None None 0 None +877 LALAIYTLL 0.0 None None 0 None +878 LAVCAFTVL 0.0 None None 0 None +879 AAAPNLRAL 0.0 None None 0 None +880 LVDSNLSVV 0.0 None None 0 None +881 VSSVQGITY 0.0 None None 0 None +882 HLMKQISSF 5.7878791982 HLMKQISS HLAFQLSS 23.0 24172|pX-rex-orf_I_{alternatively_spliced}|AAB23359.1|Human_T-lymphotropic_virus_1|11908 +883 EARGAIRGF 0.0 None None 0 None +884 LVSTSNHAY 0.0 None None 0 None +885 IAPRRWLLL 0.0 None None 0 None +886 RMAERRQEV 0.0 None None 0 None +887 YVVATTKLM 0.338384379032 YVVATTKL YAVATTIL 26.0 184713|polyprotein|AFP27208.1|Dengue_virus_4|11070 +888 FQDDFSPRF 0.0 None None 0 None +889 IGFNGNQIV 0.0 None None 0 None +890 KMFTCSKFV 0.0 None None 0 None +891 VAEVCPREV 0.0 None None 0 None +892 WAPLPGQML 0.0 None None 0 None +893 DAQQLATAI 0.0 None None 0 None +894 ILLNGDATV 0.000458453342916 ILLNGDAT VLLRLDGT 18.0 11214|possible_regulatory_protein|NP_302009.1|Mycobacterium_leprae|1769 +895 TIYDEDVLV 5.82753285036 TIYDEDVLV TMYYKDVTV 24.0 194440|envelope_glycoprotein_B|NP_044629.1|Herpes_simplex_virus_(type_1_/_strain_17)|10299 +896 WVKEDMGIV 0.0 None None 0 None +897 RKYGSTSSI 0.0 None None 0 None +898 MTDAQQLAT 0.0 None None 0 None +899 GFDQYRTLL 0.0 None None 0 None +900 NASGATAPL 0.0 None None 0 None +901 FFPEMGTKI 0.0 None None 0 None +902 NVHSSGKPI 0.305435862776 SSGKPI TSGSPI 22.0 22825|polyprotein|ABG75765.1|Dengue_virus_1|11053 +903 AALVGAEVV 0.0 None None 0 None +904 DHFSHASSI 0.0 None None 0 None +905 RAMGERLLL 0.0 None None 0 None +906 KIYDGKDKM 0.0 None None 0 None +907 WASGNERSL 22.1287414254 WASGNE WNSGHE 25.0 180440|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 +908 LATVRSHHM 0.0 None None 0 None +909 LRDHGSFLL 0.0 None None 0 None +910 TALETSAPF 0.0 None None 0 None +911 HTFSMLSRV 0.0 None None 0 None +912 KAFHGSSGL 0.0 None None 0 None +913 LAKKPGCVF 1.69047619048 PGCVF PGCSF 26.0 44833|polyprotein|BAA03375.1|Hepatitis_C_virus_subtype_1a|31646 +914 IPNPQLGPV 4.26005083762e-05 GPV GPV 17.0 154857|tegument_protein|CAB06735.1|Human_alphaherpesvirus_2|10310 +915 QQHDGAFLI 0.0 None None 0 None +916 AAFFYLDYV 0.0 None None 0 None +917 FFPEMGTKI 0.0 None None 0 None +918 SQWDHGLSI 0.0803492524925 SQWDHG TAWDFG 22.0 180726|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 +919 MSCRKIAHL 0.0 None None 0 None +920 MGFTVLTTV 0.0 None None 0 None +921 NLEVLDCRY 0.0 None None 0 None +922 LAQAVRAVL 0.0 None None 0 None +923 FMQTRYNKL 0.0 None None 0 None +924 LTHTGACPY 0.0 None None 0 None +925 KAFSDRFSL 0.0 None None 0 None +926 FLRDCSPRL 0.0 None None 0 None +927 DIFTTLKMY 0.0 None None 0 None +928 RAPPEAIAL 0.0 None None 0 None +929 STQDTPVTV 1.59510084399 STQDTPVTV ALADLPVTV 25.0 189566|glycosyl_transferase|WP_015631503.1|Mycobacterium_tuberculosis|1773 +930 QASSDWAAV 0.0 None None 0 None +931 FTRGIQTLF 0.0328747529981 RGIQTLF RGLTSLF 23.0 52652|||| +932 YRALNRVHV 0.0 None None 0 None +933 YEARLLKHM 0.0 None None 0 None +934 MELNSVNVM 0.0 None None 0 None +935 TAARLRHKV 0.0 None None 0 None +936 YAYFLDNVS 0.0 None None 0 None +937 TVLENLAVL 0.415657048035 TVLENLAVL NALDNLAVL 28.0 185447|polyprotein|AGK36298.1|Dengue_virus_2|11060 +938 HSFTHKQHL 0.0 None None 0 None +939 NMEELILAI 0.0 None None 0 None +940 IAPHRNEKL 0.0 None None 0 None +941 MMNDIVKEF 0.146493252704 MMNDIVK MINGVVK 23.0 185710|Nonstructural_protein_NS5|YP_001531176.2|Dengue_virus_3|11069 +942 FSVPLHIFL 0.133234367786 FSVPLHIFL FLVPFVVFL 25.0 139746|Dense_granule_protein_3|B6KEU8.2|Toxoplasma_gondii|5811 +943 TVMGRITTL 0.0 None None 0 None +944 FAKYWEENF 0.0 None None 0 None +945 VSDLLVLLL 0.0 None None 0 None +946 FLHVGDLVI 0.0 None None 0 None +947 EAFAHEARF 0.0 None None 0 None +948 SSLGKTQTV 0.0 None None 0 None +949 LVLIGISHV 1.0 LVLIGIS LILIGIT 26.0 59182|attachment_glycoprotein|ABQ58821.1|Human_metapneumovirus|162145 +950 FYFQVPFIY 0.0 None None 0 None +951 WSFAVAICI 0.0 None None 0 None +952 QHMIQQQAL 0.0 None None 0 None +953 FPEGYGTQV 0.38077711011 FPEGY LPEGY 25.0 31997|hypothetical_protein_FTT0484|YP_169522.1|Francisella_tularensis_subsp._tularensis_SCHU_S4|177416 +954 KPYGRNKPF 0.0 None None 0 None +955 HGFNATYHV 0.0990072203855 HGFNATY HSYGVTY 23.0 232152|rhoptry_kinase_family_protein|AFO54841.1|Toxoplasma_gondii_type_III|398031 +956 YIRTRNEFV 0.0 None None 0 None +957 YPEVFGPPL 0.511017522783 PEVFGP PEAAGP 23.0 19348|IMMUNOGENIC_PROTEIN_MPT64_(ANTIGEN_MPT64/MPB64)|CAA98382.1|Mycobacterium_tuberculosis_H37Rv|83332 +958 MVACGGTVY 0.0 None None 0 None +959 APSEHAQMV 0.0 None None 0 None +960 TRTFVEFIL 0.0 None None 0 None +961 LLSEVLLHY 0.0 None None 0 None +962 IQVGTGVTV 0.0 None None 0 None +963 LTLAFTVML 0.0 None None 0 None +964 HVGDLVIVV 0.0 None None 0 None +965 MTREELNAL 0.025913105963 MTREELNAL MTQKARNAL 23.0 150461|polyprotein|AGK36298.1|Dengue_virus_2|11060 +966 VAVQESARI 0.0 None None 0 None +967 VPSPLFSIV 0.0 None None 0 None +968 KAGGGSNEV 0.0469468239536 KAGGGSN PVGGGSS 23.0 189750|Diacylglycerol_acyltransferase/mycolyltransferase_Ag85B|SRC280000|Mycobacterium_tuberculosis|1773 +969 YMLIIVSIF 0.0 None None 0 None +970 VAPHAPVHF 0.0 None None 0 None +971 TPFHLASAV 0.0 None None 0 None +972 SARDCKDPY 0.000418357588503 SARDCKDPY SARLAGIPY 18.0 243835|glycosyl_transferase|WP_015628558.1|Mycobacterium_tuberculosis|1773 +973 FMATMPPAV 0.0 None None 0 None +974 TMVACGGTV 0.0 None None 0 None +975 NSDHVMFMV 0.0 None None 0 None +976 FMKNYFKDV 0.0 None None 0 None +977 LNVEDPVTV 0.0 None None 0 None +978 FIPINGCPI 1.34457687638 FIPINGCPI YIPLVGAPL 28.0 23365|polyprotein|BAB18806.1|Hepatitis_C_virus|11103 +979 YTSYFGYKM 1.56288713183e-05 YTSYFGYKM YTMDGEYRL 14.0 76121|polyprotein_precursor|NP_041724.2|West_Nile_virus|11082 +980 WSPHPLQIV 0.0 None None 0 None +981 YTTITPQII 0.0 None None 0 None +982 CSFYRTHTL 0.0256163049141 SFYRTHTL SFHNLHLL 22.0 79390|Protein_Tax-1|P0C213.1|Human_T-cell_lymphotropic_virus_type_1_(african_isolate)|39015 +983 NAAKNQVAM 0.0187943866999 NAAKNQVAM NASRCWVAM 21.0 21385|polyprotein|AAY82034.1|Hepatitis_C_virus_genotype_1|41856 +984 FETDGRRFL 0.0 None None 0 None +985 SVEINDIMY 0.0 None None 0 None +986 DPAPRPSLL 0.904502870813 DPAPRPSLL DPQERPRKL 24.0 110338|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 +987 QAVTEVEAV 0.138095238095 AVTEVEA AITEVEC 26.0 2102|VP1|BAF93325.1|Human_polyomavirus_1|1891762 +988 TAFQKGYGI 0.0 None None 0 None +989 ICFPVLVAL 0.27101796422 FPVLVA FPYLVA 24.0 9461|non_structural_protein_3|CAJ20172.1|Hepatitis_C_virus|11103 +990 NHVPVNHFW 0.0 None None 0 None +991 DMNDHAPEV 0.0025892563244 NDHAPEV NDFFPSV 20.0 16814|precore_protein|CAM58990.1|Hepatitis_B_virus|10407 +992 SPLPPPEQI 1.56735830397 SPLPP APLPP 26.0 179766|cell_surface_protein_(associated_with_virulence)|NP_302372.1|Mycobacterium_leprae_TN|272631 +993 LRLDGSVVI 0.915531304079 LRLDGSVV LRLDGTTL 27.0 11214|possible_regulatory_protein|NP_302009.1|Mycobacterium_leprae|1769 +994 HACSHLRQM 0.0 None None 0 None +995 FPSSQGSLY 3.38709858116 FPSSQGSL FPIVQGEL 24.0 48458|IMMUNOGENIC_PROTEIN_MPT64_(ANTIGEN_MPT64/MPB64)|CAA98382.1|Mycobacterium_tuberculosis_H37Rv|83332 +996 FNRDDCSVL 0.0 None None 0 None +997 TSFPQKVHL 0.0 None None 0 None +998 EAFAHEARF 0.0 None None 0 None +999 DAKSHELVM 0.0 None None 0 None +1000 TEYRALNRV 0.0 None None 0 None +1001 KTIWHTAEY 0.0 None None 0 None +1002 KAMLEEQLI 0.0 None None 0 None +1003 DTSDGLAVL 0.0 None None 0 None +1004 LEFGKPSTL 0.0 None None 0 None +1005 TLLEFFITL 0.0 None None 0 None +1006 FTKRQRKAM 0.0 None None 0 None +1007 FCLSTENSI 0.0 None None 0 None +1008 FQGFSVQLI 0.0 None None 0 None +1009 RVAPGYYTL 0.0 None None 0 None +1010 FYQDMMNDI 0.201754385965 YQDMMND YQQQLND 26.0 143680|Genome_polyprotein|P06441.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 +1011 CLYDSVLML 0.0 None None 0 None +1012 YTCVVSNKL 0.0 None None 0 None +1013 PAEEPTNEL 0.0 None None 0 None +1014 QVYSWLLCL 0.0 None None 0 None +1015 PANESFGHL 0.0 None None 0 None +1016 SPFAAAAAV 0.0 None None 0 None +1017 DVVHHLLSV 0.0 None None 0 None +1018 MFYPERTAL 0.0 None None 0 None +1019 VSDPACSSI 0.0 None None 0 None +1020 WAKVRTAEF 0.0 None None 0 None +1021 AALRHERAV 0.0 None None 0 None +1022 YVVATTKLM 0.22206474874 YVVATTKL YAVATTIL 26.0 184713|polyprotein|AFP27208.1|Dengue_virus_4|11070 +1023 RMLLDPNTV 0.0 None None 0 None +1024 YYDYMKPRL 0.0356673922245 YYDYM YTDYM 23.0 180681|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 +1025 FPRHCVSWM 0.0 None None 0 None +1026 YLPPDPQPF 0.802965979807 LPPDPQP VPTDPNP 27.0 70491|envelope_glycoprotein|AAC28452.1|Human_immunodeficiency_virus_1|11676 +1027 HPATRPLHV 0.0 None None 0 None +1028 MVTGILLYM 0.0 None None 0 None +1029 KPISYMAII 0.222648225888 KPISYM RPVSYL 25.0 39571|polyprotein|BAD73987.1|Hepatitis_C_virus_subtype_1b|31647 +1030 DSSQRFEVI 0.0 None None 0 None +1031 STGYAISAY 0.0 None None 0 None +1032 KQLEFHIEI 0.0 None None 0 None +1033 FFCEVPVLL 0.0 None None 0 None +1034 FSMDETGQM 0.0 None None 0 None +1035 YPRQYSLKL 0.0 None None 0 None +1036 ETAYTKDGF 0.0 None None 0 None +1037 FSNHWTFWV 0.0 None None 0 None +1038 IGYANAKIY 0.0 None None 0 None +1039 DFFEDTEHY 0.0 None None 0 None +1040 DPMKVEAHV 0.0 None None 0 None +1041 GSGEHPMDY 0.0 None None 0 None +1042 SHSRGNDTL 0.0 None None 0 None +1043 FHTSSSLTV 0.0 None None 0 None +1044 VVMRICNLI 0.0 None None 0 None +1045 TALDSSLCL 0.0 None None 0 None +1046 DSDDMDLEV 0.0 None None 0 None +1047 HSYVGPAQL 0.0206560380033 HSYVGP HSVVNP 22.0 47854|Glycoprotein_I_precursor_(Glycoprotein_IV)_(GI)_(GPIV)|P09258.1|Human_alphaherpesvirus_3|10335 +1048 EMFQRYSAF 2.07487586145 EMFQRYSAF EFFTKNSAF 24.0 44214|UL123;_IE1|AAR31448.1|Human_betaherpesvirus_5|10359 +1049 MPVSIRLVV 0.0005030251957 PVSIRLVV PASRDLVV 18.0 93224|core_protein|AAL31859.1|Hepatitis_B_virus|10407 +1050 LVDGDLGKY 0.00752911114692 GDLGKY GDAGGY 22.0 3094|Antigen_85-B_precursor_(85B)_(Extracellular_alpha-antigen)_(Antigen_85_complex_B)_(Ag85B)_(Mycolyl_transferase_85B)_(Fibronectin-binding_protein_B)_(30_kDa_extracellular_protein)|P31952|Mycobacterium_tuberculosis|1773 +1051 RSLAFPVPL 0.0223084774724 LAFPVP LSFPDP 22.0 79300|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 +1052 RAFHDLRVA 0.0 None None 0 None +1053 IYDEDVLVV 0.0 None None 0 None +1054 LAMHSIWEM 0.00687735530344 HSIWE HTLWK 23.0 24943|DNA_polymerase|CAA10434.1|Hepatitis_B_virus|10407 +1055 YCRAWCQAL 0.0 None None 0 None +1056 QAVTNHSVY 0.0 None None 0 None +1057 HSQECGSFL 0.0 None None 0 None +1058 LQHTGTSVV 0.0 None None 0 None +1059 ETRAQLARH 0.0 None None 0 None +1060 RAALVGAEV 0.0 None None 0 None +1061 IPNAQNMTI 5.34979128985 PNAQNM PGAQNL 24.0 140615|amino_acid_decarboxylase|YP_177889.1|Mycobacterium_tuberculosis_H37Rv|83332 +1062 LATCCRARY 0.0 None None 0 None +1063 LMRHSMEKI 0.384767672963 RHSMEKI RHAMEEL 27.0 419128|polyprotein|ACF49259.1|Dengue_virus_type_1_Hawaii|10000440 +1064 VSARHPQHL 1.15203265572 RHPQHL RRPKHL 25.0 66195|Nucleoprotein|P41269.1|Puumala_hantavirus|11604 +1065 YKYDAGSAA 0.0 None None 0 None +1066 IIFLLGEIV 0.0406172919483 IIFLLGEIV VLFYLGQYI 24.0 156550|E3_ubiquitin-protein_ligase_Mdm2|Q00987.1|Homo_sapiens|9606 +1067 LARSQRTQV 0.0 None None 0 None +1068 NAAVETASL 0.0 None None 0 None +1069 LACSICHVY 0.0734222777342 LACSIC IVCPIC 23.0 64819|E7_protein|ABL96585.1|Human_papillomavirus_type_16|333760 +1070 DIYDVLICL 0.804762038021 YDVLIC YDIIIC 31.0 97111|polyprotein|ABR25251.1|Hepatitis_C_virus_(isolate_H77)|63746 +1071 LTMSWLTPL 0.0 None None 0 None +1072 FHNDLMPSY 0.122946002019 NDLMPS NDFFPS 23.0 16813|External_core_antigen|SRC279980|Hepatitis_B_virus|10407 +1073 VMVSPASAI 0.0 None None 0 None +1074 VFFSLLATV 25.6111406871 FSLLATV FTLVATV 25.0 98640|trans-sialidase,_putative|EAN80840.1|Trypanosoma_cruzi|5693 +1075 EASLATQIV 0.0 None None 0 None +1076 ETLVSTSTI 0.0 None None 0 None +1077 FPYQITNEH 0.0 None None 0 None +1078 RTFLPVHLL 0.0 None None 0 None +1079 LPQPGVRSL 0.548160467495 LPQPGVR LPRPGPR 28.0 139406|polyprotein|ACT37184.1|Hepatitis_C_virus|11103 +1080 VPNNCLGKV 0.268353983445 CLGKV CLGKA 24.0 180442|Chain_B,_Dengue_Virus_Rna_Dependent_Rna_Polymerase_With_Residues_From_The_Ns5_Linker_Region|4C11_B|Dengue_virus|12637 +1081 HPLEFCLLL 0.0 None None 0 None +1082 MAFVTLTDL 0.0 None None 0 None +1083 FSVQLIRKF 0.0 None None 0 None +1084 FPQMRAMSL 0.0 None None 0 None +1085 LRLNWGEPI 0.0 None None 0 None +1086 YEEDSGEYF 0.0 None None 0 None +1087 TAKGTAQLV 0.0 None None 0 None +1088 LHFHWNWII 1.5492033712 HWNWII RWEWVV 28.0 74407|polyprotein|AAU89634.1|Hepatitis_C_virus_subtype_2a|31649 +1089 DTDGQPLLL 0.0761637873905 TDGQPLL TSGSPII 22.0 22822|NS3_protein|NP_740321.1|Dengue_virus_4|11070 +1090 AHLLCTLLL 0.211842833049 AHLLCTLLL SHFLCTFTF 27.0 41622|Genome_polyprotein|P08617.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 +1091 KAPGFEKHL 0.0 None None 0 None +1092 SSYGGTIRY 0.545454545455 YGGTIR HGGTLR 26.0 120127|unnamed_protein_product|CAA33016.1|Rubella_virus|11041 +1093 YQDMMNDIV 0.240277994375 YQDMMNDIV YQQQLNDPV 27.0 143680|Genome_polyprotein|P06441.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 +1094 MQALNLQVV 0.0 None None 0 None +1095 MHYLKNSMI 0.0 None None 0 None +1096 NAKSRGWLI 0.0 None None 0 None +1097 DSNRVVCPI 0.0 None None 0 None +1098 ISNRSVLHL 0.0 None None 0 None +1099 QAELRGRVL 0.0 None None 0 None +1100 ASFDCAIEM 0.0 None None 0 None +1101 LQIGGFSSV 0.0 None None 0 None +1102 QTWRAVTTL 0.0 None None 0 None +1103 FSAQTFYVL 0.0 None None 0 None +1104 LGDDFSSAY 0.0 None None 0 None +1105 FQCAPGYAL 0.227490636034 PGYAL PGYAL 28.0 27295|polyprotein_precursor|NP_041724.2|West_Nile_virus|11082 +1106 DRETGMHLL 0.0 None None 0 None +1107 FALQRIVQK 0.0 None None 0 None +1108 DAVGNMLNL 0.0 None None 0 None +1109 FYRLHLGTY 0.0 None None 0 None +1110 FELKSPVKM 0.0 None None 0 None +1111 VLRPRWCPV 2.53947368421 RPRWCPV RPSWGPT 26.0 36352|Polyprotein|P90247|Hepatitis_C_virus|11103 +1112 HHSSFRRHL 0.0 None None 0 None +1113 FSYLTMSWL 0.0 None None 0 None +1114 WAESVEREI 0.0 None None 0 None +1115 KADVVHVTL 0.0 None None 0 None +1116 IMEENDSNI 0.0 None None 0 None +1117 LRLPHWPII 0.0 None None 0 None +1118 EAVQDPMKV 0.0 None None 0 None +1119 LIRKFAQSI 0.0 None None 0 None +1120 SHHQCGQSL 0.0 None None 0 None +1121 CTLGLGSLY 10.1824630352 CTLGLGSLY CTCGSSDLY 28.0 7116|NS3|ABN45875.1|Hepatitis_C_virus_(isolate_H77)|63746 +1122 ELAHDSYFY 0.0 None None 0 None +1123 HAANVTQAM 0.0 None None 0 None +1124 WTFWVGPFI 0.0 None None 0 None +1125 VVEHVLTTV 0.0 None None 0 None +1126 NDHDNWCII 0.0 None None 0 None +1127 IAPLLPVAV 1.72391567608 IAPLLPV FAPALPI 24.0 422989|polyprotein|ABY67644.1|Hepatitis_C_virus_genotype_1|41856 +1128 LSGPWGSPL 0.0 None None 0 None +1129 DPADPTSNL 0.0753429944852 DPADPT DPLKPT 23.0 27241|Spike_glycoprotein_precursor|P59594.1|SARS_coronavirus|227859 +1130 FPNSDHVMF 0.0 None None 0 None +1131 EVQDIQASL 0.00328204778107 VQDIQASL VQEDAASL 19.0 423007|Genome_polyprotein|P26664.3|Hepatitis_C_virus_genotype_1|41856 +1132 RPYKQGARL 0.0 None None 0 None +1133 DVAQHGARL 0.0 None None 0 None +1134 FLEKNKDAV 0.0 None None 0 None +1135 DSELAHDSY 0.0 None None 0 None +1136 MPLWMASII 0.0 None None 0 None +1137 YHFDAIRTF 5.93421006727 FDAIRTF YDAVRTW 27.0 154164|tegument_protein|CAB06732.1|Human_alphaherpesvirus_2|10310 +1138 VSTEHCLSV 0.0 None None 0 None +1139 YEAAKLLLV 0.0 None None 0 None +1140 LVQAGVDVV 0.0 None None 0 None +1141 SATASMLSV 0.0 None None 0 None +1142 DQFTKSISI 0.0 None None 0 None +1143 CALCALSNI 0.0 None None 0 None +1144 RAKPRWRVA 0.0 None None 0 None +1145 AAMDAGFLY 0.0 None None 0 None +1146 CAMTMNKYI 0.0 None None 0 None +1147 NLEPHGYVV 0.0 None None 0 None +1148 MLLSPGQNV 0.0 None None 0 None +1149 WQIHRVDIL 0.55932505738 WQIHR WLVHR 25.0 41407|Envelope_protein|NP_739583.2|Dengue_virus_2|11060 +1150 YAELGTTTK 0.0 None None 0 None +1151 YKLNRAFML 0.0 None None 0 None +1152 FAAAAAVAA 0.0 None None 0 None +1153 KMADPNQCV 1.15009746589 KMADPNQCV RVIDPRRCL 26.0 150556|polyprotein|AGW21594.1|Dengue_virus_1|11053 +1154 DPYVKAHLL 0.0 None None 0 None +1155 WPIINTPMV 0.0 None None 0 None +1156 KYYTDPSTY 1.74983759401 KYYTDPSTY KLYQNPTTY 31.0 32268|hemagglutinin|AAK38298.1|Influenza_A_virus_(A/Bar-headed_Goose/Qinghai/61/05(H5N1))|336238 +1157 RVSSYGGTI 0.0 None None 0 None +1158 EALDAGAIY 0.0 None None 0 None +1159 EFIMAITSM 0.0 None None 0 None +1160 FPWWLARVL 0.0461652934999 WLARVL WMIRIL 24.0 185817|envelope_protein|AGW23590.1|Dengue_virus_4|11070 +1161 WTLASMELV 0.0 None None 0 None +1162 IVRCLVTSV 0.0 None None 0 None +1163 MPAFHFNIL 0.00333528511973 PAFHFNI PALVFDI 19.0 24427|polyprotein|ACX44238.1|Hepatitis_C_virus_subtype_1a|31646 +1164 YRTHTLQTL 0.0 None None 0 None +1165 HASVVAAYL 0.0131278658919 HASVVAA HARFVAA 22.0 194|Hypothetical_protein_esxG_(PE_family_protein)|O53692.1|Mycobacterium_tuberculosis|1773 +1166 ISRPSSNAL 0.0281163741936 PSSNAL PQSNAV 22.0 183229|polyprotein|AGW21594.1|Dengue_virus_1|11053 +1167 RALLGCSCV 0.0 None None 0 None +1168 DAVWSRATF 0.0 None None 0 None +1169 DVVHHLLSV 0.0 None None 0 None +1170 MSFFRLLQM 0.0 None None 0 None +1171 KIIAFRKTL 0.0 None None 0 None +1172 TVSSNLSHV 0.0 None None 0 None +1173 MSVEINDIM 0.0 None None 0 None +1174 IAICRQIGI 0.0 None None 0 None +1175 ISKPSELPI 0.0 None None 0 None +1176 DPIEKELSV 0.0 None None 0 None +1177 DHSNDPTAI 0.12924811208 DHSNDPT DHQLDPA 24.0 190466|large_surface_antigen|CAL29876.1|Hepatitis_B_virus|10407 +1178 WRLAEAEML 0.0 None None 0 None +1179 RGLPWTVRV 0.0 None None 0 None +1180 KPMPTIQWI 0.407168297158 KPMPTIQW EPEPDVAW 25.0 96257|Genome_polyprotein|SRC279960|Hepatitis_C_virus|11103 +1181 RRFNLTSTF 0.0 None None 0 None +1182 RRSHTGTFL 0.338888888889 SHTGTF SHSGSF 26.0 61077|Non-capsid_protein_NS-1|P07298.1|Human_parvovirus_B19|10798 +1183 FALDENDNA 0.0 None None 0 None +1184 NPEELEQVV 0.0 None None 0 None +1185 QAMHSFGRF 0.0 None None 0 None +1186 TAIAICRQI 0.0 None None 0 None +1187 EVMEKVLPL 0.0 None None 0 None +1188 DVLPDTFTL 0.170795867243 VLPDTFT VLPCSFT 24.0 69679|polyprotein|BAD73987.1|Hepatitis_C_virus_subtype_1b|31647 +1189 RTGDRPHTF 0.0 None None 0 None +1190 QPAVFETTV 0.0911167657101 PAVFETTV PAIFQSSM 25.0 59975|pol_protein|ACJ76655.1|Human_immunodeficiency_virus_1|11676 +1191 VMDFRFGTI 0.0 None None 0 None +1192 NEDDSTFTI 0.0 None None 0 None +1193 TALGLCEEV 0.0 None None 0 None +1194 SMLSRVLII 0.0 None None 0 None +1195 DANLHKNEL 0.0 None None 0 None +1196 DHYAVESAL 0.0 None None 0 None +1197 EVKIGKMSY 0.000778543502349 EVKIGKMSY DVKKDLISY 17.0 25929|Nonstructural_protein_NS3|NP_739587.2|Dengue_virus_2_Thailand/16681/84|31634 +1198 LANGGKVPF 1.96547847148 LANGGKVPF LSNTGEIPF 32.0 108018|polyprotein|CAB41951.1|Hepatitis_C_virus|11103 +1199 IGAKHTLTI 0.0 None None 0 None +1200 EVVGGWPVV 0.0 None None 0 None +1201 VANERISMQ 0.0 None None 0 None +1202 LSLKQVISI 0.0 None None 0 None +1203 VGFPVGDSV 0.013726318129 FPVGDSV LPVADAV 22.0 75408|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 +1204 LPLDHHLAL 0.0 None None 0 None +1205 GALPLFRKY 0.0 None None 0 None +1206 VSYHPDLGI 4.0 PDLGI PDLGV 26.0 30946|HCV-1|AAA45676.1|Hepatitis_C_virus_genotype_1|41856 +1207 HLFGTSCPY 0.0 None None 0 None +1208 TATTILIMI 0.0 None None 0 None +1209 LSFMEAQSL 0.0 None None 0 None +1210 FLSLGIASL 0.0 None None 0 None +1211 RPPPTPRKV 0.0331024442478 PPPTPRKV PPATPTSL 25.0 120093|unnamed_protein_product|CAA33016.1|Rubella_virus|11041 +1212 SQLEMPETL 0.0 None None 0 None +1213 YCRLATVHM 0.0 None None 0 None +1214 VPHEDTLSL 0.0 None None 0 None +1215 KCYKQGAFI 0.0 None None 0 None +1216 LVLAFKNQV 0.0 None None 0 None +1217 TSDDFWYHA 0.0 None None 0 None +1218 RAEHFGIA* 0.0 None None 0 None +1219 QVLPWLKAF 1.81855060575 VLPWLKAF VLAWTRAF 29.0 69394|pol|AP_000202.1|Human_adenovirus_5|28285 +1220 FSIVRADGV 0.0 None None 0 None +1221 DVHDIARFL 0.0 None None 0 None +1222 SAQRPWPRV 0.0521684604953 RPWPRV RPGPRL 23.0 139406|polyprotein|ACT37184.1|Hepatitis_C_virus|11103 +1223 CAFRSQLEM 0.0 None None 0 None +1224 IIDCLVSMV 0.0 None None 0 None +1225 NPTEARVQV 0.0 None None 0 None +1226 MVLWHLPAV 7.05423432918 LWHLPAV LWHYPCT 29.0 75636|polyprotein|AAB67037.1|Hepatitis_C_virus_(isolate_H77)|63746 +1227 KVHDSVLAL 0.0 None None 0 None +1228 FVLLLTYIL 0.0 None None 0 None +1229 RSGEPMVSL 0.0 None None 0 None +1230 LPHCGHRTL 0.0 None None 0 None +1231 MTEHRGKCY 22.1797910912 MTEHRGKCY ISEYRHYCY 26.0 28484|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 +1232 RTLRISETL 0.0 None None 0 None +1233 VSAKRVSVL 0.0 None None 0 None +1234 SVYCIRKKY 0.0 None None 0 None +1235 QSMPCLMSF 0.0 None None 0 None +1236 HRYNLTQHF 1.09592266047 HRYNLTQHF KQYNVTQAF 29.0 51250|nucleocapsid_protein|ABI96968.1|SARS_coronavirus|227859 +1237 ISLMVIEKV 0.0 None None 0 None +1238 EIYSLIDNF 0.0 None None 0 None +1239 APSNHMNLV 0.0 None None 0 None +1240 FAISHEGHM 0.0 None None 0 None +1241 LTSVLTLMF 0.0 None None 0 None +1242 YAIPSKQLE 0.0 None None 0 None +1243 QALAQRNQL 0.0 None None 0 None +1244 FNCSFVLEM 0.0 None None 0 None +1245 SPRRRAASV 0.419755381749 SPRRRAASV DPRRRSRNL 24.0 9746|Genome_polyprotein|P29846.3|Hepatitis_C_virus_genotype_1|41856 +1246 AAGAPPAKI 0.0 None None 0 None +1247 DTIPWYLRL 0.0 None None 0 None +1248 FFGNNMPEF 0.0 None None 0 None +1249 NPICCDCVI 0.00546161891463 ICCDCVI ILCLCLV 21.0 49831|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 +1250 CPYSAWCVY 0.0339459746518 CPYSAWC VPYVAWL 27.0 5952|PPE_family_protein|YP_177918.1|Mycobacterium_tuberculosis_H37Rv|83332 +1251 QMCAVNSTV 0.0 None None 0 None +1252 LQMVRLCSV 0.0 None None 0 None +1253 LTRTFVEFI 0.0 None None 0 None +1254 LSATVMLTV 0.0 None None 0 None +1255 MVPREFKPI 1.21262679539 MVPREFKP IIPSMFEP 22.0 65550|Nonstructural_protein_NS3|NP_739587.2|Dengue_virus_2_Thailand/16681/84|31634 +1256 LVIQYTVKY 0.0 None None 0 None +1257 LRFPRITFF 0.0 None None 0 None +1258 TSMPVSKML 0.0 None None 0 None +1259 LMKCPCNTF 0.0 None None 0 None +1260 IHQAMFQLL 2.96146414954 HQAMFQLL HQAAMQML 27.0 101673|gag_protein|ABO73990.1|Human_immunodeficiency_virus_1|11676 +1261 VAGRRGQQL 0.0 None None 0 None +1262 HASSIIDEL 0.0 None None 0 None +1263 YARRRWPSQ 0.0 None None 0 None +1264 SSLDHHMLV 0.0 None None 0 None +1265 DLITNIEPF 0.0157884928167 ITNIEPF ISNQEPL 20.0 10650|Nucleoprotein|P05133.1|Hantaan_virus_76-118|11602 +1266 TTILIMIVF 0.0 None None 0 None +1267 LLKSNTSTL 0.0 None None 0 None +1268 LHDVYMFCI 0.0 None None 0 None +1269 STRSPNSTV 0.0 None None 0 None +1270 QELAGVKMV 0.0 None None 0 None +1271 YVPYRDNKM 0.0 None None 0 None +1272 DPADGIRLF 0.632859149645 DGIRL DGVRL 24.0 15914|Genome_polyprotein|P27958.3|Hepatitis_C_virus_subtype_1a|31646 +1273 WRCWFNGIM 0.0204388749569 WRCWFNGI WEAVFTGL 22.0 12108|polyprotein|AAP55688.1|Hepatitis_C_virus_subtype_2a|31649 +1274 CALGLHNFV 0.0 None None 0 None +1275 MEEEFSTIL 0.0 None None 0 None +1276 MLDDAPRLL 0.0 None None 0 None +1277 LGYDMFDCV 0.0 None None 0 None +1278 FVYKSGMTS 0.0 None None 0 None +1279 ESADKTAYL 0.0 None None 0 None +1280 NLQRWVTAV 0.0 None None 0 None +1281 WKLTDMSSI 0.0 None None 0 None +1282 HTLEEIYSL 0.0 None None 0 None +1283 DAFNSTERA 0.0 None None 0 None +1284 YLYPLVLMS 0.0 None None 0 None +1285 SPFKLDATY 0.0 None None 0 None +1286 FPRIYSNSL 0.0 None None 0 None +1287 YHISEEYGL 0.0 None None 0 None +1288 ASMHRFGHI 0.0 None None 0 None +1289 AIDSASPVY 0.0 None None 0 None +1290 CTFDSPARL 0.0 None None 0 None +1291 SFMEAQSLM 0.0 None None 0 None +1292 LPYELGWLF 0.0 None None 0 None +1293 NIWECNRNI 0.0 None None 0 None +1294 SPAEETVVL 0.0 None None 0 None +1295 RQIPVVGSM 0.0354353484081 IPVVGS IPLVGA 23.0 19493|polyprotein|BAA03375.1|Hepatitis_C_virus|11103 +1296 LVWALPKTY 0.753308187545 VWALPKT LWALPHA 27.0 108277|IE62|AAP32859.1|Human_alphaherpesvirus_3|10335 +1297 QARPKGKGL 0.0 None None 0 None +1298 LHLCYEFLM 0.0368205769669 LHLCYEFLM LLLCLIFLL 22.0 37466|surface_antigen|BAF44879.1|Hepatitis_B_virus|10407 +1299 HQEDGGKAL 0.0 None None 0 None +1300 RPSSNALLI 0.286396630832 PSSNALL PQSNAVI 24.0 183229|polyprotein|AGW21594.1|Dengue_virus_1|11053 +1301 QKYDGKCPL 0.0 None None 0 None +1302 YAQFRGRHR 0.0 None None 0 None +1303 VAVYSTCVL 0.0490612481147 AVYSTC ATYSRC 23.0 149060|E2_protein|NP_751921.1|Hepatitis_C_virus_(isolate_H77)|63746 +1304 FLPPARSGI 0.0 None None 0 None +1305 QHGSLSETW 0.0 None None 0 None +1306 LGLEKTTSI 0.0 None None 0 None +1307 QTVMFMATM 0.0 None None 0 None +1308 LLKPGDRVV 0.26492774281 LKPGDRVV LQPVERVL 21.0 155928|unnamed_protein_product|CAA30115.1|Trypanosoma_cruzi|5693 +1309 MPGSPRDPV 0.0 None None 0 None +1310 LTYCTTGGI 0.0 None None 0 None +1311 FQSLLSQHM 0.0 None None 0 None +1312 KEFHFNQYL 0.0 None None 0 None +1313 SSTEWVAPL 0.0 None None 0 None +1314 RSSPATHSL 8.88487276219 PATHSL PKTHTL 24.0 184702|non-structural_protein_1|AGM49312.1|Dengue_virus|12637 +1315 ELKEWAESV 0.0 None None 0 None +1316 GVVEATLSY 0.0 None None 0 None +1317 EIAELNRTI 0.0 None None 0 None +1318 GAASMIHYI 0.0 None None 0 None +1319 LVNTCIRFV 0.0 None None 0 None +1320 QAVDTDEAL 0.0 None None 0 None +1321 AATSRGQVL 0.0 None None 0 None +1322 NPLRPRESL 0.00204486978355 PLRPRES PLCPEEK 20.0 110394|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 +1323 VSSNLSHVI 0.0 None None 0 None +1324 FTFGETEVC 0.0 None None 0 None +1325 FQDDFSPRF 0.0 None None 0 None +1326 YTVKYEQKM 0.0 None None 0 None +1327 EHSDTFINL 0.0 None None 0 None +1328 YTPKLEIKV 0.0 None None 0 None +1329 ETQETMDEL 0.0 None None 0 None +1330 DLVHHTTTL 0.00705689720887 DLVHHTT DLMCHAT 21.0 180507|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 +1331 LMFSGLWHL 0.0 None None 0 None +1332 VPHQIPKAV 0.0 None None 0 None +1333 MAPAAGTWV 0.0 None None 0 None +1334 FLITNALHF 0.0 None None 0 None +1335 SPKPPPQCV 0.0 None None 0 None +1336 SIADGRAWF 6.93354724607 IADGRAW VEDGRFW 28.0 186219|polyprotein|AGK36298.1|Dengue_virus_2|11060 +1337 MGYRVESEV 3.86373521516 MGYRVES MGYWIES 27.0 180689|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 +1338 APAPDLVVV 0.0 None None 0 None +1339 LSANARCLI 0.0 None None 0 None +1340 DTSDGLAVL 0.0 None None 0 None +1341 EARRQGAVF 0.0 None None 0 None +1342 KVPEGDSIV 0.0 None None 0 None +1343 WRPGCLWAL 4.81834181964 GCLWAL GCVWTV 28.0 6431|Genome_polyprotein|SRC279960|Hepatitis_C_virus|11103 +1344 HGLEKVPVI 3.17241105208 HGLEKVPV HGVGEIPM 25.0 131096|G1_and_G2_surface_glycoprotein_precursor|AAG22532.1|Andes_hantavirus|46607 +1345 ITIVVISLI 0.0 None None 0 None +1346 FAMELDDLH 0.0 None None 0 None +1347 LTDKVSTPA 0.0 None None 0 None +1348 LMVSAGVFI 0.0 None None 0 None +1349 LQLEVEEAV 0.0 None None 0 None +1350 SMIHYIVLI 0.0144228035657 SMIHYIVL TTIHDIIL 20.0 110373|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 +1351 FRMFVHVYI 0.0 None None 0 None +1352 HIFLFAVLL 1.02171257151 HIFLFAVLL HLFYSAVLL 29.0 98100|trans-sialidase,_putative|EAN81657.1|Trypanosoma_cruzi|5693 +1353 QQHDGAFLI 0.0 None None 0 None +1354 VELELWGVV 0.0 None None 0 None +1355 WSLQTWRAV 0.0 None None 0 None +1356 LVQEFTRGI 0.0 None None 0 None +1357 VAAFFLSLF 0.0 None None 0 None +1358 EAEEESLAL 0.0 None None 0 None +1359 HVIVRTSRV 0.0 None None 0 None +1360 ELLEPQKTY 0.208598262901 LEPQKTY LHPNNTY 23.0 141306|tegument_host_shutoff_protein|NP_044643.1|Human_alphaherpesvirus_1|10298 +1361 AMSDGRVPV 0.0 None None 0 None +1362 RPPSPKDTV 0.0269770919451 RPPSPKDTV RPSGMFDSV 17.0 177956|polyprotein|ACZ60102.1|Hepatitis_C_virus_subtype_3a|356426 +1363 VPMCHLRLL 0.0 None None 0 None +1364 LSARSVPSI 0.0 None None 0 None +1365 QVHQRMNSL 0.0 None None 0 None +1366 EALVQMQYL 0.0 None None 0 None +1367 CAQSPWCLV 1.18395973855 CAQSPWCLV CVQGDWCPI 33.0 18941|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 +1368 LSCEAHNSM 0.0 None None 0 None +1369 QARGVKKQI 0.0 None None 0 None +1370 SHHSQCSSL 0.0 None None 0 None +1371 YGGFFVISV 0.0626169731798 GGFFVI AGFFIL 23.0 69714|Large_envelope_protein|SRC279965|Hepatitis_B_virus|10407 +1372 YVYPLPVAN 0.416751180485 YVYPLPV YVYALPL 29.0 58463|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 +1373 HSYWLLKLL 0.0 None None 0 None +1374 YRTHTLQTL 0.0 None None 0 None +1375 FTTLKMYSV 0.0 None None 0 None +1376 EHMNHTCNL 0.0 None None 0 None +1377 VAIYLYPLV 0.0 None None 0 None +1378 YEGYKYEHI 1.40213483096 YKYEHI YKLKHI 24.0 39162|gag_protein|AAV53308.1|Human_immunodeficiency_virus_1|11676 +1379 DRYVAVRHL 0.274070953293 DRYVAVR SRYWAIR 21.0 60867|nucleoprotein|CAZ65591.1|Influenza_A_virus|11320 +1380 DLIDYARYM 0.159835763185 LIDYARYM LLDFVRFM 28.0 37153|Nuclear_antigen_EBNA-3C|Q69140.1|Human_gammaherpesvirus_4|10376 +1381 NLLLWVLAI 0.0 None None 0 None +1382 HLHDHYGPY 0.0 None None 0 None +1383 NTDSTAALL 0.0 None None 0 None +1384 YVKERQTVT 0.0 None None 0 None +1385 TMECWGQKY 0.0 None None 0 None +1386 KSDDSDFLA 0.0 None None 0 None +1387 MAFVRLLHS 0.0 None None 0 None +1388 LVDNLTYTL 0.122842705901 LVDNLT LLDNIT 24.0 240808|polyprotein|AAB53095.1|Tick-borne_encephalitis_virus|11084 +1389 KHSATASML 0.0 None None 0 None +1390 FEAHEVLKL 0.0 None None 0 None +1391 LVLVGCFTI 0.0083914153634 VLVGCF VLIRCY 21.0 145860|Protein_E6|P04019.1|Human_papillomavirus_type_11|10580 +1392 TTSGIGSSM 0.0 None None 0 None +1393 KSRAPPEAI 0.0 None None 0 None +1394 AALVPTQAM 0.0 None None 0 None +1395 RQRNGVAKL 0.0 None None 0 None +1396 SSDRMTSVA 0.0 None None 0 None +1397 RPSPNRPKL 0.00679026427764 RPSPNRPKL RPDYNPPLL 22.0 103563|polyprotein|BAB18806.1|Hepatitis_C_virus|11103 +1398 SSVEVLVNY 0.0 None None 0 None +1399 YCIYASLRI 0.0 None None 0 None +1400 RLLPPVSP* 1.80198471654 RLLPPVSP RLLSPLSP 31.0 54662|pX-rex-orf_I_{alternatively_spliced}|AAB23359.1|Human_T-lymphotropic_virus_1|11908 +1401 FSLGKHVCL 0.0 None None 0 None +1402 CTDKVGTEA 0.0 None None 0 None +1403 FRRSISVRI 0.0 None None 0 None +1404 LYLHTLLTI 0.0 None None 0 None +1405 LEVPAPEAI 0.0 None None 0 None +1406 LLSEMAVAV 0.0 None None 0 None +1407 VPLVRWLKV 3.69036212386 VPLVRWL VPFVQWF 27.0 37919|envelope_protein|BAF48755.1|Hepatitis_B_virus|10407 +1408 DTLPMLGNI 0.0 None None 0 None +1409 FAFGAVFSE 0.0 None None 0 None +1410 RNYQAWNFL 1.30903243738 QAWNF QQWNF 27.0 42797|6_kDa_early_secretory_antigenic_target|P0A564.2|Mycobacterium_tuberculosis|1773 +1411 DATKNQVAM 0.0 None None 0 None +1412 QTKHNAKVY 0.0 None None 0 None +1413 IEWECTMML 0.0 None None 0 None +1414 LELEFLCPL 0.0 None None 0 None +1415 QLVNRPQSI 0.0 None None 0 None +1416 TTKKSGGHY 0.247590955559 TTKKSGGHY TTRGRDAHY 23.0 66798|glycoprotein_gp35/37|AAC59622.1|Human_gammaherpesvirus_8|37296 +1417 IVEHPAGHL 0.0 None None 0 None +1418 HRYLWKILI 0.0 None None 0 None +1419 SIFEVIWSV 0.0 None None 0 None +1420 QHDDGYLEV 0.0 None None 0 None +1421 GVAPGLQVV 0.0 None None 0 None +1422 YLAMGEEIY 0.0 None None 0 None +1423 SVVCHQLGF 0.0952288061993 VCHQLG VCARLG 22.0 73177|protein_F_[Hepatitis_C_virus_subtype_1b]|ACA50643.1|Hepatitis_C_virus_(isolate_Japanese)|11116 +1424 RTKRRVFII 0.0 None None 0 None +1425 QMAERALYY 0.0 None None 0 None +1426 LISPPQEKV 0.0 None None 0 None +1427 HLIEERDTL 0.0 None None 0 None +1428 ILKQPSQTL 0.0 None None 0 None +1429 LQVVHLNAV 0.0 None None 0 None +1430 VHDIARFLY 0.0 None None 0 None +1431 RSLPIAIEM 0.0 None None 0 None +1432 NVDEVNQIM 0.0 None None 0 None +1433 GAGVEISTV 0.0 None None 0 None +1434 VPREFKPIL 0.0992866179251 VPREFKPIL VPRPDDPVL 25.0 141462|tegument_protein_UL21|NP_044622.1|Human_alphaherpesvirus_1|10298 +1435 GAQPPMPPY 3.42634928134 PPMPPY PPQPEY 27.0 48896|Genome_polyprotein|P27958.3|Hepatitis_C_virus_subtype_1a|31646 +1436 RADLLIVVF 0.0 None None 0 None +1437 WKEDMAVHV 0.0 None None 0 None +1438 FIEPHARFY 0.0 None None 0 None +1439 DEFSGVPRV 0.0268132145174 SGVPR SGLPR 23.0 58122|pol_protein|BAA32832.1|Hepatitis_B_virus|10407 +1440 RVQPAVRAL 0.0 None None 0 None +1441 ATTIVTTVY 2.66327463302e-07 VY VY 11.0 142232|POSSIBLE_CONSERVED_TRANSMEMBRANE_PROTEIN|CAB00937.1|Mycobacterium_tuberculosis|1773 +1442 FFHNPKPLF 1.02265506822 FHNPKPLF LHGPTPLL 25.0 6591|polyprotein|AAB67037.1|Hepatitis_C_virus_(isolate_H77)|63746 +1443 VTASSGIMI 0.0 None None 0 None +1444 HKAHFQYLL 0.0 None None 0 None +1445 IGVEAGRTL 0.0 None None 0 None +1446 ETMDNGFGH 0.0 None None 0 None +1447 DFWYHAVVL 1.96158586196 DFWYHAVVL DMWEHAFYL 29.0 9415|Superoxide_dismutase|P17670.1|Mycobacterium_tuberculosis|1773 +1448 FHLASAVAL 0.0 None None 0 None +1449 LAMYLSKNY 0.0 None None 0 None +1450 HLLELPQIL 0.0 None None 0 None +1451 VSVHRAPSI 0.155290102389 VHRAPSI LHHAPSL 26.0 21000|glutamine_synthetase_GLNA1_(glutamine_synthase)_(GS-I)|NP_216736.1|Mycobacterium_tuberculosis|1773 +1452 DPAAASHPI 0.0 None None 0 None +1453 SVYLRNNKL 0.0 None None 0 None +1454 INREHIPTF 0.2996637034 EHIPTF QHLPTL 24.0 64821|Protein_Tax-1|P03409.2|Human_T-lymphotropic_virus_1|11908 +1455 AQYDDPRNL 0.0 None None 0 None +1456 RPVNAYARV 0.0 None None 0 None +1457 LARLGALLL 0.0 None None 0 None +1458 SHTGTFLLV 27.0016949153 SHTGTFLL SHSGSFQI 26.0 61077|Non-capsid_protein_NS-1|P07298.1|Human_parvovirus_B19|10798 +1459 HTVAWSNGH 26.1809399136 AWSNGH SWNSGH 28.0 180440|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 +1460 TIPDSISKF 8.68426386978 IPDSISKF ITDTIDKF 25.0 12588|Glycoprotein_B_precursor_(Glycoprotein_II)|P09257.1|Human_alphaherpesvirus_3|10335 +1461 AVFEEQIKV 0.0 None None 0 None +1462 FCPLCHNPV 0.669397134211 FCPLCHN LCPHCIN 25.0 20787|Non-capsid_protein_NS-1|P07298.1|Human_parvovirus_B19|10798 +1463 RVLKCNVHL 1.08324885308 VLKCN ILKCN 27.0 47946|envelope_glycoprotein|AAC28452.1|Human_immunodeficiency_virus_1|11676 +1464 LLLPCPLLL 0.0 None None 0 None +1465 QTAEQYVFV 0.0 None None 0 None +1466 FLNSMDQQI 0.0 None None 0 None +1467 GPARGIAII 0.0 None None 0 None +1468 LASLSLKQV 0.0 None None 0 None +1469 TSVPHEDTL 0.0 None None 0 None +1470 EAEVETEAI 0.0 None None 0 None +1471 SSLSNVSQV 0.0 None None 0 None +1472 TVQNAMQIV 0.0 None None 0 None +1473 WHFIKRHIA 0.0 None None 0 None +1474 MTVAGMVLL 0.0 None None 0 None +1475 YMAGSDTTY 0.0 None None 0 None +1476 FRENFESIY 0.0 None None 0 None +1477 LATVILGAV 0.0 None None 0 None +1478 LSSGSFATM 0.0 None None 0 None +1479 DTNNLGIRI 0.0229294398523 NLGIRI DLGVRV 22.0 30946|HCV-1|AAA45676.1|Hepatitis_C_virus_genotype_1|41856 +1480 CSGCVAQVY 0.0 None None 0 None +1481 DHIRNFTTM 0.0 None None 0 None +1482 KPFISRTMM 0.0618191295436 PFISRTMM PFDKSTVM 20.0 116123|nucleocapsid_protein|ABP49342.1|Influenza_A_virus_(A/California/10/1978(H1N1))|425557 +1483 PADPAQLAV 0.0 None None 0 None +1484 YEPDTMEQY 0.0 None None 0 None +1485 EPLNDTIAI 0.0 None None 0 None +1486 QAPLAPTHM 9.89644311759 APLAPTH APVFPSH 26.0 3889|||| +1487 IHLDISSFV 0.0 None None 0 None +1488 PLMDQVSVI 0.0 None None 0 None +1489 HSLHPFPHF 0.0 None None 0 None +1490 ITFKELGAL 0.0 None None 0 None +1491 AAAREATEV 0.0 None None 0 None +1492 RTYHGRLAY 0.0 None None 0 None +1493 DADIYGKPM 0.0 None None 0 None +1494 KGYRIVVAL 0.0 None None 0 None +1495 FNMRDLSDI 0.0 None None 0 None +1496 FRKTLLNPV 0.0 None None 0 None +1497 YLAMGEEIY 0.0 None None 0 None +1498 KPFSHSCNL 0.0 None None 0 None +1499 DQATFINMY 0.0 None None 0 None +1500 ARFRIRKTI 0.0 None None 0 None +1501 RAFSFSLPC 0.081027158281 RAFSFS QAFTFS 22.0 50253|DNA_polymerase|CAA10434.1|Hepatitis_B_virus|10407 +1502 SHMCNSLLV 0.031545921554 MCNSLLV LCGMLLI 21.0 31771|Nucleoprotein|P03418.1|Human_respiratory_syncytial_virus_A2|11259 +1503 EAEEWVVSY 0.0 None None 0 None +1504 KASERFRTQ 0.0 None None 0 None +1505 QIMPHAIIF 0.226023306979 IMPHAI LLPHVI 23.0 79337|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 +1506 LLKHMPKII 0.110041217959 LKHMPKI VRHFPRI 24.0 187106|Vpr_protein|BAA93983.1|Human_immunodeficiency_virus_1|11676 +1507 ILSCNADII 0.0 None None 0 None +1508 AAQCCHKKV 0.0 None None 0 None +1509 TELDSVGPV 0.0 None None 0 None +1510 STFCGTLEY 0.0 None None 0 None +1511 GLIPPDATI 0.0516541933654 GLIPPDATI NLVPMVATV 21.0 55029|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 +1512 SAQRNAAFF 0.0 None None 0 None +1513 MDHPSGIAI 0.0 None None 0 None +1514 FTVLENLAV 0.178250809092 TVLENLAV NALDNLAV 24.0 185447|polyprotein|AGK36298.1|Dengue_virus_2|11060 +1515 KPPPQCVTL 0.502924257487 KPPPQCVTL KLTPLCVTL 28.0 32201|Gp160|Q0ED31|Human_immunodeficiency_virus_1|11676 +1516 LAIYTLLSL 0.0 None None 0 None +1517 RTVKFLMAI 0.0 None None 0 None +1518 MCLEASIPL 0.200766890345 CLEASIPL CMKTWIPL 24.0 155096|RL2|CAB06760.1|Human_alphaherpesvirus_2|10310 +1519 SAPQDSKAV 0.0 None None 0 None +1520 FIIHHRTHT 0.0 None None 0 None +1521 RKEENMESV 0.0 None None 0 None +1522 FPQVSELVL 0.0 None None 0 None +1523 YQVVAQHIY 0.0 None None 0 None +1524 DSAQRNAAF 0.0 None None 0 None +1525 KHFNNSSHF 0.0 None None 0 None +1526 EANVHGIYF 0.0 None None 0 None +1527 LSRVKAQVV 0.0 None None 0 None +1528 LENSNRSMV 0.0 None None 0 None +1529 ESKSGSPEY 10.7269076305 KSGSPEY RSGAPTY 26.0 102368|E2_protein|NP_751921.1|Hepatitis_C_virus_subtype_1a|31646 +1530 YTVKYEQKM 0.0 None None 0 None +1531 LTYGHDRQL 0.0 None None 0 None +1532 LHFHFTACY 0.0 None None 0 None +1533 DCNKTAVTI 0.0 None None 0 None +1534 QPLHSLSVL 0.547748367869 QPLHSLSV QPFHSYGV 27.0 232152|rhoptry_kinase_family_protein|AFO54841.1|Toxoplasma_gondii_type_III|398031 +1535 AACGIIQQV 0.0 None None 0 None +1536 WDQRCLHTI 0.0 None None 0 None +1537 QLQAFWKHV 0.0 None None 0 None +1538 SPHPRRRRL 0.0655592952749 PHPRRRR PEPDRQR 23.0 183813|polyprotein|AGW21594.1|Dengue_virus_1|11053 +1539 FLDKASDLL 0.0 None None 0 None +1540 SAWLFVTGI 0.0 None None 0 None +1541 FMFEMPFMQ 0.0 None None 0 None +1542 VSLQAAEEI 0.0 None None 0 None +1543 RANGNPNPT 0.0139532163774 RANGNPNP RANELVNP 21.0 154980|tegument_protein|CAB06735.1|Human_alphaherpesvirus_2|10310 +1544 ELPAFIEMM 0.0 None None 0 None +1545 CVAKCGGTV 0.0 None None 0 None +1546 LEYLAPEVL 0.0 None None 0 None +1547 TMANNPDVM 0.0 None None 0 None +1548 EAVSSASKL 0.0 None None 0 None +1549 FSLYRGWAL 0.0338147117713 FSLYRGWA FSMVGNWA 24.0 149052|E1_protein|NP_751920.1|Hepatitis_C_virus_(isolate_H77)|63746 +1550 VVIGAPYVV 0.113860246051 GAPYVV GNPYAV 22.0 110227|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 +1551 LHFHWNWII 1.13172182694 HWNWII RWEWVV 28.0 74407|polyprotein|AAU89634.1|Hepatitis_C_virus_subtype_2a|31649 +1552 MSACWSFAV 1.40795140079 SACWSF AACWGF 31.0 79506|E1_protein|BAA19893.1|Rubella_virus|11041 +1553 YIAQNDDEL 0.0 None None 0 None +1554 ETINWTLLE 0.0 None None 0 None +1555 DQYAICMKY 0.126785938088 DQYAICMK NPYAVCDK 25.0 110467|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 +1556 HAKRKTATA 0.0 None None 0 None +1557 LAAASSTAF 0.0 None None 0 None +1558 KAYGRDNTP 1.7699107108 KAYGRD KAYGTD 27.0 108230|polyprotein|AAF65953.1|Hepatitis_C_virus|11103 +1559 KHLQLYQLF 0.0 None None 0 None +1560 WAVMNHFSM 0.0 None None 0 None +1561 IERPGGSLL 0.0 None None 0 None +1562 YCFGCLSHH 0.00860509404551 YCFGCLS FCIPCMK 21.0 155096|RL2|CAB06760.1|Human_alphaherpesvirus_2|10310 +1563 QGYGGFFVI 0.00840115467717 GGFFVI AGFFIL 23.0 69714|Large_envelope_protein|SRC279965|Hepatitis_B_virus|10407 +1564 NENDLITNI 0.0 None None 0 None +1565 LPVPIIQQL 0.0 None None 0 None +1566 RLMHQLLVI 0.00726488946482 RLMHQLLVI QLFHLCLII 21.0 93431|pre-C/C_protein|ABY54138.1|Hepatitis_B_virus|10407 +1567 FHKEVFGMF 0.0 None None 0 None +1568 CTVEDGGHV 0.0 None None 0 None +1569 EVAQHLATT 0.0 None None 0 None +1570 VEHPAGHLV 3.94454377782 PAGHLV PAGHAV 28.0 23601|Genome_polyprotein|SRC279960|Hepatitis_C_virus_(isolate_H77)|63746 +1571 WKGSTECKL 0.0 None None 0 None +1572 LSDPHLTAV 0.0 None None 0 None +1573 ILTELLMVV 0.0 None None 0 None +1574 MVHLVPALV 0.00953033463174 MVHLVPAL LLHHAPSL 20.0 21000|glutamine_synthetase_GLNA1_(glutamine_synthase)_(GS-I)|NP_216736.1|Mycobacterium_tuberculosis|1773 +1575 TILENPYIM 0.0 None None 0 None +1576 DHSDSDYDF 0.0 None None 0 None +1577 NHLNIAWEL 0.76435968383 NHLNIAWEL THLYILWAV 24.0 1000|glycoprotein_gp35/37|AAC59622.1|Human_gammaherpesvirus_8|37296 +1578 FPEDVAVYT 0.0 None None 0 None +1579 YMTSSGRRF 0.0 None None 0 None +1580 SSVPLRSSV 0.0 None None 0 None +1581 LAAPPPLTE 1.95708895828 PPPLT PPPAT 25.0 120093|unnamed_protein_product|CAA33016.1|Rubella_virus|11041 +1582 VVASQPAHV 0.0 None None 0 None +1583 SMLDPHGHL 0.0 None None 0 None +1584 LVVADIHSM 0.0 None None 0 None +1585 LLYMAFVRL 0.0 None None 0 None +1586 VVTVMVTTV 0.0 None None 0 None +1587 KLIDVNHYV 0.0 None None 0 None +1588 FTQYLGLSM 0.00484909033908 FTQYLGLS FTDALGID 21.0 141277|transactivating_tegument_protein_VP16|NP_044650.1|Human_alphaherpesvirus_1|10298 +1589 FRGKHDCAL 0.0 None None 0 None +1590 EVFRHKLAM 0.0 None None 0 None +1591 RSIRLSQEI 0.0 None None 0 None +1592 HTIQKAKHM 0.0 None None 0 None +1593 PSGRPALAY 0.0 None None 0 None +1594 WQDHIRLEV 0.0 None None 0 None +1595 VLLDLRPSI 2.274058298 LLDLRP MLDLQP 24.0 110335|E7|AAD33253.1|Human_papillomavirus_type_16|333760 +1596 AVYSTCVLV 0.0927784841397 AVYSTC ATYSRC 23.0 149060|E2_protein|NP_751921.1|Hepatitis_C_virus_(isolate_H77)|63746 +1597 LALSLPACF 0.0 None None 0 None +1598 NQCPCSSDI 0.0 None None 0 None +1599 SIDPKTGVV 0.0 None None 0 None +1600 AAASHPILL 0.0 None None 0 None +1601 RLLKHMPKI 0.101153035124 LKHMPKI VRHFPRI 24.0 187106|Vpr_protein|BAA93983.1|Human_immunodeficiency_virus_1|11676 +1602 LSLTGLQVL 0.021486229198 LSLTGLQ LSLIGLK 22.0 187086|polyprotein|ABG67747.1|West_Nile_virus|11082 +1603 MSQEEKVAY 0.0 None None 0 None +1604 MIENLEHHI 0.0 None None 0 None +1605 IIATGLVTL 0.0 None None 0 None +1606 SADCGCCPM 0.0 None None 0 None +1607 CAELLSHTV 0.0 None None 0 None +1608 HISEEYGLL 0.0 None None 0 None +1609 YSFCPLCHN 0.206854960234 SFCPLCHN GLCPHCIN 25.0 20787|Non-capsid_protein_NS-1|P07298.1|Human_parvovirus_B19|10798 +1610 LPCRSLTRV 0.0 None None 0 None +1611 KVLQHGRLY 0.0 None None 0 None +1612 FLCDEEPLL 0.0 None None 0 None +1613 IPCLDDVTV 0.0 None None 0 None +1614 LASEAVSSA 0.0 None None 0 None +1615 TPTPGFSSM 0.0 None None 0 None +1616 FYLVAYAAM 0.17018469657 YLVAYA YLAAYA 26.0 74545|TcP2beta|CAA52943.1|Trypanosoma_cruzi|5693 +1617 YLKSPECFL 0.0 None None 0 None +1618 KVNTATTTM 0.0 None None 0 None +1619 LPVSTKCTV 0.0 None None 0 None +1620 SVRYAGPLY 0.297176741199 VRYAGPLY MTYAAPLF 25.0 42897|RNA_polymerase_beta-subunit|AAA21416.1|Mycobacterium_tuberculosis|1773 +1621 HTIQKAKHM 0.0 None None 0 None +1622 TFRDVAVEF 0.0366333305265 TFRDVA TWRDMA 22.0 186175|polyprotein|AFY10053.1|Dengue_virus_3|11069 +1623 DEKDLWEYI 0.0133766675551 DEKDLWEYI DQKSLENYI 25.0 28594|IMMUNOGENIC_PROTEIN_MPT64_(ANTIGEN_MPT64/MPB64)|CAA98382.1|Mycobacterium_tuberculosis_H37Rv|83332 +1624 DPADPTRDL 4.01184798055 DPADPTRDL DPAKPARLL 28.0 53405|||| +1625 EAEEWVVSY 0.0 None None 0 None +1626 CAFTVLENL 0.0 None None 0 None +1627 SWMEGQVTI 0.0 None None 0 None +1628 MTAVGYGDM 0.0 None None 0 None +1629 VSEDAKQRI 0.0 None None 0 None +1630 DVDEDGYIM 0.0 None None 0 None +1631 IVQCRVLNI 0.0 None None 0 None +1632 IASLLENIL 0.0 None None 0 None +1633 SRNWLKSIL 0.0 None None 0 None +1634 KVKPTLAMY 0.0070925003201 PTLAMY PALQMY 22.0 146260|polyprotein|ADF97231.1|Hepatitis_C_virus_subtype_3a|356426 +1635 YTMGIIFVL 0.0 None None 0 None +1636 ELKSPVKMI 0.0 None None 0 None +1637 LSLGAPSPL 0.0555525573282 LSLGAP LSLGDP 23.0 54342|UL123;_IE1|AAR31448.1|Human_betaherpesvirus_5|10359 +1638 QSIRAATEV 0.0 None None 0 None +1639 YMAATLLEF 0.0 None None 0 None +1640 CSDGSDEDA 0.319310454046 CSDGSDEDA CDDCHAQDA 21.0 6094|Genome_polyprotein|Q81495.3|Hepatitis_C_virus_(isolate_HCV-K3a/650)|356416 +1641 SYLEDVRLI 0.0 None None 0 None +1642 QVYVGDSDI 0.0 None None 0 None +1643 VIDQCLKKI 0.0 None None 0 None +1644 YPDWIRDNM 1.53360425083 YPDWI YQDWL 25.0 23288|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 +1645 RATSFGKCF 0.205486484796 SFGKCF TFGWCF 25.0 56620|Nef_protein|Q9YYU8|Human_immunodeficiency_virus_1|11676 +1646 KAGSLGIIL 0.415852219105 GSLGII GTLGIV 24.0 37573|E7_protein|ABL96585.1|Human_papillomavirus_type_16|333760 +1647 VAQQSRLVF 0.0 None None 0 None +1648 DCQSHRLTV 0.0 None None 0 None +1649 MPNVLWDLV 0.0 None None 0 None +1650 MSWLTPLMI 0.00107210420498 SWLTPLMI AWGRRLMI 18.0 181733|Antigen_85-B|P0C5B9.1|Mycobacterium_tuberculosis|1773 +1651 DANNVTCVW 0.0 None None 0 None +1652 KLLQCMSRV 0.0 None None 0 None +1653 VHLPLAVAL 0.0 None None 0 None +1654 SLYSLDATL 0.887852301761 SLYSLDATL SLYNTAATL 26.0 189286|||| +1655 FTTTQWSSL 0.276143452524 FTTTQW LSTTEW 24.0 37830|polyprotein|BAB18806.1|Hepatitis_C_virus_subtype_1b|31647 +1656 VALRDLGCL 0.0 None None 0 None +1657 MVACGGTVY 0.0 None None 0 None +1658 EMFQRYSAF 1.04802970038 EMFQRYSAF EFFTKNSAF 24.0 44214|UL123;_IE1|AAR31448.1|Human_betaherpesvirus_5|10359 +1659 DAACGIWSL 0.0 None None 0 None +1660 FTILPCTCY 0.0 None None 0 None +1661 IIYTMGIIF 0.0 None None 0 None +1662 RVYNIRGDM 0.0 None None 0 None +1663 RNDPELPTV 0.0340275143527 NDPELP NTPGLP 21.0 65497|HCV-1|AAA45676.1|Hepatitis_C_virus_genotype_1|41856 +1664 HSDSDYDFV 0.0 None None 0 None +1665 VLGEHHHHV 0.0 None None 0 None +1666 HVVDEREQM 0.0 None None 0 None +1667 GQFPYMGEV 0.000425382554656 FPYMGEV FPGGGQI 18.0 181035|||| +1668 LPPEMYVYL 0.0 None None 0 None +1669 EAYQKQLCF 0.0776136961569 YQKQLC YNKPLC 24.0 110982|E6_protein|CAB45108.1|Human_papillomavirus_type_16|333760 +1670 AATGPGEVL 0.129514787687 ATGPGEVL GTGPGNGL 25.0 47760|EBNA-1_protein|Q777E1|Human_gammaherpesvirus_4|10376 +1671 DLYATAFLV 0.0 None None 0 None +1672 GFDWKSVFI 0.0 None None 0 None +1673 FVVFSFFFV 0.0209879781055 FVVFSFF LVLFGFF 23.0 422999|polyprotein|ABD97104.1|Hepatitis_C_virus_genotype_3|356114 +1674 GRDVVHHLL 0.0 None None 0 None +1675 VTLRWYLAM 16.7007719127 TLRWYLAM TLRWFFNL 28.0 38724|Genome_polyprotein|P08617.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 +1676 LVAQYDLTV 0.0 None None 0 None +1677 RLIRGDAVV 0.0 None None 0 None +1678 FQYLVVHTE 0.0 None None 0 None +1679 KHYLMTRTL 0.0 None None 0 None +1680 FVMEHSNIV 0.0 None None 0 None +1681 HQMENNGWV 1.02571149154 QMENNGWV QMENKAWL 33.0 150399|polyprotein|AGV76873.1|Dengue_virus_2|11060 +1682 NATYSGYVY 0.0 None None 0 None +1683 KVKNSASVM 0.0 None None 0 None +1684 KQDKCFAFI 0.0 None None 0 None +1685 AQRPWPRVL 0.0843380588073 RPWPRV RPGPRL 23.0 139406|polyprotein|ACT37184.1|Hepatitis_C_virus|11103 +1686 MAATLLEFF 0.0 None None 0 None +1687 DPNTVSNSI 0.0 None None 0 None +1688 LPVSGGHVM 0.204938535034 LPVSGG MPVGGG 25.0 189750|Diacylglycerol_acyltransferase/mycolyltransferase_Ag85B|SRC280000|Mycobacterium_tuberculosis|1773 +1689 MLDDAPRLL 0.0 None None 0 None +1690 IPPDATIYF 0.0918537604584 PDATIY PDIVIY 23.0 101812|Pol_polyprotein|Q9YLQ7|Human_immunodeficiency_virus_1|11676 +1691 LHDALEVDL 0.0 None None 0 None +1692 MMEKLYPGY 0.0 None None 0 None +1693 IPFLFFTDM 0.0 None None 0 None +1694 YKLCFNTFF 0.0 None None 0 None +1695 YVTMVIDRL 0.0 None None 0 None +1696 TIYFDVVLL 0.0 None None 0 None +1697 SAWLRAISL 0.0 None None 0 None +1698 HLWPGGLSL 0.0 None None 0 None +1699 FGYMTQQRM 0.0 None None 0 None +1700 HVYILRAVF 0.0 None None 0 None +1701 LYIPALAVL 0.0 None None 0 None +1702 DPMVPLQGV 0.41651905562 DPMVPL DPTTPL 23.0 103392|polyprotein|BAB18806.1|Hepatitis_C_virus|11103 +1703 FTEEGFCAI 0.0 None None 0 None +1704 FFNDDCCEL 0.0 None None 0 None +1705 FLFHPLEFC 0.0 None None 0 None +1706 VVMWWMGIL 0.875296446467 VMWWMGIL CLWWLQYF 26.0 39591|polyprotein|AAA45677.1|Hepatitis_C_virus_(isolate_H77)|63746 +1707 KTFHHKSNF 0.0 None None 0 None +1708 QRPWPRVLL 0.245621905968 RPWPRV RPGPRL 23.0 139406|polyprotein|ACT37184.1|Hepatitis_C_virus|11103 +1709 IRVQEASTI 0.0 None None 0 None +1710 DLIDYARYM 0.484336212252 LIDYARYM LLDFVRFM 28.0 37153|Nuclear_antigen_EBNA-3C|Q69140.1|Human_gammaherpesvirus_4|10376 +1711 VTVRGFWIY 0.0 None None 0 None +1712 FMDEHAAER 0.0 None None 0 None +1713 SISDTYDPY 0.0 None None 0 None +1714 DTNDNVPEF 0.0 None None 0 None +1715 YNCTCGCSM 0.0668968271799 NCTCGCS ECTTPCS 24.0 57364|Genome_polyprotein|P26664.3|Hepatitis_C_virus|11103 +1716 LLLLASATV 0.0 None None 0 None +1717 LYMAFVRLL 0.0 None None 0 None +1718 SAEVQLSKI 0.0 None None 0 None +1719 ITACLSVLI 0.0 None None 0 None +1720 LPETKGVTL 0.440996131242 LPETKGVTL VPEVTDVTL 24.0 168240|major_paraflagellar_rod_protein|AAA30221.1|Trypanosoma_cruzi|5693 +1721 MSQEEKVAY 0.0 None None 0 None +1722 MASPQAEST 0.0 None None 0 None +1723 MSFELPYHC 0.0 None None 0 None +1724 RWNDTRATV 0.134680294585 RWNDTR RWLDAR 24.0 150538|polyprotein|AGW21594.1|Dengue_virus_1|11053 +1725 LRHERAVSM 0.0 None None 0 None +1726 LHLLVACTI 0.0 None None 0 None +1727 YGHDRQLCL 0.0 None None 0 None +1728 DATIYFDVV 0.0 None None 0 None +1729 IVCDIKEKL 0.00240549311618 IVCDIKEK IFCHSKKK 20.0 36504|polyprotein_precursor|BAA01582.1|Hepatitis_C_virus|11103 +1730 RPAQFLHEM 0.0 None None 0 None +1731 WHFVYKSGM 0.0 None None 0 None +1732 EVDPIGNLY 0.0 None None 0 None +1733 RTDGNSHEA 0.0 None None 0 None +1734 KHMPKIIHL 0.0 None None 0 None +1735 DVHDIARFL 0.0 None None 0 None +1736 PATRPLHVL 0.000259990550586 PATRPLHVL PAVGVYHIV 18.0 32663|small_hydrophobic_protein|AAM12943.1|Human_metapneumovirus|162145 +1737 LLHSNRSQI 0.0 None None 0 None +1738 PARSGIFKI 0.0 None None 0 None +1739 AALTPTEEM 0.0 None None 0 None +1740 ISAYMAATL 0.0 None None 0 None +1741 IMMSDEERI 0.0 None None 0 None +1742 KRQEGMVPV 0.581298321339 QEGMVPV DEGLLPV 25.0 140541|hypothetical_protein|NP_218210.1|Mycobacterium_tuberculosis_H37Rv|83332 +1743 LQKRATEEI 0.0136766968351 QKRATEEI QKQELDEI 20.0 327|ESAT-6-like_protein_esxB|P0A566.2|Mycobacterium_tuberculosis|1773 +1744 GKDKMTHLL 0.0 None None 0 None +1745 AQLPPWAPL 1.01158072828 AQLPPWAP AQLHVWVP 27.0 40158|polyprotein|AAA45534.1|Hepatitis_C_virus|11103 +1746 FFCEVPVLL 0.0 None None 0 None +1747 RAHKKAITT 0.0 None None 0 None +1748 FDWKSVFII 0.0 None None 0 None +1749 CLFRAARLI 0.0 None None 0 None +1750 MIEDFLRRF 0.0 None None 0 None +1751 TTTERWLRV 0.0 None None 0 None +1752 FFKDKATSK 0.0 None None 0 None +1753 HFFDAFRKF 1.97322439336 FFDAFRKF IFDRTRKF 25.0 154296|UL29|CAB06754.1|Human_alphaherpesvirus_2|10310 +1754 GALGLNRPV 0.0 None None 0 None +1755 YRTKCTLGL 0.0 None None 0 None +1756 MTVAGMVLL 0.0 None None 0 None +1757 KTLSKTAHL 0.0 None None 0 None +1758 NLYIFATCL 0.0 None None 0 None +1759 GFDTSSSSL 0.0 None None 0 None +1760 TPVLCGQPI 0.130418951884 VLCGQPI VLCLRPV 24.0 69398|X_protein|AAP06597.1|Hepatitis_B_virus|10407 +1761 WCAPGKPTL 0.0 None None 0 None +1762 ILHNQIQQV 0.629859339283 ILHNQIQQV LLHTDFEQV 25.0 37398|Non-capsid_protein_NS-1|P07298.1|Human_parvovirus_B19|10798 +1763 VVLSPEVEV 0.0 None None 0 None +1764 DSIHQVGMY 0.0155776894056 HQVGMY HAVGLF 22.0 23573|polyprotein|AAB67037.1|Hepatitis_C_virus_(isolate_H77)|63746 +1765 NHSGVGAFW 0.0 None None 0 None +1766 HNLEPHGYV 0.0 None None 0 None +1767 PSLNATTIV 0.0 None None 0 None +1768 ISGFKGDTV 0.154683020868 GFKGDTV GFPTDTV 24.0 79506|E1_protein|BAA19893.1|Rubella_virus|11041 +1769 HIASSTTSI 0.0 None None 0 None +1770 HTLHAHDPV 0.0 None None 0 None +1771 WTDYGQVFT 0.0 None None 0 None +1772 ELFRRGLRY 0.0 None None 0 None +1773 SASRTKRRV 0.0 None None 0 None +1774 NSGPSRSML 0.0 None None 0 None +1775 ESADKTAYL 0.0 None None 0 None +1776 TELEKFSKV 0.0 None None 0 None +1777 FHAQVCSLY 1.32122904181 HAQVCSLY KAKICGLY 28.0 177701|polyprotein|ACZ60104.1|Hepatitis_C_virus_subtype_3a|356426 +1778 LVVEHVLTT 0.0 None None 0 None +1779 RSYWLRLFL 0.0 None None 0 None +1780 DVDEKQLLV 0.0 None None 0 None +1781 CAIISLIFI 0.0 None None 0 None +1782 SQLEMPETL 0.0 None None 0 None +1783 NLEDVGRHL 0.0 None None 0 None +1784 HLRRIGRFI 0.0 None None 0 None +1785 KYDPDVVVM 0.0 None None 0 None +1786 KDDDCITLV 0.0 None None 0 None +1787 YDVTDSRII 0.0 None None 0 None +1788 MLLHQVAAY 0.0413203406169 MLLHQV MILHEI 24.0 196087|PPE_family_protein_PPE54|YP_177960.1|Mycobacterium_tuberculosis_H37Rv|83332 +1789 THQSGFSVI 0.0 None None 0 None +1790 DLQPVREAI 0.0 None None 0 None +1791 FAGSTQSDL 0.0 None None 0 None +1792 GSYREAQSL 0.0 None None 0 None +1793 HFMPRIQRL 0.0 None None 0 None +1794 LPLKRPGKL 0.0343305252388 LPLKRP LPFDRP 22.0 116127|Nucleoprotein|P15682.1|Influenza_A_virus_(A/Wilson-Smith/1933(H1N1))|381518 +1795 MAFPEGYGT 0.0567950827738 FPEGY LPEGY 25.0 31997|hypothetical_protein_FTT0484|YP_169522.1|Francisella_tularensis_subsp._tularensis_SCHU_S4|177416 +1796 DMQDLTEFL 0.0 None None 0 None +1797 VDFSSEVTV 0.0 None None 0 None +1798 MEVDPIGNL 0.0379279510851 MEVDPIGNL MEVTPSGTW 24.0 26273|nucleocapsid_protein|ABI96968.1|SARS_coronavirus|227859 +1799 ISRNCNSRM 0.0 None None 0 None +1800 YSLIDNFVM 0.0 None None 0 None +1801 FEMPFMQTG 0.0 None None 0 None +1802 SHELVMYIW 0.0 None None 0 None +1803 IIVSYMLII 0.0 None None 0 None +1804 AAAAAVAAL 0.0 None None 0 None +1805 LVDQKAKEV 0.0 None None 0 None +1806 FFSLLATVI 0.710550459145 FSLLATV FTLVATV 25.0 98640|trans-sialidase,_putative|EAN80840.1|Trypanosoma_cruzi|5693 +1807 IYGKPMPTI 0.0 None None 0 None +1808 YMLERLIEQ 0.0 None None 0 None +1809 CIADFLEHM 0.0 None None 0 None +1810 LPYPGSSQA 0.0 None None 0 None +1811 EAWQCQPVL 0.0 None None 0 None +1812 VATSTAQLL 0.0 None None 0 None +1813 VKYTPKLEI 0.0 None None 0 None +1814 RVSAKRVSV 0.0 None None 0 None +1815 NTWTRQMGY 0.0 None None 0 None +1816 LDFACHFTV 0.0 None None 0 None +1817 HVRIHPKLV 0.0 None None 0 None +1818 LQQNCAAYL 0.000555833253958 QQNCAAYL QDNQLAYV 19.0 150649|polyprotein|AGW21594.1|Dengue_virus_1|11053 +1819 DAVGNMLNL 0.0 None None 0 None +1820 WQAISLMVI 0.0 None None 0 None +1821 WLWKLSAVV 0.0 None None 0 None +1822 LAPTHMPEL 0.0 None None 0 None +1823 YAQTPSKTP 0.514097249368 TPSKTP TPDSTP 24.0 53041|phosphorylated_matrix_protein_(pp65)|AAA45996.1|Human_betaherpesvirus_5|10359 +1824 LLLCFLAAM 0.0771007402221 LLLCFL LLLCLI 23.0 27168|envelope_protein|BAF48755.1|Hepatitis_B_virus|10407 +1825 HMPKIIHLV 0.0 None None 0 None +1826 AQLPSYMHI 0.0 None None 0 None +1827 IKLHNPSTI 0.0 None None 0 None +1828 TLLTTHYMA 0.0 None None 0 None +1829 SYEVVIPEW 0.0 None None 0 None +1830 WVNEFGEVF 0.196334224507 WVNEFGEVF WLSDCGEAL 24.0 72790|FL-160-2_protein_-_Trypanosoma_cruzi|JH0823|Trypanosoma_cruzi|5693 +1831 LTYRHCQNF 0.0 None None 0 None +1832 LTYRHCQNF 0.0 None None 0 None +1833 RHCQNFSIL 0.0 None None 0 None +1834 YRHCQNFSI 0.0 None None 0 None +1835 YRHCQNFSI 0.0 None None 0 None +1836 FSLERIAES 0.0 None None 0 None +1837 CLHYIMGDY 0.0 None None 0 None +1838 LLACLHYIM 0.755659798581 LLACL LLACL 25.0 40262|Cytochrome_P450_2A7|P20853.1|Homo_sapiens|9606 +1839 RLLACLHYI 0.470647487397 LLACL LLACL 25.0 40262|Cytochrome_P450_2A7|P20853.1|Homo_sapiens|9606 +1840 RLLACLHYI 0.375813339906 LLACL LLACL 25.0 40262|Cytochrome_P450_2A7|P20853.1|Homo_sapiens|9606 +1841 SQSADAHSI 0.0 None None 0 None +1842 TFFSSSQSA 0.0 None None 0 None +1843 YANNHCIRT 0.0 None None 0 None +1844 FYGMTEMNY 0.197223709005 GMTEMNY ALTEMDY 25.0 418945|PPE_family_protein_PPE68|KAM81677.1|Mycobacterium_tuberculosis_H37Ra|419947 +1845 LQFYGMTEM 0.0 None None 0 None +1846 LQFYGMTEM 0.0 None None 0 None +1847 ALWMYRSLM 6.40774625238 LWMYRSLM VWLKKSMM 25.0 181036|||| +1848 ALWMYRSLM 0.855722704359 LWMYRSLM VWLKKSMM 25.0 181036|||| +1849 QALWMYRSL 0.0 None None 0 None +1850 SFRKEKRNL 0.0 None None 0 None +1851 LTSQDLAGY 0.0 None None 0 None +1852 MAGHGWGAL 0.0 None None 0 None +1853 VMSYGEQPY 0.0 None None 0 None +1854 SVSDVFHGI 0.0 None None 0 None +1855 IPNDNTLSL 0.0 None None 0 None +1856 KTIPNDNTL 0.0 None None 0 None +1857 KTIPNDNTL 0.0 None None 0 None +1858 TLSLRICTI 0.0 None None 0 None +1859 FSMRARIDV 0.0 None None 0 None +1860 RLLGQKFSM 0.0 None None 0 None +1861 IYMENERRM 0.0 None None 0 None +1862 QFLLELYSL 0.0 None None 0 None +1863 RVIRYVIGV 0.0 None None 0 None +1864 QYLSLINYY 0.0 None None 0 None +1865 STLQYLSLI 0.0 None None 0 None +1866 IAQGKPVTL 0.0 None None 0 None +1867 SVIAQGKPV 0.0 None None 0 None +1868 FAIMHAQRT 0.0922530683728 MHAQRT MHQKRT 23.0 110338|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 +1869 HTNAVFAIM 0.000248159096545 HTNAVFAIM HTTKGAALM 18.0 24986|polyprotein_precursor|NP_041724.2|West_Nile_virus|11082 +1870 NHTNAVFAI 0.0 None None 0 None +1871 HHHHHHQAW 31.6214375823 HHHHQ HHFHQ 28.0 183147|polyprotein|AGW21594.1|Dengue_virus_1|11053 +1872 QAWPPPSSA 1.66000789695 WPPPSSA WPAPSGA 32.0 144544|polyprotein_precursor|BAA01728.1|Hepatitis_C_virus|11103 +1873 AHTVARGPV 0.453229538203 HTVARGPV HPVHAGPI 24.0 24557|Gag_polyprotein|P03347.3|Human_immunodeficiency_virus_1|11676 +1874 ALQTFAHTV 0.0 None None 0 None +1875 EIYTKNHAY 0.0 None None 0 None +1876 FGYQLKEIY 0.0 None None 0 None +1877 IYTKNHAYI 0.0 None None 0 None +1878 YTKNHAYII 0.0 None None 0 None +1879 YTKNHAYII 0.0 None None 0 None +1880 HAFDRYETT 0.0 None None 0 None +1881 TTHSRPVTL 0.0 None None 0 None +1882 TTHSRPVTL 0.0 None None 0 None +1883 YETTHSRPV 0.0 None None 0 None +1884 VLFDVAGQV 5.87593218982e-05 VLFDVAGQV VIFCHPGQL 17.0 79454|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 +1885 VLFDVAGQV 9.25459319897e-05 VLFDVAGQV VIFCHPGQL 17.0 79454|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 +1886 ESKPAPAEV 0.0 None None 0 None +1887 LNVEKTEKI 0.0166822097398 VEKTEK LEKTKK 22.0 35568|Polyprotein|Q9J8D4|Dengue_virus_2|11060 +1888 MVIVFYGTL 0.0 None None 0 None +1889 MVIVFYGTL 0.0 None None 0 None +1890 SAHLTMVIV 0.0 None None 0 None +1891 YETFGAASF 0.0 None None 0 None +1892 RGVPPLRTV 0.959521069645 GVPPLRT GVPPLRA 33.0 36345|polyprotein|ABR25251.1|Hepatitis_C_virus_(isolate_H77)|63746 +1893 TAESCRSTL 0.0 None None 0 None +1894 TAESCRSTL 0.0 None None 0 None +1895 RVRAAGQRL 1.69373967722 RVRAAGQRL KIRAWGRRL 27.0 181733|Antigen_85-B|P0C5B9.1|Mycobacterium_tuberculosis|1773 +1896 DVHARESKI 0.0 None None 0 None +1897 NVPPTVQKV 0.0 None None 0 None +1898 CYYPMAGYI 0.0060192893897 YYPMAGYI YYLDRGYL 22.0 76532|outer_membrane_protein|YP_170495.1|Francisella_tularensis_subsp._tularensis_SCHU_S4|177416 +1899 CYYPMAGYI 0.0239816132828 YYPMAGYI YYLDRGYL 22.0 76532|outer_membrane_protein|YP_170495.1|Francisella_tularensis_subsp._tularensis_SCHU_S4|177416 +1900 NTRQCYYPM 0.0 None None 0 None +1901 LGYRWCLHV 0.441063931047 GYRWCL GWRWRL 25.0 37607|kaposin|AAC57155.1|Human_gammaherpesvirus_8|37296 +1902 LLLGYRWCL 5.17789244834 LLLGYRWCL LLNGWRWRL 30.0 37607|kaposin|AAC57155.1|Human_gammaherpesvirus_8|37296 +1903 TAHSSVLTL 0.0 None None 0 None +1904 TAHSSVLTL 0.0 None None 0 None +1905 FPSNHLGDL 0.0236234538092 PSNHLGD PGNGLGE 23.0 47760|EBNA-1_protein|Q777E1|Human_gammaherpesvirus_4|10376 +1906 LLLAHKKKV 0.0 None None 0 None +1907 AQILEQVEV 0.0 None None 0 None +1908 QIFKCKGTL 0.0 None None 0 None +1909 QIFKCKGTL 0.0 None None 0 None +1910 TLVGHQGPV 0.0 None None 0 None +1911 TLVGHQGPV 0.0 None None 0 None +1912 DAVELWAIV 0.0 None None 0 None +1913 VDLPLTSTI 0.00972155564068 LPLTSTI LPFHSTL 20.0 21007|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 +1914 NVVNGQMRF 0.0 None None 0 None +1915 MGAPGSEII 0.0 None None 0 None +1916 FSQFSNLKV 0.0 None None 0 None +1917 KAFSQFSNL 0.0 None None 0 None +1918 HFSVSSNLL 0.0 None None 0 None +1919 KHFSVSSNL 0.0 None None 0 None +1920 KHFSVSSNL 0.0 None None 0 None +1921 YQVLAMSTK 0.0 None None 0 None +1922 KLSSEAKTK 0.0 None None 0 None +1923 TVLRLFPFR 0.0 None None 0 None +1924 TVLRLFPFR 0.0 None None 0 None +1925 TVKDVHKAK 0.0 None None 0 None +1926 TIHNVNFSK 0.0 None None 0 None +1927 TIHNVNFSK 0.0 None None 0 None +1928 SETTFDIFV 0.0 None None 0 None +1929 GMHFSPGAR 0.0 None None 0 None +1930 FLTQPVAPK 9.05129460172 FLTQPVAP LIEKPVAP 24.0 419002|PPE_family_protein_PPE68|KAM81677.1|Mycobacterium_tuberculosis_H37Ra|419947 +1931 KAISFYMKR 0.0 None None 0 None +1932 RTVAQVTKK 0.0 None None 0 None +1933 RTVAQVTKK 0.0 None None 0 None +1934 SEDKKNTKL 0.0 None None 0 None +1935 RVAAGVQIK 0.0 None None 0 None +1936 RVAAGVQIK 0.0 None None 0 None +1937 VVGAVGVGK 0.0 None None 0 None +1938 VVGAVGVGK 0.0 None None 0 None +1939 TTTPTLKEK 0.0 None None 0 None +1940 QSLYIDRLK 0.0 None None 0 None +1941 TTIHYNYMY 0.0 None None 0 None +1942 TECIIAMSF 0.0 None None 0 None +1943 IESSYLESL 0.0 None None 0 None +1944 AEEEEEEVV 0.961625857069 AEEEEE SEEEDE 23.0 110431|E7|AAD33253.1|Human_papillomavirus_type_16|333760 +1945 TENHQPVCL 0.0 None None 0 None +1946 GQLGGLAGK 0.0 None None 0 None +1947 LSDWGPHFK 0.0 None None 0 None +1948 LSDWGPHFK 0.0 None None 0 None +1949 KPASKKEWI 0.0 None None 0 None +1950 TTKSEAIEK 0.0 None None 0 None +1951 IVRASGCEL 0.0 None None 0 None +1952 VPTELNGSM 0.0 None None 0 None +1953 VPLFPARVL 0.0 None None 0 None +1954 APAQPPMLA 32.3662874827 APAQPPM CPSQEPM 24.0 58463|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 +1955 VVGARGVGK 0.0 None None 0 None +1956 VVGARGVGK 0.0 None None 0 None +1957 KLCNSGDFR 0.0 None None 0 None +1958 HPLTENSPL 0.0 None None 0 None +1959 STVRKSPWK 0.0 None None 0 None +1960 STVRKSPWK 0.0 None None 0 None +1961 LIRMYNINK 0.0 None None 0 None +1962 LIRMYNINK 0.0 None None 0 None +1963 SPWPLSSLT 0.0 None None 0 None +1964 SLKSTRAVF 0.0 None None 0 None +1965 SVGSASSLK 0.0 None None 0 None +1966 SVGSASSLK 0.0 None None 0 None +1967 KGYGGFSRY 0.0 None None 0 None +1968 KGYGGFSRY 0.0 None None 0 None +1969 KAIGKSRPY 0.0 None None 0 None +1970 KTLRKAIGK 0.00523788333205 KTLRKAI KTILKAL 21.0 7708|gag_polyprotein|BAA00992.1|Human_immunodeficiency_virus_1|11676 +1971 KTLRKAIGK 0.00482507857332 KTLRKAI KTILKAL 21.0 7708|gag_polyprotein|BAA00992.1|Human_immunodeficiency_virus_1|11676 +1972 QALQKTLRK 0.0 None None 0 None +1973 SYQSTGDPK 0.160544975903 TGDP TGDP 24.0 2002|Large_envelope_protein|SRC279965|Hepatitis_B_virus|10407 +1974 VPEWSNNS* 0.0 None None 0 None +1975 VLETAAPGV 0.0 None None 0 None +1976 AVLDAIPLV 0.0 None None 0 None +1977 VLDAIPLVA 0.0 None None 0 None +1978 KPVVTEVRM 0.0 None None 0 None +1979 MPTNTWSGL 0.0679479043012 PTNTW PTYSW 22.0 102368|E2_protein|NP_751921.1|Hepatitis_C_virus_subtype_1a|31646 +1980 VFQGHSASI 0.0 None None 0 None +1981 SLYDFGELR 0.0 None None 0 None +1982 DSMLQTVER 0.0 None None 0 None +1983 MLQTVEREK 0.0 None None 0 None +1984 LLWKDFDQA 9.96145413497 DFDQA DFDQG 23.0 149117|envelope_glycoprotein|AAV74049.1|Hepatitis_C_virus_(isolate_H77)|63746 +1985 HVPQVADAI 0.0 None None 0 None +1986 LLEMNLMHV 0.44470519815 LLEMNLM LIEANLL 22.0 419095|polyprotein|ABR25251.1|Hepatitis_C_virus|11103 +1987 NLMHVPQVA 0.0 None None 0 None +1988 VPQVADAIL 0.0 None None 0 None +1989 FLIDGSQSV 0.0 None None 0 None +1990 FLIDGSQSV 0.0 None None 0 None +1991 SVGPEFQYV 0.0 None None 0 None +1992 LALSVTEMV 0.0 None None 0 None +1993 RLALSVTEM 0.0 None None 0 None +1994 TILQIKEEK 0.0 None None 0 None +1995 DYEAVCGHR 0.0 None None 0 None +1996 EAVCGHRAR 0.287814503571 GHRAR GHKAR 25.0 21635|gag_protein|ABO73990.1|Human_immunodeficiency_virus_1|11676 +1997 ILFQKITNR 0.0 None None 0 None +1998 KITNRGDEL 0.0 None None 0 None +1999 SPTPALGPA 0.0 None None 0 None +2000 LTPQQAQEL 0.0 None None 0 None +2001 APLGAPPPL 355.106026278 LGAPPPL LGAIPPL 29.0 73059|kaposin|AAC57155.1|Human_gammaherpesvirus_8|37296 +2002 SKTPPGAPL 1.70350167556 PPGAPL PPNAPI 27.0 93536|core_protein|AAL31859.1|Hepatitis_B_virus|10407 +2003 SKTPPGAPL 6.26781366346 PPGAPL PPNAPI 27.0 93536|core_protein|AAL31859.1|Hepatitis_B_virus|10407 +2004 MFQSLGEHI 0.0937231593112 MFQSLGEHI MEPTLGQHL 24.0 79308|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 +2005 SLGEHINTL 2.10571623096 SLGEHINTL TLGQHLPTL 30.0 79308|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 +2006 SLGEHINTL 1.0685924021 SLGEHINTL TLGQHLPTL 30.0 79308|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 +2007 AVGVGKSAL 0.0 None None 0 None +2008 YKLVVVGAV 12.5817515538 KLVVVG KLVVLG 24.0 32238|polyprotein_[Hepatitis_C_virus_subtype_1a]|ABV46251.2|Hepatitis_C_virus_(isolate_H77)|63746 +2009 AMLWALGFI 8.2714056325 MLWALGF ILWAVGL 27.0 1000|glycoprotein_gp35/37|AAC59622.1|Human_gammaherpesvirus_8|37296 +2010 FIWSVLITA 0.0 None None 0 None +2011 MLWALGFIF 3.08293386362 MLWALGF ILWAVGL 27.0 1000|glycoprotein_gp35/37|AAC59622.1|Human_gammaherpesvirus_8|37296 +2012 QTPLFIWSV 0.0 None None 0 None +2013 TPLFIWSVL 0.0 None None 0 None +2014 TQYQTPLFI 0.638287640051 QYQTP RYQTP 25.0 180617|polyprotein|AGO67248.1|Dengue_virus_2|11060 +2015 IINDGKHHV 0.0 None None 0 None +2016 GLSAEEFQL 0.0 None None 0 None +2017 SAEEFQLIR 0.0 None None 0 None +2018 APTTPKEPA 0.0115417217673 APTTPKEPA APASVYQPA 21.0 141216|envelope_glycoprotein_I|NP_044669.1|Human_alphaherpesvirus_1|10298 +2019 LLLLLLLLV 0.0 None None 0 None +2020 LLLLLLLVV 0.183789279182 LLLLLVV VLLLLVV 25.0 98540|trans-sialidase,_putative|EAN88532.1|Trypanosoma_cruzi|5693 +2021 LLLLLLVVV 0.355681484489 LLLLVVV LLLLVVM 25.0 98224|trans-sialidase,_putative|EAN82076.1|Trypanosoma_cruzi|5693 +2022 LLVVVPWGV 0.0 None None 0 None +2023 SRRHSRSPL 0.0 None None 0 None +2024 SRRHSRSPL 0.0 None None 0 None +2025 GSYSMAIPL 0.191247232974 GSYSMAIPL GLYSSTVPV 25.0 21242|polymerase|ACF94272.1|Hepatitis_B_virus|10407 +2026 MAIPLLCSY 0.0 None None 0 None +2027 NPGSYSMAI 0.0 None None 0 None +2028 RYNPGSYSM 0.0 None None 0 None +2029 RYNPGSYSM 0.0 None None 0 None +2030 SYSMAIPLL 0.0 None None 0 None +2031 CQPHAHCSL 0.0 None None 0 None +2032 HAHCSLWRR 0.0 None None 0 None +2033 IIQELTIFK 0.0 None None 0 None +2034 LPPKPVQVL 1.24074074074 PPKPVQV PPKPCGI 26.0 75376|Genome_polyprotein|P26664.3|Hepatitis_C_virus|11103 +2035 QLPPKPVQV 0.5 PPKPVQV PPKPCGI 26.0 75376|Genome_polyprotein|P26664.3|Hepatitis_C_virus|11103 +2036 GLYASLFPA 0.0 None None 0 None +2037 LFPAIIYLF 0.160615937749 FPAIIYL YPAVFYL 28.0 154041|major_capsid_protein|CAB06743.1|Human_alphaherpesvirus_2|10310 +2038 LYASLFPAI 0.0 None None 0 None +2039 PVYGLYASL 0.0 None None 0 None +2040 SLFPAIIYL 165.36965139 FPAIIYL YPAVFYL 28.0 154041|major_capsid_protein|CAB06743.1|Human_alphaherpesvirus_2|10310 +2041 SLFPAIIYL 0.19660649062 FPAIIYL YPAVFYL 28.0 154041|major_capsid_protein|CAB06743.1|Human_alphaherpesvirus_2|10310 +2042 SLFPAIIYL 0.207246371289 FPAIIYL YPAVFYL 28.0 154041|major_capsid_protein|CAB06743.1|Human_alphaherpesvirus_2|10310 +2043 VYGLYASLF 0.0 None None 0 None +2044 VYGLYASLF 0.0 None None 0 None +2045 RYNVADVSV 0.0 None None 0 None +2046 VSVAICMSL 0.0 None None 0 None +2047 YTISDDESF 0.0 None None 0 None +2048 YVQYWYYTI 0.673550706689 VQYWYY TQYWKY 28.0 141206|tegument_protein_VP11/12|NP_044648.1|Human_alphaherpesvirus_1|10298 +2049 YVQYWYYTI 0.493586768335 VQYWYY TQYWKY 28.0 141206|tegument_protein_VP11/12|NP_044648.1|Human_alphaherpesvirus_1|10298 +2050 SFYNSNRDF 0.0 None None 0 None +2051 SFYNSNRDF 0.0 None None 0 None +2052 TISFYNSNR 0.0 None None 0 None +2053 CRFELMHFK 0.0 None None 0 None +2054 ELMHFKTLY 0.00494580293464 ELMHFKTL KVLHKRTL 20.0 34101|X_protein|ACH95876.1|Hepatitis_B_virus|10407 +2055 ILGDWSNGI 0.470124959392 DWSNGI DYSNGL 26.0 51604|FL-160-2_protein_-_Trypanosoma_cruzi|JH0823|Trypanosoma_cruzi|5693 +2056 NGISALYCR 0.0 None None 0 None +2057 HIHGGTNQV 0.658346187729 HGGTN HGGTG 25.0 55336|EBNA-1|YP_401677.1|Human_gammaherpesvirus_4|10376 +2058 AFTCTSSLL 0.0 None None 0 None +2059 KAFTCTSSL 0.0 None None 0 None +2060 KAFTCTSSL 0.0 None None 0 None +2061 GDASKVWVW 0.832592284506 GDASKVWV GNASRCWV 31.0 21385|polyprotein|AAY82034.1|Hepatitis_C_virus_genotype_1|41856 +2062 STFVHGNKI 0.0 None None 0 None +2063 GEEAEASAV 0.0 None None 0 None +2064 TTSPSNTLV 0.0 None None 0 None +2065 STGLQYATK 0.0 None None 0 None +2066 SVLRCVHLL 0.0 None None 0 None +2067 GRNSFKVRV 1.9048679282 GRNSFKV GRNSFEV 32.0 37364|P53_HUMAN_Cellular_tumor_antigen_p53_(Tumor_suppressor_p53)_(Phosphoprotein_p53)_(Antigen_NY-CO-13)|P04637.2|Homo_sapiens|9606 +2068 MRTLLGDLV 0.0 None None 0 None +2069 RWDRKPMQI 0.0 None None 0 None +2070 SRSTIFMRL 0.0 None None 0 None +2071 PHLTQGNEI 0.0 None None 0 None +2072 ASTFVHGNK 0.0 None None 0 None +2073 ENAGPQNMK 0.0 None None 0 None +2074 MGQEIAALK 0.0 None None 0 None +2075 NLLGRNSFK 63.0014315849 LLGRNSFK LLGRNSFE 36.0 37364|P53_HUMAN_Cellular_tumor_antigen_p53_(Tumor_suppressor_p53)_(Phosphoprotein_p53)_(Antigen_NY-CO-13)|P04637.2|Homo_sapiens|9606 +2076 QAVCVTKPK 0.165090772535 VCVTKP ICLTHP 24.0 146317|polyprotein|ADF97231.1|Hepatitis_C_virus_subtype_3a|356426 +2077 LRCVHLLRI 0.0 None None 0 None +2078 FVHGNKIYV 0.0 None None 0 None +2079 ATKFIKKRR 0.0 None None 0 None +2080 VHLLRIFKV 0.0 None None 0 None +2081 LANAPRTLK 0.0 None None 0 None +2082 WRLTWDRHL 0.119451085397 WRLTWD WAIKWE 24.0 72233|Genome_polyprotein|P27958.3|Hepatitis_C_virus_subtype_1a|31646 +2083 CTGPPLAPR 0.0742064317743 CTGPPLAPR CGGVYLLPR 23.0 181035|||| +2084 NLTRASSKR 0.0 None None 0 None +2085 RRSGPSPTV 0.586855842399 GPSPTV GPVPAV 22.0 179799|hypothetical_protein|NP_301670.1|Mycobacterium_leprae_TN|272631 +2086 DLVAHYVHR 0.332299353923 LVAHY LVAHY 27.0 150377|polyprotein|AGS49173.1|Dengue_virus_2|11060 +2087 SSLEGFATR 0.0 None None 0 None +2088 LEDLGWANW 1.69512152692 EDLGWANW EGLGWAGW 40.0 75436|Polyprotein|P90247|Hepatitis_C_virus|11103 +2089 CVHLLRIFK 0.0 None None 0 None +2090 TIQAVCVTK 0.0 None None 0 None +2091 ITCMPGSVR 0.0886657628972 ITCMPGSV IFCHPGQL 23.0 79454|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 +2092 CSIPSICEK 0.0 None None 0 None +2093 SSRSTIFMR 0.0 None None 0 None +2094 SVTKASNLK 0.0 None None 0 None +2095 YATKFIKKR 0.0 None None 0 None +2096 FSSSDDSPR 0.0 None None 0 None +2097 VHGNKIYVL 0.0 None None 0 None +2098 WANWVLSPR 4.11764705574 WANWVLSPR WAGWLLSPR 47.0 36352|Polyprotein|P90247|Hepatitis_C_virus|11103 +2099 LSLPGGHTA 0.0 None None 0 None +2100 FRAAAEAAV 0.0 None None 0 None +2101 FRAAAEAAV 0.0 None None 0 None +2102 TSSDHSFSL 0.0 None None 0 None +2103 TSSDHSFSL 0.0 None None 0 None +2104 NHQQFYHSV 0.0 None None 0 None +2105 NHQQFYHSV 0.0 None None 0 None +2106 DYSELPHHV 0.0 None None 0 None +2107 HHVSTEQEI 0.0 None None 0 None +2108 HHVSTEQEI 0.0 None None 0 None +2109 EIISLWSPW 0.0 None None 0 None +2110 NQDPISPSL 0.243444523244 QDPISPSL EKPVAPSV 24.0 419002|PPE_family_protein_PPE68|KAM81677.1|Mycobacterium_tuberculosis_H37Ra|419947 +2111 ENASAYLTL 0.0 None None 0 None +2112 KKMENASAY 0.0 None None 0 None +2113 RRHSLPRRC 0.0 None None 0 None +2114 NMCRCLVTV 0.0 None None 0 None +2115 RLMSARLAI 0.0 None None 0 None +2116 SYSYLGLRL 0.0 None None 0 None +2117 YSYLGLRLM 0.0 None None 0 None +2118 YSYLGLRLM 0.0 None None 0 None +2119 RFSQAFFYM 0.0 None None 0 None +2120 RRFSQAFFY 0.0 None None 0 None +2121 FMMPRSSSC 0.0 None None 0 None +2122 FMMPRSSSC 0.0 None None 0 None +2123 IPAMEIFMV 0.0 None None 0 None +2124 LMAASIPAM 0.0 None None 0 None +2125 DTLQATAML 0.0 None None 0 None +2126 QATAMLDIV 0.0 None None 0 None +2127 TVTRTTATV 0.0 None None 0 None +2128 EHFPLCKTV 0.0 None None 0 None +2129 EHFPLCKTV 0.0 None None 0 None +2130 WPQCHPEEI 1.27438241384 WPQCHPEEI LPQCSPDEI 38.0 3051|UL123;_IE1|AAR31448.1|Human_betaherpesvirus_5|10359 +2131 YSYSCGHYE 0.268852568146 YSYSCGHY YPYRLWHY 24.0 10939|polyprotein|BAB18806.1|Hepatitis_C_virus_subtype_1a|31646 +2132 SHFERDYRV 0.0 None None 0 None +2133 FQTLMPDVV 0.0 None None 0 None +2134 FQTLMPDVV 0.0 None None 0 None +2135 MPDVVHQSL 2.1510778258 MPDVVHQ MPDVAHS 30.0 130953|G1_and_G2_surface_glycoprotein_precursor|AAG22532.1|Andes_hantavirus|46607 +2136 LWYTLYLMI 0.263181088307 LWYTLY LWVTVY 27.0 118|envelope_glycoprotein|ABS76372.1|Human_immunodeficiency_virus_1|11676 +2137 LYLMITTFF 0.141553469901 MITTFF MLTAFF 24.0 140651|granule_antigen_protein_GRA6|XP_002371939.1|Toxoplasma_gondii_ME49|508771 +2138 MITTFFFPL 0.390389569622 MITTFF MLTAFF 24.0 140651|granule_antigen_protein_GRA6|XP_002371939.1|Toxoplasma_gondii_ME49|508771 +2139 TLYLMITTF 1.13393265557 TLYLMITTF TLYAVATTF 31.0 150639|polyprotein|AGO67249.1|Dengue_virus_2|11060 +2140 YLMITTFFF 0.727839017994 MITTFF MLTAFF 24.0 140651|granule_antigen_protein_GRA6|XP_002371939.1|Toxoplasma_gondii_ME49|508771 +2141 YTLYLMITT 0.0 None None 0 None +2142 PTSPFQTTI 0.00448304273818 PTSPFQ PERPFQ 23.0 232154|rhoptry_protein,_putative_/_protein_kinase_domain-containing_protein|XP_002367757.1|Toxoplasma_gondii_type_II|1209523 +2143 TAERSIPTV 0.546505896162 ERSIPTV DRSYPAV 21.0 154041|major_capsid_protein|CAB06743.1|Human_alphaherpesvirus_2|10310 +2144 ERPCHREPL 2.30501930502 PCHREPL PGHEEPI 26.0 180488|polyprotein|AGO67248.1|Dengue_virus_2|11060 +2145 SSSSGPFPL 0.0 None None 0 None +2146 ELATFAKAY 0.0 None None 0 None +2147 RWDEELATF 0.0 None None 0 None +2148 ELIDLISRV 0.0 None None 0 None +2149 ELIDLISRV 0.0 None None 0 None +2150 QVNQKSSVV 0.0 None None 0 None +2151 VRLELIDLI 0.0 None None 0 None +2152 YEEYRGRLL 0.267524115073 YEEYRGRL YQDWLGRM 24.0 23288|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 +2153 YEEYRGRLL 0.0889159325107 YEEYRGRL YQDWLGRM 24.0 23288|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 +2154 CRNVHTPDL 0.0 None None 0 None +2155 YSRDQAQAL 0.0 None None 0 None +2156 YSRDQAQAL 0.0 None None 0 None +2157 FEVEGRDLL 0.0 None None 0 None +2158 FFFLCVCVF 0.0684531631414 FFFLCVCV LLILCLCL 24.0 49831|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 +2159 FFLCVCVFV 0.243568175313 FFLCVCV LILCLCL 24.0 49831|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 +2160 RRYPHKRCI 0.119202922022 YPHKRC YPPKPC 24.0 75376|Genome_polyprotein|P26664.3|Hepatitis_C_virus|11103 +2161 RRYPHKRCI 0.150450289931 YPHKRC YPPKPC 24.0 75376|Genome_polyprotein|P26664.3|Hepatitis_C_virus|11103 +2162 NMSRCCIRV 0.0 None None 0 None +2163 GLLGNGIGY 0.0 None None 0 None +2164 LLGNGIGYV 0.0 None None 0 None +2165 KILSLHLLL 0.0 None None 0 None +2166 HPAFISLAF 0.0 None None 0 None +2167 FPREKTPEV 0.911184210526 FPREKTP LPRSRTP 26.0 88849|IE62|AAP32859.1|Human_alphaherpesvirus_3|10335 +2168 WPPWLKGKY 0.578598641597 WLKGK YLKGK 22.0 419170|polyprotein|ABR25251.1|Hepatitis_C_virus|11103 +2169 IVLTGHNAY 0.0 None None 0 None +2170 IVLTGHNAY 0.0 None None 0 None +2171 VLTGHNAYL 0.0 None None 0 None +2172 QAQALGIPL 0.0 None None 0 None +2173 IVFFANNGF 0.0 None None 0 None +2174 HSESSDSEV 0.0 None None 0 None +2175 RRGSGHSEY 0.0584223726864 GSGHSE GPGHEE 24.0 180488|polyprotein|AGO67248.1|Dengue_virus_2|11060 +2176 LIMEDLVCY 0.0 None None 0 None +2177 MEDLPAACM 0.0 None None 0 None +2178 HPMASNSGG 0.00278161375312 PMASNSGG PIALLKGG 19.0 146282|polyprotein|ADF97231.1|Hepatitis_C_virus_subtype_3a|356426 +2179 DVEWRWHSY 0.0 None None 0 None +2180 DVEWRWHSY 0.0 None None 0 None +2181 ILPTCSPLV 2072.01295566 PTCSPL PACKPL 27.0 56502|polyprotein|BAD73994.1|Hepatitis_C_virus_subtype_1b|31647 +2182 LPTCSPLVF 1.81028585028 PTCSPL PACKPL 27.0 56502|polyprotein|BAD73994.1|Hepatitis_C_virus_subtype_1b|31647 +2183 VHFWPGYEY 0.0 None None 0 None +2184 SPEGDDTLY 0.0192935429649 PEGDDTLY PQGQLTAY 22.0 13701|Trans-activator_protein_BZLF1|P03206.2|Human_gammaherpesvirus_4|10376 +2185 TLVPTAPEL 0.0 None None 0 None +2186 HLIGSTTLA 2.05755395683 LIGSTTL LIGITTL 26.0 59182|attachment_glycoprotein|ABQ58821.1|Human_metapneumovirus|162145 +2187 LIGSTTLAM 0.246511627907 LIGSTTL LIGITTL 26.0 59182|attachment_glycoprotein|ABQ58821.1|Human_metapneumovirus|162145 +2188 LLMHLIGST 0.0 None None 0 None +2189 IAHQWYWTY 0.0584354508795 QWYWTY KWLWGF 23.0 62903|Genome_polyprotein|P27909.2|Dengue_virus_type_1_Hawaii|10000440 +2190 IAHQWYWTY 2.11519394372 QWYWTY KWLWGF 23.0 62903|Genome_polyprotein|P27909.2|Dengue_virus_type_1_Hawaii|10000440 +2191 LLEENGDVF 0.0 None None 0 None +2192 QRCACPHGY 0.0 None None 0 None +2193 CMYDPLGTI 0.0 None None 0 None +2194 GPHRITCMY 0.0389454916711 PHRITC PHVIFC 23.0 79337|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 +2195 NESCLSMSE 0.0 None None 0 None +2196 VANESCLSM 0.0 None None 0 None +2197 EESELYAQL 1.79691363928 EESELY EQSEFY 23.0 62355|Genome_polyprotein|P08617.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 +2198 RTAQCFLCV 0.0 None None 0 None +2199 KYSNYVWPI 10.3355467301 KYSNYVW KYTSFPW 26.0 34616|pol_protein|BAA32832.1|Hepatitis_B_virus|10407 +2200 FIFEIVGFT 0.0 None None 0 None +2201 DSSGQSNRY 1.24432386195 SSGQSNR NSGASNR 25.0 1095|glycoprotein_gp35/37|AAC59622.1|Human_gammaherpesvirus_8|37296 +2202 DSSSWSNRY 0.0 None None 0 None +2203 DSSSWSNRY 0.0 None None 0 None +2204 NRYGGGGRY 0.0 None None 0 None +2205 NRYGGGGRY 0.0 None None 0 None +2206 NEHGHRRKI 0.0 None None 0 None +2207 HTSLRGFLY 0.253521126761 HTSLRGF HLSLRGL 26.0 24302|X_protein|AAP06597.1|Hepatitis_B_virus|10407 +2208 ALNEMFCQL 0.0 None None 0 None +2209 NEMFCQLAK 0.0 None None 0 None +2210 GLYAIAVML 0.0 None None 0 None +2211 MLSFSRIAY 0.0 None None 0 None +2212 MLSFSRIAY 0.0 None None 0 None +2213 YAIAVMLSF 0.0 None None 0 None +2214 AEWDSLYVL 0.0 None None 0 None +2215 LAEWDSLYV 0.0 None None 0 None +2216 VLAEWDSLY 0.0 None None 0 None +2217 VLAEWDSLY 0.0 None None 0 None +2218 GKAFSQSAY 0.0 None None 0 None +2219 KAFSQSAYL 0.0 None None 0 None +2220 RREDLTHTL 0.0 None None 0 None +2221 RREDLTHTL 0.0 None None 0 None +2222 ERWLRQAAF 3.02094262382 RWLRQAAF RWVPGAAY 24.0 22255|polyprotein|ABR27377.1|Hepatitis_C_virus|11103 +2223 RKREEEERW 42.4491907364 KREEEE RREEEE 27.0 185491|polyprotein|AGO67248.1|Dengue_virus_2|11060 +2224 THCSPNLLF 0.0 None None 0 None +2225 HQYNIYAAL 0.351661877827 YNIYAAL YNTVAAL 23.0 189291|||| +2226 RSFTESHQY 0.0 None None 0 None +2227 ISAKIMQQW 0.0 None None 0 None +2228 YTDTISAKI 0.0 None None 0 None +2229 AAVLGMLLW 0.0 None None 0 None +2230 ISGRVVQHF 0.0 None None 0 None +2231 IAFNHGDLL 0.0 None None 0 None +2232 KYHYYGLHI 0.0 None None 0 None +2233 LSRRVTQSL 0.0 None None 0 None +2234 RRVTQSLEA 0.0 None None 0 None +2235 KTYAPLFIW 0.678885162016 TYAPLFI TYGPVFM 27.0 67349|Latent_membrane_protein_2|Q69135|Human_gammaherpesvirus_4|10376 +2236 TYAPLFIWV 1.02223796155 TYAPLFIWV TYGPVFMCL 27.0 67349|Latent_membrane_protein_2|Q69135|Human_gammaherpesvirus_4|10376 +2237 KYIAFCINI 0.587708864399 KYIAFCI RYISWCL 26.0 39591|polyprotein|AAA45677.1|Hepatitis_C_virus_(isolate_H77)|63746 +2238 YIAFCINIF 0.476894002614 YIAFCI YISWCL 24.0 423020|polyprotein|ACE82359.1|Hepatitis_C_virus_genotype_1|41856 +2239 FHYPQSIFS 0.552109387903 HYPQSIF HYMESVF 28.0 154585|ribonucleotide_reductase_large_subunit|CAB06725.1|Human_alphaherpesvirus_2|10310 +2240 MKFHYPQSI 0.0 None None 0 None +2241 NTNSNRSLI 0.0 None None 0 None +2242 FRAYQDYFL 0.0 None None 0 None +2243 FRAYQDYFL 0.0 None None 0 None +2244 LHIGKDVQL 0.0 None None 0 None +2245 QVFAAVHEW 0.000185091863979 FAAVH YAFVH 17.0 142232|POSSIBLE_CONSERVED_TRANSMEMBRANE_PROTEIN|CAB00937.1|Mycobacterium_tuberculosis|1773 +2246 RRHTDEKPY 0.465553354611 RRHTDEK QRHLDKK 25.0 110394|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 +2247 FNGNFLLSM 8.55978429414 NGNFLL NGGFLI 24.0 194567|envelope_glycoprotein_B|NP_044629.1|Herpes_simplex_virus_(type_1_/_strain_17)|10299 +2248 GSADNTVQF 0.0 None None 0 None +2249 SADNTVQFI 0.0 None None 0 None +2250 KVQREDIFY 0.0 None None 0 None +2251 YLWPSGTPA 3.65618873033 LWPSGTP LWKDGAP 27.0 140600|glutamine_synthetase_GLNA1_(glutamine_synthase)_(GS-I)|NP_216736.1|Mycobacterium_tuberculosis_H37Rv|83332 +2252 LKMVSPSPC 0.0 None None 0 None +2253 SRVARDVAM 0.0 None None 0 None +2254 QNGYSWSQF 0.0190362677864 QNGYSWS QNGACWT 26.0 6889|Agglutinin_isolectin_1_precursor|P10968.2|Triticum_aestivum|4565 +2255 SYKLSQNGY 0.355050579888 SYKLSQNG AYRIKQRG 23.0 182687|polyprotein|AGK36298.1|Dengue_virus_2|11060 +2256 WKRGKRRYF 0.438635147178 WKRGKR WTRGER 27.0 170063|polyprotein|ABU97067.1|Hepatitis_C_virus_subtype_1b|31647 +2257 CFGHCFSLY 0.36196760402 FGHCF FGWCF 25.0 56620|Nef_protein|Q9YYU8|Human_immunodeficiency_virus_1|11676 +2258 CSAIRLRNY 0.0 None None 0 None +2259 FGHCFSLYI 0.0 None None 0 None +2260 IRLRNYLCF 0.0 None None 0 None +2261 IRLRNYLCF 0.0 None None 0 None +2262 LCFGHCFSL 0.351865750194 LCFGHCF LTFGWCF 28.0 56620|Nef_protein|Q9YYU8|Human_immunodeficiency_virus_1|11676 +2263 NHLCFGHCF 643.063109635 LCFGHCF LTFGWCF 28.0 56620|Nef_protein|Q9YYU8|Human_immunodeficiency_virus_1|11676 +2264 DFVECLMWF 0.0 None None 0 None +2265 DFVECLMWF 0.0 None None 0 None +2266 NKFEPSTDL 0.0458420865757 NKFEPST NDFFPSV 19.0 16814|precore_protein|CAM58990.1|Hepatitis_B_virus|10407 +2267 AYLCCRVPL 0.256424890396 LCCRV LCCYV 24.0 11956|UL123;_IE1|AAR31448.1|Human_betaherpesvirus_5|10359 +2268 SKGTTDTPV 2.41094003631 SKGTTDTPV SPGTSGSPI 25.0 5542|Nonstructural_protein_NS3|NP_739587.2|Dengue_virus_2_Thailand/16681/84|31634 +2269 KQSNSVEPI 0.0 None None 0 None +2270 AMSAQEYYI 0.0 None None 0 None +2271 SAQEYYIDY 0.0 None None 0 None +2272 YIDYKPNHI 0.377509819097 YIDYKPN YTDYMPS 26.0 180681|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 +2273 LMLLAAAIY 0.0 None None 0 None +2274 LMLLAAAIY 0.0 None None 0 None +2275 SEDDTSYFV 0.0 None None 0 None +2276 RESVKHIGY 0.0 None None 0 None +2277 YQKVVRESV 0.0 None None 0 None +2278 SSVKTPETL 0.0 None None 0 None +2279 VIHHELQVL 0.0 None None 0 None +2280 KTDATPGRL 0.0 None None 0 None +2281 IKRLTAGSL 0.0 None None 0 None +2282 KRLTAGSLF 0.0 None None 0 None +2283 KQLSHHIGA 0.0 None None 0 None +2284 FHVNWFRRY 0.0 None None 0 None +2285 FRRYEAGHF 0.0 None None 0 None +2286 RRYEAGHFL 0.0 None None 0 None +2287 RYEAGHFLW 0.0 None None 0 None +2288 VSDHTPEQH 0.00112786319425 VSDHTPEQ LSDGNPPQ 20.0 69754|Lipoprotein_lpqH_precursor|P46733.1|Mycobacterium_avium|1764 +2289 SFHMDTQNF 0.0 None None 0 None +2290 SFHMDTQNF 0.0 None None 0 None +2291 TQNFCDIGY 0.0 None None 0 None +2292 LALSVFSKL 0.0 None None 0 None +2293 TVKLALSVF 5.19636761594e-05 TVKLALSVF TVRGLTSLF 16.0 52652|||| +2294 LQFAVGQEV 0.0 None None 0 None +2295 PQVPEHLQF 0.037697488936 PQVPEH PQYSEH 23.0 38974|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 +2296 QFAVGQEVF 0.0 None None 0 None +2297 NRYGGGGRY 0.0 None None 0 None +2298 EQLKLGAIF 4.26305904452 LKLGAI IKLGAL 23.0 423046|polyprotein|ACX44272.1|Hepatitis_C_virus_genotype_1|41856 +2299 LLMPYPVIV 0.0 None None 0 None +2300 TLLMPYPVI 0.0 None None 0 None +2301 RALKPVNKI 0.0 None None 0 None +2302 KEAMENEQF 0.0 None None 0 None +2303 LTEENKEAM 0.0 None None 0 None +2304 MEVPNIASS 0.0 None None 0 None +2305 RRFASGEKV 0.0 None None 0 None +2306 TFRDVAVEF 0.0350794875147 TFRDVA TWRDMA 22.0 186175|polyprotein|AFY10053.1|Dengue_virus_3|11069 +2307 FHISLFQYM 0.0 None None 0 None +2308 LIIDEDFHI 0.0 None None 0 None +2309 VLETAAPGV 0.0 None None 0 None +2310 ESHEKGCFW 0.0 None None 0 None +2311 MADAKGYTV 2.48831775731 MADAKGY MGDAGGY 26.0 3094|Antigen_85-B_precursor_(85B)_(Extracellular_alpha-antigen)_(Antigen_85_complex_B)_(Ag85B)_(Mycolyl_transferase_85B)_(Fibronectin-binding_protein_B)_(30_kDa_extracellular_protein)|P31952|Mycobacterium_tuberculosis|1773 +2312 KQLPRILEA 0.0 None None 0 None +2313 HTCQVNGRW 0.0130808799724 TCQVNGRW SCEGLGAW 22.0 79628|E1_protein|BAA19893.1|Rubella_virus|11041 +2314 PLLPSIISL 0.0 None None 0 None +2315 AIWEAVMSA 3.99661222935 IWEAV MWEAV 25.0 37590|VP1|BAF93325.1|Human_polyomavirus_1|1891762 +2316 AVMSALPSL 0.0 None None 0 None +2317 MSALPSLNW 0.0 None None 0 None +2318 GLDGPLVHV 0.0 None None 0 None +2319 SIRVSQKGW 0.0 None None 0 None +2320 PTDPGHFLV 0.0 None None 0 None +2321 MRGEHRFHM 0.0 None None 0 None +2322 KLSHCLSKA 0.0 None None 0 None +2323 CRPQCCQSV 32.8617887736 CRPQCCQSV CRVLCCYVL 28.0 11956|UL123;_IE1|AAR31448.1|Human_betaherpesvirus_5|10359 +2324 VRNPEPSPL 0.0 None None 0 None +2325 VLVVSPWPA 0.0 None None 0 None +2326 GMLWAMMSI 0.306314234534 GMLWAM GVLWTV 23.0 95940|polyprotein|BAA32666.1|Hepatitis_C_virus_genotype_6|42182 +2327 YMGMLWAMM 0.15801288777 GMLWAM GVLWTV 23.0 95908|Genome_polyprotein|O92529.3|Hepatitis_C_virus_genotype_6|42182 +2328 SRAVTSTTI 0.0 None None 0 None +2329 KTASWAEVV 0.0 None None 0 None +2330 WTFALTSGL 0.0 None None 0 None +2331 TDFNNGSYL 0.0 None None 0 None +2332 VTDFNNGSY 0.0 None None 0 None +2333 LLDTIPWYL 0.0 None None 0 None +2334 ASSDHTTHL 0.0 None None 0 None +2335 SHSSCVWLW 0.0 None None 0 None +2336 TGSHSSCVW 0.0 None None 0 None +2337 SIGELLQVL 0.0 None None 0 None +2338 TGFVRRPLW 0.0 None None 0 None +2339 DAEPFQRGW 0.127646462332 DAEPFQR HASPFER 24.0 23566|tegument_protein_UL7|NP_044476.1|Human_alphaherpesvirus_2|10310 +2340 FIFSDTVVL 0.0547221613587 FSDTVVL FKDNVIL 23.0 50779|N_protein|AAP13445.1|SARS_coronavirus_Urbani|228330 +2341 FIFSDTVVL 0.0775477115471 FSDTVVL FKDNVIL 23.0 50779|N_protein|AAP13445.1|SARS_coronavirus_Urbani|228330 +2342 FSDTVVLLF 0.804164436493 FSDTVVLL FKDNVILL 27.0 50779|N_protein|AAP13445.1|SARS_coronavirus_Urbani|228330 +2343 MHFIFSDTV 0.0 None None 0 None +2344 TVVLLFDFW 0.0 None None 0 None +2345 YHPGAMHCV 0.0 None None 0 None +2346 CAFSGTLPW 0.0 None None 0 None +2347 FMCAFSGTL 0.0 None None 0 None +2348 STHPSLSQW 1087.72967514 STHPSLSQW NTRPPLGNW 27.0 68601|polyprotein|AAA45534.1|Hepatitis_C_virus|11103 +2349 SRKDRAPKC 0.0 None None 0 None +2350 LMGLASTTV 0.0 None None 0 None +2351 SLLAIHQWV 0.204347866324 LAIHQWV LAVDPWV 24.0 143690|Genome_polyprotein|P06441.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 +2352 SSLLAIHQW 0.0 None None 0 None +2353 AIHIVAEKK 0.0 None None 0 None +2354 ESLPPSPTW 0.0 None None 0 None +2355 WAGNVLAPY 1.87387179047 WAGNVLAP WAGWLLSP 30.0 36352|Polyprotein|P90247|Hepatitis_C_virus|11103 +2356 QIIAGHFRK 0.0 None None 0 None +2357 STSSRSHRY 0.0 None None 0 None +2358 FHQCLSIYY 1.78908850466 FHQCLSI FHLCLII 27.0 93431|pre-C/C_protein|ABY54138.1|Hepatitis_B_virus|10407 +2359 IYYWDIRYK 0.00992413375792 YYWDIRYK HTWTEQYK 20.0 183619|nonstructural_protein_NS1|1802191G|Dengue_virus|12637 +2360 LFHQCLSIY 102.125443496 LFHQCLSI LFHLCLII 31.0 93431|pre-C/C_protein|ABY54138.1|Hepatitis_B_virus|10407 +2361 SIYYWDIRY 0.0 None None 0 None +2362 SIYYWDIRY 0.0 None None 0 None +2363 SRHTIRELL 0.0 None None 0 None +2364 QINIPIGPY 0.0 None None 0 None +2365 GGMQALGLY 0.378933871481 GGMQALGLY GGSRVEGIF 20.0 61861|Nucleoprotein|P03418.1|Human_respiratory_syncytial_virus_A2|11259 +2366 FLNLSQPRK 0.0 None None 0 None +2367 RLNSHFLNL 1.98031425281 RLNSHFLNL RVDLHFINL 31.0 119822|110_kd_polyprotein_precursor|CAA28880.1|Rubella_virus|11041 +2368 ERSLQVKRV 0.0 None None 0 None +2369 LQVKRVFVK 0.0 None None 0 None +2370 RSLQVKRVF 0.0 None None 0 None +2371 RVFVKGMKK 0.0 None None 0 None +2372 CSSSIGTIW 0.0 None None 0 None +2373 WSHASASLY 0.0 None None 0 None +2374 WSHASASLY 0.0 None None 0 None +2375 KESNAGRYY 0.0 None None 0 None +2376 VKESNAGRY 0.0 None None 0 None +2377 IVSVKPNMK 0.074476186027 VSVKPN VSIAPN 23.0 19359|IMMUNOGENIC_PROTEIN_MPT64_(ANTIGEN_MPT64/MPB64)|CAA98382.1|Mycobacterium_tuberculosis_H37Rv|83332 +2378 FSYPKRPII 0.0 None None 0 None +2379 MSHPPNILK 0.0 None None 0 None +2380 GARPGLGRY 0.0 None None 0 None +2381 ITSRDATRF 0.0 None None 0 None +2382 TRFPIIASC 0.0 None None 0 None +2383 RLLSSGTAK 0.0 None None 0 None +2384 KVLELADRF 0.0 None None 0 None +2385 RVSTGSVHK 0.0 None None 0 None +2386 VVGAVGVGK 0.0 None None 0 None +2387 LSFRSSSCR 0.0 None None 0 None +2388 EMFEHLFGK 0.533333333333 EMFEHLF DMWEHAF 26.0 9415|Superoxide_dismutase|P17670.1|Mycobacterium_tuberculosis|1773 +2389 TRAHCHLPV 0.618719512219 RAHCHLPV RKHRHLPV 32.0 75408|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 +2390 ILDYMQLRK 0.0 None None 0 None +2391 KILDYMQLR 0.0 None None 0 None +2392 TTMLDRGPK 0.0 None None 0 None +2393 IHITEEEAV 0.0 None None 0 None +2394 LVSMTYDRY 0.0 None None 0 None +2395 MTYDRYVAI 0.0764884706029 YDRYVA YKRYIS 22.0 39591|polyprotein|AAA45677.1|Hepatitis_C_virus_(isolate_H77)|63746 +2396 MVLLVSMTY 0.0 None None 0 None +2397 MVLLVSMTY 0.0 None None 0 None +2398 MVLLVSMTY 0.0 None None 0 None +2399 VSMTYDRYV 0.0 None None 0 None +2400 IHMDARLHT 0.0 None None 0 None +2401 MGMALLIHM 0.0 None None 0 None +2402 FKSKVPQTW 0.0 None None 0 None +2403 VGQQQQVLW 0.0 None None 0 None +2404 DSSSWSDRY 3.70689655172 SWSDRY TWADEY 26.0 33912|FL-160-2_protein_-_Trypanosoma_cruzi|JH0823|Trypanosoma_cruzi|5693 +2405 SGGHDSSSW 0.0 None None 0 None +2406 YEEYRGHSL 0.0 None None 0 None +2407 HTSTVRESY 0.0 None None 0 None +2408 HTSTVRESY 0.0 None None 0 None +2409 SHYGQPDRQ 0.0 None None 0 None +2410 DHEVYLKHL 0.0 None None 0 None +2411 GGLFIASNW 0.0 None None 0 None +2412 KVTRLHRRK 0.0 None None 0 None +2413 LMSTSEEEF 0.0 None None 0 None +2414 LSNNCVPQM 0.0 None None 0 None +2415 STRDEIEGL 1.14900483451 RDEIEG EDEIDG 23.0 110431|E7|AAD33253.1|Human_papillomavirus_type_16|333760 +2416 RMCTVTNYF 0.0 None None 0 None +2417 VMVSLKPDK 0.0 None None 0 None +2418 CRQEQERKF 0.0 None None 0 None +2419 EQEERREQL 0.0 None None 0 None +2420 FRLEEQKVC 0.0 None None 0 None +2421 QSLCGTRFY 0.0 None None 0 None +2422 TAAAAPTPF 0.0 None None 0 None +2423 DRNTFRHSL 0.0 None None 0 None +2424 NTFRHSLVV 0.0 None None 0 None +2425 RMNSFLHIL 0.0 None None 0 None +2426 RMNSFLHIL 0.0 None None 0 None +2427 SRMNSFLHI 0.0 None None 0 None +2428 GSFPTEYIL 0.0 None None 0 None +2429 VTNCHKNYW 0.0 None None 0 None +2430 VVTNCHKNY 0.131382703091 VVTNCHK IVTFCCK 20.0 110184|E7|AAD33253.1|Human_papillomavirus_type_16|333760 +2431 DMAPTRPRW 0.172014343171 MAPTRPRW FAPALPIW 24.0 422989|polyprotein|ABY67644.1|Hepatitis_C_virus_genotype_1|41856 +2432 FRRPQESLL 0.0 None None 0 None +2433 GINNKVCFW 0.0 None None 0 None +2434 LLTDTNSWW 0.874238307242 LLTDTNSW VLTDFKTW 26.0 69797|polyprotein|BAA09073.1|Hepatitis_C_virus_subtype_1b|31647 +2435 QLLTDTNSW 0.928593037485 LLTDTNSW VLTDFKTW 26.0 69797|polyprotein|BAA09073.1|Hepatitis_C_virus_subtype_1b|31647 +2436 HQRVHSGEK 0.0 None None 0 None +2437 QRYSHQRVH 0.0 None None 0 None +2438 VKSKLIAHY 0.0 None None 0 None +2439 SVDECELHK 0.0 None None 0 None +2440 PMPPPLEPI 0.0987361416297 MPPPLEP LPDPLKP 27.0 27241|Spike_glycoprotein_precursor|P59594.1|SARS_coronavirus|227859 +2441 KEIDVIAIP 0.0 None None 0 None +2442 YKDYAAELV 0.141859211272 YKDYAA FKDFAA 25.0 182917|polyprotein|CDF77361.1|Dengue_virus_3|11069 +2443 DNLDSDNTY 0.185784734323 NLDSDNTY HYDEDNPY 24.0 72563|polyprotein|AAB70696.1|Dengue_virus_type_1_Hawaii|10000440 +2444 LAVTLGLAL 0.0 None None 0 None +2445 HNNNRPLTM 0.0 None None 0 None +2446 WAVPPLLLA 0.411375661376 AVPPLL AIPPLV 26.0 73059|kaposin|AAC57155.1|Human_gammaherpesvirus_8|37296 +2447 RCYVRGLFH 0.0 None None 0 None +2448 KITAQRLSH 0.0 None None 0 None +2449 SSLHSEPPK 0.0 None None 0 None +2450 QAQALGIPL 0.0 None None 0 None +2451 QAQALGIPL 0.0 None None 0 None +2452 IPKSPEEAI 0.0 None None 0 None +2453 PEEPTSPAA 0.206085938541 PTSPAA PTAPCA 24.0 79628|E1_protein|BAA19893.1|Rubella_virus|11041 +2454 RVQSRPIPI 0.0396216155661 SRPIPI SEPLPV 23.0 57591|Cobalamin_(vitamin_B12)_synthesis_protein/P47K_family_protein|YP_169986.1|Francisella_tularensis_subsp._tularensis_SCHU_S4|177416 +2455 HSLQQAQSV 0.0 None None 0 None +2456 PLFTTQCGK 0.0219525875844 PLFTTQ PTFTSQ 23.0 75718|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 +2457 HMEAEMAQK 0.0 None None 0 None +2458 VQLPKVSEM 0.0 None None 0 None +2459 ITAQRLSHL 0.0 None None 0 None +2460 LLLSPPVEV 0.0 None None 0 None +2461 IPILPLIYI 0.26866979834 PILPLI PFLPLL 24.0 27345|Large_envelope_protein|P03138.3|Hepatitis_B_virus_subtype_ayw|10418 +2462 AEAQTPEDS 0.0 None None 0 None +2463 LLSPPVEVK 0.0 None None 0 None +2464 TEHDVQIYV 0.0 None None 0 None +2465 FISLKFSSK 0.0 None None 0 None +2466 IPGPIPGPI 0.0153161126032 PGPIPG PGTGPG 21.0 47760|EBNA-1_protein|Q777E1|Human_gammaherpesvirus_4|10376 +2467 KTRRTSSLH 0.0 None None 0 None +2468 EEPTSPAAA 0.0642546482275 PTSPAA PTAPCA 24.0 79628|E1_protein|BAA19893.1|Rubella_virus|11041 +2469 WILSARLLK 0.0 None None 0 None +2470 QQFPSLELL 0.0 None None 0 None +2471 RPIPILPLI 0.371841950785 PILPLI PFLPLL 24.0 27345|Large_envelope_protein|P03138.3|Hepatitis_B_virus_subtype_ayw|10418 +2472 NMKEQVVIL 0.0 None None 0 None +2473 AQRLSHLNK 0.0 None None 0 None +2474 RAYRDDTDL 0.0 None None 0 None +2475 NVFWGEHFK 0.0 None None 0 None +2476 YYKDYAAEL 0.450065235762 YKDYAA FKDFAA 25.0 182917|polyprotein|CDF77361.1|Dengue_virus_3|11069 +2477 QQFPSLELL 0.0 None None 0 None +2478 SLKFSSKIK 5.34901960784 LKFSSKI LKFYSKI 26.0 110227|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 +2479 FLFGLAQNL 0.0 None None 0 None +2480 YVRGLFHSL 0.0 None None 0 None +2481 TENSETTTA 0.056544975831 TENSETT VENLETT 24.0 149063|NS3_protease/helicase'|NP_803144.1|Hepatitis_C_virus_(isolate_H77)|63746 +2482 ALGIPLTPK 0.0 None None 0 None +2483 NENTTPSPA 0.0 None None 0 None +2484 RLPEVQLPK 8.33669952536e-05 LPEVQLPK LPSDFLPS 16.0 16836|precore/core_protein_[Hepatitis_B_virus]|AAR03815.1|Hepatitis_B_virus|10407 +2485 ISLKFSSKI 1.55102040816 LKFSSKI LKFYSKI 26.0 110227|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 +2486 KEGARNVLA 0.0 None None 0 None +2487 MPNDFWARL 2.15830070732 MPNDFWARL LPNDFFPSV 28.0 16814|precore_protein|CAM58990.1|Hepatitis_B_virus|10407 +2488 FTEHDVQIY 0.0200300974578 FTEHDVQI FTNMEVQL 22.0 183275|polyprotein|AGW21594.1|Dengue_virus_1|11053 +2489 FKFHNLPPL 0.0 None None 0 None +2490 NTYRTPSVL 0.309317439303 YRTPSV YQTPAI 24.0 180617|polyprotein|AGO67248.1|Dengue_virus_2|11060 +2491 IAIPSKCLL 0.0 None None 0 None +2492 EASSAVPTV 0.0 None None 0 None +2493 MAAAVVARL 0.0 None None 0 None +2494 QEFENIKSY 16.338826617 QEFENIKS QRFHNIRG 23.0 178247|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 +2495 FQKDPPADI 0.0 None None 0 None +2496 DMYDGRFLV 0.891117731544 MYDGRFLV LYDGSFAV 29.0 93270|hypothetical_protein|NP_218356.1|Mycobacterium_tuberculosis_H37Rv|83332 +2497 PLYKVRFSK 0.0 None None 0 None +2498 VTRPFISLK 0.0 None None 0 None +2499 IILFNRLLK 0.0 None None 0 None +2500 IPYRDSVLI 0.0 None None 0 None +2501 AEASSAVPT 0.0 None None 0 None +2502 EEMPNDFWA 1.09272457194 MPNDFW LPNDFF 28.0 16814|precore_protein|CAM58990.1|Hepatitis_B_virus|10407 +2503 KMPEMHFKA 0.0221786804353 PEMHFKA PERPFQA 20.0 232153|rhoptry_protein_18|CAJ27113.1|Toxoplasma_gondii_type_I|1209525 +2504 AYSKCFISV 0.0 None None 0 None +2505 LYLKTSQDV 0.0 None None 0 None +2506 DLLTNLMYV 0.0 None None 0 None +2507 LLTNLMYVL 0.0 None None 0 None +2508 YQFPQSIDL 0.0 None None 0 None +2509 VWQRPVLNF 113.663716399 VWQRPV IWFRPV 27.0 37507|Large_T_antigen|P03071.1|Human_polyomavirus_1|1891762 +2510 VEGTFISDY 0.0 None None 0 None +2511 EELEIFMAR 0.0 None None 0 None +2512 YEMIRTFYI 0.0 None None 0 None +2513 EEFPCHKCV 0.0 None None 0 None +2514 NYMAHLVAV 0.0 None None 0 None +2515 FADFEWHFL 5.50353283986 FADFEWHF YADRKWCF 25.0 46575|polyprotein|AAG30730.1|Dengue_virus_2|11060 +2516 SFADFEWHF 10.4336370598 SFADFEWHF NYADRKWCF 26.0 46575|polyprotein|AAG30730.1|Dengue_virus_2|11060 +2517 FEQTLEELY 0.233610324193 FEQTLEE FHQTLQD 24.0 42430|Major_surface_antigen_precursor|P03141.3|Hepatitis_B_virus|10407 +2518 IYVKPLPIL 0.166416791124 IYVKPLPI IYVYALPL 25.0 58463|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 +2519 VLQIYVKPL 0.0 None None 0 None +2520 RQWRSLTTL 0.0 None None 0 None +2521 FCLGLVVTI 0.0 None None 0 None +2522 GVFCLGLVV 0.0 None None 0 None +2523 TLGVFCLGL 1.74091147886 TLGVFCLGL TMGVLCLAI 32.0 185978|polyprotein|CDF77361.1|Dengue_virus_3|11069 +2524 IVPRLIMNF 0.0 None None 0 None +2525 LIMNFTLGV 0.0 None None 0 None +2526 GEHPYQCPY 0.0 None None 0 None +2527 VLHRHMTTI 0.0 None None 0 None +2528 HEIDFYRED 0.0 None None 0 None +2529 KLDASVQHL 0.0 None None 0 None +2530 RQLKLDASV 0.0 None None 0 None +2531 FLWLWPLDF 0.00977850494065 FLWLWPLD FLYNRPLN 18.0 98040|trans-sialidase,_putative|EAN80725.1|Trypanosoma_cruzi|5693 +2532 SEDGFLWLW 0.0 None None 0 None +2533 WLWPLDFSS 0.0 None None 0 None +2534 TFRDVAVEF 0.0366333305265 TFRDVA TWRDMA 22.0 186175|polyprotein|AFY10053.1|Dengue_virus_3|11069 +2535 AFSQSAYLI 0.0 None None 0 None +2536 AYLIQHQRF 0.0 None None 0 None +2537 KAFSQSAYL 0.0 None None 0 None +2538 QEEQQQQQL 0.0 None None 0 None +2539 YLFSPQNQF 0.0 None None 0 None +2540 YLFSPQNQF 0.0 None None 0 None +2541 QARKIDHPL 0.0 None None 0 None +2542 QARKIDHPL 0.0 None None 0 None +2543 GLFVHTPCL 0.0397343073407 FVHTPC FVYTPS 24.0 141281|tegument_protein_UL21|NP_044622.1|Human_alphaherpesvirus_1|10298 +2544 RVLPAGLFV 0.0 None None 0 None +2545 VHTPCLVGL 1.29995014283 HTPCLVGL HYPCTVNF 25.0 72566|polyprotein|BAD73987.1|Hepatitis_C_virus_subtype_1b|31647 +2546 AGLDSYPEL 0.0 None None 0 None +2547 LVVSRSVSL 0.0 None None 0 None +2548 LVVSRSVSL 0.0 None None 0 None +2549 CSVDHRSVL 0.0 None None 0 None +2550 HRSVLQRIM 0.0 None None 0 None +2551 KMWEQEEKI 0.0 None None 0 None +2552 FGIISIIFV 0.0 None None 0 None +2553 GIISIIFVV 0.0 None None 0 None +2554 IFGIISIIF 0.0 None None 0 None +2555 RIFGIISII 0.0 None None 0 None +2556 STAARIFGI 0.0 None None 0 None +2557 TAARIFGII 0.0 None None 0 None +2558 LSVQLGPTV 0.0 None None 0 None +2559 CYTFNSIII 0.0 None None 0 None +2560 SIIIFGPFL 0.0 None None 0 None +2561 SIIIFGPFL 0.0 None None 0 None +2562 YTFNSIIIF 0.0 None None 0 None +2563 LEIQTPEAV 0.0 None None 0 None +2564 YLALAAQCL 186.219838246 ALAAQCL ALAAYCL 28.0 102636|Genome_polyprotein|P27958.3|Hepatitis_C_virus_subtype_1a|31646 +2565 YLALAAQCL 2537.30645606 ALAAQCL ALAAYCL 28.0 102636|Genome_polyprotein|P27958.3|Hepatitis_C_virus_subtype_1a|31646 +2566 AGCPAAQEL 0.0 None None 0 None +2567 RARPAGCPA 0.153281835099 RARPAG RARPRG 26.0 136865|tegument_protein|CAB06735.1|Human_alphaherpesvirus_2|10310 +2568 RPAGCPAAQ 0.0553403897978 RPAGCP RPQGLP 23.0 190533|nucleocapsid_protein|AAP49024.1|SARS_coronavirus|227859 +2569 AGVDHIITM 0.405289934875 DHIITM DHTITL 24.0 42455|Probable_Na(+)-translocating_NADH-quinone_reductase_subunit_A|O84639.1|Chlamydia_trachomatis|813 +2570 LSIAGVDHI 0.19293623707 LSIAGVD LSVAGVS 25.0 120187|E1_protein|BAA19893.1|Rubella_virus|11041 +2571 PPRYIGIPI 7.34699064743 YIGIPI YYGVPV 25.0 118|envelope_glycoprotein|ABS76372.1|Human_immunodeficiency_virus_1|11676 +2572 CMLVGDSAV 0.426158812917 CMLVGDSA CKLLPDTA 22.0 164258|nucleocapsid_protein|AAA43837.1|Hantaan_virus_76-118|11602 +2573 MLSSIKCML 0.0 None None 0 None +2574 MLSSIKCML 0.0 None None 0 None +2575 FGHTYVPAF 0.0 None None 0 None +2576 GQDFGHTYV 0.0 None None 0 None +2577 YSTPQGQDF 1.31803627544 STPQGQ TTPFGQ 21.0 180643|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 +2578 FVGLAIGTL 0.0398377334692 GLAIGTL GLSPGTL 23.0 21638|protein_F|ABV46152.2|Hepatitis_C_virus_(isolate_Japanese)|11116 +2579 IGTLSGDAL 0.0 None None 0 None +2580 NMFEISNRL 0.0 None None 0 None +2581 VDLGSTTPL 0.0 None None 0 None +2582 IPLWGSPVT 2.31085692389 PLWGSPV PLFGYPV 27.0 48321|||| +2583 FVLSMQPVV 0.235323743699 FVLSMQP YVLDLQP 25.0 76334|Protein_E7|P17387.1|Human_papillomavirus_type_31|10585 +2584 FVLSMQPVV 0.215153137096 FVLSMQP YVLDLQP 25.0 76334|Protein_E7|P17387.1|Human_papillomavirus_type_31|10585 +2585 SMQPVVFQA 0.0 None None 0 None +2586 YYDPFVLSM 0.0 None None 0 None +2587 YYDPFVLSM 0.0 None None 0 None +2588 YSHQNGASY 0.0 None None 0 None +2589 AGVLLVLAL 0.651899369479 VLLVLAL ILLVLAL 27.0 21199|Circumsporozoite_protein_precursor|P08677.2|Plasmodium_vivax_strain_Belem|31273 +2590 RFAGVLLVL 0.452826067909 FAGVLLVL FLGPLLVL 25.0 178829|envelope_protein|BAJ51675.1|HBV_genotype_D|489483 +2591 VLALILPGT 0.0 None None 0 None +2592 VLLVLALIL 0.131262388183 VLLVLAL ILLVLAL 27.0 21199|Circumsporozoite_protein_precursor|P08677.2|Plasmodium_vivax_strain_Belem|31273 +2593 RQIPAQRDL 0.327777777778 PAQRDL PASRDL 26.0 93224|core_protein|AAL31859.1|Hepatitis_B_virus|10407 +2594 SYRKSVRQI 0.0 None None 0 None +2595 CYYELNQCL 4.36257309942 CYYELNQC CYEQLNDS 26.0 110431|E7|AAD33253.1|Human_papillomavirus_type_16|333760 +2596 CYYELNQCL 19.0060606061 CYYELNQC CYEQLNDS 26.0 110431|E7|AAD33253.1|Human_papillomavirus_type_16|333760 +2597 CPLCPFLTM 0.0 None None 0 None +2598 FMNRFQCPL 0.0 None None 0 None +2599 FMNRFQCPL 0.0 None None 0 None +2600 FQCPLCPFL 0.0 None None 0 None +2601 FQCPLCPFL 0.0 None None 0 None +2602 RFQCPLCPF 0.0 None None 0 None +2603 RFQCPLCPF 0.0 None None 0 None +2604 APEPLLLSW 0.0152696940155 PLLLS PLLLS 23.0 149036|E2_protein|NP_751921.1|Hepatitis_C_virus_(isolate_H77)|63746 +2605 ASLHHHHHR 0.0 None None 0 None +2606 RPPPSQASL 0.0 None None 0 None +2607 FPDHMACDL 0.0 None None 0 None +2608 ALLGNRTAL 0.0 None None 0 None +2609 GPVSAPGLL 0.0 None None 0 None +2610 HVYRNFLNK 0.0 None None 0 None +2611 RPRGDNGYT 0.0 None None 0 None +2612 SNSESEILK 0.0 None None 0 None +2613 AVDRYVAMR 0.0 None None 0 None +2614 RYVAMRHPL 0.0580304162483 RYVAMRHPL QYIYMGQPL 23.0 185327|polyprotein|ACF49259.1|Dengue_virus_type_1_Hawaii|10000440 +2615 YVAMRHPLR 0.0 None None 0 None +2616 RAGESVWPK 0.0 None None 0 None +2617 VWPKKINNI 11.2225440638 VWPKKI VWLKKL 24.0 181035|||| +2618 VVGADGVGK 0.0 None None 0 None +2619 KTETYDNYK 0.0 None None 0 None +2620 RQLTVESDK 0.0 None None 0 None +2621 ITLTATSQK 0.0 None None 0 None +2622 HPTASTLST 0.0 None None 0 None +2623 NPSHPTAST 0.0 None None 0 None +2624 LMLLQSGYK 0.0 None None 0 None +2625 HFPIYHLLL 0.0 None None 0 None +2626 LASSFVFLY 0.0 None None 0 None +2627 LISEGQRLK 0.0 None None 0 None +2628 KPLPLVTDL 0.0 None None 0 None +2629 LPLVTDLSL 0.0 None None 0 None +2630 APIAPTFYK 0.0 None None 0 None +2631 APTFYKPKL 0.0 None None 0 None +2632 IAPTFYKPK 0.0 None None 0 None +2633 TFYKPKLLK 0.0 None None 0 None +2634 VFQHIFDLI 0.0 None None 0 None +2635 AAATAVVAF 0.0 None None 0 None +2636 ALLRATDTI 0.0 None None 0 None +2637 APFDKHCAV 0.0 None None 0 None +2638 APFLNSVSI 0.00547938159601 APFLNSVS APIPASVS 18.0 179765|cell_surface_protein_(associated_with_virulence)|NP_302372.1|Mycobacterium_leprae_TN|272631 +2639 APHGEEAHL 0.0 None None 0 None +2640 APLLPRTHL 105.804891576 APLLPRT APLPPST 23.0 179766|cell_surface_protein_(associated_with_virulence)|NP_302372.1|Mycobacterium_leprae_TN|272631 +2641 APRRHSGRV 0.0 None None 0 None +2642 APSLPSPTA 0.528755892864 PSLPSPT PTLHGPT 22.0 6591|polyprotein|AAB67037.1|Hepatitis_C_virus_(isolate_H77)|63746 +2643 APVTLRGSY 0.0 None None 0 None +2644 ATGGHHQPL 0.687294743501 GHHQPL GHEEPI 25.0 180488|polyprotein|AGO67248.1|Dengue_virus_2|11060 +2645 AVMAFDLCV 0.0 None None 0 None +2646 AVMAFDRSV 0.0 None None 0 None +2647 AYQVSVCAF 0.565327595099 AYQVSVCA AYQATVCA 34.0 13518|HCV-1|AAA45676.1|Hepatitis_C_virus_genotype_1|41856 +2648 CTTPVTVEI 0.0 None None 0 None +2649 CYYYFLCLL 0.0 None None 0 None +2650 DTPRHRLLV 0.0 None None 0 None +2651 EAQQSSHCL 0.0 None None 0 None +2652 EPRITRSFV 0.0 None None 0 None +2653 ETGLALKYL 0.0 None None 0 None +2654 FSFQVDSPV 0.0 None None 0 None +2655 FSILSTALL 0.0453532771775 FSILSTALL FSIFLLALL 23.0 57894|polyprotein|BAD73987.1|Hepatitis_C_virus_subtype_1b|31647 +2656 GLRKTNMSL 0.0 None None 0 None +2657 GPNAMRYSL 0.0 None None 0 None +2658 GPRNCIGQA 0.127721163409 GPRNCI DPRRCL 23.0 150556|polyprotein|AGW21594.1|Dengue_virus_1|11053 +2659 HMSACHHSI 0.0 None None 0 None +2660 HPNAHSNST 0.0 None None 0 None +2661 HPWTTDMPA 0.0 None None 0 None +2662 HSNSTSFIF 0.0 None None 0 None +2663 HSNSTSFIF 0.0 None None 0 None +2664 HTWQMRNTV 0.0 None None 0 None +2665 HTWQMRNTV 0.0 None None 0 None +2666 IFSLGRHTW 0.0 None None 0 None +2667 INALIIFIF 0.0 None None 0 None +2668 IPHLLKLAC 0.0 None None 0 None +2669 ISASVCIQV 0.0 None None 0 None +2670 ITSTVMLEV 0.0 None None 0 None +2671 KAFNCSSFV 0.0 None None 0 None +2672 KAFSQSSNL 0.0 None None 0 None +2673 KLFSILSTA 0.0 None None 0 None +2674 KLWATAEAL 0.0 None None 0 None +2675 KTHRIVRRL 0.0 None None 0 None +2676 KTHRIVRRL 0.0 None None 0 None +2677 KTLRKSLPA 0.0 None None 0 None +2678 KTLRKSLPA 0.0 None None 0 None +2679 KYIFNNSII 0.987149197996 KYIFNNSII KYFYCNSLF 24.0 141323|multifunctional_expression_regulator|NP_044657.1|Human_alphaherpesvirus_1|10298 +2680 KYTSAAILV 0.0 None None 0 None +2681 LALSVTEMV 0.0 None None 0 None +2682 LHSPMYFFL 0.0 None None 0 None +2683 LHTPVYFLL 0.0 None None 0 None +2684 LLVSLTVTF 0.094208760953 LLVSLTV LLVCLTV 24.0 40264|Cytochrome_P450_2A6|P11509.3|Homo_sapiens|9606 +2685 LPGGVGRTL 0.0104130689254 LPGGVGRTL VPGWSRRTL 22.0 141461|ubiquitin_E3_ligase_ICP0|NP_044601.1|Human_alphaherpesvirus_1|10298 +2686 LPSDDRGSL 0.206878016438 DDRGSL DSRGSL 25.0 55709|Genome_polyprotein|P27958.3|Hepatitis_C_virus_subtype_1a|31646 +2687 LSVADQEKV 0.0 None None 0 None +2688 LWGKHQFIL 0.892559226889 LWGKHQFI LWGYLQYV 27.0 42094|telomer_length_regulation_protein_TEL1|EDV12172.1|Saccharomyces_cerevisiae|4932 +2689 MAFDLCVAI 0.0486655905336 FDLCV YDLCI 25.0 112503|E6_protein|ACV53993.1|Human_papillomavirus_type_35|10587 +2690 MAFDRSVAI 0.0 None None 0 None +2691 MAFDRSVAI 0.0 None None 0 None +2692 MIISASVCI 0.0 None None 0 None +2693 MIISASVCI 0.0 None None 0 None +2694 MLDLLTNTL 0.0 None None 0 None +2695 MTNGLCIWL 0.0 None None 0 None +2696 MVNATACAV 0.0 None None 0 None +2697 NAFQEARRL 0.0 None None 0 None +2698 PSAPKPSTL 6.16092555862 SAPKPST SAPLPSN 24.0 88377|IE62|AAP32859.1|Human_alphaherpesvirus_3|10335 +2699 QALRAGLAL 0.0 None None 0 None +2700 QALRAGLAL 0.0 None None 0 None +2701 QAVEFCQRV 0.0 None None 0 None +2702 QILVKICTI 0.0 None None 0 None +2703 QLHFIFHIL 0.0 None None 0 None +2704 QLWGKHQFI 9.62632414914 LWGKHQFI LWGYLQYV 27.0 42094|telomer_length_regulation_protein_TEL1|EDV12172.1|Saccharomyces_cerevisiae|4932 +2705 QPWEHVNAF 0.0 None None 0 None +2706 QQQMASRPF 0.0 None None 0 None +2707 QTSMSQSQV 0.0 None None 0 None +2708 RIIKLLVSL 0.0 None None 0 None +2709 RLALSTFEW 355.619732468 LSTFEW LSTTEW 27.0 37830|polyprotein|BAB18806.1|Hepatitis_C_virus_subtype_1b|31647 +2710 RLHSPMYFF 0.0 None None 0 None +2711 RLHSPMYFF 0.0 None None 0 None +2712 RLHTPVYFL 0.0 None None 0 None +2713 RSFTEENHM 0.0 None None 0 None +2714 RSFVPHLEI 0.0 None None 0 None +2715 RSFVPHLEI 0.0 None None 0 None +2716 RSVAICKPL 0.0 None None 0 None +2717 RVVLINNNL 0.0 None None 0 None +2718 SASSQSSSI 0.0 None None 0 None +2719 SASVCIQVV 0.0 None None 0 None +2720 SIIQDFFAW 0.0 None None 0 None +2721 SINALIIFI 0.0 None None 0 None +2722 SMSQSQVAL 0.0 None None 0 None +2723 SPAQAPIPY 0.108147812318 AQAPIP AQAPPP 24.0 149096|polyprotein|BAB18801.1|Hepatitis_C_virus|11103 +2724 SPGGWRSGW 83.0885140233 GGWRSGW GFWQEGW 32.0 75674|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 +2725 SSEQSIFVV 0.0 None None 0 None +2726 SSIPENEAI 0.0 None None 0 None +2727 STVMLEVPL 0.0 None None 0 None +2728 STVMLEVPL 0.0 None None 0 None +2729 SYSSLDEDF 0.0115200700311 YSSLDED YSRADEE 22.0 12585|ESAT-6-like_protein_esxB|P0A566.2|Mycobacterium_tuberculosis|1773 +2730 TPRHRLLVL 0.0 None None 0 None +2731 TSMYNEILI 0.0 None None 0 None +2732 TSVPVTTAV 0.0 None None 0 None +2733 VPADSTQTL 0.0 None None 0 None +2734 VSIETHLLF 0.0 None None 0 None +2735 VSIETHLLF 0.0 None None 0 None +2736 VSLTVTFVL 0.0 None None 0 None +2737 VTTAVSTFV 0.0 None None 0 None +2738 VTTGLMGAV 0.0 None None 0 None +2739 YSSLDEDFL 0.0 None None 0 None +2740 YVQKRSSQI 0.0 None None 0 None +2741 YYFLCLLL* 0.0 None None 0 None +2742 YYYFLCLLL 0.0 None None 0 None +2743 ASLDVTLRL 0.0 None None 0 None +2744 ISSHLSTLV 1.22721158737 SHLSTLV SHYFTLV 22.0 98466|Trans-sialidase|SRC7915|Trypanosoma_cruzi|5693 +2745 LSTLVDFAI 0.0 None None 0 None +2746 KTSVGSTKY 0.0 None None 0 None +2747 HPCERSDEV 0.0 None None 0 None +2748 ITVEEQHRI 0.0 None None 0 None +2749 ITVEEQHRI 0.0 None None 0 None +2750 MTAVQTLHL 0.0 None None 0 None +2751 PAMTAVQTL 0.0 None None 0 None +2752 RQLPAMTAV 0.0 None None 0 None +2753 ETVFTRSSW 0.0 None None 0 None +2754 FTRSSWDWI 0.0 None None 0 None +2755 VFTRSSWDW 0.0 None None 0 None +2756 EPPPPPSPL 0.0101907339737 PPPSPL PPCKPL 22.0 96366|polyprotein|ABR25251.1|Hepatitis_C_virus|11103 +2757 QTTQLSLNF 0.0 None None 0 None +2758 GAMDGATYI 0.0 None None 0 None +2759 MAFVKSVWL 0.0 None None 0 None +2760 CAVRRAAQV 0.0 None None 0 None +2761 QAVAQAVNW 0.0 None None 0 None +2762 NPKTWNTMV 0.0 None None 0 None +2763 QLYMNPKTW 4.12392711167 QLYMNPKTW RLYQNPTTY 31.0 135263|hemagglutinin|ACX31970.1|Influenza_A_virus_(A/Bar-headed_Goose/Qinghai/61/05(H5N1))|336238 +2764 RQVGFCVQW 0.0 None None 0 None +2765 KMLLAPGRF 1.4325134436 LLAPG LLAPG 25.0 59240|HCV-1|AAA45676.1|Hepatitis_C_virus_genotype_1|41856 +2766 MLLAPGRFI 0.588309359247 LLAPG LLAPG 25.0 59240|HCV-1|AAA45676.1|Hepatitis_C_virus_genotype_1|41856 +2767 FTMPEDEYM 0.0 None None 0 None +2768 FTMPEDEYM 0.0 None None 0 None +2769 MPEDEYMVY 0.0 None None 0 None +2770 IAWPADRTA 0.0 None None 0 None +2771 QALIRPTTF 0.514471687749 LIRPTTF LLRPTTL 28.0 13165|trans-sialidase,_putative|EAN81972.1|Trypanosoma_cruzi|5693 +2772 FPEYDGVDH 0.0 None None 0 None +2773 EIAEIEYSI 0.0 None None 0 None +2774 FVVSACNAT 0.0 None None 0 None +2775 WITPAQREY 2.29081841307 TPAQREY TPTLHEY 22.0 110940|Protein_E7|P03129.1|Human_papillomavirus_type_16|333760 +2776 EPVWGLEAI 0.0 None None 0 None +2777 RLSWQASSL 0.0 None None 0 None +2778 KIKELAAEF 0.0 None None 0 None +2779 VPILQSTPV 0.0416654367885 VPILQSTP LPIRYQTP 21.0 180647|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 +2780 APRGFLTNY 0.0 None None 0 None +2781 RAAEQRRAY 0.0 None None 0 None +2782 KSASWITWI 0.34874341875 SWITW QWLTW 29.0 70634|Non-capsid_protein_NS-1|P07298.1|Human_parvovirus_B19|10798 +2783 TPWSFTGTV 0.0459224896119 PWSFTG QWNFAG 24.0 42797|6_kDa_early_secretory_antigenic_target|P0A564.2|Mycobacterium_tuberculosis|1773 +2784 GPLADATPL 0.0 None None 0 None +2785 LAGERRFAF 0.0 None None 0 None +2786 IAASAMCVF 0.0 None None 0 None +2787 SSYGRNHYI 3.39831238883 GRNHYI GRSHFL 25.0 8554|Genome_polyprotein|P08617.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 +2788 IIHTGARPY 0.0 None None 0 None +2789 DTATGNCLR 0.0 None None 0 None +2790 GPYENCSVF 0.0 None None 0 None +2791 ETYQQALGK 0.102756058551 ETYQQALGK QVYQDWLGR 23.0 23288|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 +2792 YQQALGKRF 0.0447142296507 YQQALGK YQDWLGR 21.0 23288|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 +2793 YQQALGKRF 0.165670773671 YQQALGK YQDWLGR 21.0 23288|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 +2794 FAIHKIKQF 0.0 None None 0 None +2795 GYTVNIPTI 0.0 None None 0 None +2796 HSPSVASMK 0.0 None None 0 None +2797 YTDCHASNL 0.160144923269 DCHASN DCHAQD 28.0 6094|Genome_polyprotein|Q81495.3|Hepatitis_C_virus_(isolate_HCV-K3a/650)|356416 +2798 TYSSPTPNM 0.0616536351308 TYSSPT TYTFPT 23.0 232153|rhoptry_protein_18|CAJ27113.1|Toxoplasma_gondii_type_I|1209525 +2799 DAIPFGNVP 0.0 None None 0 None +2800 IPFGNVPVL 0.0 None None 0 None +2801 NYFGVQDAI 0.0 None None 0 None +2802 ETLGRGNPM 0.0 None None 0 None +2803 MALQLFLQI 0.0 None None 0 None +2804 MALQLFLQI 0.0 None None 0 None +2805 MALQLFLQI 0.0 None None 0 None +2806 KVHSAVITI 0.0 None None 0 None +2807 QAGEYSRVV 0.0 None None 0 None +2808 RVVDCYLKV 0.0 None None 0 None +2809 WQRPTLESI 0.0 None None 0 None +2810 WQRPTLESI 0.0 None None 0 None +2811 VAQLGFQPL 0.0 None None 0 None +2812 EAINCLNVA 0.0 None None 0 None +2813 VAIDIYTDM 0.0 None None 0 None +2814 HFLHSWTNL 0.349366438751 LHSWTN LHQWIN 28.0 103322|polyprotein|BAB18806.1|Hepatitis_C_virus|11103 +2815 TFKHLVHFL 0.0 None None 0 None +2816 YTFKHLVHF 0.00127547167216 YTFKHLVHF YKFMGRSHF 19.0 8554|Genome_polyprotein|P08617.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 +2817 YTFKHLVHF 0.00173099726936 YTFKHLVHF YKFMGRSHF 19.0 8554|Genome_polyprotein|P08617.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 +2818 IIMSRNAYV 0.0 None None 0 None +2819 LRYPIIMSR 0.0 None None 0 None +2820 MSRNAYVPM 0.0 None None 0 None +2821 NAPALLTPR 0.0 None None 0 None +2822 RAGSAGGTV 0.0 None None 0 None +2823 EAFTLKATV 6.35897435897 FTLKATV FTLVATV 26.0 98640|trans-sialidase,_putative|EAN80840.1|Trypanosoma_cruzi|5693 +2824 YSVIRGEAF 0.0 None None 0 None +2825 DIYSMPEGK 0.0 None None 0 None +2826 IYSMPEGKL 0.0557903921081 YSMPEGKL YSMCTGKF 23.0 150456|polyprotein|AGO67248.1|Dengue_virus_2|11060 +2827 SMPEGKLHV 0.0224344124258 MPEGKL LPQGQL 22.0 13701|Trans-activator_protein_BZLF1|P03206.2|Human_gammaherpesvirus_4|10376 +2828 YSMPEGKLH 0.292799376299 YSMPEGKL YSMCTGKF 23.0 150456|polyprotein|AGO67248.1|Dengue_virus_2|11060 +2829 FFFLCVCVF 0.100381408019 FFFLCVCV LLILCLCL 24.0 49831|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 +2830 FFFLCVCVF 0.0684531631414 FFFLCVCV LLILCLCL 24.0 49831|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 +2831 FFLCVCVFV 0.673124000294 FFLCVCV LILCLCL 24.0 49831|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 +2832 FFLCVCVFV 0.243568175313 FFLCVCV LILCLCL 24.0 49831|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 +2833 HLLQRYNEF 0.366998782491 HLLQRYNEF NLLQRANEL 28.0 154980|tegument_protein|CAB06735.1|Human_alphaherpesvirus_2|10310 +2834 RAEERRRHL 2.38489063295 AEERRRHL PEEKQRHL 30.0 110394|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 +2835 ITTTGQKLR 0.0 None None 0 None +2836 IMALAVLII 0.0 None None 0 None +2837 TALVVVSIM 0.0 None None 0 None +2838 DVLPYDAFV 0.0894142186526 VLPYDAFV VYPYDEFV 32.0 141423|envelope_glycoprotein_B|NP_044629.1|Human_alphaherpesvirus_1|10298 +2839 LTLATFSRI 0.0 None None 0 None +2840 VLTLATFSR 0.0 None None 0 None +2841 MNQRPILTI 0.0 None None 0 None +2842 NQRPILTII 0.0 None None 0 None +2843 FNVNAPDLY 0.0 None None 0 None +2844 NVNAPDLYI 0.0 None None 0 None +2845 RFNVNAPDL 0.0 None None 0 None +2846 FHWRVNFIR 0.0 None None 0 None +2847 IFHWRVNFI 0.0 None None 0 None +2848 KIFHWRVNF 0.0 None None 0 None +2849 LHDTTTRSV 0.0 None None 0 None +2850 LHNNTTRSV 0.0 None None 0 None +2851 TTTRSVHAK 0.0 None None 0 None +2852 HFKAPKISM 0.0 None None 0 None +2853 GTSSTSCSW 0.0 None None 0 None +2854 GVRAQGCYM 0.0 None None 0 None +2855 GVRAQGCYM 0.0 None None 0 None +2856 RAQGCYMDI 0.0 None None 0 None +2857 VAEKGTSKL 0.0 None None 0 None +2858 EAFSVSPEW 0.0 None None 0 None +2859 FSVSPEWAV 0.00283478309185 FSVSPEWA FSMVGNWA 22.0 149052|E1_protein|NP_751920.1|Hepatitis_C_virus_(isolate_H77)|63746 +2860 LTRPVHGAA 3.12682962682 LTRPVHGA LKEPVHGV 28.0 27125|gag-pol_fusion_polyprotein|AAN73817.1|Human_immunodeficiency_virus_1|11676 +2861 MARTAPASG 0.0 None None 0 None +2862 AHQYFAQLL 0.0968441616774 AHQYFAQLL GHQAAMQML 19.0 101673|gag_protein|ABO73990.1|Human_immunodeficiency_virus_1|11676 +2863 AHQYFAQLL 0.100003052772 AHQYFAQLL GHQAAMQML 19.0 101673|gag_protein|ABO73990.1|Human_immunodeficiency_virus_1|11676 +2864 HQYFAQLLA 0.00076046422012 HQYFAQLL HQAAMQML 19.0 101673|gag_protein|ABO73990.1|Human_immunodeficiency_virus_1|11676 +2865 LALQRQRTY 0.0 None None 0 None +2866 LALQRQRTY 0.0 None None 0 None +2867 ATVCRDPGV 0.0 None None 0 None +2868 VCRDPGVPM 0.0 None None 0 None +2869 DAPLFNTIV 0.84762355921 PLFNTIV SLFNTVV 28.0 180255|gag_protein|AAT90688.1|Human_immunodeficiency_virus_1|11676 +2870 VDAPLFNTI 0.0 None None 0 None +2871 LSETISPLW 0.0 None None 0 None +2872 WPQRPKSQV 0.0 None None 0 None +2873 MVLPGGVDI 0.0 None None 0 None +2874 FELEWLLYT 0.0 None None 0 None +2875 HSHTTGINL 0.0 None None 0 None +2876 HSHTTGINL 0.0 None None 0 None +2877 SHTTGINLV 0.0 None None 0 None +2878 STHSHTTGI 0.0 None None 0 None +2879 STHSHTTGI 0.0 None None 0 None +2880 STHSHTTGI 0.0 None None 0 None +2881 LTLVGVVVY 0.0 None None 0 None +2882 LTLVGVVVY 0.0 None None 0 None +2883 SEYFLGLTL 0.0310160688315 SEYFLGLTL KEYTFPITL 19.0 143705|Genome_polyprotein|P08617.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 +2884 EAHSFEEEM 0.0 None None 0 None +2885 SSLQEAHSF 0.0 None None 0 None +2886 SHTTLSLDL 0.0 None None 0 None +2887 KLREFFKCA 0.0 None None 0 None +2888 VAYCPAYVV 0.546466079592 AYCPAY ANCPTY 25.0 40253|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 +2889 VAYCPAYVV 0.627529983197 AYCPAY ANCPTY 25.0 40253|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 +2890 VLIPDVVAY 0.0 None None 0 None +2891 VVAYCPAYV 0.0174448489537 AYCPAY ANCPTY 25.0 40253|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 +2892 YLVLIPDVV 0.123689109937 LVLIPDVV LVLNPSVA 20.0 46755|HCV-1|AAA45676.1|Hepatitis_C_virus_genotype_1|41856 +2893 FGIGVENFI 0.0120582173391 FGIGVENFI LGYGFVNYI 21.0 36357|ELAV-like_protein_4_(Paraneoplastic_encephalomyelitis_antigen_HuD)_(Hu-antigen_D)|P26378.1|Homo_sapiens|9606 +2894 IGVENFITL 0.0 None None 0 None +2895 ITLVVFGLI 0.207698907722 VVFGLI VLFGLL 23.0 101380|BNLF2a|YP_401721.1|Human_herpesvirus_4_type_1|36352 +2896 KVARSKPYA 0.0 None None 0 None +2897 VARSKPYAM 0.0 None None 0 None +2898 KFRCDAGLG 0.0 None None 0 None +2899 GSRESNMSR 0.0 None None 0 None +2900 MSRKKKAVK 0.0 None None 0 None +2901 RKKKAVKEK 0.0 None None 0 None +2902 QSNTWSLSK 8.97866690799 QSNTWSL QQNWWTL 25.0 74886|latent_membrane_protein_1|AAS99606.1|Human_gammaherpesvirus_4|10376 +2903 YQQSNTWSL 4.15563295911 YQQSNTWSL YLQQNWWTL 30.0 74886|latent_membrane_protein_1|AAS99606.1|Human_gammaherpesvirus_4|10376 +2904 YQQSNTWSL 2.43549839174 YQQSNTWSL YLQQNWWTL 30.0 74886|latent_membrane_protein_1|AAS99606.1|Human_gammaherpesvirus_4|10376 +2905 YKLVVVGAV 16.9067084102 KLVVVG KLVVLG 24.0 32238|polyprotein_[Hepatitis_C_virus_subtype_1a]|ABV46251.2|Hepatitis_C_virus_(isolate_H77)|63746 +2906 AVRYSRGCL 0.0 None None 0 None +2907 VRYSRGCLT 0.0 None None 0 None +2908 YSRGCLTVM 0.0 None None 0 None +2909 YSRGCLTVM 0.0 None None 0 None +2910 YSRGCLTVM 0.0 None None 0 None +2911 VQYASGNRW 0.0 None None 0 None +2912 YASGNRWTF 1.46233842452 ASGNRWTF ATGITYTF 20.0 232153|rhoptry_protein_18|CAJ27113.1|Toxoplasma_gondii_type_I|1209525 +2913 YASGNRWTF 0.0162902231496 ASGNRWTF ATGITYTF 20.0 232153|rhoptry_protein_18|CAJ27113.1|Toxoplasma_gondii_type_I|1209525 +2914 AVRNAITST 0.0 None None 0 None +2915 NAITSTSVI 0.0 None None 0 None +2916 TSIAVRNAI 0.0 None None 0 None +2917 VVLPTEAPI 0.0 None None 0 None +2918 VVLPTEAPI 0.0 None None 0 None +2919 LVATSPSPV 0.0 None None 0 None +2920 LSENAVLIL 0.0 None None 0 None +2921 LSENAVLIL 0.0 None None 0 None +2922 MALSENAVL 0.00068461137038 ALSENAVL ALSLAAVL 19.0 2884|cysteine_proteinase_cruzipain_(EC_3.4.22.-)_-_Trypanosoma_cruzi|A45629|Trypanosoma_cruzi|5693 +2923 MALSENAVL 0.00103322489989 ALSENAVL ALSLAAVL 19.0 2884|cysteine_proteinase_cruzipain_(EC_3.4.22.-)_-_Trypanosoma_cruzi|A45629|Trypanosoma_cruzi|5693 +2924 SSSGWRKSF 0.0 None None 0 None +2925 FSEASQLDF 0.0 None None 0 None +2926 FSEASQLDF 0.0 None None 0 None +2927 RTKQFSEAS 0.0 None None 0 None +2928 RGFSRQSVL 0.0 None None 0 None +2929 LTRSTLSSV 0.0 None None 0 None +2930 LTRSTLSSV 0.0 None None 0 None +2931 RADHDLGRL 0.0 None None 0 None +2932 YRADHDLGR 0.0 None None 0 None +2933 ALRVNPVLA 0.0497971668364 LRVNPV IRVSPV 23.0 56198|glycoprotein_gp35/37|AAC59622.1|Human_gammaherpesvirus_8|37296 +2934 RVNPVLAEL 0.0 None None 0 None +2935 RVNPVLAEL 0.0 None None 0 None +2936 SALRVNPVL 0.109248886427 SALRVNPV TRIRVSPV 23.0 56198|glycoprotein_gp35/37|AAC59622.1|Human_gammaherpesvirus_8|37296 +2937 SSALRVNPV 3.15088690804 SSALRVNPV TTRIRVSPV 24.0 56198|glycoprotein_gp35/37|AAC59622.1|Human_gammaherpesvirus_8|37296 +2938 LLYRRTKAF 0.0 None None 0 None +2939 LLYRRTKAF 0.0 None None 0 None +2940 LYRRTKAFI 0.0 None None 0 None +2941 RTKAFIDYE 0.0 None None 0 None +2942 ATSYELHKF 0.0 None None 0 None +2943 RTQILATSY 0.0 None None 0 None +2944 TSYELHKFY 0.0 None None 0 None +2945 TSYELHKFY 0.0 None None 0 None +2946 IQKITSPNI 0.0028984223105 IQKITSPNI IEKPVAPSV 20.0 419002|PPE_family_protein_PPE68|KAM81677.1|Mycobacterium_tuberculosis_H37Ra|419947 +2947 TSVKPSQPK 0.0 None None 0 None +2948 AIFASMAHA 0.0 None None 0 None +2949 ASMAHAMQK 0.0 None None 0 None +2950 MAHAMQKYL 0.0 None None 0 None +2951 MAHAMQKYL 0.0 None None 0 None +2952 MAHAMQKYL 0.0 None None 0 None +2953 SMAHAMQKY 0.0 None None 0 None +2954 RQRLSAPPS 0.0 None None 0 None +2955 TAHGLSPTA 1.66455725447 GLSPTA GLSPTV 26.0 21139|envelope_protein|BAF48755.1|Hepatitis_B_virus|10407 +2956 GLIEGYGGW 0.0 None None 0 None +2957 QVLGLGGHI 0.0 None None 0 None +2958 AAFNPTRDF 0.0 None None 0 None +2959 AAFNPTRDF 0.0 None None 0 None +2960 KGFVCKAHF 0.0 None None 0 None +2961 SRRACSSEL 0.0 None None 0 None +2962 SPKLKMPEM 0.0 None None 0 None +2963 SNKEKWISL 0.0 None None 0 None +2964 KRWESEHIL 0.0 None None 0 None +2965 LHNEIKTLL 0.000207822443766 LHNEIKTLL IHSMNSTIL 17.0 109332|L1_protein|ACG75893.1|Human_papillomavirus_type_16|333760 +2966 FSDKMGTLT 0.0 None None 0 None +2967 LAAERKAAL 0.0 None None 0 None +2968 TPRRSRWQL 0.0 None None 0 None +2969 MNCIRQASV 0.0 None None 0 None +2970 DQRCRLCPA 0.467544317151 RCRLC RCYLC 25.0 145860|Protein_E6|P04019.1|Human_papillomavirus_type_11|10580 +2971 HTTRSLFQY 0.0 None None 0 None +2972 PHCPQPLVY 1.64017196847 HCPQPLVY HGPTPLLY 30.0 6591|polyprotein|AAB67037.1|Hepatitis_C_virus_(isolate_H77)|63746 +2973 SLEGRIWAL 1.97995031712 EGRIWAL DGRFWEL 27.0 186219|polyprotein|AGK36298.1|Dengue_virus_2|11060 +2974 YTDFLLCAS 0.0 None None 0 None +2975 VVGARGVGK 0.0 None None 0 None +2976 RGRKNRSSV 0.0 None None 0 None +2977 FEKMHQMDL 0.0 None None 0 None +2978 QVFEKMHQM 0.0 None None 0 None +2979 ARWPFGNTM 0.0 None None 0 None +2980 GALKKALAK 0.0 None None 0 None +2981 RLIAISWPL 0.00137441037811 RLIAISW RLLTKPW 18.0 161186|Nonstructural_protein_NS5|NP_739590.2|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 +2982 WPLRYVTVM 0.0 None None 0 None +2983 HILGNFLTK 0.0 None None 0 None +2984 IRCGYPTHI 0.0 None None 0 None +2985 EAGPRKGPL 2.46659552716 PRKGP PRRGP 27.0 181035|||| +2986 RLEEAGPRK 0.0 None None 0 None +2987 KLPEMKLPK 5.01765917237e-05 LPEMKLPK LPSDFLPS 16.0 16836|precore/core_protein_[Hepatitis_B_virus]|AAR03815.1|Hepatitis_B_virus|10407 +2988 MKLPKVPEM 0.0 None None 0 None +2989 DRQDQSSHY 0.0 None None 0 None +2990 SHYGQPDRQ 0.0 None None 0 None +2991 GIMPGHIQK 0.00230778161286 MPGHIQK MPSVIEK 20.0 180668|polyprotein|AGO67248.1|Dengue_virus_2|11060 +2992 IMPGHIQKK 0.0020605192972 MPGHIQK MPSVIEK 20.0 180668|polyprotein|AGO67248.1|Dengue_virus_2|11060 +2993 STMRESSPK 0.0 None None 0 None +2994 FPLFAIWPM 0.0 None None 0 None +2995 PTDPMLGLA 7.81973026172 PTDPML PDDPVL 24.0 141462|tegument_protein_UL21|NP_044622.1|Human_alphaherpesvirus_1|10298 +2996 EARSRATLA 0.0 None None 0 None +2997 FHEARSRAT 0.0 None None 0 None +2998 FSIFSTLTK 0.0 None None 0 None +2999 LPDRLTLEF 0.0 None None 0 None +3000 LPDRLTLEF 0.0 None None 0 None +3001 FSDHQSFVV 0.0794686146814 FSDHQ FPDHQ 24.0 190466|large_surface_antigen|CAL29876.1|Hepatitis_B_virus|10407 +3002 LLSQVQFPY 0.0 None None 0 None +3003 GELSVDVSF 0.0 None None 0 None +3004 LSVDVSFFF 0.0 None None 0 None +3005 LSVDVSFFF 0.0 None None 0 None +3006 SVDVSFFFK 1.57692307692 SVDVSFFFK AVDLSHFLK 26.0 5295|nef_protein|ACR27174.1|Human_immunodeficiency_virus_1|11676 +3007 VVDQGNIGK 0.0 None None 0 None +3008 MVFHKHGEK 0.0874586889695 VFHKHGEK VYHGAGSK 22.0 72039|polyprotein|CAB53095.1|Hepatitis_C_virus_subtype_1b|31647 +3009 NAYTMVFHK 0.0 None None 0 None +3010 MESNNMPFL 0.0 None None 0 None +3011 VMESNNMPF 0.0 None None 0 None +3012 IPVPVGATA 0.0 None None 0 None +3013 VPVGATASF 1.51661571138 VPVGATASF MPVGGQSSF 28.0 42342|Antigen_85-B_precursor_(85B)_(Extracellular_alpha-antigen)_(Antigen_85_complex_B)_(Ag85B)_(Mycolyl_transferase_85B)_(Fibronectin-binding_protein_B)_(30_kDa_extracellular_protein)|P31952|Mycobacterium_tuberculosis|1773 +3014 SLDLSQTNL 0.0 None None 0 None +3015 TETSSSMPG 0.0 None None 0 None +3016 HTDPHLCDF 0.0 None None 0 None +3017 SLGFKLLLR 0.884622618909 GFKLLLR NFKSLLR 22.0 52578|liver_stage_antigen-1|CAA82974.1|Plasmodium_falciparum|5833 +3018 HEQCDSSSL 0.0 None None 0 None +3019 AEKSQGPVL 0.0 None None 0 None +3020 RLLSTQAEK 0.0 None None 0 None +3021 LSDIGGLLL 0.0 None None 0 None +3022 LYLYVLSDI 0.0 None None 0 None +3023 SELSSDINL 0.0 None None 0 None +3024 MPHSQYLSA 0.0 None None 0 None +3025 EEAFVPILY 9.10107986896 AFVPILY AYVSVLY 24.0 141228|tegument_protein_VP11/12|NP_044648.1|Human_alphaherpesvirus_1|10298 +3026 QVTVSFTEM 0.0733616966506 VSFTEM VAFTEI 22.0 112697|Protein_E6|P26554.1|Human_papillomavirus_type_51|10595 +3027 TVSFTEMLK 0.0149885083017 VSFTEM VAFTEI 22.0 112697|Protein_E6|P26554.1|Human_papillomavirus_type_51|10595 +3028 VSFTEMLKK 0.0122306227742 VSFTEM VAFTEI 22.0 112697|Protein_E6|P26554.1|Human_papillomavirus_type_51|10595 +3029 LGYRCRFNK 0.0 None None 0 None +3030 LPDLFTPPL 0.625085327902 LFTPP FFTPP 25.0 10587|viral_polyprotein|AAA42941.1|Dengue_virus_2_Thailand/NGS-C/1944|11065 +3031 HTDGDTLLQ 0.00713135459058 HTDGDTLL STDSTTIL 21.0 108148|polyprotein|AAF65953.1|Hepatitis_C_virus|11103 +3032 ILAKHKSLF 0.0 None None 0 None +3033 KLTILAKHK 0.0 None None 0 None +3034 AQTHEPRQW 1.87002493797 AQTHEPRQW AVRHFPRIW 26.0 187106|Vpr_protein|BAA93983.1|Human_immunodeficiency_virus_1|11676 +3035 EAVAGHIPA 0.0 None None 0 None +3036 VAGHIPAIF 1.273 VAGHIPAI LMGYIPAV 26.0 9199|E1_protein|ABB77003.1|Hepatitis_C_virus|11103 +3037 VADLLAFTH 0.0 None None 0 None +3038 VVGAVGVGK 0.0 None None 0 None +3039 KLTSYKCKL 0.0 None None 0 None +3040 WLRVGNGAL 0.0 None None 0 None +3041 SLQLSAHRL 0.0 None None 0 None +3042 IVVISIWEI 0.0 None None 0 None +3043 SIWEIVGQA 0.228841933641 SIWEIVG STWVLVG 24.0 62004|Genome_polyprotein|P27958.3|Hepatitis_C_virus_subtype_1a|31646 +3044 YLKRGYLTL 0.0 None None 0 None +3045 MLHVDRHTL 0.0 None None 0 None +3046 VLERGQFDY 0.0 None None 0 None +3047 AALSIDHWV 0.0 None None 0 None +3048 SIDHWVAVV 0.0 None None 0 None +3049 ATAAAAAAL 0.0 None None 0 None +3050 GPATAAAAA 0.0950864586136 PATAAA PITAAA 23.0 183819|polyprotein|AGO67248.1|Dengue_virus_2|11060 +3051 LLLDTPTQL 0.0 None None 0 None +3052 HLYDTLGST 0.827970867806 HLYDTLGS RLYKTLGQ 25.0 169658|major_paraflagellar_rod_protein|AAA30221.1|Trypanosoma_cruzi|5693 +3053 LPLHLYDTL 7.53132395702 LHLYD LHLYS 23.0 190568|polymerase|AAD16253.1|Hepatitis_B_virus|10407 +3054 EEYTVWIQL 0.0 None None 0 None +3055 WEEEYTVWI 2.67996539102 WEEEYTVW WPKTHTLW 29.0 184702|non-structural_protein_1|AGM49312.1|Dengue_virus|12637 +3056 TPEDNRQPL 0.610171894935 TPEDNR TPQDNQ 27.0 150649|polyprotein|AGW21594.1|Dengue_virus_1|11053 +3057 LPEQQEGQL 0.0 None None 0 None +3058 KPMQVKTPC 0.0 None None 0 None +3059 NLQNSPLEI 0.0 None None 0 None +3060 VPNLQNSPL 0.00025151259785 VPNLQNSP VPTDPNPP 18.0 70491|envelope_glycoprotein|AAC28452.1|Human_immunodeficiency_virus_1|11676 +3061 NELYFAHVL 0.0 None None 0 None +3062 YFAHVLFSA 0.0 None None 0 None +3063 AVTRPFISL 0.0 None None 0 None +3064 FLWPLRVLS 1.97746781824 WPLRVL WMIRIL 23.0 185817|envelope_protein|AGW23590.1|Dengue_virus_4|11070 +3065 ISMKFLWPL 0.0 None None 0 None +3066 WPLRVLSQF 0.0510061316391 WPLRVLSQF WMIRILIGF 25.0 185817|envelope_protein|AGW23590.1|Dengue_virus_4|11070 +3067 REIVWEQGL 0.270327477112 VWEQG LWENG 23.0 36717|nonstructural_protein_4B|YP_001527886.1|West_Nile_virus_NY-99|10000971 +3068 TLAEKRPFM 0.000817554998277 TLAEKRPFM TLARGFPFV 22.0 64727|polyprotein_precursor|NP_041724.2|West_Nile_virus|11082 +3069 LPGHLSRAL 0.0 None None 0 None +3070 SLPGHLSRA 0.0 None None 0 None +3071 SPSSLPGHL 0.031617248785 SPSSLPGH TPDSTPCH 23.0 53041|phosphorylated_matrix_protein_(pp65)|AAA45996.1|Human_betaherpesvirus_5|10359 +3072 ALNNMFCQL 0.0 None None 0 None +3073 GPRRGSSPQ 0.0 None None 0 None +3074 SPQGAAGAA 0.0 None None 0 None +3075 KAFSQSAYL 0.0 None None 0 None +3076 FADHTVVTI 0.0 None None 0 None +3077 FADHTVVTI 0.0 None None 0 None +3078 MTAFADHTV 0.0 None None 0 None +3079 TAFADHTVV 0.0 None None 0 None +3080 GLSPRTSRH 0.140261315451 LSPRTSRH LKPGESRH 25.0 17278|Genome_polyprotein|P06441.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 +3081 LSPRTSRHI 1.36025830505 LSPRTSRH LKPGESRH 25.0 17278|Genome_polyprotein|P06441.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 +3082 RTSRHILER 0.0 None None 0 None +3083 SVQACGWRK 2.18470381235 QACGW EGCGW 28.0 75435|largest_ORF|AAB02128.1|Hepatitis_C_virus|11103 +3084 CLLSPSYYH 0.0 None None 0 None +3085 LASDRFNHI 0.0 None None 0 None +3086 QVASSPAGK 0.0 None None 0 None +3087 VASSPAGKL 0.0 None None 0 None +3088 IEYDTFGEV 0.322101512698 IEYDTF VQYDNF 24.0 32738|Liver_stage_antigen|Q25893|Plasmodium_falciparum|5833 +3089 APSSVALSL 0.0 None None 0 None +3090 NTAPSSVAL 0.0 None None 0 None +3091 EMKRHKVHI 0.0 None None 0 None +3092 ELLDYIRAV 2.20361791879 LLDYIR LLDFVR 25.0 11804|EBNA3C_latent_protein|CAD53421.1|Human_gammaherpesvirus_4|10376 +3093 PQIPPYSTF 0.0 None None 0 None +3094 ISHLHRESV 0.0 None None 0 None +3095 NLLSPDNMV 0.0 None None 0 None +3096 FASDHFLYA 0.0 None None 0 None +3097 FASDHFLYA 0.0 None None 0 None +3098 ATYVRILQR 0.0 None None 0 None +3099 FVVITATYV 0.101628132237 VITATYV VVTSTWV 24.0 14902|Genome_polyprotein|P26664.3|Hepatitis_C_virus_subtype_1a|31646 +3100 LASSSLDIV 0.0 None None 0 None +3101 FAYTILQSV 0.0 None None 0 None +3102 TILQSVPNK 0.0 None None 0 None +3103 FTLFFMAEY 0.0 None None 0 None +3104 FTLFFMAEY 0.0 None None 0 None +3105 YAAGPFTLF 0.0 None None 0 None +3106 YAAGPFTLF 0.0 None None 0 None +3107 YAAGPFTLF 0.0 None None 0 None +3108 ICSEATAAI 0.0 None None 0 None +3109 SLFNALRGK 0.437129462585 SLFNAL SLFNAV 25.0 180168|gag_protein|ABO14878.1|Human_immunodeficiency_virus_1|11676 +3110 VAIMGSTQV 0.11629553368 VAIMGST LAVMGSS 24.0 102376|Genome_polyprotein|P27958.3|Hepatitis_C_virus_subtype_1a|31646 +3111 SAYVALSNK 0.0 None None 0 None +3112 YAISARSDL 0.0 None None 0 None +3113 ATKTLRNYK 0.0 None None 0 None +3114 DVFFATKTL 0.0 None None 0 None +3115 FATKTLRNY 0.0 None None 0 None +3116 FATKTLRNY 0.0 None None 0 None +3117 FLSWCRRVV 0.0 None None 0 None +3118 LSWCRRVVL 0.0 None None 0 None +3119 RVVLELSPK 0.0 None None 0 None +3120 VVLELSPKV 0.0 None None 0 None +3121 IAIAIGAVL 0.00435035310079 IAIAIGAVL VAVAGAAIL 21.0 142231|Lipoprotein_lpqH_precursor|P0A5J0.1|Mycobacterium_tuberculosis|1773 +3122 IAIGAVLLV 0.0 None None 0 None +3123 RGMQCAICK 8.37647204165 MQCAICK LQCVQCK 27.0 148177|early_protein|CAA52585.1|Human_papillomavirus_type_52|10618 +3124 FSNADVNRL 0.0 None None 0 None +3125 MLLKPSERR 0.0 None None 0 None +3126 QLAWVPSPY 0.921133809074 AWVPS AWVPT 27.0 79628|E1_protein|BAA19893.1|Rubella_virus|11041 +3127 QLAWVPSPY 2.65839483138 AWVPS AWVPT 27.0 79628|E1_protein|BAA19893.1|Rubella_virus|11041 +3128 SSSEYMHHK 0.0 None None 0 None +3129 HIASEEPAK 0.0 None None 0 None +3130 STGFPHMLF 0.0246332875568 TGFPHML AGFYHIL 22.0 1516|Nucleoprotein|P03418.1|Human_respiratory_syncytial_virus_A2|11259 +3131 YFSTGFPHM 0.0 None None 0 None +3132 LVYMMERGK 0.0 None None 0 None +3133 VATPGRLVY 0.0 None None 0 None +3134 LLIPVAAVY 0.0 None None 0 None +3135 SAPLMELLY 0.0 None None 0 None +3136 LAMEDTGEY 0.0 None None 0 None +3137 MYLHFSDTY 0.0 None None 0 None +3138 SVSLMYLHF 1.11847247997 SLMYLH SLMYFH 28.0 180579|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 +3139 RLSISQWYR 0.0 None None 0 None +3140 SQWYRVMVK 0.0 None None 0 None +3141 STWIGNKLY 0.0 None None 0 None +3142 YMYVCTPLL 0.0 None None 0 None +3143 HQRIHTGEK 0.0 None None 0 None +3144 ALGLAQGTF 0.0191045931234 GLAQGTF GLSPGTL 21.0 21638|protein_F|ABV46152.2|Hepatitis_C_virus_(isolate_Japanese)|11116 +3145 GLAQGTFVF 0.00860509404551 GLAQGTF GLSPGTL 21.0 21638|protein_F|ABV46152.2|Hepatitis_C_virus_(isolate_Japanese)|11116 +3146 GTFVFIAHF 0.0 None None 0 None +3147 KLHQVFHSI 0.149224855724 KLHQVFHSI KLHLYSHPI 23.0 190568|polymerase|AAD16253.1|Hepatitis_B_virus|10407 +3148 VTVPEKLSF 0.0 None None 0 None +3149 HPCSQPVWL 0.0 None None 0 None +3150 FPLVRSCQM 1.72844236932 LVRSCQM LIRACML 24.0 36676|polyprotein|BAA09073.1|Hepatitis_C_virus_subtype_1b|31647 +3151 MMCRDLPGF 0.631203555857 RDLPGF RELPRF 22.0 53201|Fusion_glycoprotein_F0_precursor|P03420.1|Human_respiratory_syncytial_virus_A2|11259 +3152 RVKATIVAM 0.0 None None 0 None +3153 AQGEPLGAL 0.0 None None 0 None +3154 FQVPDLHIL 0.0 None None 0 None +3155 GMQARSVEM 0.0 None None 0 None +3156 MLHLYPGPM 0.369680851064 MLHLYPGPM LFQLYRGPL 26.0 38724|Genome_polyprotein|P08617.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 +3157 SPYSEELPL 0.0 None None 0 None +3158 YAQEGFLPH 0.408477408363 QEGFLP DEGLLP 22.0 140541|hypothetical_protein|NP_218210.1|Mycobacterium_tuberculosis_H37Rv|83332 +3159 HLLFRVIPY 0.0 None None 0 None +3160 RVIPYDQSF 0.0474258731776 IPYDQS LPFDKS 23.0 116123|nucleocapsid_protein|ABP49342.1|Influenza_A_virus_(A/California/10/1978(H1N1))|425557 +3161 SIGSSATLY 0.0 None None 0 None +3162 VQKQDNSTY 0.0 None None 0 None +3163 AQVGFTLPL 0.182777813767 GFTLPL AFTMPL 24.0 179898|cell_surface_protein_(associated_with_virulence)|NP_302372.1|Mycobacterium_leprae_TN|272631 +3164 LPTPPPPPL 2.24573975693 LPTPPPPP VPTDPNPP 31.0 70491|envelope_glycoprotein|AAC28452.1|Human_immunodeficiency_virus_1|11676 +3165 YSCAGGRLF 0.0 None None 0 None +3166 FQLDVASVI 0.0 None None 0 None +3167 LDVASVIPF 0.0 None None 0 None +3168 SVIPFDICY 1.51567816772e-05 SVIPFDIC GAIPPLVC 15.0 73059|kaposin|AAC57155.1|Human_gammaherpesvirus_8|37296 +3169 RLPNLHPSF 0.0 None None 0 None +3170 LMVAVARSA 0.0 None None 0 None +3171 TQHTSFQGY 0.0 None None 0 None +3172 EQRCSLQAF 0.0 None None 0 None +3173 KSKEREHSF 0.0 None None 0 None +3174 NIDLAREAY 0.0 None None 0 None +3175 IMSFLLSSL 0.0 None None 0 None +3176 SEKEASLLY 0.0 None None 0 None +3177 YLKEHASSL 0.0 None None 0 None +3178 LVLSGSSSL 0.0 None None 0 None +3179 FWRSSCSLF 0.403383339884 FWRSSCSL LWHYPCTL 22.0 54824|polyprotein_precursor|BAA01583.1|Hepatitis_C_virus|11103 +3180 QLADQCLTM 0.0 None None 0 None +3181 LPIKDGNTL 0.0 None None 0 None +3182 LLVDRKDAM 0.0 None None 0 None +3183 TPAIRHIML 0.848547717842 TPAIRH TPMLRH 26.0 186002|polyprotein|AGO67248.1|Dengue_virus_2|11060 +3184 MQIHMGLAL 0.0 None None 0 None +3185 ALARSSDAF 0.0 None None 0 None +3186 HQGGATRVY 1.65671617909 HQGGATRVY HDGAGKRVY 29.0 23620|Genome_polyprotein|SRC279960|Hepatitis_C_virus_genotype_1|41856 +3187 FPNAGKSSF 0.0890723848157 PNAGKS PGAGKT 23.0 180503|polyprotein|AGO67248.1|Dengue_virus_2|11060 +3188 ILQEHIGAM 0.0 None None 0 None +3189 SASAGLAAM 0.0 None None 0 None +3190 HPCVPQALV 0.0 None None 0 None +3191 ATIMETLTM 0.0 None None 0 None +3192 PSDINVSSY 0.0 None None 0 None +3193 VSSYNIYWY 9.48140414761 VSSYNIYWY ISEYRHYCY 23.0 28484|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 +3194 ESSEHEGTY 0.0 None None 0 None +3195 QAWQPTASF 31.7524708941 AWQPTA AWVPTA 29.0 79628|E1_protein|BAA19893.1|Rubella_virus|11041 +3196 FLNDRLANY 0.0 None None 0 None +3197 LQIMAGRHG 0.165211067364 MAGRHG VAGSHG 24.0 154196|tegument_protein|CAB06735.1|Human_alphaherpesvirus_2|10310 +3198 WLFPTGGSV 0.427013920926 LFPTGGSV LFPGGGQI 30.0 181035|||| +3199 LMYLQKLWM 0.0 None None 0 None +3200 SIQSPFEGF 0.0 None None 0 None +3201 LALLVSTAF 0.0 None None 0 None +3202 GLIATQLLF 0.0 None None 0 None +3203 LIATQLLFY 0.0 None None 0 None +3204 LIATQLLFY 0.0 None None 0 None +3205 AVRPTFGVL 0.0 None None 0 None +3206 AMRFHFHSM 0.0102154040423 AMRFHFHSM SARLHRHAL 21.0 28508|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 +3207 MTSGLAMRF 0.0 None None 0 None +3208 FPTTTFMCL 0.0 None None 0 None +3209 ISLFPTTTF 0.0 None None 0 None +3210 SLFPTTTFM 0.0 None None 0 None +3211 SMRSSSISG 0.0 None None 0 None +3212 VQHITGPVW 0.0 None None 0 None +3213 ASDSQEALF 0.00578652736162 SDSQEALF TDNQLAVF 21.0 52496|polyprotein_precursor|NP_041724.2|West_Nile_virus|11082 +3214 FSDISEMRT 0.0 None None 0 None +3215 TLAELLGPY 0.00117570333351 TLAELLGP TIASPKGP 19.0 23883|HCV-1|AAA45676.1|Hepatitis_C_virus_subtype_1a|31646 +3216 LVNPWGEVL 1.04441668544 VNPWGE VDPWVE 25.0 143690|Genome_polyprotein|P06441.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 +3217 LPVVLQLKL 0.0 None None 0 None +3218 AQADQVDPL 0.0 None None 0 None +3219 FCDTAPVLK 0.0 None None 0 None +3220 RLHSPMYFF 0.0 None None 0 None +3221 TMCMYFRPL 0.0 None None 0 None +3222 FLVFPFTSI 0.0 None None 0 None +3223 LMADMYLLL 0.0 None None 0 None +3224 HSHLLSHSY 2.5848832505 HLLSHS HLYSHP 23.0 190568|polymerase|AAD16253.1|Hepatitis_B_virus|10407 +3225 HSHLLSHSY 0.156318463122 HLLSHS HLYSHP 23.0 190568|polymerase|AAD16253.1|Hepatitis_B_virus|10407 +3226 TQYLVFCGM 0.0 None None 0 None +3227 YLVFCGMGL 0.0 None None 0 None +3228 LIFMYLCPA 0.0 None None 0 None +3229 VAICHPLHY 0.0 None None 0 None +3230 VLVQSLMVL 0.0 None None 0 None +3231 QAQNQSITY 0.0 None None 0 None +3232 TILTFCLSY 0.00326623801259 TILTFCLSY TIMAAILAY 20.0 150224|polyprotein|AGO67248.1|Dengue_virus_2|11060 +3233 CSIQDDLPF 0.0 None None 0 None +3234 RMSRALWTL 0.0 None None 0 None +3235 KQGWCYLVY 0.0 None None 0 None +3236 YLVYVLLPL 186.049439044 YLVYVLLPL YIIFVYIPL 31.0 110744|E5_protein|AAD24036.1|Human_papillomavirus_type_16|333760 +3237 TINSAGDLF 0.0 None None 0 None +3238 FPLDEVHAK 1.3376067584 FPLDEVHA YPLHEQHG 24.0 75356|EBNA3A_nuclear_protein|Q8AZJ8|Human_gammaherpesvirus_4|10376 +3239 LTLPPLATY 0.587666896977 LTLPPLA LTIPPTA 28.0 184643|polyprotein|AGW24534.1|Dengue_virus_2|11060 +3240 PPAPPSLSL 0.0 None None 0 None +3241 MQRASRHSQ 0.0 None None 0 None +3242 QQSQSSGPG 0.0 None None 0 None +3243 MLGDPSADY 0.0 None None 0 None +3244 SADYINANY 0.0 None None 0 None +3245 GVHKGRKPF 0.0 None None 0 None +3246 ALACFARAF 0.0 None None 0 None +3247 LTGDCCFDY 0.0 None None 0 None +3248 YPKPQVSFL 0.0 None None 0 None +3249 HPLGSLQIF 0.0 None None 0 None +3250 AVGGMIASF 0.0144532044338 GMIASF GVIAAF 22.0 98085|trans-sialidase,_putative|EAN82636.1|Trypanosoma_cruzi|5693 +3251 PTEQSLTEY 0.0 None None 0 None +3252 LLMGFSLTL 0.0 None None 0 None +3253 TQGMQCSSL 0.0365911287855 TQGMQCS TRGERCN 21.0 170063|polyprotein|ABU97067.1|Hepatitis_C_virus_subtype_1b|31647 +3254 LLNLVVTSL 0.0 None None 0 None +3255 YVKIYLLPY 0.0 None None 0 None +3256 YVKIYLLPY 0.0 None None 0 None +3257 ISVFSGSEM 0.0 None None 0 None +3258 LLDEDISVF 0.0 None None 0 None +3259 STVELVPIF 0.0 None None 0 None +3260 KSADFEGLY 0.0 None None 0 None +3261 CLFSLYTAY 0.0 None None 0 None +3262 SLYTAYHVF 0.0160929247029 SLYTAYHV KLYCSYEV 22.0 32250|FL-160-2_protein_-_Trypanosoma_cruzi|JH0823|Trypanosoma_cruzi|5693 +3263 SSHLHSDHY 0.0 None None 0 None +3264 RQKHGEAPI 0.0 None None 0 None +3265 RQDVGTYTF 0.0 None None 0 None +3266 VERQDVGTY 0.0 None None 0 None +3267 HSNSTSFIF 0.0 None None 0 None +3268 NAHSNSTSF 0.0 None None 0 None +3269 ATTESDQSF 0.0 None None 0 None +3270 FPSETKVII 0.0 None None 0 None +3271 HQVASSPGH 0.0 None None 0 None +3272 SQGGPRGTF 0.0 None None 0 None +3273 GGAPHFGHF 0.0 None None 0 None +3274 GAIALIRRY 0.0 None None 0 None +3275 DTTRYVTSK 0.0 None None 0 None +3276 EPSESDTTR 0.0 None None 0 None +3277 PSESDTTRY 0.0 None None 0 None +3278 TRYVTSKIL 0.0 None None 0 None +3279 TTRYVTSKI 0.0 None None 0 None +3280 TSCSCQSSR 0.0 None None 0 None +3281 TGDSEAAPV 0.046686577341 TGDSEAAP TGNPRTAP 22.0 154346|RL2|CAB06760.1|Human_alphaherpesvirus_2|10310 +3282 LSMEETLLL 0.0 None None 0 None +3283 WWNPALWKR 10.2327872852 PALWKR PTLWAR 26.0 149027|NS5_protein|BAA00702.1|Hepatitis_C_virus_(isolate_H77)|63746 +3284 LFQDNSSQL 0.0 None None 0 None +3285 LTPPQAQEL 0.429161842612 LTPPQAQEL LTDPNPQEV 25.0 69799|envelope_glycoprotein|BAE96221.1|Human_immunodeficiency_virus_1|11676 +3286 LTPQQAQEL 0.0 None None 0 None +3287 QAQALGIPL 0.0 None None 0 None +3288 ASRPDRLSL 0.0 None None 0 None +3289 EAQGQEASR 0.0 None None 0 None +3290 WVEPQNPVL 0.000730033295762 VEPQNPVL VSPFIPLL 17.0 58740|Major_surface_antigen_precursor|P03142.4|Hepatitis_B_virus|10407 +3291 HLPHLTHTL 0.0 None None 0 None +3292 HTLATSCRR 0.0 None None 0 None +3293 ITSFDNLFR 0.0 None None 0 None +3294 SHFHKTHEV 0.0 None None 0 None +3295 YKLVVVGAV 12.5817515538 KLVVVG KLVVLG 24.0 32238|polyprotein_[Hepatitis_C_virus_subtype_1a]|ABV46251.2|Hepatitis_C_virus_(isolate_H77)|63746 +3296 FHRRLSSSL 0.0 None None 0 None +3297 FHRRLSSSL 0.0 None None 0 None +3298 FSRRSFHRR 0.0 None None 0 None +3299 RSDVWNLGI 0.0 None None 0 None +3300 VYILILPSF 0.0 None None 0 None +3301 STTIPILTL 0.0 None None 0 None +3302 TIPILTLSL 0.0 None None 0 None +3303 LSHISHLEL 0.0 None None 0 None +3304 SHLELVESL 0.0 None None 0 None +3305 SAEVRIEPM 0.108897660016 EVRIEP QVRIKP 23.0 71266|Circumsporozoite_protein_precursor|P02893.1|Plasmodium_falciparum|5833 +3306 QSHLLIHQR 0.0 None None 0 None +3307 QVITLRKSL 0.0 None None 0 None +3308 TKKQVITLR 0.0 None None 0 None +3309 MFDASKANF 0.0 None None 0 None +3310 FLDWLRTMT 0.0 None None 0 None +3311 VDWFLDWLR 11.20129968 VDWFLDWLR ISWCLWWLQ 28.0 39591|polyprotein|AAA45677.1|Hepatitis_C_virus_(isolate_H77)|63746 +3312 WFLDWLRTM 0.137841959387 WFLDWLR WCLWWLQ 25.0 39591|polyprotein|AAA45677.1|Hepatitis_C_virus_(isolate_H77)|63746 +3313 WLRTMTNVL 0.0 None None 0 None +3314 KFLQEEPQL 0.0 None None 0 None +3315 DVFRFSPYR 0.0 None None 0 None +3316 RFSPYRGLL 0.10447761194 FSPYRGLL IAPYAGLI 26.0 25388|matrix_protein|ABP96803.1|Human_metapneumovirus|162145 +3317 DSTRPPGTR 1.52773900302 PPGTR PPGSR 26.0 136890|polyprotein|AGO67248.1|Dengue_virus_2|11060 +3318 YLGVPVFYA 0.385348721615 YLGVPVF YYGVPVW 28.0 118|envelope_glycoprotein|ABS76372.1|Human_immunodeficiency_virus_1|11676 +3319 AIHIVAEKK 0.0 None None 0 None +3320 TQFELQRNK 0.0 None None 0 None +3321 VRGTDWHLK 0.0074144902417 VRGTDWH TRGRDAH 21.0 66798|glycoprotein_gp35/37|AAC59622.1|Human_gammaherpesvirus_8|37296 +3322 GFHPDPEAL 0.149003652528 GFHPD GFFPD 24.0 190466|large_surface_antigen|CAL29876.1|Hepatitis_B_virus|10407 +3323 HIRTDTYVK 0.0 None None 0 None +3324 SRWQVHGIV 0.0 None None 0 None +3325 VPACSRAHV 0.0 None None 0 None +3326 VPACSYAHV 0.0 None None 0 None +3327 MLFFRTRYI 0.0602884044705 MLFFRTRYI VLFYLGQYI 22.0 156550|E3_ubiquitin-protein_ligase_Mdm2|Q00987.1|Homo_sapiens|9606 +3328 TRYICTTVF 0.0 None None 0 None +3329 YICTTVFYT 0.0 None None 0 None +3330 AALVPTQAM 0.0 None None 0 None +3331 MPGSPRDPV 0.0 None None 0 None +3332 RRGSGHSEY 1.07898059992 GSGHSE GPGHEE 24.0 180488|polyprotein|AGO67248.1|Dengue_virus_2|11060 +3333 RICGHIFCY 2.42597295458e-05 ICGHIFC LCLIISC 15.0 93431|pre-C/C_protein|ABY54138.1|Hepatitis_B_virus|10407 +3334 GIAPLNQWV 0.842769418953 IAPLNQW LTPLRDW 24.0 36062|polyprotein|AAB67037.1|Hepatitis_C_virus_(isolate_H77)|63746 +3335 KIIATCFAV 0.0 None None 0 None +3336 KMNEPKCLK 0.0 None None 0 None +3337 SFVPWNSYV 1.65978825128 VPWNSYV LPWYSYL 29.0 143728|Genome_polyprotein|P08617.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 +3338 VPWNSYVRL 0.33737000325 VPWNSYV LPWYSYL 29.0 143728|Genome_polyprotein|P08617.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 +3339 YQLKLFACM 0.000135204617912 YQLKLFAC YRLWHYPC 17.0 75636|polyprotein|AAB67037.1|Hepatitis_C_virus_(isolate_H77)|63746 +3340 YQLKLFACM 0.000103789830269 YQLKLFAC YRLWHYPC 17.0 75636|polyprotein|AAB67037.1|Hepatitis_C_virus_(isolate_H77)|63746 +3341 RGRGGSVSI 0.0 None None 0 None +3342 IPHTAILVT 0.0 None None 0 None +3343 SIPHTAILV 0.0 None None 0 None +3344 GLSDLELRL 0.0 None None 0 None +3345 VLLRCPNKL 0.0 None None 0 None +3346 TRLAFGLFA 0.0 None None 0 None +3347 ILIACRLNK 3.55199159767 ILIACRL VLIRCYL 21.0 145860|Protein_E6|P04019.1|Human_papillomavirus_type_11|10580 +3348 LIACRLNKK 0.0 None None 0 None +3349 RLNKKKGAY 0.0 None None 0 None +3350 TLAHEASPL 0.0 None None 0 None +3351 SAWWSFGSL 0.872449058702 WSFGSL WDFGSL 31.0 180726|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 +3352 NPEAMCSDL 55.4534482749 NPEAMC NPYAVC 25.0 110401|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 +3353 AMHPLFRKL 0.0 None None 0 None +3354 CRAMHPLFR 0.0 None None 0 None +3355 GPCRAMHPL 0.0 None None 0 None +3356 RAMHPLFRK 0.0 None None 0 None +3357 GYIHYVFYL 8.67210597487 GYIHYV GYLQYV 26.0 42094|telomer_length_regulation_protein_TEL1|EDV12172.1|Saccharomyces_cerevisiae|4932 +3358 GYIHYVFYL 0.750508588568 GYIHYV GYLQYV 26.0 42094|telomer_length_regulation_protein_TEL1|EDV12172.1|Saccharomyces_cerevisiae|4932 +3359 KGYIHYVFY 78.5423095416 GYIHYV GYLQYV 26.0 42094|telomer_length_regulation_protein_TEL1|EDV12172.1|Saccharomyces_cerevisiae|4932 +3360 YLGNGPNVI 0.0 None None 0 None +3361 SLSNKEVKK 0.0 None None 0 None +3362 GPRAINNFF 0.0 None None 0 None +3363 FRFSSQEAA 0.0 None None 0 None +3364 LLPPQDPHL 0.366181412717 LLPPQDPHL LLPRRGPRL 24.0 23224|polyprotein|BAB18806.1|Hepatitis_C_virus|11103 +3365 PPQDPHLPL 0.0 None None 0 None +3366 HVDPGTIGV 7.61077451306e-06 HVDPGTIG HISCLTFG 15.0 190443|core_protein|BAF42671.1|Hepatitis_B_virus|10407 +3367 GLMGAVNVA 0.0 None None 0 None +3368 LMGAVNVAK 0.0 None None 0 None +3369 PRMAIPWPR 0.0 None None 0 None +3370 WPRDVRKLV 0.0 None None 0 None +3371 KYYEALPEL 0.0 None None 0 None +3372 HYYHNVHAV 0.0 None None 0 None +3373 MVEHYYHNV 0.0 None None 0 None +3374 YHNVHAVVF 0.0 None None 0 None +3375 YYHNVHAVV 0.0 None None 0 None +3376 ARVWKFGPK 0.0 None None 0 None +3377 RVWKFGPKL 0.0 None None 0 None +3378 RVWKFGPKL 0.0 None None 0 None +3379 VLDKARVWK 0.180063784265 VLDKARVW VLDSFKTW 25.0 69435|Genome_polyprotein|SRC279960|Hepatitis_C_virus_(isolate_H77)|63746 +3380 CYEEYRGRL 0.0377885551771 CYEEYRGRL VYQDWLGRM 24.0 23288|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 +3381 GRYEEYRGH 0.0 None None 0 None +3382 APRGACYRA 0.0 None None 0 None +3383 YRADHDLGR 0.0 None None 0 None +3384 SYVCVVRNY 0.0 None None 0 None +3385 ARPFFFFLL 0.0529432793239 PFFFFLL PFVVFLV 22.0 148397|Dense_granule_protein_3|B6KEU8.2|Toxoplasma_gondii|5811 +3386 FFFFLLDKV 0.0 None None 0 None +3387 FFFLLDKVL 0.876549817799 FLLDKVL FLLTKIL 25.0 16753|Pre-S/S_protein|AAR99337.1|Hepatitis_B_virus|10407 +3388 FLLDKVLAS 2.38412935701 FLLDKVLA FLLTKILT 25.0 16753|Pre-S/S_protein|AAR99337.1|Hepatitis_B_virus|10407 +3389 HARPFFFFL 0.0 None None 0 None +3390 APSWRGLAE 0.00488637433335 APSWRGLA GPSLIGLA 20.0 21780|Antigen_85-B_precursor_(85B)_(Extracellular_alpha-antigen)_(Antigen_85_complex_B)_(Ag85B)_(Mycolyl_transferase_85B)_(Fibronectin-binding_protein_B)_(30_kDa_extracellular_protein)|P31952|Mycobacterium_tuberculosis|1773 +3391 LRLALMKKK 0.0 None None 0 None +3392 WLRLALMKK 0.0 None None 0 None +3393 VLIQQLEKV 0.0 None None 0 None +3394 YPGQVNRTA 0.441659094862 PGQVNRTA PGEINRVA 33.0 59153|Genome_polyprotein|P27958.3|Hepatitis_C_virus_subtype_1a|31646 +3395 MADVAMYGV 0.0 None None 0 None +3396 GLYYAEFGA 0.0 None None 0 None +3397 SVLAGLYYA 5.40222207826 LAGLYY LAGLFY 28.0 23270|polyprotein|AAB67036.1|Hepatitis_C_virus_(isolate_H77)|63746 +3398 TMWRREESL 0.0 None None 0 None +3399 CLWQLKAPV 0.0117840685959 CLWQLKAPV SLWKDGAPL 22.0 140600|glutamine_synthetase_GLNA1_(glutamine_synthase)_(GS-I)|NP_216736.1|Mycobacterium_tuberculosis_H37Rv|83332 +3400 RPRKAWAWC 5.41074531829 RPRKAW RPASAW 26.0 150534|polyprotein|AGO67248.1|Dengue_virus_2|11060 +3401 QRLKREEEK 2.19826332471 KREEEK RREEEE 23.0 185491|polyprotein|AGO67248.1|Dengue_virus_2|11060 +3402 VYHMSQSPL 0.0 None None 0 None +3403 FTMLLSLLA 0.0 None None 0 None +3404 GLAGFTMLL 0.186461334924 GFTML GFTMM 24.0 180818|Membrane_glycoprotein_precursor|NP_739582.2|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 +3405 MLLSLLAFA 0.0 None None 0 None +3406 KVHQLAITV 0.0 None None 0 None +3407 LPKSSEKAI 0.0 None None 0 None +3408 STQEPTAYV 1.33414347629 QEPTAYV QNPTTYI 27.0 135263|hemagglutinin|ACX31970.1|Influenza_A_virus_(A/Bar-headed_Goose/Qinghai/61/05(H5N1))|336238 +3409 ARMRKHIKR 0.0 None None 0 None +3410 GPARMRKHI 0.0 None None 0 None +3411 RMRKHIKRL 0.0 None None 0 None +3412 HVGKASSSM 0.0 None None 0 None +3413 QQMEAHVGK 0.0 None None 0 None +3414 VILLPQPPK 0.0 None None 0 None +3415 YLGVPVFYA 0.385348721615 YLGVPVF YYGVPVW 28.0 118|envelope_glycoprotein|ABS76372.1|Human_immunodeficiency_virus_1|11676 +3416 AIHIVAEKK 0.0 None None 0 None +3417 IVGHTGSGK 0.972587226103 HTGSGK HPGSGK 28.0 183598|polyprotein|AGW21594.1|Dengue_virus_1|11053 +3418 LPAPPGAPP 28.8454969512 LPAPPGA WPAPPGA 35.0 72928|Genome_polyprotein|P26662.3|Hepatitis_C_virus_(isolate_Japanese)|11116 +3419 VRGTDWHLK 0.0074144902417 VRGTDWH TRGRDAH 21.0 66798|glycoprotein_gp35/37|AAC59622.1|Human_gammaherpesvirus_8|37296 +3420 RRHHSPSQR 0.689680730869 HHSPS HHAPS 28.0 21000|glutamine_synthetase_GLNA1_(glutamine_synthase)_(GS-I)|NP_216736.1|Mycobacterium_tuberculosis|1773 +3421 WLQQENHEL 0.0 None None 0 None +3422 SLQPIHHDL 0.0 None None 0 None +3423 VPACSRAHV 0.0 None None 0 None +3424 VPACSYAHV 0.0 None None 0 None +3425 LLLSPPVEV 0.0 None None 0 None +3426 LLSPPVEVK 0.0 None None 0 None +3427 RPEPPETGV 1.40283044682 PEPPET PNPPEV 26.0 70491|envelope_glycoprotein|AAC28452.1|Human_immunodeficiency_virus_1|11676 +3428 RRGSGHSEY 1.07898059992 GSGHSE GPGHEE 24.0 180488|polyprotein|AGO67248.1|Dengue_virus_2|11060 +3429 GLLQRPVHL 0.0 None None 0 None +3430 HLALGRLSR 0.0 None None 0 None +3431 KIIATCFAV 0.0 None None 0 None +3432 SFVPWNSYV 1.65978825128 VPWNSYV LPWYSYL 29.0 143728|Genome_polyprotein|P08617.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 +3433 VPWNSYVRL 0.33737000325 VPWNSYV LPWYSYL 29.0 143728|Genome_polyprotein|P08617.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 +3434 YQLKLFACM 0.000135204617912 YQLKLFAC YRLWHYPC 17.0 75636|polyprotein|AAB67037.1|Hepatitis_C_virus_(isolate_H77)|63746 +3435 YQLKLFACM 0.000103789830269 YQLKLFAC YRLWHYPC 17.0 75636|polyprotein|AAB67037.1|Hepatitis_C_virus_(isolate_H77)|63746 +3436 IPHTAILVT 0.0 None None 0 None +3437 SIPHTAILV 0.0 None None 0 None +3438 SVSSCCQPV 1.40654417103 SSCCQP SECCTP 28.0 57361|Genome_polyprotein|SRC279960|Hepatitis_C_virus_(isolate_H77)|63746 +3439 WLLEWTEAA 0.223150379312 WLLEW WAIKW 24.0 72233|Genome_polyprotein|P27958.3|Hepatitis_C_virus_subtype_1a|31646 +3440 GLSDLELRL 0.0 None None 0 None +3441 VLLRCPNKL 0.0 None None 0 None +3442 TLAHEASPL 0.0 None None 0 None +3443 ILPATILVL 0.0979841141813 ILPATI MLPATL 23.0 180662|polyprotein|CDF77361.1|Dengue_virus_3|11069 +3444 TILPATILV 0.126010530119 ILPATI MLPATL 23.0 180662|polyprotein|CDF77361.1|Dengue_virus_3|11069 +3445 SAWWSFGSL 0.872449058702 WSFGSL WDFGSL 31.0 180726|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 +3446 NPEAMCSDL 55.4534482749 NPEAMC NPYAVC 25.0 110401|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 +3447 AMHPLFRKL 0.0 None None 0 None +3448 CRAMHPLFR 0.0 None None 0 None +3449 GPCRAMHPL 0.0 None None 0 None +3450 RAMHPLFRK 0.0 None None 0 None +3451 SLSNKEVKK 0.0 None None 0 None +3452 GPRAINNFF 0.0 None None 0 None +3453 LLPPQDPHL 0.366181412717 LLPPQDPHL LLPRRGPRL 24.0 23224|polyprotein|BAB18806.1|Hepatitis_C_virus|11103 +3454 PPQDPHLPL 0.0 None None 0 None +3455 GLMGAVNVA 0.0 None None 0 None +3456 LMGAVNVAK 0.0 None None 0 None +3457 KLPEVQLPK 6.62808883056e-05 LPEVQLPK LPSDFLPS 16.0 16836|precore/core_protein_[Hepatitis_B_virus]|AAR03815.1|Hepatitis_B_virus|10407 +3458 ARVWKFGPK 0.0 None None 0 None +3459 RVWKFGPKL 0.0 None None 0 None +3460 RVWKFGPKL 0.0 None None 0 None +3461 VLDKARVWK 0.180063784265 VLDKARVW VLDSFKTW 25.0 69435|Genome_polyprotein|SRC279960|Hepatitis_C_virus_(isolate_H77)|63746 +3462 APRGACYRA 0.0 None None 0 None +3463 YRADHDLGR 0.0 None None 0 None +3464 SYVCVVRNY 0.0 None None 0 None +3465 APSWRGLAE 0.00488637433335 APSWRGLA GPSLIGLA 20.0 21780|Antigen_85-B_precursor_(85B)_(Extracellular_alpha-antigen)_(Antigen_85_complex_B)_(Ag85B)_(Mycolyl_transferase_85B)_(Fibronectin-binding_protein_B)_(30_kDa_extracellular_protein)|P31952|Mycobacterium_tuberculosis|1773 +3466 VLIQQLEKV 0.0 None None 0 None +3467 GLYYAEFGA 0.0 None None 0 None +3468 SVLAGLYYA 5.40222207826 LAGLYY LAGLFY 28.0 23270|polyprotein|AAB67036.1|Hepatitis_C_virus_(isolate_H77)|63746 +3469 KPVNKILQI 0.0 None None 0 None +3470 CLWQLKAPV 0.0117840685959 CLWQLKAPV SLWKDGAPL 22.0 140600|glutamine_synthetase_GLNA1_(glutamine_synthase)_(GS-I)|NP_216736.1|Mycobacterium_tuberculosis_H37Rv|83332 +3471 RPRKAWAWC 5.41074531829 RPRKAW RPASAW 26.0 150534|polyprotein|AGO67248.1|Dengue_virus_2|11060 +3472 SLDTVAQAV 0.0 None None 0 None +3473 QRLKREEEK 2.19826332471 KREEEK RREEEE 23.0 185491|polyprotein|AGO67248.1|Dengue_virus_2|11060 +3474 RREQQLRRK 0.0 None None 0 None +3475 VYHMSQSPL 0.0 None None 0 None +3476 FTMLLSLLA 0.0 None None 0 None +3477 GLAGFTMLL 0.186461334924 GFTML GFTMM 24.0 180818|Membrane_glycoprotein_precursor|NP_739582.2|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 +3478 MLLSLLAFA 0.0 None None 0 None +3479 KVHQLAITV 0.0 None None 0 None +3480 KIMHGPFMK 0.0 None None 0 None +3481 RPRWNTHGH 0.0 None None 0 None +3482 ARMRKHIKR 0.0 None None 0 None +3483 GPARMRKHI 0.0 None None 0 None +3484 RMRKHIKRL 0.0 None None 0 None +3485 VILLPQPPK 0.0 None None 0 None +3486 TPCHCTGTL 0.0 None None 0 None +3487 TPCHCTGTL 0.0 None None 0 None +3488 IPFFGQVHL 0.0 None None 0 None +3489 ILMENKSNI 0.0 None None 0 None +3490 ILMENKSNI 0.0 None None 0 None +3491 LAYLVKKMM 0.0 None None 0 None +3492 VTISLAYLV 0.0 None None 0 None +3493 LLIESKEEM 0.0 None None 0 None +3494 WVGPWHTIV 0.0 None None 0 None +3495 WWVGPWHTI 0.0 None None 0 None +3496 KTFCGDVEY 0.0 None None 0 None +3497 AVMEQINSV 0.0 None None 0 None +3498 AVMEQINSV 0.0 None None 0 None +3499 HPRINTLGS 0.0 None None 0 None +3500 FLVAFIKKI 0.0 None None 0 None +3501 FLVAFIKKI 0.0 None None 0 None +3502 GIVSWDTFL 52.5489168518 SWDTFL KWETFL 28.0 52666|Antigen_85-B|P0C5B9.1|Mycobacterium_tuberculosis|1773 +3503 IVSWDTFLV 0.838854359979 SWDTFL KWETFL 28.0 52666|Antigen_85-B|P0C5B9.1|Mycobacterium_tuberculosis|1773 +3504 SAKLTTLVV 0.0 None None 0 None +3505 KLIWHPFSI 0.0 None None 0 None +3506 YFDENIQKL 0.0 None None 0 None +3507 SPSSGQRST 0.0 None None 0 None +3508 SAQNELTEM 0.0 None None 0 None +3509 VATNSETAM 0.0 None None 0 None +3510 PLWGGIIYI 0.24231663041 PLWGGIIYI PLFGYPVYV 25.0 48321|||| +3511 YPLWGGIIY 0.0 None None 0 None +3512 AALATLHPL 0.0 None None 0 None +3513 AALATLHPL 0.0 None None 0 None +3514 LATLHPLFL 0.0 None None 0 None +3515 GLNMLITAL 0.0 None None 0 None +3516 LLTGLNMLI 0.0 None None 0 None +3517 LMWLTYTMA 0.662873031064 LMWLTY LMWLSY 32.0 21041|Membrane_glycoprotein|Q692E0|SARS_coronavirus_TJF|284672 +3518 LTYTMAFMV 0.0585597533649 YTMAFM YTSAFV 22.0 76621|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 +3519 LTYTMAFMV 0.00186523658866 YTMAFM YTSAFV 22.0 76621|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 +3520 MLITALYSL 6.89989591232e-08 LYSL VYAF 9.0 142232|POSSIBLE_CONSERVED_TRANSMEMBRANE_PROTEIN|CAB00937.1|Mycobacterium_tuberculosis|1773 +3521 NLMWLTYTM 2.28006257564 NLMWLTY GLMWLSY 32.0 21041|Membrane_glycoprotein|Q692E0|SARS_coronavirus_TJF|284672 +3522 WLTYTMAFM 0.00930680861548 YTMAFM YTSAFV 22.0 76621|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 +3523 SANTGSSVV 0.0 None None 0 None +3524 AMGSGIQPL 0.0 None None 0 None +3525 HLLEPGQAM 0.0 None None 0 None +3526 TVVGNLGII 0.0 None None 0 None +3527 HGKPTLSTV 0.0 None None 0 None +3528 LEYNTRNAY 0.0 None None 0 None +3529 LLGLTWPVV 2.39337746242 WPVV WPVL 23.0 38427|BZLF1|AAA66529.1|Human_gammaherpesvirus_4|10376 +3530 QLLGLTWPV 0.0 None None 0 None +3531 RVLFWGHIL 0.0 None None 0 None +3532 RVLFWGHIL 0.0 None None 0 None +3533 KVFNNGADL 0.0 None None 0 None +3534 LAGEWRERL 0.0 None None 0 None +3535 MNWRPILTI 0.0 None None 0 None +3536 FSDLRSSIV 0.0 None None 0 None +3537 FSDLRSSIV 0.0 None None 0 None +3538 YFSDLRSSI 0.0 None None 0 None +3539 EANFSASRV 0.0 None None 0 None +3540 TLEGFFESL 0.0 None None 0 None +3541 KILKAQEHV 0.0 None None 0 None +3542 LLQPTPPAA 0.242418891606 PTPPAA PAPPGA 25.0 72928|Genome_polyprotein|P26662.3|Hepatitis_C_virus_(isolate_Japanese)|11116 +3543 SLQVKRVFV 0.0 None None 0 None +3544 FTLEGFFES 0.0 None None 0 None +3545 PLLRDVFNV 0.0 None None 0 None +3546 AQSEIHFQV 0.0 None None 0 None +3547 LQAHSMHEV 0.0 None None 0 None +3548 LLLQPTPPA 0.0 None None 0 None +3549 SLSFSFPLL 105.166666667 LSFSFPLL LSFALPII 26.0 39339|Nucleocapsid_protein|Q89462|Sin_Nombre_hantavirus|37705 +3550 RVWDIVPTL 137.640684863 RVWDIVPTL KPWDVVPTV 37.0 32944|polyprotein|AAW51418.1|Dengue_virus_3|11069 +3551 IVMCAMCGV 0.0 None None 0 None +3552 AMCGVPFSV 1.48904088027 AMCGVPFS SFCGSPYS 28.0 190409|polymerase|AAD16253.1|Hepatitis_B_virus|10407 +3553 RQMAARECK 0.0 None None 0 None +3554 FLVYQNILK 0.0 None None 0 None +3555 FLVYQNILK 0.0 None None 0 None +3556 KVERERLEK 0.0 None None 0 None +3557 KQIEMLEYK 0.0 None None 0 None +3558 KQIEMLEYK 0.0 None None 0 None +3559 VVGAVGVGK 0.0 None None 0 None +3560 VVGAVGVGK 0.0 None None 0 None +3561 FIDTYPPVL 0.0 None None 0 None +3562 RSAFPCAHR 0.0 None None 0 None +3563 GTPRAATMK 0.0 None None 0 None +3564 TMKAKTDLK 0.0 None None 0 None +3565 TMKAKTDLK 0.0 None None 0 None +3566 GLLFAAIKR 0.0 None None 0 None +3567 LLFAAIKRR 0.0 None None 0 None +3568 YQIDRDLHK 0.0 None None 0 None +3569 QTGEKLMAK 0.0 None None 0 None +3570 QTGEKLMAK 0.0 None None 0 None +3571 SSNLIAHVR 0.0 None None 0 None +3572 GEDVDSLAL 0.280156235348 GEDVDSLAL GEEVQVLAL 27.0 180428|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 +3573 AELVYILKH 0.0 None None 0 None +3574 KVAELVYIL 0.0 None None 0 None +3575 ISMKLVLRF 0.0 None None 0 None +3576 KSPGWSFQV 0.804206027719 PGWS PGWS 28.0 141461|ubiquitin_E3_ligase_ICP0|NP_044601.1|Human_alphaherpesvirus_1|10298 +3577 SWKSPGWSF 14.9348449335 PGWS PGWS 28.0 141461|ubiquitin_E3_ligase_ICP0|NP_044601.1|Human_alphaherpesvirus_1|10298 +3578 LTVDNITFL 0.00953450829996 TVDNITFL TVELLSFL 21.0 5191|core_protein|AAL31859.1|Hepatitis_B_virus|10407 +3579 DAATRVAMV 0.0 None None 0 None +3580 DSVDAATRV 0.0 None None 0 None +3581 VGAQIYHTI 0.0 None None 0 None +3582 GELSMLVTT 0.0 None None 0 None +3583 EELQLICQA 0.0 None None 0 None +3584 SEEELQLIC 0.0 None None 0 None +3585 CELHAQAAT 0.0 None None 0 None +3586 FTLRPGEVM 0.0 None None 0 None +3587 VYMPPPRLL 0.0 None None 0 None +3588 TFKKQWFYL 0.0 None None 0 None +3589 KANRESQSL 0.0 None None 0 None +3590 AAKARDREL 0.0 None None 0 None +3591 AARLRFFST 0.0 None None 0 None +3592 AFFSLSYIF 0.0 None None 0 None +3593 AHASLIPEF 0.200665922786 HASLIP HADVIP 24.0 97093|polyprotein|AAB66324.1|Hepatitis_C_virus_(isolate_H77)|63746 +3594 AHCGLGKIL 0.0811144143937 CGLGKIL CPLSKIL 24.0 6808|membrane_protein|AAA45887.1|Human_gammaherpesvirus_4|10376 +3595 AHIERRLHI 0.0 None None 0 None +3596 AHMETMAKL 0.0 None None 0 None +3597 AHMGVFTEL 0.0 None None 0 None +3598 AHQDALMLA 0.0 None None 0 None +3599 AHRPRARLA 0.0 None None 0 None +3600 AHTSAILTV 0.0 None None 0 None +3601 AIRPKSLAI 0.0 None None 0 None +3602 ALQRRRLSL 0.0 None None 0 None +3603 ALQRRVQRL 0.0 None None 0 None +3604 AMACMSSVF 0.0 None None 0 None +3605 AMCVIHFSF 1.41247187444 MCVIHFSF MCAVHPTL 25.0 7660|polyprotein|AAA45677.1|Hepatitis_C_virus_(isolate_H77)|63746 +3606 AMYLRASSL 0.0 None None 0 None +3607 APASRHLSA 0.0 None None 0 None +3608 APRLLRSPV 0.0 None None 0 None +3609 AQKEHSHLL 0.937305079721 AQKEHSHL AERKHRHL 28.0 75408|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 +3610 ARAAQVAGI 0.0 None None 0 None +3611 ARDPSPIQI 0.0 None None 0 None +3612 ARHERIHTK 0.0 None None 0 None +3613 ARINSIYGL 0.0624279351011 ARINSI ARLNSL 23.0 418964|PPE_family_protein_PPE68|KAM81677.1|Mycobacterium_tuberculosis_H37Ra|419947 +3614 ARKPRTREC 0.0 None None 0 None +3615 ARLQHCSAL 0.0 None None 0 None +3616 ARLQHCSAL 0.0 None None 0 None +3617 ARLYRGQAL 0.0 None None 0 None +3618 ARLYRGQAL 0.0 None None 0 None +3619 ARMQSYSTI 0.0 None None 0 None +3620 ARPEKLPEL 0.72119091728 RPEKLPEL RPRKLPQL 34.0 110338|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 +3621 ARQHLLQRM 0.0 None None 0 None +3622 ARRARLQHC 0.0 None None 0 None +3623 ARRKQSEMY 0.0 None None 0 None +3624 ARTRAKQNI 0.0 None None 0 None +3625 ARVQMQVTM 0.0 None None 0 None +3626 ASFSNHQRV 0.0695350378462 ASFSNH ASYSSH 24.0 53148|Transcription_activator_BRLF1|P03209.1|Human_herpesvirus_4_strain_B95-8|10377 +3627 ATDDKMTIF 0.0 None None 0 None +3628 AVDPMRAAY 0.0 None None 0 None +3629 AVMGRSWEV 0.0 None None 0 None +3630 AYATQLFFF 0.0 None None 0 None +3631 AYEDTVRQV 0.0 None None 0 None +3632 AYFTHSLSF 0.0 None None 0 None +3633 CAFSRRRPI 0.0 None None 0 None +3634 CFPLHGLQF 0.0590811205659 CFPLHGLQ SFPDPGLR 18.0 79300|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 +3635 CGDKISDRY 1.50652597592 CGDKIS AGDKLS 23.0 244160|surface_antigen_2_(CA-2)|XP_818927.1|Trypanosoma_cruzi_strain_CL_Brener|353153 +3636 CHFSCNNGF 0.0 None None 0 None +3637 CHQDHWSQL 0.0 None None 0 None +3638 CHQRCGGRV 0.0 None None 0 None +3639 CHSNSRDHL 18.4546845763 CHSNSRDHL CYDHAQTHL 25.0 7353|Early_antigen_protein_D|P03191.1|Human_herpesvirus_4_strain_B95-8|10377 +3640 CHYEKKTDL 1.15217391304 CHYEKK CHSKKK 26.0 36504|polyprotein_precursor|BAA01582.1|Hepatitis_C_virus|11103 +3641 CLKPHQGPV 0.0 None None 0 None +3642 CLLRNSACL 0.0 None None 0 None +3643 CLPSRTSSV 0.0 None None 0 None +3644 CLRDLFFPL 0.0 None None 0 None +3645 CMKQRDEEF 0.0 None None 0 None +3646 CPPNHIVSL 0.961374972059 CPPNHIVSL CPAGHAVGI 28.0 23601|Genome_polyprotein|SRC279960|Hepatitis_C_virus_(isolate_H77)|63746 +3647 CQFGTVQLV 0.0 None None 0 None +3648 CRAETRKTF 0.443490453045 AETRKTF GESRKTF 27.0 19435|polyprotein|CDF77361.1|Dengue_virus_3|11069 +3649 CRCPIRGLV 0.0 None None 0 None +3650 CREELAVHL 0.0 None None 0 None +3651 CREQHPAQL 0.0 None None 0 None +3652 CRKMFRRSA 0.0 None None 0 None +3653 CRKMGLRVM 0.0 None None 0 None +3654 CRPQCCQSV 21.594714567 CRPQCCQSV CRVLCCYVL 28.0 11956|UL123;_IE1|AAR31448.1|Human_betaherpesvirus_5|10359 +3655 CRRGLEQLL 0.545054613977 CRRGLEQLL CRAKFKQLL 25.0 54330|BZLF1|AAA66529.1|Human_gammaherpesvirus_4|10376 +3656 CRYGRFHKF 0.0 None None 0 None +3657 CSDTHTNEL 0.00915963725351 CSDTHTNE ASDSLNNE 19.0 4371|tegument_protein_VP11/12|NP_044516.1|Human_alphaherpesvirus_2|10310 +3658 CVLYKYVPI 0.0 None None 0 None +3659 CVMTKIFSL 0.835554412193 MTKIFSL LTKRFSL 23.0 186354|polyprotein|AGO67248.1|Dengue_virus_2|11060 +3660 CYLITVTPI 0.0 None None 0 None +3661 CYLVFIGCF 0.0 None None 0 None +3662 CYNSAIQAL 0.0 None None 0 None +3663 CYSRDQIYI 0.0 None None 0 None +3664 CYVAICGPL 0.0 None None 0 None +3665 CYYYFLCLL 0.0 None None 0 None +3666 DAKRHRKVL 0.0 None None 0 None +3667 DALCRLLGL 0.0 None None 0 None +3668 DFKKKKGSM 0.0 None None 0 None +3669 DHRDLGLSV 0.0 None None 0 None +3670 DILVHHLAV 0.0 None None 0 None +3671 DLGDKILAL 0.0 None None 0 None +3672 DLHTRHGSI 0.236111111111 LHTRHG LHEQHG 26.0 75356|EBNA3A_nuclear_protein|Q8AZJ8|Human_gammaherpesvirus_4|10376 +3673 DLKMGKKPV 0.0 None None 0 None +3674 DLLGHPQAL 0.00441766560472 DLLGHP DLVGWP 22.0 9316|HCV-1|AAA45676.1|Hepatitis_C_virus_subtype_1a|31646 +3675 DLPTKRPAL 3.09221511525 PTKRP PTERP 25.0 141402|tegument_protein_VP22|NP_044651.1|Human_alphaherpesvirus_1|10298 +3676 DLQQKILCM 0.0 None None 0 None +3677 DMMKEFISM 0.0 None None 0 None +3678 DPKERIKVA 0.0 None None 0 None +3679 DPRLKWVVL 0.0 None None 0 None +3680 DRGGCVAGV 0.0 None None 0 None +3681 DRMQRVISV 0.0 None None 0 None +3682 DRMQRVISV 0.0 None None 0 None +3683 DRNDFPVVL 0.104073443917 RNDFPVVL RGDLPVWL 23.0 180611|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 +3684 DRQLAAQLL 0.0 None None 0 None +3685 DRSGARPHL 0.0 None None 0 None +3686 DRSHTLQRM 0.0 None None 0 None +3687 DRVERNCLL 0.0 None None 0 None +3688 DSDGEEPCY 0.0 None None 0 None +3689 DSHDYVFYL 0.0 None None 0 None +3690 DTDILSYSY 0.0421563317134 DTDILSYSY NPDIVIYQY 23.0 101813|Pol_polyprotein|Q9YLQ7|Human_immunodeficiency_virus_1|11676 +3691 DTDLYHCTA 0.0 None None 0 None +3692 DTEGILTEY 0.0 None None 0 None +3693 DYMGFTLKI 0.0 None None 0 None +3694 DYPCCIFPF 0.741073093531 DYPCCI HYPCTI 26.0 54821|E2_protein|AAM33354.1|Hepatitis_C_virus_subtype_1a|31646 +3695 DYRTVNNLI 0.0 None None 0 None +3696 EAEPYYCSL 0.0 None None 0 None +3697 EAKRQNLRL 0.0 None None 0 None +3698 EALIRHLNA 0.0370757155869 ALIRHLN SLLRHHN 23.0 96897|polyprotein|ABR25251.1|Hepatitis_C_virus_(isolate_H77)|63746 +3699 EAMNNAQKI 0.0 None None 0 None +3700 EASRRYKKV 0.0 None None 0 None +3701 EFPQKYYWW 2.66043171253 FPQKYYWW FPGKTVWF 25.0 183223|polyprotein|AGW21594.1|Dengue_virus_1|11053 +3702 EGQRRPSSV 0.0 None None 0 None +3703 EHEEDGSEI 0.0 None None 0 None +3704 EHGGKTVKV 0.0 None None 0 None +3705 EHLAAPRLV 0.0 None None 0 None +3706 EHNVTVLVV 0.0 None None 0 None +3707 EHQIGPQEI 0.0 None None 0 None +3708 EHRLHTPMY 0.0 None None 0 None +3709 EIKTIVKAI 1.03630759918 EIKTIVKAI DCKTILKAL 27.0 7708|gag_polyprotein|BAA00992.1|Human_immunodeficiency_virus_1|11676 +3710 EIMNRVVNA 0.0 None None 0 None +3711 EKRFKRKSV 0.0 None None 0 None +3712 ELACYNSAI 0.0 None None 0 None +3713 ELEHMRLRY 0.0 None None 0 None +3714 ELHARGHQV 0.0 None None 0 None +3715 ELHRQVKTL 0.0005030251957 ELHRQVKTL SLHYAWKTM 18.0 183252|polyprotein|AGT63075.1|Dengue_virus_1|11053 +3716 ELKQMCNPI 0.0 None None 0 None +3717 ELLLKVFAL 0.0 None None 0 None +3718 ELQARLAAL 0.0 None None 0 None +3719 ELRAHCETL 0.0 None None 0 None +3720 ELRRYLKSG 0.0 None None 0 None +3721 EMKCREKGF 0.0 None None 0 None +3722 EMLRRQIRL 0.0 None None 0 None +3723 EMRCQYETV 2.0101481376 MRCQYETV MNCSYENM 27.0 36306|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 +3724 EMYEKGLSV 0.0 None None 0 None +3725 EPKKKEKGM 0.0 None None 0 None +3726 EPKKRKVVP 0.0 None None 0 None +3727 EPRFRLNLF 0.0 None None 0 None +3728 ERDGLERAL 0.00214622386308 ERDGLERAL ERDIPERSW 20.0 180423|polyprotein|AGW21594.1|Dengue_virus_1|11053 +3729 ERDGLHSVV 0.0 None None 0 None +3730 ERDQLKETL 0.0 None None 0 None +3731 EREKMGVTM 0.0 None None 0 None +3732 ERFWRIILL 0.0 None None 0 None +3733 ERHVAVEGV 0.0 None None 0 None +3734 ERIDTNQKC 0.0542551505549 DTNQKC DTGQAC 24.0 22633|IMMUNOGENIC_PROTEIN_MPT64_(ANTIGEN_MPT64/MPB64)|CAA98382.1|Mycobacterium_tuberculosis_H37Rv|83332 +3735 ERKTMIKKI 0.0 None None 0 None +3736 ERLQALYMI 0.0 None None 0 None +3737 ERLQNPLRV 0.0 None None 0 None +3738 ERQCHNTAL 0.0 None None 0 None +3739 ERQCHNTAL 0.0 None None 0 None +3740 ERRDCIICC 0.0 None None 0 None +3741 ERSCWVRAI 0.0 None None 0 None +3742 ERSEQPLSV 0.0 None None 0 None +3743 ERSPQAAAV 0.0 None None 0 None +3744 ERTNQKWSV 0.0 None None 0 None +3745 ERTSATLTI 0.0 None None 0 None +3746 ERTTWVQKI 0.0 None None 0 None +3747 ERYGPVFTI 106.83056401 YGPVF YGPVF 30.0 67349|Latent_membrane_protein_2|Q69135|Human_gammaherpesvirus_4|10376 +3748 ETMLHGQVM 0.0 None None 0 None +3749 ETRPTPRLL 0.840404040404 RPTPRL RPGPRL 26.0 139406|polyprotein|ACT37184.1|Hepatitis_C_virus|11103 +3750 ETVSTTLCY 0.0 None None 0 None +3751 EYIVIPSTF 0.0 None None 0 None +3752 EYLLGSWVI 0.702063562848 LLGSWV ILGGWV 27.0 68461|polyprotein|ACZ60108.1|Hepatitis_C_virus|11103 +3753 EYNANTSVL 0.0 None None 0 None +3754 EYRPRTFCF 1.18624599551 PRTFC PRTWC 27.0 141218|regulatory_protein_ICP22|NP_044663.1|Human_alphaherpesvirus_1|10298 +3755 EYVKFLHTF 0.0 None None 0 None +3756 EYVTELPSF 0.0347332864612 EYVTELPS EYTDYMPS 22.0 180681|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 +3757 FAAQHGLAV 0.0 None None 0 None +3758 FAKLRHNTQ 0.0 None None 0 None +3759 FARGQRWRL 0.121912079341 FARGQRWRL FTRGDRCNL 24.0 43937|polyprotein|AAF01178.1|Hepatitis_C_virus_subtype_2a|31649 +3760 FARGQRWRL 0.198021676537 FARGQRWRL FTRGDRCNL 24.0 43937|polyprotein|AAF01178.1|Hepatitis_C_virus_subtype_2a|31649 +3761 FCLRYGAAL 0.0 None None 0 None +3762 FCSLHCLLY 0.0 None None 0 None +3763 FCYYYFLCL 0.0 None None 0 None +3764 FEESKSYEV 0.0 None None 0 None +3765 FEFSQVLAL 0.0 None None 0 None +3766 FESHRILHL 0.0518297042583 FESHRI FQSHQL 23.0 183245|polyprotein|AGT63074.1|Dengue_virus_1|11053 +3767 FFLSYLKSL 0.0 None None 0 None +3768 FFLSYLSLV 0.0 None None 0 None +3769 FGAIRRSDA 0.0 None None 0 None +3770 FGYENSPEL 0.0 None None 0 None +3771 FHFRRPWSF 5.80280666815 HFRRPW HFPRIW 25.0 187106|Vpr_protein|BAA93983.1|Human_immunodeficiency_virus_1|11676 +3772 FHFRRPWSF 0.902255091048 HFRRPW HFPRIW 25.0 187106|Vpr_protein|BAA93983.1|Human_immunodeficiency_virus_1|11676 +3773 FHFRRPWSF 0.171144540872 HFRRPW HFPRIW 25.0 187106|Vpr_protein|BAA93983.1|Human_immunodeficiency_virus_1|11676 +3774 FHHCHPKYS 0.0 None None 0 None +3775 FHHIDSAYL 0.0124561392202 FHHIDSA FGHSDAA 21.0 79506|E1_protein|BAA19893.1|Rubella_virus|11041 +3776 FHIGSAESM 0.0 None None 0 None +3777 FHLHNAHVL 0.444444444444 LHNAHVL FHNLHLL 26.0 79390|Protein_Tax-1|P0C213.1|Human_T-cell_lymphotropic_virus_type_1_(african_isolate)|39015 +3778 FHLPYLEQK 1.18628821685 HLPYLEQ HLPYIEQ 38.0 102819|Genome_polyprotein|P27958.3|Hepatitis_C_virus_subtype_1a|31646 +3779 FHLQHWKQI 0.0 None None 0 None +3780 FHLSIHLLY 6.46174150023 SIHLLY SLHLLF 25.0 57790|Protein_Tax-1|P03409.2|Human_T-lymphotropic_virus_1|11908 +3781 FHMASGEAL 0.0 None None 0 None +3782 FHPMRTLPM 0.0 None None 0 None +3783 FHVDQATTV 0.0 None None 0 None +3784 FHYDTQLSL 0.178804383033 FHYDTQL FSYDTRC 24.0 33382|polyprotein|AAB67037.1|Hepatitis_C_virus|11103 +3785 FHYLKKQET 0.0 None None 0 None +3786 FIADKLSTL 0.0 None None 0 None +3787 FIADKLSTL 0.0 None None 0 None +3788 FICLQFWCI 0.0 None None 0 None +3789 FIMFLFVYI 0.0 None None 0 None +3790 FINNSIVYL 0.214071856287 NNSIVY NSSIVY 26.0 6817|polyprotein|AAB67037.1|Hepatitis_C_virus_(isolate_H77)|63746 +3791 FKKARWTII 0.0 None None 0 None +3792 FKNHHNRTV 0.0 None None 0 None +3793 FLARTVSTL 5.81147313029 LARTVS LARTIS 25.0 44653|6_kDa_early_secretory_antigenic_target|P0A564.2|Mycobacterium_tuberculosis|1773 +3794 FLEHGEQAY 0.0 None None 0 None +3795 FLHERKQAS 0.0 None None 0 None +3796 FLKTLWAGL 0.0 None None 0 None +3797 FLLAMLLSI 0.169887629024 LAMLLSI MAMVLSI 24.0 184736|polyprotein|AGW21594.1|Dengue_virus_1|11053 +3798 FLLEFLLPL 0.0595499389227 LEFLLP LQFLIP 25.0 22235|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 +3799 FLLFSFLFL 9.80083437792e-06 FLLFSFLFL FLVPFVVFL 15.0 139746|Dense_granule_protein_3|B6KEU8.2|Toxoplasma_gondii|5811 +3800 FLRTYKNSV 0.0 None None 0 None +3801 FLSDLTPGY 0.0 None None 0 None +3802 FLSVFYTAV 0.0 None None 0 None +3803 FLTVMLLAL 0.0 None None 0 None +3804 FLVERKTIA 0.0 None None 0 None +3805 FMAYATQLF 0.0 None None 0 None +3806 FMKYLVNFI 0.393474742824 MKYLVNF LEYLVSF 25.0 69474|core_protein|BAF42671.1|Hepatitis_B_virus|10407 +3807 FMLVMICIL 0.0 None None 0 None +3808 FMWPLHWSM 17.8722123486 FMWPLH YPWPLY 25.0 75436|Polyprotein|P90247|Hepatitis_C_virus|11103 +3809 FPAMLQAPI 0.458346535653 FPAMLQAPI FPVRPQVPL 23.0 288104|nef_protein|ACR27130.1|Human_immunodeficiency_virus_1|11676 +3810 FPIIIAWAI 0.98110662908 FPIIIAWAI FPLTFGWCF 25.0 193060|Nef_protein|Q9YYU3|Human_immunodeficiency_virus_1|11676 +3811 FPKKSLMLM 0.0 None None 0 None +3812 FPLVRSCQM 0.204347866324 LVRSCQM LIRACML 24.0 36676|polyprotein|BAA09073.1|Hepatitis_C_virus_subtype_1b|31647 +3813 FPNGRLTFL 0.0 None None 0 None +3814 FPQKYYWWF 1.4267285342 FPQKYYWW FPGKTVWF 25.0 183223|polyprotein|AGW21594.1|Dengue_virus_1|11053 +3815 FPQNRYTQE 0.0 None None 0 None +3816 FPTDCVYVM 0.0 None None 0 None +3817 FPYCRAHVL 0.0 None None 0 None +3818 FPYCRAHVL 0.0 None None 0 None +3819 FPYCRSHVF 0.0 None None 0 None +3820 FPYGSSTAL 0.0 None None 0 None +3821 FPYNSDLSL 0.0732870943231 FPYNSDL LPTNADL 22.0 141411|transactivating_tegument_protein_VP16|NP_044650.1|Human_alphaherpesvirus_1|10298 +3822 FQFGAGTQV 0.0 None None 0 None +3823 FQGRRSPSF 0.0 None None 0 None +3824 FQRKKRRKF 0.0 None None 0 None +3825 FREDPVAWV 0.0 None None 0 None +3826 FREGRPREW 0.0 None None 0 None +3827 FRGALPVQI 0.0 None None 0 None +3828 FRGDGRTCC 0.0 None None 0 None +3829 FRHSPRNLI 0.0 None None 0 None +3830 FRKELRYFL 0.0 None None 0 None +3831 FRKELRYFL 0.0 None None 0 None +3832 FRLMHNLNF 0.0 None None 0 None +3833 FRLRRVASA 0.0 None None 0 None +3834 FRLWMTTEV 0.0 None None 0 None +3835 FRNDQEETT 0.0 None None 0 None +3836 FRNGLGTGM 0.343618280556 FRNGLGTGM YLYGVGSGM 25.0 177884|polyprotein|ACZ60102.1|Hepatitis_C_virus_genotype_1|41856 +3837 FRNSRLKQC 0.0 None None 0 None +3838 FRPPAWNRL 0.0 None None 0 None +3839 FRQGHQLFH 0.0 None None 0 None +3840 FRQLEDSQV 0.0 None None 0 None +3841 FRQSRSQVV 0.0 None None 0 None +3842 FRQSRSQVV 0.0 None None 0 None +3843 FRSHVPSHL 0.0 None None 0 None +3844 FRSLQGSVF 0.0 None None 0 None +3845 FRSPEDLSL 0.0 None None 0 None +3846 FRSSASGAL 0.0 None None 0 None +3847 FRTKDGSFV 0.482142857143 FRTKDG FKTEDG 26.0 150571|polyprotein|AGO67248.1|Dengue_virus_2|11060 +3848 FRVSISQTA 0.0 None None 0 None +3849 FRYEGSLTT 3.01020070508 FRYEGS FMYEGD 23.0 126028|ATP-dependent_helicase|NP_217813.1|Mycobacterium_tuberculosis_H37Rv|83332 +3850 FSDKKTITY 0.0 None None 0 None +3851 FSFINNSIV 0.0 None None 0 None +3852 FSIPTCLMY 0.0 None None 0 None +3853 FSKAQAEYL 0.0 None None 0 None +3854 FSYPSIHRF 1.49991207554 PSIHRF PGIYRF 24.0 22046|polyprotein_precursor|BAA01582.1|Hepatitis_C_virus|11103 +3855 FTDVSRFTL 0.0953424643358 TDVSR TDVSR 24.0 181733|Antigen_85-B|P0C5B9.1|Mycobacterium_tuberculosis|1773 +3856 FTFDLYRVL 0.0 None None 0 None +3857 FTSFLLLMY 0.0 None None 0 None +3858 FVEEWTESL 0.0 None None 0 None +3859 FVQKLLFPY 0.0 None None 0 None +3860 FWCAQFTSF 1.06197345475 FWCAQFTSF FWEAVFTGL 26.0 12108|polyprotein|AAP55688.1|Hepatitis_C_virus_subtype_2a|31649 +3861 FWKKILFVI 0.0 None None 0 None +3862 FWKLFYCKF 17.0058728052 LFYCK LLYCK 25.0 25460|Fusion_glycoprotein_F0_precursor|P03420.1|Human_respiratory_syncytial_virus_A2|11259 +3863 FYADSHHCV 0.0 None None 0 None +3864 FYAIVVPML 0.114734057478 FYAIVVPM FYGKAIPL 22.0 97400|Genome_polyprotein|P26664.3|Hepatitis_C_virus|11103 +3865 FYCDDLPLL 0.0 None None 0 None +3866 FYLGTYQAV 0.681699967536 FYLGTY FYLGQY 29.0 156550|E3_ubiquitin-protein_ligase_Mdm2|Q00987.1|Homo_sapiens|9606 +3867 FYMLTCIDL 0.0 None None 0 None +3868 FYQAGSLCI 0.0 None None 0 None +3869 FYTDSSSVL 1.41214657707 TDSSSVL TDSTSIL 27.0 107894|polyprotein|CAB41951.1|Hepatitis_C_virus|11103 +3870 FYTPALFSF 0.00424010201542 FYTPALF FYCNSLF 21.0 141323|multifunctional_expression_regulator|NP_044657.1|Human_alphaherpesvirus_1|10298 +3871 GAGPRFLEL 0.0 None None 0 None +3872 GDKQHFTTL 0.0 None None 0 None +3873 GGATRVYAL 0.0 None None 0 None +3874 GHDAPRRTL 0.490665707971 HDAPRRTL HGAGTRTI 20.0 4910|polyprotein|AAB67037.1|Hepatitis_C_virus_(isolate_H77)|63746 +3875 GHKEDAGVV 0.182420233615 HKEDAGVV EEEEAGVL 23.0 185491|polyprotein|AGO67248.1|Dengue_virus_2|11060 +3876 GHKGLNQCV 0.0 None None 0 None +3877 GHLEAASCI 0.0 None None 0 None +3878 GHLQIRSLL 0.0 None None 0 None +3879 GHLSKKMTL 0.0 None None 0 None +3880 GHNSWGFGV 0.601287595144 GHNSWGFG GDTAWDFG 28.0 180726|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 +3881 GHPQDGSGL 0.0 None None 0 None +3882 GHPSLSQHL 1.07017587087 HPSLSQHL EPTLGQHL 29.0 79308|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 +3883 GHTGERHRV 0.0 None None 0 None +3884 GHTPNGRHF 0.0 None None 0 None +3885 GHVAGEQML 0.431336840656 GHVAGEQML GHQAAMQML 28.0 101673|gag_protein|ABO73990.1|Human_immunodeficiency_virus_1|11676 +3886 GLHSSFMPL 0.0 None None 0 None +3887 GLSVRPHAI 0.0 None None 0 None +3888 GMFTLRMAL 0.0 None None 0 None +3889 GNYSRSSHV 0.0 None None 0 None +3890 GPCRRRFSF 0.779795817205 GPCRRRF GPADRRF 27.0 155637|tegument_protein|CAB06732.1|Human_alphaherpesvirus_2|10310 +3891 GPLPKSYAV 0.0 None None 0 None +3892 GPRTKAWFL 1.91866745733 PRTKAWFL PSTLRWFF 25.0 38724|Genome_polyprotein|P08617.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 +3893 GRAEESVVL 0.0 None None 0 None +3894 GRAPCWQRL 0.487372385753 APCWQR APAWSR 27.0 155554|RL2|CAB06760.1|Human_alphaherpesvirus_2|10310 +3895 GREAEMQEL 0.0 None None 0 None +3896 GRMHIGDEL 0.0 None None 0 None +3897 GRMMFVGTL 0.0 None None 0 None +3898 GRNGQKAAL 0.0 None None 0 None +3899 GRVEKLLDL 0.0 None None 0 None +3900 GSDSSNGAV 0.0 None None 0 None +3901 GSEDFEDTY 0.0 None None 0 None +3902 GTNIVILEY 0.0118445772921 GTNIVILE GTQAVVLK 22.0 27981|IMMUNOGENIC_PROTEIN_MPT64_(ANTIGEN_MPT64/MPB64)|CAA98382.1|Mycobacterium_tuberculosis_H37Rv|83332 +3903 GVLECPRLI 0.0 None None 0 None +3904 HAKKKPNPV 0.718544984666 KKKPNPV KKKKNPM 28.0 142203|polyprotein|BAD73974.1|Hepatitis_C_virus_subtype_1b|31647 +3905 HHIDSAYLY 0.0 None None 0 None +3906 HHKGKMKAL 0.0 None None 0 None +3907 HHKHKELQV 0.0 None None 0 None +3908 HHRFNNFML 0.0 None None 0 None +3909 HIKDKKLPL 0.0 None None 0 None +3910 HLLSHSYCL 0.109600489264 HLLSHSYCL HLYSHPIIL 24.0 190568|polymerase|AAD16253.1|Hepatitis_B_virus|10407 +3911 HLMGQLSSL 3.88330048497 HLMGQLSSL HLAFQLSSI 27.0 24172|pX-rex-orf_I_{alternatively_spliced}|AAB23359.1|Human_T-lymphotropic_virus_1|11908 +3912 HMRLRYLAA 0.0 None None 0 None +3913 HPKYSFRRL 0.0 None None 0 None +3914 HPLRYTLIM 0.0 None None 0 None +3915 HRADVYVGV 0.0 None None 0 None +3916 HREDFEARL 0.159782640157 HREDFE HGEEFE 24.0 155811|ribonucleotide_reductase_large_subunit|CAB06725.1|Human_alphaherpesvirus_2|10310 +3917 HRGTGAVYV 27.0330536607 RGTGAVYV RGTSFVYV 29.0 27285|pol_protein|BAA32832.1|Hepatitis_B_virus|10407 +3918 HRLGESQTL 0.0 None None 0 None +3919 HRLHTPMYL 0.0 None None 0 None +3920 HRQAEVHKV 0.0 None None 0 None +3921 HRQQRGQQL 0.0 None None 0 None +3922 HRSKRGSSV 0.0 None None 0 None +3923 HRTRCLSKL 0.0 None None 0 None +3924 HRYPRVMAA 0.0 None None 0 None +3925 HRYPRVMAA 0.0 None None 0 None +3926 HSHLLSHSY 2.5848832505 HLLSHS HLYSHP 23.0 190568|polymerase|AAD16253.1|Hepatitis_B_virus|10407 +3927 HSYEAGTEI 0.0 None None 0 None +3928 HTPNGRHFY 0.701274710612 TPNGRHFY TDNNRSFY 27.0 98603|trans-sialidase,_putative|EAN82716.1|Trypanosoma_cruzi|5693 +3929 HWSMWLGVF 0.372066895841 WSMWLGV WTMKIGI 25.0 186524|polyprotein|AGW21594.1|Dengue_virus_1|11053 +3930 HYATILTSL 0.0 None None 0 None +3931 HYHHRFNNF 2.27650024439 YHHRFNN YQHKFNS 30.0 23270|polyprotein|AAB67036.1|Hepatitis_C_virus_(isolate_H77)|63746 +3932 HYISIFYAL 0.00687708027962 YISIFYA YMSPFYG 22.0 141469|envelope_glycoprotein_B|NP_044629.1|Human_alphaherpesvirus_1|10298 +3933 HYLRDVLPL 0.0 None None 0 None +3934 HYQGTWYLT 0.0 None None 0 None +3935 HYRKRGAHL 0.0 None None 0 None +3936 IAHAWWAHF 0.461739437354 HAWWAHF HARWAAF 28.0 141262|DNA_polymerase_catalytic_subunit|NP_044632.1|Human_alphaherpesvirus_1|10298 +3937 IAMYFYTTL 0.0 None None 0 None +3938 IEYGSPEEL 0.0 None None 0 None +3939 IFIASIYLL 0.0 None None 0 None +3940 IFLFVIVTI 0.0 None None 0 None +3941 IFPFALIFF 0.0 None None 0 None +3942 IFPFILIFF 0.0 None None 0 None +3943 IFSEKNRLV 0.0 None None 0 None +3944 IFSFINNSI 0.0 None None 0 None +3945 IFVSSYINI 0.0 None None 0 None +3946 IGRNRSPCM 0.0 None None 0 None +3947 IHDGAVHTI 0.552631578947 HDGAVHT QEGAMHT 26.0 50596|polyprotein|ABG75765.1|Dengue_virus_1|11053 +3948 IHDRQLRSF 0.0 None None 0 None +3949 IHEDEVDDM 0.113033351011 EDEVD EDEID 25.0 110431|E7|AAD33253.1|Human_papillomavirus_type_16|333760 +3950 IHFTKKDYV 0.0 None None 0 None +3951 IHGASNHCL 0.0 None None 0 None +3952 IHIDDNKWV 0.169553246094 DDNKWV DENPWL 25.0 31802|large_delta_antigen|AAG26087.1|Hepatitis_delta_virus_TW2667|10000523 +3953 IHLLDSLRL 0.0 None None 0 None +3954 IHLLYPPSL 0.0620423197569 IHLLYPP LHVWVPP 22.0 40158|polyprotein|AAA45534.1|Hepatitis_C_virus|11103 +3955 IHPRDRSTV 0.0 None None 0 None +3956 IHTDDNKCV 0.000134201508342 IHTDDNKCV IHDIILECV 16.0 110306|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 +3957 ILAVLPSLF 0.517090203886 AVLPSLF GIIPSMF 24.0 180407|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 +3958 ILKKRQQAA 0.0 None None 0 None +3959 ILKRRYQEP 0.0 None None 0 None +3960 ILLTQFHFL 0.852006511865 ILLTQF ILLTHF 23.0 422984|NS5B_protein|ABB72740.1|Hepatitis_C_virus_genotype_1|41856 +3961 ILMRQPLPA 0.0 None None 0 None +3962 ILRSKMKTV 0.0 None None 0 None +3963 ILRVYSGVL 0.0 None None 0 None +3964 ILSSRSRQL 0.0 None None 0 None +3965 ILSSRSRQL 0.0 None None 0 None +3966 INFNHDSSI 0.0 None None 0 None +3967 IQWSYWGVF 0.0967863310004 WSYWGVF WAYHGSY 24.0 180582|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 +3968 IRAANRRGL 0.0 None None 0 None +3969 IRDGSTMTF 0.0 None None 0 None +3970 IREYCPYTY 0.0377782116104 IREYCPYTY ISEYRHYCY 23.0 28484|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 +3971 IRFLRQYEF 0.0 None None 0 None +3972 IRHGNVIAC 0.513115695515 GNVIAC GNMSAC 24.0 133645|cell_surface_protein|NP_302626.1|Mycobacterium_leprae|1769 +3973 IRHLNATSF 0.0 None None 0 None +3974 IRIDTIHLL 0.0 None None 0 None +3975 IRLNRQRHT 0.0 None None 0 None +3976 IRNMAPDSL 0.0 None None 0 None +3977 IRPPDSRSL 0.420410333594 PPDSRSL PPGARSM 25.0 72928|Genome_polyprotein|P26662.3|Hepatitis_C_virus_(isolate_Japanese)|11116 +3978 IRRGGKHQL 0.0 None None 0 None +3979 IRRLRPSSI 0.13780610868 RRLRPS KRLEPS 22.0 50894|Genome_polyprotein|P27909.2|Dengue_virus_type_1_Hawaii|10000440 +3980 IRRLRPSSI 0.073674283114 RRLRPS KRLEPS 22.0 50894|Genome_polyprotein|P27909.2|Dengue_virus_type_1_Hawaii|10000440 +3981 IRRRGSTSL 0.0 None None 0 None +3982 IRYLHSLQI 0.0 None None 0 None +3983 ISELLFECY 0.0271004989586 ISELLFECY ISEYRHYCY 23.0 28484|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 +3984 ISFSMSEKM 0.0 None None 0 None +3985 ISKRKVSVA 0.0 None None 0 None +3986 ISLGFFLVF 0.0249581117984 ISLGFFLV LQAGFFLL 24.0 69715|envelope_protein|BAF48755.1|Hepatitis_B_virus|10407 +3987 ISSSAGLPY 0.0 None None 0 None +3988 ITIRNPLRY 0.0 None None 0 None +3989 ITMDQKKTI 0.0 None None 0 None +3990 ITMRYIHFL 0.0 None None 0 None +3991 ITTFDRLAY 13.9529411765 TFDRL TFDRL 26.0 66405|polyprotein|AAB67037.1|Hepatitis_C_virus_(isolate_H77)|63746 +3992 IVHRQFYLF 1.36497494935 IVHRQFYL LVHRQWFL 32.0 41407|Envelope_protein|NP_739583.2|Dengue_virus_2|11060 +3993 IVMGYSSGI 0.113615285052 MGYSSGI MDYSNGL 24.0 51604|FL-160-2_protein_-_Trypanosoma_cruzi|JH0823|Trypanosoma_cruzi|5693 +3994 IWFSIPTCL 0.0 None None 0 None +3995 IYAALPYVK 0.0 None None 0 None +3996 IYAFMGTPM 0.130873138164 IYAFMGTP LRAYMNTP 24.0 65497|HCV-1|AAA45676.1|Hepatitis_C_virus_genotype_1|41856 +3997 IYCRPFTTL 0.0 None None 0 None +3998 IYCVYPDSL 0.0 None None 0 None +3999 IYGLCVVIV 6.9120502655 YGLCVV YGVCIM 27.0 148117|early_protein|CAA52585.1|Human_papillomavirus_type_52|10618 +4000 IYHDSRIHV 0.0 None None 0 None +4001 IYTIVNIKI 0.0 None None 0 None +4002 IYVDKVRHV 3.30136379321 YVDKVR YLDKVR 28.0 74605|Circumsporozoite_protein_precursor|P08677.2|Plasmodium_vivax_strain_Belem|31273 +4003 KAFKRSSYL 0.0 None None 0 None +4004 KAFKRSSYL 0.0 None None 0 None +4005 KAMERSSLM 0.0 None None 0 None +4006 KHFIHLITV 0.0 None None 0 None +4007 KHLSRSNWL 0.0 None None 0 None +4008 KHNEEIRFL 0.0 None None 0 None +4009 KHRNMHCKI 0.0 None None 0 None +4010 KHRSEISMM 0.0 None None 0 None +4011 KIHIRETAI 0.0 None None 0 None +4012 KILKKRQQA 0.0 None None 0 None +4013 KISKRKVSV 0.0 None None 0 None +4014 KKRRKFWKA 0.101871750519 KRRKFW RRRKGW 25.0 55718|Probable_membrane_glycoprotein_precursor|P03218.1|Human_herpesvirus_4_strain_B95-8|10377 +4015 KLKPKKPTL 0.0 None None 0 None +4016 KLQPYFQTL 0.0163360332358 LQPYFQ LSPYYK 22.0 149024|NS2_protein|NP_751923.1|Hepatitis_C_virus_(isolate_H77)|63746 +4017 KMFRRSAHL 0.0 None None 0 None +4018 KRCALRLLV 0.0 None None 0 None +4019 KRFKRKSVV 0.0 None None 0 None +4020 KRILMPQVM 0.0 None None 0 None +4021 KRISHKAAL 0.0 None None 0 None +4022 KRQNLRLAL 0.0 None None 0 None +4023 KRQRAMETL 0.0 None None 0 None +4024 KRSPAWNEM 2.71823855445 SPAWN APAWS 24.0 155554|RL2|CAB06760.1|Human_alphaherpesvirus_2|10310 +4025 KRYLSQREV 0.951221917101 YLSQRE YLGKRE 22.0 150698|polyprotein|AGO67248.1|Dengue_virus_2|11060 +4026 KSDGLSLAV 0.0 None None 0 None +4027 KSFSKYASF 0.0 None None 0 None +4028 KWIREGYLV 0.0 None None 0 None +4029 KYMPPCSLV 0.0 None None 0 None +4030 KYPYWYQQK 0.419548617337 KYPYW KYTFW 25.0 137660|L1|ACL12325.1|Human_papillomavirus_type_58|10598 +4031 KYSTGIGWI 0.0 None None 0 None +4032 KYSTPPYLL 0.848971252603 KYSTPPYLL KYTSFPWLL 27.0 34616|pol_protein|BAA32832.1|Hepatitis_B_virus|10407 +4033 LAGQKRCAL 0.0 None None 0 None +4034 LAKVKYTAS 0.0 None None 0 None +4035 LALLKQVSV 0.0 None None 0 None +4036 LANDPIQVV 0.0 None None 0 None +4037 LAQSFFNCL 0.0 None None 0 None +4038 LCAIYFLSI 0.0 None None 0 None +4039 LCIKHFNIL 0.0 None None 0 None +4040 LEHMRLRYL 0.0 None None 0 None +4041 LFAAVVLLI 0.0 None None 0 None +4042 LFKKARWTI 0.0 None None 0 None +4043 LFLLFSFLF 0.0 None None 0 None +4044 LFPRLPSIL 6.65851410543 FPRLP FPRAP 24.0 62355|Genome_polyprotein|P08617.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 +4045 LFSFMTHCF 0.109472071245 FSFMTHC FSYDTRC 24.0 33382|polyprotein|AAB67037.1|Hepatitis_C_virus|11103 +4046 LFSFMTHRF 0.0 None None 0 None +4047 LGRNRHFGF 0.138393893319 GRNRHF GRDAHY 22.0 66798|glycoprotein_gp35/37|AAC59622.1|Human_gammaherpesvirus_8|37296 +4048 LHAPMYNLL 0.378354025976 APMYNLL VPNYNLI 24.0 150693|polyprotein|AGO67248.1|Dengue_virus_2|11060 +4049 LHAPMYNLL 0.21694931808 APMYNLL VPNYNLI 24.0 150693|polyprotein|AGO67248.1|Dengue_virus_2|11060 +4050 LHEQLGDRL 1.76159415596 LHEQLGD CYEQLGD 28.0 147561|early_protein|CAA52586.1|Human_papillomavirus_type_52|10618 +4051 LHFDAVQIC 0.0 None None 0 None +4052 LHFMPCVYI 0.0 None None 0 None +4053 LHFVQKLLF 0.183771171451 HFVQKLLF HFQRALIF 24.0 183577|polyprotein|AGK36298.1|Dengue_virus_2|11060 +4054 LHHKHKELQ 0.000432776802688 LHHKHKELQ LHEYMLDLQ 17.0 110335|E7|AAD33253.1|Human_papillomavirus_type_16|333760 +4055 LHHTHIALL 0.0 None None 0 None +4056 LHKDSNMPV 0.0 None None 0 None +4057 LHMNLLSYF 0.0 None None 0 None +4058 LHNAHVLDV 0.5 LHNAHVL FHNLHLL 26.0 79390|Protein_Tax-1|P0C213.1|Human_T-cell_lymphotropic_virus_type_1_(african_isolate)|39015 +4059 LHQCVLRFL 0.0 None None 0 None +4060 LHQGGATRV 0.0 None None 0 None +4061 LHRASGVGV 0.0 None None 0 None +4062 LHSGLQILI 0.0 None None 0 None +4063 LHTPVYFLL 0.0 None None 0 None +4064 LHTPVYFLL 0.0 None None 0 None +4065 LHTRHGSIL 0.196978634169 LHTRHG LHEQHG 26.0 75356|EBNA3A_nuclear_protein|Q8AZJ8|Human_gammaherpesvirus_4|10376 +4066 LHVGCDEVY 0.0 None None 0 None +4067 LHYEEIPEY 0.0 None None 0 None +4068 LIATQLLFY 0.0 None None 0 None +4069 LIKHKKTHI 0.679666392493 KHKKTHI KYKLKHI 21.0 34482|gag_polyprotein|BAA00992.1|Human_immunodeficiency_virus_1|11676 +4070 LIKYRQNHA 0.0 None None 0 None +4071 LIMNKRLGL 0.0 None None 0 None +4072 LKKRQQAAL 0.0 None None 0 None +4073 LKLVKRNSL 0.0 None None 0 None +4074 LLCARAWLL 0.0 None None 0 None +4075 LLDRRPHGY 0.0 None None 0 None +4076 LLESYSASL 0.0 None None 0 None +4077 LLGHKTVTI 0.0 None None 0 None +4078 LLGKKGTSA 0.473336145345 LLGKKGTSA LLGLWGTAA 25.0 37498|FL-160-2_protein_-_Trypanosoma_cruzi|JH0823|Trypanosoma_cruzi|5693 +4079 LLHTIITPM 0.0 None None 0 None +4080 LLKKLCIKL 2.09957355011 LKKLCI LRKLCI 28.0 184299|envelope_protein|AGT63061.1|Dengue_virus_3|11069 +4081 LLKSDGLSL 0.0 None None 0 None +4082 LLKTAFHPV 0.0 None None 0 None +4083 LLLMYSYAV 0.357608766066 LLLMYSYAV LLLVAHYAI 24.0 150377|polyprotein|AGS49173.1|Dengue_virus_2|11060 +4084 LLLQALQAL 0.0 None None 0 None +4085 LLMNKPYLA 1.11933186224 NKPYL NLPYL 22.0 13518|HCV-1|AAA45676.1|Hepatitis_C_virus_genotype_1|41856 +4086 LLMYTKLVV 0.0 None None 0 None +4087 LLNVHLSKL 0.0 None None 0 None +4088 LLRDFVAPL 0.0 None None 0 None +4089 LLRGHDQSA 0.0 None None 0 None +4090 LLRLLRKAM 0.0 None None 0 None +4091 LLRNDARSL 0.0 None None 0 None +4092 LLSFKRQRA 0.0 None None 0 None +4093 LLSRKDSIF 0.0 None None 0 None +4094 LLTQRLQGL 0.228736119694 LLTQRLQGL LITGRLQSL 27.0 36724|Spike_glycoprotein_precursor|P59594.1|SARS_coronavirus|227859 +4095 LMACATQLF 0.0 None None 0 None +4096 LMGQLSSLY 0.0 None None 0 None +4097 LMKMDDPSI 0.0 None None 0 None +4098 LMKQKKSSC 0.0 None None 0 None +4099 LNKLDFYVL 0.0 None None 0 None +4100 LNRQRHTPM 18.4848484848 RHTPM RHTPV 26.0 4156|polyprotein|ABR25251.1|Hepatitis_C_virus|11103 +4101 LPALRKTGV 0.0 None None 0 None +4102 LPAVHALRL 0.0 None None 0 None +4103 LPGLHFMPG 0.0 None None 0 None +4104 LPGMRGPPG 0.212348087935 GMRGP GQRGP 24.0 48915|kaposin|AAC57155.1|Human_gammaherpesvirus_8|37296 +4105 LPKDRFFAV 0.0 None None 0 None +4106 LPKEKLAAA 0.694505649699 LPKEKL LPREKL 27.0 54706|matrix_protein_2-1|AAS22094.1|Human_metapneumovirus|162145 +4107 LPMTLLLLL 0.0 None None 0 None +4108 LPQGRESPI 0.130541001792 LPQGRE LPSGRN 22.0 54709|protein_F_[Hepatitis_C_virus_subtype_1b]|ACA50643.1|Hepatitis_C_virus_(isolate_Japanese)|11116 +4109 LPRSKDTIL 0.0 None None 0 None +4110 LPRVRGTTL 0.0 None None 0 None +4111 LPSCRLAPA 0.0 None None 0 None +4112 LPTLKFQTF 0.0 None None 0 None +4113 LPYVKKTGM 0.0 None None 0 None +4114 LQKVRQEVL 0.0 None None 0 None +4115 LQLYRFSPI 0.67159130189 QLYRFSP QLFTFSP 28.0 51346|Genome_polyprotein|P29846.3|Hepatitis_C_virus|11103 +4116 LQRRRLSLL 0.0 None None 0 None +4117 LRADTSFFL 0.0 None None 0 None +4118 LRAKYRESL 0.0 None None 0 None +4119 LRAKYRESL 0.0 None None 0 None +4120 LRAPPGPQL 10.4355383797 PGPQL PGPRL 25.0 139406|polyprotein|ACT37184.1|Hepatitis_C_virus|11103 +4121 LRCHYHHRF 0.0 None None 0 None +4122 LRETRDQPL 0.0 None None 0 None +4123 LRIMLGEIL 0.0 None None 0 None +4124 LRINEVMVY 0.0 None None 0 None +4125 LRKGPIMEV 0.0 None None 0 None +4126 LRKHQILHL 0.0 None None 0 None +4127 LRKHQITHL 0.0 None None 0 None +4128 LRKPQNSEC 0.0 None None 0 None +4129 LRKQNFQPA 0.0 None None 0 None +4130 LRLALDQYL 0.0 None None 0 None +4131 LRLEINHTI 0.0 None None 0 None +4132 LRLPGGSCM 9.609030837 LRLPGGSCM VTLPTGQCL 26.0 71409|cysteine_proteinase_cruzipain_(EC_3.4.22.-)_-_Trypanosoma_cruzi|A45629|Trypanosoma_cruzi|5693 +4133 LRLRWGQII 0.0 None None 0 None +4134 LRLSEPAEI 0.0 None None 0 None +4135 LRMSDPSHI 33.5031608636 MSDPSHI LTDPSHI 32.0 59709|polyprotein|BAD73987.1|Hepatitis_C_virus_subtype_1b|31647 +4136 LRMSRSYPT 0.0 None None 0 None +4137 LRNDARSLY 0.0 None None 0 None +4138 LRPSSIETY 0.054584495544 PSSIET PESLET 23.0 184531|polyprotein|AFP27208.1|Dengue_virus_4|11070 +4139 LRQWIVVTM 0.0 None None 0 None +4140 LRRHRDVSA 0.0863636363636 LRRHRDV LRRHIDL 26.0 51526|HCV-1|AAA45676.1|Hepatitis_C_virus|11103 +4141 LRRMNSFQV 0.0074451481212 LRRMNSF LRKKSSF 21.0 116781|Nucleoprotein|P05133.1|Hantaan_virus_76-118|11602 +4142 LRRNYRCAI 0.0 None None 0 None +4143 LRRNYRCAI 0.0 None None 0 None +4144 LRRQDYQEI 0.0 None None 0 None +4145 LRRVASALL 0.0 None None 0 None +4146 LRSDAPAQL 0.0 None None 0 None +4147 LRSEEDGLV 0.0 None None 0 None +4148 LRSERNNTM 0.0 None None 0 None +4149 LRSIRVRLL 0.169857739813 SIRVRLL SVRARLL 25.0 149115|NS5_protein|BAA00702.1|Hepatitis_C_virus_(isolate_H77)|63746 +4150 LRSQAALSL 0.0 None None 0 None +4151 LRSQFPLIL 0.0 None None 0 None +4152 LRTEQNDFI 0.0 None None 0 None +4153 LRVSDGSLL 0.0 None None 0 None +4154 LRWEYGSIL 0.714053568268 WEYGSI WDFGSV 29.0 72301|envelope_protein|YP_001527880.1|West_Nile_virus_NY-99|10000971 +4155 LRYFLKHGI 0.202505548815 LRYFLKHGI MRYVLDHLI 24.0 25237|Transcription_activator_BRLF1|P03209.1|Human_herpesvirus_4_strain_B95-8|10377 +4156 LRYGAALIY 0.0 None None 0 None +4157 LSEFPEDSY 0.0 None None 0 None +4158 LSFKRQRAM 0.0 None None 0 None +4159 LSIIRFKGL 0.0 None None 0 None +4160 LSPMNHLCY 0.0 None None 0 None +4161 LSSLWYHTY 0.0419625022834 SLWYHTY DMWEHAF 22.0 9415|Superoxide_dismutase|P17670.1|Mycobacterium_tuberculosis|1773 +4162 LSTCRKLSL 0.0 None None 0 None +4163 LTDYDTRFY 0.0314758674337 LTDYDTRFY VTDNNRSFY 22.0 98603|trans-sialidase,_putative|EAN82716.1|Trypanosoma_cruzi|5693 +4164 LTEPHLRLL 0.0 None None 0 None +4165 LTGLVWQRY 0.654105044037 LTGLVWQR VSGLAWTR 27.0 54797|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 +4166 LTIYAALPY 0.0 None None 0 None +4167 LTMCMKKSL 0.0 None None 0 None +4168 LTQKQVLNY 0.0 None None 0 None +4169 LVAQHYAAL 0.0 None None 0 None +4170 LVDTVIDAY 0.0 None None 0 None +4171 LVQNSCWLI 0.0 None None 0 None +4172 LVRDRMKEL 0.0 None None 0 None +4173 LWQSCEESF 0.0 None None 0 None +4174 LYAVMGRSW 0.0 None None 0 None +4175 LYEDTLYTV 0.015462532395 YEDTLYTV YENLKYSV 22.0 186551|polyprotein|AGW21594.1|Dengue_virus_1|11053 +4176 LYEDWCQTV 0.0 None None 0 None +4177 LYEDWCQTV 0.0 None None 0 None +4178 LYFHSFIRI 0.0 None None 0 None +4179 LYFLAGQSL 0.0 None None 0 None +4180 LYFTRPVPL 0.0 None None 0 None +4181 LYGEQGHRW 0.0 None None 0 None +4182 LYGHSTHDL 0.675789473684 LYGHSTHDL LYANSAHAL 26.0 144913|Hexon_protein|P04133.3|Human_adenovirus_5|28285 +4183 LYHRDLAKW 0.0701635842114 HRDLAKW HSDAACW 24.0 79506|E1_protein|BAA19893.1|Rubella_virus|11041 +4184 LYMINHFFC 0.0 None None 0 None +4185 LYPDINNPF 0.0201559961005 PDINNPF PDYNPPL 23.0 103563|polyprotein|BAB18806.1|Hepatitis_C_virus|11103 +4186 LYPPSLPPF 61.161244788 YPPSLP FPPALP 29.0 30815|Genome_polyprotein|P26662.3|Hepatitis_C_virus|11103 +4187 LYTAYHVFF 0.0 None None 0 None +4188 LYVWKSELV 0.0 None None 0 None +4189 MACDRYVAI 0.0 None None 0 None +4190 MAEVNITYV 0.0 None None 0 None +4191 MAFDRYVAI 0.0 None None 0 None +4192 MAFDRYVAI 0.0 None None 0 None +4193 MAHERRDQL 0.0 None None 0 None +4194 MAHERRDQL 0.0 None None 0 None +4195 MAIGHFGQL 0.0 None None 0 None +4196 MAKYWNQFL 0.0 None None 0 None +4197 MAMSSRLAL 0.0 None None 0 None +4198 MATAYIRSM 0.0 None None 0 None +4199 MAYDQFLAI 0.0 None None 0 None +4200 MAYDQFLAI 0.0 None None 0 None +4201 MAYSITCPI 2.71923629545 MAYSITCPI LAYGRTCVL 24.0 17620|Early_antigen_protein_D|P03191.1|Human_herpesvirus_4_strain_B95-8|10377 +4202 MCMKKSLRL 0.0 None None 0 None +4203 MERERKAIA 0.0 None None 0 None +4204 MEVEAEQLL 0.0 None None 0 None +4205 MFATDYTTI 0.0560253733504 ATDYTTI STDSTTI 24.0 108148|polyprotein|AAF65953.1|Hepatitis_C_virus|11103 +4206 MFTLRMALF 0.0 None None 0 None +4207 MGHLQIRSL 0.0 None None 0 None +4208 MGKSTHTSM 20.3108019723 GKSTH GKSTH 28.0 20686|UL123;_IE1|AAR31448.1|Human_betaherpesvirus_5|10359 +4209 MHEEGYNKL 0.0 None None 0 None +4210 MHEYKIQGL 0.0 None None 0 None +4211 MHFCGGSFI 0.0 None None 0 None +4212 MHHPGSRKF 0.0 None None 0 None +4213 MHKTGLLGL 0.0 None None 0 None +4214 MHNLLIHRV 0.0 None None 0 None +4215 MHPDGRFEC 0.0 None None 0 None +4216 MIFILFLVI 0.0 None None 0 None +4217 MIRVKDSLI 0.0 None None 0 None +4218 MKQKKSSCL 0.0 None None 0 None +4219 MLCFYTPAL 0.00401934350471 MLCFYTPAL LMCAVHPTL 19.0 7660|polyprotein|AAA45677.1|Hepatitis_C_virus_(isolate_H77)|63746 +4220 MLHLYPGPM 0.140845070423 MLHLYPGPM LFQLYRGPL 26.0 38724|Genome_polyprotein|P08617.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 +4221 MLKTGISTV 0.0 None None 0 None +4222 MLLMNLATA 0.284963760522 LMNLAT LMNLAT 28.0 422997|preC/core_protein|CAJ33968.1|Hepatitis_B_virus|10407 +4223 MLLSILLPL 0.00626047139659 MLLSILLP MLILGLLP 20.0 41971|putative_D-ribose-binding_protein|NP_301386.1|Mycobacterium_leprae|1769 +4224 MLLSQNASI 0.0 None None 0 None +4225 MLNKVLYRL 7.66146587433e-05 MLNKVLYRL LLNGWRWRL 16.0 37607|kaposin|AAC57155.1|Human_gammaherpesvirus_8|37296 +4226 MLRELSSAF 0.0 None None 0 None +4227 MLRRQIRLL 0.0 None None 0 None +4228 MLRRQIRLL 0.0 None None 0 None +4229 MLSLRESPM 0.0 None None 0 None +4230 MLTSKVTVL 0.0 None None 0 None +4231 MLYRTVREL 0.0 None None 0 None +4232 MLYRTVREL 0.0 None None 0 None +4233 MMQCHRLSW 0.0 None None 0 None +4234 MNKRLGLEL 0.0 None None 0 None +4235 MNYKKGRAF 0.0 None None 0 None +4236 MPILKSVLI 0.0 None None 0 None +4237 MPKKVISAL 0.0 None None 0 None +4238 MPLLKLSCS 4.68242710796 MPLLKLSC VPLLAIGC 26.0 180802|polyprotein|AGO67248.1|Dengue_virus_2|11060 +4239 MPQYLASPL 0.0 None None 0 None +4240 MQFTQALEV 0.0 None None 0 None +4241 MRAAYLDDL 0.0 None None 0 None +4242 MRCQYETVL 0.840717365425 MRCQYETV MNCSYENM 27.0 36306|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 +4243 MREQRERQL 0.0 None None 0 None +4244 MRLRGGRMI 0.0 None None 0 None +4245 MRPISGVML 0.0 None None 0 None +4246 MRQPLPASM 0.0 None None 0 None +4247 MRRRQCEEV 0.695739763979 RRQCEEV KKKCDEV 25.0 24765|polyprotein_[Hepatitis_C_virus]|ABR27360.1|Hepatitis_C_virus|11103 +4248 MRRYQSRVI 0.0 None None 0 None +4249 MRRYQSRVI 0.0 None None 0 None +4250 MRSCLRLAL 0.0 None None 0 None +4251 MRSCLRLAL 0.0 None None 0 None +4252 MSEGIVKLY 0.0 None None 0 None +4253 MSPRVFFLL 0.0 None None 0 None +4254 MSQSQVALL 0.0 None None 0 None +4255 MSRSYPTGL 0.0 None None 0 None +4256 MWPLHWSMW 0.57916563282 MWPLHWSMW LWPKTHTLW 28.0 184702|non-structural_protein_1|AGM49312.1|Dengue_virus|12637 +4257 MYCLMLQCW 0.418731580108 CLMLQC CLIISC 25.0 93431|pre-C/C_protein|ABY54138.1|Hepatitis_B_virus|10407 +4258 MYCMVFLVL 0.877192982456 MYCMVFLV LLCLIFLL 26.0 37466|surface_antigen|BAF44879.1|Hepatitis_B_virus|10407 +4259 MYGAETEKF 0.0 None None 0 None +4260 MYMSVLSLI 0.0 None None 0 None +4261 MYMSVLSLI 0.0 None None 0 None +4262 MYSVVPQMV 0.0 None None 0 None +4263 MYSVVPQMV 0.0 None None 0 None +4264 MYSYAVPPL 0.236147358092 MYSYAVP IYVYALP 25.0 58463|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 +4265 MYTKLVVGF 0.0 None None 0 None +4266 NEILRRYSV 0.0138030526412 NEILRRY NKIVRMY 23.0 34304|Gag_polyprotein|P88150|Human_immunodeficiency_virus_1|11676 +4267 NFIERFWRI 0.0 None None 0 None +4268 NFIERFWRI 0.0 None None 0 None +4269 NFSINWWPI 0.882013080391 NWWPI NWWTL 29.0 74886|latent_membrane_protein_1|AAS99606.1|Human_gammaherpesvirus_4|10376 +4270 NHHNRTVEV 0.0 None None 0 None +4271 NHKDNSRIR 0.0 None None 0 None +4272 NHPYWANTV 0.0 None None 0 None +4273 NHSDLAAEL 0.0416522757017 NHSDLAAEL NHDSPDAEL 22.0 44133|Genome_polyprotein|P26664.3|Hepatitis_C_virus_genotype_1|41856 +4274 NIDLAREAY 0.0 None None 0 None +4275 NILPHYLEL 0.0 None None 0 None +4276 NIVYHTASI 0.175337715345 NIVYHTAS NLVYSTTS 27.0 96898|Genome_polyprotein|SRC279960|Hepatitis_C_virus|11103 +4277 NIYSRIREY 1.58925032505 NIYSRIREY KFYSKISEY 28.0 30892|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 +4278 NLARKEYTI 0.0 None None 0 None +4279 NLGFRFHMA 0.0 None None 0 None +4280 NLKHRKTAA 0.0 None None 0 None +4281 NLLANFSFL 0.0 None None 0 None +4282 NLLSYFNNL 0.0 None None 0 None +4283 NLMAKNNQA 1.11457402686 NLMAKN TIMAKN 22.0 103654|polyprotein|BAB18806.1|Hepatitis_C_virus|11103 +4284 NLNYRDLYY 0.0 None None 0 None +4285 NLPSKRVSL 0.679430959251 NLPSKRVS NVPYKRIE 25.0 1356|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 +4286 NMHCKISLL 0.0 None None 0 None +4287 NPLLHMVTM 0.0 None None 0 None +4288 NPLRYLAVM 0.0 None None 0 None +4289 NPLRYTSIL 0.0 None None 0 None +4290 NQKRRSESF 0.0 None None 0 None +4291 NRDKLGLQI 0.0 None None 0 None +4292 NRFSSKLLA 0.0 None None 0 None +4293 NRGPATAEV 0.0 None None 0 None +4294 NRLDLVRFY 0.166495086687 RLDLVR RVDMVR 23.0 32998|UL123;_IE1|AAR31448.1|Human_betaherpesvirus_5|10359 +4295 NRNYCVSVY 12.7901880739 RNYCVSV RHYCYSL 26.0 110846|E6_protein|CAB45108.1|Human_papillomavirus_type_16|333760 +4296 NRPEEEEQV 0.0 None None 0 None +4297 NRQRHTPMY 1.41898148148 RHTPM RHTPV 26.0 62977|polyprotein|AAB67037.1|Hepatitis_C_virus_(isolate_H77)|63746 +4298 NRVGVSSKL 0.0 None None 0 None +4299 NSDSFTGFI 0.0 None None 0 None +4300 NSINQVKLL 0.0 None None 0 None +4301 NTHRSRLSL 0.0 None None 0 None +4302 NTMAFSTDY 0.0 None None 0 None +4303 NVKKQRAGL 0.0 None None 0 None +4304 NVNQRFLNV 0.0 None None 0 None +4305 NYLEKVRSL 0.454075512249 YLEKVRS YLDKVRA 28.0 74605|Circumsporozoite_protein_precursor|P08677.2|Plasmodium_vivax_strain_Belem|31273 +4306 NYRDLYYFL 0.0 None None 0 None +4307 NYSPRPICV 7.49382142688 NYSPRP HYAPRP 28.0 25149|polyprotein|BAD73994.1|Hepatitis_C_virus_subtype_1b|31647 +4308 PASTLSLGY 3.87509767739 PASTLSLGY PASIAARGY 25.0 11063|Nonstructural_protein_NS3|NP_739587.2|Dengue_virus_2_Thailand/16681/84|31634 +4309 PFPRWLKII 0.00831776852653 PFPRWL PFVQWF 23.0 37919|envelope_protein|BAF48755.1|Hepatitis_B_virus|10407 +4310 PHWASSIVL 0.0385912911549 WASSIV WGGSVV 22.0 79351|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 +4311 PHYDFERSC 1.37387031452 PHYDFE PEYDLE 25.0 48896|Genome_polyprotein|P27958.3|Hepatitis_C_virus_subtype_1a|31646 +4312 PIEMNPEGY 0.0 None None 0 None +4313 PRIGYSLLL 0.0214674118902 PRIGYS PRASYS 22.0 53148|Transcription_activator_BRLF1|P03209.1|Human_herpesvirus_4_strain_B95-8|10377 +4314 PRLKWVVLV 0.0 None None 0 None +4315 PRNRKPLTV 21.9346414515 PRNRKPL PRSRTPI 26.0 88849|IE62|AAP32859.1|Human_alphaherpesvirus_3|10335 +4316 PRPSRCLLL 0.584858416083 RCLLL RCLLL 26.0 23566|tegument_protein_UL7|NP_044476.1|Human_alphaherpesvirus_2|10310 +4317 PRSEEAAVL 0.0 None None 0 None +4318 PRSKDTILL 0.0 None None 0 None +4319 PRSRWRDQL 0.0 None None 0 None +4320 PRWSCQEKL 0.0 None None 0 None +4321 PSQPANSFY 0.601059658223 PSQPANSFY PSQEPMSIY 23.0 58463|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 +4322 PTALSSLWY 0.0 None None 0 None +4323 PTDVLNGAA 0.0 None None 0 None +4324 PYPETPPRW 1.35529826852 YPETPP YPDAPP 30.0 141354|transcriptional_regulator_ICP4|NP_044662.1|Human_alphaherpesvirus_1|10298 +4325 PYQGRPKLL 2.71654929577 PYQGRP PYAGEP 26.0 65810|sporozoite_surface_protein_2|NP_705260.1|Plasmodium_falciparum_3D7|36329 +4326 PYQGRPKLL 0.442771084337 PYQGRP PYAGEP 26.0 65810|sporozoite_surface_protein_2|NP_705260.1|Plasmodium_falciparum_3D7|36329 +4327 PYTSVFLSV 0.0 None None 0 None +4328 QAEARLLAL 0.0 None None 0 None +4329 QAKVKFIGV 0.468283818619 VKFIGV VRFMGV 23.0 37153|Nuclear_antigen_EBNA-3C|Q69140.1|Human_gammaherpesvirus_4|10376 +4330 QEHVRCSAI 0.0 None None 0 None +4331 QFSFDGWKF 0.00828381734168 QFSFDGWKF QYSDRRWCF 19.0 53027|nonstructural_protein_3|NP_722463.1|Dengue_virus_1_Singapore/S275/1990|33741 +4332 QGRPKLLQL 0.0 None None 0 None +4333 QHCYMSRLL 0.0 None None 0 None +4334 QHDFCGLYM 1.18519018581 QHDFCGLYM KAKICGLYL 28.0 177701|polyprotein|ACZ60104.1|Hepatitis_C_virus_subtype_3a|356426 +4335 QHLLQRMSI 0.0 None None 0 None +4336 QHMHCLQDL 0.0 None None 0 None +4337 QHPNNSKDV 0.67707530484 HPNNS HPNNT 28.0 141306|tegument_host_shutoff_protein|NP_044643.1|Human_alphaherpesvirus_1|10298 +4338 QHQRLLEVL 0.0 None None 0 None +4339 QHTESLEYM 0.0 None None 0 None +4340 QHYAALQEY 0.0199846777357 HYAALQ HQAAMQ 22.0 101673|gag_protein|ABO73990.1|Human_immunodeficiency_virus_1|11676 +4341 QILSRVAAL 1.04035259267 ILSRVAAL MLSRVAAV 27.0 98253|trans-sialidase,_putative|EAN81042.1|Trypanosoma_cruzi|5693 +4342 QLMMSLLQL 0.0 None None 0 None +4343 QLREHAATL 0.0 None None 0 None +4344 QLRRSKVSV 0.0 None None 0 None +4345 QLYPRLKML 0.0 None None 0 None +4346 QLYPRLKML 0.0 None None 0 None +4347 QMLRIFKEM 0.0 None None 0 None +4348 QMYMSVLSL 0.0 None None 0 None +4349 QPAWRKASA 0.0 None None 0 None +4350 QPLRNFISV 0.0 None None 0 None +4351 QPMCRICHE 0.449806949807 MCRICH MCDECH 26.0 107790|polyprotein|AAD56189.1|Hepatitis_C_virus|11103 +4352 QRAPVGKLL 0.0 None None 0 None +4353 QRAVSRNLM 0.0 None None 0 None +4354 QRFLFIMFL 0.0 None None 0 None +4355 QRFLNVQEL 0.0264820306828 QRFLNVQEL ERYLKDQQL 22.0 14101|envelope_glycoprotein|ABI16336.1|Human_immunodeficiency_virus_1|11676 +4356 QRGEGILDM 0.0 None None 0 None +4357 QRHGFGEEI 0.00190751343828 QRHGFGEEI QTHIFAEVL 19.0 73862|EBNA-1_protein|Q777E1|Human_gammaherpesvirus_4|10376 +4358 QRIQMYMSV 0.0 None None 0 None +4359 QRIVKPTSI 0.0 None None 0 None +4360 QRLEPVYFV 0.0 None None 0 None +4361 QRLEVPIEM 0.0 None None 0 None +4362 QRMELLITF 0.0 None None 0 None +4363 QRQARQYQL 0.0 None None 0 None +4364 QRRPSSVGL 0.0 None None 0 None +4365 QRRSIPFQM 0.0 None None 0 None +4366 QRSGKPVLM 0.0 None None 0 None +4367 QRSNSETKV 0.0 None None 0 None +4368 QRSRKGDLL 0.0 None None 0 None +4369 QSEDRSHTL 0.0 None None 0 None +4370 QSQPFSMQY 0.0 None None 0 None +4371 QSQPGNALY 0.0 None None 0 None +4372 QTCKANLCY 11.2279615819 QTCKANLCY EFCRVLCCY 23.0 11956|UL123;_IE1|AAR31448.1|Human_betaherpesvirus_5|10359 +4373 QTLACNLCY 0.0 None None 0 None +4374 QVKRKVQAL 0.0 None None 0 None +4375 QYMLTLFTA 0.0 None None 0 None +4376 RAEDTALYY 0.0 None None 0 None +4377 RAIYHSCSL 0.0 None None 0 None +4378 RAKYRESLL 0.0 None None 0 None +4379 RAPQRIPSL 0.00198664006271 PQRIPSL PSRGPKL 19.0 74800|Genome_polyprotein|SRC279960|Hepatitis_C_virus_subtype_2b|31650 +4380 RARLQHCSA 0.0 None None 0 None +4381 RARYYIQVA 0.0 None None 0 None +4382 RASQRMSSV 0.0 None None 0 None +4383 RATARFHQL 0.0 None None 0 None +4384 RFFSRFTAV 0.0 None None 0 None +4385 RFHRVIKDF 0.0 None None 0 None +4386 RFKRKSVVA 0.0 None None 0 None +4387 RFLFIMFLF 0.0 None None 0 None +4388 RFLRNFPQI 0.406366189382 LRNFPQI VRHFPRI 25.0 187106|Vpr_protein|BAA93983.1|Human_immunodeficiency_virus_1|11676 +4389 RFMKYLVNF 0.219129686223 MKYLVNF LEYLVSF 25.0 69474|core_protein|BAF42671.1|Hepatitis_B_virus|10407 +4390 RFNMLNQIF 0.0 None None 0 None +4391 RFQDHRWEL 0.0 None None 0 None +4392 RHFEEALQT 0.0 None None 0 None +4393 RHFRLMHNL 0.0 None None 0 None +4394 RHIRHGNVI 0.0 None None 0 None +4395 RHLGDQMEV 17.8416258526 RHLGDQMEV RHTSDHMSI 26.0 17278|Genome_polyprotein|P06441.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 +4396 RHRCRNRFV 0.0 None None 0 None +4397 RHSPRNLIY 0.457200416329 HSPRNLIY HGPTPLLY 25.0 6591|polyprotein|AAB67037.1|Hepatitis_C_virus_(isolate_H77)|63746 +4398 RHTPMYYFL 0.0094183334308 RHTPMYY RHHNMVY 20.0 144403|polyprotein|AAK08509.1|Hepatitis_C_virus_subtype_1b|31647 +4399 RHTPMYYFL 0.00293201762289 RHTPMYY RHHNMVY 20.0 144403|polyprotein|AAK08509.1|Hepatitis_C_virus_subtype_1b|31647 +4400 RLIVKSREL 0.0 None None 0 None +4401 RLKQEIKRL 0.0 None None 0 None +4402 RLMCGPNTI 1.71760391198 LMCGPNTI ILCVPNAV 26.0 183741|polyprotein|AGS49173.1|Dengue_virus_2|11060 +4403 RLRRVASAL 0.0 None None 0 None +4404 RMCKFLQYF 0.0 None None 0 None +4405 RMSSVGANF 0.0 None None 0 None +4406 RNFPQIYIL 0.957507082153 RNFPQIY RHFPRIW 26.0 187106|Vpr_protein|BAA93983.1|Human_immunodeficiency_virus_1|11676 +4407 RNPQELWHF 0.135340359953 NPQEL NPQEV 24.0 69799|envelope_glycoprotein|BAE96221.1|Human_immunodeficiency_virus_1|11676 +4408 RNRKRFCVP 0.0 None None 0 None +4409 RPGSRGCPM 1.15273082827 RPGSRGCPM KPGTSGSPI 28.0 150341|polyprotein|AGW21594.1|Dengue_virus_1|11053 +4410 RPKYSFHRL 0.0 None None 0 None +4411 RPRARLAAL 0.0 None None 0 None +4412 RPRARYYIQ 0.0 None None 0 None +4413 RPRQGRWWL 0.0 None None 0 None +4414 RQFPKKSLM 0.0 None None 0 None +4415 RQFYLFYNF 0.0 None None 0 None +4416 RQMISELLF 0.0 None None 0 None +4417 RQQQDYWLM 0.0241357685845 QQDYWLM QQNWWTL 25.0 74886|latent_membrane_protein_1|AAS99606.1|Human_gammaherpesvirus_4|10376 +4418 RRENSLSEI 0.0 None None 0 None +4419 RRFNMLNQI 0.0 None None 0 None +4420 RRGEAEKRL 0.0 None None 0 None +4421 RRGGSGAMV 0.0 None None 0 None +4422 RRKQSEMYI 0.0 None None 0 None +4423 RRLDYDHKL 0.0 None None 0 None +4424 RRPSRAMWL 0.0 None None 0 None +4425 RRQDYQEIL 0.0 None None 0 None +4426 RRSDAEKQL 0.111181455484 RSDAEKQ RADEEQQ 22.0 70687|ESAT-6-like_protein_esxB|P0A566.2|Mycobacterium_tuberculosis|1773 +4427 RRSKVSVEM 0.0 None None 0 None +4428 RRSPSFSRV 0.0 None None 0 None +4429 RRVASALLL 0.0 None None 0 None +4430 RRVPYRGSV 0.0 None None 0 None +4431 RRYLKSGVV 0.0 None None 0 None +4432 RSADWQRKI 0.0 None None 0 None +4433 RSELNSVEY 0.0 None None 0 None +4434 RSFPAGVEM 0.0 None None 0 None +4435 RTQDAIHEL 0.0 None None 0 None +4436 RTSSIFYSF 0.0 None None 0 None +4437 RVGQMAFVF 0.0 None None 0 None +4438 RVNDCILQV 0.0 None None 0 None +4439 RVRRRGQKL 0.000560646888862 RVRRRGQK RLRPGGKK 19.0 54741|gag_polyprotein|BAA00992.1|Human_immunodeficiency_virus_1|11676 +4440 RVSDGSLLY 0.0 None None 0 None +4441 RWQGRVRTL 0.0 None None 0 None +4442 RYAALLKCW 0.0377103973581 RYAALLKCW RYMGEDGCW 22.0 185573|polyprotein|CDF77361.1|Dengue_virus_3|11069 +4443 RYARPSRLV 36.924260273 RYARPSRL RFAQPSAL 27.0 142233|ATP-dependent_helicase|NP_217813.1|Mycobacterium_tuberculosis|1773 +4444 RYCLTTLTI 0.0 None None 0 None +4445 RYFDEPVEL 0.0 None None 0 None +4446 RYFDEPVEL 0.0 None None 0 None +4447 RYFLKHGIL 0.525137542938 RYFLKHGI RYVLDHLI 22.0 25237|Transcription_activator_BRLF1|P03209.1|Human_herpesvirus_4_strain_B95-8|10377 +4448 RYILLKRSL 0.0 None None 0 None +4449 RYLENGKEM 0.0 None None 0 None +4450 RYLKSGVVL 0.0 None None 0 None +4451 RYLPDCDYL 0.48206481189 RYLPDCDYL RYAPACKPL 25.0 56502|polyprotein|BAD73994.1|Hepatitis_C_virus_subtype_1b|31647 +4452 RYRSIISDI 0.0 None None 0 None +4453 RYVAICAPL 1.06464167115 RYVAICAPL RYAPACKPL 29.0 56502|polyprotein|BAD73994.1|Hepatitis_C_virus_subtype_1b|31647 +4454 RYVASCKPL 0.477699027983 RYVASCKPL RYAPACKPL 37.0 56502|polyprotein|BAD73994.1|Hepatitis_C_virus_subtype_1b|31647 +4455 SADYINANY 0.0 None None 0 None +4456 SAEECRTEL 0.0 None None 0 None +4457 SAKQQNQIL 0.0 None None 0 None +4458 SAKQQNQIL 0.0 None None 0 None +4459 SALGREHPA 0.0 None None 0 None +4460 SARDQPSSV 0.0 None None 0 None +4461 SARLRQRAV 0.0 None None 0 None +4462 SASNNNSEL 0.0 None None 0 None +4463 SAVRRDLTF 0.0 None None 0 None +4464 SAYDGKDYI 0.0 None None 0 None +4465 SCSSNPHLL 0.0 None None 0 None +4466 SEEERGLEL 0.0 None None 0 None +4467 SEKDRPVKV 0.0 None None 0 None +4468 SESHRTSLL 0.0 None None 0 None +4469 SEVERLDVL 0.0 None None 0 None +4470 SFFNCLWEV 0.674192438284 FFNCLWEV LLNCLWSV 34.0 37536|Spike_glycoprotein_precursor|P15423.1|Human_coronavirus_229E|11137 +4471 SFPGRVREL 0.0 None None 0 None +4472 SFQTITEQF 0.0 None None 0 None +4473 SFVDAIHTF 0.0 None None 0 None +4474 SGFEFSQVL 0.0 None None 0 None +4475 SGMARVGSL 0.484375 GMARVG GMSRIG 26.0 21347|Nucleoprotein|P59595.1|SARS_coronavirus|227859 +4476 SHKEAITAL 0.0 None None 0 None +4477 SHKKQSSVI 0.0 None None 0 None +4478 SHLQRIGTI 0.0 None None 0 None +4479 SHLTIVILF 0.0 None None 0 None +4480 SHMYVATGI 0.0 None None 0 None +4481 SHNRHVPKI 0.25312133776 RHVPKI RHFPRI 25.0 187106|Vpr_protein|BAA93983.1|Human_immunodeficiency_virus_1|11676 +4482 SHPLHYTTI 0.0 None None 0 None +4483 SHPLHYTTI 0.0 None None 0 None +4484 SHQPLPGTL 0.0 None None 0 None +4485 SHRNPLLDL 0.0 None None 0 None +4486 SHSPAGELT 0.168377764503 PAGELT PQGQLT 23.0 13701|Trans-activator_protein_BZLF1|P03206.2|Human_gammaherpesvirus_4|10376 +4487 SHSSNPHLL 0.0 None None 0 None +4488 SHTLLLTQL 0.0 None None 0 None +4489 SIFYSFLPL 0.0538659105423 SIFYSFLPL SIYVYALPL 21.0 58463|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 +4490 SKFGQGTGL 0.0 None None 0 None +4491 SKQNMPQYL 0.0 None None 0 None +4492 SLAKFDAPL 0.0 None None 0 None +4493 SLDTTTWEY 0.0 None None 0 None +4494 SLFTCVLQL 0.0 None None 0 None +4495 SLGDNSEYL 0.0 None None 0 None +4496 SLHHKHKEL 0.0 None None 0 None +4497 SLIDSSRVV 0.0 None None 0 None +4498 SLKLTQSSA 0.0 None None 0 None +4499 SLLRKHQIL 56.8225353198 SLLRKHQIL SLLRNHNLV 28.0 96898|Genome_polyprotein|SRC279960|Hepatitis_C_virus|11103 +4500 SLLRKHQIT 1.76449738892 SLLRKHQI SLLRNHNL 27.0 96898|Genome_polyprotein|SRC279960|Hepatitis_C_virus|11103 +4501 SLLVHGGPL 0.203585933289 VHGGPL VHAGPI 27.0 24557|Gag_polyprotein|P03347.3|Human_immunodeficiency_virus_1|11676 +4502 SLNHRGRVM 0.0 None None 0 None +4503 SLNHRGRVM 0.0 None None 0 None +4504 SLNPKKFSI 0.0 None None 0 None +4505 SLRAEDTAL 0.0 None None 0 None +4506 SLSETVRLV 0.0 None None 0 None +4507 SLSVRTSGL 0.0 None None 0 None +4508 SLWYHTYGL 0.584082675016 YHTYGL FHSYGV 26.0 232152|rhoptry_kinase_family_protein|AFO54841.1|Toxoplasma_gondii_type_III|398031 +4509 SLYTAYHVF 0.0168850134338 SLYTAYHV KLYCSYEV 22.0 32250|FL-160-2_protein_-_Trypanosoma_cruzi|JH0823|Trypanosoma_cruzi|5693 +4510 SLYVWKSEL 0.0 None None 0 None +4511 SMAKYWNQF 0.0 None None 0 None +4512 SMKAERPPA 0.0 None None 0 None +4513 SMKNLQRAV 0.0 None None 0 None +4514 SMKVHIKAM 0.0 None None 0 None +4515 SMMTATIVF 0.0 None None 0 None +4516 SMPANFETI 0.0 None None 0 None +4517 SMREALREL 0.0 None None 0 None +4518 SMREAVREL 0.0 None None 0 None +4519 SMRYFITSV 0.0 None None 0 None +4520 SPGPFFWMF 0.0 None None 0 None +4521 SPLFYSTCM 0.620468376578 SPLFYST SPITYST 27.0 107873|Genome_polyprotein|P26664.3|Hepatitis_C_virus|11103 +4522 SPLQLPAPL 0.0 None None 0 None +4523 SPLRYISIL 0.0 None None 0 None +4524 SPMYFFLSY 0.0 None None 0 None +4525 SPRSRPSDI 0.0 None None 0 None +4526 SPRVFFLLM 0.0 None None 0 None +4527 SPSSAYLLF 0.0 None None 0 None +4528 SQHPAQQQI 0.0 None None 0 None +4529 SQMSQLMGL 0.0776138458536 SQMSQLM AQMWQLM 22.0 182599|polyprotein|AGW21594.1|Dengue_virus_1|11053 +4530 SQPGNALYF 0.0 None None 0 None +4531 SRAMWLSLF 0.0 None None 0 None +4532 SRATADPEV 0.0 None None 0 None +4533 SRCLLLPLL 5.4232325855 RCLLL RCLLL 26.0 23566|tegument_protein_UL7|NP_044476.1|Human_alphaherpesvirus_2|10310 +4534 SREDDNRER 0.0 None None 0 None +4535 SRENRWTTV 0.132816935515 RENRWT REDQWC 23.0 53476|polyprotein|AGO67248.1|Dengue_virus_2|11060 +4536 SRFCSLHCL 0.0 None None 0 None +4537 SRFTAVREF 0.0269793149431 SRFTAVR SRYWAIR 22.0 60867|nucleoprotein|CAZ65591.1|Influenza_A_virus|11320 +4538 SRFTLRCMV 1.61952838872 SRFTLRCM GRWTGRCM 26.0 110215|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 +4539 SRFVVRPLL 0.0 None None 0 None +4540 SRGQEIKTI 0.0 None None 0 None +4541 SRHDFHVDL 0.0424328495879 SRHDFHVDL TLHEYMLDL 22.0 178351|Protein_E7|P03129.1|Human_papillomavirus_type_16|333760 +4542 SRKGDLLRI 0.0 None None 0 None +4543 SRKKRRSPP 0.0 None None 0 None +4544 SRKLRKLPT 0.0 None None 0 None +4545 SRLHTPVYF 0.0 None None 0 None +4546 SRNAYSLEI 0.0 None None 0 None +4547 SRNDFEWVY 0.02135862433 SRNDFE GRNSFE 22.0 37364|P53_HUMAN_Cellular_tumor_antigen_p53_(Tumor_suppressor_p53)_(Phosphoprotein_p53)_(Antigen_NY-CO-13)|P04637.2|Homo_sapiens|9606 +4548 SRPGALEHL 0.0 None None 0 None +4549 SRPSSKQNM 0.0 None None 0 None +4550 SRQMISELL 0.0 None None 0 None +4551 SRRARGREK 0.0 None None 0 None +4552 SRRSFWSEL 0.0 None None 0 None +4553 SRSRNAYSL 0.0 None None 0 None +4554 SRSVDVTNI 0.0 None None 0 None +4555 SRTVWEEMV 0.825050427473 SRTVWE TRTVWQ 28.0 120187|E1_protein|BAA19893.1|Rubella_virus|11041 +4556 SRWRDQLLF 0.0 None None 0 None +4557 SRYARPSRL 0.939932458239 RYARPSRL RFAQPSAL 27.0 142233|ATP-dependent_helicase|NP_217813.1|Mycobacterium_tuberculosis|1773 +4558 SSASLNSNY 0.0 None None 0 None +4559 SSDEIVQEL 0.0 None None 0 None +4560 SSKQHLKPA 0.0 None None 0 None +4561 SSLARELSL 0.0 None None 0 None +4562 SSLRRMNSF 0.00406654233374 LRRMNSF LRKKSSF 21.0 116781|Nucleoprotein|P05133.1|Hantaan_virus_76-118|11602 +4563 SSRGNGKMM 0.0 None None 0 None +4564 SSTSHIPEV 0.0 None None 0 None +4565 SSYSRVALV 0.0 None None 0 None +4566 STDDATWAA 0.0 None None 0 None +4567 STERPKMTY 0.0 None None 0 None +4568 STIYIFALF 1.09241706161 TIYIFAL SIYVYAL 26.0 58463|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 +4569 STKVHIKVL 0.0 None None 0 None +4570 STQTHPLTL 4.38726372945 TQTHPLT TLTHPIT 30.0 71412|polyprotein_[Hepatitis_C_virus_subtype_1a]|ABV46251.2|Hepatitis_C_virus_subtype_1a|31646 +4571 STSHVYHLF 0.0 None None 0 None +4572 STYNETNLI 0.0 None None 0 None +4573 STYPDQQHV 2.03088323857 STYPDQQHV SYYPDQKSL 28.0 28594|IMMUNOGENIC_PROTEIN_MPT64_(ANTIGEN_MPT64/MPB64)|CAA98382.1|Mycobacterium_tuberculosis_H37Rv|83332 +4574 SVEEKGKLL 0.0 None None 0 None +4575 SVFPTQLQL 2.29326254822 SVFPTQLQL GLFPTQIQV 32.0 20865|Nucleoprotein|P41269.1|Puumala_hantavirus|11604 +4576 SVFSEQWIF 0.0264970465526 SVFSEQWIF AVFGPLWIL 23.0 96123|Genome_polyprotein|P26664.3|Hepatitis_C_virus_(isolate_H77)|63746 +4577 SVRENCCSL 0.0 None None 0 None +4578 SWMPALECL 0.05038120655 SWMPALECL SWDETWKCL 23.0 146569|polyprotein|ADF97231.1|Hepatitis_C_virus_subtype_3a|356426 +4579 SWPLWTAIF 1.22480631271 SWPLW SWCLW 27.0 39591|polyprotein|AAA45677.1|Hepatitis_C_virus_(isolate_H77)|63746 +4580 SWVSSTLGF 0.0 None None 0 None +4581 SYAKNAQDL 0.0 None None 0 None +4582 SYARILGTV 0.0 None None 0 None +4583 SYAVICNNF 0.0 None None 0 None +4584 SYFCILRTI 0.0 None None 0 None +4585 SYFGLATVF 0.0 None None 0 None +4586 SYFLATDTI 0.0 None None 0 None +4587 SYFNNLHLW 4.77360749628 FNNLHL FHNLHL 29.0 79390|Protein_Tax-1|P0C213.1|Human_T-cell_lymphotropic_virus_type_1_(african_isolate)|39015 +4588 SYGVNLYQF 5.06976518192 YGVNLYQF YGYPVYVF 22.0 23807|tax|AAG48731.1|Human_T-lymphotropic_virus_2|11909 +4589 SYIYILITI 0.0560487592099 YILITI YVILTI 23.0 186620|polyprotein|AFP27208.1|Dengue_virus_4|11070 +4590 SYKFLAPWI 0.348021972633 YKFLAPW YRFVAPG 27.0 149053|NS3_gene_product|AAB02124.1|Hepatitis_C_virus|11103 +4591 SYPSIHRFI 0.601659125972 PSIHRFI PGIYRFV 27.0 149053|NS3_gene_product|AAB02124.1|Hepatitis_C_virus|11103 +4592 SYPSQPDGF 0.0 None None 0 None +4593 SYSLISEKL 0.0 None None 0 None +4594 SYVMDHFDI 0.965095685508 YVMDHF YVLDHL 27.0 25237|Transcription_activator_BRLF1|P03209.1|Human_herpesvirus_4_strain_B95-8|10377 +4595 SYVRIGATI 0.0 None None 0 None +4596 SYWGVFAPI 0.000607367462934 SYWGVFAPI SLWKDGAPL 19.0 140600|glutamine_synthetase_GLNA1_(glutamine_synthase)_(GS-I)|NP_216736.1|Mycobacterium_tuberculosis_H37Rv|83332 +4597 SYYKIVSSI 0.0193185218111 KIVSSI KLVSSV 22.0 95262|LAMP|AAK72632.1|Human_gammaherpesvirus_8|37296 +4598 TAAIRPKSL 0.0 None None 0 None +4599 TADVGLAGY 0.0 None None 0 None +4600 TAFDESISL 0.0 None None 0 None +4601 TAMAYDQFL 0.0 None None 0 None +4602 TDKERQRLL 0.0 None None 0 None +4603 TDYDTRFYM 0.0 None None 0 None +4604 TEFGQKQKL 0.0 None None 0 None +4605 TERDQIELL 0.0 None None 0 None +4606 TFDRLAYLW 0.0 None None 0 None +4607 TFEDNLRSL 0.0 None None 0 None +4608 TFGEVNYFF 0.243387329538 GEVNYF GEADYF 25.0 24535|EBNA-1_protein|Q777E1|Human_gammaherpesvirus_4|10376 +4609 TFITSVIRF 0.0 None None 0 None +4610 TFLIAMVFI 0.0 None None 0 None +4611 TFNDWFEII 0.755265816333 FNDWFEI FKDWEEL 27.0 6556|X_protein|AAP06597.1|Hepatitis_B_virus|10407 +4612 TFSCQLHKF 0.0 None None 0 None +4613 THAPERDLC 0.0 None None 0 None +4614 THASLSNHV 0.009151449223 HASLSNH HAMSSTH 21.0 140686|ESAT-6-like_protein_esxH|P0A568.2|Mycobacterium_tuberculosis|1773 +4615 THHGPAFSI 0.0 None None 0 None +4616 THIFGLMVI 0.0 None None 0 None +4617 THIHAAACI 0.0 None None 0 None +4618 THMERVLSL 0.0 None None 0 None +4619 THMERVLSL 0.0 None None 0 None +4620 THPIYYLKI 0.0 None None 0 None +4621 THQEALMKL 0.0 None None 0 None +4622 THREGISAI 0.561269053294 THREGI NHRQGI 25.0 34642|methionine_sulfoxide_reductase_B|YP_169878.1|Francisella_tularensis_subsp._tularensis_SCHU_S4|177416 +4623 THRSRLSLG 0.0 None None 0 None +4624 THTSYQLSA 0.0 None None 0 None +4625 THYQGTWYL 0.0 None None 0 None +4626 TIKQRPKPT 0.0 None None 0 None +4627 TKFESNLCV 0.0 None None 0 None +4628 TLDKKLEYY 1.51757846321 LDKKLE LDKKVE 26.0 27000|Heat_shock_protein_HSP_90-beta|P08238.4|Homo_sapiens|9606 +4629 TLERAALRY 0.0 None None 0 None +4630 TLGLIFLCL 0.0 None None 0 None +4631 TLMVVVWVL 0.0 None None 0 None +4632 TLTIRALPA 0.0 None None 0 None +4633 TMCMYFRPL 0.0 None None 0 None +4634 TMETSFFSF 0.0 None None 0 None +4635 TMGSWTCLF 0.475156091949 SWTCL TWKCL 24.0 146569|polyprotein|ADF97231.1|Hepatitis_C_virus_subtype_3a|356426 +4636 TMRTRHFTG 0.0 None None 0 None +4637 TMRYIHFLF 0.0 None None 0 None +4638 TMSPRVFFL 0.0 None None 0 None +4639 TPGNRTKCF 2.47406881013 GNRTKCF GNASRCW 24.0 21385|polyprotein|AAY82034.1|Hepatitis_C_virus_genotype_1|41856 +4640 TPKSMQSTL 0.0 None None 0 None +4641 TPNFRRRAI 0.0 None None 0 None +4642 TPSERSKPL 1.35857438639 SERSKP SERSQP 26.0 33856|polyprotein|BAA03375.1|Hepatitis_C_virus|11103 +4643 TPSTQTHPL 0.0722037478202 TPSTQTH TPAVQTN 24.0 149037|NS4B_protein|NP_751926.1|Hepatitis_C_virus_(isolate_H77)|63746 +4644 TRAERLTWL 0.0 None None 0 None +4645 TRALHRLIV 0.0 None None 0 None +4646 TRASDRRGI 0.0 None None 0 None +4647 TRDAPGLRV 0.0 None None 0 None +4648 TREVTVNVL 0.0 None None 0 None +4649 TRFPLKTAF 0.0 None None 0 None +4650 TRFPLPEAF 0.0 None None 0 None +4651 TRFRSFSSL 0.0 None None 0 None +4652 TRFYMYEIL 0.0 None None 0 None +4653 TRGPCRRRF 7.20424999304 GPCRRRF GPADRRF 27.0 155637|tegument_protein|CAB06732.1|Human_alphaherpesvirus_2|10310 +4654 TRGPQRQIL 0.0 None None 0 None +4655 TRGRHQKKI 0.0 None None 0 None +4656 TRHGSILAC 0.0 None None 0 None +4657 TRHRCRNRF 0.0 None None 0 None +4658 TRNCNRHLC 4.92100160943 NCNRHLC NCQKPLC 28.0 110394|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 +4659 TRPSEELEL 0.0 None None 0 None +4660 TRPTASSSV 0.0 None None 0 None +4661 TRRSQKRLQ 0.0 None None 0 None +4662 TRSAEPGYL 0.0 None None 0 None +4663 TRSSKPSDM 0.0 None None 0 None +4664 TRSWGTPQL 0.114998444797 RSWGTPQ KLWESPQ 22.0 32243|C_protein|BAB60863.1|Measles_virus|11234 +4665 TRTPHSTRC 0.683754788248 TPHSTRC TPDSTPC 27.0 53041|phosphorylated_matrix_protein_(pp65)|AAA45996.1|Human_betaherpesvirus_5|10359 +4666 TRVGSKLLI 0.638888888889 TRVGSKLLI TRVGTKHAI 26.0 186041|polyprotein|AGO67248.1|Dengue_virus_2|11060 +4667 TRYSAQADI 0.0 None None 0 None +4668 TSMWRTYVM 0.0 None None 0 None +4669 TSMWRTYVM 0.0 None None 0 None +4670 TTDGRNYIV 0.479879498782 DGRNY DGVNY 22.0 56343|structural_protein|BAA00705.1|Hepatitis_C_virus|11103 +4671 TTFDRLAYL 0.61388887253 TFDRLAYL TFDRLQVL 28.0 66405|polyprotein|AAB67037.1|Hepatitis_C_virus_(isolate_H77)|63746 +4672 TTMEDQLLF 0.0 None None 0 None +4673 TVHTRNHTA 0.0 None None 0 None +4674 TVIDAYMNF 0.0 None None 0 None +4675 TVLHRPHSA 0.0 None None 0 None +4676 TVSPQPQEV 0.980041819158 SPQPQEV DPNPQEV 28.0 69799|envelope_glycoprotein|BAE96221.1|Human_immunodeficiency_virus_1|11676 +4677 TWLQVLEAI 0.0 None None 0 None +4678 TYEEPCQAI 0.0 None None 0 None +4679 TYLADRVQI 0.0 None None 0 None +4680 TYLYPPKHW 0.0 None None 0 None +4681 TYVLYYDAL 0.0 None None 0 None +4682 TYYPLKPEI 0.443101725077 YPLKPEI FPVRPQV 25.0 288104|nef_protein|ACR27130.1|Human_immunodeficiency_virus_1|11676 +4683 TYYPLKPEI 0.232710970823 YPLKPEI FPVRPQV 25.0 288104|nef_protein|ACR27130.1|Human_immunodeficiency_virus_1|11676 +4684 VAKKKEAPA 0.0 None None 0 None +4685 VARERRKAE 0.0 None None 0 None +4686 VFERDFFKI 0.0 None None 0 None +4687 VFETGTFLI 0.0 None None 0 None +4688 VFLPMTLLL 0.0 None None 0 None +4689 VFRQGHQLF 0.0 None None 0 None +4690 VFTRVSAYI 0.0107141857233 FTRVSAY FTKNSAF 21.0 44214|UL123;_IE1|AAR31448.1|Human_betaherpesvirus_5|10359 +4691 VFYTIFTPI 0.0 None None 0 None +4692 VGKKRHDPL 0.0 None None 0 None +4693 VHALRLHLY 0.0 None None 0 None +4694 VHFDHFHPC 0.867623345477 HFDHFHP HYDQDHP 29.0 180758|Nonstructural_protein_NS5|NP_739590.2|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 +4695 VHFLREVTV 0.0 None None 0 None +4696 VHHLAVSGV 1.19230769231 LAVSGV LAVSGV 26.0 419005|polyprotein|AGW21594.1|Dengue_virus_1|11053 +4697 VHIKAMQTV 0.0 None None 0 None +4698 VHIKVLQTV 0.0 None None 0 None +4699 VHKKGYNKL 0.0 None None 0 None +4700 VHKQFPITL 0.774571436042 FPITL FPITL 26.0 143705|Genome_polyprotein|P08617.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 +4701 VHKTDLERM 0.0 None None 0 None +4702 VHRGTGAVY 0.02244433038 RGTGAVY EGEGAVF 22.0 119822|110_kd_polyprotein_precursor|CAA28880.1|Rubella_virus|11041 +4703 VHSENLQNW 0.0 None None 0 None +4704 VLAIQRCPM 0.0 None None 0 None +4705 VLDEMRCQY 112.599178113 VLDEMRC VIDPRRC 24.0 150556|polyprotein|AGW21594.1|Dengue_virus_1|11053 +4706 VLKSTSCSI 0.0 None None 0 None +4707 VMKHLLSPL 0.0 None None 0 None +4708 VMSCVWFTI 0.0 None None 0 None +4709 VQMYRGHPA 0.131620119942 YRGHPA YAGEPA 23.0 65810|sporozoite_surface_protein_2|NP_705260.1|Plasmodium_falciparum_3D7|36329 +4710 VQNEDVTLL 0.0 None None 0 None +4711 VQPSQWASI 10.0381165919 PSQWA PSSWA 26.0 27878|large_surface_antigen|CAC87019.1|Hepatitis_B_virus|10407 +4712 VRDRMKELL 0.0 None None 0 None +4713 VRELRDMGI 0.0014787525281 VRELRDMG VKENFSMG 16.0 59090|nonstructural_protein_4B|YP_001527886.1|West_Nile_virus_NY-99|10000971 +4714 VRFQDESVV 0.0 None None 0 None +4715 VRFVTRYIY 0.0 None None 0 None +4716 VRFVVTITV 0.0 None None 0 None +4717 VRGTTLHLL 0.0 None None 0 None +4718 VRHQRVHQA 0.0 None None 0 None +4719 VRLKRSIQF 0.0 None None 0 None +4720 VRLSYKLTF 0.0 None None 0 None +4721 VRMEVISVT 0.0 None None 0 None +4722 VRMEVVSIT 0.0 None None 0 None +4723 VRNDHMNLR 0.0 None None 0 None +4724 VRNRCNIYI 0.0 None None 0 None +4725 VRPRARYYI 0.0 None None 0 None +4726 VRQGGVFRL 0.0 None None 0 None +4727 VRRLGPKLL 0.0 None None 0 None +4728 VRRLHCSAA 0.0 None None 0 None +4729 VRRMLTSKV 0.0 None None 0 None +4730 VRRRRRCPG 0.0 None None 0 None +4731 VRSLNLVLM 0.0 None None 0 None +4732 VRSNLEPLF 0.0 None None 0 None +4733 VRVGSDMLI 0.0 None None 0 None +4734 VRVTQKFHM 0.0 None None 0 None +4735 VSDDLVKQY 0.0 None None 0 None +4736 VSGHVSMKY 0.0 None None 0 None +4737 VSSSSSGGY 0.0 None None 0 None +4738 VTADSDPAY 0.0 None None 0 None +4739 VTAPRATTL 0.0 None None 0 None +4740 VTDVLTEPH 0.0 None None 0 None +4741 VTMDWLVRI 20.8868827501 DWLVRI SWMIRI 25.0 185817|envelope_protein|AGW23590.1|Dengue_virus_4|11070 +4742 VVAPRTLLL 0.629096369435 VVAPRTL AISPRTL 25.0 50292|gag_protein|ACR27140.1|Human_immunodeficiency_virus_1|11676 +4743 VVESLVEAY 0.0 None None 0 None +4744 VVHEVQRYL 0.0 None None 0 None +4745 VVKSKQVAL 0.0 None None 0 None +4746 VVPQMVNPF 0.0 None None 0 None +4747 VVSDVPEEL 0.0 None None 0 None +4748 VYFHMTLSF 0.0 None None 0 None +4749 VYHLFCALL 0.00735750627888 VYHLFCAL LWHYPCTL 19.0 54824|polyprotein_precursor|BAA01583.1|Hepatitis_C_virus|11103 +4750 VYISLFTCV 0.0 None None 0 None +4751 VYLRRHRDV 0.989106753813 LRRHRDV LRRHIDL 26.0 51526|HCV-1|AAA45676.1|Hepatitis_C_virus|11103 +4752 VYPRGFQEK 0.0 None None 0 None +4753 VYQVLSGGW 0.0 None None 0 None +4754 VYSEYGMDV 0.239110747927 VYSEYG TYSTYG 23.0 67471|Genome_polyprotein|Q99IB8.3|Hepatitis_C_virus_JFH-1|356411 +4755 VYSLRTRAI 0.0546114862252 VYSLRTRAI AYSQQTRGL 22.0 111816|polyprotein|BAA09072.1|Hepatitis_C_virus|11103 +4756 VYSLYWSIL 0.175675675676 VYSLYWSI LYELIWNV 26.0 108965|Prolipoprotein_diacylglyceryl_transferase|O06131.1|Mycobacterium_tuberculosis|1773 +4757 VYVVSNNNL 0.0 None None 0 None +4758 VYVVTKFLM 0.110774648364 YVVTKFLM HPITKFVM 25.0 103389|unnamed_protein_product_[Hepatitis_C_virus]|BAA14035.1|Hepatitis_C_virus|11103 +4759 VYYLLELLL 0.444897959184 YLLELL YLLEML 26.0 74774|LMP1_protein_(Epstein-Barr_virus,_putative_LYDMA_gene)|Q777A4|Human_gammaherpesvirus_4|10376 +4760 WAGSHSMRY 0.0 None None 0 None +4761 WARRKQSEM 0.0 None None 0 None +4762 WASRFSTPY 0.0 None None 0 None +4763 WFLWKQFCW 0.0 None None 0 None +4764 WGMLNSLSL 0.0 None None 0 None +4765 WHLQGPEDL 0.0 None None 0 None +4766 WHREYNFKY 0.0 None None 0 None +4767 WHSVVIQRL 0.0 None None 0 None +4768 WHVPNKPPM 0.0370999742128 WHVPNKP YHILNNP 23.0 1516|Nucleoprotein|P03418.1|Human_respiratory_syncytial_virus_A2|11259 +4769 WIEREGPEY 0.0 None None 0 None +4770 WLNENQRLV 0.0 None None 0 None +4771 WLSFRSSAS 0.0 None None 0 None +4772 WLSNFQGRY 0.0713668403123 LSNFQGRY VGNFTGLY 23.0 34027|DNA_polymerase|CAA10434.1|Hepatitis_B_virus|10407 +4773 WMEKRYLSQ 0.0 None None 0 None +4774 WMEQEGPEY 3.13980286976 QEGPEY QRGPQY 27.0 38974|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 +4775 WPLTHSQGM 39.6011817345 WPLTHSQGM WPLYGNEGM 32.0 75438|polyprotein|AAF65962.1|Hepatitis_C_virus|11103 +4776 WQRQHKLTI 3.26412079703 QRQHKLTI QRQRKVTF 26.0 159299|polyprotein|AAC03058.1|Hepatitis_C_virus_subtype_3a|356426 +4777 WRPEAVQYY 0.0 None None 0 None +4778 WSDQLSAFS 0.225160259752 WSDQLSAFS WMNRLIAFA 25.0 177647|polyprotein|ADE10208.1|Hepatitis_C_virus_subtype_3a|356426 +4779 WTDVFQIGI 0.358584414555 VFQIGI VFEVGV 24.0 59787|Hemagglutinin_glycoprotein|P08362.1|Measles_virus_strain_Edmonston|11235 +4780 WTESLAAVF 2.5146072019 WTESLAAVF WSEGEGAVF 28.0 119822|110_kd_polyprotein_precursor|CAA28880.1|Rubella_virus|11041 +4781 WVKRQKISF 0.0617858475773 VKRQKISF VKKDLISY 20.0 25929|Nonstructural_protein_NS3|NP_739587.2|Dengue_virus_2_Thailand/16681/84|31634 +4782 WVRPRRRLL 0.0 None None 0 None +4783 WVRPRRRLL 0.0 None None 0 None +4784 WYHTCGGTL 0.0 None None 0 None +4785 WYIWILLVL 0.0410194846882 WYIWIL WCLWWL 23.0 74387|Genome_polyprotein|P26664.3|Hepatitis_C_virus_(isolate_1)|11104 +4786 YAFTGLTLM 19.2063253012 FTGLT FTGLT 26.0 146213|polyprotein|ADY38595.1|Hepatitis_C_virus_subtype_1b|31647 +4787 YAMQRSWQE 2.83948962827 QRSWQ ERSWN 22.0 180440|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 +4788 YARILGTVL 0.0 None None 0 None +4789 YCDDLPLLA 0.0 None None 0 None +4790 YDDARVELV 0.0 None None 0 None +4791 YEHHHSARL 0.0 None None 0 None +4792 YFGLATVFI 0.0 None None 0 None +4793 YFHSFIRIV 0.0 None None 0 None +4794 YFTSSSRYF 0.0 None None 0 None +4795 YFYNQEEYV 0.0 None None 0 None +4796 YGVTRSKAM 0.0 None None 0 None +4797 YHCTAVNAY 0.0 None None 0 None +4798 YHDACIEEA 0.0 None None 0 None +4799 YHDVSGCYI 0.0 None None 0 None +4800 YHEAGVTAL 0.815347986631 YHEAGVT FHSYGVT 24.0 232152|rhoptry_kinase_family_protein|AFO54841.1|Toxoplasma_gondii_type_III|398031 +4801 YHFSWTSDR 0.0637106609554 HFSWTS HYAWKT 23.0 183252|polyprotein|AGT63075.1|Dengue_virus_1|11053 +4802 YHHRFNNFM 1.40756158901 YHHRFNN YQHKFNS 30.0 23270|polyprotein|AAB67036.1|Hepatitis_C_virus_(isolate_H77)|63746 +4803 YHQQNVPWA 0.0 None None 0 None +4804 YICDLRRQV 0.0 None None 0 None +4805 YINNSVLPY 0.0 None None 0 None +4806 YKGSRFHRV 1.87577517247 KGSRFHRV KKQRFHNI 25.0 110829|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 +4807 YLADRVQIV 0.0 None None 0 None +4808 YLADRVQIV 0.0 None None 0 None +4809 YLENRKETL 0.0 None None 0 None +4810 YLENRKETL 0.0 None None 0 None +4811 YLEQKPCIY 0.0 None None 0 None +4812 YLFRKELRY 0.0 None None 0 None +4813 YLKEELMCL 0.0 None None 0 None +4814 YLKENFLPW 0.0 None None 0 None +4815 YLRRHRDVS 14.1396011396 LRRHRDV LRRHIDL 26.0 51526|HCV-1|AAA45676.1|Hepatitis_C_virus|11103 +4816 YLSLVEISY 0.0 None None 0 None +4817 YLTVVSLSY 0.0 None None 0 None +4818 YMDRTPGPA 0.0 None None 0 None +4819 YMKTQSKSS 0.0 None None 0 None +4820 YMLTLFTAM 0.0 None None 0 None +4821 YNFKYVDLI 0.0 None None 0 None +4822 YNVFRQLSL 0.0 None None 0 None +4823 YPMRRRQCE 0.0 None None 0 None +4824 YPRLKMLAF 0.0 None None 0 None +4825 YPSIHRFIL 3.57700862377 PSIHRFI PGIYRFV 27.0 149053|NS3_gene_product|AAB02124.1|Hepatitis_C_virus|11103 +4826 YQLHNIQVI 0.0 None None 0 None +4827 YQMQFTQAL 0.0 None None 0 None +4828 YQMQFTQAL 0.0 None None 0 None +4829 YQSEKLCSL 0.0 None None 0 None +4830 YRAGKPTLV 0.432661229328 RAGKPT RSGAPT 23.0 102368|E2_protein|NP_751921.1|Hepatitis_C_virus_subtype_1a|31646 +4831 YRASEQKLC 0.0 None None 0 None +4832 YRDNTELPY 0.0 None None 0 None +4833 YRDVHVQKV 0.0 None None 0 None +4834 YRGPLSTTI 1.76192992766 YRGPLS YRGPLD 29.0 38724|Genome_polyprotein|P08617.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 +4835 YRGSVAPIL 0.0202594406357 YRGSVAPI YAGEPAPF 21.0 65810|sporozoite_surface_protein_2|NP_705260.1|Plasmodium_falciparum_3D7|36329 +4836 YRITVVESL 0.0 None None 0 None +4837 YRLEAVHAL 0.0 None None 0 None +4838 YRLEGDTLI 0.0 None None 0 None +4839 YRQFPKKSL 0.0 None None 0 None +4840 YRRHSLRAI 0.0 None None 0 None +4841 YRTVNNLIL 0.0 None None 0 None +4842 YSFDSLCQY 0.0 None None 0 None +4843 YSRDQIYIY 0.0 None None 0 None +4844 YSRQMISEL 0.0 None None 0 None +4845 YSRQMISEL 0.0 None None 0 None +4846 YTCEQNDQL 0.0 None None 0 None +4847 YTDSSSVLN 0.372503781182 TDSSSVLN TDSTSILG 27.0 107894|polyprotein|CAB41951.1|Hepatitis_C_virus|11103 +4848 YTEDHSASL 0.0 None None 0 None +4849 YTELWFLGL 13.1651602302 YTELW YAEMW 25.0 180077|PPE_family_protein|YP_177935.1|Mycobacterium_tuberculosis_H37Rv|83332 +4850 YTLLAFSVF 0.565506111769 LLAFSVF LLATSIF 23.0 182554|polyprotein|ACF49259.1|Dengue_virus_type_1_Hawaii|10000440 +4851 YTRKCTQAI 0.0 None None 0 None +4852 YTSMWRTYV 0.0 None None 0 None +4853 YTSMWRTYV 0.0 None None 0 None +4854 YVAICSPLF 0.0 None None 0 None +4855 YVDYMMCEF 0.0 None None 0 None +4856 YVFLHQCVL 0.0 None None 0 None +4857 YVFLHQCVL 0.0 None None 0 None +4858 YVGENVRFV 0.0 None None 0 None +4859 YVGIFHFQF 0.254817840555 VGIFHF VGVYHI 24.0 32663|small_hydrophobic_protein|AAM12943.1|Human_metapneumovirus|162145 +4860 YVLTRSKAM 0.0 None None 0 None +4861 YVTVLCLTF 0.0 None None 0 None +4862 YVYSLYWSI 159.605016198 YVYSLYWSI FLYELIWNV 29.0 108965|Prolipoprotein_diacylglyceryl_transferase|O06131.1|Mycobacterium_tuberculosis|1773 +4863 YWGVFAPIW 0.0 None None 0 None +4864 YWPPQSQPF 0.0 None None 0 None +4865 YYEKIFSTL 0.0 None None 0 None +4866 YYFLCLLL* 0.0 None None 0 None +4867 YYFLRPLL* 0.0 None None 0 None +4868 YYFLRPLL* 0.0 None None 0 None +4869 YYKIVSSIL 0.0232262868802 KIVSSI KLVSSV 22.0 95262|LAMP|AAK72632.1|Human_gammaherpesvirus_8|37296 +4870 YYLVANTKF 0.0 None None 0 None +4871 YYTNFSLEL 0.0 None None 0 None +4872 YYTNFSLEL 0.0 None None 0 None +4873 YYYFLCLLL 0.0 None None 0 None +4874 YYYFLRPLL 0.00109271035499 YYYFLRPL YIYMGQPL 21.0 185327|polyprotein|ACF49259.1|Dengue_virus_type_1_Hawaii|10000440 +4875 YYYFLRPLL 0.0362833645562 YYYFLRPL YIYMGQPL 21.0 185327|polyprotein|ACF49259.1|Dengue_virus_type_1_Hawaii|10000440 +4876 LSILVDWMI 0.0 None None 0 None +4877 LVMFLSILV 0.0 None None 0 None +4878 HWPEKEWPI 1.23491252617 HWPEKEW HTPVNSW 22.0 62977|polyprotein|AAB67037.1|Hepatitis_C_virus_(isolate_H77)|63746 +4879 WLEAMQGVI 0.0 None None 0 None +4880 MNRGRRSSL 0.597274971842 MNRGRRS MNRRKRS 25.0 183800|polyprotein|AGT63075.1|Dengue_virus_1|11053 +4881 RADHAAEQV 0.0 None None 0 None +4882 TTLSPAEPT 0.0 None None 0 None +4883 CLMVLYSLI 1.07995809695 CLMVLY CLYLLY 24.0 141222|DNA_packaging_tegument_protein_UL25|NP_044626.1|Human_alphaherpesvirus_1|10298 +4884 MTPSVYGGA 0.847766230468 TPSVYGG TPRVTGG 25.0 65749|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 +4885 FCFLVVASA 0.0 None None 0 None +4886 FLVVASAYI 0.0 None None 0 None +4887 VVASAYIKL 0.0 None None 0 None +4888 NSTIIPTLI 0.0 None None 0 None +4889 SSSGVNSTI 0.0 None None 0 None +4890 STIIPTLIL 0.0 None None 0 None +4891 NLAMCFGPV 0.0 None None 0 None +4892 MVAFINEKM 0.0 None None 0 None +4893 RHSNMVAFI 1.14135041379 RHSNMV RHHNMV 27.0 144403|polyprotein|AAK08509.1|Hepatitis_C_virus_subtype_1b|31647 +4894 SILASLSTL 0.0 None None 0 None +4895 TLQQMWISK 0.0 None None 0 None +4896 RAFADTLEV 0.0 None None 0 None +4897 VLLPVSLFI 0.0179862099621 LPVSLF LPTTLF 22.0 79180|tax_protein|AAF37566.1|Human_T-lymphotropic_virus_1|11908 +4898 LLFSVTMPK 0.0192709392451 LFSVTMP LYSSTVP 22.0 21242|polymerase|ACF94272.1|Hepatitis_B_virus|10407 +4899 VPVPPAPPL 0.748451099646 VPVPPAPP VPTDPNPP 29.0 70491|envelope_glycoprotein|AAC28452.1|Human_immunodeficiency_virus_1|11676 +4900 EIFMGLPTK 2.14751919188 IFMGLP IYMGQP 23.0 185327|polyprotein|ACF49259.1|Dengue_virus_type_1_Hawaii|10000440 +4901 VYTEIFMGL 0.0 None None 0 None +4902 YYASVYTEI 0.0 None None 0 None +4903 HMWNYMQSK 0.694505649699 MWNYMQ LWGYLQ 27.0 42094|telomer_length_regulation_protein_TEL1|EDV12172.1|Saccharomyces_cerevisiae|4932 +4904 QTYQHMWNY 1.32874030798 QHMWNY KHMWNF 34.0 103020|polyprotein|ABR25251.1|Hepatitis_C_virus|11103 +4905 SRYQTYQHM 0.0 None None 0 None +4906 MIMAQMRRI 0.0 None None 0 None +4907 RRISPFSCL 0.0731052404911 RRISPFSCL RVIDPRRCL 22.0 150556|polyprotein|AGW21594.1|Dengue_virus_1|11053 +4908 ILFDEAVKL 10.417679881 LFDEAVK LFNWAVK 21.0 169050|polyprotein|ABU97067.1|Hepatitis_C_virus_subtype_1b|31647 +4909 MKYPVKSIL 0.0 None None 0 None +4910 TLIHQFQEK 0.0 None None 0 None +4911 KLGADFIGH 0.0 None None 0 None +4912 ALGPPVLLR 8.02341413363e-05 ALGPPVLL SLGLVILL 17.0 59141|Circumsporozoite_protein_precursor|P08677.2|Plasmodium_vivax_strain_Belem|31273 +4913 PPVLLRCSL 0.0266850441922 PVLLRCSL KVLIRCYL 26.0 145860|Protein_E6|P04019.1|Human_papillomavirus_type_11|10580 +4914 FTRENTLTF 0.0 None None 0 None +4915 LTFMHLSPI 0.0 None None 0 None +4916 TFMHLSPIL 0.0 None None 0 None +4917 EFVERYHVL 0.0823067794915 VERYHVL AEEYHAL 24.0 187188|PE_family_protein_PE9|YP_177784.1|Mycobacterium_tuberculosis_H37Rv|83332 +4918 RLWARGLTV 0.0 None None 0 None +4919 RLWARGLTV 0.0 None None 0 None +4920 LVWRPLREV 0.68879469979 VWRPLRE IWLKLKE 22.0 180496|Polyprotein|NP_056776.2|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 +4921 SYVMLPCAL 0.0 None None 0 None +4922 VMLPCALPV 0.0284555239065 MLPCALP LLPAILP 23.0 41971|putative_D-ribose-binding_protein|NP_301386.1|Mycobacterium_leprae|1769 +4923 RLPEVQLPK 8.33669952536e-05 LPEVQLPK LPSDFLPS 16.0 16836|precore/core_protein_[Hepatitis_B_virus]|AAR03815.1|Hepatitis_B_virus|10407 +4924 APRGACYRA 0.0 None None 0 None +4925 APRGVCYGA 0.0482323961939 PRGVC PYGVC 24.0 148117|early_protein|CAA52585.1|Human_papillomavirus_type_52|10618 +4926 GLTWAVVLI 0.243238394937 TWAVVLI NWAKVLV 24.0 149052|E1_protein|NP_751920.1|Hepatitis_C_virus_(isolate_H77)|63746 +4927 QPLGLTWAV 0.0 None None 0 None +4928 YRNEDHWAW 0.109703755322 RNEDHWA KREDQWC 24.0 184131|polyprotein|AGO67248.1|Dengue_virus_2|11060 +4929 KCAEPSTRK 0.0 None None 0 None +4930 LLTDDLRSV 0.0 None None 0 None +4931 QMPTDYAEV 0.0 None None 0 None +4932 VVGARGVGK 0.0 None None 0 None +4933 ALFCGRSDY 0.000134140052187 ALFCGRSD AVFDRKSD 18.0 5316|EBNA-3B_nuclear_protein|CAD53420.1|Human_gammaherpesvirus_4|10376 +4934 SFLCHKALF 0.0 None None 0 None +4935 SFLCHKALF 0.0 None None 0 None +4936 SFLCHKALF 0.0 None None 0 None +4937 HHLLSLQYV 0.0 None None 0 None +4938 NHHLLSLQY 0.0 None None 0 None +4939 LRLLDRELL 0.0 None None 0 None +4940 QMPPMPPPL 0.0 None None 0 None +4941 SRVSGGTPL 0.0 None None 0 None +4942 IPLEVMEPF 29.4847656669 IPLEVME IPFEIMD 26.0 180528|polyprotein|AGO67248.1|Dengue_virus_2|11060 +4943 RHAACSVLV 0.0 None None 0 None +4944 TRHAACSVL 0.0 None None 0 None +4945 TRHAACSVL 0.0 None None 0 None +4946 IYLGAVNWI 0.25 GAVNWI GAVQWM 26.0 177647|polyprotein|ADE10208.1|Hepatitis_C_virus_subtype_3a|356426 +4947 YLGAVNWIY 5.08 GAVNWI GAVQWM 26.0 177647|polyprotein|ADE10208.1|Hepatitis_C_virus_subtype_3a|356426 +4948 MWALGIIAY 0.0905570014873 MWALGII LWKAGIL 23.0 24943|DNA_polymerase|CAA10434.1|Hepatitis_B_virus|10407 +4949 SPALNKMFY 0.0 None None 0 None +4950 IPGPIPGPI 0.00624824950737 PGPIPG PGTGPG 21.0 47760|EBNA-1_protein|Q777E1|Human_gammaherpesvirus_4|10376 +4951 IPGPIPGPI 0.0209180526986 PGPIPG PGTGPG 21.0 47760|EBNA-1_protein|Q777E1|Human_gammaherpesvirus_4|10376 +4952 NPGPIPGPI 7.77591539117 PGPIPGPI PGLSPGTL 22.0 21638|protein_F|ABV46152.2|Hepatitis_C_virus_(isolate_Japanese)|11116 +4953 AEYIVVARN 0.0 None None 0 None +4954 YIVVARNKY 0.0 None None 0 None +4955 IFWDLSKPM 0.0 None None 0 None +4956 IFWDLSKPM 0.0 None None 0 None +4957 IPTEKPTIL 0.654454704699 IPTEKPTIL LPFDKPTIM 32.0 38466|nucleocapsid_protein|ABF21284.1|Influenza_A_virus_(A/Iran/1/1957(H2N2))|488233 +4958 FLNRWMANT 1.07227470363 FLNRWM FANRWI 28.0 140561|metal_cation_transporter_P-type_ATPase_A_CtpF|NP_216513.1|Mycobacterium_tuberculosis_H37Rv|83332 +4959 WMANTLDAV 0.0 None None 0 None +4960 ALHTAVLLL 0.0 None None 0 None +4961 KMWDAVLYR 0.0 None None 0 None +4962 LSIESLTLV 0.0 None None 0 None +4963 TLSIESLTL 0.0 None None 0 None +4964 HRVNWVVFL 0.0 None None 0 None +4965 FLYQPNWRF 0.598090160823 YQPNWR YFPDWQ 24.0 101721|nef|AAA02639.1|Human_immunodeficiency_virus_1|11676 +4966 LRKRRSRKR 0.0 None None 0 None +4967 RQLRKRRSR 0.0 None None 0 None +4968 RRQEQPSIK 0.0 None None 0 None +4969 FQYKFTVQA 1.33795003856 QYKFTV NYKFTL 24.0 15242|trans-sialidase,_putative|EAN81560.1|Trypanosoma_cruzi|5693 +4970 ILGTPLSKV 0.0 None None 0 None +4971 VLSGAKIWL 0.098644741065 VLSGAKIWL VLSDFKVWL 32.0 181036|||| +4972 AVLIVTTTV 0.000402870290963 VLIVTTTV ILIGITTL 18.0 59182|attachment_glycoprotein|ABQ58821.1|Human_metapneumovirus|162145 +4973 LLESSNTNV 0.0 None None 0 None +4974 VVWATKYFL 82.9775661936 VVWATKYFL CLWWLQYFL 26.0 39591|polyprotein|AAA45677.1|Hepatitis_C_virus_(isolate_H77)|63746 +4975 AMCSAQEEI 0.0487567516051 AMCSAQEEI SICPSQEPM 21.0 58463|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 +4976 KLTPYMVVL 0.0 None None 0 None +4977 FRVRGAVSH 0.0 None None 0 None +4978 FRHSMVVPY 0.294968010535 RHSMVVP RHADVIP 25.0 97093|polyprotein|AAB66324.1|Hepatitis_C_virus_(isolate_H77)|63746 +4979 KRRRLWAAL 0.0 None None 0 None +4980 RRLWAALGP 0.0128120947675 WAALGP WLSQGP 22.0 59569|Genome_polyprotein|P26662.3|Hepatitis_C_virus_(isolate_Japanese)|11116 +4981 YLIISTFFL 0.0474258731776 YLIISTF YLLADTF 23.0 140616|membrane-associated_phospholipase_C|NP_216866.1|Mycobacterium_tuberculosis_H37Rv|83332 +4982 KIFNHPSTL 0.00530943111929 KIFNHPSTL SLYNTVSTL 20.0 189294|Gag|O89360|Human_immunodeficiency_virus_1|11676 +4983 RSPKKHGYM 0.155158512329 SPKKH SPEKH 25.0 60031|SAG1_protein|AAO72426.1|Toxoplasma_gondii_RH|383379 +4984 YMKMFEIPA 0.0 None None 0 None +4985 LSSIGRSPM 0.0 None None 0 None +4986 MVFCDFHGH 24.8831744361 MVFCDFHGH MSLADFHGE 29.0 155811|ribonucleotide_reductase_large_subunit|CAB06725.1|Human_alphaherpesvirus_2|10310 +4987 RSPMVFCDF 0.0 None None 0 None +4988 SIGRSPMVF 0.0 None None 0 None +4989 SSIGRSPMV 0.0 None None 0 None +4990 ATATAYLCR 0.0 None None 0 None +4991 ATAYLCRVK 0.0 None None 0 None +4992 RVKGNFQTI 0.0 None None 0 None +4993 TATAYLCRV 0.0 None None 0 None +4994 YLCRVKGNF 0.0 None None 0 None +4995 CVSCWNVSR 0.00917876698188 CVSCWNV CSSVFNV 21.0 13456|circumsporozoite_protein|AAN87606.1|Plasmodium_falciparum|5833 +4996 RLASLYKTL 0.0 None None 0 None +4997 TLPQSVDPL 0.351470470495 LPQSVDPL LPEGMDPF 27.0 38446|Glycoprotein_B_precursor_(Glycoprotein_II)|P09257.1|Human_alphaherpesvirus_3|10335 +4998 SSSYAIEKR 0.0 None None 0 None +4999 ISRSTFAEV 0.0 None None 0 None +5000 RLPISRSTF 0.271294816931 PISRSTF PITYSTY 22.0 107873|Genome_polyprotein|P26664.3|Hepatitis_C_virus|11103 +5001 STFAEVTGL 0.0341560998855 STFAEVT KTFEQVT 21.0 14198|UL123;_IE1|AAR31390.1|Human_betaherpesvirus_5|10359 +5002 STFAEVTGL 0.00982374389904 STFAEVT KTFEQVT 21.0 14198|UL123;_IE1|AAR31390.1|Human_betaherpesvirus_5|10359 +5003 FSWNGGSFV 26.3153973248 SWNGG SWNSG 27.0 180440|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 +5004 FSWNGGSFV 148.274767747 SWNGG SWNSG 27.0 180440|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 +5005 TINEECSEI 3.0978991727 INEECS INEDCS 30.0 103322|polyprotein|BAB18806.1|Hepatitis_C_virus|11103 +5006 ILACRWVEM 0.0 None None 0 None +5007 ESPFSSGKV 0.0 None None 0 None +5008 MLAIGCALL 0.924557240739 MLAIGC LLAIGC 29.0 180802|polyprotein|AGO67248.1|Dengue_virus_2|11060 +5009 ESIRHNVLY 0.0 None None 0 None +5010 SIRHNVLYR 0.00459874686531 SIRHNVLY GLFNNVLY 22.0 20861|Non-capsid_protein_NS-1|P07298.1|Human_parvovirus_B19|10798 +5011 LQFGPTAEG 0.0 None None 0 None +5012 QPIPSVHER 0.0 None None 0 None +5013 SVHERTDWV 0.0 None None 0 None +5014 SVHERTDWV 0.0 None None 0 None +5015 RAPSPVSFV 0.244491068542 APSPVSFV SPRPVSYL 26.0 39571|polyprotein|BAD73987.1|Hepatitis_C_virus_subtype_1b|31647 +5016 GVLVLLFTL 0.371428571429 GVLVLLFTL GILGFVFTL 26.0 20354|M1_protein|CAA30882.1|Influenza_A_virus|11320 +5017 VLAPGVLVL 0.0 None None 0 None +5018 VLAPGVLVL 0.0 None None 0 None +5019 VLVLLFTLV 0.0 None None 0 None +5020 FTFLVSLYL 0.0 None None 0 None +5021 FTFLVSLYL 0.0 None None 0 None +5022 IQAYVFTFL 0.0 None None 0 None +5023 IQAYVFTFL 0.0 None None 0 None +5024 LIQAYVFTF 0.0 None None 0 None +5025 QAYVFTFLV 0.0 None None 0 None +5026 QAYVFTFLV 0.0 None None 0 None +5027 YVFTFLVSL 0.0 None None 0 None +5028 YVFTFLVSL 0.0 None None 0 None +5029 SSSPTCSLM 0.0 None None 0 None +5030 ENWDLVTYR 0.00961312062683 ENWDLVTY QGWGPISY 20.0 8236|Genome_polyprotein|P27958.3|Hepatitis_C_virus_subtype_1a|31646 +5031 GAMENWDLV 0.0 None None 0 None +5032 LEHPGSTRF 0.758464150481 LEHPGST LRHPGFT 28.0 180818|Membrane_glycoprotein_precursor|NP_739582.2|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 +5033 QTDYVLSPL 0.0 None None 0 None +5034 VLSPLTGGL 0.000641889255728 LSPLTGG FSPGTSG 18.0 17802|Nonstructural_protein_NS3|NP_739587.2|Dengue_virus_2_Thailand/16681/84|31634 +5035 ITEILDRYV 0.0654819887488 ITEILDRY ITDTIDKF 23.0 12588|Glycoprotein_B_precursor_(Glycoprotein_II)|P09257.1|Human_alphaherpesvirus_3|10335 +5036 FNKSGFKHY 0.0509955625565 FNKSGFK FSKCGFP 23.0 23864|envelope_glycoprotein(gp21,_gp46)_-_human_T-cell_lymphotropic_virus_type_1|A45714|Human_T-lymphotropic_virus_1|11908 +5037 KSGFKHYQM 0.0 None None 0 None +5038 PVFNKSGFK 0.014495615722 FNKSGF FSKCGF 23.0 23864|envelope_glycoprotein(gp21,_gp46)_-_human_T-cell_lymphotropic_virus_type_1|A45714|Human_T-lymphotropic_virus_1|11908 +5039 VLVSGIQVL 0.0 None None 0 None +5040 VLVSGIQVL 0.0 None None 0 None +5041 RSRTGEDEV 0.0 None None 0 None +5042 LGQGELSAF 0.0 None None 0 None +5043 EAQPESEGV 0.0 None None 0 None +5044 LQDFYLGTY 32.5306568234 FYLGTY FYLGQY 29.0 156550|E3_ubiquitin-protein_ligase_Mdm2|Q00987.1|Homo_sapiens|9606 +5045 VAFPLQDFY 0.0 None None 0 None +5046 ESVNILSVL 0.0 None None 0 None +5047 GLVESVNIL 0.0 None None 0 None +5048 FTVGQTEKY 0.0 None None 0 None +5049 ESFKQTYVY 0.0 None None 0 None +5050 ESFKQTYVY 0.0 None None 0 None +5051 QTYVYSMAL 0.0 None None 0 None +5052 YVYSMALVL 0.0 None None 0 None +5053 YVYSMALVL 0.0 None None 0 None +5054 YVYSMALVL 0.0 None None 0 None +5055 FSLHKDRPV 0.0 None None 0 None +5056 ATRKLIGKV 0.0 None None 0 None +5057 HLKVRTATR 0.809264845181 HLKVRT HLRIRT 27.0 154822|ribonucleotide_reductase_large_subunit|CAB06725.1|Human_alphaherpesvirus_2|10310 +5058 TATRKLIGK 0.0 None None 0 None +5059 LLPWAHSML 0.0 None None 0 None +5060 QQNAPLLPW 1.13253012048 QQNAPLL QSNAPIM 26.0 180460|polyprotein|AGO67248.1|Dengue_virus_2|11060 +5061 RIHSDEQPY 0.0 None None 0 None +5062 AVHTVPQTI 0.0 None None 0 None +5063 DPIRRHLHI 0.0 None None 0 None +5064 HILYHCYGV 0.0 None None 0 None +5065 WTRPGSEVL 0.0 None None 0 None +5066 FPYVRNFVM 0.0 None None 0 None +5067 YVRNFVMNL 0.0 None None 0 None +5068 VAHEGMRPM 1.76923076923 AHEGMRPM AHNGLRDL 26.0 65654|polyprotein_precursor|BAA01582.1|Hepatitis_C_virus|11103 +5069 RPDKMVPVV 0.0 None None 0 None +5070 ILYLLSLFT 0.0 None None 0 None +5071 LTILYLLSL 0.0 None None 0 None +5072 YLLSLFTQT 0.0 None None 0 None +5073 AAGPHVTVL 0.0 None None 0 None +5074 RASAAGPHV 0.0 None None 0 None +5075 SAAGPHVTV 0.0 None None 0 None +5076 AVADLSCML 0.0 None None 0 None +5077 CMLVLPTRL 0.0 None None 0 None +5078 LAVADLSCM 0.0 None None 0 None +5079 MLVLPTRLV 0.0 None None 0 None +5080 VAVGTEHTL 0.0 None None 0 None +5081 SVAWTTMDV 0.0 None None 0 None +5082 TMDVATPSV 0.000405605959168 MDVA MDAA 15.0 154448|RL2|CAB06760.1|Human_alphaherpesvirus_2|10310 +5083 NLYKGSVLY 0.341399031209 NLYKGSVLY TLWKAGILY 25.0 24943|DNA_polymerase|CAA10434.1|Hepatitis_B_virus|10407 +5084 DEYNFVRTY 0.0 None None 0 None +5085 RTYECFQHR 0.0 None None 0 None +5086 LPSDPRLHL 0.0 None None 0 None +5087 FLADITHLR 0.0 None None 0 None +5088 GMRYWNMMV 0.0 None None 0 None +5089 NMMVQWWLA 1.28923492085 NMMVQW DMMMNW 23.0 72322|polyprotein|AAA86907.1|Hepatitis_C_virus|11103 +5090 TPLGKGDIV 0.0 None None 0 None +5091 KVRSCIDLI 0.0 None None 0 None +5092 YEQKVRSCI 0.0 None None 0 None +5093 ALLAFATIM 0.0 None None 0 None +5094 ATIMYVPAL 0.0 None None 0 None +5095 LAFATIMYV 0.104302556769 LAFATIMY LAYVSVLY 24.0 141341|tegument_protein_VP11/12|NP_044648.1|Human_alphaherpesvirus_1|10298 +5096 LAFATIMYV 0.0894021915166 LAFATIMY LAYVSVLY 24.0 141341|tegument_protein_VP11/12|NP_044648.1|Human_alphaherpesvirus_1|10298 +5097 YALLAFATI 0.0 None None 0 None +5098 YALLAFATI 0.0 None None 0 None +5099 LLLLLLLLV 0.0 None None 0 None +5100 LLLLLLLVV 0.183789279182 LLLLLVV VLLLLVV 25.0 98540|trans-sialidase,_putative|EAN88532.1|Trypanosoma_cruzi|5693 +5101 LLLLLLVVV 0.355681484489 LLLLVVV LLLLVVM 25.0 98224|trans-sialidase,_putative|EAN82076.1|Trypanosoma_cruzi|5693 +5102 LLVVVPWGV 0.0 None None 0 None +5103 IAATPIPAM 0.195363107976 TPIPA TPLPA 25.0 177806|polyprotein|ACZ60104.1|Hepatitis_C_virus_subtype_3a|356426 +5104 HVLEIDESV 0.0 None None 0 None +5105 HVLEIDESV 0.0 None None 0 None +5106 YFNGSTNHV 0.0 None None 0 None +5107 TPLCPGELL 0.0376303451797 LCPGELL VCWGELM 23.0 187197|Core_protein|Q9QAC5|Hepatitis_B_virus|10407 +5108 LMLGLVWTI 0.0516239227798 LMLGLVWTI LMMRTTWAL 21.0 150389|polyprotein|AGO67248.1|Dengue_virus_2|11060 +5109 LMLGLVWTI 0.0094010029801 LMLGLVWTI LMMRTTWAL 21.0 150389|polyprotein|AGO67248.1|Dengue_virus_2|11060 +5110 RLMLGLVWT 0.0383304570666 LMLGLVW LMMRTTW 19.0 150686|polyprotein|AGO67248.1|Dengue_virus_2|11060 +5111 SLTADDAFV 0.0 None None 0 None +5112 PAFSLDVLM 0.0 None None 0 None +5113 YLQAEIEPV 0.0 None None 0 None +5114 YLQAEIEPV 0.0 None None 0 None +5115 LFFVDKLYK 0.0 None None 0 None +5116 ALLPLFVVL 0.0 None None 0 None +5117 ALLPLFVVL 0.0 None None 0 None +5118 KALLPLFVV 0.0 None None 0 None +5119 VVLCGNDHV 0.458740128795 VVLCGNDHV TLVCGKDGV 25.0 65118|SAG1_protein|AAO72426.1|Toxoplasma_gondii_RH|383379 +5120 TEMKRKAPF 0.0 None None 0 None +5121 AMATYHFHF 0.26894142137 ATYHFH CSHHFH 25.0 183147|polyprotein|AGW21594.1|Dengue_virus_1|11053 +5122 ATYHFHFNL 2.521436525 TYHFHFNL SEHSHFSL 25.0 25275|Glutamate_decarboxylase_2|Q05329.1|Homo_sapiens|9606 +5123 ATYHFHFNL 3.11006375559 TYHFHFNL SEHSHFSL 25.0 25275|Glutamate_decarboxylase_2|Q05329.1|Homo_sapiens|9606 +5124 KAMATYHFH 0.0 None None 0 None +5125 LKAMATYHF 0.0 None None 0 None +5126 NVFVEVVLV 0.0 None None 0 None +5127 GVKGVNSLF 0.270014098137 VKGVNSLF VRGLTSLF 27.0 52652|||| +5128 KGVNSLFKK 0.0 None None 0 None +5129 AMSTPIYQM 0.0 None None 0 None +5130 AMSTPIYQM 0.0 None None 0 None +5131 SMAMSTPIY 0.0 None None 0 None +5132 SMAMSTPIY 0.0 None None 0 None +5133 SSMAMSTPI 0.0 None None 0 None +5134 KMADEVPLK 0.0 None None 0 None +5135 FLLAFRSGA 0.0 None None 0 None +5136 LLAFRSGAL 0.0 None None 0 None +5137 RVAEVAAQV 0.0 None None 0 None +5138 KIFWFPTGL 0.0 None None 0 None +5139 AGIFLLIHF 0.0 None None 0 None +5140 FLLIHFHPL 0.557931740375 FLLIHFHPL FCSHHFHQL 25.0 183147|polyprotein|AGW21594.1|Dengue_virus_1|11053 +5141 FLLIHFHPL 0.754446387197 FLLIHFHPL FCSHHFHQL 25.0 183147|polyprotein|AGW21594.1|Dengue_virus_1|11053 +5142 GIFLLIHFH 0.0 None None 0 None +5143 LLIHFHPLA 0.831825503832 HFHPL HFHQL 25.0 183147|polyprotein|AGW21594.1|Dengue_virus_1|11053 +5144 SIVTSTFII 0.0 None None 0 None +5145 VTSTFIISL 0.0 None None 0 None +5146 LQIHGLAVE 0.0196761894216 QIHGLAV RLHGLSA 22.0 423047|Genome_polyprotein|P27958.3|Hepatitis_C_virus_genotype_1|41856 +5147 ATVLTLPHV 0.0 None None 0 None +5148 VLTLPHVTK 0.0 None None 0 None +5149 AVSNFYLPL 0.0 None None 0 None +5150 HISAVSNFY 0.0 None None 0 None +5151 HISAVSNFY 0.0 None None 0 None +5152 SVVVIIDVK 0.0 None None 0 None +5153 VVIIDVKPK 0.0 None None 0 None +5154 FQRALVQPG 4.11642215044 FQRALV FQRALI 27.0 183577|polyprotein|AGK36298.1|Dengue_virus_2|11060 +5155 ESFTATVEF 0.0 None None 0 None +5156 LAAPRGVCY 0.0886753444311 PRGVC PYGVC 24.0 148117|early_protein|CAA52585.1|Human_papillomavirus_type_52|10618 +5157 ATGATSLCF 0.0 None None 0 None +5158 GLAMCHQEL 0.0 None None 0 None +5159 LLTLAGLAM 0.0 None None 0 None +5160 TVWPSLAPL 8.65748022982 TVWPSLAPL SLWKDGAPL 23.0 140600|glutamine_synthetase_GLNA1_(glutamine_synthase)_(GS-I)|NP_216736.1|Mycobacterium_tuberculosis_H37Rv|83332 +5161 CQHKLGKRY 0.0 None None 0 None +5162 AVWRHLLLA 0.0 None None 0 None +5163 HLLLALLLL 0.0164752006047 LALLLL LALLLL 24.0 19442|nucleocapsid_protein|ABI96968.1|SARS_coronavirus|227859 +5164 LLALLLLVL 12.4294702466 LALLLL LALLLL 24.0 19442|nucleocapsid_protein|ABI96968.1|SARS_coronavirus|227859 +5165 LLALLLLVL 7.77953412607 LALLLL LALLLL 24.0 19442|nucleocapsid_protein|ABI96968.1|SARS_coronavirus|227859 +5166 LLLALLLLV 0.264895382271 LALLLL LALLLL 24.0 19442|nucleocapsid_protein|ABI96968.1|SARS_coronavirus|227859 +5167 LTRHQRTHM 6.47908572951 TRHQRTHM SRHTSDHM 24.0 17278|Genome_polyprotein|P06441.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 +5168 EAWLFLEWV 0.0 None None 0 None +5169 SEAWLFLEW 0.0 None None 0 None +5170 WILSHTVAL 0.0 None None 0 None +5171 WILSHTVAL 0.0 None None 0 None +5172 SVRKSVSTV 0.0 None None 0 None +5173 MTVTVCPPT 0.0 None None 0 None +5174 SPMVLLLAA 0.0 None None 0 None +5175 VERGSPMVL 0.0 None None 0 None +5176 VVERGSPMV 0.0 None None 0 None +5177 FEAFDHTET 0.0 None None 0 None +5178 RLFEAFDHT 0.0 None None 0 None +5179 HTCRVMGAL 0.0 None None 0 None +5180 YKIGGIGMV 0.0 None None 0 None +5181 EELTQLNEA 0.0 None None 0 None +5182 LQSRLEEEL 0.0 None None 0 None +5183 RLEEELTQL 0.0 None None 0 None +5184 FPRLGCPWF 0.0 None None 0 None +5185 RLGCPWFTL 0.0 None None 0 None +5186 RLGCPWFTL 0.0 None None 0 None +5187 DWPVFPGLF 24.1501420113 WPVFPG WPAPPG 27.0 72928|Genome_polyprotein|P26662.3|Hepatitis_C_virus_(isolate_Japanese)|11116 +5188 FNVGDDWPV 0.0 None None 0 None +5189 NYASRTQNI 0.0140565208982 NYASRTQ NWAVRTK 21.0 6308|HCV-1|AAA45676.1|Hepatitis_C_virus_genotype_1|41856 +5190 SVSSCCQPV 0.898067608919 SSCCQP SECCTP 28.0 57361|Genome_polyprotein|SRC279960|Hepatitis_C_virus_(isolate_H77)|63746 +5191 SVSSCCQPV 1.08294722702 SSCCQP SECCTP 28.0 57361|Genome_polyprotein|SRC279960|Hepatitis_C_virus_(isolate_H77)|63746 +5192 CTLGDQLSL 0.0447254880178 GDQLSL GDKLSL 25.0 244160|surface_antigen_2_(CA-2)|XP_818927.1|Trypanosoma_cruzi_strain_CL_Brener|353153 +5193 STAPQAHGV 0.0 None None 0 None +5194 STAPQAHGV 0.0 None None 0 None +5195 VSLFYSTAI 0.0 None None 0 None +5196 VSLFYSTAI 0.0 None None 0 None +5197 YSTAISVYL 0.0 None None 0 None +5198 YSTAISVYL 0.0 None None 0 None +5199 DTAPDIVEI 0.0 None None 0 None +5200 FLWDRHVRF 0.0 None None 0 None +5201 LWDRHVRFF 0.0 None None 0 None +5202 FTCLPLGSL 0.0 None None 0 None +5203 HVWLCDLPV 7.43524726743 VWLCDLPV ARLCDLPA 30.0 4172|Glycoprotein_I_precursor_(Glycoprotein_IV)_(GI)_(GPIV)|P09258.1|Human_alphaherpesvirus_3|10335 +5204 HVWLCDLPV 46.7070308887 VWLCDLPV ARLCDLPA 30.0 4172|Glycoprotein_I_precursor_(Glycoprotein_IV)_(GI)_(GPIV)|P09258.1|Human_alphaherpesvirus_3|10335 +5205 APRGVCYGA 0.0482323961939 PRGVC PYGVC 24.0 148117|early_protein|CAA52585.1|Human_papillomavirus_type_52|10618 +5206 DPEYSPGAL 0.154024773008 YSPGAL YSPGEI 25.0 59153|Genome_polyprotein|P27958.3|Hepatitis_C_virus_subtype_1a|31646 +5207 YSPGALATF 0.0 None None 0 None +5208 VLGDFLGTV 0.0 None None 0 None +5209 AVVGTVWNV 0.0 None None 0 None +5210 NVATTGLSL 0.0 None None 0 None +5211 DTTDKGALM 0.0 None None 0 None +5212 KAVSVCPEA 0.0573665433528 KAVSVCPEA QQVSIAPNA 22.0 19359|IMMUNOGENIC_PROTEIN_MPT64_(ANTIGEN_MPT64/MPB64)|CAA98382.1|Mycobacterium_tuberculosis_H37Rv|83332 +5213 SVCPEAAPA 0.0 None None 0 None +5214 VLVVGMGPV 0.0 None None 0 None +5215 IFATKPELL 0.0 None None 0 None +5216 RIFATKPEL 0.0 None None 0 None +5217 AFSQSAYLI 0.0 None None 0 None +5218 AYLIQHQRF 0.0 None None 0 None +5219 KAFSQSAYL 0.0 None None 0 None +5220 KAFSQSAYL 0.0 None None 0 None +5221 FPAPARDDF 0.0 None None 0 None +5222 SPSVMWLVH 1.99051566923 SPSVMWL SPSSIWV 26.0 116835|Nucleoprotein|P05133.1|Hantaan_virus_76-118|11602 +5223 LAVRDVFEL 0.0 None None 0 None +5224 LAVRDVFEL 0.0 None None 0 None +5225 KTLTLAKNY 0.0 None None 0 None +5226 SSGSMCNRW 0.0888800199782 SSGSMCNRW TAGSLQGQW 23.0 9920|ESAT-6-like_protein_esxB|P0A566.2|Mycobacterium_tuberculosis|1773 +5227 TTKNDIGPY 0.0 None None 0 None +5228 LGLTNNTAM 0.0 None None 0 None +5229 FTTELTAPF 0.0995002913307 FTTELTAPF FTASVTSPL 25.0 177903|polyprotein|ACZ60102.1|Hepatitis_C_virus_subtype_3a|356426 +5230 FTTELTAPF 0.139300407863 FTTELTAPF FTASVTSPL 25.0 177903|polyprotein|ACZ60102.1|Hepatitis_C_virus_subtype_3a|356426 +5231 FTTELTAPF 0.106698184746 FTTELTAPF FTASVTSPL 25.0 177903|polyprotein|ACZ60102.1|Hepatitis_C_virus_subtype_3a|356426 +5232 MPAFTTELT 0.0 None None 0 None +5233 LMALHPALF 0.0394828895203 LMALHPAL MCAVHPTL 25.0 7660|polyprotein|AAA45677.1|Hepatitis_C_virus_(isolate_H77)|63746 +5234 QCSEHDVLF 4.32142857143 CSEHD CVEHD 26.0 120093|unnamed_protein_product|CAA33016.1|Rubella_virus|11041 +5235 EPYIDNEEF 0.0 None None 0 None +5236 VVIKAIEPY 0.0 None None 0 None +5237 QVQDSNLEY 0.0 None None 0 None +5238 QVQDSNLEY 0.0 None None 0 None +5239 LASSCGCTF 3.24598726122 LASSCGCT MYPSCCCT 24.0 59786|Large_envelope_protein|P03138.3|Hepatitis_B_virus_ayw/France/Tiollais/1979|490133 +5240 LASSCGCTF 16.2484935375 LASSCGCT MYPSCCCT 24.0 59786|Large_envelope_protein|P03138.3|Hepatitis_B_virus_ayw/France/Tiollais/1979|490133 +5241 IQLLGVFVW 0.0 None None 0 None +5242 ISIQLLGVF 0.0 None None 0 None +5243 EVDFTCWKY 0.0 None None 0 None +5244 HPTAASQSR 0.0 None None 0 None +5245 IIETANVSY 0.0 None None 0 None +5246 VSYTNAWAL 0.121870305999 SYTNAWAL SYAQMWSL 26.0 180579|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 +5247 FFIHSFTLM 0.0 None None 0 None +5248 MFFIHSFTL 0.0344792251349 MFFIHSFT LFYQHKFN 22.0 23270|polyprotein|AAB67036.1|Hepatitis_C_virus_(isolate_H77)|63746 +5249 MFNPIIYIF 0.0584094317908 MFNPIIY LFNNVLY 24.0 20861|Non-capsid_protein_NS-1|P07298.1|Human_parvovirus_B19|10798 +5250 LPTPVEPTV 0.987770214465 LPTPVEPT LPDPLKPT 31.0 27241|Spike_glycoprotein_precursor|P59594.1|SARS_coronavirus|227859 +5251 TPVEPTVAC 0.234271638656 TPVEPT TPYKPT 24.0 68229|EBNA3B_(EBNA4A)_latent_protein|CAA24858.1|Human_gammaherpesvirus_4|10376 +5252 HPDNVSSSY 0.0 None None 0 None +5253 LLAAARPLW 1.30039551297 LLAAARPLW ITAAAVTLW 24.0 36717|nonstructural_protein_4B|YP_001527886.1|West_Nile_virus_NY-99|10000971 +5254 SPVALQLRY 0.0 None None 0 None +5255 YQIGTDSAL 0.0 None None 0 None +5256 EAHHHFPSL 3.68937388497 HHFPSL HHAPSL 29.0 21000|glutamine_synthetase_GLNA1_(glutamine_synthase)_(GS-I)|NP_216736.1|Mycobacterium_tuberculosis|1773 +5257 EAHHHFPSL 5.17245410388 HHFPSL HHAPSL 29.0 21000|glutamine_synthetase_GLNA1_(glutamine_synthase)_(GS-I)|NP_216736.1|Mycobacterium_tuberculosis|1773 +5258 GSGEAHHHF 0.0 None None 0 None +5259 RVSSLTLHF 0.0 None None 0 None +5260 KPFSQSCEF 0.0 None None 0 None +5261 KPLLSGPWA 0.348123132681 KPLLSGP KPTLHGP 27.0 6591|polyprotein|AAB67037.1|Hepatitis_C_virus_(isolate_H77)|63746 +5262 LSMTSITSV 0.0 None None 0 None +5263 IDTDQVHTL 0.0 None None 0 None +5264 TWKDTPYYI 0.0 None None 0 None +5265 KLILTLSAI 0.0 None None 0 None +5266 SYQMSNKLI 0.0 None None 0 None +5267 YQMSNKLIL 0.0 None None 0 None +5268 YQMSNKLIL 0.0 None None 0 None +5269 LMWSVTWPK 0.418780213276 WSVTW WAIKW 25.0 149105|E2_protein|NP_751921.1|Hepatitis_C_virus_(isolate_H77)|63746 +5270 SQSETNSAV 0.0 None None 0 None +5271 SHASHLHLF 0.0 None None 0 None +5272 SHASHLHLF 0.0 None None 0 None +5273 KVLISVHLI 0.0 None None 0 None +5274 DHYLVDRTL 0.0 None None 0 None +5275 YIKPLVPPA 0.0 None None 0 None +5276 RPGQSPGQL 1.15887751873 PGQSPGQL PGLSPGTL 31.0 21638|protein_F|ABV46152.2|Hepatitis_C_virus_(isolate_Japanese)|11116 +5277 HLFESSQLV 0.0 None None 0 None +5278 HLFESSQLV 0.0 None None 0 None +5279 GVYLWEDPV 6.47717900666 LWEDP LWESP 27.0 32243|C_protein|BAB60863.1|Measles_virus|11234 +5280 YLWEDPVCG 47.588178133 LWEDP LWESP 27.0 32243|C_protein|BAB60863.1|Measles_virus|11234 +5281 RILYMADEV 0.0 None None 0 None +5282 SLLDACLIL 0.0 None None 0 None +5283 APLPMPNPL 0.226485551842 LPMPNPL IPMTGPL 24.0 180531|polyprotein|AGO67248.1|Dengue_virus_2|11060 +5284 LLLWAPLPM 0.0 None None 0 None +5285 MQLRKAPNV 0.0 None None 0 None +5286 AHACAHALL 0.0 None None 0 None +5287 GAHACAHAL 0.0 None None 0 None +5288 VLNGWLRSV 7.1854641519 VLNGW LLNGW 28.0 37607|kaposin|AAC57155.1|Human_gammaherpesvirus_8|37296 +5289 AIDDHVCMA 0.0 None None 0 None +5290 LMVPRLEYV 0.0 None None 0 None +5291 FINARGRLL 0.0 None None 0 None +5292 AIPLRGFPV 7.52036422648 IPLRGFPV LSLRGLPV 27.0 24302|X_protein|AAP06597.1|Hepatitis_B_virus|10407 +5293 FVDENNEKL 0.0 None None 0 None +5294 FVDENNEKL 0.0 None None 0 None +5295 HTARLFYFV 0.0 None None 0 None +5296 LPSTAGPEM 6.14013666685 LPSTAGP LPEAAGP 28.0 43447|IMMUNOGENIC_PROTEIN_MPT64_(ANTIGEN_MPT64/MPB64)|CAA98382.1|Mycobacterium_tuberculosis_H37Rv|83332 +5297 LPSTAGPEM 6.97269757083 LPSTAGP LPEAAGP 28.0 43447|IMMUNOGENIC_PROTEIN_MPT64_(ANTIGEN_MPT64/MPB64)|CAA98382.1|Mycobacterium_tuberculosis_H37Rv|83332 +5298 TAANGSEVM 0.0 None None 0 None +5299 TAANGSEVM 0.0 None None 0 None +5300 MADATFQSL 0.0 None None 0 None +5301 MADATFQSL 0.0 None None 0 None +5302 WFNMADATF 0.0 None None 0 None +5303 ICIWNVSKL 0.0 None None 0 None +5304 EPTITDASL 0.0 None None 0 None +5305 IFDEWLKRF 0.0 None None 0 None +5306 FTGGIVNKL 0.0472701242502 FTGGIVNKL FMGVLVNSL 24.0 139747|granule_antigen_protein_GRA6|XP_002371939.1|Toxoplasma_gondii_ME49|508771 +5307 GIVNKLCAL 0.0 None None 0 None +5308 FGSLLGTCL 0.0 None None 0 None +5309 ISGPRSPTY 0.157560426259 ISGPRSPTY INGIRRPKH 20.0 66195|Nucleoprotein|P41269.1|Puumala_hantavirus|11604 +5310 MSLNSYIKL 0.0 None None 0 None +5311 YMVIMSPRL 0.0 None None 0 None +5312 EILWTTELY 0.0 None None 0 None +5313 LEILWTTEL 0.0 None None 0 None +5314 LGTSDVRIL 0.0 None None 0 None +5315 VAFLGTSDV 0.0 None None 0 None +5316 IMIAVVDSM 0.0 None None 0 None +5317 IMIAVVDSM 0.0 None None 0 None +5318 EASVHSVPI 0.0 None None 0 None +5319 FFSSNLPTY 0.0 None None 0 None +5320 FSSNLPTYY 12.750272737 NLPTYY SLPSYY 27.0 28594|IMMUNOGENIC_PROTEIN_MPT64_(ANTIGEN_MPT64/MPB64)|CAA98382.1|Mycobacterium_tuberculosis_H37Rv|83332 +5321 VALVPESSV 0.0 None None 0 None +5322 ISRNHNSRM 0.0 None None 0 None +5323 KTFGISRNH 0.0 None None 0 None +5324 RNHNSRMNK 0.0 None None 0 None +5325 LTDLQGVIV 0.0 None None 0 None +5326 IRHEMSTFA 0.0 None None 0 None +5327 VVSDSWGSK 0.0 None None 0 None +5328 IRAANVSAL 0.0 None None 0 None +5329 IRAANVSAL 0.0 None None 0 None +5330 RAANVSALY 0.0 None None 0 None +5331 GYRERGHPY 0.0 None None 0 None +5332 VVGAVGVGK 0.0 None None 0 None +5333 LTNTLTTSK 0.0 None None 0 None +5334 AAASTSSPK 0.0 None None 0 None +5335 TSITTSTQK 0.0 None None 0 None +5336 SHPGSAEIV 0.0 None None 0 None +5337 SYYSCVAAM 0.0 None None 0 None +5338 SYYSCVAAM 0.0 None None 0 None +5339 AHTFKQRRI 0.0 None None 0 None +5340 HTFKQRRIK 0.0 None None 0 None +5341 RYEEYRGRF 0.0254287796016 YEEYRGRF YQDWLGRM 22.0 23288|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 +5342 YEEYRGRFL 0.00584663400753 YEEYRGRF YQDWLGRM 22.0 23288|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 +5343 MTTGSVFFY 0.0 None None 0 None +5344 MTTGSVFFY 0.0 None None 0 None +5345 HVLSLAETK 0.0 None None 0 None +5346 SLAETKTLY 0.0 None None 0 None +5347 KLKTVSQTK 0.0 None None 0 None +5348 ASYDQSLRV 0.0 None None 0 None +5349 FSASYDQSL 0.0 None None 0 None +5350 HLKEPLQKL 0.0 None None 0 None +5351 HLYEQGGHL 0.0 None None 0 None +5352 HQCVHTGAK 0.0 None None 0 None +5353 IAHAWWACF 0.624917866388 HAWWACF HARWAAF 30.0 141262|DNA_polymerase_catalytic_subunit|NP_044632.1|Human_alphaherpesvirus_1|10298 +5354 AMWNRCADL 0.0 None None 0 None +5355 AYTFWTYIM 0.850753683829 AYTFW KYTFW 29.0 137660|L1|ACL12325.1|Human_papillomavirus_type_58|10598 +5356 IMNARSKNV 0.0 None None 0 None +5357 YAYTFWTYI 6.89162833838 AYTFW KYTFW 29.0 137660|L1|ACL12325.1|Human_papillomavirus_type_58|10598 +5358 YAYTFWTYI 1.32063005669 AYTFW KYTFW 29.0 137660|L1|ACL12325.1|Human_papillomavirus_type_58|10598 +5359 KAARIAAKV 0.0 None None 0 None +5360 KVGQSSMWI 0.0 None None 0 None +5361 PSTSTSRPV 0.0 None None 0 None +5362 CLAAMALSI 0.0 None None 0 None +5363 WLTPVIPTL 0.234315353622 WLTPVIP WLSLLVP 24.0 62477|HBsAg_protein|ABF71024.1|Hepatitis_B_virus|10407 +5364 GLFHCTRSV 0.0 None None 0 None +5365 RNWDVCKVI 0.0 None None 0 None +5366 KIPIRLPPV 0.0 None None 0 None +5367 FMLGITPNL 0.0 None None 0 None +5368 HRHHHRCRR 0.0 None None 0 None +5369 FLAGSSLPV 0.0 None None 0 None +5370 FLAGSSLPV 0.0 None None 0 None +5371 SSFLAGSSL 0.0 None None 0 None +5372 KLPSDPDAL 0.0 None None 0 None +5373 VYAVTVVTL 0.0 None None 0 None +5374 YAVTVVTLL 0.0 None None 0 None +5375 YAVTVVTLL 0.0 None None 0 None +5376 FILICCLII 0.0653826258252 LICCLII VLCCYVL 25.0 11956|UL123;_IE1|AAR31448.1|Human_betaherpesvirus_5|10359 +5377 ILICCLIIL 0.465751713705 LICCLII VLCCYVL 25.0 11956|UL123;_IE1|AAR31448.1|Human_betaherpesvirus_5|10359 +5378 LIILENIFV 0.0 None None 0 None +5379 VFILICCLI 0.300679700821 ILICCLI ILIRCII 24.0 137656|E6_protein|ACT36477.1|Human_papillomavirus_type_58|10598 +5380 PAMKFSCSL 0.0 None None 0 None +5381 FLSLIIDAT 0.0 None None 0 None +5382 LIIDATKFI 0.0 None None 0 None +5383 LIIDATKFI 0.0 None None 0 None +5384 IMMSSEDDI 0.0 None None 0 None +5385 YLDGQPQEA 0.0825589178834 YLDGQP YRDGNP 24.0 110227|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 +5386 GLAPPQLLI 0.0 None None 0 None +5387 ARIERPHNY 0.0 None None 0 None +5388 FTSSEPSRM 0.0 None None 0 None +5389 ESEGHTIEL 0.0 None None 0 None +5390 KMQEGLLAV 0.0819874238225 QEGLLAV QNGALAI 21.0 51685|Nuclear_antigen_EBNA-3C|Q69140.1|Human_gammaherpesvirus_4|10376 diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/run.sh b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/run.sh new file mode 100755 index 00000000..cbcf44cf --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/run.sh @@ -0,0 +1,24 @@ +############################################## +# Compute neoantigen quality +# +# Directory structure: +# +# data: +# neoantigen-data file and iebd-epitope file. +# +# alignments: +# precomputed blastp alignments for all neoantigens, split into files for each sample. +# blastp -query -db data/iedb.fasta -outfmt 5 -evalue 100000000 -gapopen 11 -gapextend 1 > +# +# src: +# source code folder +# +# output: +# source code output folder +############################################## + +# fitness model paramaters +a=26. +k=1. + +python src/main.py data/SupplementaryTable1.txt alignments $a $k > output/neontigenQuality.txt diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/src/.DS_Store b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/src/.DS_Store new file mode 100755 index 0000000000000000000000000000000000000000..5008ddfcf53c02e82d7eee2e57c38e5672ef89f6 GIT binary patch literal 6148 zcmeH~Jr2S!425mzP>H1@V-^m;4Wg<&0T*E43hX&L&p$$qDprKhvt+--jT7}7np#A3 zem<@ulZcFPQ@L2!n>{z**++&mCkOWA81W14cNZlEfg7;MkzE(HCqgga^y>{tEnwC%0;vJ&^%eQ zLs35+`xjp>T0 + + NeoantigenQuality + + + + + + org.python.pydev.PyDevBuilder + + + + + + org.python.pydev.pythonNature + + diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/src/.pydevproject b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/src/.pydevproject new file mode 100755 index 00000000..037bd251 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/src/.pydevproject @@ -0,0 +1,8 @@ + + + +/${PROJECT_DIR_NAME} + +python 2.7 +Default + diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/src/Aligner.py b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/src/Aligner.py new file mode 100755 index 00000000..fbca6a36 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/src/Aligner.py @@ -0,0 +1,108 @@ +''' +Created on Jul 26, 2017 + +@author: Marta Luksza, mluksza@ias.edu +''' +from math import log, exp + +from Bio import pairwise2 +from Bio.Blast import NCBIXML +from Bio.SubsMat import MatrixInfo as matlist + + +class Aligner(object): + ''' + Class to align neoantigens with IEDB epitopes and compute TCR-recognition + probabilities. + ''' + INF = float("inf") + + @staticmethod + def align(seq1, seq2): + ''' + Smith-Waterman alignment with default parameters. + ''' + matrix = matlist.blosum62 + gap_open = -11 + gap_extend = -1 + aln = pairwise2.align.localds(seq1.upper(), seq2.upper(), matrix, gap_open, gap_extend) + return aln + + @staticmethod + def logSum(v): + ''' + compute the logarithm of a sum of exponentials + ''' + if len(v) == 0: + return -Aligner.INF + ma = max(v) + if ma == -Aligner.INF: + return -Aligner.INF + return log(sum([exp(x - ma) for x in v])) + ma + + def __init__(self): + # dictionary of computed Ri-values mapped to neoantigen identifiers + self.Ri = {} + # dictionary of IEDB epitope alignments mapped to neoantigen identifiers + self.alignments = {} + # dictionary of the highest scoring alignments mapped to neoantigen identifiers + self.maximum_alignment = {} + + def readAllBlastAlignments(self, xmlpath): + ''' + Read precomputed blastp alignments from xml files, + compute alignment scores, + find the highest scoring alignment for each neoantigen. + ''' + f = open(xmlpath) + blast_records = NCBIXML.parse(f) + maxscore = {} + try: + for brecord in blast_records: + nid = int(str(brecord.query).split("_")[1]) + for alignment in brecord.alignments: + if not nid in self.alignments: + self.alignments[nid] = {} + self.maximum_alignment[nid] = None + self.maximum_alignment[nid] = 0 + maxscore[nid] = 0 + species = " ".join((str(alignment).split())[1:-3]) + for hsp in alignment.hsps: + if not "-" in hsp.query and not "-" in hsp.sbjct: + al = Aligner.align(hsp.query, hsp.sbjct) + if len(al) > 0: + al = al[0] + self.alignments[nid][species] = al + if al[2] > maxscore[nid]: + self.maximum_alignment[nid] = species + maxscore[nid] = al[2] + except ValueError: + pass + f.close() + + def computeR(self, a=26, k=1): + ''' + Compute TCR-recognition probabilities for each neoantigen. + ''' + # iterate over all neoantigens + for i in self.alignments: + # energies of all bound states of neoantigen i + bindingEnergies = [-k * (a - el[2]) for el in list(self.alignments[i].values())] + # partition function, over all bound states and an unbound state + lZ = Aligner.logSum(bindingEnergies + [0]) + lGb = Aligner.logSum(bindingEnergies) + R = exp(lGb - lZ) + self.Ri[i] = R + + def getR(self, i): + ''' + Return precomputed R value and the highest scoring alignment + for a given neoantigen i. + ''' + emptyAlignment = [None, None, 0] + if i in self.Ri: + species = self.maximum_alignment[i] + al = self.alignments[i][species] + species = str(species).replace(" ", "_") + return [self.Ri[i], species, al] + return [0., None, emptyAlignment] diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/src/__init__.py b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/src/__init__.py new file mode 100755 index 00000000..e69de29b diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/src/main.py b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/src/main.py new file mode 100755 index 00000000..3a0b9934 --- /dev/null +++ b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/src/main.py @@ -0,0 +1,71 @@ +''' +Created on Jul 27, 2017 + +@author: Marta Luksza, mluksza@ias.edu +''' +import sys + +from .Aligner import Aligner + + +def main(): + ''' + command line parameters: + neofile - text file with neoantigen data (supplementary data) + alignmentDirectory - folder with precomputed alignments (SI) + a - midpoint parameter of the logistic function, alignment score threshold + k - slope parameter of the logistic function + ''' + neofile = sys.argv[1] + alignmentDirectory = sys.argv[2] + + a = float(sys.argv[3]) + k = float(sys.argv[4]) + + # Compute MHC amplitudes for all neoantigens + f = open(neofile) + lines = f.readlines() + Ai = {} + data = {} + samples = set() + for line in lines[1:]: + [i, sample, _, _, _, _, mtpeptide, _, _, kdwt, kdmt] = line.strip().split() + i = int(i) + data[i] = mtpeptide.upper() + Ai[i] = float(kdwt) / float(kdmt) + samples.add(sample) + f.close() + + # Compute TCR-recognition probabilities for all neoantigens + aligner = Aligner() + for sample in samples: + xmlpath = alignmentDirectory + "/neoantigens_" + sample + "_iedb.xml" + aligner.readAllBlastAlignments(xmlpath) + aligner.computeR(a, k) + + # Compute neoantigen quality + nids = list(Ai.keys()) + nids.sort() + header = ["NeoantigenID", "MT.Peptide.Form", "NeoantigenQuality", + "NeoantigenAlignment", "IEDB_EpitopeAlignment", "AlignmentScore", "IEDB_Epitope"] + header = "\t".join(header) + print(header) + for i in nids: + A = Ai[i] + [R, species, alignment] = aligner.getR(i) + + neoAlignment = alignment[0] + epitopeAlignment = alignment[1] + score = alignment[2] + + l = [i, data[i], A * R, neoAlignment, epitopeAlignment, score, species] + l = "\t".join([str(s) for s in l]) + print(l) + + +if __name__ == '__main__': + if len(sys.argv) != 5: + print("Run as:") + print("python src/main.py ") + else: + main() From 9745e6f2e74b14208f37ad875aafd10bd149ff79 Mon Sep 17 00:00:00 2001 From: Pablo Riesgo Ferreiro Date: Sat, 6 Jun 2020 21:11:39 +0200 Subject: [PATCH 042/105] added generated code from avro models + conversion from/to iCaM and CSV --- input/command_line.py | 176 +++++----- input/helpers/data_import.py | 56 --- input/model_avro/Gene.avsc | 19 + input/model_avro/Mutation.avsc | 34 ++ input/model_avro/Neoantigen.avsc | 76 ++++ input/model_avro/README.md | 28 ++ input/model_avro/__init__.py | 24 ++ input/model_avro/generate_source_code.py | 8 + .../model_avro/neoantigen.avdl | 168 ++++----- input/model_avro/neoantigen.avpr | 81 +++++ input/model_avro/neoantigen/__init__.py | 4 + input/model_avro/schema.avsc | 1 + input/model_avro/schema_classes.py | 332 ++++++++++++++++++ input/model_avro/schema_conversion.py | 178 ++++++++++ input/predict_all_epitopes.py | 4 +- .../test_schema_conversion.py | 22 ++ .../unit_tests/test_schema_conversion.py | 116 ++++++ setup.py | 101 +++--- 18 files changed, 1150 insertions(+), 278 deletions(-) create mode 100644 input/model_avro/Gene.avsc create mode 100644 input/model_avro/Mutation.avsc create mode 100644 input/model_avro/Neoantigen.avsc create mode 100755 input/model_avro/README.md create mode 100644 input/model_avro/__init__.py create mode 100755 input/model_avro/generate_source_code.py rename model/neoepitope.avdl => input/model_avro/neoantigen.avdl (70%) create mode 100644 input/model_avro/neoantigen.avpr create mode 100644 input/model_avro/neoantigen/__init__.py create mode 100644 input/model_avro/schema.avsc create mode 100644 input/model_avro/schema_classes.py create mode 100755 input/model_avro/schema_conversion.py create mode 100755 input/tests/integration_tests/test_schema_conversion.py create mode 100755 input/tests/unit_tests/test_schema_conversion.py diff --git a/input/command_line.py b/input/command_line.py index 14545218..2c8bc478 100755 --- a/input/command_line.py +++ b/input/command_line.py @@ -1,87 +1,89 @@ -from argparse import ArgumentParser - -from logzero import logger - -from input.predict_all_epitopes import BunchEpitopes - - -def input_cli(): - parser = ArgumentParser(description='adds patient information given in sample file of a cohort to merged icam file') - parser.add_argument('-i', '--icam_file', dest='icam_file', help='define iCaM file which should be annotated', - required=True) - parser.add_argument('-a', '--allele_file', dest='allele_file', help='define file with hla alleles of patients', - required=True) - parser.add_argument('-t', '--tissue', dest='tissue', help='define tissue of cancer origin', default="skin") - parser.add_argument('-f', '--frameshift', dest='frameshift', - help='indicate by true or false if frameshift mutations or SNVs are to be considered', - default=False) - parser.add_argument('-tc', '--tumour_content', dest='tumour_content', - help='pass csv file with tumour content of patient; e.g. patient_overview file ', default=False) - args = parser.parse_args() - - icam_file = args.icam_file - allele_file = args.allele_file - tissue = args.tissue - indel = args.frameshift - if args.tumour_content: - tumour_content_file = args.tumour_content - else: - tumour_content_file = "" - - indel = False - - bunchepitopes = BunchEpitopes() - logger.info("Starting INPuT...") - bunchepitopes.wrapper_table_add_feature_annotation(icam_file, indel, allele_file, tissue, tumour_content_file) - logger.info("Finished INPuT...") - ''' - file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/INPuT/nonprogramm_files/test_SD.csv" - # file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/INPuT/nonprogramm_files/test_fulldat.txt" - #file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/20170713_IS_IM_data.complete.update_Dv10.csv.annotation.csv_v2.csv" - # file = "/projects/SUMMIT/WP1.2/Literature_Cohorts/data_analysis/20190117_hugo_prelim_sample_annot.txt" - #file = "/projects/SUMMIT/WP1.2/Literature_Cohorts/data_analysis/20190121_hugo_merged_dat.txt" - indel = False - fasta_proteome = "/projects/data/human/2018_uniprot_with_isoforms/uniprot_human_with_isoforms.fasta" - ref_file = "/projects/CM27_IND_patients/GTEX_normal_tissue_data/Skin .csv" - path_to_hla_file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/indels/RB_0004_labHLA_V2.csv" - #path_to_hla_file = "/projects/SUMMIT/WP1.2/Literature_Cohorts/data_analysis/alleles.csv" - - - Bunchepitopes().main(file, indel, fasta_proteome, ref_file, path_to_hla_file) - ''' - -# def epitope_cli(): -# # file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/INPuT2/nonprogramm_files/test_SD.csv" -# # file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/INPuT2/nonprogramm_files/test_fulldat.txt" -# indel = False -# fasta_proteome = "/projects/data/human/2018_uniprot_with_isoforms/uniprot_human_with_isoforms.fasta" -# ref_file = "/projects/CM27_IND_patients/GTEX_normal_tissue_data/Skin .csv" -# file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/MHC_prediction_netmhcpan4/testdat_ott.txt" -# hla_file = "/projects/SUMMIT/WP1.2/Literature_Cohorts/data_analysis/cohorts/ott/icam_ott/alleles.csv" -# -# # predfeatallBunchepitopes -# predictAll = Bunchepitopes() -# # args = parser.parse_args() -# subprocess.call(["predict_all_epitopes", '-i', file, '-a', hla_file]) -# -# # z = Epitope().main(dat[0], dat[1][ii], self.proteome_dictionary, self.rna_reference, self.aa_frequency, self.fourmer_frequency, self.aa_index1_dict, self.aa_index2_dict, self.provean_matrix, self.hla_available_alleles, self.patient_hla_I_allels) -# -# predictAll.main() - i -# endTime = datetime.now() -# print >> sys.stderr, "start: " + str(startTime) + "\nend: " + str(endTime) + "\nneeded: " + str( -# endTime - startTime) -# # print dat -# # x = Epitope() -# # x = Epitope(dat[1][1], dat[0]) -# # print vars(x) -# # print dat[1][1][1] -# # print dat[0][1] -# -# # for ii,i in enumerate(dat[1]): -# # Epitope().main(dat[0],dat[1][ii]) -# # print x.tricks -# -# # x.main(dat[0], dat[1][1]) -# # print x.tricks -# # print x.tricks["transcript_position"] -# # print dir(x) +from argparse import ArgumentParser + +from logzero import logger + +from input.predict_all_epitopes import BunchEpitopes + + +def input_cli(): + parser = ArgumentParser(description='adds patient information given in sample file of a cohort to merged icam file') + parser.add_argument('-i', '--icam_file', dest='icam_file', help='define iCaM file which should be annotated', + required=True) + parser.add_argument('-a', '--allele_file', dest='allele_file', help='define file with hla alleles of patients', + required=True) + parser.add_argument('-t', '--tissue', dest='tissue', help='define tissue of cancer origin', default="skin") + parser.add_argument('-f', '--frameshift', dest='frameshift', + help='indicate by true or false if frameshift mutations or SNVs are to be considered', + default=False) + parser.add_argument('-tc', '--tumour_content', dest='tumour_content', + help='pass csv file with tumour content of patient; e.g. patient_overview file ', default=False) + args = parser.parse_args() + + icam_file = args.icam_file + allele_file = args.allele_file + tissue = args.tissue + indel = args.frameshift + if args.tumour_content: + tumour_content_file = args.tumour_content + else: + tumour_content_file = "" + + # TODO: this is overriding the value of the parameter frameshift, do we want to activate this Franziska? + # otherwise we may want to just delete the parameter + indel = False + + bunchepitopes = BunchEpitopes() + logger.info("Starting INPuT...") + bunchepitopes.wrapper_table_add_feature_annotation(icam_file, indel, allele_file, tissue, tumour_content_file) + logger.info("Finished INPuT...") + ''' + file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/INPuT/nonprogramm_files/test_SD.csv" + # file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/INPuT/nonprogramm_files/test_fulldat.txt" + #file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/20170713_IS_IM_data.complete.update_Dv10.csv.annotation.csv_v2.csv" + # file = "/projects/SUMMIT/WP1.2/Literature_Cohorts/data_analysis/20190117_hugo_prelim_sample_annot.txt" + #file = "/projects/SUMMIT/WP1.2/Literature_Cohorts/data_analysis/20190121_hugo_merged_dat.txt" + indel = False + fasta_proteome = "/projects/data/human/2018_uniprot_with_isoforms/uniprot_human_with_isoforms.fasta" + ref_file = "/projects/CM27_IND_patients/GTEX_normal_tissue_data/Skin .csv" + path_to_hla_file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/indels/RB_0004_labHLA_V2.csv" + #path_to_hla_file = "/projects/SUMMIT/WP1.2/Literature_Cohorts/data_analysis/alleles.csv" + + + Bunchepitopes().main(file, indel, fasta_proteome, ref_file, path_to_hla_file) + ''' + +# def epitope_cli(): +# # file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/INPuT2/nonprogramm_files/test_SD.csv" +# # file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/INPuT2/nonprogramm_files/test_fulldat.txt" +# indel = False +# fasta_proteome = "/projects/data/human/2018_uniprot_with_isoforms/uniprot_human_with_isoforms.fasta" +# ref_file = "/projects/CM27_IND_patients/GTEX_normal_tissue_data/Skin .csv" +# file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/MHC_prediction_netmhcpan4/testdat_ott.txt" +# hla_file = "/projects/SUMMIT/WP1.2/Literature_Cohorts/data_analysis/cohorts/ott/icam_ott/alleles.csv" +# +# # predfeatallBunchepitopes +# predictAll = Bunchepitopes() +# # args = parser.parse_args() +# subprocess.call(["predict_all_epitopes", '-i', file, '-a', hla_file]) +# +# # z = Epitope().main(dat[0], dat[1][ii], self.proteome_dictionary, self.rna_reference, self.aa_frequency, self.fourmer_frequency, self.aa_index1_dict, self.aa_index2_dict, self.provean_matrix, self.hla_available_alleles, self.patient_hla_I_allels) +# +# predictAll.main() - i +# endTime = datetime.now() +# print >> sys.stderr, "start: " + str(startTime) + "\nend: " + str(endTime) + "\nneeded: " + str( +# endTime - startTime) +# # print dat +# # x = Epitope() +# # x = Epitope(dat[1][1], dat[0]) +# # print vars(x) +# # print dat[1][1][1] +# # print dat[0][1] +# +# # for ii,i in enumerate(dat[1]): +# # Epitope().main(dat[0],dat[1][ii]) +# # print x.tricks +# +# # x.main(dat[0], dat[1][1]) +# # print x.tricks +# # print x.tricks["transcript_position"] +# # print dir(x) diff --git a/input/helpers/data_import.py b/input/helpers/data_import.py index c5d563ca..e68da6bf 100755 --- a/input/helpers/data_import.py +++ b/input/helpers/data_import.py @@ -107,49 +107,6 @@ def import_dat_general(in_file): return header, data -def import_as_dict(in_file, key): - '''Reads csv file and returns dictionary. specifiy what is key, remaining is value - ''' - d = {} - c = 0 - with open(in_file) as f: - for line in f: - w = line.replace('"', "").rstrip("\r\n").split(";") - if c == 0: - header = w - keyIndex = int(header.index(key)) - c += 1 - continue - if c > 0: - d[w[keyIndex]] = w[:keyIndex] + w[keyIndex + 1:] - c += 1 - return d - - -def import_allele_file(allele_file): - '''imports allele.csv file in form of dictionary''' - d = {} - with open(allele_file) as f: - for line in f: - w = line.replace('"', "").rstrip("\r\n").rstrip(';').split(";") - d[w[0] + "_" + w[1]] = w[2:] - return d - - -def get_header_from_tuple(tuple_dat_head): - ''' - get columnnames/header of data frame stored in tuple - ''' - return tuple_dat_head[0] - - -def get_data_from_tuple(tuple_dat_head): - ''' - get columnnames/header of data frame stored in tuple - ''' - return tuple_dat_head[1] - - def change_col_names(tuple_dat_head): """This function changes the names of columns if table hat not been importet to R before.""" dat_new = tuple_dat_head[1] @@ -232,16 +189,3 @@ def append_patient(tuple_dat_head, in_file): dat_new[ii].append(pat) head_new.append("patient") return head_new, dat_new - - -if __name__ == '__main__': - import sys - - f = sys.argv[1] - dat = import_dat(f) - dat = change_col_names(dat) - dat = append_patient(dat, f) - print(subst_semicolon(dat)) - # write_ouptut_to_file(dat) -else: - import sys diff --git a/input/model_avro/Gene.avsc b/input/model_avro/Gene.avsc new file mode 100644 index 00000000..474fae97 --- /dev/null +++ b/input/model_avro/Gene.avsc @@ -0,0 +1,19 @@ +{ + "type" : "record", + "name" : "Gene", + "namespace" : "neoantigen", + "fields" : [ { + "name" : "assembly", + "type" : "string", + "doc" : "The genome assembly to which the gene definition refers to (e.g.: GRCh37, GRCh38)", + "default" : "GRCh37" + }, { + "name" : "gene", + "type" : [ "null", "string" ], + "doc" : "The gene symbol or gene identifier, optional as the transcript unequivocally identifies a gene" + }, { + "name" : "transcriptIdentifier", + "type" : "string", + "doc" : "The transcript identifier to which this neoepitope definition refers (e.g.: Ensembl transcript id)" + } ] +} diff --git a/input/model_avro/Mutation.avsc b/input/model_avro/Mutation.avsc new file mode 100644 index 00000000..48f885ca --- /dev/null +++ b/input/model_avro/Mutation.avsc @@ -0,0 +1,34 @@ +{ + "type" : "record", + "name" : "Mutation", + "namespace" : "neoantigen", + "fields" : [ { + "name" : "position", + "type" : "int", + "doc" : "The aminoacid position within the protein. 1-based, starting in the N-terminus" + }, { + "name" : "wildTypeAminoacid", + "type" : "string", + "doc" : "IUPAC code for the wild type aminoacid in this position" + }, { + "name" : "mutatedAminoacid", + "type" : "string", + "doc" : "IUPAC code for the mutated aminoacid in this position" + }, { + "name" : "leftFlankingRegion", + "type" : "string", + "doc" : "The left flanking region of variable size in IUPAC codes" + }, { + "name" : "sizeLeftFlankingRegion", + "type" : [ "null", "int" ], + "doc" : "The size of the left flanking region" + }, { + "name" : "rightFlankingRegion", + "type" : "string", + "doc" : "The right flanking region of variable size in IUPAC codes" + }, { + "name" : "sizeRightFlankingRegion", + "type" : [ "null", "int" ], + "doc" : "The size of the right flanking region" + } ] +} diff --git a/input/model_avro/Neoantigen.avsc b/input/model_avro/Neoantigen.avsc new file mode 100644 index 00000000..6b4881ac --- /dev/null +++ b/input/model_avro/Neoantigen.avsc @@ -0,0 +1,76 @@ +{ + "type" : "record", + "name" : "Neoantigen", + "namespace" : "neoantigen", + "doc" : "A neoantigen minimal definition", + "fields" : [ { + "name" : "gene", + "type" : { + "type" : "record", + "name" : "Gene", + "fields" : [ { + "name" : "assembly", + "type" : "string", + "doc" : "The genome assembly to which the gene definition refers to (e.g.: GRCh37, GRCh38)", + "default" : "GRCh37" + }, { + "name" : "gene", + "type" : [ "null", "string" ], + "doc" : "The gene symbol or gene identifier, optional as the transcript unequivocally identifies a gene" + }, { + "name" : "transcriptIdentifier", + "type" : "string", + "doc" : "The transcript identifier to which this neoepitope definition refers (e.g.: Ensembl transcript id)" + } ] + }, + "doc" : "The gene where the neoepitope corresponds" + }, { + "name" : "mutation", + "type" : { + "type" : "record", + "name" : "Mutation", + "fields" : [ { + "name" : "position", + "type" : "int", + "doc" : "The aminoacid position within the protein. 1-based, starting in the N-terminus" + }, { + "name" : "wildTypeAminoacid", + "type" : "string", + "doc" : "IUPAC code for the wild type aminoacid in this position" + }, { + "name" : "mutatedAminoacid", + "type" : "string", + "doc" : "IUPAC code for the mutated aminoacid in this position" + }, { + "name" : "leftFlankingRegion", + "type" : "string", + "doc" : "The left flanking region of variable size in IUPAC codes" + }, { + "name" : "sizeLeftFlankingRegion", + "type" : [ "null", "int" ], + "doc" : "The size of the left flanking region" + }, { + "name" : "rightFlankingRegion", + "type" : "string", + "doc" : "The right flanking region of variable size in IUPAC codes" + }, { + "name" : "sizeRightFlankingRegion", + "type" : [ "null", "int" ], + "doc" : "The size of the right flanking region" + } ] + }, + "doc" : "The mutation" + }, { + "name" : "expressionValue", + "type" : [ "null", "float" ], + "doc" : "Expression value of the transcript (any more definition on type of expression?\r\n\t\tie: digital from RNAseq, from microarrays, etc.)" + }, { + "name" : "clonalityEstimation", + "type" : [ "null", "boolean" ], + "doc" : "Clonality estimation. At the moment this is a boolean indicating whether there is clonality or not,\r\n\t\tthere is no quantitive measurement at the moment." + }, { + "name" : "variantAlleleFrequency", + "type" : [ "null", "float" ], + "doc" : "Variant allele frequency in the range [0.0, 1.0]" + } ] +} diff --git a/input/model_avro/README.md b/input/model_avro/README.md new file mode 100755 index 00000000..d07c56b9 --- /dev/null +++ b/input/model_avro/README.md @@ -0,0 +1,28 @@ + +Download avro tools from https://apache.lauf-forum.at/avro/avro-1.9.2/java/avro-tools-1.9.2.jar + +Convert the neoepitope.avdl files into neoepitope.avpr: +``` +java -jar ~/bin/avro-tools-1.9.2.jar idl neoepitope.avdl neoepitope.avpr +``` + +Convert the neoepitope.avdl files into Neoepitope.avsc: +``` +java -jar ~/bin/avro-tools-1.9.2.jar idl2schemata neoepitope.avdl +``` + +Installed avrodoc following instructions here https://github.com/ept/avrodoc + +Generate Python code using the following script: +``` +import json +from avrogen import write_schema_files + + +schema_json = json.dumps(json.load(open('Neoepitope.avsc', 'r'))) +output_directory = '../input/model' +write_schema_files(schema_json, output_directory) +``` + + + diff --git a/input/model_avro/__init__.py b/input/model_avro/__init__.py new file mode 100644 index 00000000..ae67fc33 --- /dev/null +++ b/input/model_avro/__init__.py @@ -0,0 +1,24 @@ + + +from .schema_classes import SchemaClasses, SCHEMA as my_schema, get_schema_type +from avro.io import DatumReader + + +class SpecificDatumReader(DatumReader): + SCHEMA_TYPES = { + "neoantigen.Gene": SchemaClasses.neoantigen.GeneClass, + "neoantigen.Mutation": SchemaClasses.neoantigen.MutationClass, + "neoantigen.Neoantigen": SchemaClasses.neoantigen.NeoantigenClass, + } + def __init__(self, readers_schema=None, **kwargs): + writers_schema = kwargs.pop("writers_schema", readers_schema) + writers_schema = kwargs.pop("writer_schema", writers_schema) + super(SpecificDatumReader, self).__init__(writers_schema, readers_schema, **kwargs) + def read_record(self, writers_schema, readers_schema, decoder): + + result = super(SpecificDatumReader, self).read_record(writers_schema, readers_schema, decoder) + + if readers_schema.fullname in SpecificDatumReader.SCHEMA_TYPES: + result = SpecificDatumReader.SCHEMA_TYPES[readers_schema.fullname](result) + + return result \ No newline at end of file diff --git a/input/model_avro/generate_source_code.py b/input/model_avro/generate_source_code.py new file mode 100755 index 00000000..2e664adc --- /dev/null +++ b/input/model_avro/generate_source_code.py @@ -0,0 +1,8 @@ +#!/bin/python +import json +from avrogen import write_schema_files + + +schema_json = json.dumps(json.load(open('Neoantigen.avsc', 'r'))) +output_directory = '.' +write_schema_files(schema_json, output_directory) diff --git a/model/neoepitope.avdl b/input/model_avro/neoantigen.avdl similarity index 70% rename from model/neoepitope.avdl rename to input/model_avro/neoantigen.avdl index c6e3f784..756f4139 100755 --- a/model/neoepitope.avdl +++ b/input/model_avro/neoantigen.avdl @@ -1,83 +1,85 @@ -/** - * An example protocol in Avro IDL for defining neoepitopes - */ -@namespace("tron.neoepitope") -protocol Neoepitope { - - record Gene { - /** - The genome assembly to which the gene definition refers to (e.g.: GRCh37, GRCh38) - */ - string assembly = "GRCh37"; - /** - The gene symbol or gene identifier, optional as the transcript unequivocally identifies a gene - */ - union {string, null} gene; - /** - The transcript identifier to which this neoepitope definition refers (e.g.: Ensembl transcript id) - */ - string transcriptIdentifier; - } - - record Mutation { - /** - The aminoacid position within the protein. 1-based, starting in the N-terminus - */ - int position; - /** - IUPAC code for the wild type aminoacid in this position - */ - string wildTypeAminoacid; - /** - IUPAC code for the mutated aminoacid in this position - */ - string mutatedAminoacid; - - /** - The left flanking region of variable size in IUPAC codes - */ - string leftFlankingRegion; - /** - The size of the left flanking region - */ - union {string, null} sizeLeftFlankingRegion; - /** - The right flanking region of variable size in IUPAC codes - */ - string rightFlankingRegion; - /** - The size of the right flanking region - */ - union {string, null} sizeRightlankingRegion; - } - - /** - A neoepitope minimal definition - */ - record Neoepitope { - - /** - The gene where the neoepitope corresponds - */ - Gene gene; - - /** - The mutation - */ - Mutation mutation; - - // OPTIONAL - /** - Expression value of the transcript (any more definition on type of expression? ie: digital from RNAseq, from microarrays, etc.) - */ - union {float, null} expressionValue; - /** - Clonality estimation (any more definition on the method?) - */ - union {float, null} clonalityEstimation; - /** - Variant allele frequency in the range [0.0, 1.0] - */ - union {float, null} variantAlleleFrequency; - } -} +/** + * An example protocol in Avro IDL for defining neoepitopes + */ +@namespace("neoantigen") +protocol Neoantigen { + + record Gene { + /** + The genome assembly to which the gene definition refers to (e.g.: GRCh37, GRCh38) + */ + string assembly = "GRCh37"; + /** + The gene symbol or gene identifier, optional as the transcript unequivocally identifies a gene + */ + union {null, string} gene; + /** + The transcript identifier to which this neoepitope definition refers (e.g.: Ensembl transcript id) + */ + string transcriptIdentifier; + } + + record Mutation { + /** + The aminoacid position within the protein. 1-based, starting in the N-terminus + */ + int position; + /** + IUPAC code for the wild type aminoacid in this position + */ + string wildTypeAminoacid; + /** + IUPAC code for the mutated aminoacid in this position + */ + string mutatedAminoacid; + + /** + The left flanking region of variable size in IUPAC codes + */ + string leftFlankingRegion; + /** + The size of the left flanking region + */ + union {null, int} sizeLeftFlankingRegion; + /** + The right flanking region of variable size in IUPAC codes + */ + string rightFlankingRegion; + /** + The size of the right flanking region + */ + union {null, int} sizeRightFlankingRegion; + } + + /** + A neoantigen minimal definition + */ + record Neoantigen { + + /** + The gene where the neoepitope corresponds + */ + Gene gene; + + /** + The mutation + */ + Mutation mutation; + + // OPTIONAL + /** + Expression value of the transcript (any more definition on type of expression? + ie: digital from RNAseq, from microarrays, etc.) + */ + union {null, float} expressionValue; + /** + Clonality estimation. At the moment this is a boolean indicating whether there is clonality or not, + there is no quantitive measurement at the moment. + */ + union {null, boolean} clonalityEstimation; + /** + Variant allele frequency in the range [0.0, 1.0] + */ + union {null, float} variantAlleleFrequency; + } +} diff --git a/input/model_avro/neoantigen.avpr b/input/model_avro/neoantigen.avpr new file mode 100644 index 00000000..1c0e8d75 --- /dev/null +++ b/input/model_avro/neoantigen.avpr @@ -0,0 +1,81 @@ +{ + "protocol" : "Neoantigen", + "namespace" : "neoantigen", + "doc" : "* An example protocol in Avro IDL for defining neoepitopes", + "types" : [ { + "type" : "record", + "name" : "Gene", + "fields" : [ { + "name" : "assembly", + "type" : "string", + "doc" : "The genome assembly to which the gene definition refers to (e.g.: GRCh37, GRCh38)", + "default" : "GRCh37" + }, { + "name" : "gene", + "type" : [ "null", "string" ], + "doc" : "The gene symbol or gene identifier, optional as the transcript unequivocally identifies a gene" + }, { + "name" : "transcriptIdentifier", + "type" : "string", + "doc" : "The transcript identifier to which this neoepitope definition refers (e.g.: Ensembl transcript id)" + } ] + }, { + "type" : "record", + "name" : "Mutation", + "fields" : [ { + "name" : "position", + "type" : "int", + "doc" : "The aminoacid position within the protein. 1-based, starting in the N-terminus" + }, { + "name" : "wildTypeAminoacid", + "type" : "string", + "doc" : "IUPAC code for the wild type aminoacid in this position" + }, { + "name" : "mutatedAminoacid", + "type" : "string", + "doc" : "IUPAC code for the mutated aminoacid in this position" + }, { + "name" : "leftFlankingRegion", + "type" : "string", + "doc" : "The left flanking region of variable size in IUPAC codes" + }, { + "name" : "sizeLeftFlankingRegion", + "type" : [ "null", "int" ], + "doc" : "The size of the left flanking region" + }, { + "name" : "rightFlankingRegion", + "type" : "string", + "doc" : "The right flanking region of variable size in IUPAC codes" + }, { + "name" : "sizeRightFlankingRegion", + "type" : [ "null", "int" ], + "doc" : "The size of the right flanking region" + } ] + }, { + "type" : "record", + "name" : "Neoantigen", + "doc" : "A neoantigen minimal definition", + "fields" : [ { + "name" : "gene", + "type" : "Gene", + "doc" : "The gene where the neoepitope corresponds" + }, { + "name" : "mutation", + "type" : "Mutation", + "doc" : "The mutation" + }, { + "name" : "expressionValue", + "type" : [ "null", "float" ], + "doc" : "Expression value of the transcript (any more definition on type of expression?\r\n\t\tie: digital from RNAseq, from microarrays, etc.)" + }, { + "name" : "clonalityEstimation", + "type" : [ "null", "boolean" ], + "doc" : "Clonality estimation. At the moment this is a boolean indicating whether there is clonality or not,\r\n\t\tthere is no quantitive measurement at the moment." + }, { + "name" : "variantAlleleFrequency", + "type" : [ "null", "float" ], + "doc" : "Variant allele frequency in the range [0.0, 1.0]" + } ] + } ], + "messages" : { } +} \ No newline at end of file diff --git a/input/model_avro/neoantigen/__init__.py b/input/model_avro/neoantigen/__init__.py new file mode 100644 index 00000000..7b30002e --- /dev/null +++ b/input/model_avro/neoantigen/__init__.py @@ -0,0 +1,4 @@ +from ..schema_classes import SchemaClasses +Gene = SchemaClasses.neoantigen.GeneClass +Mutation = SchemaClasses.neoantigen.MutationClass +Neoantigen = SchemaClasses.neoantigen.NeoantigenClass diff --git a/input/model_avro/schema.avsc b/input/model_avro/schema.avsc new file mode 100644 index 00000000..1bd09b48 --- /dev/null +++ b/input/model_avro/schema.avsc @@ -0,0 +1 @@ +{"type": "record", "name": "Neoantigen", "namespace": "neoantigen", "doc": "A neoantigen minimal definition", "fields": [{"name": "gene", "type": {"type": "record", "name": "Gene", "fields": [{"name": "assembly", "type": "string", "doc": "The genome assembly to which the gene definition refers to (e.g.: GRCh37, GRCh38)", "default": "GRCh37"}, {"name": "gene", "type": ["null", "string"], "doc": "The gene symbol or gene identifier, optional as the transcript unequivocally identifies a gene"}, {"name": "transcriptIdentifier", "type": "string", "doc": "The transcript identifier to which this neoepitope definition refers (e.g.: Ensembl transcript id)"}]}, "doc": "The gene where the neoepitope corresponds"}, {"name": "mutation", "type": {"type": "record", "name": "Mutation", "fields": [{"name": "position", "type": "int", "doc": "The aminoacid position within the protein. 1-based, starting in the N-terminus"}, {"name": "wildTypeAminoacid", "type": "string", "doc": "IUPAC code for the wild type aminoacid in this position"}, {"name": "mutatedAminoacid", "type": "string", "doc": "IUPAC code for the mutated aminoacid in this position"}, {"name": "leftFlankingRegion", "type": "string", "doc": "The left flanking region of variable size in IUPAC codes"}, {"name": "sizeLeftFlankingRegion", "type": ["null", "int"], "doc": "The size of the left flanking region"}, {"name": "rightFlankingRegion", "type": "string", "doc": "The right flanking region of variable size in IUPAC codes"}, {"name": "sizeRightFlankingRegion", "type": ["null", "int"], "doc": "The size of the right flanking region"}]}, "doc": "The mutation"}, {"name": "expressionValue", "type": ["null", "float"], "doc": "Expression value of the transcript (any more definition on type of expression?\r\n\t\tie: digital from RNAseq, from microarrays, etc.)"}, {"name": "clonalityEstimation", "type": ["null", "boolean"], "doc": "Clonality estimation. At the moment this is a boolean indicating whether there is clonality or not,\r\n\t\tthere is no quantitive measurement at the moment."}, {"name": "variantAlleleFrequency", "type": ["null", "float"], "doc": "Variant allele frequency in the range [0.0, 1.0]"}]} \ No newline at end of file diff --git a/input/model_avro/schema_classes.py b/input/model_avro/schema_classes.py new file mode 100644 index 00000000..9bc4a9c3 --- /dev/null +++ b/input/model_avro/schema_classes.py @@ -0,0 +1,332 @@ +import json +import os.path +import decimal +import datetime +import six +from avrogen.dict_wrapper import DictWrapper +from avrogen import avrojson +from avro import schema as avro_schema +if six.PY3: from avro.schema import SchemaFromJSONData as make_avsc_object + +else: + from avro.schema import make_avsc_object + + + +def __read_file(file_name): + with open(file_name, "r") as f: + return f.read() + +def __get_names_and_schema(file_name): + names = avro_schema.Names() + schema = make_avsc_object(json.loads(__read_file(file_name)), names) + return names, schema + +__NAMES, SCHEMA = __get_names_and_schema(os.path.join(os.path.dirname(__file__), "schema.avsc")) +__SCHEMAS = {} +def get_schema_type(fullname): + return __SCHEMAS.get(fullname) +__SCHEMAS = dict((n.fullname.lstrip("."), n) for n in six.itervalues(__NAMES.names)) + + +class SchemaClasses(object): + + + pass + class neoantigen(object): + + class GeneClass(DictWrapper): + + """ + + """ + + + RECORD_SCHEMA = get_schema_type("neoantigen.Gene") + + + def __init__(self, inner_dict=None): + super(SchemaClasses.neoantigen.GeneClass, self).__init__(inner_dict) + if inner_dict is None: + self.assembly = SchemaClasses.neoantigen.GeneClass.RECORD_SCHEMA.fields[0].default + self.gene = None + self.transcriptIdentifier = str() + + + @property + def assembly(self): + """ + :rtype: str + """ + return self._inner_dict.get('assembly') + + @assembly.setter + def assembly(self, value): + #""" + #:param str value: + #""" + self._inner_dict['assembly'] = value + + + @property + def gene(self): + """ + :rtype: str + """ + return self._inner_dict.get('gene') + + @gene.setter + def gene(self, value): + #""" + #:param str value: + #""" + self._inner_dict['gene'] = value + + + @property + def transcriptIdentifier(self): + """ + :rtype: str + """ + return self._inner_dict.get('transcriptIdentifier') + + @transcriptIdentifier.setter + def transcriptIdentifier(self, value): + #""" + #:param str value: + #""" + self._inner_dict['transcriptIdentifier'] = value + + + class MutationClass(DictWrapper): + + """ + + """ + + + RECORD_SCHEMA = get_schema_type("neoantigen.Mutation") + + + def __init__(self, inner_dict=None): + super(SchemaClasses.neoantigen.MutationClass, self).__init__(inner_dict) + if inner_dict is None: + self.position = int() + self.wildTypeAminoacid = str() + self.mutatedAminoacid = str() + self.leftFlankingRegion = str() + self.sizeLeftFlankingRegion = None + self.rightFlankingRegion = str() + self.sizeRightFlankingRegion = None + + + @property + def position(self): + """ + :rtype: int + """ + return self._inner_dict.get('position') + + @position.setter + def position(self, value): + #""" + #:param int value: + #""" + self._inner_dict['position'] = value + + + @property + def wildTypeAminoacid(self): + """ + :rtype: str + """ + return self._inner_dict.get('wildTypeAminoacid') + + @wildTypeAminoacid.setter + def wildTypeAminoacid(self, value): + #""" + #:param str value: + #""" + self._inner_dict['wildTypeAminoacid'] = value + + + @property + def mutatedAminoacid(self): + """ + :rtype: str + """ + return self._inner_dict.get('mutatedAminoacid') + + @mutatedAminoacid.setter + def mutatedAminoacid(self, value): + #""" + #:param str value: + #""" + self._inner_dict['mutatedAminoacid'] = value + + + @property + def leftFlankingRegion(self): + """ + :rtype: str + """ + return self._inner_dict.get('leftFlankingRegion') + + @leftFlankingRegion.setter + def leftFlankingRegion(self, value): + #""" + #:param str value: + #""" + self._inner_dict['leftFlankingRegion'] = value + + + @property + def sizeLeftFlankingRegion(self): + """ + :rtype: int + """ + return self._inner_dict.get('sizeLeftFlankingRegion') + + @sizeLeftFlankingRegion.setter + def sizeLeftFlankingRegion(self, value): + #""" + #:param int value: + #""" + self._inner_dict['sizeLeftFlankingRegion'] = value + + + @property + def rightFlankingRegion(self): + """ + :rtype: str + """ + return self._inner_dict.get('rightFlankingRegion') + + @rightFlankingRegion.setter + def rightFlankingRegion(self, value): + #""" + #:param str value: + #""" + self._inner_dict['rightFlankingRegion'] = value + + + @property + def sizeRightFlankingRegion(self): + """ + :rtype: int + """ + return self._inner_dict.get('sizeRightFlankingRegion') + + @sizeRightFlankingRegion.setter + def sizeRightFlankingRegion(self, value): + #""" + #:param int value: + #""" + self._inner_dict['sizeRightFlankingRegion'] = value + + + class NeoantigenClass(DictWrapper): + + """ + A neoantigen minimal definition + """ + + + RECORD_SCHEMA = get_schema_type("neoantigen.Neoantigen") + + + def __init__(self, inner_dict=None): + super(SchemaClasses.neoantigen.NeoantigenClass, self).__init__(inner_dict) + if inner_dict is None: + self.gene = SchemaClasses.neoantigen.GeneClass() + self.mutation = SchemaClasses.neoantigen.MutationClass() + self.expressionValue = None + self.clonalityEstimation = None + self.variantAlleleFrequency = None + + + @property + def gene(self): + """ + :rtype: SchemaClasses.neoantigen.GeneClass + """ + return self._inner_dict.get('gene') + + @gene.setter + def gene(self, value): + #""" + #:param SchemaClasses.neoantigen.GeneClass value: + #""" + self._inner_dict['gene'] = value + + + @property + def mutation(self): + """ + :rtype: SchemaClasses.neoantigen.MutationClass + """ + return self._inner_dict.get('mutation') + + @mutation.setter + def mutation(self, value): + #""" + #:param SchemaClasses.neoantigen.MutationClass value: + #""" + self._inner_dict['mutation'] = value + + + @property + def expressionValue(self): + """ + :rtype: float + """ + return self._inner_dict.get('expressionValue') + + @expressionValue.setter + def expressionValue(self, value): + #""" + #:param float value: + #""" + self._inner_dict['expressionValue'] = value + + + @property + def clonalityEstimation(self): + """ + :rtype: bool + """ + return self._inner_dict.get('clonalityEstimation') + + @clonalityEstimation.setter + def clonalityEstimation(self, value): + #""" + #:param bool value: + #""" + self._inner_dict['clonalityEstimation'] = value + + + @property + def variantAlleleFrequency(self): + """ + :rtype: float + """ + return self._inner_dict.get('variantAlleleFrequency') + + @variantAlleleFrequency.setter + def variantAlleleFrequency(self, value): + #""" + #:param float value: + #""" + self._inner_dict['variantAlleleFrequency'] = value + + + pass + +__SCHEMA_TYPES = { +'neoantigen.Gene': SchemaClasses.neoantigen.GeneClass, + 'neoantigen.Mutation': SchemaClasses.neoantigen.MutationClass, + 'neoantigen.Neoantigen': SchemaClasses.neoantigen.NeoantigenClass, + +} +_json_converter = avrojson.AvroJsonConverter(use_logical_types=False, schema_types=__SCHEMA_TYPES) + diff --git a/input/model_avro/schema_conversion.py b/input/model_avro/schema_conversion.py new file mode 100755 index 00000000..88480149 --- /dev/null +++ b/input/model_avro/schema_conversion.py @@ -0,0 +1,178 @@ +import pandas as pd +from pandas.io.json import json_normalize +import re +import os +import difflib +import json +from collections import defaultdict + +from avro_validator.schema import Schema +from input.model_avro.neoantigen import Neoantigen, Gene, Mutation + +NEOANTIGEN_AVSC = 'Neoantigen.avsc' +GENE_AVSC = 'Gene.avsc' +MUTATION_AVSC = 'Mutation.avsc' + + +class SchemaConverter(object): + + def __init__(self): + + self.neoantigen_schema = self._initialise_schema(NEOANTIGEN_AVSC) + self.gene_schema = self._initialise_schema(GENE_AVSC) + self.mutation_schema = self._initialise_schema(MUTATION_AVSC) + + def _initialise_schema(self, avsc): + schema_file = os.path.join(os.path.abspath(os.path.dirname(__file__)), avsc) + schema = Schema(schema_file) + return schema.parse() + + def validate(self, model): + if isinstance(model, Neoantigen): + valid = self.neoantigen_schema.validate(model) \ + and self.mutation_schema.validate(model.mutation) and self.gene_schema.validate(model.gene) + elif isinstance(model, Gene): + valid = self.gene_schema.validate(model) + elif isinstance(model, Mutation): + valid = self.mutation_schema.validate(model) + else: + raise ValueError("Unexpected type for validation {}".format(type(model))) + if not valid: + raise ValueError("Invalid model_avro due to unknown reasons") + return valid + + def icam2model(self, icam_file): + """ + :param icam_file: the path to an iCaM output file + :type icam_file: str + :rtype: list[Neoepitope] + """ + data = pd.read_csv(icam_file, sep='\t') + SchemaConverter._enrich_icam_table(data) + neoantigens = [] + for _, icam_entry in data.iterrows(): + neoantigens.append(self._icam_entry2model(icam_entry)) + for neoantigen in neoantigens: + self.neoantigen_schema.validate(neoantigen) + return neoantigens + + @staticmethod + def model2json(neoantigens): + """ + :param neoantigens: the list of objects of class Neoantigen + :type: neoepitopes: list[Neoantigen] + :return: the list of dict + :rtype: list[dict] + """ + json_data = [] + for neoantigen in neoantigens: + temp_data = neoantigen._inner_dict + if isinstance(neoantigen.gene, Gene): + temp_data['gene'] = neoantigen.gene._inner_dict + if isinstance(neoantigen.mutation, Mutation): + temp_data['mutation'] = neoantigen.mutation._inner_dict + json_data.append(temp_data) + return json_data + + @staticmethod + def json2model(json_file): + """ + :param json_file: the path to a CSV file with the defined column names + :type json_file: str + :rtype: list[Neoantigen] + """ + data = json.load(open(json_file)) + neoantigens = [] + for entry in data: + neoantigen = Neoantigen(entry) + neoantigen.gene = Gene(entry['gene']) + neoantigen.mutation = Gene(entry['mutation']) + neoantigens.append(neoantigen) + return neoantigens + + @staticmethod + def model2csv(neoantigens): + """ + :param neoantigens: list of objects of class Neoantigen + :type neoantigens: list[Neoantigen] + :rtype: pd.Dataframe + """ + return json_normalize(data=SchemaConverter.model2json(neoantigens)) + + @staticmethod + def csv2model(dataframe): + """ + :param dataframe: the input CSV in a dataframe + :type dataframe: pd.Dataframe + :return: the list of objects of type Neoantigen + :rtype: list[Neoantigen] + """ + neoantigens = [] + for _, row in dataframe.iterrows(): + dict_data = row.to_dict() + nested_dict = SchemaConverter._flat_dict2nested_dict(flat_dict=dict_data) + n = Neoantigen(nested_dict) + neoantigens.append(n) + return neoantigens + + @staticmethod + def _flat_dict2nested_dict(flat_dict): + """ + :type flat_dict: dict + :return: + """ + nested_dict = defaultdict(lambda: {}) + for k, v in flat_dict.items(): + splitted_k = k.split('.') + if len(splitted_k) > 2: + raise NotImplemented("Support for dictionaries nested more than one level is not implemented") + if len(splitted_k) == 2: + nested_dict[splitted_k[0]][splitted_k[1]] = v + else: + nested_dict[k] = v + return dict(nested_dict) + + def _icam_entry2model(self, icam_entry): + + gene = Gene({ + 'assembly': 'hg19', + 'gene': icam_entry.get('gene'), + 'transcriptIdentifier': icam_entry.get('UCSC_transcript') + }) + + mutation = Mutation({ + 'position': icam_entry.get('position'), + 'wildTypeAminoacid': icam_entry.get('wild_type_aminoacid'), + 'mutatedAminoacid': icam_entry.get('mutated_aminoacid'), + 'leftFlankingRegion': icam_entry.get('left_flanking_region'), + 'rightFlankingRegion': icam_entry.get('right_flanking_region'), + 'sizeLeftFlankingRegion': len(icam_entry.get('left_flanking_region')), + 'sizeRightFlankingRegion': len(icam_entry.get('right_flanking_region')) + }) + + neoantigen = Neoantigen({ + 'mutation': mutation._inner_dict, + 'gene': gene._inner_dict, + 'clonalityEstimation': None, # TODO: where do we get this from? + 'expressionValue': icam_entry.get('transcript_expression'), # TODO: or do we want exon expression? + 'variantAlleleFrequency': icam_entry.get('VAF_in_tumor') # TODO: or do we want VAF in RNA? + }) + return neoantigen + + @staticmethod + def _enrich_icam_table(data): + data['wild_type_aminoacid'] = data['substitution'].transform(lambda x: re.search("(\w)\d+\w", x).group(1)) + data['mutated_aminoacid'] = data['substitution'].transform(lambda x: re.search("\w\d+(\w)", x).group(1)) + data['position'] = data['substitution'].transform(lambda x: int(re.search("\w(\d+)\w", x).group(1))) + data['left_flanking_region'] = data[[ + '+-13_AA_(SNV)_/_-15_AA_to_STOP_(INDEL)', '[WT]_+-13_AA_(SNV)_/_-15_AA_to_STOP_(INDEL)']].apply( + lambda x: SchemaConverter._get_matching_region(x[0], x[1]), axis=1) + data['right_flanking_region'] = data[[ + '+-13_AA_(SNV)_/_-15_AA_to_STOP_(INDEL)', '[WT]_+-13_AA_(SNV)_/_-15_AA_to_STOP_(INDEL)']].apply( + lambda x: SchemaConverter._get_matching_region(x[0], x[1], match=1), axis=1) + + @staticmethod + def _get_matching_region(sequence1, sequence2, match=0): + match = difflib.SequenceMatcher(None, sequence1, sequence2).get_matching_blocks()[match] + return sequence1[match.a : match.a + match.size] + diff --git a/input/predict_all_epitopes.py b/input/predict_all_epitopes.py index 29aa4d72..902ef4fe 100755 --- a/input/predict_all_epitopes.py +++ b/input/predict_all_epitopes.py @@ -51,8 +51,8 @@ def load_rna_reference(rna_reference_file, tissue): """ rna_dict = {} ref_tuple = data_import.import_dat_general(rna_reference_file) - ref = data_import.get_data_from_tuple(ref_tuple) - ref_head = data_import.get_header_from_tuple(ref_tuple) + ref = ref_tuple[1] + ref_head = ref_tuple[0] tissue = tissue.lower() head_cols = [col for col in ref_head if col.startswith(tissue)] cols_expr = [ref_head.index(col) for col in head_cols] diff --git a/input/tests/integration_tests/test_schema_conversion.py b/input/tests/integration_tests/test_schema_conversion.py new file mode 100755 index 00000000..60bbb694 --- /dev/null +++ b/input/tests/integration_tests/test_schema_conversion.py @@ -0,0 +1,22 @@ +from unittest import TestCase + +from input.model_avro.schema_conversion import SchemaConverter +from input.model_avro.neoantigen import Neoantigen, Gene, Mutation + + +class SchemaConverterTest(TestCase): + + def test_icam2model(self): + self.icam_file = '/projects/SUMMIT/WP1.2/input/development/Pt29.sequences4testing.txt' + # self.icam_file = '\\\\192.168.171.199\\projects$\\SUMMIT\\WP1.2\\input\\development\\Pt29.sequences4testing.txt' + with open(self.icam_file) as f: + self.count_lines = len(f.readlines()) + neoantigens = SchemaConverter().icam2model(self.icam_file) + self.assertIsNotNone(neoantigens) + self.assertEqual(self.count_lines - 1, len(neoantigens)) + for n in neoantigens: + self.assertIsInstance(n, Neoantigen) + g = Gene(n.gene) + self.assertTrue(g.transcriptIdentifier is not None and len(g.transcriptIdentifier) > 0) + m = Mutation(n.mutation) + self.assertTrue(m.mutatedAminoacid is not None and len(m.mutatedAminoacid) > 0) \ No newline at end of file diff --git a/input/tests/unit_tests/test_schema_conversion.py b/input/tests/unit_tests/test_schema_conversion.py new file mode 100755 index 00000000..c1b7104b --- /dev/null +++ b/input/tests/unit_tests/test_schema_conversion.py @@ -0,0 +1,116 @@ +import random +from unittest import TestCase + +from Bio.Data import IUPACData +import json +import numpy as np + +from pandas.io.json import json_normalize + +from input.model_avro.schema_conversion import SchemaConverter +from input.helpers import intermediate_files +from input.model_avro.neoantigen import Neoantigen, Gene, Mutation + + +class SchemaConverterTest(TestCase): + + def test_model2json(self): + neoantigens = [_get_random_neoantigen() for _ in range(5)] + json_data = SchemaConverter.model2json(neoantigens) + self.assertIsInstance(json_data, list) + self.assertEqual(5, len(json_data)) + self._assert_lists_equal([Neoantigen(j) for j in json_data], neoantigens) + + def test_json2model(self): + json_file = intermediate_files.create_temp_file(prefix='test_') + neoantigens = [_get_random_neoantigen() for _ in range(5)] + json_data = SchemaConverter.model2json(neoantigens) + with open(json_file, 'w') as fd: + fd.write(json.dumps(json_data)) + neoantigens2 = SchemaConverter.json2model(json_file) + self.assertIsNotNone(neoantigens2) + self._assert_lists_equal(neoantigens, neoantigens2) + + def test_model2csv(self): + neoantigens = [_get_random_neoantigen() for _ in range(5)] + csv_data = json_normalize(data=SchemaConverter.model2json(neoantigens)) + self.assertIsNotNone(csv_data) + self.assertEqual(csv_data.shape[0], len(neoantigens)) + for n in neoantigens: + self.assertEqual(n.variantAlleleFrequency, + csv_data[ + (csv_data['mutation.position'] == n.mutation['position']) & + (csv_data['mutation.mutatedAminoacid'] == n.mutation['mutatedAminoacid']) + ].variantAlleleFrequency.iloc[0]) + + def test_csv2model(self): + neoantigens = [_get_random_neoantigen() for _ in range(5)] + csv_data = json_normalize(data=SchemaConverter.model2json(neoantigens)) + neoantigens2 = SchemaConverter.csv2model(csv_data) + self._assert_lists_equal(neoantigens, neoantigens2) + + def _assert_lists_equal(self, neoantigens, neoantigens2): + self.assertEqual(len(neoantigens), len(neoantigens2)) + for n1, n2, in zip(neoantigens, neoantigens2): + self.assertEqual(n1.expressionValue, n2.expressionValue) + self.assertEqual(n1.variantAlleleFrequency, n2.variantAlleleFrequency) + self.assertEqual(n1.clonalityEstimation, n2.clonalityEstimation) + self.assertEqual(n1.mutation, n2.mutation) + self.assertEqual(n1.gene, n2.gene) + + +class SchemaValidationTest(TestCase): + + def test_validation(self): + neoantigens = [_get_random_neoantigen() for _ in range(5)] + schema_converter = SchemaConverter() + for n in neoantigens: + self.assertTrue(schema_converter.validate(n)) + + def test_field_not_in_the_model(self): + neoantigen = _get_random_neoantigen() + neoantigen._inner_dict['my_field_out_of_model'] = 5.7 # this field does not exist + schema_converter = SchemaConverter() + with self.assertRaises(ValueError): + schema_converter.validate(neoantigen) + + def test_field_invalid_type(self): + neoantigen = _get_random_neoantigen() + neoantigen.expressionValue = "5.7" # should be a float + schema_converter = SchemaConverter() + with self.assertRaises(ValueError): + schema_converter.validate(neoantigen) + + def test_missing_non_nullable_field(self): + neoantigen = _get_random_neoantigen() + neoantigen.mutation = None # non nullable field + schema_converter = SchemaConverter() + with self.assertRaises(ValueError): + schema_converter.validate(neoantigen) + + def test_missing_non_nullable_nested_field(self): + neoantigen = _get_random_neoantigen() + mutation = Mutation() + mutation.position = None # non nullable field + neoantigen.mutation = mutation + schema_converter = SchemaConverter() + with self.assertRaises(ValueError): + schema_converter.validate(neoantigen) + + +def _get_random_neoantigen(): + neoantigen = Neoantigen() + neoantigen.variantAlleleFrequency = np.random.uniform(0, 1) + neoantigen.expressionValue = np.random.uniform(0, 50) + neoantigen.clonalityEstimation = None + mutation = Mutation() + mutation.mutatedAminoacid = random.choices(list(IUPACData.protein_letters), k=1)[0] + mutation.wildTypeAminoacid = random.choices(list(IUPACData.protein_letters), k=1)[0] + mutation.position = np.random.randint(0, 1000) + neoantigen.mutation = mutation + gene = Gene() + gene.gene = "BRCA2" + gene.transcriptIdentifier = "ENST1234567" + gene.assembly = "hg19" + neoantigen.gene = gene + return neoantigen diff --git a/setup.py b/setup.py index 22fe636f..b4360ecc 100755 --- a/setup.py +++ b/setup.py @@ -1,50 +1,51 @@ -from setuptools import find_packages, setup, Command -import distutils.command.build -from distutils.dist import Distribution -# from wheel.bdist_wheel import bdist_wheel as _bdist_wheel -# import xmlrunner -import unittest -import sys -import os -# import dotenv -import logging -import glob -from datetime import datetime -import input - -# Build the Python package -setup( - name='input', - version=input.VERSION, - packages=find_packages(), - include_package_data=True, - entry_points={ - 'console_scripts': [ - 'input=input.command_line:input_cli' - ], - }, - author='Franziska Lang', - description='TODO', - requires=[], - # NOTE: always specify versions to ensure build reproducibility - # NOTE2: sklearn==0.19.0 is a hidden dependency as it is required by Classifier.pickle - - install_requires=[ - 'biopython==1.76', - 'mock', - 'pandas==0.24.2', - 'numpy==1.16.2', - 'scipy==1.4.1', - 'pickle-mixin', - 'scikit-learn==0.20.3', - 'logzero==1.5.0' - ], - setup_requires=[], - classifiers=[ - 'Development Status :: 3 - Alpha', # Chose either "3 - Alpha", "4 - Beta" or "5 - Production/Stable" as the current state of your package - 'Intended Audience :: Healthcare Industry', - 'Intended Audience :: Science/Research', - 'Topic :: Scientific/Engineering :: Bio-Informatics', - 'Programming Language :: Python :: 3' - ] -) +from setuptools import find_packages, setup, Command +import distutils.command.build +from distutils.dist import Distribution +# from wheel.bdist_wheel import bdist_wheel as _bdist_wheel +# import xmlrunner +import unittest +import sys +import os +# import dotenv +import logging +import glob +from datetime import datetime +import input + +# Build the Python package +setup( + name='input', + version=input.VERSION, + packages=find_packages(), + include_package_data=True, + entry_points={ + 'console_scripts': [ + 'input=input.command_line:input_cli' + ], + }, + author='Franziska Lang', + description='TODO', + requires=[], + # NOTE: always specify versions to ensure build reproducibility + # NOTE2: sklearn==0.19.0 is a hidden dependency as it is required by Classifier.pickle + + install_requires=[ + 'biopython==1.76', + 'mock', + 'pandas==0.24.2', + 'numpy==1.16.2', + 'scipy==1.4.1', + 'pickle-mixin', + 'scikit-learn==0.20.3', + 'logzero==1.5.0', + 'avro_validator' + ], + setup_requires=[], + classifiers=[ + 'Development Status :: 3 - Alpha', # Chose either "3 - Alpha", "4 - Beta" or "5 - Production/Stable" as the current state of your package + 'Intended Audience :: Healthcare Industry', + 'Intended Audience :: Science/Research', + 'Topic :: Scientific/Engineering :: Bio-Informatics', + 'Programming Language :: Python :: 3' + ] +) From 7dbbbbf5b5e305f0d5978e6c85bb99c9c3847bd0 Mon Sep 17 00:00:00 2001 From: Pablo Riesgo Ferreiro Date: Tue, 9 Jun 2020 22:45:20 +0200 Subject: [PATCH 043/105] added generated code from proto models + conversion from/to iCaM and CSV --- input/model_protobuf/README.md | 18 +++ input/model_protobuf/__init__.py | 0 input/model_protobuf/neoantigen.proto | 77 ++++++++++++ input/model_protobuf/neoantigen.py | 57 +++++++++ input/model_protobuf/schema_conversion.py | 117 ++++++++++++++++++ ...sion.py => test_schema_conversion_avro.py} | 0 .../test_schema_conversion_proto.py | 22 ++++ ...sion.py => test_schema_conversion_avro.py} | 0 .../test_schema_conversion_proto.py | 82 ++++++++++++ setup.py | 3 +- 10 files changed, 375 insertions(+), 1 deletion(-) create mode 100755 input/model_protobuf/README.md create mode 100644 input/model_protobuf/__init__.py create mode 100755 input/model_protobuf/neoantigen.proto create mode 100644 input/model_protobuf/neoantigen.py create mode 100755 input/model_protobuf/schema_conversion.py rename input/tests/integration_tests/{test_schema_conversion.py => test_schema_conversion_avro.py} (100%) create mode 100755 input/tests/integration_tests/test_schema_conversion_proto.py rename input/tests/unit_tests/{test_schema_conversion.py => test_schema_conversion_avro.py} (100%) create mode 100755 input/tests/unit_tests/test_schema_conversion_proto.py diff --git a/input/model_protobuf/README.md b/input/model_protobuf/README.md new file mode 100755 index 00000000..f5164d18 --- /dev/null +++ b/input/model_protobuf/README.md @@ -0,0 +1,18 @@ + +Install the protocol buffers compiler. Download and unzip from the releases page https://github.com/protocolbuffers/protobuf/releases/tag/v3.12.3 + +Install the tool betterproto to make generated Python source code a bit better: +``` +pip install "betterproto[compiler]" +``` + +Generate Python source code from neoepitope.proto: +``` +protoc -I . --python_betterproto_out=. neoantigen.proto +``` + +This will generate `neoantigen.py` and `__init__.py` files. + + + + diff --git a/input/model_protobuf/__init__.py b/input/model_protobuf/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/input/model_protobuf/neoantigen.proto b/input/model_protobuf/neoantigen.proto new file mode 100755 index 00000000..ca74ff34 --- /dev/null +++ b/input/model_protobuf/neoantigen.proto @@ -0,0 +1,77 @@ +syntax = "proto3"; + +package neoantigen; + +message Gene { + /** + The genome assembly to which the gene definition refers to (e.g.: GRCh37, GRCh38) + */ + string assembly = 1; + /** + The gene symbol or gene identifier, optional as the transcript unequivocally identifies a gene + */ + string gene = 2; + /** + The transcript identifier to which this neoepitope definition refers (e.g.: Ensembl transcript id) + */ + string transcriptIdentifier = 3; +} + +message Mutation { + /** + The aminoacid position within the protein. 1-based, starting in the N-terminus + */ + int32 position = 1; + /** + IUPAC code for the wild type aminoacid in this position + */ + string wildTypeAminoacid = 2; + /** + IUPAC code for the mutated aminoacid in this position + */ + string mutatedAminoacid = 3; + /** + The left flanking region of variable size in IUPAC codes + */ + string leftFlankingRegion = 4; + /** + The size of the left flanking region + */ + int32 sizeLeftFlankingRegion = 5; + /** + The right flanking region of variable size in IUPAC codes + */ + string rightFlankingRegion = 6; + /** + The size of the right flanking region + */ + int32 sizeRightFlankingRegion = 7; +} + +/** +A neoantigen minimal definition +*/ +message Neoantigen { + /** + The gene where the neoepitope corresponds + */ + Gene gene = 1; + /** + The mutation + */ + Mutation mutation = 2; + /** + Expression value of the transcript (any more definition on type of expression? + ie: digital from RNAseq, from microarrays, etc.) + */ + float expressionValue = 3; + /** + Clonality estimation. At the moment this is a boolean indicating whether there is clonality or not, + there is no quantitive measurement at the moment. + */ + bool clonalityEstimation = 4; + /** + Variant allele frequency in the range [0.0, 1.0] + */ + float variantAlleleFrequency = 5; +} \ No newline at end of file diff --git a/input/model_protobuf/neoantigen.py b/input/model_protobuf/neoantigen.py new file mode 100644 index 00000000..b2b4dc94 --- /dev/null +++ b/input/model_protobuf/neoantigen.py @@ -0,0 +1,57 @@ +# Generated by the protocol buffer compiler. DO NOT EDIT! +# sources: neoantigen.proto +# plugin: python-betterproto +from dataclasses import dataclass + +import betterproto + + +@dataclass +class Gene(betterproto.Message): + # * The genome assembly to which the gene definition refers to (e.g.: GRCh37, + # GRCh38) + assembly: str = betterproto.string_field(1) + # * The gene symbol or gene identifier, optional as the transcript + # unequivocally identifies a gene + gene: str = betterproto.string_field(2) + # * The transcript identifier to which this neoepitope definition refers + # (e.g.: Ensembl transcript id) + transcript_identifier: str = betterproto.string_field(3) + + +@dataclass +class Mutation(betterproto.Message): + # * The aminoacid position within the protein. 1-based, starting in the + # N-terminus + position: int = betterproto.int32_field(1) + # * IUPAC code for the wild type aminoacid in this position + wild_type_aminoacid: str = betterproto.string_field(2) + # * IUPAC code for the mutated aminoacid in this position + mutated_aminoacid: str = betterproto.string_field(3) + # * The left flanking region of variable size in IUPAC codes + left_flanking_region: str = betterproto.string_field(4) + # * The size of the left flanking region + size_left_flanking_region: int = betterproto.int32_field(5) + # * The right flanking region of variable size in IUPAC codes + right_flanking_region: str = betterproto.string_field(6) + # * The size of the right flanking region + size_right_flanking_region: int = betterproto.int32_field(7) + + +@dataclass +class Neoantigen(betterproto.Message): + """* A neoantigen minimal definition""" + + # * The gene where the neoepitope corresponds + gene: "Gene" = betterproto.message_field(1) + # * The mutation + mutation: "Mutation" = betterproto.message_field(2) + # * Expression value of the transcript (any more definition on type of + # expression? ie: digital from RNAseq, from microarrays, etc.) + expression_value: float = betterproto.float_field(3) + # * Clonality estimation. At the moment this is a boolean indicating whether + # there is clonality or not, there is no quantitive measurement at the + # moment. + clonality_estimation: bool = betterproto.bool_field(4) + # * Variant allele frequency in the range [0.0, 1.0] + variant_allele_frequency: float = betterproto.float_field(5) diff --git a/input/model_protobuf/schema_conversion.py b/input/model_protobuf/schema_conversion.py new file mode 100755 index 00000000..25b77efc --- /dev/null +++ b/input/model_protobuf/schema_conversion.py @@ -0,0 +1,117 @@ +import pandas as pd +from pandas.io.json import json_normalize +import re +import difflib +from collections import defaultdict + +from input.model_protobuf.neoantigen import Neoantigen, Gene, Mutation + + +class SchemaConverter(object): + + @staticmethod + def validate(model): + """ + :type model: betterproto.Message + :return: + """ + return model.__bytes__() + + @staticmethod + def icam2model(icam_file): + """ + :param icam_file: the path to an iCaM output file + :type icam_file: str + :rtype: list[Neoepitope] + """ + data = pd.read_csv(icam_file, sep='\t') + SchemaConverter._enrich_icam_table(data) + neoantigens = [] + for _, icam_entry in data.iterrows(): + neoantigens.append(SchemaConverter._icam_entry2model(icam_entry)) + for n in neoantigens: + SchemaConverter.validate(n) + return neoantigens + + @staticmethod + def model2csv(neoantigens): + """ + :param neoantigens: list of objects of class Neoantigen + :type neoantigens: list[Neoantigen] + :rtype: pd.Dataframe + """ + return json_normalize(data=[n.to_dict() for n in neoantigens]) + + @staticmethod + def csv2model(dataframe): + """ + :param dataframe: the input CSV in a dataframe + :type dataframe: pd.Dataframe + :return: the list of objects of type Neoantigen + :rtype: list[Neoantigen] + """ + neoantigens = [] + for _, row in dataframe.iterrows(): + neoantigens.append(Neoantigen().from_dict(SchemaConverter._flat_dict2nested_dict(flat_dict=row.to_dict()))) + return neoantigens + + @staticmethod + def _flat_dict2nested_dict(flat_dict): + """ + :type flat_dict: dict + :return: + """ + nested_dict = defaultdict(lambda: {}) + for k, v in flat_dict.items(): + splitted_k = k.split('.') + if len(splitted_k) > 2: + raise NotImplemented("Support for dictionaries nested more than one level is not implemented") + if len(splitted_k) == 2: + nested_dict[splitted_k[0]][splitted_k[1]] = v + else: + nested_dict[k] = v + return dict(nested_dict) + + @staticmethod + def _icam_entry2model(icam_entry): + + gene = Gene() + gene.assembly = 'hg19' + gene.gene = icam_entry.get('gene') + gene.transcript_identifier = icam_entry.get('UCSC_transcript') + + mutation = Mutation() + mutation.position = icam_entry.get('position') + mutation.wild_type_aminoacid = icam_entry.get('wild_type_aminoacid') + mutation.mutated_aminoacid = icam_entry.get('mutated_aminoacid') + mutation.left_flanking_region = icam_entry.get('left_flanking_region') + mutation.right_flanking_region = icam_entry.get('right_flanking_region') + mutation.size_left_flanking_region = len(icam_entry.get('left_flanking_region')) + mutation.size_right_flanking_region = len(icam_entry.get('right_flanking_region')) + + neoantigen = Neoantigen() + neoantigen.mutation = mutation + neoantigen.gene = gene + neoantigen.clonality_estimation = None # TODO: where do we get this from? + neoantigen.expression_value = icam_entry.get('transcript_expression') # TODO: or do we want exon expression? + neoantigen.variant_allele_frequency = icam_entry.get('VAF_in_tumor') # TODO: or do we want VAF in RNA? + + return neoantigen + + @staticmethod + def _enrich_icam_table(data): + data['wild_type_aminoacid'] = data['substitution'].transform(lambda x: re.search("(\w)\d+\w", x).group(1)) + data['mutated_aminoacid'] = data['substitution'].transform(lambda x: re.search("\w\d+(\w)", x).group(1)) + data['position'] = data['substitution'].transform(lambda x: int(re.search("\w(\d+)\w", x).group(1))) + data['left_flanking_region'] = data[[ + '+-13_AA_(SNV)_/_-15_AA_to_STOP_(INDEL)', '[WT]_+-13_AA_(SNV)_/_-15_AA_to_STOP_(INDEL)']].apply( + lambda x: SchemaConverter._get_matching_region(x[0], x[1]), axis=1) + data['right_flanking_region'] = data[[ + '+-13_AA_(SNV)_/_-15_AA_to_STOP_(INDEL)', '[WT]_+-13_AA_(SNV)_/_-15_AA_to_STOP_(INDEL)']].apply( + lambda x: SchemaConverter._get_matching_region(x[0], x[1], match=1), axis=1) + + @staticmethod + def _get_matching_region(sequence1, sequence2, match=0): + match = difflib.SequenceMatcher(None, sequence1, sequence2).get_matching_blocks()[match] + return sequence1[match.a : match.a + match.size] + diff --git a/input/tests/integration_tests/test_schema_conversion.py b/input/tests/integration_tests/test_schema_conversion_avro.py similarity index 100% rename from input/tests/integration_tests/test_schema_conversion.py rename to input/tests/integration_tests/test_schema_conversion_avro.py diff --git a/input/tests/integration_tests/test_schema_conversion_proto.py b/input/tests/integration_tests/test_schema_conversion_proto.py new file mode 100755 index 00000000..2e07931e --- /dev/null +++ b/input/tests/integration_tests/test_schema_conversion_proto.py @@ -0,0 +1,22 @@ +from unittest import TestCase + +from input.model_protobuf.schema_conversion import SchemaConverter +from input.model_protobuf.neoantigen import Neoantigen, Gene, Mutation + + +class SchemaConverterTest(TestCase): + + def test_icam2model(self): + # self.icam_file = '/projects/SUMMIT/WP1.2/input/development/Pt29.sequences4testing.txt' + self.icam_file = '\\\\192.168.171.199\\projects$\\SUMMIT\\WP1.2\\input\\development\\Pt29.sequences4testing.txt' + with open(self.icam_file) as f: + self.count_lines = len(f.readlines()) + neoantigens = SchemaConverter().icam2model(self.icam_file) + self.assertIsNotNone(neoantigens) + self.assertEqual(self.count_lines - 1, len(neoantigens)) + for n in neoantigens: + self.assertIsInstance(n, Neoantigen) + self.assertIsInstance(n.gene, Gene) + self.assertIsInstance(n.mutation, Mutation) + self.assertTrue(n.gene.transcript_identifier is not None and len(n.gene.transcript_identifier) > 0) + self.assertTrue(n.mutation.mutated_aminoacid is not None and len(n.mutation.mutated_aminoacid) == 1) diff --git a/input/tests/unit_tests/test_schema_conversion.py b/input/tests/unit_tests/test_schema_conversion_avro.py similarity index 100% rename from input/tests/unit_tests/test_schema_conversion.py rename to input/tests/unit_tests/test_schema_conversion_avro.py diff --git a/input/tests/unit_tests/test_schema_conversion_proto.py b/input/tests/unit_tests/test_schema_conversion_proto.py new file mode 100755 index 00000000..f3ae9f74 --- /dev/null +++ b/input/tests/unit_tests/test_schema_conversion_proto.py @@ -0,0 +1,82 @@ +import random +import struct +from unittest import TestCase + +from Bio.Data import IUPACData +import numpy as np + +from input.model_protobuf.schema_conversion import SchemaConverter +from input.model_protobuf.neoantigen import Neoantigen, Gene, Mutation + + +class SchemaConverterTest(TestCase): + + def test_model2json(self): + neoantigens = [_get_random_neoantigen() for _ in range(5)] + json_data = [n.to_json() for n in neoantigens] + self.assertIsInstance(json_data, list) + self.assertEqual(5, len(json_data)) + neoantigens2 = [Neoantigen().from_json(j) for j in json_data] + self._assert_lists_equal(neoantigens, neoantigens2) + + def test_model2dict(self): + neoantigens = [_get_random_neoantigen() for _ in range(5)] + json_data = [n.to_dict() for n in neoantigens] + self.assertIsInstance(json_data, list) + self.assertEqual(5, len(json_data)) + neoantigens2 = [Neoantigen().from_dict(j) for j in json_data] + self._assert_lists_equal(neoantigens, neoantigens2) + + def test_model2csv(self): + neoantigens = [_get_random_neoantigen() for _ in range(5)] + csv_data = SchemaConverter.model2csv(neoantigens) + self.assertIsNotNone(csv_data) + self.assertEqual(csv_data.shape[0], len(neoantigens)) + for n in neoantigens: + self.assertEqual(n.variant_allele_frequency, + csv_data[ + (csv_data['mutation.position'] == n.mutation.position) & + (csv_data['mutation.mutatedAminoacid'] == n.mutation.mutated_aminoacid) + ].variantAlleleFrequency.iloc[0]) + + def test_csv2model(self): + neoantigens = [_get_random_neoantigen() for _ in range(5)] + csv_data = SchemaConverter.model2csv(neoantigens) + neoantigens2 = SchemaConverter.csv2model(csv_data) + self._assert_lists_equal(neoantigens, neoantigens2) + + def _assert_lists_equal(self, neoantigens, neoantigens2): + self.assertEqual(len(neoantigens), len(neoantigens2)) + for n1, n2, in zip(neoantigens, neoantigens2): + self.assertEqual(n1, n2) + + +class SchemaValidationTest(TestCase): + + def test_validation(self): + neoantigens = [_get_random_neoantigen() for _ in range(5)] + for n in neoantigens: + SchemaConverter.validate(n) + + def test_field_invalid_type(self): + neoantigen = _get_random_neoantigen() + neoantigen.expression_value = "5.7" # should be a float + with self.assertRaises(struct.error): + SchemaConverter.validate(neoantigen) + + +def _get_random_neoantigen(): + neoantigen = Neoantigen() + neoantigen.variant_allele_frequency = np.random.uniform(0, 1) + neoantigen.expression_value = np.random.uniform(0, 50) + mutation = Mutation() + mutation.mutated_aminoacid = random.choices(list(IUPACData.protein_letters), k=1)[0] + mutation.wild_type_aminoacid = random.choices(list(IUPACData.protein_letters), k=1)[0] + mutation.position = np.random.randint(0, 1000) + neoantigen.mutation = mutation + gene = Gene() + gene.gene = "BRCA2" + gene.transcript_identifier = "ENST1234567" + gene.assembly = "hg19" + neoantigen.gene = gene + return neoantigen diff --git a/setup.py b/setup.py index b4360ecc..d829163a 100755 --- a/setup.py +++ b/setup.py @@ -38,7 +38,8 @@ 'pickle-mixin', 'scikit-learn==0.20.3', 'logzero==1.5.0', - 'avro_validator' + 'avro_validator', + 'betterproto' ], setup_requires=[], classifiers=[ From aac028712958173a79dc295c79ab89c7b45acebc Mon Sep 17 00:00:00 2001 From: Pablo Riesgo Ferreiro Date: Thu, 11 Jun 2020 06:40:39 +0200 Subject: [PATCH 044/105] generated HTML documentation from models --- input/model_protobuf/README.md | 11 + input/model_protobuf/doc/index.html | 583 ++++++++++++++++++++++++++++ 2 files changed, 594 insertions(+) create mode 100644 input/model_protobuf/doc/index.html diff --git a/input/model_protobuf/README.md b/input/model_protobuf/README.md index f5164d18..959e9fb0 100755 --- a/input/model_protobuf/README.md +++ b/input/model_protobuf/README.md @@ -1,4 +1,7 @@ + +## Compiling the models and generating source code + Install the protocol buffers compiler. Download and unzip from the releases page https://github.com/protocolbuffers/protobuf/releases/tag/v3.12.3 Install the tool betterproto to make generated Python source code a bit better: @@ -13,6 +16,14 @@ protoc -I . --python_betterproto_out=. neoantigen.proto This will generate `neoantigen.py` and `__init__.py` files. +## Documentation + +Documentation is generated using this tool https://github.com/pseudomuto/protoc-gen-doc. Follow the instructions in the README for installation and then add the binary to your PATH. +Run: +``` +mkdir doc +protoc --doc_out=./doc --doc_opt=html,index.html neoantigen.proto +``` diff --git a/input/model_protobuf/doc/index.html b/input/model_protobuf/doc/index.html new file mode 100644 index 00000000..061e9f35 --- /dev/null +++ b/input/model_protobuf/doc/index.html @@ -0,0 +1,583 @@ + + + + + Protocol Documentation + + + + + + + + + + +

Protocol Documentation

+ +

Table of Contents

+ +
+ +
+ + + +
+

neoantigen.proto

Top +
+

+ + +

Gene

+

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
FieldTypeLabelDescription
assemblystring

+The genome assembly to which the gene definition refers to (e.g.: GRCh37, GRCh38)

genestring

+The gene symbol or gene identifier, optional as the transcript unequivocally identifies a gene

transcriptIdentifierstring

+The transcript identifier to which this neoepitope definition refers (e.g.: Ensembl transcript id)

+ + + + + +

Mutation

+

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
FieldTypeLabelDescription
positionint32

+The aminoacid position within the protein. 1-based, starting in the N-terminus

wildTypeAminoacidstring

+IUPAC code for the wild type aminoacid in this position

mutatedAminoacidstring

+IUPAC code for the mutated aminoacid in this position

leftFlankingRegionstring

+The left flanking region of variable size in IUPAC codes

sizeLeftFlankingRegionint32

+The size of the left flanking region

rightFlankingRegionstring

+The right flanking region of variable size in IUPAC codes

sizeRightFlankingRegionint32

+The size of the right flanking region

+ + + + + +

Neoantigen

+

A neoantigen minimal definition

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
FieldTypeLabelDescription
geneGene

+The gene where the neoepitope corresponds

mutationMutation

+The mutation

expressionValuefloat

+Expression value of the transcript (any more definition on type of expression? +ie: digital from RNAseq, from microarrays, etc.)

clonalityEstimationbool

+Clonality estimation. At the moment this is a boolean indicating whether there is clonality or not, +there is no quantitive measurement at the moment.

variantAlleleFrequencyfloat

+Variant allele frequency in the range [0.0, 1.0]

+ + + + + + + + + + + + + +

Scalar Value Types

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
.proto TypeNotesC++JavaPythonGoC#PHPRuby
doubledoubledoublefloatfloat64doublefloatFloat
floatfloatfloatfloatfloat32floatfloatFloat
int32Uses variable-length encoding. Inefficient for encoding negative numbers – if your field is likely to have negative values, use sint32 instead.int32intintint32intintegerBignum or Fixnum (as required)
int64Uses variable-length encoding. Inefficient for encoding negative numbers – if your field is likely to have negative values, use sint64 instead.int64longint/longint64longinteger/stringBignum
uint32Uses variable-length encoding.uint32intint/longuint32uintintegerBignum or Fixnum (as required)
uint64Uses variable-length encoding.uint64longint/longuint64ulonginteger/stringBignum or Fixnum (as required)
sint32Uses variable-length encoding. Signed int value. These more efficiently encode negative numbers than regular int32s.int32intintint32intintegerBignum or Fixnum (as required)
sint64Uses variable-length encoding. Signed int value. These more efficiently encode negative numbers than regular int64s.int64longint/longint64longinteger/stringBignum
fixed32Always four bytes. More efficient than uint32 if values are often greater than 2^28.uint32intintuint32uintintegerBignum or Fixnum (as required)
fixed64Always eight bytes. More efficient than uint64 if values are often greater than 2^56.uint64longint/longuint64ulonginteger/stringBignum
sfixed32Always four bytes.int32intintint32intintegerBignum or Fixnum (as required)
sfixed64Always eight bytes.int64longint/longint64longinteger/stringBignum
boolboolbooleanbooleanboolboolbooleanTrueClass/FalseClass
stringA string must always contain UTF-8 encoded or 7-bit ASCII text.stringStringstr/unicodestringstringstringString (UTF-8)
bytesMay contain any arbitrary sequence of bytes.stringByteStringstr[]byteByteStringstringString (ASCII-8BIT)
+ + + From 6a79a294cd0be92432aef54c358f45927fa63868 Mon Sep 17 00:00:00 2001 From: Pablo Riesgo Ferreiro Date: Tue, 16 Jun 2020 12:18:08 +0200 Subject: [PATCH 045/105] rmeove balachandran folder --- .../.DS_Store | Bin 6148 -> 0 bytes .../__init__.py | 0 .../alignments/.DS_Store | Bin 6148 -> 0 bytes .../alignments/neoantigens_s_112032_1_T.fasta | 76 - .../neoantigens_s_112032_1_T_iedb.xml | 1246 - .../alignments/neoantigens_s_113413_1_T.fasta | 120 - .../neoantigens_s_113413_1_T_iedb.xml | 2156 - .../alignments/neoantigens_s_113520_1_T.fasta | 56 - .../neoantigens_s_113520_1_T_iedb.xml | 1106 - .../alignments/neoantigens_s_114296_1_T.fasta | 160 - .../neoantigens_s_114296_1_T_iedb.xml | 3362 -- .../alignments/neoantigens_s_114432_1_T.fasta | 198 - .../neoantigens_s_114432_1_T_iedb.xml | 3164 -- .../alignments/neoantigens_s_114445_1_T.fasta | 40 - .../neoantigens_s_114445_1_T_iedb.xml | 866 - .../alignments/neoantigens_s_114843_1_T.fasta | 10 - .../neoantigens_s_114843_1_T_iedb.xml | 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input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_135773_1_T.fasta delete mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_135773_1_T_iedb.xml delete mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_136103_1_T.fasta delete mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_136103_1_T_iedb.xml delete mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_136546_2_T.fasta delete mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_136546_2_T_iedb.xml delete mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_136587_1_T.fasta delete mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_136587_1_T_iedb.xml delete mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_137814_1_T.fasta delete mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_137814_1_T_iedb.xml delete mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_137854_2_T.fasta delete mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_137854_2_T_iedb.xml delete mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_138385_2_T.fasta delete mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_138385_2_T_iedb.xml delete mode 100755 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input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_139936_1_T_iedb.xml delete mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_140531_2_T.fasta delete mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_140531_2_T_iedb.xml delete mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_141002_2_T.fasta delete mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_141002_2_T_iedb.xml delete mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_141146_2_T.fasta delete mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_141146_2_T_iedb.xml delete mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/data/.DS_Store delete mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/data/SupplementaryTable1.txt delete mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/data/iedb.fasta delete mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/output/NeoantigenQuality.txt delete mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/run.sh delete mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/src/.DS_Store delete mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/src/.project delete mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/src/.pydevproject delete mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/src/Aligner.py delete mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/src/__init__.py delete mode 100755 input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/src/main.py diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/.DS_Store b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/.DS_Store deleted file mode 100755 index 29498513331c9590ed766731a6b095eb0acf43ae..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 6148 zcmeHK%TB{U3>?!4RdDH%H1@V-^m;4Wg<&0T*E43hX&L&p$$qDprKhvt+--jT7}7np#A3 zem<@ulZcFPQ@L2!n>{z**++&mCkOWA81W14cNZlEfg7;MkzE(HCqgga^y>{tEnwC%0;vJ&^%eQ zLs35+`xjp>T0M_1 -HIQDLYTVL ->M_2 -GYYTLLNVF ->M_3 -LTLFGYYTL ->M_4 -TLFGYYTLL ->M_5 -YYTLLNVFL ->M_6 -LAVRPSKIK ->M_7 -PTYGNSTKL ->M_8 -TASNVEFAI ->M_9 -TSSDSISHM ->M_10 -RFRALNQEL ->M_11 -HRNHIDRAL ->M_12 -FALLFGHRF ->M_13 -HRFDYRDPV ->M_14 -VADSTLLLM ->M_15 -FKMGAHTEV ->M_16 -FEGFPQSLL ->M_17 -FEGFPQSLL ->M_18 -GAQDRNSSF ->M_19 -FTHLRLQEF ->M_20 -LAASGPTLV ->M_21 -MIVGRTYTL ->M_22 -VAAENEAVL ->M_23 -IERNLINSL ->M_24 -GEAGTIERV ->M_25 -VAIFLGFYV ->M_26 -YSIFQLAFV ->M_27 -MALNYNRAF ->M_28 -TVFGGLMAL ->M_29 -LSSRLSDTL ->M_30 -SRLSDTLSF ->M_31 -KRTSPEELL ->M_32 -HALHLRRMM ->M_33 -MAGFMGMAV ->M_34 -RMMAGFMGM ->M_35 -FVSTIIHLL ->M_36 -YLVPGFSPY ->M_37 -YLVPGFSPY ->M_38 -KASFDHACL diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_112032_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_112032_1_T_iedb.xml deleted file mode 100755 index 91a7ccb8..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_112032_1_T_iedb.xml +++ /dev/null @@ -1,1246 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_1 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_1 - 9 - - - 1 - gnl|BL_ORD_ID|86 - 6373|Genome polyprotein|SRC279960|Hepatitis C virus subtype 3a|356426 - 86 - 10 - - - 1 - 15.3938 - 28 - 0.84849 - 1 - 9 - 2 - 10 - 0 - 0 - 6 - 6 - 0 - 9 - HIQDLYTVL - HAQDATTVL - H QD TVL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 2 - Query_2 - M_2 - 9 - - - 1 - gnl|BL_ORD_ID|23 - 1516|Nucleoprotein|P03418.1|Human respiratory syncytial virus A2|11259 - 23 - 14 - - - 1 - 13.4678 - 23 - 7.59625 - 1 - 7 - 2 - 8 - 0 - 0 - 4 - 6 - 0 - 7 - GYYTLLN - GFYHILN - G+Y +LN - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 3 - Query_3 - M_3 - 9 - - - 1 - gnl|BL_ORD_ID|1677 - 149024|NS2 protein|NP_751923.1|Hepatitis C virus (isolate H77)|63746 - 1677 - 9 - - - 1 - 12.3122 - 20 - 64.7664 - 1 - 7 - 2 - 8 - 0 - 0 - 5 - 5 - 0 - 7 - LTLFGYY - LTLSPYY - LTL YY - - - - - 2 - gnl|BL_ORD_ID|639 - 37991|polyprotein|AAY82034.1|Hepatitis C virus genotype 1|41856 - 639 - 13 - - - 1 - 11.927 - 19 - 78.6478 - 1 - 7 - 4 - 10 - 0 - 0 - 5 - 5 - 0 - 7 - LTLFGYY - LTLSPYY - LTL YY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 4 - Query_4 - M_4 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_5 - 9 - - - 1 - gnl|BL_ORD_ID|1867 - 180464|polyprotein|CDF77361.1|Dengue virus 3|11069 - 1867 - 10 - - - 1 - 12.3122 - 20 - 44.794 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 7 - 0 - 8 - YTLLNVFL - FTILALFL - +T+L +FL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 6 - Query_6 - M_6 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_7 - 9 - - - 1 - gnl|BL_ORD_ID|1143 - 75436|Polyprotein|P90247|Hepatitis C virus|11103 - 1143 - 20 - - - 1 - 13.4678 - 23 - 11.6549 - 1 - 6 - 4 - 9 - 0 - 0 - 4 - 4 - 0 - 6 - PTYGNS - PLYGNE - P YGN - - - - - 2 - gnl|BL_ORD_ID|1144 - 75438|polyprotein|AAF65962.1|Hepatitis C virus|11103 - 1144 - 20 - - - 1 - 13.4678 - 23 - 11.8474 - 1 - 6 - 4 - 9 - 0 - 0 - 4 - 4 - 0 - 6 - PTYGNS - PLYGNE - P YGN - - - - - 3 - gnl|BL_ORD_ID|1142 - 75435|largest ORF|AAB02128.1|Hepatitis C virus|11103 - 1142 - 20 - - - 1 - 13.4678 - 23 - 12.0429 - 1 - 6 - 4 - 9 - 0 - 0 - 4 - 4 - 0 - 6 - PTYGNS - PLYGNE - P YGN - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 8 - Query_8 - M_8 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_9 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_10 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_11 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_12 - 9 - - - 1 - gnl|BL_ORD_ID|606 - 37251|||| - 606 - 9 - - - 1 - 13.853 - 24 - 4.4402 - 3 - 7 - 1 - 5 - 0 - 0 - 5 - 5 - 0 - 5 - LLFGH - LLFGH - LLFGH - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 13 - Query_13 - M_13 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_14 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_15 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_16 - 9 - - - 1 - gnl|BL_ORD_ID|389 - 23807|tax|AAG48731.1|Human T-lymphotropic virus 2|11909 - 389 - 23 - - - 1 - 15.779 - 29 - 0.429649 - 1 - 9 - 2 - 10 - 0 - 0 - 7 - 7 - 0 - 9 - FEGFPQSLL - FPGFGQSLL - F GF QSLL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 17 - Query_17 - M_17 - 9 - - - 1 - gnl|BL_ORD_ID|389 - 23807|tax|AAG48731.1|Human T-lymphotropic virus 2|11909 - 389 - 23 - - - 1 - 15.779 - 29 - 0.429649 - 1 - 9 - 2 - 10 - 0 - 0 - 7 - 7 - 0 - 9 - FEGFPQSLL - FPGFGQSLL - F GF QSLL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 18 - Query_18 - M_18 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_19 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_20 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_21 - 9 - - - 1 - gnl|BL_ORD_ID|301 - 20354|M1 protein|CAA30882.1|Influenza A virus|11320 - 301 - 9 - - - 1 - 11.927 - 19 - 70.3445 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 6 - 0 - 8 - IVGRTYTL - ILGFVFTL - I+G +TL - - - - - 2 - gnl|BL_ORD_ID|302 - 20355|Matrix protein 1|P03485.1|Influenza A virus (A/Puerto Rico/8/1934(H1N1))|211044 - 302 - 10 - - - 1 - 11.927 - 19 - 85.0569 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 6 - 0 - 8 - IVGRTYTL - ILGFVFTL - I+G +TL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 22 - Query_22 - M_22 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_23 - 9 - - - 1 - gnl|BL_ORD_ID|1972 - 182938|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1972 - 10 - - - 1 - 15.779 - 29 - 0.43293 - 2 - 9 - 3 - 10 - 0 - 0 - 6 - 7 - 0 - 8 - ERNLINSL - EENLVNSL - E NL+NSL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 24 - Query_24 - M_24 - 9 - - - 1 - gnl|BL_ORD_ID|2223 - 194242|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis|1773 - 2223 - 9 - - - 1 - 15.3938 - 28 - 0.819689 - 2 - 9 - 2 - 9 - 0 - 0 - 5 - 6 - 0 - 8 - EAGTIERV - EAGNFERI - EAG ER+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 25 - Query_25 - M_25 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_26 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_27 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 28 - Query_28 - M_28 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 29 - Query_29 - M_29 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 30 - Query_30 - M_30 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 31 - Query_31 - M_31 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 32 - Query_32 - M_32 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 33 - Query_33 - M_33 - 9 - - - 1 - gnl|BL_ORD_ID|1357 - 108153|polyprotein|AAF65950.1|Hepatitis C virus|11103 - 1357 - 10 - - - 1 - 12.6974 - 21 - 36.0093 - 1 - 6 - 5 - 10 - 0 - 0 - 4 - 4 - 0 - 6 - MAGFMG - MTGFTG - M GF G - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 34 - Query_34 - M_34 - 9 - - - 1 - gnl|BL_ORD_ID|1357 - 108153|polyprotein|AAF65950.1|Hepatitis C virus|11103 - 1357 - 10 - - - 1 - 13.0826 - 22 - 15.0326 - 2 - 8 - 4 - 10 - 0 - 0 - 4 - 5 - 0 - 7 - MMAGFMG - LMTGFTG - +M GF G - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 35 - Query_35 - M_35 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 36 - Query_36 - M_36 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 37 - Query_37 - M_37 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 38 - Query_38 - M_38 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_113413_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_113413_1_T.fasta deleted file mode 100755 index b7f441ce..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_113413_1_T.fasta +++ /dev/null @@ -1,120 +0,0 @@ ->M_39 -EFHDIASHV ->M_40 -MCDNGSGLV ->M_41 -IQNAGGSVI ->M_42 -TQDGALMNV ->M_43 -TLGIICLLL ->M_44 -WNDKVKEAL ->M_45 -QNAGGSVII ->M_46 -SDYLHWEVV ->M_47 -SSVPVLNML ->M_48 -WALEVLLNA ->M_49 -YETQDGALM ->M_50 -NMELPYFVL ->M_51 -LSTPAPQVF ->M_52 -VSDTEFHPL ->M_53 -MVVAGQRAV ->M_54 -YLHWEVVEL ->M_55 -ANFPWALEV ->M_56 -WYLRDVSEV ->M_57 -FHDIASHVK ->M_58 -FPWALEVLL ->M_59 -GTLGIICLL ->M_60 -YLHWEVVEL ->M_61 -LQFSRMEQL ->M_62 -VHLESNATV ->M_63 -QMFVHLQLL ->M_64 -VHLESNATV ->M_65 -TQDGALMNV ->M_66 -VAFCLKCNL ->M_67 -STDSLSTPA ->M_68 -DILEKSSSV ->M_69 -NMVGFSDRV ->M_70 -NLGSKLQLV ->M_71 -FPWALEVLL ->M_72 -TKDTFMMEL ->M_73 -HCANFPWAL ->M_74 -ESSSETSTY ->M_75 -QMFVHLQLL ->M_76 -QPLKYTWLL ->M_77 -SLTTLLQAL ->M_78 -SLSTPAPQV ->M_79 -FAINFFKEV ->M_80 -YTWLLAAKV ->M_81 -DLENMELPY ->M_82 -EKSSSVPVL ->M_83 -WLCDHPVPV ->M_84 -LLMSTLGIL ->M_85 -IQNAGGSVI ->M_86 -YTWLLAAKV ->M_87 -FSQEPADQM ->M_88 -ILSWLVSQL ->M_89 -LLLMSTLGI ->M_90 -FYIFNVSSI ->M_91 -GLGECITQV ->M_92 -LAMRRHSRI ->M_93 -LAKDSGAPV ->M_94 -YLHWEVVEL ->M_95 -FMMELLNRV ->M_96 -WLCDHPVPV ->M_97 -FAINFFKEV ->M_98 -FMMELLNRV diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_113413_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_113413_1_T_iedb.xml deleted file mode 100755 index 417ce7e1..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_113413_1_T_iedb.xml +++ /dev/null @@ -1,2156 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_39 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_39 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_40 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_41 - 9 - - - 1 - gnl|BL_ORD_ID|2016 - 183843|envelope protein|AGW23576.1|Dengue virus 3|11069 - 2016 - 10 - - - 1 - 15.779 - 29 - 0.401267 - 1 - 9 - 1 - 9 - 0 - 0 - 6 - 8 - 0 - 9 - IQNAGGSVI - IQNSGGTSI - IQN+GG+ I - - - - - 2 - gnl|BL_ORD_ID|461 - 27981|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 - 461 - 20 - - - 1 - 15.0086 - 27 - 1.13532 - 2 - 7 - 15 - 20 - 0 - 0 - 5 - 6 - 0 - 6 - QNAGGS - QNAGGT - QNAGG+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 4 - Query_4 - M_42 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_43 - 9 - - - 1 - gnl|BL_ORD_ID|979 - 64818|E7|AAD33253.1|Human papillomavirus type 16|333760 - 979 - 8 - - - 1 - 15.0086 - 27 - 1.52888 - 1 - 6 - 1 - 6 - 0 - 0 - 5 - 6 - 0 - 6 - TLGIIC - TLGIVC - TLGI+C - - - - - 2 - gnl|BL_ORD_ID|980 - 64819|E7 protein|ABL96585.1|Human papillomavirus type 16|333760 - 980 - 9 - - - 1 - 14.6234 - 26 - 2.04484 - 1 - 6 - 1 - 6 - 0 - 0 - 5 - 6 - 0 - 6 - TLGIIC - TLGIVC - TLGI+C - - - - - 3 - gnl|BL_ORD_ID|2102 - 185978|polyprotein|CDF77361.1|Dengue virus 3|11069 - 2102 - 10 - - - 1 - 14.6234 - 26 - 2.17971 - 1 - 7 - 1 - 7 - 0 - 0 - 4 - 7 - 0 - 7 - TLGIICL - TMGVLCL - T+G++CL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 6 - Query_6 - M_44 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_45 - 9 - - - 1 - gnl|BL_ORD_ID|461 - 27981|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 - 461 - 20 - - - 1 - 15.0086 - 27 - 1.13532 - 1 - 6 - 15 - 20 - 0 - 0 - 5 - 6 - 0 - 6 - QNAGGS - QNAGGT - QNAGG+ - - - - - 2 - gnl|BL_ORD_ID|2016 - 183843|envelope protein|AGW23576.1|Dengue virus 3|11069 - 2016 - 10 - - - 1 - 14.6234 - 26 - 1.84513 - 1 - 9 - 2 - 10 - 0 - 0 - 5 - 7 - 0 - 9 - QNAGGSVII - QNSGGTSIF - QN+GG+ I - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 8 - Query_8 - M_46 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_47 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_48 - 9 - - - 1 - gnl|BL_ORD_ID|637 - 37960|membrane protein|AAA45887.1|Human gammaherpesvirus 4|10376 - 637 - 9 - - - 1 - 12.3122 - 20 - 60.6092 - 1 - 7 - 3 - 9 - 0 - 0 - 5 - 5 - 0 - 7 - WALEVLL - WTLVVLL - W L VLL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 11 - Query_11 - M_49 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_50 - 9 - - - 1 - gnl|BL_ORD_ID|184 - 13518|HCV-1|AAA45676.1|Hepatitis C virus genotype 1|41856 - 184 - 20 - - - 1 - 12.6974 - 21 - 23.6647 - 4 - 8 - 3 - 7 - 0 - 0 - 4 - 4 - 0 - 5 - LPYFV - LPYLV - LPY V - - - - - 2 - gnl|BL_ORD_ID|183 - 13516|Genome polyprotein|P26664.3|Hepatitis C virus subtype 1a|31646 - 183 - 9 - - - 1 - 12.3122 - 20 - 47.1713 - 4 - 8 - 3 - 7 - 0 - 0 - 4 - 4 - 0 - 5 - LPYFV - LPYLV - LPY V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 13 - Query_13 - M_51 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_52 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_53 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_54 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_55 - 9 - - - 1 - gnl|BL_ORD_ID|561 - 34616|pol protein|BAA32832.1|Hepatitis B virus|10407 - 561 - 9 - - - 1 - 14.2382 - 25 - 3.05306 - 1 - 7 - 3 - 9 - 0 - 0 - 4 - 5 - 0 - 7 - ANFPWAL - TSFPWLL - +FPW L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 18 - Query_18 - M_56 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_57 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_58 - 9 - - - 1 - gnl|BL_ORD_ID|637 - 37960|membrane protein|AAA45887.1|Human gammaherpesvirus 4|10376 - 637 - 9 - - - 1 - 12.3122 - 20 - 66.9453 - 3 - 9 - 3 - 9 - 0 - 0 - 5 - 5 - 0 - 7 - WALEVLL - WTLVVLL - W L VLL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 21 - Query_21 - M_59 - 9 - - - 1 - gnl|BL_ORD_ID|979 - 64818|E7|AAD33253.1|Human papillomavirus type 16|333760 - 979 - 8 - - - 1 - 14.6234 - 26 - 1.73882 - 2 - 7 - 1 - 6 - 0 - 0 - 5 - 6 - 0 - 6 - TLGIIC - TLGIVC - TLGI+C - - - - - 2 - gnl|BL_ORD_ID|980 - 64819|E7 protein|ABL96585.1|Human papillomavirus type 16|333760 - 980 - 9 - - - 1 - 14.6234 - 26 - 2.33479 - 2 - 7 - 1 - 6 - 0 - 0 - 5 - 6 - 0 - 6 - TLGIIC - TLGIVC - TLGI+C - - - - - 3 - gnl|BL_ORD_ID|2102 - 185978|polyprotein|CDF77361.1|Dengue virus 3|11069 - 2102 - 10 - - - 1 - 14.6234 - 26 - 2.37049 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 7 - 0 - 7 - TLGIICL - TMGVLCL - T+G++CL - - - - - 4 - gnl|BL_ORD_ID|627 - 37573|E7 protein|ABL96585.1|Human papillomavirus type 16|333760 - 627 - 9 - - - 1 - 13.853 - 24 - 5.95161 - 1 - 6 - 4 - 9 - 0 - 0 - 5 - 6 - 0 - 6 - GTLGII - GTLGIV - GTLGI+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 22 - Query_22 - M_60 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_61 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_62 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_63 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_64 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_65 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 28 - Query_28 - M_66 - 9 - - - 1 - gnl|BL_ORD_ID|1382 - 110184|E7|AAD33253.1|Human papillomavirus type 16|333760 - 1382 - 35 - - - 1 - 13.4678 - 23 - 9.19861 - 1 - 8 - 14 - 21 - 0 - 0 - 5 - 6 - 0 - 8 - VAFCLKCN - VTFCCKCD - V FC KC+ - - - - - 2 - gnl|BL_ORD_ID|1400 - 110467|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1400 - 25 - - - 1 - 11.5418 - 18 - 93.0417 - 2 - 7 - 8 - 13 - 0 - 0 - 4 - 4 - 0 - 6 - AFCLKC - AVCDKC - A C KC - - - - - 3 - gnl|BL_ORD_ID|1387 - 110227|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1387 - 33 - - - 1 - 11.1566 - 17 - 143.577 - 2 - 7 - 15 - 20 - 0 - 0 - 4 - 4 - 0 - 6 - AFCLKC - AVCDKC - A C KC - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 29 - Query_29 - M_67 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 30 - Query_30 - M_68 - 9 - - - 1 - gnl|BL_ORD_ID|181 - 13456|circumsporozoite protein|AAN87606.1|Plasmodium falciparum|5833 - 181 - 20 - - - 1 - 13.4678 - 23 - 9.72555 - 3 - 9 - 11 - 17 - 0 - 0 - 5 - 6 - 0 - 7 - LEKSSSV - MEKCSSV - +EK SSV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 31 - Query_31 - M_69 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 32 - Query_32 - M_70 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 33 - Query_33 - M_71 - 9 - - - 1 - gnl|BL_ORD_ID|637 - 37960|membrane protein|AAA45887.1|Human gammaherpesvirus 4|10376 - 637 - 9 - - - 1 - 12.3122 - 20 - 66.9453 - 3 - 9 - 3 - 9 - 0 - 0 - 5 - 5 - 0 - 7 - WALEVLL - WTLVVLL - W L VLL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 34 - Query_34 - M_72 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 35 - Query_35 - M_73 - 9 - - - 1 - gnl|BL_ORD_ID|561 - 34616|pol protein|BAA32832.1|Hepatitis B virus|10407 - 561 - 9 - - - 1 - 14.2382 - 25 - 2.95178 - 3 - 9 - 3 - 9 - 0 - 0 - 4 - 5 - 0 - 7 - ANFPWAL - TSFPWLL - +FPW L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 36 - Query_36 - M_74 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 37 - Query_37 - M_75 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 38 - Query_38 - M_76 - 9 - - - 1 - gnl|BL_ORD_ID|1020 - 68229|EBNA3B (EBNA4A) latent protein|CAA24858.1|Human gammaherpesvirus 4|10376 - 1020 - 10 - - - 1 - 11.927 - 19 - 68.8532 - 2 - 7 - 5 - 10 - 0 - 0 - 4 - 4 - 0 - 6 - PLKYTW - PYKPTW - P K TW - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 39 - Query_39 - M_77 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 40 - Query_40 - M_78 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 41 - Query_41 - M_79 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 42 - Query_42 - M_80 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 43 - Query_43 - M_81 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 44 - Query_44 - M_82 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 45 - Query_45 - M_83 - 9 - - - 1 - gnl|BL_ORD_ID|1944 - 180818|Membrane glycoprotein precursor|NP_739582.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1944 - 15 - - - 1 - 13.4678 - 23 - 9.36117 - 1 - 6 - 1 - 6 - 0 - 0 - 3 - 4 - 0 - 6 - WLCDHP - WILRHP - W+ HP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 46 - Query_46 - M_84 - 9 - - - 1 - gnl|BL_ORD_ID|627 - 37573|E7 protein|ABL96585.1|Human papillomavirus type 16|333760 - 627 - 9 - - - 1 - 15.3938 - 28 - 0.565591 - 1 - 9 - 1 - 9 - 0 - 0 - 7 - 8 - 0 - 9 - LLMSTLGIL - LLMGTLGIV - LLM TLGI+ - - - - - 2 - gnl|BL_ORD_ID|1718 - 150391|polyprotein|AGS49173.1|Dengue virus 2|11060 - 1718 - 10 - - - 1 - 14.6234 - 26 - 1.64355 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 9 - 0 - 9 - LLMSTLGIL - LMMTTIGIV - L+M+T+GI+ - - - - - 3 - gnl|BL_ORD_ID|1722 - 150448|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1722 - 9 - - - 1 - 13.4678 - 23 - 8.56958 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 7 - 0 - 7 - LMSTLGI - MMATIGI - +M+T+GI - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 47 - Query_47 - M_85 - 9 - - - 1 - gnl|BL_ORD_ID|2016 - 183843|envelope protein|AGW23576.1|Dengue virus 3|11069 - 2016 - 10 - - - 1 - 15.779 - 29 - 0.401267 - 1 - 9 - 1 - 9 - 0 - 0 - 6 - 8 - 0 - 9 - IQNAGGSVI - IQNSGGTSI - IQN+GG+ I - - - - - 2 - gnl|BL_ORD_ID|461 - 27981|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 - 461 - 20 - - - 1 - 15.0086 - 27 - 1.13532 - 2 - 7 - 15 - 20 - 0 - 0 - 5 - 6 - 0 - 6 - QNAGGS - QNAGGT - QNAGG+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 48 - Query_48 - M_86 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 49 - Query_49 - M_87 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 50 - Query_50 - M_88 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 51 - Query_51 - M_89 - 9 - - - 1 - gnl|BL_ORD_ID|627 - 37573|E7 protein|ABL96585.1|Human papillomavirus type 16|333760 - 627 - 9 - - - 1 - 15.3938 - 28 - 0.690962 - 2 - 9 - 1 - 8 - 0 - 0 - 7 - 7 - 0 - 8 - LLMSTLGI - LLMGTLGI - LLM TLGI - - - - - 2 - gnl|BL_ORD_ID|1718 - 150391|polyprotein|AGS49173.1|Dengue virus 2|11060 - 1718 - 10 - - - 1 - 14.6234 - 26 - 2.17971 - 2 - 9 - 1 - 8 - 0 - 0 - 5 - 8 - 0 - 8 - LLMSTLGI - LMMTTIGI - L+M+T+GI - - - - - 3 - gnl|BL_ORD_ID|1722 - 150448|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1722 - 9 - - - 1 - 13.4678 - 23 - 8.56958 - 3 - 9 - 1 - 7 - 0 - 0 - 4 - 7 - 0 - 7 - LMSTLGI - MMATIGI - +M+T+GI - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 52 - Query_52 - M_90 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 53 - Query_53 - M_91 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 54 - Query_54 - M_92 - 9 - - - 1 - gnl|BL_ORD_ID|2274 - 419017|polyprotein|AFY10034.1|Dengue virus 4|11070 - 2274 - 10 - - - 1 - 13.4678 - 23 - 10.9961 - 2 - 7 - 3 - 8 - 0 - 0 - 4 - 6 - 0 - 6 - AMRRHS - AMKRYS - AM+R+S - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 55 - Query_55 - M_93 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 56 - Query_56 - M_94 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 57 - Query_57 - M_95 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 58 - Query_58 - M_96 - 9 - - - 1 - gnl|BL_ORD_ID|1944 - 180818|Membrane glycoprotein precursor|NP_739582.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1944 - 15 - - - 1 - 13.4678 - 23 - 9.36117 - 1 - 6 - 1 - 6 - 0 - 0 - 3 - 4 - 0 - 6 - WLCDHP - WILRHP - W+ HP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 59 - Query_59 - M_97 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 60 - Query_60 - M_98 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_113520_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_113520_1_T.fasta deleted file mode 100755 index 5c7319a5..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_113520_1_T.fasta +++ /dev/null @@ -1,56 +0,0 @@ ->M_99 -TVAEKRGWK ->M_100 -RLLPDTFVL ->M_101 -RLLPDTFVL ->M_102 -SSMAAGLEH ->M_103 -MIYRLAQAK ->M_104 -TPMYRTRPA ->M_105 -ITYYCHGGY ->M_106 -KLGSSITYY ->M_107 -FPVSYGVPA ->M_108 -IMFPVSYGV ->M_109 -ISDTILKTK ->M_110 -RLQTHTIYK ->M_111 -ELFHVDWHV ->M_112 -LPRQYWEAL ->M_113 -MPHRATVYA ->M_114 -KLLECSLTK ->M_115 -RPQGQRPAL ->M_116 -SSDCIIEKK ->M_117 -TSSDCIIEK ->M_118 -GLMGHTLHR ->M_119 -LPGHAPGIL ->M_120 -YAYHVEWEK ->M_121 -WVRWHKGCL ->M_122 -SSSIRIHER ->M_123 -FLSSSFSML ->M_124 -FSMLKDHIK ->M_125 -LSSSFSMLK ->M_126 -VVGADGVGK diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_113520_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_113520_1_T_iedb.xml deleted file mode 100755 index 8f3d16ac..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_113520_1_T_iedb.xml +++ /dev/null @@ -1,1106 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_99 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_99 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_100 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_101 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_102 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_103 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_104 - 9 - - - 1 - gnl|BL_ORD_ID|1284 - 102150|nef protein|ACR27119.1|Human immunodeficiency virus 1|11676 - 1284 - 9 - - - 1 - 10.7714 - 16 - 449.273 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 4 - 0 - 8 - TPMYRTRP - TPQVPLRP - TP RP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 7 - Query_7 - M_105 - 9 - - - 1 - gnl|BL_ORD_ID|1176 - 79454|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 1176 - 15 - - - 1 - 13.0826 - 22 - 20.7204 - 4 - 8 - 3 - 7 - 0 - 0 - 3 - 4 - 0 - 5 - YCHGG - FCHPG - +CH G - - - - - 2 - gnl|BL_ORD_ID|1160 - 76532|outer membrane protein|YP_170495.1|Francisella tularensis subsp. tularensis SCHU S4|177416 - 1160 - 10 - - - 1 - 11.5418 - 18 - 146.048 - 3 - 9 - 1 - 7 - 0 - 0 - 4 - 4 - 0 - 7 - YYCHGGY - YYLDRGY - YY GY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 8 - Query_8 - M_106 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_107 - 9 - - - 1 - gnl|BL_ORD_ID|1 - 118|envelope glycoprotein|ABS76372.1|Human immunodeficiency virus 1|11676 - 1 - 20 - - - 1 - 13.853 - 24 - 6.85717 - 3 - 8 - 9 - 14 - 0 - 0 - 5 - 5 - 0 - 6 - VSYGVP - VYYGVP - V YGVP - - - - - 2 - gnl|BL_ORD_ID|1831 - 179823|cell surface protein (associated with virulence)|NP_302372.1|Mycobacterium leprae TN|272631 - 1831 - 9 - - - 1 - 11.927 - 19 - 112.786 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 4 - 0 - 9 - FPVSYGVPA - IPASVSAPA - P S PA - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 10 - Query_10 - M_108 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_109 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_110 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_111 - 9 - - - 1 - gnl|BL_ORD_ID|686 - 41407|Envelope protein|NP_739583.2|Dengue virus 2|11060 - 686 - 15 - - - 1 - 10.3862 - 15 - 487.414 - 2 - 7 - 7 - 12 - 0 - 0 - 3 - 3 - 0 - 6 - LFHVDW - LVHRQW - L H W - - - - - 2 - gnl|BL_ORD_ID|1746 - 150725|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1746 - 9 - - - 1 - 10.001 - 14 - 843.115 - 2 - 7 - 2 - 7 - 0 - 0 - 3 - 3 - 0 - 6 - LFHVDW - LVHRQW - L H W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 14 - Query_14 - M_112 - 9 - - - 1 - gnl|BL_ORD_ID|502 - 31997|hypothetical protein FTT0484|YP_169522.1|Francisella tularensis subsp. tularensis SCHU S4|177416 - 502 - 9 - - - 1 - 13.853 - 24 - 5.65074 - 1 - 6 - 3 - 8 - 0 - 0 - 4 - 4 - 0 - 6 - LPRQYW - LPEGYW - LP YW - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 15 - Query_15 - M_113 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_114 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_115 - 9 - - - 1 - gnl|BL_ORD_ID|1739 - 150643|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1739 - 10 - - - 1 - 14.2382 - 25 - 3.50259 - 2 - 9 - 2 - 9 - 0 - 0 - 5 - 6 - 0 - 8 - PQGQRPAL - PEGIIPAL - P+G PAL - - - - - 2 - gnl|BL_ORD_ID|2075 - 185125|polyprotein|AGW21594.1|Dengue virus 1|11053 - 2075 - 10 - - - 1 - 14.2382 - 25 - 4.23087 - 2 - 9 - 3 - 10 - 0 - 0 - 5 - 6 - 0 - 8 - PQGQRPAL - PEGIIPAL - P+G PAL - - - - - 3 - gnl|BL_ORD_ID|577 - 36352|Polyprotein|P90247|Hepatitis C virus|11103 - 577 - 20 - - - 1 - 13.853 - 24 - 4.57317 - 2 - 9 - 10 - 17 - 0 - 0 - 4 - 6 - 0 - 8 - PQGQRPAL - PRGSRPSW - P+G RP+ - - - - - 4 - gnl|BL_ORD_ID|566 - 35237|nonstructural protein 3|NP_722463.1|Dengue virus type 1 Hawaii|10000440 - 566 - 20 - - - 1 - 13.853 - 24 - 5.14963 - 2 - 9 - 7 - 14 - 0 - 0 - 5 - 6 - 0 - 8 - PQGQRPAL - PEGIIPAL - P+G PAL - - - - - 5 - gnl|BL_ORD_ID|1107 - 72929|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 - 1107 - 15 - - - 1 - 13.0826 - 22 - 19.7105 - 2 - 6 - 4 - 8 - 0 - 0 - 4 - 4 - 0 - 5 - PQGQR - PQGSR - PQG R - - - - - 6 - gnl|BL_ORD_ID|131 - 9316|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 - 131 - 15 - - - 1 - 13.0826 - 22 - 20.0418 - 2 - 6 - 8 - 12 - 0 - 0 - 4 - 4 - 0 - 5 - PQGQR - PQGSR - PQG R - - - - - 7 - gnl|BL_ORD_ID|1933 - 180778|polyprotein|AFP27208.1|Dengue virus 4|11070 - 1933 - 10 - - - 1 - 12.6974 - 21 - 24.7764 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - PQGQRPAL - PEGIIPTL - P+G P L - - - - - 8 - gnl|BL_ORD_ID|1948 - 180850|polyprotein|AFP27208.1|Dengue virus 4|11070 - 1948 - 10 - - - 1 - 12.6974 - 21 - 26.5293 - 2 - 9 - 3 - 10 - 0 - 0 - 4 - 5 - 0 - 8 - PQGQRPAL - PEGIIPTL - P+G P L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 18 - Query_18 - M_116 - 9 - - - 1 - gnl|BL_ORD_ID|1007 - 66405|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 1007 - 20 - - - 1 - 10.7714 - 16 - 316.686 - 2 - 9 - 4 - 11 - 0 - 0 - 4 - 5 - 0 - 8 - SDCIIEKK - SACQRQKK - S C +KK - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 19 - Query_19 - M_117 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_118 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_119 - 9 - - - 1 - gnl|BL_ORD_ID|741 - 47760|EBNA-1 protein|Q777E1|Human gammaherpesvirus 4|10376 - 741 - 15 - - - 1 - 12.3122 - 20 - 43.2075 - 2 - 7 - 1 - 6 - 0 - 0 - 4 - 4 - 0 - 6 - PGHAPG - PGTGPG - PG PG - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 22 - Query_22 - M_120 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_121 - 9 - - - 1 - gnl|BL_ORD_ID|1944 - 180818|Membrane glycoprotein precursor|NP_739582.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1944 - 15 - - - 1 - 11.927 - 19 - 77.3377 - 1 - 7 - 1 - 7 - 0 - 0 - 3 - 4 - 0 - 7 - WVRWHKG - WILRHPG - W+ H G - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 24 - Query_24 - M_122 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_123 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_124 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_125 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 28 - Query_28 - M_126 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114296_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114296_1_T.fasta deleted file mode 100755 index 2b03eb9e..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114296_1_T.fasta +++ /dev/null @@ -1,160 +0,0 @@ ->M_127 -AVDLSSAGM ->M_128 -GMAGVLIGY ->M_129 -SSAGMAGVL ->M_130 -KAAPIYKLV ->M_131 -VTKAAPIYK ->M_132 -FLPSWLLGI ->M_133 -RMAFTDHQL ->M_134 -RMAFTDHQL ->M_135 -ALQPQLGCY ->M_136 -YQQALQPQL ->M_137 -YQQALQPQL ->M_138 -YQLKMLIKI ->M_139 -ILLVVYNNV ->M_140 -LLVVYNNVL ->M_141 -LLVVYNNVL ->M_142 -LVVYNNVLK ->M_143 -LSGHSTQDL ->M_144 -QALSKFKAM ->M_145 -LSVDRMRKV ->M_146 -LGVAARWDL ->M_147 -HAVQAAVQY ->M_148 -HAVQAAVQY ->M_149 -KIMNSLPEM ->M_150 -KIMNSLPEM ->M_151 -LPEMKVQLV ->M_152 -SLPEMKVQL ->M_153 -LTISGECPK ->M_154 -AMYDVLTFA ->M_155 -ATDQAMYDV ->M_156 -KIHATDQAM ->M_157 -QAMYDVLTF ->M_158 -QAMYDVLTF ->M_159 -LICFLTPVK ->M_160 -NLICFLTPV ->M_161 -IAHIFGGAR ->M_162 -LLEISKWFR ->M_163 -FSDDGVLGP ->M_164 -GSFSDDGVL ->M_165 -VLGPVLTTF ->M_166 -ATSIPAGSM ->M_167 -IPAGSMPTV ->M_168 -IMDLRNGTF ->M_169 -CLSGYCSVF ->M_170 -CSVFAYKPM ->M_171 -GYCSVFAYK ->M_172 -SGYCSVFAY ->M_173 -LIMALVWSL ->M_174 -LIMALVWSL ->M_175 -LIMALVWSL ->M_176 -LVWSLPCGF ->M_177 -ESDYLINEM ->M_178 -YLINEMYL* ->M_179 -TQMVDIWSV ->M_180 -MVAFFSSHT ->M_181 -VAFFSSHTY ->M_182 -VAFFSSHTY ->M_183 -VAFFSSHTY ->M_184 -VTFSTSSQL ->M_185 -WVDFADSVT ->M_186 -YQTFKDWGI ->M_187 -ISMGQEEKK ->M_188 -WISMGQEEK ->M_189 -FSWQSHLLI ->M_190 -QSHLLIHQR ->M_191 -FYIIECIAM ->M_192 -TAFYIIECI ->M_193 -YIIECIAMS ->M_194 -ASTYSQLKL ->M_195 -SASTYSQLK ->M_196 -VSASTYSQL ->M_197 -YSQLKLWNV ->M_198 -FYQHLNLMR ->M_199 -YQHLNLMRV ->M_200 -KPAPHPQAL ->M_201 -MADSGPIYN ->M_202 -GLGFYNDVV ->M_203 -FCENDAEVL ->M_204 -RTTQQENPR ->M_205 -AMDDLDTDM ->M_206 -EECGKTFYR diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114296_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114296_1_T_iedb.xml deleted file mode 100755 index 5a71dc1f..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114296_1_T_iedb.xml +++ /dev/null @@ -1,3362 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_127 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_127 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_128 - 9 - - - 1 - gnl|BL_ORD_ID|339 - 21275|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 - 339 - 9 - - - 1 - 11.5418 - 18 - 157.499 - 1 - 8 - 1 - 8 - 0 - 0 - 5 - 5 - 0 - 8 - GMAGVLIG - GMGPSLIG - GM LIG - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 3 - Query_3 - M_129 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_130 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_131 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_132 - 9 - - - 1 - gnl|BL_ORD_ID|174 - 13215|Antigen 85-B|P0C5B9.1|Mycobacterium tuberculosis|1773 - 174 - 10 - - - 1 - 13.4678 - 23 - 12.4198 - 2 - 6 - 2 - 6 - 0 - 0 - 4 - 4 - 0 - 5 - LPSWL - LPQWL - LP WL - - - - - 2 - gnl|BL_ORD_ID|2172 - 189727|Antigen 85-B|P0C5B9.1|Mycobacterium tuberculosis|1773 - 2172 - 9 - - - 1 - 13.0826 - 22 - 14.1983 - 2 - 6 - 1 - 5 - 0 - 0 - 4 - 4 - 0 - 5 - LPSWL - LPQWL - LP WL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 7 - Query_7 - M_133 - 9 - - - 1 - gnl|BL_ORD_ID|2185 - 190466|large surface antigen|CAL29876.1|Hepatitis B virus|10407 - 2185 - 15 - - - 1 - 15.3938 - 28 - 0.751673 - 4 - 9 - 4 - 9 - 0 - 0 - 5 - 5 - 0 - 6 - FTDHQL - FPDHQL - F DHQL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 8 - Query_8 - M_134 - 9 - - - 1 - gnl|BL_ORD_ID|2185 - 190466|large surface antigen|CAL29876.1|Hepatitis B virus|10407 - 2185 - 15 - - - 1 - 15.3938 - 28 - 0.751673 - 4 - 9 - 4 - 9 - 0 - 0 - 5 - 5 - 0 - 6 - FTDHQL - FPDHQL - F DHQL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 9 - Query_9 - M_135 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_136 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_137 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_138 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_139 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_140 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_141 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_142 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_143 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_144 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_145 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_146 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_147 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 22 - Query_22 - M_148 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_149 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_150 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_151 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_152 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_153 - 9 - - - 1 - gnl|BL_ORD_ID|2309 - 423011|polyprotein|AER51001.1|Hepatitis C virus genotype 1|41856 - 2309 - 9 - - - 1 - 13.4678 - 23 - 10.0233 - 3 - 8 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - ISGECP - MSGEVP - +SGE P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 28 - Query_28 - M_154 - 9 - - - 1 - gnl|BL_ORD_ID|45 - 3019|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 - 45 - 9 - - - 1 - 15.0086 - 27 - 1.12298 - 1 - 7 - 1 - 7 - 0 - 0 - 5 - 7 - 0 - 7 - AMYDVLT - ALYDVVT - A+YDV+T - - - - - 2 - gnl|BL_ORD_ID|1382 - 110184|E7|AAD33253.1|Human papillomavirus type 16|333760 - 1382 - 35 - - - 1 - 14.6234 - 26 - 2.14504 - 1 - 8 - 9 - 16 - 0 - 0 - 4 - 7 - 0 - 8 - AMYDVLTF - AHYNIVTF - A Y+++TF - - - - - 3 - gnl|BL_ORD_ID|43 - 3017|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 43 - 9 - - - 1 - 13.853 - 24 - 5.09494 - 1 - 7 - 1 - 7 - 0 - 0 - 4 - 7 - 0 - 7 - AMYDVLT - ALYDVVS - A+YDV++ - - - - - 4 - gnl|BL_ORD_ID|44 - 3018|polyprotein|BAA25076.1|Hepatitis C virus (isolate H77)|63746 - 44 - 9 - - - 1 - 13.853 - 24 - 6.37844 - 1 - 7 - 1 - 7 - 0 - 0 - 4 - 7 - 0 - 7 - AMYDVLT - ALYDVVS - A+YDV++ - - - - - 5 - gnl|BL_ORD_ID|682 - 41085|polyprotein|ABR25251.1|Hepatitis C virus|11103 - 682 - 15 - - - 1 - 13.853 - 24 - 6.52084 - 1 - 7 - 2 - 8 - 0 - 0 - 4 - 7 - 0 - 7 - AMYDVLT - ALYDVVS - A+YDV++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 29 - Query_29 - M_155 - 9 - - - 1 - gnl|BL_ORD_ID|1398 - 110431|E7|AAD33253.1|Human papillomavirus type 16|333760 - 1398 - 36 - - - 1 - 11.927 - 19 - 54.6787 - 3 - 9 - 29 - 35 - 0 - 0 - 3 - 6 - 0 - 7 - DQAMYDV - DRAHYNI - D+A Y++ - - - - - 2 - gnl|BL_ORD_ID|1382 - 110184|E7|AAD33253.1|Human papillomavirus type 16|333760 - 1382 - 35 - - - 1 - 11.927 - 19 - 69.4128 - 3 - 9 - 7 - 13 - 0 - 0 - 3 - 6 - 0 - 7 - DQAMYDV - DRAHYNI - D+A Y++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 30 - Query_30 - M_156 - 9 - - - 1 - gnl|BL_ORD_ID|1339 - 107925|polyprotein|AAF65964.1|Hepatitis C virus|11103 - 1339 - 10 - - - 1 - 12.6974 - 21 - 26.9859 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 4 - 0 - 6 - KIHATD - KAHGTD - K H TD - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 31 - Query_31 - M_157 - 9 - - - 1 - gnl|BL_ORD_ID|45 - 3019|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 - 45 - 9 - - - 1 - 15.0086 - 27 - 0.989407 - 2 - 8 - 1 - 7 - 0 - 0 - 5 - 7 - 0 - 7 - AMYDVLT - ALYDVVT - A+YDV+T - - - - - 2 - gnl|BL_ORD_ID|1382 - 110184|E7|AAD33253.1|Human papillomavirus type 16|333760 - 1382 - 35 - - - 1 - 15.0086 - 27 - 1.26448 - 1 - 9 - 8 - 16 - 0 - 0 - 4 - 8 - 0 - 9 - QAMYDVLTF - RAHYNIVTF - +A Y+++TF - - - - - 3 - gnl|BL_ORD_ID|43 - 3017|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 43 - 9 - - - 1 - 14.2382 - 25 - 4.3647 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 7 - 0 - 7 - AMYDVLT - ALYDVVS - A+YDV++ - - - - - 4 - gnl|BL_ORD_ID|44 - 3018|polyprotein|BAA25076.1|Hepatitis C virus (isolate H77)|63746 - 44 - 9 - - - 1 - 13.853 - 24 - 5.45887 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 7 - 0 - 7 - AMYDVLT - ALYDVVS - A+YDV++ - - - - - 5 - gnl|BL_ORD_ID|682 - 41085|polyprotein|ABR25251.1|Hepatitis C virus|11103 - 682 - 15 - - - 1 - 13.853 - 24 - 5.48445 - 2 - 8 - 2 - 8 - 0 - 0 - 4 - 7 - 0 - 7 - AMYDVLT - ALYDVVS - A+YDV++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 32 - Query_32 - M_158 - 9 - - - 1 - gnl|BL_ORD_ID|45 - 3019|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 - 45 - 9 - - - 1 - 15.0086 - 27 - 0.989407 - 2 - 8 - 1 - 7 - 0 - 0 - 5 - 7 - 0 - 7 - AMYDVLT - ALYDVVT - A+YDV+T - - - - - 2 - gnl|BL_ORD_ID|1382 - 110184|E7|AAD33253.1|Human papillomavirus type 16|333760 - 1382 - 35 - - - 1 - 15.0086 - 27 - 1.26448 - 1 - 9 - 8 - 16 - 0 - 0 - 4 - 8 - 0 - 9 - QAMYDVLTF - RAHYNIVTF - +A Y+++TF - - - - - 3 - gnl|BL_ORD_ID|43 - 3017|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 43 - 9 - - - 1 - 14.2382 - 25 - 4.3647 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 7 - 0 - 7 - AMYDVLT - ALYDVVS - A+YDV++ - - - - - 4 - gnl|BL_ORD_ID|44 - 3018|polyprotein|BAA25076.1|Hepatitis C virus (isolate H77)|63746 - 44 - 9 - - - 1 - 13.853 - 24 - 5.45887 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 7 - 0 - 7 - AMYDVLT - ALYDVVS - A+YDV++ - - - - - 5 - gnl|BL_ORD_ID|682 - 41085|polyprotein|ABR25251.1|Hepatitis C virus|11103 - 682 - 15 - - - 1 - 13.853 - 24 - 5.48445 - 2 - 8 - 2 - 8 - 0 - 0 - 4 - 7 - 0 - 7 - AMYDVLT - ALYDVVS - A+YDV++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 33 - Query_33 - M_159 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 34 - Query_34 - M_160 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 35 - Query_35 - M_161 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 36 - Query_36 - M_162 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 37 - Query_37 - M_163 - 9 - - - 1 - gnl|BL_ORD_ID|1136 - 75040|Protein P|P03159.1|Hepatitis B virus|10407 - 1136 - 9 - - - 1 - 13.4678 - 23 - 8.42175 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 6 - 0 - 9 - FSDDGVLGP - YMDDVVLGA - + DD VLG - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 38 - Query_38 - M_164 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 39 - Query_39 - M_165 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 40 - Query_40 - M_166 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 41 - Query_41 - M_167 - 9 - - - 1 - gnl|BL_ORD_ID|233 - 16796|HBcAg|ABE97049.1|Hepatitis B virus|10407 - 233 - 10 - - - 1 - 13.4678 - 23 - 11.9953 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 6 - 0 - 9 - IPAGSMPTV - LPADFFPSV - +PA P+V - - - - - 2 - gnl|BL_ORD_ID|1933 - 180778|polyprotein|AFP27208.1|Dengue virus 4|11070 - 1933 - 10 - - - 1 - 13.0826 - 22 - 20.8706 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 6 - 0 - 8 - PAGSMPTV - PEGIIPTL - P G +PT+ - - - - - 3 - gnl|BL_ORD_ID|1948 - 180850|polyprotein|AFP27208.1|Dengue virus 4|11070 - 1948 - 10 - - - 1 - 13.0826 - 22 - 21.9749 - 2 - 9 - 3 - 10 - 0 - 0 - 4 - 6 - 0 - 8 - PAGSMPTV - PEGIIPTL - P G +PT+ - - - - - 4 - gnl|BL_ORD_ID|232 - 16795|precore/core protein|AAP57273.1|Hepatitis B virus|10407 - 232 - 10 - - - 1 - 12.6974 - 21 - 23.5358 - 1 - 9 - 2 - 10 - 0 - 0 - 3 - 6 - 0 - 9 - IPAGSMPTV - LPADFFPSI - +PA P++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 42 - Query_42 - M_168 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 43 - Query_43 - M_169 - 9 - - - 1 - gnl|BL_ORD_ID|1196 - 95281|polyprotein|ACE82433.1|Hepatitis C virus genotype 1|41856 - 1196 - 9 - - - 1 - 13.4678 - 23 - 8.87313 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - CLSGYC - CISGVC - C+SG C - - - - - 2 - gnl|BL_ORD_ID|784 - 52509|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 - 784 - 15 - - - 1 - 12.6974 - 21 - 26.5542 - 1 - 6 - 7 - 12 - 0 - 0 - 3 - 5 - 0 - 6 - CLSGYC - CINGVC - C++G C - - - - - 3 - gnl|BL_ORD_ID|66 - 4910|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 66 - 20 - - - 1 - 12.6974 - 21 - 32.3697 - 1 - 6 - 3 - 8 - 0 - 0 - 3 - 5 - 0 - 6 - CLSGYC - CINGVC - C++G C - - - - - 4 - gnl|BL_ORD_ID|1674 - 148619|unnamed protein product|BAA14233.1|Hepatitis C virus|11103 - 1674 - 45 - - - 1 - 12.3122 - 20 - 32.7965 - 1 - 6 - 36 - 41 - 0 - 0 - 3 - 5 - 0 - 6 - CLSGYC - CVNGVC - C++G C - - - - - 5 - gnl|BL_ORD_ID|91 - 6435|polyprotein|BAB18806.1|Hepatitis C virus|11103 - 91 - 9 - - - 1 - 12.6974 - 21 - 35.3877 - 1 - 6 - 1 - 6 - 0 - 0 - 3 - 5 - 0 - 6 - CLSGYC - CINGVC - C++G C - - - - - 6 - gnl|BL_ORD_ID|90 - 6433|Genome polyprotein|SRC279960|Hepatitis C virus subtype 1a|31646 - 90 - 9 - - - 1 - 12.6974 - 21 - 39.1808 - 1 - 6 - 1 - 6 - 0 - 0 - 3 - 5 - 0 - 6 - CLSGYC - CINGVC - C++G C - - - - - 7 - gnl|BL_ORD_ID|89 - 6432|polyprotein [Hepatitis C virus]|CAL46125.1|Hepatitis C virus (isolate H77)|63746 - 89 - 9 - - - 1 - 12.6974 - 21 - 39.8499 - 1 - 6 - 1 - 6 - 0 - 0 - 3 - 5 - 0 - 6 - CLSGYC - CINGLC - C++G C - - - - - 8 - gnl|BL_ORD_ID|65 - 4909|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 - 65 - 15 - - - 1 - 12.3122 - 20 - 39.8759 - 1 - 6 - 3 - 8 - 0 - 0 - 3 - 5 - 0 - 6 - CLSGYC - CINGVC - C++G C - - - - - 9 - gnl|BL_ORD_ID|1194 - 95279|polyprotein|BAG31965.1|Hepatitis C virus|11103 - 1194 - 9 - - - 1 - 12.3122 - 20 - 40.5299 - 1 - 6 - 1 - 6 - 0 - 0 - 3 - 5 - 0 - 6 - CLSGYC - CINGVC - C++G C - - - - - 10 - gnl|BL_ORD_ID|1193 - 95278|polyprotein|BAC67110.1|Hepatitis C virus|11103 - 1193 - 9 - - - 1 - 12.3122 - 20 - 41.221 - 1 - 6 - 1 - 6 - 0 - 0 - 3 - 5 - 0 - 6 - CLSGYC - CINGVC - C++G C - - - - - 11 - gnl|BL_ORD_ID|87 - 6430|polyprotein|BAB18810.1|Hepatitis C virus genotype 1|41856 - 87 - 9 - - - 1 - 12.3122 - 20 - 49.6079 - 1 - 6 - 1 - 6 - 0 - 0 - 3 - 5 - 0 - 6 - CLSGYC - CINGAC - C++G C - - - - - 12 - gnl|BL_ORD_ID|107 - 7292|polyprotein|AAA75355.1|Hepatitis C virus subtype 1b|31647 - 107 - 9 - - - 1 - 12.3122 - 20 - 55.769 - 1 - 6 - 1 - 6 - 0 - 0 - 3 - 5 - 0 - 6 - CLSGYC - CVNGVC - C++G C - - - - - 13 - gnl|BL_ORD_ID|1632 - 146246|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 - 1632 - 17 - - - 1 - 11.927 - 19 - 62.8517 - 1 - 6 - 5 - 10 - 0 - 0 - 3 - 5 - 0 - 6 - CLSGYC - CVNGVC - C++G C - - - - - 14 - gnl|BL_ORD_ID|1198 - 95298|Genome polyprotein|Q913V3.1|Hepatitis C virus (isolate 1)|11104 - 1198 - 9 - - - 1 - 11.927 - 19 - 76.3762 - 1 - 6 - 1 - 6 - 0 - 0 - 3 - 5 - 0 - 6 - CLSGYC - CVNGAC - C++G C - - - - - 15 - gnl|BL_ORD_ID|106 - 7291|neuramindase|AAT73327.1|Influenza A virus (A/Puerto Rico/8/1934(H1N1))|211044 - 106 - 9 - - - 1 - 11.927 - 19 - 91.4136 - 1 - 6 - 1 - 6 - 0 - 0 - 3 - 5 - 0 - 6 - CLSGYC - CVNGSC - C++G C - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 44 - Query_44 - M_170 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 45 - Query_45 - M_171 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 46 - Query_46 - M_172 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 47 - Query_47 - M_173 - 9 - - - 1 - gnl|BL_ORD_ID|2038 - 184453|polyprotein|AFP27207.1|Dengue virus 4|11070 - 2038 - 10 - - - 1 - 11.5418 - 18 - 178.729 - 1 - 9 - 2 - 10 - 0 - 0 - 3 - 5 - 0 - 9 - LIMALVWSL - LLMRTTWAF - L+M W+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 48 - Query_48 - M_174 - 9 - - - 1 - gnl|BL_ORD_ID|2038 - 184453|polyprotein|AFP27207.1|Dengue virus 4|11070 - 2038 - 10 - - - 1 - 11.5418 - 18 - 178.729 - 1 - 9 - 2 - 10 - 0 - 0 - 3 - 5 - 0 - 9 - LIMALVWSL - LLMRTTWAF - L+M W+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 49 - Query_49 - M_175 - 9 - - - 1 - gnl|BL_ORD_ID|2038 - 184453|polyprotein|AFP27207.1|Dengue virus 4|11070 - 2038 - 10 - - - 1 - 11.5418 - 18 - 178.729 - 1 - 9 - 2 - 10 - 0 - 0 - 3 - 5 - 0 - 9 - LIMALVWSL - LLMRTTWAF - L+M W+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 50 - Query_50 - M_176 - 9 - - - 1 - gnl|BL_ORD_ID|832 - 54820|polyprotein precursor|BAA02756.1|Hepatitis C virus|11103 - 832 - 9 - - - 1 - 15.3938 - 28 - 0.794531 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - VWSLPCGF - LWHYPCTF - +W PC F - - - - - 2 - gnl|BL_ORD_ID|1149 - 75636|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 1149 - 10 - - - 1 - 13.4678 - 23 - 9.90554 - 2 - 7 - 3 - 8 - 0 - 0 - 3 - 4 - 0 - 6 - VWSLPC - LWHYPC - +W PC - - - - - 3 - gnl|BL_ORD_ID|831 - 54819|JK3|CAA43789.1|Hepatitis C virus|11103 - 831 - 9 - - - 1 - 13.4678 - 23 - 11.5219 - 2 - 7 - 2 - 7 - 0 - 0 - 3 - 4 - 0 - 6 - VWSLPC - LWHYPC - +W PC - - - - - 4 - gnl|BL_ORD_ID|834 - 54824|polyprotein precursor|BAA01583.1|Hepatitis C virus|11103 - 834 - 9 - - - 1 - 13.4678 - 23 - 12.1399 - 2 - 7 - 2 - 7 - 0 - 0 - 3 - 4 - 0 - 6 - VWSLPC - LWHYPC - +W PC - - - - - 5 - gnl|BL_ORD_ID|833 - 54821|E2 protein|AAM33354.1|Hepatitis C virus subtype 1a|31646 - 833 - 9 - - - 1 - 13.4678 - 23 - 12.3531 - 2 - 7 - 2 - 7 - 0 - 0 - 3 - 4 - 0 - 6 - VWSLPC - LWHYPC - +W PC - - - - - 6 - gnl|BL_ORD_ID|835 - 54825|polyprotein|BAA03375.1|Hepatitis C virus|11103 - 835 - 9 - - - 1 - 13.4678 - 23 - 13.2439 - 2 - 7 - 2 - 7 - 0 - 0 - 3 - 4 - 0 - 6 - VWSLPC - LWHYPC - +W PC - - - - - 7 - gnl|BL_ORD_ID|1372 - 108277|IE62|AAP32859.1|Human alphaherpesvirus 3|10335 - 1372 - 9 - - - 1 - 12.6974 - 21 - 30.8766 - 2 - 6 - 2 - 6 - 0 - 0 - 3 - 5 - 0 - 5 - VWSLP - LWALP - +W+LP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 51 - Query_51 - M_177 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 52 - Query_52 - M_178 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 53 - Query_53 - M_179 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 54 - Query_54 - M_180 - 9 - - - 1 - gnl|BL_ORD_ID|419 - 25275|Glutamate decarboxylase 2|Q05329.1|Homo sapiens|9606 - 419 - 13 - - - 1 - 12.6974 - 21 - 35.1136 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 6 - 0 - 8 - VAFFSSHT - IAFTSEHS - +AF S H+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 55 - Query_55 - M_181 - 9 - - - 1 - gnl|BL_ORD_ID|419 - 25275|Glutamate decarboxylase 2|Q05329.1|Homo sapiens|9606 - 419 - 13 - - - 1 - 13.0826 - 22 - 13.9136 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 7 - 0 - 9 - VAFFSSHTY - IAFTSEHSH - +AF S H++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 56 - Query_56 - M_182 - 9 - - - 1 - gnl|BL_ORD_ID|419 - 25275|Glutamate decarboxylase 2|Q05329.1|Homo sapiens|9606 - 419 - 13 - - - 1 - 13.0826 - 22 - 13.9136 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 7 - 0 - 9 - VAFFSSHTY - IAFTSEHSH - +AF S H++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 57 - Query_57 - M_183 - 9 - - - 1 - gnl|BL_ORD_ID|419 - 25275|Glutamate decarboxylase 2|Q05329.1|Homo sapiens|9606 - 419 - 13 - - - 1 - 13.0826 - 22 - 13.9136 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 7 - 0 - 9 - VAFFSSHTY - IAFTSEHSH - +AF S H++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 58 - Query_58 - M_184 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 59 - Query_59 - M_185 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 60 - Query_60 - M_186 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 61 - Query_61 - M_187 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 62 - Query_62 - M_188 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 63 - Query_63 - M_189 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 64 - Query_64 - M_190 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 65 - Query_65 - M_191 - 9 - - - 1 - gnl|BL_ORD_ID|399 - 24457|polyprotein|BAA09072.1|Hepatitis C virus|11103 - 399 - 15 - - - 1 - 12.3122 - 20 - 44.6122 - 2 - 8 - 6 - 12 - 0 - 0 - 3 - 6 - 0 - 7 - YIIECIA - YIMACMS - YI+ C++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 66 - Query_66 - M_192 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 67 - Query_67 - M_193 - 9 - - - 1 - gnl|BL_ORD_ID|399 - 24457|polyprotein|BAA09072.1|Hepatitis C virus|11103 - 399 - 15 - - - 1 - 12.3122 - 20 - 45.3306 - 1 - 7 - 6 - 12 - 0 - 0 - 3 - 6 - 0 - 7 - YIIECIA - YIMACMS - YI+ C++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 68 - Query_68 - M_194 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 69 - Query_69 - M_195 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 70 - Query_70 - M_196 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 71 - Query_71 - M_197 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 72 - Query_72 - M_198 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 73 - Query_73 - M_199 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 74 - Query_74 - M_200 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 75 - Query_75 - M_201 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 76 - Query_76 - M_202 - 9 - - - 1 - gnl|BL_ORD_ID|579 - 36358|ELAV-like protein 1|Q15717.2|Homo sapiens|9606 - 579 - 9 - - - 1 - 11.5418 - 18 - 130.247 - 1 - 8 - 2 - 9 - 0 - 0 - 5 - 5 - 0 - 8 - GLGFYNDV - GYGFVNYV - G GF N V - - - - - 2 - gnl|BL_ORD_ID|578 - 36357|ELAV-like protein 4 (Paraneoplastic encephalomyelitis antigen HuD) (Hu-antigen D)|P26378.1|Homo sapiens|9606 - 578 - 9 - - - 1 - 11.1566 - 17 - 215.083 - 1 - 8 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - GLGFYNDV - GYGFVNYI - G GF N + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 77 - Query_77 - M_203 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 78 - Query_78 - M_204 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 79 - Query_79 - M_205 - 9 - - - 1 - gnl|BL_ORD_ID|984 - 64967|Circumsporozoite protein precursor|P08677.2|Plasmodium vivax strain Belem|31273 - 984 - 9 - - - 1 - 13.4678 - 23 - 9.68021 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 8 - 0 - 9 - AMDDLDTDM - TLNDLETDV - ++DL+TD+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 80 - Query_80 - M_206 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114432_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114432_1_T.fasta deleted file mode 100755 index b6881013..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114432_1_T.fasta +++ /dev/null @@ -1,198 +0,0 @@ ->M_207 -MITQFELQK ->M_208 -CTAMRVAAK ->M_209 -HFERLTRAL ->M_210 -RLKFGNKHK ->M_211 -ASQQGMAAL ->M_212 -LDYASQQGM ->M_213 -YASQQGMAA ->M_214 -GVRAGRLQL ->M_215 -VRAGRLQLF ->M_216 -LFIHHIQGL ->M_217 -FCSIYITLL ->M_218 -HHSPSTHVM ->M_219 -RSFWSHVVR ->M_220 -AEVEVADKL ->M_221 -KLLENLAKV ->M_222 -MAEAKRMKL ->M_223 -SMAEAKRMK ->M_224 -SYESCDAHF ->M_225 -ASFVPSMGK ->M_226 -FVPSMGKNL ->M_227 -IPASFVPSM ->M_228 -SVSIPASFV ->M_229 -HLGVPVTLR ->M_230 -RVQHLGVPV ->M_231 -NPNTGSVYM ->M_232 -VYMNSQQSL ->M_233 -VYMNSQQSL ->M_234 -EMAKFKVTI ->M_235 -KLFGYEMAK ->M_236 -MAKFKVTIK ->M_237 -HRTIPYLDL ->M_238 -IVWEHRQKL ->M_239 -GMVAPDVVK ->M_240 -HPGVSSQFL ->M_241 -SPRGGPPPL ->M_242 -IVHPLKPQM ->M_243 -KPQMNYQTA ->M_244 -AYCSYCYYF ->M_245 -NAYCSYCYY ->M_246 -SPAPERCMV ->M_247 -ALMDMYPHV ->M_248 -IGVDDRRRL ->M_249 -RRRLCILRM ->M_250 -HFQWILFFV ->M_251 -HVPGAVPNL ->M_252 -SLTGDVSPL ->M_253 -HMVERIQFV ->M_254 -HFERLTRAL ->M_255 -ASQQGMAAL ->M_256 -LDYASQQGM ->M_257 -YASQQGMAA ->M_258 -GVRAGRLQL ->M_259 -VRAGRLQLF ->M_260 -APAGGTASA ->M_261 -HHSPSTHVM ->M_262 -FGHITHPCM ->M_263 -RSFWSHVVR ->M_264 -AAAAAAAAT ->M_265 -VSSKSQKLL ->M_266 -YSLSPVSSK ->M_267 -AEVEVADKL ->M_268 -KLLENLAKV ->M_269 -MAEAKRMKL ->M_270 -SMAEAKRMK ->M_271 -YRWCGFPQL ->M_272 -YRWCGFPQL ->M_273 -SYESCDAHF ->M_274 -FLVGLWSHL ->M_275 -KPRFLVGLW ->M_276 -LVGLWSHLL ->M_277 -MPPYYVGPL ->M_278 -TALPTYPPY ->M_279 -FEGFPQSPL ->M_280 -NPNTGSVYM ->M_281 -VYMNSQQSL ->M_282 -VYMNSQQSL ->M_283 -KRQQFGSQF ->M_284 -DPFALFFMA ->M_285 -EYAADPFAL ->M_286 -YAADPFALF ->M_287 -HRTIPYLDL ->M_288 -IVWEHRQKL ->M_289 -HSVAIVSPF ->M_290 -RIGFVGLFH ->M_291 -HPGVSSQFL ->M_292 -IVHPLKPQM ->M_293 -KPQMNYQTA ->M_294 -AYCSYCYYF ->M_295 -NAYCSYCYY ->M_296 -SPAPERCMV ->M_297 -LTLAVYLSF ->M_298 -ALMDMYPHV ->M_299 -IGVDDRRRL ->M_300 -RRRLCILRM ->M_301 -DTAWDTLEL ->M_302 -TAWDTLELI ->M_303 -TAWDTLELI ->M_304 -MSVSQKLTL ->M_305 -HQRAHTGEK diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114432_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114432_1_T_iedb.xml deleted file mode 100755 index 12a5b419..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114432_1_T_iedb.xml +++ /dev/null @@ -1,3164 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_207 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_207 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_208 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_209 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_210 - 9 - - - 1 - gnl|BL_ORD_ID|829 - 54741|gag polyprotein|BAA00992.1|Human immunodeficiency virus 1|11676 - 829 - 9 - - - 1 - 12.3122 - 20 - 52.1643 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 6 - 0 - 9 - RLKFGNKHK - RLRPGGKKK - RL+ G K K - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 5 - Query_5 - M_211 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_212 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_213 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_214 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_215 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_216 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_217 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_218 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_219 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_220 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_221 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_222 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_223 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_224 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_225 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_226 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_227 - 9 - - - 1 - gnl|BL_ORD_ID|232 - 16795|precore/core protein|AAP57273.1|Hepatitis B virus|10407 - 232 - 10 - - - 1 - 15.3938 - 28 - 0.822133 - 1 - 9 - 2 - 10 - 0 - 0 - 5 - 7 - 0 - 9 - IPASFVPSM - LPADFFPSI - +PA F PS+ - - - - - 2 - gnl|BL_ORD_ID|233 - 16796|HBcAg|ABE97049.1|Hepatitis B virus|10407 - 233 - 10 - - - 1 - 15.0086 - 27 - 1.04324 - 1 - 9 - 2 - 10 - 0 - 0 - 5 - 7 - 0 - 9 - IPASFVPSM - LPADFFPSV - +PA F PS+ - - - - - 3 - gnl|BL_ORD_ID|566 - 35237|nonstructural protein 3|NP_722463.1|Dengue virus type 1 Hawaii|10000440 - 566 - 20 - - - 1 - 13.4678 - 23 - 10.3889 - 1 - 8 - 11 - 18 - 0 - 0 - 5 - 5 - 0 - 8 - IPASFVPS - IPALFEPE - IPA F P - - - - - 4 - gnl|BL_ORD_ID|993 - 65550|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 993 - 15 - - - 1 - 12.3122 - 20 - 50.6727 - 1 - 8 - 6 - 13 - 0 - 0 - 4 - 5 - 0 - 8 - IPASFVPS - IPSMFEPE - IP+ F P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 22 - Query_22 - M_228 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_229 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_230 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_231 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_232 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_233 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 28 - Query_28 - M_234 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 29 - Query_29 - M_235 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 30 - Query_30 - M_236 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 31 - Query_31 - M_237 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 32 - Query_32 - M_238 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 33 - Query_33 - M_239 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 34 - Query_34 - M_240 - 9 - - - 1 - gnl|BL_ORD_ID|1152 - 75718|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 1152 - 11 - - - 1 - 14.6234 - 26 - 2.31378 - 1 - 8 - 4 - 11 - 0 - 0 - 4 - 6 - 0 - 8 - HPGVSSQF - HPTFTSQY - HP +SQ+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 35 - Query_35 - M_241 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 36 - Query_36 - M_242 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 37 - Query_37 - M_243 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 38 - Query_38 - M_244 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 39 - Query_39 - M_245 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 40 - Query_40 - M_246 - 9 - - - 1 - gnl|BL_ORD_ID|859 - 56310|polyprotein|AGO67248.1|Dengue virus 2|11060 - 859 - 10 - - - 1 - 13.853 - 24 - 5.38895 - 4 - 8 - 5 - 9 - 0 - 0 - 4 - 4 - 0 - 5 - PERCM - PRRCM - P RCM - - - - - 2 - gnl|BL_ORD_ID|2076 - 185200|polyprotein|AGO67248.1|Dengue virus 2|11060 - 2076 - 10 - - - 1 - 13.853 - 24 - 6.19145 - 4 - 8 - 1 - 5 - 0 - 0 - 4 - 4 - 0 - 5 - PERCM - PRRCM - P RCM - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 41 - Query_41 - M_247 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 42 - Query_42 - M_248 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 43 - Query_43 - M_249 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 44 - Query_44 - M_250 - 9 - - - 1 - gnl|BL_ORD_ID|325 - 21041|Membrane glycoprotein|Q692E0|SARS coronavirus TJF|284672 - 325 - 9 - - - 1 - 11.927 - 19 - 104.062 - 2 - 9 - 2 - 9 - 0 - 0 - 3 - 5 - 0 - 8 - FQWILFFV - LMWLSYFV - W+ +FV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 45 - Query_45 - M_251 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 46 - Query_46 - M_252 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 47 - Query_47 - M_253 - 9 - - - 1 - gnl|BL_ORD_ID|1799 - 164551|envelope glycoprotein B|NP_044629.1|Herpes simplex virus (type 1 / strain 17)|10299 - 1799 - 9 - - - 1 - 11.5418 - 18 - 159.996 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 6 - 0 - 8 - MVERIQFV - MLEDHEFV - M+E +FV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 48 - Query_48 - M_254 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 49 - Query_49 - M_255 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 50 - Query_50 - M_256 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 51 - Query_51 - M_257 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 52 - Query_52 - M_258 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 53 - Query_53 - M_259 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 54 - Query_54 - M_260 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 55 - Query_55 - M_261 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 56 - Query_56 - M_262 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 57 - Query_57 - M_263 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 58 - Query_58 - M_264 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 59 - Query_59 - M_265 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 60 - Query_60 - M_266 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 61 - Query_61 - M_267 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 62 - Query_62 - M_268 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 63 - Query_63 - M_269 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 64 - Query_64 - M_270 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 65 - Query_65 - M_271 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 66 - Query_66 - M_272 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 67 - Query_67 - M_273 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 68 - Query_68 - M_274 - 9 - - - 1 - gnl|BL_ORD_ID|1114 - 73862|EBNA-1 protein|Q777E1|Human gammaherpesvirus 4|10376 - 1114 - 15 - - - 1 - 13.0826 - 22 - 17.2424 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 7 - 0 - 9 - FLVGLWSHL - FMVFLQTHI - F+V L +H+ - - - - - 2 - gnl|BL_ORD_ID|254 - 17110|EBNA-1 protein|Q777E1|Human gammaherpesvirus 4|10376 - 254 - 9 - - - 1 - 13.0826 - 22 - 19.071 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 7 - 0 - 9 - FLVGLWSHL - FMVFLQTHI - F+V L +H+ - - - - - 3 - gnl|BL_ORD_ID|623 - 37498|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 - 623 - 10 - - - 1 - 12.6974 - 21 - 25.2038 - 1 - 7 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - FLVGLWS - LLLGLWG - L+GLW - - - - - 4 - gnl|BL_ORD_ID|616 - 37351|trans-sialidase, putative|EAN81560.1|Trypanosoma cruzi|5693 - 616 - 10 - - - 1 - 12.6974 - 21 - 34.2302 - 2 - 6 - 1 - 5 - 0 - 0 - 4 - 5 - 0 - 5 - LVGLW - LLGLW - L+GLW - - - - - 5 - gnl|BL_ORD_ID|615 - 37350|trans-sialidase|XP_818394.1|Trypanosoma cruzi|5693 - 615 - 10 - - - 1 - 12.6974 - 21 - 34.2302 - 2 - 7 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - LVGLWS - LLGLWG - L+GLW - - - - - 6 - gnl|BL_ORD_ID|614 - 37347|Sialidase 85-1.1 precursor|P18269.2|Trypanosoma cruzi|5693 - 614 - 10 - - - 1 - 12.6974 - 21 - 34.2302 - 2 - 7 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - LVGLWS - LLGLWG - L+GLW - - - - - 7 - gnl|BL_ORD_ID|1253 - 98223|trans-sialidase, putative|EAN80725.1|Trypanosoma cruzi|5693 - 1253 - 9 - - - 1 - 12.6974 - 21 - 35.3877 - 2 - 7 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - LVGLWS - LLGLWG - L+GLW - - - - - 8 - gnl|BL_ORD_ID|918 - 59766|Genome polyprotein|P27958.3|Hepatitis C virus (isolate H)|11108 - 918 - 9 - - - 1 - 12.3122 - 20 - 46.3849 - 2 - 9 - 2 - 9 - 0 - 0 - 3 - 6 - 0 - 8 - LVGLWSHL - MVGNWAKV - +VG W+ + - - - - - 9 - gnl|BL_ORD_ID|919 - 59767|polyprotein|BAB18806.1|Hepatitis C virus subtype 1a|31646 - 919 - 10 - - - 1 - 12.3122 - 20 - 56.5271 - 2 - 9 - 2 - 9 - 0 - 0 - 3 - 6 - 0 - 8 - LVGLWSHL - MVGNWAKV - +VG W+ + - - - - - 10 - gnl|BL_ORD_ID|1686 - 149052|E1 protein|NP_751920.1|Hepatitis C virus (isolate H77)|63746 - 1686 - 18 - - - 1 - 11.927 - 19 - 66.2126 - 2 - 9 - 7 - 14 - 0 - 0 - 3 - 6 - 0 - 8 - LVGLWSHL - MVGNWAKV - +VG W+ + - - - - - 11 - gnl|BL_ORD_ID|321 - 21004|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 - 321 - 10 - - - 1 - 7.30463 - 7 - 12470.7 - 5 - 6 - 7 - 8 - 0 - 0 - 2 - 2 - 0 - 2 - LW - LW - LW - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 69 - Query_69 - M_275 - 9 - - - 1 - gnl|BL_ORD_ID|2086 - 185468|polyprotein|AGW21594.1|Dengue virus 1|11053 - 2086 - 10 - - - 1 - 14.2382 - 25 - 3.44317 - 1 - 8 - 1 - 8 - 0 - 0 - 5 - 6 - 0 - 8 - KPRFLVGL - RPMFAVGL - +P F VGL - - - - - 2 - gnl|BL_ORD_ID|2277 - 419037|polyprotein|AEF01538.1|Dengue virus 1|11053 - 2277 - 10 - - - 1 - 13.4678 - 23 - 9.90554 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 6 - 0 - 8 - KPRFLVGL - RPMFAVGI - +P F VG+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 70 - Query_70 - M_276 - 9 - - - 1 - gnl|BL_ORD_ID|919 - 59767|polyprotein|BAB18806.1|Hepatitis C virus subtype 1a|31646 - 919 - 10 - - - 1 - 13.4678 - 23 - 9.23902 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 7 - 0 - 9 - LVGLWSHLL - MVGNWAKVL - +VG W+ +L - - - - - 2 - gnl|BL_ORD_ID|1686 - 149052|E1 protein|NP_751920.1|Hepatitis C virus (isolate H77)|63746 - 1686 - 18 - - - 1 - 13.0826 - 22 - 12.6766 - 1 - 9 - 7 - 15 - 0 - 0 - 4 - 7 - 0 - 9 - LVGLWSHLL - MVGNWAKVL - +VG W+ +L - - - - - 3 - gnl|BL_ORD_ID|623 - 37498|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 - 623 - 10 - - - 1 - 12.3122 - 20 - 39.1729 - 1 - 6 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - LVGLWS - LLGLWG - L+GLW - - - - - 4 - gnl|BL_ORD_ID|615 - 37350|trans-sialidase|XP_818394.1|Trypanosoma cruzi|5693 - 615 - 10 - - - 1 - 12.3122 - 20 - 39.1729 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - LVGLWS - LLGLWG - L+GLW - - - - - 5 - gnl|BL_ORD_ID|614 - 37347|Sialidase 85-1.1 precursor|P18269.2|Trypanosoma cruzi|5693 - 614 - 10 - - - 1 - 12.3122 - 20 - 39.1729 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - LVGLWS - LLGLWG - L+GLW - - - - - 6 - gnl|BL_ORD_ID|616 - 37351|trans-sialidase, putative|EAN81560.1|Trypanosoma cruzi|5693 - 616 - 10 - - - 1 - 12.3122 - 20 - 39.8368 - 1 - 5 - 1 - 5 - 0 - 0 - 4 - 5 - 0 - 5 - LVGLW - LLGLW - L+GLW - - - - - 7 - gnl|BL_ORD_ID|1253 - 98223|trans-sialidase, putative|EAN80725.1|Trypanosoma cruzi|5693 - 1253 - 9 - - - 1 - 12.3122 - 20 - 41.221 - 1 - 6 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - LVGLWS - LLGLWG - L+GLW - - - - - 8 - gnl|BL_ORD_ID|918 - 59766|Genome polyprotein|P27958.3|Hepatitis C virus (isolate H)|11108 - 918 - 9 - - - 1 - 12.3122 - 20 - 47.1713 - 1 - 8 - 2 - 9 - 0 - 0 - 3 - 6 - 0 - 8 - LVGLWSHL - MVGNWAKV - +VG W+ + - - - - - 9 - gnl|BL_ORD_ID|321 - 21004|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 - 321 - 10 - - - 1 - 7.68983 - 8 - 12187.2 - 4 - 5 - 7 - 8 - 0 - 0 - 2 - 2 - 0 - 2 - LW - LW - LW - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 71 - Query_71 - M_277 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 72 - Query_72 - M_278 - 9 - - - 1 - gnl|BL_ORD_ID|471 - 28594|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 - 471 - 20 - - - 1 - 12.3122 - 20 - 38.3641 - 2 - 8 - 2 - 8 - 0 - 0 - 4 - 6 - 0 - 7 - ALPTYPP - SLPSYYP - +LP+Y P - - - - - 2 - gnl|BL_ORD_ID|776 - 51643|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 - 776 - 20 - - - 1 - 12.3122 - 20 - 53.6149 - 2 - 8 - 12 - 18 - 0 - 0 - 4 - 6 - 0 - 7 - ALPTYPP - SLPSYYP - +LP+Y P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 73 - Query_73 - M_279 - 9 - - - 1 - gnl|BL_ORD_ID|273 - 18390|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 273 - 20 - - - 1 - 14.2382 - 25 - 3.85699 - 4 - 9 - 3 - 8 - 0 - 0 - 4 - 6 - 0 - 6 - FPQSPL - FPRAPL - FP++PL - - - - - 2 - gnl|BL_ORD_ID|946 - 62355|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 946 - 20 - - - 1 - 13.853 - 24 - 4.4203 - 4 - 9 - 10 - 15 - 0 - 0 - 4 - 6 - 0 - 6 - FPQSPL - FPRAPL - FP++PL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 74 - Query_74 - M_280 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 75 - Query_75 - M_281 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 76 - Query_76 - M_282 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 77 - Query_77 - M_283 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 78 - Query_78 - M_284 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 79 - Query_79 - M_285 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 80 - Query_80 - M_286 - 9 - - - 1 - gnl|BL_ORD_ID|1587 - 141484|capsid maturation protease|NP_044627.1|Human alphaherpesvirus 1|10298 - 1587 - 9 - - - 1 - 10.3862 - 15 - 583.315 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 5 - 0 - 9 - YAADPFALF - YVAGFLALY - Y A AL+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 81 - Query_81 - M_287 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 82 - Query_82 - M_288 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 83 - Query_83 - M_289 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 84 - Query_84 - M_290 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 85 - Query_85 - M_291 - 9 - - - 1 - gnl|BL_ORD_ID|1152 - 75718|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 1152 - 11 - - - 1 - 14.6234 - 26 - 2.31378 - 1 - 8 - 4 - 11 - 0 - 0 - 4 - 6 - 0 - 8 - HPGVSSQF - HPTFTSQY - HP +SQ+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 86 - Query_86 - M_292 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 87 - Query_87 - M_293 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 88 - Query_88 - M_294 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 89 - Query_89 - M_295 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 90 - Query_90 - M_296 - 9 - - - 1 - gnl|BL_ORD_ID|859 - 56310|polyprotein|AGO67248.1|Dengue virus 2|11060 - 859 - 10 - - - 1 - 13.853 - 24 - 5.38895 - 4 - 8 - 5 - 9 - 0 - 0 - 4 - 4 - 0 - 5 - PERCM - PRRCM - P RCM - - - - - 2 - gnl|BL_ORD_ID|2076 - 185200|polyprotein|AGO67248.1|Dengue virus 2|11060 - 2076 - 10 - - - 1 - 13.853 - 24 - 6.19145 - 4 - 8 - 1 - 5 - 0 - 0 - 4 - 4 - 0 - 5 - PERCM - PRRCM - P RCM - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 91 - Query_91 - M_297 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 92 - Query_92 - M_298 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 93 - Query_93 - M_299 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 94 - Query_94 - M_300 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 95 - Query_95 - M_301 - 9 - - - 1 - gnl|BL_ORD_ID|1924 - 180726|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1924 - 15 - - - 1 - 15.0086 - 27 - 0.917715 - 1 - 5 - 7 - 11 - 0 - 0 - 5 - 5 - 0 - 5 - DTAWD - DTAWD - DTAWD - - - - - 2 - gnl|BL_ORD_ID|439 - 27061|envelope glycoprotein|ABU89742.1|Dengue virus 2 Thailand/16681/84|31634 - 439 - 10 - - - 1 - 15.0086 - 27 - 1.37261 - 1 - 5 - 4 - 8 - 0 - 0 - 5 - 5 - 0 - 5 - DTAWD - DTAWD - DTAWD - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 96 - Query_96 - M_302 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 97 - Query_97 - M_303 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 98 - Query_98 - M_304 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 99 - Query_99 - M_305 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114445_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114445_1_T.fasta deleted file mode 100755 index 4d08ad1b..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114445_1_T.fasta +++ /dev/null @@ -1,40 +0,0 @@ ->M_306 -AVATITQAL ->M_307 -TTVNGNTAL ->M_308 -EYYSQTTGL ->M_309 -YYSQTTGLC ->M_310 -CPSEPNTPM ->M_311 -TPMARTFDW ->M_312 -GHYEVRASL ->M_313 -HYEVRASLL ->M_314 -MYWRRSQCC ->M_315 -DYPNAYTTW ->M_316 -RYSDYPNAY ->M_317 -AADLPILTW ->M_318 -WLLAADLPI ->M_319 -IPPEANITI ->M_320 -TVHNLCHIL ->M_321 -FFVEKRHAF ->M_322 -LPLTRSMSI ->M_323 -AAAAATSAL ->M_324 -SIYAYHVEW ->M_325 -AYPQYVIEY diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114445_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114445_1_T_iedb.xml deleted file mode 100755 index 59c917ba..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114445_1_T_iedb.xml +++ /dev/null @@ -1,866 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_306 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_306 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_307 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_308 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_309 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_310 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_311 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_312 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_313 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_314 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_315 - 9 - - - 1 - gnl|BL_ORD_ID|2124 - 186550|polyprotein|AFY10039.1|Dengue virus 4|11070 - 2124 - 10 - - - 1 - 14.2382 - 25 - 4.23087 - 1 - 9 - 2 - 10 - 0 - 0 - 5 - 5 - 0 - 9 - DYPNAYTTW - DQENPYRTW - D N Y TW - - - - - 2 - gnl|BL_ORD_ID|1174 - 79351|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 1174 - 17 - - - 1 - 13.4678 - 23 - 10.1282 - 3 - 9 - 1 - 7 - 0 - 0 - 4 - 4 - 0 - 7 - PNAYTTW - QNLYTLW - N YT W - - - - - 3 - gnl|BL_ORD_ID|1097 - 72563|polyprotein|AAB70696.1|Dengue virus type 1 Hawaii|10000440 - 1097 - 20 - - - 1 - 13.0826 - 22 - 14.6415 - 1 - 9 - 4 - 12 - 0 - 0 - 5 - 5 - 0 - 9 - DYPNAYTTW - DEDNPYKTW - D N Y TW - - - - - 4 - gnl|BL_ORD_ID|2189 - 190533|nucleocapsid protein|AAP49024.1|SARS coronavirus|227859 - 2189 - 15 - - - 1 - 12.3122 - 20 - 57.5015 - 3 - 9 - 7 - 13 - 0 - 0 - 3 - 4 - 0 - 7 - PNAYTTW - PNNIASW - PN +W - - - - - 5 - gnl|BL_ORD_ID|850 - 55683|nucleocapsid protein|ABI96968.1|SARS coronavirus|227859 - 850 - 15 - - - 1 - 11.5418 - 18 - 120.288 - 3 - 9 - 7 - 13 - 0 - 0 - 3 - 4 - 0 - 7 - PNAYTTW - PNNTASW - PN +W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 11 - Query_11 - M_316 - 9 - - - 1 - gnl|BL_ORD_ID|878 - 57703|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 - 878 - 15 - - - 1 - 13.4678 - 23 - 7.23267 - 3 - 7 - 1 - 5 - 0 - 0 - 4 - 5 - 0 - 5 - SDYPN - SEYPN - S+YPN - - - - - 2 - gnl|BL_ORD_ID|559 - 34598|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 559 - 15 - - - 1 - 12.6974 - 21 - 22.89 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 6 - 0 - 9 - RYSDYPNAY - KYSPFRNGY - +YS + N Y - - - - - 3 - gnl|BL_ORD_ID|657 - 38974|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 657 - 11 - - - 1 - 12.6974 - 21 - 27.7331 - 1 - 6 - 6 - 11 - 0 - 0 - 3 - 6 - 0 - 6 - RYSDYP - QYSEHP - +YS++P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 12 - Query_12 - M_317 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_318 - 9 - - - 1 - gnl|BL_ORD_ID|1438 - 120093|unnamed protein product|CAA33016.1|Rubella virus|11041 - 1438 - 21 - - - 1 - 11.927 - 19 - 61.829 - 1 - 8 - 4 - 11 - 0 - 0 - 3 - 4 - 0 - 8 - WLLAADLP - WCVEHDRP - W + D P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 14 - Query_14 - M_319 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_320 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_321 - 9 - - - 1 - gnl|BL_ORD_ID|2009 - 183781|polyprotein|AGO67248.1|Dengue virus 2|11060 - 2009 - 10 - - - 1 - 14.2382 - 25 - 4.15863 - 3 - 9 - 4 - 10 - 0 - 0 - 4 - 5 - 0 - 7 - VEKRHAF - LEKRHVL - +EKRH - - - - - 2 - gnl|BL_ORD_ID|2055 - 184755|polyprotein|AGO67248.1|Dengue virus 2|11060 - 2055 - 9 - - - 1 - 13.853 - 24 - 4.75595 - 3 - 9 - 3 - 9 - 0 - 0 - 4 - 5 - 0 - 7 - VEKRHAF - LEKRHVL - +EKRH - - - - - 3 - gnl|BL_ORD_ID|2031 - 184337|polyprotein|AGO67248.1|Dengue virus 2|11060 - 2031 - 10 - - - 1 - 13.853 - 24 - 5.38895 - 3 - 9 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - VEKRHAF - LEKRHVL - +EKRH - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 17 - Query_17 - M_322 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_323 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_324 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_325 - 9 - - - 1 - gnl|BL_ORD_ID|608 - 37254|||| - 608 - 9 - - - 1 - 13.853 - 24 - 7.58732 - 1 - 6 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - AYPQYV - GYPRYV - YP+YV - - - - - 2 - gnl|BL_ORD_ID|1170 - 79294|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 1170 - 15 - - - 1 - 12.3122 - 20 - 46.8002 - 1 - 6 - 4 - 9 - 0 - 0 - 4 - 4 - 0 - 6 - AYPQYV - GYPVYV - YP YV - - - - - 3 - gnl|BL_ORD_ID|389 - 23807|tax|AAG48731.1|Human T-lymphotropic virus 2|11909 - 389 - 23 - - - 1 - 12.3122 - 20 - 48.9251 - 1 - 7 - 12 - 18 - 0 - 0 - 4 - 4 - 0 - 7 - AYPQYVI - GYPVYVF - YP YV - - - - - 4 - gnl|BL_ORD_ID|572 - 35845|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 572 - 9 - - - 1 - 12.3122 - 20 - 61.624 - 1 - 6 - 3 - 8 - 0 - 0 - 4 - 4 - 0 - 6 - AYPQYV - GYPVYV - YP YV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114843_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114843_1_T.fasta deleted file mode 100755 index da28f85e..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114843_1_T.fasta +++ /dev/null @@ -1,10 +0,0 @@ ->M_326 -FSSKPSSIY ->M_327 -SIYGGLVLI ->M_328 -SAESGAQLL ->M_329 -GIICLDYKL ->M_330 -FEDIGDEDL diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114843_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114843_1_T_iedb.xml deleted file mode 100755 index 0b436b58..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_114843_1_T_iedb.xml +++ /dev/null @@ -1,150 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_326 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_326 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_327 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_328 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_329 - 9 - - - 1 - gnl|BL_ORD_ID|2102 - 185978|polyprotein|CDF77361.1|Dengue virus 3|11069 - 2102 - 10 - - - 1 - 12.3122 - 20 - 44.0514 - 1 - 5 - 3 - 7 - 0 - 0 - 3 - 5 - 0 - 5 - GIICL - GVLCL - G++CL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 5 - Query_5 - M_330 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116261_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116261_1_T.fasta deleted file mode 100755 index 8d96174b..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116261_1_T.fasta +++ /dev/null @@ -1,64 +0,0 @@ ->M_331 -IRVEESMHL ->M_332 -AMEKLLSGK ->M_333 -ARTGHLPAM ->M_334 -GHLPAMEKL ->M_335 -QVYHWVCEK ->M_336 -HRWNRFTMI ->M_337 -THRWNRFTM ->M_338 -ITSGLEVIY ->M_339 -ARRFWGKIM ->M_340 -RFWGKIMAK ->M_341 -TYEEATVYI ->M_342 -EHAAALWAL ->M_343 -LVLMNWTKK ->M_344 -FTDTAAESA ->M_345 -NIEDSASFY ->M_346 -SRSDAAKHL ->M_347 -LRWRHCQRL ->M_348 -WRHCQRLDV ->M_349 -VRLGPVKSI ->M_350 -SMQAHIKAL ->M_351 -ESFKQTDFY ->M_352 -QTDFYSMAL ->M_353 -LPWMRLLLL ->M_354 -MRLLLLLLV ->M_355 -PRLPWMRLL ->M_356 -WMRLLLLLL ->M_357 -AIALHRLSL ->M_358 -MRGHDWRML ->M_359 -QMRGHDWRM ->M_360 -HLETHNTDK ->M_361 -CSKLKHRDL ->M_362 -VVGAVGVGK diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116261_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116261_1_T_iedb.xml deleted file mode 100755 index 4883d2fe..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116261_1_T_iedb.xml +++ /dev/null @@ -1,1019 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_331 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_331 - 9 - - - 1 - gnl|BL_ORD_ID|665 - 40158|polyprotein|AAA45534.1|Hepatitis C virus|11103 - 665 - 15 - - - 1 - 13.4678 - 23 - 7.74893 - 2 - 9 - 3 - 10 - 0 - 0 - 4 - 6 - 0 - 8 - RVEESMHL - RVEAQLHV - RVE +H+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 2 - Query_2 - M_332 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_333 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_334 - 9 - - - 1 - gnl|BL_ORD_ID|1271 - 101673|gag protein|ABO73990.1|Human immunodeficiency virus 1|11676 - 1271 - 9 - - - 1 - 13.853 - 24 - 6.83656 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 6 - 0 - 9 - GHLPAMEKL - GHQAAMQML - GH AM+ L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 5 - Query_5 - M_335 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_336 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_337 - 9 - - - 1 - gnl|BL_ORD_ID|1297 - 103389|unnamed protein product [Hepatitis C virus]|BAA14035.1|Hepatitis C virus|11103 - 1297 - 20 - - - 1 - 14.2382 - 25 - 3.035 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 5 - 0 - 9 - THRWNRFTM - THPITKFVM - TH +F M - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 8 - Query_8 - M_338 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_339 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_340 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_341 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_342 - 9 - - - 1 - gnl|BL_ORD_ID|1994 - 183594|polyprotein|AGT63075.1|Dengue virus 1|11053 - 1994 - 10 - - - 1 - 12.6974 - 21 - 30.9217 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 5 - 0 - 8 - HAAALWAL - HPASAWTL - H A+ W L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 13 - Query_13 - M_343 - 9 - - - 1 - gnl|BL_ORD_ID|692 - 42152|polyprotein|AAY82055.1|Hepatitis C virus (isolate H77)|63746 - 692 - 9 - - - 1 - 13.0826 - 22 - 13.4763 - 2 - 8 - 1 - 7 - 0 - 0 - 3 - 6 - 0 - 7 - VLMNWTK - MMMNWSP - ++MNW+ - - - - - 2 - gnl|BL_ORD_ID|1096 - 72322|polyprotein|AAA86907.1|Hepatitis C virus|11103 - 1096 - 15 - - - 1 - 13.0826 - 22 - 15.8531 - 2 - 8 - 3 - 9 - 0 - 0 - 3 - 6 - 0 - 7 - VLMNWTK - MMMNWSP - ++MNW+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 14 - Query_14 - M_344 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_345 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_346 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_347 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_348 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_349 - 9 - - - 1 - gnl|BL_ORD_ID|1651 - 146528|NS3/4A protein|CAM56207.1|Hepatitis C virus|11103 - 1651 - 9 - - - 1 - 15.779 - 29 - 0.508093 - 2 - 8 - 1 - 7 - 0 - 0 - 5 - 7 - 0 - 7 - RLGPVKS - RLGPVQN - RLGPV++ - - - - - 2 - gnl|BL_ORD_ID|2291 - 419325|Genome polyprotein|O92532.3|Hepatitis C virus|11103 - 2291 - 9 - - - 1 - 15.779 - 29 - 0.523878 - 2 - 8 - 1 - 7 - 0 - 0 - 5 - 7 - 0 - 7 - RLGPVKS - RLGPVQN - RLGPV++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 20 - Query_20 - M_350 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_351 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 22 - Query_22 - M_352 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_353 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_354 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_355 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_356 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_357 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 28 - Query_28 - M_358 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 29 - Query_29 - M_359 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 30 - Query_30 - M_360 - 9 - - - 1 - gnl|BL_ORD_ID|1224 - 97111|polyprotein|ABR25251.1|Hepatitis C virus (isolate H77)|63746 - 1224 - 18 - - - 1 - 13.4678 - 23 - 12.4678 - 3 - 9 - 8 - 14 - 0 - 0 - 4 - 5 - 0 - 7 - ETHNTDK - ECHSTDA - E H+TD - - - - - 2 - gnl|BL_ORD_ID|1337 - 107901|Genome polyprotein|P26664.3|Hepatitis C virus|11103 - 1337 - 10 - - - 1 - 13.0826 - 22 - 15.8345 - 3 - 8 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - ETHNTD - ECHSTD - E H+TD - - - - - 3 - gnl|BL_ORD_ID|1320 - 107780|Genome polyprotein|P26664.3|Hepatitis C virus|11103 - 1320 - 10 - - - 1 - 12.6974 - 21 - 30.4011 - 3 - 8 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - ETHNTD - ECHSTD - E H+TD - - - - - 4 - gnl|BL_ORD_ID|1321 - 107781|polyprotein|AAF65953.1|Hepatitis C virus|11103 - 1321 - 10 - - - 1 - 12.6974 - 21 - 35.4066 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - ETHNTDK - ECHSTDS - E H+TD - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 31 - Query_31 - M_361 - 9 - - - 1 - gnl|BL_ORD_ID|470 - 28508|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 470 - 15 - - - 1 - 11.5418 - 18 - 125.819 - 1 - 7 - 6 - 12 - 0 - 0 - 4 - 4 - 0 - 7 - CSKLKHR - CSARLHR - CS HR - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 32 - Query_32 - M_362 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116397_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116397_1_T.fasta deleted file mode 100755 index d653256b..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116397_1_T.fasta +++ /dev/null @@ -1,44 +0,0 @@ ->M_363 -AHPDGSWTF ->M_364 -WGRERGARV ->M_365 -KADIPRDSY ->M_366 -NVLQSSVPV ->M_367 -IITESGEVI ->M_368 -WVYDAIITE ->M_369 -FPPNILDDI ->M_370 -MASQRPLQF ->M_371 -DMHVAVKIV ->M_372 -FARPASPSR ->M_373 -IVFEVFGHH ->M_374 -TTAVLTATF ->M_375 -MAAAVVARL ->M_376 -FSLPPSRKK ->M_377 -LPMCWAMEV ->M_378 -LTYSCLDNK ->M_379 -LLNSGGDII ->M_380 -DIYCITDFV ->M_381 -FVEELADTV ->M_382 -TISCTSLKK ->M_383 -VTISCTSLK ->M_384 -IIIKCQLPK diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116397_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116397_1_T_iedb.xml deleted file mode 100755 index db2f2c3b..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116397_1_T_iedb.xml +++ /dev/null @@ -1,655 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_363 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_363 - 9 - - - 1 - gnl|BL_ORD_ID|1994 - 183594|polyprotein|AGT63075.1|Dengue virus 1|11053 - 1994 - 10 - - - 1 - 15.3938 - 28 - 0.809281 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 5 - 0 - 8 - HPDGSWTF - HPASAWTL - HP +WT - - - - - 2 - gnl|BL_ORD_ID|431 - 26273|nucleocapsid protein|ABI96968.1|SARS coronavirus|227859 - 431 - 15 - - - 1 - 13.4678 - 23 - 11.689 - 3 - 7 - 7 - 11 - 0 - 0 - 3 - 4 - 0 - 5 - PDGSW - PSGTW - P G+W - - - - - 3 - gnl|BL_ORD_ID|2187 - 190494|nucleocapsid protein|ABI96968.1|SARS coronavirus|227859 - 2187 - 10 - - - 1 - 13.0826 - 22 - 14.0252 - 3 - 7 - 5 - 9 - 0 - 0 - 3 - 4 - 0 - 5 - PDGSW - PSGTW - P G+W - - - - - 4 - gnl|BL_ORD_ID|1931 - 180758|Nonstructural protein NS5|NP_739590.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1931 - 15 - - - 1 - 13.0826 - 22 - 16.3955 - 2 - 9 - 8 - 15 - 0 - 0 - 3 - 5 - 0 - 8 - HPDGSWTF - HPYKTWAY - HP +W + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 2 - Query_2 - M_364 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_365 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_366 - 9 - - - 1 - gnl|BL_ORD_ID|1259 - 98308|trans-sialidase, putative|EAN80840.1|Trypanosoma cruzi|5693 - 1259 - 9 - - - 1 - 12.3122 - 20 - 52.1643 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 7 - 0 - 9 - NVLQSSVPV - NVMLVTLPV - NV+ ++PV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 5 - Query_5 - M_367 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_368 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_369 - 9 - - - 1 - gnl|BL_ORD_ID|1917 - 180682|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1917 - 9 - - - 1 - 12.6974 - 21 - 28.3449 - 3 - 9 - 2 - 8 - 0 - 0 - 5 - 5 - 0 - 7 - PNILDDI - PEIEDDI - P I DDI - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 8 - Query_8 - M_370 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_371 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_372 - 9 - - - 1 - gnl|BL_ORD_ID|803 - 53405|||| - 803 - 15 - - - 1 - 13.0826 - 22 - 16.6732 - 4 - 9 - 3 - 8 - 0 - 0 - 4 - 5 - 0 - 6 - PASPSR - PAKPAR - PA P+R - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 11 - Query_11 - M_373 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_374 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_375 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_376 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_377 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_378 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_379 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_380 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_381 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_382 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_383 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 22 - Query_22 - M_384 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116644_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116644_1_T.fasta deleted file mode 100755 index ca704e0b..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116644_1_T.fasta +++ /dev/null @@ -1,60 +0,0 @@ ->M_385 -RYGAGQQNL ->M_386 -TPYAACPAI ->M_387 -SPFNTTFPF ->M_388 -QVARRVQEL ->M_389 -HREARGRAL ->M_390 -AIFGPSNTY ->M_391 -DLFQFPKAY ->M_392 -LPEDPKCEF ->M_393 -SFQPKAAVF ->M_394 -PPSETGGIF ->M_395 -NAGEMVIEY ->M_396 -APTSSDYEF ->M_397 -LFCGLPFSI ->M_398 -VPVASSEAS ->M_399 -DPSPGIMAF ->M_400 -LTYSLLTPL ->M_401 -TYSLLTPLL ->M_402 -CYVAICNPF ->M_403 -LAAMAIDCY ->M_404 -MAIDCYVAI ->M_405 -YFFLGNLAF ->M_406 -FPVEDRRGV ->M_407 -FAQLINNKM ->M_408 -RVASVVVSF ->M_409 -RVASVVVSF ->M_410 -FYLRYFEK* ->M_411 -FFSSNLPTY ->M_412 -FSSNLPTYY ->M_413 -NPYKAPMAE ->M_414 -AFLQKAHLI diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116644_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116644_1_T_iedb.xml deleted file mode 100755 index d99c60f6..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116644_1_T_iedb.xml +++ /dev/null @@ -1,1173 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_385 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_385 - 9 - - - 1 - gnl|BL_ORD_ID|79 - 5783|Nucleoprotein|P03418.1|Human respiratory syncytial virus A2|11259 - 79 - 14 - - - 1 - 14.6234 - 26 - 1.47122 - 2 - 9 - 2 - 9 - 0 - 0 - 6 - 6 - 0 - 8 - YGAGQQNL - YGAGQVML - YGAGQ L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 2 - Query_2 - M_386 - 9 - - - 1 - gnl|BL_ORD_ID|1397 - 110401|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1397 - 25 - - - 1 - 13.853 - 24 - 4.88128 - 1 - 6 - 20 - 25 - 0 - 0 - 4 - 4 - 0 - 6 - TPYAAC - NPYAVC - PYA C - - - - - 2 - gnl|BL_ORD_ID|1387 - 110227|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1387 - 33 - - - 1 - 13.853 - 24 - 5.78904 - 2 - 6 - 13 - 17 - 0 - 0 - 4 - 4 - 0 - 5 - PYAAC - PYAVC - PYA C - - - - - 3 - gnl|BL_ORD_ID|1400 - 110467|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1400 - 25 - - - 1 - 13.853 - 24 - 5.83535 - 1 - 6 - 5 - 10 - 0 - 0 - 4 - 4 - 0 - 6 - TPYAAC - NPYAVC - PYA C - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 3 - Query_3 - M_387 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_388 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_389 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_390 - 9 - - - 1 - gnl|BL_ORD_ID|1205 - 96123|Genome polyprotein|P26664.3|Hepatitis C virus (isolate H77)|63746 - 1205 - 9 - - - 1 - 14.2382 - 25 - 3.80667 - 1 - 5 - 1 - 5 - 0 - 0 - 4 - 5 - 0 - 5 - AIFGP - AVFGP - A+FGP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 7 - Query_7 - M_391 - 9 - - - 1 - gnl|BL_ORD_ID|273 - 18390|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 273 - 20 - - - 1 - 13.0826 - 22 - 14.1742 - 3 - 8 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - FQFPKA - FYFPRA - F FP+A - - - - - 2 - gnl|BL_ORD_ID|946 - 62355|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 946 - 20 - - - 1 - 13.0826 - 22 - 20.1922 - 3 - 8 - 8 - 13 - 0 - 0 - 4 - 5 - 0 - 6 - FQFPKA - FYFPRA - F FP+A - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 8 - Query_8 - M_392 - 9 - - - 1 - gnl|BL_ORD_ID|1179 - 79628|E1 protein|BAA19893.1|Rubella virus|11041 - 1179 - 21 - - - 1 - 12.6974 - 21 - 24.4562 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 4 - 0 - 7 - PEDPKCE - PTDVSCE - P D CE - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 9 - Query_9 - M_393 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_394 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_395 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_396 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_397 - 9 - - - 1 - gnl|BL_ORD_ID|2182 - 190409|polymerase|AAD16253.1|Hepatitis B virus|10407 - 2182 - 15 - - - 1 - 16.5494 - 31 - 0.211832 - 2 - 8 - 8 - 14 - 0 - 0 - 5 - 6 - 0 - 7 - FCGLPFS - FCGSPYS - FCG P+S - - - - - 2 - gnl|BL_ORD_ID|390 - 23864|envelope glycoprotein(gp21, gp46) - human T-cell lymphotropic virus type 1|A45714|Human T-lymphotropic virus 1|11908 - 390 - 9 - - - 1 - 14.2382 - 25 - 3.37936 - 3 - 7 - 5 - 9 - 0 - 0 - 4 - 4 - 0 - 5 - CGLPF - CGFPF - CG PF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 14 - Query_14 - M_398 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_399 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_400 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_401 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_402 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_403 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_404 - 9 - - - 1 - gnl|BL_ORD_ID|2292 - 419366|polyprotein|BAA00792.1|Hepatitis C virus|11103 - 2292 - 9 - - - 1 - 14.2382 - 25 - 2.66858 - 3 - 9 - 3 - 9 - 0 - 0 - 5 - 6 - 0 - 7 - IDCYVAI - IDCNVAV - IDC VA+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 21 - Query_21 - M_405 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 22 - Query_22 - M_406 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_407 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_408 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_409 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_410 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_411 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 28 - Query_28 - M_412 - 9 - - - 1 - gnl|BL_ORD_ID|471 - 28594|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 - 471 - 20 - - - 1 - 13.4678 - 23 - 8.80594 - 4 - 9 - 2 - 7 - 0 - 0 - 4 - 6 - 0 - 6 - NLPTYY - SLPSYY - +LP+YY - - - - - 2 - gnl|BL_ORD_ID|1971 - 182926|polyprotein|AFP27208.1|Dengue virus 4|11070 - 1971 - 9 - - - 1 - 13.4678 - 23 - 9.18751 - 3 - 8 - 3 - 8 - 0 - 0 - 4 - 6 - 0 - 6 - SNLPTY - ASLPTY - ++LPTY - - - - - 3 - gnl|BL_ORD_ID|2100 - 185881|polyprotein|AFP27208.1|Dengue virus 4|11070 - 2100 - 10 - - - 1 - 13.4678 - 23 - 9.73455 - 3 - 8 - 4 - 9 - 0 - 0 - 4 - 6 - 0 - 6 - SNLPTY - ASLPTY - ++LPTY - - - - - 4 - gnl|BL_ORD_ID|776 - 51643|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 - 776 - 20 - - - 1 - 13.4678 - 23 - 10.5613 - 5 - 9 - 13 - 17 - 0 - 0 - 4 - 5 - 0 - 5 - LPTYY - LPSYY - LP+YY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 29 - Query_29 - M_413 - 9 - - - 1 - gnl|BL_ORD_ID|2141 - 187163|Gag polyprotein|P88150|Human immunodeficiency virus 1|11676 - 2141 - 11 - - - 1 - 11.5418 - 18 - 130.32 - 1 - 7 - 4 - 10 - 0 - 0 - 4 - 4 - 0 - 7 - NPYKAPM - NPEVIPM - NP PM - - - - - 2 - gnl|BL_ORD_ID|2139 - 187158|Gag protein|Q1KW74|Human immunodeficiency virus 1|11676 - 2139 - 11 - - - 1 - 11.5418 - 18 - 156.929 - 1 - 7 - 4 - 10 - 0 - 0 - 4 - 4 - 0 - 7 - NPYKAPM - NPEIIPM - NP PM - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 30 - Query_30 - M_414 - 9 - - - 1 - gnl|BL_ORD_ID|2055 - 184755|polyprotein|AGO67248.1|Dengue virus 2|11060 - 2055 - 9 - - - 1 - 11.927 - 19 - 104.062 - 3 - 9 - 3 - 9 - 0 - 0 - 3 - 6 - 0 - 7 - LQKAHLI - LEKRHVL - L+K H++ - - - - - 2 - gnl|BL_ORD_ID|2031 - 184337|polyprotein|AGO67248.1|Dengue virus 2|11060 - 2031 - 10 - - - 1 - 11.927 - 19 - 104.808 - 3 - 9 - 1 - 7 - 0 - 0 - 3 - 6 - 0 - 7 - LQKAHLI - LEKRHVL - L+K H++ - - - - - 3 - gnl|BL_ORD_ID|2009 - 183781|polyprotein|AGO67248.1|Dengue virus 2|11060 - 2009 - 10 - - - 1 - 11.927 - 19 - 108.205 - 3 - 9 - 4 - 10 - 0 - 0 - 3 - 6 - 0 - 7 - LQKAHLI - LEKRHVL - L+K H++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116732_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116732_1_T.fasta deleted file mode 100755 index ab50cfd0..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116732_1_T.fasta +++ /dev/null @@ -1,56 +0,0 @@ ->M_415 -FQGYLKDPV ->M_416 -SEVLGYWAF ->M_417 -SEVLGYWAF ->M_418 -RRFGWLQTA ->M_419 -GHEEKITFI ->M_420 -EESIAVGTM ->M_421 -EESIAVGTM ->M_422 -FRYLGKCNI ->M_423 -FEVGGAALF ->M_424 -FEVGGAALF ->M_425 -GMCVLEMAV ->M_426 -VLEMAVLEI ->M_427 -FLMVSRDCL ->M_428 -SRDCLRTVL ->M_429 -VSRDCLRTV ->M_430 -ALREFKFRV ->M_431 -REFKFRVSA ->M_432 -REFKFRVSA ->M_433 -YEALREFKF ->M_434 -NQMDKLAAF ->M_435 -YRMSPSNQM ->M_436 -KVISYPVAL ->M_437 -TERTKVISY ->M_438 -LHLRRKEIM ->M_439 -QTSCHVFMV ->M_440 -GEAGAGGTA ->M_441 -EHMPNNSRL ->M_442 -PRKPRSQNF diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116732_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116732_1_T_iedb.xml deleted file mode 100755 index 5aa795f9..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116732_1_T_iedb.xml +++ /dev/null @@ -1,832 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_415 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_415 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_416 - 9 - - - 1 - gnl|BL_ORD_ID|1253 - 98223|trans-sialidase, putative|EAN80725.1|Trypanosoma cruzi|5693 - 1253 - 9 - - - 1 - 13.853 - 24 - 7.58732 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - VLGYWAF - LLGLWGF - +LG W F - - - - - 2 - gnl|BL_ORD_ID|616 - 37351|trans-sialidase, putative|EAN81560.1|Trypanosoma cruzi|5693 - 616 - 10 - - - 1 - 13.4678 - 23 - 7.89871 - 3 - 9 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - VLGYWAF - LLGLWVF - +LG W F - - - - - 3 - gnl|BL_ORD_ID|614 - 37347|Sialidase 85-1.1 precursor|P18269.2|Trypanosoma cruzi|5693 - 614 - 10 - - - 1 - 11.927 - 19 - 77.1759 - 3 - 9 - 1 - 7 - 0 - 0 - 3 - 4 - 0 - 7 - VLGYWAF - LLGLWGL - +LG W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 3 - Query_3 - M_417 - 9 - - - 1 - gnl|BL_ORD_ID|1253 - 98223|trans-sialidase, putative|EAN80725.1|Trypanosoma cruzi|5693 - 1253 - 9 - - - 1 - 13.853 - 24 - 7.58732 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - VLGYWAF - LLGLWGF - +LG W F - - - - - 2 - gnl|BL_ORD_ID|616 - 37351|trans-sialidase, putative|EAN81560.1|Trypanosoma cruzi|5693 - 616 - 10 - - - 1 - 13.4678 - 23 - 7.89871 - 3 - 9 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - VLGYWAF - LLGLWVF - +LG W F - - - - - 3 - gnl|BL_ORD_ID|614 - 37347|Sialidase 85-1.1 precursor|P18269.2|Trypanosoma cruzi|5693 - 614 - 10 - - - 1 - 11.927 - 19 - 77.1759 - 3 - 9 - 1 - 7 - 0 - 0 - 3 - 4 - 0 - 7 - VLGYWAF - LLGLWGL - +LG W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 4 - Query_4 - M_418 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_419 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_420 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_421 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_422 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_423 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_424 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_425 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_426 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_427 - 9 - - - 1 - gnl|BL_ORD_ID|1492 - 136837|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 - 1492 - 11 - - - 1 - 11.5418 - 18 - 156.929 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 5 - 0 - 9 - FLMVSRDCL - FLLALLSCL - FL+ CL - - - - - 2 - gnl|BL_ORD_ID|428 - 26111|polyprotein|BAD73987.1|Hepatitis C virus subtype 1b|31647 - 428 - 10 - - - 1 - 11.5418 - 18 - 170.632 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 5 - 0 - 9 - FLMVSRDCL - FLLALLSCL - FL+ CL - - - - - 3 - gnl|BL_ORD_ID|225 - 16706|structural protein|BAA00705.1|Hepatitis C virus|11103 - 225 - 9 - - - 1 - 11.5418 - 18 - 187.089 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 5 - 0 - 9 - FLMVSRDCL - FLLALLSCL - FL+ CL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 14 - Query_14 - M_428 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_429 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_430 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_431 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_432 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_433 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_434 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_435 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 22 - Query_22 - M_436 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_437 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_438 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_439 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_440 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_441 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 28 - Query_28 - M_442 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116846_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116846_1_T.fasta deleted file mode 100755 index c4edc2b0..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116846_1_T.fasta +++ /dev/null @@ -1,56 +0,0 @@ ->M_443 -RQWPRLSHK ->M_444 -ISLAYLVKK ->M_445 -TISLAYLVK ->M_446 -MFLWTVAVI ->M_447 -TVAVIPILF ->M_448 -KIRQLKKKK ->M_449 -NEKTTPSPA ->M_450 -NENATPSPA ->M_451 -RERTANENA ->M_452 -CYLQIFATR ->M_453 -LPPSLQGAV ->M_454 -RVARSHCQR ->M_455 -VPSEPSSSV ->M_456 -EEWCSLWAG ->M_457 -WEEWCSLWA ->M_458 -RLPSYMVEK ->M_459 -SYMVEKREF ->M_460 -GENFCTAVK ->M_461 -MEGYMKAKV ->M_462 -CPLPRPPPI ->M_463 -AEEAGYPLS ->M_464 -EEAGYPLSC ->M_465 -GVYLLFALR ->M_466 -VYLLFALRL ->M_467 -QEASNKHAE ->M_468 -SEYSSSLGR ->M_469 -RESGSFLST ->M_470 -LYQLHNLVV diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116846_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116846_1_T_iedb.xml deleted file mode 100755 index d3bf813a..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_116846_1_T_iedb.xml +++ /dev/null @@ -1,882 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_443 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_443 - 9 - - - 1 - gnl|BL_ORD_ID|1173 - 79337|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 1173 - 15 - - - 1 - 13.853 - 24 - 5.77703 - 2 - 8 - 4 - 10 - 0 - 0 - 4 - 4 - 0 - 7 - QWPRLSH - TWPLLPH - WP L H - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 2 - Query_2 - M_444 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_445 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_446 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_447 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_448 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_449 - 9 - - - 1 - gnl|BL_ORD_ID|2288 - 419298|RNA-dependent RNA polymerase|ACH97782.1|Hepatitis C virus|11103 - 2288 - 9 - - - 1 - 11.927 - 19 - 76.3762 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 4 - 0 - 6 - NEKTTP - NSKRTP - N K TP - - - - - 2 - gnl|BL_ORD_ID|1598 - 142244|polyprotein|ACJ37184.1|Hepatitis C virus subtype 1a|31646 - 1598 - 9 - - - 1 - 11.927 - 19 - 84.261 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 4 - 0 - 6 - NEKTTP - NSKKTP - N K TP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 8 - Query_8 - M_450 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_451 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_452 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_453 - 9 - - - 1 - gnl|BL_ORD_ID|746 - 48836|EBNA-1 protein|Q777E1|Human gammaherpesvirus 4|10376 - 746 - 15 - - - 1 - 13.4678 - 23 - 8.59146 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 6 - 0 - 8 - PPSLQGAV - PPMVEGAA - PP ++GA - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 12 - Query_12 - M_454 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_455 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_456 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_457 - 9 - - - 1 - gnl|BL_ORD_ID|2051 - 184702|non-structural protein 1|AGM49312.1|Dengue virus|12637 - 2051 - 9 - - - 1 - 10.7714 - 16 - 469.42 - 1 - 8 - 2 - 9 - 0 - 0 - 3 - 5 - 0 - 8 - WEEWCSLW - WPKTHTLW - W + +LW - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 16 - Query_16 - M_458 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_459 - 9 - - - 1 - gnl|BL_ORD_ID|1799 - 164551|envelope glycoprotein B|NP_044629.1|Herpes simplex virus (type 1 / strain 17)|10299 - 1799 - 9 - - - 1 - 12.6974 - 21 - 23.4633 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - MVEKREF - MLEDHEF - M+E EF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 18 - Query_18 - M_460 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_461 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_462 - 9 - - - 1 - gnl|BL_ORD_ID|1508 - 139406|polyprotein|ACT37184.1|Hepatitis C virus|11103 - 1508 - 10 - - - 1 - 12.3122 - 20 - 39.8368 - 3 - 8 - 3 - 8 - 0 - 0 - 5 - 5 - 0 - 6 - LPRPPP - LPRPGP - LPRP P - - - - - 2 - gnl|BL_ORD_ID|1438 - 120093|unnamed protein product|CAA33016.1|Rubella virus|11041 - 1438 - 21 - - - 1 - 11.927 - 19 - 68.5496 - 5 - 8 - 10 - 13 - 0 - 0 - 4 - 4 - 0 - 4 - RPPP - RPPP - RPPP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 21 - Query_21 - M_463 - 9 - - - 1 - gnl|BL_ORD_ID|2258 - 288104|nef protein|ACR27130.1|Human immunodeficiency virus 1|11676 - 2258 - 18 - - - 1 - 13.0826 - 22 - 13.7716 - 3 - 9 - 1 - 7 - 0 - 0 - 3 - 5 - 0 - 7 - EAGYPLS - EVGFPVR - E G+P+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 22 - Query_22 - M_464 - 9 - - - 1 - gnl|BL_ORD_ID|2258 - 288104|nef protein|ACR27130.1|Human immunodeficiency virus 1|11676 - 2258 - 18 - - - 1 - 13.0826 - 22 - 14.4713 - 2 - 8 - 1 - 7 - 0 - 0 - 3 - 5 - 0 - 7 - EAGYPLS - EVGFPVR - E G+P+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 23 - Query_23 - M_465 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_466 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_467 - 9 - - - 1 - gnl|BL_ORD_ID|53 - 3935|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis|1773 - 53 - 20 - - - 1 - 14.2382 - 25 - 3.6022 - 1 - 7 - 9 - 15 - 0 - 0 - 5 - 6 - 0 - 7 - QEASNKH - QEAANKQ - QEA+NK - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 26 - Query_26 - M_468 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_469 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 28 - Query_28 - M_470 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_118562_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_118562_1_T.fasta deleted file mode 100755 index babdc234..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_118562_1_T.fasta +++ /dev/null @@ -1,2712 +0,0 @@ ->M_471 -YAAPQLHSI ->M_472 -HLHDHYGPY ->M_473 -FAEDGACTV ->M_474 -HVIGTIGHF ->M_475 -FADDEHSMV ->M_476 -YANERPKSL ->M_477 -FACHFTVFV ->M_478 -NALDYICTV ->M_479 -LAYQELPTV ->M_480 -FVMEHSNIV ->M_481 -VAFCTMNVI ->M_482 -FTIRAIQVY ->M_483 -MAISVVKHI ->M_484 -RALEKLNHV ->M_485 -FADMERHHI ->M_486 -FANRRKEEV ->M_487 -LAIDSASPV ->M_488 -RALGPGHTV ->M_489 -FAKVLIRTY ->M_490 -SSDDNDAFY ->M_491 -YPKGRPSHI ->M_492 -WALPKTYTI ->M_493 -LARHWRVHI ->M_494 -FSYSASSEI ->M_495 -FSFFFVNIF ->M_496 -YSFDGMWKV ->M_497 -DSIHQVGMY ->M_498 -MTYDLASVV ->M_499 -LAFPVPLYY ->M_500 -YAALAMGTL ->M_501 -YLFRELATI ->M_502 -YMDLMGFSY ->M_503 -FAISHEGHM ->M_504 -FSSPRLRPI ->M_505 -FVYLHLNMV ->M_506 -MANNPDVMI ->M_507 -AALPAAQTV ->M_508 -FAWKNMDFL ->M_509 -FAAQGPTVF ->M_510 -LALSNLPTV ->M_511 -FTLEFLVCI ->M_512 -FSVDFPRIY ->M_513 -FTIFWTVYY ->M_514 -MADPNQCVI ->M_515 -RAFWAGSVV ->M_516 -YHFDAIRTF ->M_517 -FAKGWLLKL ->M_518 -NAQNMTITV ->M_519 -RALNRVHVL ->M_520 -MAPELISHL ->M_521 -KAFYHPRLI ->M_522 -LAFVIVLLV ->M_523 -CTAVVLLVY ->M_524 -FTEFCDSCY ->M_525 -LAREPVNEL ->M_526 -YTRKRTQSI ->M_527 -FAPSCANSL ->M_528 -KVYDLVHSV ->M_529 -QAPPLMGTI ->M_530 -QAFRRSISV ->M_531 -FVLDHSRLV ->M_532 -FIKRHIAPI ->M_533 -YSQPFYTSY ->M_534 -FAQDVDRMF ->M_535 -QAPEFLQTL ->M_536 -LSDISRSCY ->M_537 -NAYARVLRF ->M_538 -FANFFNTFL ->M_539 -FIYDAVGNM ->M_540 -LARECGSPL ->M_541 -WHGPARPSL ->M_542 -HVMFMVAFY ->M_543 -MAITSMNPV ->M_544 -TAVEFIMAI ->M_545 -QAYGGPRYL ->M_546 -FTIRAIQVY ->M_547 -YLDYVSISY ->M_548 -SAYMHHSKI ->M_549 -YLMEFGQLL ->M_550 -KAEELKETV ->M_551 -FALGVGTAL ->M_552 -LVFPNSDHV ->M_553 -FTLQNPSAV ->M_554 -EIVDQQGHM ->M_555 -FTIFWTVYY ->M_556 -FPNSCLSTL ->M_557 -YSISDWTSI ->M_558 -FTACYIRIV ->M_559 -FEFDHIRNF ->M_560 -YTPDELHAM ->M_561 -FVHPATRPL ->M_562 -KALRITNVY ->M_563 -QARDQGSPV ->M_564 -FIYDAVGNM ->M_565 -EAFPEDVAV ->M_566 -YATADSSSL ->M_567 -RAREHSDTF ->M_568 -IAIQLITHM ->M_569 -MAFENNAGL ->M_570 -FGHENRVSI ->M_571 -NATTIVTTV ->M_572 -VTFPGINLM ->M_573 -DAYPRQYSL ->M_574 -YIQEGFLAV ->M_575 -FATTACHTL ->M_576 -RANQCFAFV ->M_577 -MTQPVWSTI ->M_578 -FTEEGFCAI ->M_579 -FADHPQAPF ->M_580 -VAMGSAALV ->M_581 -TAKDYRVYV ->M_582 -EAEEWVVSY ->M_583 -FTLPLMDQV ->M_584 -MQMPCTIKI ->M_585 -YRYFCRVPV ->M_586 -WAHAWPSPY ->M_587 -IAIISVLVI ->M_588 -MASCPFAKV ->M_589 -NHDRFHYLL ->M_590 -FTIFWTVYY ->M_591 -VASQPAHVV ->M_592 -EAFNCESKM ->M_593 -FSSEVTVAL ->M_594 -ETIKQLQEL ->M_595 -YFMDPMVPL ->M_596 -NVYHVGMHI ->M_597 -AAMEGRLPV ->M_598 -NHDDDDVEI ->M_599 -NASVNVSHL ->M_600 -EALDAGAIY ->M_601 -YGRDDWEVI ->M_602 -VALDKDALV ->M_603 -LPFSLGKHV ->M_604 -MANNPCSRY ->M_605 -YEEPNTATF ->M_606 -MALYHCVAI ->M_607 -YTLAPGVPL ->M_608 -KIHPFFETI ->M_609 -NMDFLIAEY ->M_610 -LCIPWTNPV ->M_611 -SAQEHLLFV ->M_612 -QSVHPVVTV ->M_613 -YVASDIQYM ->M_614 -FHMRQVNIV ->M_615 -LAKHSTSAV ->M_616 -FSHQPKEKV ->M_617 -YLYIPALAV ->M_618 -VALFMAITI ->M_619 -VAFYGLGAV ->M_620 -EVDPIGNLY ->M_621 -WALSIHVSV ->M_622 -ITYPSQAPV ->M_623 -CIALWSLAY ->M_624 -FLFYVMTEV ->M_625 -HAEQDSTTV ->M_626 -DTNDNVPEF ->M_627 -NSYGSRRTL ->M_628 -NARCLIVHL ->M_629 -FWYRNCHHV ->M_630 -DADPSTPHL ->M_631 -DSYIHVTYI ->M_632 -DVFDALDLM ->M_633 -FSMDETGQM ->M_634 -RTFNKPESV ->M_635 -YSLQEMEVL ->M_636 -QTVMFMATM ->M_637 -VTIDGIRFI ->M_638 -RALSHPQSL ->M_639 -TAAGFWLMV ->M_640 -FMEELGECV ->M_641 -YLESNPGTI ->M_642 -VPSNFVEHV ->M_643 -FTEELRRTF ->M_644 -YGRSRGITV ->M_645 -FSMACNTPL ->M_646 -QAADEPQLL ->M_647 -YEFALQRIV ->M_648 -TAAPTSASV ->M_649 -LACRKAREI ->M_650 -FIEPLNDTI ->M_651 -SALRAITRV ->M_652 -RAAPKAMVL ->M_653 -VADEGLNNL ->M_654 -LSNDECKTI ->M_655 -NAWAVMNHF ->M_656 -VASNAWAVM ->M_657 -LSRNLIRTI ->M_658 -HSKEEIKVI ->M_659 -DSELNFNEY ->M_660 -DAAERECHL ->M_661 -ISYTEVPTY ->M_662 -IASDHVVDM ->M_663 -IAILICTMI ->M_664 -MAKTGRFHI ->M_665 -EVMEKVLPL ->M_666 -FENNAGLPV ->M_667 -FLHEMVAAM ->M_668 -QAEPKKKPV ->M_669 -YVLHSKEEI ->M_670 -FFFHNPKPL ->M_671 -FHWNWIIVL ->M_672 -YTMGIIFVL ->M_673 -YVGKDIESV ->M_674 -YQHYFRLLV ->M_675 -MSNSMINTM ->M_676 -FSMLSRVLI ->M_677 -FVDYPGDPV ->M_678 -STAPLYSGM ->M_679 -DTVQLNVKY ->M_680 -SAYMAATLL ->M_681 -QAWNFLRAM ->M_682 -CAFGAMCAV ->M_683 -IMEEEFSTI ->M_684 -HAANVTQAM ->M_685 -MAKQIKTKV ->M_686 -KAKGIYNSI ->M_687 -HAPVHFLVI ->M_688 -EVLQSMQRF ->M_689 -YVASDIQYM ->M_690 -YAAMDLSCL ->M_691 -TPMTCSNTI ->M_692 -EAPPGRVTF ->M_693 -DTHSGAGKF ->M_694 -YKYRYFCRV ->M_695 -LSDPHLTAV ->M_696 -WAGLGGRHV ->M_697 -QHTGTSVVL ->M_698 -STFCGTLEY ->M_699 -TMYRCGPLI ->M_700 -WHNQCSGHL ->M_701 -FPLRNRPFY ->M_702 -YVGPAQLSV ->M_703 -VAQHLATTY ->M_704 -LVYPRFLYL ->M_705 -FSREEMHNM ->M_706 -YYPPGVVFY ->M_707 -YLMSFFRLL ->M_708 -RVFPLRGKI ->M_709 -YPLPVANGM ->M_710 -RAVCFSMEI ->M_711 -QALPLDHHL ->M_712 -FIEPHARFY ->M_713 -FFYCIYASL ->M_714 -CHDDYLVML ->M_715 -KALFWTVAM ->M_716 -EYYEPPHRI ->M_717 -PTSPMPYTY ->M_718 -EAVEARGAI ->M_719 -NVVRLVATI ->M_720 -YLKNSMIAV ->M_721 -LQAEIVETM ->M_722 -FHHKSNFLL ->M_723 -KPIPAFEMV ->M_724 -FLVDSNLSV ->M_725 -FIDRQLTMV ->M_726 -YSASSEIII ->M_727 -YTPDELHAM ->M_728 -FFYLDYVSI ->M_729 -YIAPMMEKL ->M_730 -EAFDRTETH ->M_731 -SIVDVSIMY ->M_732 -IPYTTVLHL ->M_733 -EVFRHKLAM ->M_734 -VMDRWNETV ->M_735 -LLLDHGVHV ->M_736 -VIFNVVRLV ->M_737 -LAIKVTPSV ->M_738 -LTDRQPLMH ->M_739 -KPLPFNREV ->M_740 -LNFGDITTV ->M_741 -QAIDSTFYL ->M_742 -LALNKGRAY ->M_743 -IARQVVTAM ->M_744 -GAFAFGAVF ->M_745 -KSFPFQSLL ->M_746 -RAGGSSVVI ->M_747 -DTIPWYLRL ->M_748 -MAVDGKPEY ->M_749 -YLQDVVMQV ->M_750 -FMVRNYEFL ->M_751 -YMAGSDTTY ->M_752 -VVYVLMTSV ->M_753 -MPAERNGAI ->M_754 -WPLQPVDHI ->M_755 -MLDPHGHLI ->M_756 -FISNSLNIL ->M_757 -RADGDLTLI ->M_758 -YQEEMIQCY ->M_759 -FILDCHPKY ->M_760 -GAYVYPLPV ->M_761 -FKEAWKHTI ->M_762 -LAGVKMVMI ->M_763 -DAKQRIRLL ->M_764 -LYYPPGVVF ->M_765 -RASEDDRVL ->M_766 -SALEYLLPL ->M_767 -AAVEPERTL ->M_768 -GTDCLLLAF ->M_769 -FVQLPVPII ->M_770 -RIYPDRHRI ->M_771 -KVDKNISHI ->M_772 -RHSQWDHGL ->M_773 -MLYSRDHSV ->M_774 -AARPLSRMV ->M_775 -HAQVCSLYI ->M_776 -YSQPFYTSY ->M_777 -MSDFQYLVV ->M_778 -SANARCLIV ->M_779 -SAIAIVQIL ->M_780 -WMFYHFDAI ->M_781 -YSKVIKCVV ->M_782 -AARARGNKV ->M_783 -TAYERLYLW ->M_784 -TTASGVWAF ->M_785 -KVREEVVTM ->M_786 -MYYRVRDTM ->M_787 -YVDRLLQHF ->M_788 -PAIARPQAI ->M_789 -YLLRAGVHL ->M_790 -LVTPHMAEV ->M_791 -EHVSDDDLL ->M_792 -SFYHLVSTV ->M_793 -FSAGNEANV ->M_794 -KPGDRVVLV ->M_795 -YSRGSSRCI ->M_796 -YSTCVLVVL ->M_797 -YSTHQTFMV ->M_798 -WSLDGKYIV ->M_799 -HAWRDLSSM ->M_800 -FASSLWETT ->M_801 -FDYPSLFCI ->M_802 -KAPPLTDVL ->M_803 -DVFDALDLM ->M_804 -ALYCRLATV ->M_805 -MVYLQIGGF ->M_806 -EPFSGTASV ->M_807 -ETMDELELL ->M_808 -SMLNWFSPV ->M_809 -NMLNLTHTY ->M_810 -HSFNPEAQV ->M_811 -SAYGSSGEL ->M_812 -FSIPWAHAW ->M_813 -MASSAQEHL ->M_814 -RHSREMALL ->M_815 -WVLHHMGGM ->M_816 -VADSDRQLV ->M_817 -IAAAWALSF ->M_818 -KAESTPEIV ->M_819 -LHLGHMFSL ->M_820 -QRINLPHLL ->M_821 -YALMRHRHT ->M_822 -RLYPLANSL ->M_823 -DHFSHASSI ->M_824 -ISMEKGYNI ->M_825 -FLHEMVAAM ->M_826 -YVALEAQAI ->M_827 -YLMTRTLPM ->M_828 -QTFPQVSEL ->M_829 -YPESIKAPV ->M_830 -VHSKTSQLL ->M_831 -TSSDRMTSV ->M_832 -QMAERALYY ->M_833 -LASPFATTA ->M_834 -AAYTSYTPY ->M_835 -VSCRPVVYV ->M_836 -RTYHGRLAY ->M_837 -LARHSAAFL ->M_838 -RSEALPVSY ->M_839 -ETKPFGLVV ->M_840 -DVKNFWQGM ->M_841 -FAELKSARM ->M_842 -YMKPRLRTT ->M_843 -STFCGTLEY ->M_844 -HAATGPGEV ->M_845 -PSQNRFLTY ->M_846 -YISAWLDSL ->M_847 -VPFPPKEPL ->M_848 -KSHELVMYI ->M_849 -LMLGRTNTL ->M_850 -VARHTFSML ->M_851 -LAIFMPPTY ->M_852 -WAVVTMTAV ->M_853 -FPRASQSLV ->M_854 -YDFLCLSLV ->M_855 -NKFPGDSMV ->M_856 -FSLLATVIL ->M_857 -SSSDNRNFI ->M_858 -KSRNWLKSI ->M_859 -QALNLQVVL ->M_860 -FPVLLLDTI ->M_861 -VTDFHNHSV ->M_862 -LSDSMPLWM ->M_863 -QSTKVNMLY ->M_864 -MANHLGVGV ->M_865 -HMDVEESQY ->M_866 -LADPIEKEL ->M_867 -MAITILVAL ->M_868 -YRDNKMTRI ->M_869 -FQMAERALY ->M_870 -RINENTGIV ->M_871 -EAGEESTSV ->M_872 -RGMPPPPTV ->M_873 -RLFRMFVHV ->M_874 -FLTDMAKQI ->M_875 -ISMQFLSSL ->M_876 -HTDTNNLGI ->M_877 -LALAIYTLL ->M_878 -LAVCAFTVL ->M_879 -AAAPNLRAL ->M_880 -LVDSNLSVV ->M_881 -VSSVQGITY ->M_882 -HLMKQISSF ->M_883 -EARGAIRGF ->M_884 -LVSTSNHAY ->M_885 -IAPRRWLLL ->M_886 -RMAERRQEV ->M_887 -YVVATTKLM ->M_888 -FQDDFSPRF ->M_889 -IGFNGNQIV ->M_890 -KMFTCSKFV ->M_891 -VAEVCPREV ->M_892 -WAPLPGQML ->M_893 -DAQQLATAI ->M_894 -ILLNGDATV ->M_895 -TIYDEDVLV ->M_896 -WVKEDMGIV ->M_897 -RKYGSTSSI ->M_898 -MTDAQQLAT ->M_899 -GFDQYRTLL ->M_900 -NASGATAPL ->M_901 -FFPEMGTKI ->M_902 -NVHSSGKPI ->M_903 -AALVGAEVV ->M_904 -DHFSHASSI ->M_905 -RAMGERLLL ->M_906 -KIYDGKDKM ->M_907 -WASGNERSL ->M_908 -LATVRSHHM ->M_909 -LRDHGSFLL ->M_910 -TALETSAPF ->M_911 -HTFSMLSRV ->M_912 -KAFHGSSGL ->M_913 -LAKKPGCVF ->M_914 -IPNPQLGPV ->M_915 -QQHDGAFLI ->M_916 -AAFFYLDYV ->M_917 -FFPEMGTKI ->M_918 -SQWDHGLSI ->M_919 -MSCRKIAHL ->M_920 -MGFTVLTTV ->M_921 -NLEVLDCRY ->M_922 -LAQAVRAVL ->M_923 -FMQTRYNKL ->M_924 -LTHTGACPY ->M_925 -KAFSDRFSL ->M_926 -FLRDCSPRL ->M_927 -DIFTTLKMY ->M_928 -RAPPEAIAL ->M_929 -STQDTPVTV ->M_930 -QASSDWAAV ->M_931 -FTRGIQTLF ->M_932 -YRALNRVHV ->M_933 -YEARLLKHM ->M_934 -MELNSVNVM ->M_935 -TAARLRHKV ->M_936 -YAYFLDNVS ->M_937 -TVLENLAVL ->M_938 -HSFTHKQHL ->M_939 -NMEELILAI ->M_940 -IAPHRNEKL ->M_941 -MMNDIVKEF ->M_942 -FSVPLHIFL ->M_943 -TVMGRITTL ->M_944 -FAKYWEENF ->M_945 -VSDLLVLLL ->M_946 -FLHVGDLVI ->M_947 -EAFAHEARF ->M_948 -SSLGKTQTV ->M_949 -LVLIGISHV ->M_950 -FYFQVPFIY ->M_951 -WSFAVAICI ->M_952 -QHMIQQQAL ->M_953 -FPEGYGTQV ->M_954 -KPYGRNKPF ->M_955 -HGFNATYHV ->M_956 -YIRTRNEFV ->M_957 -YPEVFGPPL ->M_958 -MVACGGTVY ->M_959 -APSEHAQMV ->M_960 -TRTFVEFIL ->M_961 -LLSEVLLHY ->M_962 -IQVGTGVTV ->M_963 -LTLAFTVML ->M_964 -HVGDLVIVV ->M_965 -MTREELNAL ->M_966 -VAVQESARI ->M_967 -VPSPLFSIV ->M_968 -KAGGGSNEV ->M_969 -YMLIIVSIF ->M_970 -VAPHAPVHF ->M_971 -TPFHLASAV ->M_972 -SARDCKDPY ->M_973 -FMATMPPAV ->M_974 -TMVACGGTV ->M_975 -NSDHVMFMV ->M_976 -FMKNYFKDV ->M_977 -LNVEDPVTV ->M_978 -FIPINGCPI ->M_979 -YTSYFGYKM ->M_980 -WSPHPLQIV ->M_981 -YTTITPQII ->M_982 -CSFYRTHTL ->M_983 -NAAKNQVAM ->M_984 -FETDGRRFL ->M_985 -SVEINDIMY ->M_986 -DPAPRPSLL ->M_987 -QAVTEVEAV ->M_988 -TAFQKGYGI ->M_989 -ICFPVLVAL ->M_990 -NHVPVNHFW ->M_991 -DMNDHAPEV ->M_992 -SPLPPPEQI ->M_993 -LRLDGSVVI ->M_994 -HACSHLRQM ->M_995 -FPSSQGSLY ->M_996 -FNRDDCSVL ->M_997 -TSFPQKVHL ->M_998 -EAFAHEARF ->M_999 -DAKSHELVM ->M_1000 -TEYRALNRV ->M_1001 -KTIWHTAEY ->M_1002 -KAMLEEQLI ->M_1003 -DTSDGLAVL ->M_1004 -LEFGKPSTL ->M_1005 -TLLEFFITL ->M_1006 -FTKRQRKAM ->M_1007 -FCLSTENSI ->M_1008 -FQGFSVQLI ->M_1009 -RVAPGYYTL ->M_1010 -FYQDMMNDI ->M_1011 -CLYDSVLML ->M_1012 -YTCVVSNKL ->M_1013 -PAEEPTNEL ->M_1014 -QVYSWLLCL ->M_1015 -PANESFGHL ->M_1016 -SPFAAAAAV ->M_1017 -DVVHHLLSV ->M_1018 -MFYPERTAL ->M_1019 -VSDPACSSI ->M_1020 -WAKVRTAEF ->M_1021 -AALRHERAV ->M_1022 -YVVATTKLM ->M_1023 -RMLLDPNTV ->M_1024 -YYDYMKPRL ->M_1025 -FPRHCVSWM ->M_1026 -YLPPDPQPF ->M_1027 -HPATRPLHV ->M_1028 -MVTGILLYM ->M_1029 -KPISYMAII ->M_1030 -DSSQRFEVI ->M_1031 -STGYAISAY ->M_1032 -KQLEFHIEI ->M_1033 -FFCEVPVLL ->M_1034 -FSMDETGQM ->M_1035 -YPRQYSLKL ->M_1036 -ETAYTKDGF ->M_1037 -FSNHWTFWV ->M_1038 -IGYANAKIY ->M_1039 -DFFEDTEHY ->M_1040 -DPMKVEAHV ->M_1041 -GSGEHPMDY ->M_1042 -SHSRGNDTL ->M_1043 -FHTSSSLTV ->M_1044 -VVMRICNLI ->M_1045 -TALDSSLCL ->M_1046 -DSDDMDLEV ->M_1047 -HSYVGPAQL ->M_1048 -EMFQRYSAF ->M_1049 -MPVSIRLVV ->M_1050 -LVDGDLGKY ->M_1051 -RSLAFPVPL ->M_1052 -RAFHDLRVA ->M_1053 -IYDEDVLVV ->M_1054 -LAMHSIWEM ->M_1055 -YCRAWCQAL ->M_1056 -QAVTNHSVY ->M_1057 -HSQECGSFL ->M_1058 -LQHTGTSVV ->M_1059 -ETRAQLARH ->M_1060 -RAALVGAEV ->M_1061 -IPNAQNMTI ->M_1062 -LATCCRARY ->M_1063 -LMRHSMEKI ->M_1064 -VSARHPQHL ->M_1065 -YKYDAGSAA ->M_1066 -IIFLLGEIV ->M_1067 -LARSQRTQV ->M_1068 -NAAVETASL ->M_1069 -LACSICHVY ->M_1070 -DIYDVLICL ->M_1071 -LTMSWLTPL ->M_1072 -FHNDLMPSY ->M_1073 -VMVSPASAI ->M_1074 -VFFSLLATV ->M_1075 -EASLATQIV ->M_1076 -ETLVSTSTI ->M_1077 -FPYQITNEH ->M_1078 -RTFLPVHLL ->M_1079 -LPQPGVRSL ->M_1080 -VPNNCLGKV ->M_1081 -HPLEFCLLL ->M_1082 -MAFVTLTDL ->M_1083 -FSVQLIRKF ->M_1084 -FPQMRAMSL ->M_1085 -LRLNWGEPI ->M_1086 -YEEDSGEYF ->M_1087 -TAKGTAQLV ->M_1088 -LHFHWNWII ->M_1089 -DTDGQPLLL ->M_1090 -AHLLCTLLL ->M_1091 -KAPGFEKHL ->M_1092 -SSYGGTIRY ->M_1093 -YQDMMNDIV ->M_1094 -MQALNLQVV ->M_1095 -MHYLKNSMI ->M_1096 -NAKSRGWLI ->M_1097 -DSNRVVCPI ->M_1098 -ISNRSVLHL ->M_1099 -QAELRGRVL ->M_1100 -ASFDCAIEM ->M_1101 -LQIGGFSSV ->M_1102 -QTWRAVTTL ->M_1103 -FSAQTFYVL ->M_1104 -LGDDFSSAY ->M_1105 -FQCAPGYAL ->M_1106 -DRETGMHLL ->M_1107 -FALQRIVQK ->M_1108 -DAVGNMLNL ->M_1109 -FYRLHLGTY ->M_1110 -FELKSPVKM ->M_1111 -VLRPRWCPV ->M_1112 -HHSSFRRHL ->M_1113 -FSYLTMSWL ->M_1114 -WAESVEREI ->M_1115 -KADVVHVTL ->M_1116 -IMEENDSNI ->M_1117 -LRLPHWPII ->M_1118 -EAVQDPMKV ->M_1119 -LIRKFAQSI ->M_1120 -SHHQCGQSL ->M_1121 -CTLGLGSLY ->M_1122 -ELAHDSYFY ->M_1123 -HAANVTQAM ->M_1124 -WTFWVGPFI ->M_1125 -VVEHVLTTV ->M_1126 -NDHDNWCII ->M_1127 -IAPLLPVAV ->M_1128 -LSGPWGSPL ->M_1129 -DPADPTSNL ->M_1130 -FPNSDHVMF ->M_1131 -EVQDIQASL ->M_1132 -RPYKQGARL ->M_1133 -DVAQHGARL ->M_1134 -FLEKNKDAV ->M_1135 -DSELAHDSY ->M_1136 -MPLWMASII ->M_1137 -YHFDAIRTF ->M_1138 -VSTEHCLSV ->M_1139 -YEAAKLLLV ->M_1140 -LVQAGVDVV ->M_1141 -SATASMLSV ->M_1142 -DQFTKSISI ->M_1143 -CALCALSNI ->M_1144 -RAKPRWRVA ->M_1145 -AAMDAGFLY ->M_1146 -CAMTMNKYI ->M_1147 -NLEPHGYVV ->M_1148 -MLLSPGQNV ->M_1149 -WQIHRVDIL ->M_1150 -YAELGTTTK ->M_1151 -YKLNRAFML ->M_1152 -FAAAAAVAA ->M_1153 -KMADPNQCV ->M_1154 -DPYVKAHLL ->M_1155 -WPIINTPMV ->M_1156 -KYYTDPSTY ->M_1157 -RVSSYGGTI ->M_1158 -EALDAGAIY ->M_1159 -EFIMAITSM ->M_1160 -FPWWLARVL ->M_1161 -WTLASMELV ->M_1162 -IVRCLVTSV ->M_1163 -MPAFHFNIL ->M_1164 -YRTHTLQTL ->M_1165 -HASVVAAYL ->M_1166 -ISRPSSNAL ->M_1167 -RALLGCSCV ->M_1168 -DAVWSRATF ->M_1169 -DVVHHLLSV ->M_1170 -MSFFRLLQM ->M_1171 -KIIAFRKTL ->M_1172 -TVSSNLSHV ->M_1173 -MSVEINDIM ->M_1174 -IAICRQIGI ->M_1175 -ISKPSELPI ->M_1176 -DPIEKELSV ->M_1177 -DHSNDPTAI ->M_1178 -WRLAEAEML ->M_1179 -RGLPWTVRV ->M_1180 -KPMPTIQWI ->M_1181 -RRFNLTSTF ->M_1182 -RRSHTGTFL ->M_1183 -FALDENDNA ->M_1184 -NPEELEQVV ->M_1185 -QAMHSFGRF ->M_1186 -TAIAICRQI ->M_1187 -EVMEKVLPL ->M_1188 -DVLPDTFTL ->M_1189 -RTGDRPHTF ->M_1190 -QPAVFETTV ->M_1191 -VMDFRFGTI ->M_1192 -NEDDSTFTI ->M_1193 -TALGLCEEV ->M_1194 -SMLSRVLII ->M_1195 -DANLHKNEL ->M_1196 -DHYAVESAL ->M_1197 -EVKIGKMSY ->M_1198 -LANGGKVPF ->M_1199 -IGAKHTLTI ->M_1200 -EVVGGWPVV ->M_1201 -VANERISMQ ->M_1202 -LSLKQVISI ->M_1203 -VGFPVGDSV ->M_1204 -LPLDHHLAL ->M_1205 -GALPLFRKY ->M_1206 -VSYHPDLGI ->M_1207 -HLFGTSCPY ->M_1208 -TATTILIMI ->M_1209 -LSFMEAQSL ->M_1210 -FLSLGIASL ->M_1211 -RPPPTPRKV ->M_1212 -SQLEMPETL ->M_1213 -YCRLATVHM ->M_1214 -VPHEDTLSL ->M_1215 -KCYKQGAFI ->M_1216 -LVLAFKNQV ->M_1217 -TSDDFWYHA ->M_1218 -RAEHFGIA* ->M_1219 -QVLPWLKAF ->M_1220 -FSIVRADGV ->M_1221 -DVHDIARFL ->M_1222 -SAQRPWPRV ->M_1223 -CAFRSQLEM ->M_1224 -IIDCLVSMV ->M_1225 -NPTEARVQV ->M_1226 -MVLWHLPAV ->M_1227 -KVHDSVLAL ->M_1228 -FVLLLTYIL ->M_1229 -RSGEPMVSL ->M_1230 -LPHCGHRTL ->M_1231 -MTEHRGKCY ->M_1232 -RTLRISETL ->M_1233 -VSAKRVSVL ->M_1234 -SVYCIRKKY ->M_1235 -QSMPCLMSF ->M_1236 -HRYNLTQHF ->M_1237 -ISLMVIEKV ->M_1238 -EIYSLIDNF ->M_1239 -APSNHMNLV ->M_1240 -FAISHEGHM ->M_1241 -LTSVLTLMF ->M_1242 -YAIPSKQLE ->M_1243 -QALAQRNQL ->M_1244 -FNCSFVLEM ->M_1245 -SPRRRAASV ->M_1246 -AAGAPPAKI ->M_1247 -DTIPWYLRL ->M_1248 -FFGNNMPEF ->M_1249 -NPICCDCVI ->M_1250 -CPYSAWCVY ->M_1251 -QMCAVNSTV ->M_1252 -LQMVRLCSV ->M_1253 -LTRTFVEFI ->M_1254 -LSATVMLTV ->M_1255 -MVPREFKPI ->M_1256 -LVIQYTVKY ->M_1257 -LRFPRITFF ->M_1258 -TSMPVSKML ->M_1259 -LMKCPCNTF ->M_1260 -IHQAMFQLL ->M_1261 -VAGRRGQQL ->M_1262 -HASSIIDEL ->M_1263 -YARRRWPSQ ->M_1264 -SSLDHHMLV ->M_1265 -DLITNIEPF ->M_1266 -TTILIMIVF ->M_1267 -LLKSNTSTL ->M_1268 -LHDVYMFCI ->M_1269 -STRSPNSTV ->M_1270 -QELAGVKMV ->M_1271 -YVPYRDNKM ->M_1272 -DPADGIRLF ->M_1273 -WRCWFNGIM ->M_1274 -CALGLHNFV ->M_1275 -MEEEFSTIL ->M_1276 -MLDDAPRLL ->M_1277 -LGYDMFDCV ->M_1278 -FVYKSGMTS ->M_1279 -ESADKTAYL ->M_1280 -NLQRWVTAV ->M_1281 -WKLTDMSSI ->M_1282 -HTLEEIYSL ->M_1283 -DAFNSTERA ->M_1284 -YLYPLVLMS ->M_1285 -SPFKLDATY ->M_1286 -FPRIYSNSL ->M_1287 -YHISEEYGL ->M_1288 -ASMHRFGHI ->M_1289 -AIDSASPVY ->M_1290 -CTFDSPARL ->M_1291 -SFMEAQSLM ->M_1292 -LPYELGWLF ->M_1293 -NIWECNRNI ->M_1294 -SPAEETVVL ->M_1295 -RQIPVVGSM ->M_1296 -LVWALPKTY ->M_1297 -QARPKGKGL ->M_1298 -LHLCYEFLM ->M_1299 -HQEDGGKAL ->M_1300 -RPSSNALLI ->M_1301 -QKYDGKCPL ->M_1302 -YAQFRGRHR ->M_1303 -VAVYSTCVL ->M_1304 -FLPPARSGI ->M_1305 -QHGSLSETW ->M_1306 -LGLEKTTSI ->M_1307 -QTVMFMATM ->M_1308 -LLKPGDRVV ->M_1309 -MPGSPRDPV ->M_1310 -LTYCTTGGI ->M_1311 -FQSLLSQHM ->M_1312 -KEFHFNQYL ->M_1313 -SSTEWVAPL ->M_1314 -RSSPATHSL ->M_1315 -ELKEWAESV ->M_1316 -GVVEATLSY ->M_1317 -EIAELNRTI ->M_1318 -GAASMIHYI ->M_1319 -LVNTCIRFV ->M_1320 -QAVDTDEAL ->M_1321 -AATSRGQVL ->M_1322 -NPLRPRESL ->M_1323 -VSSNLSHVI ->M_1324 -FTFGETEVC ->M_1325 -FQDDFSPRF ->M_1326 -YTVKYEQKM ->M_1327 -EHSDTFINL ->M_1328 -YTPKLEIKV ->M_1329 -ETQETMDEL ->M_1330 -DLVHHTTTL ->M_1331 -LMFSGLWHL ->M_1332 -VPHQIPKAV ->M_1333 -MAPAAGTWV ->M_1334 -FLITNALHF ->M_1335 -SPKPPPQCV ->M_1336 -SIADGRAWF ->M_1337 -MGYRVESEV ->M_1338 -APAPDLVVV ->M_1339 -LSANARCLI ->M_1340 -DTSDGLAVL ->M_1341 -EARRQGAVF ->M_1342 -KVPEGDSIV ->M_1343 -WRPGCLWAL ->M_1344 -HGLEKVPVI ->M_1345 -ITIVVISLI ->M_1346 -FAMELDDLH ->M_1347 -LTDKVSTPA ->M_1348 -LMVSAGVFI ->M_1349 -LQLEVEEAV ->M_1350 -SMIHYIVLI ->M_1351 -FRMFVHVYI ->M_1352 -HIFLFAVLL ->M_1353 -QQHDGAFLI ->M_1354 -VELELWGVV ->M_1355 -WSLQTWRAV ->M_1356 -LVQEFTRGI ->M_1357 -VAAFFLSLF ->M_1358 -EAEEESLAL ->M_1359 -HVIVRTSRV ->M_1360 -ELLEPQKTY ->M_1361 -AMSDGRVPV ->M_1362 -RPPSPKDTV ->M_1363 -VPMCHLRLL ->M_1364 -LSARSVPSI ->M_1365 -QVHQRMNSL ->M_1366 -EALVQMQYL ->M_1367 -CAQSPWCLV ->M_1368 -LSCEAHNSM ->M_1369 -QARGVKKQI ->M_1370 -SHHSQCSSL ->M_1371 -YGGFFVISV ->M_1372 -YVYPLPVAN ->M_1373 -HSYWLLKLL ->M_1374 -YRTHTLQTL ->M_1375 -FTTLKMYSV ->M_1376 -EHMNHTCNL ->M_1377 -VAIYLYPLV ->M_1378 -YEGYKYEHI ->M_1379 -DRYVAVRHL ->M_1380 -DLIDYARYM ->M_1381 -NLLLWVLAI ->M_1382 -HLHDHYGPY ->M_1383 -NTDSTAALL ->M_1384 -YVKERQTVT ->M_1385 -TMECWGQKY ->M_1386 -KSDDSDFLA ->M_1387 -MAFVRLLHS ->M_1388 -LVDNLTYTL ->M_1389 -KHSATASML ->M_1390 -FEAHEVLKL ->M_1391 -LVLVGCFTI ->M_1392 -TTSGIGSSM ->M_1393 -KSRAPPEAI ->M_1394 -AALVPTQAM ->M_1395 -RQRNGVAKL ->M_1396 -SSDRMTSVA ->M_1397 -RPSPNRPKL ->M_1398 -SSVEVLVNY ->M_1399 -YCIYASLRI ->M_1400 -RLLPPVSP* ->M_1401 -FSLGKHVCL ->M_1402 -CTDKVGTEA ->M_1403 -FRRSISVRI ->M_1404 -LYLHTLLTI ->M_1405 -LEVPAPEAI ->M_1406 -LLSEMAVAV ->M_1407 -VPLVRWLKV ->M_1408 -DTLPMLGNI ->M_1409 -FAFGAVFSE ->M_1410 -RNYQAWNFL ->M_1411 -DATKNQVAM ->M_1412 -QTKHNAKVY ->M_1413 -IEWECTMML ->M_1414 -LELEFLCPL ->M_1415 -QLVNRPQSI ->M_1416 -TTKKSGGHY ->M_1417 -IVEHPAGHL ->M_1418 -HRYLWKILI ->M_1419 -SIFEVIWSV ->M_1420 -QHDDGYLEV ->M_1421 -GVAPGLQVV ->M_1422 -YLAMGEEIY ->M_1423 -SVVCHQLGF ->M_1424 -RTKRRVFII ->M_1425 -QMAERALYY ->M_1426 -LISPPQEKV ->M_1427 -HLIEERDTL ->M_1428 -ILKQPSQTL ->M_1429 -LQVVHLNAV ->M_1430 -VHDIARFLY ->M_1431 -RSLPIAIEM ->M_1432 -NVDEVNQIM ->M_1433 -GAGVEISTV ->M_1434 -VPREFKPIL ->M_1435 -GAQPPMPPY ->M_1436 -RADLLIVVF ->M_1437 -WKEDMAVHV ->M_1438 -FIEPHARFY ->M_1439 -DEFSGVPRV ->M_1440 -RVQPAVRAL ->M_1441 -ATTIVTTVY ->M_1442 -FFHNPKPLF ->M_1443 -VTASSGIMI ->M_1444 -HKAHFQYLL ->M_1445 -IGVEAGRTL ->M_1446 -ETMDNGFGH ->M_1447 -DFWYHAVVL ->M_1448 -FHLASAVAL ->M_1449 -LAMYLSKNY ->M_1450 -HLLELPQIL ->M_1451 -VSVHRAPSI ->M_1452 -DPAAASHPI ->M_1453 -SVYLRNNKL ->M_1454 -INREHIPTF ->M_1455 -AQYDDPRNL ->M_1456 -RPVNAYARV ->M_1457 -LARLGALLL ->M_1458 -SHTGTFLLV ->M_1459 -HTVAWSNGH ->M_1460 -TIPDSISKF ->M_1461 -AVFEEQIKV ->M_1462 -FCPLCHNPV ->M_1463 -RVLKCNVHL ->M_1464 -LLLPCPLLL ->M_1465 -QTAEQYVFV ->M_1466 -FLNSMDQQI ->M_1467 -GPARGIAII ->M_1468 -LASLSLKQV ->M_1469 -TSVPHEDTL ->M_1470 -EAEVETEAI ->M_1471 -SSLSNVSQV ->M_1472 -TVQNAMQIV ->M_1473 -WHFIKRHIA ->M_1474 -MTVAGMVLL ->M_1475 -YMAGSDTTY ->M_1476 -FRENFESIY ->M_1477 -LATVILGAV ->M_1478 -LSSGSFATM ->M_1479 -DTNNLGIRI ->M_1480 -CSGCVAQVY ->M_1481 -DHIRNFTTM ->M_1482 -KPFISRTMM ->M_1483 -PADPAQLAV ->M_1484 -YEPDTMEQY ->M_1485 -EPLNDTIAI ->M_1486 -QAPLAPTHM ->M_1487 -IHLDISSFV ->M_1488 -PLMDQVSVI ->M_1489 -HSLHPFPHF ->M_1490 -ITFKELGAL ->M_1491 -AAAREATEV ->M_1492 -RTYHGRLAY ->M_1493 -DADIYGKPM ->M_1494 -KGYRIVVAL ->M_1495 -FNMRDLSDI ->M_1496 -FRKTLLNPV ->M_1497 -YLAMGEEIY ->M_1498 -KPFSHSCNL ->M_1499 -DQATFINMY ->M_1500 -ARFRIRKTI ->M_1501 -RAFSFSLPC ->M_1502 -SHMCNSLLV ->M_1503 -EAEEWVVSY ->M_1504 -KASERFRTQ ->M_1505 -QIMPHAIIF ->M_1506 -LLKHMPKII ->M_1507 -ILSCNADII ->M_1508 -AAQCCHKKV ->M_1509 -TELDSVGPV ->M_1510 -STFCGTLEY ->M_1511 -GLIPPDATI ->M_1512 -SAQRNAAFF ->M_1513 -MDHPSGIAI ->M_1514 -FTVLENLAV ->M_1515 -KPPPQCVTL ->M_1516 -LAIYTLLSL ->M_1517 -RTVKFLMAI ->M_1518 -MCLEASIPL ->M_1519 -SAPQDSKAV ->M_1520 -FIIHHRTHT ->M_1521 -RKEENMESV ->M_1522 -FPQVSELVL ->M_1523 -YQVVAQHIY ->M_1524 -DSAQRNAAF ->M_1525 -KHFNNSSHF ->M_1526 -EANVHGIYF ->M_1527 -LSRVKAQVV ->M_1528 -LENSNRSMV ->M_1529 -ESKSGSPEY ->M_1530 -YTVKYEQKM ->M_1531 -LTYGHDRQL ->M_1532 -LHFHFTACY ->M_1533 -DCNKTAVTI ->M_1534 -QPLHSLSVL ->M_1535 -AACGIIQQV ->M_1536 -WDQRCLHTI ->M_1537 -QLQAFWKHV ->M_1538 -SPHPRRRRL ->M_1539 -FLDKASDLL ->M_1540 -SAWLFVTGI ->M_1541 -FMFEMPFMQ ->M_1542 -VSLQAAEEI ->M_1543 -RANGNPNPT ->M_1544 -ELPAFIEMM ->M_1545 -CVAKCGGTV ->M_1546 -LEYLAPEVL ->M_1547 -TMANNPDVM ->M_1548 -EAVSSASKL ->M_1549 -FSLYRGWAL ->M_1550 -VVIGAPYVV ->M_1551 -LHFHWNWII ->M_1552 -MSACWSFAV ->M_1553 -YIAQNDDEL ->M_1554 -ETINWTLLE ->M_1555 -DQYAICMKY ->M_1556 -HAKRKTATA ->M_1557 -LAAASSTAF ->M_1558 -KAYGRDNTP ->M_1559 -KHLQLYQLF ->M_1560 -WAVMNHFSM ->M_1561 -IERPGGSLL ->M_1562 -YCFGCLSHH ->M_1563 -QGYGGFFVI ->M_1564 -NENDLITNI ->M_1565 -LPVPIIQQL ->M_1566 -RLMHQLLVI ->M_1567 -FHKEVFGMF ->M_1568 -CTVEDGGHV ->M_1569 -EVAQHLATT ->M_1570 -VEHPAGHLV ->M_1571 -WKGSTECKL ->M_1572 -LSDPHLTAV ->M_1573 -ILTELLMVV ->M_1574 -MVHLVPALV ->M_1575 -TILENPYIM ->M_1576 -DHSDSDYDF ->M_1577 -NHLNIAWEL ->M_1578 -FPEDVAVYT ->M_1579 -YMTSSGRRF ->M_1580 -SSVPLRSSV ->M_1581 -LAAPPPLTE ->M_1582 -VVASQPAHV ->M_1583 -SMLDPHGHL ->M_1584 -LVVADIHSM ->M_1585 -LLYMAFVRL ->M_1586 -VVTVMVTTV ->M_1587 -KLIDVNHYV ->M_1588 -FTQYLGLSM ->M_1589 -FRGKHDCAL ->M_1590 -EVFRHKLAM ->M_1591 -RSIRLSQEI ->M_1592 -HTIQKAKHM ->M_1593 -PSGRPALAY ->M_1594 -WQDHIRLEV ->M_1595 -VLLDLRPSI ->M_1596 -AVYSTCVLV ->M_1597 -LALSLPACF ->M_1598 -NQCPCSSDI ->M_1599 -SIDPKTGVV ->M_1600 -AAASHPILL ->M_1601 -RLLKHMPKI ->M_1602 -LSLTGLQVL ->M_1603 -MSQEEKVAY ->M_1604 -MIENLEHHI ->M_1605 -IIATGLVTL ->M_1606 -SADCGCCPM ->M_1607 -CAELLSHTV ->M_1608 -HISEEYGLL ->M_1609 -YSFCPLCHN ->M_1610 -LPCRSLTRV ->M_1611 -KVLQHGRLY ->M_1612 -FLCDEEPLL ->M_1613 -IPCLDDVTV ->M_1614 -LASEAVSSA ->M_1615 -TPTPGFSSM ->M_1616 -FYLVAYAAM ->M_1617 -YLKSPECFL ->M_1618 -KVNTATTTM ->M_1619 -LPVSTKCTV ->M_1620 -SVRYAGPLY ->M_1621 -HTIQKAKHM ->M_1622 -TFRDVAVEF ->M_1623 -DEKDLWEYI ->M_1624 -DPADPTRDL ->M_1625 -EAEEWVVSY ->M_1626 -CAFTVLENL ->M_1627 -SWMEGQVTI ->M_1628 -MTAVGYGDM ->M_1629 -VSEDAKQRI ->M_1630 -DVDEDGYIM ->M_1631 -IVQCRVLNI ->M_1632 -IASLLENIL ->M_1633 -SRNWLKSIL ->M_1634 -KVKPTLAMY ->M_1635 -YTMGIIFVL ->M_1636 -ELKSPVKMI ->M_1637 -LSLGAPSPL ->M_1638 -QSIRAATEV ->M_1639 -YMAATLLEF ->M_1640 -CSDGSDEDA ->M_1641 -SYLEDVRLI ->M_1642 -QVYVGDSDI ->M_1643 -VIDQCLKKI ->M_1644 -YPDWIRDNM ->M_1645 -RATSFGKCF ->M_1646 -KAGSLGIIL ->M_1647 -VAQQSRLVF ->M_1648 -DCQSHRLTV ->M_1649 -MPNVLWDLV ->M_1650 -MSWLTPLMI ->M_1651 -DANNVTCVW ->M_1652 -KLLQCMSRV ->M_1653 -VHLPLAVAL ->M_1654 -SLYSLDATL ->M_1655 -FTTTQWSSL ->M_1656 -VALRDLGCL ->M_1657 -MVACGGTVY ->M_1658 -EMFQRYSAF ->M_1659 -DAACGIWSL ->M_1660 -FTILPCTCY ->M_1661 -IIYTMGIIF ->M_1662 -RVYNIRGDM ->M_1663 -RNDPELPTV ->M_1664 -HSDSDYDFV ->M_1665 -VLGEHHHHV ->M_1666 -HVVDEREQM ->M_1667 -GQFPYMGEV ->M_1668 -LPPEMYVYL ->M_1669 -EAYQKQLCF ->M_1670 -AATGPGEVL ->M_1671 -DLYATAFLV ->M_1672 -GFDWKSVFI ->M_1673 -FVVFSFFFV ->M_1674 -GRDVVHHLL ->M_1675 -VTLRWYLAM ->M_1676 -LVAQYDLTV ->M_1677 -RLIRGDAVV ->M_1678 -FQYLVVHTE ->M_1679 -KHYLMTRTL ->M_1680 -FVMEHSNIV ->M_1681 -HQMENNGWV ->M_1682 -NATYSGYVY ->M_1683 -KVKNSASVM ->M_1684 -KQDKCFAFI ->M_1685 -AQRPWPRVL ->M_1686 -MAATLLEFF ->M_1687 -DPNTVSNSI ->M_1688 -LPVSGGHVM ->M_1689 -MLDDAPRLL ->M_1690 -IPPDATIYF ->M_1691 -LHDALEVDL ->M_1692 -MMEKLYPGY ->M_1693 -IPFLFFTDM ->M_1694 -YKLCFNTFF ->M_1695 -YVTMVIDRL ->M_1696 -TIYFDVVLL ->M_1697 -SAWLRAISL ->M_1698 -HLWPGGLSL ->M_1699 -FGYMTQQRM ->M_1700 -HVYILRAVF ->M_1701 -LYIPALAVL ->M_1702 -DPMVPLQGV ->M_1703 -FTEEGFCAI ->M_1704 -FFNDDCCEL ->M_1705 -FLFHPLEFC ->M_1706 -VVMWWMGIL ->M_1707 -KTFHHKSNF ->M_1708 -QRPWPRVLL ->M_1709 -IRVQEASTI ->M_1710 -DLIDYARYM ->M_1711 -VTVRGFWIY ->M_1712 -FMDEHAAER ->M_1713 -SISDTYDPY ->M_1714 -DTNDNVPEF ->M_1715 -YNCTCGCSM ->M_1716 -LLLLASATV ->M_1717 -LYMAFVRLL ->M_1718 -SAEVQLSKI ->M_1719 -ITACLSVLI ->M_1720 -LPETKGVTL ->M_1721 -MSQEEKVAY ->M_1722 -MASPQAEST ->M_1723 -MSFELPYHC ->M_1724 -RWNDTRATV ->M_1725 -LRHERAVSM ->M_1726 -LHLLVACTI ->M_1727 -YGHDRQLCL ->M_1728 -DATIYFDVV ->M_1729 -IVCDIKEKL ->M_1730 -RPAQFLHEM ->M_1731 -WHFVYKSGM ->M_1732 -EVDPIGNLY ->M_1733 -RTDGNSHEA ->M_1734 -KHMPKIIHL ->M_1735 -DVHDIARFL ->M_1736 -PATRPLHVL ->M_1737 -LLHSNRSQI ->M_1738 -PARSGIFKI ->M_1739 -AALTPTEEM ->M_1740 -ISAYMAATL ->M_1741 -IMMSDEERI ->M_1742 -KRQEGMVPV ->M_1743 -LQKRATEEI ->M_1744 -GKDKMTHLL ->M_1745 -AQLPPWAPL ->M_1746 -FFCEVPVLL ->M_1747 -RAHKKAITT ->M_1748 -FDWKSVFII ->M_1749 -CLFRAARLI ->M_1750 -MIEDFLRRF ->M_1751 -TTTERWLRV ->M_1752 -FFKDKATSK ->M_1753 -HFFDAFRKF ->M_1754 -GALGLNRPV ->M_1755 -YRTKCTLGL ->M_1756 -MTVAGMVLL ->M_1757 -KTLSKTAHL ->M_1758 -NLYIFATCL ->M_1759 -GFDTSSSSL ->M_1760 -TPVLCGQPI ->M_1761 -WCAPGKPTL ->M_1762 -ILHNQIQQV ->M_1763 -VVLSPEVEV ->M_1764 -DSIHQVGMY ->M_1765 -NHSGVGAFW ->M_1766 -HNLEPHGYV ->M_1767 -PSLNATTIV ->M_1768 -ISGFKGDTV ->M_1769 -HIASSTTSI ->M_1770 -HTLHAHDPV ->M_1771 -WTDYGQVFT ->M_1772 -ELFRRGLRY ->M_1773 -SASRTKRRV ->M_1774 -NSGPSRSML ->M_1775 -ESADKTAYL ->M_1776 -TELEKFSKV ->M_1777 -FHAQVCSLY ->M_1778 -LVVEHVLTT ->M_1779 -RSYWLRLFL ->M_1780 -DVDEKQLLV ->M_1781 -CAIISLIFI ->M_1782 -SQLEMPETL ->M_1783 -NLEDVGRHL ->M_1784 -HLRRIGRFI ->M_1785 -KYDPDVVVM ->M_1786 -KDDDCITLV ->M_1787 -YDVTDSRII ->M_1788 -MLLHQVAAY ->M_1789 -THQSGFSVI ->M_1790 -DLQPVREAI ->M_1791 -FAGSTQSDL ->M_1792 -GSYREAQSL ->M_1793 -HFMPRIQRL ->M_1794 -LPLKRPGKL ->M_1795 -MAFPEGYGT ->M_1796 -DMQDLTEFL ->M_1797 -VDFSSEVTV ->M_1798 -MEVDPIGNL ->M_1799 -ISRNCNSRM ->M_1800 -YSLIDNFVM ->M_1801 -FEMPFMQTG ->M_1802 -SHELVMYIW ->M_1803 -IIVSYMLII ->M_1804 -AAAAAVAAL ->M_1805 -LVDQKAKEV ->M_1806 -FFSLLATVI ->M_1807 -IYGKPMPTI ->M_1808 -YMLERLIEQ ->M_1809 -CIADFLEHM ->M_1810 -LPYPGSSQA ->M_1811 -EAWQCQPVL ->M_1812 -VATSTAQLL ->M_1813 -VKYTPKLEI ->M_1814 -RVSAKRVSV ->M_1815 -NTWTRQMGY ->M_1816 -LDFACHFTV ->M_1817 -HVRIHPKLV ->M_1818 -LQQNCAAYL ->M_1819 -DAVGNMLNL ->M_1820 -WQAISLMVI ->M_1821 -WLWKLSAVV ->M_1822 -LAPTHMPEL ->M_1823 -YAQTPSKTP ->M_1824 -LLLCFLAAM ->M_1825 -HMPKIIHLV ->M_1826 -AQLPSYMHI diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_118562_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_118562_1_T_iedb.xml deleted file mode 100755 index e5875335..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_118562_1_T_iedb.xml +++ /dev/null @@ -1,45067 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_471 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_471 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_472 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_473 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_474 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_475 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_476 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_477 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_478 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_479 - 9 - - - 1 - gnl|BL_ORD_ID|1152 - 75718|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 1152 - 11 - - - 1 - 12.3122 - 20 - 42.1867 - 3 - 8 - 1 - 6 - 0 - 0 - 4 - 4 - 0 - 6 - YQELPT - YSEHPT - Y E PT - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 10 - Query_10 - M_480 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_481 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_482 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_483 - 9 - - - 1 - gnl|BL_ORD_ID|1903 - 180641|polyprotein|AFJ91714.1|Dengue virus 1|11053 - 1903 - 9 - - - 1 - 12.6974 - 21 - 37.875 - 1 - 7 - 1 - 7 - 0 - 0 - 4 - 6 - 0 - 7 - MAISVVK - MALSIVS - MA+S+V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 14 - Query_14 - M_484 - 9 - - - 1 - gnl|BL_ORD_ID|33 - 2506|M protein, serotype 5 precursor|P02977.2|Streptococcus pyogenes serotype M5|301449 - 33 - 9 - - - 1 - 14.6234 - 26 - 1.88321 - 2 - 7 - 1 - 6 - 0 - 0 - 6 - 6 - 0 - 6 - ALEKLN - ALEKLN - ALEKLN - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 15 - Query_15 - M_485 - 9 - - - 1 - gnl|BL_ORD_ID|2009 - 183781|polyprotein|AGO67248.1|Dengue virus 2|11060 - 2009 - 10 - - - 1 - 13.4678 - 23 - 8.61729 - 3 - 9 - 3 - 9 - 0 - 0 - 3 - 6 - 0 - 7 - DMERHHI - DLEKRHV - D+E+ H+ - - - - - 2 - gnl|BL_ORD_ID|2055 - 184755|polyprotein|AGO67248.1|Dengue virus 2|11060 - 2055 - 9 - - - 1 - 13.4678 - 23 - 8.87313 - 3 - 9 - 2 - 8 - 0 - 0 - 3 - 6 - 0 - 7 - DMERHHI - DLEKRHV - D+E+ H+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 16 - Query_16 - M_486 - 9 - - - 1 - gnl|BL_ORD_ID|4 - 327|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis|1773 - 4 - 20 - - - 1 - 13.853 - 24 - 4.4203 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 8 - 0 - 8 - ANRRKEEV - ANKQKQEL - AN++K+E+ - - - - - 2 - gnl|BL_ORD_ID|53 - 3935|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis|1773 - 53 - 20 - - - 1 - 13.853 - 24 - 4.97811 - 2 - 9 - 12 - 19 - 0 - 0 - 4 - 8 - 0 - 8 - ANRRKEEV - ANKQKQEL - AN++K+E+ - - - - - 3 - gnl|BL_ORD_ID|304 - 20415|circumsporozoite protein|AAN87606.1|Plasmodium falciparum|5833 - 304 - 20 - - - 1 - 13.4678 - 23 - 10.3889 - 2 - 9 - 11 - 18 - 0 - 0 - 4 - 7 - 0 - 8 - ANRRKEEV - ANKPKDEL - AN+ K+E+ - - - - - 4 - gnl|BL_ORD_ID|434 - 26870|Circumsporozoite protein precursor|P02893.1|Plasmodium falciparum|5833 - 434 - 20 - - - 1 - 13.4678 - 23 - 11.4655 - 2 - 9 - 6 - 13 - 0 - 0 - 4 - 7 - 0 - 8 - ANRRKEEV - ANKPKDEL - AN+ K+E+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 17 - Query_17 - M_487 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_488 - 9 - - - 1 - gnl|BL_ORD_ID|530 - 32663|small hydrophobic protein|AAM12943.1|Human metapneumovirus|162145 - 530 - 10 - - - 1 - 10.7714 - 16 - 390.249 - 2 - 9 - 3 - 10 - 0 - 0 - 4 - 5 - 0 - 8 - ALGPGHTV - AVGVYHIV - A+G H V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 19 - Query_19 - M_489 - 9 - - - 1 - gnl|BL_ORD_ID|1621 - 145860|Protein E6|P04019.1|Human papillomavirus type 11|10580 - 1621 - 9 - - - 1 - 15.3938 - 28 - 0.556982 - 3 - 9 - 1 - 7 - 0 - 0 - 6 - 6 - 0 - 7 - KVLIRTY - KVLIRCY - KVLIR Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 20 - Query_20 - M_490 - 9 - - - 1 - gnl|BL_ORD_ID|1265 - 98603|trans-sialidase, putative|EAN82716.1|Trypanosoma cruzi|5693 - 1265 - 9 - - - 1 - 14.2382 - 25 - 4.3647 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 7 - 0 - 8 - SDDNDAFY - TDNNRSFY - +D+N +FY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 21 - Query_21 - M_491 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 22 - Query_22 - M_492 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_493 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_494 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_495 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_496 - 9 - - - 1 - gnl|BL_ORD_ID|1654 - 146570|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 - 1654 - 17 - - - 1 - 15.3938 - 28 - 0.651332 - 2 - 9 - 1 - 8 - 0 - 0 - 5 - 6 - 0 - 8 - SFDGMWKV - SWDQMWKC - S+D MWK - - - - - 2 - gnl|BL_ORD_ID|1653 - 146569|polyprotein|ADF97231.1|Hepatitis C virus subtype 3a|356426 - 1653 - 17 - - - 1 - 13.0826 - 22 - 15.9108 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 5 - 0 - 8 - SFDGMWKV - SWDETWKC - S+D WK - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 27 - Query_27 - M_497 - 9 - - - 1 - gnl|BL_ORD_ID|382 - 23573|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 382 - 9 - - - 1 - 13.0826 - 22 - 14.7007 - 4 - 9 - 1 - 6 - 0 - 0 - 3 - 5 - 0 - 6 - HQVGMY - HAVGLF - H VG++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 28 - Query_28 - M_498 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 29 - Query_29 - M_499 - 9 - - - 1 - gnl|BL_ORD_ID|743 - 47946|envelope glycoprotein|AAC28452.1|Human immunodeficiency virus 1|11676 - 743 - 20 - - - 1 - 14.2382 - 25 - 4.20027 - 4 - 9 - 1 - 6 - 0 - 0 - 3 - 6 - 0 - 6 - PVPLYY - PIPIHY - P+P++Y - - - - - 2 - gnl|BL_ORD_ID|1001 - 65817|envelope glycoprotein|AAL59843.1|Human immunodeficiency virus 1|11676 - 1001 - 20 - - - 1 - 13.853 - 24 - 5.41768 - 4 - 9 - 11 - 16 - 0 - 0 - 3 - 6 - 0 - 6 - PVPLYY - PIPIHY - P+P++Y - - - - - 3 - gnl|BL_ORD_ID|1171 - 79300|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 1171 - 15 - - - 1 - 12.6974 - 21 - 29.7824 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - LAFPVP - LSFPDP - L+FP P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 30 - Query_30 - M_500 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 31 - Query_31 - M_501 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 32 - Query_32 - M_502 - 9 - - - 1 - gnl|BL_ORD_ID|255 - 17117|matrix protein|AAN09804.1|Measles virus strain Edmonston|11235 - 255 - 9 - - - 1 - 12.6974 - 21 - 27.8632 - 1 - 6 - 3 - 8 - 0 - 0 - 4 - 5 - 0 - 6 - YMDLMG - YMSLLG - YM L+G - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 33 - Query_33 - M_503 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 34 - Query_34 - M_504 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 35 - Query_35 - M_505 - 9 - - - 1 - gnl|BL_ORD_ID|41 - 2903|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 - 41 - 15 - - - 1 - 13.853 - 24 - 5.48445 - 1 - 9 - 6 - 14 - 0 - 0 - 4 - 7 - 0 - 9 - FVYLHLNMV - LIHLHQNIV - ++LH N+V - - - - - 2 - gnl|BL_ORD_ID|316 - 20921|polyprotein|BAA03375.1|Hepatitis C virus|11103 - 316 - 15 - - - 1 - 13.4678 - 23 - 11.2975 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 7 - 0 - 9 - FVYLHLNMV - LIHLHQNIV - ++LH N+V - - - - - 3 - gnl|BL_ORD_ID|1816 - 177843|polyprotein|ACZ60102.1|Hepatitis C virus subtype 3a|356426 - 1816 - 17 - - - 1 - 13.0826 - 22 - 17.2821 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 7 - 0 - 9 - FVYLHLNMV - LIHLHQNIV - ++LH N+V - - - - - 4 - gnl|BL_ORD_ID|1016 - 67503|Genome polyprotein|P26662.3|Hepatitis C virus|11103 - 1016 - 10 - - - 1 - 12.3122 - 20 - 47.8854 - 1 - 7 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - FVYLHLN - YVYDHLT - +VY HL - - - - - 5 - gnl|BL_ORD_ID|573 - 36062|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 573 - 20 - - - 1 - 12.3122 - 20 - 48.9705 - 1 - 7 - 8 - 14 - 0 - 0 - 4 - 5 - 0 - 7 - FVYLHLN - YVYNHLT - +VY HL - - - - - 6 - gnl|BL_ORD_ID|279 - 18678|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 - 279 - 15 - - - 1 - 12.3122 - 20 - 55.7176 - 1 - 7 - 7 - 13 - 0 - 0 - 4 - 5 - 0 - 7 - FVYLHLN - YVYNHLT - +VY HL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 36 - Query_36 - M_506 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 37 - Query_37 - M_507 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 38 - Query_38 - M_508 - 9 - - - 1 - gnl|BL_ORD_ID|949 - 62504|HBsAg protein|ABF71024.1|Hepatitis B virus|10407 - 949 - 9 - - - 1 - 12.6974 - 21 - 31.9494 - 3 - 9 - 3 - 9 - 0 - 0 - 3 - 6 - 0 - 7 - WKNMDFL - WTSLNFL - W +++FL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 39 - Query_39 - M_509 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 40 - Query_40 - M_510 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 41 - Query_41 - M_511 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 42 - Query_42 - M_512 - 9 - - - 1 - gnl|BL_ORD_ID|2137 - 187106|Vpr protein|BAA93983.1|Human immunodeficiency virus 1|11676 - 2137 - 9 - - - 1 - 14.2382 - 25 - 4.1461 - 5 - 9 - 5 - 9 - 0 - 0 - 4 - 5 - 0 - 5 - FPRIY - FPRIW - FPRI+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 43 - Query_43 - M_513 - 9 - - - 1 - gnl|BL_ORD_ID|1633 - 146249|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 - 1633 - 17 - - - 1 - 15.0086 - 27 - 0.838218 - 3 - 9 - 9 - 15 - 0 - 0 - 4 - 6 - 0 - 7 - IFWTVYY - VMWTVYH - + WTVY+ - - - - - 2 - gnl|BL_ORD_ID|66 - 4910|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 66 - 20 - - - 1 - 15.0086 - 27 - 1.19565 - 3 - 9 - 7 - 13 - 0 - 0 - 4 - 6 - 0 - 7 - IFWTVYY - VCWTVYH - + WTVY+ - - - - - 3 - gnl|BL_ORD_ID|65 - 4909|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 - 65 - 15 - - - 1 - 15.0086 - 27 - 1.24275 - 3 - 9 - 7 - 13 - 0 - 0 - 4 - 6 - 0 - 7 - IFWTVYY - VCWTVYH - + WTVY+ - - - - - 4 - gnl|BL_ORD_ID|1632 - 146246|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 - 1632 - 17 - - - 1 - 14.6234 - 26 - 1.81173 - 3 - 9 - 9 - 15 - 0 - 0 - 4 - 6 - 0 - 7 - IFWTVYY - VCWTVYH - + WTVY+ - - - - - 5 - gnl|BL_ORD_ID|1674 - 148619|unnamed protein product|BAA14233.1|Hepatitis C virus|11103 - 1674 - 45 - - - 1 - 14.2382 - 25 - 3.72943 - 3 - 8 - 40 - 45 - 0 - 0 - 4 - 5 - 0 - 6 - IFWTVY - VCWTVY - + WTVY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 44 - Query_44 - M_514 - 9 - - - 1 - gnl|BL_ORD_ID|1731 - 150556|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1731 - 10 - - - 1 - 13.853 - 24 - 6.99268 - 3 - 8 - 4 - 9 - 0 - 0 - 3 - 5 - 0 - 6 - DPNQCV - DPRRCL - DP +C+ - - - - - 2 - gnl|BL_ORD_ID|859 - 56310|polyprotein|AGO67248.1|Dengue virus 2|11060 - 859 - 10 - - - 1 - 13.4678 - 23 - 9.56649 - 3 - 8 - 4 - 9 - 0 - 0 - 3 - 5 - 0 - 6 - DPNQCV - DPRRCM - DP +C+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 45 - Query_45 - M_515 - 9 - - - 1 - gnl|BL_ORD_ID|1174 - 79351|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 1174 - 17 - - - 1 - 15.0086 - 27 - 1.02766 - 2 - 9 - 5 - 12 - 0 - 0 - 5 - 5 - 0 - 8 - AFWAGSVV - TLWGGSVV - W GSVV - - - - - 2 - gnl|BL_ORD_ID|2018 - 184130|polyprotein|AFP27208.1|Dengue virus 4|11070 - 2018 - 10 - - - 1 - 12.6974 - 21 - 24.356 - 3 - 8 - 5 - 10 - 0 - 0 - 3 - 4 - 0 - 6 - FWAGSV - LWCGSL - W GS+ - - - - - 3 - gnl|BL_ORD_ID|1921 - 180718|polyprotein|AFP27208.1|Dengue virus 4|11070 - 1921 - 9 - - - 1 - 12.6974 - 21 - 27.8632 - 3 - 8 - 4 - 9 - 0 - 0 - 3 - 4 - 0 - 6 - FWAGSV - LWCGSL - W GS+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 46 - Query_46 - M_516 - 9 - - - 1 - gnl|BL_ORD_ID|1756 - 154164|tegument protein|CAB06732.1|Human alphaherpesvirus 2|10310 - 1756 - 15 - - - 1 - 15.779 - 29 - 0.460848 - 3 - 9 - 9 - 15 - 0 - 0 - 4 - 7 - 0 - 7 - FDAIRTF - YDAVRTW - +DA+RT+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 47 - Query_47 - M_517 - 9 - - - 1 - gnl|BL_ORD_ID|120 - 8236|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 - 120 - 15 - - - 1 - 14.2382 - 25 - 2.60034 - 1 - 5 - 2 - 6 - 0 - 0 - 4 - 5 - 0 - 5 - FAKGW - FAQGW - FA+GW - - - - - 2 - gnl|BL_ORD_ID|2057 - 184814|polyprotein|AGO67248.1|Dengue virus 2|11060 - 2057 - 9 - - - 1 - 12.3122 - 20 - 43.3628 - 1 - 7 - 3 - 9 - 0 - 0 - 4 - 4 - 0 - 7 - FAKGWLL - LGKGWPL - KGW L - - - - - 3 - gnl|BL_ORD_ID|1716 - 150387|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1716 - 10 - - - 1 - 12.3122 - 20 - 46.3152 - 1 - 7 - 4 - 10 - 0 - 0 - 4 - 4 - 0 - 7 - FAKGWLL - LGKGWPL - KGW L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 48 - Query_48 - M_518 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 49 - Query_49 - M_519 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 50 - Query_50 - M_520 - 9 - - - 1 - gnl|BL_ORD_ID|1172 - 79308|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 1172 - 16 - - - 1 - 12.6974 - 21 - 24.3923 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 5 - 0 - 9 - MAPELISHL - MEPTLGQHL - M P L HL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 51 - Query_51 - M_521 - 9 - - - 1 - gnl|BL_ORD_ID|273 - 18390|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 273 - 20 - - - 1 - 13.4678 - 23 - 7.7086 - 3 - 7 - 1 - 5 - 0 - 0 - 4 - 4 - 0 - 5 - FYHPR - FYFPR - FY PR - - - - - 2 - gnl|BL_ORD_ID|946 - 62355|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 946 - 20 - - - 1 - 13.4678 - 23 - 9.25482 - 3 - 7 - 8 - 12 - 0 - 0 - 4 - 4 - 0 - 5 - FYHPR - FYFPR - FY PR - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 52 - Query_52 - M_522 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 53 - Query_53 - M_523 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 54 - Query_54 - M_524 - 9 - - - 1 - gnl|BL_ORD_ID|1338 - 107905|Genome polyprotein|P26664.3|Hepatitis C virus|11103 - 1338 - 10 - - - 1 - 13.0826 - 22 - 17.265 - 4 - 9 - 3 - 8 - 0 - 0 - 3 - 4 - 0 - 6 - FCDSCY - ICDECH - CD C+ - - - - - 2 - gnl|BL_ORD_ID|1323 - 107790|polyprotein|AAD56189.1|Hepatitis C virus|11103 - 1323 - 10 - - - 1 - 13.0826 - 22 - 19.1489 - 4 - 9 - 4 - 9 - 0 - 0 - 3 - 4 - 0 - 6 - FCDSCY - MCDECH - CD C+ - - - - - 3 - gnl|BL_ORD_ID|1337 - 107901|Genome polyprotein|P26664.3|Hepatitis C virus|11103 - 1337 - 10 - - - 1 - 13.0826 - 22 - 20.5146 - 4 - 9 - 1 - 6 - 0 - 0 - 3 - 4 - 0 - 6 - FCDSCY - ICDECH - CD C+ - - - - - 4 - gnl|BL_ORD_ID|1224 - 97111|polyprotein|ABR25251.1|Hepatitis C virus (isolate H77)|63746 - 1224 - 18 - - - 1 - 13.0826 - 22 - 21.0784 - 4 - 9 - 5 - 10 - 0 - 0 - 3 - 4 - 0 - 6 - FCDSCY - ICDECH - CD C+ - - - - - 5 - gnl|BL_ORD_ID|1366 - 108218|Genome polyprotein|P26664.3|Hepatitis C virus|11103 - 1366 - 10 - - - 1 - 12.6974 - 21 - 29.385 - 4 - 9 - 5 - 10 - 0 - 0 - 3 - 4 - 0 - 6 - FCDSCY - ICDECH - CD C+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 55 - Query_55 - M_525 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 56 - Query_56 - M_526 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 57 - Query_57 - M_527 - 9 - - - 1 - gnl|BL_ORD_ID|148 - 10962|envelope glycoprotein|AAU04921.1|Human T-lymphotropic virus 1|11908 - 148 - 9 - - - 1 - 13.0826 - 22 - 20.4374 - 1 - 7 - 2 - 8 - 0 - 0 - 3 - 5 - 0 - 7 - FAPSCAN - YSPSCCT - ++PSC - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 58 - Query_58 - M_528 - 9 - - - 1 - gnl|BL_ORD_ID|849 - 55620|EBNA3C latent protein|CAD53421.1|Human gammaherpesvirus 4|10376 - 849 - 9 - - - 1 - 14.2382 - 25 - 4.21767 - 1 - 7 - 2 - 8 - 0 - 0 - 3 - 6 - 0 - 7 - KVYDLVH - RIYDLIE - ++YDL+ - - - - - 2 - gnl|BL_ORD_ID|1518 - 140597|MCE-family protein MCE4A|YP_177977.1|Mycobacterium tuberculosis H37Rv|83332 - 1518 - 9 - - - 1 - 12.3122 - 20 - 63.7024 - 4 - 9 - 4 - 9 - 0 - 0 - 3 - 5 - 0 - 6 - DLVHSV - DLLHKI - DL+H + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 59 - Query_59 - M_529 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 60 - Query_60 - M_530 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 61 - Query_61 - M_531 - 9 - - - 1 - gnl|BL_ORD_ID|418 - 25237|Transcription activator BRLF1|P03209.1|Human herpesvirus 4 strain B95-8|10377 - 418 - 15 - - - 1 - 13.853 - 24 - 6.52084 - 1 - 5 - 9 - 13 - 0 - 0 - 4 - 5 - 0 - 5 - FVLDH - YVLDH - +VLDH - - - - - 2 - gnl|BL_ORD_ID|1156 - 76333|BRLF1|ABB89247.1|Human gammaherpesvirus 4|10376 - 1156 - 9 - - - 1 - 13.4678 - 23 - 9.85027 - 1 - 5 - 1 - 5 - 0 - 0 - 4 - 5 - 0 - 5 - FVLDH - YVLDH - +VLDH - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 62 - Query_62 - M_532 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 63 - Query_63 - M_533 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 64 - Query_64 - M_534 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 65 - Query_65 - M_535 - 9 - - - 1 - gnl|BL_ORD_ID|2045 - 184531|polyprotein|AFP27208.1|Dengue virus 4|11070 - 2045 - 10 - - - 1 - 13.4678 - 23 - 10.4367 - 3 - 9 - 2 - 8 - 0 - 0 - 5 - 6 - 0 - 7 - PEFLQTL - PESLETL - PE L+TL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 66 - Query_66 - M_536 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 67 - Query_67 - M_537 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 68 - Query_68 - M_538 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 69 - Query_69 - M_539 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 70 - Query_70 - M_540 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 71 - Query_71 - M_541 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 72 - Query_72 - M_542 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 73 - Query_73 - M_543 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 74 - Query_74 - M_544 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 75 - Query_75 - M_545 - 9 - - - 1 - gnl|BL_ORD_ID|654 - 38724|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 654 - 20 - - - 1 - 12.6974 - 21 - 29.0269 - 1 - 6 - 13 - 18 - 0 - 0 - 4 - 4 - 0 - 6 - QAYGGP - QLYRGP - Q Y GP - - - - - 2 - gnl|BL_ORD_ID|638 - 37970|tax|AAG48731.1|Human T-lymphotropic virus 2|11909 - 638 - 9 - - - 1 - 11.927 - 19 - 100.753 - 3 - 9 - 3 - 9 - 0 - 0 - 4 - 5 - 0 - 7 - YGGPRYL - YGYPVYV - YG P Y+ - - - - - 3 - gnl|BL_ORD_ID|389 - 23807|tax|AAG48731.1|Human T-lymphotropic virus 2|11909 - 389 - 23 - - - 1 - 11.5418 - 18 - 106.416 - 3 - 9 - 11 - 17 - 0 - 0 - 4 - 5 - 0 - 7 - YGGPRYL - YGYPVYV - YG P Y+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 76 - Query_76 - M_546 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 77 - Query_77 - M_547 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 78 - Query_78 - M_548 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 79 - Query_79 - M_549 - 9 - - - 1 - gnl|BL_ORD_ID|1040 - 69474|core protein|BAF42671.1|Hepatitis B virus|10407 - 1040 - 10 - - - 1 - 13.0826 - 22 - 13.5467 - 1 - 6 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - YLMEFG - YLVSFG - YL+ FG - - - - - 2 - gnl|BL_ORD_ID|201 - 15061|core protein|BAF42671.1|Hepatitis B virus|10407 - 201 - 9 - - - 1 - 13.0826 - 22 - 16.035 - 1 - 6 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - YLMEFG - YLVSFG - YL+ FG - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 80 - Query_80 - M_550 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 81 - Query_81 - M_551 - 9 - - - 1 - gnl|BL_ORD_ID|1351 - 108127|Genome polyprotein|P26664.3|Hepatitis C virus|11103 - 1351 - 10 - - - 1 - 14.2382 - 25 - 4.08767 - 3 - 9 - 3 - 9 - 0 - 0 - 5 - 6 - 0 - 7 - LGVGTAL - LGIGTVL - LG+GT L - - - - - 2 - gnl|BL_ORD_ID|1361 - 108169|Genome polyprotein|P26664.3|Hepatitis C virus|11103 - 1361 - 10 - - - 1 - 13.853 - 24 - 4.61192 - 3 - 9 - 4 - 10 - 0 - 0 - 5 - 6 - 0 - 7 - LGVGTAL - LGIGTVL - LG+GT L - - - - - 3 - gnl|BL_ORD_ID|1362 - 108171|polyprotein|AAF65953.1|Hepatitis C virus|11103 - 1362 - 10 - - - 1 - 13.853 - 24 - 4.94204 - 3 - 9 - 4 - 10 - 0 - 0 - 5 - 6 - 0 - 7 - LGVGTAL - LGIGTVL - LG+GT L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 82 - Query_82 - M_552 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 83 - Query_83 - M_553 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 84 - Query_84 - M_554 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 85 - Query_85 - M_555 - 9 - - - 1 - gnl|BL_ORD_ID|1633 - 146249|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 - 1633 - 17 - - - 1 - 15.0086 - 27 - 0.838218 - 3 - 9 - 9 - 15 - 0 - 0 - 4 - 6 - 0 - 7 - IFWTVYY - VMWTVYH - + WTVY+ - - - - - 2 - gnl|BL_ORD_ID|66 - 4910|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 66 - 20 - - - 1 - 15.0086 - 27 - 1.19565 - 3 - 9 - 7 - 13 - 0 - 0 - 4 - 6 - 0 - 7 - IFWTVYY - VCWTVYH - + WTVY+ - - - - - 3 - gnl|BL_ORD_ID|65 - 4909|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 - 65 - 15 - - - 1 - 15.0086 - 27 - 1.24275 - 3 - 9 - 7 - 13 - 0 - 0 - 4 - 6 - 0 - 7 - IFWTVYY - VCWTVYH - + WTVY+ - - - - - 4 - gnl|BL_ORD_ID|1632 - 146246|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 - 1632 - 17 - - - 1 - 14.6234 - 26 - 1.81173 - 3 - 9 - 9 - 15 - 0 - 0 - 4 - 6 - 0 - 7 - IFWTVYY - VCWTVYH - + WTVY+ - - - - - 5 - gnl|BL_ORD_ID|1674 - 148619|unnamed protein product|BAA14233.1|Hepatitis C virus|11103 - 1674 - 45 - - - 1 - 14.2382 - 25 - 3.72943 - 3 - 8 - 40 - 45 - 0 - 0 - 4 - 5 - 0 - 6 - IFWTVY - VCWTVY - + WTVY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 86 - Query_86 - M_556 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 87 - Query_87 - M_557 - 9 - - - 1 - gnl|BL_ORD_ID|949 - 62504|HBsAg protein|ABF71024.1|Hepatitis B virus|10407 - 949 - 9 - - - 1 - 11.1566 - 17 - 215.083 - 6 - 9 - 3 - 6 - 0 - 0 - 3 - 4 - 0 - 4 - WTSI - WTSL - WTS+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 88 - Query_88 - M_558 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 89 - Query_89 - M_559 - 9 - - - 1 - gnl|BL_ORD_ID|1758 - 154296|UL29|CAB06754.1|Human alphaherpesvirus 2|10310 - 1758 - 15 - - - 1 - 12.6974 - 21 - 24.0543 - 3 - 9 - 6 - 12 - 0 - 0 - 4 - 4 - 0 - 7 - FDHIRNF - FDRTRKF - FD R F - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 90 - Query_90 - M_560 - 9 - - - 1 - gnl|BL_ORD_ID|1474 - 130953|G1 and G2 surface glycoprotein precursor|AAG22532.1|Andes hantavirus|46607 - 1474 - 9 - - - 1 - 11.927 - 19 - 107.472 - 3 - 9 - 3 - 9 - 0 - 0 - 3 - 5 - 0 - 7 - PDELHAM - PDVAHSL - PD H++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 91 - Query_91 - M_561 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 92 - Query_92 - M_562 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 93 - Query_93 - M_563 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 94 - Query_94 - M_564 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 95 - Query_95 - M_565 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 96 - Query_96 - M_566 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 97 - Query_97 - M_567 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 98 - Query_98 - M_568 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 99 - Query_99 - M_569 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 100 - Query_100 - M_570 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 101 - Query_101 - M_571 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 102 - Query_102 - M_572 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 103 - Query_103 - M_573 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 104 - Query_104 - M_574 - 9 - - - 1 - gnl|BL_ORD_ID|777 - 51685|Nuclear antigen EBNA-3C|Q69140.1|Human gammaherpesvirus 4|10376 - 777 - 10 - - - 1 - 12.3122 - 20 - 49.5064 - 3 - 9 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - QEGFLAV - QNGALAI - Q G LA+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 105 - Query_105 - M_575 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 106 - Query_106 - M_576 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 107 - Query_107 - M_577 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 108 - Query_108 - M_578 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 109 - Query_109 - M_579 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 110 - Query_110 - M_580 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 111 - Query_111 - M_581 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 112 - Query_112 - M_582 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 113 - Query_113 - M_583 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 114 - Query_114 - M_584 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 115 - Query_115 - M_585 - 9 - - - 1 - gnl|BL_ORD_ID|1770 - 155131|ribonucleotide reductase large subunit|CAB06725.1|Human alphaherpesvirus 2|10310 - 1770 - 15 - - - 1 - 13.853 - 24 - 7.10896 - 3 - 6 - 5 - 8 - 0 - 0 - 4 - 4 - 0 - 4 - YFCR - YFCR - YFCR - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 116 - Query_116 - M_586 - 9 - - - 1 - gnl|BL_ORD_ID|1097 - 72563|polyprotein|AAB70696.1|Dengue virus type 1 Hawaii|10000440 - 1097 - 20 - - - 1 - 10.3862 - 15 - 509.034 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 5 - 0 - 9 - WAHAWPSPY - WHYDEDNPY - W + +PY - - - - - 2 - gnl|BL_ORD_ID|1943 - 180817|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1943 - 9 - - - 1 - 10.001 - 14 - 955.526 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 4 - 0 - 9 - WAHAWPSPY - WHYDQDHPY - W + PY - - - - - 3 - gnl|BL_ORD_ID|1931 - 180758|Nonstructural protein NS5|NP_739590.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1931 - 15 - - - 1 - 9.23063 - 12 - 1403.43 - 1 - 9 - 2 - 10 - 0 - 0 - 3 - 4 - 0 - 9 - WAHAWPSPY - WHYDQDHPY - W + PY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 117 - Query_117 - M_587 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 118 - Query_118 - M_588 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 119 - Query_119 - M_589 - 9 - - - 1 - gnl|BL_ORD_ID|134 - 9461|non structural protein 3|CAJ20172.1|Hepatitis C virus|11103 - 134 - 9 - - - 1 - 12.6974 - 21 - 31.4086 - 3 - 9 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - DRFHYLL - DNFPYLV - D F YL+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 120 - Query_120 - M_590 - 9 - - - 1 - gnl|BL_ORD_ID|1633 - 146249|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 - 1633 - 17 - - - 1 - 15.0086 - 27 - 0.838218 - 3 - 9 - 9 - 15 - 0 - 0 - 4 - 6 - 0 - 7 - IFWTVYY - VMWTVYH - + WTVY+ - - - - - 2 - gnl|BL_ORD_ID|66 - 4910|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 66 - 20 - - - 1 - 15.0086 - 27 - 1.19565 - 3 - 9 - 7 - 13 - 0 - 0 - 4 - 6 - 0 - 7 - IFWTVYY - VCWTVYH - + WTVY+ - - - - - 3 - gnl|BL_ORD_ID|65 - 4909|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 - 65 - 15 - - - 1 - 15.0086 - 27 - 1.24275 - 3 - 9 - 7 - 13 - 0 - 0 - 4 - 6 - 0 - 7 - IFWTVYY - VCWTVYH - + WTVY+ - - - - - 4 - gnl|BL_ORD_ID|1632 - 146246|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 - 1632 - 17 - - - 1 - 14.6234 - 26 - 1.81173 - 3 - 9 - 9 - 15 - 0 - 0 - 4 - 6 - 0 - 7 - IFWTVYY - VCWTVYH - + WTVY+ - - - - - 5 - gnl|BL_ORD_ID|1674 - 148619|unnamed protein product|BAA14233.1|Hepatitis C virus|11103 - 1674 - 45 - - - 1 - 14.2382 - 25 - 3.72943 - 3 - 8 - 40 - 45 - 0 - 0 - 4 - 5 - 0 - 6 - IFWTVY - VCWTVY - + WTVY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 121 - Query_121 - M_591 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 122 - Query_122 - M_592 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 123 - Query_123 - M_593 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 124 - Query_124 - M_594 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 125 - Query_125 - M_595 - 9 - - - 1 - gnl|BL_ORD_ID|1298 - 103392|polyprotein|BAB18806.1|Hepatitis C virus|11103 - 1298 - 9 - - - 1 - 13.0826 - 22 - 17.1877 - 4 - 9 - 4 - 9 - 0 - 0 - 4 - 4 - 0 - 6 - DPMVPL - DPTTPL - DP PL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 126 - Query_126 - M_596 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 127 - Query_127 - M_597 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 128 - Query_128 - M_598 - 9 - - - 1 - gnl|BL_ORD_ID|715 - 44133|Genome polyprotein|P26664.3|Hepatitis C virus genotype 1|41856 - 715 - 9 - - - 1 - 15.0086 - 27 - 1.21609 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 6 - 0 - 9 - NHDDDDVEI - NHDSPDAEL - NHD D E+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 129 - Query_129 - M_599 - 9 - - - 1 - gnl|BL_ORD_ID|1999 - 183670|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1999 - 10 - - - 1 - 14.2382 - 25 - 3.05549 - 1 - 7 - 3 - 9 - 0 - 0 - 6 - 7 - 0 - 7 - NASVNVS - NSSVNVS - N+SVNVS - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 130 - Query_130 - M_600 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 131 - Query_131 - M_601 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 132 - Query_132 - M_602 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 133 - Query_133 - M_603 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 134 - Query_134 - M_604 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 135 - Query_135 - M_605 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 136 - Query_136 - M_606 - 9 - - - 1 - gnl|BL_ORD_ID|2156 - 189292|gag protein|ABC40295.1|Human immunodeficiency virus 1|11676 - 2156 - 9 - - - 1 - 14.2382 - 25 - 3.05306 - 2 - 9 - 1 - 8 - 0 - 0 - 5 - 7 - 0 - 8 - ALYHCVAI - SLYNTVAI - +LY+ VAI - - - - - 2 - gnl|BL_ORD_ID|2201 - 190829|gag protein|BAB88077.1|Human immunodeficiency virus 1|11676 - 2201 - 10 - - - 1 - 13.853 - 24 - 5.77604 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 7 - 0 - 8 - ALYHCVAI - SLYNTVAV - +LY+ VA+ - - - - - 3 - gnl|BL_ORD_ID|1465 - 127003|gag polyprotein|BAB88551.1|Human immunodeficiency virus 1|11676 - 1465 - 10 - - - 1 - 13.853 - 24 - 6.19145 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 7 - 0 - 8 - ALYHCVAI - SLYNTVAV - +LY+ VA+ - - - - - 4 - gnl|BL_ORD_ID|2151 - 189287|gag protein|ADO94802.1|Human immunodeficiency virus 1|11676 - 2151 - 9 - - - 1 - 13.853 - 24 - 6.37844 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 7 - 0 - 8 - ALYHCVAI - SLYNTIAI - +LY+ +AI - - - - - 5 - gnl|BL_ORD_ID|2157 - 189293|gag protein|BAB88077.1|Human immunodeficiency virus 1|11676 - 2157 - 9 - - - 1 - 13.853 - 24 - 7.32819 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 7 - 0 - 8 - ALYHCVAI - SLYNTVAV - +LY+ VA+ - - - - - 6 - gnl|BL_ORD_ID|1466 - 127004|gag polyprotein|BAB88551.1|Human immunodeficiency virus 1|11676 - 1466 - 11 - - - 1 - 13.4678 - 23 - 7.61059 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 7 - 0 - 8 - ALYHCVAI - SLYNTVAV - +LY+ VA+ - - - - - 7 - gnl|BL_ORD_ID|1455 - 126492|gag protein|BAB88077.1|Human immunodeficiency virus 1|11676 - 1455 - 11 - - - 1 - 13.4678 - 23 - 7.61059 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 7 - 0 - 8 - ALYHCVAI - SLYNTVAV - +LY+ VA+ - - - - - 8 - gnl|BL_ORD_ID|2212 - 190981|gag protein|BAB88077.1|Human immunodeficiency virus 1|11676 - 2212 - 10 - - - 1 - 13.4678 - 23 - 9.40133 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 7 - 0 - 8 - ALYHCVAI - SLYNTVAV - +LY+ VA+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 137 - Query_137 - M_607 - 9 - - - 1 - gnl|BL_ORD_ID|974 - 64727|polyprotein precursor|NP_041724.2|West Nile virus|11082 - 974 - 9 - - - 1 - 13.4678 - 23 - 8.87313 - 2 - 9 - 1 - 8 - 0 - 0 - 5 - 5 - 0 - 8 - TLAPGVPL - TLARGFPF - TLA G P - - - - - 2 - gnl|BL_ORD_ID|652 - 38556|Genome polyprotein|Q00269.3|Hepatitis C virus|11103 - 652 - 9 - - - 1 - 12.6974 - 21 - 33.058 - 5 - 9 - 5 - 9 - 0 - 0 - 4 - 4 - 0 - 5 - PGVPL - PGVPF - PGVP - - - - - 3 - gnl|BL_ORD_ID|452 - 27345|Large envelope protein|P03138.3|Hepatitis B virus subtype ayw|10418 - 452 - 9 - - - 1 - 11.927 - 19 - 99.1366 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 6 - 0 - 7 - LAPGVPL - LSPFLPL - L+P +PL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 138 - Query_138 - M_608 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 139 - Query_139 - M_609 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 140 - Query_140 - M_610 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 141 - Query_141 - M_611 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 142 - Query_142 - M_612 - 9 - - - 1 - gnl|BL_ORD_ID|306 - 20686|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 - 306 - 11 - - - 1 - 15.779 - 29 - 0.466791 - 1 - 8 - 2 - 9 - 0 - 0 - 5 - 7 - 0 - 8 - QSVHPVVT - KSTHPMVT - +S HP+VT - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 143 - Query_143 - M_613 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 144 - Query_144 - M_614 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 145 - Query_145 - M_615 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 146 - Query_146 - M_616 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 147 - Query_147 - M_617 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 148 - Query_148 - M_618 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 149 - Query_149 - M_619 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 150 - Query_150 - M_620 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 151 - Query_151 - M_621 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 152 - Query_152 - M_622 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 153 - Query_153 - M_623 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 154 - Query_154 - M_624 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 155 - Query_155 - M_625 - 9 - - - 1 - gnl|BL_ORD_ID|86 - 6373|Genome polyprotein|SRC279960|Hepatitis C virus subtype 3a|356426 - 86 - 10 - - - 1 - 13.853 - 24 - 4.53299 - 4 - 9 - 4 - 9 - 0 - 0 - 5 - 6 - 0 - 6 - QDSTTV - QDATTV - QD+TTV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 156 - Query_156 - M_626 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 157 - Query_157 - M_627 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 158 - Query_158 - M_628 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 159 - Query_159 - M_629 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 160 - Query_160 - M_630 - 9 - - - 1 - gnl|BL_ORD_ID|1298 - 103392|polyprotein|BAB18806.1|Hepatitis C virus|11103 - 1298 - 9 - - - 1 - 13.0826 - 22 - 13.7128 - 3 - 7 - 4 - 8 - 0 - 0 - 4 - 5 - 0 - 5 - DPSTP - DPTTP - DP+TP - - - - - 2 - gnl|BL_ORD_ID|811 - 54342|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 - 811 - 20 - - - 1 - 12.3122 - 20 - 56.0891 - 2 - 9 - 11 - 18 - 0 - 0 - 4 - 4 - 0 - 8 - ADPSTPHL - GDPLFPEL - DP P L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 161 - Query_161 - M_631 - 9 - - - 1 - gnl|BL_ORD_ID|1083 - 71663|Spike glycoprotein precursor|P59594.1|SARS coronavirus|227859 - 1083 - 9 - - - 1 - 15.0086 - 27 - 1.17789 - 3 - 9 - 3 - 9 - 0 - 0 - 4 - 7 - 0 - 7 - YIHVTYI - FLHVTYV - ++HVTY+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 162 - Query_162 - M_632 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 163 - Query_163 - M_633 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 164 - Query_164 - M_634 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 165 - Query_165 - M_635 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 166 - Query_166 - M_636 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 167 - Query_167 - M_637 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 168 - Query_168 - M_638 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 169 - Query_169 - M_639 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 170 - Query_170 - M_640 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 171 - Query_171 - M_641 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 172 - Query_172 - M_642 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 173 - Query_173 - M_643 - 9 - - - 1 - gnl|BL_ORD_ID|658 - 39095|nonstructural protein 3|NP_722463.1|Dengue virus type 1 Hawaii|10000440 - 658 - 15 - - - 1 - 11.5418 - 18 - 108.251 - 1 - 7 - 9 - 15 - 0 - 0 - 4 - 5 - 0 - 7 - FTEELRR - FVELMRR - F E +RR - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 174 - Query_174 - M_644 - 9 - - - 1 - gnl|BL_ORD_ID|685 - 41269|kaposin|AAC57155.1|Human gammaherpesvirus 8|37296 - 685 - 15 - - - 1 - 12.6974 - 21 - 23.272 - 4 - 9 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - SRGITV - DRGLTV - RG+TV - - - - - 2 - gnl|BL_ORD_ID|1595 - 142231|Lipoprotein lpqH precursor|P0A5J0.1|Mycobacterium tuberculosis|1773 - 1595 - 24 - - - 1 - 12.6974 - 21 - 27.2634 - 5 - 9 - 3 - 7 - 0 - 0 - 4 - 5 - 0 - 5 - RGITV - RGLTV - RG+TV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 175 - Query_175 - M_645 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 176 - Query_176 - M_646 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 177 - Query_177 - M_647 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 178 - Query_178 - M_648 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 179 - Query_179 - M_649 - 9 - - - 1 - gnl|BL_ORD_ID|1770 - 155131|ribonucleotide reductase large subunit|CAB06725.1|Human alphaherpesvirus 2|10310 - 1770 - 15 - - - 1 - 13.0826 - 22 - 18.437 - 3 - 8 - 7 - 12 - 0 - 0 - 5 - 5 - 0 - 6 - CRKARE - CRCARE - CR ARE - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 180 - Query_180 - M_650 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 181 - Query_181 - M_651 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 182 - Query_182 - M_652 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 183 - Query_183 - M_653 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 184 - Query_184 - M_654 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 185 - Query_185 - M_655 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 186 - Query_186 - M_656 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 187 - Query_187 - M_657 - 9 - - - 1 - gnl|BL_ORD_ID|959 - 63010|6 kDa early secretory antigenic target|P0A564.2|Mycobacterium tuberculosis|1773 - 959 - 20 - - - 1 - 13.853 - 24 - 4.57317 - 3 - 9 - 10 - 16 - 0 - 0 - 5 - 6 - 0 - 7 - RNLIRTI - QNLARTI - +NL RTI - - - - - 2 - gnl|BL_ORD_ID|656 - 38922|6 kDa early secretory antigenic target|P0A564.2|Mycobacterium tuberculosis|1773 - 656 - 8 - - - 1 - 13.4678 - 23 - 11.0044 - 3 - 9 - 2 - 8 - 0 - 0 - 5 - 6 - 0 - 7 - RNLIRTI - QNLARTI - +NL RTI - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 188 - Query_188 - M_658 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 189 - Query_189 - M_659 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 190 - Query_190 - M_660 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 191 - Query_191 - M_661 - 9 - - - 1 - gnl|BL_ORD_ID|475 - 29186|polyprotein precursor|NP_041724.2|West Nile virus|11082 - 475 - 9 - - - 1 - 13.853 - 24 - 7.45662 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 7 - 0 - 9 - ISYTEVPTY - ITYTDVLRY - I+YT+V Y - - - - - 2 - gnl|BL_ORD_ID|1152 - 75718|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 1152 - 11 - - - 1 - 13.4678 - 23 - 11.9608 - 3 - 9 - 1 - 7 - 0 - 0 - 4 - 6 - 0 - 7 - YTEVPTY - YSEHPTF - Y+E PT+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 192 - Query_192 - M_662 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 193 - Query_193 - M_663 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 194 - Query_194 - M_664 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 195 - Query_195 - M_665 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 196 - Query_196 - M_666 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 197 - Query_197 - M_667 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 198 - Query_198 - M_668 - 9 - - - 1 - gnl|BL_ORD_ID|2282 - 419124|polyprotein|ACF49259.1|Dengue virus type 1 Hawaii|10000440 - 2282 - 9 - - - 1 - 11.927 - 19 - 84.261 - 3 - 8 - 3 - 8 - 0 - 0 - 4 - 4 - 0 - 6 - EPKKKP - EPGKNP - EP K P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 199 - Query_199 - M_669 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 200 - Query_200 - M_670 - 9 - - - 1 - gnl|BL_ORD_ID|707 - 43447|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 - 707 - 20 - - - 1 - 12.6974 - 21 - 22.9279 - 1 - 9 - 5 - 13 - 0 - 0 - 5 - 5 - 0 - 9 - FFFHNPKPL - IFFFNPGEL - FF NP L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 201 - Query_201 - M_671 - 9 - - - 1 - gnl|BL_ORD_ID|1121 - 74407|polyprotein|AAU89634.1|Hepatitis C virus subtype 2a|31649 - 1121 - 9 - - - 1 - 12.3122 - 20 - 54.8462 - 2 - 7 - 4 - 9 - 0 - 0 - 2 - 4 - 0 - 6 - HWNWII - RWEWVV - W W++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 202 - Query_202 - M_672 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 203 - Query_203 - M_673 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 204 - Query_204 - M_674 - 9 - - - 1 - gnl|BL_ORD_ID|1435 - 116781|Nucleoprotein|P05133.1|Hantaan virus 76-118|11602 - 1435 - 15 - - - 1 - 12.6974 - 21 - 26.9941 - 1 - 6 - 8 - 13 - 0 - 0 - 4 - 4 - 0 - 6 - YQHYFR - YQSYLR - YQ Y R - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 205 - Query_205 - M_675 - 9 - - - 1 - gnl|BL_ORD_ID|2259 - 294287|gag protein|ABI20203.1|Human immunodeficiency virus 1|11676 - 2259 - 17 - - - 1 - 13.4678 - 23 - 9.7917 - 3 - 9 - 8 - 14 - 0 - 0 - 4 - 7 - 0 - 7 - NSMINTM - NTMLNTV - N+M+NT+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 206 - Query_206 - M_676 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 207 - Query_207 - M_677 - 9 - - - 1 - gnl|BL_ORD_ID|1206 - 96156|polyprotein|ABR25251.1|Hepatitis C virus (isolate H77)|63746 - 1206 - 21 - - - 1 - 13.0826 - 22 - 17.0133 - 2 - 9 - 6 - 13 - 0 - 0 - 4 - 5 - 0 - 8 - VDYPGDPV - VDFSLDPT - VD+ DP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 208 - Query_208 - M_678 - 9 - - - 1 - gnl|BL_ORD_ID|1258 - 98254|trans-sialidase, putative|EAN81042.1|Trypanosoma cruzi|5693 - 1258 - 9 - - - 1 - 12.6974 - 21 - 26.4654 - 2 - 7 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - TAPLYS - TLPVYS - T P+YS - - - - - 2 - gnl|BL_ORD_ID|1255 - 98242|trans-sialidase, putative|EAN81042.1|Trypanosoma cruzi|5693 - 1255 - 9 - - - 1 - 12.6974 - 21 - 27.8632 - 2 - 7 - 3 - 8 - 0 - 0 - 4 - 5 - 0 - 6 - TAPLYS - TLPVYS - T P+YS - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 209 - Query_209 - M_679 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 210 - Query_210 - M_680 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 211 - Query_211 - M_681 - 9 - - - 1 - gnl|BL_ORD_ID|701 - 42797|6 kDa early secretory antigenic target|P0A564.2|Mycobacterium tuberculosis|1773 - 701 - 20 - - - 1 - 13.853 - 24 - 5.6992 - 1 - 5 - 4 - 8 - 0 - 0 - 4 - 4 - 0 - 5 - QAWNF - QQWNF - Q WNF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 212 - Query_212 - M_682 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 213 - Query_213 - M_683 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 214 - Query_214 - M_684 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 215 - Query_215 - M_685 - 9 - - - 1 - gnl|BL_ORD_ID|126 - 8920|M protein, serotype 5 precursor|P02977.2|Streptococcus pyogenes serotype M5|301449 - 126 - 18 - - - 1 - 11.5418 - 18 - 105.162 - 1 - 8 - 3 - 10 - 0 - 0 - 4 - 7 - 0 - 8 - MAKQIKTK - LAKEQKSK - +AK+ K+K - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 216 - Query_216 - M_686 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 217 - Query_217 - M_687 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 218 - Query_218 - M_688 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 219 - Query_219 - M_689 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 220 - Query_220 - M_690 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 221 - Query_221 - M_691 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 222 - Query_222 - M_692 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 223 - Query_223 - M_693 - 9 - - - 1 - gnl|BL_ORD_ID|386 - 23621|Genome polyprotein|P26664.3|Hepatitis C virus (isolate 1)|11104 - 386 - 11 - - - 1 - 14.2382 - 25 - 3.03901 - 3 - 8 - 1 - 6 - 0 - 0 - 5 - 5 - 0 - 6 - HSGAGK - HDGAGK - H GAGK - - - - - 2 - gnl|BL_ORD_ID|1874 - 180503|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1874 - 10 - - - 1 - 14.2382 - 25 - 3.21576 - 3 - 8 - 1 - 6 - 0 - 0 - 5 - 5 - 0 - 6 - HSGAGK - HPGAGK - H GAGK - - - - - 3 - gnl|BL_ORD_ID|385 - 23620|Genome polyprotein|SRC279960|Hepatitis C virus genotype 1|41856 - 385 - 10 - - - 1 - 14.2382 - 25 - 3.56308 - 3 - 8 - 1 - 6 - 0 - 0 - 5 - 5 - 0 - 6 - HSGAGK - HDGAGK - H GAGK - - - - - 4 - gnl|BL_ORD_ID|384 - 23619|Genome polyprotein|P27958.3|Hepatitis C virus (isolate H)|11108 - 384 - 9 - - - 1 - 14.2382 - 25 - 3.87216 - 3 - 8 - 1 - 6 - 0 - 0 - 5 - 5 - 0 - 6 - HSGAGK - HDGAGK - H GAGK - - - - - 5 - gnl|BL_ORD_ID|1015 - 67471|Genome polyprotein|Q99IB8.3|Hepatitis C virus JFH-1|356411 - 1015 - 9 - - - 1 - 13.853 - 24 - 5.45887 - 2 - 9 - 1 - 8 - 0 - 0 - 5 - 6 - 0 - 8 - THSGAGKF - TYSTYGKF - T+S GKF - - - - - 6 - gnl|BL_ORD_ID|474 - 29182|polyprotein|BAD73991.1|Hepatitis C virus subtype 1b|31647 - 474 - 9 - - - 1 - 13.853 - 24 - 5.45887 - 2 - 9 - 2 - 9 - 0 - 0 - 5 - 6 - 0 - 8 - THSGAGKF - TYSTYGKF - T+S GKF - - - - - 7 - gnl|BL_ORD_ID|1995 - 183598|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1995 - 10 - - - 1 - 13.0826 - 22 - 15.2954 - 3 - 8 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - HSGAGK - HPGSGK - H G+GK - - - - - 8 - gnl|BL_ORD_ID|847 - 55336|EBNA-1|YP_401677.1|Human gammaherpesvirus 4|10376 - 847 - 15 - - - 1 - 12.3122 - 20 - 58.4135 - 2 - 7 - 10 - 15 - 0 - 0 - 4 - 4 - 0 - 6 - THSGAG - THGGTG - TH G G - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 224 - Query_224 - M_694 - 9 - - - 1 - gnl|BL_ORD_ID|1770 - 155131|ribonucleotide reductase large subunit|CAB06725.1|Human alphaherpesvirus 2|10310 - 1770 - 15 - - - 1 - 13.4678 - 23 - 10.0248 - 4 - 8 - 4 - 8 - 0 - 0 - 4 - 4 - 0 - 5 - RYFCR - EYFCR - YFCR - - - - - 2 - gnl|BL_ORD_ID|469 - 28484|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 469 - 9 - - - 1 - 13.0826 - 22 - 21.8994 - 2 - 7 - 3 - 8 - 0 - 0 - 3 - 6 - 0 - 6 - KYRYFC - EYRHYC - +YR++C - - - - - 3 - gnl|BL_ORD_ID|1406 - 110846|E6 protein|CAB45108.1|Human papillomavirus type 16|333760 - 1406 - 9 - - - 1 - 13.0826 - 22 - 22.2806 - 2 - 7 - 1 - 6 - 0 - 0 - 3 - 6 - 0 - 6 - KYRYFC - EYRHYC - +YR++C - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 225 - Query_225 - M_695 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 226 - Query_226 - M_696 - 9 - - - 1 - gnl|BL_ORD_ID|160 - 12183|EBNA3C latent protein|CAD53421.1|Human gammaherpesvirus 4|10376 - 160 - 9 - - - 1 - 11.927 - 19 - 97.5444 - 3 - 8 - 3 - 8 - 0 - 0 - 4 - 5 - 0 - 6 - GLGGRH - GVGWRH - G+G RH - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 227 - Query_227 - M_697 - 9 - - - 1 - gnl|BL_ORD_ID|1760 - 154387|RL2|CAB06760.1|Human alphaherpesvirus 2|10310 - 1760 - 15 - - - 1 - 13.0826 - 22 - 13.39 - 2 - 9 - 6 - 13 - 0 - 0 - 5 - 5 - 0 - 8 - HTGTSVVL - HIGAYVVL - H G VVL - - - - - 2 - gnl|BL_ORD_ID|1764 - 154725|RL2|CAB06760.1|Human alphaherpesvirus 2|10310 - 1764 - 15 - - - 1 - 13.0826 - 22 - 17.5339 - 2 - 9 - 2 - 9 - 0 - 0 - 5 - 5 - 0 - 8 - HTGTSVVL - HIGAYVVL - H G VVL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 228 - Query_228 - M_698 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 229 - Query_229 - M_699 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 230 - Query_230 - M_700 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 231 - Query_231 - M_701 - 9 - - - 1 - gnl|BL_ORD_ID|1265 - 98603|trans-sialidase, putative|EAN82716.1|Trypanosoma cruzi|5693 - 1265 - 9 - - - 1 - 13.0826 - 22 - 15.7589 - 5 - 9 - 5 - 9 - 0 - 0 - 4 - 4 - 0 - 5 - NRPFY - NRSFY - NR FY - - - - - 2 - gnl|BL_ORD_ID|1981 - 183231|polyprotein|AFP27208.1|Dengue virus 4|11070 - 1981 - 10 - - - 1 - 13.0826 - 22 - 18.4997 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 4 - 0 - 8 - FPLRNRPF - FPQSNSPI - FP N P - - - - - 3 - gnl|BL_ORD_ID|1866 - 180460|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1866 - 10 - - - 1 - 12.6974 - 21 - 28.8893 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 4 - 0 - 8 - FPLRNRPF - FPQSNAPI - FP N P - - - - - 4 - gnl|BL_ORD_ID|1704 - 150217|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1704 - 9 - - - 1 - 12.6974 - 21 - 33.6262 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 4 - 0 - 8 - FPLRNRPF - FPQSNAPI - FP N P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 232 - Query_232 - M_702 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 233 - Query_233 - M_703 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 234 - Query_234 - M_704 - 9 - - - 1 - gnl|BL_ORD_ID|1755 - 154041|major capsid protein|CAB06743.1|Human alphaherpesvirus 2|10310 - 1755 - 15 - - - 1 - 11.927 - 19 - 87.4721 - 3 - 9 - 7 - 13 - 0 - 0 - 4 - 4 - 0 - 7 - YPRFLYL - YPAVFYL - YP YL - - - - - 2 - gnl|BL_ORD_ID|855 - 55779|fusion protein|BAB60865.1|Measles virus|11234 - 855 - 9 - - - 1 - 11.927 - 19 - 91.4136 - 3 - 9 - 3 - 9 - 0 - 0 - 4 - 5 - 0 - 7 - YPRFLYL - YPDAVYL - YP +YL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 235 - Query_235 - M_705 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 236 - Query_236 - M_706 - 9 - - - 1 - gnl|BL_ORD_ID|1948 - 180850|polyprotein|AFP27208.1|Dengue virus 4|11070 - 1948 - 10 - - - 1 - 12.3122 - 20 - 52.9061 - 1 - 7 - 1 - 7 - 0 - 0 - 3 - 5 - 0 - 7 - YYPPGVV - YTPEGII - Y P G++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 237 - Query_237 - M_707 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 238 - Query_238 - M_708 - 9 - - - 1 - gnl|BL_ORD_ID|1950 - 181035|||| - 1950 - 44 - - - 1 - 12.6974 - 21 - 25.8912 - 1 - 9 - 11 - 19 - 0 - 0 - 4 - 7 - 0 - 9 - RVFPLRGKI - KLFPGGGQI - ++FP G+I - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 239 - Query_239 - M_709 - 9 - - - 1 - gnl|BL_ORD_ID|1139 - 75356|EBNA3A nuclear protein|Q8AZJ8|Human gammaherpesvirus 4|10376 - 1139 - 9 - - - 1 - 14.6234 - 26 - 2.22125 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 6 - 0 - 9 - YPLPVANGM - YPLHEQHGM - YPL +GM - - - - - 2 - gnl|BL_ORD_ID|1144 - 75438|polyprotein|AAF65962.1|Hepatitis C virus|11103 - 1144 - 20 - - - 1 - 10.3862 - 15 - 376.551 - 1 - 9 - 3 - 11 - 0 - 0 - 4 - 5 - 0 - 9 - YPLPVANGM - WPLYGNEGM - +PL GM - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 240 - Query_240 - M_710 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 241 - Query_241 - M_711 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 242 - Query_242 - M_712 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 243 - Query_243 - M_713 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 244 - Query_244 - M_714 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 245 - Query_245 - M_715 - 9 - - - 1 - gnl|BL_ORD_ID|1449 - 126486|gag protein|ADK33372.1|Human immunodeficiency virus 1|11676 - 1449 - 10 - - - 1 - 15.0086 - 27 - 0.933082 - 1 - 9 - 1 - 9 - 0 - 0 - 6 - 8 - 0 - 9 - KALFWTVAM - KSLFNTVAV - K+LF TVA+ - - - - - 2 - gnl|BL_ORD_ID|1450 - 126487|gag protein|ADK33372.1|Human immunodeficiency virus 1|11676 - 1450 - 11 - - - 1 - 15.0086 - 27 - 1.06128 - 1 - 9 - 1 - 9 - 0 - 0 - 6 - 8 - 0 - 9 - KALFWTVAM - KSLFNTVAV - K+LF TVA+ - - - - - 3 - gnl|BL_ORD_ID|1447 - 126484|gag protein|AAW03034.1|Human immunodeficiency virus 1|11676 - 1447 - 10 - - - 1 - 15.0086 - 27 - 1.32867 - 1 - 8 - 1 - 8 - 0 - 0 - 6 - 7 - 0 - 8 - KALFWTVA - KSLFNTVA - K+LF TVA - - - - - 4 - gnl|BL_ORD_ID|1448 - 126485|gag protein|AAW03034.1|Human immunodeficiency virus 1|11676 - 1448 - 11 - - - 1 - 14.6234 - 26 - 1.54725 - 1 - 8 - 1 - 8 - 0 - 0 - 6 - 7 - 0 - 8 - KALFWTVA - KSLFNTVA - K+LF TVA - - - - - 5 - gnl|BL_ORD_ID|1445 - 126482|gag protein|AAY98604.1|Human immunodeficiency virus 1|11676 - 1445 - 10 - - - 1 - 14.6234 - 26 - 1.7557 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 8 - 0 - 9 - KALFWTVAM - KSLFNTIAV - K+LF T+A+ - - - - - 6 - gnl|BL_ORD_ID|1446 - 126483|gag protein|AAY98604.1|Human immunodeficiency virus 1|11676 - 1446 - 11 - - - 1 - 14.6234 - 26 - 2.02142 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 8 - 0 - 9 - KALFWTVAM - KSLFNTIAV - K+LF T+A+ - - - - - 7 - gnl|BL_ORD_ID|2198 - 190826|gag polyprotein|CAB81949.1|Human immunodeficiency virus 1|11676 - 2198 - 10 - - - 1 - 14.6234 - 26 - 2.33097 - 1 - 8 - 1 - 8 - 0 - 0 - 5 - 7 - 0 - 8 - KALFWTVA - KSLFNTIA - K+LF T+A - - - - - 8 - gnl|BL_ORD_ID|2204 - 190961|gag protein|BAC45024.1|Human immunodeficiency virus 1|11676 - 2204 - 10 - - - 1 - 14.2382 - 25 - 2.75947 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 8 - 0 - 9 - KALFWTVAM - RSLFNTVAV - ++LF TVA+ - - - - - 9 - gnl|BL_ORD_ID|1444 - 126481|gag polyprotein p17 region|BAA83653.1|Human immunodeficiency virus 1|11676 - 1444 - 11 - - - 1 - 14.2382 - 25 - 2.78989 - 1 - 8 - 1 - 8 - 0 - 0 - 5 - 7 - 0 - 8 - KALFWTVA - KSLFNTIA - K+LF T+A - - - - - 10 - gnl|BL_ORD_ID|1460 - 126997|gag protein|BAC45024.1|Human immunodeficiency virus 1|11676 - 1460 - 11 - - - 1 - 14.2382 - 25 - 3.14502 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 8 - 0 - 9 - KALFWTVAM - RSLFNTVAV - ++LF TVA+ - - - - - 11 - gnl|BL_ORD_ID|1458 - 126995|gag polyprotein|BAB19171.1|Human immunodeficiency virus 1|11676 - 1458 - 10 - - - 1 - 14.2382 - 25 - 4.08767 - 1 - 8 - 1 - 8 - 0 - 0 - 5 - 7 - 0 - 8 - KALFWTVA - RSLFNTVA - ++LF TVA - - - - - 12 - gnl|BL_ORD_ID|1459 - 126996|Gag protein|Q9YYH6|Human immunodeficiency virus 1|11676 - 1459 - 11 - - - 1 - 13.853 - 24 - 4.67708 - 1 - 8 - 1 - 8 - 0 - 0 - 5 - 7 - 0 - 8 - KALFWTVA - RSLFNTVA - ++LF TVA - - - - - 13 - gnl|BL_ORD_ID|2203 - 190960|gag-pol polyprotein|BAC02551.1|Human immunodeficiency virus 1|11676 - 2203 - 10 - - - 1 - 13.853 - 24 - 5.38895 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 8 - 0 - 9 - KALFWTVAM - RSLFNTIAV - ++LF T+A+ - - - - - 14 - gnl|BL_ORD_ID|1457 - 126994|gag-pol polyprotein|BAC02551.1|Human immunodeficiency virus 1|11676 - 1457 - 11 - - - 1 - 13.853 - 24 - 6.17581 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 8 - 0 - 9 - KALFWTVAM - RSLFNTIAV - ++LF T+A+ - - - - - 15 - gnl|BL_ORD_ID|2202 - 190959|gag polyprotein|BAB19174.1|Human immunodeficiency virus 1|11676 - 2202 - 10 - - - 1 - 13.4678 - 23 - 7.49677 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 7 - 0 - 8 - KALFWTVA - RSLFNTIA - ++LF T+A - - - - - 16 - gnl|BL_ORD_ID|1456 - 126993|gag polyprotein|BAB19174.1|Human immunodeficiency virus 1|11676 - 1456 - 11 - - - 1 - 13.4678 - 23 - 8.59697 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 7 - 0 - 8 - KALFWTVA - RSLFNTIA - ++LF T+A - - - - - 17 - gnl|BL_ORD_ID|1847 - 180236|gag|BAC81459.1|Human immunodeficiency virus 1|11676 - 1847 - 9 - - - 1 - 13.0826 - 22 - 17.1877 - 2 - 9 - 1 - 8 - 0 - 0 - 5 - 7 - 0 - 8 - ALFWTVAM - SLFNTVAV - +LF TVA+ - - - - - 18 - gnl|BL_ORD_ID|2208 - 190975|gag protein|BAC45024.1|Human immunodeficiency virus 1|11676 - 2208 - 10 - - - 1 - 13.0826 - 22 - 19.4818 - 2 - 9 - 1 - 8 - 0 - 0 - 5 - 7 - 0 - 8 - ALFWTVAM - SLFNTVAV - +LF TVA+ - - - - - 19 - gnl|BL_ORD_ID|1846 - 180233|gag protein|ACZ34075.1|Human immunodeficiency virus 1|11676 - 1846 - 9 - - - 1 - 13.0826 - 22 - 22.6682 - 2 - 8 - 1 - 7 - 0 - 0 - 5 - 6 - 0 - 7 - ALFWTVA - SLFNTVA - +LF TVA - - - - - 20 - gnl|BL_ORD_ID|1475 - 131070|Gag protein|Q9IN85|HIV-1 M:A|505184 - 1475 - 9 - - - 1 - 12.6974 - 21 - 23.4633 - 2 - 8 - 1 - 7 - 0 - 0 - 5 - 6 - 0 - 7 - ALFWTVA - SLFNTVA - +LF TVA - - - - - 21 - gnl|BL_ORD_ID|1468 - 127083|Gag protein|Q9YYH6|Human immunodeficiency virus 1|11676 - 1468 - 10 - - - 1 - 12.6974 - 21 - 26.9859 - 2 - 8 - 1 - 7 - 0 - 0 - 5 - 6 - 0 - 7 - ALFWTVA - SLFNTVA - +LF TVA - - - - - 22 - gnl|BL_ORD_ID|2145 - 189204|||| - 2145 - 9 - - - 1 - 12.6974 - 21 - 29.3325 - 2 - 8 - 1 - 7 - 0 - 0 - 5 - 6 - 0 - 7 - ALFWTVA - ALYNTVA - AL+ TVA - - - - - 23 - gnl|BL_ORD_ID|2147 - 189277|gag protein|AAY98604.1|Human immunodeficiency virus 1|11676 - 2147 - 9 - - - 1 - 12.6974 - 21 - 31.4086 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 7 - 0 - 8 - ALFWTVAM - SLFNTIAV - +LF T+A+ - - - - - 24 - gnl|BL_ORD_ID|1467 - 127082|gag-pol polyprotein|BAC02551.1|Human immunodeficiency virus 1|11676 - 1467 - 10 - - - 1 - 12.6974 - 21 - 36.0093 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 7 - 0 - 8 - ALFWTVAM - SLFNTIAV - +LF T+A+ - - - - - 25 - gnl|BL_ORD_ID|1845 - 180191|gag polyprotein|BAB19174.1|Human immunodeficiency virus 1|11676 - 1845 - 9 - - - 1 - 12.3122 - 20 - 44.1001 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 6 - 0 - 7 - ALFWTVA - SLFNTIA - +LF T+A - - - - - 26 - gnl|BL_ORD_ID|2207 - 190974|gag polyprotein|BAB19174.1|Human immunodeficiency virus 1|11676 - 2207 - 10 - - - 1 - 12.3122 - 20 - 50.3363 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 6 - 0 - 7 - ALFWTVA - SLFNTIA - +LF T+A - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 246 - Query_246 - M_716 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 247 - Query_247 - M_717 - 9 - - - 1 - gnl|BL_ORD_ID|545 - 33382|polyprotein|AAB67037.1|Hepatitis C virus|11103 - 545 - 15 - - - 1 - 12.6974 - 21 - 25.6947 - 3 - 9 - 5 - 11 - 0 - 0 - 3 - 6 - 0 - 7 - SPMPYTY - TPMGFSY - +PM ++Y - - - - - 2 - gnl|BL_ORD_ID|1068 - 70491|envelope glycoprotein|AAC28452.1|Human immunodeficiency virus 1|11676 - 1068 - 10 - - - 1 - 11.5418 - 18 - 141.547 - 1 - 6 - 2 - 7 - 0 - 0 - 4 - 4 - 0 - 6 - PTSPMP - PTDPNP - PT P P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 248 - Query_248 - M_718 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 249 - Query_249 - M_719 - 9 - - - 1 - gnl|BL_ORD_ID|722 - 44920|tegument protein pp65|YP_002608275.1|Human betaherpesvirus 5|10359 - 722 - 9 - - - 1 - 13.853 - 24 - 4.4402 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 8 - 0 - 9 - NVVRLVATI - NLVPMVATV - N+V +VAT+ - - - - - 2 - gnl|BL_ORD_ID|838 - 55029|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 838 - 11 - - - 1 - 13.853 - 24 - 4.75889 - 1 - 9 - 2 - 10 - 0 - 0 - 5 - 8 - 0 - 9 - NVVRLVATI - NLVPMVATV - N+V +VAT+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 250 - Query_250 - M_720 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 251 - Query_251 - M_721 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 252 - Query_252 - M_722 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 253 - Query_253 - M_723 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 254 - Query_254 - M_724 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 255 - Query_255 - M_725 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 256 - Query_256 - M_726 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 257 - Query_257 - M_727 - 9 - - - 1 - gnl|BL_ORD_ID|1474 - 130953|G1 and G2 surface glycoprotein precursor|AAG22532.1|Andes hantavirus|46607 - 1474 - 9 - - - 1 - 11.927 - 19 - 107.472 - 3 - 9 - 3 - 9 - 0 - 0 - 3 - 5 - 0 - 7 - PDELHAM - PDVAHSL - PD H++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 258 - Query_258 - M_728 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 259 - Query_259 - M_729 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 260 - Query_260 - M_730 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 261 - Query_261 - M_731 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 262 - Query_262 - M_732 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 263 - Query_263 - M_733 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 264 - Query_264 - M_734 - 9 - - - 1 - gnl|BL_ORD_ID|284 - 19337|gag protein|AAW57872.1|Human immunodeficiency virus 1|11676 - 284 - 9 - - - 1 - 13.0826 - 22 - 16.035 - 2 - 7 - 3 - 8 - 0 - 0 - 3 - 5 - 0 - 6 - MDRWNE - LDRWEK - +DRW + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 265 - Query_265 - M_735 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 266 - Query_266 - M_736 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 267 - Query_267 - M_737 - 9 - - - 1 - gnl|BL_ORD_ID|672 - 40288|kaposin|AAC57155.1|Human gammaherpesvirus 8|37296 - 672 - 15 - - - 1 - 13.0826 - 22 - 18.437 - 1 - 7 - 5 - 11 - 0 - 0 - 5 - 5 - 0 - 7 - LAIKVTP - LAISVVP - LAI V P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 268 - Query_268 - M_738 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 269 - Query_269 - M_739 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 270 - Query_270 - M_740 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 271 - Query_271 - M_741 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 272 - Query_272 - M_742 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 273 - Query_273 - M_743 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 274 - Query_274 - M_744 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 275 - Query_275 - M_745 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 276 - Query_276 - M_746 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 277 - Query_277 - M_747 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 278 - Query_278 - M_748 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 279 - Query_279 - M_749 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 280 - Query_280 - M_750 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 281 - Query_281 - M_751 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 282 - Query_282 - M_752 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 283 - Query_283 - M_753 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 284 - Query_284 - M_754 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 285 - Query_285 - M_755 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 286 - Query_286 - M_756 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 287 - Query_287 - M_757 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 288 - Query_288 - M_758 - 9 - - - 1 - gnl|BL_ORD_ID|1763 - 154585|ribonucleotide reductase large subunit|CAB06725.1|Human alphaherpesvirus 2|10310 - 1763 - 15 - - - 1 - 12.3122 - 20 - 42.5209 - 1 - 9 - 5 - 13 - 0 - 0 - 4 - 5 - 0 - 9 - YQEEMIQCY - YMESVFQMY - Y E + Q Y - - - - - 2 - gnl|BL_ORD_ID|1586 - 141480|ribonucleotide reductase subunit 1|NP_044641.1|Human alphaherpesvirus 1|10298 - 1586 - 9 - - - 1 - 11.927 - 19 - 77.6399 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 5 - 0 - 9 - YQEEMIQCY - YMESVFQMY - Y E + Q Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 289 - Query_289 - M_759 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 290 - Query_290 - M_760 - 9 - - - 1 - gnl|BL_ORD_ID|889 - 58463|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 889 - 20 - - - 1 - 13.853 - 24 - 5.89466 - 3 - 9 - 12 - 18 - 0 - 0 - 5 - 6 - 0 - 7 - YVYPLPV - YVYALPL - YVY LP+ - - - - - 2 - gnl|BL_ORD_ID|338 - 21242|polymerase|ACF94272.1|Hepatitis B virus|10407 - 338 - 9 - - - 1 - 11.1566 - 17 - 287.485 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 5 - 0 - 9 - GAYVYPLPV - GLYSSTVPV - G Y +PV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 291 - Query_291 - M_761 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 292 - Query_292 - M_762 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 293 - Query_293 - M_763 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 294 - Query_294 - M_764 - 9 - - - 1 - gnl|BL_ORD_ID|1948 - 180850|polyprotein|AFP27208.1|Dengue virus 4|11070 - 1948 - 10 - - - 1 - 12.3122 - 20 - 49.5064 - 2 - 8 - 1 - 7 - 0 - 0 - 3 - 5 - 0 - 7 - YYPPGVV - YTPEGII - Y P G++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 295 - Query_295 - M_765 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 296 - Query_296 - M_766 - 9 - - - 1 - gnl|BL_ORD_ID|356 - 22235|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 356 - 15 - - - 1 - 16.1642 - 30 - 0.297937 - 1 - 8 - 6 - 13 - 0 - 0 - 5 - 8 - 0 - 8 - SALEYLLP - SALQFLIP - SAL++L+P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 297 - Query_297 - M_767 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 298 - Query_298 - M_768 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 299 - Query_299 - M_769 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 300 - Query_300 - M_770 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 301 - Query_301 - M_771 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 302 - Query_302 - M_772 - 9 - - - 1 - gnl|BL_ORD_ID|1924 - 180726|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1924 - 15 - - - 1 - 13.0826 - 22 - 20.3784 - 3 - 8 - 8 - 13 - 0 - 0 - 3 - 4 - 0 - 6 - SQWDHG - TAWDFG - + WD G - - - - - 2 - gnl|BL_ORD_ID|439 - 27061|envelope glycoprotein|ABU89742.1|Dengue virus 2 Thailand/16681/84|31634 - 439 - 10 - - - 1 - 12.6974 - 21 - 29.385 - 3 - 8 - 5 - 10 - 0 - 0 - 3 - 4 - 0 - 6 - SQWDHG - TAWDFG - + WD G - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 303 - Query_303 - M_773 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 304 - Query_304 - M_774 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 305 - Query_305 - M_775 - 9 - - - 1 - gnl|BL_ORD_ID|1813 - 177701|polyprotein|ACZ60104.1|Hepatitis C virus subtype 3a|356426 - 1813 - 18 - - - 1 - 16.1642 - 30 - 0.340428 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 7 - 0 - 9 - HAQVCSLYI - KAKICGLYL - A++C LY+ - - - - - 2 - gnl|BL_ORD_ID|1793 - 164264|nucleocapsid protein|AAA43837.1|Hantaan virus 76-118|11602 - 1793 - 15 - - - 1 - 13.4678 - 23 - 11.1066 - 1 - 8 - 7 - 14 - 0 - 0 - 4 - 4 - 0 - 8 - HAQVCSLY - RTAVCGLY - VC LY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 306 - Query_306 - M_776 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 307 - Query_307 - M_777 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 308 - Query_308 - M_778 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 309 - Query_309 - M_779 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 310 - Query_310 - M_780 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 311 - Query_311 - M_781 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 312 - Query_312 - M_782 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 313 - Query_313 - M_783 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 314 - Query_314 - M_784 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 315 - Query_315 - M_785 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 316 - Query_316 - M_786 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 317 - Query_317 - M_787 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 318 - Query_318 - M_788 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 319 - Query_319 - M_789 - 9 - - - 1 - gnl|BL_ORD_ID|227 - 16751|pol protein|BAA32832.1|Hepatitis B virus|10407 - 227 - 9 - - - 1 - 15.0086 - 27 - 1.21609 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 7 - 0 - 9 - YLLRAGVHL - FLLSLGIHL - +LL G+HL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 320 - Query_320 - M_790 - 9 - - - 1 - gnl|BL_ORD_ID|1715 - 150378|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1715 - 9 - - - 1 - 13.4678 - 23 - 7.85574 - 1 - 6 - 4 - 9 - 0 - 0 - 5 - 5 - 0 - 6 - LVTPHM - LVTPSM - LVTP M - - - - - 2 - gnl|BL_ORD_ID|1908 - 180657|polyprotein|CDF77361.1|Dengue virus 3|11069 - 1908 - 9 - - - 1 - 13.4678 - 23 - 7.99354 - 1 - 7 - 2 - 8 - 0 - 0 - 5 - 5 - 0 - 7 - LVTPHMA - LVTPSMT - LVTP M - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 321 - Query_321 - M_791 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 322 - Query_322 - M_792 - 9 - - - 1 - gnl|BL_ORD_ID|23 - 1516|Nucleoprotein|P03418.1|Human respiratory syncytial virus A2|11259 - 23 - 14 - - - 1 - 13.853 - 24 - 6.4996 - 1 - 8 - 2 - 9 - 0 - 0 - 3 - 6 - 0 - 8 - SFYHLVST - GFYHILNN - FYH+++ - - - - - 2 - gnl|BL_ORD_ID|2158 - 189294|Gag|O89360|Human immunodeficiency virus 1|11676 - 2158 - 9 - - - 1 - 13.4678 - 23 - 10.1994 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 7 - 0 - 9 - SFYHLVSTV - SLYNTVSTL - S Y+ VST+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 323 - Query_323 - M_793 - 9 - - - 1 - gnl|BL_ORD_ID|14 - 1090|Transcription activator BRLF1|P03209.1|Human herpesvirus 4 strain B95-8|10377 - 14 - 9 - - - 1 - 11.927 - 19 - 88.4863 - 2 - 7 - 3 - 8 - 0 - 0 - 4 - 6 - 0 - 6 - SAGNEA - NAGNDA - +AGN+A - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 324 - Query_324 - M_794 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 325 - Query_325 - M_795 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 326 - Query_326 - M_796 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 327 - Query_327 - M_797 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 328 - Query_328 - M_798 - 9 - - - 1 - gnl|BL_ORD_ID|1092 - 72233|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 - 1092 - 15 - - - 1 - 13.0826 - 22 - 16.9555 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 7 - 0 - 9 - WSLDGKYIV - WAIKWEYVV - W++ +Y+V - - - - - 2 - gnl|BL_ORD_ID|1097 - 72563|polyprotein|AAB70696.1|Dengue virus type 1 Hawaii|10000440 - 1097 - 20 - - - 1 - 12.6974 - 21 - 22.9279 - 1 - 9 - 12 - 20 - 0 - 0 - 4 - 5 - 0 - 9 - WSLDGKYIV - WAYHGSYEV - W+ G Y V - - - - - 3 - gnl|BL_ORD_ID|2285 - 419170|polyprotein|ABR25251.1|Hepatitis C virus|11103 - 2285 - 9 - - - 1 - 12.6974 - 21 - 26.9236 - 1 - 7 - 3 - 9 - 0 - 0 - 4 - 5 - 0 - 7 - WSLDGKY - WYLKGKW - W L GK+ - - - - - 4 - gnl|BL_ORD_ID|1941 - 180814|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1941 - 9 - - - 1 - 12.3122 - 20 - 48.7826 - 1 - 7 - 1 - 7 - 0 - 0 - 3 - 4 - 0 - 7 - WSLDGKY - WAYHGSY - W+ G Y - - - - - 5 - gnl|BL_ORD_ID|1888 - 180582|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1888 - 15 - - - 1 - 12.3122 - 20 - 50.6727 - 1 - 7 - 3 - 9 - 0 - 0 - 3 - 4 - 0 - 7 - WSLDGKY - WAYHGSY - W+ G Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 329 - Query_329 - M_799 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 330 - Query_330 - M_800 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 331 - Query_331 - M_801 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 332 - Query_332 - M_802 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 333 - Query_333 - M_803 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 334 - Query_334 - M_804 - 9 - - - 1 - gnl|BL_ORD_ID|2199 - 190827|gag protein|AAN08336.1|Human immunodeficiency virus 1|11676 - 2199 - 10 - - - 1 - 12.3122 - 20 - 59.3959 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 7 - 0 - 9 - ALYCRLATV - SLYNTIATL - +LY +AT+ - - - - - 2 - gnl|BL_ORD_ID|2152 - 189288|gag protein|AAV53168.1|Human immunodeficiency virus 1|11676 - 2152 - 9 - - - 1 - 12.3122 - 20 - 64.7664 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 7 - 0 - 9 - ALYCRLATV - SLYNTIATL - +LY +AT+ - - - - - 3 - gnl|BL_ORD_ID|1451 - 126488|gag protein|AAV53168.1|Human immunodeficiency virus 1|11676 - 1451 - 11 - - - 1 - 11.927 - 19 - 67.9126 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 7 - 0 - 9 - ALYCRLATV - SLYNTIATL - +LY +AT+ - - - - - 4 - gnl|BL_ORD_ID|2209 - 190978|gag protein|AAV53168.1|Human immunodeficiency virus 1|11676 - 2209 - 10 - - - 1 - 11.927 - 19 - 73.4989 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 7 - 0 - 9 - ALYCRLATV - SLYNTIATL - +LY +AT+ - - - - - 5 - gnl|BL_ORD_ID|2205 - 190962|gag polyprotein|BAB88540.1|Human immunodeficiency virus 1|11676 - 2205 - 10 - - - 1 - 11.927 - 19 - 78.4397 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 7 - 0 - 9 - ALYCRLATV - SLYNTIATL - +LY +AT+ - - - - - 6 - gnl|BL_ORD_ID|1461 - 126999|gag polyprotein|BAB88540.1|Human immunodeficiency virus 1|11676 - 1461 - 11 - - - 1 - 11.927 - 19 - 85.0874 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 7 - 0 - 9 - ALYCRLATV - SLYNTIATL - +LY +AT+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 335 - Query_335 - M_805 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 336 - Query_336 - M_806 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 337 - Query_337 - M_807 - 9 - - - 1 - gnl|BL_ORD_ID|2083 - 185419|envelope protein|AGW23591.1|Dengue virus 3|11069 - 2083 - 9 - - - 1 - 13.4678 - 23 - 10.9354 - 3 - 8 - 4 - 9 - 0 - 0 - 5 - 6 - 0 - 6 - MDELEL - MDKLEL - MD+LEL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 338 - Query_338 - M_808 - 9 - - - 1 - gnl|BL_ORD_ID|624 - 37507|Large T antigen|P03071.1|Human polyomavirus 1|1891762 - 624 - 9 - - - 1 - 15.3938 - 28 - 0.690962 - 2 - 9 - 2 - 9 - 0 - 0 - 5 - 6 - 0 - 8 - MLNWFSPV - LLIWFRPV - +L WF PV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 339 - Query_339 - M_809 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 340 - Query_340 - M_810 - 9 - - - 1 - gnl|BL_ORD_ID|2139 - 187158|Gag protein|Q1KW74|Human immunodeficiency virus 1|11676 - 2139 - 11 - - - 1 - 13.853 - 24 - 5.66142 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - HSFNPE - KAFNPE - +FNPE - - - - - 2 - gnl|BL_ORD_ID|2141 - 187163|Gag polyprotein|P88150|Human immunodeficiency virus 1|11676 - 2141 - 11 - - - 1 - 13.4678 - 23 - 8.0187 - 1 - 7 - 1 - 7 - 0 - 0 - 4 - 4 - 0 - 7 - HSFNPEA - KGFNPEV - FNPE - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 341 - Query_341 - M_811 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 342 - Query_342 - M_812 - 9 - - - 1 - gnl|BL_ORD_ID|730 - 46480|DNA polymerase|CAA10434.1|Hepatitis B virus|10407 - 730 - 9 - - - 1 - 15.779 - 29 - 0.439716 - 1 - 7 - 2 - 8 - 0 - 0 - 5 - 5 - 0 - 7 - FSIPWAH - VSIPWTH - SIPW H - - - - - 2 - gnl|BL_ORD_ID|879 - 57723|polyprotein|CAB53095.1|Hepatitis C virus|11103 - 879 - 10 - - - 1 - 12.3122 - 20 - 44.0514 - 1 - 8 - 2 - 9 - 0 - 0 - 3 - 5 - 0 - 8 - FSIPWAHA - FAIKWEYV - F+I W + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 343 - Query_343 - M_813 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 344 - Query_344 - M_814 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 345 - Query_345 - M_815 - 9 - - - 1 - gnl|BL_ORD_ID|1944 - 180818|Membrane glycoprotein precursor|NP_739582.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1944 - 15 - - - 1 - 14.2382 - 25 - 3.31511 - 1 - 7 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - WVLHHMG - WILRHPG - W+L H G - - - - - 2 - gnl|BL_ORD_ID|1481 - 133645|cell surface protein|NP_302626.1|Mycobacterium leprae|1769 - 1481 - 15 - - - 1 - 11.5418 - 18 - 101.887 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 5 - 0 - 8 - VLHHMGGM - MLDHAGNM - +L H G M - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 346 - Query_346 - M_816 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 347 - Query_347 - M_817 - 9 - - - 1 - gnl|BL_ORD_ID|2014 - 183819|polyprotein|AGO67248.1|Dengue virus 2|11060 - 2014 - 10 - - - 1 - 12.3122 - 20 - 52.9061 - 2 - 7 - 5 - 10 - 0 - 0 - 5 - 5 - 0 - 6 - AAAWAL - AAAWYL - AAAW L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 348 - Query_348 - M_818 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 349 - Query_349 - M_819 - 9 - - - 1 - gnl|BL_ORD_ID|904 - 59459|Trans-sialidase|SRC7915|Trypanosoma cruzi|5693 - 904 - 9 - - - 1 - 12.3122 - 20 - 53.0441 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - LGHMFSL - LSHYFTL - L H F+L - - - - - 2 - gnl|BL_ORD_ID|1262 - 98466|Trans-sialidase|SRC7915|Trypanosoma cruzi|5693 - 1262 - 10 - - - 1 - 12.3122 - 20 - 56.5271 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - LGHMFSL - LSHYFTL - L H F+L - - - - - 3 - gnl|BL_ORD_ID|247 - 16890|trans-sialidase|XP_810777.1|Trypanosoma cruzi|5693 - 247 - 9 - - - 1 - 11.927 - 19 - 102.395 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - LGHMFSL - LSHNFTL - L H F+L - - - - - 4 - gnl|BL_ORD_ID|1242 - 98039|Trans-sialidase|SRC7915|Trypanosoma cruzi|5693 - 1242 - 10 - - - 1 - 11.5418 - 18 - 117.155 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - LGHMFSL - LSHNFTL - L H F+L - - - - - 5 - gnl|BL_ORD_ID|246 - 16889|trans-sialidase, putative|EAN82636.1|Trypanosoma cruzi|5693 - 246 - 9 - - - 1 - 11.5418 - 18 - 143.267 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - LGHMFSL - LSHDFTL - L H F+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 350 - Query_350 - M_820 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 351 - Query_351 - M_821 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 352 - Query_352 - M_822 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 353 - Query_353 - M_823 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 354 - Query_354 - M_824 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 355 - Query_355 - M_825 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 356 - Query_356 - M_826 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 357 - Query_357 - M_827 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 358 - Query_358 - M_828 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 359 - Query_359 - M_829 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 360 - Query_360 - M_830 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 361 - Query_361 - M_831 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 362 - Query_362 - M_832 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 363 - Query_363 - M_833 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 364 - Query_364 - M_834 - 9 - - - 1 - gnl|BL_ORD_ID|1916 - 180681|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1916 - 15 - - - 1 - 13.0826 - 22 - 14.8197 - 1 - 8 - 2 - 9 - 0 - 0 - 4 - 4 - 0 - 8 - AAYTSYTP - EEYTDYMP - YT Y P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 365 - Query_365 - M_835 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 366 - Query_366 - M_836 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 367 - Query_367 - M_837 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 368 - Query_368 - M_838 - 9 - - - 1 - gnl|BL_ORD_ID|2273 - 419006|PPE family protein PPE68|KAM81677.1|Mycobacterium tuberculosis H37Ra|419947 - 2273 - 10 - - - 1 - 13.4678 - 23 - 10.0795 - 1 - 6 - 3 - 8 - 0 - 0 - 4 - 6 - 0 - 6 - RSEALP - RAESLP - R+E+LP - - - - - 2 - gnl|BL_ORD_ID|328 - 21078|Antigen 85-B precursor|P21160.1|Mycobacterium kansasii|1768 - 328 - 9 - - - 1 - 13.0826 - 22 - 18.7436 - 4 - 9 - 1 - 6 - 0 - 0 - 4 - 4 - 0 - 6 - ALPVSY - GLPVEY - LPV Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 369 - Query_369 - M_839 - 9 - - - 1 - gnl|BL_ORD_ID|490 - 30946|HCV-1|AAA45676.1|Hepatitis C virus genotype 1|41856 - 490 - 20 - - - 1 - 11.1566 - 17 - 183.47 - 3 - 9 - 5 - 11 - 0 - 0 - 4 - 5 - 0 - 7 - KPFGLVV - KPARLIV - KP L+V - - - - - 2 - gnl|BL_ORD_ID|1414 - 111448|polyprotein precursor|BAA02756.1|Hepatitis C virus|11103 - 1414 - 15 - - - 1 - 11.1566 - 17 - 190.157 - 3 - 9 - 5 - 11 - 0 - 0 - 4 - 5 - 0 - 7 - KPFGLVV - KPARLIV - KP L+V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 370 - Query_370 - M_840 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 371 - Query_371 - M_841 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 372 - Query_372 - M_842 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 373 - Query_373 - M_843 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 374 - Query_374 - M_844 - 9 - - - 1 - gnl|BL_ORD_ID|1659 - 146644|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 - 1659 - 10 - - - 1 - 13.853 - 24 - 6.29996 - 1 - 8 - 3 - 10 - 0 - 0 - 5 - 6 - 0 - 8 - HAATGPGE - HAPTGSGK - HA TG G+ - - - - - 2 - gnl|BL_ORD_ID|394 - 24219|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 - 394 - 15 - - - 1 - 13.4678 - 23 - 7.61659 - 1 - 8 - 3 - 10 - 0 - 0 - 5 - 6 - 0 - 8 - HAATGPGE - HAPTGSGK - HA TG G+ - - - - - 3 - gnl|BL_ORD_ID|393 - 24218|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 - 393 - 10 - - - 1 - 13.4678 - 23 - 8.92274 - 1 - 8 - 3 - 10 - 0 - 0 - 5 - 6 - 0 - 8 - HAATGPGE - HAPTGSGK - HA TG G+ - - - - - 4 - gnl|BL_ORD_ID|741 - 47760|EBNA-1 protein|Q777E1|Human gammaherpesvirus 4|10376 - 741 - 15 - - - 1 - 12.3122 - 20 - 51.4826 - 3 - 8 - 2 - 7 - 0 - 0 - 4 - 4 - 0 - 6 - ATGPGE - GTGPGN - TGPG - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 375 - Query_375 - M_845 - 9 - - - 1 - gnl|BL_ORD_ID|1916 - 180681|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1916 - 15 - - - 1 - 13.0826 - 22 - 20.0418 - 1 - 6 - 9 - 14 - 0 - 0 - 4 - 4 - 0 - 6 - PSQNRF - PSMKRF - PS RF - - - - - 2 - gnl|BL_ORD_ID|1911 - 180667|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1911 - 10 - - - 1 - 13.0826 - 22 - 21.2326 - 1 - 6 - 2 - 7 - 0 - 0 - 4 - 4 - 0 - 6 - PSQNRF - PSMKRF - PS RF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 376 - Query_376 - M_846 - 9 - - - 1 - gnl|BL_ORD_ID|488 - 30903|prM protein|YP_001527879.1|West Nile virus NY-99|10000971 - 488 - 16 - - - 1 - 14.2382 - 25 - 3.11811 - 3 - 8 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - SAWLDS - GAWMDS - AW+DS - - - - - 2 - gnl|BL_ORD_ID|484 - 30266|Transcriptional regulator IE63 homolog|Q04360.1|Human herpesvirus 4 strain B95-8|10377 - 484 - 9 - - - 1 - 11.927 - 19 - 95.9763 - 4 - 8 - 3 - 7 - 0 - 0 - 3 - 4 - 0 - 5 - AWLDS - TWLDA - WLD+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 377 - Query_377 - M_847 - 9 - - - 1 - gnl|BL_ORD_ID|1936 - 180789|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1936 - 15 - - - 1 - 11.927 - 19 - 61.2314 - 1 - 6 - 8 - 13 - 0 - 0 - 3 - 5 - 0 - 6 - VPFPPK - IPYDPK - +P+ PK - - - - - 2 - gnl|BL_ORD_ID|1211 - 96366|polyprotein|ABR25251.1|Hepatitis C virus|11103 - 1211 - 12 - - - 1 - 11.1566 - 17 - 174.36 - 4 - 9 - 5 - 10 - 0 - 0 - 4 - 5 - 0 - 6 - PPKEPL - PPCKPL - PP +PL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 378 - Query_378 - M_848 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 379 - Query_379 - M_849 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 380 - Query_380 - M_850 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 381 - Query_381 - M_851 - 9 - - - 1 - gnl|BL_ORD_ID|1583 - 141469|envelope glycoprotein B|NP_044629.1|Human alphaherpesvirus 1|10298 - 1583 - 9 - - - 1 - 11.927 - 19 - 76.3762 - 3 - 9 - 1 - 7 - 0 - 0 - 3 - 5 - 0 - 7 - IFMPPTY - VYMSPFY - ++M P Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 382 - Query_382 - M_852 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 383 - Query_383 - M_853 - 9 - - - 1 - gnl|BL_ORD_ID|389 - 23807|tax|AAG48731.1|Human T-lymphotropic virus 2|11909 - 389 - 23 - - - 1 - 14.2382 - 25 - 4.20595 - 1 - 9 - 2 - 10 - 0 - 0 - 5 - 6 - 0 - 9 - FPRASQSLV - FPGFGQSLL - FP QSL+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 384 - Query_384 - M_854 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 385 - Query_385 - M_855 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 386 - Query_386 - M_856 - 9 - - - 1 - gnl|BL_ORD_ID|1266 - 98640|trans-sialidase, putative|EAN80840.1|Trypanosoma cruzi|5693 - 1266 - 9 - - - 1 - 13.853 - 24 - 7.20201 - 1 - 7 - 3 - 9 - 0 - 0 - 5 - 7 - 0 - 7 - FSLLATV - FTLVATV - F+L+ATV - - - - - 2 - gnl|BL_ORD_ID|1245 - 98044|trans-sialidase, putative|EAN80840.1|Trypanosoma cruzi|5693 - 1245 - 9 - - - 1 - 13.4678 - 23 - 7.99354 - 1 - 7 - 1 - 7 - 0 - 0 - 5 - 7 - 0 - 7 - FSLLATV - FTLVATV - F+L+ATV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 387 - Query_387 - M_857 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 388 - Query_388 - M_858 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 389 - Query_389 - M_859 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 390 - Query_390 - M_860 - 9 - - - 1 - gnl|BL_ORD_ID|1689 - 149063|NS3 protease/helicase'|NP_803144.1|Hepatitis C virus (isolate H77)|63746 - 1689 - 18 - - - 1 - 10.7714 - 16 - 272.739 - 2 - 8 - 7 - 13 - 0 - 0 - 4 - 5 - 0 - 7 - PVLLLDT - PVENLET - PV L+T - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 391 - Query_391 - M_861 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 392 - Query_392 - M_862 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 393 - Query_393 - M_863 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 394 - Query_394 - M_864 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 395 - Query_395 - M_865 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 396 - Query_396 - M_866 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 397 - Query_397 - M_867 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 398 - Query_398 - M_868 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 399 - Query_399 - M_869 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 400 - Query_400 - M_870 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 401 - Query_401 - M_871 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 402 - Query_402 - M_872 - 9 - - - 1 - gnl|BL_ORD_ID|1438 - 120093|unnamed protein product|CAA33016.1|Rubella virus|11041 - 1438 - 21 - - - 1 - 11.1566 - 17 - 146.584 - 4 - 8 - 11 - 15 - 0 - 0 - 4 - 4 - 0 - 5 - PPPPT - PPPAT - PPP T - - - - - 2 - gnl|BL_ORD_ID|1276 - 101821|vif protein|ACC96167.1|Human immunodeficiency virus 1|11676 - 1276 - 11 - - - 1 - 11.1566 - 17 - 185.696 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 6 - 0 - 9 - RGMPPPPTV - KTKPPLPSV - + PP P+V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 403 - Query_403 - M_873 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 404 - Query_404 - M_874 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 405 - Query_405 - M_875 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 406 - Query_406 - M_876 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 407 - Query_407 - M_877 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 408 - Query_408 - M_878 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 409 - Query_409 - M_879 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 410 - Query_410 - M_880 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 411 - Query_411 - M_881 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 412 - Query_412 - M_882 - 9 - - - 1 - gnl|BL_ORD_ID|392 - 24172|pX-rex-orf I {alternatively spliced}|AAB23359.1|Human T-lymphotropic virus 1|11908 - 392 - 9 - - - 1 - 12.6974 - 21 - 35.3877 - 1 - 8 - 1 - 8 - 0 - 0 - 5 - 6 - 0 - 8 - HLMKQISS - HLAFQLSS - HL Q+SS - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 413 - Query_413 - M_883 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 414 - Query_414 - M_884 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 415 - Query_415 - M_885 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 416 - Query_416 - M_886 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 417 - Query_417 - M_887 - 9 - - - 1 - gnl|BL_ORD_ID|2052 - 184713|polyprotein|AFP27208.1|Dengue virus 4|11070 - 2052 - 9 - - - 1 - 13.4678 - 23 - 10.1994 - 1 - 8 - 2 - 9 - 0 - 0 - 6 - 6 - 0 - 8 - YVVATTKL - YAVATTIL - Y VATT L - - - - - 2 - gnl|BL_ORD_ID|1484 - 133716|polyprotein|ABG75765.1|Dengue virus 1|11053 - 1484 - 9 - - - 1 - 12.6974 - 21 - 25.5715 - 1 - 6 - 3 - 8 - 0 - 0 - 5 - 5 - 0 - 6 - YVVATT - YAVATT - Y VATT - - - - - 3 - gnl|BL_ORD_ID|1738 - 150639|polyprotein|AGO67249.1|Dengue virus 2|11060 - 1738 - 10 - - - 1 - 12.6974 - 21 - 26.9859 - 1 - 6 - 3 - 8 - 0 - 0 - 5 - 5 - 0 - 6 - YVVATT - YAVATT - Y VATT - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 418 - Query_418 - M_888 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 419 - Query_419 - M_889 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 420 - Query_420 - M_890 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 421 - Query_421 - M_891 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 422 - Query_422 - M_892 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 423 - Query_423 - M_893 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 424 - Query_424 - M_894 - 9 - - - 1 - gnl|BL_ORD_ID|152 - 11214|possible regulatory protein|NP_302009.1|Mycobacterium leprae|1769 - 152 - 15 - - - 1 - 11.1566 - 17 - 239.5 - 1 - 8 - 3 - 10 - 0 - 0 - 4 - 5 - 0 - 8 - ILLNGDAT - VLLRLDGT - +LL D T - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 425 - Query_425 - M_895 - 9 - - - 1 - gnl|BL_ORD_ID|2225 - 194440|envelope glycoprotein B|NP_044629.1|Herpes simplex virus (type 1 / strain 17)|10299 - 2225 - 9 - - - 1 - 12.6974 - 21 - 27.8632 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 7 - 0 - 9 - TIYDEDVLV - TMYYKDVTV - T+Y +DV V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 426 - Query_426 - M_896 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 427 - Query_427 - M_897 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 428 - Query_428 - M_898 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 429 - Query_429 - M_899 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 430 - Query_430 - M_900 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 431 - Query_431 - M_901 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 432 - Query_432 - M_902 - 9 - - - 1 - gnl|BL_ORD_ID|367 - 22825|polyprotein|ABG75765.1|Dengue virus 1|11053 - 367 - 10 - - - 1 - 12.6974 - 21 - 30.9217 - 4 - 9 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - SSGKPI - TSGSPI - +SG PI - - - - - 2 - gnl|BL_ORD_ID|75 - 5542|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 75 - 15 - - - 1 - 12.6974 - 21 - 31.2769 - 4 - 9 - 10 - 15 - 0 - 0 - 4 - 5 - 0 - 6 - SSGKPI - TSGSPI - +SG PI - - - - - 3 - gnl|BL_ORD_ID|366 - 22824|polyprotein|AAG30730.1|Dengue virus 2|11060 - 366 - 10 - - - 1 - 12.6974 - 21 - 31.4509 - 4 - 9 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - SSGKPI - TSGSPI - +SG PI - - - - - 4 - gnl|BL_ORD_ID|363 - 22820|Nonstructural protein NS3|YP_001531172.2|Dengue virus 3|11069 - 363 - 10 - - - 1 - 12.6974 - 21 - 33.0913 - 4 - 9 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - SSGKPI - TSGSPI - +SG PI - - - - - 5 - gnl|BL_ORD_ID|365 - 22823|NS3 protein|NP_739587.1|Dengue virus 2|11060 - 365 - 10 - - - 1 - 12.6974 - 21 - 35.4066 - 4 - 9 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - SSGKPI - TSGSPI - +SG PI - - - - - 6 - gnl|BL_ORD_ID|364 - 22822|NS3 protein|NP_740321.1|Dengue virus 4|11070 - 364 - 11 - - - 1 - 12.6974 - 21 - 36.919 - 4 - 9 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - SSGKPI - TSGSPI - +SG PI - - - - - 7 - gnl|BL_ORD_ID|361 - 22818|Nonstructural protein NS3|NP_739587.2|Dengue virus 2|11060 - 361 - 10 - - - 1 - 12.6974 - 21 - 37.8768 - 4 - 9 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - SSGKPI - TSGSPI - +SG PI - - - - - 8 - gnl|BL_ORD_ID|360 - 22817|polyprotein|AAK49562.1|Dengue virus 2|11060 - 360 - 11 - - - 1 - 12.3122 - 20 - 38.8163 - 4 - 9 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - SSGKPI - TSGSPI - +SG PI - - - - - 9 - gnl|BL_ORD_ID|362 - 22819|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 362 - 11 - - - 1 - 12.3122 - 20 - 40.8064 - 4 - 9 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - SSGKPI - TSGSPI - +SG PI - - - - - 10 - gnl|BL_ORD_ID|260 - 17802|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 260 - 15 - - - 1 - 12.3122 - 20 - 51.4826 - 4 - 9 - 5 - 10 - 0 - 0 - 4 - 5 - 0 - 6 - SSGKPI - TSGSPI - +SG PI - - - - - 11 - gnl|BL_ORD_ID|1712 - 150341|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1712 - 9 - - - 1 - 12.3122 - 20 - 55.769 - 4 - 9 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - SSGKPI - TSGSPI - +SG PI - - - - - 12 - gnl|BL_ORD_ID|1929 - 180750|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1929 - 15 - - - 1 - 12.3122 - 20 - 59.339 - 4 - 9 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - SSGKPI - TSGSPI - +SG PI - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 433 - Query_433 - M_903 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 434 - Query_434 - M_904 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 435 - Query_435 - M_905 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 436 - Query_436 - M_906 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 437 - Query_437 - M_907 - 9 - - - 1 - gnl|BL_ORD_ID|1861 - 180440|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1861 - 15 - - - 1 - 12.6974 - 21 - 31.2769 - 1 - 6 - 9 - 14 - 0 - 0 - 4 - 5 - 0 - 6 - WASGNE - WNSGHE - W SG+E - - - - - 2 - gnl|BL_ORD_ID|1926 - 180734|Nonstructural protein NS3|NP_739587.2|Dengue virus 2|11060 - 1926 - 9 - - - 1 - 12.6974 - 21 - 39.8499 - 1 - 6 - 3 - 8 - 0 - 0 - 4 - 5 - 0 - 6 - WASGNE - WNSGHE - W SG+E - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 438 - Query_438 - M_908 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 439 - Query_439 - M_909 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 440 - Query_440 - M_910 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 441 - Query_441 - M_911 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 442 - Query_442 - M_912 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 443 - Query_443 - M_913 - 9 - - - 1 - gnl|BL_ORD_ID|721 - 44833|polyprotein|BAA03375.1|Hepatitis C virus subtype 1a|31646 - 721 - 9 - - - 1 - 14.2382 - 25 - 4.3647 - 5 - 9 - 3 - 7 - 0 - 0 - 4 - 4 - 0 - 5 - PGCVF - PGCSF - PGC F - - - - - 2 - gnl|BL_ORD_ID|651 - 38494|polyprotein|BAA03375.1|Hepatitis C virus|11103 - 651 - 9 - - - 1 - 13.853 - 24 - 6.26888 - 5 - 9 - 2 - 6 - 0 - 0 - 4 - 4 - 0 - 5 - PGCVF - PGCSF - PGC F - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 444 - Query_444 - M_914 - 9 - - - 1 - gnl|BL_ORD_ID|1766 - 154857|tegument protein|CAB06735.1|Human alphaherpesvirus 2|10310 - 1766 - 16 - - - 1 - 5.37863 - 2 - 67403 - 7 - 9 - 14 - 16 - 0 - 0 - 3 - 3 - 0 - 3 - GPV - GPV - GPV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 445 - Query_445 - M_915 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 446 - Query_446 - M_916 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 447 - Query_447 - M_917 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 448 - Query_448 - M_918 - 9 - - - 1 - gnl|BL_ORD_ID|1924 - 180726|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1924 - 15 - - - 1 - 12.6974 - 21 - 25.6947 - 1 - 6 - 8 - 13 - 0 - 0 - 3 - 4 - 0 - 6 - SQWDHG - TAWDFG - + WD G - - - - - 2 - gnl|BL_ORD_ID|439 - 27061|envelope glycoprotein|ABU89742.1|Dengue virus 2 Thailand/16681/84|31634 - 439 - 10 - - - 1 - 12.6974 - 21 - 37.8768 - 1 - 6 - 5 - 10 - 0 - 0 - 3 - 4 - 0 - 6 - SQWDHG - TAWDFG - + WD G - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 449 - Query_449 - M_919 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 450 - Query_450 - M_920 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 451 - Query_451 - M_921 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 452 - Query_452 - M_922 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 453 - Query_453 - M_923 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 454 - Query_454 - M_924 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 455 - Query_455 - M_925 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 456 - Query_456 - M_926 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 457 - Query_457 - M_927 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 458 - Query_458 - M_928 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 459 - Query_459 - M_929 - 9 - - - 1 - gnl|BL_ORD_ID|2165 - 189566|glycosyl transferase|WP_015631503.1|Mycobacterium tuberculosis|1773 - 2165 - 9 - - - 1 - 13.853 - 24 - 6.37844 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 6 - 0 - 9 - STQDTPVTV - ALADLPVTV - + D PVTV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 460 - Query_460 - M_930 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 461 - Query_461 - M_931 - 9 - - - 1 - gnl|BL_ORD_ID|786 - 52652|||| - 786 - 27 - - - 1 - 13.4678 - 23 - 11.7097 - 3 - 9 - 14 - 20 - 0 - 0 - 4 - 6 - 0 - 7 - RGIQTLF - RGLTSLF - RG+ +LF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 462 - Query_462 - M_932 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 463 - Query_463 - M_933 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 464 - Query_464 - M_934 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 465 - Query_465 - M_935 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 466 - Query_466 - M_936 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 467 - Query_467 - M_937 - 9 - - - 1 - gnl|BL_ORD_ID|2084 - 185447|polyprotein|AGK36298.1|Dengue virus 2|11060 - 2084 - 10 - - - 1 - 14.6234 - 26 - 1.93939 - 1 - 9 - 2 - 10 - 0 - 0 - 6 - 7 - 0 - 9 - TVLENLAVL - NALDNLAVL - L+NLAVL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 468 - Query_468 - M_938 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 469 - Query_469 - M_939 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 470 - Query_470 - M_940 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 471 - Query_471 - M_941 - 9 - - - 1 - gnl|BL_ORD_ID|2093 - 185710|Nonstructural protein NS5|YP_001531176.2|Dengue virus 3|11069 - 2093 - 9 - - - 1 - 13.0826 - 22 - 19.404 - 1 - 7 - 2 - 8 - 0 - 0 - 4 - 6 - 0 - 7 - MMNDIVK - MINGVVK - M+N +VK - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 472 - Query_472 - M_942 - 9 - - - 1 - gnl|BL_ORD_ID|1509 - 139746|Dense granule protein 3|B6KEU8.2|Toxoplasma gondii|5811 - 1509 - 9 - - - 1 - 12.6974 - 21 - 39.1808 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 6 - 0 - 9 - FSVPLHIFL - FLVPFVVFL - F VP +FL - - - - - 2 - gnl|BL_ORD_ID|1672 - 148397|Dense granule protein 3|B6KEU8.2|Toxoplasma gondii|5811 - 1672 - 9 - - - 1 - 11.5418 - 18 - 120.255 - 3 - 9 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - VPLHIFL - VPFVVFL - VP +FL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 473 - Query_473 - M_943 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 474 - Query_474 - M_944 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 475 - Query_475 - M_945 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 476 - Query_476 - M_946 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 477 - Query_477 - M_947 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 478 - Query_478 - M_948 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 479 - Query_479 - M_949 - 9 - - - 1 - gnl|BL_ORD_ID|901 - 59182|attachment glycoprotein|ABQ58821.1|Human metapneumovirus|162145 - 901 - 10 - - - 1 - 13.4678 - 23 - 9.23902 - 1 - 7 - 2 - 8 - 0 - 0 - 5 - 7 - 0 - 7 - LVLIGIS - LILIGIT - L+LIGI+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 480 - Query_480 - M_950 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 481 - Query_481 - M_951 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 482 - Query_482 - M_952 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 483 - Query_483 - M_953 - 9 - - - 1 - gnl|BL_ORD_ID|502 - 31997|hypothetical protein FTT0484|YP_169522.1|Francisella tularensis subsp. tularensis SCHU S4|177416 - 502 - 9 - - - 1 - 13.853 - 24 - 5.55396 - 1 - 5 - 3 - 7 - 0 - 0 - 4 - 4 - 0 - 5 - FPEGY - LPEGY - PEGY - - - - - 2 - gnl|BL_ORD_ID|1640 - 146287|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 - 1640 - 18 - - - 1 - 11.1566 - 17 - 184.539 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 6 - 0 - 8 - PEGYGTQV - PKGPITQM - P+G TQ+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 484 - Query_484 - M_954 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 485 - Query_485 - M_955 - 9 - - - 1 - gnl|BL_ORD_ID|1408 - 110940|Protein E7|P03129.1|Human papillomavirus type 16|333760 - 1408 - 15 - - - 1 - 11.927 - 19 - 60.2782 - 1 - 8 - 2 - 9 - 0 - 0 - 4 - 4 - 0 - 8 - HGFNATYH - HGDTPTLH - HG T H - - - - - 2 - gnl|BL_ORD_ID|1392 - 110335|E7|AAD33253.1|Human papillomavirus type 16|333760 - 1392 - 32 - - - 1 - 11.5418 - 18 - 87.5281 - 1 - 8 - 2 - 9 - 0 - 0 - 4 - 4 - 0 - 8 - HGFNATYH - HGDTPTLH - HG T H - - - - - 3 - gnl|BL_ORD_ID|2243 - 232152|rhoptry kinase family protein|AFO54841.1|Toxoplasma gondii type III|398031 - 2243 - 19 - - - 1 - 11.5418 - 18 - 130.88 - 1 - 7 - 7 - 13 - 0 - 0 - 3 - 4 - 0 - 7 - HGFNATY - HSYGVTY - H + TY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 486 - Query_486 - M_956 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 487 - Query_487 - M_957 - 9 - - - 1 - gnl|BL_ORD_ID|285 - 19348|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 - 285 - 20 - - - 1 - 12.6974 - 21 - 33.3894 - 2 - 7 - 5 - 10 - 0 - 0 - 4 - 4 - 0 - 6 - PEVFGP - PEAAGP - PE GP - - - - - 2 - gnl|BL_ORD_ID|866 - 56620|Nef protein|Q9YYU8|Human immunodeficiency virus 1|11676 - 866 - 10 - - - 1 - 12.6974 - 21 - 38.5196 - 1 - 6 - 2 - 7 - 0 - 0 - 4 - 4 - 0 - 6 - YPEVFG - YPLTFG - YP FG - - - - - 3 - gnl|BL_ORD_ID|1281 - 102046|nef protein|ACQ72180.1|Human immunodeficiency virus 1|11676 - 1281 - 8 - - - 1 - 12.6974 - 21 - 38.9267 - 1 - 6 - 2 - 7 - 0 - 0 - 4 - 4 - 0 - 6 - YPEVFG - YPLTFG - YP FG - - - - - 4 - gnl|BL_ORD_ID|1288 - 102254|nef protein|ACQ72180.1|Human immunodeficiency virus 1|11676 - 1288 - 9 - - - 1 - 12.3122 - 20 - 43.3628 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 4 - 0 - 6 - YPEVFG - YPLTFG - YP FG - - - - - 5 - gnl|BL_ORD_ID|707 - 43447|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 - 707 - 20 - - - 1 - 11.927 - 19 - 78.9367 - 2 - 7 - 15 - 20 - 0 - 0 - 4 - 4 - 0 - 6 - PEVFGP - PEAAGP - PE GP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 488 - Query_488 - M_958 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 489 - Query_489 - M_959 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 490 - Query_490 - M_960 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 491 - Query_491 - M_961 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 492 - Query_492 - M_962 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 493 - Query_493 - M_963 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 494 - Query_494 - M_964 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 495 - Query_495 - M_965 - 9 - - - 1 - gnl|BL_ORD_ID|1726 - 150461|polyprotein|AGK36298.1|Dengue virus 2|11060 - 1726 - 9 - - - 1 - 13.0826 - 22 - 14.4474 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 7 - 0 - 9 - MTREELNAL - MTQKARNAL - MT++ NAL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 496 - Query_496 - M_966 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 497 - Query_497 - M_967 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 498 - Query_498 - M_968 - 9 - - - 1 - gnl|BL_ORD_ID|2175 - 189750|Diacylglycerol acyltransferase/mycolyltransferase Ag85B|SRC280000|Mycobacterium tuberculosis|1773 - 2175 - 9 - - - 1 - 11.5418 - 18 - 147.871 - 1 - 7 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - KAGGGSN - PVGGGSS - GGGS+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 499 - Query_499 - M_969 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 500 - Query_500 - M_970 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 501 - Query_501 - M_971 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 502 - Query_502 - M_972 - 9 - - - 1 - gnl|BL_ORD_ID|2251 - 243835|glycosyl transferase|WP_015628558.1|Mycobacterium tuberculosis|1773 - 2251 - 9 - - - 1 - 13.0826 - 22 - 18.4218 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 5 - 0 - 9 - SARDCKDPY - SARLAGIPY - SAR PY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 503 - Query_503 - M_973 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 504 - Query_504 - M_974 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 505 - Query_505 - M_975 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 506 - Query_506 - M_976 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 507 - Query_507 - M_977 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 508 - Query_508 - M_978 - 9 - - - 1 - gnl|BL_ORD_ID|378 - 23365|polyprotein|BAB18806.1|Hepatitis C virus|11103 - 378 - 10 - - - 1 - 14.6234 - 26 - 2.00506 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 7 - 0 - 9 - FIPINGCPI - YIPLVGAPL - +IP+ G P+ - - - - - 2 - gnl|BL_ORD_ID|296 - 19493|polyprotein|BAA03375.1|Hepatitis C virus|11103 - 296 - 15 - - - 1 - 13.853 - 24 - 4.45371 - 1 - 8 - 8 - 15 - 0 - 0 - 4 - 6 - 0 - 8 - FIPINGCP - YIPLVGAP - +IP+ G P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 509 - Query_509 - M_979 - 9 - - - 1 - gnl|BL_ORD_ID|1153 - 76121|polyprotein precursor|NP_041724.2|West Nile virus|11082 - 1153 - 9 - - - 1 - 8.46023 - 10 - 5101.61 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 5 - 0 - 9 - YTSYFGYKM - YTMDGEYRL - YT Y++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 510 - Query_510 - M_980 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 511 - Query_511 - M_981 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 512 - Query_512 - M_982 - 9 - - - 1 - gnl|BL_ORD_ID|1175 - 79390|Protein Tax-1|P0C213.1|Human T-cell lymphotropic virus type 1 (african isolate)|39015 - 1175 - 15 - - - 1 - 11.927 - 19 - 69.3823 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 5 - 0 - 8 - SFYRTHTL - SFHNLHLL - SF+ H L - - - - - 2 - gnl|BL_ORD_ID|880 - 57790|Protein Tax-1|P03409.2|Human T-lymphotropic virus 1|11908 - 880 - 9 - - - 1 - 11.5418 - 18 - 122.194 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 5 - 0 - 8 - SFYRTHTL - SFHSLHLL - SF+ H L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 513 - Query_513 - M_983 - 9 - - - 1 - gnl|BL_ORD_ID|341 - 21385|polyprotein|AAY82034.1|Hepatitis C virus genotype 1|41856 - 341 - 10 - - - 1 - 13.853 - 24 - 7.36741 - 1 - 9 - 2 - 10 - 0 - 0 - 5 - 7 - 0 - 9 - NAAKNQVAM - NASRCWVAM - NA++ VAM - - - - - 2 - gnl|BL_ORD_ID|706 - 43310|polyprotein|AAW78019.1|Hepatitis C virus (isolate H77)|63746 - 706 - 9 - - - 1 - 13.4678 - 23 - 7.85574 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 7 - 0 - 9 - NAAKNQVAM - NASRCWVAM - NA++ VAM - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 514 - Query_514 - M_984 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 515 - Query_515 - M_985 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 516 - Query_516 - M_986 - 9 - - - 1 - gnl|BL_ORD_ID|1171 - 79300|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 1171 - 15 - - - 1 - 12.3122 - 20 - 43.2075 - 1 - 9 - 5 - 13 - 0 - 0 - 5 - 5 - 0 - 9 - DPAPRPSLL - DPGLRPQNL - DP RP L - - - - - 2 - gnl|BL_ORD_ID|1393 - 110338|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1393 - 33 - - - 1 - 11.927 - 19 - 64.3353 - 1 - 9 - 11 - 19 - 0 - 0 - 5 - 5 - 0 - 9 - DPAPRPSLL - DPQERPRKL - DP RP L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 517 - Query_517 - M_987 - 9 - - - 1 - gnl|BL_ORD_ID|29 - 2102|VP1|BAF93325.1|Human polyomavirus 1|1891762 - 29 - 9 - - - 1 - 13.853 - 24 - 5.00793 - 2 - 8 - 1 - 7 - 0 - 0 - 5 - 6 - 0 - 7 - AVTEVEA - AITEVEC - A+TEVE - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 518 - Query_518 - M_988 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 519 - Query_519 - M_989 - 9 - - - 1 - gnl|BL_ORD_ID|134 - 9461|non structural protein 3|CAJ20172.1|Hepatitis C virus|11103 - 134 - 9 - - - 1 - 13.4678 - 23 - 7.85574 - 3 - 8 - 3 - 8 - 0 - 0 - 5 - 5 - 0 - 6 - FPVLVA - FPYLVA - FP LVA - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 520 - Query_520 - M_990 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 521 - Query_521 - M_991 - 9 - - - 1 - gnl|BL_ORD_ID|235 - 16814|precore protein|CAM58990.1|Hepatitis B virus|10407 - 235 - 10 - - - 1 - 12.6974 - 21 - 28.8893 - 3 - 9 - 4 - 10 - 0 - 0 - 4 - 4 - 0 - 7 - NDHAPEV - NDFFPSV - ND P V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 522 - Query_522 - M_992 - 9 - - - 1 - gnl|BL_ORD_ID|1827 - 179766|cell surface protein (associated with virulence)|NP_302372.1|Mycobacterium leprae TN|272631 - 1827 - 9 - - - 1 - 12.3122 - 20 - 59.6102 - 1 - 5 - 1 - 5 - 0 - 0 - 4 - 5 - 0 - 5 - SPLPP - APLPP - +PLPP - - - - - 2 - gnl|BL_ORD_ID|1395 - 110394|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1395 - 32 - - - 1 - 11.927 - 19 - 60.6476 - 2 - 8 - 8 - 14 - 0 - 0 - 4 - 5 - 0 - 7 - PLPPPEQ - PLCPEEK - PL P E+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 523 - Query_523 - M_993 - 9 - - - 1 - gnl|BL_ORD_ID|152 - 11214|possible regulatory protein|NP_302009.1|Mycobacterium leprae|1769 - 152 - 15 - - - 1 - 15.0086 - 27 - 0.94895 - 1 - 8 - 5 - 12 - 0 - 0 - 5 - 7 - 0 - 8 - LRLDGSVV - LRLDGTTL - LRLDG+ + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 524 - Query_524 - M_994 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 525 - Query_525 - M_995 - 9 - - - 1 - gnl|BL_ORD_ID|745 - 48458|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 - 745 - 20 - - - 1 - 13.853 - 24 - 4.81213 - 1 - 8 - 6 - 13 - 0 - 0 - 5 - 5 - 0 - 8 - FPSSQGSL - FPIVQGEL - FP QG L - - - - - 2 - gnl|BL_ORD_ID|1994 - 183594|polyprotein|AGT63075.1|Dengue virus 1|11053 - 1994 - 10 - - - 1 - 13.0826 - 22 - 16.9691 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 6 - 0 - 8 - PSSQGSLY - PASAWTLY - P+S +LY - - - - - 3 - gnl|BL_ORD_ID|1729 - 150534|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1729 - 9 - - - 1 - 13.0826 - 22 - 18.1053 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 6 - 0 - 8 - PSSQGSLY - PASAWTLY - P+S +LY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 526 - Query_526 - M_996 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 527 - Query_527 - M_997 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 528 - Query_528 - M_998 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 529 - Query_529 - M_999 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 530 - Query_530 - M_1000 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 531 - Query_531 - M_1001 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 532 - Query_532 - M_1002 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 533 - Query_533 - M_1003 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 534 - Query_534 - M_1004 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 535 - Query_535 - M_1005 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 536 - Query_536 - M_1006 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 537 - Query_537 - M_1007 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 538 - Query_538 - M_1008 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 539 - Query_539 - M_1009 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 540 - Query_540 - M_1010 - 9 - - - 1 - gnl|BL_ORD_ID|1606 - 143680|Genome polyprotein|P06441.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 1606 - 21 - - - 1 - 13.853 - 24 - 5.97959 - 2 - 8 - 12 - 18 - 0 - 0 - 4 - 5 - 0 - 7 - YQDMMND - YQQQLND - YQ +ND - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 541 - Query_541 - M_1011 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 542 - Query_542 - M_1012 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 543 - Query_543 - M_1013 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 544 - Query_544 - M_1014 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 545 - Query_545 - M_1015 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 546 - Query_546 - M_1016 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 547 - Query_547 - M_1017 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 548 - Query_548 - M_1018 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 549 - Query_549 - M_1019 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 550 - Query_550 - M_1020 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 551 - Query_551 - M_1021 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 552 - Query_552 - M_1022 - 9 - - - 1 - gnl|BL_ORD_ID|2052 - 184713|polyprotein|AFP27208.1|Dengue virus 4|11070 - 2052 - 9 - - - 1 - 13.4678 - 23 - 10.1994 - 1 - 8 - 2 - 9 - 0 - 0 - 6 - 6 - 0 - 8 - YVVATTKL - YAVATTIL - Y VATT L - - - - - 2 - gnl|BL_ORD_ID|1484 - 133716|polyprotein|ABG75765.1|Dengue virus 1|11053 - 1484 - 9 - - - 1 - 12.6974 - 21 - 25.5715 - 1 - 6 - 3 - 8 - 0 - 0 - 5 - 5 - 0 - 6 - YVVATT - YAVATT - Y VATT - - - - - 3 - gnl|BL_ORD_ID|1738 - 150639|polyprotein|AGO67249.1|Dengue virus 2|11060 - 1738 - 10 - - - 1 - 12.6974 - 21 - 26.9859 - 1 - 6 - 3 - 8 - 0 - 0 - 5 - 5 - 0 - 6 - YVVATT - YAVATT - Y VATT - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 553 - Query_553 - M_1023 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 554 - Query_554 - M_1024 - 9 - - - 1 - gnl|BL_ORD_ID|1916 - 180681|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1916 - 15 - - - 1 - 11.927 - 19 - 61.2314 - 1 - 5 - 4 - 8 - 0 - 0 - 4 - 4 - 0 - 5 - YYDYM - YTDYM - Y DYM - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 555 - Query_555 - M_1025 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 556 - Query_556 - M_1026 - 9 - - - 1 - gnl|BL_ORD_ID|1068 - 70491|envelope glycoprotein|AAC28452.1|Human immunodeficiency virus 1|11676 - 1068 - 10 - - - 1 - 12.3122 - 20 - 65.5527 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - LPPDPQP - VPTDPNP - +P DP P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 557 - Query_557 - M_1027 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 558 - Query_558 - M_1028 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 559 - Query_559 - M_1029 - 9 - - - 1 - gnl|BL_ORD_ID|661 - 39571|polyprotein|BAD73987.1|Hepatitis C virus subtype 1b|31647 - 661 - 10 - - - 1 - 13.853 - 24 - 5.38895 - 1 - 6 - 4 - 9 - 0 - 0 - 3 - 6 - 0 - 6 - KPISYM - RPVSYL - +P+SY+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 560 - Query_560 - M_1030 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 561 - Query_561 - M_1031 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 562 - Query_562 - M_1032 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 563 - Query_563 - M_1033 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 564 - Query_564 - M_1034 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 565 - Query_565 - M_1035 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 566 - Query_566 - M_1036 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 567 - Query_567 - M_1037 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 568 - Query_568 - M_1038 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 569 - Query_569 - M_1039 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 570 - Query_570 - M_1040 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 571 - Query_571 - M_1041 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 572 - Query_572 - M_1042 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 573 - Query_573 - M_1043 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 574 - Query_574 - M_1044 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 575 - Query_575 - M_1045 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 576 - Query_576 - M_1046 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 577 - Query_577 - M_1047 - 9 - - - 1 - gnl|BL_ORD_ID|742 - 47854|Glycoprotein I precursor (Glycoprotein IV) (GI) (GPIV)|P09258.1|Human alphaherpesvirus 3|10335 - 742 - 10 - - - 1 - 12.6974 - 21 - 37.2442 - 1 - 6 - 2 - 7 - 0 - 0 - 4 - 4 - 0 - 6 - HSYVGP - HSVVNP - HS V P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 578 - Query_578 - M_1048 - 9 - - - 1 - gnl|BL_ORD_ID|716 - 44214|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 - 716 - 11 - - - 1 - 13.4678 - 23 - 7.61059 - 1 - 9 - 3 - 11 - 0 - 0 - 5 - 6 - 0 - 9 - EMFQRYSAF - EFFTKNSAF - E F + SAF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 579 - Query_579 - M_1049 - 9 - - - 1 - gnl|BL_ORD_ID|1184 - 93224|core protein|AAL31859.1|Hepatitis B virus|10407 - 1184 - 14 - - - 1 - 11.5418 - 18 - 149.079 - 2 - 9 - 4 - 11 - 0 - 0 - 5 - 5 - 0 - 8 - PVSIRLVV - PASRDLVV - P S LVV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 580 - Query_580 - M_1050 - 9 - - - 1 - gnl|BL_ORD_ID|50 - 3094|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 - 50 - 9 - - - 1 - 11.927 - 19 - 109.216 - 4 - 9 - 3 - 8 - 0 - 0 - 4 - 4 - 0 - 6 - GDLGKY - GDAGGY - GD G Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 581 - Query_581 - M_1051 - 9 - - - 1 - gnl|BL_ORD_ID|1171 - 79300|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 1171 - 15 - - - 1 - 12.6974 - 21 - 34.4815 - 3 - 8 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - LAFPVP - LSFPDP - L+FP P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 582 - Query_582 - M_1052 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 583 - Query_583 - M_1053 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 584 - Query_584 - M_1054 - 9 - - - 1 - gnl|BL_ORD_ID|413 - 24943|DNA polymerase|CAA10434.1|Hepatitis B virus|10407 - 413 - 11 - - - 1 - 12.3122 - 20 - 43.6113 - 4 - 8 - 1 - 5 - 0 - 0 - 2 - 5 - 0 - 5 - HSIWE - HTLWK - H++W+ - - - - - 2 - gnl|BL_ORD_ID|1983 - 183252|polyprotein|AGT63075.1|Dengue virus 1|11053 - 1983 - 10 - - - 1 - 11.5418 - 18 - 126.796 - 1 - 8 - 1 - 8 - 0 - 0 - 2 - 5 - 0 - 8 - LAMHSIWE - FSLHYAWK - ++H W+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 585 - Query_585 - M_1055 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 586 - Query_586 - M_1056 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 587 - Query_587 - M_1057 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 588 - Query_588 - M_1058 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 589 - Query_589 - M_1059 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 590 - Query_590 - M_1060 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 591 - Query_591 - M_1061 - 9 - - - 1 - gnl|BL_ORD_ID|1521 - 140615|amino acid decarboxylase|YP_177889.1|Mycobacterium tuberculosis H37Rv|83332 - 1521 - 9 - - - 1 - 13.853 - 24 - 5.65074 - 2 - 7 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - PNAQNM - PGAQNL - P AQN+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 592 - Query_592 - M_1062 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 593 - Query_593 - M_1063 - 9 - - - 1 - gnl|BL_ORD_ID|2284 - 419128|polyprotein|ACF49259.1|Dengue virus type 1 Hawaii|10000440 - 2284 - 9 - - - 1 - 14.6234 - 26 - 1.91441 - 3 - 9 - 3 - 9 - 0 - 0 - 4 - 7 - 0 - 7 - RHSMEKI - RHAMEEL - RH+ME++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 594 - Query_594 - M_1064 - 9 - - - 1 - gnl|BL_ORD_ID|1006 - 66195|Nucleoprotein|P41269.1|Puumala hantavirus|11604 - 1006 - 15 - - - 1 - 13.853 - 24 - 5.02902 - 4 - 9 - 10 - 15 - 0 - 0 - 4 - 5 - 0 - 6 - RHPQHL - RRPKHL - R P+HL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 595 - Query_595 - M_1065 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 596 - Query_596 - M_1066 - 9 - - - 1 - gnl|BL_ORD_ID|1781 - 156550|E3 ubiquitin-protein ligase Mdm2|Q00987.1|Homo sapiens|9606 - 1781 - 9 - - - 1 - 12.6974 - 21 - 26.9236 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 7 - 0 - 9 - IIFLLGEIV - VLFYLGQYI - ++F LG+ + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 597 - Query_597 - M_1067 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 598 - Query_598 - M_1068 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 599 - Query_599 - M_1069 - 9 - - - 1 - gnl|BL_ORD_ID|980 - 64819|E7 protein|ABL96585.1|Human papillomavirus type 16|333760 - 980 - 9 - - - 1 - 11.5418 - 18 - 147.871 - 1 - 6 - 4 - 9 - 0 - 0 - 3 - 4 - 0 - 6 - LACSIC - IVCPIC - + C IC - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 600 - Query_600 - M_1070 - 9 - - - 1 - gnl|BL_ORD_ID|1224 - 97111|polyprotein|ABR25251.1|Hepatitis C virus (isolate H77)|63746 - 1224 - 18 - - - 1 - 14.6234 - 26 - 2.18552 - 3 - 8 - 1 - 6 - 0 - 0 - 4 - 6 - 0 - 6 - YDVLIC - YDIIIC - YD++IC - - - - - 2 - gnl|BL_ORD_ID|1366 - 108218|Genome polyprotein|P26664.3|Hepatitis C virus|11103 - 1366 - 10 - - - 1 - 14.2382 - 25 - 3.38479 - 3 - 8 - 1 - 6 - 0 - 0 - 4 - 6 - 0 - 6 - YDVLIC - YDIIIC - YD++IC - - - - - 3 - gnl|BL_ORD_ID|1317 - 107760|polyprotein|AAD56189.1|Hepatitis C virus|11103 - 1317 - 10 - - - 1 - 13.4678 - 23 - 12.2057 - 3 - 8 - 2 - 7 - 0 - 0 - 3 - 6 - 0 - 6 - YDVLIC - YDIIMC - YD+++C - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 601 - Query_601 - M_1071 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 602 - Query_602 - M_1072 - 9 - - - 1 - gnl|BL_ORD_ID|234 - 16813|External core antigen|SRC279980|Hepatitis B virus|10407 - 234 - 10 - - - 1 - 13.0826 - 22 - 18.1832 - 3 - 8 - 4 - 9 - 0 - 0 - 4 - 4 - 0 - 6 - NDLMPS - NDFFPS - ND PS - - - - - 2 - gnl|BL_ORD_ID|235 - 16814|precore protein|CAM58990.1|Hepatitis B virus|10407 - 235 - 10 - - - 1 - 13.0826 - 22 - 19.1489 - 3 - 8 - 4 - 9 - 0 - 0 - 4 - 4 - 0 - 6 - NDLMPS - NDFFPS - ND PS - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 603 - Query_603 - M_1073 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 604 - Query_604 - M_1074 - 9 - - - 1 - gnl|BL_ORD_ID|1266 - 98640|trans-sialidase, putative|EAN80840.1|Trypanosoma cruzi|5693 - 1266 - 9 - - - 1 - 13.4678 - 23 - 9.02895 - 3 - 9 - 3 - 9 - 0 - 0 - 5 - 7 - 0 - 7 - FSLLATV - FTLVATV - F+L+ATV - - - - - 2 - gnl|BL_ORD_ID|1245 - 98044|trans-sialidase, putative|EAN80840.1|Trypanosoma cruzi|5693 - 1245 - 9 - - - 1 - 13.4678 - 23 - 10.561 - 3 - 9 - 1 - 7 - 0 - 0 - 5 - 7 - 0 - 7 - FSLLATV - FTLVATV - F+L+ATV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 605 - Query_605 - M_1075 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 606 - Query_606 - M_1076 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 607 - Query_607 - M_1077 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 608 - Query_608 - M_1078 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 609 - Query_609 - M_1079 - 9 - - - 1 - gnl|BL_ORD_ID|1171 - 79300|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 1171 - 15 - - - 1 - 14.2382 - 25 - 3.03951 - 1 - 7 - 3 - 9 - 0 - 0 - 4 - 5 - 0 - 7 - LPQPGVR - FPDPGLR - P PG+R - - - - - 2 - gnl|BL_ORD_ID|2238 - 230028|Protein Nef|P04603.3|Human immunodeficiency virus 1|11676 - 2238 - 10 - - - 1 - 13.853 - 24 - 5.02829 - 2 - 7 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - PQPGVR - PGPGIR - P PG+R - - - - - 3 - gnl|BL_ORD_ID|2239 - 230029|Protein Nef|P03404.4|Human immunodeficiency virus 1|11676 - 2239 - 10 - - - 1 - 13.853 - 24 - 5.11607 - 2 - 7 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - PQPGVR - PGPGIR - P PG+R - - - - - 4 - gnl|BL_ORD_ID|1508 - 139406|polyprotein|ACT37184.1|Hepatitis C virus|11103 - 1508 - 10 - - - 1 - 13.853 - 24 - 5.67669 - 1 - 7 - 3 - 9 - 0 - 0 - 5 - 6 - 0 - 7 - LPQPGVR - LPRPGPR - LP+PG R - - - - - 5 - gnl|BL_ORD_ID|1106 - 72928|Genome polyprotein|P26662.3|Hepatitis C virus (isolate Japanese)|11116 - 1106 - 10 - - - 1 - 13.853 - 24 - 7.36741 - 4 - 9 - 5 - 10 - 0 - 0 - 4 - 5 - 0 - 6 - PGVRSL - PGARSM - PG RS+ - - - - - 6 - gnl|BL_ORD_ID|2240 - 230030|Nef protein|BAA86664.1|Human immunodeficiency virus 1|11676 - 2240 - 10 - - - 1 - 13.0826 - 22 - 16.9691 - 2 - 7 - 4 - 9 - 0 - 0 - 4 - 4 - 0 - 6 - PQPGVR - PGPGTR - P PG R - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 610 - Query_610 - M_1080 - 9 - - - 1 - gnl|BL_ORD_ID|1862 - 180442|Chain B, Dengue Virus Rna Dependent Rna Polymerase With Residues From The Ns5 Linker Region|4C11_B|Dengue virus|12637 - 1862 - 10 - - - 1 - 13.4678 - 23 - 12.4198 - 5 - 9 - 4 - 8 - 0 - 0 - 4 - 4 - 0 - 5 - CLGKV - CLGKA - CLGK - - - - - 2 - gnl|BL_ORD_ID|193 - 14324|Chain B, Dengue Virus Rna Dependent Rna Polymerase With Residues From The Ns5 Linker Region|4C11_B|Dengue virus|12637 - 193 - 9 - - - 1 - 13.0826 - 22 - 14.1983 - 5 - 9 - 4 - 8 - 0 - 0 - 4 - 4 - 0 - 5 - CLGKV - CLGKA - CLGK - - - - - 3 - gnl|BL_ORD_ID|741 - 47760|EBNA-1 protein|Q777E1|Human gammaherpesvirus 4|10376 - 741 - 15 - - - 1 - 12.6974 - 21 - 22.89 - 2 - 8 - 5 - 11 - 0 - 0 - 4 - 5 - 0 - 7 - PNNCLGK - PGNGLGE - P N LG+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 611 - Query_611 - M_1081 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 612 - Query_612 - M_1082 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 613 - Query_613 - M_1083 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 614 - Query_614 - M_1084 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 615 - Query_615 - M_1085 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 616 - Query_616 - M_1086 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 617 - Query_617 - M_1087 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 618 - Query_618 - M_1088 - 9 - - - 1 - gnl|BL_ORD_ID|1121 - 74407|polyprotein|AAU89634.1|Hepatitis C virus subtype 2a|31649 - 1121 - 9 - - - 1 - 12.3122 - 20 - 44.8495 - 4 - 9 - 4 - 9 - 0 - 0 - 2 - 4 - 0 - 6 - HWNWII - RWEWVV - W W++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 619 - Query_619 - M_1089 - 9 - - - 1 - gnl|BL_ORD_ID|364 - 22822|NS3 protein|NP_740321.1|Dengue virus 4|11070 - 364 - 11 - - - 1 - 13.0826 - 22 - 15.2395 - 2 - 8 - 2 - 8 - 0 - 0 - 3 - 5 - 0 - 7 - TDGQPLL - TSGSPII - T G P++ - - - - - 2 - gnl|BL_ORD_ID|363 - 22820|Nonstructural protein NS3|YP_001531172.2|Dengue virus 3|11069 - 363 - 10 - - - 1 - 13.0826 - 22 - 16.9691 - 2 - 8 - 2 - 8 - 0 - 0 - 3 - 5 - 0 - 7 - TDGQPLL - TSGSPII - T G P++ - - - - - 3 - gnl|BL_ORD_ID|362 - 22819|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 362 - 11 - - - 1 - 13.0826 - 22 - 21.123 - 2 - 8 - 2 - 8 - 0 - 0 - 3 - 5 - 0 - 7 - TDGQPLL - TSGSPII - T G P++ - - - - - 4 - gnl|BL_ORD_ID|361 - 22818|Nonstructural protein NS3|NP_739587.2|Dengue virus 2|11060 - 361 - 10 - - - 1 - 13.0826 - 22 - 22.3554 - 2 - 8 - 2 - 8 - 0 - 0 - 3 - 5 - 0 - 7 - TDGQPLL - TSGSPII - T G P++ - - - - - 5 - gnl|BL_ORD_ID|1929 - 180750|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1929 - 15 - - - 1 - 12.6974 - 21 - 22.89 - 2 - 8 - 4 - 10 - 0 - 0 - 3 - 5 - 0 - 7 - TDGQPLL - TSGSPII - T G P++ - - - - - 6 - gnl|BL_ORD_ID|260 - 17802|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 260 - 15 - - - 1 - 12.6974 - 21 - 22.89 - 2 - 8 - 5 - 11 - 0 - 0 - 3 - 5 - 0 - 7 - TDGQPLL - TSGSPII - T G P++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 620 - Query_620 - M_1090 - 9 - - - 1 - gnl|BL_ORD_ID|688 - 41622|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 688 - 20 - - - 1 - 15.3938 - 28 - 0.534339 - 1 - 9 - 4 - 12 - 0 - 0 - 4 - 5 - 0 - 9 - AHLLCTLLL - SHFLCTFTF - +H LCT - - - - - 2 - gnl|BL_ORD_ID|123 - 8554|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 123 - 20 - - - 1 - 15.0086 - 27 - 1.09683 - 1 - 9 - 12 - 20 - 0 - 0 - 4 - 5 - 0 - 9 - AHLLCTLLL - SHFLCTFTF - +H LCT - - - - - 3 - gnl|BL_ORD_ID|388 - 23797|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 388 - 20 - - - 1 - 14.6234 - 26 - 1.80994 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 4 - 0 - 8 - HLLCTLLL - HFLCTFTF - H LCT - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 621 - Query_621 - M_1091 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 622 - Query_622 - M_1092 - 9 - - - 1 - gnl|BL_ORD_ID|1440 - 120127|unnamed protein product|CAA33016.1|Rubella virus|11041 - 1440 - 25 - - - 1 - 14.2382 - 25 - 3.45818 - 3 - 8 - 9 - 14 - 0 - 0 - 4 - 6 - 0 - 6 - YGGTIR - HGGTLR - +GGT+R - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 623 - Query_623 - M_1093 - 9 - - - 1 - gnl|BL_ORD_ID|1606 - 143680|Genome polyprotein|P06441.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 1606 - 21 - - - 1 - 15.0086 - 27 - 1.33185 - 1 - 9 - 12 - 20 - 0 - 0 - 5 - 6 - 0 - 9 - YQDMMNDIV - YQQQLNDPV - YQ +ND V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 624 - Query_624 - M_1094 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 625 - Query_625 - M_1095 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 626 - Query_626 - M_1096 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 627 - Query_627 - M_1097 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 628 - Query_628 - M_1098 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 629 - Query_629 - M_1099 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 630 - Query_630 - M_1100 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 631 - Query_631 - M_1101 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 632 - Query_632 - M_1102 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 633 - Query_633 - M_1103 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 634 - Query_634 - M_1104 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 635 - Query_635 - M_1105 - 9 - - - 1 - gnl|BL_ORD_ID|451 - 27295|polyprotein precursor|NP_041724.2|West Nile virus|11082 - 451 - 9 - - - 1 - 14.6234 - 26 - 1.76369 - 5 - 9 - 5 - 9 - 0 - 0 - 5 - 5 - 0 - 5 - PGYAL - PGYAL - PGYAL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 636 - Query_636 - M_1106 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 637 - Query_637 - M_1107 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 638 - Query_638 - M_1108 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 639 - Query_639 - M_1109 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 640 - Query_640 - M_1110 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 641 - Query_641 - M_1111 - 9 - - - 1 - gnl|BL_ORD_ID|577 - 36352|Polyprotein|P90247|Hepatitis C virus|11103 - 577 - 20 - - - 1 - 13.853 - 24 - 4.81213 - 3 - 9 - 14 - 20 - 0 - 0 - 4 - 4 - 0 - 7 - RPRWCPV - RPSWGPT - RP W P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 642 - Query_642 - M_1112 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 643 - Query_643 - M_1113 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 644 - Query_644 - M_1114 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 645 - Query_645 - M_1115 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 646 - Query_646 - M_1116 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 647 - Query_647 - M_1117 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 648 - Query_648 - M_1118 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 649 - Query_649 - M_1119 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 650 - Query_650 - M_1120 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 651 - Query_651 - M_1121 - 9 - - - 1 - gnl|BL_ORD_ID|104 - 7116|NS3|ABN45875.1|Hepatitis C virus (isolate H77)|63746 - 104 - 9 - - - 1 - 13.4678 - 23 - 9.02895 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 5 - 0 - 9 - CTLGLGSLY - CTCGSSDLY - CT G LY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 652 - Query_652 - M_1122 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 653 - Query_653 - M_1123 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 654 - Query_654 - M_1124 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 655 - Query_655 - M_1125 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 656 - Query_656 - M_1126 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 657 - Query_657 - M_1127 - 9 - - - 1 - gnl|BL_ORD_ID|2300 - 422989|polyprotein|ABY67644.1|Hepatitis C virus genotype 1|41856 - 2300 - 10 - - - 1 - 12.6974 - 21 - 37.8768 - 1 - 7 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - IAPLLPV - FAPALPI - AP LP+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 658 - Query_658 - M_1128 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 659 - Query_659 - M_1129 - 9 - - - 1 - gnl|BL_ORD_ID|448 - 27241|Spike glycoprotein precursor|P59594.1|SARS coronavirus|227859 - 448 - 9 - - - 1 - 12.3122 - 20 - 68.0606 - 1 - 6 - 4 - 9 - 0 - 0 - 4 - 4 - 0 - 6 - DPADPT - DPLKPT - DP PT - - - - - 2 - gnl|BL_ORD_ID|1635 - 146280|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 - 1635 - 10 - - - 1 - 10.7714 - 16 - 471.24 - 1 - 8 - 3 - 10 - 0 - 0 - 4 - 4 - 0 - 8 - DPADPTSN - DPNIRTGN - DP T N - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 660 - Query_660 - M_1130 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 661 - Query_661 - M_1131 - 9 - - - 1 - gnl|BL_ORD_ID|2307 - 423007|Genome polyprotein|P26664.3|Hepatitis C virus genotype 1|41856 - 2307 - 10 - - - 1 - 11.5418 - 18 - 175.991 - 2 - 9 - 2 - 9 - 0 - 0 - 5 - 6 - 0 - 8 - VQDIQASL - VQEDAASL - VQ+ ASL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 662 - Query_662 - M_1132 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 663 - Query_663 - M_1133 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 664 - Query_664 - M_1134 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 665 - Query_665 - M_1135 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 666 - Query_666 - M_1136 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 667 - Query_667 - M_1137 - 9 - - - 1 - gnl|BL_ORD_ID|1756 - 154164|tegument protein|CAB06732.1|Human alphaherpesvirus 2|10310 - 1756 - 15 - - - 1 - 15.779 - 29 - 0.460848 - 3 - 9 - 9 - 15 - 0 - 0 - 4 - 7 - 0 - 7 - FDAIRTF - YDAVRTW - +DA+RT+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 668 - Query_668 - M_1138 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 669 - Query_669 - M_1139 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 670 - Query_670 - M_1140 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 671 - Query_671 - M_1141 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 672 - Query_672 - M_1142 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 673 - Query_673 - M_1143 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 674 - Query_674 - M_1144 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 675 - Query_675 - M_1145 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 676 - Query_676 - M_1146 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 677 - Query_677 - M_1147 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 678 - Query_678 - M_1148 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 679 - Query_679 - M_1149 - 9 - - - 1 - gnl|BL_ORD_ID|686 - 41407|Envelope protein|NP_739583.2|Dengue virus 2|11060 - 686 - 15 - - - 1 - 12.3122 - 20 - 43.2075 - 1 - 5 - 6 - 10 - 0 - 0 - 3 - 4 - 0 - 5 - WQIHR - WLVHR - W +HR - - - - - 2 - gnl|BL_ORD_ID|1746 - 150725|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1746 - 9 - - - 1 - 12.3122 - 20 - 63.7024 - 1 - 5 - 1 - 5 - 0 - 0 - 3 - 4 - 0 - 5 - WQIHR - WLVHR - W +HR - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 680 - Query_680 - M_1150 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 681 - Query_681 - M_1151 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 682 - Query_682 - M_1152 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 683 - Query_683 - M_1153 - 9 - - - 1 - gnl|BL_ORD_ID|1731 - 150556|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1731 - 10 - - - 1 - 14.6234 - 26 - 2.108 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 7 - 0 - 9 - KMADPNQCV - RVIDPRRCL - ++ DP +C+ - - - - - 2 - gnl|BL_ORD_ID|859 - 56310|polyprotein|AGO67248.1|Dengue virus 2|11060 - 859 - 10 - - - 1 - 14.2382 - 25 - 3.75112 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 7 - 0 - 9 - KMADPNQCV - RVIDPRRCM - ++ DP +C+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 684 - Query_684 - M_1154 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 685 - Query_685 - M_1155 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 686 - Query_686 - M_1156 - 9 - - - 1 - gnl|BL_ORD_ID|527 - 32268|hemagglutinin|AAK38298.1|Influenza A virus (A/Bar-headed Goose/Qinghai/61/05(H5N1))|336238 - 527 - 10 - - - 1 - 15.0086 - 27 - 1.06007 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 7 - 0 - 9 - KYYTDPSTY - KLYQNPTTY - K Y +P+TY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 687 - Query_687 - M_1157 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 688 - Query_688 - M_1158 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 689 - Query_689 - M_1159 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 690 - Query_690 - M_1160 - 9 - - - 1 - gnl|BL_ORD_ID|2098 - 185817|envelope protein|AGW23590.1|Dengue virus 4|11070 - 2098 - 10 - - - 1 - 12.3122 - 20 - 48.6895 - 4 - 9 - 2 - 7 - 0 - 0 - 3 - 5 - 0 - 6 - WLARVL - WMIRIL - W+ R+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 691 - Query_691 - M_1161 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 692 - Query_692 - M_1162 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 693 - Query_693 - M_1163 - 9 - - - 1 - gnl|BL_ORD_ID|398 - 24427|polyprotein|ACX44238.1|Hepatitis C virus subtype 1a|31646 - 398 - 9 - - - 1 - 11.927 - 19 - 75.1319 - 2 - 8 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - PAFHFNI - PALVFDI - PA F+I - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 694 - Query_694 - M_1164 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 695 - Query_695 - M_1165 - 9 - - - 1 - gnl|BL_ORD_ID|3 - 194|Hypothetical protein esxG (PE family protein)|O53692.1|Mycobacterium tuberculosis|1773 - 3 - 9 - - - 1 - 11.927 - 19 - 102.395 - 1 - 7 - 3 - 9 - 0 - 0 - 5 - 5 - 0 - 7 - HASVVAA - HARFVAA - HA VAA - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 696 - Query_696 - M_1166 - 9 - - - 1 - gnl|BL_ORD_ID|1980 - 183229|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1980 - 10 - - - 1 - 13.0826 - 22 - 22.3554 - 4 - 9 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - PSSNAL - PQSNAV - P SNA+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 697 - Query_697 - M_1167 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 698 - Query_698 - M_1168 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 699 - Query_699 - M_1169 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 700 - Query_700 - M_1170 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 701 - Query_701 - M_1171 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 702 - Query_702 - M_1172 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 703 - Query_703 - M_1173 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 704 - Query_704 - M_1174 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 705 - Query_705 - M_1175 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 706 - Query_706 - M_1176 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 707 - Query_707 - M_1177 - 9 - - - 1 - gnl|BL_ORD_ID|2185 - 190466|large surface antigen|CAL29876.1|Hepatitis B virus|10407 - 2185 - 15 - - - 1 - 13.0826 - 22 - 16.6732 - 1 - 7 - 6 - 12 - 0 - 0 - 4 - 4 - 0 - 7 - DHSNDPT - DHQLDPA - DH DP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 708 - Query_708 - M_1178 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 709 - Query_709 - M_1179 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 710 - Query_710 - M_1180 - 9 - - - 1 - gnl|BL_ORD_ID|1207 - 96257|Genome polyprotein|SRC279960|Hepatitis C virus|11103 - 1207 - 8 - - - 1 - 13.4678 - 23 - 13.562 - 1 - 8 - 1 - 8 - 0 - 0 - 3 - 5 - 0 - 8 - KPMPTIQW - EPEPDVAW - +P P + W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 711 - Query_711 - M_1181 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 712 - Query_712 - M_1182 - 9 - - - 1 - gnl|BL_ORD_ID|931 - 61077|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 - 931 - 9 - - - 1 - 14.2382 - 25 - 3.61702 - 3 - 8 - 2 - 7 - 0 - 0 - 4 - 6 - 0 - 6 - SHTGTF - SHSGSF - SH+G+F - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 713 - Query_713 - M_1183 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 714 - Query_714 - M_1184 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 715 - Query_715 - M_1185 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 716 - Query_716 - M_1186 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 717 - Query_717 - M_1187 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 718 - Query_718 - M_1188 - 9 - - - 1 - gnl|BL_ORD_ID|1049 - 69679|polyprotein|BAD73987.1|Hepatitis C virus subtype 1b|31647 - 1049 - 9 - - - 1 - 13.853 - 24 - 6.26888 - 2 - 8 - 1 - 7 - 0 - 0 - 5 - 6 - 0 - 7 - VLPDTFT - VLPCSFT - VLP +FT - - - - - 2 - gnl|BL_ORD_ID|447 - 27239|polyprotein|BAB18806.1|Hepatitis C virus subtype 1b|31647 - 447 - 9 - - - 1 - 13.4678 - 23 - 11.7244 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 6 - 0 - 7 - VLPDTFT - ILPCSFT - +LP +FT - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 719 - Query_719 - M_1189 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 720 - Query_720 - M_1190 - 9 - - - 1 - gnl|BL_ORD_ID|922 - 59975|pol protein|ACJ76655.1|Human immunodeficiency virus 1|11676 - 922 - 9 - - - 1 - 14.6234 - 26 - 1.52328 - 2 - 9 - 2 - 9 - 0 - 0 - 3 - 8 - 0 - 8 - PAVFETTV - PAIFQSSM - PA+F++++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 721 - Query_721 - M_1191 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 722 - Query_722 - M_1192 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 723 - Query_723 - M_1193 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 724 - Query_724 - M_1194 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 725 - Query_725 - M_1195 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 726 - Query_726 - M_1196 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 727 - Query_727 - M_1197 - 9 - - - 1 - gnl|BL_ORD_ID|427 - 25929|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 427 - 15 - - - 1 - 10.7714 - 16 - 355.4 - 1 - 9 - 7 - 15 - 0 - 0 - 4 - 6 - 0 - 9 - EVKIGKMSY - DVKKDLISY - +VK +SY - - - - - 2 - gnl|BL_ORD_ID|9 - 790|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 9 - 15 - - - 1 - 10.001 - 14 - 663.673 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 6 - 0 - 9 - EVKIGKMSY - DVKKDLISY - +VK +SY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 728 - Query_728 - M_1198 - 9 - - - 1 - gnl|BL_ORD_ID|1346 - 108018|polyprotein|CAB41951.1|Hepatitis C virus|11103 - 1346 - 10 - - - 1 - 17.3198 - 33 - 0.18734 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 8 - 0 - 9 - LANGGKVPF - LSNTGEIPF - L+N G++PF - - - - - 2 - gnl|BL_ORD_ID|1312 - 107738|polyprotein|CAB41951.1|Hepatitis C virus|11103 - 1312 - 10 - - - 1 - 16.9346 - 32 - 0.197903 - 1 - 9 - 2 - 10 - 0 - 0 - 5 - 8 - 0 - 9 - LANGGKVPF - LSNTGEIPF - L+N G++PF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 729 - Query_729 - M_1199 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 730 - Query_730 - M_1200 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 731 - Query_731 - M_1201 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 732 - Query_732 - M_1202 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 733 - Query_733 - M_1203 - 9 - - - 1 - gnl|BL_ORD_ID|1141 - 75408|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 1141 - 20 - - - 1 - 13.853 - 24 - 5.99481 - 3 - 9 - 12 - 18 - 0 - 0 - 4 - 5 - 0 - 7 - FPVGDSV - LPVADAV - PV D+V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 734 - Query_734 - M_1204 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 735 - Query_735 - M_1205 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 736 - Query_736 - M_1206 - 9 - - - 1 - gnl|BL_ORD_ID|490 - 30946|HCV-1|AAA45676.1|Hepatitis C virus genotype 1|41856 - 490 - 20 - - - 1 - 14.2382 - 25 - 3.66432 - 5 - 9 - 13 - 17 - 0 - 0 - 4 - 5 - 0 - 5 - PDLGI - PDLGV - PDLG+ - - - - - 2 - gnl|BL_ORD_ID|816 - 54605|HCV-1|AAA45676.1|Hepatitis C virus|11103 - 816 - 10 - - - 1 - 14.2382 - 25 - 4.15863 - 5 - 9 - 6 - 10 - 0 - 0 - 4 - 5 - 0 - 5 - PDLGI - PDLGV - PDLG+ - - - - - 3 - gnl|BL_ORD_ID|471 - 28594|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 - 471 - 20 - - - 1 - 13.853 - 24 - 4.81213 - 2 - 6 - 5 - 9 - 0 - 0 - 4 - 5 - 0 - 5 - SYHPD - SYYPD - SY+PD - - - - - 4 - gnl|BL_ORD_ID|776 - 51643|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 - 776 - 20 - - - 1 - 13.4678 - 23 - 8.10378 - 2 - 6 - 15 - 19 - 0 - 0 - 4 - 5 - 0 - 5 - SYHPD - SYYPD - SY+PD - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 737 - Query_737 - M_1207 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 738 - Query_738 - M_1208 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 739 - Query_739 - M_1209 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 740 - Query_740 - M_1210 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 741 - Query_741 - M_1211 - 9 - - - 1 - gnl|BL_ORD_ID|1438 - 120093|unnamed protein product|CAA33016.1|Rubella virus|11041 - 1438 - 21 - - - 1 - 11.927 - 19 - 77.0667 - 2 - 9 - 12 - 19 - 0 - 0 - 4 - 5 - 0 - 8 - PPPTPRKV - PPATPTSL - PP TP + - - - - - 2 - gnl|BL_ORD_ID|1298 - 103392|polyprotein|BAB18806.1|Hepatitis C virus|11103 - 1298 - 9 - - - 1 - 11.1566 - 17 - 246.948 - 1 - 6 - 3 - 8 - 0 - 0 - 4 - 4 - 0 - 6 - RPPPTP - RDPTTP - R P TP - - - - - 3 - gnl|BL_ORD_ID|1573 - 141402|tegument protein VP22|NP_044651.1|Human alphaherpesvirus 1|10298 - 1573 - 10 - - - 1 - 10.001 - 14 - 1133.68 - 1 - 7 - 1 - 7 - 0 - 0 - 4 - 4 - 0 - 7 - RPPPTPR - RPTERPR - RP PR - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 742 - Query_742 - M_1212 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 743 - Query_743 - M_1213 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 744 - Query_744 - M_1214 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 745 - Query_745 - M_1215 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 746 - Query_746 - M_1216 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 747 - Query_747 - M_1217 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 748 - Query_748 - M_1218 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 749 - Query_749 - M_1219 - 9 - - - 1 - gnl|BL_ORD_ID|1035 - 69394|pol|AP_000202.1|Human adenovirus 5|28285 - 1035 - 9 - - - 1 - 15.0086 - 27 - 0.973936 - 2 - 9 - 1 - 8 - 0 - 0 - 5 - 6 - 0 - 8 - VLPWLKAF - VLAWTRAF - VL W +AF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 750 - Query_750 - M_1220 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 751 - Query_751 - M_1221 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 752 - Query_752 - M_1222 - 9 - - - 1 - gnl|BL_ORD_ID|1508 - 139406|polyprotein|ACT37184.1|Hepatitis C virus|11103 - 1508 - 10 - - - 1 - 12.6974 - 21 - 27.4501 - 4 - 9 - 5 - 10 - 0 - 0 - 4 - 5 - 0 - 6 - RPWPRV - RPGPRL - RP PR+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 753 - Query_753 - M_1223 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 754 - Query_754 - M_1224 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 755 - Query_755 - M_1225 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 756 - Query_756 - M_1226 - 9 - - - 1 - gnl|BL_ORD_ID|1149 - 75636|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 1149 - 10 - - - 1 - 15.0086 - 27 - 1.44144 - 3 - 9 - 3 - 9 - 0 - 0 - 4 - 4 - 0 - 7 - LWHLPAV - LWHYPCT - LWH P - - - - - 2 - gnl|BL_ORD_ID|832 - 54820|polyprotein precursor|BAA02756.1|Hepatitis C virus|11103 - 832 - 9 - - - 1 - 14.6234 - 26 - 1.52328 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 4 - 0 - 7 - LWHLPAV - LWHYPCT - LWH P - - - - - 3 - gnl|BL_ORD_ID|831 - 54819|JK3|CAA43789.1|Hepatitis C virus|11103 - 831 - 9 - - - 1 - 14.6234 - 26 - 1.6522 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 4 - 0 - 7 - LWHLPAV - LWHYPCT - LWH P - - - - - 4 - gnl|BL_ORD_ID|833 - 54821|E2 protein|AAM33354.1|Hepatitis C virus subtype 1a|31646 - 833 - 9 - - - 1 - 14.6234 - 26 - 1.67935 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 4 - 0 - 7 - LWHLPAV - LWHYPCT - LWH P - - - - - 5 - gnl|BL_ORD_ID|835 - 54825|polyprotein|BAA03375.1|Hepatitis C virus|11103 - 835 - 9 - - - 1 - 14.6234 - 26 - 1.73509 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 4 - 0 - 7 - LWHLPAV - LWHYPCT - LWH P - - - - - 6 - gnl|BL_ORD_ID|834 - 54824|polyprotein precursor|BAA01583.1|Hepatitis C virus|11103 - 834 - 9 - - - 1 - 14.6234 - 26 - 1.88321 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 4 - 0 - 7 - LWHLPAV - LWHYPCT - LWH P - - - - - 7 - gnl|BL_ORD_ID|1010 - 67210|NS3 protein|NP_739587.1|Dengue virus 2 Thailand/NGS-C/1944|11065 - 1010 - 9 - - - 1 - 12.6974 - 21 - 39.1808 - 3 - 9 - 2 - 8 - 0 - 0 - 2 - 6 - 0 - 7 - LWHLPAV - VWFVPSI - +W +P++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 757 - Query_757 - M_1227 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 758 - Query_758 - M_1228 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 759 - Query_759 - M_1229 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 760 - Query_760 - M_1230 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 761 - Query_761 - M_1231 - 9 - - - 1 - gnl|BL_ORD_ID|469 - 28484|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 469 - 9 - - - 1 - 14.2382 - 25 - 4.3647 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 7 - 0 - 9 - MTEHRGKCY - ISEYRHYCY - ++E+R CY - - - - - 2 - gnl|BL_ORD_ID|1406 - 110846|E6 protein|CAB45108.1|Human papillomavirus type 16|333760 - 1406 - 9 - - - 1 - 12.6974 - 21 - 30.8766 - 3 - 9 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - EHRGKCY - EYRHYCY - E+R CY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 762 - Query_762 - M_1232 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 763 - Query_763 - M_1233 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 764 - Query_764 - M_1234 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 765 - Query_765 - M_1235 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 766 - Query_766 - M_1236 - 9 - - - 1 - gnl|BL_ORD_ID|764 - 51250|nucleocapsid protein|ABI96968.1|SARS coronavirus|227859 - 764 - 15 - - - 1 - 15.779 - 29 - 0.411155 - 1 - 9 - 7 - 15 - 0 - 0 - 5 - 7 - 0 - 9 - HRYNLTQHF - KQYNVTQAF - +YN+TQ F - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 767 - Query_767 - M_1237 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 768 - Query_768 - M_1238 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 769 - Query_769 - M_1239 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 770 - Query_770 - M_1240 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 771 - Query_771 - M_1241 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 772 - Query_772 - M_1242 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 773 - Query_773 - M_1243 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 774 - Query_774 - M_1244 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 775 - Query_775 - M_1245 - 9 - - - 1 - gnl|BL_ORD_ID|135 - 9746|Genome polyprotein|P29846.3|Hepatitis C virus genotype 1|41856 - 135 - 9 - - - 1 - 13.0826 - 22 - 21.5246 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 7 - 0 - 9 - SPRRRAASV - DPRRRSRNL - PRRR+ ++ - - - - - 2 - gnl|BL_ORD_ID|1757 - 154196|tegument protein|CAB06735.1|Human alphaherpesvirus 2|10310 - 1757 - 16 - - - 1 - 12.6974 - 21 - 34.8463 - 4 - 9 - 4 - 9 - 0 - 0 - 5 - 6 - 0 - 6 - RRAASV - RRSASV - RR+ASV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 776 - Query_776 - M_1246 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 777 - Query_777 - M_1247 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 778 - Query_778 - M_1248 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 779 - Query_779 - M_1249 - 9 - - - 1 - gnl|BL_ORD_ID|750 - 49831|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 - 750 - 15 - - - 1 - 10.001 - 14 - 757.359 - 3 - 9 - 6 - 12 - 0 - 0 - 3 - 5 - 0 - 7 - ICCDCVI - ILCLCLV - I C C++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 780 - Query_780 - M_1250 - 9 - - - 1 - gnl|BL_ORD_ID|82 - 5952|PPE family protein|YP_177918.1|Mycobacterium tuberculosis H37Rv|83332 - 82 - 9 - - - 1 - 13.853 - 24 - 7.58732 - 1 - 7 - 3 - 9 - 0 - 0 - 4 - 4 - 0 - 7 - CPYSAWC - VPYVAWL - PY AW - - - - - 2 - gnl|BL_ORD_ID|1097 - 72563|polyprotein|AAB70696.1|Dengue virus type 1 Hawaii|10000440 - 1097 - 20 - - - 1 - 12.6974 - 21 - 21.8633 - 2 - 9 - 8 - 15 - 0 - 0 - 3 - 4 - 0 - 8 - PYSAWCVY - PYKTWAYH - PY W + - - - - - 3 - gnl|BL_ORD_ID|1931 - 180758|Nonstructural protein NS5|NP_739590.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1931 - 15 - - - 1 - 12.6974 - 21 - 27.8948 - 2 - 7 - 9 - 14 - 0 - 0 - 3 - 3 - 0 - 6 - PYSAWC - PYKTWA - PY W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 781 - Query_781 - M_1251 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 782 - Query_782 - M_1252 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 783 - Query_783 - M_1253 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 784 - Query_784 - M_1254 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 785 - Query_785 - M_1255 - 9 - - - 1 - gnl|BL_ORD_ID|566 - 35237|nonstructural protein 3|NP_722463.1|Dengue virus type 1 Hawaii|10000440 - 566 - 20 - - - 1 - 11.5418 - 18 - 95.4438 - 1 - 8 - 10 - 17 - 0 - 0 - 3 - 6 - 0 - 8 - MVPREFKP - IIPALFEP - ++P F+P - - - - - 2 - gnl|BL_ORD_ID|993 - 65550|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 993 - 15 - - - 1 - 11.5418 - 18 - 100.351 - 1 - 8 - 5 - 12 - 0 - 0 - 3 - 6 - 0 - 8 - MVPREFKP - IIPSMFEP - ++P F+P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 786 - Query_786 - M_1256 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 787 - Query_787 - M_1257 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 788 - Query_788 - M_1258 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 789 - Query_789 - M_1259 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 790 - Query_790 - M_1260 - 9 - - - 1 - gnl|BL_ORD_ID|1271 - 101673|gag protein|ABO73990.1|Human immunodeficiency virus 1|11676 - 1271 - 9 - - - 1 - 13.853 - 24 - 5.09494 - 2 - 9 - 2 - 9 - 0 - 0 - 5 - 6 - 0 - 8 - HQAMFQLL - HQAAMQML - HQA Q+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 791 - Query_791 - M_1261 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 792 - Query_792 - M_1262 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 793 - Query_793 - M_1263 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 794 - Query_794 - M_1264 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 795 - Query_795 - M_1265 - 9 - - - 1 - gnl|BL_ORD_ID|142 - 10650|Nucleoprotein|P05133.1|Hantaan virus 76-118|11602 - 142 - 15 - - - 1 - 13.0826 - 22 - 15.0718 - 3 - 9 - 7 - 13 - 0 - 0 - 4 - 5 - 0 - 7 - ITNIEPF - ISNQEPL - I+N EP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 796 - Query_796 - M_1266 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 797 - Query_797 - M_1267 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 798 - Query_798 - M_1268 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 799 - Query_799 - M_1269 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 800 - Query_800 - M_1270 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 801 - Query_801 - M_1271 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 802 - Query_802 - M_1272 - 9 - - - 1 - gnl|BL_ORD_ID|215 - 15914|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 - 215 - 15 - - - 1 - 13.4678 - 23 - 8.0204 - 4 - 8 - 6 - 10 - 0 - 0 - 4 - 5 - 0 - 5 - DGIRL - DGVRL - DG+RL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 803 - Query_803 - M_1273 - 9 - - - 1 - gnl|BL_ORD_ID|159 - 12108|polyprotein|AAP55688.1|Hepatitis C virus subtype 2a|31649 - 159 - 10 - - - 1 - 12.3122 - 20 - 49.5064 - 1 - 8 - 3 - 10 - 0 - 0 - 3 - 4 - 0 - 8 - WRCWFNGI - WEAVFTGL - W F G+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 804 - Query_804 - M_1274 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 805 - Query_805 - M_1275 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 806 - Query_806 - M_1276 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 807 - Query_807 - M_1277 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 808 - Query_808 - M_1278 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 809 - Query_809 - M_1279 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 810 - Query_810 - M_1280 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 811 - Query_811 - M_1281 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 812 - Query_812 - M_1282 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 813 - Query_813 - M_1283 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 814 - Query_814 - M_1284 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 815 - Query_815 - M_1285 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 816 - Query_816 - M_1286 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 817 - Query_817 - M_1287 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 818 - Query_818 - M_1288 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 819 - Query_819 - M_1289 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 820 - Query_820 - M_1290 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 821 - Query_821 - M_1291 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 822 - Query_822 - M_1292 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 823 - Query_823 - M_1293 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 824 - Query_824 - M_1294 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 825 - Query_825 - M_1295 - 9 - - - 1 - gnl|BL_ORD_ID|296 - 19493|polyprotein|BAA03375.1|Hepatitis C virus|11103 - 296 - 15 - - - 1 - 13.0826 - 22 - 14.8197 - 3 - 8 - 9 - 14 - 0 - 0 - 4 - 6 - 0 - 6 - IPVVGS - IPLVGA - IP+VG+ - - - - - 2 - gnl|BL_ORD_ID|378 - 23365|polyprotein|BAB18806.1|Hepatitis C virus|11103 - 378 - 10 - - - 1 - 13.0826 - 22 - 19.8203 - 3 - 8 - 3 - 8 - 0 - 0 - 4 - 6 - 0 - 6 - IPVVGS - IPLVGA - IP+VG+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 826 - Query_826 - M_1296 - 9 - - - 1 - gnl|BL_ORD_ID|1372 - 108277|IE62|AAP32859.1|Human alphaherpesvirus 3|10335 - 1372 - 9 - - - 1 - 13.853 - 24 - 7.20201 - 2 - 8 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - VWALPKT - LWALPHA - +WALP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 827 - Query_827 - M_1297 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 828 - Query_828 - M_1298 - 9 - - - 1 - gnl|BL_ORD_ID|621 - 37466|surface antigen|BAF44879.1|Hepatitis B virus|10407 - 621 - 9 - - - 1 - 11.5418 - 18 - 155.038 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 6 - 0 - 9 - LHLCYEFLM - LLLCLIFLL - L LC FL+ - - - - - 2 - gnl|BL_ORD_ID|596 - 37120|Major surface antigen precursor|P17399.3|Hepatitis B virus|10407 - 596 - 9 - - - 1 - 11.1566 - 17 - 208.544 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - LCYEFLM - LCLIFLL - LC FL+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 829 - Query_829 - M_1299 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 830 - Query_830 - M_1300 - 9 - - - 1 - gnl|BL_ORD_ID|1980 - 183229|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1980 - 10 - - - 1 - 13.853 - 24 - 6.8721 - 2 - 8 - 2 - 8 - 0 - 0 - 4 - 6 - 0 - 7 - PSSNALL - PQSNAVI - P SNA++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 831 - Query_831 - M_1301 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 832 - Query_832 - M_1302 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 833 - Query_833 - M_1303 - 9 - - - 1 - gnl|BL_ORD_ID|1688 - 149060|E2 protein|NP_751921.1|Hepatitis C virus (isolate H77)|63746 - 1688 - 9 - - - 1 - 12.6974 - 21 - 26.0147 - 2 - 7 - 4 - 9 - 0 - 0 - 4 - 4 - 0 - 6 - AVYSTC - ATYSRC - A YS C - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 834 - Query_834 - M_1304 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 835 - Query_835 - M_1305 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 836 - Query_836 - M_1306 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 837 - Query_837 - M_1307 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 838 - Query_838 - M_1308 - 9 - - - 1 - gnl|BL_ORD_ID|1778 - 155928|unnamed protein product|CAA30115.1|Trypanosoma cruzi|5693 - 1778 - 9 - - - 1 - 12.6974 - 21 - 23.8709 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 7 - 0 - 8 - LKPGDRVV - LQPVERVL - L+P +RV+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 839 - Query_839 - M_1309 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 840 - Query_840 - M_1310 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 841 - Query_841 - M_1311 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 842 - Query_842 - M_1312 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 843 - Query_843 - M_1313 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 844 - Query_844 - M_1314 - 9 - - - 1 - gnl|BL_ORD_ID|2051 - 184702|non-structural protein 1|AGM49312.1|Dengue virus|12637 - 2051 - 9 - - - 1 - 13.4678 - 23 - 9.02895 - 4 - 9 - 3 - 8 - 0 - 0 - 4 - 5 - 0 - 6 - PATHSL - PKTHTL - P TH+L - - - - - 2 - gnl|BL_ORD_ID|1333 - 107873|Genome polyprotein|P26664.3|Hepatitis C virus|11103 - 1333 - 10 - - - 1 - 12.3122 - 20 - 56.5271 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - SSPATHS - GSPITYS - SP T+S - - - - - 3 - gnl|BL_ORD_ID|965 - 63963|HCV-1|AAA45676.1|Hepatitis C virus|11103 - 965 - 10 - - - 1 - 12.3122 - 20 - 63.4362 - 3 - 8 - 3 - 8 - 0 - 0 - 4 - 5 - 0 - 6 - SPATHS - SPITYS - SP T+S - - - - - 4 - gnl|BL_ORD_ID|972 - 64489|polyprotein|BAA03375.1|Hepatitis C virus|11103 - 972 - 11 - - - 1 - 12.3122 - 20 - 63.6416 - 3 - 8 - 6 - 11 - 0 - 0 - 4 - 5 - 0 - 6 - SPATHS - SPITYS - SP T+S - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 845 - Query_845 - M_1315 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 846 - Query_846 - M_1316 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 847 - Query_847 - M_1317 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 848 - Query_848 - M_1318 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 849 - Query_849 - M_1319 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 850 - Query_850 - M_1320 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 851 - Query_851 - M_1321 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 852 - Query_852 - M_1322 - 9 - - - 1 - gnl|BL_ORD_ID|1395 - 110394|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1395 - 32 - - - 1 - 11.1566 - 17 - 134.202 - 2 - 8 - 8 - 14 - 0 - 0 - 4 - 4 - 0 - 7 - PLRPRES - PLCPEEK - PL P E - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 853 - Query_853 - M_1323 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 854 - Query_854 - M_1324 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 855 - Query_855 - M_1325 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 856 - Query_856 - M_1326 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 857 - Query_857 - M_1327 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 858 - Query_858 - M_1328 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 859 - Query_859 - M_1329 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 860 - Query_860 - M_1330 - 9 - - - 1 - gnl|BL_ORD_ID|1876 - 180507|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1876 - 15 - - - 1 - 11.5418 - 18 - 131.587 - 1 - 7 - 8 - 14 - 0 - 0 - 4 - 5 - 0 - 7 - DLVHHTT - DLMCHAT - DL+ H T - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 861 - Query_861 - M_1331 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 862 - Query_862 - M_1332 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 863 - Query_863 - M_1333 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 864 - Query_864 - M_1334 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 865 - Query_865 - M_1335 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 866 - Query_866 - M_1336 - 9 - - - 1 - gnl|BL_ORD_ID|2111 - 186219|polyprotein|AGK36298.1|Dengue virus 2|11060 - 2111 - 9 - - - 1 - 14.6234 - 26 - 2.33479 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - IADGRAW - VEDGRFW - + DGR W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 867 - Query_867 - M_1337 - 9 - - - 1 - gnl|BL_ORD_ID|1919 - 180689|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1919 - 15 - - - 1 - 15.3938 - 28 - 0.680841 - 1 - 7 - 8 - 14 - 0 - 0 - 5 - 6 - 0 - 7 - MGYRVES - MGYWIES - MGY +ES - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 868 - Query_868 - M_1338 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 869 - Query_869 - M_1339 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 870 - Query_870 - M_1340 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 871 - Query_871 - M_1341 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 872 - Query_872 - M_1342 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 873 - Query_873 - M_1343 - 9 - - - 1 - gnl|BL_ORD_ID|1729 - 150534|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1729 - 9 - - - 1 - 13.4678 - 23 - 9.02895 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 4 - 0 - 8 - RPGCLWAL - RPASAWTL - RP W L - - - - - 2 - gnl|BL_ORD_ID|88 - 6431|Genome polyprotein|SRC279960|Hepatitis C virus|11103 - 88 - 9 - - - 1 - 13.4678 - 23 - 12.1399 - 4 - 9 - 4 - 9 - 0 - 0 - 3 - 5 - 0 - 6 - GCLWAL - GCVWTV - GC+W + - - - - - 3 - gnl|BL_ORD_ID|708 - 43619|Genome polyprotein|P26664.3|Hepatitis C virus|11103 - 708 - 9 - - - 1 - 12.6974 - 21 - 26.4654 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 4 - 0 - 7 - RPGCLWA - NEGCGWA - GC WA - - - - - 4 - gnl|BL_ORD_ID|626 - 37536|Spike glycoprotein precursor|P15423.1|Human coronavirus 229E|11137 - 626 - 9 - - - 1 - 12.6974 - 21 - 34.7909 - 4 - 9 - 4 - 9 - 0 - 0 - 3 - 5 - 0 - 6 - GCLWAL - NCLWSV - CLW++ - - - - - 5 - gnl|BL_ORD_ID|664 - 39591|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 - 664 - 20 - - - 1 - 11.5418 - 18 - 101.139 - 5 - 9 - 12 - 16 - 0 - 0 - 4 - 4 - 0 - 5 - CLWAL - CLWWL - CLW L - - - - - 6 - gnl|BL_ORD_ID|1120 - 74387|Genome polyprotein|P26664.3|Hepatitis C virus (isolate 1)|11104 - 1120 - 9 - - - 1 - 11.5418 - 18 - 152.614 - 5 - 9 - 5 - 9 - 0 - 0 - 4 - 4 - 0 - 5 - CLWAL - CLWWL - CLW L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 874 - Query_874 - M_1344 - 9 - - - 1 - gnl|BL_ORD_ID|1476 - 131096|G1 and G2 surface glycoprotein precursor|AAG22532.1|Andes hantavirus|46607 - 1476 - 10 - - - 1 - 13.0826 - 22 - 15.0326 - 1 - 8 - 3 - 10 - 0 - 0 - 3 - 7 - 0 - 8 - HGLEKVPV - HGVGEIPM - HG+ ++P+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 875 - Query_875 - M_1345 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 876 - Query_876 - M_1346 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 877 - Query_877 - M_1347 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 878 - Query_878 - M_1348 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 879 - Query_879 - M_1349 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 880 - Query_880 - M_1350 - 9 - - - 1 - gnl|BL_ORD_ID|1394 - 110373|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1394 - 25 - - - 1 - 11.927 - 19 - 62.6597 - 1 - 8 - 13 - 20 - 0 - 0 - 4 - 6 - 0 - 8 - SMIHYIVL - TTIHDIIL - + IH I+L - - - - - 2 - gnl|BL_ORD_ID|1411 - 111251|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1411 - 15 - - - 1 - 11.5418 - 18 - 103.444 - 1 - 8 - 4 - 11 - 0 - 0 - 4 - 6 - 0 - 8 - SMIHYIVL - TTIHDIIL - + IH I+L - - - - - 3 - gnl|BL_ORD_ID|1390 - 110306|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1390 - 32 - - - 1 - 11.5418 - 18 - 109.949 - 1 - 8 - 11 - 18 - 0 - 0 - 4 - 6 - 0 - 8 - SMIHYIVL - TTIHDIIL - + IH I+L - - - - - 4 - gnl|BL_ORD_ID|1403 - 110720|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1403 - 9 - - - 1 - 11.1566 - 17 - 208.544 - 3 - 8 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - IHYIVL - IHDIIL - IH I+L - - - - - 5 - gnl|BL_ORD_ID|968 - 64320|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 968 - 10 - - - 1 - 11.1566 - 17 - 218.136 - 3 - 8 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - IHYIVL - IHDIIL - IH I+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 881 - Query_881 - M_1351 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 882 - Query_882 - M_1352 - 9 - - - 1 - gnl|BL_ORD_ID|1249 - 98100|trans-sialidase, putative|EAN81657.1|Trypanosoma cruzi|5693 - 1249 - 9 - - - 1 - 13.853 - 24 - 5.95161 - 1 - 9 - 1 - 9 - 0 - 0 - 6 - 7 - 0 - 9 - HIFLFAVLL - HLFYSAVLL - H+F AVLL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 883 - Query_883 - M_1353 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 884 - Query_884 - M_1354 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 885 - Query_885 - M_1355 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 886 - Query_886 - M_1356 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 887 - Query_887 - M_1357 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 888 - Query_888 - M_1358 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 889 - Query_889 - M_1359 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 890 - Query_890 - M_1360 - 9 - - - 1 - gnl|BL_ORD_ID|1563 - 141306|tegument host shutoff protein|NP_044643.1|Human alphaherpesvirus 1|10298 - 1563 - 10 - - - 1 - 13.853 - 24 - 5.98008 - 3 - 9 - 4 - 10 - 0 - 0 - 4 - 4 - 0 - 7 - LEPQKTY - LHPNNTY - L P TY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 891 - Query_891 - M_1361 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 892 - Query_892 - M_1362 - 9 - - - 1 - gnl|BL_ORD_ID|1820 - 177956|polyprotein|ACZ60102.1|Hepatitis C virus subtype 3a|356426 - 1820 - 17 - - - 1 - 11.927 - 19 - 68.8968 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 5 - 0 - 9 - RPPSPKDTV - RPSGMFDSV - RP D+V - - - - - 2 - gnl|BL_ORD_ID|1819 - 177955|polyprotein|ACZ60102.1|Hepatitis C virus subtype 3a|356426 - 1819 - 11 - - - 1 - 11.927 - 19 - 93.6338 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 5 - 0 - 9 - RPPSPKDTV - RPSGMFDSV - RP D+V - - - - - 3 - gnl|BL_ORD_ID|1656 - 146592|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 - 1656 - 16 - - - 1 - 11.5418 - 18 - 127.377 - 1 - 9 - 6 - 14 - 0 - 0 - 4 - 5 - 0 - 9 - RPPSPKDTV - RPSGMFDSV - RP D+V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 893 - Query_893 - M_1363 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 894 - Query_894 - M_1364 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 895 - Query_895 - M_1365 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 896 - Query_896 - M_1366 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 897 - Query_897 - M_1367 - 9 - - - 1 - gnl|BL_ORD_ID|281 - 18941|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 281 - 15 - - - 1 - 14.6234 - 26 - 1.39982 - 1 - 9 - 3 - 11 - 0 - 0 - 4 - 5 - 0 - 9 - CAQSPWCLV - CVQGDWCPI - C Q WC + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 898 - Query_898 - M_1368 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 899 - Query_899 - M_1369 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 900 - Query_900 - M_1370 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 901 - Query_901 - M_1371 - 9 - - - 1 - gnl|BL_ORD_ID|1050 - 69714|Large envelope protein|SRC279965|Hepatitis B virus|10407 - 1050 - 9 - - - 1 - 12.3122 - 20 - 54.8462 - 2 - 7 - 4 - 9 - 0 - 0 - 3 - 5 - 0 - 6 - GGFFVI - AGFFIL - GFF++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 902 - Query_902 - M_1372 - 9 - - - 1 - gnl|BL_ORD_ID|889 - 58463|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 889 - 20 - - - 1 - 13.853 - 24 - 5.41768 - 1 - 7 - 12 - 18 - 0 - 0 - 5 - 6 - 0 - 7 - YVYPLPV - YVYALPL - YVY LP+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 903 - Query_903 - M_1373 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 904 - Query_904 - M_1374 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 905 - Query_905 - M_1375 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 906 - Query_906 - M_1376 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 907 - Query_907 - M_1377 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 908 - Query_908 - M_1378 - 9 - - - 1 - gnl|BL_ORD_ID|659 - 39162|gag protein|AAV53308.1|Human immunodeficiency virus 1|11676 - 659 - 15 - - - 1 - 12.6974 - 21 - 23.6601 - 4 - 9 - 9 - 14 - 0 - 0 - 4 - 5 - 0 - 6 - YKYEHI - YKLKHI - YK +HI - - - - - 2 - gnl|BL_ORD_ID|2125 - 186551|polyprotein|AGW21594.1|Dengue virus 1|11053 - 2125 - 10 - - - 1 - 12.6974 - 21 - 26.5293 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 5 - 0 - 9 - YEGYKYEHI - YENLKYSVI - YE KY I - - - - - 3 - gnl|BL_ORD_ID|558 - 34482|gag polyprotein|BAA00992.1|Human immunodeficiency virus 1|11676 - 558 - 9 - - - 1 - 12.3122 - 20 - 40.5299 - 4 - 9 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - YKYEHI - YKLKHI - YK +HI - - - - - 4 - gnl|BL_ORD_ID|1016 - 67503|Genome polyprotein|P26662.3|Hepatitis C virus|11103 - 1016 - 10 - - - 1 - 11.927 - 19 - 66.6359 - 4 - 9 - 2 - 7 - 0 - 0 - 3 - 5 - 0 - 6 - YKYEHI - YVYDHL - Y Y+H+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 909 - Query_909 - M_1379 - 9 - - - 1 - gnl|BL_ORD_ID|929 - 60867|nucleoprotein|CAZ65591.1|Influenza A virus|11320 - 929 - 9 - - - 1 - 12.6974 - 21 - 24.2855 - 1 - 7 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - DRYVAVR - SRYWAIR - RY A+R - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 910 - Query_910 - M_1380 - 9 - - - 1 - gnl|BL_ORD_ID|601 - 37153|Nuclear antigen EBNA-3C|Q69140.1|Human gammaherpesvirus 4|10376 - 601 - 10 - - - 1 - 15.779 - 29 - 0.523411 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 7 - 0 - 8 - LIDYARYM - LLDFVRFM - L+D+ R+M - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 911 - Query_911 - M_1381 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 912 - Query_912 - M_1382 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 913 - Query_913 - M_1383 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 914 - Query_914 - M_1384 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 915 - Query_915 - M_1385 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 916 - Query_916 - M_1386 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 917 - Query_917 - M_1387 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 918 - Query_918 - M_1388 - 9 - - - 1 - gnl|BL_ORD_ID|2250 - 240808|polyprotein|AAB53095.1|Tick-borne encephalitis virus|11084 - 2250 - 9 - - - 1 - 12.3122 - 20 - 42.6373 - 1 - 6 - 2 - 7 - 0 - 0 - 4 - 6 - 0 - 6 - LVDNLT - LLDNIT - L+DN+T - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 919 - Query_919 - M_1389 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 920 - Query_920 - M_1390 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 921 - Query_921 - M_1391 - 9 - - - 1 - gnl|BL_ORD_ID|1621 - 145860|Protein E6|P04019.1|Human papillomavirus type 11|10580 - 1621 - 9 - - - 1 - 11.927 - 19 - 105.754 - 2 - 7 - 2 - 7 - 0 - 0 - 3 - 5 - 0 - 6 - VLVGCF - VLIRCY - VL+ C+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 922 - Query_922 - M_1392 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 923 - Query_923 - M_1393 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 924 - Query_924 - M_1394 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 925 - Query_925 - M_1395 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 926 - Query_926 - M_1396 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 927 - Query_927 - M_1397 - 9 - - - 1 - gnl|BL_ORD_ID|1936 - 180789|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1936 - 15 - - - 1 - 11.927 - 19 - 86.1406 - 2 - 9 - 7 - 14 - 0 - 0 - 4 - 4 - 0 - 8 - PSPNRPKL - PIPYDPKF - P P PK - - - - - 2 - gnl|BL_ORD_ID|1299 - 103563|polyprotein|BAB18806.1|Hepatitis C virus|11103 - 1299 - 9 - - - 1 - 11.1566 - 17 - 287.485 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 5 - 0 - 9 - RPSPNRPKL - RPDYNPPLL - RP N P L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 928 - Query_928 - M_1398 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 929 - Query_929 - M_1399 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 930 - Query_930 - M_1400 - 9 - - - 1 - gnl|BL_ORD_ID|819 - 54662|pX-rex-orf I {alternatively spliced}|AAB23359.1|Human T-lymphotropic virus 1|11908 - 819 - 9 - - - 1 - 15.0086 - 27 - 1.45111 - 1 - 8 - 1 - 8 - 0 - 0 - 6 - 7 - 0 - 8 - RLLPPVSP - RLLSPLSP - RLL P+SP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 931 - Query_931 - M_1401 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 932 - Query_932 - M_1402 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 933 - Query_933 - M_1403 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 934 - Query_934 - M_1404 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 935 - Query_935 - M_1405 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 936 - Query_936 - M_1406 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 937 - Query_937 - M_1407 - 9 - - - 1 - gnl|BL_ORD_ID|636 - 37919|envelope protein|BAF48755.1|Hepatitis B virus|10407 - 636 - 10 - - - 1 - 14.2382 - 25 - 3.16139 - 1 - 7 - 3 - 9 - 0 - 0 - 4 - 5 - 0 - 7 - VPLVRWL - VPFVQWF - VP V+W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 938 - Query_938 - M_1408 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 939 - Query_939 - M_1409 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 940 - Query_940 - M_1410 - 9 - - - 1 - gnl|BL_ORD_ID|701 - 42797|6 kDa early secretory antigenic target|P0A564.2|Mycobacterium tuberculosis|1773 - 701 - 20 - - - 1 - 13.4678 - 23 - 8.9532 - 4 - 8 - 4 - 8 - 0 - 0 - 4 - 4 - 0 - 5 - QAWNF - QQWNF - Q WNF - - - - - 2 - gnl|BL_ORD_ID|1538 - 140760|LOW MOLECULAR WEIGHT PROTEIN ANTIGEN 7 ESXH (10 kDa ANTIGEN) (CFP-7) (PROTEIN TB10.4)|CAA17363.1|Mycobacterium tuberculosis H37Rv|83332 - 1538 - 9 - - - 1 - 13.4678 - 23 - 11.9303 - 2 - 7 - 1 - 6 - 0 - 0 - 4 - 4 - 0 - 6 - NYQAWN - TYQAWQ - YQAW - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 941 - Query_941 - M_1411 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 942 - Query_942 - M_1412 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 943 - Query_943 - M_1413 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 944 - Query_944 - M_1414 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 945 - Query_945 - M_1415 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 946 - Query_946 - M_1416 - 9 - - - 1 - gnl|BL_ORD_ID|1008 - 66798|glycoprotein gp35/37|AAC59622.1|Human gammaherpesvirus 8|37296 - 1008 - 15 - - - 1 - 12.6974 - 21 - 27.8948 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 5 - 0 - 9 - TTKKSGGHY - TTRGRDAHY - TT+ HY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 947 - Query_947 - M_1417 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 948 - Query_948 - M_1418 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 949 - Query_949 - M_1419 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 950 - Query_950 - M_1420 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 951 - Query_951 - M_1421 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 952 - Query_952 - M_1422 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 953 - Query_953 - M_1423 - 9 - - - 1 - gnl|BL_ORD_ID|1111 - 73177|protein F [Hepatitis C virus subtype 1b]|ACA50643.1|Hepatitis C virus (isolate Japanese)|11116 - 1111 - 9 - - - 1 - 13.0826 - 22 - 20.7937 - 3 - 8 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - VCHQLG - VCARLG - VC +LG - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 954 - Query_954 - M_1424 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 955 - Query_955 - M_1425 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 956 - Query_956 - M_1426 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 957 - Query_957 - M_1427 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 958 - Query_958 - M_1428 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 959 - Query_959 - M_1429 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 960 - Query_960 - M_1430 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 961 - Query_961 - M_1431 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 962 - Query_962 - M_1432 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 963 - Query_963 - M_1433 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 964 - Query_964 - M_1434 - 9 - - - 1 - gnl|BL_ORD_ID|1581 - 141462|tegument protein UL21|NP_044622.1|Human alphaherpesvirus 1|10298 - 1581 - 9 - - - 1 - 13.4678 - 23 - 8.42175 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 6 - 0 - 9 - VPREFKPIL - VPRPDDPVL - VPR P+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 965 - Query_965 - M_1435 - 9 - - - 1 - gnl|BL_ORD_ID|747 - 48896|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 - 747 - 15 - - - 1 - 12.3122 - 20 - 53.9857 - 4 - 9 - 1 - 6 - 0 - 0 - 4 - 4 - 0 - 6 - PPMPPY - PPQPEY - PP P Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 966 - Query_966 - M_1436 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 967 - Query_967 - M_1437 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 968 - Query_968 - M_1438 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 969 - Query_969 - M_1439 - 9 - - - 1 - gnl|BL_ORD_ID|886 - 58122|pol protein|BAA32832.1|Hepatitis B virus|10407 - 886 - 10 - - - 1 - 13.4678 - 23 - 9.73455 - 4 - 8 - 1 - 5 - 0 - 0 - 4 - 5 - 0 - 5 - SGVPR - SGLPR - SG+PR - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 970 - Query_970 - M_1440 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 971 - Query_971 - M_1441 - 9 - - - 1 - gnl|BL_ORD_ID|1596 - 142232|POSSIBLE CONSERVED TRANSMEMBRANE PROTEIN|CAB00937.1|Mycobacterium tuberculosis|1773 - 1596 - 19 - - - 1 - 6.53423 - 5 - 16334.9 - 8 - 9 - 13 - 14 - 0 - 0 - 2 - 2 - 0 - 2 - VY - VY - VY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 972 - Query_972 - M_1442 - 9 - - - 1 - gnl|BL_ORD_ID|96 - 6591|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 96 - 18 - - - 1 - 14.2382 - 25 - 3.03664 - 2 - 9 - 9 - 16 - 0 - 0 - 4 - 4 - 0 - 8 - FHNPKPLF - LHGPTPLL - H P PL - - - - - 2 - gnl|BL_ORD_ID|707 - 43447|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 - 707 - 20 - - - 1 - 13.0826 - 22 - 19.8728 - 1 - 9 - 6 - 14 - 0 - 0 - 5 - 5 - 0 - 9 - FFHNPKPLF - FFFNPGELL - FF NP L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 973 - Query_973 - M_1443 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 974 - Query_974 - M_1444 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 975 - Query_975 - M_1445 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 976 - Query_976 - M_1446 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 977 - Query_977 - M_1447 - 9 - - - 1 - gnl|BL_ORD_ID|133 - 9415|Superoxide dismutase|P17670.1|Mycobacterium tuberculosis|1773 - 133 - 10 - - - 1 - 13.853 - 24 - 4.3044 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 5 - 0 - 9 - DFWYHAVVL - DMWEHAFYL - D W HA L - - - - - 2 - gnl|BL_ORD_ID|132 - 9414|Superoxide dismutase|P17670.1|Mycobacterium tuberculosis|1773 - 132 - 9 - - - 1 - 13.853 - 24 - 5.45887 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 5 - 0 - 9 - DFWYHAVVL - DMWEHAFYL - D W HA L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 978 - Query_978 - M_1448 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 979 - Query_979 - M_1449 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 980 - Query_980 - M_1450 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 981 - Query_981 - M_1451 - 9 - - - 1 - gnl|BL_ORD_ID|320 - 21000|glutamine synthetase GLNA1 (glutamine synthase) (GS-I)|NP_216736.1|Mycobacterium tuberculosis|1773 - 320 - 9 - - - 1 - 14.2382 - 25 - 4.07578 - 3 - 9 - 3 - 9 - 0 - 0 - 4 - 6 - 0 - 7 - VHRAPSI - LHHAPSL - +H APS+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 982 - Query_982 - M_1452 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 983 - Query_983 - M_1453 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 984 - Query_984 - M_1454 - 9 - - - 1 - gnl|BL_ORD_ID|981 - 64821|Protein Tax-1|P03409.2|Human T-lymphotropic virus 1|11908 - 981 - 9 - - - 1 - 13.853 - 24 - 7.20201 - 4 - 9 - 4 - 9 - 0 - 0 - 3 - 5 - 0 - 6 - EHIPTF - QHLPTL - +H+PT - - - - - 2 - gnl|BL_ORD_ID|1172 - 79308|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 1172 - 16 - - - 1 - 13.0826 - 22 - 12.7581 - 4 - 9 - 7 - 12 - 0 - 0 - 3 - 5 - 0 - 6 - EHIPTF - QHLPTL - +H+PT - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 985 - Query_985 - M_1455 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 986 - Query_986 - M_1456 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 987 - Query_987 - M_1457 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 988 - Query_988 - M_1458 - 9 - - - 1 - gnl|BL_ORD_ID|931 - 61077|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 - 931 - 9 - - - 1 - 14.6234 - 26 - 2.07889 - 1 - 8 - 2 - 9 - 0 - 0 - 4 - 7 - 0 - 8 - SHTGTFLL - SHSGSFQI - SH+G+F + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 989 - Query_989 - M_1459 - 9 - - - 1 - gnl|BL_ORD_ID|1861 - 180440|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1861 - 15 - - - 1 - 12.6974 - 21 - 22.514 - 4 - 9 - 8 - 13 - 0 - 0 - 3 - 6 - 0 - 6 - AWSNGH - SWNSGH - +W++GH - - - - - 2 - gnl|BL_ORD_ID|1926 - 180734|Nonstructural protein NS3|NP_739587.2|Dengue virus 2|11060 - 1926 - 9 - - - 1 - 12.3122 - 20 - 40.5299 - 4 - 9 - 2 - 7 - 0 - 0 - 3 - 6 - 0 - 6 - AWSNGH - SWNSGH - +W++GH - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 990 - Query_990 - M_1460 - 9 - - - 1 - gnl|BL_ORD_ID|163 - 12588|Glycoprotein B precursor (Glycoprotein II)|P09257.1|Human alphaherpesvirus 3|10335 - 163 - 11 - - - 1 - 14.2382 - 25 - 3.80034 - 2 - 9 - 2 - 9 - 0 - 0 - 5 - 6 - 0 - 8 - IPDSISKF - ITDTIDKF - I D+I KF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 991 - Query_991 - M_1461 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 992 - Query_992 - M_1462 - 9 - - - 1 - gnl|BL_ORD_ID|1036 - 69398|X protein|AAP06597.1|Hepatitis B virus|10407 - 1036 - 9 - - - 1 - 11.927 - 19 - 87.0561 - 4 - 9 - 2 - 7 - 0 - 0 - 4 - 4 - 0 - 6 - LCHNPV - LCLRPV - LC PV - - - - - 2 - gnl|BL_ORD_ID|310 - 20787|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 - 310 - 10 - - - 1 - 11.927 - 19 - 93.6922 - 1 - 7 - 2 - 8 - 0 - 0 - 4 - 4 - 0 - 7 - FCPLCHN - LCPHCIN - CP C N - - - - - 3 - gnl|BL_ORD_ID|309 - 20786|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 - 309 - 9 - - - 1 - 11.927 - 19 - 102.395 - 1 - 7 - 2 - 8 - 0 - 0 - 4 - 4 - 0 - 7 - FCPLCHN - LCPHCIN - CP C N - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 993 - Query_993 - M_1463 - 9 - - - 1 - gnl|BL_ORD_ID|743 - 47946|envelope glycoprotein|AAC28452.1|Human immunodeficiency virus 1|11676 - 743 - 20 - - - 1 - 13.853 - 24 - 5.6992 - 2 - 6 - 14 - 18 - 0 - 0 - 4 - 5 - 0 - 5 - VLKCN - ILKCN - +LKCN - - - - - 2 - gnl|BL_ORD_ID|1570 - 141396|ribonucleotide reductase subunit 1|NP_044641.1|Human alphaherpesvirus 1|10298 - 1570 - 9 - - - 1 - 13.0826 - 22 - 22.6682 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 6 - 0 - 9 - RVLKCNVHL - RILGVLVHL - R+L VHL - - - - - 3 - gnl|BL_ORD_ID|156 - 11956|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 - 156 - 11 - - - 1 - 11.927 - 19 - 69.0218 - 1 - 7 - 4 - 10 - 0 - 0 - 5 - 5 - 0 - 7 - RVLKCNV - RVLCCYV - RVL C V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 994 - Query_994 - M_1464 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 995 - Query_995 - M_1465 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 996 - Query_996 - M_1466 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 997 - Query_997 - M_1467 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 998 - Query_998 - M_1468 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 999 - Query_999 - M_1469 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1000 - Query_1000 - M_1470 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1001 - Query_1001 - M_1471 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1002 - Query_1002 - M_1472 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1003 - Query_1003 - M_1473 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1004 - Query_1004 - M_1474 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1005 - Query_1005 - M_1475 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1006 - Query_1006 - M_1476 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1007 - Query_1007 - M_1477 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1008 - Query_1008 - M_1478 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1009 - Query_1009 - M_1479 - 9 - - - 1 - gnl|BL_ORD_ID|490 - 30946|HCV-1|AAA45676.1|Hepatitis C virus genotype 1|41856 - 490 - 20 - - - 1 - 12.6974 - 21 - 22.5677 - 4 - 9 - 14 - 19 - 0 - 0 - 3 - 6 - 0 - 6 - NLGIRI - DLGVRV - +LG+R+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1010 - Query_1010 - M_1480 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1011 - Query_1011 - M_1481 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1012 - Query_1012 - M_1482 - 9 - - - 1 - gnl|BL_ORD_ID|1432 - 116123|nucleocapsid protein|ABP49342.1|Influenza A virus (A/California/10/1978(H1N1))|425557 - 1432 - 9 - - - 1 - 11.927 - 19 - 82.8955 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - PFISRTMM - PFDKSTVM - PF T+M - - - - - 2 - gnl|BL_ORD_ID|1232 - 97467|nucleocapsid protein|ACP44251.1|Influenza A virus (A/Fujian/411/2002(H3N2))|293090 - 1232 - 9 - - - 1 - 11.927 - 19 - 94.432 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - PFISRTMM - PFEKSTIM - PF T+M - - - - - 3 - gnl|BL_ORD_ID|649 - 38471|nucleocapsid protein|ABC46569.1|Influenza A virus (A/Memphis/4/1980(H3N2))|383578 - 649 - 9 - - - 1 - 11.927 - 19 - 99.1366 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - PFISRTMM - PFEKSTVM - PF T+M - - - - - 4 - gnl|BL_ORD_ID|647 - 38466|nucleocapsid protein|ABF21284.1|Influenza A virus (A/Iran/1/1957(H2N2))|488233 - 647 - 9 - - - 1 - 11.5418 - 18 - 165.102 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - PFISRTMM - PFDKPTIM - PF T+M - - - - - 5 - gnl|BL_ORD_ID|648 - 38468|nucleoprotein|CAA24268.1|Influenza A virus (A/Puerto Rico/8/1934(H1N1))|211044 - 648 - 9 - - - 1 - 11.5418 - 18 - 181.349 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - PFISRTMM - PFDRTTIM - PF T+M - - - - - 6 - gnl|BL_ORD_ID|650 - 38472|nucleoprotein|AAV48837.1|Influenza A virus (A/Brevig Mission/1/1918(H1N1))|88776 - 650 - 9 - - - 1 - 11.5418 - 18 - 187.089 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - PFISRTMM - PFERATIM - PF T+M - - - - - 7 - gnl|BL_ORD_ID|1434 - 116136|nucleocapsid protein|ACS34671.1|Influenza A virus (A/Auckland/1/2009(H1N1))|642794 - 1434 - 9 - - - 1 - 11.1566 - 17 - 199.082 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - PFISRTMM - PFERATVM - PF T+M - - - - - 8 - gnl|BL_ORD_ID|1433 - 116127|Nucleoprotein|P15682.1|Influenza A virus (A/Wilson-Smith/1933(H1N1))|381518 - 1433 - 9 - - - 1 - 11.1566 - 17 - 291.863 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - PFISRTMM - PFDRPTIM - PF T+M - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1013 - Query_1013 - M_1483 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1014 - Query_1014 - M_1484 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1015 - Query_1015 - M_1485 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1016 - Query_1016 - M_1486 - 9 - - - 1 - gnl|BL_ORD_ID|1395 - 110394|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1395 - 32 - - - 1 - 13.4678 - 23 - 8.60866 - 1 - 6 - 6 - 11 - 0 - 0 - 4 - 4 - 0 - 6 - QAPLAP - QKPLCP - Q PL P - - - - - 2 - gnl|BL_ORD_ID|52 - 3889|||| - 52 - 9 - - - 1 - 13.0826 - 22 - 16.035 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 6 - 0 - 7 - APLAPTH - APVFPSH - AP+ P+H - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1017 - Query_1017 - M_1487 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1018 - Query_1018 - M_1488 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1019 - Query_1019 - M_1489 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1020 - Query_1020 - M_1490 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1021 - Query_1021 - M_1491 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1022 - Query_1022 - M_1492 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1023 - Query_1023 - M_1493 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1024 - Query_1024 - M_1494 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1025 - Query_1025 - M_1495 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1026 - Query_1026 - M_1496 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1027 - Query_1027 - M_1497 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1028 - Query_1028 - M_1498 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1029 - Query_1029 - M_1499 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1030 - Query_1030 - M_1500 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1031 - Query_1031 - M_1501 - 9 - - - 1 - gnl|BL_ORD_ID|755 - 50253|DNA polymerase|CAA10434.1|Hepatitis B virus|10407 - 755 - 10 - - - 1 - 12.6974 - 21 - 29.8889 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 6 - 0 - 6 - RAFSFS - QAFTFS - +AF+FS - - - - - 2 - gnl|BL_ORD_ID|539 - 32955|P protein|P31870.1|Hepatitis B virus|10407 - 539 - 15 - - - 1 - 12.6974 - 21 - 32.8422 - 1 - 6 - 2 - 7 - 0 - 0 - 4 - 6 - 0 - 6 - RAFSFS - QAFTFS - +AF+FS - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1032 - Query_1032 - M_1502 - 9 - - - 1 - gnl|BL_ORD_ID|494 - 31771|Nucleoprotein|P03418.1|Human respiratory syncytial virus A2|11259 - 494 - 14 - - - 1 - 11.5418 - 18 - 158.243 - 3 - 9 - 2 - 8 - 0 - 0 - 3 - 5 - 0 - 7 - MCNSLLV - LCGMLLI - +C LL+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1033 - Query_1033 - M_1503 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1034 - Query_1034 - M_1504 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1035 - Query_1035 - M_1505 - 9 - - - 1 - gnl|BL_ORD_ID|1173 - 79337|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 1173 - 15 - - - 1 - 11.927 - 19 - 66.2133 - 2 - 7 - 7 - 12 - 0 - 0 - 3 - 5 - 0 - 6 - IMPHAI - LLPHVI - ++PH I - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1036 - Query_1036 - M_1506 - 9 - - - 1 - gnl|BL_ORD_ID|2137 - 187106|Vpr protein|BAA93983.1|Human immunodeficiency virus 1|11676 - 2137 - 9 - - - 1 - 14.2382 - 25 - 4.1461 - 2 - 8 - 2 - 8 - 0 - 0 - 3 - 6 - 0 - 7 - LKHMPKI - VRHFPRI - ++H P+I - - - - - 2 - gnl|BL_ORD_ID|798 - 53148|Transcription activator BRLF1|P03209.1|Human herpesvirus 4 strain B95-8|10377 - 798 - 15 - - - 1 - 11.927 - 19 - 90.193 - 1 - 7 - 3 - 9 - 0 - 0 - 3 - 6 - 0 - 7 - LLKHMPK - LIKTLPR - L+K +P+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1037 - Query_1037 - M_1507 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1038 - Query_1038 - M_1508 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1039 - Query_1039 - M_1509 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1040 - Query_1040 - M_1510 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1041 - Query_1041 - M_1511 - 9 - - - 1 - gnl|BL_ORD_ID|838 - 55029|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 838 - 11 - - - 1 - 12.3122 - 20 - 44.3407 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 6 - 0 - 9 - GLIPPDATI - NLVPMVATV - L+P AT+ - - - - - 2 - gnl|BL_ORD_ID|722 - 44920|tegument protein pp65|YP_002608275.1|Human betaherpesvirus 5|10359 - 722 - 9 - - - 1 - 12.3122 - 20 - 60.6092 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 6 - 0 - 9 - GLIPPDATI - NLVPMVATV - L+P AT+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1042 - Query_1042 - M_1512 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1043 - Query_1043 - M_1513 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1044 - Query_1044 - M_1514 - 9 - - - 1 - gnl|BL_ORD_ID|2084 - 185447|polyprotein|AGK36298.1|Dengue virus 2|11060 - 2084 - 10 - - - 1 - 13.4678 - 23 - 11.1891 - 2 - 9 - 2 - 9 - 0 - 0 - 5 - 6 - 0 - 8 - TVLENLAV - NALDNLAV - L+NLAV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1045 - Query_1045 - M_1515 - 9 - - - 1 - gnl|BL_ORD_ID|516 - 32201|Gp160|Q0ED31|Human immunodeficiency virus 1|11676 - 516 - 9 - - - 1 - 14.6234 - 26 - 2.37398 - 1 - 9 - 1 - 9 - 0 - 0 - 6 - 6 - 0 - 9 - KPPPQCVTL - KLTPLCVTL - K P CVTL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1046 - Query_1046 - M_1516 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1047 - Query_1047 - M_1517 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1048 - Query_1048 - M_1518 - 9 - - - 1 - gnl|BL_ORD_ID|1769 - 155096|RL2|CAB06760.1|Human alphaherpesvirus 2|10310 - 1769 - 15 - - - 1 - 13.4678 - 23 - 8.30114 - 2 - 9 - 8 - 15 - 0 - 0 - 4 - 6 - 0 - 8 - CLEASIPL - CMKTWIPL - C++ IPL - - - - - 2 - gnl|BL_ORD_ID|1381 - 110125|E2 protein|ACS92695.1|Human papillomavirus type 16|333760 - 1381 - 10 - - - 1 - 13.4678 - 23 - 10.0795 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 7 - 0 - 9 - MCLEASIPL - ICEEASVTV - +C EAS+ + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1049 - Query_1049 - M_1519 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1050 - Query_1050 - M_1520 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1051 - Query_1051 - M_1521 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1052 - Query_1052 - M_1522 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1053 - Query_1053 - M_1523 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1054 - Query_1054 - M_1524 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1055 - Query_1055 - M_1525 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1056 - Query_1056 - M_1526 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1057 - Query_1057 - M_1527 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1058 - Query_1058 - M_1528 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1059 - Query_1059 - M_1529 - 9 - - - 1 - gnl|BL_ORD_ID|1289 - 102368|E2 protein|NP_751921.1|Hepatitis C virus subtype 1a|31646 - 1289 - 15 - - - 1 - 14.6234 - 26 - 2.26419 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 6 - 0 - 7 - KSGSPEY - RSGAPTY - +SG+P Y - - - - - 2 - gnl|BL_ORD_ID|1696 - 149098|E2 protein|NP_751921.1|Hepatitis C virus (isolate H77)|63746 - 1696 - 9 - - - 1 - 14.2382 - 25 - 2.80642 - 3 - 9 - 1 - 7 - 0 - 0 - 4 - 6 - 0 - 7 - KSGSPEY - RSGAPTY - +SG+P Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1060 - Query_1060 - M_1530 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1061 - Query_1061 - M_1531 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1062 - Query_1062 - M_1532 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1063 - Query_1063 - M_1533 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1064 - Query_1064 - M_1534 - 9 - - - 1 - gnl|BL_ORD_ID|2243 - 232152|rhoptry kinase family protein|AFO54841.1|Toxoplasma gondii type III|398031 - 2243 - 19 - - - 1 - 15.779 - 29 - 0.404157 - 1 - 8 - 4 - 11 - 0 - 0 - 5 - 5 - 0 - 8 - QPLHSLSV - QPFHSYGV - QP HS V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1065 - Query_1065 - M_1535 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1066 - Query_1066 - M_1536 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1067 - Query_1067 - M_1537 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1068 - Query_1068 - M_1538 - 9 - - - 1 - gnl|BL_ORD_ID|2013 - 183813|polyprotein|AGW21594.1|Dengue virus 1|11053 - 2013 - 10 - - - 1 - 12.3122 - 20 - 53.7901 - 2 - 8 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - PHPRRRR - PEPDRQR - P P R+R - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1069 - Query_1069 - M_1539 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1070 - Query_1070 - M_1540 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1071 - Query_1071 - M_1541 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1072 - Query_1072 - M_1542 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1073 - Query_1073 - M_1543 - 9 - - - 1 - gnl|BL_ORD_ID|1767 - 154980|tegument protein|CAB06735.1|Human alphaherpesvirus 2|10310 - 1767 - 15 - - - 1 - 11.927 - 19 - 78.5415 - 1 - 8 - 6 - 13 - 0 - 0 - 5 - 5 - 0 - 8 - RANGNPNP - RANELVNP - RAN NP - - - - - 2 - gnl|BL_ORD_ID|559 - 34598|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 559 - 15 - - - 1 - 11.5418 - 18 - 143.868 - 3 - 9 - 7 - 13 - 0 - 0 - 4 - 4 - 0 - 7 - NGNPNPT - NGYMEPT - NG PT - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1074 - Query_1074 - M_1544 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1075 - Query_1075 - M_1545 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1076 - Query_1076 - M_1546 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1077 - Query_1077 - M_1547 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1078 - Query_1078 - M_1548 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1079 - Query_1079 - M_1549 - 9 - - - 1 - gnl|BL_ORD_ID|1686 - 149052|E1 protein|NP_751920.1|Hepatitis C virus (isolate H77)|63746 - 1686 - 18 - - - 1 - 13.0826 - 22 - 19.4353 - 1 - 8 - 5 - 12 - 0 - 0 - 4 - 5 - 0 - 8 - FSLYRGWA - FSMVGNWA - FS+ WA - - - - - 2 - gnl|BL_ORD_ID|2312 - 423020|polyprotein|ACE82359.1|Hepatitis C virus genotype 1|41856 - 2312 - 9 - - - 1 - 11.927 - 19 - 71.5135 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 4 - 0 - 8 - SLYRGWAL - KLYISWCL - LY W L - - - - - 3 - gnl|BL_ORD_ID|164 - 12616|gag protein|AAV53308.1|Human immunodeficiency virus 1|11676 - 164 - 8 - - - 1 - 11.927 - 19 - 100.945 - 2 - 9 - 1 - 8 - 0 - 0 - 2 - 5 - 0 - 8 - SLYRGWAL - EIYKRWII - +Y+ W + - - - - - 4 - gnl|BL_ORD_ID|47 - 3026|polyprotein|CAB53095.1|Hepatitis C virus subtype 1b|31647 - 47 - 9 - - - 1 - 11.5418 - 18 - 155.038 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 5 - 0 - 8 - SLYRGWAL - ALYGVWPL - +LY W L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1080 - Query_1080 - M_1550 - 9 - - - 1 - gnl|BL_ORD_ID|1387 - 110227|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1387 - 33 - - - 1 - 13.853 - 24 - 8.26714 - 4 - 9 - 11 - 16 - 0 - 0 - 4 - 4 - 0 - 6 - GAPYVV - GNPYAV - G PY V - - - - - 2 - gnl|BL_ORD_ID|1400 - 110467|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1400 - 25 - - - 1 - 13.0826 - 22 - 17.2955 - 4 - 9 - 4 - 9 - 0 - 0 - 4 - 4 - 0 - 6 - GAPYVV - GNPYAV - G PY V - - - - - 3 - gnl|BL_ORD_ID|1397 - 110401|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1397 - 25 - - - 1 - 13.0826 - 22 - 21.086 - 4 - 9 - 19 - 24 - 0 - 0 - 4 - 4 - 0 - 6 - GAPYVV - GNPYAV - G PY V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1081 - Query_1081 - M_1551 - 9 - - - 1 - gnl|BL_ORD_ID|1121 - 74407|polyprotein|AAU89634.1|Hepatitis C virus subtype 2a|31649 - 1121 - 9 - - - 1 - 12.3122 - 20 - 44.8495 - 4 - 9 - 4 - 9 - 0 - 0 - 2 - 4 - 0 - 6 - HWNWII - RWEWVV - W W++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1082 - Query_1082 - M_1552 - 9 - - - 1 - gnl|BL_ORD_ID|1177 - 79506|E1 protein|BAA19893.1|Rubella virus|11041 - 1177 - 20 - - - 1 - 15.0086 - 27 - 1.42104 - 2 - 7 - 7 - 12 - 0 - 0 - 4 - 5 - 0 - 6 - SACWSF - AACWGF - +ACW F - - - - - 2 - gnl|BL_ORD_ID|1198 - 95298|Genome polyprotein|Q913V3.1|Hepatitis C virus (isolate 1)|11104 - 1198 - 9 - - - 1 - 12.6974 - 21 - 35.3877 - 2 - 6 - 4 - 8 - 0 - 0 - 3 - 4 - 0 - 5 - SACWS - GACWT - ACW+ - - - - - 3 - gnl|BL_ORD_ID|87 - 6430|polyprotein|BAB18810.1|Hepatitis C virus genotype 1|41856 - 87 - 9 - - - 1 - 12.6974 - 21 - 35.3877 - 2 - 6 - 4 - 8 - 0 - 0 - 3 - 4 - 0 - 5 - SACWS - GACWT - ACW+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1083 - Query_1083 - M_1553 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1084 - Query_1084 - M_1554 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1085 - Query_1085 - M_1555 - 9 - - - 1 - gnl|BL_ORD_ID|1400 - 110467|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1400 - 25 - - - 1 - 13.4678 - 23 - 11.7461 - 1 - 8 - 5 - 12 - 0 - 0 - 4 - 6 - 0 - 8 - DQYAICMK - NPYAVCDK - + YA+C K - - - - - 2 - gnl|BL_ORD_ID|1387 - 110227|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1387 - 33 - - - 1 - 13.0826 - 22 - 15.9056 - 1 - 8 - 12 - 19 - 0 - 0 - 4 - 6 - 0 - 8 - DQYAICMK - NPYAVCDK - + YA+C K - - - - - 3 - gnl|BL_ORD_ID|2035 - 184412|envelope protein|AGW23591.1|Dengue virus 3|11069 - 2035 - 10 - - - 1 - 12.6974 - 21 - 36.0093 - 2 - 7 - 5 - 10 - 0 - 0 - 3 - 5 - 0 - 6 - QYAICM - SYAMCL - YA+C+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1086 - Query_1086 - M_1556 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1087 - Query_1087 - M_1557 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1088 - Query_1088 - M_1558 - 9 - - - 1 - gnl|BL_ORD_ID|1370 - 108230|polyprotein|AAF65953.1|Hepatitis C virus|11103 - 1370 - 10 - - - 1 - 14.2382 - 25 - 3.62465 - 1 - 6 - 4 - 9 - 0 - 0 - 5 - 5 - 0 - 6 - KAYGRD - KAYGTD - KAYG D - - - - - 2 - gnl|BL_ORD_ID|1339 - 107925|polyprotein|AAF65964.1|Hepatitis C virus|11103 - 1339 - 10 - - - 1 - 12.6974 - 21 - 32.5356 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - KAYGRD - KAHGTD - KA+G D - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1089 - Query_1089 - M_1559 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1090 - Query_1090 - M_1560 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1091 - Query_1091 - M_1561 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1092 - Query_1092 - M_1562 - 9 - - - 1 - gnl|BL_ORD_ID|1769 - 155096|RL2|CAB06760.1|Human alphaherpesvirus 2|10310 - 1769 - 15 - - - 1 - 11.927 - 19 - 86.1406 - 1 - 7 - 4 - 10 - 0 - 0 - 2 - 4 - 0 - 7 - YCFGCLS - FCIPCMK - +C C+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1093 - Query_1093 - M_1563 - 9 - - - 1 - gnl|BL_ORD_ID|1050 - 69714|Large envelope protein|SRC279965|Hepatitis B virus|10407 - 1050 - 9 - - - 1 - 12.3122 - 20 - 53.938 - 4 - 9 - 4 - 9 - 0 - 0 - 3 - 5 - 0 - 6 - GGFFVI - AGFFIL - GFF++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1094 - Query_1094 - M_1564 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1095 - Query_1095 - M_1565 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1096 - Query_1096 - M_1566 - 9 - - - 1 - gnl|BL_ORD_ID|1186 - 93431|pre-C/C protein|ABY54138.1|Hepatitis B virus|10407 - 1186 - 20 - - - 1 - 11.5418 - 18 - 98.2529 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 6 - 0 - 9 - RLMHQLLVI - QLFHLCLII - +L H L+I - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1097 - Query_1097 - M_1567 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1098 - Query_1098 - M_1568 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1099 - Query_1099 - M_1569 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1100 - Query_1100 - M_1570 - 9 - - - 1 - gnl|BL_ORD_ID|383 - 23601|Genome polyprotein|SRC279960|Hepatitis C virus (isolate H77)|63746 - 383 - 21 - - - 1 - 14.2382 - 25 - 3.66708 - 4 - 9 - 3 - 8 - 0 - 0 - 5 - 5 - 0 - 6 - PAGHLV - PAGHAV - PAGH V - - - - - 2 - gnl|BL_ORD_ID|597 - 37127|polyprotein|AAY82030.1|Hepatitis C virus genotype 1|41856 - 597 - 9 - - - 1 - 13.853 - 24 - 5.00793 - 4 - 9 - 4 - 9 - 0 - 0 - 5 - 5 - 0 - 6 - PAGHLV - PAGHAV - PAGH V - - - - - 3 - gnl|BL_ORD_ID|598 - 37136|Genome polyprotein|P27958.3|Hepatitis C virus|11103 - 598 - 9 - - - 1 - 12.6974 - 21 - 38.5226 - 4 - 9 - 4 - 9 - 0 - 0 - 4 - 4 - 0 - 6 - PAGHLV - PTGHAV - P GH V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1101 - Query_1101 - M_1571 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1102 - Query_1102 - M_1572 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1103 - Query_1103 - M_1573 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1104 - Query_1104 - M_1574 - 9 - - - 1 - gnl|BL_ORD_ID|320 - 21000|glutamine synthetase GLNA1 (glutamine synthase) (GS-I)|NP_216736.1|Mycobacterium tuberculosis|1773 - 320 - 9 - - - 1 - 11.5418 - 18 - 150.225 - 1 - 8 - 2 - 9 - 0 - 0 - 3 - 6 - 0 - 8 - MVHLVPAL - LLHHAPSL - ++H P+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1105 - Query_1105 - M_1575 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1106 - Query_1106 - M_1576 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1107 - Query_1107 - M_1577 - 9 - - - 1 - gnl|BL_ORD_ID|10 - 1000|glycoprotein gp35/37|AAC59622.1|Human gammaherpesvirus 8|37296 - 10 - 15 - - - 1 - 13.0826 - 22 - 21.0678 - 1 - 9 - 5 - 13 - 0 - 0 - 4 - 5 - 0 - 9 - NHLNIAWEL - THLYILWAV - HL I W + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1108 - Query_1108 - M_1578 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1109 - Query_1109 - M_1579 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1110 - Query_1110 - M_1580 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1111 - Query_1111 - M_1581 - 9 - - - 1 - gnl|BL_ORD_ID|1438 - 120093|unnamed protein product|CAA33016.1|Rubella virus|11041 - 1438 - 21 - - - 1 - 11.5418 - 18 - 101.431 - 4 - 8 - 11 - 15 - 0 - 0 - 4 - 4 - 0 - 5 - PPPLT - PPPAT - PPP T - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1112 - Query_1112 - M_1582 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1113 - Query_1113 - M_1583 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1114 - Query_1114 - M_1584 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1115 - Query_1115 - M_1585 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1116 - Query_1116 - M_1586 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1117 - Query_1117 - M_1587 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1118 - Query_1118 - M_1588 - 9 - - - 1 - gnl|BL_ORD_ID|1561 - 141277|transactivating tegument protein VP16|NP_044650.1|Human alphaherpesvirus 1|10298 - 1561 - 10 - - - 1 - 12.6974 - 21 - 26.0802 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 5 - 0 - 8 - FTQYLGLS - FTDALGID - FT LG+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1119 - Query_1119 - M_1589 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1120 - Query_1120 - M_1590 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1121 - Query_1121 - M_1591 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1122 - Query_1122 - M_1592 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1123 - Query_1123 - M_1593 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1124 - Query_1124 - M_1594 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1125 - Query_1125 - M_1595 - 9 - - - 1 - gnl|BL_ORD_ID|1392 - 110335|E7|AAD33253.1|Human papillomavirus type 16|333760 - 1392 - 32 - - - 1 - 14.2382 - 25 - 4.6455 - 2 - 7 - 12 - 17 - 0 - 0 - 4 - 6 - 0 - 6 - LLDLRP - MLDLQP - +LDL+P - - - - - 2 - gnl|BL_ORD_ID|1138 - 75075|E7 protein|ABL96585.1|Human papillomavirus type 16|333760 - 1138 - 10 - - - 1 - 13.853 - 24 - 6.08483 - 2 - 8 - 2 - 8 - 0 - 0 - 4 - 6 - 0 - 7 - LLDLRPS - MLDLQPE - +LDL+P - - - - - 3 - gnl|BL_ORD_ID|1823 - 178351|Protein E7|P03129.1|Human papillomavirus type 16|333760 - 1823 - 15 - - - 1 - 13.853 - 24 - 6.40908 - 2 - 8 - 8 - 14 - 0 - 0 - 4 - 6 - 0 - 7 - LLDLRPS - MLDLQPE - +LDL+P - - - - - 4 - gnl|BL_ORD_ID|1137 - 75074|Protein E7|P03129.1|Human papillomavirus type 16|333760 - 1137 - 9 - - - 1 - 13.853 - 24 - 6.83656 - 2 - 8 - 2 - 8 - 0 - 0 - 4 - 6 - 0 - 7 - LLDLRPS - MLDLQPE - +LDL+P - - - - - 5 - gnl|BL_ORD_ID|1117 - 74288|Protein E7|P36831.1|Human papillomavirus type 52|10618 - 1117 - 10 - - - 1 - 13.4678 - 23 - 9.07951 - 2 - 8 - 2 - 8 - 0 - 0 - 4 - 6 - 0 - 7 - LLDLRPS - ILDLQPE - +LDL+P - - - - - 6 - gnl|BL_ORD_ID|1157 - 76334|Protein E7|P17387.1|Human papillomavirus type 31|10585 - 1157 - 10 - - - 1 - 13.4678 - 23 - 12.2057 - 2 - 8 - 2 - 8 - 0 - 0 - 4 - 6 - 0 - 7 - LLDLRPS - VLDLQPE - +LDL+P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1126 - Query_1126 - M_1596 - 9 - - - 1 - gnl|BL_ORD_ID|1688 - 149060|E2 protein|NP_751921.1|Hepatitis C virus (isolate H77)|63746 - 1688 - 9 - - - 1 - 12.6974 - 21 - 26.0147 - 1 - 6 - 4 - 9 - 0 - 0 - 4 - 4 - 0 - 6 - AVYSTC - ATYSRC - A YS C - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1127 - Query_1127 - M_1597 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1128 - Query_1128 - M_1598 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1129 - Query_1129 - M_1599 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1130 - Query_1130 - M_1600 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1131 - Query_1131 - M_1601 - 9 - - - 1 - gnl|BL_ORD_ID|2137 - 187106|Vpr protein|BAA93983.1|Human immunodeficiency virus 1|11676 - 2137 - 9 - - - 1 - 13.853 - 24 - 5.74926 - 3 - 9 - 2 - 8 - 0 - 0 - 3 - 6 - 0 - 7 - LKHMPKI - VRHFPRI - ++H P+I - - - - - 2 - gnl|BL_ORD_ID|798 - 53148|Transcription activator BRLF1|P03209.1|Human herpesvirus 4 strain B95-8|10377 - 798 - 15 - - - 1 - 11.927 - 19 - 90.193 - 2 - 8 - 3 - 9 - 0 - 0 - 3 - 6 - 0 - 7 - LLKHMPK - LIKTLPR - L+K +P+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1132 - Query_1132 - M_1602 - 9 - - - 1 - gnl|BL_ORD_ID|2136 - 187086|polyprotein|ABG67747.1|West Nile virus|11082 - 2136 - 9 - - - 1 - 12.6974 - 21 - 33.058 - 1 - 7 - 3 - 9 - 0 - 0 - 5 - 6 - 0 - 7 - LSLTGLQ - LSLIGLK - LSL GL+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1133 - Query_1133 - M_1603 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1134 - Query_1134 - M_1604 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1135 - Query_1135 - M_1605 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1136 - Query_1136 - M_1606 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1137 - Query_1137 - M_1607 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1138 - Query_1138 - M_1608 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1139 - Query_1139 - M_1609 - 9 - - - 1 - gnl|BL_ORD_ID|310 - 20787|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 - 310 - 10 - - - 1 - 12.3122 - 20 - 42.6014 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 4 - 0 - 8 - SFCPLCHN - GLCPHCIN - CP C N - - - - - 2 - gnl|BL_ORD_ID|309 - 20786|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 - 309 - 9 - - - 1 - 12.3122 - 20 - 51.2985 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 4 - 0 - 8 - SFCPLCHN - GLCPHCIN - CP C N - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1140 - Query_1140 - M_1610 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1141 - Query_1141 - M_1611 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1142 - Query_1142 - M_1612 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1143 - Query_1143 - M_1613 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1144 - Query_1144 - M_1614 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1145 - Query_1145 - M_1615 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1146 - Query_1146 - M_1616 - 9 - - - 1 - gnl|BL_ORD_ID|1122 - 74545|TcP2beta|CAA52943.1|Trypanosoma cruzi|5693 - 1122 - 10 - - - 1 - 12.6974 - 21 - 37.8768 - 2 - 7 - 1 - 6 - 0 - 0 - 5 - 5 - 0 - 6 - YLVAYA - YLAAYA - YL AYA - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1147 - Query_1147 - M_1617 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1148 - Query_1148 - M_1618 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1149 - Query_1149 - M_1619 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1150 - Query_1150 - M_1620 - 9 - - - 1 - gnl|BL_ORD_ID|703 - 42897|RNA polymerase beta-subunit|AAA21416.1|Mycobacterium tuberculosis|1773 - 703 - 9 - - - 1 - 14.2382 - 25 - 4.1461 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 6 - 0 - 8 - VRYAGPLY - MTYAAPLF - + YA PL+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1151 - Query_1151 - M_1621 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1152 - Query_1152 - M_1622 - 9 - - - 1 - gnl|BL_ORD_ID|2108 - 186175|polyprotein|AFY10053.1|Dengue virus 3|11069 - 2108 - 10 - - - 1 - 13.853 - 24 - 6.08483 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 6 - 0 - 6 - TFRDVA - TWRDMA - T+RD+A - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1153 - Query_1153 - M_1623 - 9 - - - 1 - gnl|BL_ORD_ID|471 - 28594|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 - 471 - 20 - - - 1 - 13.853 - 24 - 4.57317 - 1 - 9 - 9 - 17 - 0 - 0 - 5 - 6 - 0 - 9 - DEKDLWEYI - DQKSLENYI - D+K L YI - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1154 - Query_1154 - M_1624 - 9 - - - 1 - gnl|BL_ORD_ID|803 - 53405|||| - 803 - 15 - - - 1 - 15.3938 - 28 - 0.751673 - 1 - 9 - 2 - 10 - 0 - 0 - 6 - 6 - 0 - 9 - DPADPTRDL - DPAKPARLL - DPA P R L - - - - - 2 - gnl|BL_ORD_ID|694 - 42295|Circumsporozoite protein precursor|P02893.1|Plasmodium falciparum|5833 - 694 - 9 - - - 1 - 13.853 - 24 - 4.6749 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 6 - 0 - 8 - PADPTRDL - PNDPNRNV - P DP R++ - - - - - 3 - gnl|BL_ORD_ID|765 - 51311|X protein|ABR68906.1|Hepatitis B virus|10407 - 765 - 9 - - - 1 - 13.0826 - 22 - 17.1877 - 4 - 9 - 3 - 8 - 0 - 0 - 4 - 5 - 0 - 6 - DPTRDL - DPARDV - DP RD+ - - - - - 4 - gnl|BL_ORD_ID|448 - 27241|Spike glycoprotein precursor|P59594.1|SARS coronavirus|227859 - 448 - 9 - - - 1 - 11.927 - 19 - 82.8955 - 1 - 6 - 4 - 9 - 0 - 0 - 4 - 4 - 0 - 6 - DPADPT - DPLKPT - DP PT - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1155 - Query_1155 - M_1625 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1156 - Query_1156 - M_1626 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1157 - Query_1157 - M_1627 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1158 - Query_1158 - M_1628 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1159 - Query_1159 - M_1629 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1160 - Query_1160 - M_1630 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1161 - Query_1161 - M_1631 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1162 - Query_1162 - M_1632 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1163 - Query_1163 - M_1633 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1164 - Query_1164 - M_1634 - 9 - - - 1 - gnl|BL_ORD_ID|1634 - 146260|polyprotein|ADF97231.1|Hepatitis C virus subtype 3a|356426 - 1634 - 18 - - - 1 - 13.0826 - 22 - 13.1042 - 4 - 9 - 5 - 10 - 0 - 0 - 4 - 4 - 0 - 6 - PTLAMY - PALQMY - P L MY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1165 - Query_1165 - M_1635 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1166 - Query_1166 - M_1636 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1167 - Query_1167 - M_1637 - 9 - - - 1 - gnl|BL_ORD_ID|811 - 54342|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 - 811 - 20 - - - 1 - 13.0826 - 22 - 16.1327 - 1 - 6 - 8 - 13 - 0 - 0 - 5 - 5 - 0 - 6 - LSLGAP - LSLGDP - LSLG P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1168 - Query_1168 - M_1638 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1169 - Query_1169 - M_1639 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1170 - Query_1170 - M_1640 - 9 - - - 1 - gnl|BL_ORD_ID|83 - 6094|Genome polyprotein|Q81495.3|Hepatitis C virus (isolate HCV-K3a/650)|356416 - 83 - 15 - - - 1 - 10.7714 - 16 - 331.488 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 5 - 0 - 9 - CSDGSDEDA - CDDCHAQDA - C D +DA - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1171 - Query_1171 - M_1641 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1172 - Query_1172 - M_1642 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1173 - Query_1173 - M_1643 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1174 - Query_1174 - M_1644 - 9 - - - 1 - gnl|BL_ORD_ID|376 - 23288|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 - 376 - 15 - - - 1 - 12.6974 - 21 - 22.1438 - 1 - 5 - 7 - 11 - 0 - 0 - 3 - 4 - 0 - 5 - YPDWI - YQDWL - Y DW+ - - - - - 2 - gnl|BL_ORD_ID|1256 - 98244|trans-sialidase, putative|EAN80840.1|Trypanosoma cruzi|5693 - 1256 - 9 - - - 1 - 12.3122 - 20 - 43.3628 - 4 - 8 - 2 - 6 - 0 - 0 - 3 - 4 - 0 - 5 - WIRDN - WLTDN - W+ DN - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1175 - Query_1175 - M_1645 - 9 - - - 1 - gnl|BL_ORD_ID|866 - 56620|Nef protein|Q9YYU8|Human immunodeficiency virus 1|11676 - 866 - 10 - - - 1 - 13.853 - 24 - 7.36741 - 4 - 9 - 5 - 10 - 0 - 0 - 4 - 5 - 0 - 6 - SFGKCF - TFGWCF - +FG CF - - - - - 2 - gnl|BL_ORD_ID|2214 - 193060|Nef protein|Q9YYU3|Human immunodeficiency virus 1|11676 - 2214 - 10 - - - 1 - 13.4678 - 23 - 9.07951 - 4 - 9 - 5 - 10 - 0 - 0 - 4 - 5 - 0 - 6 - SFGKCF - TFGWCF - +FG CF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1176 - Query_1176 - M_1646 - 9 - - - 1 - gnl|BL_ORD_ID|627 - 37573|E7 protein|ABL96585.1|Human papillomavirus type 16|333760 - 627 - 9 - - - 1 - 13.0826 - 22 - 21.1561 - 3 - 8 - 4 - 9 - 0 - 0 - 4 - 6 - 0 - 6 - GSLGII - GTLGIV - G+LGI+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1177 - Query_1177 - M_1647 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1178 - Query_1178 - M_1648 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1179 - Query_1179 - M_1649 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1180 - Query_1180 - M_1650 - 9 - - - 1 - gnl|BL_ORD_ID|1956 - 181733|Antigen 85-B|P0C5B9.1|Mycobacterium tuberculosis|1773 - 1956 - 40 - - - 1 - 11.5418 - 18 - 88.9423 - 2 - 9 - 10 - 17 - 0 - 0 - 4 - 5 - 0 - 8 - SWLTPLMI - AWGRRLMI - +W LMI - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1181 - Query_1181 - M_1651 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1182 - Query_1182 - M_1652 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1183 - Query_1183 - M_1653 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1184 - Query_1184 - M_1654 - 9 - - - 1 - gnl|BL_ORD_ID|2150 - 189286|||| - 2150 - 9 - - - 1 - 13.4678 - 23 - 8.87313 - 1 - 9 - 1 - 9 - 0 - 0 - 6 - 7 - 0 - 9 - SLYSLDATL - SLYNTAATL - SLY+ ATL - - - - - 2 - gnl|BL_ORD_ID|1463 - 127001|gag polyprotein|BAA00992.1|Human immunodeficiency virus 1|11676 - 1463 - 10 - - - 1 - 13.0826 - 22 - 14.0252 - 1 - 9 - 2 - 10 - 0 - 0 - 6 - 7 - 0 - 9 - SLYSLDATL - SLYNTVATL - SLY+ ATL - - - - - 3 - gnl|BL_ORD_ID|1453 - 126490|Gag protein|Q1KW74|Human immunodeficiency virus 1|11676 - 1453 - 10 - - - 1 - 13.0826 - 22 - 14.5203 - 1 - 9 - 2 - 10 - 0 - 0 - 6 - 7 - 0 - 9 - SLYSLDATL - SLYNTVATL - SLY+ ATL - - - - - 4 - gnl|BL_ORD_ID|2205 - 190962|gag polyprotein|BAB88540.1|Human immunodeficiency virus 1|11676 - 2205 - 10 - - - 1 - 13.0826 - 22 - 15.0326 - 1 - 9 - 2 - 10 - 0 - 0 - 6 - 7 - 0 - 9 - SLYSLDATL - SLYNTIATL - SLY+ ATL - - - - - 5 - gnl|BL_ORD_ID|2199 - 190827|gag protein|AAN08336.1|Human immunodeficiency virus 1|11676 - 2199 - 10 - - - 1 - 13.0826 - 22 - 15.5626 - 1 - 9 - 2 - 10 - 0 - 0 - 6 - 7 - 0 - 9 - SLYSLDATL - SLYNTIATL - SLY+ ATL - - - - - 6 - gnl|BL_ORD_ID|1464 - 127002|gag protein|AAV53342.1|Human immunodeficiency virus 1|11676 - 1464 - 11 - - - 1 - 13.0826 - 22 - 15.7745 - 1 - 9 - 2 - 10 - 0 - 0 - 6 - 7 - 0 - 9 - SLYSLDATL - SLYNTVATL - SLY+ ATL - - - - - 7 - gnl|BL_ORD_ID|1454 - 126491|gag protein|AAV53216.1|Human immunodeficiency virus 1|11676 - 1454 - 11 - - - 1 - 13.0826 - 22 - 16.0488 - 1 - 9 - 2 - 10 - 0 - 0 - 6 - 7 - 0 - 9 - SLYSLDATL - SLYNTVATL - SLY+ ATL - - - - - 8 - gnl|BL_ORD_ID|913 - 59613|Gag polyprotein|P03347.3|Human immunodeficiency virus 1|11676 - 913 - 9 - - - 1 - 13.0826 - 22 - 16.3158 - 1 - 9 - 1 - 9 - 0 - 0 - 6 - 7 - 0 - 9 - SLYSLDATL - SLYNTVATL - SLY+ ATL - - - - - 9 - gnl|BL_ORD_ID|1461 - 126999|gag polyprotein|BAB88540.1|Human immunodeficiency virus 1|11676 - 1461 - 11 - - - 1 - 13.0826 - 22 - 16.3278 - 1 - 9 - 2 - 10 - 0 - 0 - 6 - 7 - 0 - 9 - SLYSLDATL - SLYNTIATL - SLY+ ATL - - - - - 10 - gnl|BL_ORD_ID|2152 - 189288|gag protein|AAV53168.1|Human immunodeficiency virus 1|11676 - 2152 - 9 - - - 1 - 13.0826 - 22 - 17.1877 - 1 - 9 - 1 - 9 - 0 - 0 - 6 - 7 - 0 - 9 - SLYSLDATL - SLYNTIATL - SLY+ ATL - - - - - 11 - gnl|BL_ORD_ID|1451 - 126488|gag protein|AAV53168.1|Human immunodeficiency virus 1|11676 - 1451 - 11 - - - 1 - 13.0826 - 22 - 17.1933 - 1 - 9 - 2 - 10 - 0 - 0 - 6 - 7 - 0 - 9 - SLYSLDATL - SLYNTIATL - SLY+ ATL - - - - - 12 - gnl|BL_ORD_ID|2211 - 190980|gag protein|AAV53216.1|Human immunodeficiency virus 1|11676 - 2211 - 10 - - - 1 - 13.0826 - 22 - 18.8216 - 1 - 9 - 1 - 9 - 0 - 0 - 6 - 7 - 0 - 9 - SLYSLDATL - SLYNTVATL - SLY+ ATL - - - - - 13 - gnl|BL_ORD_ID|2209 - 190978|gag protein|AAV53168.1|Human immunodeficiency virus 1|11676 - 2209 - 10 - - - 1 - 13.0826 - 22 - 19.4818 - 1 - 9 - 1 - 9 - 0 - 0 - 6 - 7 - 0 - 9 - SLYSLDATL - SLYNTIATL - SLY+ ATL - - - - - 14 - gnl|BL_ORD_ID|2160 - 189297|||| - 2160 - 9 - - - 1 - 12.6974 - 21 - 23.4633 - 1 - 9 - 1 - 9 - 0 - 0 - 6 - 6 - 0 - 9 - SLYSLDATL - SLYQTVATL - SLY ATL - - - - - 15 - gnl|BL_ORD_ID|2149 - 189285|gag protein|AAK30999.1|Human immunodeficiency virus 1|11676 - 2149 - 9 - - - 1 - 12.3122 - 20 - 41.221 - 1 - 9 - 1 - 9 - 0 - 0 - 6 - 7 - 0 - 9 - SLYSLDATL - SLYNSVATL - SLY+ ATL - - - - - 16 - gnl|BL_ORD_ID|2161 - 189300|gag polyprotein|BAB88548.1|Human immunodeficiency virus 1|11676 - 2161 - 9 - - - 1 - 12.3122 - 20 - 52.1643 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 7 - 0 - 9 - SLYSLDATL - SVYNTVATL - S+Y+ ATL - - - - - 17 - gnl|BL_ORD_ID|2145 - 189204|||| - 2145 - 9 - - - 1 - 12.3122 - 20 - 64.7664 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 7 - 0 - 9 - SLYSLDATL - ALYNTVATL - +LY+ ATL - - - - - 18 - gnl|BL_ORD_ID|1458 - 126995|gag polyprotein|BAB19171.1|Human immunodeficiency virus 1|11676 - 1458 - 10 - - - 1 - 12.3122 - 20 - 65.5527 - 1 - 9 - 2 - 10 - 0 - 0 - 5 - 7 - 0 - 9 - SLYSLDATL - SLFNTVATL - SL++ ATL - - - - - 19 - gnl|BL_ORD_ID|1447 - 126484|gag protein|AAW03034.1|Human immunodeficiency virus 1|11676 - 1447 - 10 - - - 1 - 11.927 - 19 - 66.6359 - 1 - 9 - 2 - 10 - 0 - 0 - 5 - 7 - 0 - 9 - SLYSLDATL - SLFNTVATL - SL++ ATL - - - - - 20 - gnl|BL_ORD_ID|2202 - 190959|gag polyprotein|BAB19174.1|Human immunodeficiency virus 1|11676 - 2202 - 10 - - - 1 - 11.927 - 19 - 67.736 - 1 - 9 - 2 - 10 - 0 - 0 - 5 - 7 - 0 - 9 - SLYSLDATL - SLFNTIATL - SL++ ATL - - - - - 21 - gnl|BL_ORD_ID|2198 - 190826|gag polyprotein|CAB81949.1|Human immunodeficiency virus 1|11676 - 2198 - 10 - - - 1 - 11.927 - 19 - 68.8532 - 1 - 9 - 2 - 10 - 0 - 0 - 5 - 7 - 0 - 9 - SLYSLDATL - SLFNTIATL - SL++ ATL - - - - - 22 - gnl|BL_ORD_ID|1845 - 180191|gag polyprotein|BAB19174.1|Human immunodeficiency virus 1|11676 - 1845 - 9 - - - 1 - 11.927 - 19 - 80.227 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 7 - 0 - 9 - SLYSLDATL - SLFNTIATL - SL++ ATL - - - - - 23 - gnl|BL_ORD_ID|1475 - 131070|Gag protein|Q9IN85|HIV-1 M:A|505184 - 1475 - 9 - - - 1 - 11.927 - 19 - 80.227 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 7 - 0 - 9 - SLYSLDATL - SLFNTVATL - SL++ ATL - - - - - 24 - gnl|BL_ORD_ID|1844 - 180168|gag protein|ABO14878.1|Human immunodeficiency virus 1|11676 - 1844 - 9 - - - 1 - 11.927 - 19 - 81.5509 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 7 - 0 - 9 - SLYSLDATL - SLFNAVATL - SL++ ATL - - - - - 25 - gnl|BL_ORD_ID|1459 - 126996|Gag protein|Q9YYH6|Human immunodeficiency virus 1|11676 - 1459 - 11 - - - 1 - 11.927 - 19 - 86.4589 - 1 - 9 - 2 - 10 - 0 - 0 - 5 - 7 - 0 - 9 - SLYSLDATL - SLFNTVATL - SL++ ATL - - - - - 26 - gnl|BL_ORD_ID|1448 - 126485|gag protein|AAW03034.1|Human immunodeficiency virus 1|11676 - 1448 - 11 - - - 1 - 11.927 - 19 - 87.8512 - 1 - 9 - 2 - 10 - 0 - 0 - 5 - 7 - 0 - 9 - SLYSLDATL - SLFNTVATL - SL++ ATL - - - - - 27 - gnl|BL_ORD_ID|1456 - 126993|gag polyprotein|BAB19174.1|Human immunodeficiency virus 1|11676 - 1456 - 11 - - - 1 - 11.927 - 19 - 89.2645 - 1 - 9 - 2 - 10 - 0 - 0 - 5 - 7 - 0 - 9 - SLYSLDATL - SLFNTIATL - SL++ ATL - - - - - 28 - gnl|BL_ORD_ID|1444 - 126481|gag polyprotein p17 region|BAA83653.1|Human immunodeficiency virus 1|11676 - 1444 - 11 - - - 1 - 11.927 - 19 - 89.2645 - 1 - 9 - 2 - 10 - 0 - 0 - 5 - 7 - 0 - 9 - SLYSLDATL - SLFNTIATL - SL++ ATL - - - - - 29 - gnl|BL_ORD_ID|2207 - 190974|gag polyprotein|BAB19174.1|Human immunodeficiency virus 1|11676 - 2207 - 10 - - - 1 - 11.927 - 19 - 99.9004 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 7 - 0 - 9 - SLYSLDATL - SLFNTIATL - SL++ ATL - - - - - 30 - gnl|BL_ORD_ID|1468 - 127083|Gag protein|Q9YYH6|Human immunodeficiency virus 1|11676 - 1468 - 10 - - - 1 - 11.927 - 19 - 99.9004 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 7 - 0 - 9 - SLYSLDATL - SLFNTVATL - SL++ ATL - - - - - 31 - gnl|BL_ORD_ID|2148 - 189280|||| - 2148 - 9 - - - 1 - 11.5418 - 18 - 152.614 - 1 - 9 - 1 - 9 - 0 - 0 - 6 - 6 - 0 - 9 - SLYSLDATL - SLYLTVATL - SLY ATL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1185 - Query_1185 - M_1655 - 9 - - - 1 - gnl|BL_ORD_ID|634 - 37830|polyprotein|BAB18806.1|Hepatitis C virus subtype 1b|31647 - 634 - 9 - - - 1 - 12.3122 - 20 - 62.655 - 1 - 6 - 2 - 7 - 0 - 0 - 3 - 5 - 0 - 6 - FTTTQW - LSTTEW - +TT+W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1186 - Query_1186 - M_1656 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1187 - Query_1187 - M_1657 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1188 - Query_1188 - M_1658 - 9 - - - 1 - gnl|BL_ORD_ID|716 - 44214|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 - 716 - 11 - - - 1 - 13.4678 - 23 - 7.61059 - 1 - 9 - 3 - 11 - 0 - 0 - 5 - 6 - 0 - 9 - EMFQRYSAF - EFFTKNSAF - E F + SAF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1189 - Query_1189 - M_1659 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1190 - Query_1190 - M_1660 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1191 - Query_1191 - M_1661 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1192 - Query_1192 - M_1662 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1193 - Query_1193 - M_1663 - 9 - - - 1 - gnl|BL_ORD_ID|990 - 65497|HCV-1|AAA45676.1|Hepatitis C virus genotype 1|41856 - 990 - 20 - - - 1 - 12.3122 - 20 - 40.7919 - 2 - 7 - 14 - 19 - 0 - 0 - 4 - 4 - 0 - 6 - NDPELP - NTPGLP - N P LP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1194 - Query_1194 - M_1664 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1195 - Query_1195 - M_1665 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1196 - Query_1196 - M_1666 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1197 - Query_1197 - M_1667 - 9 - - - 1 - gnl|BL_ORD_ID|1950 - 181035|||| - 1950 - 44 - - - 1 - 10.7714 - 16 - 169.864 - 3 - 9 - 13 - 19 - 0 - 0 - 3 - 5 - 0 - 7 - FPYMGEV - FPGGGQI - FP G++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1198 - Query_1198 - M_1668 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1199 - Query_1199 - M_1669 - 9 - - - 1 - gnl|BL_ORD_ID|1409 - 110982|E6 protein|CAB45108.1|Human papillomavirus type 16|333760 - 1409 - 10 - - - 1 - 13.0826 - 22 - 17.5659 - 3 - 8 - 2 - 7 - 0 - 0 - 4 - 4 - 0 - 6 - YQKQLC - YNKPLC - Y K LC - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1200 - Query_1200 - M_1670 - 9 - - - 1 - gnl|BL_ORD_ID|741 - 47760|EBNA-1 protein|Q777E1|Human gammaherpesvirus 4|10376 - 741 - 15 - - - 1 - 13.0826 - 22 - 14.3275 - 2 - 9 - 2 - 9 - 0 - 0 - 5 - 5 - 0 - 8 - ATGPGEVL - GTGPGNGL - TGPG L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1201 - Query_1201 - M_1671 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1202 - Query_1202 - M_1672 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1203 - Query_1203 - M_1673 - 9 - - - 1 - gnl|BL_ORD_ID|2305 - 422999|polyprotein|ABD97104.1|Hepatitis C virus genotype 3|356114 - 2305 - 9 - - - 1 - 11.1566 - 17 - 211.79 - 1 - 7 - 3 - 9 - 0 - 0 - 4 - 5 - 0 - 7 - FVVFSFF - LVLFGFF - V+F FF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1204 - Query_1204 - M_1674 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1205 - Query_1205 - M_1675 - 9 - - - 1 - gnl|BL_ORD_ID|654 - 38724|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 654 - 20 - - - 1 - 15.0086 - 27 - 1.19565 - 2 - 9 - 4 - 11 - 0 - 0 - 4 - 6 - 0 - 8 - TLRWYLAM - TLRWFFNL - TLRW+ + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1206 - Query_1206 - M_1676 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1207 - Query_1207 - M_1677 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1208 - Query_1208 - M_1678 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1209 - Query_1209 - M_1679 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1210 - Query_1210 - M_1680 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1211 - Query_1211 - M_1681 - 9 - - - 1 - gnl|BL_ORD_ID|1719 - 150399|polyprotein|AGV76873.1|Dengue virus 2|11060 - 1719 - 10 - - - 1 - 16.5494 - 31 - 0.283519 - 2 - 9 - 2 - 9 - 0 - 0 - 5 - 6 - 0 - 8 - QMENNGWV - QMENKAWL - QMEN W+ - - - - - 2 - gnl|BL_ORD_ID|2040 - 184467|polyprotein|AGO67248.1|Dengue virus 2|11060 - 2040 - 10 - - - 1 - 15.779 - 29 - 0.499796 - 2 - 9 - 3 - 10 - 0 - 0 - 4 - 6 - 0 - 8 - QMENNGWV - QMEDKAWL - QME+ W+ - - - - - 3 - gnl|BL_ORD_ID|686 - 41407|Envelope protein|NP_739583.2|Dengue virus 2|11060 - 686 - 15 - - - 1 - 14.6234 - 26 - 2.07692 - 3 - 9 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - MENNGWV - MENKAWL - MEN W+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1212 - Query_1212 - M_1682 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1213 - Query_1213 - M_1683 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1214 - Query_1214 - M_1684 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1215 - Query_1215 - M_1685 - 9 - - - 1 - gnl|BL_ORD_ID|1508 - 139406|polyprotein|ACT37184.1|Hepatitis C virus|11103 - 1508 - 10 - - - 1 - 12.6974 - 21 - 29.8889 - 3 - 8 - 5 - 10 - 0 - 0 - 4 - 5 - 0 - 6 - RPWPRV - RPGPRL - RP PR+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1216 - Query_1216 - M_1686 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1217 - Query_1217 - M_1687 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1218 - Query_1218 - M_1688 - 9 - - - 1 - gnl|BL_ORD_ID|2175 - 189750|Diacylglycerol acyltransferase/mycolyltransferase Ag85B|SRC280000|Mycobacterium tuberculosis|1773 - 2175 - 9 - - - 1 - 12.6974 - 21 - 26.0147 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - LPVSGG - MPVGGG - +PV GG - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1219 - Query_1219 - M_1689 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1220 - Query_1220 - M_1690 - 9 - - - 1 - gnl|BL_ORD_ID|1274 - 101812|Pol polyprotein|Q9YLQ7|Human immunodeficiency virus 1|11676 - 1274 - 9 - - - 1 - 12.6974 - 21 - 35.9943 - 3 - 8 - 4 - 9 - 0 - 0 - 4 - 4 - 0 - 6 - PDATIY - PDIVIY - PD IY - - - - - 2 - gnl|BL_ORD_ID|1275 - 101813|Pol polyprotein|Q9YLQ7|Human immunodeficiency virus 1|11676 - 1275 - 11 - - - 1 - 12.6974 - 21 - 37.5414 - 3 - 8 - 4 - 9 - 0 - 0 - 4 - 4 - 0 - 6 - PDATIY - PDIVIY - PD IY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1221 - Query_1221 - M_1691 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1222 - Query_1222 - M_1692 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1223 - Query_1223 - M_1693 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1224 - Query_1224 - M_1694 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1225 - Query_1225 - M_1695 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1226 - Query_1226 - M_1696 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1227 - Query_1227 - M_1697 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1228 - Query_1228 - M_1698 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1229 - Query_1229 - M_1699 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1230 - Query_1230 - M_1700 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1231 - Query_1231 - M_1701 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1232 - Query_1232 - M_1702 - 9 - - - 1 - gnl|BL_ORD_ID|1298 - 103392|polyprotein|BAB18806.1|Hepatitis C virus|11103 - 1298 - 9 - - - 1 - 13.0826 - 22 - 20.0871 - 1 - 6 - 4 - 9 - 0 - 0 - 4 - 4 - 0 - 6 - DPMVPL - DPTTPL - DP PL - - - - - 2 - gnl|BL_ORD_ID|2258 - 288104|nef protein|ACR27130.1|Human immunodeficiency virus 1|11676 - 2258 - 18 - - - 1 - 11.927 - 19 - 58.6274 - 2 - 7 - 8 - 13 - 0 - 0 - 4 - 5 - 0 - 6 - PMVPLQ - PQVPLR - P VPL+ - - - - - 3 - gnl|BL_ORD_ID|1284 - 102150|nef protein|ACR27119.1|Human immunodeficiency virus 1|11676 - 1284 - 9 - - - 1 - 11.927 - 19 - 87.0561 - 2 - 7 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - PMVPLQ - PQVPLR - P VPL+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1233 - Query_1233 - M_1703 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1234 - Query_1234 - M_1704 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1235 - Query_1235 - M_1705 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1236 - Query_1236 - M_1706 - 9 - - - 1 - gnl|BL_ORD_ID|413 - 24943|DNA polymerase|CAA10434.1|Hepatitis B virus|10407 - 413 - 11 - - - 1 - 12.3122 - 20 - 39.4691 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - VMWWMGIL - TLWKAGIL - +W GIL - - - - - 2 - gnl|BL_ORD_ID|988 - 65148|DNA polymerase|CAA10434.1|Hepatitis B virus|10407 - 988 - 10 - - - 1 - 12.3122 - 20 - 48.6895 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 5 - 0 - 8 - VMWWMGIL - TLWKAGIL - +W GIL - - - - - 3 - gnl|BL_ORD_ID|664 - 39591|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 - 664 - 20 - - - 1 - 11.5418 - 18 - 132.799 - 2 - 9 - 12 - 19 - 0 - 0 - 2 - 4 - 0 - 8 - VMWWMGIL - CLWWLQYF - +WW+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1237 - Query_1237 - M_1707 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1238 - Query_1238 - M_1708 - 9 - - - 1 - gnl|BL_ORD_ID|1508 - 139406|polyprotein|ACT37184.1|Hepatitis C virus|11103 - 1508 - 10 - - - 1 - 12.6974 - 21 - 31.4509 - 2 - 7 - 5 - 10 - 0 - 0 - 4 - 5 - 0 - 6 - RPWPRV - RPGPRL - RP PR+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1239 - Query_1239 - M_1709 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1240 - Query_1240 - M_1710 - 9 - - - 1 - gnl|BL_ORD_ID|601 - 37153|Nuclear antigen EBNA-3C|Q69140.1|Human gammaherpesvirus 4|10376 - 601 - 10 - - - 1 - 15.779 - 29 - 0.523411 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 7 - 0 - 8 - LIDYARYM - LLDFVRFM - L+D+ R+M - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1241 - Query_1241 - M_1711 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1242 - Query_1242 - M_1712 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1243 - Query_1243 - M_1713 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1244 - Query_1244 - M_1714 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1245 - Query_1245 - M_1715 - 9 - - - 1 - gnl|BL_ORD_ID|1296 - 103322|polyprotein|BAB18806.1|Hepatitis C virus|11103 - 1296 - 20 - - - 1 - 11.1566 - 17 - 199.383 - 2 - 8 - 10 - 16 - 0 - 0 - 3 - 5 - 0 - 7 - NCTCGCS - DCSTPCS - +C+ CS - - - - - 2 - gnl|BL_ORD_ID|873 - 57364|Genome polyprotein|P26664.3|Hepatitis C virus|11103 - 873 - 11 - - - 1 - 11.1566 - 17 - 222.638 - 2 - 8 - 2 - 8 - 0 - 0 - 4 - 4 - 0 - 7 - NCTCGCS - ECTTPCS - CT CS - - - - - 3 - gnl|BL_ORD_ID|1679 - 149029|polyprotein|ABR25251.1|Hepatitis C virus (isolate H77)|63746 - 1679 - 9 - - - 1 - 10.7714 - 16 - 354.707 - 3 - 8 - 1 - 6 - 0 - 0 - 4 - 4 - 0 - 6 - CTCGCS - CTTPCS - CT CS - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1246 - Query_1246 - M_1716 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1247 - Query_1247 - M_1717 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1248 - Query_1248 - M_1718 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1249 - Query_1249 - M_1719 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1250 - Query_1250 - M_1720 - 9 - - - 1 - gnl|BL_ORD_ID|1801 - 168240|major paraflagellar rod protein|AAA30221.1|Trypanosoma cruzi|5693 - 1801 - 10 - - - 1 - 13.4678 - 23 - 8.76869 - 1 - 9 - 2 - 10 - 0 - 0 - 5 - 6 - 0 - 9 - LPETKGVTL - VPEVTDVTL - +PE VTL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1251 - Query_1251 - M_1721 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1252 - Query_1252 - M_1722 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1253 - Query_1253 - M_1723 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1254 - Query_1254 - M_1724 - 9 - - - 1 - gnl|BL_ORD_ID|1730 - 150538|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1730 - 9 - - - 1 - 12.3122 - 20 - 46.3849 - 1 - 6 - 3 - 8 - 0 - 0 - 4 - 4 - 0 - 6 - RWNDTR - RWLDAR - RW D R - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1255 - Query_1255 - M_1725 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1256 - Query_1256 - M_1726 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1257 - Query_1257 - M_1727 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1258 - Query_1258 - M_1728 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1259 - Query_1259 - M_1729 - 9 - - - 1 - gnl|BL_ORD_ID|582 - 36504|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 - 582 - 9 - - - 1 - 11.5418 - 18 - 126.161 - 1 - 8 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - IVCDIKEK - IFCHSKKK - I C K+K - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1260 - Query_1260 - M_1730 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1261 - Query_1261 - M_1731 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1262 - Query_1262 - M_1732 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1263 - Query_1263 - M_1733 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1264 - Query_1264 - M_1734 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1265 - Query_1265 - M_1735 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1266 - Query_1266 - M_1736 - 9 - - - 1 - gnl|BL_ORD_ID|530 - 32663|small hydrophobic protein|AAM12943.1|Human metapneumovirus|162145 - 530 - 10 - - - 1 - 11.1566 - 17 - 238.931 - 1 - 9 - 2 - 10 - 0 - 0 - 3 - 5 - 0 - 9 - PATRPLHVL - PAVGVYHIV - PA H++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1267 - Query_1267 - M_1737 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1268 - Query_1268 - M_1738 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1269 - Query_1269 - M_1739 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1270 - Query_1270 - M_1740 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1271 - Query_1271 - M_1741 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1272 - Query_1272 - M_1742 - 9 - - - 1 - gnl|BL_ORD_ID|1512 - 140541|hypothetical protein|NP_218210.1|Mycobacterium tuberculosis H37Rv|83332 - 1512 - 9 - - - 1 - 14.2382 - 25 - 3.00197 - 3 - 9 - 3 - 9 - 0 - 0 - 4 - 6 - 0 - 7 - QEGMVPV - DEGLLPV - EG++PV - - - - - 2 - gnl|BL_ORD_ID|604 - 37187|surface antigen|BAF44879.1|Hepatitis B virus|10407 - 604 - 10 - - - 1 - 13.853 - 24 - 4.3044 - 4 - 9 - 5 - 10 - 0 - 0 - 4 - 6 - 0 - 6 - EGMVPV - QGMLPV - +GM+PV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1273 - Query_1273 - M_1743 - 9 - - - 1 - gnl|BL_ORD_ID|4 - 327|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis|1773 - 4 - 20 - - - 1 - 11.1566 - 17 - 210.697 - 2 - 9 - 5 - 12 - 0 - 0 - 4 - 6 - 0 - 8 - QKRATEEI - QKQELDEI - QK+ +EI - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1274 - Query_1274 - M_1744 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1275 - Query_1275 - M_1745 - 9 - - - 1 - gnl|BL_ORD_ID|665 - 40158|polyprotein|AAA45534.1|Hepatitis C virus|11103 - 665 - 15 - - - 1 - 13.853 - 24 - 5.87794 - 1 - 8 - 6 - 13 - 0 - 0 - 5 - 5 - 0 - 8 - AQLPPWAP - AQLHVWVP - AQL W P - - - - - 2 - gnl|BL_ORD_ID|1187 - 93536|core protein|AAL31859.1|Hepatitis B virus|10407 - 1187 - 11 - - - 1 - 12.3122 - 20 - 55.8493 - 1 - 9 - 2 - 10 - 0 - 0 - 5 - 6 - 0 - 9 - AQLPPWAPL - AYRPPNAPI - A PP AP+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1276 - Query_1276 - M_1746 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1277 - Query_1277 - M_1747 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1278 - Query_1278 - M_1748 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1279 - Query_1279 - M_1749 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1280 - Query_1280 - M_1750 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1281 - Query_1281 - M_1751 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1282 - Query_1282 - M_1752 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1283 - Query_1283 - M_1753 - 9 - - - 1 - gnl|BL_ORD_ID|1758 - 154296|UL29|CAB06754.1|Human alphaherpesvirus 2|10310 - 1758 - 15 - - - 1 - 13.0826 - 22 - 17.8301 - 2 - 9 - 5 - 12 - 0 - 0 - 5 - 5 - 0 - 8 - FFDAFRKF - IFDRTRKF - FD RKF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1284 - Query_1284 - M_1754 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1285 - Query_1285 - M_1755 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1286 - Query_1286 - M_1756 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1287 - Query_1287 - M_1757 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1288 - Query_1288 - M_1758 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1289 - Query_1289 - M_1759 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1290 - Query_1290 - M_1760 - 9 - - - 1 - gnl|BL_ORD_ID|1036 - 69398|X protein|AAP06597.1|Hepatitis B virus|10407 - 1036 - 9 - - - 1 - 13.0826 - 22 - 20.7937 - 3 - 9 - 1 - 7 - 0 - 0 - 4 - 6 - 0 - 7 - VLCGQPI - VLCLRPV - VLC +P+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1291 - Query_1291 - M_1761 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1292 - Query_1292 - M_1762 - 9 - - - 1 - gnl|BL_ORD_ID|619 - 37398|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 - 619 - 10 - - - 1 - 13.853 - 24 - 6.52279 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 6 - 0 - 9 - ILHNQIQQV - LLHTDFEQV - +LH +QV - - - - - 2 - gnl|BL_ORD_ID|618 - 37397|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 - 618 - 9 - - - 1 - 13.853 - 24 - 6.83656 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 6 - 0 - 9 - ILHNQIQQV - LLHTDFEQV - +LH +QV - - - - - 3 - gnl|BL_ORD_ID|581 - 36432|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 - 581 - 9 - - - 1 - 13.0826 - 22 - 16.8921 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 5 - 0 - 8 - LHNQIQQV - LHTDFEQV - LH +QV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1293 - Query_1293 - M_1763 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1294 - Query_1294 - M_1764 - 9 - - - 1 - gnl|BL_ORD_ID|382 - 23573|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 382 - 9 - - - 1 - 13.0826 - 22 - 14.7007 - 4 - 9 - 1 - 6 - 0 - 0 - 3 - 5 - 0 - 6 - HQVGMY - HAVGLF - H VG++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1295 - Query_1295 - M_1765 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1296 - Query_1296 - M_1766 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1297 - Query_1297 - M_1767 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1298 - Query_1298 - M_1768 - 9 - - - 1 - gnl|BL_ORD_ID|1177 - 79506|E1 protein|BAA19893.1|Rubella virus|11041 - 1177 - 20 - - - 1 - 13.853 - 24 - 7.09074 - 3 - 9 - 11 - 17 - 0 - 0 - 5 - 5 - 0 - 7 - GFKGDTV - GFPTDTV - GF DTV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1299 - Query_1299 - M_1769 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1300 - Query_1300 - M_1770 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1301 - Query_1301 - M_1771 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1302 - Query_1302 - M_1772 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1303 - Query_1303 - M_1773 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1304 - Query_1304 - M_1774 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1305 - Query_1305 - M_1775 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1306 - Query_1306 - M_1776 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1307 - Query_1307 - M_1777 - 9 - - - 1 - gnl|BL_ORD_ID|1813 - 177701|polyprotein|ACZ60104.1|Hepatitis C virus subtype 3a|356426 - 1813 - 18 - - - 1 - 15.3938 - 28 - 0.594437 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 6 - 0 - 8 - HAQVCSLY - KAKICGLY - A++C LY - - - - - 2 - gnl|BL_ORD_ID|1793 - 164264|nucleocapsid protein|AAA43837.1|Hantaan virus 76-118|11602 - 1793 - 15 - - - 1 - 14.6234 - 26 - 2.07692 - 1 - 9 - 6 - 14 - 0 - 0 - 4 - 5 - 0 - 9 - FHAQVCSLY - YRTAVCGLY - + VC LY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1308 - Query_1308 - M_1778 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1309 - Query_1309 - M_1779 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1310 - Query_1310 - M_1780 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1311 - Query_1311 - M_1781 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1312 - Query_1312 - M_1782 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1313 - Query_1313 - M_1783 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1314 - Query_1314 - M_1784 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1315 - Query_1315 - M_1785 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1316 - Query_1316 - M_1786 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1317 - Query_1317 - M_1787 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1318 - Query_1318 - M_1788 - 9 - - - 1 - gnl|BL_ORD_ID|2232 - 196087|PPE family protein PPE54|YP_177960.1|Mycobacterium tuberculosis H37Rv|83332 - 2232 - 11 - - - 1 - 13.0826 - 22 - 14.9787 - 1 - 6 - 5 - 10 - 0 - 0 - 3 - 6 - 0 - 6 - MLLHQV - MILHEI - M+LH++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1319 - Query_1319 - M_1789 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1320 - Query_1320 - M_1790 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1321 - Query_1321 - M_1791 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1322 - Query_1322 - M_1792 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1323 - Query_1323 - M_1793 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1324 - Query_1324 - M_1794 - 9 - - - 1 - gnl|BL_ORD_ID|1433 - 116127|Nucleoprotein|P15682.1|Influenza A virus (A/Wilson-Smith/1933(H1N1))|381518 - 1433 - 9 - - - 1 - 13.0826 - 22 - 19.7427 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 4 - 0 - 6 - LPLKRP - LPFDRP - LP RP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1325 - Query_1325 - M_1795 - 9 - - - 1 - gnl|BL_ORD_ID|502 - 31997|hypothetical protein FTT0484|YP_169522.1|Francisella tularensis subsp. tularensis SCHU S4|177416 - 502 - 9 - - - 1 - 13.853 - 24 - 5.55396 - 3 - 7 - 3 - 7 - 0 - 0 - 4 - 4 - 0 - 5 - FPEGY - LPEGY - PEGY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1326 - Query_1326 - M_1796 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1327 - Query_1327 - M_1797 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1328 - Query_1328 - M_1798 - 9 - - - 1 - gnl|BL_ORD_ID|431 - 26273|nucleocapsid protein|ABI96968.1|SARS coronavirus|227859 - 431 - 15 - - - 1 - 14.2382 - 25 - 2.55569 - 1 - 9 - 3 - 11 - 0 - 0 - 5 - 5 - 0 - 9 - MEVDPIGNL - MEVTPSGTW - MEV P G - - - - - 2 - gnl|BL_ORD_ID|2187 - 190494|nucleocapsid protein|ABI96968.1|SARS coronavirus|227859 - 2187 - 10 - - - 1 - 14.2382 - 25 - 3.10797 - 1 - 8 - 1 - 8 - 0 - 0 - 5 - 5 - 0 - 8 - MEVDPIGN - MEVTPSGT - MEV P G - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1329 - Query_1329 - M_1799 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1330 - Query_1330 - M_1800 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1331 - Query_1331 - M_1801 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1332 - Query_1332 - M_1802 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1333 - Query_1333 - M_1803 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1334 - Query_1334 - M_1804 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1335 - Query_1335 - M_1805 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1336 - Query_1336 - M_1806 - 9 - - - 1 - gnl|BL_ORD_ID|1266 - 98640|trans-sialidase, putative|EAN80840.1|Trypanosoma cruzi|5693 - 1266 - 9 - - - 1 - 13.4678 - 23 - 8.13377 - 2 - 8 - 3 - 9 - 0 - 0 - 5 - 7 - 0 - 7 - FSLLATV - FTLVATV - F+L+ATV - - - - - 2 - gnl|BL_ORD_ID|1245 - 98044|trans-sialidase, putative|EAN80840.1|Trypanosoma cruzi|5693 - 1245 - 9 - - - 1 - 13.4678 - 23 - 9.34888 - 2 - 8 - 1 - 7 - 0 - 0 - 5 - 7 - 0 - 7 - FSLLATV - FTLVATV - F+L+ATV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1337 - Query_1337 - M_1807 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1338 - Query_1338 - M_1808 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1339 - Query_1339 - M_1809 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1340 - Query_1340 - M_1810 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1341 - Query_1341 - M_1811 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1342 - Query_1342 - M_1812 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1343 - Query_1343 - M_1813 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1344 - Query_1344 - M_1814 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1345 - Query_1345 - M_1815 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1346 - Query_1346 - M_1816 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1347 - Query_1347 - M_1817 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1348 - Query_1348 - M_1818 - 9 - - - 1 - gnl|BL_ORD_ID|1741 - 150649|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1741 - 10 - - - 1 - 11.1566 - 17 - 228.313 - 2 - 9 - 3 - 10 - 0 - 0 - 4 - 5 - 0 - 8 - QQNCAAYL - QDNQLAYV - Q N AY+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1349 - Query_1349 - M_1819 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1350 - Query_1350 - M_1820 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1351 - Query_1351 - M_1821 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1352 - Query_1352 - M_1822 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1353 - Query_1353 - M_1823 - 9 - - - 1 - gnl|BL_ORD_ID|910 - 59585|polymerase|AAD16253.1|Hepatitis B virus|10407 - 910 - 9 - - - 1 - 13.0826 - 22 - 18.4218 - 1 - 6 - 3 - 8 - 0 - 0 - 4 - 5 - 0 - 6 - YAQTPS - YADSPS - YA +PS - - - - - 2 - gnl|BL_ORD_ID|793 - 53041|phosphorylated matrix protein (pp65)|AAA45996.1|Human betaherpesvirus 5|10359 - 793 - 11 - - - 1 - 12.3122 - 20 - 59.6252 - 4 - 9 - 3 - 8 - 0 - 0 - 4 - 4 - 0 - 6 - TPSKTP - TPDSTP - TP TP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1354 - Query_1354 - M_1824 - 9 - - - 1 - gnl|BL_ORD_ID|442 - 27168|envelope protein|BAF48755.1|Hepatitis B virus|10407 - 442 - 9 - - - 1 - 10.7714 - 16 - 411.363 - 1 - 6 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - LLLCFL - LLLCLI - LLLC + - - - - - 2 - gnl|BL_ORD_ID|621 - 37466|surface antigen|BAF44879.1|Hepatitis B virus|10407 - 621 - 9 - - - 1 - 10.7714 - 16 - 497.585 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - LLLCFL - LLLCLI - LLLC + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1355 - Query_1355 - M_1825 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1356 - Query_1356 - M_1826 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_118813_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_118813_1_T.fasta deleted file mode 100755 index 6e1ccdb0..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_118813_1_T.fasta +++ /dev/null @@ -1,188 +0,0 @@ ->M_1827 -IKLHNPSTI ->M_1828 -TLLTTHYMA ->M_1829 -SYEVVIPEW ->M_1830 -WVNEFGEVF ->M_1831 -LTYRHCQNF ->M_1832 -LTYRHCQNF ->M_1833 -RHCQNFSIL ->M_1834 -YRHCQNFSI ->M_1835 -YRHCQNFSI ->M_1836 -FSLERIAES ->M_1837 -CLHYIMGDY ->M_1838 -LLACLHYIM ->M_1839 -RLLACLHYI ->M_1840 -RLLACLHYI ->M_1841 -SQSADAHSI ->M_1842 -TFFSSSQSA ->M_1843 -YANNHCIRT ->M_1844 -FYGMTEMNY ->M_1845 -LQFYGMTEM ->M_1846 -LQFYGMTEM ->M_1847 -ALWMYRSLM ->M_1848 -ALWMYRSLM ->M_1849 -QALWMYRSL ->M_1850 -SFRKEKRNL ->M_1851 -LTSQDLAGY ->M_1852 -MAGHGWGAL ->M_1853 -VMSYGEQPY ->M_1854 -SVSDVFHGI ->M_1855 -IPNDNTLSL ->M_1856 -KTIPNDNTL ->M_1857 -KTIPNDNTL ->M_1858 -TLSLRICTI ->M_1859 -FSMRARIDV ->M_1860 -RLLGQKFSM ->M_1861 -IYMENERRM ->M_1862 -QFLLELYSL ->M_1863 -RVIRYVIGV ->M_1864 -QYLSLINYY ->M_1865 -STLQYLSLI ->M_1866 -IAQGKPVTL ->M_1867 -SVIAQGKPV ->M_1868 -FAIMHAQRT ->M_1869 -HTNAVFAIM ->M_1870 -NHTNAVFAI ->M_1871 -HHHHHHQAW ->M_1872 -QAWPPPSSA ->M_1873 -AHTVARGPV ->M_1874 -ALQTFAHTV ->M_1875 -EIYTKNHAY ->M_1876 -FGYQLKEIY ->M_1877 -IYTKNHAYI ->M_1878 -YTKNHAYII ->M_1879 -YTKNHAYII ->M_1880 -HAFDRYETT ->M_1881 -TTHSRPVTL ->M_1882 -TTHSRPVTL ->M_1883 -YETTHSRPV ->M_1884 -VLFDVAGQV ->M_1885 -VLFDVAGQV ->M_1886 -ESKPAPAEV ->M_1887 -LNVEKTEKI ->M_1888 -MVIVFYGTL ->M_1889 -MVIVFYGTL ->M_1890 -SAHLTMVIV ->M_1891 -YETFGAASF ->M_1892 -RGVPPLRTV ->M_1893 -TAESCRSTL ->M_1894 -TAESCRSTL ->M_1895 -RVRAAGQRL ->M_1896 -DVHARESKI ->M_1897 -NVPPTVQKV ->M_1898 -CYYPMAGYI ->M_1899 -CYYPMAGYI ->M_1900 -NTRQCYYPM ->M_1901 -LGYRWCLHV ->M_1902 -LLLGYRWCL ->M_1903 -TAHSSVLTL ->M_1904 -TAHSSVLTL ->M_1905 -FPSNHLGDL ->M_1906 -LLLAHKKKV ->M_1907 -AQILEQVEV ->M_1908 -QIFKCKGTL ->M_1909 -QIFKCKGTL ->M_1910 -TLVGHQGPV ->M_1911 -TLVGHQGPV ->M_1912 -DAVELWAIV ->M_1913 -VDLPLTSTI ->M_1914 -NVVNGQMRF ->M_1915 -MGAPGSEII ->M_1916 -FSQFSNLKV ->M_1917 -KAFSQFSNL ->M_1918 -HFSVSSNLL ->M_1919 -KHFSVSSNL ->M_1920 -KHFSVSSNL diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_118813_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_118813_1_T_iedb.xml deleted file mode 100755 index 0c91beb3..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_118813_1_T_iedb.xml +++ /dev/null @@ -1,2608 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_1827 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_1827 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_1828 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_1829 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_1830 - 9 - - - 1 - gnl|BL_ORD_ID|1103 - 72790|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 - 1103 - 9 - - - 1 - 13.853 - 24 - 5.65074 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 6 - 0 - 9 - WVNEFGEVF - WLSDCGEAL - W+++ GE - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 5 - Query_5 - M_1831 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_1832 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_1833 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_1834 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_1835 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_1836 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_1837 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_1838 - 9 - - - 1 - gnl|BL_ORD_ID|669 - 40262|Cytochrome P450 2A7|P20853.1|Homo sapiens|9606 - 669 - 10 - - - 1 - 12.6974 - 21 - 31.4509 - 1 - 5 - 4 - 8 - 0 - 0 - 5 - 5 - 0 - 5 - LLACL - LLACL - LLACL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 13 - Query_13 - M_1839 - 9 - - - 1 - gnl|BL_ORD_ID|669 - 40262|Cytochrome P450 2A7|P20853.1|Homo sapiens|9606 - 669 - 10 - - - 1 - 12.6974 - 21 - 28.8893 - 2 - 6 - 4 - 8 - 0 - 0 - 5 - 5 - 0 - 5 - LLACL - LLACL - LLACL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 14 - Query_14 - M_1840 - 9 - - - 1 - gnl|BL_ORD_ID|669 - 40262|Cytochrome P450 2A7|P20853.1|Homo sapiens|9606 - 669 - 10 - - - 1 - 12.6974 - 21 - 28.8893 - 2 - 6 - 4 - 8 - 0 - 0 - 5 - 5 - 0 - 5 - LLACL - LLACL - LLACL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 15 - Query_15 - M_1841 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_1842 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_1843 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_1844 - 9 - - - 1 - gnl|BL_ORD_ID|2264 - 418945|PPE family protein PPE68|KAM81677.1|Mycobacterium tuberculosis H37Ra|419947 - 2264 - 9 - - - 1 - 14.2382 - 25 - 2.62424 - 3 - 9 - 1 - 7 - 0 - 0 - 4 - 6 - 0 - 7 - GMTEMNY - ALTEMDY - +TEM+Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 19 - Query_19 - M_1845 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_1846 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_1847 - 9 - - - 1 - gnl|BL_ORD_ID|1951 - 181036|||| - 1951 - 20 - - - 1 - 13.0826 - 22 - 13.0672 - 2 - 9 - 7 - 14 - 0 - 0 - 3 - 7 - 0 - 8 - LWMYRSLM - VWLKKSMM - +W+ +S+M - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 22 - Query_22 - M_1848 - 9 - - - 1 - gnl|BL_ORD_ID|1951 - 181036|||| - 1951 - 20 - - - 1 - 13.0826 - 22 - 13.0672 - 2 - 9 - 7 - 14 - 0 - 0 - 3 - 7 - 0 - 8 - LWMYRSLM - VWLKKSMM - +W+ +S+M - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 23 - Query_23 - M_1849 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_1850 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_1851 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_1852 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_1853 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 28 - Query_28 - M_1854 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 29 - Query_29 - M_1855 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 30 - Query_30 - M_1856 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 31 - Query_31 - M_1857 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 32 - Query_32 - M_1858 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 33 - Query_33 - M_1859 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 34 - Query_34 - M_1860 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 35 - Query_35 - M_1861 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 36 - Query_36 - M_1862 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 37 - Query_37 - M_1863 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 38 - Query_38 - M_1864 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 39 - Query_39 - M_1865 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 40 - Query_40 - M_1866 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 41 - Query_41 - M_1867 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 42 - Query_42 - M_1868 - 9 - - - 1 - gnl|BL_ORD_ID|1393 - 110338|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1393 - 33 - - - 1 - 13.0826 - 22 - 15.4552 - 4 - 9 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - MHAQRT - MHQKRT - MH +RT - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 43 - Query_43 - M_1869 - 9 - - - 1 - gnl|BL_ORD_ID|414 - 24986|polyprotein precursor|NP_041724.2|West Nile virus|11082 - 414 - 9 - - - 1 - 11.1566 - 17 - 221.814 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 5 - 0 - 9 - HTNAVFAIM - HTTKGAALM - HT A+M - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 44 - Query_44 - M_1870 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 45 - Query_45 - M_1871 - 9 - - - 1 - gnl|BL_ORD_ID|1975 - 183147|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1975 - 9 - - - 1 - 10.7714 - 16 - 349.459 - 3 - 7 - 4 - 8 - 0 - 0 - 4 - 4 - 0 - 5 - HHHHQ - HHFHQ - HH HQ - - - - - 2 - gnl|BL_ORD_ID|1576 - 141418|tegument protein VP11/12|NP_044648.1|Human alphaherpesvirus 1|10298 - 1576 - 9 - - - 1 - 10.3862 - 15 - 574.99 - 3 - 7 - 4 - 8 - 0 - 0 - 4 - 4 - 0 - 5 - HHHHQ - HHHAQ - HHH Q - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 46 - Query_46 - M_1872 - 9 - - - 1 - gnl|BL_ORD_ID|1618 - 144544|polyprotein precursor|BAA01728.1|Hepatitis C virus|11103 - 1618 - 10 - - - 1 - 14.2382 - 25 - 4.01795 - 3 - 9 - 1 - 7 - 0 - 0 - 5 - 5 - 0 - 7 - WPPPSSA - WPAPSGA - WP PS A - - - - - 2 - gnl|BL_ORD_ID|665 - 40158|polyprotein|AAA45534.1|Hepatitis C virus|11103 - 665 - 15 - - - 1 - 12.3122 - 20 - 51.4826 - 1 - 6 - 9 - 14 - 0 - 0 - 3 - 3 - 0 - 6 - QAWPPP - HVWVPP - W PP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 47 - Query_47 - M_1873 - 9 - - - 1 - gnl|BL_ORD_ID|403 - 24557|Gag polyprotein|P03347.3|Human immunodeficiency virus 1|11676 - 403 - 9 - - - 1 - 12.6974 - 21 - 39.8499 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 5 - 0 - 8 - HTVARGPV - HPVHAGPI - H V GP+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 48 - Query_48 - M_1874 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 49 - Query_49 - M_1875 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 50 - Query_50 - M_1876 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 51 - Query_51 - M_1877 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 52 - Query_52 - M_1878 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 53 - Query_53 - M_1879 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 54 - Query_54 - M_1880 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 55 - Query_55 - M_1881 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 56 - Query_56 - M_1882 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 57 - Query_57 - M_1883 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 58 - Query_58 - M_1884 - 9 - - - 1 - gnl|BL_ORD_ID|1176 - 79454|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 1176 - 15 - - - 1 - 11.5418 - 18 - 141.75 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 6 - 0 - 9 - VLFDVAGQV - VIFCHPGQL - V+F GQ+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 59 - Query_59 - M_1885 - 9 - - - 1 - gnl|BL_ORD_ID|1176 - 79454|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 1176 - 15 - - - 1 - 11.5418 - 18 - 141.75 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 6 - 0 - 9 - VLFDVAGQV - VIFCHPGQL - V+F GQ+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 60 - Query_60 - M_1886 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 61 - Query_61 - M_1887 - 9 - - - 1 - gnl|BL_ORD_ID|569 - 35568|Polyprotein|Q9J8D4|Dengue virus 2|11060 - 569 - 8 - - - 1 - 11.5418 - 18 - 135.128 - 3 - 8 - 1 - 6 - 0 - 0 - 4 - 6 - 0 - 6 - VEKTEK - LEKTKK - +EKT+K - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 62 - Query_62 - M_1888 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 63 - Query_63 - M_1889 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 64 - Query_64 - M_1890 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 65 - Query_65 - M_1891 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 66 - Query_66 - M_1892 - 9 - - - 1 - gnl|BL_ORD_ID|576 - 36345|polyprotein|ABR25251.1|Hepatitis C virus (isolate H77)|63746 - 576 - 10 - - - 1 - 16.1642 - 30 - 0.338287 - 2 - 8 - 2 - 8 - 0 - 0 - 6 - 6 - 0 - 7 - GVPPLRT - GVPPLRA - GVPPLR - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 67 - Query_67 - M_1893 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 68 - Query_68 - M_1894 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 69 - Query_69 - M_1895 - 9 - - - 1 - gnl|BL_ORD_ID|1956 - 181733|Antigen 85-B|P0C5B9.1|Mycobacterium tuberculosis|1773 - 1956 - 40 - - - 1 - 14.6234 - 26 - 2.9583 - 1 - 9 - 7 - 15 - 0 - 0 - 5 - 8 - 0 - 9 - RVRAAGQRL - KIRAWGRRL - ++RA G+RL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 70 - Query_70 - M_1896 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 71 - Query_71 - M_1897 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 72 - Query_72 - M_1898 - 9 - - - 1 - gnl|BL_ORD_ID|1160 - 76532|outer membrane protein|YP_170495.1|Francisella tularensis subsp. tularensis SCHU S4|177416 - 1160 - 10 - - - 1 - 11.1566 - 17 - 190.083 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 5 - 0 - 8 - YYPMAGYI - YYLDRGYL - YY GY+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 73 - Query_73 - M_1899 - 9 - - - 1 - gnl|BL_ORD_ID|1160 - 76532|outer membrane protein|YP_170495.1|Francisella tularensis subsp. tularensis SCHU S4|177416 - 1160 - 10 - - - 1 - 11.1566 - 17 - 190.083 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 5 - 0 - 8 - YYPMAGYI - YYLDRGYL - YY GY+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 74 - Query_74 - M_1900 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 75 - Query_75 - M_1901 - 9 - - - 1 - gnl|BL_ORD_ID|629 - 37607|kaposin|AAC57155.1|Human gammaherpesvirus 8|37296 - 629 - 9 - - - 1 - 12.6974 - 21 - 23.4633 - 2 - 7 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - GYRWCL - GWRWRL - G+RW L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 76 - Query_76 - M_1902 - 9 - - - 1 - gnl|BL_ORD_ID|629 - 37607|kaposin|AAC57155.1|Human gammaherpesvirus 8|37296 - 629 - 9 - - - 1 - 14.2382 - 25 - 3.87216 - 1 - 9 - 1 - 9 - 0 - 0 - 6 - 7 - 0 - 9 - LLLGYRWCL - LLNGWRWRL - LL G+RW L - - - - - 2 - gnl|BL_ORD_ID|626 - 37536|Spike glycoprotein precursor|P15423.1|Human coronavirus 229E|11137 - 626 - 9 - - - 1 - 9.61583 - 13 - 1239.7 - 1 - 7 - 1 - 7 - 0 - 0 - 4 - 4 - 0 - 7 - LLLGYRW - LLLNCLW - LLL W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 77 - Query_77 - M_1903 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 78 - Query_78 - M_1904 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 79 - Query_79 - M_1905 - 9 - - - 1 - gnl|BL_ORD_ID|741 - 47760|EBNA-1 protein|Q777E1|Human gammaherpesvirus 4|10376 - 741 - 15 - - - 1 - 13.0826 - 22 - 16.6732 - 2 - 8 - 5 - 11 - 0 - 0 - 4 - 5 - 0 - 7 - PSNHLGD - PGNGLGE - P N LG+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 80 - Query_80 - M_1906 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 81 - Query_81 - M_1907 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 82 - Query_82 - M_1908 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 83 - Query_83 - M_1909 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 84 - Query_84 - M_1910 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 85 - Query_85 - M_1911 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 86 - Query_86 - M_1912 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 87 - Query_87 - M_1913 - 9 - - - 1 - gnl|BL_ORD_ID|322 - 21007|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 322 - 9 - - - 1 - 12.3122 - 20 - 56.7066 - 3 - 9 - 3 - 9 - 0 - 0 - 4 - 5 - 0 - 7 - LPLTSTI - LPFHSTL - LP ST+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 88 - Query_88 - M_1914 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 89 - Query_89 - M_1915 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 90 - Query_90 - M_1916 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 91 - Query_91 - M_1917 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 92 - Query_92 - M_1918 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 93 - Query_93 - M_1919 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 94 - Query_94 - M_1920 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_119118_2_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_119118_2_T.fasta deleted file mode 100755 index a2c43fcd..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_119118_2_T.fasta +++ /dev/null @@ -1,50 +0,0 @@ ->M_1921 -YQVLAMSTK ->M_1922 -KLSSEAKTK ->M_1923 -TVLRLFPFR ->M_1924 -TVLRLFPFR ->M_1925 -TVKDVHKAK ->M_1926 -TIHNVNFSK ->M_1927 -TIHNVNFSK ->M_1928 -SETTFDIFV ->M_1929 -GMHFSPGAR ->M_1930 -FLTQPVAPK ->M_1931 -KAISFYMKR ->M_1932 -RTVAQVTKK ->M_1933 -RTVAQVTKK ->M_1934 -SEDKKNTKL ->M_1935 -RVAAGVQIK ->M_1936 -RVAAGVQIK ->M_1937 -VVGAVGVGK ->M_1938 -VVGAVGVGK ->M_1939 -TTTPTLKEK ->M_1940 -QSLYIDRLK ->M_1941 -TTIHYNYMY ->M_1942 -TECIIAMSF ->M_1943 -IESSYLESL ->M_1944 -AEEEEEEVV ->M_1945 -TENHQPVCL diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_119118_2_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_119118_2_T_iedb.xml deleted file mode 100755 index 6c7a7c78..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_119118_2_T_iedb.xml +++ /dev/null @@ -1,577 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_1921 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_1921 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_1922 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_1923 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_1924 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_1925 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_1926 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_1927 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_1928 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_1929 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_1930 - 9 - - - 1 - gnl|BL_ORD_ID|2271 - 419002|PPE family protein PPE68|KAM81677.1|Mycobacterium tuberculosis H37Ra|419947 - 2271 - 10 - - - 1 - 13.4678 - 23 - 7.76238 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 6 - 0 - 8 - FLTQPVAP - LIEKPVAP - + +PVAP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 11 - Query_11 - M_1931 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_1932 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_1933 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_1934 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_1935 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_1936 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_1937 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_1938 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_1939 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_1940 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_1941 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 22 - Query_22 - M_1942 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_1943 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_1944 - 9 - - - 1 - gnl|BL_ORD_ID|1398 - 110431|E7|AAD33253.1|Human papillomavirus type 16|333760 - 1398 - 36 - - - 1 - 10.7714 - 16 - 242.357 - 1 - 6 - 13 - 18 - 0 - 0 - 4 - 6 - 0 - 6 - AEEEEE - SEEEDE - +EEE+E - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 25 - Query_25 - M_1945 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_119914_2_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_119914_2_T.fasta deleted file mode 100755 index 34547d25..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_119914_2_T.fasta +++ /dev/null @@ -1,58 +0,0 @@ ->M_1946 -GQLGGLAGK ->M_1947 -LSDWGPHFK ->M_1948 -LSDWGPHFK ->M_1949 -KPASKKEWI ->M_1950 -TTKSEAIEK ->M_1951 -IVRASGCEL ->M_1952 -VPTELNGSM ->M_1953 -VPLFPARVL ->M_1954 -APAQPPMLA ->M_1955 -VVGARGVGK ->M_1956 -VVGARGVGK ->M_1957 -KLCNSGDFR ->M_1958 -HPLTENSPL ->M_1959 -STVRKSPWK ->M_1960 -STVRKSPWK ->M_1961 -LIRMYNINK ->M_1962 -LIRMYNINK ->M_1963 -SPWPLSSLT ->M_1964 -SLKSTRAVF ->M_1965 -SVGSASSLK ->M_1966 -SVGSASSLK ->M_1967 -KGYGGFSRY ->M_1968 -KGYGGFSRY ->M_1969 -KAIGKSRPY ->M_1970 -KTLRKAIGK ->M_1971 -KTLRKAIGK ->M_1972 -QALQKTLRK ->M_1973 -SYQSTGDPK ->M_1974 -VPEWSNNS* diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_119914_2_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_119914_2_T_iedb.xml deleted file mode 100755 index 6278990d..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_119914_2_T_iedb.xml +++ /dev/null @@ -1,739 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_1946 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_1946 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_1947 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_1948 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_1949 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_1950 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_1951 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_1952 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_1953 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_1954 - 9 - - - 1 - gnl|BL_ORD_ID|889 - 58463|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 889 - 20 - - - 1 - 13.0826 - 22 - 16.1327 - 1 - 7 - 3 - 9 - 0 - 0 - 4 - 5 - 0 - 7 - APAQPPM - CPSQEPM - P+Q PM - - - - - 2 - gnl|BL_ORD_ID|749 - 49485|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 749 - 11 - - - 1 - 13.0826 - 22 - 16.8999 - 2 - 7 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - PAQPPM - PSQEPM - P+Q PM - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 10 - Query_10 - M_1955 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_1956 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_1957 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_1958 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_1959 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_1960 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_1961 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_1962 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_1963 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_1964 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_1965 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_1966 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 22 - Query_22 - M_1967 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_1968 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_1969 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_1970 - 9 - - - 1 - gnl|BL_ORD_ID|115 - 7708|gag polyprotein|BAA00992.1|Human immunodeficiency virus 1|11676 - 115 - 9 - - - 1 - 11.5418 - 18 - 165.102 - 1 - 7 - 3 - 9 - 0 - 0 - 4 - 6 - 0 - 7 - KTLRKAI - KTILKAL - KT+ KA+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 26 - Query_26 - M_1971 - 9 - - - 1 - gnl|BL_ORD_ID|115 - 7708|gag polyprotein|BAA00992.1|Human immunodeficiency virus 1|11676 - 115 - 9 - - - 1 - 11.5418 - 18 - 165.102 - 1 - 7 - 3 - 9 - 0 - 0 - 4 - 6 - 0 - 7 - KTLRKAI - KTILKAL - KT+ KA+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 27 - Query_27 - M_1972 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 28 - Query_28 - M_1973 - 9 - - - 1 - gnl|BL_ORD_ID|26 - 2002|Large envelope protein|SRC279965|Hepatitis B virus|10407 - 26 - 10 - - - 1 - 13.4678 - 23 - 10.0795 - 5 - 8 - 6 - 9 - 0 - 0 - 4 - 4 - 0 - 4 - TGDP - TGDP - TGDP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 29 - Query_29 - M_1974 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_119995_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_119995_1_T.fasta deleted file mode 100755 index f889c16c..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_119995_1_T.fasta +++ /dev/null @@ -1,172 +0,0 @@ ->M_1975 -VLETAAPGV ->M_1976 -AVLDAIPLV ->M_1977 -VLDAIPLVA ->M_1978 -KPVVTEVRM ->M_1979 -MPTNTWSGL ->M_1980 -VFQGHSASI ->M_1981 -SLYDFGELR ->M_1982 -DSMLQTVER ->M_1983 -MLQTVEREK ->M_1984 -LLWKDFDQA ->M_1985 -HVPQVADAI ->M_1986 -LLEMNLMHV ->M_1987 -NLMHVPQVA ->M_1988 -VPQVADAIL ->M_1989 -FLIDGSQSV ->M_1990 -FLIDGSQSV ->M_1991 -SVGPEFQYV ->M_1992 -LALSVTEMV ->M_1993 -RLALSVTEM ->M_1994 -TILQIKEEK ->M_1995 -DYEAVCGHR ->M_1996 -EAVCGHRAR ->M_1997 -ILFQKITNR ->M_1998 -KITNRGDEL ->M_1999 -SPTPALGPA ->M_2000 -LTPQQAQEL ->M_2001 -APLGAPPPL ->M_2002 -SKTPPGAPL ->M_2003 -SKTPPGAPL ->M_2004 -MFQSLGEHI ->M_2005 -SLGEHINTL ->M_2006 -SLGEHINTL ->M_2007 -AVGVGKSAL ->M_2008 -YKLVVVGAV ->M_2009 -AMLWALGFI ->M_2010 -FIWSVLITA ->M_2011 -MLWALGFIF ->M_2012 -QTPLFIWSV ->M_2013 -TPLFIWSVL ->M_2014 -TQYQTPLFI ->M_2015 -IINDGKHHV ->M_2016 -GLSAEEFQL ->M_2017 -SAEEFQLIR ->M_2018 -APTTPKEPA ->M_2019 -LLLLLLLLV ->M_2020 -LLLLLLLVV ->M_2021 -LLLLLLVVV ->M_2022 -LLVVVPWGV ->M_2023 -SRRHSRSPL ->M_2024 -SRRHSRSPL ->M_2025 -GSYSMAIPL ->M_2026 -MAIPLLCSY ->M_2027 -NPGSYSMAI ->M_2028 -RYNPGSYSM ->M_2029 -RYNPGSYSM ->M_2030 -SYSMAIPLL ->M_2031 -CQPHAHCSL ->M_2032 -HAHCSLWRR ->M_2033 -IIQELTIFK ->M_2034 -LPPKPVQVL ->M_2035 -QLPPKPVQV ->M_2036 -GLYASLFPA ->M_2037 -LFPAIIYLF ->M_2038 -LYASLFPAI ->M_2039 -PVYGLYASL ->M_2040 -SLFPAIIYL ->M_2041 -SLFPAIIYL ->M_2042 -SLFPAIIYL ->M_2043 -VYGLYASLF ->M_2044 -VYGLYASLF ->M_2045 -RYNVADVSV ->M_2046 -VSVAICMSL ->M_2047 -YTISDDESF ->M_2048 -YVQYWYYTI ->M_2049 -YVQYWYYTI ->M_2050 -SFYNSNRDF ->M_2051 -SFYNSNRDF ->M_2052 -TISFYNSNR ->M_2053 -CRFELMHFK ->M_2054 -ELMHFKTLY ->M_2055 -ILGDWSNGI ->M_2056 -NGISALYCR ->M_2057 -HIHGGTNQV ->M_2058 -AFTCTSSLL ->M_2059 -KAFTCTSSL ->M_2060 -KAFTCTSSL diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_119995_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_119995_1_T_iedb.xml deleted file mode 100755 index 2c8c8541..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_119995_1_T_iedb.xml +++ /dev/null @@ -1,3002 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_1975 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_1975 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_1976 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_1977 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_1978 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_1979 - 9 - - - 1 - gnl|BL_ORD_ID|1289 - 102368|E2 protein|NP_751921.1|Hepatitis C virus subtype 1a|31646 - 1289 - 15 - - - 1 - 11.5418 - 18 - 98.8375 - 2 - 6 - 6 - 10 - 0 - 0 - 3 - 4 - 0 - 5 - PTNTW - PTYSW - PT +W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 6 - Query_6 - M_1980 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_1981 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_1982 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_1983 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_1984 - 9 - - - 1 - gnl|BL_ORD_ID|1699 - 149117|envelope glycoprotein|AAV74049.1|Hepatitis C virus (isolate H77)|63746 - 1699 - 18 - - - 1 - 13.4678 - 23 - 11.4723 - 5 - 9 - 2 - 6 - 0 - 0 - 4 - 4 - 0 - 5 - DFDQA - DFDQG - DFDQ - - - - - 2 - gnl|BL_ORD_ID|103 - 6936|Genome polyprotein|P26664.3|Hepatitis C virus (isolate 1)|11104 - 103 - 11 - - - 1 - 13.0826 - 22 - 18.7359 - 5 - 9 - 6 - 10 - 0 - 0 - 4 - 4 - 0 - 5 - DFDQA - DFDQG - DFDQ - - - - - 3 - gnl|BL_ORD_ID|841 - 55226|HCV-1|AAA45676.1|Hepatitis C virus|11103 - 841 - 10 - - - 1 - 13.0826 - 22 - 19.8203 - 5 - 9 - 5 - 9 - 0 - 0 - 4 - 4 - 0 - 5 - DFDQA - DFDQG - DFDQ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 11 - Query_11 - M_1985 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_1986 - 9 - - - 1 - gnl|BL_ORD_ID|2280 - 419095|polyprotein|ABR25251.1|Hepatitis C virus|11103 - 2280 - 10 - - - 1 - 11.927 - 19 - 66.6359 - 1 - 7 - 3 - 9 - 0 - 0 - 4 - 6 - 0 - 7 - LLEMNLM - LIEANLL - L+E NL+ - - - - - 2 - gnl|BL_ORD_ID|168 - 13091|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 168 - 9 - - - 1 - 11.927 - 19 - 82.8955 - 1 - 7 - 2 - 8 - 0 - 0 - 4 - 6 - 0 - 7 - LLEMNLM - LIEANLL - L+E NL+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 13 - Query_13 - M_1987 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_1988 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_1989 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_1990 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_1991 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_1992 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_1993 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_1994 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_1995 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 22 - Query_22 - M_1996 - 9 - - - 1 - gnl|BL_ORD_ID|343 - 21635|gag protein|ABO73990.1|Human immunodeficiency virus 1|11676 - 343 - 9 - - - 1 - 13.4678 - 23 - 10.3786 - 5 - 9 - 3 - 7 - 0 - 0 - 4 - 5 - 0 - 5 - GHRAR - GHKAR - GH+AR - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 23 - Query_23 - M_1997 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_1998 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_1999 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_2000 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_2001 - 9 - - - 1 - gnl|BL_ORD_ID|1110 - 73059|kaposin|AAC57155.1|Human gammaherpesvirus 8|37296 - 1110 - 15 - - - 1 - 14.2382 - 25 - 2.93584 - 3 - 9 - 5 - 11 - 0 - 0 - 6 - 6 - 0 - 7 - LGAPPPL - LGAIPPL - LGA PPL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 28 - Query_28 - M_2002 - 9 - - - 1 - gnl|BL_ORD_ID|1187 - 93536|core protein|AAL31859.1|Hepatitis B virus|10407 - 1187 - 11 - - - 1 - 12.6974 - 21 - 26.8092 - 4 - 9 - 5 - 10 - 0 - 0 - 4 - 5 - 0 - 6 - PPGAPL - PPNAPI - PP AP+ - - - - - 2 - gnl|BL_ORD_ID|1316 - 107754|Genome polyprotein|P26664.3|Hepatitis C virus|11103 - 1316 - 10 - - - 1 - 12.6974 - 21 - 30.9217 - 3 - 7 - 2 - 6 - 0 - 0 - 4 - 5 - 0 - 5 - TPPGA - TPPGS - TPPG+ - - - - - 3 - gnl|BL_ORD_ID|1766 - 154857|tegument protein|CAB06735.1|Human alphaherpesvirus 2|10310 - 1766 - 16 - - - 1 - 4.99343 - 1 - 101281 - 8 - 9 - 15 - 16 - 0 - 0 - 1 - 2 - 0 - 2 - PL - PV - P+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 29 - Query_29 - M_2003 - 9 - - - 1 - gnl|BL_ORD_ID|1187 - 93536|core protein|AAL31859.1|Hepatitis B virus|10407 - 1187 - 11 - - - 1 - 12.6974 - 21 - 26.8092 - 4 - 9 - 5 - 10 - 0 - 0 - 4 - 5 - 0 - 6 - PPGAPL - PPNAPI - PP AP+ - - - - - 2 - gnl|BL_ORD_ID|1316 - 107754|Genome polyprotein|P26664.3|Hepatitis C virus|11103 - 1316 - 10 - - - 1 - 12.6974 - 21 - 30.9217 - 3 - 7 - 2 - 6 - 0 - 0 - 4 - 5 - 0 - 5 - TPPGA - TPPGS - TPPG+ - - - - - 3 - gnl|BL_ORD_ID|1766 - 154857|tegument protein|CAB06735.1|Human alphaherpesvirus 2|10310 - 1766 - 16 - - - 1 - 4.99343 - 1 - 101281 - 8 - 9 - 15 - 16 - 0 - 0 - 1 - 2 - 0 - 2 - PL - PV - P+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 30 - Query_30 - M_2004 - 9 - - - 1 - gnl|BL_ORD_ID|1172 - 79308|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 1172 - 16 - - - 1 - 13.853 - 24 - 7.02995 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 7 - 0 - 9 - MFQSLGEHI - MEPTLGQHL - M +LG+H+ - - - - - 2 - gnl|BL_ORD_ID|981 - 64821|Protein Tax-1|P03409.2|Human T-lymphotropic virus 1|11908 - 981 - 9 - - - 1 - 13.0826 - 22 - 20.0871 - 4 - 9 - 1 - 6 - 0 - 0 - 3 - 6 - 0 - 6 - SLGEHI - TLGQHL - +LG+H+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 31 - Query_31 - M_2005 - 9 - - - 1 - gnl|BL_ORD_ID|1172 - 79308|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 1172 - 16 - - - 1 - 16.1642 - 30 - 0.328782 - 1 - 9 - 4 - 12 - 0 - 0 - 5 - 8 - 0 - 9 - SLGEHINTL - TLGQHLPTL - +LG+H+ TL - - - - - 2 - gnl|BL_ORD_ID|981 - 64821|Protein Tax-1|P03409.2|Human T-lymphotropic virus 1|11908 - 981 - 9 - - - 1 - 15.779 - 29 - 0.48278 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 8 - 0 - 9 - SLGEHINTL - TLGQHLPTL - +LG+H+ TL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 32 - Query_32 - M_2006 - 9 - - - 1 - gnl|BL_ORD_ID|1172 - 79308|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 1172 - 16 - - - 1 - 16.1642 - 30 - 0.328782 - 1 - 9 - 4 - 12 - 0 - 0 - 5 - 8 - 0 - 9 - SLGEHINTL - TLGQHLPTL - +LG+H+ TL - - - - - 2 - gnl|BL_ORD_ID|981 - 64821|Protein Tax-1|P03409.2|Human T-lymphotropic virus 1|11908 - 981 - 9 - - - 1 - 15.779 - 29 - 0.48278 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 8 - 0 - 9 - SLGEHINTL - TLGQHLPTL - +LG+H+ TL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 33 - Query_33 - M_2007 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 34 - Query_34 - M_2008 - 9 - - - 1 - gnl|BL_ORD_ID|524 - 32238|polyprotein [Hepatitis C virus subtype 1a]|ABV46251.2|Hepatitis C virus (isolate H77)|63746 - 524 - 10 - - - 1 - 12.6974 - 21 - 30.9217 - 2 - 7 - 1 - 6 - 0 - 0 - 5 - 6 - 0 - 6 - KLVVVG - KLVVLG - KLVV+G - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 35 - Query_35 - M_2009 - 9 - - - 1 - gnl|BL_ORD_ID|10 - 1000|glycoprotein gp35/37|AAC59622.1|Human gammaherpesvirus 8|37296 - 10 - 15 - - - 1 - 13.853 - 24 - 5.67783 - 2 - 8 - 9 - 15 - 0 - 0 - 4 - 6 - 0 - 7 - MLWALGF - ILWAVGL - +LWA+G - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 36 - Query_36 - M_2010 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 37 - Query_37 - M_2011 - 9 - - - 1 - gnl|BL_ORD_ID|10 - 1000|glycoprotein gp35/37|AAC59622.1|Human gammaherpesvirus 8|37296 - 10 - 15 - - - 1 - 13.853 - 24 - 4.94253 - 1 - 7 - 9 - 15 - 0 - 0 - 4 - 6 - 0 - 7 - MLWALGF - ILWAVGL - +LWA+G - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 38 - Query_38 - M_2012 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 39 - Query_39 - M_2013 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 40 - Query_40 - M_2014 - 9 - - - 1 - gnl|BL_ORD_ID|1897 - 180617|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1897 - 10 - - - 1 - 13.4678 - 23 - 9.40133 - 2 - 6 - 4 - 8 - 0 - 0 - 4 - 5 - 0 - 5 - QYQTP - RYQTP - +YQTP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 41 - Query_41 - M_2015 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 42 - Query_42 - M_2016 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 43 - Query_43 - M_2017 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 44 - Query_44 - M_2018 - 9 - - - 1 - gnl|BL_ORD_ID|305 - 20417|HCV-1|AAA45676.1|Hepatitis C virus genotype 1|41856 - 305 - 20 - - - 1 - 11.927 - 19 - 61.3622 - 3 - 9 - 10 - 16 - 0 - 0 - 4 - 4 - 0 - 7 - TTPKEPA - TLPGNPA - T P PA - - - - - 2 - gnl|BL_ORD_ID|1545 - 141216|envelope glycoprotein I|NP_044669.1|Human alphaherpesvirus 1|10298 - 1545 - 9 - - - 1 - 11.5418 - 18 - 134.458 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 6 - 0 - 9 - APTTPKEPA - APASVYQPA - AP + +PA - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 45 - Query_45 - M_2019 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 46 - Query_46 - M_2020 - 9 - - - 1 - gnl|BL_ORD_ID|1263 - 98540|trans-sialidase, putative|EAN88532.1|Trypanosoma cruzi|5693 - 1263 - 10 - - - 1 - 11.1566 - 17 - 242.571 - 3 - 9 - 4 - 10 - 0 - 0 - 6 - 7 - 0 - 7 - LLLLLVV - VLLLLVV - +LLLLVV - - - - - 2 - gnl|BL_ORD_ID|1254 - 98224|trans-sialidase, putative|EAN82076.1|Trypanosoma cruzi|5693 - 1254 - 10 - - - 1 - 11.1566 - 17 - 286.165 - 4 - 9 - 1 - 6 - 0 - 0 - 6 - 6 - 0 - 6 - LLLLVV - LLLLVV - LLLLVV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 47 - Query_47 - M_2021 - 9 - - - 1 - gnl|BL_ORD_ID|1263 - 98540|trans-sialidase, putative|EAN88532.1|Trypanosoma cruzi|5693 - 1263 - 10 - - - 1 - 11.1566 - 17 - 231.802 - 3 - 8 - 5 - 10 - 0 - 0 - 6 - 6 - 0 - 6 - LLLLVV - LLLLVV - LLLLVV - - - - - 2 - gnl|BL_ORD_ID|1254 - 98224|trans-sialidase, putative|EAN82076.1|Trypanosoma cruzi|5693 - 1254 - 10 - - - 1 - 11.1566 - 17 - 250.006 - 3 - 9 - 1 - 7 - 0 - 0 - 6 - 7 - 0 - 7 - LLLLVVV - LLLLVVM - LLLLVV+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 48 - Query_48 - M_2022 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 49 - Query_49 - M_2023 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 50 - Query_50 - M_2024 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 51 - Query_51 - M_2025 - 9 - - - 1 - gnl|BL_ORD_ID|338 - 21242|polymerase|ACF94272.1|Hepatitis B virus|10407 - 338 - 9 - - - 1 - 13.0826 - 22 - 19.071 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 6 - 0 - 9 - GSYSMAIPL - GLYSSTVPV - G YS +P+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 52 - Query_52 - M_2026 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 53 - Query_53 - M_2027 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 54 - Query_54 - M_2028 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 55 - Query_55 - M_2029 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 56 - Query_56 - M_2030 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 57 - Query_57 - M_2031 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 58 - Query_58 - M_2032 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 59 - Query_59 - M_2033 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 60 - Query_60 - M_2034 - 9 - - - 1 - gnl|BL_ORD_ID|1140 - 75376|Genome polyprotein|P26664.3|Hepatitis C virus|11103 - 1140 - 8 - - - 1 - 13.0826 - 22 - 15.3199 - 2 - 8 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - PPKPVQV - PPKPCGI - PPKP + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 61 - Query_61 - M_2035 - 9 - - - 1 - gnl|BL_ORD_ID|1140 - 75376|Genome polyprotein|P26664.3|Hepatitis C virus|11103 - 1140 - 8 - - - 1 - 13.0826 - 22 - 14.7957 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - PPKPVQV - PPKPCGI - PPKP + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 62 - Query_62 - M_2036 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 63 - Query_63 - M_2037 - 9 - - - 1 - gnl|BL_ORD_ID|1755 - 154041|major capsid protein|CAB06743.1|Human alphaherpesvirus 2|10310 - 1755 - 15 - - - 1 - 14.2382 - 25 - 3.03951 - 2 - 8 - 7 - 13 - 0 - 0 - 4 - 6 - 0 - 7 - FPAIIYL - YPAVFYL - +PA+ YL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 64 - Query_64 - M_2038 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 65 - Query_65 - M_2039 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 66 - Query_66 - M_2040 - 9 - - - 1 - gnl|BL_ORD_ID|1755 - 154041|major capsid protein|CAB06743.1|Human alphaherpesvirus 2|10310 - 1755 - 15 - - - 1 - 14.6234 - 26 - 2.04141 - 3 - 9 - 7 - 13 - 0 - 0 - 4 - 6 - 0 - 7 - FPAIIYL - YPAVFYL - +PA+ YL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 67 - Query_67 - M_2041 - 9 - - - 1 - gnl|BL_ORD_ID|1755 - 154041|major capsid protein|CAB06743.1|Human alphaherpesvirus 2|10310 - 1755 - 15 - - - 1 - 14.6234 - 26 - 2.04141 - 3 - 9 - 7 - 13 - 0 - 0 - 4 - 6 - 0 - 7 - FPAIIYL - YPAVFYL - +PA+ YL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 68 - Query_68 - M_2042 - 9 - - - 1 - gnl|BL_ORD_ID|1755 - 154041|major capsid protein|CAB06743.1|Human alphaherpesvirus 2|10310 - 1755 - 15 - - - 1 - 14.6234 - 26 - 2.04141 - 3 - 9 - 7 - 13 - 0 - 0 - 4 - 6 - 0 - 7 - FPAIIYL - YPAVFYL - +PA+ YL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 69 - Query_69 - M_2043 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 70 - Query_70 - M_2044 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 71 - Query_71 - M_2045 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 72 - Query_72 - M_2046 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 73 - Query_73 - M_2047 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 74 - Query_74 - M_2048 - 9 - - - 1 - gnl|BL_ORD_ID|1541 - 141206|tegument protein VP11/12|NP_044648.1|Human alphaherpesvirus 1|10298 - 1541 - 9 - - - 1 - 12.6974 - 21 - 31.9494 - 2 - 7 - 4 - 9 - 0 - 0 - 4 - 4 - 0 - 6 - VQYWYY - TQYWKY - QYW Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 75 - Query_75 - M_2049 - 9 - - - 1 - gnl|BL_ORD_ID|1541 - 141206|tegument protein VP11/12|NP_044648.1|Human alphaherpesvirus 1|10298 - 1541 - 9 - - - 1 - 12.6974 - 21 - 31.9494 - 2 - 7 - 4 - 9 - 0 - 0 - 4 - 4 - 0 - 6 - VQYWYY - TQYWKY - QYW Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 76 - Query_76 - M_2050 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 77 - Query_77 - M_2051 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 78 - Query_78 - M_2052 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 79 - Query_79 - M_2053 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 80 - Query_80 - M_2054 - 9 - - - 1 - gnl|BL_ORD_ID|555 - 34101|X protein|ACH95876.1|Hepatitis B virus|10407 - 555 - 10 - - - 1 - 11.5418 - 18 - 115.311 - 1 - 8 - 1 - 8 - 0 - 0 - 3 - 7 - 0 - 8 - ELMHFKTL - KVLHKRTL - +++H +TL - - - - - 2 - gnl|BL_ORD_ID|1042 - 69524|X protein|ACH95876.1|Hepatitis B virus|10407 - 1042 - 9 - - - 1 - 11.1566 - 17 - 221.814 - 2 - 8 - 1 - 7 - 0 - 0 - 3 - 6 - 0 - 7 - LMHFKTL - VLHKRTL - ++H +TL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 81 - Query_81 - M_2055 - 9 - - - 1 - gnl|BL_ORD_ID|775 - 51604|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 - 775 - 10 - - - 1 - 14.6234 - 26 - 1.78499 - 4 - 9 - 3 - 8 - 0 - 0 - 4 - 6 - 0 - 6 - DWSNGI - DYSNGL - D+SNG+ - - - - - 2 - gnl|BL_ORD_ID|623 - 37498|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 - 623 - 10 - - - 1 - 10.7714 - 16 - 303.747 - 1 - 8 - 2 - 9 - 0 - 0 - 3 - 4 - 0 - 8 - ILGDWSNG - LLGLWGTA - +LG W - - - - - 3 - gnl|BL_ORD_ID|615 - 37350|trans-sialidase|XP_818394.1|Trypanosoma cruzi|5693 - 615 - 10 - - - 1 - 10.7714 - 16 - 303.747 - 1 - 8 - 1 - 8 - 0 - 0 - 3 - 4 - 0 - 8 - ILGDWSNG - LLGLWGTA - +LG W - - - - - 4 - gnl|BL_ORD_ID|321 - 21004|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 - 321 - 10 - - - 1 - 7.30463 - 7 - 14472.4 - 4 - 5 - 7 - 8 - 0 - 0 - 1 - 1 - 0 - 2 - DW - LW - W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 82 - Query_82 - M_2056 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 83 - Query_83 - M_2057 - 9 - - - 1 - gnl|BL_ORD_ID|847 - 55336|EBNA-1|YP_401677.1|Human gammaherpesvirus 4|10376 - 847 - 15 - - - 1 - 12.3122 - 20 - 58.4135 - 3 - 7 - 11 - 15 - 0 - 0 - 4 - 4 - 0 - 5 - HGGTN - HGGTG - HGGT - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 84 - Query_84 - M_2058 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 85 - Query_85 - M_2059 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 86 - Query_86 - M_2060 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_120070_2_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_120070_2_T.fasta deleted file mode 100755 index 415651ea..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_120070_2_T.fasta +++ /dev/null @@ -1,76 +0,0 @@ ->M_2061 -GDASKVWVW ->M_2062 -STFVHGNKI ->M_2063 -GEEAEASAV ->M_2064 -TTSPSNTLV ->M_2065 -STGLQYATK ->M_2066 -SVLRCVHLL ->M_2067 -GRNSFKVRV ->M_2068 -MRTLLGDLV ->M_2069 -RWDRKPMQI ->M_2070 -SRSTIFMRL ->M_2071 -PHLTQGNEI ->M_2072 -ASTFVHGNK ->M_2073 -ENAGPQNMK ->M_2074 -MGQEIAALK ->M_2075 -NLLGRNSFK ->M_2076 -QAVCVTKPK ->M_2077 -LRCVHLLRI ->M_2078 -FVHGNKIYV ->M_2079 -ATKFIKKRR ->M_2080 -VHLLRIFKV ->M_2081 -LANAPRTLK ->M_2082 -WRLTWDRHL ->M_2083 -CTGPPLAPR ->M_2084 -NLTRASSKR ->M_2085 -RRSGPSPTV ->M_2086 -DLVAHYVHR ->M_2087 -SSLEGFATR ->M_2088 -LEDLGWANW ->M_2089 -CVHLLRIFK ->M_2090 -TIQAVCVTK ->M_2091 -ITCMPGSVR ->M_2092 -CSIPSICEK ->M_2093 -SSRSTIFMR ->M_2094 -SVTKASNLK ->M_2095 -YATKFIKKR ->M_2096 -FSSSDDSPR ->M_2097 -VHGNKIYVL ->M_2098 -WANWVLSPR diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_120070_2_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_120070_2_T_iedb.xml deleted file mode 100755 index 22e96f0f..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_120070_2_T_iedb.xml +++ /dev/null @@ -1,1584 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_2061 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_2061 - 9 - - - 1 - gnl|BL_ORD_ID|341 - 21385|polyprotein|AAY82034.1|Hepatitis C virus genotype 1|41856 - 341 - 10 - - - 1 - 15.779 - 29 - 0.401267 - 1 - 8 - 1 - 8 - 0 - 0 - 5 - 7 - 0 - 8 - GDASKVWV - GNASRCWV - G+AS+ WV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 2 - Query_2 - M_2062 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_2063 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_2064 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_2065 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_2066 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_2067 - 9 - - - 1 - gnl|BL_ORD_ID|617 - 37364|P53_HUMAN Cellular tumor antigen p53 (Tumor suppressor p53) (Phosphoprotein p53) (Antigen NY-CO-13)|P04637.2|Homo sapiens|9606 - 617 - 9 - - - 1 - 16.5494 - 31 - 0.265948 - 1 - 7 - 3 - 9 - 0 - 0 - 6 - 7 - 0 - 7 - GRNSFKV - GRNSFEV - GRNSF+V - - - - - 2 - gnl|BL_ORD_ID|1613 - 143740|polyprotein|ACF60462.1|Hepatovirus A|12092 - 1613 - 9 - - - 1 - 13.0826 - 22 - 14.4474 - 2 - 7 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - RNSFKV - RNEFRV - RN F+V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 8 - Query_8 - M_2068 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_2069 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_2070 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_2071 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_2072 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_2073 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_2074 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_2075 - 9 - - - 1 - gnl|BL_ORD_ID|617 - 37364|P53_HUMAN Cellular tumor antigen p53 (Tumor suppressor p53) (Phosphoprotein p53) (Antigen NY-CO-13)|P04637.2|Homo sapiens|9606 - 617 - 9 - - - 1 - 18.0902 - 35 - 0.111589 - 2 - 9 - 1 - 8 - 0 - 0 - 7 - 8 - 0 - 8 - LLGRNSFK - LLGRNSFE - LLGRNSF+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 16 - Query_16 - M_2076 - 9 - - - 1 - gnl|BL_ORD_ID|1645 - 146317|polyprotein|ADF97231.1|Hepatitis C virus subtype 3a|356426 - 1645 - 9 - - - 1 - 13.0826 - 22 - 13.7128 - 3 - 8 - 1 - 6 - 0 - 0 - 3 - 5 - 0 - 6 - VCVTKP - ICLTHP - +C+T P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 17 - Query_17 - M_2077 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_2078 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_2079 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_2080 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_2081 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 22 - Query_22 - M_2082 - 9 - - - 1 - gnl|BL_ORD_ID|1539 - 140769|LOW MOLECULAR WEIGHT PROTEIN ANTIGEN 7 ESXH (10 kDa ANTIGEN) (CFP-7) (PROTEIN TB10.4)|CAA17363.1|Mycobacterium tuberculosis H37Rv|83332 - 1539 - 9 - - - 1 - 12.3122 - 20 - 59.6102 - 1 - 9 - 1 - 9 - 0 - 0 - 2 - 6 - 0 - 9 - WRLTWDRHL - WQAQWNQAM - W+ W++ + - - - - - 2 - gnl|BL_ORD_ID|1092 - 72233|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 - 1092 - 15 - - - 1 - 11.1566 - 17 - 190.157 - 1 - 6 - 1 - 6 - 0 - 0 - 2 - 4 - 0 - 6 - WRLTWD - WAIKWE - W + W+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 23 - Query_23 - M_2083 - 9 - - - 1 - gnl|BL_ORD_ID|1950 - 181035|||| - 1950 - 44 - - - 1 - 13.4678 - 23 - 10.2905 - 1 - 9 - 20 - 28 - 0 - 0 - 5 - 5 - 0 - 9 - CTGPPLAPR - CGGVYLLPR - C G L PR - - - - - 2 - gnl|BL_ORD_ID|344 - 21638|protein F|ABV46152.2|Hepatitis C virus (isolate Japanese)|11116 - 344 - 9 - - - 1 - 11.927 - 19 - 95.9763 - 3 - 8 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - GPPLAP - GPGLSP - GP L+P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 24 - Query_24 - M_2084 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_2085 - 9 - - - 1 - gnl|BL_ORD_ID|1829 - 179799|hypothetical protein|NP_301670.1|Mycobacterium leprae TN|272631 - 1829 - 9 - - - 1 - 12.3122 - 20 - 53.938 - 4 - 9 - 1 - 6 - 0 - 0 - 4 - 4 - 0 - 6 - GPSPTV - GPVPAV - GP P V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 26 - Query_26 - M_2086 - 9 - - - 1 - gnl|BL_ORD_ID|1714 - 150377|polyprotein|AGS49173.1|Dengue virus 2|11060 - 1714 - 9 - - - 1 - 13.853 - 24 - 7.45662 - 2 - 6 - 3 - 7 - 0 - 0 - 5 - 5 - 0 - 5 - LVAHY - LVAHY - LVAHY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 27 - Query_27 - M_2087 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 28 - Query_28 - M_2088 - 9 - - - 1 - gnl|BL_ORD_ID|1143 - 75436|Polyprotein|P90247|Hepatitis C virus|11103 - 1143 - 20 - - - 1 - 16.5494 - 31 - 0.231862 - 2 - 9 - 9 - 16 - 0 - 0 - 6 - 6 - 0 - 8 - EDLGWANW - EGLGWAGW - E LGWA W - - - - - 2 - gnl|BL_ORD_ID|1144 - 75438|polyprotein|AAF65962.1|Hepatitis C virus|11103 - 1144 - 20 - - - 1 - 16.1642 - 30 - 0.347768 - 2 - 9 - 9 - 16 - 0 - 0 - 5 - 6 - 0 - 8 - EDLGWANW - EGMGWAGW - E +GWA W - - - - - 3 - gnl|BL_ORD_ID|710 - 43624|Genome polyprotein|P26660.3|Hepatitis C virus isolate HC-J6|11113 - 710 - 9 - - - 1 - 16.1642 - 30 - 0.349175 - 2 - 9 - 2 - 9 - 0 - 0 - 6 - 6 - 0 - 8 - EDLGWANW - EGLGWAGW - E LGWA W - - - - - 4 - gnl|BL_ORD_ID|116 - 7999|core protein|BAA82580.1|Hepatitis C virus|11103 - 116 - 9 - - - 1 - 16.1642 - 30 - 0.356759 - 2 - 9 - 2 - 9 - 0 - 0 - 6 - 6 - 0 - 8 - EDLGWANW - EGLGWAGW - E LGWA W - - - - - 5 - gnl|BL_ORD_ID|712 - 43628|polyprotein|BAA03375.1|Hepatitis C virus subtype 1b|31647 - 712 - 9 - - - 1 - 15.779 - 29 - 0.457844 - 2 - 9 - 2 - 9 - 0 - 0 - 5 - 6 - 0 - 8 - EDLGWANW - EGMGWAGW - E +GWA W - - - - - 6 - gnl|BL_ORD_ID|713 - 43756|Genome polyprotein|SRC279960|Hepatitis C virus subtype 2a|31649 - 713 - 9 - - - 1 - 15.0086 - 27 - 1.05395 - 2 - 9 - 2 - 9 - 0 - 0 - 5 - 5 - 0 - 8 - EDLGWANW - ETCGWAGW - E GWA W - - - - - 7 - gnl|BL_ORD_ID|577 - 36352|Polyprotein|P90247|Hepatitis C virus|11103 - 577 - 20 - - - 1 - 15.0086 - 27 - 1.17519 - 4 - 9 - 1 - 6 - 0 - 0 - 5 - 5 - 0 - 6 - LGWANW - LGWAGW - LGWA W - - - - - 8 - gnl|BL_ORD_ID|708 - 43619|Genome polyprotein|P26664.3|Hepatitis C virus|11103 - 708 - 9 - - - 1 - 15.0086 - 27 - 1.21609 - 2 - 9 - 2 - 9 - 0 - 0 - 5 - 5 - 0 - 8 - EDLGWANW - EGCGWAGW - E GWA W - - - - - 9 - gnl|BL_ORD_ID|711 - 43627|core protein|AAX68853.1|Hepatitis C virus subtype 1b|31647 - 711 - 9 - - - 1 - 15.0086 - 27 - 1.2556 - 2 - 9 - 2 - 9 - 0 - 0 - 5 - 5 - 0 - 8 - EDLGWANW - EGLGWTGW - E LGW W - - - - - 10 - gnl|BL_ORD_ID|2120 - 186453|polyprotein|AFP27208.1|Dengue virus 4|11070 - 2120 - 10 - - - 1 - 13.4678 - 23 - 7.76238 - 5 - 9 - 6 - 10 - 0 - 0 - 4 - 4 - 0 - 5 - GWANW - GWKNW - GW NW - - - - - 11 - gnl|BL_ORD_ID|315 - 20894|polyprotein [Hepatitis C virus]|BAF91806.1|Hepatitis C virus|11103 - 315 - 9 - - - 1 - 13.4678 - 23 - 10.0233 - 4 - 9 - 2 - 7 - 0 - 0 - 4 - 4 - 0 - 6 - LGWANW - LGWVGW - LGW W - - - - - 12 - gnl|BL_ORD_ID|160 - 12183|EBNA3C latent protein|CAD53421.1|Human gammaherpesvirus 4|10376 - 160 - 9 - - - 1 - 12.6974 - 21 - 32.4991 - 4 - 9 - 4 - 9 - 0 - 0 - 3 - 5 - 0 - 6 - LGWANW - VGWRHW - +GW +W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 29 - Query_29 - M_2089 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 30 - Query_30 - M_2090 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 31 - Query_31 - M_2091 - 9 - - - 1 - gnl|BL_ORD_ID|1176 - 79454|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 1176 - 15 - - - 1 - 13.853 - 24 - 7.10896 - 1 - 8 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - ITCMPGSV - IFCHPGQL - I C PG + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 32 - Query_32 - M_2092 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 33 - Query_33 - M_2093 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 34 - Query_34 - M_2094 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 35 - Query_35 - M_2095 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 36 - Query_36 - M_2096 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 37 - Query_37 - M_2097 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 38 - Query_38 - M_2098 - 9 - - - 1 - gnl|BL_ORD_ID|577 - 36352|Polyprotein|P90247|Hepatitis C virus|11103 - 577 - 20 - - - 1 - 19.631 - 39 - 0.0260695 - 1 - 9 - 3 - 11 - 0 - 0 - 7 - 8 - 0 - 9 - WANWVLSPR - WAGWLLSPR - WA W+LSPR - - - - - 2 - gnl|BL_ORD_ID|1144 - 75438|polyprotein|AAF65962.1|Hepatitis C virus|11103 - 1144 - 20 - - - 1 - 17.3198 - 33 - 0.118837 - 1 - 8 - 13 - 20 - 0 - 0 - 6 - 7 - 0 - 8 - WANWVLSP - WAGWLLSP - WA W+LSP - - - - - 3 - gnl|BL_ORD_ID|1143 - 75436|Polyprotein|P90247|Hepatitis C virus|11103 - 1143 - 20 - - - 1 - 17.3198 - 33 - 0.120923 - 1 - 8 - 13 - 20 - 0 - 0 - 6 - 7 - 0 - 8 - WANWVLSP - WAGWLLSP - WA W+LSP - - - - - 4 - gnl|BL_ORD_ID|1142 - 75435|largest ORF|AAB02128.1|Hepatitis C virus|11103 - 1142 - 20 - - - 1 - 15.779 - 29 - 0.412688 - 1 - 8 - 13 - 20 - 0 - 0 - 5 - 6 - 0 - 8 - WANWVLSP - WMGWLLSP - W W+LSP - - - - - 5 - gnl|BL_ORD_ID|315 - 20894|polyprotein [Hepatitis C virus]|BAF91806.1|Hepatitis C virus|11103 - 315 - 9 - - - 1 - 12.3122 - 20 - 65.8473 - 1 - 6 - 4 - 9 - 0 - 0 - 3 - 4 - 0 - 6 - WANWVL - WVGWLL - W W+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_120920_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_120920_1_T.fasta deleted file mode 100755 index bb5924de..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_120920_1_T.fasta +++ /dev/null @@ -1,126 +0,0 @@ ->M_2099 -LSLPGGHTA ->M_2100 -FRAAAEAAV ->M_2101 -FRAAAEAAV ->M_2102 -TSSDHSFSL ->M_2103 -TSSDHSFSL ->M_2104 -NHQQFYHSV ->M_2105 -NHQQFYHSV ->M_2106 -DYSELPHHV ->M_2107 -HHVSTEQEI ->M_2108 -HHVSTEQEI ->M_2109 -EIISLWSPW ->M_2110 -NQDPISPSL ->M_2111 -ENASAYLTL ->M_2112 -KKMENASAY ->M_2113 -RRHSLPRRC ->M_2114 -NMCRCLVTV ->M_2115 -RLMSARLAI ->M_2116 -SYSYLGLRL ->M_2117 -YSYLGLRLM ->M_2118 -YSYLGLRLM ->M_2119 -RFSQAFFYM ->M_2120 -RRFSQAFFY ->M_2121 -FMMPRSSSC ->M_2122 -FMMPRSSSC ->M_2123 -IPAMEIFMV ->M_2124 -LMAASIPAM ->M_2125 -DTLQATAML ->M_2126 -QATAMLDIV ->M_2127 -TVTRTTATV ->M_2128 -EHFPLCKTV ->M_2129 -EHFPLCKTV ->M_2130 -WPQCHPEEI ->M_2131 -YSYSCGHYE ->M_2132 -SHFERDYRV ->M_2133 -FQTLMPDVV ->M_2134 -FQTLMPDVV ->M_2135 -MPDVVHQSL ->M_2136 -LWYTLYLMI ->M_2137 -LYLMITTFF ->M_2138 -MITTFFFPL ->M_2139 -TLYLMITTF ->M_2140 -YLMITTFFF ->M_2141 -YTLYLMITT ->M_2142 -PTSPFQTTI ->M_2143 -TAERSIPTV ->M_2144 -ERPCHREPL ->M_2145 -SSSSGPFPL ->M_2146 -ELATFAKAY ->M_2147 -RWDEELATF ->M_2148 -ELIDLISRV ->M_2149 -ELIDLISRV ->M_2150 -QVNQKSSVV ->M_2151 -VRLELIDLI ->M_2152 -YEEYRGRLL ->M_2153 -YEEYRGRLL ->M_2154 -CRNVHTPDL ->M_2155 -YSRDQAQAL ->M_2156 -YSRDQAQAL ->M_2157 -FEVEGRDLL ->M_2158 -FFFLCVCVF ->M_2159 -FFLCVCVFV ->M_2160 -RRYPHKRCI ->M_2161 -RRYPHKRCI diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_120920_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_120920_1_T_iedb.xml deleted file mode 100755 index ae438936..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_120920_1_T_iedb.xml +++ /dev/null @@ -1,1853 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_2099 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_2099 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_2100 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_2101 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_2102 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_2103 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_2104 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_2105 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_2106 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_2107 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_2108 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_2109 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_2110 - 9 - - - 1 - gnl|BL_ORD_ID|2271 - 419002|PPE family protein PPE68|KAM81677.1|Mycobacterium tuberculosis H37Ra|419947 - 2271 - 10 - - - 1 - 13.4678 - 23 - 9.40133 - 2 - 9 - 3 - 10 - 0 - 0 - 3 - 7 - 0 - 8 - QDPISPSL - EKPVAPSV - + P++PS+ - - - - - 2 - gnl|BL_ORD_ID|811 - 54342|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 - 811 - 20 - - - 1 - 13.0826 - 22 - 14.406 - 3 - 9 - 12 - 18 - 0 - 0 - 4 - 5 - 0 - 7 - DPISPSL - DPLFPEL - DP+ P L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 13 - Query_13 - M_2111 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_2112 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_2113 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_2114 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_2115 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_2116 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_2117 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_2118 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_2119 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 22 - Query_22 - M_2120 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_2121 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_2122 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_2123 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_2124 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_2125 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 28 - Query_28 - M_2126 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 29 - Query_29 - M_2127 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 30 - Query_30 - M_2128 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 31 - Query_31 - M_2129 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 32 - Query_32 - M_2130 - 9 - - - 1 - gnl|BL_ORD_ID|48 - 3051|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 - 48 - 20 - - - 1 - 18.8606 - 37 - 0.0470713 - 1 - 9 - 8 - 16 - 0 - 0 - 6 - 7 - 0 - 9 - WPQCHPEEI - LPQCSPDEI - PQC P+EI - - - - - 2 - gnl|BL_ORD_ID|20 - 1230|gag protein|AAW03034.1|Human immunodeficiency virus 1|11676 - 20 - 9 - - - 1 - 13.0826 - 22 - 14.9585 - 1 - 6 - 3 - 8 - 0 - 0 - 3 - 4 - 0 - 6 - WPQCHP - WDRVHP - W + HP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 33 - Query_33 - M_2131 - 9 - - - 1 - gnl|BL_ORD_ID|147 - 10939|polyprotein|BAB18806.1|Hepatitis C virus subtype 1a|31646 - 147 - 9 - - - 1 - 12.3122 - 20 - 42.6373 - 1 - 8 - 2 - 9 - 0 - 0 - 4 - 4 - 0 - 8 - YSYSCGHY - YPYRLWHY - Y Y HY - - - - - 2 - gnl|BL_ORD_ID|1145 - 75448|polyprotein|BAB18806.1|Hepatitis C virus|11103 - 1145 - 8 - - - 1 - 12.3122 - 20 - 45.3667 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 4 - 0 - 8 - YSYSCGHY - YPYRLWHY - Y Y HY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 34 - Query_34 - M_2132 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 35 - Query_35 - M_2133 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 36 - Query_36 - M_2134 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 37 - Query_37 - M_2135 - 9 - - - 1 - gnl|BL_ORD_ID|1474 - 130953|G1 and G2 surface glycoprotein precursor|AAG22532.1|Andes hantavirus|46607 - 1474 - 9 - - - 1 - 15.3938 - 28 - 0.556982 - 1 - 7 - 2 - 8 - 0 - 0 - 5 - 5 - 0 - 7 - MPDVVHQ - MPDVAHS - MPDV H - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 38 - Query_38 - M_2136 - 9 - - - 1 - gnl|BL_ORD_ID|1 - 118|envelope glycoprotein|ABS76372.1|Human immunodeficiency virus 1|11676 - 1 - 20 - - - 1 - 12.6974 - 21 - 24.4238 - 1 - 6 - 5 - 10 - 0 - 0 - 4 - 5 - 0 - 6 - LWYTLY - LWVTVY - LW T+Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 39 - Query_39 - M_2137 - 9 - - - 1 - gnl|BL_ORD_ID|1525 - 140651|granule antigen protein GRA6|XP_002371939.1|Toxoplasma gondii ME49|508771 - 1525 - 9 - - - 1 - 12.6974 - 21 - 28.8346 - 4 - 9 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - MITTFF - MLTAFF - M+T FF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 40 - Query_40 - M_2138 - 9 - - - 1 - gnl|BL_ORD_ID|1525 - 140651|granule antigen protein GRA6|XP_002371939.1|Toxoplasma gondii ME49|508771 - 1525 - 9 - - - 1 - 12.6974 - 21 - 33.058 - 1 - 6 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - MITTFF - MLTAFF - M+T FF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 41 - Query_41 - M_2139 - 9 - - - 1 - gnl|BL_ORD_ID|1738 - 150639|polyprotein|AGO67249.1|Dengue virus 2|11060 - 1738 - 10 - - - 1 - 14.6234 - 26 - 1.97194 - 1 - 9 - 1 - 9 - 0 - 0 - 6 - 7 - 0 - 9 - TLYLMITTF - TLYAVATTF - TLY + TTF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 42 - Query_42 - M_2140 - 9 - - - 1 - gnl|BL_ORD_ID|1525 - 140651|granule antigen protein GRA6|XP_002371939.1|Toxoplasma gondii ME49|508771 - 1525 - 9 - - - 1 - 12.6974 - 21 - 35.3877 - 3 - 8 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - MITTFF - MLTAFF - M+T FF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 43 - Query_43 - M_2141 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 44 - Query_44 - M_2142 - 9 - - - 1 - gnl|BL_ORD_ID|2245 - 232154|rhoptry protein, putative / protein kinase domain-containing protein|XP_002367757.1|Toxoplasma gondii type II|1209523 - 2245 - 19 - - - 1 - 13.0826 - 22 - 18.5716 - 1 - 6 - 2 - 7 - 0 - 0 - 4 - 4 - 0 - 6 - PTSPFQ - PERPFQ - P PFQ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 45 - Query_45 - M_2143 - 9 - - - 1 - gnl|BL_ORD_ID|1755 - 154041|major capsid protein|CAB06743.1|Human alphaherpesvirus 2|10310 - 1755 - 15 - - - 1 - 13.4678 - 23 - 11.1066 - 3 - 9 - 4 - 10 - 0 - 0 - 4 - 5 - 0 - 7 - ERSIPTV - DRSYPAV - +RS P V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 46 - Query_46 - M_2144 - 9 - - - 1 - gnl|BL_ORD_ID|1871 - 180488|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1871 - 10 - - - 1 - 13.853 - 24 - 6.41039 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - PCHREPL - PGHEEPI - P H EP+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 47 - Query_47 - M_2145 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 48 - Query_48 - M_2146 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 49 - Query_49 - M_2147 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 50 - Query_50 - M_2148 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 51 - Query_51 - M_2149 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 52 - Query_52 - M_2150 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 53 - Query_53 - M_2151 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 54 - Query_54 - M_2152 - 9 - - - 1 - gnl|BL_ORD_ID|376 - 23288|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 - 376 - 15 - - - 1 - 13.853 - 24 - 5.98058 - 1 - 8 - 7 - 14 - 0 - 0 - 3 - 7 - 0 - 8 - YEEYRGRL - YQDWLGRM - Y+++ GR+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 55 - Query_55 - M_2153 - 9 - - - 1 - gnl|BL_ORD_ID|376 - 23288|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 - 376 - 15 - - - 1 - 13.853 - 24 - 5.98058 - 1 - 8 - 7 - 14 - 0 - 0 - 3 - 7 - 0 - 8 - YEEYRGRL - YQDWLGRM - Y+++ GR+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 56 - Query_56 - M_2154 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 57 - Query_57 - M_2155 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 58 - Query_58 - M_2156 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 59 - Query_59 - M_2157 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 60 - Query_60 - M_2158 - 9 - - - 1 - gnl|BL_ORD_ID|750 - 49831|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 - 750 - 15 - - - 1 - 11.927 - 19 - 74.9817 - 1 - 8 - 4 - 11 - 0 - 0 - 3 - 5 - 0 - 8 - FFFLCVCV - LLILCLCL - LC+C+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 61 - Query_61 - M_2159 - 9 - - - 1 - gnl|BL_ORD_ID|750 - 49831|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 - 750 - 15 - - - 1 - 11.5418 - 18 - 131.587 - 1 - 7 - 5 - 11 - 0 - 0 - 3 - 5 - 0 - 7 - FFLCVCV - LILCLCL - LC+C+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 62 - Query_62 - M_2160 - 9 - - - 1 - gnl|BL_ORD_ID|1140 - 75376|Genome polyprotein|P26664.3|Hepatitis C virus|11103 - 1140 - 8 - - - 1 - 12.6974 - 21 - 24.9053 - 3 - 8 - 1 - 6 - 0 - 0 - 4 - 4 - 0 - 6 - YPHKRC - YPPKPC - YP K C - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 63 - Query_63 - M_2161 - 9 - - - 1 - gnl|BL_ORD_ID|1140 - 75376|Genome polyprotein|P26664.3|Hepatitis C virus|11103 - 1140 - 8 - - - 1 - 12.6974 - 21 - 24.9053 - 3 - 8 - 1 - 6 - 0 - 0 - 4 - 4 - 0 - 6 - YPHKRC - YPPKPC - YP K C - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_121511_2_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_121511_2_T.fasta deleted file mode 100755 index ac5e8004..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_121511_2_T.fasta +++ /dev/null @@ -1,116 +0,0 @@ ->M_2162 -NMSRCCIRV ->M_2163 -GLLGNGIGY ->M_2164 -LLGNGIGYV ->M_2165 -KILSLHLLL ->M_2166 -HPAFISLAF ->M_2167 -FPREKTPEV ->M_2168 -WPPWLKGKY ->M_2169 -IVLTGHNAY ->M_2170 -IVLTGHNAY ->M_2171 -VLTGHNAYL ->M_2172 -QAQALGIPL ->M_2173 -IVFFANNGF ->M_2174 -HSESSDSEV ->M_2175 -RRGSGHSEY ->M_2176 -LIMEDLVCY ->M_2177 -MEDLPAACM ->M_2178 -HPMASNSGG ->M_2179 -DVEWRWHSY ->M_2180 -DVEWRWHSY ->M_2181 -ILPTCSPLV ->M_2182 -LPTCSPLVF ->M_2183 -VHFWPGYEY ->M_2184 -SPEGDDTLY ->M_2185 -TLVPTAPEL ->M_2186 -HLIGSTTLA ->M_2187 -LIGSTTLAM ->M_2188 -LLMHLIGST ->M_2189 -IAHQWYWTY ->M_2190 -IAHQWYWTY ->M_2191 -LLEENGDVF ->M_2192 -QRCACPHGY ->M_2193 -CMYDPLGTI ->M_2194 -GPHRITCMY ->M_2195 -NESCLSMSE ->M_2196 -VANESCLSM ->M_2197 -EESELYAQL ->M_2198 -RTAQCFLCV ->M_2199 -KYSNYVWPI ->M_2200 -FIFEIVGFT ->M_2201 -DSSGQSNRY ->M_2202 -DSSSWSNRY ->M_2203 -DSSSWSNRY ->M_2204 -NRYGGGGRY ->M_2205 -NRYGGGGRY ->M_2206 -NEHGHRRKI ->M_2207 -HTSLRGFLY ->M_2208 -ALNEMFCQL ->M_2209 -NEMFCQLAK ->M_2210 -GLYAIAVML ->M_2211 -MLSFSRIAY ->M_2212 -MLSFSRIAY ->M_2213 -YAIAVMLSF ->M_2214 -AEWDSLYVL ->M_2215 -LAEWDSLYV ->M_2216 -VLAEWDSLY ->M_2217 -VLAEWDSLY ->M_2218 -GKAFSQSAY ->M_2219 -KAFSQSAYL diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_121511_2_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_121511_2_T_iedb.xml deleted file mode 100755 index bbcebff2..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_121511_2_T_iedb.xml +++ /dev/null @@ -1,1923 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_2162 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_2162 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_2163 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_2164 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_2165 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_2166 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_2167 - 9 - - - 1 - gnl|BL_ORD_ID|1181 - 88849|IE62|AAP32859.1|Human alphaherpesvirus 3|10335 - 1181 - 9 - - - 1 - 14.2382 - 25 - 2.85402 - 1 - 7 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - FPREKTP - LPRSRTP - PR +TP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 7 - Query_7 - M_2168 - 9 - - - 1 - gnl|BL_ORD_ID|2285 - 419170|polyprotein|ABR25251.1|Hepatitis C virus|11103 - 2285 - 9 - - - 1 - 11.1566 - 17 - 202.191 - 4 - 8 - 4 - 8 - 0 - 0 - 4 - 5 - 0 - 5 - WLKGK - YLKGK - +LKGK - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 8 - Query_8 - M_2169 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_2170 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_2171 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_2172 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_2173 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_2174 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_2175 - 9 - - - 1 - gnl|BL_ORD_ID|1871 - 180488|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1871 - 10 - - - 1 - 13.0826 - 22 - 16.3922 - 3 - 8 - 1 - 6 - 0 - 0 - 4 - 4 - 0 - 6 - GSGHSE - GPGHEE - G GH E - - - - - 2 - gnl|BL_ORD_ID|657 - 38974|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 657 - 11 - - - 1 - 12.3122 - 20 - 38.8163 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 7 - 0 - 9 - RRGSGHSEY - QRGPQYSEH - +RG +SE+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 15 - Query_15 - M_2176 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_2177 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_2178 - 9 - - - 1 - gnl|BL_ORD_ID|1636 - 146282|polyprotein|ADF97231.1|Hepatitis C virus subtype 3a|356426 - 1636 - 17 - - - 1 - 12.3122 - 20 - 54.7088 - 2 - 9 - 5 - 12 - 0 - 0 - 4 - 5 - 0 - 8 - PMASNSGG - PIALLKGG - P+A GG - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 18 - Query_18 - M_2179 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_2180 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_2181 - 9 - - - 1 - gnl|BL_ORD_ID|863 - 56502|polyprotein|BAD73994.1|Hepatitis C virus subtype 1b|31647 - 863 - 9 - - - 1 - 13.853 - 24 - 6.16125 - 3 - 8 - 4 - 9 - 0 - 0 - 4 - 4 - 0 - 6 - PTCSPL - PACKPL - P C PL - - - - - 2 - gnl|BL_ORD_ID|1211 - 96366|polyprotein|ABR25251.1|Hepatitis C virus|11103 - 1211 - 12 - - - 1 - 13.4678 - 23 - 11.0162 - 3 - 9 - 5 - 11 - 0 - 0 - 4 - 5 - 0 - 7 - PTCSPLV - PPCKPLL - P C PL+ - - - - - 3 - gnl|BL_ORD_ID|745 - 48458|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 - 745 - 20 - - - 1 - 11.5418 - 18 - 98.2529 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - LPTCSPLV - LPVVFPIV - LP P+V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 21 - Query_21 - M_2182 - 9 - - - 1 - gnl|BL_ORD_ID|863 - 56502|polyprotein|BAD73994.1|Hepatitis C virus subtype 1b|31647 - 863 - 9 - - - 1 - 13.853 - 24 - 6.16125 - 2 - 7 - 4 - 9 - 0 - 0 - 4 - 4 - 0 - 6 - PTCSPL - PACKPL - P C PL - - - - - 2 - gnl|BL_ORD_ID|1211 - 96366|polyprotein|ABR25251.1|Hepatitis C virus|11103 - 1211 - 12 - - - 1 - 13.4678 - 23 - 11.0162 - 2 - 8 - 5 - 11 - 0 - 0 - 4 - 5 - 0 - 7 - PTCSPLV - PPCKPLL - P C PL+ - - - - - 3 - gnl|BL_ORD_ID|745 - 48458|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 - 745 - 20 - - - 1 - 11.5418 - 18 - 107.151 - 1 - 8 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - LPTCSPLV - LPVVFPIV - LP P+V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 22 - Query_22 - M_2183 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_2184 - 9 - - - 1 - gnl|BL_ORD_ID|186 - 13701|Trans-activator protein BZLF1|P03206.2|Human gammaherpesvirus 4|10376 - 186 - 11 - - - 1 - 12.6974 - 21 - 24.627 - 2 - 9 - 4 - 11 - 0 - 0 - 4 - 5 - 0 - 8 - PEGDDTLY - PQGQLTAY - P+G T Y - - - - - 2 - gnl|BL_ORD_ID|2045 - 184531|polyprotein|AFP27208.1|Dengue virus 4|11070 - 2045 - 10 - - - 1 - 12.3122 - 20 - 61.3845 - 2 - 8 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - PEGDDTL - PESLETL - PE +TL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 24 - Query_24 - M_2185 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_2186 - 9 - - - 1 - gnl|BL_ORD_ID|901 - 59182|attachment glycoprotein|ABQ58821.1|Human metapneumovirus|162145 - 901 - 10 - - - 1 - 13.4678 - 23 - 12.859 - 2 - 8 - 4 - 10 - 0 - 0 - 6 - 6 - 0 - 7 - LIGSTTL - LIGITTL - LIG TTL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 26 - Query_26 - M_2187 - 9 - - - 1 - gnl|BL_ORD_ID|901 - 59182|attachment glycoprotein|ABQ58821.1|Human metapneumovirus|162145 - 901 - 10 - - - 1 - 13.0826 - 22 - 16.3922 - 1 - 7 - 4 - 10 - 0 - 0 - 6 - 6 - 0 - 7 - LIGSTTL - LIGITTL - LIG TTL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 27 - Query_27 - M_2188 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 28 - Query_28 - M_2189 - 9 - - - 1 - gnl|BL_ORD_ID|957 - 62903|Genome polyprotein|P27909.2|Dengue virus type 1 Hawaii|10000440 - 957 - 20 - - - 1 - 11.5418 - 18 - 98.2529 - 4 - 9 - 3 - 8 - 0 - 0 - 2 - 4 - 0 - 6 - QWYWTY - KWLWGF - +W W + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 29 - Query_29 - M_2190 - 9 - - - 1 - gnl|BL_ORD_ID|957 - 62903|Genome polyprotein|P27909.2|Dengue virus type 1 Hawaii|10000440 - 957 - 20 - - - 1 - 11.5418 - 18 - 98.2529 - 4 - 9 - 3 - 8 - 0 - 0 - 2 - 4 - 0 - 6 - QWYWTY - KWLWGF - +W W + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 30 - Query_30 - M_2191 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 31 - Query_31 - M_2192 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 32 - Query_32 - M_2193 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 33 - Query_33 - M_2194 - 9 - - - 1 - gnl|BL_ORD_ID|1173 - 79337|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 1173 - 15 - - - 1 - 12.3122 - 20 - 38.6124 - 2 - 7 - 9 - 14 - 0 - 0 - 4 - 4 - 0 - 6 - PHRITC - PHVIFC - PH I C - - - - - 2 - gnl|BL_ORD_ID|1332 - 107872|Genome polyprotein|P26664.3|Hepatitis C virus|11103 - 1332 - 10 - - - 1 - 11.927 - 19 - 106.494 - 1 - 7 - 1 - 7 - 0 - 0 - 4 - 4 - 0 - 7 - GPHRITC - GRHLIFC - G H I C - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 34 - Query_34 - M_2195 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 35 - Query_35 - M_2196 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 36 - Query_36 - M_2197 - 9 - - - 1 - gnl|BL_ORD_ID|946 - 62355|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 946 - 20 - - - 1 - 13.0826 - 22 - 20.1922 - 1 - 6 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - EESELY - EQSEFY - E+SE Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 37 - Query_37 - M_2198 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 38 - Query_38 - M_2199 - 9 - - - 1 - gnl|BL_ORD_ID|561 - 34616|pol protein|BAA32832.1|Hepatitis B virus|10407 - 561 - 9 - - - 1 - 12.6974 - 21 - 26.4654 - 1 - 7 - 1 - 7 - 0 - 0 - 3 - 6 - 0 - 7 - KYSNYVW - KYTSFPW - KY+++ W - - - - - 2 - gnl|BL_ORD_ID|1915 - 180675|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1915 - 15 - - - 1 - 10.7714 - 16 - 257.204 - 3 - 9 - 2 - 8 - 0 - 0 - 3 - 4 - 0 - 7 - SNYVWPI - STYGWNL - S Y W + - - - - - 3 - gnl|BL_ORD_ID|1711 - 150309|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1711 - 10 - - - 1 - 10.3862 - 15 - 485 - 3 - 7 - 4 - 8 - 0 - 0 - 3 - 3 - 0 - 5 - SNYVW - STYGW - S Y W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 39 - Query_39 - M_2200 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 40 - Query_40 - M_2201 - 9 - - - 1 - gnl|BL_ORD_ID|1995 - 183598|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1995 - 10 - - - 1 - 13.4678 - 23 - 9.90554 - 3 - 9 - 4 - 10 - 0 - 0 - 4 - 6 - 0 - 7 - SGQSNRY - SGKTRRY - SG++ RY - - - - - 2 - gnl|BL_ORD_ID|15 - 1095|glycoprotein gp35/37|AAC59622.1|Human gammaherpesvirus 8|37296 - 15 - 15 - - - 1 - 13.0826 - 22 - 16.6732 - 2 - 8 - 6 - 12 - 0 - 0 - 5 - 6 - 0 - 7 - SSGQSNR - NSGASNR - +SG SNR - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 41 - Query_41 - M_2202 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 42 - Query_42 - M_2203 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 43 - Query_43 - M_2204 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 44 - Query_44 - M_2205 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 45 - Query_45 - M_2206 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 46 - Query_46 - M_2207 - 9 - - - 1 - gnl|BL_ORD_ID|396 - 24302|X protein|AAP06597.1|Hepatitis B virus|10407 - 396 - 9 - - - 1 - 14.2382 - 25 - 2.75966 - 1 - 7 - 1 - 7 - 0 - 0 - 5 - 5 - 0 - 7 - HTSLRGF - HLSLRGL - H SLRG - - - - - 2 - gnl|BL_ORD_ID|395 - 24299|X protein|BAF81690.1|Hepatitis B virus|10407 - 395 - 9 - - - 1 - 14.2382 - 25 - 3.74233 - 1 - 7 - 1 - 7 - 0 - 0 - 5 - 5 - 0 - 7 - HTSLRGF - HLSLRGL - H SLRG - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 47 - Query_47 - M_2208 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 48 - Query_48 - M_2209 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 49 - Query_49 - M_2210 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 50 - Query_50 - M_2211 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 51 - Query_51 - M_2212 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 52 - Query_52 - M_2213 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 53 - Query_53 - M_2214 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 54 - Query_54 - M_2215 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 55 - Query_55 - M_2216 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 56 - Query_56 - M_2217 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 57 - Query_57 - M_2218 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 58 - Query_58 - M_2219 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_122176_2_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_122176_2_T.fasta deleted file mode 100755 index 5fe42885..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_122176_2_T.fasta +++ /dev/null @@ -1,54 +0,0 @@ ->M_2220 -RREDLTHTL ->M_2221 -RREDLTHTL ->M_2222 -ERWLRQAAF ->M_2223 -RKREEEERW ->M_2224 -THCSPNLLF ->M_2225 -HQYNIYAAL ->M_2226 -RSFTESHQY ->M_2227 -ISAKIMQQW ->M_2228 -YTDTISAKI ->M_2229 -AAVLGMLLW ->M_2230 -ISGRVVQHF ->M_2231 -IAFNHGDLL ->M_2232 -KYHYYGLHI ->M_2233 -LSRRVTQSL ->M_2234 -RRVTQSLEA ->M_2235 -KTYAPLFIW ->M_2236 -TYAPLFIWV ->M_2237 -KYIAFCINI ->M_2238 -YIAFCINIF ->M_2239 -FHYPQSIFS ->M_2240 -MKFHYPQSI ->M_2241 -NTNSNRSLI ->M_2242 -FRAYQDYFL ->M_2243 -FRAYQDYFL ->M_2244 -LHIGKDVQL ->M_2245 -QVFAAVHEW ->M_2246 -RRHTDEKPY diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_122176_2_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_122176_2_T_iedb.xml deleted file mode 100755 index 503d1aad..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_122176_2_T_iedb.xml +++ /dev/null @@ -1,1281 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_2220 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_2220 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_2221 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_2222 - 9 - - - 1 - gnl|BL_ORD_ID|357 - 22255|polyprotein|ABR27377.1|Hepatitis C virus|11103 - 357 - 9 - - - 1 - 13.853 - 24 - 5.95161 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 6 - 0 - 8 - RWLRQAAF - RWVPGAAY - RW+ AA+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 4 - Query_4 - M_2223 - 9 - - - 1 - gnl|BL_ORD_ID|2088 - 185491|polyprotein|AGO67248.1|Dengue virus 2|11060 - 2088 - 10 - - - 1 - 12.3122 - 20 - 62.4024 - 2 - 7 - 1 - 6 - 0 - 0 - 5 - 6 - 0 - 6 - KREEEE - RREEEE - +REEEE - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 5 - Query_5 - M_2224 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_2225 - 9 - - - 1 - gnl|BL_ORD_ID|790 - 52886|pp65|AAA45994.1|Human betaherpesvirus 5|10359 - 790 - 9 - - - 1 - 12.6974 - 21 - 23.4633 - 2 - 9 - 1 - 8 - 0 - 0 - 5 - 6 - 0 - 8 - QYNIYAAL - QYDPVAAL - QY+ AAL - - - - - 2 - gnl|BL_ORD_ID|2155 - 189291|||| - 2155 - 9 - - - 1 - 12.6974 - 21 - 26.0147 - 3 - 9 - 3 - 9 - 0 - 0 - 5 - 5 - 0 - 7 - YNIYAAL - YNTVAAL - YN AAL - - - - - 3 - gnl|BL_ORD_ID|791 - 52888|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 791 - 11 - - - 1 - 12.6974 - 21 - 29.1766 - 2 - 9 - 1 - 8 - 0 - 0 - 5 - 6 - 0 - 8 - QYNIYAAL - QYDPVAAL - QY+ AAL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 7 - Query_7 - M_2226 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_2227 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_2228 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_2229 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_2230 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_2231 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_2232 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_2233 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_2234 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_2235 - 9 - - - 1 - gnl|BL_ORD_ID|1011 - 67349|Latent membrane protein 2|Q69135|Human gammaherpesvirus 4|10376 - 1011 - 9 - - - 1 - 14.6234 - 26 - 1.85254 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 6 - 0 - 7 - TYAPLFI - TYGPVFM - TY P+F+ - - - - - 2 - gnl|BL_ORD_ID|2312 - 423020|polyprotein|ACE82359.1|Hepatitis C virus genotype 1|41856 - 2312 - 9 - - - 1 - 10.001 - 14 - 866.983 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 4 - 0 - 9 - KTYAPLFIW - KLYISWCLW - K Y +W - - - - - 3 - gnl|BL_ORD_ID|664 - 39591|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 - 664 - 20 - - - 1 - 9.61583 - 13 - 985.051 - 1 - 9 - 6 - 14 - 0 - 0 - 3 - 4 - 0 - 9 - KTYAPLFIW - KRYISWCLW - K Y +W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 17 - Query_17 - M_2236 - 9 - - - 1 - gnl|BL_ORD_ID|1011 - 67349|Latent membrane protein 2|Q69135|Human gammaherpesvirus 4|10376 - 1011 - 9 - - - 1 - 14.6234 - 26 - 1.62552 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 7 - 0 - 9 - TYAPLFIWV - TYGPVFMCL - TY P+F+ + - - - - - 2 - gnl|BL_ORD_ID|82 - 5952|PPE family protein|YP_177918.1|Mycobacterium tuberculosis H37Rv|83332 - 82 - 9 - - - 1 - 11.1566 - 17 - 211.79 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 4 - 0 - 9 - TYAPLFIWV - AYVPYVAWL - Y P W+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 18 - Query_18 - M_2237 - 9 - - - 1 - gnl|BL_ORD_ID|664 - 39591|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 - 664 - 20 - - - 1 - 14.2382 - 25 - 3.035 - 1 - 7 - 7 - 13 - 0 - 0 - 3 - 7 - 0 - 7 - KYIAFCI - RYISWCL - +YI++C+ - - - - - 2 - gnl|BL_ORD_ID|2312 - 423020|polyprotein|ACE82359.1|Hepatitis C virus genotype 1|41856 - 2312 - 9 - - - 1 - 13.4678 - 23 - 10.7466 - 2 - 7 - 3 - 8 - 0 - 0 - 3 - 6 - 0 - 6 - YIAFCI - YISWCL - YI++C+ - - - - - 3 - gnl|BL_ORD_ID|1120 - 74387|Genome polyprotein|P26664.3|Hepatitis C virus (isolate 1)|11104 - 1120 - 9 - - - 1 - 13.4678 - 23 - 11.5219 - 2 - 7 - 1 - 6 - 0 - 0 - 3 - 6 - 0 - 6 - YIAFCI - YISWCL - YI++C+ - - - - - 4 - gnl|BL_ORD_ID|1119 - 74386|HCV-1|AAA45676.1|Hepatitis C virus|11103 - 1119 - 8 - - - 1 - 13.4678 - 23 - 12.8716 - 2 - 7 - 1 - 6 - 0 - 0 - 3 - 6 - 0 - 6 - YIAFCI - YISWCL - YI++C+ - - - - - 5 - gnl|BL_ORD_ID|399 - 24457|polyprotein|BAA09072.1|Hepatitis C virus|11103 - 399 - 15 - - - 1 - 13.0826 - 22 - 13.39 - 1 - 8 - 5 - 12 - 0 - 0 - 4 - 6 - 0 - 8 - KYIAFCIN - KYIMACMS - KYI C++ - - - - - 6 - gnl|BL_ORD_ID|1297 - 103389|unnamed protein product [Hepatitis C virus]|BAA14035.1|Hepatitis C virus|11103 - 1297 - 20 - - - 1 - 11.5418 - 18 - 116.798 - 1 - 8 - 7 - 14 - 0 - 0 - 2 - 6 - 0 - 8 - KYIAFCIN - KFVMACMS - K++ C++ - - - - - 7 - gnl|BL_ORD_ID|1502 - 137660|L1|ACL12325.1|Human papillomavirus type 58|10598 - 1502 - 9 - - - 1 - 11.5418 - 18 - 150.225 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 6 - 0 - 9 - KYIAFCINI - KYTFWEVNL - KY + +N+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 19 - Query_19 - M_2238 - 9 - - - 1 - gnl|BL_ORD_ID|2312 - 423020|polyprotein|ACE82359.1|Hepatitis C virus genotype 1|41856 - 2312 - 9 - - - 1 - 13.4678 - 23 - 11.5219 - 1 - 6 - 3 - 8 - 0 - 0 - 3 - 6 - 0 - 6 - YIAFCI - YISWCL - YI++C+ - - - - - 2 - gnl|BL_ORD_ID|1120 - 74387|Genome polyprotein|P26664.3|Hepatitis C virus (isolate 1)|11104 - 1120 - 9 - - - 1 - 13.4678 - 23 - 13.0154 - 1 - 6 - 1 - 6 - 0 - 0 - 3 - 6 - 0 - 6 - YIAFCI - YISWCL - YI++C+ - - - - - 3 - gnl|BL_ORD_ID|664 - 39591|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 - 664 - 20 - - - 1 - 13.0826 - 22 - 13.0672 - 1 - 6 - 8 - 13 - 0 - 0 - 3 - 6 - 0 - 6 - YIAFCI - YISWCL - YI++C+ - - - - - 4 - gnl|BL_ORD_ID|1119 - 74386|HCV-1|AAA45676.1|Hepatitis C virus|11103 - 1119 - 8 - - - 1 - 13.4678 - 23 - 13.8002 - 1 - 6 - 1 - 6 - 0 - 0 - 3 - 6 - 0 - 6 - YIAFCI - YISWCL - YI++C+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 20 - Query_20 - M_2239 - 9 - - - 1 - gnl|BL_ORD_ID|1763 - 154585|ribonucleotide reductase large subunit|CAB06725.1|Human alphaherpesvirus 2|10310 - 1763 - 15 - - - 1 - 14.2382 - 25 - 2.38473 - 2 - 8 - 4 - 10 - 0 - 0 - 4 - 6 - 0 - 7 - HYPQSIF - HYMESVF - HY +S+F - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 21 - Query_21 - M_2240 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 22 - Query_22 - M_2241 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_2242 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_2243 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_2244 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_2245 - 9 - - - 1 - gnl|BL_ORD_ID|1596 - 142232|POSSIBLE CONSERVED TRANSMEMBRANE PROTEIN|CAB00937.1|Mycobacterium tuberculosis|1773 - 1596 - 19 - - - 1 - 10.001 - 14 - 683.554 - 3 - 7 - 14 - 18 - 0 - 0 - 3 - 4 - 0 - 5 - FAAVH - YAFVH - +A VH - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 27 - Query_27 - M_2246 - 9 - - - 1 - gnl|BL_ORD_ID|1395 - 110394|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1395 - 32 - - - 1 - 12.6974 - 21 - 25.5546 - 1 - 7 - 15 - 21 - 0 - 0 - 4 - 6 - 0 - 7 - RRHTDEK - QRHLDKK - +RH D+K - - - - - 2 - gnl|BL_ORD_ID|1405 - 110829|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1405 - 15 - - - 1 - 12.6974 - 21 - 26.1211 - 1 - 7 - 3 - 9 - 0 - 0 - 4 - 6 - 0 - 7 - RRHTDEK - QRHLDKK - +RH D+K - - - - - 3 - gnl|BL_ORD_ID|1385 - 110215|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1385 - 25 - - - 1 - 12.6974 - 21 - 28.4868 - 2 - 8 - 4 - 10 - 0 - 0 - 4 - 5 - 0 - 7 - RHTDEKP - RHLDKKQ - RH D+K - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_123126_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_123126_1_T.fasta deleted file mode 100755 index eda51dc1..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_123126_1_T.fasta +++ /dev/null @@ -1,120 +0,0 @@ ->M_2247 -FNGNFLLSM ->M_2248 -GSADNTVQF ->M_2249 -SADNTVQFI ->M_2250 -KVQREDIFY ->M_2251 -YLWPSGTPA ->M_2252 -LKMVSPSPC ->M_2253 -SRVARDVAM ->M_2254 -QNGYSWSQF ->M_2255 -SYKLSQNGY ->M_2256 -WKRGKRRYF ->M_2257 -CFGHCFSLY ->M_2258 -CSAIRLRNY ->M_2259 -FGHCFSLYI ->M_2260 -IRLRNYLCF ->M_2261 -IRLRNYLCF ->M_2262 -LCFGHCFSL ->M_2263 -NHLCFGHCF ->M_2264 -DFVECLMWF ->M_2265 -DFVECLMWF ->M_2266 -NKFEPSTDL ->M_2267 -AYLCCRVPL ->M_2268 -SKGTTDTPV ->M_2269 -KQSNSVEPI ->M_2270 -AMSAQEYYI ->M_2271 -SAQEYYIDY ->M_2272 -YIDYKPNHI ->M_2273 -LMLLAAAIY ->M_2274 -LMLLAAAIY ->M_2275 -SEDDTSYFV ->M_2276 -RESVKHIGY ->M_2277 -YQKVVRESV ->M_2278 -SSVKTPETL ->M_2279 -VIHHELQVL ->M_2280 -KTDATPGRL ->M_2281 -IKRLTAGSL ->M_2282 -KRLTAGSLF ->M_2283 -KQLSHHIGA ->M_2284 -FHVNWFRRY ->M_2285 -FRRYEAGHF ->M_2286 -RRYEAGHFL ->M_2287 -RYEAGHFLW ->M_2288 -VSDHTPEQH ->M_2289 -SFHMDTQNF ->M_2290 -SFHMDTQNF ->M_2291 -TQNFCDIGY ->M_2292 -LALSVFSKL ->M_2293 -TVKLALSVF ->M_2294 -LQFAVGQEV ->M_2295 -PQVPEHLQF ->M_2296 -QFAVGQEVF ->M_2297 -NRYGGGGRY ->M_2298 -EQLKLGAIF ->M_2299 -LLMPYPVIV ->M_2300 -TLLMPYPVI ->M_2301 -RALKPVNKI ->M_2302 -KEAMENEQF ->M_2303 -LTEENKEAM ->M_2304 -MEVPNIASS ->M_2305 -RRFASGEKV ->M_2306 -TFRDVAVEF diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_123126_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_123126_1_T_iedb.xml deleted file mode 100755 index 6f4861f5..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_123126_1_T_iedb.xml +++ /dev/null @@ -1,2774 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_2247 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_2247 - 9 - - - 1 - gnl|BL_ORD_ID|2229 - 194567|envelope glycoprotein B|NP_044629.1|Herpes simplex virus (type 1 / strain 17)|10299 - 2229 - 9 - - - 1 - 12.6974 - 21 - 35.9943 - 2 - 7 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - NGNFLL - NGGFLI - NG FL+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 2 - Query_2 - M_2248 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_2249 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_2250 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_2251 - 9 - - - 1 - gnl|BL_ORD_ID|1520 - 140600|glutamine synthetase GLNA1 (glutamine synthase) (GS-I)|NP_216736.1|Mycobacterium tuberculosis H37Rv|83332 - 1520 - 9 - - - 1 - 13.853 - 24 - 6.48995 - 2 - 8 - 2 - 8 - 0 - 0 - 4 - 4 - 0 - 7 - LWPSGTP - LWKDGAP - LW G P - - - - - 2 - gnl|BL_ORD_ID|2041 - 184512|polyprotein|AGO67248.1|Dengue virus 2|11060 - 2041 - 10 - - - 1 - 11.927 - 19 - 90.726 - 2 - 8 - 2 - 8 - 0 - 0 - 3 - 4 - 0 - 7 - LWPSGTP - MWKQITP - +W TP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 6 - Query_6 - M_2252 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_2253 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_2254 - 9 - - - 1 - gnl|BL_ORD_ID|101 - 6889|Agglutinin isolectin 1 precursor|P10968.2|Triticum aestivum|4565 - 101 - 9 - - - 1 - 14.2382 - 25 - 3.49608 - 1 - 7 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - QNGYSWS - QNGACWT - QNG W+ - - - - - 2 - gnl|BL_ORD_ID|1194 - 95279|polyprotein|BAG31965.1|Hepatitis C virus|11103 - 1194 - 9 - - - 1 - 13.853 - 24 - 6.48995 - 2 - 7 - 3 - 8 - 0 - 0 - 4 - 4 - 0 - 6 - NGYSWS - NGVCWS - NG WS - - - - - 3 - gnl|BL_ORD_ID|1193 - 95278|polyprotein|BAC67110.1|Hepatitis C virus|11103 - 1193 - 9 - - - 1 - 13.853 - 24 - 6.48995 - 2 - 7 - 3 - 8 - 0 - 0 - 4 - 4 - 0 - 6 - NGYSWS - NGVCWS - NG WS - - - - - 4 - gnl|BL_ORD_ID|66 - 4910|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 66 - 20 - - - 1 - 13.4678 - 23 - 8.23977 - 2 - 9 - 5 - 12 - 0 - 0 - 3 - 5 - 0 - 8 - NGYSWSQF - NGVCWTVY - NG W+ + - - - - - 5 - gnl|BL_ORD_ID|65 - 4909|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 - 65 - 15 - - - 1 - 13.4678 - 23 - 9.20205 - 2 - 9 - 5 - 12 - 0 - 0 - 3 - 5 - 0 - 8 - NGYSWSQF - NGVCWTVY - NG W+ + - - - - - 6 - gnl|BL_ORD_ID|1632 - 146246|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 - 1632 - 17 - - - 1 - 13.4678 - 23 - 10.4757 - 2 - 9 - 7 - 14 - 0 - 0 - 3 - 5 - 0 - 8 - NGYSWSQF - NGVCWTVY - NG W+ + - - - - - 7 - gnl|BL_ORD_ID|784 - 52509|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 - 784 - 15 - - - 1 - 13.4678 - 23 - 12.0936 - 2 - 7 - 9 - 14 - 0 - 0 - 3 - 4 - 0 - 6 - NGYSWS - NGVCWT - NG W+ - - - - - 8 - gnl|BL_ORD_ID|107 - 7292|polyprotein|AAA75355.1|Hepatitis C virus subtype 1b|31647 - 107 - 9 - - - 1 - 13.0826 - 22 - 16.035 - 2 - 7 - 3 - 8 - 0 - 0 - 3 - 4 - 0 - 6 - NGYSWS - NGVCWT - NG W+ - - - - - 9 - gnl|BL_ORD_ID|89 - 6432|polyprotein [Hepatitis C virus]|CAL46125.1|Hepatitis C virus (isolate H77)|63746 - 89 - 9 - - - 1 - 13.0826 - 22 - 16.035 - 2 - 7 - 3 - 8 - 0 - 0 - 3 - 4 - 0 - 6 - NGYSWS - NGLCWT - NG W+ - - - - - 10 - gnl|BL_ORD_ID|1674 - 148619|unnamed protein product|BAA14233.1|Hepatitis C virus|11103 - 1674 - 45 - - - 1 - 13.0826 - 22 - 16.0472 - 2 - 9 - 38 - 45 - 0 - 0 - 3 - 5 - 0 - 8 - NGYSWSQF - NGVCWTVY - NG W+ + - - - - - 11 - gnl|BL_ORD_ID|91 - 6435|polyprotein|BAB18806.1|Hepatitis C virus|11103 - 91 - 9 - - - 1 - 13.0826 - 22 - 16.6015 - 2 - 7 - 3 - 8 - 0 - 0 - 3 - 4 - 0 - 6 - NGYSWS - NGVCWT - NG W+ - - - - - 12 - gnl|BL_ORD_ID|1197 - 95297|polyprotein|BAA09072.1|Hepatitis C virus genotype 1|41856 - 1197 - 9 - - - 1 - 13.0826 - 22 - 18.4218 - 2 - 7 - 3 - 8 - 0 - 0 - 3 - 4 - 0 - 6 - NGYSWS - NGVCWT - NG W+ - - - - - 13 - gnl|BL_ORD_ID|90 - 6433|Genome polyprotein|SRC279960|Hepatitis C virus subtype 1a|31646 - 90 - 9 - - - 1 - 13.0826 - 22 - 19.404 - 2 - 7 - 3 - 8 - 0 - 0 - 3 - 4 - 0 - 6 - NGYSWS - NGVCWT - NG W+ - - - - - 14 - gnl|BL_ORD_ID|1195 - 95280|Genome polyprotein|O39928.3|Hepatitis C virus genotype 5|33746 - 1195 - 9 - - - 1 - 12.6974 - 21 - 38.5226 - 2 - 7 - 3 - 8 - 0 - 0 - 3 - 4 - 0 - 6 - NGYSWS - NGVMWT - NG W+ - - - - - 15 - gnl|BL_ORD_ID|1192 - 95265|polyprotein|ABL63009.1|Hepatitis C virus genotype 4|33745 - 1192 - 9 - - - 1 - 12.3122 - 20 - 40.5299 - 2 - 7 - 3 - 8 - 0 - 0 - 3 - 4 - 0 - 6 - NGYSWS - NGVMWT - NG W+ - - - - - 16 - gnl|BL_ORD_ID|27 - 2033|polyprotein|BAA32665.1|Hepatitis C virus genotype 6|42182 - 27 - 9 - - - 1 - 12.3122 - 20 - 40.5299 - 2 - 7 - 3 - 8 - 0 - 0 - 3 - 4 - 0 - 6 - NGYSWS - NGVMWT - NG W+ - - - - - 17 - gnl|BL_ORD_ID|1199 - 95854|Genome polyprotein|O39927.3|Hepatitis C virus genotype 6|42182 - 1199 - 9 - - - 1 - 12.3122 - 20 - 49.6079 - 2 - 7 - 3 - 8 - 0 - 0 - 3 - 4 - 0 - 6 - NGYSWS - NGVMWT - NG W+ - - - - - 18 - gnl|BL_ORD_ID|1200 - 95890|polyprotein|ABE98152.1|Hepatitis C virus genotype 6|42182 - 1200 - 9 - - - 1 - 12.3122 - 20 - 51.2985 - 2 - 7 - 3 - 8 - 0 - 0 - 3 - 4 - 0 - 6 - NGYSWS - NGVMWT - NG W+ - - - - - 19 - gnl|BL_ORD_ID|397 - 24390|Major capsid protein L1|P50816.2|Human papillomavirus type 44|10592 - 397 - 9 - - - 1 - 11.927 - 19 - 102.395 - 1 - 8 - 2 - 9 - 0 - 0 - 3 - 3 - 0 - 8 - QNGYSWSQ - NNGICWGN - NG W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 9 - Query_9 - M_2255 - 9 - - - 1 - gnl|BL_ORD_ID|1961 - 182687|polyprotein|AGK36298.1|Dengue virus 2|11060 - 1961 - 10 - - - 1 - 13.4678 - 23 - 9.40133 - 1 - 8 - 1 - 8 - 0 - 0 - 3 - 6 - 0 - 8 - SYKLSQNG - AYRIKQRG - +Y++ Q G - - - - - 2 - gnl|BL_ORD_ID|1888 - 180582|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1888 - 15 - - - 1 - 12.3122 - 20 - 41.1784 - 1 - 8 - 8 - 15 - 0 - 0 - 4 - 5 - 0 - 8 - SYKLSQNG - SYETKQTG - SY+ Q G - - - - - 3 - gnl|BL_ORD_ID|2287 - 419229|polyprotein|ACF49259.1|Dengue virus type 1 Hawaii|10000440 - 2287 - 9 - - - 1 - 12.3122 - 20 - 61.624 - 2 - 8 - 2 - 8 - 0 - 0 - 3 - 5 - 0 - 7 - YKLSQNG - YRILQRG - Y++ Q G - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 10 - Query_10 - M_2256 - 9 - - - 1 - gnl|BL_ORD_ID|1811 - 170063|polyprotein|ABU97067.1|Hepatitis C virus subtype 1b|31647 - 1811 - 9 - - - 1 - 13.853 - 24 - 7.07804 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - WKRGKR - WTRGER - W RG+R - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 11 - Query_11 - M_2257 - 9 - - - 1 - gnl|BL_ORD_ID|866 - 56620|Nef protein|Q9YYU8|Human immunodeficiency virus 1|11676 - 866 - 10 - - - 1 - 12.6974 - 21 - 25.6384 - 2 - 6 - 6 - 10 - 0 - 0 - 4 - 4 - 0 - 5 - FGHCF - FGWCF - FG CF - - - - - 2 - gnl|BL_ORD_ID|2214 - 193060|Nef protein|Q9YYU3|Human immunodeficiency virus 1|11676 - 2214 - 10 - - - 1 - 12.6974 - 21 - 30.4011 - 2 - 6 - 6 - 10 - 0 - 0 - 4 - 4 - 0 - 5 - FGHCF - FGWCF - FG CF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 12 - Query_12 - M_2258 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_2259 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_2260 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_2261 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_2262 - 9 - - - 1 - gnl|BL_ORD_ID|866 - 56620|Nef protein|Q9YYU8|Human immunodeficiency virus 1|11676 - 866 - 10 - - - 1 - 14.2382 - 25 - 3.50259 - 1 - 7 - 4 - 10 - 0 - 0 - 5 - 5 - 0 - 7 - LCFGHCF - LTFGWCF - L FG CF - - - - - 2 - gnl|BL_ORD_ID|2214 - 193060|Nef protein|Q9YYU3|Human immunodeficiency virus 1|11676 - 2214 - 10 - - - 1 - 14.2382 - 25 - 4.15863 - 1 - 7 - 4 - 10 - 0 - 0 - 5 - 5 - 0 - 7 - LCFGHCF - LTFGWCF - L FG CF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 17 - Query_17 - M_2263 - 9 - - - 1 - gnl|BL_ORD_ID|866 - 56620|Nef protein|Q9YYU8|Human immunodeficiency virus 1|11676 - 866 - 10 - - - 1 - 14.2382 - 25 - 2.66759 - 3 - 9 - 4 - 10 - 0 - 0 - 5 - 5 - 0 - 7 - LCFGHCF - LTFGWCF - L FG CF - - - - - 2 - gnl|BL_ORD_ID|2214 - 193060|Nef protein|Q9YYU3|Human immunodeficiency virus 1|11676 - 2214 - 10 - - - 1 - 14.2382 - 25 - 3.16139 - 3 - 9 - 4 - 10 - 0 - 0 - 5 - 5 - 0 - 7 - LCFGHCF - LTFGWCF - L FG CF - - - - - 3 - gnl|BL_ORD_ID|1332 - 107872|Genome polyprotein|P26664.3|Hepatitis C virus|11103 - 1332 - 10 - - - 1 - 10.7714 - 16 - 373.491 - 1 - 7 - 2 - 8 - 0 - 0 - 4 - 4 - 0 - 7 - NHLCFGH - RHLIFCH - HL F H - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 18 - Query_18 - M_2264 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_2265 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_2266 - 9 - - - 1 - gnl|BL_ORD_ID|235 - 16814|precore protein|CAM58990.1|Hepatitis B virus|10407 - 235 - 10 - - - 1 - 11.5418 - 18 - 113.495 - 1 - 7 - 4 - 10 - 0 - 0 - 4 - 4 - 0 - 7 - NKFEPST - NDFFPSV - N F PS - - - - - 2 - gnl|BL_ORD_ID|234 - 16813|External core antigen|SRC279980|Hepatitis B virus|10407 - 234 - 10 - - - 1 - 11.5418 - 18 - 137.176 - 1 - 7 - 4 - 10 - 0 - 0 - 4 - 4 - 0 - 7 - NKFEPST - NDFFPSA - N F PS - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 21 - Query_21 - M_2267 - 9 - - - 1 - gnl|BL_ORD_ID|156 - 11956|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 - 156 - 11 - - - 1 - 11.1566 - 17 - 203.388 - 3 - 7 - 6 - 10 - 0 - 0 - 4 - 4 - 0 - 5 - LCCRV - LCCYV - LCC V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 22 - Query_22 - M_2268 - 9 - - - 1 - gnl|BL_ORD_ID|75 - 5542|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 75 - 15 - - - 1 - 13.4678 - 23 - 10.9188 - 1 - 9 - 7 - 15 - 0 - 0 - 4 - 7 - 0 - 9 - SKGTTDTPV - SPGTSGSPI - S GT+ +P+ - - - - - 2 - gnl|BL_ORD_ID|260 - 17802|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 260 - 15 - - - 1 - 13.0826 - 22 - 13.6187 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 7 - 0 - 9 - SKGTTDTPV - SPGTSGSPI - S GT+ +P+ - - - - - 3 - gnl|BL_ORD_ID|1929 - 180750|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1929 - 15 - - - 1 - 13.0826 - 22 - 15.8531 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 7 - 0 - 9 - SKGTTDTPV - SPGTSGSPI - S GT+ +P+ - - - - - 4 - gnl|BL_ORD_ID|364 - 22822|NS3 protein|NP_740321.1|Dengue virus 4|11070 - 364 - 11 - - - 1 - 12.6974 - 21 - 29.6736 - 3 - 9 - 1 - 7 - 0 - 0 - 3 - 6 - 0 - 7 - GTTDTPV - GTSGSPI - GT+ +P+ - - - - - 5 - gnl|BL_ORD_ID|363 - 22820|Nonstructural protein NS3|YP_001531172.2|Dengue virus 3|11069 - 363 - 10 - - - 1 - 12.6974 - 21 - 33.6561 - 3 - 9 - 1 - 7 - 0 - 0 - 3 - 6 - 0 - 7 - GTTDTPV - GTSGSPI - GT+ +P+ - - - - - 6 - gnl|BL_ORD_ID|367 - 22825|polyprotein|ABG75765.1|Dengue virus 1|11053 - 367 - 10 - - - 1 - 12.6974 - 21 - 37.2442 - 3 - 9 - 1 - 7 - 0 - 0 - 3 - 6 - 0 - 7 - GTTDTPV - GTSGSPI - GT+ +P+ - - - - - 7 - gnl|BL_ORD_ID|360 - 22817|polyprotein|AAK49562.1|Dengue virus 2|11060 - 360 - 11 - - - 1 - 12.6974 - 21 - 37.5414 - 3 - 9 - 1 - 7 - 0 - 0 - 3 - 6 - 0 - 7 - GTTDTPV - GTSGSPI - GT+ +P+ - - - - - 8 - gnl|BL_ORD_ID|362 - 22819|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 362 - 11 - - - 1 - 12.3122 - 20 - 40.1325 - 3 - 9 - 1 - 7 - 0 - 0 - 3 - 6 - 0 - 7 - GTTDTPV - GTSGSPI - GT+ +P+ - - - - - 9 - gnl|BL_ORD_ID|361 - 22818|Nonstructural protein NS3|NP_739587.2|Dengue virus 2|11060 - 361 - 10 - - - 1 - 12.3122 - 20 - 46.3152 - 3 - 9 - 1 - 7 - 0 - 0 - 3 - 6 - 0 - 7 - GTTDTPV - GTSGSPI - GT+ +P+ - - - - - 10 - gnl|BL_ORD_ID|1712 - 150341|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1712 - 9 - - - 1 - 12.3122 - 20 - 47.1713 - 3 - 9 - 3 - 9 - 0 - 0 - 3 - 6 - 0 - 7 - GTTDTPV - GTSGSPI - GT+ +P+ - - - - - 11 - gnl|BL_ORD_ID|366 - 22824|polyprotein|AAG30730.1|Dengue virus 2|11060 - 366 - 10 - - - 1 - 12.3122 - 20 - 50.3363 - 3 - 9 - 1 - 7 - 0 - 0 - 3 - 6 - 0 - 7 - GTTDTPV - GTSGSPI - GT+ +P+ - - - - - 12 - gnl|BL_ORD_ID|365 - 22823|NS3 protein|NP_739587.1|Dengue virus 2|11060 - 365 - 10 - - - 1 - 12.3122 - 20 - 51.1794 - 3 - 9 - 1 - 7 - 0 - 0 - 3 - 6 - 0 - 7 - GTTDTPV - GTSGSPI - GT+ +P+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 23 - Query_23 - M_2269 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_2270 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_2271 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_2272 - 9 - - - 1 - gnl|BL_ORD_ID|1916 - 180681|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1916 - 15 - - - 1 - 13.4678 - 23 - 9.20205 - 1 - 7 - 4 - 10 - 0 - 0 - 4 - 5 - 0 - 7 - YIDYKPN - YTDYMPS - Y DY P+ - - - - - 2 - gnl|BL_ORD_ID|558 - 34482|gag polyprotein|BAA00992.1|Human immunodeficiency virus 1|11676 - 558 - 9 - - - 1 - 11.927 - 19 - 84.261 - 3 - 9 - 1 - 7 - 0 - 0 - 4 - 4 - 0 - 7 - DYKPNHI - KYKLKHI - YK HI - - - - - 3 - gnl|BL_ORD_ID|659 - 39162|gag protein|AAV53308.1|Human immunodeficiency virus 1|11676 - 659 - 15 - - - 1 - 11.5418 - 18 - 108.251 - 3 - 9 - 8 - 14 - 0 - 0 - 4 - 4 - 0 - 7 - DYKPNHI - KYKLKHI - YK HI - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 27 - Query_27 - M_2273 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 28 - Query_28 - M_2274 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 29 - Query_29 - M_2275 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 30 - Query_30 - M_2276 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 31 - Query_31 - M_2277 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 32 - Query_32 - M_2278 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 33 - Query_33 - M_2279 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 34 - Query_34 - M_2280 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 35 - Query_35 - M_2281 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 36 - Query_36 - M_2282 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 37 - Query_37 - M_2283 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 38 - Query_38 - M_2284 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 39 - Query_39 - M_2285 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 40 - Query_40 - M_2286 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 41 - Query_41 - M_2287 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 42 - Query_42 - M_2288 - 9 - - - 1 - gnl|BL_ORD_ID|1057 - 69754|Lipoprotein lpqH precursor|P46733.1|Mycobacterium avium|1764 - 1057 - 10 - - - 1 - 12.6974 - 21 - 36.6217 - 1 - 8 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - VSDHTPEQ - LSDGNPPQ - +SD P Q - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 43 - Query_43 - M_2289 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 44 - Query_44 - M_2290 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 45 - Query_45 - M_2291 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 46 - Query_46 - M_2292 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 47 - Query_47 - M_2293 - 9 - - - 1 - gnl|BL_ORD_ID|786 - 52652|||| - 786 - 27 - - - 1 - 10.3862 - 15 - 322.823 - 1 - 9 - 12 - 20 - 0 - 0 - 4 - 6 - 0 - 9 - TVKLALSVF - TVRGLTSLF - TV+ S+F - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 48 - Query_48 - M_2294 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 49 - Query_49 - M_2295 - 9 - - - 1 - gnl|BL_ORD_ID|657 - 38974|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 657 - 11 - - - 1 - 12.3122 - 20 - 51.4474 - 1 - 6 - 5 - 10 - 0 - 0 - 4 - 4 - 0 - 6 - PQVPEH - PQYSEH - PQ EH - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 50 - Query_50 - M_2296 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 51 - Query_51 - M_2297 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 52 - Query_52 - M_2298 - 9 - - - 1 - gnl|BL_ORD_ID|2319 - 423046|polyprotein|ACX44272.1|Hepatitis C virus genotype 1|41856 - 2319 - 10 - - - 1 - 12.6974 - 21 - 37.8768 - 3 - 8 - 5 - 10 - 0 - 0 - 4 - 6 - 0 - 6 - LKLGAI - IKLGAL - +KLGA+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 53 - Query_53 - M_2299 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 54 - Query_54 - M_2300 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 55 - Query_55 - M_2301 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 56 - Query_56 - M_2302 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 57 - Query_57 - M_2303 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 58 - Query_58 - M_2304 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 59 - Query_59 - M_2305 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 60 - Query_60 - M_2306 - 9 - - - 1 - gnl|BL_ORD_ID|2108 - 186175|polyprotein|AFY10053.1|Dengue virus 3|11069 - 2108 - 10 - - - 1 - 13.853 - 24 - 6.08483 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 6 - 0 - 6 - TFRDVA - TWRDMA - T+RD+A - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_124242_3_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_124242_3_T.fasta deleted file mode 100755 index bd231bd7..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_124242_3_T.fasta +++ /dev/null @@ -1,92 +0,0 @@ ->M_2307 -FHISLFQYM ->M_2308 -LIIDEDFHI ->M_2309 -VLETAAPGV ->M_2310 -ESHEKGCFW ->M_2311 -MADAKGYTV ->M_2312 -KQLPRILEA ->M_2313 -HTCQVNGRW ->M_2314 -PLLPSIISL ->M_2315 -AIWEAVMSA ->M_2316 -AVMSALPSL ->M_2317 -MSALPSLNW ->M_2318 -GLDGPLVHV ->M_2319 -SIRVSQKGW ->M_2320 -PTDPGHFLV ->M_2321 -MRGEHRFHM ->M_2322 -KLSHCLSKA ->M_2323 -CRPQCCQSV ->M_2324 -VRNPEPSPL ->M_2325 -VLVVSPWPA ->M_2326 -GMLWAMMSI ->M_2327 -YMGMLWAMM ->M_2328 -SRAVTSTTI ->M_2329 -KTASWAEVV ->M_2330 -WTFALTSGL ->M_2331 -TDFNNGSYL ->M_2332 -VTDFNNGSY ->M_2333 -LLDTIPWYL ->M_2334 -ASSDHTTHL ->M_2335 -SHSSCVWLW ->M_2336 -TGSHSSCVW ->M_2337 -SIGELLQVL ->M_2338 -TGFVRRPLW ->M_2339 -DAEPFQRGW ->M_2340 -FIFSDTVVL ->M_2341 -FIFSDTVVL ->M_2342 -FSDTVVLLF ->M_2343 -MHFIFSDTV ->M_2344 -TVVLLFDFW ->M_2345 -YHPGAMHCV ->M_2346 -CAFSGTLPW ->M_2347 -FMCAFSGTL ->M_2348 -STHPSLSQW ->M_2349 -SRKDRAPKC ->M_2350 -LMGLASTTV ->M_2351 -SLLAIHQWV ->M_2352 -SSLLAIHQW diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_124242_3_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_124242_3_T_iedb.xml deleted file mode 100755 index 1e232a20..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_124242_3_T_iedb.xml +++ /dev/null @@ -1,1631 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_2307 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_2307 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_2308 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_2309 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_2310 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_2311 - 9 - - - 1 - gnl|BL_ORD_ID|50 - 3094|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 - 50 - 9 - - - 1 - 14.2382 - 25 - 3.37936 - 1 - 7 - 2 - 8 - 0 - 0 - 5 - 5 - 0 - 7 - MADAKGY - MGDAGGY - M DA GY - - - - - 2 - gnl|BL_ORD_ID|1639 - 146285|polyprotein|ADF97231.1|Hepatitis C virus subtype 3a|356426 - 1639 - 18 - - - 1 - 12.6974 - 21 - 28.603 - 4 - 9 - 12 - 17 - 0 - 0 - 4 - 5 - 0 - 6 - AKGYTV - AQGYNV - A+GY V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 6 - Query_6 - M_2312 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_2313 - 9 - - - 1 - gnl|BL_ORD_ID|1179 - 79628|E1 protein|BAA19893.1|Rubella virus|11041 - 1179 - 21 - - - 1 - 11.927 - 19 - 77.0667 - 2 - 9 - 5 - 12 - 0 - 0 - 3 - 5 - 0 - 8 - TCQVNGRW - SCEGLGAW - +C+ G W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 8 - Query_8 - M_2314 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_2315 - 9 - - - 1 - gnl|BL_ORD_ID|628 - 37590|VP1|BAF93325.1|Human polyomavirus 1|1891762 - 628 - 9 - - - 1 - 13.0826 - 22 - 21.8994 - 2 - 6 - 3 - 7 - 0 - 0 - 4 - 5 - 0 - 5 - IWEAV - MWEAV - +WEAV - - - - - 2 - gnl|BL_ORD_ID|446 - 27217|VP1|AAL37677.1|JC polyomavirus|10632 - 446 - 9 - - - 1 - 13.0826 - 22 - 22.6682 - 2 - 6 - 3 - 7 - 0 - 0 - 4 - 5 - 0 - 5 - IWEAV - MWEAV - +WEAV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 10 - Query_10 - M_2316 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_2317 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_2318 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_2319 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_2320 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_2321 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_2322 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_2323 - 9 - - - 1 - gnl|BL_ORD_ID|156 - 11956|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 - 156 - 11 - - - 1 - 12.3122 - 20 - 38.8163 - 1 - 9 - 3 - 11 - 0 - 0 - 4 - 5 - 0 - 9 - CRPQCCQSV - CRVLCCYVL - CR CC + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 18 - Query_18 - M_2324 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_2325 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_2326 - 9 - - - 1 - gnl|BL_ORD_ID|1203 - 95940|polyprotein|BAA32666.1|Hepatitis C virus genotype 6|42182 - 1203 - 9 - - - 1 - 12.3122 - 20 - 43.3628 - 1 - 6 - 4 - 9 - 0 - 0 - 3 - 5 - 0 - 6 - GMLWAM - GVLWTV - G+LW + - - - - - 2 - gnl|BL_ORD_ID|1201 - 95908|Genome polyprotein|O92529.3|Hepatitis C virus genotype 6|42182 - 1201 - 9 - - - 1 - 12.3122 - 20 - 44.8495 - 1 - 6 - 4 - 9 - 0 - 0 - 3 - 5 - 0 - 6 - GMLWAM - GVLWTV - G+LW + - - - - - 3 - gnl|BL_ORD_ID|1191 - 95264|Genome polyprotein|O92532.3|Hepatitis C virus genotype 6|42182 - 1191 - 9 - - - 1 - 12.3122 - 20 - 53.0441 - 1 - 6 - 4 - 9 - 0 - 0 - 3 - 5 - 0 - 6 - GMLWAM - GVLWTV - G+LW + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 21 - Query_21 - M_2327 - 9 - - - 1 - gnl|BL_ORD_ID|1201 - 95908|Genome polyprotein|O92529.3|Hepatitis C virus genotype 6|42182 - 1201 - 9 - - - 1 - 12.6974 - 21 - 39.1808 - 3 - 8 - 4 - 9 - 0 - 0 - 3 - 5 - 0 - 6 - GMLWAM - GVLWTV - G+LW + - - - - - 2 - gnl|BL_ORD_ID|1203 - 95940|polyprotein|BAA32666.1|Hepatitis C virus genotype 6|42182 - 1203 - 9 - - - 1 - 12.6974 - 21 - 39.8499 - 3 - 8 - 4 - 9 - 0 - 0 - 3 - 5 - 0 - 6 - GMLWAM - GVLWTV - G+LW + - - - - - 3 - gnl|BL_ORD_ID|223 - 16623|gag protein|AAV53308.1|Human immunodeficiency virus 1|11676 - 223 - 10 - - - 1 - 12.3122 - 20 - 44.794 - 1 - 7 - 1 - 7 - 0 - 0 - 2 - 5 - 0 - 7 - YMGMLWA - FLGKIWP - ++G +W - - - - - 4 - gnl|BL_ORD_ID|1191 - 95264|Genome polyprotein|O92532.3|Hepatitis C virus genotype 6|42182 - 1191 - 9 - - - 1 - 12.3122 - 20 - 47.1713 - 3 - 8 - 4 - 9 - 0 - 0 - 3 - 5 - 0 - 6 - GMLWAM - GVLWTV - G+LW + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 22 - Query_22 - M_2328 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_2329 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_2330 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_2331 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_2332 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_2333 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 28 - Query_28 - M_2334 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 29 - Query_29 - M_2335 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 30 - Query_30 - M_2336 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 31 - Query_31 - M_2337 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 32 - Query_32 - M_2338 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 33 - Query_33 - M_2339 - 9 - - - 1 - gnl|BL_ORD_ID|381 - 23566|tegument protein UL7|NP_044476.1|Human alphaherpesvirus 2|10310 - 381 - 13 - - - 1 - 13.853 - 24 - 5.01075 - 1 - 7 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - DAEPFQR - HASPFER - A PF+R - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 34 - Query_34 - M_2340 - 9 - - - 1 - gnl|BL_ORD_ID|760 - 50779|N protein|AAP13445.1|SARS coronavirus Urbani|228330 - 760 - 9 - - - 1 - 13.0826 - 22 - 15.4875 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - FSDTVVL - FKDNVIL - F D V+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 35 - Query_35 - M_2341 - 9 - - - 1 - gnl|BL_ORD_ID|760 - 50779|N protein|AAP13445.1|SARS coronavirus Urbani|228330 - 760 - 9 - - - 1 - 13.0826 - 22 - 15.4875 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - FSDTVVL - FKDNVIL - F D V+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 36 - Query_36 - M_2342 - 9 - - - 1 - gnl|BL_ORD_ID|760 - 50779|N protein|AAP13445.1|SARS coronavirus Urbani|228330 - 760 - 9 - - - 1 - 14.6234 - 26 - 2.01137 - 1 - 8 - 2 - 9 - 0 - 0 - 5 - 6 - 0 - 8 - FSDTVVLL - FKDNVILL - F D V+LL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 37 - Query_37 - M_2343 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 38 - Query_38 - M_2344 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 39 - Query_39 - M_2345 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 40 - Query_40 - M_2346 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 41 - Query_41 - M_2347 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 42 - Query_42 - M_2348 - 9 - - - 1 - gnl|BL_ORD_ID|1028 - 68601|polyprotein|AAA45534.1|Hepatitis C virus|11103 - 1028 - 15 - - - 1 - 14.6234 - 26 - 2.00652 - 1 - 9 - 6 - 14 - 0 - 0 - 4 - 5 - 0 - 9 - STHPSLSQW - NTRPPLGNW - +T P L W - - - - - 2 - gnl|BL_ORD_ID|729 - 46243|E2 protein|NP_751921.1|Hepatitis C virus (isolate H77)|63746 - 729 - 10 - - - 1 - 14.2382 - 25 - 2.80664 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 5 - 0 - 9 - STHPSLSQW - NTRPPLGNW - +T P L W - - - - - 3 - gnl|BL_ORD_ID|1600 - 142246|polyprotein|BAB18810.1|Hepatitis C virus subtype 1a|31646 - 1600 - 9 - - - 1 - 14.2382 - 25 - 3.10506 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 5 - 0 - 9 - STHPSLSQW - NTRPPLGNW - +T P L W - - - - - 4 - gnl|BL_ORD_ID|1601 - 142247|envelope protein 2|ACY64760.1|Hepatitis C virus subtype 1a|31646 - 1601 - 9 - - - 1 - 13.4678 - 23 - 7.72035 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 5 - 0 - 9 - STHPSLSQW - NTRPPMGNW - +T P + W - - - - - 5 - gnl|BL_ORD_ID|1599 - 142245|polyprotein|ACJ37204.1|Hepatitis C virus subtype 1a|31646 - 1599 - 9 - - - 1 - 12.3122 - 20 - 56.7066 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 4 - 0 - 9 - STHPSLSQW - NTRPPAGNW - +T P W - - - - - 6 - gnl|BL_ORD_ID|1603 - 142249|polyprotein|AAY82036.1|Hepatitis C virus subtype 1a|31646 - 1603 - 9 - - - 1 - 12.3122 - 20 - 60.6092 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 4 - 0 - 9 - STHPSLSQW - NTRPPRGNW - +T P W - - - - - 7 - gnl|BL_ORD_ID|1602 - 142248|polyprotein|BAB18806.1|Hepatitis C virus subtype 1a|31646 - 1602 - 9 - - - 1 - 11.927 - 19 - 110.987 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 4 - 0 - 9 - STHPSLSQW - NTRPPQGNW - +T P W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 43 - Query_43 - M_2349 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 44 - Query_44 - M_2350 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 45 - Query_45 - M_2351 - 9 - - - 1 - gnl|BL_ORD_ID|1607 - 143690|Genome polyprotein|P06441.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 1607 - 9 - - - 1 - 13.4678 - 23 - 13.0154 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - LAIHQWV - LAVDPWV - LA+ WV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 46 - Query_46 - M_2352 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_124756_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_124756_1_T.fasta deleted file mode 100755 index 90bf1be6..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_124756_1_T.fasta +++ /dev/null @@ -1,174 +0,0 @@ ->M_2353 -AIHIVAEKK ->M_2354 -ESLPPSPTW ->M_2355 -WAGNVLAPY ->M_2356 -QIIAGHFRK ->M_2357 -STSSRSHRY ->M_2358 -FHQCLSIYY ->M_2359 -IYYWDIRYK ->M_2360 -LFHQCLSIY ->M_2361 -SIYYWDIRY ->M_2362 -SIYYWDIRY ->M_2363 -SRHTIRELL ->M_2364 -QINIPIGPY ->M_2365 -GGMQALGLY ->M_2366 -FLNLSQPRK ->M_2367 -RLNSHFLNL ->M_2368 -ERSLQVKRV ->M_2369 -LQVKRVFVK ->M_2370 -RSLQVKRVF ->M_2371 -RVFVKGMKK ->M_2372 -CSSSIGTIW ->M_2373 -WSHASASLY ->M_2374 -WSHASASLY ->M_2375 -KESNAGRYY ->M_2376 -VKESNAGRY ->M_2377 -IVSVKPNMK ->M_2378 -FSYPKRPII ->M_2379 -MSHPPNILK ->M_2380 -GARPGLGRY ->M_2381 -ITSRDATRF ->M_2382 -TRFPIIASC ->M_2383 -RLLSSGTAK ->M_2384 -KVLELADRF ->M_2385 -RVSTGSVHK ->M_2386 -VVGAVGVGK ->M_2387 -LSFRSSSCR ->M_2388 -EMFEHLFGK ->M_2389 -TRAHCHLPV ->M_2390 -ILDYMQLRK ->M_2391 -KILDYMQLR ->M_2392 -TTMLDRGPK ->M_2393 -IHITEEEAV ->M_2394 -LVSMTYDRY ->M_2395 -MTYDRYVAI ->M_2396 -MVLLVSMTY ->M_2397 -MVLLVSMTY ->M_2398 -MVLLVSMTY ->M_2399 -VSMTYDRYV ->M_2400 -IHMDARLHT ->M_2401 -MGMALLIHM ->M_2402 -FKSKVPQTW ->M_2403 -VGQQQQVLW ->M_2404 -DSSSWSDRY ->M_2405 -SGGHDSSSW ->M_2406 -YEEYRGHSL ->M_2407 -HTSTVRESY ->M_2408 -HTSTVRESY ->M_2409 -SHYGQPDRQ ->M_2410 -DHEVYLKHL ->M_2411 -GGLFIASNW ->M_2412 -KVTRLHRRK ->M_2413 -LMSTSEEEF ->M_2414 -LSNNCVPQM ->M_2415 -STRDEIEGL ->M_2416 -RMCTVTNYF ->M_2417 -VMVSLKPDK ->M_2418 -CRQEQERKF ->M_2419 -EQEERREQL ->M_2420 -FRLEEQKVC ->M_2421 -QSLCGTRFY ->M_2422 -TAAAAPTPF ->M_2423 -DRNTFRHSL ->M_2424 -NTFRHSLVV ->M_2425 -RMNSFLHIL ->M_2426 -RMNSFLHIL ->M_2427 -SRMNSFLHI ->M_2428 -GSFPTEYIL ->M_2429 -VTNCHKNYW ->M_2430 -VVTNCHKNY ->M_2431 -DMAPTRPRW ->M_2432 -FRRPQESLL ->M_2433 -GINNKVCFW ->M_2434 -LLTDTNSWW ->M_2435 -QLLTDTNSW ->M_2436 -HQRVHSGEK ->M_2437 -QRYSHQRVH ->M_2438 -VKSKLIAHY ->M_2439 -SVDECELHK diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_124756_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_124756_1_T_iedb.xml deleted file mode 100755 index 2842ee1f..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_124756_1_T_iedb.xml +++ /dev/null @@ -1,2615 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_2353 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_2353 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_2354 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_2355 - 9 - - - 1 - gnl|BL_ORD_ID|577 - 36352|Polyprotein|P90247|Hepatitis C virus|11103 - 577 - 20 - - - 1 - 14.2382 - 25 - 2.6 - 1 - 8 - 3 - 10 - 0 - 0 - 5 - 7 - 0 - 8 - WAGNVLAP - WAGWLLSP - WAG +L+P - - - - - 2 - gnl|BL_ORD_ID|1144 - 75438|polyprotein|AAF65962.1|Hepatitis C virus|11103 - 1144 - 20 - - - 1 - 14.2382 - 25 - 2.64513 - 1 - 8 - 13 - 20 - 0 - 0 - 5 - 7 - 0 - 8 - WAGNVLAP - WAGWLLSP - WAG +L+P - - - - - 3 - gnl|BL_ORD_ID|1143 - 75436|Polyprotein|P90247|Hepatitis C virus|11103 - 1143 - 20 - - - 1 - 14.2382 - 25 - 2.69103 - 1 - 8 - 13 - 20 - 0 - 0 - 5 - 7 - 0 - 8 - WAGNVLAP - WAGWLLSP - WAG +L+P - - - - - 4 - gnl|BL_ORD_ID|2293 - 419410|polyprotein|ABR25251.1|Hepatitis C virus|11103 - 2293 - 9 - - - 1 - 13.4678 - 23 - 11.1275 - 1 - 6 - 1 - 6 - 0 - 0 - 3 - 5 - 0 - 6 - WAGNVL - WLGNII - W GN++ - - - - - 5 - gnl|BL_ORD_ID|1102 - 72722|polyprotein|AAF01178.1|Hepatitis C virus subtype 2a|31649 - 1102 - 9 - - - 1 - 13.4678 - 23 - 11.5219 - 1 - 6 - 1 - 6 - 0 - 0 - 3 - 5 - 0 - 6 - WAGNVL - WLGNII - W GN++ - - - - - 6 - gnl|BL_ORD_ID|1142 - 75435|largest ORF|AAB02128.1|Hepatitis C virus|11103 - 1142 - 20 - - - 1 - 12.6974 - 21 - 22.9279 - 1 - 8 - 13 - 20 - 0 - 0 - 4 - 6 - 0 - 8 - WAGNVLAP - WMGWLLSP - W G +L+P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 4 - Query_4 - M_2356 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_2357 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_2358 - 9 - - - 1 - gnl|BL_ORD_ID|1186 - 93431|pre-C/C protein|ABY54138.1|Hepatitis B virus|10407 - 1186 - 20 - - - 1 - 13.4678 - 23 - 12.4431 - 1 - 7 - 4 - 10 - 0 - 0 - 5 - 5 - 0 - 7 - FHQCLSI - FHLCLII - FH CL I - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 7 - Query_7 - M_2359 - 9 - - - 1 - gnl|BL_ORD_ID|1996 - 183619|nonstructural protein NS1|1802191G|Dengue virus|12637 - 1996 - 9 - - - 1 - 11.1566 - 17 - 266.5 - 2 - 9 - 1 - 8 - 0 - 0 - 3 - 5 - 0 - 8 - YYWDIRYK - HTWTEQYK - + W +YK - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 8 - Query_8 - M_2360 - 9 - - - 1 - gnl|BL_ORD_ID|1186 - 93431|pre-C/C protein|ABY54138.1|Hepatitis B virus|10407 - 1186 - 20 - - - 1 - 14.6234 - 26 - 2.38548 - 1 - 8 - 3 - 10 - 0 - 0 - 6 - 6 - 0 - 8 - LFHQCLSI - LFHLCLII - LFH CL I - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 9 - Query_9 - M_2361 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_2362 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_2363 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_2364 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_2365 - 9 - - - 1 - gnl|BL_ORD_ID|938 - 61861|Nucleoprotein|P03418.1|Human respiratory syncytial virus A2|11259 - 938 - 14 - - - 1 - 11.5418 - 18 - 140.41 - 1 - 9 - 4 - 12 - 0 - 0 - 3 - 6 - 0 - 9 - GGMQALGLY - GGSRVEGIF - GG + G++ - - - - - 2 - gnl|BL_ORD_ID|1950 - 181035|||| - 1950 - 44 - - - 1 - 9.61583 - 13 - 724.877 - 1 - 9 - 16 - 24 - 0 - 0 - 4 - 5 - 0 - 9 - GGMQALGLY - GGQICGGVY - GG G+Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 14 - Query_14 - M_2366 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_2367 - 9 - - - 1 - gnl|BL_ORD_ID|1437 - 119822|110 kd polyprotein precursor|CAA28880.1|Rubella virus|11041 - 1437 - 29 - - - 1 - 16.9346 - 32 - 0.172633 - 1 - 9 - 19 - 27 - 0 - 0 - 5 - 8 - 0 - 9 - RLNSHFLNL - RVDLHFINL - R++ HF+NL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 16 - Query_16 - M_2368 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_2369 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_2370 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_2371 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_2372 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_2373 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 22 - Query_22 - M_2374 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_2375 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_2376 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_2377 - 9 - - - 1 - gnl|BL_ORD_ID|287 - 19359|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 - 287 - 20 - - - 1 - 13.4678 - 23 - 9.25482 - 2 - 7 - 11 - 16 - 0 - 0 - 4 - 5 - 0 - 6 - VSVKPN - VSIAPN - VS+ PN - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 26 - Query_26 - M_2378 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_2379 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 28 - Query_28 - M_2380 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 29 - Query_29 - M_2381 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 30 - Query_30 - M_2382 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 31 - Query_31 - M_2383 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 32 - Query_32 - M_2384 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 33 - Query_33 - M_2385 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 34 - Query_34 - M_2386 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 35 - Query_35 - M_2387 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 36 - Query_36 - M_2388 - 9 - - - 1 - gnl|BL_ORD_ID|133 - 9415|Superoxide dismutase|P17670.1|Mycobacterium tuberculosis|1773 - 133 - 10 - - - 1 - 13.853 - 24 - 5.02829 - 1 - 7 - 1 - 7 - 0 - 0 - 4 - 6 - 0 - 7 - EMFEHLF - DMWEHAF - +M+EH F - - - - - 2 - gnl|BL_ORD_ID|132 - 9414|Superoxide dismutase|P17670.1|Mycobacterium tuberculosis|1773 - 132 - 9 - - - 1 - 13.853 - 24 - 5.65074 - 1 - 7 - 1 - 7 - 0 - 0 - 4 - 6 - 0 - 7 - EMFEHLF - DMWEHAF - +M+EH F - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 37 - Query_37 - M_2389 - 9 - - - 1 - gnl|BL_ORD_ID|1141 - 75408|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 1141 - 20 - - - 1 - 15.779 - 29 - 0.419784 - 2 - 9 - 7 - 14 - 0 - 0 - 6 - 6 - 0 - 8 - RAHCHLPV - RKHRHLPV - R H HLPV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 38 - Query_38 - M_2390 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 39 - Query_39 - M_2391 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 40 - Query_40 - M_2392 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 41 - Query_41 - M_2393 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 42 - Query_42 - M_2394 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 43 - Query_43 - M_2395 - 9 - - - 1 - gnl|BL_ORD_ID|664 - 39591|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 - 664 - 20 - - - 1 - 12.6974 - 21 - 32.8758 - 3 - 8 - 5 - 10 - 0 - 0 - 3 - 5 - 0 - 6 - YDRYVA - YKRYIS - Y RY++ - - - - - 2 - gnl|BL_ORD_ID|663 - 39590|polyprotein|AAY82030.1|Hepatitis C virus|11103 - 663 - 11 - - - 1 - 12.3122 - 20 - 45.0816 - 3 - 8 - 5 - 10 - 0 - 0 - 3 - 5 - 0 - 6 - YDRYVA - YKRYIS - Y RY++ - - - - - 3 - gnl|BL_ORD_ID|662 - 39589|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 662 - 10 - - - 1 - 12.3122 - 20 - 45.5485 - 3 - 8 - 5 - 10 - 0 - 0 - 3 - 5 - 0 - 6 - YDRYVA - YKRYIS - Y RY++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 44 - Query_44 - M_2396 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 45 - Query_45 - M_2397 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 46 - Query_46 - M_2398 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 47 - Query_47 - M_2399 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 48 - Query_48 - M_2400 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 49 - Query_49 - M_2401 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 50 - Query_50 - M_2402 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 51 - Query_51 - M_2403 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 52 - Query_52 - M_2404 - 9 - - - 1 - gnl|BL_ORD_ID|552 - 33912|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 - 552 - 10 - - - 1 - 13.4678 - 23 - 8.03745 - 4 - 9 - 2 - 7 - 0 - 0 - 3 - 5 - 0 - 6 - SWSDRY - TWADEY - +W+D Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 53 - Query_53 - M_2405 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 54 - Query_54 - M_2406 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 55 - Query_55 - M_2407 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 56 - Query_56 - M_2408 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 57 - Query_57 - M_2409 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 58 - Query_58 - M_2410 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 59 - Query_59 - M_2411 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 60 - Query_60 - M_2412 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 61 - Query_61 - M_2413 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 62 - Query_62 - M_2414 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 63 - Query_63 - M_2415 - 9 - - - 1 - gnl|BL_ORD_ID|1398 - 110431|E7|AAD33253.1|Human papillomavirus type 16|333760 - 1398 - 36 - - - 1 - 12.6974 - 21 - 32.5473 - 3 - 8 - 16 - 21 - 0 - 0 - 4 - 5 - 0 - 6 - RDEIEG - EDEIDG - DEI+G - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 64 - Query_64 - M_2416 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 65 - Query_65 - M_2417 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 66 - Query_66 - M_2418 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 67 - Query_67 - M_2419 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 68 - Query_68 - M_2420 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 69 - Query_69 - M_2421 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 70 - Query_70 - M_2422 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 71 - Query_71 - M_2423 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 72 - Query_72 - M_2424 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 73 - Query_73 - M_2425 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 74 - Query_74 - M_2426 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 75 - Query_75 - M_2427 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 76 - Query_76 - M_2428 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 77 - Query_77 - M_2429 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 78 - Query_78 - M_2430 - 9 - - - 1 - gnl|BL_ORD_ID|1382 - 110184|E7|AAD33253.1|Human papillomavirus type 16|333760 - 1382 - 35 - - - 1 - 11.1566 - 17 - 179.88 - 1 - 7 - 13 - 19 - 0 - 0 - 4 - 5 - 0 - 7 - VVTNCHK - IVTFCCK - +VT C K - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 79 - Query_79 - M_2431 - 9 - - - 1 - gnl|BL_ORD_ID|2300 - 422989|polyprotein|ABY67644.1|Hepatitis C virus genotype 1|41856 - 2300 - 10 - - - 1 - 12.6974 - 21 - 26.9859 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 4 - 0 - 8 - MAPTRPRW - FAPALPIW - AP P W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 80 - Query_80 - M_2432 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 81 - Query_81 - M_2433 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 82 - Query_82 - M_2434 - 9 - - - 1 - gnl|BL_ORD_ID|1054 - 69750|polyprotein|AAC03058.1|Hepatitis C virus genotype 3|356114 - 1054 - 9 - - - 1 - 13.0826 - 22 - 19.7427 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 6 - 0 - 8 - LLTDTNSW - VLSDFKSW - +L+D SW - - - - - 2 - gnl|BL_ORD_ID|1058 - 69797|polyprotein|BAA09073.1|Hepatitis C virus subtype 1b|31647 - 1058 - 9 - - - 1 - 12.6974 - 21 - 24.707 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 6 - 0 - 8 - LLTDTNSW - VLTDFKTW - +LTD +W - - - - - 3 - gnl|BL_ORD_ID|1055 - 69751|polyprotein|BAB18806.1|Hepatitis C virus genotype 1|41856 - 1055 - 9 - - - 1 - 11.927 - 19 - 114.611 - 1 - 8 - 1 - 8 - 0 - 0 - 3 - 6 - 0 - 8 - LLTDTNSW - VLSDFKTW - +L+D +W - - - - - 4 - gnl|BL_ORD_ID|1056 - 69753|polyprotein|AAK49500.1|Hepatitis C virus genotype 3|356114 - 1056 - 9 - - - 1 - 11.5418 - 18 - 120.255 - 1 - 8 - 1 - 8 - 0 - 0 - 3 - 6 - 0 - 8 - LLTDTNSW - VLSDFRTW - +L+D +W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 83 - Query_83 - M_2435 - 9 - - - 1 - gnl|BL_ORD_ID|1054 - 69750|polyprotein|AAC03058.1|Hepatitis C virus genotype 3|356114 - 1054 - 9 - - - 1 - 13.4678 - 23 - 10.561 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 6 - 0 - 8 - LLTDTNSW - VLSDFKSW - +L+D SW - - - - - 2 - gnl|BL_ORD_ID|1058 - 69797|polyprotein|BAA09073.1|Hepatitis C virus subtype 1b|31647 - 1058 - 9 - - - 1 - 13.4678 - 23 - 13.2439 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 6 - 0 - 8 - LLTDTNSW - VLTDFKTW - +LTD +W - - - - - 3 - gnl|BL_ORD_ID|1055 - 69751|polyprotein|BAB18806.1|Hepatitis C virus genotype 1|41856 - 1055 - 9 - - - 1 - 12.3122 - 20 - 61.624 - 2 - 9 - 1 - 8 - 0 - 0 - 3 - 6 - 0 - 8 - LLTDTNSW - VLSDFKTW - +L+D +W - - - - - 4 - gnl|BL_ORD_ID|1056 - 69753|polyprotein|AAK49500.1|Hepatitis C virus genotype 3|356114 - 1056 - 9 - - - 1 - 12.3122 - 20 - 66.9453 - 2 - 9 - 1 - 8 - 0 - 0 - 3 - 6 - 0 - 8 - LLTDTNSW - VLSDFRTW - +L+D +W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 84 - Query_84 - M_2436 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 85 - Query_85 - M_2437 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 86 - Query_86 - M_2438 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 87 - Query_87 - M_2439 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_125196_3_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_125196_3_T.fasta deleted file mode 100755 index 67783270..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_125196_3_T.fasta +++ /dev/null @@ -1,126 +0,0 @@ ->M_2440 -PMPPPLEPI ->M_2441 -KEIDVIAIP ->M_2442 -YKDYAAELV ->M_2443 -DNLDSDNTY ->M_2444 -LAVTLGLAL ->M_2445 -HNNNRPLTM ->M_2446 -WAVPPLLLA ->M_2447 -RCYVRGLFH ->M_2448 -KITAQRLSH ->M_2449 -SSLHSEPPK ->M_2450 -QAQALGIPL ->M_2451 -QAQALGIPL ->M_2452 -IPKSPEEAI ->M_2453 -PEEPTSPAA ->M_2454 -RVQSRPIPI ->M_2455 -HSLQQAQSV ->M_2456 -PLFTTQCGK ->M_2457 -HMEAEMAQK ->M_2458 -VQLPKVSEM ->M_2459 -ITAQRLSHL ->M_2460 -LLLSPPVEV ->M_2461 -IPILPLIYI ->M_2462 -AEAQTPEDS ->M_2463 -LLSPPVEVK ->M_2464 -TEHDVQIYV ->M_2465 -FISLKFSSK ->M_2466 -IPGPIPGPI ->M_2467 -KTRRTSSLH ->M_2468 -EEPTSPAAA ->M_2469 -WILSARLLK ->M_2470 -QQFPSLELL ->M_2471 -RPIPILPLI ->M_2472 -NMKEQVVIL ->M_2473 -AQRLSHLNK ->M_2474 -RAYRDDTDL ->M_2475 -NVFWGEHFK ->M_2476 -YYKDYAAEL ->M_2477 -QQFPSLELL ->M_2478 -SLKFSSKIK ->M_2479 -FLFGLAQNL ->M_2480 -YVRGLFHSL ->M_2481 -TENSETTTA ->M_2482 -ALGIPLTPK ->M_2483 -NENTTPSPA ->M_2484 -RLPEVQLPK ->M_2485 -ISLKFSSKI ->M_2486 -KEGARNVLA ->M_2487 -MPNDFWARL ->M_2488 -FTEHDVQIY ->M_2489 -FKFHNLPPL ->M_2490 -NTYRTPSVL ->M_2491 -IAIPSKCLL ->M_2492 -EASSAVPTV ->M_2493 -MAAAVVARL ->M_2494 -QEFENIKSY ->M_2495 -FQKDPPADI ->M_2496 -DMYDGRFLV ->M_2497 -PLYKVRFSK ->M_2498 -VTRPFISLK ->M_2499 -IILFNRLLK ->M_2500 -IPYRDSVLI ->M_2501 -AEASSAVPT ->M_2502 -EEMPNDFWA diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_125196_3_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_125196_3_T_iedb.xml deleted file mode 100755 index 0ae81462..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_125196_3_T_iedb.xml +++ /dev/null @@ -1,2325 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_2440 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_2440 - 9 - - - 1 - gnl|BL_ORD_ID|448 - 27241|Spike glycoprotein precursor|P59594.1|SARS coronavirus|227859 - 448 - 9 - - - 1 - 11.927 - 19 - 77.6399 - 2 - 8 - 2 - 8 - 0 - 0 - 4 - 6 - 0 - 7 - MPPPLEP - LPDPLKP - +P PL+P - - - - - 2 - gnl|BL_ORD_ID|1581 - 141462|tegument protein UL21|NP_044622.1|Human alphaherpesvirus 1|10298 - 1581 - 9 - - - 1 - 10.3862 - 15 - 702.182 - 2 - 9 - 1 - 8 - 0 - 0 - 3 - 6 - 0 - 8 - MPPPLEPI - VPRPDDPV - +P P +P+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 2 - Query_2 - M_2441 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_2442 - 9 - - - 1 - gnl|BL_ORD_ID|1970 - 182917|polyprotein|CDF77361.1|Dengue virus 3|11069 - 1970 - 9 - - - 1 - 14.2382 - 25 - 4.1461 - 1 - 6 - 2 - 7 - 0 - 0 - 4 - 6 - 0 - 6 - YKDYAA - FKDFAA - +KD+AA - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 4 - Query_4 - M_2443 - 9 - - - 1 - gnl|BL_ORD_ID|1097 - 72563|polyprotein|AAB70696.1|Dengue virus type 1 Hawaii|10000440 - 1097 - 20 - - - 1 - 12.6974 - 21 - 29.0269 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - NLDSDNTY - HYDEDNPY - + D DN Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 5 - Query_5 - M_2444 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_2445 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_2446 - 9 - - - 1 - gnl|BL_ORD_ID|1110 - 73059|kaposin|AAC57155.1|Human gammaherpesvirus 8|37296 - 1110 - 15 - - - 1 - 13.0826 - 22 - 17.5339 - 2 - 7 - 7 - 12 - 0 - 0 - 4 - 6 - 0 - 6 - AVPPLL - AIPPLV - A+PPL+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 8 - Query_8 - M_2447 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_2448 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_2449 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_2450 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_2451 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_2452 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_2453 - 9 - - - 1 - gnl|BL_ORD_ID|1179 - 79628|E1 protein|BAA19893.1|Rubella virus|11041 - 1179 - 21 - - - 1 - 12.3122 - 20 - 39.4328 - 4 - 9 - 14 - 19 - 0 - 0 - 4 - 5 - 0 - 6 - PTSPAA - PTAPCA - PT+P A - - - - - 2 - gnl|BL_ORD_ID|1573 - 141402|tegument protein VP22|NP_044651.1|Human alphaherpesvirus 1|10298 - 1573 - 10 - - - 1 - 11.927 - 19 - 68.8532 - 2 - 8 - 4 - 10 - 0 - 0 - 4 - 5 - 0 - 7 - EEPTSPA - ERPRAPA - E P +PA - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 15 - Query_15 - M_2454 - 9 - - - 1 - gnl|BL_ORD_ID|876 - 57591|Cobalamin (vitamin B12) synthesis protein/P47K family protein|YP_169986.1|Francisella tularensis subsp. tularensis SCHU S4|177416 - 876 - 10 - - - 1 - 12.6974 - 21 - 25.2038 - 4 - 9 - 1 - 6 - 0 - 0 - 3 - 5 - 0 - 6 - SRPIPI - SEPLPV - S P+P+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 16 - Query_16 - M_2455 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_2456 - 9 - - - 1 - gnl|BL_ORD_ID|1152 - 75718|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 1152 - 11 - - - 1 - 13.0826 - 22 - 16.3278 - 1 - 6 - 5 - 10 - 0 - 0 - 4 - 5 - 0 - 6 - PLFTTQ - PTFTSQ - P FT+Q - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 18 - Query_18 - M_2457 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_2458 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_2459 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_2460 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 22 - Query_22 - M_2461 - 9 - - - 1 - gnl|BL_ORD_ID|452 - 27345|Large envelope protein|P03138.3|Hepatitis B virus subtype ayw|10418 - 452 - 9 - - - 1 - 11.927 - 19 - 82.8955 - 2 - 7 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - PILPLI - PFLPLL - P LPL+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 23 - Query_23 - M_2462 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_2463 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_2464 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_2465 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_2466 - 9 - - - 1 - gnl|BL_ORD_ID|741 - 47760|EBNA-1 protein|Q777E1|Human gammaherpesvirus 4|10376 - 741 - 15 - - - 1 - 10.3862 - 15 - 419.458 - 2 - 7 - 1 - 6 - 0 - 0 - 4 - 4 - 0 - 6 - PGPIPG - PGTGPG - PG PG - - - - - 2 - gnl|BL_ORD_ID|75 - 5542|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 75 - 15 - - - 1 - 10.001 - 14 - 709.084 - 2 - 9 - 8 - 15 - 0 - 0 - 4 - 4 - 0 - 8 - PGPIPGPI - PGTSGSPI - PG PI - - - - - 3 - gnl|BL_ORD_ID|1929 - 180750|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1929 - 15 - - - 1 - 10.001 - 14 - 819.307 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 4 - 0 - 8 - PGPIPGPI - PGTSGSPI - PG PI - - - - - 4 - gnl|BL_ORD_ID|260 - 17802|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 260 - 15 - - - 1 - 10.001 - 14 - 830.077 - 2 - 9 - 3 - 10 - 0 - 0 - 4 - 4 - 0 - 8 - PGPIPGPI - PGTSGSPI - PG PI - - - - - 5 - gnl|BL_ORD_ID|1712 - 150341|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1712 - 9 - - - 1 - 9.61583 - 13 - 1362.74 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 4 - 0 - 8 - PGPIPGPI - PGTSGSPI - PG PI - - - - - 6 - gnl|BL_ORD_ID|1766 - 154857|tegument protein|CAB06735.1|Human alphaherpesvirus 2|10310 - 1766 - 16 - - - 1 - 4.99343 - 1 - 89081.4 - 7 - 9 - 14 - 16 - 0 - 0 - 2 - 3 - 0 - 3 - GPI - GPV - GP+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 28 - Query_28 - M_2467 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 29 - Query_29 - M_2468 - 9 - - - 1 - gnl|BL_ORD_ID|1179 - 79628|E1 protein|BAA19893.1|Rubella virus|11041 - 1179 - 21 - - - 1 - 12.6974 - 21 - 30.3943 - 3 - 8 - 14 - 19 - 0 - 0 - 4 - 5 - 0 - 6 - PTSPAA - PTAPCA - PT+P A - - - - - 2 - gnl|BL_ORD_ID|1573 - 141402|tegument protein VP22|NP_044651.1|Human alphaherpesvirus 1|10298 - 1573 - 10 - - - 1 - 12.3122 - 20 - 62.4024 - 1 - 7 - 4 - 10 - 0 - 0 - 4 - 5 - 0 - 7 - EEPTSPA - ERPRAPA - E P +PA - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 30 - Query_30 - M_2469 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 31 - Query_31 - M_2470 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 32 - Query_32 - M_2471 - 9 - - - 1 - gnl|BL_ORD_ID|452 - 27345|Large envelope protein|P03138.3|Hepatitis B virus subtype ayw|10418 - 452 - 9 - - - 1 - 11.927 - 19 - 105.754 - 4 - 9 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - PILPLI - PFLPLL - P LPL+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 33 - Query_33 - M_2472 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 34 - Query_34 - M_2473 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 35 - Query_35 - M_2474 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 36 - Query_36 - M_2475 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 37 - Query_37 - M_2476 - 9 - - - 1 - gnl|BL_ORD_ID|1970 - 182917|polyprotein|CDF77361.1|Dengue virus 3|11069 - 1970 - 9 - - - 1 - 13.853 - 24 - 4.59527 - 2 - 7 - 2 - 7 - 0 - 0 - 4 - 6 - 0 - 6 - YKDYAA - FKDFAA - +KD+AA - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 38 - Query_38 - M_2477 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 39 - Query_39 - M_2478 - 9 - - - 1 - gnl|BL_ORD_ID|1387 - 110227|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1387 - 33 - - - 1 - 14.6234 - 26 - 2.38904 - 2 - 8 - 21 - 27 - 0 - 0 - 6 - 6 - 0 - 7 - LKFSSKI - LKFYSKI - LKF SKI - - - - - 2 - gnl|BL_ORD_ID|1400 - 110467|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1400 - 25 - - - 1 - 14.6234 - 26 - 2.651 - 1 - 8 - 13 - 20 - 0 - 0 - 6 - 6 - 0 - 8 - SLKFSSKI - CLKFYSKI - LKF SKI - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 40 - Query_40 - M_2479 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 41 - Query_41 - M_2480 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 42 - Query_42 - M_2481 - 9 - - - 1 - gnl|BL_ORD_ID|1689 - 149063|NS3 protease/helicase'|NP_803144.1|Hepatitis C virus (isolate H77)|63746 - 1689 - 18 - - - 1 - 12.6974 - 21 - 27.7051 - 1 - 7 - 8 - 14 - 0 - 0 - 5 - 5 - 0 - 7 - TENSETT - VENLETT - EN ETT - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 43 - Query_43 - M_2482 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 44 - Query_44 - M_2483 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 45 - Query_45 - M_2484 - 9 - - - 1 - gnl|BL_ORD_ID|241 - 16836|precore/core protein [Hepatitis B virus]|AAR03815.1|Hepatitis B virus|10407 - 241 - 10 - - - 1 - 10.3862 - 15 - 499.131 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 4 - 0 - 8 - LPEVQLPK - LPSDFLPS - LP LP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 46 - Query_46 - M_2485 - 9 - - - 1 - gnl|BL_ORD_ID|1387 - 110227|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1387 - 33 - - - 1 - 15.0086 - 27 - 1.24899 - 3 - 9 - 21 - 27 - 0 - 0 - 6 - 6 - 0 - 7 - LKFSSKI - LKFYSKI - LKF SKI - - - - - 2 - gnl|BL_ORD_ID|1400 - 110467|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1400 - 25 - - - 1 - 14.2382 - 25 - 2.9789 - 3 - 9 - 14 - 20 - 0 - 0 - 6 - 6 - 0 - 7 - LKFSSKI - LKFYSKI - LKF SKI - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 47 - Query_47 - M_2486 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 48 - Query_48 - M_2487 - 9 - - - 1 - gnl|BL_ORD_ID|235 - 16814|precore protein|CAM58990.1|Hepatitis B virus|10407 - 235 - 10 - - - 1 - 15.3938 - 28 - 0.822133 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 7 - 0 - 9 - MPNDFWARL - LPNDFFPSV - +PNDF+ + - - - - - 2 - gnl|BL_ORD_ID|234 - 16813|External core antigen|SRC279980|Hepatitis B virus|10407 - 234 - 10 - - - 1 - 15.0086 - 27 - 1.18631 - 1 - 6 - 2 - 7 - 0 - 0 - 4 - 6 - 0 - 6 - MPNDFW - LPNDFF - +PNDF+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 49 - Query_49 - M_2488 - 9 - - - 1 - gnl|BL_ORD_ID|1984 - 183275|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1984 - 10 - - - 1 - 13.0826 - 22 - 16.111 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 6 - 0 - 8 - FTEHDVQI - FTNMEVQL - FT +VQ+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 50 - Query_50 - M_2489 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 51 - Query_51 - M_2490 - 9 - - - 1 - gnl|BL_ORD_ID|1897 - 180617|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1897 - 10 - - - 1 - 13.4678 - 23 - 12.2057 - 3 - 8 - 5 - 10 - 0 - 0 - 3 - 6 - 0 - 6 - YRTPSV - YQTPAI - Y+TP++ - - - - - 2 - gnl|BL_ORD_ID|2153 - 189289|gag protein|ADO93742.1|Human immunodeficiency virus 1|11676 - 2153 - 9 - - - 1 - 12.3122 - 20 - 44.8495 - 3 - 9 - 3 - 9 - 0 - 0 - 5 - 5 - 0 - 7 - YRTPSVL - YNTISVL - Y T SVL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 52 - Query_52 - M_2491 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 53 - Query_53 - M_2492 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 54 - Query_54 - M_2493 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 55 - Query_55 - M_2494 - 9 - - - 1 - gnl|BL_ORD_ID|1822 - 178247|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1822 - 15 - - - 1 - 14.2382 - 25 - 3.43226 - 1 - 8 - 6 - 13 - 0 - 0 - 4 - 5 - 0 - 8 - QEFENIKS - QRFHNIRG - Q F NI+ - - - - - 2 - gnl|BL_ORD_ID|1384 - 110205|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1384 - 32 - - - 1 - 14.2382 - 25 - 4.11038 - 1 - 7 - 4 - 10 - 0 - 0 - 4 - 5 - 0 - 7 - QEFENIK - QRFHNIR - Q F NI+ - - - - - 3 - gnl|BL_ORD_ID|1385 - 110215|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1385 - 25 - - - 1 - 14.2382 - 25 - 4.57287 - 1 - 8 - 10 - 17 - 0 - 0 - 4 - 5 - 0 - 8 - QEFENIKS - QRFHNIRG - Q F NI+ - - - - - 4 - gnl|BL_ORD_ID|1395 - 110394|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1395 - 32 - - - 1 - 13.0826 - 22 - 18.1365 - 1 - 7 - 22 - 28 - 0 - 0 - 4 - 5 - 0 - 7 - QEFENIK - QRFHNIR - Q F NI+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 56 - Query_56 - M_2495 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 57 - Query_57 - M_2496 - 9 - - - 1 - gnl|BL_ORD_ID|1185 - 93270|hypothetical protein|NP_218356.1|Mycobacterium tuberculosis H37Rv|83332 - 1185 - 9 - - - 1 - 15.0086 - 27 - 0.92904 - 2 - 9 - 2 - 9 - 0 - 0 - 5 - 6 - 0 - 8 - MYDGRFLV - LYDGSFAV - +YDG F V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 58 - Query_58 - M_2497 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 59 - Query_59 - M_2498 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 60 - Query_60 - M_2499 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 61 - Query_61 - M_2500 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 62 - Query_62 - M_2501 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 63 - Query_63 - M_2502 - 9 - - - 1 - gnl|BL_ORD_ID|235 - 16814|precore protein|CAM58990.1|Hepatitis B virus|10407 - 235 - 10 - - - 1 - 15.0086 - 27 - 0.948031 - 3 - 8 - 2 - 7 - 0 - 0 - 4 - 6 - 0 - 6 - MPNDFW - LPNDFF - +PNDF+ - - - - - 2 - gnl|BL_ORD_ID|234 - 16813|External core antigen|SRC279980|Hepatitis B virus|10407 - 234 - 10 - - - 1 - 15.0086 - 27 - 0.978697 - 3 - 8 - 2 - 7 - 0 - 0 - 4 - 6 - 0 - 6 - MPNDFW - LPNDFF - +PNDF+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_126613_2_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_126613_2_T.fasta deleted file mode 100755 index 73fb9895..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_126613_2_T.fasta +++ /dev/null @@ -1,70 +0,0 @@ ->M_2503 -KMPEMHFKA ->M_2504 -AYSKCFISV ->M_2505 -LYLKTSQDV ->M_2506 -DLLTNLMYV ->M_2507 -LLTNLMYVL ->M_2508 -YQFPQSIDL ->M_2509 -VWQRPVLNF ->M_2510 -VEGTFISDY ->M_2511 -EELEIFMAR ->M_2512 -YEMIRTFYI ->M_2513 -EEFPCHKCV ->M_2514 -NYMAHLVAV ->M_2515 -FADFEWHFL ->M_2516 -SFADFEWHF ->M_2517 -FEQTLEELY ->M_2518 -IYVKPLPIL ->M_2519 -VLQIYVKPL ->M_2520 -RQWRSLTTL ->M_2521 -FCLGLVVTI ->M_2522 -GVFCLGLVV ->M_2523 -TLGVFCLGL ->M_2524 -IVPRLIMNF ->M_2525 -LIMNFTLGV ->M_2526 -GEHPYQCPY ->M_2527 -VLHRHMTTI ->M_2528 -HEIDFYRED ->M_2529 -KLDASVQHL ->M_2530 -RQLKLDASV ->M_2531 -FLWLWPLDF ->M_2532 -SEDGFLWLW ->M_2533 -WLWPLDFSS ->M_2534 -TFRDVAVEF ->M_2535 -AFSQSAYLI ->M_2536 -AYLIQHQRF ->M_2537 -KAFSQSAYL diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_126613_2_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_126613_2_T_iedb.xml deleted file mode 100755 index 2a4695b8..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_126613_2_T_iedb.xml +++ /dev/null @@ -1,1190 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_2503 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_2503 - 9 - - - 1 - gnl|BL_ORD_ID|2244 - 232153|rhoptry protein 18|CAJ27113.1|Toxoplasma gondii type I|1209525 - 2244 - 19 - - - 1 - 12.3122 - 20 - 38.4826 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - PEMHFKA - PERPFQA - PE F+A - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 2 - Query_2 - M_2504 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_2505 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_2506 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_2507 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_2508 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_2509 - 9 - - - 1 - gnl|BL_ORD_ID|624 - 37507|Large T antigen|P03071.1|Human polyomavirus 1|1891762 - 624 - 9 - - - 1 - 13.853 - 24 - 5.95161 - 1 - 6 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - VWQRPV - IWFRPV - +W RPV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 8 - Query_8 - M_2510 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_2511 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_2512 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_2513 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_2514 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_2515 - 9 - - - 1 - gnl|BL_ORD_ID|732 - 46575|polyprotein|AAG30730.1|Dengue virus 2|11060 - 732 - 9 - - - 1 - 13.4678 - 23 - 7.85574 - 1 - 8 - 2 - 9 - 0 - 0 - 4 - 6 - 0 - 8 - FADFEWHF - YADRKWCF - +AD +W F - - - - - 2 - gnl|BL_ORD_ID|456 - 27770|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 456 - 10 - - - 1 - 13.4678 - 23 - 10.4367 - 1 - 8 - 3 - 10 - 0 - 0 - 4 - 5 - 0 - 8 - FADFEWHF - YADRRWCF - +AD W F - - - - - 3 - gnl|BL_ORD_ID|1850 - 180360|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1850 - 15 - - - 1 - 13.4678 - 23 - 11.2975 - 1 - 8 - 7 - 14 - 0 - 0 - 4 - 5 - 0 - 8 - FADFEWHF - YADRRWCF - +AD W F - - - - - 4 - gnl|BL_ORD_ID|733 - 46576|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 733 - 9 - - - 1 - 13.4678 - 23 - 11.9303 - 1 - 8 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - FADFEWHF - YADRRWCF - +AD W F - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 14 - Query_14 - M_2516 - 9 - - - 1 - gnl|BL_ORD_ID|732 - 46575|polyprotein|AAG30730.1|Dengue virus 2|11060 - 732 - 9 - - - 1 - 13.853 - 24 - 4.92244 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 7 - 0 - 9 - SFADFEWHF - NYADRKWCF - ++AD +W F - - - - - 2 - gnl|BL_ORD_ID|456 - 27770|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 456 - 10 - - - 1 - 13.853 - 24 - 5.98008 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 6 - 0 - 9 - SFADFEWHF - NYADRRWCF - ++AD W F - - - - - 3 - gnl|BL_ORD_ID|1850 - 180360|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1850 - 15 - - - 1 - 13.853 - 24 - 6.40908 - 1 - 9 - 6 - 14 - 0 - 0 - 4 - 6 - 0 - 9 - SFADFEWHF - NYADRRWCF - ++AD W F - - - - - 4 - gnl|BL_ORD_ID|733 - 46576|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 733 - 9 - - - 1 - 13.853 - 24 - 6.95623 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 6 - 0 - 9 - SFADFEWHF - NYADRRWCF - ++AD W F - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 15 - Query_15 - M_2517 - 9 - - - 1 - gnl|BL_ORD_ID|697 - 42430|Major surface antigen precursor|P03141.3|Hepatitis B virus|10407 - 697 - 15 - - - 1 - 13.4678 - 23 - 7.23267 - 1 - 7 - 8 - 14 - 0 - 0 - 4 - 6 - 0 - 7 - FEQTLEE - FHQTLQD - F QTL++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 16 - Query_16 - M_2518 - 9 - - - 1 - gnl|BL_ORD_ID|889 - 58463|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 889 - 20 - - - 1 - 12.6974 - 21 - 31.8709 - 1 - 8 - 11 - 18 - 0 - 0 - 5 - 6 - 0 - 8 - IYVKPLPI - IYVYALPL - IYV LP+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 17 - Query_17 - M_2519 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_2520 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_2521 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_2522 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_2523 - 9 - - - 1 - gnl|BL_ORD_ID|2102 - 185978|polyprotein|CDF77361.1|Dengue virus 3|11069 - 2102 - 10 - - - 1 - 15.3938 - 28 - 0.539796 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 7 - 0 - 9 - TLGVFCLGL - TMGVLCLAI - T+GV CL + - - - - - 2 - gnl|BL_ORD_ID|979 - 64818|E7|AAD33253.1|Human papillomavirus type 16|333760 - 979 - 8 - - - 1 - 13.4678 - 23 - 12.6494 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - TLGVFC - TLGIVC - TLG+ C - - - - - 3 - gnl|BL_ORD_ID|980 - 64819|E7 protein|ABL96585.1|Human papillomavirus type 16|333760 - 980 - 9 - - - 1 - 13.0826 - 22 - 17.1877 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - TLGVFC - TLGIVC - TLG+ C - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 22 - Query_22 - M_2524 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_2525 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_2526 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_2527 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_2528 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_2529 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 28 - Query_28 - M_2530 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 29 - Query_29 - M_2531 - 9 - - - 1 - gnl|BL_ORD_ID|1243 - 98040|trans-sialidase, putative|EAN80725.1|Trypanosoma cruzi|5693 - 1243 - 9 - - - 1 - 13.0826 - 22 - 22.6682 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 6 - 0 - 8 - FLWLWPLD - FLYNRPLN - FL+ PL+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 30 - Query_30 - M_2532 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 31 - Query_31 - M_2533 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 32 - Query_32 - M_2534 - 9 - - - 1 - gnl|BL_ORD_ID|2108 - 186175|polyprotein|AFY10053.1|Dengue virus 3|11069 - 2108 - 10 - - - 1 - 13.853 - 24 - 6.08483 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 6 - 0 - 6 - TFRDVA - TWRDMA - T+RD+A - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 33 - Query_33 - M_2535 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 34 - Query_34 - M_2536 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 35 - Query_35 - M_2537 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_126796_3_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_126796_3_T.fasta deleted file mode 100755 index d1c98dee..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_126796_3_T.fasta +++ /dev/null @@ -1,132 +0,0 @@ ->M_2538 -QEEQQQQQL ->M_2539 -YLFSPQNQF ->M_2540 -YLFSPQNQF ->M_2541 -QARKIDHPL ->M_2542 -QARKIDHPL ->M_2543 -GLFVHTPCL ->M_2544 -RVLPAGLFV ->M_2545 -VHTPCLVGL ->M_2546 -AGLDSYPEL ->M_2547 -LVVSRSVSL ->M_2548 -LVVSRSVSL ->M_2549 -CSVDHRSVL ->M_2550 -HRSVLQRIM ->M_2551 -KMWEQEEKI ->M_2552 -FGIISIIFV ->M_2553 -GIISIIFVV ->M_2554 -IFGIISIIF ->M_2555 -RIFGIISII ->M_2556 -STAARIFGI ->M_2557 -TAARIFGII ->M_2558 -LSVQLGPTV ->M_2559 -CYTFNSIII ->M_2560 -SIIIFGPFL ->M_2561 -SIIIFGPFL ->M_2562 -YTFNSIIIF ->M_2563 -LEIQTPEAV ->M_2564 -YLALAAQCL ->M_2565 -YLALAAQCL ->M_2566 -AGCPAAQEL ->M_2567 -RARPAGCPA ->M_2568 -RPAGCPAAQ ->M_2569 -AGVDHIITM ->M_2570 -LSIAGVDHI ->M_2571 -PPRYIGIPI ->M_2572 -CMLVGDSAV ->M_2573 -MLSSIKCML ->M_2574 -MLSSIKCML ->M_2575 -FGHTYVPAF ->M_2576 -GQDFGHTYV ->M_2577 -YSTPQGQDF ->M_2578 -FVGLAIGTL ->M_2579 -IGTLSGDAL ->M_2580 -NMFEISNRL ->M_2581 -VDLGSTTPL ->M_2582 -IPLWGSPVT ->M_2583 -FVLSMQPVV ->M_2584 -FVLSMQPVV ->M_2585 -SMQPVVFQA ->M_2586 -YYDPFVLSM ->M_2587 -YYDPFVLSM ->M_2588 -YSHQNGASY ->M_2589 -AGVLLVLAL ->M_2590 -RFAGVLLVL ->M_2591 -VLALILPGT ->M_2592 -VLLVLALIL ->M_2593 -RQIPAQRDL ->M_2594 -SYRKSVRQI ->M_2595 -CYYELNQCL ->M_2596 -CYYELNQCL ->M_2597 -CPLCPFLTM ->M_2598 -FMNRFQCPL ->M_2599 -FMNRFQCPL ->M_2600 -FQCPLCPFL ->M_2601 -FQCPLCPFL ->M_2602 -RFQCPLCPF ->M_2603 -RFQCPLCPF diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_126796_3_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_126796_3_T_iedb.xml deleted file mode 100755 index fed7e106..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_126796_3_T_iedb.xml +++ /dev/null @@ -1,2526 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_2538 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_2538 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_2539 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_2540 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_2541 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_2542 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_2543 - 9 - - - 1 - gnl|BL_ORD_ID|1562 - 141281|tegument protein UL21|NP_044622.1|Human alphaherpesvirus 1|10298 - 1562 - 10 - - - 1 - 13.4678 - 23 - 10.6199 - 3 - 8 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - FVHTPC - FVYTPS - FV+TP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 7 - Query_7 - M_2544 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_2545 - 9 - - - 1 - gnl|BL_ORD_ID|1099 - 72566|polyprotein|BAD73987.1|Hepatitis C virus subtype 1b|31647 - 1099 - 9 - - - 1 - 14.2382 - 25 - 3.61702 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 4 - 0 - 8 - HTPCLVGL - HYPCTVNF - H PC V - - - - - 2 - gnl|BL_ORD_ID|417 - 25186|polyprotein|AAK32686.1|Hepatitis C virus|11103 - 417 - 10 - - - 1 - 13.853 - 24 - 4.3044 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 4 - 0 - 8 - HTPCLVGL - HYPCTVNF - H PC V - - - - - 3 - gnl|BL_ORD_ID|1413 - 111407|polyprotein|BAA00792.1|Hepatitis C virus|11103 - 1413 - 10 - - - 1 - 13.4678 - 23 - 8.46851 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 4 - 0 - 7 - HTPCLVG - HYPCTVN - H PC V - - - - - 4 - gnl|BL_ORD_ID|835 - 54825|polyprotein|BAA03375.1|Hepatitis C virus|11103 - 835 - 9 - - - 1 - 13.0826 - 22 - 14.1983 - 2 - 7 - 4 - 9 - 0 - 0 - 4 - 4 - 0 - 6 - HTPCLV - HYPCTV - H PC V - - - - - 5 - gnl|BL_ORD_ID|1149 - 75636|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 1149 - 10 - - - 1 - 13.0826 - 22 - 20.1646 - 2 - 7 - 5 - 10 - 0 - 0 - 3 - 4 - 0 - 6 - HTPCLV - HYPCTI - H PC + - - - - - 6 - gnl|BL_ORD_ID|833 - 54821|E2 protein|AAM33354.1|Hepatitis C virus subtype 1a|31646 - 833 - 9 - - - 1 - 12.6974 - 21 - 24.2855 - 2 - 7 - 4 - 9 - 0 - 0 - 3 - 4 - 0 - 6 - HTPCLV - HYPCTI - H PC + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 9 - Query_9 - M_2546 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_2547 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_2548 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_2549 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_2550 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_2551 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_2552 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_2553 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_2554 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_2555 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_2556 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_2557 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_2558 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 22 - Query_22 - M_2559 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_2560 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_2561 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_2562 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_2563 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_2564 - 9 - - - 1 - gnl|BL_ORD_ID|1292 - 102636|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 - 1292 - 15 - - - 1 - 13.4678 - 23 - 10.1977 - 3 - 9 - 8 - 14 - 0 - 0 - 6 - 6 - 0 - 7 - ALAAQCL - ALAAYCL - ALAA CL - - - - - 2 - gnl|BL_ORD_ID|1033 - 69349|Genome polyprotein|P29846.3|Hepatitis C virus (isolate Taiwan)|31645 - 1033 - 10 - - - 1 - 13.4678 - 23 - 12.859 - 3 - 9 - 4 - 10 - 0 - 0 - 6 - 6 - 0 - 7 - ALAAQCL - ALAAYCL - ALAA CL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 28 - Query_28 - M_2565 - 9 - - - 1 - gnl|BL_ORD_ID|1292 - 102636|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 - 1292 - 15 - - - 1 - 13.4678 - 23 - 10.1977 - 3 - 9 - 8 - 14 - 0 - 0 - 6 - 6 - 0 - 7 - ALAAQCL - ALAAYCL - ALAA CL - - - - - 2 - gnl|BL_ORD_ID|1033 - 69349|Genome polyprotein|P29846.3|Hepatitis C virus (isolate Taiwan)|31645 - 1033 - 10 - - - 1 - 13.4678 - 23 - 12.859 - 3 - 9 - 4 - 10 - 0 - 0 - 6 - 6 - 0 - 7 - ALAAQCL - ALAAYCL - ALAA CL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 29 - Query_29 - M_2566 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 30 - Query_30 - M_2567 - 9 - - - 1 - gnl|BL_ORD_ID|1493 - 136865|tegument protein|CAB06735.1|Human alphaherpesvirus 2|10310 - 1493 - 15 - - - 1 - 13.4678 - 23 - 10.1977 - 1 - 6 - 3 - 8 - 0 - 0 - 5 - 5 - 0 - 6 - RARPAG - RARPRG - RARP G - - - - - 2 - gnl|BL_ORD_ID|2189 - 190533|nucleocapsid protein|AAP49024.1|SARS coronavirus|227859 - 2189 - 15 - - - 1 - 13.4678 - 23 - 10.3735 - 3 - 8 - 2 - 7 - 0 - 0 - 4 - 4 - 0 - 6 - RPAGCP - RPQGLP - RP G P - - - - - 3 - gnl|BL_ORD_ID|850 - 55683|nucleocapsid protein|ABI96968.1|SARS coronavirus|227859 - 850 - 15 - - - 1 - 13.4678 - 23 - 10.9188 - 3 - 8 - 2 - 7 - 0 - 0 - 4 - 4 - 0 - 6 - RPAGCP - RPQGLP - RP G P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 31 - Query_31 - M_2568 - 9 - - - 1 - gnl|BL_ORD_ID|2189 - 190533|nucleocapsid protein|AAP49024.1|SARS coronavirus|227859 - 2189 - 15 - - - 1 - 13.4678 - 23 - 11.1066 - 1 - 6 - 2 - 7 - 0 - 0 - 4 - 4 - 0 - 6 - RPAGCP - RPQGLP - RP G P - - - - - 2 - gnl|BL_ORD_ID|850 - 55683|nucleocapsid protein|ABI96968.1|SARS coronavirus|227859 - 850 - 15 - - - 1 - 13.4678 - 23 - 11.689 - 1 - 6 - 2 - 7 - 0 - 0 - 4 - 4 - 0 - 6 - RPAGCP - RPQGLP - RP G P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 32 - Query_32 - M_2569 - 9 - - - 1 - gnl|BL_ORD_ID|698 - 42455|Probable Na(+)-translocating NADH-quinone reductase subunit A|O84639.1|Chlamydia trachomatis|813 - 698 - 9 - - - 1 - 13.0826 - 22 - 20.4374 - 4 - 9 - 3 - 8 - 0 - 0 - 4 - 5 - 0 - 6 - DHIITM - DHTITL - DH IT+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 33 - Query_33 - M_2570 - 9 - - - 1 - gnl|BL_ORD_ID|1441 - 120187|E1 protein|BAA19893.1|Rubella virus|11041 - 1441 - 21 - - - 1 - 14.2382 - 25 - 3.04044 - 1 - 7 - 14 - 20 - 0 - 0 - 5 - 6 - 0 - 7 - LSIAGVD - LSVAGVS - LS+AGV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 34 - Query_34 - M_2571 - 9 - - - 1 - gnl|BL_ORD_ID|1 - 118|envelope glycoprotein|ABS76372.1|Human immunodeficiency virus 1|11676 - 1 - 20 - - - 1 - 13.0826 - 22 - 14.6415 - 4 - 9 - 10 - 15 - 0 - 0 - 3 - 5 - 0 - 6 - YIGIPI - YYGVPV - Y G+P+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 35 - Query_35 - M_2572 - 9 - - - 1 - gnl|BL_ORD_ID|1792 - 164258|nucleocapsid protein|AAA43837.1|Hantaan virus 76-118|11602 - 1792 - 15 - - - 1 - 13.4678 - 23 - 11.689 - 1 - 8 - 4 - 11 - 0 - 0 - 4 - 6 - 0 - 8 - CMLVGDSA - CKLLPDTA - C L+ D+A - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 36 - Query_36 - M_2573 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 37 - Query_37 - M_2574 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 38 - Query_38 - M_2575 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 39 - Query_39 - M_2576 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 40 - Query_40 - M_2577 - 9 - - - 1 - gnl|BL_ORD_ID|1904 - 180643|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1904 - 15 - - - 1 - 11.927 - 19 - 61.2314 - 2 - 7 - 6 - 11 - 0 - 0 - 4 - 5 - 0 - 6 - STPQGQ - TTPFGQ - +TP GQ - - - - - 2 - gnl|BL_ORD_ID|1856 - 180411|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1856 - 9 - - - 1 - 11.5418 - 18 - 138.797 - 2 - 7 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - STPQGQ - TTPFGQ - +TP GQ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 41 - Query_41 - M_2578 - 9 - - - 1 - gnl|BL_ORD_ID|344 - 21638|protein F|ABV46152.2|Hepatitis C virus (isolate Japanese)|11116 - 344 - 9 - - - 1 - 13.0826 - 22 - 18.7436 - 3 - 9 - 3 - 9 - 0 - 0 - 5 - 6 - 0 - 7 - GLAIGTL - GLSPGTL - GL+ GTL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 42 - Query_42 - M_2579 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 43 - Query_43 - M_2580 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 44 - Query_44 - M_2581 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 45 - Query_45 - M_2582 - 9 - - - 1 - gnl|BL_ORD_ID|744 - 48321|||| - 744 - 9 - - - 1 - 15.0086 - 27 - 1.49881 - 2 - 8 - 1 - 7 - 0 - 0 - 5 - 6 - 0 - 7 - PLWGSPV - PLFGYPV - PL+G PV - - - - - 2 - gnl|BL_ORD_ID|378 - 23365|polyprotein|BAB18806.1|Hepatitis C virus|11103 - 378 - 10 - - - 1 - 14.2382 - 25 - 2.57891 - 1 - 8 - 3 - 10 - 0 - 0 - 5 - 7 - 0 - 8 - IPLWGSPV - IPLVGAPL - IPL G+P+ - - - - - 3 - gnl|BL_ORD_ID|296 - 19493|polyprotein|BAA03375.1|Hepatitis C virus|11103 - 296 - 15 - - - 1 - 14.2382 - 25 - 3.14687 - 1 - 7 - 9 - 15 - 0 - 0 - 5 - 6 - 0 - 7 - IPLWGSP - IPLVGAP - IPL G+P - - - - - 4 - gnl|BL_ORD_ID|1149 - 75636|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 1149 - 10 - - - 1 - 13.0826 - 22 - 15.0326 - 3 - 9 - 3 - 9 - 0 - 0 - 4 - 4 - 0 - 7 - LWGSPVT - LWHYPCT - LW P T - - - - - 5 - gnl|BL_ORD_ID|832 - 54820|polyprotein precursor|BAA02756.1|Hepatitis C virus|11103 - 832 - 9 - - - 1 - 13.0826 - 22 - 16.6015 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 4 - 0 - 7 - LWGSPVT - LWHYPCT - LW P T - - - - - 6 - gnl|BL_ORD_ID|833 - 54821|E2 protein|AAM33354.1|Hepatitis C virus subtype 1a|31646 - 833 - 9 - - - 1 - 13.0826 - 22 - 18.4218 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 4 - 0 - 7 - LWGSPVT - LWHYPCT - LW P T - - - - - 7 - gnl|BL_ORD_ID|831 - 54819|JK3|CAA43789.1|Hepatitis C virus|11103 - 831 - 9 - - - 1 - 13.0826 - 22 - 18.4218 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 4 - 0 - 7 - LWGSPVT - LWHYPCT - LW P T - - - - - 8 - gnl|BL_ORD_ID|834 - 54824|polyprotein precursor|BAA01583.1|Hepatitis C virus|11103 - 834 - 9 - - - 1 - 13.0826 - 22 - 18.7436 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 4 - 0 - 7 - LWGSPVT - LWHYPCT - LW P T - - - - - 9 - gnl|BL_ORD_ID|835 - 54825|polyprotein|BAA03375.1|Hepatitis C virus|11103 - 835 - 9 - - - 1 - 13.0826 - 22 - 19.7427 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 4 - 0 - 7 - LWGSPVT - LWHYPCT - LW P T - - - - - 10 - gnl|BL_ORD_ID|609 - 37255|||| - 609 - 9 - - - 1 - 12.6974 - 21 - 26.0147 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - LWGSPVT - LFGYPVA - L+G PV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 46 - Query_46 - M_2583 - 9 - - - 1 - gnl|BL_ORD_ID|1157 - 76334|Protein E7|P17387.1|Human papillomavirus type 31|10585 - 1157 - 10 - - - 1 - 14.6234 - 26 - 1.81479 - 1 - 7 - 1 - 7 - 0 - 0 - 4 - 6 - 0 - 7 - FVLSMQP - YVLDLQP - +VL +QP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 47 - Query_47 - M_2584 - 9 - - - 1 - gnl|BL_ORD_ID|1157 - 76334|Protein E7|P17387.1|Human papillomavirus type 31|10585 - 1157 - 10 - - - 1 - 14.6234 - 26 - 1.81479 - 1 - 7 - 1 - 7 - 0 - 0 - 4 - 6 - 0 - 7 - FVLSMQP - YVLDLQP - +VL +QP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 48 - Query_48 - M_2585 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 49 - Query_49 - M_2586 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 50 - Query_50 - M_2587 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 51 - Query_51 - M_2588 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 52 - Query_52 - M_2589 - 9 - - - 1 - gnl|BL_ORD_ID|336 - 21199|Circumsporozoite protein precursor|P08677.2|Plasmodium vivax strain Belem|31273 - 336 - 10 - - - 1 - 12.6974 - 21 - 30.4011 - 3 - 9 - 4 - 10 - 0 - 0 - 6 - 7 - 0 - 7 - VLLVLAL - ILLVLAL - +LLVLAL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 53 - Query_53 - M_2590 - 9 - - - 1 - gnl|BL_ORD_ID|1824 - 178829|envelope protein|BAJ51675.1|HBV genotype D|489483 - 1824 - 10 - - - 1 - 12.6974 - 21 - 25.6384 - 2 - 9 - 1 - 8 - 0 - 0 - 6 - 6 - 0 - 8 - FAGVLLVL - FLGPLLVL - F G LLVL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 54 - Query_54 - M_2591 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 55 - Query_55 - M_2592 - 9 - - - 1 - gnl|BL_ORD_ID|336 - 21199|Circumsporozoite protein precursor|P08677.2|Plasmodium vivax strain Belem|31273 - 336 - 10 - - - 1 - 12.3122 - 20 - 46.3152 - 1 - 7 - 4 - 10 - 0 - 0 - 6 - 7 - 0 - 7 - VLLVLAL - ILLVLAL - +LLVLAL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 56 - Query_56 - M_2593 - 9 - - - 1 - gnl|BL_ORD_ID|1184 - 93224|core protein|AAL31859.1|Hepatitis B virus|10407 - 1184 - 14 - - - 1 - 15.0086 - 27 - 1.285 - 4 - 9 - 4 - 9 - 0 - 0 - 5 - 5 - 0 - 6 - PAQRDL - PASRDL - PA RDL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 57 - Query_57 - M_2594 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 58 - Query_58 - M_2595 - 9 - - - 1 - gnl|BL_ORD_ID|1398 - 110431|E7|AAD33253.1|Human papillomavirus type 16|333760 - 1398 - 36 - - - 1 - 13.0826 - 22 - 14.7121 - 1 - 8 - 5 - 12 - 0 - 0 - 4 - 5 - 0 - 8 - CYYELNQC - CYEQLNDS - CY +LN - - - - - 2 - gnl|BL_ORD_ID|1392 - 110335|E7|AAD33253.1|Human papillomavirus type 16|333760 - 1392 - 32 - - - 1 - 13.0826 - 22 - 19.4872 - 1 - 8 - 24 - 31 - 0 - 0 - 4 - 5 - 0 - 8 - CYYELNQC - CYEQLNDS - CY +LN - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 59 - Query_59 - M_2596 - 9 - - - 1 - gnl|BL_ORD_ID|1398 - 110431|E7|AAD33253.1|Human papillomavirus type 16|333760 - 1398 - 36 - - - 1 - 13.0826 - 22 - 14.7121 - 1 - 8 - 5 - 12 - 0 - 0 - 4 - 5 - 0 - 8 - CYYELNQC - CYEQLNDS - CY +LN - - - - - 2 - gnl|BL_ORD_ID|1392 - 110335|E7|AAD33253.1|Human papillomavirus type 16|333760 - 1392 - 32 - - - 1 - 13.0826 - 22 - 19.4872 - 1 - 8 - 24 - 31 - 0 - 0 - 4 - 5 - 0 - 8 - CYYELNQC - CYEQLNDS - CY +LN - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 60 - Query_60 - M_2597 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 61 - Query_61 - M_2598 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 62 - Query_62 - M_2599 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 63 - Query_63 - M_2600 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 64 - Query_64 - M_2601 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 65 - Query_65 - M_2602 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 66 - Query_66 - M_2603 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_127486_2_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_127486_2_T.fasta deleted file mode 100755 index 86c0b387..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_127486_2_T.fasta +++ /dev/null @@ -1,62 +0,0 @@ ->M_2604 -APEPLLLSW ->M_2605 -ASLHHHHHR ->M_2606 -RPPPSQASL ->M_2607 -FPDHMACDL ->M_2608 -ALLGNRTAL ->M_2609 -GPVSAPGLL ->M_2610 -HVYRNFLNK ->M_2611 -RPRGDNGYT ->M_2612 -SNSESEILK ->M_2613 -AVDRYVAMR ->M_2614 -RYVAMRHPL ->M_2615 -YVAMRHPLR ->M_2616 -RAGESVWPK ->M_2617 -VWPKKINNI ->M_2618 -VVGADGVGK ->M_2619 -KTETYDNYK ->M_2620 -RQLTVESDK ->M_2621 -ITLTATSQK ->M_2622 -HPTASTLST ->M_2623 -NPSHPTAST ->M_2624 -LMLLQSGYK ->M_2625 -HFPIYHLLL ->M_2626 -LASSFVFLY ->M_2627 -LISEGQRLK ->M_2628 -KPLPLVTDL ->M_2629 -LPLVTDLSL ->M_2630 -APIAPTFYK ->M_2631 -APTFYKPKL ->M_2632 -IAPTFYKPK ->M_2633 -TFYKPKLLK ->M_2634 -VFQHIFDLI diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_127486_2_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_127486_2_T_iedb.xml deleted file mode 100755 index cb107982..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_127486_2_T_iedb.xml +++ /dev/null @@ -1,724 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_2604 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_2604 - 9 - - - 1 - gnl|BL_ORD_ID|1682 - 149036|E2 protein|NP_751921.1|Hepatitis C virus (isolate H77)|63746 - 1682 - 9 - - - 1 - 12.3122 - 20 - 55.769 - 4 - 8 - 4 - 8 - 0 - 0 - 5 - 5 - 0 - 5 - PLLLS - PLLLS - PLLLS - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 2 - Query_2 - M_2605 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_2606 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_2607 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_2608 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_2609 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_2610 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_2611 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_2612 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_2613 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_2614 - 9 - - - 1 - gnl|BL_ORD_ID|2080 - 185327|polyprotein|ACF49259.1|Dengue virus type 1 Hawaii|10000440 - 2080 - 9 - - - 1 - 13.853 - 24 - 5.18352 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 6 - 0 - 9 - RYVAMRHPL - QYIYMGQPL - +Y+ M PL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 12 - Query_12 - M_2615 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_2616 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_2617 - 9 - - - 1 - gnl|BL_ORD_ID|1950 - 181035|||| - 1950 - 44 - - - 1 - 13.4678 - 23 - 8.97754 - 1 - 6 - 7 - 12 - 0 - 0 - 4 - 5 - 0 - 6 - VWPKKI - VWLKKL - VW KK+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 15 - Query_15 - M_2618 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_2619 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_2620 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_2621 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_2622 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_2623 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_2624 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 22 - Query_22 - M_2625 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_2626 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_2627 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_2628 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_2629 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_2630 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 28 - Query_28 - M_2631 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 29 - Query_29 - M_2632 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 30 - Query_30 - M_2633 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 31 - Query_31 - M_2634 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_128984_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_128984_1_T.fasta deleted file mode 100755 index 288816ea..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_128984_1_T.fasta +++ /dev/null @@ -1,216 +0,0 @@ ->M_2635 -AAATAVVAF ->M_2636 -ALLRATDTI ->M_2637 -APFDKHCAV ->M_2638 -APFLNSVSI ->M_2639 -APHGEEAHL ->M_2640 -APLLPRTHL ->M_2641 -APRRHSGRV ->M_2642 -APSLPSPTA ->M_2643 -APVTLRGSY ->M_2644 -ATGGHHQPL ->M_2645 -AVMAFDLCV ->M_2646 -AVMAFDRSV ->M_2647 -AYQVSVCAF ->M_2648 -CTTPVTVEI ->M_2649 -CYYYFLCLL ->M_2650 -DTPRHRLLV ->M_2651 -EAQQSSHCL ->M_2652 -EPRITRSFV ->M_2653 -ETGLALKYL ->M_2654 -FSFQVDSPV ->M_2655 -FSILSTALL ->M_2656 -GLRKTNMSL ->M_2657 -GPNAMRYSL ->M_2658 -GPRNCIGQA ->M_2659 -HMSACHHSI ->M_2660 -HPNAHSNST ->M_2661 -HPWTTDMPA ->M_2662 -HSNSTSFIF ->M_2663 -HSNSTSFIF ->M_2664 -HTWQMRNTV ->M_2665 -HTWQMRNTV ->M_2666 -IFSLGRHTW ->M_2667 -INALIIFIF ->M_2668 -IPHLLKLAC ->M_2669 -ISASVCIQV ->M_2670 -ITSTVMLEV ->M_2671 -KAFNCSSFV ->M_2672 -KAFSQSSNL ->M_2673 -KLFSILSTA ->M_2674 -KLWATAEAL ->M_2675 -KTHRIVRRL ->M_2676 -KTHRIVRRL ->M_2677 -KTLRKSLPA ->M_2678 -KTLRKSLPA ->M_2679 -KYIFNNSII ->M_2680 -KYTSAAILV ->M_2681 -LALSVTEMV ->M_2682 -LHSPMYFFL ->M_2683 -LHTPVYFLL ->M_2684 -LLVSLTVTF ->M_2685 -LPGGVGRTL ->M_2686 -LPSDDRGSL ->M_2687 -LSVADQEKV ->M_2688 -LWGKHQFIL ->M_2689 -MAFDLCVAI ->M_2690 -MAFDRSVAI ->M_2691 -MAFDRSVAI ->M_2692 -MIISASVCI ->M_2693 -MIISASVCI ->M_2694 -MLDLLTNTL ->M_2695 -MTNGLCIWL ->M_2696 -MVNATACAV ->M_2697 -NAFQEARRL ->M_2698 -PSAPKPSTL ->M_2699 -QALRAGLAL ->M_2700 -QALRAGLAL ->M_2701 -QAVEFCQRV ->M_2702 -QILVKICTI ->M_2703 -QLHFIFHIL ->M_2704 -QLWGKHQFI ->M_2705 -QPWEHVNAF ->M_2706 -QQQMASRPF ->M_2707 -QTSMSQSQV ->M_2708 -RIIKLLVSL ->M_2709 -RLALSTFEW ->M_2710 -RLHSPMYFF ->M_2711 -RLHSPMYFF ->M_2712 -RLHTPVYFL ->M_2713 -RSFTEENHM ->M_2714 -RSFVPHLEI ->M_2715 -RSFVPHLEI ->M_2716 -RSVAICKPL ->M_2717 -RVVLINNNL ->M_2718 -SASSQSSSI ->M_2719 -SASVCIQVV ->M_2720 -SIIQDFFAW ->M_2721 -SINALIIFI ->M_2722 -SMSQSQVAL ->M_2723 -SPAQAPIPY ->M_2724 -SPGGWRSGW ->M_2725 -SSEQSIFVV ->M_2726 -SSIPENEAI ->M_2727 -STVMLEVPL ->M_2728 -STVMLEVPL ->M_2729 -SYSSLDEDF ->M_2730 -TPRHRLLVL ->M_2731 -TSMYNEILI ->M_2732 -TSVPVTTAV ->M_2733 -VPADSTQTL ->M_2734 -VSIETHLLF ->M_2735 -VSIETHLLF ->M_2736 -VSLTVTFVL ->M_2737 -VTTAVSTFV ->M_2738 -VTTGLMGAV ->M_2739 -YSSLDEDFL ->M_2740 -YVQKRSSQI ->M_2741 -YYFLCLLL* ->M_2742 -YYYFLCLLL diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_128984_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_128984_1_T_iedb.xml deleted file mode 100755 index ef42d15d..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_128984_1_T_iedb.xml +++ /dev/null @@ -1,3116 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_2635 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_2635 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_2636 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_2637 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_2638 - 9 - - - 1 - gnl|BL_ORD_ID|1826 - 179765|cell surface protein (associated with virulence)|NP_302372.1|Mycobacterium leprae TN|272631 - 1826 - 9 - - - 1 - 11.1566 - 17 - 202.191 - 1 - 8 - 1 - 8 - 0 - 0 - 5 - 5 - 0 - 8 - APFLNSVS - APIPASVS - AP SVS - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 5 - Query_5 - M_2639 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_2640 - 9 - - - 1 - gnl|BL_ORD_ID|1827 - 179766|cell surface protein (associated with virulence)|NP_302372.1|Mycobacterium leprae TN|272631 - 1827 - 9 - - - 1 - 12.3122 - 20 - 57.6592 - 1 - 7 - 1 - 7 - 0 - 0 - 5 - 5 - 0 - 7 - APLLPRT - APLPPST - APL P T - - - - - 2 - gnl|BL_ORD_ID|789 - 52760|nef protein|ACR27174.1|Human immunodeficiency virus 1|11676 - 789 - 10 - - - 1 - 11.927 - 19 - 86.442 - 1 - 8 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - APLLPRTH - VPLRPMTY - PL P T+ - - - - - 3 - gnl|BL_ORD_ID|1067 - 70365|Truncated Nef protein|P04601.4|Human immunodeficiency virus 1|11676 - 1067 - 9 - - - 1 - 11.927 - 19 - 97.5444 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 5 - 0 - 8 - APLLPRTH - VPLRPMTY - PL P T+ - - - - - 4 - gnl|BL_ORD_ID|2258 - 288104|nef protein|ACR27130.1|Human immunodeficiency virus 1|11676 - 2258 - 18 - - - 1 - 10.7714 - 16 - 330.264 - 1 - 7 - 10 - 16 - 0 - 0 - 4 - 4 - 0 - 7 - APLLPRT - VPLRPMT - PL P T - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 7 - Query_7 - M_2641 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_2642 - 9 - - - 1 - gnl|BL_ORD_ID|96 - 6591|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 96 - 18 - - - 1 - 11.927 - 19 - 82.9694 - 2 - 8 - 7 - 13 - 0 - 0 - 4 - 5 - 0 - 7 - PSLPSPT - PTLHGPT - P+L PT - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 9 - Query_9 - M_2643 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_2644 - 9 - - - 1 - gnl|BL_ORD_ID|1871 - 180488|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1871 - 10 - - - 1 - 12.6974 - 21 - 22.7423 - 4 - 9 - 3 - 8 - 0 - 0 - 3 - 5 - 0 - 6 - GHHQPL - GHEEPI - GH +P+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 11 - Query_11 - M_2645 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_2646 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_2647 - 9 - - - 1 - gnl|BL_ORD_ID|184 - 13518|HCV-1|AAA45676.1|Hepatitis C virus genotype 1|41856 - 184 - 20 - - - 1 - 16.5494 - 31 - 0.218227 - 1 - 8 - 8 - 15 - 0 - 0 - 6 - 7 - 0 - 8 - AYQVSVCA - AYQATVCA - AYQ +VCA - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 14 - Query_14 - M_2648 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_2649 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_2650 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_2651 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_2652 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_2653 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_2654 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_2655 - 9 - - - 1 - gnl|BL_ORD_ID|883 - 57894|polyprotein|BAD73987.1|Hepatitis C virus subtype 1b|31647 - 883 - 10 - - - 1 - 11.927 - 19 - 79.723 - 1 - 9 - 2 - 10 - 0 - 0 - 6 - 6 - 0 - 9 - FSILSTALL - FSIFLLALL - FSI ALL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 22 - Query_22 - M_2656 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_2657 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_2658 - 9 - - - 1 - gnl|BL_ORD_ID|1731 - 150556|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1731 - 10 - - - 1 - 12.6974 - 21 - 25.6384 - 1 - 6 - 4 - 9 - 0 - 0 - 3 - 4 - 0 - 6 - GPRNCI - DPRRCL - PR C+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 25 - Query_25 - M_2659 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_2660 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_2661 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 28 - Query_28 - M_2662 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 29 - Query_29 - M_2663 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 30 - Query_30 - M_2664 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 31 - Query_31 - M_2665 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 32 - Query_32 - M_2666 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 33 - Query_33 - M_2667 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 34 - Query_34 - M_2668 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 35 - Query_35 - M_2669 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 36 - Query_36 - M_2670 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 37 - Query_37 - M_2671 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 38 - Query_38 - M_2672 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 39 - Query_39 - M_2673 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 40 - Query_40 - M_2674 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 41 - Query_41 - M_2675 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 42 - Query_42 - M_2676 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 43 - Query_43 - M_2677 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 44 - Query_44 - M_2678 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 45 - Query_45 - M_2679 - 9 - - - 1 - gnl|BL_ORD_ID|1565 - 141323|multifunctional expression regulator|NP_044657.1|Human alphaherpesvirus 1|10298 - 1565 - 9 - - - 1 - 13.0826 - 22 - 15.7589 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 6 - 0 - 9 - KYIFNNSII - KYFYCNSLF - KY + NS+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 46 - Query_46 - M_2680 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 47 - Query_47 - M_2681 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 48 - Query_48 - M_2682 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 49 - Query_49 - M_2683 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 50 - Query_50 - M_2684 - 9 - - - 1 - gnl|BL_ORD_ID|670 - 40264|Cytochrome P450 2A6|P11509.3|Homo sapiens|9606 - 670 - 10 - - - 1 - 12.6974 - 21 - 34.8136 - 1 - 7 - 4 - 10 - 0 - 0 - 6 - 6 - 0 - 7 - LLVSLTV - LLVCLTV - LLV LTV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 51 - Query_51 - M_2685 - 9 - - - 1 - gnl|BL_ORD_ID|1580 - 141461|ubiquitin E3 ligase ICP0|NP_044601.1|Human alphaherpesvirus 1|10298 - 1580 - 9 - - - 1 - 13.0826 - 22 - 14.4474 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 6 - 0 - 9 - LPGGVGRTL - VPGWSRRTL - +PG RTL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 52 - Query_52 - M_2686 - 9 - - - 1 - gnl|BL_ORD_ID|851 - 55709|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 - 851 - 15 - - - 1 - 13.0826 - 22 - 12.5116 - 4 - 9 - 5 - 10 - 0 - 0 - 5 - 5 - 0 - 6 - DDRGSL - DSRGSL - D RGSL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 53 - Query_53 - M_2687 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 54 - Query_54 - M_2688 - 9 - - - 1 - gnl|BL_ORD_ID|691 - 42094|telomer length regulation protein TEL1|EDV12172.1|Saccharomyces cerevisiae|4932 - 691 - 9 - - - 1 - 14.2382 - 25 - 3.87216 - 1 - 8 - 2 - 9 - 0 - 0 - 4 - 6 - 0 - 8 - LWGKHQFI - LWGYLQYV - LWG Q++ - - - - - 2 - gnl|BL_ORD_ID|1295 - 103020|polyprotein|ABR25251.1|Hepatitis C virus|11103 - 1295 - 10 - - - 1 - 12.6974 - 21 - 38.5196 - 1 - 5 - 2 - 6 - 0 - 0 - 3 - 3 - 0 - 5 - LWGKH - FWAKH - W KH - - - - - 3 - gnl|BL_ORD_ID|1029 - 68605|Genome polyprotein|P26662.3|Hepatitis C virus|11103 - 1029 - 10 - - - 1 - 12.3122 - 20 - 39.1729 - 1 - 5 - 2 - 6 - 0 - 0 - 3 - 3 - 0 - 5 - LWGKH - FWAKH - W KH - - - - - 4 - gnl|BL_ORD_ID|195 - 14381|polyprotein|BAA25076.1|Hepatitis C virus|11103 - 195 - 9 - - - 1 - 12.3122 - 20 - 41.221 - 1 - 7 - 3 - 9 - 0 - 0 - 3 - 4 - 0 - 7 - LWGKHQF - FWAKHMW - W KH + - - - - - 5 - gnl|BL_ORD_ID|272 - 18337|polyprotein|BAD73987.1|Hepatitis C virus subtype 1b|31647 - 272 - 9 - - - 1 - 12.3122 - 20 - 43.3628 - 1 - 5 - 1 - 5 - 0 - 0 - 3 - 3 - 0 - 5 - LWGKH - FWAKH - W KH - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 55 - Query_55 - M_2689 - 9 - - - 1 - gnl|BL_ORD_ID|1422 - 112503|E6 protein|ACV53993.1|Human papillomavirus type 35|10587 - 1422 - 10 - - - 1 - 13.0826 - 22 - 18.1832 - 3 - 7 - 4 - 8 - 0 - 0 - 3 - 5 - 0 - 5 - FDLCV - YDLCI - +DLC+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 56 - Query_56 - M_2690 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 57 - Query_57 - M_2691 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 58 - Query_58 - M_2692 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 59 - Query_59 - M_2693 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 60 - Query_60 - M_2694 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 61 - Query_61 - M_2695 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 62 - Query_62 - M_2696 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 63 - Query_63 - M_2697 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 64 - Query_64 - M_2698 - 9 - - - 1 - gnl|BL_ORD_ID|1180 - 88377|IE62|AAP32859.1|Human alphaherpesvirus 3|10335 - 1180 - 9 - - - 1 - 12.3122 - 20 - 55.769 - 2 - 8 - 1 - 7 - 0 - 0 - 5 - 5 - 0 - 7 - SAPKPST - SAPLPSN - SAP PS - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 65 - Query_65 - M_2699 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 66 - Query_66 - M_2700 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 67 - Query_67 - M_2701 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 68 - Query_68 - M_2702 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 69 - Query_69 - M_2703 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 70 - Query_70 - M_2704 - 9 - - - 1 - gnl|BL_ORD_ID|691 - 42094|telomer length regulation protein TEL1|EDV12172.1|Saccharomyces cerevisiae|4932 - 691 - 9 - - - 1 - 14.2382 - 25 - 3.26672 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 6 - 0 - 8 - LWGKHQFI - LWGYLQYV - LWG Q++ - - - - - 2 - gnl|BL_ORD_ID|195 - 14381|polyprotein|BAA25076.1|Hepatitis C virus|11103 - 195 - 9 - - - 1 - 12.6974 - 21 - 37.875 - 2 - 8 - 3 - 9 - 0 - 0 - 3 - 4 - 0 - 7 - LWGKHQF - FWAKHMW - W KH + - - - - - 3 - gnl|BL_ORD_ID|1029 - 68605|Genome polyprotein|P26662.3|Hepatitis C virus|11103 - 1029 - 10 - - - 1 - 12.6974 - 21 - 38.5196 - 2 - 7 - 2 - 7 - 0 - 0 - 3 - 3 - 0 - 6 - LWGKHQ - FWAKHM - W KH - - - - - 4 - gnl|BL_ORD_ID|1295 - 103020|polyprotein|ABR25251.1|Hepatitis C virus|11103 - 1295 - 10 - - - 1 - 12.3122 - 20 - 39.1729 - 2 - 6 - 2 - 6 - 0 - 0 - 3 - 3 - 0 - 5 - LWGKH - FWAKH - W KH - - - - - 5 - gnl|BL_ORD_ID|272 - 18337|polyprotein|BAD73987.1|Hepatitis C virus subtype 1b|31647 - 272 - 9 - - - 1 - 12.3122 - 20 - 44.8495 - 2 - 6 - 1 - 5 - 0 - 0 - 3 - 3 - 0 - 5 - LWGKH - FWAKH - W KH - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 71 - Query_71 - M_2705 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 72 - Query_72 - M_2706 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 73 - Query_73 - M_2707 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 74 - Query_74 - M_2708 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 75 - Query_75 - M_2709 - 9 - - - 1 - gnl|BL_ORD_ID|1711 - 150309|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1711 - 10 - - - 1 - 13.4678 - 23 - 7.76238 - 2 - 9 - 1 - 8 - 0 - 0 - 3 - 6 - 0 - 8 - LALSTFEW - IPMSTYGW - + +ST+ W - - - - - 2 - gnl|BL_ORD_ID|634 - 37830|polyprotein|BAB18806.1|Hepatitis C virus subtype 1b|31647 - 634 - 9 - - - 1 - 13.4678 - 23 - 8.13377 - 4 - 9 - 2 - 7 - 0 - 0 - 5 - 5 - 0 - 6 - LSTFEW - LSTTEW - LST EW - - - - - 3 - gnl|BL_ORD_ID|1915 - 180675|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1915 - 15 - - - 1 - 13.0826 - 22 - 17.2424 - 4 - 9 - 1 - 6 - 0 - 0 - 3 - 5 - 0 - 6 - LSTFEW - MSTYGW - +ST+ W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 76 - Query_76 - M_2710 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 77 - Query_77 - M_2711 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 78 - Query_78 - M_2712 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 79 - Query_79 - M_2713 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 80 - Query_80 - M_2714 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 81 - Query_81 - M_2715 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 82 - Query_82 - M_2716 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 83 - Query_83 - M_2717 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 84 - Query_84 - M_2718 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 85 - Query_85 - M_2719 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 86 - Query_86 - M_2720 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 87 - Query_87 - M_2721 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 88 - Query_88 - M_2722 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 89 - Query_89 - M_2723 - 9 - - - 1 - gnl|BL_ORD_ID|1694 - 149096|polyprotein|BAB18801.1|Hepatitis C virus|11103 - 1694 - 9 - - - 1 - 11.927 - 19 - 95.9763 - 3 - 8 - 2 - 7 - 0 - 0 - 5 - 5 - 0 - 6 - AQAPIP - AQAPPP - AQAP P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 90 - Query_90 - M_2724 - 9 - - - 1 - gnl|BL_ORD_ID|1151 - 75674|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 - 1151 - 15 - - - 1 - 13.0826 - 22 - 16.1221 - 3 - 9 - 6 - 12 - 0 - 0 - 4 - 5 - 0 - 7 - GGWRSGW - GFWQEGW - G W+ GW - - - - - 2 - gnl|BL_ORD_ID|800 - 53246|polyprotein precursor|AAF20092.2|West Nile virus|11082 - 800 - 9 - - - 1 - 10.7714 - 16 - 393.541 - 4 - 9 - 2 - 7 - 0 - 0 - 3 - 4 - 0 - 6 - GWRSGW - AWNSGY - W SG+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 91 - Query_91 - M_2725 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 92 - Query_92 - M_2726 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 93 - Query_93 - M_2727 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 94 - Query_94 - M_2728 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 95 - Query_95 - M_2729 - 9 - - - 1 - gnl|BL_ORD_ID|162 - 12585|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis|1773 - 162 - 20 - - - 1 - 12.6974 - 21 - 34.4393 - 2 - 8 - 13 - 19 - 0 - 0 - 4 - 5 - 0 - 7 - YSSLDED - YSRADEE - YS DE+ - - - - - 2 - gnl|BL_ORD_ID|1071 - 70687|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis|1773 - 1071 - 20 - - - 1 - 12.3122 - 20 - 42.7067 - 2 - 8 - 3 - 9 - 0 - 0 - 4 - 5 - 0 - 7 - YSSLDED - YSRADEE - YS DE+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 96 - Query_96 - M_2730 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 97 - Query_97 - M_2731 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 98 - Query_98 - M_2732 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 99 - Query_99 - M_2733 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 100 - Query_100 - M_2734 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 101 - Query_101 - M_2735 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 102 - Query_102 - M_2736 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 103 - Query_103 - M_2737 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 104 - Query_104 - M_2738 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 105 - Query_105 - M_2739 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 106 - Query_106 - M_2740 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 107 - Query_107 - M_2741 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 108 - Query_108 - M_2742 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_129049_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_129049_1_T.fasta deleted file mode 100755 index 29de5645..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_129049_1_T.fasta +++ /dev/null @@ -1,54 +0,0 @@ ->M_2743 -ASLDVTLRL ->M_2744 -ISSHLSTLV ->M_2745 -LSTLVDFAI ->M_2746 -KTSVGSTKY ->M_2747 -HPCERSDEV ->M_2748 -ITVEEQHRI ->M_2749 -ITVEEQHRI ->M_2750 -MTAVQTLHL ->M_2751 -PAMTAVQTL ->M_2752 -RQLPAMTAV ->M_2753 -ETVFTRSSW ->M_2754 -FTRSSWDWI ->M_2755 -VFTRSSWDW ->M_2756 -EPPPPPSPL ->M_2757 -QTTQLSLNF ->M_2758 -GAMDGATYI ->M_2759 -MAFVKSVWL ->M_2760 -CAVRRAAQV ->M_2761 -QAVAQAVNW ->M_2762 -NPKTWNTMV ->M_2763 -QLYMNPKTW ->M_2764 -RQVGFCVQW ->M_2765 -KMLLAPGRF ->M_2766 -MLLAPGRFI ->M_2767 -FTMPEDEYM ->M_2768 -FTMPEDEYM ->M_2769 -MPEDEYMVY diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_129049_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_129049_1_T_iedb.xml deleted file mode 100755 index 30ba0cad..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_129049_1_T_iedb.xml +++ /dev/null @@ -1,754 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_2743 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_2743 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_2744 - 9 - - - 1 - gnl|BL_ORD_ID|1262 - 98466|Trans-sialidase|SRC7915|Trypanosoma cruzi|5693 - 1262 - 10 - - - 1 - 12.3122 - 20 - 49.5064 - 3 - 9 - 3 - 9 - 0 - 0 - 5 - 5 - 0 - 7 - SHLSTLV - SHYFTLV - SH TLV - - - - - 2 - gnl|BL_ORD_ID|904 - 59459|Trans-sialidase|SRC7915|Trypanosoma cruzi|5693 - 904 - 9 - - - 1 - 12.3122 - 20 - 63.7024 - 3 - 9 - 3 - 9 - 0 - 0 - 5 - 5 - 0 - 7 - SHLSTLV - SHYFTLV - SH TLV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 3 - Query_3 - M_2745 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_2746 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_2747 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_2748 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_2749 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_2750 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_2751 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_2752 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_2753 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_2754 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_2755 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_2756 - 9 - - - 1 - gnl|BL_ORD_ID|1211 - 96366|polyprotein|ABR25251.1|Hepatitis C virus|11103 - 1211 - 12 - - - 1 - 10.3862 - 15 - 463.357 - 4 - 9 - 5 - 10 - 0 - 0 - 4 - 4 - 0 - 6 - PPPSPL - PPCKPL - PP PL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 15 - Query_15 - M_2757 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_2758 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_2759 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_2760 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_2761 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_2762 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_2763 - 9 - - - 1 - gnl|BL_ORD_ID|1486 - 135263|hemagglutinin|ACX31970.1|Influenza A virus (A/Bar-headed Goose/Qinghai/61/05(H5N1))|336238 - 1486 - 10 - - - 1 - 16.1642 - 30 - 0.390189 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 7 - 0 - 9 - QLYMNPKTW - RLYQNPTTY - +LY NP T+ - - - - - 2 - gnl|BL_ORD_ID|527 - 32268|hemagglutinin|AAK38298.1|Influenza A virus (A/Bar-headed Goose/Qinghai/61/05(H5N1))|336238 - 527 - 10 - - - 1 - 15.779 - 29 - 0.412579 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 7 - 0 - 9 - QLYMNPKTW - KLYQNPTTY - +LY NP T+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 22 - Query_22 - M_2764 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_2765 - 9 - - - 1 - gnl|BL_ORD_ID|902 - 59240|HCV-1|AAA45676.1|Hepatitis C virus genotype 1|41856 - 902 - 11 - - - 1 - 13.853 - 24 - 5.19029 - 3 - 7 - 2 - 6 - 0 - 0 - 5 - 5 - 0 - 5 - LLAPG - LLAPG - LLAPG - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 24 - Query_24 - M_2766 - 9 - - - 1 - gnl|BL_ORD_ID|902 - 59240|HCV-1|AAA45676.1|Hepatitis C virus genotype 1|41856 - 902 - 11 - - - 1 - 13.853 - 24 - 5.28123 - 2 - 6 - 2 - 6 - 0 - 0 - 5 - 5 - 0 - 5 - LLAPG - LLAPG - LLAPG - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 25 - Query_25 - M_2767 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_2768 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_2769 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_129675_2_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_129675_2_T.fasta deleted file mode 100755 index 708278e5..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_129675_2_T.fasta +++ /dev/null @@ -1,38 +0,0 @@ ->M_2770 -IAWPADRTA ->M_2771 -QALIRPTTF ->M_2772 -FPEYDGVDH ->M_2773 -EIAEIEYSI ->M_2774 -FVVSACNAT ->M_2775 -WITPAQREY ->M_2776 -EPVWGLEAI ->M_2777 -RLSWQASSL ->M_2778 -KIKELAAEF ->M_2779 -VPILQSTPV ->M_2780 -APRGFLTNY ->M_2781 -RAAEQRRAY ->M_2782 -KSASWITWI ->M_2783 -TPWSFTGTV ->M_2784 -GPLADATPL ->M_2785 -LAGERRFAF ->M_2786 -IAASAMCVF ->M_2787 -SSYGRNHYI ->M_2788 -IIHTGARPY diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_129675_2_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_129675_2_T_iedb.xml deleted file mode 100755 index c4cadf10..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_129675_2_T_iedb.xml +++ /dev/null @@ -1,845 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_2770 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_2770 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_2771 - 9 - - - 1 - gnl|BL_ORD_ID|172 - 13165|trans-sialidase, putative|EAN81972.1|Trypanosoma cruzi|5693 - 172 - 9 - - - 1 - 15.0086 - 27 - 1.19683 - 3 - 9 - 2 - 8 - 0 - 0 - 5 - 6 - 0 - 7 - LIRPTTF - LLRPTTL - L+RPTT - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 3 - Query_3 - M_2772 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_2773 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_2774 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_2775 - 9 - - - 1 - gnl|BL_ORD_ID|1408 - 110940|Protein E7|P03129.1|Human papillomavirus type 16|333760 - 1408 - 15 - - - 1 - 13.0826 - 22 - 13.39 - 3 - 9 - 5 - 11 - 0 - 0 - 4 - 4 - 0 - 7 - TPAQREY - TPTLHEY - TP EY - - - - - 2 - gnl|BL_ORD_ID|1392 - 110335|E7|AAD33253.1|Human papillomavirus type 16|333760 - 1392 - 32 - - - 1 - 13.0826 - 22 - 19.7687 - 3 - 9 - 5 - 11 - 0 - 0 - 4 - 4 - 0 - 7 - TPAQREY - TPTLHEY - TP EY - - - - - 3 - gnl|BL_ORD_ID|1823 - 178351|Protein E7|P03129.1|Human papillomavirus type 16|333760 - 1823 - 15 - - - 1 - 12.6974 - 21 - 31.7906 - 3 - 9 - 1 - 7 - 0 - 0 - 4 - 4 - 0 - 7 - TPAQREY - TPTLHEY - TP EY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 7 - Query_7 - M_2776 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_2777 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_2778 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_2779 - 9 - - - 1 - gnl|BL_ORD_ID|1906 - 180647|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1906 - 15 - - - 1 - 11.927 - 19 - 77.3377 - 1 - 8 - 8 - 15 - 0 - 0 - 4 - 5 - 0 - 8 - VPILQSTP - LPIRYQTP - +PI TP - - - - - 2 - gnl|BL_ORD_ID|1897 - 180617|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1897 - 10 - - - 1 - 11.5418 - 18 - 128.811 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 5 - 0 - 9 - VPILQSTPV - LPIRYQTPA - +PI TP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 11 - Query_11 - M_2780 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_2781 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_2782 - 9 - - - 1 - gnl|BL_ORD_ID|1142 - 75435|largest ORF|AAB02128.1|Hepatitis C virus|11103 - 1142 - 20 - - - 1 - 12.6974 - 21 - 27.6963 - 1 - 9 - 9 - 17 - 0 - 0 - 2 - 5 - 0 - 9 - KSASWITWI - EGCGWMGWL - + W+ W+ - - - - - 2 - gnl|BL_ORD_ID|1070 - 70634|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 - 1070 - 9 - - - 1 - 12.6974 - 21 - 35.3877 - 4 - 8 - 3 - 7 - 0 - 0 - 3 - 4 - 0 - 5 - SWITW - QWLTW - W+TW - - - - - 3 - gnl|BL_ORD_ID|315 - 20894|polyprotein [Hepatitis C virus]|BAF91806.1|Hepatitis C virus|11103 - 315 - 9 - - - 1 - 11.927 - 19 - 82.8955 - 4 - 9 - 3 - 8 - 0 - 0 - 2 - 4 - 0 - 6 - SWITWI - GWVGWL - W+ W+ - - - - - 4 - gnl|BL_ORD_ID|1277 - 101967|pol protein|ACJ76655.1|Human immunodeficiency virus 1|11676 - 1277 - 10 - - - 1 - 11.927 - 19 - 108.205 - 1 - 8 - 3 - 10 - 0 - 0 - 3 - 5 - 0 - 8 - KSASWITW - QKETWETW - + +W TW - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 14 - Query_14 - M_2783 - 9 - - - 1 - gnl|BL_ORD_ID|701 - 42797|6 kDa early secretory antigenic target|P0A564.2|Mycobacterium tuberculosis|1773 - 701 - 20 - - - 1 - 13.0826 - 22 - 15.1234 - 2 - 7 - 5 - 10 - 0 - 0 - 3 - 4 - 0 - 6 - PWSFTG - QWNFAG - W+F G - - - - - 2 - gnl|BL_ORD_ID|1471 - 127792|6 kDa early secretory antigenic target|P0A564.2|Mycobacterium tuberculosis|1773 - 1471 - 10 - - - 1 - 13.0826 - 22 - 21.2326 - 3 - 7 - 2 - 6 - 0 - 0 - 3 - 4 - 0 - 5 - WSFTG - WNFAG - W+F G - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 15 - Query_15 - M_2784 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_2785 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_2786 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_2787 - 9 - - - 1 - gnl|BL_ORD_ID|123 - 8554|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 123 - 20 - - - 1 - 13.853 - 24 - 5.06317 - 4 - 9 - 10 - 15 - 0 - 0 - 3 - 6 - 0 - 6 - GRNHYI - GRSHFL - GR+H++ - - - - - 2 - gnl|BL_ORD_ID|688 - 41622|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 688 - 20 - - - 1 - 13.853 - 24 - 6.41204 - 4 - 9 - 2 - 7 - 0 - 0 - 3 - 6 - 0 - 6 - GRNHYI - GRSHFL - GR+H++ - - - - - 3 - gnl|BL_ORD_ID|578 - 36357|ELAV-like protein 4 (Paraneoplastic encephalomyelitis antigen HuD) (Hu-antigen D)|P26378.1|Homo sapiens|9606 - 578 - 9 - - - 1 - 10.7714 - 16 - 324.284 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - SYGRNHYI - GYGFVNYI - YG +YI - - - - - 4 - gnl|BL_ORD_ID|579 - 36358|ELAV-like protein 1|Q15717.2|Homo sapiens|9606 - 579 - 9 - - - 1 - 10.3862 - 15 - 617.74 - 2 - 9 - 2 - 9 - 0 - 0 - 3 - 5 - 0 - 8 - SYGRNHYI - GYGFVNYV - YG +Y+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 19 - Query_19 - M_2788 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_131144_2_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_131144_2_T.fasta deleted file mode 100755 index 3e7a8fb1..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_131144_2_T.fasta +++ /dev/null @@ -1,120 +0,0 @@ ->M_2789 -DTATGNCLR ->M_2790 -GPYENCSVF ->M_2791 -ETYQQALGK ->M_2792 -YQQALGKRF ->M_2793 -YQQALGKRF ->M_2794 -FAIHKIKQF ->M_2795 -GYTVNIPTI ->M_2796 -HSPSVASMK ->M_2797 -YTDCHASNL ->M_2798 -TYSSPTPNM ->M_2799 -DAIPFGNVP ->M_2800 -IPFGNVPVL ->M_2801 -NYFGVQDAI ->M_2802 -ETLGRGNPM ->M_2803 -MALQLFLQI ->M_2804 -MALQLFLQI ->M_2805 -MALQLFLQI ->M_2806 -KVHSAVITI ->M_2807 -QAGEYSRVV ->M_2808 -RVVDCYLKV ->M_2809 -WQRPTLESI ->M_2810 -WQRPTLESI ->M_2811 -VAQLGFQPL ->M_2812 -EAINCLNVA ->M_2813 -VAIDIYTDM ->M_2814 -HFLHSWTNL ->M_2815 -TFKHLVHFL ->M_2816 -YTFKHLVHF ->M_2817 -YTFKHLVHF ->M_2818 -IIMSRNAYV ->M_2819 -LRYPIIMSR ->M_2820 -MSRNAYVPM ->M_2821 -NAPALLTPR ->M_2822 -RAGSAGGTV ->M_2823 -EAFTLKATV ->M_2824 -YSVIRGEAF ->M_2825 -DIYSMPEGK ->M_2826 -IYSMPEGKL ->M_2827 -SMPEGKLHV ->M_2828 -YSMPEGKLH ->M_2829 -FFFLCVCVF ->M_2830 -FFFLCVCVF ->M_2831 -FFLCVCVFV ->M_2832 -FFLCVCVFV ->M_2833 -HLLQRYNEF ->M_2834 -RAEERRRHL ->M_2835 -ITTTGQKLR ->M_2836 -IMALAVLII ->M_2837 -TALVVVSIM ->M_2838 -DVLPYDAFV ->M_2839 -LTLATFSRI ->M_2840 -VLTLATFSR ->M_2841 -MNQRPILTI ->M_2842 -NQRPILTII ->M_2843 -FNVNAPDLY ->M_2844 -NVNAPDLYI ->M_2845 -RFNVNAPDL ->M_2846 -FHWRVNFIR ->M_2847 -IFHWRVNFI ->M_2848 -KIFHWRVNF diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_131144_2_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_131144_2_T_iedb.xml deleted file mode 100755 index 7034a12b..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_131144_2_T_iedb.xml +++ /dev/null @@ -1,1820 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_2789 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_2789 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_2790 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_2791 - 9 - - - 1 - gnl|BL_ORD_ID|376 - 23288|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 - 376 - 15 - - - 1 - 13.853 - 24 - 5.58032 - 1 - 9 - 5 - 13 - 0 - 0 - 4 - 6 - 0 - 9 - ETYQQALGK - QVYQDWLGR - + YQ LG+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 4 - Query_4 - M_2792 - 9 - - - 1 - gnl|BL_ORD_ID|376 - 23288|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 - 376 - 15 - - - 1 - 12.6974 - 21 - 26.9941 - 1 - 7 - 7 - 13 - 0 - 0 - 4 - 5 - 0 - 7 - YQQALGK - YQDWLGR - YQ LG+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 5 - Query_5 - M_2793 - 9 - - - 1 - gnl|BL_ORD_ID|376 - 23288|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 - 376 - 15 - - - 1 - 12.6974 - 21 - 26.9941 - 1 - 7 - 7 - 13 - 0 - 0 - 4 - 5 - 0 - 7 - YQQALGK - YQDWLGR - YQ LG+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 6 - Query_6 - M_2794 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_2795 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_2796 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_2797 - 9 - - - 1 - gnl|BL_ORD_ID|83 - 6094|Genome polyprotein|Q81495.3|Hepatitis C virus (isolate HCV-K3a/650)|356416 - 83 - 15 - - - 1 - 14.2382 - 25 - 3.49239 - 3 - 8 - 3 - 8 - 0 - 0 - 4 - 5 - 0 - 6 - DCHASN - DCHAQD - DCHA + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 10 - Query_10 - M_2798 - 9 - - - 1 - gnl|BL_ORD_ID|2244 - 232153|rhoptry protein 18|CAJ27113.1|Toxoplasma gondii type I|1209525 - 2244 - 19 - - - 1 - 11.927 - 19 - 88.393 - 1 - 6 - 12 - 17 - 0 - 0 - 4 - 5 - 0 - 6 - TYSSPT - TYTFPT - TY+ PT - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 11 - Query_11 - M_2799 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_2800 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_2801 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_2802 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_2803 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_2804 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_2805 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_2806 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_2807 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_2808 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_2809 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 22 - Query_22 - M_2810 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_2811 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_2812 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_2813 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_2814 - 9 - - - 1 - gnl|BL_ORD_ID|1296 - 103322|polyprotein|BAB18806.1|Hepatitis C virus|11103 - 1296 - 20 - - - 1 - 13.4678 - 23 - 11.4655 - 3 - 8 - 3 - 8 - 0 - 0 - 4 - 4 - 0 - 6 - LHSWTN - LHQWIN - LH W N - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 27 - Query_27 - M_2815 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 28 - Query_28 - M_2816 - 9 - - - 1 - gnl|BL_ORD_ID|123 - 8554|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 123 - 20 - - - 1 - 10.001 - 14 - 536.103 - 1 - 9 - 6 - 14 - 0 - 0 - 4 - 4 - 0 - 9 - YTFKHLVHF - YKFMGRSHF - Y F HF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 29 - Query_29 - M_2817 - 9 - - - 1 - gnl|BL_ORD_ID|123 - 8554|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 123 - 20 - - - 1 - 10.001 - 14 - 536.103 - 1 - 9 - 6 - 14 - 0 - 0 - 4 - 4 - 0 - 9 - YTFKHLVHF - YKFMGRSHF - Y F HF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 30 - Query_30 - M_2818 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 31 - Query_31 - M_2819 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 32 - Query_32 - M_2820 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 33 - Query_33 - M_2821 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 34 - Query_34 - M_2822 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 35 - Query_35 - M_2823 - 9 - - - 1 - gnl|BL_ORD_ID|1266 - 98640|trans-sialidase, putative|EAN80840.1|Trypanosoma cruzi|5693 - 1266 - 9 - - - 1 - 13.853 - 24 - 5.65074 - 3 - 9 - 3 - 9 - 0 - 0 - 6 - 6 - 0 - 7 - FTLKATV - FTLVATV - FTL ATV - - - - - 2 - gnl|BL_ORD_ID|1245 - 98044|trans-sialidase, putative|EAN80840.1|Trypanosoma cruzi|5693 - 1245 - 9 - - - 1 - 13.853 - 24 - 5.65074 - 3 - 9 - 1 - 7 - 0 - 0 - 6 - 6 - 0 - 7 - FTLKATV - FTLVATV - FTL ATV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 36 - Query_36 - M_2824 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 37 - Query_37 - M_2825 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 38 - Query_38 - M_2826 - 9 - - - 1 - gnl|BL_ORD_ID|1725 - 150456|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1725 - 10 - - - 1 - 14.2382 - 25 - 2.71312 - 2 - 9 - 3 - 10 - 0 - 0 - 5 - 5 - 0 - 8 - YSMPEGKL - YSMCTGKF - YSM GK - - - - - 2 - gnl|BL_ORD_ID|186 - 13701|Trans-activator protein BZLF1|P03206.2|Human gammaherpesvirus 4|10376 - 186 - 11 - - - 1 - 13.0826 - 22 - 18.1034 - 4 - 9 - 3 - 8 - 0 - 0 - 3 - 6 - 0 - 6 - MPEGKL - LPQGQL - +P+G+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 39 - Query_39 - M_2827 - 9 - - - 1 - gnl|BL_ORD_ID|186 - 13701|Trans-activator protein BZLF1|P03206.2|Human gammaherpesvirus 4|10376 - 186 - 11 - - - 1 - 13.0826 - 22 - 16.6114 - 2 - 7 - 3 - 8 - 0 - 0 - 3 - 6 - 0 - 6 - MPEGKL - LPQGQL - +P+G+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 40 - Query_40 - M_2828 - 9 - - - 1 - gnl|BL_ORD_ID|1725 - 150456|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1725 - 10 - - - 1 - 14.2382 - 25 - 2.75947 - 1 - 8 - 3 - 10 - 0 - 0 - 5 - 5 - 0 - 8 - YSMPEGKL - YSMCTGKF - YSM GK - - - - - 2 - gnl|BL_ORD_ID|186 - 13701|Trans-activator protein BZLF1|P03206.2|Human gammaherpesvirus 4|10376 - 186 - 11 - - - 1 - 13.0826 - 22 - 17.4916 - 3 - 8 - 3 - 8 - 0 - 0 - 3 - 6 - 0 - 6 - MPEGKL - LPQGQL - +P+G+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 41 - Query_41 - M_2829 - 9 - - - 1 - gnl|BL_ORD_ID|750 - 49831|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 - 750 - 15 - - - 1 - 11.927 - 19 - 74.9817 - 1 - 8 - 4 - 11 - 0 - 0 - 3 - 5 - 0 - 8 - FFFLCVCV - LLILCLCL - LC+C+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 42 - Query_42 - M_2830 - 9 - - - 1 - gnl|BL_ORD_ID|750 - 49831|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 - 750 - 15 - - - 1 - 11.927 - 19 - 74.9817 - 1 - 8 - 4 - 11 - 0 - 0 - 3 - 5 - 0 - 8 - FFFLCVCV - LLILCLCL - LC+C+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 43 - Query_43 - M_2831 - 9 - - - 1 - gnl|BL_ORD_ID|750 - 49831|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 - 750 - 15 - - - 1 - 11.5418 - 18 - 131.587 - 1 - 7 - 5 - 11 - 0 - 0 - 3 - 5 - 0 - 7 - FFLCVCV - LILCLCL - LC+C+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 44 - Query_44 - M_2832 - 9 - - - 1 - gnl|BL_ORD_ID|750 - 49831|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 - 750 - 15 - - - 1 - 11.5418 - 18 - 131.587 - 1 - 7 - 5 - 11 - 0 - 0 - 3 - 5 - 0 - 7 - FFLCVCV - LILCLCL - LC+C+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 45 - Query_45 - M_2833 - 9 - - - 1 - gnl|BL_ORD_ID|1767 - 154980|tegument protein|CAB06735.1|Human alphaherpesvirus 2|10310 - 1767 - 15 - - - 1 - 16.1642 - 30 - 0.279828 - 1 - 9 - 2 - 10 - 0 - 0 - 6 - 7 - 0 - 9 - HLLQRYNEF - NLLQRANEL - +LLQR NE - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 46 - Query_46 - M_2834 - 9 - - - 1 - gnl|BL_ORD_ID|1395 - 110394|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1395 - 32 - - - 1 - 15.0086 - 27 - 1.766 - 2 - 9 - 11 - 18 - 0 - 0 - 5 - 7 - 0 - 8 - AEERRRHL - PEEKQRHL - EE++RHL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 47 - Query_47 - M_2835 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 48 - Query_48 - M_2836 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 49 - Query_49 - M_2837 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 50 - Query_50 - M_2838 - 9 - - - 1 - gnl|BL_ORD_ID|1578 - 141423|envelope glycoprotein B|NP_044629.1|Human alphaherpesvirus 1|10298 - 1578 - 9 - - - 1 - 15.779 - 29 - 0.442703 - 2 - 9 - 2 - 9 - 0 - 0 - 6 - 6 - 0 - 8 - VLPYDAFV - VYPYDEFV - V PYD FV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 51 - Query_51 - M_2839 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 52 - Query_52 - M_2840 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 53 - Query_53 - M_2841 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 54 - Query_54 - M_2842 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 55 - Query_55 - M_2843 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 56 - Query_56 - M_2844 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 57 - Query_57 - M_2845 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 58 - Query_58 - M_2846 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 59 - Query_59 - M_2847 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 60 - Query_60 - M_2848 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_131327_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_131327_1_T.fasta deleted file mode 100755 index ec8b2bf3..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_131327_1_T.fasta +++ /dev/null @@ -1,224 +0,0 @@ ->M_2849 -LHDTTTRSV ->M_2850 -LHNNTTRSV ->M_2851 -TTTRSVHAK ->M_2852 -HFKAPKISM ->M_2853 -GTSSTSCSW ->M_2854 -GVRAQGCYM ->M_2855 -GVRAQGCYM ->M_2856 -RAQGCYMDI ->M_2857 -VAEKGTSKL ->M_2858 -EAFSVSPEW ->M_2859 -FSVSPEWAV ->M_2860 -LTRPVHGAA ->M_2861 -MARTAPASG ->M_2862 -AHQYFAQLL ->M_2863 -AHQYFAQLL ->M_2864 -HQYFAQLLA ->M_2865 -LALQRQRTY ->M_2866 -LALQRQRTY ->M_2867 -ATVCRDPGV ->M_2868 -VCRDPGVPM ->M_2869 -DAPLFNTIV ->M_2870 -VDAPLFNTI ->M_2871 -LSETISPLW ->M_2872 -WPQRPKSQV ->M_2873 -MVLPGGVDI ->M_2874 -FELEWLLYT ->M_2875 -HSHTTGINL ->M_2876 -HSHTTGINL ->M_2877 -SHTTGINLV ->M_2878 -STHSHTTGI ->M_2879 -STHSHTTGI ->M_2880 -STHSHTTGI ->M_2881 -LTLVGVVVY ->M_2882 -LTLVGVVVY ->M_2883 -SEYFLGLTL ->M_2884 -EAHSFEEEM ->M_2885 -SSLQEAHSF ->M_2886 -SHTTLSLDL ->M_2887 -KLREFFKCA ->M_2888 -VAYCPAYVV ->M_2889 -VAYCPAYVV ->M_2890 -VLIPDVVAY ->M_2891 -VVAYCPAYV ->M_2892 -YLVLIPDVV ->M_2893 -FGIGVENFI ->M_2894 -IGVENFITL ->M_2895 -ITLVVFGLI ->M_2896 -KVARSKPYA ->M_2897 -VARSKPYAM ->M_2898 -KFRCDAGLG ->M_2899 -GSRESNMSR ->M_2900 -MSRKKKAVK ->M_2901 -RKKKAVKEK ->M_2902 -QSNTWSLSK ->M_2903 -YQQSNTWSL ->M_2904 -YQQSNTWSL ->M_2905 -YKLVVVGAV ->M_2906 -AVRYSRGCL ->M_2907 -VRYSRGCLT ->M_2908 -YSRGCLTVM ->M_2909 -YSRGCLTVM ->M_2910 -YSRGCLTVM ->M_2911 -VQYASGNRW ->M_2912 -YASGNRWTF ->M_2913 -YASGNRWTF ->M_2914 -AVRNAITST ->M_2915 -NAITSTSVI ->M_2916 -TSIAVRNAI ->M_2917 -VVLPTEAPI ->M_2918 -VVLPTEAPI ->M_2919 -LVATSPSPV ->M_2920 -LSENAVLIL ->M_2921 -LSENAVLIL ->M_2922 -MALSENAVL ->M_2923 -MALSENAVL ->M_2924 -SSSGWRKSF ->M_2925 -FSEASQLDF ->M_2926 -FSEASQLDF ->M_2927 -RTKQFSEAS ->M_2928 -RGFSRQSVL ->M_2929 -LTRSTLSSV ->M_2930 -LTRSTLSSV ->M_2931 -RADHDLGRL ->M_2932 -YRADHDLGR ->M_2933 -ALRVNPVLA ->M_2934 -RVNPVLAEL ->M_2935 -RVNPVLAEL ->M_2936 -SALRVNPVL ->M_2937 -SSALRVNPV ->M_2938 -LLYRRTKAF ->M_2939 -LLYRRTKAF ->M_2940 -LYRRTKAFI ->M_2941 -RTKAFIDYE ->M_2942 -ATSYELHKF ->M_2943 -RTQILATSY ->M_2944 -TSYELHKFY ->M_2945 -TSYELHKFY ->M_2946 -IQKITSPNI ->M_2947 -TSVKPSQPK ->M_2948 -AIFASMAHA ->M_2949 -ASMAHAMQK ->M_2950 -MAHAMQKYL ->M_2951 -MAHAMQKYL ->M_2952 -MAHAMQKYL ->M_2953 -SMAHAMQKY ->M_2954 -RQRLSAPPS ->M_2955 -TAHGLSPTA ->M_2956 -GLIEGYGGW ->M_2957 -QVLGLGGHI ->M_2958 -AAFNPTRDF ->M_2959 -AAFNPTRDF ->M_2960 -KGFVCKAHF diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_131327_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_131327_1_T_iedb.xml deleted file mode 100755 index 651f706c..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_131327_1_T_iedb.xml +++ /dev/null @@ -1,3217 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_2849 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_2849 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_2850 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_2851 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_2852 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_2853 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_2854 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_2855 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_2856 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_2857 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_2858 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_2859 - 9 - - - 1 - gnl|BL_ORD_ID|1686 - 149052|E1 protein|NP_751920.1|Hepatitis C virus (isolate H77)|63746 - 1686 - 18 - - - 1 - 13.0826 - 22 - 17.338 - 1 - 8 - 5 - 12 - 0 - 0 - 4 - 5 - 0 - 8 - FSVSPEWA - FSMVGNWA - FS+ WA - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 12 - Query_12 - M_2860 - 9 - - - 1 - gnl|BL_ORD_ID|441 - 27125|gag-pol fusion polyprotein|AAN73817.1|Human immunodeficiency virus 1|11676 - 441 - 9 - - - 1 - 15.3938 - 28 - 0.845687 - 1 - 8 - 2 - 9 - 0 - 0 - 5 - 5 - 0 - 8 - LTRPVHGA - LKEPVHGV - L PVHG - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 13 - Query_13 - M_2861 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_2862 - 9 - - - 1 - gnl|BL_ORD_ID|1271 - 101673|gag protein|ABO73990.1|Human immunodeficiency virus 1|11676 - 1271 - 9 - - - 1 - 11.5418 - 18 - 152.614 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 5 - 0 - 9 - AHQYFAQLL - GHQAAMQML - HQ Q+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 15 - Query_15 - M_2863 - 9 - - - 1 - gnl|BL_ORD_ID|1271 - 101673|gag protein|ABO73990.1|Human immunodeficiency virus 1|11676 - 1271 - 9 - - - 1 - 11.5418 - 18 - 152.614 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 5 - 0 - 9 - AHQYFAQLL - GHQAAMQML - HQ Q+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 16 - Query_16 - M_2864 - 9 - - - 1 - gnl|BL_ORD_ID|1271 - 101673|gag protein|ABO73990.1|Human immunodeficiency virus 1|11676 - 1271 - 9 - - - 1 - 11.1566 - 17 - 199.082 - 1 - 8 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - HQYFAQLL - HQAAMQML - HQ Q+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 17 - Query_17 - M_2865 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_2866 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_2867 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_2868 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_2869 - 9 - - - 1 - gnl|BL_ORD_ID|1848 - 180255|gag protein|AAT90688.1|Human immunodeficiency virus 1|11676 - 1848 - 9 - - - 1 - 14.6234 - 26 - 1.85254 - 3 - 9 - 1 - 7 - 0 - 0 - 5 - 6 - 0 - 7 - PLFNTIV - SLFNTVV - LFNT+V - - - - - 2 - gnl|BL_ORD_ID|2159 - 189295|gag protein|AEB70304.1|Human immunodeficiency virus 1|11676 - 2159 - 9 - - - 1 - 13.853 - 24 - 6.16125 - 3 - 9 - 1 - 7 - 0 - 0 - 4 - 6 - 0 - 7 - PLFNTIV - SLYNTVV - L+NT+V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 22 - Query_22 - M_2870 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_2871 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_2872 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_2873 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_2874 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_2875 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 28 - Query_28 - M_2876 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 29 - Query_29 - M_2877 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 30 - Query_30 - M_2878 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 31 - Query_31 - M_2879 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 32 - Query_32 - M_2880 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 33 - Query_33 - M_2881 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 34 - Query_34 - M_2882 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 35 - Query_35 - M_2883 - 9 - - - 1 - gnl|BL_ORD_ID|1608 - 143705|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 1608 - 9 - - - 1 - 11.5418 - 18 - 132.337 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 5 - 0 - 9 - SEYFLGLTL - KEYTFPITL - EY +TL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 36 - Query_36 - M_2884 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 37 - Query_37 - M_2885 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 38 - Query_38 - M_2886 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 39 - Query_39 - M_2887 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 40 - Query_40 - M_2888 - 9 - - - 1 - gnl|BL_ORD_ID|668 - 40253|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 - 668 - 15 - - - 1 - 13.0826 - 22 - 15.3281 - 2 - 7 - 6 - 11 - 0 - 0 - 4 - 4 - 0 - 6 - AYCPAY - ANCPTY - A CP Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 41 - Query_41 - M_2889 - 9 - - - 1 - gnl|BL_ORD_ID|668 - 40253|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 - 668 - 15 - - - 1 - 13.0826 - 22 - 15.3281 - 2 - 7 - 6 - 11 - 0 - 0 - 4 - 4 - 0 - 6 - AYCPAY - ANCPTY - A CP Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 42 - Query_42 - M_2890 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 43 - Query_43 - M_2891 - 9 - - - 1 - gnl|BL_ORD_ID|668 - 40253|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 - 668 - 15 - - - 1 - 13.0826 - 22 - 15.3281 - 3 - 8 - 6 - 11 - 0 - 0 - 4 - 4 - 0 - 6 - AYCPAY - ANCPTY - A CP Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 44 - Query_44 - M_2892 - 9 - - - 1 - gnl|BL_ORD_ID|737 - 46755|HCV-1|AAA45676.1|Hepatitis C virus genotype 1|41856 - 737 - 20 - - - 1 - 12.3122 - 20 - 47.5082 - 2 - 9 - 12 - 19 - 0 - 0 - 5 - 5 - 0 - 8 - LVLIPDVV - LVLNPSVA - LVL P V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 45 - Query_45 - M_2893 - 9 - - - 1 - gnl|BL_ORD_ID|578 - 36357|ELAV-like protein 4 (Paraneoplastic encephalomyelitis antigen HuD) (Hu-antigen D)|P26378.1|Homo sapiens|9606 - 578 - 9 - - - 1 - 11.5418 - 18 - 187.089 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 5 - 0 - 9 - FGIGVENFI - LGYGFVNYI - G G N+I - - - - - 2 - gnl|BL_ORD_ID|579 - 36358|ELAV-like protein 1|Q15717.2|Homo sapiens|9606 - 579 - 9 - - - 1 - 10.7714 - 16 - 339.179 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 5 - 0 - 9 - FGIGVENFI - LGYGFVNYV - G G N++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 46 - Query_46 - M_2894 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 47 - Query_47 - M_2895 - 9 - - - 1 - gnl|BL_ORD_ID|2326 - 423068|polyprotein|ACX44241.1|Hepatitis C virus genotype 1|41856 - 2326 - 10 - - - 1 - 12.3122 - 20 - 51.1794 - 4 - 9 - 1 - 6 - 0 - 0 - 4 - 6 - 0 - 6 - VVFGLI - VLFGLM - V+FGL+ - - - - - 2 - gnl|BL_ORD_ID|1269 - 101380|BNLF2a|YP_401721.1|Human herpesvirus 4 type 1|36352 - 1269 - 9 - - - 1 - 12.3122 - 20 - 58.627 - 4 - 9 - 1 - 6 - 0 - 0 - 4 - 6 - 0 - 6 - VVFGLI - VLFGLL - V+FGL+ - - - - - 3 - gnl|BL_ORD_ID|2331 - 423075|polyprotein|ACX44241.1|Hepatitis C virus genotype 1|41856 - 2331 - 9 - - - 1 - 12.3122 - 20 - 68.0606 - 4 - 9 - 2 - 7 - 0 - 0 - 4 - 6 - 0 - 6 - VVFGLI - VLFGLM - V+FGL+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 48 - Query_48 - M_2896 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 49 - Query_49 - M_2897 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 50 - Query_50 - M_2898 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 51 - Query_51 - M_2899 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 52 - Query_52 - M_2900 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 53 - Query_53 - M_2901 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 54 - Query_54 - M_2902 - 9 - - - 1 - gnl|BL_ORD_ID|1132 - 74886|latent membrane protein 1|AAS99606.1|Human gammaherpesvirus 4|10376 - 1132 - 9 - - - 1 - 12.6974 - 21 - 33.058 - 1 - 7 - 3 - 9 - 0 - 0 - 4 - 5 - 0 - 7 - QSNTWSL - QQNWWTL - Q N W+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 55 - Query_55 - M_2903 - 9 - - - 1 - gnl|BL_ORD_ID|1132 - 74886|latent membrane protein 1|AAS99606.1|Human gammaherpesvirus 4|10376 - 1132 - 9 - - - 1 - 13.853 - 24 - 7.20201 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 6 - 0 - 9 - YQQSNTWSL - YLQQNWWTL - Y Q N W+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 56 - Query_56 - M_2904 - 9 - - - 1 - gnl|BL_ORD_ID|1132 - 74886|latent membrane protein 1|AAS99606.1|Human gammaherpesvirus 4|10376 - 1132 - 9 - - - 1 - 13.853 - 24 - 7.20201 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 6 - 0 - 9 - YQQSNTWSL - YLQQNWWTL - Y Q N W+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 57 - Query_57 - M_2905 - 9 - - - 1 - gnl|BL_ORD_ID|524 - 32238|polyprotein [Hepatitis C virus subtype 1a]|ABV46251.2|Hepatitis C virus (isolate H77)|63746 - 524 - 10 - - - 1 - 12.6974 - 21 - 30.9217 - 2 - 7 - 1 - 6 - 0 - 0 - 5 - 6 - 0 - 6 - KLVVVG - KLVVLG - KLVV+G - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 58 - Query_58 - M_2906 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 59 - Query_59 - M_2907 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 60 - Query_60 - M_2908 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 61 - Query_61 - M_2909 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 62 - Query_62 - M_2910 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 63 - Query_63 - M_2911 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 64 - Query_64 - M_2912 - 9 - - - 1 - gnl|BL_ORD_ID|2244 - 232153|rhoptry protein 18|CAJ27113.1|Toxoplasma gondii type I|1209525 - 2244 - 19 - - - 1 - 12.3122 - 20 - 39.084 - 2 - 9 - 8 - 15 - 0 - 0 - 4 - 6 - 0 - 8 - ASGNRWTF - ATGITYTF - A+G +TF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 65 - Query_65 - M_2913 - 9 - - - 1 - gnl|BL_ORD_ID|2244 - 232153|rhoptry protein 18|CAJ27113.1|Toxoplasma gondii type I|1209525 - 2244 - 19 - - - 1 - 12.3122 - 20 - 39.084 - 2 - 9 - 8 - 15 - 0 - 0 - 4 - 6 - 0 - 8 - ASGNRWTF - ATGITYTF - A+G +TF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 66 - Query_66 - M_2914 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 67 - Query_67 - M_2915 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 68 - Query_68 - M_2916 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 69 - Query_69 - M_2917 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 70 - Query_70 - M_2918 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 71 - Query_71 - M_2919 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 72 - Query_72 - M_2920 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 73 - Query_73 - M_2921 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 74 - Query_74 - M_2922 - 9 - - - 1 - gnl|BL_ORD_ID|40 - 2884|cysteine proteinase cruzipain (EC 3.4.22.-) - Trypanosoma cruzi|A45629|Trypanosoma cruzi|5693 - 40 - 10 - - - 1 - 11.5418 - 18 - 139.346 - 2 - 9 - 1 - 8 - 0 - 0 - 6 - 6 - 0 - 8 - ALSENAVL - ALSLAAVL - ALS AVL - - - - - 2 - gnl|BL_ORD_ID|39 - 2883|cysteine proteinase cruzipain (EC 3.4.22.-) - Trypanosoma cruzi|A45629|Trypanosoma cruzi|5693 - 39 - 9 - - - 1 - 11.5418 - 18 - 157.499 - 2 - 9 - 1 - 8 - 0 - 0 - 6 - 6 - 0 - 8 - ALSENAVL - ALSLAAVL - ALS AVL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 75 - Query_75 - M_2923 - 9 - - - 1 - gnl|BL_ORD_ID|40 - 2884|cysteine proteinase cruzipain (EC 3.4.22.-) - Trypanosoma cruzi|A45629|Trypanosoma cruzi|5693 - 40 - 10 - - - 1 - 11.5418 - 18 - 139.346 - 2 - 9 - 1 - 8 - 0 - 0 - 6 - 6 - 0 - 8 - ALSENAVL - ALSLAAVL - ALS AVL - - - - - 2 - gnl|BL_ORD_ID|39 - 2883|cysteine proteinase cruzipain (EC 3.4.22.-) - Trypanosoma cruzi|A45629|Trypanosoma cruzi|5693 - 39 - 9 - - - 1 - 11.5418 - 18 - 157.499 - 2 - 9 - 1 - 8 - 0 - 0 - 6 - 6 - 0 - 8 - ALSENAVL - ALSLAAVL - ALS AVL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 76 - Query_76 - M_2924 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 77 - Query_77 - M_2925 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 78 - Query_78 - M_2926 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 79 - Query_79 - M_2927 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 80 - Query_80 - M_2928 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 81 - Query_81 - M_2929 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 82 - Query_82 - M_2930 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 83 - Query_83 - M_2931 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 84 - Query_84 - M_2932 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 85 - Query_85 - M_2933 - 9 - - - 1 - gnl|BL_ORD_ID|857 - 56198|glycoprotein gp35/37|AAC59622.1|Human gammaherpesvirus 8|37296 - 857 - 15 - - - 1 - 13.0826 - 22 - 17.2424 - 2 - 7 - 5 - 10 - 0 - 0 - 4 - 6 - 0 - 6 - LRVNPV - IRVSPV - +RV+PV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 86 - Query_86 - M_2934 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 87 - Query_87 - M_2935 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 88 - Query_88 - M_2936 - 9 - - - 1 - gnl|BL_ORD_ID|857 - 56198|glycoprotein gp35/37|AAC59622.1|Human gammaherpesvirus 8|37296 - 857 - 15 - - - 1 - 13.0826 - 22 - 17.2424 - 1 - 8 - 3 - 10 - 0 - 0 - 4 - 7 - 0 - 8 - SALRVNPV - TRIRVSPV - + +RV+PV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 89 - Query_89 - M_2937 - 9 - - - 1 - gnl|BL_ORD_ID|857 - 56198|glycoprotein gp35/37|AAC59622.1|Human gammaherpesvirus 8|37296 - 857 - 15 - - - 1 - 13.4678 - 23 - 8.0204 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 8 - 0 - 9 - SSALRVNPV - TTRIRVSPV - ++ +RV+PV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 90 - Query_90 - M_2938 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 91 - Query_91 - M_2939 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 92 - Query_92 - M_2940 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 93 - Query_93 - M_2941 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 94 - Query_94 - M_2942 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 95 - Query_95 - M_2943 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 96 - Query_96 - M_2944 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 97 - Query_97 - M_2945 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 98 - Query_98 - M_2946 - 9 - - - 1 - gnl|BL_ORD_ID|2271 - 419002|PPE family protein PPE68|KAM81677.1|Mycobacterium tuberculosis H37Ra|419947 - 2271 - 10 - - - 1 - 11.927 - 19 - 81.0261 - 1 - 9 - 2 - 10 - 0 - 0 - 3 - 7 - 0 - 9 - IQKITSPNI - IEKPVAPSV - I+K +P++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 99 - Query_99 - M_2947 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 100 - Query_100 - M_2948 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 101 - Query_101 - M_2949 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 102 - Query_102 - M_2950 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 103 - Query_103 - M_2951 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 104 - Query_104 - M_2952 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 105 - Query_105 - M_2953 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 106 - Query_106 - M_2954 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 107 - Query_107 - M_2955 - 9 - - - 1 - gnl|BL_ORD_ID|332 - 21139|envelope protein|BAF48755.1|Hepatitis B virus|10407 - 332 - 10 - - - 1 - 14.2382 - 25 - 3.10797 - 4 - 9 - 1 - 6 - 0 - 0 - 5 - 5 - 0 - 6 - GLSPTA - GLSPTV - GLSPT - - - - - 2 - gnl|BL_ORD_ID|331 - 21137|Major surface antigen precursor|P03142.4|Hepatitis B virus subtype adw|106821 - 331 - 10 - - - 1 - 14.2382 - 25 - 3.68732 - 4 - 9 - 1 - 6 - 0 - 0 - 5 - 5 - 0 - 6 - GLSPTA - GLSPTV - GLSPT - - - - - 3 - gnl|BL_ORD_ID|1392 - 110335|E7|AAD33253.1|Human papillomavirus type 16|333760 - 1392 - 32 - - - 1 - 13.0826 - 22 - 19.2096 - 3 - 8 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - HGLSPT - HGDTPT - HG +PT - - - - - 4 - gnl|BL_ORD_ID|1408 - 110940|Protein E7|P03129.1|Human papillomavirus type 16|333760 - 1408 - 15 - - - 1 - 12.6974 - 21 - 27.8948 - 3 - 8 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - HGLSPT - HGDTPT - HG +PT - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 108 - Query_108 - M_2956 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 109 - Query_109 - M_2957 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 110 - Query_110 - M_2958 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 111 - Query_111 - M_2959 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 112 - Query_112 - M_2960 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_131909_2_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_131909_2_T.fasta deleted file mode 100755 index c4488424..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_131909_2_T.fasta +++ /dev/null @@ -1,76 +0,0 @@ ->M_2961 -SRRACSSEL ->M_2962 -SPKLKMPEM ->M_2963 -SNKEKWISL ->M_2964 -KRWESEHIL ->M_2965 -LHNEIKTLL ->M_2966 -FSDKMGTLT ->M_2967 -LAAERKAAL ->M_2968 -TPRRSRWQL ->M_2969 -MNCIRQASV ->M_2970 -DQRCRLCPA ->M_2971 -HTTRSLFQY ->M_2972 -PHCPQPLVY ->M_2973 -SLEGRIWAL ->M_2974 -YTDFLLCAS ->M_2975 -VVGARGVGK ->M_2976 -RGRKNRSSV ->M_2977 -FEKMHQMDL ->M_2978 -QVFEKMHQM ->M_2979 -ARWPFGNTM ->M_2980 -GALKKALAK ->M_2981 -RLIAISWPL ->M_2982 -WPLRYVTVM ->M_2983 -HILGNFLTK ->M_2984 -IRCGYPTHI ->M_2985 -EAGPRKGPL ->M_2986 -RLEEAGPRK ->M_2987 -KLPEMKLPK ->M_2988 -MKLPKVPEM ->M_2989 -DRQDQSSHY ->M_2990 -SHYGQPDRQ ->M_2991 -GIMPGHIQK ->M_2992 -IMPGHIQKK ->M_2993 -STMRESSPK ->M_2994 -FPLFAIWPM ->M_2995 -PTDPMLGLA ->M_2996 -EARSRATLA ->M_2997 -FHEARSRAT ->M_2998 -FSIFSTLTK diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_131909_2_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_131909_2_T_iedb.xml deleted file mode 100755 index 40c7799e..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_131909_2_T_iedb.xml +++ /dev/null @@ -1,1221 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_2961 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_2961 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_2962 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_2963 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_2964 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_2965 - 9 - - - 1 - gnl|BL_ORD_ID|1378 - 109332|L1 protein|ACG75893.1|Human papillomavirus type 16|333760 - 1378 - 9 - - - 1 - 9.61583 - 13 - 1457.43 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 6 - 0 - 9 - LHNEIKTLL - IHSMNSTIL - +H+ T+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 6 - Query_6 - M_2966 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_2967 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_2968 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_2969 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_2970 - 9 - - - 1 - gnl|BL_ORD_ID|1621 - 145860|Protein E6|P04019.1|Human papillomavirus type 11|10580 - 1621 - 9 - - - 1 - 12.6974 - 21 - 39.1808 - 3 - 7 - 5 - 9 - 0 - 0 - 4 - 4 - 0 - 5 - RCRLC - RCYLC - RC LC - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 11 - Query_11 - M_2971 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_2972 - 9 - - - 1 - gnl|BL_ORD_ID|96 - 6591|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 96 - 18 - - - 1 - 15.0086 - 27 - 1.3941 - 2 - 9 - 10 - 17 - 0 - 0 - 5 - 6 - 0 - 8 - HCPQPLVY - HGPTPLLY - H P PL+Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 13 - Query_13 - M_2973 - 9 - - - 1 - gnl|BL_ORD_ID|2111 - 186219|polyprotein|AGK36298.1|Dengue virus 2|11060 - 2111 - 9 - - - 1 - 14.2382 - 25 - 3.43721 - 3 - 9 - 3 - 9 - 0 - 0 - 4 - 5 - 0 - 7 - EGRIWAL - DGRFWEL - +GR W L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 14 - Query_14 - M_2974 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_2975 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_2976 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_2977 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_2978 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_2979 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_2980 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_2981 - 9 - - - 1 - gnl|BL_ORD_ID|1787 - 161186|Nonstructural protein NS5|NP_739590.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1787 - 15 - - - 1 - 11.1566 - 17 - 239.5 - 1 - 7 - 1 - 7 - 0 - 0 - 3 - 4 - 0 - 7 - RLIAISW - RLLTKPW - RL+ W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 22 - Query_22 - M_2982 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_2983 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_2984 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_2985 - 9 - - - 1 - gnl|BL_ORD_ID|1950 - 181035|||| - 1950 - 44 - - - 1 - 14.2382 - 25 - 5.04563 - 4 - 8 - 27 - 31 - 0 - 0 - 4 - 5 - 0 - 5 - PRKGP - PRRGP - PR+GP - - - - - 2 - gnl|BL_ORD_ID|1130 - 74798|polyprotein|BAA03375.1|Hepatitis C virus|11103 - 1130 - 10 - - - 1 - 13.853 - 24 - 5.77604 - 4 - 8 - 4 - 8 - 0 - 0 - 4 - 5 - 0 - 5 - PRKGP - PRRGP - PR+GP - - - - - 3 - gnl|BL_ORD_ID|374 - 23224|polyprotein|BAB18806.1|Hepatitis C virus|11103 - 374 - 15 - - - 1 - 13.853 - 24 - 5.77703 - 4 - 8 - 6 - 10 - 0 - 0 - 4 - 5 - 0 - 5 - PRKGP - PRRGP - PR+GP - - - - - 4 - gnl|BL_ORD_ID|630 - 37685|polyprotein|BAA03375.1|Hepatitis C virus|11103 - 630 - 9 - - - 1 - 13.853 - 24 - 6.83656 - 4 - 8 - 3 - 7 - 0 - 0 - 4 - 5 - 0 - 5 - PRKGP - PRRGP - PR+GP - - - - - 5 - gnl|BL_ORD_ID|1129 - 74797|polyprotein|BAA09073.1|Hepatitis C virus subtype 1b|31647 - 1129 - 9 - - - 1 - 13.853 - 24 - 6.95623 - 4 - 8 - 4 - 8 - 0 - 0 - 4 - 5 - 0 - 5 - PRKGP - PRRGP - PR+GP - - - - - 6 - gnl|BL_ORD_ID|1508 - 139406|polyprotein|ACT37184.1|Hepatitis C virus|11103 - 1508 - 10 - - - 1 - 12.3122 - 20 - 54.6881 - 4 - 8 - 4 - 8 - 0 - 0 - 4 - 4 - 0 - 5 - PRKGP - PRPGP - PR GP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 26 - Query_26 - M_2986 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_2987 - 9 - - - 1 - gnl|BL_ORD_ID|241 - 16836|precore/core protein [Hepatitis B virus]|AAR03815.1|Hepatitis B virus|10407 - 241 - 10 - - - 1 - 10.7714 - 16 - 451.277 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 4 - 0 - 8 - LPEMKLPK - LPSDFLPS - LP LP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 28 - Query_28 - M_2988 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 29 - Query_29 - M_2989 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 30 - Query_30 - M_2990 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 31 - Query_31 - M_2991 - 9 - - - 1 - gnl|BL_ORD_ID|1912 - 180668|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1912 - 10 - - - 1 - 12.6974 - 21 - 26.0802 - 3 - 9 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - MPGHIQK - MPSVIEK - MP I+K - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 32 - Query_32 - M_2992 - 9 - - - 1 - gnl|BL_ORD_ID|1912 - 180668|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1912 - 10 - - - 1 - 12.6974 - 21 - 35.4066 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - MPGHIQK - MPSVIEK - MP I+K - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 33 - Query_33 - M_2993 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 34 - Query_34 - M_2994 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 35 - Query_35 - M_2995 - 9 - - - 1 - gnl|BL_ORD_ID|242 - 16839|External core antigen|SRC279980|Hepatitis B virus|10407 - 242 - 10 - - - 1 - 12.6974 - 21 - 26.0802 - 1 - 8 - 3 - 10 - 0 - 0 - 4 - 6 - 0 - 8 - PTDPMLGL - PSDTNMGL - P+D +GL - - - - - 2 - gnl|BL_ORD_ID|1581 - 141462|tegument protein UL21|NP_044622.1|Human alphaherpesvirus 1|10298 - 1581 - 9 - - - 1 - 12.3122 - 20 - 40.5299 - 1 - 6 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - PTDPML - PDDPVL - P DP+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 36 - Query_36 - M_2996 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 37 - Query_37 - M_2997 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 38 - Query_38 - M_2998 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132080_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132080_1_T.fasta deleted file mode 100755 index 7703bccd..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132080_1_T.fasta +++ /dev/null @@ -1,80 +0,0 @@ ->M_2999 -LPDRLTLEF ->M_3000 -LPDRLTLEF ->M_3001 -FSDHQSFVV ->M_3002 -LLSQVQFPY ->M_3003 -GELSVDVSF ->M_3004 -LSVDVSFFF ->M_3005 -LSVDVSFFF ->M_3006 -SVDVSFFFK ->M_3007 -VVDQGNIGK ->M_3008 -MVFHKHGEK ->M_3009 -NAYTMVFHK ->M_3010 -MESNNMPFL ->M_3011 -VMESNNMPF ->M_3012 -IPVPVGATA ->M_3013 -VPVGATASF ->M_3014 -SLDLSQTNL ->M_3015 -TETSSSMPG ->M_3016 -HTDPHLCDF ->M_3017 -SLGFKLLLR ->M_3018 -HEQCDSSSL ->M_3019 -AEKSQGPVL ->M_3020 -RLLSTQAEK ->M_3021 -LSDIGGLLL ->M_3022 -LYLYVLSDI ->M_3023 -SELSSDINL ->M_3024 -MPHSQYLSA ->M_3025 -EEAFVPILY ->M_3026 -QVTVSFTEM ->M_3027 -TVSFTEMLK ->M_3028 -VSFTEMLKK ->M_3029 -LGYRCRFNK ->M_3030 -LPDLFTPPL ->M_3031 -HTDGDTLLQ ->M_3032 -ILAKHKSLF ->M_3033 -KLTILAKHK ->M_3034 -AQTHEPRQW ->M_3035 -EAVAGHIPA ->M_3036 -VAGHIPAIF ->M_3037 -VADLLAFTH ->M_3038 -VVGAVGVGK diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132080_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132080_1_T_iedb.xml deleted file mode 100755 index 5a5e9535..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132080_1_T_iedb.xml +++ /dev/null @@ -1,1566 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_2999 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_2999 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_3000 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_3001 - 9 - - - 1 - gnl|BL_ORD_ID|2185 - 190466|large surface antigen|CAL29876.1|Hepatitis B virus|10407 - 2185 - 15 - - - 1 - 13.4678 - 23 - 7.48645 - 1 - 5 - 4 - 8 - 0 - 0 - 4 - 4 - 0 - 5 - FSDHQ - FPDHQ - F DHQ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 4 - Query_4 - M_3002 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_3003 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_3004 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_3005 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_3006 - 9 - - - 1 - gnl|BL_ORD_ID|72 - 5295|nef protein|ACR27174.1|Human immunodeficiency virus 1|11676 - 72 - 9 - - - 1 - 14.6234 - 26 - 1.88321 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 7 - 0 - 9 - SVDVSFFFK - AVDLSHFLK - +VD+S F K - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 9 - Query_9 - M_3007 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_3008 - 9 - - - 1 - gnl|BL_ORD_ID|1090 - 72039|polyprotein|CAB53095.1|Hepatitis C virus subtype 1b|31647 - 1090 - 10 - - - 1 - 12.6974 - 21 - 23.5358 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 5 - 0 - 8 - VFHKHGEK - VYHGAGSK - V+H G K - - - - - 2 - gnl|BL_ORD_ID|1089 - 72038|Polyprotein|Q9IZA3|Hepatitis C virus subtype 2a|31649 - 1089 - 10 - - - 1 - 12.6974 - 21 - 27.922 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 5 - 0 - 8 - VFHKHGEK - VYHGAGNK - V+H G K - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 11 - Query_11 - M_3009 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_3010 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_3011 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_3012 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_3013 - 9 - - - 1 - gnl|BL_ORD_ID|696 - 42342|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 - 696 - 9 - - - 1 - 15.3938 - 28 - 0.610749 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 7 - 0 - 9 - VPVGATASF - MPVGGQSSF - +PVG +SF - - - - - 2 - gnl|BL_ORD_ID|2175 - 189750|Diacylglycerol acyltransferase/mycolyltransferase Ag85B|SRC280000|Mycobacterium tuberculosis|1773 - 2175 - 9 - - - 1 - 15.0086 - 27 - 1.15928 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 7 - 0 - 9 - VPVGATASF - MPVGGGSSF - +PVG +SF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 16 - Query_16 - M_3014 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_3015 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_3016 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_3017 - 9 - - - 1 - gnl|BL_ORD_ID|785 - 52578|liver stage antigen-1|CAA82974.1|Plasmodium falciparum|5833 - 785 - 9 - - - 1 - 12.6974 - 21 - 30.8766 - 3 - 9 - 3 - 9 - 0 - 0 - 5 - 5 - 0 - 7 - GFKLLLR - NFKSLLR - FK LLR - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 20 - Query_20 - M_3018 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_3019 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 22 - Query_22 - M_3020 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_3021 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_3022 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_3023 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_3024 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_3025 - 9 - - - 1 - gnl|BL_ORD_ID|1553 - 141228|tegument protein VP11/12|NP_044648.1|Human alphaherpesvirus 1|10298 - 1553 - 9 - - - 1 - 13.4678 - 23 - 8.56958 - 3 - 9 - 1 - 7 - 0 - 0 - 4 - 6 - 0 - 7 - AFVPILY - AYVSVLY - A+V +LY - - - - - 2 - gnl|BL_ORD_ID|1568 - 141341|tegument protein VP11/12|NP_044648.1|Human alphaherpesvirus 1|10298 - 1568 - 9 - - - 1 - 13.4678 - 23 - 11.9303 - 3 - 9 - 3 - 9 - 0 - 0 - 4 - 6 - 0 - 7 - AFVPILY - AYVSVLY - A+V +LY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 28 - Query_28 - M_3026 - 9 - - - 1 - gnl|BL_ORD_ID|1427 - 112697|Protein E6|P26554.1|Human papillomavirus type 51|10595 - 1427 - 10 - - - 1 - 13.0826 - 22 - 16.6782 - 4 - 9 - 1 - 6 - 0 - 0 - 4 - 6 - 0 - 6 - VSFTEM - VAFTEI - V+FTE+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 29 - Query_29 - M_3027 - 9 - - - 1 - gnl|BL_ORD_ID|1427 - 112697|Protein E6|P26554.1|Human papillomavirus type 51|10595 - 1427 - 10 - - - 1 - 13.0826 - 22 - 14.2707 - 2 - 7 - 1 - 6 - 0 - 0 - 4 - 6 - 0 - 6 - VSFTEM - VAFTEI - V+FTE+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 30 - Query_30 - M_3028 - 9 - - - 1 - gnl|BL_ORD_ID|1427 - 112697|Protein E6|P26554.1|Human papillomavirus type 51|10595 - 1427 - 10 - - - 1 - 13.4678 - 23 - 11.9953 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 6 - 0 - 6 - VSFTEM - VAFTEI - V+FTE+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 31 - Query_31 - M_3029 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 32 - Query_32 - M_3030 - 9 - - - 1 - gnl|BL_ORD_ID|141 - 10587|viral polyprotein|AAA42941.1|Dengue virus 2 Thailand/NGS-C/1944|11065 - 141 - 9 - - - 1 - 13.0826 - 22 - 23.0624 - 4 - 8 - 3 - 7 - 0 - 0 - 4 - 4 - 0 - 5 - LFTPP - FFTPP - FTPP - - - - - 2 - gnl|BL_ORD_ID|235 - 16814|precore protein|CAM58990.1|Hepatitis B virus|10407 - 235 - 10 - - - 1 - 10.7714 - 16 - 347.035 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 6 - 0 - 9 - LPDLFTPPL - LPNDFFPSV - LP+ F P + - - - - - 3 - gnl|BL_ORD_ID|234 - 16813|External core antigen|SRC279980|Hepatitis B virus|10407 - 234 - 10 - - - 1 - 10.7714 - 16 - 384.587 - 1 - 7 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - LPDLFTP - LPNDFFP - LP+ F P - - - - - 4 - gnl|BL_ORD_ID|239 - 16832|core protein|BAF42671.1|Hepatitis B virus|10407 - 239 - 10 - - - 1 - 10.3862 - 15 - 626.674 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 5 - 0 - 9 - LPDLFTPPL - LPSDFFPSI - LP F P + - - - - - 5 - gnl|BL_ORD_ID|69 - 5191|core protein|AAL31859.1|Hepatitis B virus|10407 - 69 - 17 - - - 1 - 10.001 - 14 - 641.761 - 1 - 9 - 9 - 17 - 0 - 0 - 4 - 5 - 0 - 9 - LPDLFTPPL - LPSDFFPSV - LP F P + - - - - - 6 - gnl|BL_ORD_ID|241 - 16836|precore/core protein [Hepatitis B virus]|AAR03815.1|Hepatitis B virus|10407 - 241 - 10 - - - 1 - 10.3862 - 15 - 731.165 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 5 - 0 - 9 - LPDLFTPPL - LPSDFLPSV - LP F P + - - - - - 7 - gnl|BL_ORD_ID|240 - 16833|core protein|CAL29866.1|Hepatitis B virus|10407 - 240 - 10 - - - 1 - 10.001 - 14 - 817.025 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 5 - 0 - 9 - LPDLFTPPL - LPSDFFPSV - LP F P + - - - - - 8 - gnl|BL_ORD_ID|653 - 38701|core protein|AAL31859.1|Hepatitis B virus|10407 - 653 - 9 - - - 1 - 10.001 - 14 - 831.41 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 5 - 0 - 9 - LPDLFTPPL - LPSDFFPSV - LP F P + - - - - - 9 - gnl|BL_ORD_ID|238 - 16831|External core antigen|SRC279980|Hepatitis B virus|10407 - 238 - 10 - - - 1 - 10.001 - 14 - 887.43 - 1 - 7 - 2 - 8 - 0 - 0 - 4 - 4 - 0 - 7 - LPDLFTP - LPSDFFP - LP F P - - - - - 10 - gnl|BL_ORD_ID|237 - 16827|External core antigen|SRC279980|Hepatitis B virus|10407 - 237 - 10 - - - 1 - 10.001 - 14 - 887.43 - 1 - 7 - 2 - 8 - 0 - 0 - 4 - 4 - 0 - 7 - LPDLFTP - LPSDFFP - LP F P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 33 - Query_33 - M_3031 - 9 - - - 1 - gnl|BL_ORD_ID|1355 - 108148|polyprotein|AAF65953.1|Hepatitis C virus|11103 - 1355 - 10 - - - 1 - 11.5418 - 18 - 175.991 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 5 - 0 - 8 - HTDGDTLL - STDSTTIL - TD T+L - - - - - 2 - gnl|BL_ORD_ID|1359 - 108158|polyprotein|AAF65953.1|Hepatitis C virus|11103 - 1359 - 10 - - - 1 - 11.1566 - 17 - 253.803 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - TDGDTLL - TDSTTIL - TD T+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 34 - Query_34 - M_3032 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 35 - Query_35 - M_3033 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 36 - Query_36 - M_3034 - 9 - - - 1 - gnl|BL_ORD_ID|2137 - 187106|Vpr protein|BAA93983.1|Human immunodeficiency virus 1|11676 - 2137 - 9 - - - 1 - 14.2382 - 25 - 3.55601 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 5 - 0 - 9 - AQTHEPRQW - AVRHFPRIW - A H PR W - - - - - 2 - gnl|BL_ORD_ID|1931 - 180758|Nonstructural protein NS5|NP_739590.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1931 - 15 - - - 1 - 10.7714 - 16 - 365.404 - 2 - 9 - 6 - 13 - 0 - 0 - 3 - 4 - 0 - 8 - QTHEPRQW - QDHPYKTW - Q H + W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 37 - Query_37 - M_3035 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 38 - Query_38 - M_3036 - 9 - - - 1 - gnl|BL_ORD_ID|128 - 9199|E1 protein|ABB77003.1|Hepatitis C virus|11103 - 128 - 9 - - - 1 - 14.2382 - 25 - 3.32254 - 1 - 8 - 2 - 9 - 0 - 0 - 4 - 7 - 0 - 8 - VAGHIPAI - LMGYIPAV - + G+IPA+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 39 - Query_39 - M_3037 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 40 - Query_40 - M_3038 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132221_2_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132221_2_T.fasta deleted file mode 100755 index 04e045d2..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132221_2_T.fasta +++ /dev/null @@ -1,74 +0,0 @@ ->M_3039 -KLTSYKCKL ->M_3040 -WLRVGNGAL ->M_3041 -SLQLSAHRL ->M_3042 -IVVISIWEI ->M_3043 -SIWEIVGQA ->M_3044 -YLKRGYLTL ->M_3045 -MLHVDRHTL ->M_3046 -VLERGQFDY ->M_3047 -AALSIDHWV ->M_3048 -SIDHWVAVV ->M_3049 -ATAAAAAAL ->M_3050 -GPATAAAAA ->M_3051 -LLLDTPTQL ->M_3052 -HLYDTLGST ->M_3053 -LPLHLYDTL ->M_3054 -EEYTVWIQL ->M_3055 -WEEEYTVWI ->M_3056 -TPEDNRQPL ->M_3057 -LPEQQEGQL ->M_3058 -KPMQVKTPC ->M_3059 -NLQNSPLEI ->M_3060 -VPNLQNSPL ->M_3061 -NELYFAHVL ->M_3062 -YFAHVLFSA ->M_3063 -AVTRPFISL ->M_3064 -FLWPLRVLS ->M_3065 -ISMKFLWPL ->M_3066 -WPLRVLSQF ->M_3067 -REIVWEQGL ->M_3068 -TLAEKRPFM ->M_3069 -LPGHLSRAL ->M_3070 -SLPGHLSRA ->M_3071 -SPSSLPGHL ->M_3072 -ALNNMFCQL ->M_3073 -GPRRGSSPQ ->M_3074 -SPQGAAGAA ->M_3075 -KAFSQSAYL diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132221_2_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132221_2_T_iedb.xml deleted file mode 100755 index 1c80711c..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132221_2_T_iedb.xml +++ /dev/null @@ -1,1367 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_3039 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_3039 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_3040 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_3041 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_3042 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_3043 - 9 - - - 1 - gnl|BL_ORD_ID|939 - 62004|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 - 939 - 15 - - - 1 - 12.6974 - 21 - 27.8948 - 1 - 7 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - SIWEIVG - STWVLVG - S W +VG - - - - - 2 - gnl|BL_ORD_ID|2122 - 186474|polyprotein|AGO67248.1|Dengue virus 2|11060 - 2122 - 10 - - - 1 - 11.5418 - 18 - 155.455 - 3 - 9 - 1 - 7 - 0 - 0 - 3 - 5 - 0 - 7 - WEIVGQA - WKTWGKA - W+ G+A - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 6 - Query_6 - M_3044 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_3045 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_3046 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_3047 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_3048 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_3049 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_3050 - 9 - - - 1 - gnl|BL_ORD_ID|2014 - 183819|polyprotein|AGO67248.1|Dengue virus 2|11060 - 2014 - 10 - - - 1 - 11.927 - 19 - 68.8532 - 2 - 7 - 2 - 7 - 0 - 0 - 5 - 5 - 0 - 6 - PATAAA - PITAAA - P TAAA - - - - - 2 - gnl|BL_ORD_ID|1882 - 180538|Nonstructural protein NS2B|NP_739586.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1882 - 15 - - - 1 - 11.927 - 19 - 73.829 - 2 - 7 - 10 - 15 - 0 - 0 - 5 - 5 - 0 - 6 - PATAAA - PITAAA - P TAAA - - - - - 3 - gnl|BL_ORD_ID|1880 - 180529|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1880 - 9 - - - 1 - 11.927 - 19 - 82.8955 - 2 - 7 - 2 - 7 - 0 - 0 - 5 - 5 - 0 - 6 - PATAAA - PITAAA - P TAAA - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 13 - Query_13 - M_3051 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_3052 - 9 - - - 1 - gnl|BL_ORD_ID|1808 - 169658|major paraflagellar rod protein|AAA30221.1|Trypanosoma cruzi|5693 - 1808 - 9 - - - 1 - 14.2382 - 25 - 3.05306 - 1 - 8 - 1 - 8 - 0 - 0 - 5 - 5 - 0 - 8 - HLYDTLGS - RLYKTLGQ - LY TLG - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 15 - Query_15 - M_3053 - 9 - - - 1 - gnl|BL_ORD_ID|2191 - 190568|polymerase|AAD16253.1|Hepatitis B virus|10407 - 2191 - 20 - - - 1 - 12.3122 - 20 - 44.0299 - 3 - 7 - 6 - 10 - 0 - 0 - 4 - 4 - 0 - 5 - LHLYD - LHLYS - LHLY - - - - - 2 - gnl|BL_ORD_ID|498 - 31898|P protein|P17100.1|Hepatitis B virus|10407 - 498 - 9 - - - 1 - 11.927 - 19 - 75.1319 - 3 - 7 - 2 - 6 - 0 - 0 - 4 - 4 - 0 - 5 - LHLYD - LHLYS - LHLY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 16 - Query_16 - M_3054 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_3055 - 9 - - - 1 - gnl|BL_ORD_ID|2051 - 184702|non-structural protein 1|AGM49312.1|Dengue virus|12637 - 2051 - 9 - - - 1 - 13.4678 - 23 - 9.85027 - 1 - 8 - 2 - 9 - 0 - 0 - 3 - 6 - 0 - 8 - WEEEYTVW - WPKTHTLW - W + +T+W - - - - - 2 - gnl|BL_ORD_ID|552 - 33912|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 - 552 - 10 - - - 1 - 11.927 - 19 - 81.0261 - 1 - 5 - 3 - 7 - 0 - 0 - 3 - 4 - 0 - 5 - WEEEY - WADEY - W +EY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 18 - Query_18 - M_3056 - 9 - - - 1 - gnl|BL_ORD_ID|1741 - 150649|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1741 - 10 - - - 1 - 14.2382 - 25 - 3.44317 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 6 - 0 - 6 - TPEDNR - TPQDNQ - TP+DN+ - - - - - 2 - gnl|BL_ORD_ID|1934 - 180780|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1934 - 9 - - - 1 - 14.2382 - 25 - 4.0067 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 6 - 0 - 6 - TPEDNR - TPQDNQ - TP+DN+ - - - - - 3 - gnl|BL_ORD_ID|1935 - 180781|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1935 - 9 - - - 1 - 13.853 - 24 - 4.75595 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 6 - 0 - 6 - TPEDNR - TPQDNQ - TP+DN+ - - - - - 4 - gnl|BL_ORD_ID|2105 - 186029|envelope protein|ABV59122.1|Dengue virus 3|11069 - 2105 - 9 - - - 1 - 13.0826 - 22 - 13.9535 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 6 - 0 - 9 - TPEDNRQPL - TPTWNRKEL - TP NR+ L - - - - - 5 - gnl|BL_ORD_ID|1494 - 136890|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1494 - 9 - - - 1 - 12.6974 - 21 - 30.3534 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 5 - 0 - 9 - TPEDNRQPL - TPPGSRDPF - TP +R P - - - - - 6 - gnl|BL_ORD_ID|2013 - 183813|polyprotein|AGW21594.1|Dengue virus 1|11053 - 2013 - 10 - - - 1 - 11.927 - 19 - 75.9314 - 2 - 7 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - PEDNRQ - PEPDRQ - PE +RQ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 19 - Query_19 - M_3057 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_3058 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_3059 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 22 - Query_22 - M_3060 - 9 - - - 1 - gnl|BL_ORD_ID|1068 - 70491|envelope glycoprotein|AAC28452.1|Human immunodeficiency virus 1|11676 - 1068 - 10 - - - 1 - 10.3862 - 15 - 691.436 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 4 - 0 - 8 - VPNLQNSP - VPTDPNPP - VP N P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 23 - Query_23 - M_3061 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_3062 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_3063 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_3064 - 9 - - - 1 - gnl|BL_ORD_ID|2098 - 185817|envelope protein|AGW23590.1|Dengue virus 4|11070 - 2098 - 10 - - - 1 - 12.3122 - 20 - 52.9061 - 3 - 8 - 2 - 7 - 0 - 0 - 3 - 5 - 0 - 6 - WPLRVL - WMIRIL - W +R+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 27 - Query_27 - M_3065 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 28 - Query_28 - M_3066 - 9 - - - 1 - gnl|BL_ORD_ID|2098 - 185817|envelope protein|AGW23590.1|Dengue virus 4|11070 - 2098 - 10 - - - 1 - 13.4678 - 23 - 7.62841 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 6 - 0 - 9 - WPLRVLSQF - WMIRILIGF - W +R+L F - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 29 - Query_29 - M_3067 - 9 - - - 1 - gnl|BL_ORD_ID|588 - 36717|nonstructural protein 4B|YP_001527886.1|West Nile virus NY-99|10000971 - 588 - 18 - - - 1 - 12.3122 - 20 - 41.1077 - 4 - 8 - 9 - 13 - 0 - 0 - 3 - 4 - 0 - 5 - VWEQG - LWENG - +WE G - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 30 - Query_30 - M_3068 - 9 - - - 1 - gnl|BL_ORD_ID|974 - 64727|polyprotein precursor|NP_041724.2|West Nile virus|11082 - 974 - 9 - - - 1 - 13.4678 - 23 - 10.7466 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 6 - 0 - 9 - TLAEKRPFM - TLARGFPFV - TLA PF+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 31 - Query_31 - M_3069 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 32 - Query_32 - M_3070 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 33 - Query_33 - M_3071 - 9 - - - 1 - gnl|BL_ORD_ID|793 - 53041|phosphorylated matrix protein (pp65)|AAA45996.1|Human betaherpesvirus 5|10359 - 793 - 11 - - - 1 - 13.0826 - 22 - 14.7222 - 1 - 8 - 3 - 10 - 0 - 0 - 4 - 5 - 0 - 8 - SPSSLPGH - TPDSTPCH - +P S P H - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 34 - Query_34 - M_3072 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 35 - Query_35 - M_3073 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 36 - Query_36 - M_3074 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 37 - Query_37 - M_3075 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132607_2_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132607_2_T.fasta deleted file mode 100755 index 517f5990..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132607_2_T.fasta +++ /dev/null @@ -1,98 +0,0 @@ ->M_3076 -FADHTVVTI ->M_3077 -FADHTVVTI ->M_3078 -MTAFADHTV ->M_3079 -TAFADHTVV ->M_3080 -GLSPRTSRH ->M_3081 -LSPRTSRHI ->M_3082 -RTSRHILER ->M_3083 -SVQACGWRK ->M_3084 -CLLSPSYYH ->M_3085 -LASDRFNHI ->M_3086 -QVASSPAGK ->M_3087 -VASSPAGKL ->M_3088 -IEYDTFGEV ->M_3089 -APSSVALSL ->M_3090 -NTAPSSVAL ->M_3091 -EMKRHKVHI ->M_3092 -ELLDYIRAV ->M_3093 -PQIPPYSTF ->M_3094 -ISHLHRESV ->M_3095 -NLLSPDNMV ->M_3096 -FASDHFLYA ->M_3097 -FASDHFLYA ->M_3098 -ATYVRILQR ->M_3099 -FVVITATYV ->M_3100 -LASSSLDIV ->M_3101 -FAYTILQSV ->M_3102 -TILQSVPNK ->M_3103 -FTLFFMAEY ->M_3104 -FTLFFMAEY ->M_3105 -YAAGPFTLF ->M_3106 -YAAGPFTLF ->M_3107 -YAAGPFTLF ->M_3108 -ICSEATAAI ->M_3109 -SLFNALRGK ->M_3110 -VAIMGSTQV ->M_3111 -SAYVALSNK ->M_3112 -YAISARSDL ->M_3113 -ATKTLRNYK ->M_3114 -DVFFATKTL ->M_3115 -FATKTLRNY ->M_3116 -FATKTLRNY ->M_3117 -FLSWCRRVV ->M_3118 -LSWCRRVVL ->M_3119 -RVVLELSPK ->M_3120 -VVLELSPKV ->M_3121 -IAIAIGAVL ->M_3122 -IAIGAVLLV ->M_3123 -RGMQCAICK ->M_3124 -FSNADVNRL diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132607_2_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132607_2_T_iedb.xml deleted file mode 100755 index 29c73261..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132607_2_T_iedb.xml +++ /dev/null @@ -1,1665 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_3076 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_3076 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_3077 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_3078 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_3079 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_3080 - 9 - - - 1 - gnl|BL_ORD_ID|256 - 17278|Genome polyprotein|P06441.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 256 - 20 - - - 1 - 13.4678 - 23 - 10.9145 - 2 - 9 - 4 - 11 - 0 - 0 - 5 - 5 - 0 - 8 - LSPRTSRH - LKPGESRH - L P SRH - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 6 - Query_6 - M_3081 - 9 - - - 1 - gnl|BL_ORD_ID|664 - 39591|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 - 664 - 20 - - - 1 - 15.0086 - 27 - 1.23765 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 6 - 0 - 9 - LSPRTSRHI - LSPYYKRYI - LSP R+I - - - - - 2 - gnl|BL_ORD_ID|663 - 39590|polyprotein|AAY82030.1|Hepatitis C virus|11103 - 663 - 11 - - - 1 - 14.2382 - 25 - 2.83796 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 6 - 0 - 9 - LSPRTSRHI - LSPYYKRYI - LSP R+I - - - - - 3 - gnl|BL_ORD_ID|662 - 39589|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 662 - 10 - - - 1 - 14.2382 - 25 - 3.68732 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 6 - 0 - 9 - LSPRTSRHI - LSPYYKRYI - LSP R+I - - - - - 4 - gnl|BL_ORD_ID|256 - 17278|Genome polyprotein|P06441.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 256 - 20 - - - 1 - 13.853 - 24 - 6.63101 - 1 - 8 - 4 - 11 - 0 - 0 - 5 - 5 - 0 - 8 - LSPRTSRH - LKPGESRH - L P SRH - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 7 - Query_7 - M_3082 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_3083 - 9 - - - 1 - gnl|BL_ORD_ID|1142 - 75435|largest ORF|AAB02128.1|Hepatitis C virus|11103 - 1142 - 20 - - - 1 - 13.4678 - 23 - 8.80594 - 3 - 7 - 9 - 13 - 0 - 0 - 3 - 4 - 0 - 5 - QACGW - EGCGW - + CGW - - - - - 2 - gnl|BL_ORD_ID|709 - 43621|largest ORF|AAB02128.1|Hepatitis C virus (isolate H77)|63746 - 709 - 9 - - - 1 - 13.4678 - 23 - 12.1399 - 3 - 7 - 2 - 6 - 0 - 0 - 3 - 4 - 0 - 5 - QACGW - EGCGW - + CGW - - - - - 3 - gnl|BL_ORD_ID|708 - 43619|Genome polyprotein|P26664.3|Hepatitis C virus|11103 - 708 - 9 - - - 1 - 13.0826 - 22 - 14.1983 - 3 - 7 - 2 - 6 - 0 - 0 - 3 - 4 - 0 - 5 - QACGW - EGCGW - + CGW - - - - - 4 - gnl|BL_ORD_ID|713 - 43756|Genome polyprotein|SRC279960|Hepatitis C virus subtype 2a|31649 - 713 - 9 - - - 1 - 13.0826 - 22 - 14.7007 - 3 - 7 - 2 - 6 - 0 - 0 - 3 - 4 - 0 - 5 - QACGW - ETCGW - + CGW - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 9 - Query_9 - M_3084 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_3085 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_3086 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_3087 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_3088 - 9 - - - 1 - gnl|BL_ORD_ID|531 - 32738|Liver stage antigen|Q25893|Plasmodium falciparum|5833 - 531 - 9 - - - 1 - 13.4678 - 23 - 10.7466 - 1 - 6 - 4 - 9 - 0 - 0 - 3 - 5 - 0 - 6 - IEYDTF - VQYDNF - ++YD F - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 14 - Query_14 - M_3089 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_3090 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_3091 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_3092 - 9 - - - 1 - gnl|BL_ORD_ID|155 - 11804|EBNA3C latent protein|CAD53421.1|Human gammaherpesvirus 4|10376 - 155 - 10 - - - 1 - 14.2382 - 25 - 3.88217 - 2 - 7 - 4 - 9 - 0 - 0 - 4 - 6 - 0 - 6 - LLDYIR - LLDFVR - LLD++R - - - - - 2 - gnl|BL_ORD_ID|601 - 37153|Nuclear antigen EBNA-3C|Q69140.1|Human gammaherpesvirus 4|10376 - 601 - 10 - - - 1 - 14.2382 - 25 - 4.01795 - 2 - 7 - 1 - 6 - 0 - 0 - 4 - 6 - 0 - 6 - LLDYIR - LLDFVR - LLD++R - - - - - 3 - gnl|BL_ORD_ID|1127 - 74768|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 - 1127 - 9 - - - 1 - 12.6974 - 21 - 26.0147 - 2 - 8 - 2 - 8 - 0 - 0 - 5 - 6 - 0 - 7 - LLDYIRA - LLDGLRA - LLD +RA - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 18 - Query_18 - M_3093 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_3094 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_3095 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_3096 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 22 - Query_22 - M_3097 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_3098 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_3099 - 9 - - - 1 - gnl|BL_ORD_ID|200 - 14902|Genome polyprotein|P26664.3|Hepatitis C virus subtype 1a|31646 - 200 - 9 - - - 1 - 13.0826 - 22 - 16.6015 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 7 - 0 - 7 - VITATYV - VVTSTWV - V+T+T+V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 25 - Query_25 - M_3100 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_3101 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_3102 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 28 - Query_28 - M_3103 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 29 - Query_29 - M_3104 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 30 - Query_30 - M_3105 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 31 - Query_31 - M_3106 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 32 - Query_32 - M_3107 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 33 - Query_33 - M_3108 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 34 - Query_34 - M_3109 - 9 - - - 1 - gnl|BL_ORD_ID|1844 - 180168|gag protein|ABO14878.1|Human immunodeficiency virus 1|11676 - 1844 - 9 - - - 1 - 13.853 - 24 - 5.36545 - 1 - 6 - 1 - 6 - 0 - 0 - 5 - 6 - 0 - 6 - SLFNAL - SLFNAV - SLFNA+ - - - - - 2 - gnl|BL_ORD_ID|2146 - 189275|gag protein|AAO84847.1|Human immunodeficiency virus 1|11676 - 2146 - 9 - - - 1 - 13.853 - 24 - 5.45887 - 1 - 6 - 1 - 6 - 0 - 0 - 5 - 6 - 0 - 6 - SLFNAL - SLFNAV - SLFNA+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 35 - Query_35 - M_3110 - 9 - - - 1 - gnl|BL_ORD_ID|1290 - 102376|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 - 1290 - 15 - - - 1 - 13.853 - 24 - 5.77703 - 1 - 7 - 8 - 14 - 0 - 0 - 4 - 7 - 0 - 7 - VAIMGST - LAVMGSS - +A+MGS+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 36 - Query_36 - M_3111 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 37 - Query_37 - M_3112 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 38 - Query_38 - M_3113 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 39 - Query_39 - M_3114 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 40 - Query_40 - M_3115 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 41 - Query_41 - M_3116 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 42 - Query_42 - M_3117 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 43 - Query_43 - M_3118 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 44 - Query_44 - M_3119 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 45 - Query_45 - M_3120 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 46 - Query_46 - M_3121 - 9 - - - 1 - gnl|BL_ORD_ID|1595 - 142231|Lipoprotein lpqH precursor|P0A5J0.1|Mycobacterium tuberculosis|1773 - 1595 - 24 - - - 1 - 10.3862 - 15 - 335.171 - 1 - 9 - 7 - 15 - 0 - 0 - 4 - 7 - 0 - 9 - IAIAIGAVL - VAVAGAAIL - +A+A A+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 47 - Query_47 - M_3122 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 48 - Query_48 - M_3123 - 9 - - - 1 - gnl|BL_ORD_ID|2035 - 184412|envelope protein|AGW23591.1|Dengue virus 3|11069 - 2035 - 10 - - - 1 - 13.4678 - 23 - 8.32231 - 1 - 8 - 2 - 9 - 0 - 0 - 4 - 6 - 0 - 8 - RGMQCAIC - KGMSYAMC - +GM A+C - - - - - 2 - gnl|BL_ORD_ID|1388 - 110282|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1388 - 25 - - - 1 - 13.0826 - 22 - 15.2941 - 3 - 9 - 5 - 11 - 0 - 0 - 3 - 5 - 0 - 7 - MQCAICK - LECVYCK - ++C CK - - - - - 3 - gnl|BL_ORD_ID|1671 - 148177|early protein|CAA52585.1|Human papillomavirus type 52|10618 - 1671 - 9 - - - 1 - 12.6974 - 21 - 24.707 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - MQCAICK - LQCVQCK - +QC CK - - - - - 4 - gnl|BL_ORD_ID|1661 - 147835|early protein|CAA52585.1|Human papillomavirus type 52|10618 - 1661 - 9 - - - 1 - 11.927 - 19 - 85.6478 - 3 - 9 - 3 - 9 - 0 - 0 - 3 - 6 - 0 - 7 - MQCAICK - IRCIICQ - ++C IC+ - - - - - 5 - gnl|BL_ORD_ID|1499 - 137656|E6 protein|ACT36477.1|Human papillomavirus type 58|10598 - 1499 - 9 - - - 1 - 11.927 - 19 - 87.0561 - 3 - 9 - 3 - 9 - 0 - 0 - 3 - 6 - 0 - 7 - MQCAICK - IRCIICQ - ++C IC+ - - - - - 6 - gnl|BL_ORD_ID|1390 - 110306|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1390 - 32 - - - 1 - 11.5418 - 18 - 120.694 - 3 - 9 - 18 - 24 - 0 - 0 - 3 - 5 - 0 - 7 - MQCAICK - LECVYCK - ++C CK - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 49 - Query_49 - M_3124 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132916_2_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132916_2_T.fasta deleted file mode 100755 index 797c1d82..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132916_2_T.fasta +++ /dev/null @@ -1,38 +0,0 @@ ->M_3125 -MLLKPSERR ->M_3126 -QLAWVPSPY ->M_3127 -QLAWVPSPY ->M_3128 -SSSEYMHHK ->M_3129 -HIASEEPAK ->M_3130 -STGFPHMLF ->M_3131 -YFSTGFPHM ->M_3132 -LVYMMERGK ->M_3133 -VATPGRLVY ->M_3134 -LLIPVAAVY ->M_3135 -SAPLMELLY ->M_3136 -LAMEDTGEY ->M_3137 -MYLHFSDTY ->M_3138 -SVSLMYLHF ->M_3139 -RLSISQWYR ->M_3140 -SQWYRVMVK ->M_3141 -STWIGNKLY ->M_3142 -YMYVCTPLL ->M_3143 -HQRIHTGEK diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132916_2_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132916_2_T_iedb.xml deleted file mode 100755 index fc0cf64a..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132916_2_T_iedb.xml +++ /dev/null @@ -1,511 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_3125 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_3125 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_3126 - 9 - - - 1 - gnl|BL_ORD_ID|1179 - 79628|E1 protein|BAA19893.1|Rubella virus|11041 - 1179 - 21 - - - 1 - 13.853 - 24 - 6.94735 - 3 - 7 - 11 - 15 - 0 - 0 - 4 - 5 - 0 - 5 - AWVPS - AWVPT - AWVP+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 3 - Query_3 - M_3127 - 9 - - - 1 - gnl|BL_ORD_ID|1179 - 79628|E1 protein|BAA19893.1|Rubella virus|11041 - 1179 - 21 - - - 1 - 13.853 - 24 - 6.94735 - 3 - 7 - 11 - 15 - 0 - 0 - 4 - 5 - 0 - 5 - AWVPS - AWVPT - AWVP+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 4 - Query_4 - M_3128 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_3129 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_3130 - 9 - - - 1 - gnl|BL_ORD_ID|23 - 1516|Nucleoprotein|P03418.1|Human respiratory syncytial virus A2|11259 - 23 - 14 - - - 1 - 12.6974 - 21 - 30.4718 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - TGFPHML - AGFYHIL - GF H+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 7 - Query_7 - M_3131 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_3132 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_3133 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_3134 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_3135 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_3136 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_3137 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_3138 - 9 - - - 1 - gnl|BL_ORD_ID|1887 - 180579|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1887 - 15 - - - 1 - 14.6234 - 26 - 2.26419 - 3 - 8 - 8 - 13 - 0 - 0 - 5 - 5 - 0 - 6 - SLMYLH - SLMYFH - SLMY H - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 15 - Query_15 - M_3139 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_3140 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_3141 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_3142 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_3143 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132940_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132940_1_T.fasta deleted file mode 100755 index 4ee0029b..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132940_1_T.fasta +++ /dev/null @@ -1,262 +0,0 @@ ->M_3144 -ALGLAQGTF ->M_3145 -GLAQGTFVF ->M_3146 -GTFVFIAHF ->M_3147 -KLHQVFHSI ->M_3148 -VTVPEKLSF ->M_3149 -HPCSQPVWL ->M_3150 -FPLVRSCQM ->M_3151 -MMCRDLPGF ->M_3152 -RVKATIVAM ->M_3153 -AQGEPLGAL ->M_3154 -FQVPDLHIL ->M_3155 -GMQARSVEM ->M_3156 -MLHLYPGPM ->M_3157 -SPYSEELPL ->M_3158 -YAQEGFLPH ->M_3159 -HLLFRVIPY ->M_3160 -RVIPYDQSF ->M_3161 -SIGSSATLY ->M_3162 -VQKQDNSTY ->M_3163 -AQVGFTLPL ->M_3164 -LPTPPPPPL ->M_3165 -YSCAGGRLF ->M_3166 -FQLDVASVI ->M_3167 -LDVASVIPF ->M_3168 -SVIPFDICY ->M_3169 -RLPNLHPSF ->M_3170 -LMVAVARSA ->M_3171 -TQHTSFQGY ->M_3172 -EQRCSLQAF ->M_3173 -KSKEREHSF ->M_3174 -NIDLAREAY ->M_3175 -IMSFLLSSL ->M_3176 -SEKEASLLY ->M_3177 -YLKEHASSL ->M_3178 -LVLSGSSSL ->M_3179 -FWRSSCSLF ->M_3180 -QLADQCLTM ->M_3181 -LPIKDGNTL ->M_3182 -LLVDRKDAM ->M_3183 -TPAIRHIML ->M_3184 -MQIHMGLAL ->M_3185 -ALARSSDAF ->M_3186 -HQGGATRVY ->M_3187 -FPNAGKSSF ->M_3188 -ILQEHIGAM ->M_3189 -SASAGLAAM ->M_3190 -HPCVPQALV ->M_3191 -ATIMETLTM ->M_3192 -PSDINVSSY ->M_3193 -VSSYNIYWY ->M_3194 -ESSEHEGTY ->M_3195 -QAWQPTASF ->M_3196 -FLNDRLANY ->M_3197 -LQIMAGRHG ->M_3198 -WLFPTGGSV ->M_3199 -LMYLQKLWM ->M_3200 -SIQSPFEGF ->M_3201 -LALLVSTAF ->M_3202 -GLIATQLLF ->M_3203 -LIATQLLFY ->M_3204 -LIATQLLFY ->M_3205 -AVRPTFGVL ->M_3206 -AMRFHFHSM ->M_3207 -MTSGLAMRF ->M_3208 -FPTTTFMCL ->M_3209 -ISLFPTTTF ->M_3210 -SLFPTTTFM ->M_3211 -SMRSSSISG ->M_3212 -VQHITGPVW ->M_3213 -ASDSQEALF ->M_3214 -FSDISEMRT ->M_3215 -TLAELLGPY ->M_3216 -LVNPWGEVL ->M_3217 -LPVVLQLKL ->M_3218 -AQADQVDPL ->M_3219 -FCDTAPVLK ->M_3220 -RLHSPMYFF ->M_3221 -TMCMYFRPL ->M_3222 -FLVFPFTSI ->M_3223 -LMADMYLLL ->M_3224 -HSHLLSHSY ->M_3225 -HSHLLSHSY ->M_3226 -TQYLVFCGM ->M_3227 -YLVFCGMGL ->M_3228 -LIFMYLCPA ->M_3229 -VAICHPLHY ->M_3230 -VLVQSLMVL ->M_3231 -QAQNQSITY ->M_3232 -TILTFCLSY ->M_3233 -CSIQDDLPF ->M_3234 -RMSRALWTL ->M_3235 -KQGWCYLVY ->M_3236 -YLVYVLLPL ->M_3237 -TINSAGDLF ->M_3238 -FPLDEVHAK ->M_3239 -LTLPPLATY ->M_3240 -PPAPPSLSL ->M_3241 -MQRASRHSQ ->M_3242 -QQSQSSGPG ->M_3243 -MLGDPSADY ->M_3244 -SADYINANY ->M_3245 -GVHKGRKPF ->M_3246 -ALACFARAF ->M_3247 -LTGDCCFDY ->M_3248 -YPKPQVSFL ->M_3249 -HPLGSLQIF ->M_3250 -AVGGMIASF ->M_3251 -PTEQSLTEY ->M_3252 -LLMGFSLTL ->M_3253 -TQGMQCSSL ->M_3254 -LLNLVVTSL ->M_3255 -YVKIYLLPY ->M_3256 -YVKIYLLPY ->M_3257 -ISVFSGSEM ->M_3258 -LLDEDISVF ->M_3259 -STVELVPIF ->M_3260 -KSADFEGLY ->M_3261 -CLFSLYTAY ->M_3262 -SLYTAYHVF ->M_3263 -SSHLHSDHY ->M_3264 -RQKHGEAPI ->M_3265 -RQDVGTYTF ->M_3266 -VERQDVGTY ->M_3267 -HSNSTSFIF ->M_3268 -NAHSNSTSF ->M_3269 -ATTESDQSF ->M_3270 -FPSETKVII ->M_3271 -HQVASSPGH ->M_3272 -SQGGPRGTF ->M_3273 -GGAPHFGHF ->M_3274 -GAIALIRRY diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132940_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132940_1_T_iedb.xml deleted file mode 100755 index ca2e9615..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_132940_1_T_iedb.xml +++ /dev/null @@ -1,4011 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_3144 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_3144 - 9 - - - 1 - gnl|BL_ORD_ID|344 - 21638|protein F|ABV46152.2|Hepatitis C virus (isolate Japanese)|11116 - 344 - 9 - - - 1 - 12.3122 - 20 - 49.6079 - 3 - 9 - 3 - 9 - 0 - 0 - 4 - 5 - 0 - 7 - GLAQGTF - GLSPGTL - GL+ GT - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 2 - Query_2 - M_3145 - 9 - - - 1 - gnl|BL_ORD_ID|344 - 21638|protein F|ABV46152.2|Hepatitis C virus (isolate Japanese)|11116 - 344 - 9 - - - 1 - 12.6974 - 21 - 37.2378 - 1 - 7 - 3 - 9 - 0 - 0 - 4 - 5 - 0 - 7 - GLAQGTF - GLSPGTL - GL+ GT - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 3 - Query_3 - M_3146 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_3147 - 9 - - - 1 - gnl|BL_ORD_ID|2191 - 190568|polymerase|AAD16253.1|Hepatitis B virus|10407 - 2191 - 20 - - - 1 - 11.927 - 19 - 77.7846 - 1 - 9 - 5 - 13 - 0 - 0 - 5 - 5 - 0 - 9 - KLHQVFHSI - KLHLYSHPI - KLH H I - - - - - 2 - gnl|BL_ORD_ID|498 - 31898|P protein|P17100.1|Hepatitis B virus|10407 - 498 - 9 - - - 1 - 11.927 - 19 - 92.9112 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 5 - 0 - 9 - KLHQVFHSI - KLHLYSHPI - KLH H I - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 5 - Query_5 - M_3148 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_3149 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_3150 - 9 - - - 1 - gnl|BL_ORD_ID|586 - 36676|polyprotein|BAA09073.1|Hepatitis C virus subtype 1b|31647 - 586 - 9 - - - 1 - 13.0826 - 22 - 18.1053 - 3 - 9 - 1 - 7 - 0 - 0 - 3 - 6 - 0 - 7 - LVRSCQM - LIRACML - L+R+C + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 8 - Query_8 - M_3151 - 9 - - - 1 - gnl|BL_ORD_ID|799 - 53201|Fusion glycoprotein F0 precursor|P03420.1|Human respiratory syncytial virus A2|11259 - 799 - 9 - - - 1 - 13.0826 - 22 - 14.1983 - 4 - 9 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - RDLPGF - RELPRF - R+LP F - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 9 - Query_9 - M_3152 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_3153 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_3154 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_3155 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_3156 - 9 - - - 1 - gnl|BL_ORD_ID|654 - 38724|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 654 - 20 - - - 1 - 14.2382 - 25 - 2.55563 - 1 - 9 - 11 - 19 - 0 - 0 - 4 - 6 - 0 - 9 - MLHLYPGPM - LFQLYRGPL - + LY GP+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 14 - Query_14 - M_3157 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_3158 - 9 - - - 1 - gnl|BL_ORD_ID|1512 - 140541|hypothetical protein|NP_218210.1|Mycobacterium tuberculosis H37Rv|83332 - 1512 - 9 - - - 1 - 13.4678 - 23 - 11.1275 - 3 - 8 - 3 - 8 - 0 - 0 - 4 - 4 - 0 - 6 - QEGFLP - DEGLLP - EG LP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 16 - Query_16 - M_3159 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_3160 - 9 - - - 1 - gnl|BL_ORD_ID|1432 - 116123|nucleocapsid protein|ABP49342.1|Influenza A virus (A/California/10/1978(H1N1))|425557 - 1432 - 9 - - - 1 - 13.4678 - 23 - 7.72035 - 3 - 8 - 1 - 6 - 0 - 0 - 3 - 6 - 0 - 6 - IPYDQS - LPFDKS - +P+D+S - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 18 - Query_18 - M_3161 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_3162 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_3163 - 9 - - - 1 - gnl|BL_ORD_ID|1841 - 179898|cell surface protein (associated with virulence)|NP_302372.1|Mycobacterium leprae TN|272631 - 1841 - 9 - - - 1 - 13.853 - 24 - 5.18352 - 4 - 9 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - GFTLPL - AFTMPL - FT+PL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 21 - Query_21 - M_3164 - 9 - - - 1 - gnl|BL_ORD_ID|1068 - 70491|envelope glycoprotein|AAC28452.1|Human immunodeficiency virus 1|11676 - 1068 - 10 - - - 1 - 11.927 - 19 - 95.2093 - 1 - 8 - 1 - 8 - 0 - 0 - 5 - 6 - 0 - 8 - LPTPPPPP - VPTDPNPP - +PT P PP - - - - - 2 - gnl|BL_ORD_ID|1276 - 101821|vif protein|ACC96167.1|Human immunodeficiency virus 1|11676 - 1276 - 11 - - - 1 - 9.61583 - 13 - 1292.96 - 3 - 8 - 2 - 7 - 0 - 0 - 4 - 4 - 0 - 6 - TPPPPP - TKPPLP - T PP P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 22 - Query_22 - M_3165 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_3166 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_3167 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_3168 - 9 - - - 1 - gnl|BL_ORD_ID|1110 - 73059|kaposin|AAC57155.1|Human gammaherpesvirus 8|37296 - 1110 - 15 - - - 1 - 10.3862 - 15 - 500.815 - 1 - 8 - 6 - 13 - 0 - 0 - 3 - 4 - 0 - 8 - SVIPFDIC - GAIPPLVC - IP +C - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 26 - Query_26 - M_3169 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_3170 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 28 - Query_28 - M_3171 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 29 - Query_29 - M_3172 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 30 - Query_30 - M_3173 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 31 - Query_31 - M_3174 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 32 - Query_32 - M_3175 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 33 - Query_33 - M_3176 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 34 - Query_34 - M_3177 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 35 - Query_35 - M_3178 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 36 - Query_36 - M_3179 - 9 - - - 1 - gnl|BL_ORD_ID|834 - 54824|polyprotein precursor|BAA01583.1|Hepatitis C virus|11103 - 834 - 9 - - - 1 - 12.6974 - 21 - 25.1356 - 1 - 8 - 2 - 9 - 0 - 0 - 3 - 4 - 0 - 8 - FWRSSCSL - LWHYPCTL - W C+L - - - - - 2 - gnl|BL_ORD_ID|1149 - 75636|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 1149 - 10 - - - 1 - 11.927 - 19 - 66.6359 - 1 - 8 - 3 - 10 - 0 - 0 - 2 - 4 - 0 - 8 - FWRSSCSL - LWHYPCTI - W C++ - - - - - 3 - gnl|BL_ORD_ID|833 - 54821|E2 protein|AAM33354.1|Hepatitis C virus subtype 1a|31646 - 833 - 9 - - - 1 - 11.927 - 19 - 73.9069 - 1 - 8 - 2 - 9 - 0 - 0 - 2 - 4 - 0 - 8 - FWRSSCSL - LWHYPCTI - W C++ - - - - - 4 - gnl|BL_ORD_ID|835 - 54825|polyprotein|BAA03375.1|Hepatitis C virus|11103 - 835 - 9 - - - 1 - 11.927 - 19 - 110.987 - 1 - 8 - 2 - 9 - 0 - 0 - 2 - 4 - 0 - 8 - FWRSSCSL - LWHYPCTV - W C++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 37 - Query_37 - M_3180 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 38 - Query_38 - M_3181 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 39 - Query_39 - M_3182 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 40 - Query_40 - M_3183 - 9 - - - 1 - gnl|BL_ORD_ID|2103 - 186002|polyprotein|AGO67248.1|Dengue virus 2|11060 - 2103 - 9 - - - 1 - 13.853 - 24 - 5.74926 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - TPAIRH - TPMLRH - TP +RH - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 41 - Query_41 - M_3184 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 42 - Query_42 - M_3185 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 43 - Query_43 - M_3186 - 9 - - - 1 - gnl|BL_ORD_ID|385 - 23620|Genome polyprotein|SRC279960|Hepatitis C virus genotype 1|41856 - 385 - 10 - - - 1 - 15.0086 - 27 - 1.14868 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 5 - 0 - 9 - HQGGATRVY - HDGAGKRVY - H G RVY - - - - - 2 - gnl|BL_ORD_ID|386 - 23621|Genome polyprotein|P26664.3|Hepatitis C virus (isolate 1)|11104 - 386 - 11 - - - 1 - 15.0086 - 27 - 1.29055 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 5 - 0 - 9 - HQGGATRVY - HDGAGKRVY - H G RVY - - - - - 3 - gnl|BL_ORD_ID|384 - 23619|Genome polyprotein|P27958.3|Hepatitis C virus (isolate H)|11108 - 384 - 9 - - - 1 - 15.0086 - 27 - 1.33879 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 5 - 0 - 9 - HQGGATRVY - HDGAGKRVY - H G RVY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 44 - Query_44 - M_3187 - 9 - - - 1 - gnl|BL_ORD_ID|1874 - 180503|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1874 - 10 - - - 1 - 13.0826 - 22 - 18.1832 - 2 - 7 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - PNAGKS - PGAGKT - P AGK+ - - - - - 2 - gnl|BL_ORD_ID|389 - 23807|tax|AAG48731.1|Human T-lymphotropic virus 2|11909 - 389 - 23 - - - 1 - 12.6974 - 21 - 26.0558 - 1 - 7 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - FPNAGKS - FPGFGQS - FP G+S - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 45 - Query_45 - M_3188 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 46 - Query_46 - M_3189 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 47 - Query_47 - M_3190 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 48 - Query_48 - M_3191 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 49 - Query_49 - M_3192 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 50 - Query_50 - M_3193 - 9 - - - 1 - gnl|BL_ORD_ID|469 - 28484|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 469 - 9 - - - 1 - 11.5418 - 18 - 150.225 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 5 - 0 - 9 - VSSYNIYWY - ISEYRHYCY - +S Y Y Y - - - - - 2 - gnl|BL_ORD_ID|353 - 21960|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 - 353 - 10 - - - 1 - 10.001 - 14 - 976.635 - 2 - 9 - 3 - 10 - 0 - 0 - 4 - 5 - 0 - 8 - SSYNIYWY - SSFYSDWY - SS+ WY - - - - - 3 - gnl|BL_ORD_ID|782 - 52431|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 - 782 - 9 - - - 1 - 10.001 - 14 - 1142.49 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - SSYNIYWY - SSFYSDWY - SS+ WY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 51 - Query_51 - M_3194 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 52 - Query_52 - M_3195 - 9 - - - 1 - gnl|BL_ORD_ID|1179 - 79628|E1 protein|BAA19893.1|Rubella virus|11041 - 1179 - 21 - - - 1 - 14.2382 - 25 - 2.93831 - 2 - 7 - 11 - 16 - 0 - 0 - 5 - 5 - 0 - 6 - AWQPTA - AWVPTA - AW PTA - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 53 - Query_53 - M_3196 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 54 - Query_54 - M_3197 - 9 - - - 1 - gnl|BL_ORD_ID|1757 - 154196|tegument protein|CAB06735.1|Human alphaherpesvirus 2|10310 - 1757 - 16 - - - 1 - 12.6974 - 21 - 35.41 - 4 - 9 - 9 - 14 - 0 - 0 - 4 - 5 - 0 - 6 - MAGRHG - VAGSHG - +AG HG - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 55 - Query_55 - M_3198 - 9 - - - 1 - gnl|BL_ORD_ID|1950 - 181035|||| - 1950 - 44 - - - 1 - 15.3938 - 28 - 1.11573 - 2 - 9 - 12 - 19 - 0 - 0 - 5 - 6 - 0 - 8 - LFPTGGSV - LFPGGGQI - LFP GG + - - - - - 2 - gnl|BL_ORD_ID|1177 - 79506|E1 protein|BAA19893.1|Rubella virus|11041 - 1177 - 20 - - - 1 - 13.0826 - 22 - 15.1234 - 1 - 5 - 10 - 14 - 0 - 0 - 4 - 4 - 0 - 5 - WLFPT - WGFPT - W FPT - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 56 - Query_56 - M_3199 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 57 - Query_57 - M_3200 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 58 - Query_58 - M_3201 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 59 - Query_59 - M_3202 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 60 - Query_60 - M_3203 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 61 - Query_61 - M_3204 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 62 - Query_62 - M_3205 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 63 - Query_63 - M_3206 - 9 - - - 1 - gnl|BL_ORD_ID|470 - 28508|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 470 - 15 - - - 1 - 12.3122 - 20 - 46.8002 - 1 - 9 - 7 - 15 - 0 - 0 - 3 - 6 - 0 - 9 - AMRFHFHSM - SARLHRHAL - + R H H++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 64 - Query_64 - M_3207 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 65 - Query_65 - M_3208 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 66 - Query_66 - M_3209 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 67 - Query_67 - M_3210 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 68 - Query_68 - M_3211 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 69 - Query_69 - M_3212 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 70 - Query_70 - M_3213 - 9 - - - 1 - gnl|BL_ORD_ID|783 - 52496|polyprotein precursor|NP_041724.2|West Nile virus|11082 - 783 - 9 - - - 1 - 13.0826 - 22 - 21.5246 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 7 - 0 - 8 - SDSQEALF - TDNQLAVF - +D+Q A+F - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 71 - Query_71 - M_3214 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 72 - Query_72 - M_3215 - 9 - - - 1 - gnl|BL_ORD_ID|391 - 23883|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 - 391 - 15 - - - 1 - 11.927 - 19 - 68.3105 - 1 - 8 - 7 - 14 - 0 - 0 - 4 - 5 - 0 - 8 - TLAELLGP - TIASPKGP - T+A GP - - - - - 2 - gnl|BL_ORD_ID|1005 - 66106|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 - 1005 - 15 - - - 1 - 11.927 - 19 - 74.9817 - 1 - 8 - 3 - 10 - 0 - 0 - 4 - 5 - 0 - 8 - TLAELLGP - TIASPKGP - T+A GP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 73 - Query_73 - M_3216 - 9 - - - 1 - gnl|BL_ORD_ID|1607 - 143690|Genome polyprotein|P06441.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 1607 - 9 - - - 1 - 13.0826 - 22 - 16.035 - 2 - 7 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - VNPWGE - VDPWVE - V+PW E - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 74 - Query_74 - M_3217 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 75 - Query_75 - M_3218 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 76 - Query_76 - M_3219 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 77 - Query_77 - M_3220 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 78 - Query_78 - M_3221 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 79 - Query_79 - M_3222 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 80 - Query_80 - M_3223 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 81 - Query_81 - M_3224 - 9 - - - 1 - gnl|BL_ORD_ID|2191 - 190568|polymerase|AAD16253.1|Hepatitis B virus|10407 - 2191 - 20 - - - 1 - 11.1566 - 17 - 207.813 - 3 - 8 - 7 - 12 - 0 - 0 - 4 - 4 - 0 - 6 - HLLSHS - HLYSHP - HL SH - - - - - 2 - gnl|BL_ORD_ID|580 - 36402|P protein|Q05486.1|Hepatitis B virus|10407 - 580 - 15 - - - 1 - 10.7714 - 16 - 300.51 - 3 - 8 - 2 - 7 - 0 - 0 - 4 - 4 - 0 - 6 - HLLSHS - HLYSHP - HL SH - - - - - 3 - gnl|BL_ORD_ID|498 - 31898|P protein|P17100.1|Hepatitis B virus|10407 - 498 - 9 - - - 1 - 10.7714 - 16 - 354.707 - 3 - 8 - 3 - 8 - 0 - 0 - 4 - 4 - 0 - 6 - HLLSHS - HLYSHP - HL SH - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 82 - Query_82 - M_3225 - 9 - - - 1 - gnl|BL_ORD_ID|2191 - 190568|polymerase|AAD16253.1|Hepatitis B virus|10407 - 2191 - 20 - - - 1 - 11.1566 - 17 - 207.813 - 3 - 8 - 7 - 12 - 0 - 0 - 4 - 4 - 0 - 6 - HLLSHS - HLYSHP - HL SH - - - - - 2 - gnl|BL_ORD_ID|580 - 36402|P protein|Q05486.1|Hepatitis B virus|10407 - 580 - 15 - - - 1 - 10.7714 - 16 - 300.51 - 3 - 8 - 2 - 7 - 0 - 0 - 4 - 4 - 0 - 6 - HLLSHS - HLYSHP - HL SH - - - - - 3 - gnl|BL_ORD_ID|498 - 31898|P protein|P17100.1|Hepatitis B virus|10407 - 498 - 9 - - - 1 - 10.7714 - 16 - 354.707 - 3 - 8 - 3 - 8 - 0 - 0 - 4 - 4 - 0 - 6 - HLLSHS - HLYSHP - HL SH - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 83 - Query_83 - M_3226 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 84 - Query_84 - M_3227 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 85 - Query_85 - M_3228 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 86 - Query_86 - M_3229 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 87 - Query_87 - M_3230 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 88 - Query_88 - M_3231 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 89 - Query_89 - M_3232 - 9 - - - 1 - gnl|BL_ORD_ID|1705 - 150224|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1705 - 10 - - - 1 - 11.927 - 19 - 86.442 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 6 - 0 - 9 - TILTFCLSY - TIMAAILAY - TI+ L+Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 90 - Query_90 - M_3233 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 91 - Query_91 - M_3234 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 92 - Query_92 - M_3235 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 93 - Query_93 - M_3236 - 9 - - - 1 - gnl|BL_ORD_ID|1404 - 110744|E5 protein|AAD24036.1|Human papillomavirus type 16|333760 - 1404 - 9 - - - 1 - 13.853 - 24 - 5.65074 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 8 - 0 - 9 - YLVYVLLPL - YIIFVYIPL - Y+++V +PL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 94 - Query_94 - M_3237 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 95 - Query_95 - M_3238 - 9 - - - 1 - gnl|BL_ORD_ID|1139 - 75356|EBNA3A nuclear protein|Q8AZJ8|Human gammaherpesvirus 4|10376 - 1139 - 9 - - - 1 - 13.853 - 24 - 5.55396 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 5 - 0 - 8 - FPLDEVHA - YPLHEQHG - +PL E H - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 96 - Query_96 - M_3239 - 9 - - - 1 - gnl|BL_ORD_ID|2049 - 184643|polyprotein|AGW24534.1|Dengue virus 2|11060 - 2049 - 10 - - - 1 - 13.4678 - 23 - 8.32231 - 1 - 7 - 1 - 7 - 0 - 0 - 5 - 6 - 0 - 7 - LTLPPLA - LTIPPTA - LT+PP A - - - - - 2 - gnl|BL_ORD_ID|1560 - 141276|tegument protein VP13/14|NP_044649.1|Human alphaherpesvirus 1|10298 - 1560 - 9 - - - 1 - 13.0826 - 22 - 14.4474 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 5 - 0 - 9 - LTLPPLATY - FTAPEVGTY - T P + TY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 97 - Query_97 - M_3240 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 98 - Query_98 - M_3241 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 99 - Query_99 - M_3242 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 100 - Query_100 - M_3243 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 101 - Query_101 - M_3244 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 102 - Query_102 - M_3245 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 103 - Query_103 - M_3246 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 104 - Query_104 - M_3247 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 105 - Query_105 - M_3248 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 106 - Query_106 - M_3249 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 107 - Query_107 - M_3250 - 9 - - - 1 - gnl|BL_ORD_ID|1248 - 98085|trans-sialidase, putative|EAN82636.1|Trypanosoma cruzi|5693 - 1248 - 10 - - - 1 - 12.3122 - 20 - 40.5114 - 4 - 9 - 1 - 6 - 0 - 0 - 4 - 6 - 0 - 6 - GMIASF - GVIAAF - G+IA+F - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 108 - Query_108 - M_3251 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 109 - Query_109 - M_3252 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 110 - Query_110 - M_3253 - 9 - - - 1 - gnl|BL_ORD_ID|1811 - 170063|polyprotein|ABU97067.1|Hepatitis C virus subtype 1b|31647 - 1811 - 9 - - - 1 - 12.3122 - 20 - 44.1001 - 1 - 7 - 2 - 8 - 0 - 0 - 3 - 6 - 0 - 7 - TQGMQCS - TRGERCN - T+G +C+ - - - - - 2 - gnl|BL_ORD_ID|714 - 43937|polyprotein|AAF01178.1|Hepatitis C virus subtype 2a|31649 - 714 - 10 - - - 1 - 12.3122 - 20 - 51.1794 - 1 - 7 - 3 - 9 - 0 - 0 - 3 - 6 - 0 - 7 - TQGMQCS - TRGDRCN - T+G +C+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 111 - Query_111 - M_3254 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 112 - Query_112 - M_3255 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 113 - Query_113 - M_3256 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 114 - Query_114 - M_3257 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 115 - Query_115 - M_3258 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 116 - Query_116 - M_3259 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 117 - Query_117 - M_3260 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 118 - Query_118 - M_3261 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 119 - Query_119 - M_3262 - 9 - - - 1 - gnl|BL_ORD_ID|526 - 32250|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 - 526 - 9 - - - 1 - 12.6974 - 21 - 33.058 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 5 - 0 - 8 - SLYTAYHV - KLYCSYEV - LY +Y V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 120 - Query_120 - M_3263 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 121 - Query_121 - M_3264 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 122 - Query_122 - M_3265 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 123 - Query_123 - M_3266 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 124 - Query_124 - M_3267 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 125 - Query_125 - M_3268 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 126 - Query_126 - M_3269 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 127 - Query_127 - M_3270 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 128 - Query_128 - M_3271 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 129 - Query_129 - M_3272 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 130 - Query_130 - M_3273 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 131 - Query_131 - M_3274 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_133761_2_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_133761_2_T.fasta deleted file mode 100755 index ef93e997..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_133761_2_T.fasta +++ /dev/null @@ -1,86 +0,0 @@ ->M_3275 -DTTRYVTSK ->M_3276 -EPSESDTTR ->M_3277 -PSESDTTRY ->M_3278 -TRYVTSKIL ->M_3279 -TTRYVTSKI ->M_3280 -TSCSCQSSR ->M_3281 -TGDSEAAPV ->M_3282 -LSMEETLLL ->M_3283 -WWNPALWKR ->M_3284 -LFQDNSSQL ->M_3285 -LTPPQAQEL ->M_3286 -LTPQQAQEL ->M_3287 -QAQALGIPL ->M_3288 -ASRPDRLSL ->M_3289 -EAQGQEASR ->M_3290 -WVEPQNPVL ->M_3291 -HLPHLTHTL ->M_3292 -HTLATSCRR ->M_3293 -ITSFDNLFR ->M_3294 -SHFHKTHEV ->M_3295 -YKLVVVGAV ->M_3296 -FHRRLSSSL ->M_3297 -FHRRLSSSL ->M_3298 -FSRRSFHRR ->M_3299 -RSDVWNLGI ->M_3300 -VYILILPSF ->M_3301 -STTIPILTL ->M_3302 -TIPILTLSL ->M_3303 -LSHISHLEL ->M_3304 -SHLELVESL ->M_3305 -SAEVRIEPM ->M_3306 -QSHLLIHQR ->M_3307 -QVITLRKSL ->M_3308 -TKKQVITLR ->M_3309 -MFDASKANF ->M_3310 -FLDWLRTMT ->M_3311 -VDWFLDWLR ->M_3312 -WFLDWLRTM ->M_3313 -WLRTMTNVL ->M_3314 -KFLQEEPQL ->M_3315 -DVFRFSPYR ->M_3316 -RFSPYRGLL ->M_3317 -DSTRPPGTR diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_133761_2_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_133761_2_T_iedb.xml deleted file mode 100755 index 6e8c146f..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_133761_2_T_iedb.xml +++ /dev/null @@ -1,1517 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_3275 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_3275 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_3276 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_3277 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_3278 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_3279 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_3280 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_3281 - 9 - - - 1 - gnl|BL_ORD_ID|1759 - 154346|RL2|CAB06760.1|Human alphaherpesvirus 2|10310 - 1759 - 15 - - - 1 - 13.0826 - 22 - 18.437 - 1 - 8 - 5 - 12 - 0 - 0 - 4 - 5 - 0 - 8 - TGDSEAAP - TGNPRTAP - TG+ AP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 8 - Query_8 - M_3282 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_3283 - 9 - - - 1 - gnl|BL_ORD_ID|549 - 33681|||| - 549 - 10 - - - 1 - 15.0086 - 27 - 0.933082 - 3 - 9 - 4 - 10 - 0 - 0 - 4 - 6 - 0 - 7 - NPALWKR - GPAIYKR - PA++KR - - - - - 2 - gnl|BL_ORD_ID|1678 - 149027|NS5 protein|BAA00702.1|Hepatitis C virus (isolate H77)|63746 - 1678 - 18 - - - 1 - 13.4678 - 23 - 8.48241 - 4 - 9 - 2 - 7 - 0 - 0 - 4 - 4 - 0 - 6 - PALWKR - PTLWAR - P LW R - - - - - 3 - gnl|BL_ORD_ID|1615 - 144207|polyprotein|CAB41951.1|Hepatitis C virus|11103 - 1615 - 10 - - - 1 - 13.0826 - 22 - 14.7743 - 4 - 9 - 2 - 7 - 0 - 0 - 4 - 4 - 0 - 6 - PALWKR - PTLWAR - P LW R - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 10 - Query_10 - M_3284 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_3285 - 9 - - - 1 - gnl|BL_ORD_ID|1060 - 69799|envelope glycoprotein|BAE96221.1|Human immunodeficiency virus 1|11676 - 1060 - 10 - - - 1 - 13.0826 - 22 - 16.6782 - 1 - 9 - 2 - 10 - 0 - 0 - 5 - 6 - 0 - 9 - LTPPQAQEL - LTDPNPQEV - LT P QE+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 12 - Query_12 - M_3286 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_3287 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_3288 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_3289 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_3290 - 9 - - - 1 - gnl|BL_ORD_ID|891 - 58740|Major surface antigen precursor|P03142.4|Hepatitis B virus|10407 - 891 - 10 - - - 1 - 10.7714 - 16 - 368.054 - 2 - 9 - 3 - 10 - 0 - 0 - 4 - 5 - 0 - 8 - VEPQNPVL - VSPFIPLL - V P P+L - - - - - 2 - gnl|BL_ORD_ID|478 - 29455|Major surface antigen precursor|P03141.3|Hepatitis B virus subtype adw2|10408 - 478 - 9 - - - 1 - 10.7714 - 16 - 393.541 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - VEPQNPVL - VSPFIPLL - V P P+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 17 - Query_17 - M_3291 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_3292 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_3293 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_3294 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_3295 - 9 - - - 1 - gnl|BL_ORD_ID|524 - 32238|polyprotein [Hepatitis C virus subtype 1a]|ABV46251.2|Hepatitis C virus (isolate H77)|63746 - 524 - 10 - - - 1 - 12.6974 - 21 - 30.9217 - 2 - 7 - 1 - 6 - 0 - 0 - 5 - 6 - 0 - 6 - KLVVVG - KLVVLG - KLVV+G - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 22 - Query_22 - M_3296 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_3297 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_3298 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_3299 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_3300 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_3301 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 28 - Query_28 - M_3302 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 29 - Query_29 - M_3303 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 30 - Query_30 - M_3304 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 31 - Query_31 - M_3305 - 9 - - - 1 - gnl|BL_ORD_ID|1075 - 71266|Circumsporozoite protein precursor|P02893.1|Plasmodium falciparum|5833 - 1075 - 20 - - - 1 - 13.853 - 24 - 4.4203 - 3 - 8 - 8 - 13 - 0 - 0 - 4 - 6 - 0 - 6 - EVRIEP - QVRIKP - +VRI+P - - - - - 2 - gnl|BL_ORD_ID|304 - 20415|circumsporozoite protein|AAN87606.1|Plasmodium falciparum|5833 - 304 - 20 - - - 1 - 13.853 - 24 - 7.45549 - 3 - 8 - 3 - 8 - 0 - 0 - 4 - 6 - 0 - 6 - EVRIEP - QVRIKP - +VRI+P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 32 - Query_32 - M_3306 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 33 - Query_33 - M_3307 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 34 - Query_34 - M_3308 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 35 - Query_35 - M_3309 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 36 - Query_36 - M_3310 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 37 - Query_37 - M_3311 - 9 - - - 1 - gnl|BL_ORD_ID|664 - 39591|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 - 664 - 20 - - - 1 - 12.3122 - 20 - 56.0891 - 1 - 9 - 9 - 17 - 0 - 0 - 4 - 6 - 0 - 9 - VDWFLDWLR - ISWCLWWLQ - + W L WL+ - - - - - 2 - gnl|BL_ORD_ID|1120 - 74387|Genome polyprotein|P26664.3|Hepatitis C virus (isolate 1)|11104 - 1120 - 9 - - - 1 - 11.5418 - 18 - 138.797 - 1 - 8 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - VDWFLDWL - ISWCLWWL - + W L WL - - - - - 3 - gnl|BL_ORD_ID|1697 - 149105|E2 protein|NP_751921.1|Hepatitis C virus (isolate H77)|63746 - 1697 - 9 - - - 1 - 10.7714 - 16 - 365.422 - 1 - 7 - 3 - 9 - 0 - 0 - 2 - 3 - 0 - 7 - VDWFLDW - ASWAIKW - W + W - - - - - 4 - gnl|BL_ORD_ID|1119 - 74386|HCV-1|AAA45676.1|Hepatitis C virus|11103 - 1119 - 8 - - - 1 - 10.3862 - 15 - 795.381 - 1 - 7 - 2 - 8 - 0 - 0 - 3 - 4 - 0 - 7 - VDWFLDW - ISWCLWW - + W L W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 38 - Query_38 - M_3312 - 9 - - - 1 - gnl|BL_ORD_ID|664 - 39591|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 - 664 - 20 - - - 1 - 10.3862 - 15 - 413.002 - 1 - 7 - 11 - 17 - 0 - 0 - 4 - 5 - 0 - 7 - WFLDWLR - WCLWWLQ - W L WL+ - - - - - 2 - gnl|BL_ORD_ID|1120 - 74387|Genome polyprotein|P26664.3|Hepatitis C virus (isolate 1)|11104 - 1120 - 9 - - - 1 - 10.001 - 14 - 968.836 - 1 - 6 - 4 - 9 - 0 - 0 - 4 - 4 - 0 - 6 - WFLDWL - WCLWWL - W L WL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 39 - Query_39 - M_3313 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 40 - Query_40 - M_3314 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 41 - Query_41 - M_3315 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 42 - Query_42 - M_3316 - 9 - - - 1 - gnl|BL_ORD_ID|421 - 25388|matrix protein|ABP96803.1|Human metapneumovirus|162145 - 421 - 10 - - - 1 - 14.6234 - 26 - 1.59035 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 6 - 0 - 8 - FSPYRGLL - IAPYAGLI - +PY GL+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 43 - Query_43 - M_3317 - 9 - - - 1 - gnl|BL_ORD_ID|1494 - 136890|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1494 - 9 - - - 1 - 13.0826 - 22 - 13.4763 - 5 - 9 - 2 - 6 - 0 - 0 - 4 - 5 - 0 - 5 - PPGTR - PPGSR - PPG+R - - - - - 2 - gnl|BL_ORD_ID|1106 - 72928|Genome polyprotein|P26662.3|Hepatitis C virus (isolate Japanese)|11116 - 1106 - 10 - - - 1 - 13.0826 - 22 - 15.8345 - 5 - 9 - 4 - 8 - 0 - 0 - 4 - 4 - 0 - 5 - PPGTR - PPGAR - PPG R - - - - - 3 - gnl|BL_ORD_ID|1599 - 142245|polyprotein|ACJ37204.1|Hepatitis C virus subtype 1a|31646 - 1599 - 9 - - - 1 - 13.0826 - 22 - 18.1053 - 2 - 7 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - STRPPG - NTRPPA - +TRPP - - - - - 4 - gnl|BL_ORD_ID|1601 - 142247|envelope protein 2|ACY64760.1|Hepatitis C virus subtype 1a|31646 - 1601 - 9 - - - 1 - 13.0826 - 22 - 19.071 - 2 - 6 - 1 - 5 - 0 - 0 - 4 - 5 - 0 - 5 - STRPP - NTRPP - +TRPP - - - - - 5 - gnl|BL_ORD_ID|1602 - 142248|polyprotein|BAB18806.1|Hepatitis C virus subtype 1a|31646 - 1602 - 9 - - - 1 - 13.0826 - 22 - 19.404 - 2 - 6 - 1 - 5 - 0 - 0 - 4 - 5 - 0 - 5 - STRPP - NTRPP - +TRPP - - - - - 6 - gnl|BL_ORD_ID|1603 - 142249|polyprotein|AAY82036.1|Hepatitis C virus subtype 1a|31646 - 1603 - 9 - - - 1 - 13.0826 - 22 - 23.0624 - 2 - 6 - 1 - 5 - 0 - 0 - 4 - 5 - 0 - 5 - STRPP - NTRPP - +TRPP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_133954_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_133954_1_T.fasta deleted file mode 100755 index 43cd5767..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_133954_1_T.fasta +++ /dev/null @@ -1,336 +0,0 @@ ->M_3318 -YLGVPVFYA ->M_3319 -AIHIVAEKK ->M_3320 -TQFELQRNK ->M_3321 -VRGTDWHLK ->M_3322 -GFHPDPEAL ->M_3323 -HIRTDTYVK ->M_3324 -SRWQVHGIV ->M_3325 -VPACSRAHV ->M_3326 -VPACSYAHV ->M_3327 -MLFFRTRYI ->M_3328 -TRYICTTVF ->M_3329 -YICTTVFYT ->M_3330 -AALVPTQAM ->M_3331 -MPGSPRDPV ->M_3332 -RRGSGHSEY ->M_3333 -RICGHIFCY ->M_3334 -GIAPLNQWV ->M_3335 -KIIATCFAV ->M_3336 -KMNEPKCLK ->M_3337 -SFVPWNSYV ->M_3338 -VPWNSYVRL ->M_3339 -YQLKLFACM ->M_3340 -YQLKLFACM ->M_3341 -RGRGGSVSI ->M_3342 -IPHTAILVT ->M_3343 -SIPHTAILV ->M_3344 -GLSDLELRL ->M_3345 -VLLRCPNKL ->M_3346 -TRLAFGLFA ->M_3347 -ILIACRLNK ->M_3348 -LIACRLNKK ->M_3349 -RLNKKKGAY ->M_3350 -TLAHEASPL ->M_3351 -SAWWSFGSL ->M_3352 -NPEAMCSDL ->M_3353 -AMHPLFRKL ->M_3354 -CRAMHPLFR ->M_3355 -GPCRAMHPL ->M_3356 -RAMHPLFRK ->M_3357 -GYIHYVFYL ->M_3358 -GYIHYVFYL ->M_3359 -KGYIHYVFY ->M_3360 -YLGNGPNVI ->M_3361 -SLSNKEVKK ->M_3362 -GPRAINNFF ->M_3363 -FRFSSQEAA ->M_3364 -LLPPQDPHL ->M_3365 -PPQDPHLPL ->M_3366 -HVDPGTIGV ->M_3367 -GLMGAVNVA ->M_3368 -LMGAVNVAK ->M_3369 -PRMAIPWPR ->M_3370 -WPRDVRKLV ->M_3371 -KYYEALPEL ->M_3372 -HYYHNVHAV ->M_3373 -MVEHYYHNV ->M_3374 -YHNVHAVVF ->M_3375 -YYHNVHAVV ->M_3376 -ARVWKFGPK ->M_3377 -RVWKFGPKL ->M_3378 -RVWKFGPKL ->M_3379 -VLDKARVWK ->M_3380 -CYEEYRGRL ->M_3381 -GRYEEYRGH ->M_3382 -APRGACYRA ->M_3383 -YRADHDLGR ->M_3384 -SYVCVVRNY ->M_3385 -ARPFFFFLL ->M_3386 -FFFFLLDKV ->M_3387 -FFFLLDKVL ->M_3388 -FLLDKVLAS ->M_3389 -HARPFFFFL ->M_3390 -APSWRGLAE ->M_3391 -LRLALMKKK ->M_3392 -WLRLALMKK ->M_3393 -VLIQQLEKV ->M_3394 -YPGQVNRTA ->M_3395 -MADVAMYGV ->M_3396 -GLYYAEFGA ->M_3397 -SVLAGLYYA ->M_3398 -TMWRREESL ->M_3399 -CLWQLKAPV ->M_3400 -RPRKAWAWC ->M_3401 -QRLKREEEK ->M_3402 -VYHMSQSPL ->M_3403 -FTMLLSLLA ->M_3404 -GLAGFTMLL ->M_3405 -MLLSLLAFA ->M_3406 -KVHQLAITV ->M_3407 -LPKSSEKAI ->M_3408 -STQEPTAYV ->M_3409 -ARMRKHIKR ->M_3410 -GPARMRKHI ->M_3411 -RMRKHIKRL ->M_3412 -HVGKASSSM ->M_3413 -QQMEAHVGK ->M_3414 -VILLPQPPK ->M_3415 -YLGVPVFYA ->M_3416 -AIHIVAEKK ->M_3417 -IVGHTGSGK ->M_3418 -LPAPPGAPP ->M_3419 -VRGTDWHLK ->M_3420 -RRHHSPSQR ->M_3421 -WLQQENHEL ->M_3422 -SLQPIHHDL ->M_3423 -VPACSRAHV ->M_3424 -VPACSYAHV ->M_3425 -LLLSPPVEV ->M_3426 -LLSPPVEVK ->M_3427 -RPEPPETGV ->M_3428 -RRGSGHSEY ->M_3429 -GLLQRPVHL ->M_3430 -HLALGRLSR ->M_3431 -KIIATCFAV ->M_3432 -SFVPWNSYV ->M_3433 -VPWNSYVRL ->M_3434 -YQLKLFACM ->M_3435 -YQLKLFACM ->M_3436 -IPHTAILVT ->M_3437 -SIPHTAILV ->M_3438 -SVSSCCQPV ->M_3439 -WLLEWTEAA ->M_3440 -GLSDLELRL ->M_3441 -VLLRCPNKL ->M_3442 -TLAHEASPL ->M_3443 -ILPATILVL ->M_3444 -TILPATILV ->M_3445 -SAWWSFGSL ->M_3446 -NPEAMCSDL ->M_3447 -AMHPLFRKL ->M_3448 -CRAMHPLFR ->M_3449 -GPCRAMHPL ->M_3450 -RAMHPLFRK ->M_3451 -SLSNKEVKK ->M_3452 -GPRAINNFF ->M_3453 -LLPPQDPHL ->M_3454 -PPQDPHLPL ->M_3455 -GLMGAVNVA ->M_3456 -LMGAVNVAK ->M_3457 -KLPEVQLPK ->M_3458 -ARVWKFGPK ->M_3459 -RVWKFGPKL ->M_3460 -RVWKFGPKL ->M_3461 -VLDKARVWK ->M_3462 -APRGACYRA ->M_3463 -YRADHDLGR ->M_3464 -SYVCVVRNY ->M_3465 -APSWRGLAE ->M_3466 -VLIQQLEKV ->M_3467 -GLYYAEFGA ->M_3468 -SVLAGLYYA ->M_3469 -KPVNKILQI ->M_3470 -CLWQLKAPV ->M_3471 -RPRKAWAWC ->M_3472 -SLDTVAQAV ->M_3473 -QRLKREEEK ->M_3474 -RREQQLRRK ->M_3475 -VYHMSQSPL ->M_3476 -FTMLLSLLA ->M_3477 -GLAGFTMLL ->M_3478 -MLLSLLAFA ->M_3479 -KVHQLAITV ->M_3480 -KIMHGPFMK ->M_3481 -RPRWNTHGH ->M_3482 -ARMRKHIKR ->M_3483 -GPARMRKHI ->M_3484 -RMRKHIKRL ->M_3485 -VILLPQPPK diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_133954_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_133954_1_T_iedb.xml deleted file mode 100755 index 23b6434e..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_133954_1_T_iedb.xml +++ /dev/null @@ -1,6405 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_3318 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_3318 - 9 - - - 1 - gnl|BL_ORD_ID|1 - 118|envelope glycoprotein|ABS76372.1|Human immunodeficiency virus 1|11676 - 1 - 20 - - - 1 - 14.6234 - 26 - 1.57628 - 1 - 7 - 10 - 16 - 0 - 0 - 5 - 6 - 0 - 7 - YLGVPVF - YYGVPVW - Y GVPV+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 2 - Query_2 - M_3319 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_3320 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_3321 - 9 - - - 1 - gnl|BL_ORD_ID|1008 - 66798|glycoprotein gp35/37|AAC59622.1|Human gammaherpesvirus 8|37296 - 1008 - 15 - - - 1 - 12.6974 - 21 - 22.1438 - 1 - 7 - 2 - 8 - 0 - 0 - 4 - 4 - 0 - 7 - VRGTDWH - TRGRDAH - RG D H - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 5 - Query_5 - M_3322 - 9 - - - 1 - gnl|BL_ORD_ID|2185 - 190466|large surface antigen|CAL29876.1|Hepatitis B virus|10407 - 2185 - 15 - - - 1 - 12.6974 - 21 - 30.2729 - 1 - 5 - 2 - 6 - 0 - 0 - 4 - 4 - 0 - 5 - GFHPD - GFFPD - GF PD - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 6 - Query_6 - M_3323 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_3324 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_3325 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_3326 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_3327 - 9 - - - 1 - gnl|BL_ORD_ID|1781 - 156550|E3 ubiquitin-protein ligase Mdm2|Q00987.1|Homo sapiens|9606 - 1781 - 9 - - - 1 - 12.6974 - 21 - 30.3534 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 7 - 0 - 9 - MLFFRTRYI - VLFYLGQYI - +LF+ +YI - - - - - 2 - gnl|BL_ORD_ID|608 - 37254|||| - 608 - 9 - - - 1 - 12.3122 - 20 - 62.655 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 6 - 0 - 9 - MLFFRTRYI - LLFGYPRYV - +LF RY+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 11 - Query_11 - M_3328 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_3329 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_3330 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_3331 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_3332 - 9 - - - 1 - gnl|BL_ORD_ID|1871 - 180488|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1871 - 10 - - - 1 - 13.0826 - 22 - 16.3922 - 3 - 8 - 1 - 6 - 0 - 0 - 4 - 4 - 0 - 6 - GSGHSE - GPGHEE - G GH E - - - - - 2 - gnl|BL_ORD_ID|657 - 38974|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 657 - 11 - - - 1 - 12.3122 - 20 - 38.8163 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 7 - 0 - 9 - RRGSGHSEY - QRGPQYSEH - +RG +SE+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 16 - Query_16 - M_3333 - 9 - - - 1 - gnl|BL_ORD_ID|1186 - 93431|pre-C/C protein|ABY54138.1|Hepatitis B virus|10407 - 1186 - 20 - - - 1 - 8.84543 - 11 - 2528.11 - 2 - 8 - 6 - 12 - 0 - 0 - 3 - 4 - 0 - 7 - ICGHIFC - LCLIISC - +C I C - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 17 - Query_17 - M_3334 - 9 - - - 1 - gnl|BL_ORD_ID|573 - 36062|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 573 - 20 - - - 1 - 13.0826 - 22 - 15.1234 - 2 - 8 - 13 - 19 - 0 - 0 - 3 - 4 - 0 - 7 - IAPLNQW - LTPLRDW - + PL W - - - - - 2 - gnl|BL_ORD_ID|996 - 65654|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 - 996 - 15 - - - 1 - 12.3122 - 20 - 41.8446 - 3 - 9 - 1 - 7 - 0 - 0 - 3 - 3 - 0 - 7 - APLNQWV - TPLRDWA - PL W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 18 - Query_18 - M_3335 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_3336 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_3337 - 9 - - - 1 - gnl|BL_ORD_ID|1610 - 143728|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 1610 - 9 - - - 1 - 14.2382 - 25 - 3.00197 - 3 - 9 - 1 - 7 - 0 - 0 - 4 - 6 - 0 - 7 - VPWNSYV - LPWYSYL - +PW SY+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 21 - Query_21 - M_3338 - 9 - - - 1 - gnl|BL_ORD_ID|1610 - 143728|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 1610 - 9 - - - 1 - 14.2382 - 25 - 3.05306 - 1 - 7 - 1 - 7 - 0 - 0 - 4 - 6 - 0 - 7 - VPWNSYV - LPWYSYL - +PW SY+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 22 - Query_22 - M_3339 - 9 - - - 1 - gnl|BL_ORD_ID|1149 - 75636|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 1149 - 10 - - - 1 - 11.5418 - 18 - 153.051 - 1 - 8 - 1 - 8 - 0 - 0 - 3 - 5 - 0 - 8 - YQLKLFAC - YRLWHYPC - Y+L + C - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 23 - Query_23 - M_3340 - 9 - - - 1 - gnl|BL_ORD_ID|1149 - 75636|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 1149 - 10 - - - 1 - 11.5418 - 18 - 153.051 - 1 - 8 - 1 - 8 - 0 - 0 - 3 - 5 - 0 - 8 - YQLKLFAC - YRLWHYPC - Y+L + C - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 24 - Query_24 - M_3341 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_3342 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_3343 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_3344 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 28 - Query_28 - M_3345 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 29 - Query_29 - M_3346 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 30 - Query_30 - M_3347 - 9 - - - 1 - gnl|BL_ORD_ID|1621 - 145860|Protein E6|P04019.1|Human papillomavirus type 11|10580 - 1621 - 9 - - - 1 - 11.1566 - 17 - 208.544 - 1 - 7 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - ILIACRL - VLIRCYL - +LI C L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 31 - Query_31 - M_3348 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 32 - Query_32 - M_3349 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 33 - Query_33 - M_3350 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 34 - Query_34 - M_3351 - 9 - - - 1 - gnl|BL_ORD_ID|1924 - 180726|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1924 - 15 - - - 1 - 15.0086 - 27 - 1.14188 - 4 - 9 - 10 - 15 - 0 - 0 - 5 - 5 - 0 - 6 - WSFGSL - WDFGSL - W FGSL - - - - - 2 - gnl|BL_ORD_ID|1095 - 72301|envelope protein|YP_001527880.1|West Nile virus NY-99|10000971 - 1095 - 18 - - - 1 - 13.4678 - 23 - 7.53558 - 4 - 9 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - WSFGSL - WDFGSV - W FGS+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 35 - Query_35 - M_3352 - 9 - - - 1 - gnl|BL_ORD_ID|1397 - 110401|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1397 - 25 - - - 1 - 14.2382 - 25 - 3.81797 - 1 - 6 - 20 - 25 - 0 - 0 - 4 - 5 - 0 - 6 - NPEAMC - NPYAVC - NP A+C - - - - - 2 - gnl|BL_ORD_ID|1400 - 110467|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1400 - 25 - - - 1 - 14.2382 - 25 - 3.88133 - 1 - 6 - 5 - 10 - 0 - 0 - 4 - 5 - 0 - 6 - NPEAMC - NPYAVC - NP A+C - - - - - 3 - gnl|BL_ORD_ID|1387 - 110227|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1387 - 33 - - - 1 - 14.2382 - 25 - 4.76191 - 1 - 6 - 12 - 17 - 0 - 0 - 4 - 5 - 0 - 6 - NPEAMC - NPYAVC - NP A+C - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 36 - Query_36 - M_3353 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 37 - Query_37 - M_3354 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 38 - Query_38 - M_3355 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 39 - Query_39 - M_3356 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 40 - Query_40 - M_3357 - 9 - - - 1 - gnl|BL_ORD_ID|691 - 42094|telomer length regulation protein TEL1|EDV12172.1|Saccharomyces cerevisiae|4932 - 691 - 9 - - - 1 - 13.0826 - 22 - 15.4875 - 1 - 6 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - GYIHYV - GYLQYV - GY+ YV - - - - - 2 - gnl|BL_ORD_ID|579 - 36358|ELAV-like protein 1|Q15717.2|Homo sapiens|9606 - 579 - 9 - - - 1 - 12.3122 - 20 - 53.0441 - 1 - 6 - 4 - 9 - 0 - 0 - 3 - 6 - 0 - 6 - GYIHYV - GFVNYV - G+++YV - - - - - 3 - gnl|BL_ORD_ID|578 - 36357|ELAV-like protein 4 (Paraneoplastic encephalomyelitis antigen HuD) (Hu-antigen D)|P26378.1|Homo sapiens|9606 - 578 - 9 - - - 1 - 11.927 - 19 - 109.216 - 1 - 6 - 4 - 9 - 0 - 0 - 2 - 6 - 0 - 6 - GYIHYV - GFVNYI - G+++Y+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 41 - Query_41 - M_3358 - 9 - - - 1 - gnl|BL_ORD_ID|691 - 42094|telomer length regulation protein TEL1|EDV12172.1|Saccharomyces cerevisiae|4932 - 691 - 9 - - - 1 - 13.0826 - 22 - 15.4875 - 1 - 6 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - GYIHYV - GYLQYV - GY+ YV - - - - - 2 - gnl|BL_ORD_ID|579 - 36358|ELAV-like protein 1|Q15717.2|Homo sapiens|9606 - 579 - 9 - - - 1 - 12.3122 - 20 - 53.0441 - 1 - 6 - 4 - 9 - 0 - 0 - 3 - 6 - 0 - 6 - GYIHYV - GFVNYV - G+++YV - - - - - 3 - gnl|BL_ORD_ID|578 - 36357|ELAV-like protein 4 (Paraneoplastic encephalomyelitis antigen HuD) (Hu-antigen D)|P26378.1|Homo sapiens|9606 - 578 - 9 - - - 1 - 11.927 - 19 - 109.216 - 1 - 6 - 4 - 9 - 0 - 0 - 2 - 6 - 0 - 6 - GYIHYV - GFVNYI - G+++Y+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 42 - Query_42 - M_3359 - 9 - - - 1 - gnl|BL_ORD_ID|691 - 42094|telomer length regulation protein TEL1|EDV12172.1|Saccharomyces cerevisiae|4932 - 691 - 9 - - - 1 - 13.0826 - 22 - 14.7007 - 2 - 7 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - GYIHYV - GYLQYV - GY+ YV - - - - - 2 - gnl|BL_ORD_ID|579 - 36358|ELAV-like protein 1|Q15717.2|Homo sapiens|9606 - 579 - 9 - - - 1 - 12.3122 - 20 - 51.2985 - 2 - 7 - 4 - 9 - 0 - 0 - 3 - 6 - 0 - 6 - GYIHYV - GFVNYV - G+++YV - - - - - 3 - gnl|BL_ORD_ID|389 - 23807|tax|AAG48731.1|Human T-lymphotropic virus 2|11909 - 389 - 23 - - - 1 - 11.927 - 19 - 72.4855 - 2 - 8 - 12 - 18 - 0 - 0 - 5 - 5 - 0 - 7 - GYIHYVF - GYPVYVF - GY YVF - - - - - 4 - gnl|BL_ORD_ID|578 - 36357|ELAV-like protein 4 (Paraneoplastic encephalomyelitis antigen HuD) (Hu-antigen D)|P26378.1|Homo sapiens|9606 - 578 - 9 - - - 1 - 11.927 - 19 - 104.062 - 2 - 7 - 4 - 9 - 0 - 0 - 2 - 6 - 0 - 6 - GYIHYV - GFVNYI - G+++Y+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 43 - Query_43 - M_3360 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 44 - Query_44 - M_3361 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 45 - Query_45 - M_3362 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 46 - Query_46 - M_3363 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 47 - Query_47 - M_3364 - 9 - - - 1 - gnl|BL_ORD_ID|374 - 23224|polyprotein|BAB18806.1|Hepatitis C virus|11103 - 374 - 15 - - - 1 - 13.853 - 24 - 6.75013 - 1 - 9 - 4 - 12 - 0 - 0 - 5 - 6 - 0 - 9 - LLPPQDPHL - LLPRRGPRL - LLP + P L - - - - - 2 - gnl|BL_ORD_ID|1950 - 181035|||| - 1950 - 44 - - - 1 - 13.4678 - 23 - 10.7201 - 1 - 9 - 25 - 33 - 0 - 0 - 5 - 6 - 0 - 9 - LLPPQDPHL - LLPRRGPRL - LLP + P L - - - - - 3 - gnl|BL_ORD_ID|1130 - 74798|polyprotein|BAA03375.1|Hepatitis C virus|11103 - 1130 - 10 - - - 1 - 13.0826 - 22 - 16.3922 - 1 - 9 - 2 - 10 - 0 - 0 - 5 - 6 - 0 - 9 - LLPPQDPHL - LLPRRGPRL - LLP + P L - - - - - 4 - gnl|BL_ORD_ID|630 - 37685|polyprotein|BAA03375.1|Hepatitis C virus|11103 - 630 - 9 - - - 1 - 13.0826 - 22 - 18.1053 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 6 - 0 - 9 - LLPPQDPHL - LLPRRGPRL - LLP + P L - - - - - 5 - gnl|BL_ORD_ID|1508 - 139406|polyprotein|ACT37184.1|Hepatitis C virus|11103 - 1508 - 10 - - - 1 - 10.7714 - 16 - 299.259 - 1 - 9 - 2 - 10 - 0 - 0 - 5 - 5 - 0 - 9 - LLPPQDPHL - LLPRPGPRL - LLP P L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 48 - Query_48 - M_3365 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 49 - Query_49 - M_3366 - 9 - - - 1 - gnl|BL_ORD_ID|2183 - 190443|core protein|BAF42671.1|Hepatitis B virus|10407 - 2183 - 9 - - - 1 - 10.7714 - 16 - 370.892 - 1 - 8 - 1 - 8 - 0 - 0 - 3 - 4 - 0 - 8 - HVDPGTIG - HISCLTFG - H+ T G - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 50 - Query_50 - M_3367 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 51 - Query_51 - M_3368 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 52 - Query_52 - M_3369 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 53 - Query_53 - M_3370 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 54 - Query_54 - M_3371 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 55 - Query_55 - M_3372 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 56 - Query_56 - M_3373 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 57 - Query_57 - M_3374 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 58 - Query_58 - M_3375 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 59 - Query_59 - M_3376 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 60 - Query_60 - M_3377 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 61 - Query_61 - M_3378 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 62 - Query_62 - M_3379 - 9 - - - 1 - gnl|BL_ORD_ID|1038 - 69435|Genome polyprotein|SRC279960|Hepatitis C virus (isolate H77)|63746 - 1038 - 9 - - - 1 - 13.4678 - 23 - 11.5219 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 5 - 0 - 8 - VLDKARVW - VLDSFKTW - VLD + W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 63 - Query_63 - M_3380 - 9 - - - 1 - gnl|BL_ORD_ID|376 - 23288|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 - 376 - 15 - - - 1 - 14.2382 - 25 - 3.37317 - 1 - 9 - 6 - 14 - 0 - 0 - 3 - 7 - 0 - 9 - CYEEYRGRL - VYQDWLGRM - Y+++ GR+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 64 - Query_64 - M_3381 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 65 - Query_65 - M_3382 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 66 - Query_66 - M_3383 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 67 - Query_67 - M_3384 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 68 - Query_68 - M_3385 - 9 - - - 1 - gnl|BL_ORD_ID|1672 - 148397|Dense granule protein 3|B6KEU8.2|Toxoplasma gondii|5811 - 1672 - 9 - - - 1 - 11.927 - 19 - 76.3762 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - PFFFFLL - PFVVFLV - PF FL+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 69 - Query_69 - M_3386 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 70 - Query_70 - M_3387 - 9 - - - 1 - gnl|BL_ORD_ID|228 - 16753|Pre-S/S protein|AAR99337.1|Hepatitis B virus|10407 - 228 - 9 - - - 1 - 13.0826 - 22 - 18.4218 - 3 - 9 - 1 - 7 - 0 - 0 - 5 - 6 - 0 - 7 - FLLDKVL - FLLTKIL - FLL K+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 71 - Query_71 - M_3388 - 9 - - - 1 - gnl|BL_ORD_ID|228 - 16753|Pre-S/S protein|AAR99337.1|Hepatitis B virus|10407 - 228 - 9 - - - 1 - 13.853 - 24 - 7.07804 - 1 - 8 - 1 - 8 - 0 - 0 - 5 - 6 - 0 - 8 - FLLDKVLA - FLLTKILT - FLL K+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 72 - Query_72 - M_3389 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 73 - Query_73 - M_3390 - 9 - - - 1 - gnl|BL_ORD_ID|350 - 21780|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 - 350 - 9 - - - 1 - 13.0826 - 22 - 17.4884 - 1 - 8 - 1 - 8 - 0 - 0 - 5 - 5 - 0 - 8 - APSWRGLA - GPSLIGLA - PS GLA - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 74 - Query_74 - M_3391 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 75 - Query_75 - M_3392 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 76 - Query_76 - M_3393 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 77 - Query_77 - M_3394 - 9 - - - 1 - gnl|BL_ORD_ID|899 - 59153|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 - 899 - 15 - - - 1 - 17.705 - 34 - 0.120504 - 2 - 9 - 7 - 14 - 0 - 0 - 5 - 7 - 0 - 8 - PGQVNRTA - PGEINRVA - PG++NR A - - - - - 2 - gnl|BL_ORD_ID|925 - 60059|Genome polyprotein|P27958.3|Hepatitis C virus genotype 1|41856 - 925 - 10 - - - 1 - 17.3198 - 33 - 0.174505 - 2 - 9 - 2 - 9 - 0 - 0 - 5 - 7 - 0 - 8 - PGQVNRTA - PGEINRVA - PG++NR A - - - - - 3 - gnl|BL_ORD_ID|1089 - 72038|Polyprotein|Q9IZA3|Hepatitis C virus subtype 2a|31649 - 1089 - 10 - - - 1 - 12.3122 - 20 - 64.4862 - 1 - 8 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - YPGQVNRT - YHGAGNKT - Y G N+T - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 78 - Query_78 - M_3395 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 79 - Query_79 - M_3396 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 80 - Query_80 - M_3397 - 9 - - - 1 - gnl|BL_ORD_ID|375 - 23270|polyprotein|AAB67036.1|Hepatitis C virus (isolate H77)|63746 - 375 - 15 - - - 1 - 14.6234 - 26 - 2.2254 - 3 - 8 - 3 - 8 - 0 - 0 - 5 - 6 - 0 - 6 - LAGLYY - LAGLFY - LAGL+Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 81 - Query_81 - M_3398 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 82 - Query_82 - M_3399 - 9 - - - 1 - gnl|BL_ORD_ID|1520 - 140600|glutamine synthetase GLNA1 (glutamine synthase) (GS-I)|NP_216736.1|Mycobacterium tuberculosis H37Rv|83332 - 1520 - 9 - - - 1 - 13.0826 - 22 - 18.1053 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 6 - 0 - 9 - CLWQLKAPV - SLWKDGAPL - LW+ AP+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 83 - Query_83 - M_3400 - 9 - - - 1 - gnl|BL_ORD_ID|1729 - 150534|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1729 - 9 - - - 1 - 12.6974 - 21 - 24.707 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 4 - 0 - 6 - RPRKAW - RPASAW - RP AW - - - - - 2 - gnl|BL_ORD_ID|928 - 60238|Gag polyprotein|P03347.3|Human immunodeficiency virus 1|11676 - 928 - 9 - - - 1 - 11.927 - 19 - 80.227 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 4 - 0 - 8 - PRKAWAWC - PRTLNAWV - PR AW - - - - - 3 - gnl|BL_ORD_ID|756 - 50292|gag protein|ACR27140.1|Human immunodeficiency virus 1|11676 - 756 - 11 - - - 1 - 11.927 - 19 - 106.287 - 2 - 8 - 5 - 11 - 0 - 0 - 4 - 4 - 0 - 7 - PRKAWAW - PRTLNAW - PR AW - - - - - 4 - gnl|BL_ORD_ID|472 - 28657|gag protein|CAB00235.1|Human immunodeficiency virus 1|11676 - 472 - 9 - - - 1 - 11.927 - 19 - 107.472 - 2 - 8 - 3 - 9 - 0 - 0 - 4 - 4 - 0 - 7 - PRKAWAW - PRTLNAW - PR AW - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 84 - Query_84 - M_3401 - 9 - - - 1 - gnl|BL_ORD_ID|2088 - 185491|polyprotein|AGO67248.1|Dengue virus 2|11060 - 2088 - 10 - - - 1 - 11.1566 - 17 - 205.223 - 4 - 9 - 1 - 6 - 0 - 0 - 4 - 6 - 0 - 6 - KREEEK - RREEEE - +REEE+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 85 - Query_85 - M_3402 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 86 - Query_86 - M_3403 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 87 - Query_87 - M_3404 - 9 - - - 1 - gnl|BL_ORD_ID|1944 - 180818|Membrane glycoprotein precursor|NP_739582.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1944 - 15 - - - 1 - 13.0826 - 22 - 12.5116 - 4 - 8 - 7 - 11 - 0 - 0 - 4 - 5 - 0 - 5 - GFTML - GFTMM - GFTM+ - - - - - 2 - gnl|BL_ORD_ID|1686 - 149052|E1 protein|NP_751920.1|Hepatitis C virus (isolate H77)|63746 - 1686 - 18 - - - 1 - 13.0826 - 22 - 15.2048 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 7 - 0 - 8 - GLAGFTML - GIAYFSMV - G+A F+M+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 88 - Query_88 - M_3405 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 89 - Query_89 - M_3406 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 90 - Query_90 - M_3407 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 91 - Query_91 - M_3408 - 9 - - - 1 - gnl|BL_ORD_ID|1486 - 135263|hemagglutinin|ACX31970.1|Influenza A virus (A/Bar-headed Goose/Qinghai/61/05(H5N1))|336238 - 1486 - 10 - - - 1 - 14.2382 - 25 - 2.71312 - 3 - 9 - 4 - 10 - 0 - 0 - 4 - 5 - 0 - 7 - QEPTAYV - QNPTTYI - Q PT Y+ - - - - - 2 - gnl|BL_ORD_ID|527 - 32268|hemagglutinin|AAK38298.1|Influenza A virus (A/Bar-headed Goose/Qinghai/61/05(H5N1))|336238 - 527 - 10 - - - 1 - 14.2382 - 25 - 2.71312 - 3 - 9 - 4 - 10 - 0 - 0 - 4 - 5 - 0 - 7 - QEPTAYV - QNPTTYI - Q PT Y+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 92 - Query_92 - M_3409 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 93 - Query_93 - M_3410 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 94 - Query_94 - M_3411 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 95 - Query_95 - M_3412 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 96 - Query_96 - M_3413 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 97 - Query_97 - M_3414 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 98 - Query_98 - M_3415 - 9 - - - 1 - gnl|BL_ORD_ID|1 - 118|envelope glycoprotein|ABS76372.1|Human immunodeficiency virus 1|11676 - 1 - 20 - - - 1 - 14.6234 - 26 - 1.57628 - 1 - 7 - 10 - 16 - 0 - 0 - 5 - 6 - 0 - 7 - YLGVPVF - YYGVPVW - Y GVPV+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 99 - Query_99 - M_3416 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 100 - Query_100 - M_3417 - 9 - - - 1 - gnl|BL_ORD_ID|1995 - 183598|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1995 - 10 - - - 1 - 13.853 - 24 - 5.02829 - 4 - 9 - 1 - 6 - 0 - 0 - 5 - 5 - 0 - 6 - HTGSGK - HPGSGK - H GSGK - - - - - 2 - gnl|BL_ORD_ID|386 - 23621|Genome polyprotein|P26664.3|Hepatitis C virus (isolate 1)|11104 - 386 - 11 - - - 1 - 13.0826 - 22 - 16.0488 - 4 - 9 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - HTGSGK - HDGAGK - H G+GK - - - - - 3 - gnl|BL_ORD_ID|385 - 23620|Genome polyprotein|SRC279960|Hepatitis C virus genotype 1|41856 - 385 - 10 - - - 1 - 13.0826 - 22 - 17.5659 - 4 - 9 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - HTGSGK - HDGAGK - H G+GK - - - - - 4 - gnl|BL_ORD_ID|384 - 23619|Genome polyprotein|P27958.3|Hepatitis C virus (isolate H)|11108 - 384 - 9 - - - 1 - 13.0826 - 22 - 20.4374 - 4 - 9 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - HTGSGK - HDGAGK - H G+GK - - - - - 5 - gnl|BL_ORD_ID|1874 - 180503|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1874 - 10 - - - 1 - 12.6974 - 21 - 23.1358 - 4 - 9 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - HTGSGK - HPGAGK - H G+GK - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 101 - Query_101 - M_3418 - 9 - - - 1 - gnl|BL_ORD_ID|1106 - 72928|Genome polyprotein|P26662.3|Hepatitis C virus (isolate Japanese)|11116 - 1106 - 10 - - - 1 - 14.6234 - 26 - 1.61671 - 1 - 7 - 1 - 7 - 0 - 0 - 6 - 6 - 0 - 7 - LPAPPGA - WPAPPGA - PAPPGA - - - - - 2 - gnl|BL_ORD_ID|1187 - 93536|core protein|AAL31859.1|Hepatitis B virus|10407 - 1187 - 11 - - - 1 - 11.1566 - 17 - 185.696 - 4 - 8 - 5 - 9 - 0 - 0 - 4 - 4 - 0 - 5 - PPGAP - PPNAP - PP AP - - - - - 3 - gnl|BL_ORD_ID|1831 - 179823|cell surface protein (associated with virulence)|NP_302372.1|Mycobacterium leprae TN|272631 - 1831 - 9 - - - 1 - 10.7714 - 16 - 339.179 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 5 - 0 - 8 - LPAPPGAP - IPASVSAP - +PA AP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 102 - Query_102 - M_3419 - 9 - - - 1 - gnl|BL_ORD_ID|1008 - 66798|glycoprotein gp35/37|AAC59622.1|Human gammaherpesvirus 8|37296 - 1008 - 15 - - - 1 - 12.6974 - 21 - 22.1438 - 1 - 7 - 2 - 8 - 0 - 0 - 4 - 4 - 0 - 7 - VRGTDWH - TRGRDAH - RG D H - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 103 - Query_103 - M_3420 - 9 - - - 1 - gnl|BL_ORD_ID|320 - 21000|glutamine synthetase GLNA1 (glutamine synthase) (GS-I)|NP_216736.1|Mycobacterium tuberculosis|1773 - 320 - 9 - - - 1 - 13.853 - 24 - 6.71897 - 3 - 7 - 4 - 8 - 0 - 0 - 4 - 5 - 0 - 5 - HHSPS - HHAPS - HH+PS - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 104 - Query_104 - M_3421 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 105 - Query_105 - M_3422 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 106 - Query_106 - M_3423 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 107 - Query_107 - M_3424 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 108 - Query_108 - M_3425 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 109 - Query_109 - M_3426 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 110 - Query_110 - M_3427 - 9 - - - 1 - gnl|BL_ORD_ID|1827 - 179766|cell surface protein (associated with virulence)|NP_302372.1|Mycobacterium leprae TN|272631 - 1827 - 9 - - - 1 - 11.927 - 19 - 82.8955 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 4 - 0 - 8 - PEPPETGV - PLPPSTAT - P PP T - - - - - 2 - gnl|BL_ORD_ID|1068 - 70491|envelope glycoprotein|AAC28452.1|Human immunodeficiency virus 1|11676 - 1068 - 10 - - - 1 - 11.927 - 19 - 85.0569 - 2 - 7 - 5 - 10 - 0 - 0 - 4 - 4 - 0 - 6 - PEPPET - PNPPEV - P PPE - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 111 - Query_111 - M_3428 - 9 - - - 1 - gnl|BL_ORD_ID|1871 - 180488|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1871 - 10 - - - 1 - 13.0826 - 22 - 16.3922 - 3 - 8 - 1 - 6 - 0 - 0 - 4 - 4 - 0 - 6 - GSGHSE - GPGHEE - G GH E - - - - - 2 - gnl|BL_ORD_ID|657 - 38974|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 657 - 11 - - - 1 - 12.3122 - 20 - 38.8163 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 7 - 0 - 9 - RRGSGHSEY - QRGPQYSEH - +RG +SE+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 112 - Query_112 - M_3429 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 113 - Query_113 - M_3430 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 114 - Query_114 - M_3431 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 115 - Query_115 - M_3432 - 9 - - - 1 - gnl|BL_ORD_ID|1610 - 143728|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 1610 - 9 - - - 1 - 14.2382 - 25 - 3.00197 - 3 - 9 - 1 - 7 - 0 - 0 - 4 - 6 - 0 - 7 - VPWNSYV - LPWYSYL - +PW SY+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 116 - Query_116 - M_3433 - 9 - - - 1 - gnl|BL_ORD_ID|1610 - 143728|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 1610 - 9 - - - 1 - 14.2382 - 25 - 3.05306 - 1 - 7 - 1 - 7 - 0 - 0 - 4 - 6 - 0 - 7 - VPWNSYV - LPWYSYL - +PW SY+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 117 - Query_117 - M_3434 - 9 - - - 1 - gnl|BL_ORD_ID|1149 - 75636|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 1149 - 10 - - - 1 - 11.5418 - 18 - 153.051 - 1 - 8 - 1 - 8 - 0 - 0 - 3 - 5 - 0 - 8 - YQLKLFAC - YRLWHYPC - Y+L + C - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 118 - Query_118 - M_3435 - 9 - - - 1 - gnl|BL_ORD_ID|1149 - 75636|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 1149 - 10 - - - 1 - 11.5418 - 18 - 153.051 - 1 - 8 - 1 - 8 - 0 - 0 - 3 - 5 - 0 - 8 - YQLKLFAC - YRLWHYPC - Y+L + C - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 119 - Query_119 - M_3436 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 120 - Query_120 - M_3437 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 121 - Query_121 - M_3438 - 9 - - - 1 - gnl|BL_ORD_ID|872 - 57361|Genome polyprotein|SRC279960|Hepatitis C virus (isolate H77)|63746 - 872 - 11 - - - 1 - 12.6974 - 21 - 28.2065 - 3 - 8 - 1 - 6 - 0 - 0 - 4 - 4 - 0 - 6 - SSCCQP - SECCTP - S CC P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 122 - Query_122 - M_3439 - 9 - - - 1 - gnl|BL_ORD_ID|664 - 39591|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 - 664 - 20 - - - 1 - 10.3862 - 15 - 495.983 - 1 - 7 - 11 - 17 - 0 - 0 - 3 - 4 - 0 - 7 - WLLEWTE - WCLWWLQ - W L W + - - - - - 2 - gnl|BL_ORD_ID|1092 - 72233|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 - 1092 - 15 - - - 1 - 10.001 - 14 - 852.012 - 1 - 5 - 1 - 5 - 0 - 0 - 2 - 4 - 0 - 5 - WLLEW - WAIKW - W ++W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 123 - Query_123 - M_3440 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 124 - Query_124 - M_3441 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 125 - Query_125 - M_3442 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 126 - Query_126 - M_3443 - 9 - - - 1 - gnl|BL_ORD_ID|1910 - 180662|polyprotein|CDF77361.1|Dengue virus 3|11069 - 1910 - 10 - - - 1 - 13.0826 - 22 - 22.3554 - 1 - 6 - 3 - 8 - 0 - 0 - 4 - 6 - 0 - 6 - ILPATI - MLPATL - +LPAT+ - - - - - 2 - gnl|BL_ORD_ID|1853 - 180390|polyprotein|CDF77361.1|Dengue virus 3|11069 - 1853 - 10 - - - 1 - 12.6974 - 21 - 22.7423 - 1 - 6 - 5 - 10 - 0 - 0 - 4 - 6 - 0 - 6 - ILPATI - MLPATL - +LPAT+ - - - - - 3 - gnl|BL_ORD_ID|1894 - 180609|polyprotein|ABK30845.1|Dengue virus 3|11069 - 1894 - 9 - - - 1 - 12.6974 - 21 - 24.2855 - 1 - 6 - 4 - 9 - 0 - 0 - 4 - 6 - 0 - 6 - ILPATI - MLPATL - +LPAT+ - - - - - 4 - gnl|BL_ORD_ID|1909 - 180660|polyprotein|CDF77361.1|Dengue virus 3|11069 - 1909 - 9 - - - 1 - 12.6974 - 21 - 24.707 - 1 - 6 - 2 - 7 - 0 - 0 - 4 - 6 - 0 - 6 - ILPATI - MLPATL - +LPAT+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 127 - Query_127 - M_3444 - 9 - - - 1 - gnl|BL_ORD_ID|1910 - 180662|polyprotein|CDF77361.1|Dengue virus 3|11069 - 1910 - 10 - - - 1 - 13.0826 - 22 - 20.1646 - 2 - 7 - 3 - 8 - 0 - 0 - 4 - 6 - 0 - 6 - ILPATI - MLPATL - +LPAT+ - - - - - 2 - gnl|BL_ORD_ID|1853 - 180390|polyprotein|CDF77361.1|Dengue virus 3|11069 - 1853 - 10 - - - 1 - 13.0826 - 22 - 21.6006 - 2 - 7 - 5 - 10 - 0 - 0 - 4 - 6 - 0 - 6 - ILPATI - MLPATL - +LPAT+ - - - - - 3 - gnl|BL_ORD_ID|1909 - 180660|polyprotein|CDF77361.1|Dengue virus 3|11069 - 1909 - 9 - - - 1 - 13.0826 - 22 - 21.8994 - 2 - 7 - 2 - 7 - 0 - 0 - 4 - 6 - 0 - 6 - ILPATI - MLPATL - +LPAT+ - - - - - 4 - gnl|BL_ORD_ID|1894 - 180609|polyprotein|ABK30845.1|Dengue virus 3|11069 - 1894 - 9 - - - 1 - 13.0826 - 22 - 22.2806 - 2 - 7 - 4 - 9 - 0 - 0 - 4 - 6 - 0 - 6 - ILPATI - MLPATL - +LPAT+ - - - - - 5 - gnl|BL_ORD_ID|983 - 64948|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 - 983 - 9 - - - 1 - 11.927 - 19 - 104.062 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 7 - 0 - 9 - TILPATILV - TLLYATVEV - T+L AT+ V - - - - - 6 - gnl|BL_ORD_ID|6 - 449|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 - 6 - 10 - - - 1 - 11.5418 - 18 - 157.893 - 1 - 7 - 4 - 10 - 0 - 0 - 4 - 6 - 0 - 7 - TILPATI - TLLYATV - T+L AT+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 128 - Query_128 - M_3445 - 9 - - - 1 - gnl|BL_ORD_ID|1924 - 180726|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1924 - 15 - - - 1 - 15.0086 - 27 - 1.14188 - 4 - 9 - 10 - 15 - 0 - 0 - 5 - 5 - 0 - 6 - WSFGSL - WDFGSL - W FGSL - - - - - 2 - gnl|BL_ORD_ID|1095 - 72301|envelope protein|YP_001527880.1|West Nile virus NY-99|10000971 - 1095 - 18 - - - 1 - 13.4678 - 23 - 7.53558 - 4 - 9 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - WSFGSL - WDFGSV - W FGS+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 129 - Query_129 - M_3446 - 9 - - - 1 - gnl|BL_ORD_ID|1397 - 110401|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1397 - 25 - - - 1 - 14.2382 - 25 - 3.81797 - 1 - 6 - 20 - 25 - 0 - 0 - 4 - 5 - 0 - 6 - NPEAMC - NPYAVC - NP A+C - - - - - 2 - gnl|BL_ORD_ID|1400 - 110467|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1400 - 25 - - - 1 - 14.2382 - 25 - 3.88133 - 1 - 6 - 5 - 10 - 0 - 0 - 4 - 5 - 0 - 6 - NPEAMC - NPYAVC - NP A+C - - - - - 3 - gnl|BL_ORD_ID|1387 - 110227|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1387 - 33 - - - 1 - 14.2382 - 25 - 4.76191 - 1 - 6 - 12 - 17 - 0 - 0 - 4 - 5 - 0 - 6 - NPEAMC - NPYAVC - NP A+C - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 130 - Query_130 - M_3447 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 131 - Query_131 - M_3448 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 132 - Query_132 - M_3449 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 133 - Query_133 - M_3450 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 134 - Query_134 - M_3451 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 135 - Query_135 - M_3452 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 136 - Query_136 - M_3453 - 9 - - - 1 - gnl|BL_ORD_ID|374 - 23224|polyprotein|BAB18806.1|Hepatitis C virus|11103 - 374 - 15 - - - 1 - 13.853 - 24 - 6.75013 - 1 - 9 - 4 - 12 - 0 - 0 - 5 - 6 - 0 - 9 - LLPPQDPHL - LLPRRGPRL - LLP + P L - - - - - 2 - gnl|BL_ORD_ID|1950 - 181035|||| - 1950 - 44 - - - 1 - 13.4678 - 23 - 10.7201 - 1 - 9 - 25 - 33 - 0 - 0 - 5 - 6 - 0 - 9 - LLPPQDPHL - LLPRRGPRL - LLP + P L - - - - - 3 - gnl|BL_ORD_ID|1130 - 74798|polyprotein|BAA03375.1|Hepatitis C virus|11103 - 1130 - 10 - - - 1 - 13.0826 - 22 - 16.3922 - 1 - 9 - 2 - 10 - 0 - 0 - 5 - 6 - 0 - 9 - LLPPQDPHL - LLPRRGPRL - LLP + P L - - - - - 4 - gnl|BL_ORD_ID|630 - 37685|polyprotein|BAA03375.1|Hepatitis C virus|11103 - 630 - 9 - - - 1 - 13.0826 - 22 - 18.1053 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 6 - 0 - 9 - LLPPQDPHL - LLPRRGPRL - LLP + P L - - - - - 5 - gnl|BL_ORD_ID|1508 - 139406|polyprotein|ACT37184.1|Hepatitis C virus|11103 - 1508 - 10 - - - 1 - 10.7714 - 16 - 299.259 - 1 - 9 - 2 - 10 - 0 - 0 - 5 - 5 - 0 - 9 - LLPPQDPHL - LLPRPGPRL - LLP P L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 137 - Query_137 - M_3454 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 138 - Query_138 - M_3455 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 139 - Query_139 - M_3456 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 140 - Query_140 - M_3457 - 9 - - - 1 - gnl|BL_ORD_ID|241 - 16836|precore/core protein [Hepatitis B virus]|AAR03815.1|Hepatitis B virus|10407 - 241 - 10 - - - 1 - 10.3862 - 15 - 506.338 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 4 - 0 - 8 - LPEVQLPK - LPSDFLPS - LP LP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 141 - Query_141 - M_3458 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 142 - Query_142 - M_3459 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 143 - Query_143 - M_3460 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 144 - Query_144 - M_3461 - 9 - - - 1 - gnl|BL_ORD_ID|1038 - 69435|Genome polyprotein|SRC279960|Hepatitis C virus (isolate H77)|63746 - 1038 - 9 - - - 1 - 13.4678 - 23 - 11.5219 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 5 - 0 - 8 - VLDKARVW - VLDSFKTW - VLD + W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 145 - Query_145 - M_3462 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 146 - Query_146 - M_3463 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 147 - Query_147 - M_3464 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 148 - Query_148 - M_3465 - 9 - - - 1 - gnl|BL_ORD_ID|350 - 21780|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 - 350 - 9 - - - 1 - 13.0826 - 22 - 17.4884 - 1 - 8 - 1 - 8 - 0 - 0 - 5 - 5 - 0 - 8 - APSWRGLA - GPSLIGLA - PS GLA - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 149 - Query_149 - M_3466 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 150 - Query_150 - M_3467 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 151 - Query_151 - M_3468 - 9 - - - 1 - gnl|BL_ORD_ID|375 - 23270|polyprotein|AAB67036.1|Hepatitis C virus (isolate H77)|63746 - 375 - 15 - - - 1 - 14.6234 - 26 - 2.2254 - 3 - 8 - 3 - 8 - 0 - 0 - 5 - 6 - 0 - 6 - LAGLYY - LAGLFY - LAGL+Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 152 - Query_152 - M_3469 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 153 - Query_153 - M_3470 - 9 - - - 1 - gnl|BL_ORD_ID|1520 - 140600|glutamine synthetase GLNA1 (glutamine synthase) (GS-I)|NP_216736.1|Mycobacterium tuberculosis H37Rv|83332 - 1520 - 9 - - - 1 - 13.0826 - 22 - 18.1053 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 6 - 0 - 9 - CLWQLKAPV - SLWKDGAPL - LW+ AP+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 154 - Query_154 - M_3471 - 9 - - - 1 - gnl|BL_ORD_ID|1729 - 150534|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1729 - 9 - - - 1 - 12.6974 - 21 - 24.707 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 4 - 0 - 6 - RPRKAW - RPASAW - RP AW - - - - - 2 - gnl|BL_ORD_ID|928 - 60238|Gag polyprotein|P03347.3|Human immunodeficiency virus 1|11676 - 928 - 9 - - - 1 - 11.927 - 19 - 80.227 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 4 - 0 - 8 - PRKAWAWC - PRTLNAWV - PR AW - - - - - 3 - gnl|BL_ORD_ID|756 - 50292|gag protein|ACR27140.1|Human immunodeficiency virus 1|11676 - 756 - 11 - - - 1 - 11.927 - 19 - 106.287 - 2 - 8 - 5 - 11 - 0 - 0 - 4 - 4 - 0 - 7 - PRKAWAW - PRTLNAW - PR AW - - - - - 4 - gnl|BL_ORD_ID|472 - 28657|gag protein|CAB00235.1|Human immunodeficiency virus 1|11676 - 472 - 9 - - - 1 - 11.927 - 19 - 107.472 - 2 - 8 - 3 - 9 - 0 - 0 - 4 - 4 - 0 - 7 - PRKAWAW - PRTLNAW - PR AW - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 155 - Query_155 - M_3472 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 156 - Query_156 - M_3473 - 9 - - - 1 - gnl|BL_ORD_ID|2088 - 185491|polyprotein|AGO67248.1|Dengue virus 2|11060 - 2088 - 10 - - - 1 - 11.1566 - 17 - 205.223 - 4 - 9 - 1 - 6 - 0 - 0 - 4 - 6 - 0 - 6 - KREEEK - RREEEE - +REEE+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 157 - Query_157 - M_3474 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 158 - Query_158 - M_3475 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 159 - Query_159 - M_3476 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 160 - Query_160 - M_3477 - 9 - - - 1 - gnl|BL_ORD_ID|1944 - 180818|Membrane glycoprotein precursor|NP_739582.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1944 - 15 - - - 1 - 13.0826 - 22 - 12.5116 - 4 - 8 - 7 - 11 - 0 - 0 - 4 - 5 - 0 - 5 - GFTML - GFTMM - GFTM+ - - - - - 2 - gnl|BL_ORD_ID|1686 - 149052|E1 protein|NP_751920.1|Hepatitis C virus (isolate H77)|63746 - 1686 - 18 - - - 1 - 13.0826 - 22 - 15.2048 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 7 - 0 - 8 - GLAGFTML - GIAYFSMV - G+A F+M+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 161 - Query_161 - M_3478 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 162 - Query_162 - M_3479 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 163 - Query_163 - M_3480 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 164 - Query_164 - M_3481 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 165 - Query_165 - M_3482 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 166 - Query_166 - M_3483 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 167 - Query_167 - M_3484 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 168 - Query_168 - M_3485 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134127_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134127_1_T.fasta deleted file mode 100755 index b2113c0f..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134127_1_T.fasta +++ /dev/null @@ -1,108 +0,0 @@ ->M_3486 -TPCHCTGTL ->M_3487 -TPCHCTGTL ->M_3488 -IPFFGQVHL ->M_3489 -ILMENKSNI ->M_3490 -ILMENKSNI ->M_3491 -LAYLVKKMM ->M_3492 -VTISLAYLV ->M_3493 -LLIESKEEM ->M_3494 -WVGPWHTIV ->M_3495 -WWVGPWHTI ->M_3496 -KTFCGDVEY ->M_3497 -AVMEQINSV ->M_3498 -AVMEQINSV ->M_3499 -HPRINTLGS ->M_3500 -FLVAFIKKI ->M_3501 -FLVAFIKKI ->M_3502 -GIVSWDTFL ->M_3503 -IVSWDTFLV ->M_3504 -SAKLTTLVV ->M_3505 -KLIWHPFSI ->M_3506 -YFDENIQKL ->M_3507 -SPSSGQRST ->M_3508 -SAQNELTEM ->M_3509 -VATNSETAM ->M_3510 -PLWGGIIYI ->M_3511 -YPLWGGIIY ->M_3512 -AALATLHPL ->M_3513 -AALATLHPL ->M_3514 -LATLHPLFL ->M_3515 -GLNMLITAL ->M_3516 -LLTGLNMLI ->M_3517 -LMWLTYTMA ->M_3518 -LTYTMAFMV ->M_3519 -LTYTMAFMV ->M_3520 -MLITALYSL ->M_3521 -NLMWLTYTM ->M_3522 -WLTYTMAFM ->M_3523 -SANTGSSVV ->M_3524 -AMGSGIQPL ->M_3525 -HLLEPGQAM ->M_3526 -TVVGNLGII ->M_3527 -HGKPTLSTV ->M_3528 -LEYNTRNAY ->M_3529 -LLGLTWPVV ->M_3530 -QLLGLTWPV ->M_3531 -RVLFWGHIL ->M_3532 -RVLFWGHIL ->M_3533 -KVFNNGADL ->M_3534 -LAGEWRERL ->M_3535 -MNWRPILTI ->M_3536 -FSDLRSSIV ->M_3537 -FSDLRSSIV ->M_3538 -YFSDLRSSI ->M_3539 -EANFSASRV diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134127_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134127_1_T_iedb.xml deleted file mode 100755 index 70b4f12a..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134127_1_T_iedb.xml +++ /dev/null @@ -1,1681 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_3486 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_3486 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_3487 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_3488 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_3489 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_3490 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_3491 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_3492 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_3493 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_3494 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_3495 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_3496 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_3497 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_3498 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_3499 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_3500 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_3501 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_3502 - 9 - - - 1 - gnl|BL_ORD_ID|787 - 52666|Antigen 85-B|P0C5B9.1|Mycobacterium tuberculosis|1773 - 787 - 9 - - - 1 - 14.2382 - 25 - 3.10506 - 4 - 9 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - SWDTFL - KWETFL - W+TFL - - - - - 2 - gnl|BL_ORD_ID|317 - 20929|Circumsporozoite protein precursor|P02893.1|Plasmodium falciparum|5833 - 317 - 9 - - - 1 - 10.3862 - 15 - 712.196 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 6 - 0 - 9 - GIVSWDTFL - GLIMVLSFL - G++ +FL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 18 - Query_18 - M_3503 - 9 - - - 1 - gnl|BL_ORD_ID|787 - 52666|Antigen 85-B|P0C5B9.1|Mycobacterium tuberculosis|1773 - 787 - 9 - - - 1 - 14.2382 - 25 - 3.05306 - 3 - 8 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - SWDTFL - KWETFL - W+TFL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 19 - Query_19 - M_3504 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_3505 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_3506 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 22 - Query_22 - M_3507 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_3508 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_3509 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_3510 - 9 - - - 1 - gnl|BL_ORD_ID|744 - 48321|||| - 744 - 9 - - - 1 - 13.4678 - 23 - 12.57 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 7 - 0 - 9 - PLWGGIIYI - PLFGYPVYV - PL+G +Y+ - - - - - 2 - gnl|BL_ORD_ID|606 - 37251|||| - 606 - 9 - - - 1 - 11.5418 - 18 - 165.102 - 2 - 9 - 2 - 9 - 0 - 0 - 3 - 6 - 0 - 8 - LWGGIIYI - LFGHPVYV - L+G +Y+ - - - - - 3 - gnl|BL_ORD_ID|607 - 37253|||| - 607 - 9 - - - 1 - 11.1566 - 17 - 202.191 - 2 - 9 - 2 - 9 - 0 - 0 - 3 - 6 - 0 - 8 - LWGGIIYI - LFGYAVYV - L+G +Y+ - - - - - 4 - gnl|BL_ORD_ID|389 - 23807|tax|AAG48731.1|Human T-lymphotropic virus 2|11909 - 389 - 23 - - - 1 - 10.7714 - 16 - 238.868 - 2 - 9 - 10 - 17 - 0 - 0 - 3 - 6 - 0 - 8 - LWGGIIYI - LYGYPVYV - L+G +Y+ - - - - - 5 - gnl|BL_ORD_ID|638 - 37970|tax|AAG48731.1|Human T-lymphotropic virus 2|11909 - 638 - 9 - - - 1 - 10.7714 - 16 - 376.438 - 2 - 9 - 2 - 9 - 0 - 0 - 3 - 6 - 0 - 8 - LWGGIIYI - LYGYPVYV - L+G +Y+ - - - - - 6 - gnl|BL_ORD_ID|2036 - 184429|||| - 2036 - 9 - - - 1 - 10.7714 - 16 - 393.541 - 2 - 9 - 2 - 9 - 0 - 0 - 3 - 6 - 0 - 8 - LWGGIIYI - LFGFPVYV - L+G +Y+ - - - - - 7 - gnl|BL_ORD_ID|1170 - 79294|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 1170 - 15 - - - 1 - 10.3862 - 15 - 443.083 - 2 - 9 - 2 - 9 - 0 - 0 - 3 - 6 - 0 - 8 - LWGGIIYI - LFGYPVYV - L+G +Y+ - - - - - 8 - gnl|BL_ORD_ID|572 - 35845|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 572 - 9 - - - 1 - 10.7714 - 16 - 497.585 - 2 - 9 - 1 - 8 - 0 - 0 - 3 - 6 - 0 - 8 - LWGGIIYI - LFGYPVYV - L+G +Y+ - - - - - 9 - gnl|BL_ORD_ID|571 - 35844|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 571 - 8 - - - 1 - 10.7714 - 16 - 522.979 - 2 - 9 - 1 - 8 - 0 - 0 - 3 - 6 - 0 - 8 - LWGGIIYI - LFGYPVYV - L+G +Y+ - - - - - 10 - gnl|BL_ORD_ID|610 - 37257|Protein Tax-1|P03409.2|Human T-lymphotropic virus 1|11908 - 610 - 9 - - - 1 - 10.3862 - 15 - 534.993 - 2 - 9 - 2 - 9 - 0 - 0 - 3 - 6 - 0 - 8 - LWGGIIYI - LFGYPVYV - L+G +Y+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 26 - Query_26 - M_3511 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_3512 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 28 - Query_28 - M_3513 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 29 - Query_29 - M_3514 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 30 - Query_30 - M_3515 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 31 - Query_31 - M_3516 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 32 - Query_32 - M_3517 - 9 - - - 1 - gnl|BL_ORD_ID|325 - 21041|Membrane glycoprotein|Q692E0|SARS coronavirus TJF|284672 - 325 - 9 - - - 1 - 15.3938 - 28 - 0.807007 - 1 - 6 - 2 - 7 - 0 - 0 - 5 - 6 - 0 - 6 - LMWLTY - LMWLSY - LMWL+Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 33 - Query_33 - M_3518 - 9 - - - 1 - gnl|BL_ORD_ID|1162 - 76621|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 1162 - 11 - - - 1 - 11.927 - 19 - 70.1482 - 3 - 8 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - YTMAFM - YTSAFV - YT AF+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 34 - Query_34 - M_3519 - 9 - - - 1 - gnl|BL_ORD_ID|1162 - 76621|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 1162 - 11 - - - 1 - 11.927 - 19 - 70.1482 - 3 - 8 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - YTMAFM - YTSAFV - YT AF+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 35 - Query_35 - M_3520 - 9 - - - 1 - gnl|BL_ORD_ID|1596 - 142232|POSSIBLE CONSERVED TRANSMEMBRANE PROTEIN|CAB00937.1|Mycobacterium tuberculosis|1773 - 1596 - 19 - - - 1 - 7.68983 - 8 - 7255.43 - 6 - 9 - 13 - 16 - 0 - 0 - 1 - 3 - 0 - 4 - LYSL - VYAF - +Y+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 36 - Query_36 - M_3521 - 9 - - - 1 - gnl|BL_ORD_ID|325 - 21041|Membrane glycoprotein|Q692E0|SARS coronavirus TJF|284672 - 325 - 9 - - - 1 - 15.779 - 29 - 0.548509 - 1 - 7 - 1 - 7 - 0 - 0 - 5 - 6 - 0 - 7 - NLMWLTY - GLMWLSY - LMWL+Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 37 - Query_37 - M_3522 - 9 - - - 1 - gnl|BL_ORD_ID|1812 - 177647|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 - 1812 - 16 - - - 1 - 12.3122 - 20 - 47.9018 - 1 - 8 - 6 - 13 - 0 - 0 - 3 - 5 - 0 - 8 - WLTYTMAF - WMNRLIAF - W+ +AF - - - - - 2 - gnl|BL_ORD_ID|1162 - 76621|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 1162 - 11 - - - 1 - 11.927 - 19 - 65.7443 - 4 - 9 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - YTMAFM - YTSAFV - YT AF+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 38 - Query_38 - M_3523 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 39 - Query_39 - M_3524 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 40 - Query_40 - M_3525 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 41 - Query_41 - M_3526 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 42 - Query_42 - M_3527 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 43 - Query_43 - M_3528 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 44 - Query_44 - M_3529 - 9 - - - 1 - gnl|BL_ORD_ID|645 - 38427|BZLF1|AAA66529.1|Human gammaherpesvirus 4|10376 - 645 - 9 - - - 1 - 11.5418 - 18 - 132.337 - 6 - 9 - 6 - 9 - 0 - 0 - 3 - 4 - 0 - 4 - WPVV - WPVL - WPV+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 45 - Query_45 - M_3530 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 46 - Query_46 - M_3531 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 47 - Query_47 - M_3532 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 48 - Query_48 - M_3533 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 49 - Query_49 - M_3534 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 50 - Query_50 - M_3535 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 51 - Query_51 - M_3536 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 52 - Query_52 - M_3537 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 53 - Query_53 - M_3538 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 54 - Query_54 - M_3539 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134510_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134510_1_T.fasta deleted file mode 100755 index 9d7ce536..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134510_1_T.fasta +++ /dev/null @@ -1,26 +0,0 @@ ->M_3540 -TLEGFFESL ->M_3541 -KILKAQEHV ->M_3542 -LLQPTPPAA ->M_3543 -SLQVKRVFV ->M_3544 -FTLEGFFES ->M_3545 -PLLRDVFNV ->M_3546 -AQSEIHFQV ->M_3547 -LQAHSMHEV ->M_3548 -LLLQPTPPA ->M_3549 -SLSFSFPLL ->M_3550 -RVWDIVPTL ->M_3551 -IVMCAMCGV ->M_3552 -AMCGVPFSV diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134510_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134510_1_T_iedb.xml deleted file mode 100755 index 32faa078..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134510_1_T_iedb.xml +++ /dev/null @@ -1,615 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_3540 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_3540 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_3541 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_3542 - 9 - - - 1 - gnl|BL_ORD_ID|1106 - 72928|Genome polyprotein|P26662.3|Hepatitis C virus (isolate Japanese)|11116 - 1106 - 10 - - - 1 - 12.3122 - 20 - 62.4024 - 4 - 9 - 2 - 7 - 0 - 0 - 4 - 4 - 0 - 6 - PTPPAA - PAPPGA - P PP A - - - - - 2 - gnl|BL_ORD_ID|1179 - 79628|E1 protein|BAA19893.1|Rubella virus|11041 - 1179 - 21 - - - 1 - 11.5418 - 18 - 116.985 - 4 - 9 - 14 - 19 - 0 - 0 - 4 - 4 - 0 - 6 - PTPPAA - PTAPCA - PT P A - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 4 - Query_4 - M_3543 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_3544 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_3545 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_3546 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_3547 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_3548 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_3549 - 9 - - - 1 - gnl|BL_ORD_ID|660 - 39339|Nucleocapsid protein|Q89462|Sin Nombre hantavirus|37705 - 660 - 15 - - - 1 - 13.853 - 24 - 7.10896 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 7 - 0 - 8 - LSFSFPLL - LSFALPII - LSF+ P++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 11 - Query_11 - M_3550 - 9 - - - 1 - gnl|BL_ORD_ID|538 - 32944|polyprotein|AAW51418.1|Dengue virus 3|11069 - 538 - 9 - - - 1 - 16.9346 - 32 - 0.261971 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 8 - 0 - 9 - RVWDIVPTL - KPWDVVPTV - + WD+VPT+ - - - - - 2 - gnl|BL_ORD_ID|536 - 32942|Polyprotein|Q9J8D4|Dengue virus 2|11060 - 536 - 9 - - - 1 - 15.779 - 29 - 0.485957 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 8 - 0 - 9 - RVWDIVPTL - KPWDVLPTV - + WD++PT+ - - - - - 3 - gnl|BL_ORD_ID|1787 - 161186|Nonstructural protein NS5|NP_739590.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1787 - 15 - - - 1 - 15.0086 - 27 - 1.12275 - 3 - 7 - 7 - 11 - 0 - 0 - 4 - 5 - 0 - 5 - WDIVP - WDVVP - WD+VP - - - - - 4 - gnl|BL_ORD_ID|533 - 32939|polyprotein|AAK67712.1|Dengue virus 2|11060 - 533 - 9 - - - 1 - 15.0086 - 27 - 1.17789 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 7 - 0 - 9 - RVWDIVPTL - KPWDIIPMV - + WDI+P + - - - - - 5 - gnl|BL_ORD_ID|537 - 32943|polyprotein|AAL96681.1|Dengue virus 2|11060 - 537 - 9 - - - 1 - 15.0086 - 27 - 1.45111 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 7 - 0 - 9 - RVWDIVPTL - KPWDVVPMV - + WD+VP + - - - - - 6 - gnl|BL_ORD_ID|534 - 32940|polyprotein|ABG75765.1|Dengue virus type 1 Hawaii|10000440 - 534 - 9 - - - 1 - 14.2382 - 25 - 2.71372 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 7 - 0 - 9 - RVWDIVPTL - KPWDVIPMV - + WD++P + - - - - - 7 - gnl|BL_ORD_ID|535 - 32941|DEN polyprotein|AAC40835.1|Dengue virus 2|11060 - 535 - 9 - - - 1 - 13.853 - 24 - 5.95161 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 7 - 0 - 9 - RVWDIVPTL - KPWDVLPMV - + WD++P + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 12 - Query_12 - M_3551 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_3552 - 9 - - - 1 - gnl|BL_ORD_ID|2182 - 190409|polymerase|AAD16253.1|Hepatitis B virus|10407 - 2182 - 15 - - - 1 - 15.3938 - 28 - 0.658828 - 1 - 8 - 7 - 14 - 0 - 0 - 4 - 6 - 0 - 8 - AMCGVPFS - SFCGSPYS - + CG P+S - - - - - 2 - gnl|BL_ORD_ID|390 - 23864|envelope glycoprotein(gp21, gp46) - human T-cell lymphotropic virus type 1|A45714|Human T-lymphotropic virus 1|11908 - 390 - 9 - - - 1 - 14.6234 - 26 - 2.45448 - 1 - 7 - 3 - 9 - 0 - 0 - 4 - 5 - 0 - 7 - AMCGVPF - SKCGFPF - + CG PF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134611_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134611_1_T.fasta deleted file mode 100755 index 9830ebcb..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134611_1_T.fasta +++ /dev/null @@ -1,38 +0,0 @@ ->M_3553 -RQMAARECK ->M_3554 -FLVYQNILK ->M_3555 -FLVYQNILK ->M_3556 -KVERERLEK ->M_3557 -KQIEMLEYK ->M_3558 -KQIEMLEYK ->M_3559 -VVGAVGVGK ->M_3560 -VVGAVGVGK ->M_3561 -FIDTYPPVL ->M_3562 -RSAFPCAHR ->M_3563 -GTPRAATMK ->M_3564 -TMKAKTDLK ->M_3565 -TMKAKTDLK ->M_3566 -GLLFAAIKR ->M_3567 -LLFAAIKRR ->M_3568 -YQIDRDLHK ->M_3569 -QTGEKLMAK ->M_3570 -QTGEKLMAK ->M_3571 -SSNLIAHVR diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134611_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134611_1_T_iedb.xml deleted file mode 100755 index 155a1ef3..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134611_1_T_iedb.xml +++ /dev/null @@ -1,403 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_3553 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_3553 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_3554 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_3555 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_3556 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_3557 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_3558 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_3559 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_3560 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_3561 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_3562 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_3563 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_3564 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_3565 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_3566 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_3567 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_3568 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_3569 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_3570 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_3571 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134702_2_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134702_2_T.fasta deleted file mode 100755 index d6a788c6..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134702_2_T.fasta +++ /dev/null @@ -1,36 +0,0 @@ ->M_3572 -GEDVDSLAL ->M_3573 -AELVYILKH ->M_3574 -KVAELVYIL ->M_3575 -ISMKLVLRF ->M_3576 -KSPGWSFQV ->M_3577 -SWKSPGWSF ->M_3578 -LTVDNITFL ->M_3579 -DAATRVAMV ->M_3580 -DSVDAATRV ->M_3581 -VGAQIYHTI ->M_3582 -GELSMLVTT ->M_3583 -EELQLICQA ->M_3584 -SEEELQLIC ->M_3585 -CELHAQAAT ->M_3586 -FTLRPGEVM ->M_3587 -VYMPPPRLL ->M_3588 -TFKKQWFYL ->M_3589 -KANRESQSL diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134702_2_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134702_2_T_iedb.xml deleted file mode 100755 index da61382f..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_134702_2_T_iedb.xml +++ /dev/null @@ -1,519 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_3572 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_3572 - 9 - - - 1 - gnl|BL_ORD_ID|1858 - 180428|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1858 - 15 - - - 1 - 15.0086 - 27 - 1.35294 - 1 - 9 - 7 - 15 - 0 - 0 - 6 - 7 - 0 - 9 - GEDVDSLAL - GEEVQVLAL - GE+V LAL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 2 - Query_2 - M_3573 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_3574 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_3575 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_3576 - 9 - - - 1 - gnl|BL_ORD_ID|1580 - 141461|ubiquitin E3 ligase ICP0|NP_044601.1|Human alphaherpesvirus 1|10298 - 1580 - 9 - - - 1 - 13.853 - 24 - 4.51705 - 3 - 6 - 2 - 5 - 0 - 0 - 4 - 4 - 0 - 4 - PGWS - PGWS - PGWS - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 6 - Query_6 - M_3577 - 9 - - - 1 - gnl|BL_ORD_ID|1580 - 141461|ubiquitin E3 ligase ICP0|NP_044601.1|Human alphaherpesvirus 1|10298 - 1580 - 9 - - - 1 - 13.4678 - 23 - 9.18751 - 5 - 8 - 2 - 5 - 0 - 0 - 4 - 4 - 0 - 4 - PGWS - PGWS - PGWS - - - - - 2 - gnl|BL_ORD_ID|951 - 62616|Chain A, Dengue Virus 4 Ns3 Helicase In Complex With Ssrna|2JLU_A|Dengue virus 4 Thailand/0348/1991|408688 - 951 - 9 - - - 1 - 13.0826 - 22 - 22.6682 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 5 - 0 - 9 - SWKSPGWSF - SYKDREWCF - S+K W F - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 7 - Query_7 - M_3578 - 9 - - - 1 - gnl|BL_ORD_ID|69 - 5191|core protein|AAL31859.1|Hepatitis B virus|10407 - 69 - 17 - - - 1 - 11.927 - 19 - 75.4827 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 7 - 0 - 8 - TVDNITFL - TVELLSFL - TV+ ++FL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 8 - Query_8 - M_3579 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_3580 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_3581 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_3582 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_3583 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_3584 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_3585 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_3586 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_3587 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_3588 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_3589 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_135773_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_135773_1_T.fasta deleted file mode 100755 index c0cf645e..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_135773_1_T.fasta +++ /dev/null @@ -1,2572 +0,0 @@ ->M_3590 -AAKARDREL ->M_3591 -AARLRFFST ->M_3592 -AFFSLSYIF ->M_3593 -AHASLIPEF ->M_3594 -AHCGLGKIL ->M_3595 -AHIERRLHI ->M_3596 -AHMETMAKL ->M_3597 -AHMGVFTEL ->M_3598 -AHQDALMLA ->M_3599 -AHRPRARLA ->M_3600 -AHTSAILTV ->M_3601 -AIRPKSLAI ->M_3602 -ALQRRRLSL ->M_3603 -ALQRRVQRL ->M_3604 -AMACMSSVF ->M_3605 -AMCVIHFSF ->M_3606 -AMYLRASSL ->M_3607 -APASRHLSA ->M_3608 -APRLLRSPV ->M_3609 -AQKEHSHLL ->M_3610 -ARAAQVAGI ->M_3611 -ARDPSPIQI ->M_3612 -ARHERIHTK ->M_3613 -ARINSIYGL ->M_3614 -ARKPRTREC ->M_3615 -ARLQHCSAL ->M_3616 -ARLQHCSAL ->M_3617 -ARLYRGQAL ->M_3618 -ARLYRGQAL ->M_3619 -ARMQSYSTI ->M_3620 -ARPEKLPEL ->M_3621 -ARQHLLQRM ->M_3622 -ARRARLQHC ->M_3623 -ARRKQSEMY ->M_3624 -ARTRAKQNI ->M_3625 -ARVQMQVTM ->M_3626 -ASFSNHQRV ->M_3627 -ATDDKMTIF ->M_3628 -AVDPMRAAY ->M_3629 -AVMGRSWEV ->M_3630 -AYATQLFFF ->M_3631 -AYEDTVRQV ->M_3632 -AYFTHSLSF ->M_3633 -CAFSRRRPI ->M_3634 -CFPLHGLQF ->M_3635 -CGDKISDRY ->M_3636 -CHFSCNNGF ->M_3637 -CHQDHWSQL ->M_3638 -CHQRCGGRV ->M_3639 -CHSNSRDHL ->M_3640 -CHYEKKTDL ->M_3641 -CLKPHQGPV ->M_3642 -CLLRNSACL ->M_3643 -CLPSRTSSV ->M_3644 -CLRDLFFPL ->M_3645 -CMKQRDEEF ->M_3646 -CPPNHIVSL ->M_3647 -CQFGTVQLV ->M_3648 -CRAETRKTF ->M_3649 -CRCPIRGLV ->M_3650 -CREELAVHL ->M_3651 -CREQHPAQL ->M_3652 -CRKMFRRSA ->M_3653 -CRKMGLRVM ->M_3654 -CRPQCCQSV ->M_3655 -CRRGLEQLL ->M_3656 -CRYGRFHKF ->M_3657 -CSDTHTNEL ->M_3658 -CVLYKYVPI ->M_3659 -CVMTKIFSL ->M_3660 -CYLITVTPI ->M_3661 -CYLVFIGCF ->M_3662 -CYNSAIQAL ->M_3663 -CYSRDQIYI ->M_3664 -CYVAICGPL ->M_3665 -CYYYFLCLL ->M_3666 -DAKRHRKVL ->M_3667 -DALCRLLGL ->M_3668 -DFKKKKGSM ->M_3669 -DHRDLGLSV ->M_3670 -DILVHHLAV ->M_3671 -DLGDKILAL ->M_3672 -DLHTRHGSI ->M_3673 -DLKMGKKPV ->M_3674 -DLLGHPQAL ->M_3675 -DLPTKRPAL ->M_3676 -DLQQKILCM ->M_3677 -DMMKEFISM ->M_3678 -DPKERIKVA ->M_3679 -DPRLKWVVL ->M_3680 -DRGGCVAGV ->M_3681 -DRMQRVISV ->M_3682 -DRMQRVISV ->M_3683 -DRNDFPVVL ->M_3684 -DRQLAAQLL ->M_3685 -DRSGARPHL ->M_3686 -DRSHTLQRM ->M_3687 -DRVERNCLL ->M_3688 -DSDGEEPCY ->M_3689 -DSHDYVFYL ->M_3690 -DTDILSYSY ->M_3691 -DTDLYHCTA ->M_3692 -DTEGILTEY ->M_3693 -DYMGFTLKI ->M_3694 -DYPCCIFPF ->M_3695 -DYRTVNNLI ->M_3696 -EAEPYYCSL ->M_3697 -EAKRQNLRL ->M_3698 -EALIRHLNA ->M_3699 -EAMNNAQKI ->M_3700 -EASRRYKKV ->M_3701 -EFPQKYYWW ->M_3702 -EGQRRPSSV ->M_3703 -EHEEDGSEI ->M_3704 -EHGGKTVKV ->M_3705 -EHLAAPRLV ->M_3706 -EHNVTVLVV ->M_3707 -EHQIGPQEI ->M_3708 -EHRLHTPMY ->M_3709 -EIKTIVKAI ->M_3710 -EIMNRVVNA ->M_3711 -EKRFKRKSV ->M_3712 -ELACYNSAI ->M_3713 -ELEHMRLRY ->M_3714 -ELHARGHQV ->M_3715 -ELHRQVKTL ->M_3716 -ELKQMCNPI ->M_3717 -ELLLKVFAL ->M_3718 -ELQARLAAL ->M_3719 -ELRAHCETL ->M_3720 -ELRRYLKSG ->M_3721 -EMKCREKGF ->M_3722 -EMLRRQIRL ->M_3723 -EMRCQYETV ->M_3724 -EMYEKGLSV ->M_3725 -EPKKKEKGM ->M_3726 -EPKKRKVVP ->M_3727 -EPRFRLNLF ->M_3728 -ERDGLERAL ->M_3729 -ERDGLHSVV ->M_3730 -ERDQLKETL ->M_3731 -EREKMGVTM ->M_3732 -ERFWRIILL ->M_3733 -ERHVAVEGV ->M_3734 -ERIDTNQKC ->M_3735 -ERKTMIKKI ->M_3736 -ERLQALYMI ->M_3737 -ERLQNPLRV ->M_3738 -ERQCHNTAL ->M_3739 -ERQCHNTAL ->M_3740 -ERRDCIICC ->M_3741 -ERSCWVRAI ->M_3742 -ERSEQPLSV ->M_3743 -ERSPQAAAV ->M_3744 -ERTNQKWSV ->M_3745 -ERTSATLTI ->M_3746 -ERTTWVQKI ->M_3747 -ERYGPVFTI ->M_3748 -ETMLHGQVM ->M_3749 -ETRPTPRLL ->M_3750 -ETVSTTLCY ->M_3751 -EYIVIPSTF ->M_3752 -EYLLGSWVI ->M_3753 -EYNANTSVL ->M_3754 -EYRPRTFCF ->M_3755 -EYVKFLHTF ->M_3756 -EYVTELPSF ->M_3757 -FAAQHGLAV ->M_3758 -FAKLRHNTQ ->M_3759 -FARGQRWRL ->M_3760 -FARGQRWRL ->M_3761 -FCLRYGAAL ->M_3762 -FCSLHCLLY ->M_3763 -FCYYYFLCL ->M_3764 -FEESKSYEV ->M_3765 -FEFSQVLAL ->M_3766 -FESHRILHL ->M_3767 -FFLSYLKSL ->M_3768 -FFLSYLSLV ->M_3769 -FGAIRRSDA ->M_3770 -FGYENSPEL ->M_3771 -FHFRRPWSF ->M_3772 -FHFRRPWSF ->M_3773 -FHFRRPWSF ->M_3774 -FHHCHPKYS ->M_3775 -FHHIDSAYL ->M_3776 -FHIGSAESM ->M_3777 -FHLHNAHVL ->M_3778 -FHLPYLEQK ->M_3779 -FHLQHWKQI ->M_3780 -FHLSIHLLY ->M_3781 -FHMASGEAL ->M_3782 -FHPMRTLPM ->M_3783 -FHVDQATTV ->M_3784 -FHYDTQLSL ->M_3785 -FHYLKKQET ->M_3786 -FIADKLSTL ->M_3787 -FIADKLSTL ->M_3788 -FICLQFWCI ->M_3789 -FIMFLFVYI ->M_3790 -FINNSIVYL ->M_3791 -FKKARWTII ->M_3792 -FKNHHNRTV ->M_3793 -FLARTVSTL ->M_3794 -FLEHGEQAY ->M_3795 -FLHERKQAS ->M_3796 -FLKTLWAGL ->M_3797 -FLLAMLLSI ->M_3798 -FLLEFLLPL ->M_3799 -FLLFSFLFL ->M_3800 -FLRTYKNSV ->M_3801 -FLSDLTPGY ->M_3802 -FLSVFYTAV ->M_3803 -FLTVMLLAL ->M_3804 -FLVERKTIA ->M_3805 -FMAYATQLF ->M_3806 -FMKYLVNFI ->M_3807 -FMLVMICIL ->M_3808 -FMWPLHWSM ->M_3809 -FPAMLQAPI ->M_3810 -FPIIIAWAI ->M_3811 -FPKKSLMLM ->M_3812 -FPLVRSCQM ->M_3813 -FPNGRLTFL ->M_3814 -FPQKYYWWF ->M_3815 -FPQNRYTQE ->M_3816 -FPTDCVYVM ->M_3817 -FPYCRAHVL ->M_3818 -FPYCRAHVL ->M_3819 -FPYCRSHVF ->M_3820 -FPYGSSTAL ->M_3821 -FPYNSDLSL ->M_3822 -FQFGAGTQV ->M_3823 -FQGRRSPSF ->M_3824 -FQRKKRRKF ->M_3825 -FREDPVAWV ->M_3826 -FREGRPREW ->M_3827 -FRGALPVQI ->M_3828 -FRGDGRTCC ->M_3829 -FRHSPRNLI ->M_3830 -FRKELRYFL ->M_3831 -FRKELRYFL ->M_3832 -FRLMHNLNF ->M_3833 -FRLRRVASA ->M_3834 -FRLWMTTEV ->M_3835 -FRNDQEETT ->M_3836 -FRNGLGTGM ->M_3837 -FRNSRLKQC ->M_3838 -FRPPAWNRL ->M_3839 -FRQGHQLFH ->M_3840 -FRQLEDSQV ->M_3841 -FRQSRSQVV ->M_3842 -FRQSRSQVV ->M_3843 -FRSHVPSHL ->M_3844 -FRSLQGSVF ->M_3845 -FRSPEDLSL ->M_3846 -FRSSASGAL ->M_3847 -FRTKDGSFV ->M_3848 -FRVSISQTA ->M_3849 -FRYEGSLTT ->M_3850 -FSDKKTITY ->M_3851 -FSFINNSIV ->M_3852 -FSIPTCLMY ->M_3853 -FSKAQAEYL ->M_3854 -FSYPSIHRF ->M_3855 -FTDVSRFTL ->M_3856 -FTFDLYRVL ->M_3857 -FTSFLLLMY ->M_3858 -FVEEWTESL ->M_3859 -FVQKLLFPY ->M_3860 -FWCAQFTSF ->M_3861 -FWKKILFVI ->M_3862 -FWKLFYCKF ->M_3863 -FYADSHHCV ->M_3864 -FYAIVVPML ->M_3865 -FYCDDLPLL ->M_3866 -FYLGTYQAV ->M_3867 -FYMLTCIDL ->M_3868 -FYQAGSLCI ->M_3869 -FYTDSSSVL ->M_3870 -FYTPALFSF ->M_3871 -GAGPRFLEL ->M_3872 -GDKQHFTTL ->M_3873 -GGATRVYAL ->M_3874 -GHDAPRRTL ->M_3875 -GHKEDAGVV ->M_3876 -GHKGLNQCV ->M_3877 -GHLEAASCI ->M_3878 -GHLQIRSLL ->M_3879 -GHLSKKMTL ->M_3880 -GHNSWGFGV ->M_3881 -GHPQDGSGL ->M_3882 -GHPSLSQHL ->M_3883 -GHTGERHRV ->M_3884 -GHTPNGRHF ->M_3885 -GHVAGEQML ->M_3886 -GLHSSFMPL ->M_3887 -GLSVRPHAI ->M_3888 -GMFTLRMAL ->M_3889 -GNYSRSSHV ->M_3890 -GPCRRRFSF ->M_3891 -GPLPKSYAV ->M_3892 -GPRTKAWFL ->M_3893 -GRAEESVVL ->M_3894 -GRAPCWQRL ->M_3895 -GREAEMQEL ->M_3896 -GRMHIGDEL ->M_3897 -GRMMFVGTL ->M_3898 -GRNGQKAAL ->M_3899 -GRVEKLLDL ->M_3900 -GSDSSNGAV ->M_3901 -GSEDFEDTY ->M_3902 -GTNIVILEY ->M_3903 -GVLECPRLI ->M_3904 -HAKKKPNPV ->M_3905 -HHIDSAYLY ->M_3906 -HHKGKMKAL ->M_3907 -HHKHKELQV ->M_3908 -HHRFNNFML ->M_3909 -HIKDKKLPL ->M_3910 -HLLSHSYCL ->M_3911 -HLMGQLSSL ->M_3912 -HMRLRYLAA ->M_3913 -HPKYSFRRL ->M_3914 -HPLRYTLIM ->M_3915 -HRADVYVGV ->M_3916 -HREDFEARL ->M_3917 -HRGTGAVYV ->M_3918 -HRLGESQTL ->M_3919 -HRLHTPMYL ->M_3920 -HRQAEVHKV ->M_3921 -HRQQRGQQL ->M_3922 -HRSKRGSSV ->M_3923 -HRTRCLSKL ->M_3924 -HRYPRVMAA ->M_3925 -HRYPRVMAA ->M_3926 -HSHLLSHSY ->M_3927 -HSYEAGTEI ->M_3928 -HTPNGRHFY ->M_3929 -HWSMWLGVF ->M_3930 -HYATILTSL ->M_3931 -HYHHRFNNF ->M_3932 -HYISIFYAL ->M_3933 -HYLRDVLPL ->M_3934 -HYQGTWYLT ->M_3935 -HYRKRGAHL ->M_3936 -IAHAWWAHF ->M_3937 -IAMYFYTTL ->M_3938 -IEYGSPEEL ->M_3939 -IFIASIYLL ->M_3940 -IFLFVIVTI ->M_3941 -IFPFALIFF ->M_3942 -IFPFILIFF ->M_3943 -IFSEKNRLV ->M_3944 -IFSFINNSI ->M_3945 -IFVSSYINI ->M_3946 -IGRNRSPCM ->M_3947 -IHDGAVHTI ->M_3948 -IHDRQLRSF ->M_3949 -IHEDEVDDM ->M_3950 -IHFTKKDYV ->M_3951 -IHGASNHCL ->M_3952 -IHIDDNKWV ->M_3953 -IHLLDSLRL ->M_3954 -IHLLYPPSL ->M_3955 -IHPRDRSTV ->M_3956 -IHTDDNKCV ->M_3957 -ILAVLPSLF ->M_3958 -ILKKRQQAA ->M_3959 -ILKRRYQEP ->M_3960 -ILLTQFHFL ->M_3961 -ILMRQPLPA ->M_3962 -ILRSKMKTV ->M_3963 -ILRVYSGVL ->M_3964 -ILSSRSRQL ->M_3965 -ILSSRSRQL ->M_3966 -INFNHDSSI ->M_3967 -IQWSYWGVF ->M_3968 -IRAANRRGL ->M_3969 -IRDGSTMTF ->M_3970 -IREYCPYTY ->M_3971 -IRFLRQYEF ->M_3972 -IRHGNVIAC ->M_3973 -IRHLNATSF ->M_3974 -IRIDTIHLL ->M_3975 -IRLNRQRHT ->M_3976 -IRNMAPDSL ->M_3977 -IRPPDSRSL ->M_3978 -IRRGGKHQL ->M_3979 -IRRLRPSSI ->M_3980 -IRRLRPSSI ->M_3981 -IRRRGSTSL ->M_3982 -IRYLHSLQI ->M_3983 -ISELLFECY ->M_3984 -ISFSMSEKM ->M_3985 -ISKRKVSVA ->M_3986 -ISLGFFLVF ->M_3987 -ISSSAGLPY ->M_3988 -ITIRNPLRY ->M_3989 -ITMDQKKTI ->M_3990 -ITMRYIHFL ->M_3991 -ITTFDRLAY ->M_3992 -IVHRQFYLF ->M_3993 -IVMGYSSGI ->M_3994 -IWFSIPTCL ->M_3995 -IYAALPYVK ->M_3996 -IYAFMGTPM ->M_3997 -IYCRPFTTL ->M_3998 -IYCVYPDSL ->M_3999 -IYGLCVVIV ->M_4000 -IYHDSRIHV ->M_4001 -IYTIVNIKI ->M_4002 -IYVDKVRHV ->M_4003 -KAFKRSSYL ->M_4004 -KAFKRSSYL ->M_4005 -KAMERSSLM ->M_4006 -KHFIHLITV ->M_4007 -KHLSRSNWL ->M_4008 -KHNEEIRFL ->M_4009 -KHRNMHCKI ->M_4010 -KHRSEISMM ->M_4011 -KIHIRETAI ->M_4012 -KILKKRQQA ->M_4013 -KISKRKVSV ->M_4014 -KKRRKFWKA ->M_4015 -KLKPKKPTL ->M_4016 -KLQPYFQTL ->M_4017 -KMFRRSAHL ->M_4018 -KRCALRLLV ->M_4019 -KRFKRKSVV ->M_4020 -KRILMPQVM ->M_4021 -KRISHKAAL ->M_4022 -KRQNLRLAL ->M_4023 -KRQRAMETL ->M_4024 -KRSPAWNEM ->M_4025 -KRYLSQREV ->M_4026 -KSDGLSLAV ->M_4027 -KSFSKYASF ->M_4028 -KWIREGYLV ->M_4029 -KYMPPCSLV ->M_4030 -KYPYWYQQK ->M_4031 -KYSTGIGWI ->M_4032 -KYSTPPYLL ->M_4033 -LAGQKRCAL ->M_4034 -LAKVKYTAS ->M_4035 -LALLKQVSV ->M_4036 -LANDPIQVV ->M_4037 -LAQSFFNCL ->M_4038 -LCAIYFLSI ->M_4039 -LCIKHFNIL ->M_4040 -LEHMRLRYL ->M_4041 -LFAAVVLLI ->M_4042 -LFKKARWTI ->M_4043 -LFLLFSFLF ->M_4044 -LFPRLPSIL ->M_4045 -LFSFMTHCF ->M_4046 -LFSFMTHRF ->M_4047 -LGRNRHFGF ->M_4048 -LHAPMYNLL ->M_4049 -LHAPMYNLL ->M_4050 -LHEQLGDRL ->M_4051 -LHFDAVQIC ->M_4052 -LHFMPCVYI ->M_4053 -LHFVQKLLF ->M_4054 -LHHKHKELQ ->M_4055 -LHHTHIALL ->M_4056 -LHKDSNMPV ->M_4057 -LHMNLLSYF ->M_4058 -LHNAHVLDV ->M_4059 -LHQCVLRFL ->M_4060 -LHQGGATRV ->M_4061 -LHRASGVGV ->M_4062 -LHSGLQILI ->M_4063 -LHTPVYFLL ->M_4064 -LHTPVYFLL ->M_4065 -LHTRHGSIL ->M_4066 -LHVGCDEVY ->M_4067 -LHYEEIPEY ->M_4068 -LIATQLLFY ->M_4069 -LIKHKKTHI ->M_4070 -LIKYRQNHA ->M_4071 -LIMNKRLGL ->M_4072 -LKKRQQAAL ->M_4073 -LKLVKRNSL ->M_4074 -LLCARAWLL ->M_4075 -LLDRRPHGY ->M_4076 -LLESYSASL ->M_4077 -LLGHKTVTI ->M_4078 -LLGKKGTSA ->M_4079 -LLHTIITPM ->M_4080 -LLKKLCIKL ->M_4081 -LLKSDGLSL ->M_4082 -LLKTAFHPV ->M_4083 -LLLMYSYAV ->M_4084 -LLLQALQAL ->M_4085 -LLMNKPYLA ->M_4086 -LLMYTKLVV ->M_4087 -LLNVHLSKL ->M_4088 -LLRDFVAPL ->M_4089 -LLRGHDQSA ->M_4090 -LLRLLRKAM ->M_4091 -LLRNDARSL ->M_4092 -LLSFKRQRA ->M_4093 -LLSRKDSIF ->M_4094 -LLTQRLQGL ->M_4095 -LMACATQLF ->M_4096 -LMGQLSSLY ->M_4097 -LMKMDDPSI ->M_4098 -LMKQKKSSC ->M_4099 -LNKLDFYVL ->M_4100 -LNRQRHTPM ->M_4101 -LPALRKTGV ->M_4102 -LPAVHALRL ->M_4103 -LPGLHFMPG ->M_4104 -LPGMRGPPG ->M_4105 -LPKDRFFAV ->M_4106 -LPKEKLAAA ->M_4107 -LPMTLLLLL ->M_4108 -LPQGRESPI ->M_4109 -LPRSKDTIL ->M_4110 -LPRVRGTTL ->M_4111 -LPSCRLAPA ->M_4112 -LPTLKFQTF ->M_4113 -LPYVKKTGM ->M_4114 -LQKVRQEVL ->M_4115 -LQLYRFSPI ->M_4116 -LQRRRLSLL ->M_4117 -LRADTSFFL ->M_4118 -LRAKYRESL ->M_4119 -LRAKYRESL ->M_4120 -LRAPPGPQL ->M_4121 -LRCHYHHRF ->M_4122 -LRETRDQPL ->M_4123 -LRIMLGEIL ->M_4124 -LRINEVMVY ->M_4125 -LRKGPIMEV ->M_4126 -LRKHQILHL ->M_4127 -LRKHQITHL ->M_4128 -LRKPQNSEC ->M_4129 -LRKQNFQPA ->M_4130 -LRLALDQYL ->M_4131 -LRLEINHTI ->M_4132 -LRLPGGSCM ->M_4133 -LRLRWGQII ->M_4134 -LRLSEPAEI ->M_4135 -LRMSDPSHI ->M_4136 -LRMSRSYPT ->M_4137 -LRNDARSLY ->M_4138 -LRPSSIETY ->M_4139 -LRQWIVVTM ->M_4140 -LRRHRDVSA ->M_4141 -LRRMNSFQV ->M_4142 -LRRNYRCAI ->M_4143 -LRRNYRCAI ->M_4144 -LRRQDYQEI ->M_4145 -LRRVASALL ->M_4146 -LRSDAPAQL ->M_4147 -LRSEEDGLV ->M_4148 -LRSERNNTM ->M_4149 -LRSIRVRLL ->M_4150 -LRSQAALSL ->M_4151 -LRSQFPLIL ->M_4152 -LRTEQNDFI ->M_4153 -LRVSDGSLL ->M_4154 -LRWEYGSIL ->M_4155 -LRYFLKHGI ->M_4156 -LRYGAALIY ->M_4157 -LSEFPEDSY ->M_4158 -LSFKRQRAM ->M_4159 -LSIIRFKGL ->M_4160 -LSPMNHLCY ->M_4161 -LSSLWYHTY ->M_4162 -LSTCRKLSL ->M_4163 -LTDYDTRFY ->M_4164 -LTEPHLRLL ->M_4165 -LTGLVWQRY ->M_4166 -LTIYAALPY ->M_4167 -LTMCMKKSL ->M_4168 -LTQKQVLNY ->M_4169 -LVAQHYAAL ->M_4170 -LVDTVIDAY ->M_4171 -LVQNSCWLI ->M_4172 -LVRDRMKEL ->M_4173 -LWQSCEESF ->M_4174 -LYAVMGRSW ->M_4175 -LYEDTLYTV ->M_4176 -LYEDWCQTV ->M_4177 -LYEDWCQTV ->M_4178 -LYFHSFIRI ->M_4179 -LYFLAGQSL ->M_4180 -LYFTRPVPL ->M_4181 -LYGEQGHRW ->M_4182 -LYGHSTHDL ->M_4183 -LYHRDLAKW ->M_4184 -LYMINHFFC ->M_4185 -LYPDINNPF ->M_4186 -LYPPSLPPF ->M_4187 -LYTAYHVFF ->M_4188 -LYVWKSELV ->M_4189 -MACDRYVAI ->M_4190 -MAEVNITYV ->M_4191 -MAFDRYVAI ->M_4192 -MAFDRYVAI ->M_4193 -MAHERRDQL ->M_4194 -MAHERRDQL ->M_4195 -MAIGHFGQL ->M_4196 -MAKYWNQFL ->M_4197 -MAMSSRLAL ->M_4198 -MATAYIRSM ->M_4199 -MAYDQFLAI ->M_4200 -MAYDQFLAI ->M_4201 -MAYSITCPI ->M_4202 -MCMKKSLRL ->M_4203 -MERERKAIA ->M_4204 -MEVEAEQLL ->M_4205 -MFATDYTTI ->M_4206 -MFTLRMALF ->M_4207 -MGHLQIRSL ->M_4208 -MGKSTHTSM ->M_4209 -MHEEGYNKL ->M_4210 -MHEYKIQGL ->M_4211 -MHFCGGSFI ->M_4212 -MHHPGSRKF ->M_4213 -MHKTGLLGL ->M_4214 -MHNLLIHRV ->M_4215 -MHPDGRFEC ->M_4216 -MIFILFLVI ->M_4217 -MIRVKDSLI ->M_4218 -MKQKKSSCL ->M_4219 -MLCFYTPAL ->M_4220 -MLHLYPGPM ->M_4221 -MLKTGISTV ->M_4222 -MLLMNLATA ->M_4223 -MLLSILLPL ->M_4224 -MLLSQNASI ->M_4225 -MLNKVLYRL ->M_4226 -MLRELSSAF ->M_4227 -MLRRQIRLL ->M_4228 -MLRRQIRLL ->M_4229 -MLSLRESPM ->M_4230 -MLTSKVTVL ->M_4231 -MLYRTVREL ->M_4232 -MLYRTVREL ->M_4233 -MMQCHRLSW ->M_4234 -MNKRLGLEL ->M_4235 -MNYKKGRAF ->M_4236 -MPILKSVLI ->M_4237 -MPKKVISAL ->M_4238 -MPLLKLSCS ->M_4239 -MPQYLASPL ->M_4240 -MQFTQALEV ->M_4241 -MRAAYLDDL ->M_4242 -MRCQYETVL ->M_4243 -MREQRERQL ->M_4244 -MRLRGGRMI ->M_4245 -MRPISGVML ->M_4246 -MRQPLPASM ->M_4247 -MRRRQCEEV ->M_4248 -MRRYQSRVI ->M_4249 -MRRYQSRVI ->M_4250 -MRSCLRLAL ->M_4251 -MRSCLRLAL ->M_4252 -MSEGIVKLY ->M_4253 -MSPRVFFLL ->M_4254 -MSQSQVALL ->M_4255 -MSRSYPTGL ->M_4256 -MWPLHWSMW ->M_4257 -MYCLMLQCW ->M_4258 -MYCMVFLVL ->M_4259 -MYGAETEKF ->M_4260 -MYMSVLSLI ->M_4261 -MYMSVLSLI ->M_4262 -MYSVVPQMV ->M_4263 -MYSVVPQMV ->M_4264 -MYSYAVPPL ->M_4265 -MYTKLVVGF ->M_4266 -NEILRRYSV ->M_4267 -NFIERFWRI ->M_4268 -NFIERFWRI ->M_4269 -NFSINWWPI ->M_4270 -NHHNRTVEV ->M_4271 -NHKDNSRIR ->M_4272 -NHPYWANTV ->M_4273 -NHSDLAAEL ->M_4274 -NIDLAREAY ->M_4275 -NILPHYLEL ->M_4276 -NIVYHTASI ->M_4277 -NIYSRIREY ->M_4278 -NLARKEYTI ->M_4279 -NLGFRFHMA ->M_4280 -NLKHRKTAA ->M_4281 -NLLANFSFL ->M_4282 -NLLSYFNNL ->M_4283 -NLMAKNNQA ->M_4284 -NLNYRDLYY ->M_4285 -NLPSKRVSL ->M_4286 -NMHCKISLL ->M_4287 -NPLLHMVTM ->M_4288 -NPLRYLAVM ->M_4289 -NPLRYTSIL ->M_4290 -NQKRRSESF ->M_4291 -NRDKLGLQI ->M_4292 -NRFSSKLLA ->M_4293 -NRGPATAEV ->M_4294 -NRLDLVRFY ->M_4295 -NRNYCVSVY ->M_4296 -NRPEEEEQV ->M_4297 -NRQRHTPMY ->M_4298 -NRVGVSSKL ->M_4299 -NSDSFTGFI ->M_4300 -NSINQVKLL ->M_4301 -NTHRSRLSL ->M_4302 -NTMAFSTDY ->M_4303 -NVKKQRAGL ->M_4304 -NVNQRFLNV ->M_4305 -NYLEKVRSL ->M_4306 -NYRDLYYFL ->M_4307 -NYSPRPICV ->M_4308 -PASTLSLGY ->M_4309 -PFPRWLKII ->M_4310 -PHWASSIVL ->M_4311 -PHYDFERSC ->M_4312 -PIEMNPEGY ->M_4313 -PRIGYSLLL ->M_4314 -PRLKWVVLV ->M_4315 -PRNRKPLTV ->M_4316 -PRPSRCLLL ->M_4317 -PRSEEAAVL ->M_4318 -PRSKDTILL ->M_4319 -PRSRWRDQL ->M_4320 -PRWSCQEKL ->M_4321 -PSQPANSFY ->M_4322 -PTALSSLWY ->M_4323 -PTDVLNGAA ->M_4324 -PYPETPPRW ->M_4325 -PYQGRPKLL ->M_4326 -PYQGRPKLL ->M_4327 -PYTSVFLSV ->M_4328 -QAEARLLAL ->M_4329 -QAKVKFIGV ->M_4330 -QEHVRCSAI ->M_4331 -QFSFDGWKF ->M_4332 -QGRPKLLQL ->M_4333 -QHCYMSRLL ->M_4334 -QHDFCGLYM ->M_4335 -QHLLQRMSI ->M_4336 -QHMHCLQDL ->M_4337 -QHPNNSKDV ->M_4338 -QHQRLLEVL ->M_4339 -QHTESLEYM ->M_4340 -QHYAALQEY ->M_4341 -QILSRVAAL ->M_4342 -QLMMSLLQL ->M_4343 -QLREHAATL ->M_4344 -QLRRSKVSV ->M_4345 -QLYPRLKML ->M_4346 -QLYPRLKML ->M_4347 -QMLRIFKEM ->M_4348 -QMYMSVLSL ->M_4349 -QPAWRKASA ->M_4350 -QPLRNFISV ->M_4351 -QPMCRICHE ->M_4352 -QRAPVGKLL ->M_4353 -QRAVSRNLM ->M_4354 -QRFLFIMFL ->M_4355 -QRFLNVQEL ->M_4356 -QRGEGILDM ->M_4357 -QRHGFGEEI ->M_4358 -QRIQMYMSV ->M_4359 -QRIVKPTSI ->M_4360 -QRLEPVYFV ->M_4361 -QRLEVPIEM ->M_4362 -QRMELLITF ->M_4363 -QRQARQYQL ->M_4364 -QRRPSSVGL ->M_4365 -QRRSIPFQM ->M_4366 -QRSGKPVLM ->M_4367 -QRSNSETKV ->M_4368 -QRSRKGDLL ->M_4369 -QSEDRSHTL ->M_4370 -QSQPFSMQY ->M_4371 -QSQPGNALY ->M_4372 -QTCKANLCY ->M_4373 -QTLACNLCY ->M_4374 -QVKRKVQAL ->M_4375 -QYMLTLFTA ->M_4376 -RAEDTALYY ->M_4377 -RAIYHSCSL ->M_4378 -RAKYRESLL ->M_4379 -RAPQRIPSL ->M_4380 -RARLQHCSA ->M_4381 -RARYYIQVA ->M_4382 -RASQRMSSV ->M_4383 -RATARFHQL ->M_4384 -RFFSRFTAV ->M_4385 -RFHRVIKDF ->M_4386 -RFKRKSVVA ->M_4387 -RFLFIMFLF ->M_4388 -RFLRNFPQI ->M_4389 -RFMKYLVNF ->M_4390 -RFNMLNQIF ->M_4391 -RFQDHRWEL ->M_4392 -RHFEEALQT ->M_4393 -RHFRLMHNL ->M_4394 -RHIRHGNVI ->M_4395 -RHLGDQMEV ->M_4396 -RHRCRNRFV ->M_4397 -RHSPRNLIY ->M_4398 -RHTPMYYFL ->M_4399 -RHTPMYYFL ->M_4400 -RLIVKSREL ->M_4401 -RLKQEIKRL ->M_4402 -RLMCGPNTI ->M_4403 -RLRRVASAL ->M_4404 -RMCKFLQYF ->M_4405 -RMSSVGANF ->M_4406 -RNFPQIYIL ->M_4407 -RNPQELWHF ->M_4408 -RNRKRFCVP ->M_4409 -RPGSRGCPM ->M_4410 -RPKYSFHRL ->M_4411 -RPRARLAAL ->M_4412 -RPRARYYIQ ->M_4413 -RPRQGRWWL ->M_4414 -RQFPKKSLM ->M_4415 -RQFYLFYNF ->M_4416 -RQMISELLF ->M_4417 -RQQQDYWLM ->M_4418 -RRENSLSEI ->M_4419 -RRFNMLNQI ->M_4420 -RRGEAEKRL ->M_4421 -RRGGSGAMV ->M_4422 -RRKQSEMYI ->M_4423 -RRLDYDHKL ->M_4424 -RRPSRAMWL ->M_4425 -RRQDYQEIL ->M_4426 -RRSDAEKQL ->M_4427 -RRSKVSVEM ->M_4428 -RRSPSFSRV ->M_4429 -RRVASALLL ->M_4430 -RRVPYRGSV ->M_4431 -RRYLKSGVV ->M_4432 -RSADWQRKI ->M_4433 -RSELNSVEY ->M_4434 -RSFPAGVEM ->M_4435 -RTQDAIHEL ->M_4436 -RTSSIFYSF ->M_4437 -RVGQMAFVF ->M_4438 -RVNDCILQV ->M_4439 -RVRRRGQKL ->M_4440 -RVSDGSLLY ->M_4441 -RWQGRVRTL ->M_4442 -RYAALLKCW ->M_4443 -RYARPSRLV ->M_4444 -RYCLTTLTI ->M_4445 -RYFDEPVEL ->M_4446 -RYFDEPVEL ->M_4447 -RYFLKHGIL ->M_4448 -RYILLKRSL ->M_4449 -RYLENGKEM ->M_4450 -RYLKSGVVL ->M_4451 -RYLPDCDYL ->M_4452 -RYRSIISDI ->M_4453 -RYVAICAPL ->M_4454 -RYVASCKPL ->M_4455 -SADYINANY ->M_4456 -SAEECRTEL ->M_4457 -SAKQQNQIL ->M_4458 -SAKQQNQIL ->M_4459 -SALGREHPA ->M_4460 -SARDQPSSV ->M_4461 -SARLRQRAV ->M_4462 -SASNNNSEL ->M_4463 -SAVRRDLTF ->M_4464 -SAYDGKDYI ->M_4465 -SCSSNPHLL ->M_4466 -SEEERGLEL ->M_4467 -SEKDRPVKV ->M_4468 -SESHRTSLL ->M_4469 -SEVERLDVL ->M_4470 -SFFNCLWEV ->M_4471 -SFPGRVREL ->M_4472 -SFQTITEQF ->M_4473 -SFVDAIHTF ->M_4474 -SGFEFSQVL ->M_4475 -SGMARVGSL ->M_4476 -SHKEAITAL ->M_4477 -SHKKQSSVI ->M_4478 -SHLQRIGTI ->M_4479 -SHLTIVILF ->M_4480 -SHMYVATGI ->M_4481 -SHNRHVPKI ->M_4482 -SHPLHYTTI ->M_4483 -SHPLHYTTI ->M_4484 -SHQPLPGTL ->M_4485 -SHRNPLLDL ->M_4486 -SHSPAGELT ->M_4487 -SHSSNPHLL ->M_4488 -SHTLLLTQL ->M_4489 -SIFYSFLPL ->M_4490 -SKFGQGTGL ->M_4491 -SKQNMPQYL ->M_4492 -SLAKFDAPL ->M_4493 -SLDTTTWEY ->M_4494 -SLFTCVLQL ->M_4495 -SLGDNSEYL ->M_4496 -SLHHKHKEL ->M_4497 -SLIDSSRVV ->M_4498 -SLKLTQSSA ->M_4499 -SLLRKHQIL ->M_4500 -SLLRKHQIT ->M_4501 -SLLVHGGPL ->M_4502 -SLNHRGRVM ->M_4503 -SLNHRGRVM ->M_4504 -SLNPKKFSI ->M_4505 -SLRAEDTAL ->M_4506 -SLSETVRLV ->M_4507 -SLSVRTSGL ->M_4508 -SLWYHTYGL ->M_4509 -SLYTAYHVF ->M_4510 -SLYVWKSEL ->M_4511 -SMAKYWNQF ->M_4512 -SMKAERPPA ->M_4513 -SMKNLQRAV ->M_4514 -SMKVHIKAM ->M_4515 -SMMTATIVF ->M_4516 -SMPANFETI ->M_4517 -SMREALREL ->M_4518 -SMREAVREL ->M_4519 -SMRYFITSV ->M_4520 -SPGPFFWMF ->M_4521 -SPLFYSTCM ->M_4522 -SPLQLPAPL ->M_4523 -SPLRYISIL ->M_4524 -SPMYFFLSY ->M_4525 -SPRSRPSDI ->M_4526 -SPRVFFLLM ->M_4527 -SPSSAYLLF ->M_4528 -SQHPAQQQI ->M_4529 -SQMSQLMGL ->M_4530 -SQPGNALYF ->M_4531 -SRAMWLSLF ->M_4532 -SRATADPEV ->M_4533 -SRCLLLPLL ->M_4534 -SREDDNRER ->M_4535 -SRENRWTTV ->M_4536 -SRFCSLHCL ->M_4537 -SRFTAVREF ->M_4538 -SRFTLRCMV ->M_4539 -SRFVVRPLL ->M_4540 -SRGQEIKTI ->M_4541 -SRHDFHVDL ->M_4542 -SRKGDLLRI ->M_4543 -SRKKRRSPP ->M_4544 -SRKLRKLPT ->M_4545 -SRLHTPVYF ->M_4546 -SRNAYSLEI ->M_4547 -SRNDFEWVY ->M_4548 -SRPGALEHL ->M_4549 -SRPSSKQNM ->M_4550 -SRQMISELL ->M_4551 -SRRARGREK ->M_4552 -SRRSFWSEL ->M_4553 -SRSRNAYSL ->M_4554 -SRSVDVTNI ->M_4555 -SRTVWEEMV ->M_4556 -SRWRDQLLF ->M_4557 -SRYARPSRL ->M_4558 -SSASLNSNY ->M_4559 -SSDEIVQEL ->M_4560 -SSKQHLKPA ->M_4561 -SSLARELSL ->M_4562 -SSLRRMNSF ->M_4563 -SSRGNGKMM ->M_4564 -SSTSHIPEV ->M_4565 -SSYSRVALV ->M_4566 -STDDATWAA ->M_4567 -STERPKMTY ->M_4568 -STIYIFALF ->M_4569 -STKVHIKVL ->M_4570 -STQTHPLTL ->M_4571 -STSHVYHLF ->M_4572 -STYNETNLI ->M_4573 -STYPDQQHV ->M_4574 -SVEEKGKLL ->M_4575 -SVFPTQLQL ->M_4576 -SVFSEQWIF ->M_4577 -SVRENCCSL ->M_4578 -SWMPALECL ->M_4579 -SWPLWTAIF ->M_4580 -SWVSSTLGF ->M_4581 -SYAKNAQDL ->M_4582 -SYARILGTV ->M_4583 -SYAVICNNF ->M_4584 -SYFCILRTI ->M_4585 -SYFGLATVF ->M_4586 -SYFLATDTI ->M_4587 -SYFNNLHLW ->M_4588 -SYGVNLYQF ->M_4589 -SYIYILITI ->M_4590 -SYKFLAPWI ->M_4591 -SYPSIHRFI ->M_4592 -SYPSQPDGF ->M_4593 -SYSLISEKL ->M_4594 -SYVMDHFDI ->M_4595 -SYVRIGATI ->M_4596 -SYWGVFAPI ->M_4597 -SYYKIVSSI ->M_4598 -TAAIRPKSL ->M_4599 -TADVGLAGY ->M_4600 -TAFDESISL ->M_4601 -TAMAYDQFL ->M_4602 -TDKERQRLL ->M_4603 -TDYDTRFYM ->M_4604 -TEFGQKQKL ->M_4605 -TERDQIELL ->M_4606 -TFDRLAYLW ->M_4607 -TFEDNLRSL ->M_4608 -TFGEVNYFF ->M_4609 -TFITSVIRF ->M_4610 -TFLIAMVFI ->M_4611 -TFNDWFEII ->M_4612 -TFSCQLHKF ->M_4613 -THAPERDLC ->M_4614 -THASLSNHV ->M_4615 -THHGPAFSI ->M_4616 -THIFGLMVI ->M_4617 -THIHAAACI ->M_4618 -THMERVLSL ->M_4619 -THMERVLSL ->M_4620 -THPIYYLKI ->M_4621 -THQEALMKL ->M_4622 -THREGISAI ->M_4623 -THRSRLSLG ->M_4624 -THTSYQLSA ->M_4625 -THYQGTWYL ->M_4626 -TIKQRPKPT ->M_4627 -TKFESNLCV ->M_4628 -TLDKKLEYY ->M_4629 -TLERAALRY ->M_4630 -TLGLIFLCL ->M_4631 -TLMVVVWVL ->M_4632 -TLTIRALPA ->M_4633 -TMCMYFRPL ->M_4634 -TMETSFFSF ->M_4635 -TMGSWTCLF ->M_4636 -TMRTRHFTG ->M_4637 -TMRYIHFLF ->M_4638 -TMSPRVFFL ->M_4639 -TPGNRTKCF ->M_4640 -TPKSMQSTL ->M_4641 -TPNFRRRAI ->M_4642 -TPSERSKPL ->M_4643 -TPSTQTHPL ->M_4644 -TRAERLTWL ->M_4645 -TRALHRLIV ->M_4646 -TRASDRRGI ->M_4647 -TRDAPGLRV ->M_4648 -TREVTVNVL ->M_4649 -TRFPLKTAF ->M_4650 -TRFPLPEAF ->M_4651 -TRFRSFSSL ->M_4652 -TRFYMYEIL ->M_4653 -TRGPCRRRF ->M_4654 -TRGPQRQIL ->M_4655 -TRGRHQKKI ->M_4656 -TRHGSILAC ->M_4657 -TRHRCRNRF ->M_4658 -TRNCNRHLC ->M_4659 -TRPSEELEL ->M_4660 -TRPTASSSV ->M_4661 -TRRSQKRLQ ->M_4662 -TRSAEPGYL ->M_4663 -TRSSKPSDM ->M_4664 -TRSWGTPQL ->M_4665 -TRTPHSTRC ->M_4666 -TRVGSKLLI ->M_4667 -TRYSAQADI ->M_4668 -TSMWRTYVM ->M_4669 -TSMWRTYVM ->M_4670 -TTDGRNYIV ->M_4671 -TTFDRLAYL ->M_4672 -TTMEDQLLF ->M_4673 -TVHTRNHTA ->M_4674 -TVIDAYMNF ->M_4675 -TVLHRPHSA ->M_4676 -TVSPQPQEV ->M_4677 -TWLQVLEAI ->M_4678 -TYEEPCQAI ->M_4679 -TYLADRVQI ->M_4680 -TYLYPPKHW ->M_4681 -TYVLYYDAL ->M_4682 -TYYPLKPEI ->M_4683 -TYYPLKPEI ->M_4684 -VAKKKEAPA ->M_4685 -VARERRKAE ->M_4686 -VFERDFFKI ->M_4687 -VFETGTFLI ->M_4688 -VFLPMTLLL ->M_4689 -VFRQGHQLF ->M_4690 -VFTRVSAYI ->M_4691 -VFYTIFTPI ->M_4692 -VGKKRHDPL ->M_4693 -VHALRLHLY ->M_4694 -VHFDHFHPC ->M_4695 -VHFLREVTV ->M_4696 -VHHLAVSGV ->M_4697 -VHIKAMQTV ->M_4698 -VHIKVLQTV ->M_4699 -VHKKGYNKL ->M_4700 -VHKQFPITL ->M_4701 -VHKTDLERM ->M_4702 -VHRGTGAVY ->M_4703 -VHSENLQNW ->M_4704 -VLAIQRCPM ->M_4705 -VLDEMRCQY ->M_4706 -VLKSTSCSI ->M_4707 -VMKHLLSPL ->M_4708 -VMSCVWFTI ->M_4709 -VQMYRGHPA ->M_4710 -VQNEDVTLL ->M_4711 -VQPSQWASI ->M_4712 -VRDRMKELL ->M_4713 -VRELRDMGI ->M_4714 -VRFQDESVV ->M_4715 -VRFVTRYIY ->M_4716 -VRFVVTITV ->M_4717 -VRGTTLHLL ->M_4718 -VRHQRVHQA ->M_4719 -VRLKRSIQF ->M_4720 -VRLSYKLTF ->M_4721 -VRMEVISVT ->M_4722 -VRMEVVSIT ->M_4723 -VRNDHMNLR ->M_4724 -VRNRCNIYI ->M_4725 -VRPRARYYI ->M_4726 -VRQGGVFRL ->M_4727 -VRRLGPKLL ->M_4728 -VRRLHCSAA ->M_4729 -VRRMLTSKV ->M_4730 -VRRRRRCPG ->M_4731 -VRSLNLVLM ->M_4732 -VRSNLEPLF ->M_4733 -VRVGSDMLI ->M_4734 -VRVTQKFHM ->M_4735 -VSDDLVKQY ->M_4736 -VSGHVSMKY ->M_4737 -VSSSSSGGY ->M_4738 -VTADSDPAY ->M_4739 -VTAPRATTL ->M_4740 -VTDVLTEPH ->M_4741 -VTMDWLVRI ->M_4742 -VVAPRTLLL ->M_4743 -VVESLVEAY ->M_4744 -VVHEVQRYL ->M_4745 -VVKSKQVAL ->M_4746 -VVPQMVNPF ->M_4747 -VVSDVPEEL ->M_4748 -VYFHMTLSF ->M_4749 -VYHLFCALL ->M_4750 -VYISLFTCV ->M_4751 -VYLRRHRDV ->M_4752 -VYPRGFQEK ->M_4753 -VYQVLSGGW ->M_4754 -VYSEYGMDV ->M_4755 -VYSLRTRAI ->M_4756 -VYSLYWSIL ->M_4757 -VYVVSNNNL ->M_4758 -VYVVTKFLM ->M_4759 -VYYLLELLL ->M_4760 -WAGSHSMRY ->M_4761 -WARRKQSEM ->M_4762 -WASRFSTPY ->M_4763 -WFLWKQFCW ->M_4764 -WGMLNSLSL ->M_4765 -WHLQGPEDL ->M_4766 -WHREYNFKY ->M_4767 -WHSVVIQRL ->M_4768 -WHVPNKPPM ->M_4769 -WIEREGPEY ->M_4770 -WLNENQRLV ->M_4771 -WLSFRSSAS ->M_4772 -WLSNFQGRY ->M_4773 -WMEKRYLSQ ->M_4774 -WMEQEGPEY ->M_4775 -WPLTHSQGM ->M_4776 -WQRQHKLTI ->M_4777 -WRPEAVQYY ->M_4778 -WSDQLSAFS ->M_4779 -WTDVFQIGI ->M_4780 -WTESLAAVF ->M_4781 -WVKRQKISF ->M_4782 -WVRPRRRLL ->M_4783 -WVRPRRRLL ->M_4784 -WYHTCGGTL ->M_4785 -WYIWILLVL ->M_4786 -YAFTGLTLM ->M_4787 -YAMQRSWQE ->M_4788 -YARILGTVL ->M_4789 -YCDDLPLLA ->M_4790 -YDDARVELV ->M_4791 -YEHHHSARL ->M_4792 -YFGLATVFI ->M_4793 -YFHSFIRIV ->M_4794 -YFTSSSRYF ->M_4795 -YFYNQEEYV ->M_4796 -YGVTRSKAM ->M_4797 -YHCTAVNAY ->M_4798 -YHDACIEEA ->M_4799 -YHDVSGCYI ->M_4800 -YHEAGVTAL ->M_4801 -YHFSWTSDR ->M_4802 -YHHRFNNFM ->M_4803 -YHQQNVPWA ->M_4804 -YICDLRRQV ->M_4805 -YINNSVLPY ->M_4806 -YKGSRFHRV ->M_4807 -YLADRVQIV ->M_4808 -YLADRVQIV ->M_4809 -YLENRKETL ->M_4810 -YLENRKETL ->M_4811 -YLEQKPCIY ->M_4812 -YLFRKELRY ->M_4813 -YLKEELMCL ->M_4814 -YLKENFLPW ->M_4815 -YLRRHRDVS ->M_4816 -YLSLVEISY ->M_4817 -YLTVVSLSY ->M_4818 -YMDRTPGPA ->M_4819 -YMKTQSKSS ->M_4820 -YMLTLFTAM ->M_4821 -YNFKYVDLI ->M_4822 -YNVFRQLSL ->M_4823 -YPMRRRQCE ->M_4824 -YPRLKMLAF ->M_4825 -YPSIHRFIL ->M_4826 -YQLHNIQVI ->M_4827 -YQMQFTQAL ->M_4828 -YQMQFTQAL ->M_4829 -YQSEKLCSL ->M_4830 -YRAGKPTLV ->M_4831 -YRASEQKLC ->M_4832 -YRDNTELPY ->M_4833 -YRDVHVQKV ->M_4834 -YRGPLSTTI ->M_4835 -YRGSVAPIL ->M_4836 -YRITVVESL ->M_4837 -YRLEAVHAL ->M_4838 -YRLEGDTLI ->M_4839 -YRQFPKKSL ->M_4840 -YRRHSLRAI ->M_4841 -YRTVNNLIL ->M_4842 -YSFDSLCQY ->M_4843 -YSRDQIYIY ->M_4844 -YSRQMISEL ->M_4845 -YSRQMISEL ->M_4846 -YTCEQNDQL ->M_4847 -YTDSSSVLN ->M_4848 -YTEDHSASL ->M_4849 -YTELWFLGL ->M_4850 -YTLLAFSVF ->M_4851 -YTRKCTQAI ->M_4852 -YTSMWRTYV ->M_4853 -YTSMWRTYV ->M_4854 -YVAICSPLF ->M_4855 -YVDYMMCEF ->M_4856 -YVFLHQCVL ->M_4857 -YVFLHQCVL ->M_4858 -YVGENVRFV ->M_4859 -YVGIFHFQF ->M_4860 -YVLTRSKAM ->M_4861 -YVTVLCLTF ->M_4862 -YVYSLYWSI ->M_4863 -YWGVFAPIW ->M_4864 -YWPPQSQPF ->M_4865 -YYEKIFSTL ->M_4866 -YYFLCLLL* ->M_4867 -YYFLRPLL* ->M_4868 -YYFLRPLL* ->M_4869 -YYKIVSSIL ->M_4870 -YYLVANTKF ->M_4871 -YYTNFSLEL ->M_4872 -YYTNFSLEL ->M_4873 -YYYFLCLLL ->M_4874 -YYYFLRPLL ->M_4875 -YYYFLRPLL diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_135773_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_135773_1_T_iedb.xml deleted file mode 100755 index c0028a47..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_135773_1_T_iedb.xml +++ /dev/null @@ -1,41743 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_3590 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_3590 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_3591 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_3592 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_3593 - 9 - - - 1 - gnl|BL_ORD_ID|1223 - 97093|polyprotein|AAB66324.1|Hepatitis C virus (isolate H77)|63746 - 1223 - 10 - - - 1 - 13.4678 - 23 - 8.17864 - 2 - 7 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - HASLIP - HADVIP - HA +IP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 5 - Query_5 - M_3594 - 9 - - - 1 - gnl|BL_ORD_ID|99 - 6808|membrane protein|AAA45887.1|Human gammaherpesvirus 4|10376 - 99 - 8 - - - 1 - 13.853 - 24 - 7.77379 - 3 - 9 - 1 - 7 - 0 - 0 - 5 - 5 - 0 - 7 - CGLGKIL - CPLSKIL - C L KIL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 6 - Query_6 - M_3595 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_3596 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_3597 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_3598 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_3599 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_3600 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_3601 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_3602 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_3603 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_3604 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_3605 - 9 - - - 1 - gnl|BL_ORD_ID|114 - 7660|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 - 114 - 20 - - - 1 - 13.0826 - 22 - 16.9313 - 2 - 9 - 7 - 14 - 0 - 0 - 3 - 5 - 0 - 8 - MCVIHFSF - MCAVHPTL - MC +H + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 17 - Query_17 - M_3606 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_3607 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_3608 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_3609 - 9 - - - 1 - gnl|BL_ORD_ID|1141 - 75408|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 1141 - 20 - - - 1 - 13.853 - 24 - 5.60382 - 1 - 8 - 5 - 12 - 0 - 0 - 4 - 7 - 0 - 8 - AQKEHSHL - AERKHRHL - A+++H HL - - - - - 2 - gnl|BL_ORD_ID|419 - 25275|Glutamate decarboxylase 2|Q05329.1|Homo sapiens|9606 - 419 - 13 - - - 1 - 13.0826 - 22 - 16.789 - 4 - 8 - 6 - 10 - 0 - 0 - 4 - 4 - 0 - 5 - EHSHL - EHSHF - EHSH - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 21 - Query_21 - M_3610 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 22 - Query_22 - M_3611 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_3612 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_3613 - 9 - - - 1 - gnl|BL_ORD_ID|2266 - 418964|PPE family protein PPE68|KAM81677.1|Mycobacterium tuberculosis H37Ra|419947 - 2266 - 9 - - - 1 - 13.4678 - 23 - 10.0233 - 1 - 6 - 4 - 9 - 0 - 0 - 4 - 6 - 0 - 6 - ARINSI - ARLNSL - AR+NS+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 25 - Query_25 - M_3614 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_3615 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_3616 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 28 - Query_28 - M_3617 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 29 - Query_29 - M_3618 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 30 - Query_30 - M_3619 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 31 - Query_31 - M_3620 - 9 - - - 1 - gnl|BL_ORD_ID|1393 - 110338|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1393 - 33 - - - 1 - 16.5494 - 31 - 0.25572 - 2 - 9 - 15 - 22 - 0 - 0 - 6 - 7 - 0 - 8 - RPEKLPEL - RPRKLPQL - RP KLP+L - - - - - 2 - gnl|BL_ORD_ID|1428 - 113122|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1428 - 10 - - - 1 - 16.1642 - 30 - 0.350719 - 2 - 9 - 3 - 10 - 0 - 0 - 6 - 7 - 0 - 8 - RPEKLPEL - RPRKLPQL - RP KLP+L - - - - - 3 - gnl|BL_ORD_ID|1394 - 110373|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1394 - 25 - - - 1 - 14.6234 - 26 - 1.89486 - 3 - 9 - 1 - 7 - 0 - 0 - 5 - 6 - 0 - 7 - PEKLPEL - PRKLPQL - P KLP+L - - - - - 4 - gnl|BL_ORD_ID|2189 - 190533|nucleocapsid protein|AAP49024.1|SARS coronavirus|227859 - 2189 - 15 - - - 1 - 13.853 - 24 - 6.19118 - 2 - 8 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - RPEKLPE - RPQGLPN - RP+ LP - - - - - 5 - gnl|BL_ORD_ID|850 - 55683|nucleocapsid protein|ABI96968.1|SARS coronavirus|227859 - 850 - 15 - - - 1 - 13.853 - 24 - 6.40908 - 2 - 8 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - RPEKLPE - RPQGLPN - RP+ LP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 32 - Query_32 - M_3621 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 33 - Query_33 - M_3622 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 34 - Query_34 - M_3623 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 35 - Query_35 - M_3624 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 36 - Query_36 - M_3625 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 37 - Query_37 - M_3626 - 9 - - - 1 - gnl|BL_ORD_ID|798 - 53148|Transcription activator BRLF1|P03209.1|Human herpesvirus 4 strain B95-8|10377 - 798 - 15 - - - 1 - 13.4678 - 23 - 12.0936 - 1 - 6 - 10 - 15 - 0 - 0 - 4 - 6 - 0 - 6 - ASFSNH - ASYSSH - AS+S+H - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 38 - Query_38 - M_3627 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 39 - Query_39 - M_3628 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 40 - Query_40 - M_3629 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 41 - Query_41 - M_3630 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 42 - Query_42 - M_3631 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 43 - Query_43 - M_3632 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 44 - Query_44 - M_3633 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 45 - Query_45 - M_3634 - 9 - - - 1 - gnl|BL_ORD_ID|1171 - 79300|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 1171 - 15 - - - 1 - 11.927 - 19 - 83.5344 - 1 - 8 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - CFPLHGLQ - SFPDPGLR - FP GL+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 46 - Query_46 - M_3635 - 9 - - - 1 - gnl|BL_ORD_ID|2252 - 244160|surface antigen 2 (CA-2)|XP_818927.1|Trypanosoma cruzi strain CL Brener|353153 - 2252 - 9 - - - 1 - 13.0826 - 22 - 13.4763 - 1 - 6 - 3 - 8 - 0 - 0 - 4 - 5 - 0 - 6 - CGDKIS - AGDKLS - GDK+S - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 47 - Query_47 - M_3636 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 48 - Query_48 - M_3637 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 49 - Query_49 - M_3638 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 50 - Query_50 - M_3639 - 9 - - - 1 - gnl|BL_ORD_ID|109 - 7353|Early antigen protein D|P03191.1|Human herpesvirus 4 strain B95-8|10377 - 109 - 9 - - - 1 - 12.3122 - 20 - 45.611 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 7 - 0 - 9 - CHSNSRDHL - CYDHAQTHL - C+ +++ HL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 51 - Query_51 - M_3640 - 9 - - - 1 - gnl|BL_ORD_ID|582 - 36504|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 - 582 - 9 - - - 1 - 12.6974 - 21 - 26.0147 - 1 - 6 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - CHYEKK - CHSKKK - CH +KK - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 52 - Query_52 - M_3641 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 53 - Query_53 - M_3642 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 54 - Query_54 - M_3643 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 55 - Query_55 - M_3644 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 56 - Query_56 - M_3645 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 57 - Query_57 - M_3646 - 9 - - - 1 - gnl|BL_ORD_ID|383 - 23601|Genome polyprotein|SRC279960|Hepatitis C virus (isolate H77)|63746 - 383 - 21 - - - 1 - 15.0086 - 27 - 1.18025 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 5 - 0 - 9 - CPPNHIVSL - CPAGHAVGI - CP H V + - - - - - 2 - gnl|BL_ORD_ID|597 - 37127|polyprotein|AAY82030.1|Hepatitis C virus genotype 1|41856 - 597 - 9 - - - 1 - 13.853 - 24 - 7.07804 - 1 - 7 - 3 - 9 - 0 - 0 - 4 - 4 - 0 - 7 - CPPNHIV - CPAGHAV - CP H V - - - - - 3 - gnl|BL_ORD_ID|598 - 37136|Genome polyprotein|P27958.3|Hepatitis C virus|11103 - 598 - 9 - - - 1 - 13.4678 - 23 - 9.5131 - 1 - 7 - 3 - 9 - 0 - 0 - 4 - 4 - 0 - 7 - CPPNHIV - CPTGHAV - CP H V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 58 - Query_58 - M_3647 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 59 - Query_59 - M_3648 - 9 - - - 1 - gnl|BL_ORD_ID|291 - 19435|polyprotein|CDF77361.1|Dengue virus 3|11069 - 291 - 10 - - - 1 - 15.0086 - 27 - 1.14868 - 3 - 9 - 1 - 7 - 0 - 0 - 5 - 6 - 0 - 7 - AETRKTF - GESRKTF - E+RKTF - - - - - 2 - gnl|BL_ORD_ID|290 - 19434|Genome polyprotein|P27915.1|Dengue virus 3|11069 - 290 - 9 - - - 1 - 15.0086 - 27 - 1.29649 - 3 - 9 - 1 - 7 - 0 - 0 - 5 - 6 - 0 - 7 - AETRKTF - GESRKTF - E+RKTF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 60 - Query_60 - M_3649 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 61 - Query_61 - M_3650 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 62 - Query_62 - M_3651 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 63 - Query_63 - M_3652 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 64 - Query_64 - M_3653 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 65 - Query_65 - M_3654 - 9 - - - 1 - gnl|BL_ORD_ID|156 - 11956|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 - 156 - 11 - - - 1 - 12.3122 - 20 - 38.8163 - 1 - 9 - 3 - 11 - 0 - 0 - 4 - 5 - 0 - 9 - CRPQCCQSV - CRVLCCYVL - CR CC + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 66 - Query_66 - M_3655 - 9 - - - 1 - gnl|BL_ORD_ID|810 - 54330|BZLF1|AAA66529.1|Human gammaherpesvirus 4|10376 - 810 - 13 - - - 1 - 13.853 - 24 - 5.6596 - 1 - 9 - 3 - 11 - 0 - 0 - 5 - 6 - 0 - 9 - CRRGLEQLL - CRAKFKQLL - CR +QLL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 67 - Query_67 - M_3656 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 68 - Query_68 - M_3657 - 9 - - - 1 - gnl|BL_ORD_ID|61 - 4371|tegument protein VP11/12|NP_044516.1|Human alphaherpesvirus 2|10310 - 61 - 9 - - - 1 - 11.927 - 19 - 112.786 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 5 - 0 - 8 - CSDTHTNE - ASDSLNNE - SD+ NE - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 69 - Query_69 - M_3658 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 70 - Query_70 - M_3659 - 9 - - - 1 - gnl|BL_ORD_ID|2118 - 186354|polyprotein|AGO67248.1|Dengue virus 2|11060 - 2118 - 10 - - - 1 - 13.4678 - 23 - 10.9961 - 3 - 9 - 4 - 10 - 0 - 0 - 5 - 6 - 0 - 7 - MTKIFSL - LTKRFSL - +TK FSL - - - - - 2 - gnl|BL_ORD_ID|445 - 27216|polyprotein|BAD73987.1|Hepatitis C virus subtype 1b|31647 - 445 - 9 - - - 1 - 12.6974 - 21 - 31.4086 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 6 - 0 - 8 - VMTKIFSL - LMTHFFSI - +MT FS+ - - - - - 3 - gnl|BL_ORD_ID|1678 - 149027|NS5 protein|BAA00702.1|Hepatitis C virus (isolate H77)|63746 - 1678 - 18 - - - 1 - 12.3122 - 20 - 40.471 - 2 - 9 - 10 - 17 - 0 - 0 - 4 - 6 - 0 - 8 - VMTKIFSL - LMTHFFSV - +MT FS+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 71 - Query_71 - M_3660 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 72 - Query_72 - M_3661 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 73 - Query_73 - M_3662 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 74 - Query_74 - M_3663 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 75 - Query_75 - M_3664 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 76 - Query_76 - M_3665 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 77 - Query_77 - M_3666 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 78 - Query_78 - M_3667 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 79 - Query_79 - M_3668 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 80 - Query_80 - M_3669 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 81 - Query_81 - M_3670 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 82 - Query_82 - M_3671 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 83 - Query_83 - M_3672 - 9 - - - 1 - gnl|BL_ORD_ID|1139 - 75356|EBNA3A nuclear protein|Q8AZJ8|Human gammaherpesvirus 4|10376 - 1139 - 9 - - - 1 - 13.4678 - 23 - 12.7908 - 2 - 7 - 3 - 8 - 0 - 0 - 4 - 5 - 0 - 6 - LHTRHG - LHEQHG - LH +HG - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 84 - Query_84 - M_3673 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 85 - Query_85 - M_3674 - 9 - - - 1 - gnl|BL_ORD_ID|131 - 9316|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 - 131 - 15 - - - 1 - 13.4678 - 23 - 11.8896 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - DLLGHP - DLVGWP - DL+G P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 86 - Query_86 - M_3675 - 9 - - - 1 - gnl|BL_ORD_ID|1573 - 141402|tegument protein VP22|NP_044651.1|Human alphaherpesvirus 1|10298 - 1573 - 10 - - - 1 - 12.6974 - 21 - 27.4501 - 3 - 7 - 2 - 6 - 0 - 0 - 4 - 5 - 0 - 5 - PTKRP - PTERP - PT+RP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 87 - Query_87 - M_3676 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 88 - Query_88 - M_3677 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 89 - Query_89 - M_3678 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 90 - Query_90 - M_3679 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 91 - Query_91 - M_3680 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 92 - Query_92 - M_3681 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 93 - Query_93 - M_3682 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 94 - Query_94 - M_3683 - 9 - - - 1 - gnl|BL_ORD_ID|1895 - 180611|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1895 - 15 - - - 1 - 14.2382 - 25 - 3.25804 - 2 - 9 - 4 - 11 - 0 - 0 - 5 - 5 - 0 - 8 - RNDFPVVL - RGDLPVWL - R D PV L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 95 - Query_95 - M_3684 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 96 - Query_96 - M_3685 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 97 - Query_97 - M_3686 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 98 - Query_98 - M_3687 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 99 - Query_99 - M_3688 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 100 - Query_100 - M_3689 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 101 - Query_101 - M_3690 - 9 - - - 1 - gnl|BL_ORD_ID|1275 - 101813|Pol polyprotein|Q9YLQ7|Human immunodeficiency virus 1|11676 - 1275 - 11 - - - 1 - 13.0826 - 22 - 19.3899 - 1 - 9 - 3 - 11 - 0 - 0 - 4 - 6 - 0 - 9 - DTDILSYSY - NPDIVIYQY - + DI+ Y Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 102 - Query_102 - M_3691 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 103 - Query_103 - M_3692 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 104 - Query_104 - M_3693 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 105 - Query_105 - M_3694 - 9 - - - 1 - gnl|BL_ORD_ID|833 - 54821|E2 protein|AAM33354.1|Hepatitis C virus subtype 1a|31646 - 833 - 9 - - - 1 - 13.0826 - 22 - 15.4875 - 1 - 6 - 4 - 9 - 0 - 0 - 4 - 4 - 0 - 6 - DYPCCI - HYPCTI - YPC I - - - - - 2 - gnl|BL_ORD_ID|1149 - 75636|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 1149 - 10 - - - 1 - 13.0826 - 22 - 16.111 - 1 - 6 - 5 - 10 - 0 - 0 - 4 - 4 - 0 - 6 - DYPCCI - HYPCTI - YPC I - - - - - 3 - gnl|BL_ORD_ID|835 - 54825|polyprotein|BAA03375.1|Hepatitis C virus|11103 - 835 - 9 - - - 1 - 12.6974 - 21 - 29.3325 - 1 - 6 - 4 - 9 - 0 - 0 - 3 - 4 - 0 - 6 - DYPCCI - HYPCTV - YPC + - - - - - 4 - gnl|BL_ORD_ID|417 - 25186|polyprotein|AAK32686.1|Hepatitis C virus|11103 - 417 - 10 - - - 1 - 12.6974 - 21 - 29.385 - 2 - 6 - 2 - 6 - 0 - 0 - 3 - 4 - 0 - 5 - YPCCI - YPCTV - YPC + - - - - - 5 - gnl|BL_ORD_ID|1099 - 72566|polyprotein|BAD73987.1|Hepatitis C virus subtype 1b|31647 - 1099 - 9 - - - 1 - 12.6974 - 21 - 30.8766 - 1 - 6 - 2 - 7 - 0 - 0 - 3 - 4 - 0 - 6 - DYPCCI - HYPCTV - YPC + - - - - - 6 - gnl|BL_ORD_ID|1413 - 111407|polyprotein|BAA00792.1|Hepatitis C virus|11103 - 1413 - 10 - - - 1 - 12.6974 - 21 - 33.6561 - 2 - 6 - 2 - 6 - 0 - 0 - 3 - 4 - 0 - 5 - YPCCI - YPCTV - YPC + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 106 - Query_106 - M_3695 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 107 - Query_107 - M_3696 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 108 - Query_108 - M_3697 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 109 - Query_109 - M_3698 - 9 - - - 1 - gnl|BL_ORD_ID|1218 - 96897|polyprotein|ABR25251.1|Hepatitis C virus (isolate H77)|63746 - 1218 - 17 - - - 1 - 12.6974 - 21 - 22.1036 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 6 - 0 - 7 - ALIRHLN - SLLRHHN - +L+RH N - - - - - 2 - gnl|BL_ORD_ID|1616 - 144403|polyprotein|AAK08509.1|Hepatitis C virus subtype 1b|31647 - 1616 - 9 - - - 1 - 11.927 - 19 - 95.9763 - 3 - 8 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - LIRHLN - LLRHHN - L+RH N - - - - - 3 - gnl|BL_ORD_ID|1785 - 159290|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 - 1785 - 9 - - - 1 - 11.927 - 19 - 109.216 - 3 - 8 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - LIRHLN - LLRHHN - L+RH N - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 110 - Query_110 - M_3699 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 111 - Query_111 - M_3700 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 112 - Query_112 - M_3701 - 9 - - - 1 - gnl|BL_ORD_ID|1979 - 183223|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1979 - 10 - - - 1 - 13.0826 - 22 - 16.6782 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 5 - 0 - 8 - FPQKYYWW - FPGKTVWF - FP K W+ - - - - - 2 - gnl|BL_ORD_ID|2214 - 193060|Nef protein|Q9YYU3|Human immunodeficiency virus 1|11676 - 2214 - 10 - - - 1 - 11.927 - 19 - 86.442 - 1 - 8 - 1 - 8 - 0 - 0 - 3 - 4 - 0 - 8 - EFPQKYYW - RFPLTFGW - FP + W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 113 - Query_113 - M_3702 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 114 - Query_114 - M_3703 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 115 - Query_115 - M_3704 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 116 - Query_116 - M_3705 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 117 - Query_117 - M_3706 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 118 - Query_118 - M_3707 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 119 - Query_119 - M_3708 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 120 - Query_120 - M_3709 - 9 - - - 1 - gnl|BL_ORD_ID|115 - 7708|gag polyprotein|BAA00992.1|Human immunodeficiency virus 1|11676 - 115 - 9 - - - 1 - 14.6234 - 26 - 2.04484 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 8 - 0 - 9 - EIKTIVKAI - DCKTILKAL - + KTI+KA+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 121 - Query_121 - M_3710 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 122 - Query_122 - M_3711 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 123 - Query_123 - M_3712 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 124 - Query_124 - M_3713 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 125 - Query_125 - M_3714 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 126 - Query_126 - M_3715 - 9 - - - 1 - gnl|BL_ORD_ID|1983 - 183252|polyprotein|AGT63075.1|Dengue virus 1|11053 - 1983 - 10 - - - 1 - 12.6974 - 21 - 36.0093 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 5 - 0 - 9 - ELHRQVKTL - SLHYAWKTM - LH KT+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 127 - Query_127 - M_3716 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 128 - Query_128 - M_3717 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 129 - Query_129 - M_3718 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 130 - Query_130 - M_3719 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 131 - Query_131 - M_3720 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 132 - Query_132 - M_3721 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 133 - Query_133 - M_3722 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 134 - Query_134 - M_3723 - 9 - - - 1 - gnl|BL_ORD_ID|176 - 13262|gag polyprotein|BAA00992.1|Human immunodeficiency virus 1|11676 - 176 - 9 - - - 1 - 14.6234 - 26 - 1.76369 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 6 - 0 - 9 - EMRCQYETV - ELRSLYNTV - E+R Y TV - - - - - 2 - gnl|BL_ORD_ID|575 - 36306|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 - 575 - 15 - - - 1 - 14.2382 - 25 - 2.38473 - 2 - 9 - 4 - 11 - 0 - 0 - 4 - 5 - 0 - 8 - MRCQYETV - MNCSYENM - M C YE + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 135 - Query_135 - M_3724 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 136 - Query_136 - M_3725 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 137 - Query_137 - M_3726 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 138 - Query_138 - M_3727 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 139 - Query_139 - M_3728 - 9 - - - 1 - gnl|BL_ORD_ID|1857 - 180423|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1857 - 10 - - - 1 - 12.6974 - 21 - 37.2442 - 1 - 9 - 2 - 10 - 0 - 0 - 5 - 6 - 0 - 9 - ERDGLERAL - ERDIPERSW - ERD ER+ - - - - - 2 - gnl|BL_ORD_ID|1861 - 180440|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1861 - 15 - - - 1 - 10.7714 - 16 - 260.888 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 6 - 0 - 9 - ERDGLERAL - EREIPERSW - ER+ ER+ - - - - - 3 - gnl|BL_ORD_ID|1968 - 182898|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1968 - 10 - - - 1 - 10.7714 - 16 - 362.692 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 6 - 0 - 9 - ERDGLERAL - EREIPERSW - ER+ ER+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 140 - Query_140 - M_3729 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 141 - Query_141 - M_3730 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 142 - Query_142 - M_3731 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 143 - Query_143 - M_3732 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 144 - Query_144 - M_3733 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 145 - Query_145 - M_3734 - 9 - - - 1 - gnl|BL_ORD_ID|358 - 22633|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 - 358 - 20 - - - 1 - 13.4678 - 23 - 12.2414 - 4 - 9 - 3 - 8 - 0 - 0 - 4 - 4 - 0 - 6 - DTNQKC - DTGQAC - DT Q C - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 146 - Query_146 - M_3735 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 147 - Query_147 - M_3736 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 148 - Query_148 - M_3737 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 149 - Query_149 - M_3738 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 150 - Query_150 - M_3739 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 151 - Query_151 - M_3740 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 152 - Query_152 - M_3741 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 153 - Query_153 - M_3742 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 154 - Query_154 - M_3743 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 155 - Query_155 - M_3744 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 156 - Query_156 - M_3745 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 157 - Query_157 - M_3746 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 158 - Query_158 - M_3747 - 9 - - - 1 - gnl|BL_ORD_ID|1011 - 67349|Latent membrane protein 2|Q69135|Human gammaherpesvirus 4|10376 - 1011 - 9 - - - 1 - 15.3938 - 28 - 0.690962 - 3 - 7 - 2 - 6 - 0 - 0 - 5 - 5 - 0 - 5 - YGPVF - YGPVF - YGPVF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 159 - Query_159 - M_3748 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 160 - Query_160 - M_3749 - 9 - - - 1 - gnl|BL_ORD_ID|1508 - 139406|polyprotein|ACT37184.1|Hepatitis C virus|11103 - 1508 - 10 - - - 1 - 13.853 - 24 - 6.99268 - 3 - 8 - 5 - 10 - 0 - 0 - 5 - 5 - 0 - 6 - RPTPRL - RPGPRL - RP PRL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 161 - Query_161 - M_3750 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 162 - Query_162 - M_3751 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 163 - Query_163 - M_3752 - 9 - - - 1 - gnl|BL_ORD_ID|1179 - 79628|E1 protein|BAA19893.1|Rubella virus|11041 - 1179 - 21 - - - 1 - 13.853 - 24 - 7.30211 - 4 - 8 - 9 - 13 - 0 - 0 - 4 - 5 - 0 - 5 - LGSWV - LGAWV - LG+WV - - - - - 2 - gnl|BL_ORD_ID|1022 - 68461|polyprotein|ACZ60108.1|Hepatitis C virus|11103 - 1022 - 10 - - - 1 - 13.4678 - 23 - 12.6375 - 3 - 8 - 5 - 10 - 0 - 0 - 4 - 5 - 0 - 6 - LLGSWV - ILGGWV - +LG WV - - - - - 3 - gnl|BL_ORD_ID|1213 - 96547|Genome polyprotein|Q913D4.3|Hepatitis C virus (isolate H77)|63746 - 1213 - 10 - - - 1 - 13.0826 - 22 - 13.7839 - 3 - 8 - 5 - 10 - 0 - 0 - 4 - 5 - 0 - 6 - LLGSWV - ILGGWV - +LG WV - - - - - 4 - gnl|BL_ORD_ID|616 - 37351|trans-sialidase, putative|EAN81560.1|Trypanosoma cruzi|5693 - 616 - 10 - - - 1 - 13.0826 - 22 - 15.8345 - 3 - 8 - 1 - 6 - 0 - 0 - 5 - 5 - 0 - 6 - LLGSWV - LLGLWV - LLG WV - - - - - 5 - gnl|BL_ORD_ID|612 - 37286|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 - 612 - 10 - - - 1 - 13.0826 - 22 - 16.3922 - 3 - 8 - 5 - 10 - 0 - 0 - 4 - 5 - 0 - 6 - LLGSWV - ILGGWV - +LG WV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 164 - Query_164 - M_3753 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 165 - Query_165 - M_3754 - 9 - - - 1 - gnl|BL_ORD_ID|1547 - 141218|regulatory protein ICP22|NP_044663.1|Human alphaherpesvirus 1|10298 - 1547 - 9 - - - 1 - 14.6234 - 26 - 2.04484 - 4 - 8 - 2 - 6 - 0 - 0 - 4 - 5 - 0 - 5 - PRTFC - PRTWC - PRT+C - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 166 - Query_166 - M_3755 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 167 - Query_167 - M_3756 - 9 - - - 1 - gnl|BL_ORD_ID|1916 - 180681|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1916 - 15 - - - 1 - 12.6974 - 21 - 30.771 - 1 - 8 - 3 - 10 - 0 - 0 - 4 - 5 - 0 - 8 - EYVTELPS - EYTDYMPS - EY +PS - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 168 - Query_168 - M_3757 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 169 - Query_169 - M_3758 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 170 - Query_170 - M_3759 - 9 - - - 1 - gnl|BL_ORD_ID|714 - 43937|polyprotein|AAF01178.1|Hepatitis C virus subtype 2a|31649 - 714 - 10 - - - 1 - 14.6234 - 26 - 1.7557 - 1 - 9 - 2 - 10 - 0 - 0 - 5 - 5 - 0 - 9 - FARGQRWRL - FTRGDRCNL - F RG R L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 171 - Query_171 - M_3760 - 9 - - - 1 - gnl|BL_ORD_ID|714 - 43937|polyprotein|AAF01178.1|Hepatitis C virus subtype 2a|31649 - 714 - 10 - - - 1 - 14.6234 - 26 - 1.7557 - 1 - 9 - 2 - 10 - 0 - 0 - 5 - 5 - 0 - 9 - FARGQRWRL - FTRGDRCNL - F RG R L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 172 - Query_172 - M_3761 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 173 - Query_173 - M_3762 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 174 - Query_174 - M_3763 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 175 - Query_175 - M_3764 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 176 - Query_176 - M_3765 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 177 - Query_177 - M_3766 - 9 - - - 1 - gnl|BL_ORD_ID|1982 - 183245|polyprotein|AGT63074.1|Dengue virus 1|11053 - 1982 - 10 - - - 1 - 13.0826 - 22 - 20.1646 - 1 - 6 - 1 - 6 - 0 - 0 - 3 - 6 - 0 - 6 - FESHRI - FQSHQL - F+SH++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 178 - Query_178 - M_3767 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 179 - Query_179 - M_3768 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 180 - Query_180 - M_3769 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 181 - Query_181 - M_3770 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 182 - Query_182 - M_3771 - 9 - - - 1 - gnl|BL_ORD_ID|2137 - 187106|Vpr protein|BAA93983.1|Human immunodeficiency virus 1|11676 - 2137 - 9 - - - 1 - 11.927 - 19 - 80.227 - 2 - 7 - 4 - 9 - 0 - 0 - 4 - 4 - 0 - 6 - HFRRPW - HFPRIW - HF R W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 183 - Query_183 - M_3772 - 9 - - - 1 - gnl|BL_ORD_ID|2137 - 187106|Vpr protein|BAA93983.1|Human immunodeficiency virus 1|11676 - 2137 - 9 - - - 1 - 11.927 - 19 - 80.227 - 2 - 7 - 4 - 9 - 0 - 0 - 4 - 4 - 0 - 6 - HFRRPW - HFPRIW - HF R W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 184 - Query_184 - M_3773 - 9 - - - 1 - gnl|BL_ORD_ID|2137 - 187106|Vpr protein|BAA93983.1|Human immunodeficiency virus 1|11676 - 2137 - 9 - - - 1 - 11.927 - 19 - 80.227 - 2 - 7 - 4 - 9 - 0 - 0 - 4 - 4 - 0 - 6 - HFRRPW - HFPRIW - HF R W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 185 - Query_185 - M_3774 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 186 - Query_186 - M_3775 - 9 - - - 1 - gnl|BL_ORD_ID|1177 - 79506|E1 protein|BAA19893.1|Rubella virus|11041 - 1177 - 20 - - - 1 - 12.3122 - 20 - 52.8131 - 1 - 7 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - FHHIDSA - FGHSDAA - F H D+A - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 187 - Query_187 - M_3776 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 188 - Query_188 - M_3777 - 9 - - - 1 - gnl|BL_ORD_ID|1175 - 79390|Protein Tax-1|P0C213.1|Human T-cell lymphotropic virus type 1 (african isolate)|39015 - 1175 - 15 - - - 1 - 12.3122 - 20 - 53.1389 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - LHNAHVL - FHNLHLL - HN H+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 189 - Query_189 - M_3778 - 9 - - - 1 - gnl|BL_ORD_ID|1293 - 102819|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 - 1293 - 15 - - - 1 - 18.0902 - 35 - 0.0792643 - 2 - 8 - 3 - 9 - 0 - 0 - 6 - 7 - 0 - 7 - HLPYLEQ - HLPYIEQ - HLPY+EQ - - - - - 2 - gnl|BL_ORD_ID|1214 - 96601|polyprotein|ABR25251.1|Hepatitis C virus (isolate H77)|63746 - 1214 - 10 - - - 1 - 15.3938 - 28 - 0.630146 - 3 - 8 - 1 - 6 - 0 - 0 - 5 - 6 - 0 - 6 - LPYLEQ - LPYIEQ - LPY+EQ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 190 - Query_190 - M_3779 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 191 - Query_191 - M_3780 - 9 - - - 1 - gnl|BL_ORD_ID|880 - 57790|Protein Tax-1|P03409.2|Human T-lymphotropic virus 1|11908 - 880 - 9 - - - 1 - 12.3122 - 20 - 43.3628 - 4 - 9 - 4 - 9 - 0 - 0 - 4 - 6 - 0 - 6 - SIHLLY - SLHLLF - S+HLL+ - - - - - 2 - gnl|BL_ORD_ID|1175 - 79390|Protein Tax-1|P0C213.1|Human T-cell lymphotropic virus type 1 (african isolate)|39015 - 1175 - 15 - - - 1 - 11.1566 - 17 - 161.906 - 4 - 9 - 4 - 9 - 0 - 0 - 3 - 6 - 0 - 6 - SIHLLY - NLHLLF - ++HLL+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 192 - Query_192 - M_3781 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 193 - Query_193 - M_3782 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 194 - Query_194 - M_3783 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 195 - Query_195 - M_3784 - 9 - - - 1 - gnl|BL_ORD_ID|545 - 33382|polyprotein|AAB67037.1|Hepatitis C virus|11103 - 545 - 15 - - - 1 - 13.853 - 24 - 4.45371 - 1 - 7 - 9 - 15 - 0 - 0 - 4 - 5 - 0 - 7 - FHYDTQL - FSYDTRC - F YDT+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 196 - Query_196 - M_3785 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 197 - Query_197 - M_3786 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 198 - Query_198 - M_3787 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 199 - Query_199 - M_3788 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 200 - Query_200 - M_3789 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 201 - Query_201 - M_3790 - 9 - - - 1 - gnl|BL_ORD_ID|100 - 6817|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 100 - 8 - - - 1 - 13.4678 - 23 - 9.40947 - 3 - 8 - 3 - 8 - 0 - 0 - 5 - 6 - 0 - 6 - NNSIVY - NSSIVY - N+SIVY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 202 - Query_202 - M_3791 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 203 - Query_203 - M_3792 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 204 - Query_204 - M_3793 - 9 - - - 1 - gnl|BL_ORD_ID|719 - 44653|6 kDa early secretory antigenic target|P0A564.2|Mycobacterium tuberculosis|1773 - 719 - 20 - - - 1 - 14.2382 - 25 - 3.36386 - 2 - 7 - 2 - 7 - 0 - 0 - 5 - 6 - 0 - 6 - LARTVS - LARTIS - LART+S - - - - - 2 - gnl|BL_ORD_ID|959 - 63010|6 kDa early secretory antigenic target|P0A564.2|Mycobacterium tuberculosis|1773 - 959 - 20 - - - 1 - 14.2382 - 25 - 3.42196 - 2 - 7 - 12 - 17 - 0 - 0 - 5 - 6 - 0 - 6 - LARTVS - LARTIS - LART+S - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 205 - Query_205 - M_3794 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 206 - Query_206 - M_3795 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 207 - Query_207 - M_3796 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 208 - Query_208 - M_3797 - 9 - - - 1 - gnl|BL_ORD_ID|2053 - 184736|polyprotein|AGW21594.1|Dengue virus 1|11053 - 2053 - 9 - - - 1 - 13.0826 - 22 - 16.3158 - 3 - 9 - 1 - 7 - 0 - 0 - 5 - 7 - 0 - 7 - LAMLLSI - MAMVLSI - +AM+LSI - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 209 - Query_209 - M_3798 - 9 - - - 1 - gnl|BL_ORD_ID|356 - 22235|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 356 - 15 - - - 1 - 13.4678 - 23 - 9.68748 - 3 - 8 - 8 - 13 - 0 - 0 - 4 - 6 - 0 - 6 - LEFLLP - LQFLIP - L+FL+P - - - - - 2 - gnl|BL_ORD_ID|1976 - 183162|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1976 - 10 - - - 1 - 11.1566 - 17 - 202.108 - 1 - 8 - 2 - 9 - 0 - 0 - 4 - 6 - 0 - 8 - FLLEFLLP - FLMVLLIP - FL+ L+P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 210 - Query_210 - M_3799 - 9 - - - 1 - gnl|BL_ORD_ID|1509 - 139746|Dense granule protein 3|B6KEU8.2|Toxoplasma gondii|5811 - 1509 - 9 - - - 1 - 7.68983 - 8 - 11881 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 6 - 0 - 9 - FLLFSFLFL - FLVPFVVFL - FL+ +FL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 211 - Query_211 - M_3800 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 212 - Query_212 - M_3801 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 213 - Query_213 - M_3802 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 214 - Query_214 - M_3803 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 215 - Query_215 - M_3804 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 216 - Query_216 - M_3805 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 217 - Query_217 - M_3806 - 9 - - - 1 - gnl|BL_ORD_ID|1040 - 69474|core protein|BAF42671.1|Hepatitis B virus|10407 - 1040 - 10 - - - 1 - 13.853 - 24 - 6.8721 - 2 - 8 - 2 - 8 - 0 - 0 - 4 - 7 - 0 - 7 - MKYLVNF - LEYLVSF - ++YLV+F - - - - - 2 - gnl|BL_ORD_ID|2322 - 423053|core protein|AAL31859.1|Hepatitis B virus|10407 - 2322 - 11 - - - 1 - 13.4678 - 23 - 9.05775 - 2 - 8 - 5 - 11 - 0 - 0 - 4 - 7 - 0 - 7 - MKYLVNF - IEYLVSF - ++YLV+F - - - - - 3 - gnl|BL_ORD_ID|201 - 15061|core protein|BAF42671.1|Hepatitis B virus|10407 - 201 - 9 - - - 1 - 13.0826 - 22 - 21.5246 - 3 - 8 - 1 - 6 - 0 - 0 - 4 - 6 - 0 - 6 - KYLVNF - EYLVSF - +YLV+F - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 218 - Query_218 - M_3807 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 219 - Query_219 - M_3808 - 9 - - - 1 - gnl|BL_ORD_ID|1143 - 75436|Polyprotein|P90247|Hepatitis C virus|11103 - 1143 - 20 - - - 1 - 12.3122 - 20 - 38.3641 - 1 - 6 - 1 - 6 - 0 - 0 - 3 - 5 - 0 - 6 - FMWPLH - YPWPLY - + WPL+ - - - - - 2 - gnl|BL_ORD_ID|1144 - 75438|polyprotein|AAF65962.1|Hepatitis C virus|11103 - 1144 - 20 - - - 1 - 12.3122 - 20 - 39.5605 - 1 - 6 - 1 - 6 - 0 - 0 - 3 - 5 - 0 - 6 - FMWPLH - YPWPLY - + WPL+ - - - - - 3 - gnl|BL_ORD_ID|1142 - 75435|largest ORF|AAB02128.1|Hepatitis C virus|11103 - 1142 - 20 - - - 1 - 12.3122 - 20 - 41.421 - 1 - 6 - 1 - 6 - 0 - 0 - 3 - 5 - 0 - 6 - FMWPLH - YPWPLY - + WPL+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 220 - Query_220 - M_3809 - 9 - - - 1 - gnl|BL_ORD_ID|2258 - 288104|nef protein|ACR27130.1|Human immunodeficiency virus 1|11676 - 2258 - 18 - - - 1 - 12.3122 - 20 - 45.1301 - 1 - 9 - 4 - 12 - 0 - 0 - 4 - 5 - 0 - 9 - FPAMLQAPI - FPVRPQVPL - FP Q P+ - - - - - 2 - gnl|BL_ORD_ID|1831 - 179823|cell surface protein (associated with virulence)|NP_302372.1|Mycobacterium leprae TN|272631 - 1831 - 9 - - - 1 - 12.3122 - 20 - 50.4464 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 5 - 0 - 8 - FPAMLQAP - IPASVSAP - PA + AP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 221 - Query_221 - M_3810 - 9 - - - 1 - gnl|BL_ORD_ID|2214 - 193060|Nef protein|Q9YYU3|Human immunodeficiency virus 1|11676 - 2214 - 10 - - - 1 - 14.2382 - 25 - 4.08767 - 1 - 9 - 2 - 10 - 0 - 0 - 3 - 4 - 0 - 9 - FPIIIAWAI - FPLTFGWCF - FP+ W - - - - - 2 - gnl|BL_ORD_ID|2215 - 193071|Nef protein|Q9WPU2|Human immunodeficiency virus 1|11676 - 2215 - 10 - - - 1 - 13.853 - 24 - 6.29996 - 1 - 9 - 2 - 10 - 0 - 0 - 2 - 5 - 0 - 9 - FPIIIAWAI - YPLTLGWCF - +P+ + W - - - - - 3 - gnl|BL_ORD_ID|866 - 56620|Nef protein|Q9YYU8|Human immunodeficiency virus 1|11676 - 866 - 10 - - - 1 - 13.0826 - 22 - 16.111 - 1 - 9 - 2 - 10 - 0 - 0 - 2 - 4 - 0 - 9 - FPIIIAWAI - YPLTFGWCF - +P+ W - - - - - 4 - gnl|BL_ORD_ID|1288 - 102254|nef protein|ACQ72180.1|Human immunodeficiency virus 1|11676 - 1288 - 9 - - - 1 - 13.0826 - 22 - 18.7436 - 1 - 8 - 1 - 8 - 0 - 0 - 2 - 4 - 0 - 8 - FPIIIAWA - YPLTFGWC - +P+ W - - - - - 5 - gnl|BL_ORD_ID|1281 - 102046|nef protein|ACQ72180.1|Human immunodeficiency virus 1|11676 - 1281 - 8 - - - 1 - 12.6974 - 21 - 26.6862 - 1 - 7 - 2 - 8 - 0 - 0 - 2 - 4 - 0 - 7 - FPIIIAW - YPLTFGW - +P+ W - - - - - 6 - gnl|BL_ORD_ID|459 - 27878|large surface antigen|CAC87019.1|Hepatitis B virus|10407 - 459 - 9 - - - 1 - 11.927 - 19 - 92.9112 - 2 - 8 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - PIIIAWA - PIPSSWA - PI +WA - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 222 - Query_222 - M_3811 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 223 - Query_223 - M_3812 - 9 - - - 1 - gnl|BL_ORD_ID|586 - 36676|polyprotein|BAA09073.1|Hepatitis C virus subtype 1b|31647 - 586 - 9 - - - 1 - 13.0826 - 22 - 18.1053 - 3 - 9 - 1 - 7 - 0 - 0 - 3 - 6 - 0 - 7 - LVRSCQM - LIRACML - L+R+C + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 224 - Query_224 - M_3813 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 225 - Query_225 - M_3814 - 9 - - - 1 - gnl|BL_ORD_ID|1979 - 183223|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1979 - 10 - - - 1 - 12.6974 - 21 - 23.5358 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 5 - 0 - 8 - FPQKYYWW - FPGKTVWF - FP K W+ - - - - - 2 - gnl|BL_ORD_ID|2214 - 193060|Nef protein|Q9YYU3|Human immunodeficiency virus 1|11676 - 2214 - 10 - - - 1 - 12.6974 - 21 - 27.922 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 5 - 0 - 9 - FPQKYYWWF - FPLTFGWCF - FP + W F - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 226 - Query_226 - M_3815 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 227 - Query_227 - M_3816 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 228 - Query_228 - M_3817 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 229 - Query_229 - M_3818 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 230 - Query_230 - M_3819 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 231 - Query_231 - M_3820 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 232 - Query_232 - M_3821 - 9 - - - 1 - gnl|BL_ORD_ID|1575 - 141411|transactivating tegument protein VP16|NP_044650.1|Human alphaherpesvirus 1|10298 - 1575 - 10 - - - 1 - 13.0826 - 22 - 13.3135 - 1 - 7 - 3 - 9 - 0 - 0 - 4 - 5 - 0 - 7 - FPYNSDL - LPTNADL - P N+DL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 233 - Query_233 - M_3822 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 234 - Query_234 - M_3823 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 235 - Query_235 - M_3824 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 236 - Query_236 - M_3825 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 237 - Query_237 - M_3826 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 238 - Query_238 - M_3827 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 239 - Query_239 - M_3828 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 240 - Query_240 - M_3829 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 241 - Query_241 - M_3830 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 242 - Query_242 - M_3831 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 243 - Query_243 - M_3832 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 244 - Query_244 - M_3833 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 245 - Query_245 - M_3834 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 246 - Query_246 - M_3835 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 247 - Query_247 - M_3836 - 9 - - - 1 - gnl|BL_ORD_ID|1817 - 177884|polyprotein|ACZ60102.1|Hepatitis C virus genotype 1|41856 - 1817 - 18 - - - 1 - 13.4678 - 23 - 12.4678 - 1 - 9 - 7 - 15 - 0 - 0 - 4 - 7 - 0 - 9 - FRNGLGTGM - YLYGVGSGM - + G+G+GM - - - - - 2 - gnl|BL_ORD_ID|807 - 53953|kaposin|AAC57155.1|Human gammaherpesvirus 8|37296 - 807 - 15 - - - 1 - 12.6974 - 21 - 31.2769 - 1 - 8 - 6 - 13 - 0 - 0 - 4 - 5 - 0 - 8 - FRNGLGTG - FRTRVATG - FR + TG - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 248 - Query_248 - M_3837 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 249 - Query_249 - M_3838 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 250 - Query_250 - M_3839 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 251 - Query_251 - M_3840 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 252 - Query_252 - M_3841 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 253 - Query_253 - M_3842 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 254 - Query_254 - M_3843 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 255 - Query_255 - M_3844 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 256 - Query_256 - M_3845 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 257 - Query_257 - M_3846 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 258 - Query_258 - M_3847 - 9 - - - 1 - gnl|BL_ORD_ID|1732 - 150571|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1732 - 10 - - - 1 - 14.2382 - 25 - 3.00394 - 1 - 6 - 4 - 9 - 0 - 0 - 4 - 6 - 0 - 6 - FRTKDG - FKTEDG - F+T+DG - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 259 - Query_259 - M_3848 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 260 - Query_260 - M_3849 - 9 - - - 1 - gnl|BL_ORD_ID|1443 - 126028|ATP-dependent helicase|NP_217813.1|Mycobacterium tuberculosis H37Rv|83332 - 1443 - 9 - - - 1 - 13.0826 - 22 - 15.4875 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 4 - 0 - 6 - FRYEGS - FMYEGD - F YEG - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 261 - Query_261 - M_3850 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 262 - Query_262 - M_3851 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 263 - Query_263 - M_3852 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 264 - Query_264 - M_3853 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 265 - Query_265 - M_3854 - 9 - - - 1 - gnl|BL_ORD_ID|355 - 22046|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 - 355 - 10 - - - 1 - 13.853 - 24 - 5.67669 - 4 - 9 - 5 - 10 - 0 - 0 - 4 - 5 - 0 - 6 - PSIHRF - PGIYRF - P I+RF - - - - - 2 - gnl|BL_ORD_ID|1687 - 149053|NS3 gene product|AAB02124.1|Hepatitis C virus|11103 - 1687 - 18 - - - 1 - 13.4678 - 23 - 8.34044 - 4 - 9 - 5 - 10 - 0 - 0 - 4 - 5 - 0 - 6 - PSIHRF - PGIYRF - P I+RF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 266 - Query_266 - M_3855 - 9 - - - 1 - gnl|BL_ORD_ID|1956 - 181733|Antigen 85-B|P0C5B9.1|Mycobacterium tuberculosis|1773 - 1956 - 40 - - - 1 - 14.6234 - 26 - 3.22525 - 2 - 6 - 2 - 6 - 0 - 0 - 5 - 5 - 0 - 5 - TDVSR - TDVSR - TDVSR - - - - - 2 - gnl|BL_ORD_ID|221 - 16548|Glycoprotein GP110 precursor|P03188.1|Human herpesvirus 4 strain B95-8|10377 - 221 - 9 - - - 1 - 11.5418 - 18 - 159.996 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 5 - 0 - 9 - FTDVSRFTL - FLDKGTYTL - F D +TL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 267 - Query_267 - M_3856 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 268 - Query_268 - M_3857 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 269 - Query_269 - M_3858 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 270 - Query_270 - M_3859 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 271 - Query_271 - M_3860 - 9 - - - 1 - gnl|BL_ORD_ID|159 - 12108|polyprotein|AAP55688.1|Hepatitis C virus subtype 2a|31649 - 159 - 10 - - - 1 - 13.4678 - 23 - 8.46851 - 1 - 9 - 2 - 10 - 0 - 0 - 5 - 5 - 0 - 9 - FWCAQFTSF - FWEAVFTGL - FW A FT - - - - - 2 - gnl|BL_ORD_ID|1628 - 146188|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 - 1628 - 18 - - - 1 - 12.3122 - 20 - 36.8413 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 5 - 0 - 9 - FWCAQFTSF - FWESVFTGL - FW + FT - - - - - 3 - gnl|BL_ORD_ID|1630 - 146213|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 - 1630 - 18 - - - 1 - 12.3122 - 20 - 38.0157 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 5 - 0 - 9 - FWCAQFTSF - FWESVFTGL - FW + FT - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 272 - Query_272 - M_3861 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 273 - Query_273 - M_3862 - 9 - - - 1 - gnl|BL_ORD_ID|422 - 25460|Fusion glycoprotein F0 precursor|P03420.1|Human respiratory syncytial virus A2|11259 - 422 - 11 - - - 1 - 13.4678 - 23 - 10.7778 - 4 - 8 - 6 - 10 - 0 - 0 - 4 - 4 - 0 - 5 - LFYCK - LLYCK - L YCK - - - - - 2 - gnl|BL_ORD_ID|1960 - 182599|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1960 - 9 - - - 1 - 12.3122 - 20 - 45.611 - 1 - 6 - 3 - 8 - 0 - 0 - 3 - 4 - 0 - 6 - FWKLFY - MWQLMY - W+L Y - - - - - 3 - gnl|BL_ORD_ID|1887 - 180579|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1887 - 15 - - - 1 - 11.5418 - 18 - 98.8375 - 1 - 6 - 6 - 11 - 0 - 0 - 3 - 3 - 0 - 6 - FWKLFY - MWSLMY - W L Y - - - - - 4 - gnl|BL_ORD_ID|1945 - 180828|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1945 - 10 - - - 1 - 11.5418 - 18 - 137.176 - 1 - 6 - 4 - 9 - 0 - 0 - 3 - 3 - 0 - 6 - FWKLFY - MWSLMY - W L Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 274 - Query_274 - M_3863 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 275 - Query_275 - M_3864 - 9 - - - 1 - gnl|BL_ORD_ID|1231 - 97400|Genome polyprotein|P26664.3|Hepatitis C virus|11103 - 1231 - 10 - - - 1 - 12.6974 - 21 - 25.2038 - 1 - 8 - 3 - 10 - 0 - 0 - 3 - 5 - 0 - 8 - FYAIVVPM - FYGKAIPL - FY +P+ - - - - - 2 - gnl|BL_ORD_ID|274 - 18397|Genome polyprotein|P26662.3|Hepatitis C virus|11103 - 274 - 11 - - - 1 - 12.6974 - 21 - 35.1103 - 1 - 8 - 1 - 8 - 0 - 0 - 3 - 5 - 0 - 8 - FYAIVVPM - FYGKAIPI - FY +P+ - - - - - 3 - gnl|BL_ORD_ID|1230 - 97399|polyprotein|ACZ60108.1|Hepatitis C virus subtype 3a|356426 - 1230 - 10 - - - 1 - 12.3122 - 20 - 51.1794 - 1 - 8 - 3 - 10 - 0 - 0 - 3 - 5 - 0 - 8 - FYAIVVPM - FYGKAIPI - FY +P+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 276 - Query_276 - M_3865 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 277 - Query_277 - M_3866 - 9 - - - 1 - gnl|BL_ORD_ID|1781 - 156550|E3 ubiquitin-protein ligase Mdm2|Q00987.1|Homo sapiens|9606 - 1781 - 9 - - - 1 - 14.2382 - 25 - 3.55601 - 1 - 6 - 3 - 8 - 0 - 0 - 5 - 5 - 0 - 6 - FYLGTY - FYLGQY - FYLG Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 278 - Query_278 - M_3867 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 279 - Query_279 - M_3868 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 280 - Query_280 - M_3869 - 9 - - - 1 - gnl|BL_ORD_ID|1336 - 107894|polyprotein|CAB41951.1|Hepatitis C virus|11103 - 1336 - 10 - - - 1 - 14.2382 - 25 - 4.23087 - 3 - 9 - 3 - 9 - 0 - 0 - 5 - 7 - 0 - 7 - TDSSSVL - TDSTSIL - TDS+S+L - - - - - 2 - gnl|BL_ORD_ID|1226 - 97227|polyprotein|CAB41951.1|Hepatitis C virus|11103 - 1226 - 10 - - - 1 - 14.2382 - 25 - 4.23087 - 3 - 9 - 4 - 10 - 0 - 0 - 5 - 7 - 0 - 7 - TDSSSVL - TDSTSIL - TDS+S+L - - - - - 3 - gnl|BL_ORD_ID|1224 - 97111|polyprotein|ABR25251.1|Hepatitis C virus (isolate H77)|63746 - 1224 - 18 - - - 1 - 13.4678 - 23 - 11.4723 - 3 - 9 - 12 - 18 - 0 - 0 - 4 - 7 - 0 - 7 - TDSSSVL - TDATSIL - TD++S+L - - - - - 4 - gnl|BL_ORD_ID|1225 - 97226|Genome polyprotein|P26664.3|Hepatitis C virus|11103 - 1225 - 10 - - - 1 - 13.4678 - 23 - 12.4198 - 3 - 9 - 4 - 10 - 0 - 0 - 4 - 7 - 0 - 7 - TDSSSVL - TDATSIL - TD++S+L - - - - - 5 - gnl|BL_ORD_ID|1354 - 108147|Genome polyprotein|P26664.3|Hepatitis C virus|11103 - 1354 - 10 - - - 1 - 13.4678 - 23 - 12.859 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 7 - 0 - 7 - TDSSSVL - TDATSIL - TD++S+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 281 - Query_281 - M_3870 - 9 - - - 1 - gnl|BL_ORD_ID|1565 - 141323|multifunctional expression regulator|NP_044657.1|Human alphaherpesvirus 1|10298 - 1565 - 9 - - - 1 - 12.3122 - 20 - 60.6092 - 1 - 7 - 3 - 9 - 0 - 0 - 4 - 5 - 0 - 7 - FYTPALF - FYCNSLF - FY +LF - - - - - 2 - gnl|BL_ORD_ID|545 - 33382|polyprotein|AAB67037.1|Hepatitis C virus|11103 - 545 - 15 - - - 1 - 11.927 - 19 - 65.1875 - 3 - 9 - 5 - 11 - 0 - 0 - 4 - 5 - 0 - 7 - TPALFSF - TPMGFSY - TP FS+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 282 - Query_282 - M_3871 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 283 - Query_283 - M_3872 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 284 - Query_284 - M_3873 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 285 - Query_285 - M_3874 - 9 - - - 1 - gnl|BL_ORD_ID|66 - 4910|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 66 - 20 - - - 1 - 12.6974 - 21 - 27.2657 - 2 - 9 - 13 - 20 - 0 - 0 - 4 - 5 - 0 - 8 - HDAPRRTL - HGAGTRTI - H A RT+ - - - - - 2 - gnl|BL_ORD_ID|1089 - 72038|Polyprotein|Q9IZA3|Hepatitis C virus subtype 2a|31649 - 1089 - 10 - - - 1 - 12.6974 - 21 - 35.4066 - 2 - 9 - 3 - 10 - 0 - 0 - 4 - 5 - 0 - 8 - HDAPRRTL - HGAGNKTL - H A +TL - - - - - 3 - gnl|BL_ORD_ID|1090 - 72039|polyprotein|CAB53095.1|Hepatitis C virus subtype 1b|31647 - 1090 - 10 - - - 1 - 12.3122 - 20 - 41.8935 - 2 - 9 - 3 - 10 - 0 - 0 - 4 - 5 - 0 - 8 - HDAPRRTL - HGAGSKTL - H A +TL - - - - - 4 - gnl|BL_ORD_ID|391 - 23883|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 - 391 - 15 - - - 1 - 11.5418 - 18 - 100.351 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 5 - 0 - 8 - HDAPRRTL - HGAGTRTI - H A RT+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 286 - Query_286 - M_3875 - 9 - - - 1 - gnl|BL_ORD_ID|2088 - 185491|polyprotein|AGO67248.1|Dengue virus 2|11060 - 2088 - 10 - - - 1 - 13.0826 - 22 - 19.8203 - 2 - 9 - 3 - 10 - 0 - 0 - 4 - 7 - 0 - 8 - HKEDAGVV - EEEEAGVL - +E+AGV+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 287 - Query_287 - M_3876 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 288 - Query_288 - M_3877 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 289 - Query_289 - M_3878 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 290 - Query_290 - M_3879 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 291 - Query_291 - M_3880 - 9 - - - 1 - gnl|BL_ORD_ID|1924 - 180726|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1924 - 15 - - - 1 - 14.2382 - 25 - 2.60034 - 1 - 8 - 6 - 13 - 0 - 0 - 4 - 5 - 0 - 8 - GHNSWGFG - GDTAWDFG - G +W FG - - - - - 2 - gnl|BL_ORD_ID|439 - 27061|envelope glycoprotein|ABU89742.1|Dengue virus 2 Thailand/16681/84|31634 - 439 - 10 - - - 1 - 14.2382 - 25 - 4.15863 - 1 - 8 - 3 - 10 - 0 - 0 - 4 - 5 - 0 - 8 - GHNSWGFG - GDTAWDFG - G +W FG - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 292 - Query_292 - M_3881 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 293 - Query_293 - M_3882 - 9 - - - 1 - gnl|BL_ORD_ID|1172 - 79308|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 1172 - 16 - - - 1 - 14.6234 - 26 - 1.40835 - 2 - 9 - 2 - 9 - 0 - 0 - 5 - 6 - 0 - 8 - HPSLSQHL - EPTLGQHL - P+L QHL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 294 - Query_294 - M_3883 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 295 - Query_295 - M_3884 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 296 - Query_296 - M_3885 - 9 - - - 1 - gnl|BL_ORD_ID|1271 - 101673|gag protein|ABO73990.1|Human immunodeficiency virus 1|11676 - 1271 - 9 - - - 1 - 14.2382 - 25 - 2.75966 - 1 - 9 - 1 - 9 - 0 - 0 - 6 - 6 - 0 - 9 - GHVAGEQML - GHQAAMQML - GH A QML - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 297 - Query_297 - M_3886 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 298 - Query_298 - M_3887 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 299 - Query_299 - M_3888 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 300 - Query_300 - M_3889 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 301 - Query_301 - M_3890 - 9 - - - 1 - gnl|BL_ORD_ID|1775 - 155637|tegument protein|CAB06732.1|Human alphaherpesvirus 2|10310 - 1775 - 15 - - - 1 - 14.6234 - 26 - 1.37617 - 1 - 7 - 3 - 9 - 0 - 0 - 5 - 5 - 0 - 7 - GPCRRRF - GPADRRF - GP RRF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 302 - Query_302 - M_3891 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 303 - Query_303 - M_3892 - 9 - - - 1 - gnl|BL_ORD_ID|654 - 38724|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 654 - 20 - - - 1 - 13.0826 - 22 - 20.5164 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 4 - 0 - 8 - PRTKAWFL - PSTLRWFF - P T WF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 304 - Query_304 - M_3893 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 305 - Query_305 - M_3894 - 9 - - - 1 - gnl|BL_ORD_ID|1774 - 155554|RL2|CAB06760.1|Human alphaherpesvirus 2|10310 - 1774 - 15 - - - 1 - 13.853 - 24 - 4.61107 - 3 - 8 - 4 - 9 - 0 - 0 - 4 - 4 - 0 - 6 - APCWQR - APAWSR - AP W R - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 306 - Query_306 - M_3895 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 307 - Query_307 - M_3896 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 308 - Query_308 - M_3897 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 309 - Query_309 - M_3898 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 310 - Query_310 - M_3899 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 311 - Query_311 - M_3900 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 312 - Query_312 - M_3901 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 313 - Query_313 - M_3902 - 9 - - - 1 - gnl|BL_ORD_ID|461 - 27981|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 - 461 - 20 - - - 1 - 12.6974 - 21 - 21.519 - 1 - 8 - 5 - 12 - 0 - 0 - 4 - 6 - 0 - 8 - GTNIVILE - GTQAVVLK - GT V+L+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 314 - Query_314 - M_3903 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 315 - Query_315 - M_3904 - 9 - - - 1 - gnl|BL_ORD_ID|1589 - 142203|polyprotein|BAD73974.1|Hepatitis C virus subtype 1b|31647 - 1589 - 9 - - - 1 - 13.0826 - 22 - 16.6015 - 3 - 9 - 1 - 7 - 0 - 0 - 5 - 6 - 0 - 7 - KKKPNPV - KKKKNPM - KKK NP+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 316 - Query_316 - M_3905 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 317 - Query_317 - M_3906 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 318 - Query_318 - M_3907 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 319 - Query_319 - M_3908 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 320 - Query_320 - M_3909 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 321 - Query_321 - M_3910 - 9 - - - 1 - gnl|BL_ORD_ID|2191 - 190568|polymerase|AAD16253.1|Hepatitis B virus|10407 - 2191 - 20 - - - 1 - 12.3122 - 20 - 44.7058 - 1 - 9 - 7 - 15 - 0 - 0 - 5 - 5 - 0 - 9 - HLLSHSYCL - HLYSHPIIL - HL SH L - - - - - 2 - gnl|BL_ORD_ID|580 - 36402|P protein|Q05486.1|Hepatitis B virus|10407 - 580 - 15 - - - 1 - 12.3122 - 20 - 49.8749 - 1 - 9 - 2 - 10 - 0 - 0 - 5 - 5 - 0 - 9 - HLLSHSYCL - HLYSHPIIL - HL SH L - - - - - 3 - gnl|BL_ORD_ID|498 - 31898|P protein|P17100.1|Hepatitis B virus|10407 - 498 - 9 - - - 1 - 11.1566 - 17 - 199.082 - 1 - 6 - 3 - 8 - 0 - 0 - 4 - 4 - 0 - 6 - HLLSHS - HLYSHP - HL SH - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 322 - Query_322 - M_3911 - 9 - - - 1 - gnl|BL_ORD_ID|392 - 24172|pX-rex-orf I {alternatively spliced}|AAB23359.1|Human T-lymphotropic virus 1|11908 - 392 - 9 - - - 1 - 14.2382 - 25 - 3.21187 - 1 - 9 - 1 - 9 - 0 - 0 - 6 - 7 - 0 - 9 - HLMGQLSSL - HLAFQLSSI - HL QLSS+ - - - - - 2 - gnl|BL_ORD_ID|2031 - 184337|polyprotein|AGO67248.1|Dengue virus 2|11060 - 2031 - 10 - - - 1 - 12.3122 - 20 - 44.0514 - 1 - 6 - 5 - 10 - 0 - 0 - 3 - 6 - 0 - 6 - HLMGQL - HVLGRL - H++G+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 323 - Query_323 - M_3912 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 324 - Query_324 - M_3913 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 325 - Query_325 - M_3914 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 326 - Query_326 - M_3915 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 327 - Query_327 - M_3916 - 9 - - - 1 - gnl|BL_ORD_ID|1776 - 155811|ribonucleotide reductase large subunit|CAB06725.1|Human alphaherpesvirus 2|10310 - 1776 - 15 - - - 1 - 12.6974 - 21 - 28.3557 - 1 - 6 - 8 - 13 - 0 - 0 - 4 - 5 - 0 - 6 - HREDFE - HGEEFE - H E+FE - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 328 - Query_328 - M_3917 - 9 - - - 1 - gnl|BL_ORD_ID|450 - 27285|pol protein|BAA32832.1|Hepatitis B virus|10407 - 450 - 10 - - - 1 - 15.0086 - 27 - 0.948031 - 2 - 9 - 3 - 10 - 0 - 0 - 6 - 6 - 0 - 8 - RGTGAVYV - RGTSFVYV - RGT VYV - - - - - 2 - gnl|BL_ORD_ID|1437 - 119822|110 kd polyprotein precursor|CAA28880.1|Rubella virus|11041 - 1437 - 29 - - - 1 - 13.0826 - 22 - 19.5886 - 2 - 8 - 11 - 17 - 0 - 0 - 4 - 5 - 0 - 7 - RGTGAVY - EGEGAVF - G GAV+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 329 - Query_329 - M_3918 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 330 - Query_330 - M_3919 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 331 - Query_331 - M_3920 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 332 - Query_332 - M_3921 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 333 - Query_333 - M_3922 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 334 - Query_334 - M_3923 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 335 - Query_335 - M_3924 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 336 - Query_336 - M_3925 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 337 - Query_337 - M_3926 - 9 - - - 1 - gnl|BL_ORD_ID|2191 - 190568|polymerase|AAD16253.1|Hepatitis B virus|10407 - 2191 - 20 - - - 1 - 11.1566 - 17 - 207.813 - 3 - 8 - 7 - 12 - 0 - 0 - 4 - 4 - 0 - 6 - HLLSHS - HLYSHP - HL SH - - - - - 2 - gnl|BL_ORD_ID|580 - 36402|P protein|Q05486.1|Hepatitis B virus|10407 - 580 - 15 - - - 1 - 10.7714 - 16 - 300.51 - 3 - 8 - 2 - 7 - 0 - 0 - 4 - 4 - 0 - 6 - HLLSHS - HLYSHP - HL SH - - - - - 3 - gnl|BL_ORD_ID|498 - 31898|P protein|P17100.1|Hepatitis B virus|10407 - 498 - 9 - - - 1 - 10.7714 - 16 - 354.707 - 3 - 8 - 3 - 8 - 0 - 0 - 4 - 4 - 0 - 6 - HLLSHS - HLYSHP - HL SH - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 338 - Query_338 - M_3927 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 339 - Query_339 - M_3928 - 9 - - - 1 - gnl|BL_ORD_ID|1265 - 98603|trans-sialidase, putative|EAN82716.1|Trypanosoma cruzi|5693 - 1265 - 9 - - - 1 - 14.6234 - 26 - 1.6522 - 2 - 9 - 2 - 9 - 0 - 0 - 5 - 5 - 0 - 8 - TPNGRHFY - TDNNRSFY - T N R FY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 340 - Query_340 - M_3929 - 9 - - - 1 - gnl|BL_ORD_ID|2123 - 186524|polyprotein|AGW21594.1|Dengue virus 1|11053 - 2123 - 10 - - - 1 - 12.6974 - 21 - 23.5358 - 2 - 8 - 1 - 7 - 0 - 0 - 3 - 6 - 0 - 7 - WSMWLGV - WTMKIGI - W+M +G+ - - - - - 2 - gnl|BL_ORD_ID|2121 - 186470|envelope protein|AGT63061.1|Dengue virus 3|11069 - 2121 - 10 - - - 1 - 11.1566 - 17 - 184.324 - 2 - 8 - 1 - 7 - 0 - 0 - 3 - 5 - 0 - 7 - WSMWLGV - WIMKIGI - W M +G+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 341 - Query_341 - M_3930 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 342 - Query_342 - M_3931 - 9 - - - 1 - gnl|BL_ORD_ID|375 - 23270|polyprotein|AAB67036.1|Hepatitis C virus (isolate H77)|63746 - 375 - 15 - - - 1 - 14.6234 - 26 - 1.57759 - 2 - 8 - 8 - 14 - 0 - 0 - 4 - 6 - 0 - 7 - YHHRFNN - YQHKFNS - Y H+FN+ - - - - - 2 - gnl|BL_ORD_ID|23 - 1516|Nucleoprotein|P03418.1|Human respiratory syncytial virus A2|11259 - 23 - 14 - - - 1 - 11.1566 - 17 - 170.435 - 2 - 8 - 3 - 9 - 0 - 0 - 3 - 5 - 0 - 7 - YHHRFNN - FYHILNN - ++H NN - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 343 - Query_343 - M_3932 - 9 - - - 1 - gnl|BL_ORD_ID|1583 - 141469|envelope glycoprotein B|NP_044629.1|Human alphaherpesvirus 1|10298 - 1583 - 9 - - - 1 - 12.3122 - 20 - 46.3849 - 2 - 8 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - YISIFYA - YMSPFYG - Y+S FY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 344 - Query_344 - M_3933 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 345 - Query_345 - M_3934 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 346 - Query_346 - M_3935 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 347 - Query_347 - M_3936 - 9 - - - 1 - gnl|BL_ORD_ID|1556 - 141262|DNA polymerase catalytic subunit|NP_044632.1|Human alphaherpesvirus 1|10298 - 1556 - 10 - - - 1 - 12.6974 - 21 - 25.6384 - 3 - 9 - 4 - 10 - 0 - 0 - 5 - 5 - 0 - 7 - HAWWAHF - HARWAAF - HA WA F - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 348 - Query_348 - M_3937 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 349 - Query_349 - M_3938 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 350 - Query_350 - M_3939 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 351 - Query_351 - M_3940 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 352 - Query_352 - M_3941 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 353 - Query_353 - M_3942 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 354 - Query_354 - M_3943 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 355 - Query_355 - M_3944 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 356 - Query_356 - M_3945 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 357 - Query_357 - M_3946 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 358 - Query_358 - M_3947 - 9 - - - 1 - gnl|BL_ORD_ID|759 - 50596|polyprotein|ABG75765.1|Dengue virus 1|11053 - 759 - 9 - - - 1 - 14.2382 - 25 - 4.0067 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 6 - 0 - 7 - HDGAVHT - QEGAMHT - +GA+HT - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 359 - Query_359 - M_3948 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 360 - Query_360 - M_3949 - 9 - - - 1 - gnl|BL_ORD_ID|1398 - 110431|E7|AAD33253.1|Human papillomavirus type 16|333760 - 1398 - 36 - - - 1 - 12.3122 - 20 - 43.3992 - 3 - 7 - 16 - 20 - 0 - 0 - 4 - 5 - 0 - 5 - EDEVD - EDEID - EDE+D - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 361 - Query_361 - M_3950 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 362 - Query_362 - M_3951 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 363 - Query_363 - M_3952 - 9 - - - 1 - gnl|BL_ORD_ID|495 - 31802|large delta antigen|AAG26087.1|Hepatitis delta virus TW2667|10000523 - 495 - 9 - - - 1 - 13.0826 - 22 - 21.8994 - 4 - 9 - 4 - 9 - 0 - 0 - 3 - 5 - 0 - 6 - DDNKWV - DENPWL - D+N W+ - - - - - 2 - gnl|BL_ORD_ID|1919 - 180689|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1919 - 15 - - - 1 - 12.6974 - 21 - 22.89 - 1 - 9 - 4 - 12 - 0 - 0 - 3 - 5 - 0 - 9 - IHIDDNKWV - VHADMGYWI - +H D W+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 364 - Query_364 - M_3953 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 365 - Query_365 - M_3954 - 9 - - - 1 - gnl|BL_ORD_ID|665 - 40158|polyprotein|AAA45534.1|Hepatitis C virus|11103 - 665 - 15 - - - 1 - 12.3122 - 20 - 57.5015 - 1 - 7 - 8 - 14 - 0 - 0 - 3 - 5 - 0 - 7 - IHLLYPP - LHVWVPP - +H+ PP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 366 - Query_366 - M_3955 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 367 - Query_367 - M_3956 - 9 - - - 1 - gnl|BL_ORD_ID|1390 - 110306|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1390 - 32 - - - 1 - 10.001 - 14 - 635.848 - 1 - 9 - 13 - 21 - 0 - 0 - 4 - 5 - 0 - 9 - IHTDDNKCV - IHDIILECV - IH +CV - - - - - 2 - gnl|BL_ORD_ID|1394 - 110373|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1394 - 25 - - - 1 - 9.61583 - 13 - 777.964 - 1 - 9 - 15 - 23 - 0 - 0 - 4 - 5 - 0 - 9 - IHTDDNKCV - IHDIILECV - IH +CV - - - - - 3 - gnl|BL_ORD_ID|1411 - 111251|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1411 - 15 - - - 1 - 10.001 - 14 - 909.224 - 1 - 9 - 6 - 14 - 0 - 0 - 4 - 5 - 0 - 9 - IHTDDNKCV - IHDIILECV - IH +CV - - - - - 4 - gnl|BL_ORD_ID|968 - 64320|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 968 - 10 - - - 1 - 9.61583 - 13 - 1245.43 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 5 - 0 - 9 - IHTDDNKCV - IHDIILECV - IH +CV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 368 - Query_368 - M_3957 - 9 - - - 1 - gnl|BL_ORD_ID|1854 - 180407|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1854 - 15 - - - 1 - 13.853 - 24 - 4.3017 - 3 - 9 - 8 - 14 - 0 - 0 - 3 - 6 - 0 - 7 - AVLPSLF - GIIPSMF - ++PS+F - - - - - 2 - gnl|BL_ORD_ID|567 - 35238|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 567 - 15 - - - 1 - 13.853 - 24 - 5.39022 - 3 - 9 - 9 - 15 - 0 - 0 - 3 - 6 - 0 - 7 - AVLPSLF - GIIPSMF - ++PS+F - - - - - 3 - gnl|BL_ORD_ID|993 - 65550|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 993 - 15 - - - 1 - 13.853 - 24 - 5.67783 - 3 - 9 - 4 - 10 - 0 - 0 - 3 - 6 - 0 - 7 - AVLPSLF - GIIPSMF - ++PS+F - - - - - 4 - gnl|BL_ORD_ID|1740 - 150644|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1740 - 10 - - - 1 - 13.853 - 24 - 6.99268 - 3 - 9 - 4 - 10 - 0 - 0 - 3 - 6 - 0 - 7 - AVLPSLF - GIIPSMF - ++PS+F - - - - - 5 - gnl|BL_ORD_ID|1933 - 180778|polyprotein|AFP27208.1|Dengue virus 4|11070 - 1933 - 10 - - - 1 - 13.0826 - 22 - 13.0843 - 3 - 9 - 4 - 10 - 0 - 0 - 3 - 6 - 0 - 7 - AVLPSLF - GIIPTLF - ++P+LF - - - - - 6 - gnl|BL_ORD_ID|566 - 35237|nonstructural protein 3|NP_722463.1|Dengue virus type 1 Hawaii|10000440 - 566 - 20 - - - 1 - 13.0826 - 22 - 15.8745 - 3 - 9 - 9 - 15 - 0 - 0 - 3 - 6 - 0 - 7 - AVLPSLF - GIIPALF - ++P+LF - - - - - 7 - gnl|BL_ORD_ID|1739 - 150643|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1739 - 10 - - - 1 - 13.0826 - 22 - 20.8706 - 3 - 9 - 4 - 10 - 0 - 0 - 3 - 6 - 0 - 7 - AVLPSLF - GIIPALF - ++P+LF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 369 - Query_369 - M_3958 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 370 - Query_370 - M_3959 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 371 - Query_371 - M_3960 - 9 - - - 1 - gnl|BL_ORD_ID|2298 - 422984|NS5B protein|ABB72740.1|Hepatitis C virus genotype 1|41856 - 2298 - 9 - - - 1 - 12.6974 - 21 - 35.3877 - 1 - 6 - 4 - 9 - 0 - 0 - 5 - 5 - 0 - 6 - ILLTQF - ILLTHF - ILLT F - - - - - 2 - gnl|BL_ORD_ID|2329 - 423072|polyprotein|ACJ37172.1|Hepatitis C virus genotype 1|41856 - 2329 - 9 - - - 1 - 12.6974 - 21 - 39.1808 - 1 - 6 - 4 - 9 - 0 - 0 - 5 - 5 - 0 - 6 - ILLTQF - ILLTHF - ILLT F - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 372 - Query_372 - M_3961 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 373 - Query_373 - M_3962 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 374 - Query_374 - M_3963 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 375 - Query_375 - M_3964 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 376 - Query_376 - M_3965 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 377 - Query_377 - M_3966 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 378 - Query_378 - M_3967 - 9 - - - 1 - gnl|BL_ORD_ID|1888 - 180582|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1888 - 15 - - - 1 - 12.3122 - 20 - 38.6124 - 3 - 9 - 3 - 9 - 0 - 0 - 3 - 5 - 0 - 7 - WSYWGVF - WAYHGSY - W+Y G + - - - - - 2 - gnl|BL_ORD_ID|1097 - 72563|polyprotein|AAB70696.1|Dengue virus type 1 Hawaii|10000440 - 1097 - 20 - - - 1 - 11.927 - 19 - 78.9367 - 3 - 9 - 12 - 18 - 0 - 0 - 3 - 5 - 0 - 7 - WSYWGVF - WAYHGSY - W+Y G + - - - - - 3 - gnl|BL_ORD_ID|160 - 12183|EBNA3C latent protein|CAD53421.1|Human gammaherpesvirus 4|10376 - 160 - 9 - - - 1 - 11.5418 - 18 - 145.552 - 1 - 6 - 4 - 9 - 0 - 0 - 2 - 4 - 0 - 6 - IQWSYW - VGWRHW - + W +W - - - - - 4 - gnl|BL_ORD_ID|1244 - 98042|trans-sialidase, putative|EAN80840.1|Trypanosoma cruzi|5693 - 1244 - 10 - - - 1 - 11.1566 - 17 - 265.518 - 3 - 8 - 5 - 10 - 0 - 0 - 3 - 4 - 0 - 6 - WSYWGV - WAEWPV - W+ W V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 379 - Query_379 - M_3968 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 380 - Query_380 - M_3969 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 381 - Query_381 - M_3970 - 9 - - - 1 - gnl|BL_ORD_ID|469 - 28484|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 469 - 9 - - - 1 - 10.7714 - 16 - 354.707 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 5 - 0 - 9 - IREYCPYTY - ISEYRHYCY - I EY Y Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 382 - Query_382 - M_3971 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 383 - Query_383 - M_3972 - 9 - - - 1 - gnl|BL_ORD_ID|1481 - 133645|cell surface protein|NP_302626.1|Mycobacterium leprae|1769 - 1481 - 15 - - - 1 - 13.0826 - 22 - 17.8301 - 4 - 9 - 6 - 11 - 0 - 0 - 4 - 5 - 0 - 6 - GNVIAC - GNMSAC - GN+ AC - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 384 - Query_384 - M_3973 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 385 - Query_385 - M_3974 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 386 - Query_386 - M_3975 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 387 - Query_387 - M_3976 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 388 - Query_388 - M_3977 - 9 - - - 1 - gnl|BL_ORD_ID|1106 - 72928|Genome polyprotein|P26662.3|Hepatitis C virus (isolate Japanese)|11116 - 1106 - 10 - - - 1 - 13.853 - 24 - 6.75361 - 3 - 9 - 4 - 10 - 0 - 0 - 4 - 6 - 0 - 7 - PPDSRSL - PPGARSM - PP +RS+ - - - - - 2 - gnl|BL_ORD_ID|256 - 17278|Genome polyprotein|P06441.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 256 - 20 - - - 1 - 11.927 - 19 - 67.0972 - 1 - 7 - 4 - 10 - 0 - 0 - 3 - 6 - 0 - 7 - IRPPDSR - LKPGESR - ++P +SR - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 389 - Query_389 - M_3978 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 390 - Query_390 - M_3979 - 9 - - - 1 - gnl|BL_ORD_ID|761 - 50894|Genome polyprotein|P27909.2|Dengue virus type 1 Hawaii|10000440 - 761 - 20 - - - 1 - 13.4678 - 23 - 11.8474 - 2 - 7 - 3 - 8 - 0 - 0 - 4 - 5 - 0 - 6 - RRLRPS - KRLEPS - +RL PS - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 391 - Query_391 - M_3980 - 9 - - - 1 - gnl|BL_ORD_ID|761 - 50894|Genome polyprotein|P27909.2|Dengue virus type 1 Hawaii|10000440 - 761 - 20 - - - 1 - 13.4678 - 23 - 11.8474 - 2 - 7 - 3 - 8 - 0 - 0 - 4 - 5 - 0 - 6 - RRLRPS - KRLEPS - +RL PS - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 392 - Query_392 - M_3981 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 393 - Query_393 - M_3982 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 394 - Query_394 - M_3983 - 9 - - - 1 - gnl|BL_ORD_ID|469 - 28484|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 469 - 9 - - - 1 - 12.6974 - 21 - 31.4086 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 5 - 0 - 9 - ISELLFECY - ISEYRHYCY - ISE CY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 395 - Query_395 - M_3984 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 396 - Query_396 - M_3985 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 397 - Query_397 - M_3986 - 9 - - - 1 - gnl|BL_ORD_ID|1051 - 69715|envelope protein|BAF48755.1|Hepatitis B virus|10407 - 1051 - 9 - - - 1 - 11.927 - 19 - 72.7009 - 1 - 8 - 2 - 9 - 0 - 0 - 4 - 6 - 0 - 8 - ISLGFFLV - LQAGFFLL - + GFFL+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 398 - Query_398 - M_3987 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 399 - Query_399 - M_3988 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 400 - Query_400 - M_3989 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 401 - Query_401 - M_3990 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 402 - Query_402 - M_3991 - 9 - - - 1 - gnl|BL_ORD_ID|1007 - 66405|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 1007 - 20 - - - 1 - 14.6234 - 26 - 1.71852 - 3 - 7 - 13 - 17 - 0 - 0 - 5 - 5 - 0 - 5 - TFDRL - TFDRL - TFDRL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 403 - Query_403 - M_3992 - 9 - - - 1 - gnl|BL_ORD_ID|686 - 41407|Envelope protein|NP_739583.2|Dengue virus 2|11060 - 686 - 15 - - - 1 - 16.9346 - 32 - 0.201842 - 1 - 8 - 7 - 14 - 0 - 0 - 5 - 8 - 0 - 8 - IVHRQFYL - LVHRQWFL - +VHRQ++L - - - - - 2 - gnl|BL_ORD_ID|1746 - 150725|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1746 - 9 - - - 1 - 16.5494 - 31 - 0.331977 - 1 - 8 - 2 - 9 - 0 - 0 - 5 - 8 - 0 - 8 - IVHRQFYL - LVHRQWFL - +VHRQ++L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 404 - Query_404 - M_3993 - 9 - - - 1 - gnl|BL_ORD_ID|775 - 51604|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 - 775 - 10 - - - 1 - 13.4678 - 23 - 8.92274 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 6 - 0 - 7 - MGYSSGI - MDYSNGL - M YS+G+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 405 - Query_405 - M_3994 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 406 - Query_406 - M_3995 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 407 - Query_407 - M_3996 - 9 - - - 1 - gnl|BL_ORD_ID|990 - 65497|HCV-1|AAA45676.1|Hepatitis C virus genotype 1|41856 - 990 - 20 - - - 1 - 13.853 - 24 - 5.50999 - 1 - 8 - 9 - 16 - 0 - 0 - 4 - 6 - 0 - 8 - IYAFMGTP - LRAYMNTP - + A+M TP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 408 - Query_408 - M_3997 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 409 - Query_409 - M_3998 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 410 - Query_410 - M_3999 - 9 - - - 1 - gnl|BL_ORD_ID|1667 - 148117|early protein|CAA52585.1|Human papillomavirus type 52|10618 - 1667 - 9 - - - 1 - 12.6974 - 21 - 26.0147 - 2 - 7 - 2 - 7 - 0 - 0 - 3 - 6 - 0 - 6 - YGLCVV - YGVCIM - YG+C++ - - - - - 2 - gnl|BL_ORD_ID|389 - 23807|tax|AAG48731.1|Human T-lymphotropic virus 2|11909 - 389 - 23 - - - 1 - 11.5418 - 18 - 117.383 - 1 - 6 - 17 - 22 - 0 - 0 - 3 - 5 - 0 - 6 - IYGLCV - VFGDCV - ++G CV - - - - - 3 - gnl|BL_ORD_ID|1170 - 79294|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 1170 - 15 - - - 1 - 11.5418 - 18 - 135.568 - 1 - 6 - 9 - 14 - 0 - 0 - 3 - 5 - 0 - 6 - IYGLCV - VFGDCV - ++G CV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 411 - Query_411 - M_4000 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 412 - Query_412 - M_4001 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 413 - Query_413 - M_4002 - 9 - - - 1 - gnl|BL_ORD_ID|1125 - 74605|Circumsporozoite protein precursor|P08677.2|Plasmodium vivax strain Belem|31273 - 1125 - 9 - - - 1 - 14.6234 - 26 - 1.6522 - 2 - 7 - 1 - 6 - 0 - 0 - 5 - 6 - 0 - 6 - YVDKVR - YLDKVR - Y+DKVR - - - - - 2 - gnl|BL_ORD_ID|837 - 54965|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 - 837 - 10 - - - 1 - 12.3122 - 20 - 39.1729 - 1 - 8 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - IYVDKVRH - MYVGGVEH - +YV V H - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 414 - Query_414 - M_4003 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 415 - Query_415 - M_4004 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 416 - Query_416 - M_4005 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 417 - Query_417 - M_4006 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 418 - Query_418 - M_4007 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 419 - Query_419 - M_4008 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 420 - Query_420 - M_4009 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 421 - Query_421 - M_4010 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 422 - Query_422 - M_4011 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 423 - Query_423 - M_4012 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 424 - Query_424 - M_4013 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 425 - Query_425 - M_4014 - 9 - - - 1 - gnl|BL_ORD_ID|852 - 55718|Probable membrane glycoprotein precursor|P03218.1|Human herpesvirus 4 strain B95-8|10377 - 852 - 9 - - - 1 - 11.927 - 19 - 70.3445 - 2 - 7 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - KRRKFW - RRRKGW - +RRK W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 426 - Query_426 - M_4015 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 427 - Query_427 - M_4016 - 9 - - - 1 - gnl|BL_ORD_ID|1677 - 149024|NS2 protein|NP_751923.1|Hepatitis C virus (isolate H77)|63746 - 1677 - 9 - - - 1 - 12.6974 - 21 - 25.1356 - 2 - 7 - 4 - 9 - 0 - 0 - 3 - 5 - 0 - 6 - LQPYFQ - LSPYYK - L PY++ - - - - - 2 - gnl|BL_ORD_ID|639 - 37991|polyprotein|AAY82034.1|Hepatitis C virus genotype 1|41856 - 639 - 13 - - - 1 - 12.6974 - 21 - 26.4786 - 2 - 7 - 6 - 11 - 0 - 0 - 3 - 5 - 0 - 6 - LQPYFQ - LSPYYK - L PY++ - - - - - 3 - gnl|BL_ORD_ID|662 - 39589|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 662 - 10 - - - 1 - 12.6974 - 21 - 28.8893 - 2 - 7 - 1 - 6 - 0 - 0 - 3 - 5 - 0 - 6 - LQPYFQ - LSPYYK - L PY++ - - - - - 4 - gnl|BL_ORD_ID|663 - 39590|polyprotein|AAY82030.1|Hepatitis C virus|11103 - 663 - 11 - - - 1 - 12.6974 - 21 - 29.6736 - 2 - 7 - 1 - 6 - 0 - 0 - 3 - 5 - 0 - 6 - LQPYFQ - LSPYYK - L PY++ - - - - - 5 - gnl|BL_ORD_ID|664 - 39591|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 - 664 - 20 - - - 1 - 12.3122 - 20 - 49.7173 - 2 - 7 - 1 - 6 - 0 - 0 - 3 - 5 - 0 - 6 - LQPYFQ - LSPYYK - L PY++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 428 - Query_428 - M_4017 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 429 - Query_429 - M_4018 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 430 - Query_430 - M_4019 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 431 - Query_431 - M_4020 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 432 - Query_432 - M_4021 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 433 - Query_433 - M_4022 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 434 - Query_434 - M_4023 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 435 - Query_435 - M_4024 - 9 - - - 1 - gnl|BL_ORD_ID|1774 - 155554|RL2|CAB06760.1|Human alphaherpesvirus 2|10310 - 1774 - 15 - - - 1 - 12.6974 - 21 - 26.5542 - 3 - 7 - 4 - 8 - 0 - 0 - 3 - 5 - 0 - 5 - SPAWN - APAWS - +PAW+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 436 - Query_436 - M_4025 - 9 - - - 1 - gnl|BL_ORD_ID|1745 - 150698|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1745 - 10 - - - 1 - 13.0826 - 22 - 20.5146 - 3 - 8 - 3 - 8 - 0 - 0 - 4 - 5 - 0 - 6 - YLSQRE - YLGKRE - YL +RE - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 437 - Query_437 - M_4026 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 438 - Query_438 - M_4027 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 439 - Query_439 - M_4028 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 440 - Query_440 - M_4029 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 441 - Query_441 - M_4030 - 9 - - - 1 - gnl|BL_ORD_ID|1502 - 137660|L1|ACL12325.1|Human papillomavirus type 58|10598 - 1502 - 9 - - - 1 - 12.6974 - 21 - 36.611 - 1 - 5 - 1 - 5 - 0 - 0 - 3 - 4 - 0 - 5 - KYPYW - KYTFW - KY +W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 442 - Query_442 - M_4031 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 443 - Query_443 - M_4032 - 9 - - - 1 - gnl|BL_ORD_ID|561 - 34616|pol protein|BAA32832.1|Hepatitis B virus|10407 - 561 - 9 - - - 1 - 14.6234 - 26 - 1.91441 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 8 - 0 - 9 - KYSTPPYLL - KYTSFPWLL - KY++ P+LL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 444 - Query_444 - M_4033 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 445 - Query_445 - M_4034 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 446 - Query_446 - M_4035 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 447 - Query_447 - M_4036 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 448 - Query_448 - M_4037 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 449 - Query_449 - M_4038 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 450 - Query_450 - M_4039 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 451 - Query_451 - M_4040 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 452 - Query_452 - M_4041 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 453 - Query_453 - M_4042 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 454 - Query_454 - M_4043 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 455 - Query_455 - M_4044 - 9 - - - 1 - gnl|BL_ORD_ID|946 - 62355|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 946 - 20 - - - 1 - 13.853 - 24 - 7.33195 - 2 - 6 - 10 - 14 - 0 - 0 - 4 - 4 - 0 - 5 - FPRLP - FPRAP - FPR P - - - - - 2 - gnl|BL_ORD_ID|273 - 18390|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 273 - 20 - - - 1 - 13.4678 - 23 - 9.40925 - 2 - 6 - 3 - 7 - 0 - 0 - 4 - 4 - 0 - 5 - FPRLP - FPRAP - FPR P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 456 - Query_456 - M_4045 - 9 - - - 1 - gnl|BL_ORD_ID|545 - 33382|polyprotein|AAB67037.1|Hepatitis C virus|11103 - 545 - 15 - - - 1 - 13.4678 - 23 - 9.20205 - 2 - 8 - 9 - 15 - 0 - 0 - 4 - 5 - 0 - 7 - FSFMTHC - FSYDTRC - FS+ T C - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 457 - Query_457 - M_4046 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 458 - Query_458 - M_4047 - 9 - - - 1 - gnl|BL_ORD_ID|1008 - 66798|glycoprotein gp35/37|AAC59622.1|Human gammaherpesvirus 8|37296 - 1008 - 15 - - - 1 - 12.3122 - 20 - 37.995 - 2 - 7 - 4 - 9 - 0 - 0 - 3 - 5 - 0 - 6 - GRNRHF - GRDAHY - GR+ H+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 459 - Query_459 - M_4048 - 9 - - - 1 - gnl|BL_ORD_ID|1744 - 150693|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1744 - 9 - - - 1 - 12.6974 - 21 - 26.4654 - 3 - 9 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - APMYNLL - VPNYNLI - P YNL+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 460 - Query_460 - M_4049 - 9 - - - 1 - gnl|BL_ORD_ID|1744 - 150693|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1744 - 9 - - - 1 - 12.6974 - 21 - 26.4654 - 3 - 9 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - APMYNLL - VPNYNLI - P YNL+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 461 - Query_461 - M_4050 - 9 - - - 1 - gnl|BL_ORD_ID|1660 - 147561|early protein|CAA52586.1|Human papillomavirus type 52|10618 - 1660 - 9 - - - 1 - 15.3938 - 28 - 0.819689 - 1 - 7 - 1 - 7 - 0 - 0 - 5 - 6 - 0 - 7 - LHEQLGD - CYEQLGD - +EQLGD - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 462 - Query_462 - M_4051 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 463 - Query_463 - M_4052 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 464 - Query_464 - M_4053 - 9 - - - 1 - gnl|BL_ORD_ID|1992 - 183577|polyprotein|AGK36298.1|Dengue virus 2|11060 - 1992 - 10 - - - 1 - 12.3122 - 20 - 43.3206 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 6 - 0 - 8 - HFVQKLLF - HFQRALIF - HF + L+F - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 465 - Query_465 - M_4054 - 9 - - - 1 - gnl|BL_ORD_ID|1392 - 110335|E7|AAD33253.1|Human papillomavirus type 16|333760 - 1392 - 32 - - - 1 - 10.001 - 14 - 438.401 - 1 - 9 - 8 - 16 - 0 - 0 - 4 - 5 - 0 - 9 - LHHKHKELQ - LHEYMLDLQ - LH +LQ - - - - - 2 - gnl|BL_ORD_ID|1823 - 178351|Protein E7|P03129.1|Human papillomavirus type 16|333760 - 1823 - 15 - - - 1 - 10.3862 - 15 - 565.448 - 1 - 9 - 4 - 12 - 0 - 0 - 4 - 5 - 0 - 9 - LHHKHKELQ - LHEYMLDLQ - LH +LQ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 466 - Query_466 - M_4055 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 467 - Query_467 - M_4056 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 468 - Query_468 - M_4057 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 469 - Query_469 - M_4058 - 9 - - - 1 - gnl|BL_ORD_ID|1175 - 79390|Protein Tax-1|P0C213.1|Human T-cell lymphotropic virus type 1 (african isolate)|39015 - 1175 - 15 - - - 1 - 12.6974 - 21 - 21.4208 - 1 - 7 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - LHNAHVL - FHNLHLL - HN H+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 470 - Query_470 - M_4059 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 471 - Query_471 - M_4060 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 472 - Query_472 - M_4061 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 473 - Query_473 - M_4062 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 474 - Query_474 - M_4063 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 475 - Query_475 - M_4064 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 476 - Query_476 - M_4065 - 9 - - - 1 - gnl|BL_ORD_ID|1139 - 75356|EBNA3A nuclear protein|Q8AZJ8|Human gammaherpesvirus 4|10376 - 1139 - 9 - - - 1 - 13.4678 - 23 - 12.57 - 1 - 6 - 3 - 8 - 0 - 0 - 4 - 5 - 0 - 6 - LHTRHG - LHEQHG - LH +HG - - - - - 2 - gnl|BL_ORD_ID|1377 - 109331|L1|ABP99807.1|Human papillomavirus type 18|333761 - 1377 - 9 - - - 1 - 12.6974 - 21 - 33.058 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 7 - 0 - 9 - LHTRHGSIL - IHSMNSSIL - +H+ + SIL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 477 - Query_477 - M_4066 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 478 - Query_478 - M_4067 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 479 - Query_479 - M_4068 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 480 - Query_480 - M_4069 - 9 - - - 1 - gnl|BL_ORD_ID|558 - 34482|gag polyprotein|BAA00992.1|Human immunodeficiency virus 1|11676 - 558 - 9 - - - 1 - 10.7714 - 16 - 497.585 - 3 - 9 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - KHKKTHI - KYKLKHI - K+K HI - - - - - 2 - gnl|BL_ORD_ID|659 - 39162|gag protein|AAV53308.1|Human immunodeficiency virus 1|11676 - 659 - 15 - - - 1 - 10.3862 - 15 - 507.643 - 3 - 9 - 8 - 14 - 0 - 0 - 4 - 5 - 0 - 7 - KHKKTHI - KYKLKHI - K+K HI - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 481 - Query_481 - M_4070 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 482 - Query_482 - M_4071 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 483 - Query_483 - M_4072 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 484 - Query_484 - M_4073 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 485 - Query_485 - M_4074 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 486 - Query_486 - M_4075 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 487 - Query_487 - M_4076 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 488 - Query_488 - M_4077 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 489 - Query_489 - M_4078 - 9 - - - 1 - gnl|BL_ORD_ID|623 - 37498|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 - 623 - 10 - - - 1 - 13.853 - 24 - 4.69227 - 1 - 9 - 2 - 10 - 0 - 0 - 6 - 7 - 0 - 9 - LLGKKGTSA - LLGLWGTAA - LLG GT+A - - - - - 2 - gnl|BL_ORD_ID|615 - 37350|trans-sialidase|XP_818394.1|Trypanosoma cruzi|5693 - 615 - 10 - - - 1 - 13.853 - 24 - 4.69227 - 1 - 9 - 1 - 9 - 0 - 0 - 6 - 7 - 0 - 9 - LLGKKGTSA - LLGLWGTAA - LLG GT+A - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 490 - Query_490 - M_4079 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 491 - Query_491 - M_4080 - 9 - - - 1 - gnl|BL_ORD_ID|2027 - 184299|envelope protein|AGT63061.1|Dengue virus 3|11069 - 2027 - 9 - - - 1 - 13.853 - 24 - 5.00793 - 2 - 7 - 4 - 9 - 0 - 0 - 5 - 6 - 0 - 6 - LKKLCI - LRKLCI - L+KLCI - - - - - 2 - gnl|BL_ORD_ID|2028 - 184300|envelope protein|AFN87749.1|Dengue virus 2|11060 - 2028 - 9 - - - 1 - 12.6974 - 21 - 34.7909 - 2 - 7 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - LKKLCI - LRKYCI - L+K CI - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 492 - Query_492 - M_4081 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 493 - Query_493 - M_4082 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 494 - Query_494 - M_4083 - 9 - - - 1 - gnl|BL_ORD_ID|1714 - 150377|polyprotein|AGS49173.1|Dengue virus 2|11060 - 1714 - 9 - - - 1 - 12.3122 - 20 - 51.2985 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 7 - 0 - 9 - LLLMYSYAV - LLLVAHYAI - LLL+ YA+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 495 - Query_495 - M_4084 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 496 - Query_496 - M_4085 - 9 - - - 1 - gnl|BL_ORD_ID|184 - 13518|HCV-1|AAA45676.1|Hepatitis C virus genotype 1|41856 - 184 - 20 - - - 1 - 11.927 - 19 - 57.7977 - 4 - 8 - 2 - 6 - 0 - 0 - 4 - 4 - 0 - 5 - NKPYL - NLPYL - N PYL - - - - - 2 - gnl|BL_ORD_ID|183 - 13516|Genome polyprotein|P26664.3|Hepatitis C virus subtype 1a|31646 - 183 - 9 - - - 1 - 11.927 - 19 - 88.4863 - 4 - 8 - 2 - 6 - 0 - 0 - 4 - 4 - 0 - 5 - NKPYL - NLPYL - N PYL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 497 - Query_497 - M_4086 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 498 - Query_498 - M_4087 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 499 - Query_499 - M_4088 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 500 - Query_500 - M_4089 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 501 - Query_501 - M_4090 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 502 - Query_502 - M_4091 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 503 - Query_503 - M_4092 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 504 - Query_504 - M_4093 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 505 - Query_505 - M_4094 - 9 - - - 1 - gnl|BL_ORD_ID|590 - 36724|Spike glycoprotein precursor|P59594.1|SARS coronavirus|227859 - 590 - 9 - - - 1 - 13.853 - 24 - 6.48995 - 1 - 9 - 1 - 9 - 0 - 0 - 6 - 7 - 0 - 9 - LLTQRLQGL - LITGRLQSL - L+T RLQ L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 506 - Query_506 - M_4095 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 507 - Query_507 - M_4096 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 508 - Query_508 - M_4097 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 509 - Query_509 - M_4098 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 510 - Query_510 - M_4099 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 511 - Query_511 - M_4100 - 9 - - - 1 - gnl|BL_ORD_ID|55 - 4156|polyprotein|ABR25251.1|Hepatitis C virus|11103 - 55 - 9 - - - 1 - 14.2382 - 25 - 4.29054 - 5 - 9 - 2 - 6 - 0 - 0 - 4 - 5 - 0 - 5 - RHTPM - RHTPV - RHTP+ - - - - - 2 - gnl|BL_ORD_ID|958 - 62977|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 958 - 10 - - - 1 - 13.853 - 24 - 4.37925 - 5 - 9 - 3 - 7 - 0 - 0 - 4 - 5 - 0 - 5 - RHTPM - RHTPV - RHTP+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 512 - Query_512 - M_4101 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 513 - Query_513 - M_4102 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 514 - Query_514 - M_4103 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 515 - Query_515 - M_4104 - 9 - - - 1 - gnl|BL_ORD_ID|75 - 5542|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 75 - 15 - - - 1 - 12.3122 - 20 - 41.1784 - 2 - 8 - 8 - 14 - 0 - 0 - 4 - 4 - 0 - 7 - PGMRGPP - PGTSGSP - PG G P - - - - - 2 - gnl|BL_ORD_ID|748 - 48915|kaposin|AAC57155.1|Human gammaherpesvirus 8|37296 - 748 - 15 - - - 1 - 12.3122 - 20 - 46.8002 - 3 - 7 - 4 - 8 - 0 - 0 - 4 - 4 - 0 - 5 - GMRGP - GQRGP - G RGP - - - - - 3 - gnl|BL_ORD_ID|260 - 17802|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 260 - 15 - - - 1 - 12.3122 - 20 - 55.7176 - 2 - 8 - 3 - 9 - 0 - 0 - 4 - 4 - 0 - 7 - PGMRGPP - PGTSGSP - PG G P - - - - - 4 - gnl|BL_ORD_ID|1929 - 180750|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1929 - 15 - - - 1 - 12.3122 - 20 - 57.5015 - 2 - 8 - 2 - 8 - 0 - 0 - 4 - 4 - 0 - 7 - PGMRGPP - PGTSGSP - PG G P - - - - - 5 - gnl|BL_ORD_ID|1494 - 136890|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1494 - 9 - - - 1 - 11.927 - 19 - 78.9234 - 2 - 7 - 3 - 8 - 0 - 0 - 4 - 4 - 0 - 6 - PGMRGP - PGSRDP - PG R P - - - - - 6 - gnl|BL_ORD_ID|1712 - 150341|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1712 - 9 - - - 1 - 11.927 - 19 - 92.9112 - 2 - 8 - 2 - 8 - 0 - 0 - 4 - 4 - 0 - 7 - PGMRGPP - PGTSGSP - PG G P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 516 - Query_516 - M_4105 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 517 - Query_517 - M_4106 - 9 - - - 1 - gnl|BL_ORD_ID|825 - 54706|matrix protein 2-1|AAS22094.1|Human metapneumovirus|162145 - 825 - 9 - - - 1 - 14.2382 - 25 - 3.32254 - 1 - 6 - 2 - 7 - 0 - 0 - 5 - 6 - 0 - 6 - LPKEKL - LPREKL - LP+EKL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 518 - Query_518 - M_4107 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 519 - Query_519 - M_4108 - 9 - - - 1 - gnl|BL_ORD_ID|826 - 54709|protein F [Hepatitis C virus subtype 1b]|ACA50643.1|Hepatitis C virus (isolate Japanese)|11116 - 826 - 9 - - - 1 - 12.6974 - 21 - 24.2855 - 1 - 6 - 2 - 7 - 0 - 0 - 4 - 4 - 0 - 6 - LPQGRE - LPSGRN - LP GR - - - - - 2 - gnl|BL_ORD_ID|1871 - 180488|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1871 - 10 - - - 1 - 12.3122 - 20 - 41.8935 - 4 - 9 - 3 - 8 - 0 - 0 - 4 - 4 - 0 - 6 - GRESPI - GHEEPI - G E PI - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 520 - Query_520 - M_4109 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 521 - Query_521 - M_4110 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 522 - Query_522 - M_4111 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 523 - Query_523 - M_4112 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 524 - Query_524 - M_4113 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 525 - Query_525 - M_4114 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 526 - Query_526 - M_4115 - 9 - - - 1 - gnl|BL_ORD_ID|215 - 15914|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 - 215 - 15 - - - 1 - 15.0086 - 27 - 0.858443 - 1 - 8 - 8 - 15 - 0 - 0 - 4 - 8 - 0 - 8 - LQLYRFSP - VRLHRFAP - ++L+RF+P - - - - - 2 - gnl|BL_ORD_ID|767 - 51346|Genome polyprotein|P29846.3|Hepatitis C virus|11103 - 767 - 9 - - - 1 - 14.6234 - 26 - 1.62552 - 2 - 8 - 1 - 7 - 0 - 0 - 5 - 6 - 0 - 7 - QLYRFSP - QLFTFSP - QL+ FSP - - - - - 3 - gnl|BL_ORD_ID|1079 - 71616|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 1079 - 15 - - - 1 - 13.0826 - 22 - 14.3275 - 1 - 8 - 4 - 11 - 0 - 0 - 4 - 6 - 0 - 8 - LQLYRFSP - MYLYQLSP - + LY+ SP - - - - - 4 - gnl|BL_ORD_ID|1135 - 75024|Protein Tax-1|P03409.2|Human T-lymphotropic virus 1|11908 - 1135 - 9 - - - 1 - 12.6974 - 21 - 26.9236 - 3 - 8 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - LYRFSP - LYQLSP - LY+ SP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 527 - Query_527 - M_4116 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 528 - Query_528 - M_4117 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 529 - Query_529 - M_4118 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 530 - Query_530 - M_4119 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 531 - Query_531 - M_4120 - 9 - - - 1 - gnl|BL_ORD_ID|1508 - 139406|polyprotein|ACT37184.1|Hepatitis C virus|11103 - 1508 - 10 - - - 1 - 12.6974 - 21 - 34.2302 - 5 - 9 - 6 - 10 - 0 - 0 - 4 - 5 - 0 - 5 - PGPQL - PGPRL - PGP+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 532 - Query_532 - M_4121 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 533 - Query_533 - M_4122 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 534 - Query_534 - M_4123 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 535 - Query_535 - M_4124 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 536 - Query_536 - M_4125 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 537 - Query_537 - M_4126 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 538 - Query_538 - M_4127 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 539 - Query_539 - M_4128 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 540 - Query_540 - M_4129 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 541 - Query_541 - M_4130 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 542 - Query_542 - M_4131 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 543 - Query_543 - M_4132 - 9 - - - 1 - gnl|BL_ORD_ID|1077 - 71409|cysteine proteinase cruzipain (EC 3.4.22.-) - Trypanosoma cruzi|A45629|Trypanosoma cruzi|5693 - 1077 - 9 - - - 1 - 14.2382 - 25 - 3.43721 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 6 - 0 - 9 - LRLPGGSCM - VTLPTGQCL - + LP G C+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 544 - Query_544 - M_4133 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 545 - Query_545 - M_4134 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 546 - Query_546 - M_4135 - 9 - - - 1 - gnl|BL_ORD_ID|915 - 59709|polyprotein|BAD73987.1|Hepatitis C virus subtype 1b|31647 - 915 - 9 - - - 1 - 16.1642 - 30 - 0.354217 - 3 - 9 - 3 - 9 - 0 - 0 - 5 - 7 - 0 - 7 - MSDPSHI - LTDPSHI - ++DPSHI - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 547 - Query_547 - M_4136 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 548 - Query_548 - M_4137 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 549 - Query_549 - M_4138 - 9 - - - 1 - gnl|BL_ORD_ID|2045 - 184531|polyprotein|AFP27208.1|Dengue virus 4|11070 - 2045 - 10 - - - 1 - 13.0826 - 22 - 18.4997 - 3 - 8 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - PSSIET - PESLET - P S+ET - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 550 - Query_550 - M_4139 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 551 - Query_551 - M_4140 - 9 - - - 1 - gnl|BL_ORD_ID|771 - 51526|HCV-1|AAA45676.1|Hepatitis C virus|11103 - 771 - 10 - - - 1 - 13.853 - 24 - 7.36741 - 1 - 7 - 2 - 8 - 0 - 0 - 5 - 6 - 0 - 7 - LRRHRDV - LRRHIDL - LRRH D+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 552 - Query_552 - M_4141 - 9 - - - 1 - gnl|BL_ORD_ID|1435 - 116781|Nucleoprotein|P05133.1|Hantaan virus 76-118|11602 - 1435 - 15 - - - 1 - 12.3122 - 20 - 41.1784 - 1 - 7 - 1 - 7 - 0 - 0 - 4 - 6 - 0 - 7 - LRRMNSF - LRKKSSF - LR+ +SF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 553 - Query_553 - M_4142 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 554 - Query_554 - M_4143 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 555 - Query_555 - M_4144 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 556 - Query_556 - M_4145 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 557 - Query_557 - M_4146 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 558 - Query_558 - M_4147 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 559 - Query_559 - M_4148 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 560 - Query_560 - M_4149 - 9 - - - 1 - gnl|BL_ORD_ID|1698 - 149115|NS5 protein|BAA00702.1|Hepatitis C virus (isolate H77)|63746 - 1698 - 9 - - - 1 - 13.4678 - 23 - 11.9303 - 3 - 9 - 1 - 7 - 0 - 0 - 5 - 6 - 0 - 7 - SIRVRLL - SVRARLL - S+R RLL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 561 - Query_561 - M_4150 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 562 - Query_562 - M_4151 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 563 - Query_563 - M_4152 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 564 - Query_564 - M_4153 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 565 - Query_565 - M_4154 - 9 - - - 1 - gnl|BL_ORD_ID|1095 - 72301|envelope protein|YP_001527880.1|West Nile virus NY-99|10000971 - 1095 - 18 - - - 1 - 15.0086 - 27 - 1.37027 - 3 - 8 - 1 - 6 - 0 - 0 - 3 - 6 - 0 - 6 - WEYGSI - WDFGSV - W++GS+ - - - - - 2 - gnl|BL_ORD_ID|1924 - 180726|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1924 - 15 - - - 1 - 14.6234 - 26 - 2.14985 - 3 - 8 - 10 - 15 - 0 - 0 - 3 - 6 - 0 - 6 - WEYGSI - WDFGSL - W++GS+ - - - - - 3 - gnl|BL_ORD_ID|1110 - 73059|kaposin|AAC57155.1|Human gammaherpesvirus 8|37296 - 1110 - 15 - - - 1 - 13.853 - 24 - 4.45371 - 2 - 8 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - RWEYGSI - RWRLGAI - RW G+I - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 566 - Query_566 - M_4155 - 9 - - - 1 - gnl|BL_ORD_ID|418 - 25237|Transcription activator BRLF1|P03209.1|Human herpesvirus 4 strain B95-8|10377 - 418 - 15 - - - 1 - 14.2382 - 25 - 2.88535 - 1 - 9 - 7 - 15 - 0 - 0 - 5 - 6 - 0 - 9 - LRYFLKHGI - MRYVLDHLI - +RY L H I - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 567 - Query_567 - M_4156 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 568 - Query_568 - M_4157 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 569 - Query_569 - M_4158 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 570 - Query_570 - M_4159 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 571 - Query_571 - M_4160 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 572 - Query_572 - M_4161 - 9 - - - 1 - gnl|BL_ORD_ID|133 - 9415|Superoxide dismutase|P17670.1|Mycobacterium tuberculosis|1773 - 133 - 10 - - - 1 - 11.927 - 19 - 75.9314 - 3 - 9 - 1 - 7 - 0 - 0 - 2 - 4 - 0 - 7 - SLWYHTY - DMWEHAF - +W H + - - - - - 2 - gnl|BL_ORD_ID|132 - 9414|Superoxide dismutase|P17670.1|Mycobacterium tuberculosis|1773 - 132 - 9 - - - 1 - 11.927 - 19 - 91.4136 - 3 - 9 - 1 - 7 - 0 - 0 - 2 - 4 - 0 - 7 - SLWYHTY - DMWEHAF - +W H + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 573 - Query_573 - M_4162 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 574 - Query_574 - M_4163 - 9 - - - 1 - gnl|BL_ORD_ID|1265 - 98603|trans-sialidase, putative|EAN82716.1|Trypanosoma cruzi|5693 - 1265 - 9 - - - 1 - 12.3122 - 20 - 62.655 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 6 - 0 - 9 - LTDYDTRFY - VTDNNRSFY - +TD + FY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 575 - Query_575 - M_4164 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 576 - Query_576 - M_4165 - 9 - - - 1 - gnl|BL_ORD_ID|830 - 54797|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 830 - 11 - - - 1 - 14.2382 - 25 - 3.36866 - 1 - 8 - 4 - 11 - 0 - 0 - 4 - 6 - 0 - 8 - LTGLVWQR - VSGLAWTR - ++GL W R - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 577 - Query_577 - M_4166 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 578 - Query_578 - M_4167 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 579 - Query_579 - M_4168 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 580 - Query_580 - M_4169 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 581 - Query_581 - M_4170 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 582 - Query_582 - M_4171 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 583 - Query_583 - M_4172 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 584 - Query_584 - M_4173 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 585 - Query_585 - M_4174 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 586 - Query_586 - M_4175 - 9 - - - 1 - gnl|BL_ORD_ID|2125 - 186551|polyprotein|AGW21594.1|Dengue virus 1|11053 - 2125 - 10 - - - 1 - 12.3122 - 20 - 48.6895 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 6 - 0 - 8 - YEDTLYTV - YENLKYSV - YE+ Y+V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 587 - Query_587 - M_4176 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 588 - Query_588 - M_4177 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 589 - Query_589 - M_4178 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 590 - Query_590 - M_4179 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 591 - Query_591 - M_4180 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 592 - Query_592 - M_4181 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 593 - Query_593 - M_4182 - 9 - - - 1 - gnl|BL_ORD_ID|1619 - 144913|Hexon protein|P04133.3|Human adenovirus 5|28285 - 1619 - 10 - - - 1 - 14.2382 - 25 - 3.62465 - 1 - 9 - 2 - 10 - 0 - 0 - 5 - 6 - 0 - 9 - LYGHSTHDL - LYANSAHAL - LY +S H L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 594 - Query_594 - M_4183 - 9 - - - 1 - gnl|BL_ORD_ID|1177 - 79506|E1 protein|BAA19893.1|Rubella virus|11041 - 1177 - 20 - - - 1 - 13.4678 - 23 - 8.37795 - 3 - 9 - 4 - 10 - 0 - 0 - 4 - 4 - 0 - 7 - HRDLAKW - HSDAACW - H D A W - - - - - 2 - gnl|BL_ORD_ID|1384 - 110205|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1384 - 32 - - - 1 - 10.7714 - 16 - 223.475 - 2 - 9 - 6 - 13 - 0 - 0 - 2 - 4 - 0 - 8 - YHRDLAKW - FHNIRGRW - +H +W - - - - - 3 - gnl|BL_ORD_ID|1395 - 110394|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1395 - 32 - - - 1 - 10.7714 - 16 - 260.809 - 2 - 9 - 24 - 31 - 0 - 0 - 2 - 4 - 0 - 8 - YHRDLAKW - FHNIRGRW - +H +W - - - - - 4 - gnl|BL_ORD_ID|1385 - 110215|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1385 - 25 - - - 1 - 10.7714 - 16 - 308.682 - 2 - 9 - 12 - 19 - 0 - 0 - 2 - 4 - 0 - 8 - YHRDLAKW - FHNIRGRW - +H +W - - - - - 5 - gnl|BL_ORD_ID|1822 - 178247|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1822 - 15 - - - 1 - 10.3862 - 15 - 443.083 - 2 - 9 - 8 - 15 - 0 - 0 - 2 - 4 - 0 - 8 - YHRDLAKW - FHNIRGRW - +H +W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 595 - Query_595 - M_4184 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 596 - Query_596 - M_4185 - 9 - - - 1 - gnl|BL_ORD_ID|1299 - 103563|polyprotein|BAB18806.1|Hepatitis C virus|11103 - 1299 - 9 - - - 1 - 11.927 - 19 - 114.611 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 4 - 0 - 7 - PDINNPF - PDYNPPL - PD N P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 597 - Query_597 - M_4186 - 9 - - - 1 - gnl|BL_ORD_ID|486 - 30815|Genome polyprotein|P26662.3|Hepatitis C virus|11103 - 486 - 9 - - - 1 - 13.4678 - 23 - 13.2439 - 2 - 7 - 2 - 7 - 0 - 0 - 4 - 6 - 0 - 6 - YPPSLP - FPPALP - +PP+LP - - - - - 2 - gnl|BL_ORD_ID|1882 - 180538|Nonstructural protein NS2B|NP_739586.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1882 - 15 - - - 1 - 12.6974 - 21 - 21.7795 - 1 - 7 - 4 - 10 - 0 - 0 - 4 - 6 - 0 - 7 - LYPPSLP - LFPVSIP - L+P S+P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 598 - Query_598 - M_4187 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 599 - Query_599 - M_4188 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 600 - Query_600 - M_4189 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 601 - Query_601 - M_4190 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 602 - Query_602 - M_4191 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 603 - Query_603 - M_4192 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 604 - Query_604 - M_4193 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 605 - Query_605 - M_4194 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 606 - Query_606 - M_4195 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 607 - Query_607 - M_4196 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 608 - Query_608 - M_4197 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 609 - Query_609 - M_4198 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 610 - Query_610 - M_4199 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 611 - Query_611 - M_4200 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 612 - Query_612 - M_4201 - 9 - - - 1 - gnl|BL_ORD_ID|259 - 17620|Early antigen protein D|P03191.1|Human herpesvirus 4 strain B95-8|10377 - 259 - 15 - - - 1 - 13.853 - 24 - 5.11701 - 1 - 9 - 4 - 12 - 0 - 0 - 4 - 6 - 0 - 9 - MAYSITCPI - LAYGRTCVL - +AY TC + - - - - - 2 - gnl|BL_ORD_ID|258 - 17619|Early antigen protein D|P03191.1|Human herpesvirus 4 strain B95-8|10377 - 258 - 14 - - - 1 - 13.853 - 24 - 5.3697 - 1 - 9 - 4 - 12 - 0 - 0 - 4 - 6 - 0 - 9 - MAYSITCPI - LAYGRTCVL - +AY TC + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 613 - Query_613 - M_4202 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 614 - Query_614 - M_4203 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 615 - Query_615 - M_4204 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 616 - Query_616 - M_4205 - 9 - - - 1 - gnl|BL_ORD_ID|1355 - 108148|polyprotein|AAF65953.1|Hepatitis C virus|11103 - 1355 - 10 - - - 1 - 13.0826 - 22 - 20.8706 - 3 - 9 - 1 - 7 - 0 - 0 - 5 - 6 - 0 - 7 - ATDYTTI - STDSTTI - +TD TTI - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 617 - Query_617 - M_4206 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 618 - Query_618 - M_4207 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 619 - Query_619 - M_4208 - 9 - - - 1 - gnl|BL_ORD_ID|306 - 20686|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 - 306 - 11 - - - 1 - 14.2382 - 25 - 3.14502 - 2 - 6 - 1 - 5 - 0 - 0 - 5 - 5 - 0 - 5 - GKSTH - GKSTH - GKSTH - - - - - 2 - gnl|BL_ORD_ID|256 - 17278|Genome polyprotein|P06441.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 256 - 20 - - - 1 - 13.853 - 24 - 5.14963 - 2 - 8 - 7 - 13 - 0 - 0 - 5 - 6 - 0 - 7 - GKSTHTS - GESRHTS - G+S HTS - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 620 - Query_620 - M_4209 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 621 - Query_621 - M_4210 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 622 - Query_622 - M_4211 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 623 - Query_623 - M_4212 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 624 - Query_624 - M_4213 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 625 - Query_625 - M_4214 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 626 - Query_626 - M_4215 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 627 - Query_627 - M_4216 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 628 - Query_628 - M_4217 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 629 - Query_629 - M_4218 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 630 - Query_630 - M_4219 - 9 - - - 1 - gnl|BL_ORD_ID|114 - 7660|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 - 114 - 20 - - - 1 - 11.1566 - 17 - 164.091 - 1 - 9 - 6 - 14 - 0 - 0 - 3 - 5 - 0 - 9 - MLCFYTPAL - LMCAVHPTL - ++C P L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 631 - Query_631 - M_4220 - 9 - - - 1 - gnl|BL_ORD_ID|654 - 38724|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 654 - 20 - - - 1 - 14.2382 - 25 - 2.55563 - 1 - 9 - 11 - 19 - 0 - 0 - 4 - 6 - 0 - 9 - MLHLYPGPM - LFQLYRGPL - + LY GP+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 632 - Query_632 - M_4221 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 633 - Query_633 - M_4222 - 9 - - - 1 - gnl|BL_ORD_ID|2303 - 422997|preC/core protein|CAJ33968.1|Hepatitis B virus|10407 - 2303 - 9 - - - 1 - 14.6234 - 26 - 2.11355 - 3 - 8 - 3 - 8 - 0 - 0 - 6 - 6 - 0 - 6 - LMNLAT - LMNLAT - LMNLAT - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 634 - Query_634 - M_4223 - 9 - - - 1 - gnl|BL_ORD_ID|690 - 41971|putative D-ribose-binding protein|NP_301386.1|Mycobacterium leprae|1769 - 690 - 15 - - - 1 - 10.001 - 14 - 757.359 - 1 - 8 - 1 - 8 - 0 - 0 - 5 - 6 - 0 - 8 - MLLSILLP - MLILGLLP - ML+ LLP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 635 - Query_635 - M_4224 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 636 - Query_636 - M_4225 - 9 - - - 1 - gnl|BL_ORD_ID|629 - 37607|kaposin|AAC57155.1|Human gammaherpesvirus 8|37296 - 629 - 9 - - - 1 - 11.5418 - 18 - 124.163 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 6 - 0 - 9 - MLNKVLYRL - LLNGWRWRL - +LN +RL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 637 - Query_637 - M_4226 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 638 - Query_638 - M_4227 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 639 - Query_639 - M_4228 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 640 - Query_640 - M_4229 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 641 - Query_641 - M_4230 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 642 - Query_642 - M_4231 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 643 - Query_643 - M_4232 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 644 - Query_644 - M_4233 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 645 - Query_645 - M_4234 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 646 - Query_646 - M_4235 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 647 - Query_647 - M_4236 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 648 - Query_648 - M_4237 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 649 - Query_649 - M_4238 - 9 - - - 1 - gnl|BL_ORD_ID|1938 - 180802|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1938 - 9 - - - 1 - 13.853 - 24 - 4.92244 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 6 - 0 - 8 - MPLLKLSC - VPLLAIGC - +PLL + C - - - - - 2 - gnl|BL_ORD_ID|1939 - 180803|polyprotein|AFP27208.1|Dengue virus 4|11070 - 1939 - 9 - - - 1 - 13.853 - 24 - 6.71897 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 6 - 0 - 8 - MPLLKLSC - VPLLAMGC - +PLL + C - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 650 - Query_650 - M_4239 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 651 - Query_651 - M_4240 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 652 - Query_652 - M_4241 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 653 - Query_653 - M_4242 - 9 - - - 1 - gnl|BL_ORD_ID|575 - 36306|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 - 575 - 15 - - - 1 - 14.6234 - 26 - 2.07692 - 1 - 8 - 4 - 11 - 0 - 0 - 4 - 5 - 0 - 8 - MRCQYETV - MNCSYENM - M C YE + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 654 - Query_654 - M_4243 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 655 - Query_655 - M_4244 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 656 - Query_656 - M_4245 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 657 - Query_657 - M_4246 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 658 - Query_658 - M_4247 - 9 - - - 1 - gnl|BL_ORD_ID|409 - 24765|polyprotein [Hepatitis C virus]|ABR27360.1|Hepatitis C virus|11103 - 409 - 9 - - - 1 - 13.853 - 24 - 6.37844 - 3 - 9 - 3 - 9 - 0 - 0 - 3 - 7 - 0 - 7 - RRQCEEV - KKKCDEV - +++C+EV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 659 - Query_659 - M_4248 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 660 - Query_660 - M_4249 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 661 - Query_661 - M_4250 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 662 - Query_662 - M_4251 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 663 - Query_663 - M_4252 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 664 - Query_664 - M_4253 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 665 - Query_665 - M_4254 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 666 - Query_666 - M_4255 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 667 - Query_667 - M_4256 - 9 - - - 1 - gnl|BL_ORD_ID|2051 - 184702|non-structural protein 1|AGM49312.1|Dengue virus|12637 - 2051 - 9 - - - 1 - 11.5418 - 18 - 130.247 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 6 - 0 - 9 - MWPLHWSMW - LWPKTHTLW - +WP ++W - - - - - 2 - gnl|BL_ORD_ID|2310 - 423016|NS5A|ACX46481.1|Hepatitis C virus genotype 1|41856 - 2310 - 9 - - - 1 - 11.1566 - 17 - 296.302 - 2 - 9 - 2 - 9 - 0 - 0 - 3 - 5 - 0 - 8 - WPLHWSMW - FPLAMPVW - +PL +W - - - - - 3 - gnl|BL_ORD_ID|664 - 39591|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 - 664 - 20 - - - 1 - 10.7714 - 16 - 334.087 - 4 - 9 - 9 - 14 - 0 - 0 - 2 - 4 - 0 - 6 - LHWSMW - ISWCLW - + W +W - - - - - 4 - gnl|BL_ORD_ID|2312 - 423020|polyprotein|ACE82359.1|Hepatitis C virus genotype 1|41856 - 2312 - 9 - - - 1 - 10.7714 - 16 - 365.422 - 4 - 9 - 4 - 9 - 0 - 0 - 2 - 4 - 0 - 6 - LHWSMW - ISWCLW - + W +W - - - - - 5 - gnl|BL_ORD_ID|1120 - 74387|Genome polyprotein|P26664.3|Hepatitis C virus (isolate 1)|11104 - 1120 - 9 - - - 1 - 10.3862 - 15 - 504.867 - 4 - 9 - 2 - 7 - 0 - 0 - 2 - 4 - 0 - 6 - LHWSMW - ISWCLW - + W +W - - - - - 6 - gnl|BL_ORD_ID|1119 - 74386|HCV-1|AAA45676.1|Hepatitis C virus|11103 - 1119 - 8 - - - 1 - 10.7714 - 16 - 530.711 - 4 - 9 - 2 - 7 - 0 - 0 - 2 - 4 - 0 - 6 - LHWSMW - ISWCLW - + W +W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 668 - Query_668 - M_4257 - 9 - - - 1 - gnl|BL_ORD_ID|1186 - 93431|pre-C/C protein|ABY54138.1|Hepatitis B virus|10407 - 1186 - 20 - - - 1 - 11.927 - 19 - 74.4218 - 3 - 8 - 7 - 12 - 0 - 0 - 3 - 5 - 0 - 6 - CLMLQC - CLIISC - CL++ C - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 669 - Query_669 - M_4258 - 9 - - - 1 - gnl|BL_ORD_ID|621 - 37466|surface antigen|BAF44879.1|Hepatitis B virus|10407 - 621 - 9 - - - 1 - 12.6974 - 21 - 28.8346 - 1 - 8 - 2 - 9 - 0 - 0 - 3 - 7 - 0 - 8 - MYCMVFLV - LLCLIFLL - + C++FL+ - - - - - 2 - gnl|BL_ORD_ID|596 - 37120|Major surface antigen precursor|P17399.3|Hepatitis B virus|10407 - 596 - 9 - - - 1 - 12.6974 - 21 - 33.6262 - 1 - 8 - 1 - 8 - 0 - 0 - 3 - 7 - 0 - 8 - MYCMVFLV - LLCLIFLL - + C++FL+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 670 - Query_670 - M_4259 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 671 - Query_671 - M_4260 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 672 - Query_672 - M_4261 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 673 - Query_673 - M_4262 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 674 - Query_674 - M_4263 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 675 - Query_675 - M_4264 - 9 - - - 1 - gnl|BL_ORD_ID|889 - 58463|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 889 - 20 - - - 1 - 12.6974 - 21 - 25.6057 - 1 - 7 - 11 - 17 - 0 - 0 - 4 - 6 - 0 - 7 - MYSYAVP - IYVYALP - +Y YA+P - - - - - 2 - gnl|BL_ORD_ID|338 - 21242|polymerase|ACF94272.1|Hepatitis B virus|10407 - 338 - 9 - - - 1 - 12.3122 - 20 - 45.611 - 1 - 7 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - MYSYAVP - LYSSTVP - +YS VP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 676 - Query_676 - M_4265 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 677 - Query_677 - M_4266 - 9 - - - 1 - gnl|BL_ORD_ID|557 - 34304|Gag polyprotein|P88150|Human immunodeficiency virus 1|11676 - 557 - 14 - - - 1 - 13.0826 - 22 - 17.8721 - 1 - 7 - 8 - 14 - 0 - 0 - 4 - 6 - 0 - 7 - NEILRRY - NKIVRMY - N+I+R Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 678 - Query_678 - M_4267 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 679 - Query_679 - M_4268 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 680 - Query_680 - M_4269 - 9 - - - 1 - gnl|BL_ORD_ID|1132 - 74886|latent membrane protein 1|AAS99606.1|Human gammaherpesvirus 4|10376 - 1132 - 9 - - - 1 - 12.6974 - 21 - 31.9494 - 5 - 9 - 5 - 9 - 0 - 0 - 3 - 4 - 0 - 5 - NWWPI - NWWTL - NWW + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 681 - Query_681 - M_4270 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 682 - Query_682 - M_4271 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 683 - Query_683 - M_4272 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 684 - Query_684 - M_4273 - 9 - - - 1 - gnl|BL_ORD_ID|715 - 44133|Genome polyprotein|P26664.3|Hepatitis C virus genotype 1|41856 - 715 - 9 - - - 1 - 11.927 - 19 - 69.1936 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 5 - 0 - 9 - NHSDLAAEL - NHDSPDAEL - NH AEL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 685 - Query_685 - M_4274 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 686 - Query_686 - M_4275 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 687 - Query_687 - M_4276 - 9 - - - 1 - gnl|BL_ORD_ID|1219 - 96898|Genome polyprotein|SRC279960|Hepatitis C virus|11103 - 1219 - 17 - - - 1 - 13.853 - 24 - 4.23286 - 1 - 8 - 7 - 14 - 0 - 0 - 5 - 6 - 0 - 8 - NIVYHTAS - NLVYSTTS - N+VY T S - - - - - 2 - gnl|BL_ORD_ID|1218 - 96897|polyprotein|ABR25251.1|Hepatitis C virus (isolate H77)|63746 - 1218 - 17 - - - 1 - 13.853 - 24 - 5.7721 - 1 - 8 - 7 - 14 - 0 - 0 - 5 - 6 - 0 - 8 - NIVYHTAS - NLVYSTTS - N+VY T S - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 688 - Query_688 - M_4277 - 9 - - - 1 - gnl|BL_ORD_ID|487 - 30892|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 487 - 9 - - - 1 - 14.6234 - 26 - 1.76369 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 6 - 0 - 9 - NIYSRIREY - KFYSKISEY - YS+I EY - - - - - 2 - gnl|BL_ORD_ID|1400 - 110467|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1400 - 25 - - - 1 - 14.6234 - 26 - 2.69562 - 2 - 9 - 16 - 23 - 0 - 0 - 5 - 6 - 0 - 8 - IYSRIREY - FYSKISEY - YS+I EY - - - - - 3 - gnl|BL_ORD_ID|1387 - 110227|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1387 - 33 - - - 1 - 14.2382 - 25 - 3.62324 - 1 - 9 - 22 - 30 - 0 - 0 - 5 - 6 - 0 - 9 - NIYSRIREY - KFYSKISEY - YS+I EY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 689 - Query_689 - M_4278 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 690 - Query_690 - M_4279 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 691 - Query_691 - M_4280 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 692 - Query_692 - M_4281 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 693 - Query_693 - M_4282 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 694 - Query_694 - M_4283 - 9 - - - 1 - gnl|BL_ORD_ID|1300 - 103654|polyprotein|BAB18806.1|Hepatitis C virus|11103 - 1300 - 9 - - - 1 - 12.6974 - 21 - 26.0147 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - NLMAKN - TIMAKN - +MAKN - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 695 - Query_695 - M_4284 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 696 - Query_696 - M_4285 - 9 - - - 1 - gnl|BL_ORD_ID|21 - 1356|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 21 - 15 - - - 1 - 14.6234 - 26 - 1.63256 - 1 - 8 - 5 - 12 - 0 - 0 - 4 - 6 - 0 - 8 - NLPSKRVS - NVPYKRIE - N+P KR+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 697 - Query_697 - M_4286 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 698 - Query_698 - M_4287 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 699 - Query_699 - M_4288 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 700 - Query_700 - M_4289 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 701 - Query_701 - M_4290 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 702 - Query_702 - M_4291 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 703 - Query_703 - M_4292 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 704 - Query_704 - M_4293 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 705 - Query_705 - M_4294 - 9 - - - 1 - gnl|BL_ORD_ID|540 - 32998|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 - 540 - 11 - - - 1 - 13.4678 - 23 - 12.17 - 2 - 7 - 6 - 11 - 0 - 0 - 4 - 6 - 0 - 6 - RLDLVR - RVDMVR - R+D+VR - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 706 - Query_706 - M_4295 - 9 - - - 1 - gnl|BL_ORD_ID|1406 - 110846|E6 protein|CAB45108.1|Human papillomavirus type 16|333760 - 1406 - 9 - - - 1 - 13.853 - 24 - 6.71897 - 2 - 8 - 3 - 9 - 0 - 0 - 4 - 6 - 0 - 7 - RNYCVSV - RHYCYSL - R+YC S+ - - - - - 2 - gnl|BL_ORD_ID|855 - 55779|fusion protein|BAB60865.1|Measles virus|11234 - 855 - 9 - - - 1 - 11.5418 - 18 - 175.774 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 5 - 0 - 8 - RNYCVSVY - RRYPDAVY - R Y +VY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 707 - Query_707 - M_4296 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 708 - Query_708 - M_4297 - 9 - - - 1 - gnl|BL_ORD_ID|958 - 62977|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 958 - 10 - - - 1 - 13.853 - 24 - 4.37925 - 4 - 8 - 3 - 7 - 0 - 0 - 4 - 5 - 0 - 5 - RHTPM - RHTPV - RHTP+ - - - - - 2 - gnl|BL_ORD_ID|55 - 4156|polyprotein|ABR25251.1|Hepatitis C virus|11103 - 55 - 9 - - - 1 - 13.853 - 24 - 4.51705 - 4 - 8 - 2 - 6 - 0 - 0 - 4 - 5 - 0 - 5 - RHTPM - RHTPV - RHTP+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 709 - Query_709 - M_4298 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 710 - Query_710 - M_4299 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 711 - Query_711 - M_4300 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 712 - Query_712 - M_4301 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 713 - Query_713 - M_4302 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 714 - Query_714 - M_4303 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 715 - Query_715 - M_4304 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 716 - Query_716 - M_4305 - 9 - - - 1 - gnl|BL_ORD_ID|1125 - 74605|Circumsporozoite protein precursor|P08677.2|Plasmodium vivax strain Belem|31273 - 1125 - 9 - - - 1 - 15.3938 - 28 - 0.735125 - 2 - 8 - 1 - 7 - 0 - 0 - 5 - 7 - 0 - 7 - YLEKVRS - YLDKVRA - YL+KVR+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 717 - Query_717 - M_4306 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 718 - Query_718 - M_4307 - 9 - - - 1 - gnl|BL_ORD_ID|416 - 25149|polyprotein|BAD73994.1|Hepatitis C virus subtype 1b|31647 - 416 - 9 - - - 1 - 14.6234 - 26 - 2.07889 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 6 - 0 - 6 - NYSPRP - HYAPRP - +Y+PRP - - - - - 2 - gnl|BL_ORD_ID|1551 - 141226|tegument protein UL37|ADD60080.1|Human alphaherpesvirus 1|10298 - 1551 - 9 - - - 1 - 13.853 - 24 - 5.84954 - 2 - 7 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - YSPRPI - YLPRPV - Y PRP+ - - - - - 3 - gnl|BL_ORD_ID|2240 - 230030|Nef protein|BAA86664.1|Human immunodeficiency virus 1|11676 - 2240 - 10 - - - 1 - 13.4678 - 23 - 7.76238 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - NYSPRP - NYTPGP - NY+P P - - - - - 4 - gnl|BL_ORD_ID|2238 - 230028|Protein Nef|P04603.3|Human immunodeficiency virus 1|11676 - 2238 - 10 - - - 1 - 13.4678 - 23 - 7.89871 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - NYSPRP - NYTPGP - NY+P P - - - - - 5 - gnl|BL_ORD_ID|2239 - 230029|Protein Nef|P03404.4|Human immunodeficiency virus 1|11676 - 2239 - 10 - - - 1 - 13.4678 - 23 - 9.73455 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - NYSPRP - NYTPGP - NY+P P - - - - - 6 - gnl|BL_ORD_ID|1011 - 67349|Latent membrane protein 2|Q69135|Human gammaherpesvirus 4|10376 - 1011 - 9 - - - 1 - 11.927 - 19 - 92.9112 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 5 - 0 - 9 - NYSPRPICV - TYGPVFMCL - Y P +C+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 719 - Query_719 - M_4308 - 9 - - - 1 - gnl|BL_ORD_ID|150 - 11063|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 150 - 15 - - - 1 - 14.2382 - 25 - 4.08331 - 1 - 9 - 7 - 15 - 0 - 0 - 5 - 6 - 0 - 9 - PASTLSLGY - PASIAARGY - PAS + GY - - - - - 2 - gnl|BL_ORD_ID|1855 - 180408|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1855 - 10 - - - 1 - 13.853 - 24 - 4.61192 - 1 - 9 - 2 - 10 - 0 - 0 - 5 - 6 - 0 - 9 - PASTLSLGY - PASIAARGY - PAS + GY - - - - - 3 - gnl|BL_ORD_ID|1639 - 146285|polyprotein|ADF97231.1|Hepatitis C virus subtype 3a|356426 - 1639 - 18 - - - 1 - 13.4678 - 23 - 11.4723 - 1 - 9 - 7 - 15 - 0 - 0 - 4 - 7 - 0 - 9 - PASTLSLGY - PAAYVAQGY - PA+ ++ GY - - - - - 4 - gnl|BL_ORD_ID|1638 - 146284|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 - 1638 - 18 - - - 1 - 12.3122 - 20 - 44.435 - 1 - 9 - 7 - 15 - 0 - 0 - 4 - 6 - 0 - 9 - PASTLSLGY - PAAYAAQGY - PA+ + GY - - - - - 5 - gnl|BL_ORD_ID|737 - 46755|HCV-1|AAA45676.1|Hepatitis C virus genotype 1|41856 - 737 - 20 - - - 1 - 11.927 - 19 - 58.6701 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 6 - 0 - 9 - PASTLSLGY - PAAYAAQGY - PA+ + GY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 720 - Query_720 - M_4309 - 9 - - - 1 - gnl|BL_ORD_ID|636 - 37919|envelope protein|BAF48755.1|Hepatitis B virus|10407 - 636 - 10 - - - 1 - 12.3122 - 20 - 47.0941 - 1 - 6 - 4 - 9 - 0 - 0 - 3 - 4 - 0 - 6 - PFPRWL - PFVQWF - PF +W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 721 - Query_721 - M_4310 - 9 - - - 1 - gnl|BL_ORD_ID|1174 - 79351|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 1174 - 17 - - - 1 - 12.6974 - 21 - 34.1537 - 3 - 8 - 7 - 12 - 0 - 0 - 3 - 4 - 0 - 6 - WASSIV - WGGSVV - W S+V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 722 - Query_722 - M_4311 - 9 - - - 1 - gnl|BL_ORD_ID|747 - 48896|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 - 747 - 15 - - - 1 - 13.853 - 24 - 4.22764 - 1 - 6 - 4 - 9 - 0 - 0 - 4 - 4 - 0 - 6 - PHYDFE - PEYDLE - P YD E - - - - - 2 - gnl|BL_ORD_ID|619 - 37398|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 - 619 - 10 - - - 1 - 13.853 - 24 - 7.36741 - 2 - 7 - 3 - 8 - 0 - 0 - 4 - 5 - 0 - 6 - HYDFER - HTDFEQ - H DFE+ - - - - - 3 - gnl|BL_ORD_ID|581 - 36432|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 - 581 - 9 - - - 1 - 13.4678 - 23 - 8.56958 - 2 - 7 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - HYDFER - HTDFEQ - H DFE+ - - - - - 4 - gnl|BL_ORD_ID|618 - 37397|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 - 618 - 9 - - - 1 - 13.4678 - 23 - 8.72003 - 2 - 7 - 3 - 8 - 0 - 0 - 4 - 5 - 0 - 6 - HYDFER - HTDFEQ - H DFE+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 723 - Query_723 - M_4312 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 724 - Query_724 - M_4313 - 9 - - - 1 - gnl|BL_ORD_ID|798 - 53148|Transcription activator BRLF1|P03209.1|Human herpesvirus 4 strain B95-8|10377 - 798 - 15 - - - 1 - 13.4678 - 23 - 12.0936 - 1 - 6 - 8 - 13 - 0 - 0 - 4 - 4 - 0 - 6 - PRIGYS - PRASYS - PR YS - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 725 - Query_725 - M_4314 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 726 - Query_726 - M_4315 - 9 - - - 1 - gnl|BL_ORD_ID|854 - 55744|polyprotein precursor|NP_041724.2|West Nile virus|11082 - 854 - 9 - - - 1 - 14.2382 - 25 - 3.74233 - 2 - 9 - 2 - 9 - 0 - 0 - 5 - 7 - 0 - 8 - RNRKPLTV - RSRRSLTV - R+R+ LTV - - - - - 2 - gnl|BL_ORD_ID|1181 - 88849|IE62|AAP32859.1|Human alphaherpesvirus 3|10335 - 1181 - 9 - - - 1 - 13.853 - 24 - 7.20201 - 1 - 7 - 3 - 9 - 0 - 0 - 4 - 6 - 0 - 7 - PRNRKPL - PRSRTPI - PR+R P+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 727 - Query_727 - M_4316 - 9 - - - 1 - gnl|BL_ORD_ID|381 - 23566|tegument protein UL7|NP_044476.1|Human alphaherpesvirus 2|10310 - 381 - 13 - - - 1 - 13.4678 - 23 - 10.7509 - 5 - 9 - 9 - 13 - 0 - 0 - 5 - 5 - 0 - 5 - RCLLL - RCLLL - RCLLL - - - - - 2 - gnl|BL_ORD_ID|1731 - 150556|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1731 - 10 - - - 1 - 12.6974 - 21 - 26.5293 - 3 - 7 - 5 - 9 - 0 - 0 - 4 - 4 - 0 - 5 - PSRCL - PRRCL - P RCL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 728 - Query_728 - M_4317 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 729 - Query_729 - M_4318 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 730 - Query_730 - M_4319 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 731 - Query_731 - M_4320 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 732 - Query_732 - M_4321 - 9 - - - 1 - gnl|BL_ORD_ID|889 - 58463|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 889 - 20 - - - 1 - 12.6974 - 21 - 33.9105 - 1 - 9 - 4 - 12 - 0 - 0 - 5 - 5 - 0 - 9 - PSQPANSFY - PSQEPMSIY - PSQ S Y - - - - - 2 - gnl|BL_ORD_ID|749 - 49485|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 749 - 11 - - - 1 - 12.3122 - 20 - 50.6074 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 5 - 0 - 9 - PSQPANSFY - PSQEPMSIY - PSQ S Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 733 - Query_733 - M_4322 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 734 - Query_734 - M_4323 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 735 - Query_735 - M_4324 - 9 - - - 1 - gnl|BL_ORD_ID|1569 - 141354|transcriptional regulator ICP4|NP_044662.1|Human alphaherpesvirus 1|10298 - 1569 - 10 - - - 1 - 13.4678 - 23 - 8.46851 - 2 - 7 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - YPETPP - YPDAPP - YP+ PP - - - - - 2 - gnl|BL_ORD_ID|1759 - 154346|RL2|CAB06760.1|Human alphaherpesvirus 2|10310 - 1759 - 15 - - - 1 - 12.3122 - 20 - 59.339 - 3 - 8 - 8 - 13 - 0 - 0 - 4 - 4 - 0 - 6 - PETPPR - PRTAPR - P T PR - - - - - 3 - gnl|BL_ORD_ID|1438 - 120093|unnamed protein product|CAA33016.1|Rubella virus|11041 - 1438 - 21 - - - 1 - 10.001 - 14 - 777.216 - 1 - 6 - 11 - 16 - 0 - 0 - 4 - 4 - 0 - 6 - PYPETP - PPPATP - P P TP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 736 - Query_736 - M_4325 - 9 - - - 1 - gnl|BL_ORD_ID|1000 - 65810|sporozoite surface protein 2|NP_705260.1|Plasmodium falciparum 3D7|36329 - 1000 - 10 - - - 1 - 13.4678 - 23 - 8.61729 - 1 - 6 - 2 - 7 - 0 - 0 - 4 - 4 - 0 - 6 - PYQGRP - PYAGEP - PY G P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 737 - Query_737 - M_4326 - 9 - - - 1 - gnl|BL_ORD_ID|1000 - 65810|sporozoite surface protein 2|NP_705260.1|Plasmodium falciparum 3D7|36329 - 1000 - 10 - - - 1 - 13.4678 - 23 - 8.61729 - 1 - 6 - 2 - 7 - 0 - 0 - 4 - 4 - 0 - 6 - PYQGRP - PYAGEP - PY G P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 738 - Query_738 - M_4327 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 739 - Query_739 - M_4328 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 740 - Query_740 - M_4329 - 9 - - - 1 - gnl|BL_ORD_ID|601 - 37153|Nuclear antigen EBNA-3C|Q69140.1|Human gammaherpesvirus 4|10376 - 601 - 10 - - - 1 - 13.0826 - 22 - 14.2707 - 4 - 9 - 5 - 10 - 0 - 0 - 4 - 6 - 0 - 6 - VKFIGV - VRFMGV - V+F+GV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 741 - Query_741 - M_4330 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 742 - Query_742 - M_4331 - 9 - - - 1 - gnl|BL_ORD_ID|792 - 53027|nonstructural protein 3|NP_722463.1|Dengue virus 1 Singapore/S275/1990|33741 - 792 - 9 - - - 1 - 11.1566 - 17 - 254.603 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 5 - 0 - 9 - QFSFDGWKF - QYSDRRWCF - Q+S W F - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 743 - Query_743 - M_4332 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 744 - Query_744 - M_4333 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 745 - Query_745 - M_4334 - 9 - - - 1 - gnl|BL_ORD_ID|1813 - 177701|polyprotein|ACZ60104.1|Hepatitis C virus subtype 3a|356426 - 1813 - 18 - - - 1 - 15.3938 - 28 - 0.691719 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 6 - 0 - 9 - QHDFCGLYM - KAKICGLYL - + CGLY+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 746 - Query_746 - M_4335 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 747 - Query_747 - M_4336 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 748 - Query_748 - M_4337 - 9 - - - 1 - gnl|BL_ORD_ID|1563 - 141306|tegument host shutoff protein|NP_044643.1|Human alphaherpesvirus 1|10298 - 1563 - 10 - - - 1 - 13.853 - 24 - 5.48318 - 2 - 6 - 5 - 9 - 0 - 0 - 4 - 5 - 0 - 5 - HPNNS - HPNNT - HPNN+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 749 - Query_749 - M_4338 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 750 - Query_750 - M_4339 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 751 - Query_751 - M_4340 - 9 - - - 1 - gnl|BL_ORD_ID|1271 - 101673|gag protein|ABO73990.1|Human immunodeficiency virus 1|11676 - 1271 - 9 - - - 1 - 11.927 - 19 - 71.5135 - 2 - 7 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - HYAALQ - HQAAMQ - H AA+Q - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 752 - Query_752 - M_4341 - 9 - - - 1 - gnl|BL_ORD_ID|1257 - 98253|trans-sialidase, putative|EAN81042.1|Trypanosoma cruzi|5693 - 1257 - 9 - - - 1 - 14.6234 - 26 - 1.57352 - 2 - 9 - 1 - 8 - 0 - 0 - 6 - 8 - 0 - 8 - ILSRVAAL - MLSRVAAV - +LSRVAA+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 753 - Query_753 - M_4342 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 754 - Query_754 - M_4343 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 755 - Query_755 - M_4344 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 756 - Query_756 - M_4345 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 757 - Query_757 - M_4346 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 758 - Query_758 - M_4347 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 759 - Query_759 - M_4348 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 760 - Query_760 - M_4349 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 761 - Query_761 - M_4350 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 762 - Query_762 - M_4351 - 9 - - - 1 - gnl|BL_ORD_ID|1323 - 107790|polyprotein|AAD56189.1|Hepatitis C virus|11103 - 1323 - 10 - - - 1 - 12.6974 - 21 - 37.8768 - 3 - 8 - 4 - 9 - 0 - 0 - 4 - 4 - 0 - 6 - MCRICH - MCDECH - MC CH - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 763 - Query_763 - M_4352 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 764 - Query_764 - M_4353 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 765 - Query_765 - M_4354 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 766 - Query_766 - M_4355 - 9 - - - 1 - gnl|BL_ORD_ID|191 - 14101|envelope glycoprotein|ABI16336.1|Human immunodeficiency virus 1|11676 - 191 - 9 - - - 1 - 12.6974 - 21 - 30.8766 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 7 - 0 - 9 - QRFLNVQEL - ERYLKDQQL - +R+L Q+L - - - - - 2 - gnl|BL_ORD_ID|864 - 56574|envelope glycoprotein|ABI16336.1|Human immunodeficiency virus 1|11676 - 864 - 9 - - - 1 - 11.927 - 19 - 69.1936 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 6 - 0 - 8 - RFLNVQEL - RYLKDQQL - R+L Q+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 767 - Query_767 - M_4356 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 768 - Query_768 - M_4357 - 9 - - - 1 - gnl|BL_ORD_ID|1114 - 73862|EBNA-1 protein|Q777E1|Human gammaherpesvirus 4|10376 - 1114 - 15 - - - 1 - 13.0826 - 22 - 16.3955 - 1 - 9 - 7 - 15 - 0 - 0 - 4 - 5 - 0 - 9 - QRHGFGEEI - QTHIFAEVL - Q H F E + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 769 - Query_769 - M_4358 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 770 - Query_770 - M_4359 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 771 - Query_771 - M_4360 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 772 - Query_772 - M_4361 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 773 - Query_773 - M_4362 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 774 - Query_774 - M_4363 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 775 - Query_775 - M_4364 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 776 - Query_776 - M_4365 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 777 - Query_777 - M_4366 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 778 - Query_778 - M_4367 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 779 - Query_779 - M_4368 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 780 - Query_780 - M_4369 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 781 - Query_781 - M_4370 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 782 - Query_782 - M_4371 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 783 - Query_783 - M_4372 - 9 - - - 1 - gnl|BL_ORD_ID|1674 - 148619|unnamed protein product|BAA14233.1|Hepatitis C virus|11103 - 1674 - 45 - - - 1 - 11.927 - 19 - 52.3928 - 2 - 9 - 35 - 42 - 0 - 0 - 3 - 5 - 0 - 8 - TCKANLCY - TCVNGVCW - TC +C+ - - - - - 2 - gnl|BL_ORD_ID|1632 - 146246|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 - 1632 - 17 - - - 1 - 11.927 - 19 - 83.9093 - 2 - 9 - 4 - 11 - 0 - 0 - 3 - 5 - 0 - 8 - TCKANLCY - TCVNGVCW - TC +C+ - - - - - 3 - gnl|BL_ORD_ID|66 - 4910|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 66 - 20 - - - 1 - 11.927 - 19 - 86.1921 - 2 - 9 - 2 - 9 - 0 - 0 - 3 - 5 - 0 - 8 - TCKANLCY - TCINGVCW - TC +C+ - - - - - 4 - gnl|BL_ORD_ID|784 - 52509|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 - 784 - 15 - - - 1 - 11.927 - 19 - 94.4229 - 2 - 9 - 6 - 13 - 0 - 0 - 3 - 5 - 0 - 8 - TCKANLCY - TCINGVCW - TC +C+ - - - - - 5 - gnl|BL_ORD_ID|65 - 4909|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 - 65 - 15 - - - 1 - 11.5418 - 18 - 101.887 - 2 - 9 - 2 - 9 - 0 - 0 - 3 - 5 - 0 - 8 - TCKANLCY - TCINGVCW - TC +C+ - - - - - 6 - gnl|BL_ORD_ID|156 - 11956|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 - 156 - 11 - - - 1 - 11.5418 - 18 - 152.168 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 5 - 0 - 9 - QTCKANLCY - EFCRVLCCY - + C+ CY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 784 - Query_784 - M_4373 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 785 - Query_785 - M_4374 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 786 - Query_786 - M_4375 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 787 - Query_787 - M_4376 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 788 - Query_788 - M_4377 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 789 - Query_789 - M_4378 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 790 - Query_790 - M_4379 - 9 - - - 1 - gnl|BL_ORD_ID|1131 - 74800|Genome polyprotein|SRC279960|Hepatitis C virus subtype 2b|31650 - 1131 - 10 - - - 1 - 11.1566 - 17 - 199.037 - 3 - 9 - 4 - 10 - 0 - 0 - 4 - 4 - 0 - 7 - PQRIPSL - PSRGPKL - P R P L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 791 - Query_791 - M_4380 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 792 - Query_792 - M_4381 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 793 - Query_793 - M_4382 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 794 - Query_794 - M_4383 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 795 - Query_795 - M_4384 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 796 - Query_796 - M_4385 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 797 - Query_797 - M_4386 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 798 - Query_798 - M_4387 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 799 - Query_799 - M_4388 - 9 - - - 1 - gnl|BL_ORD_ID|2137 - 187106|Vpr protein|BAA93983.1|Human immunodeficiency virus 1|11676 - 2137 - 9 - - - 1 - 14.2382 - 25 - 4.21767 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 7 - 0 - 7 - LRNFPQI - VRHFPRI - +R+FP+I - - - - - 2 - gnl|BL_ORD_ID|48 - 3051|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 - 48 - 20 - - - 1 - 14.2382 - 25 - 4.2724 - 3 - 8 - 5 - 10 - 0 - 0 - 4 - 5 - 0 - 6 - LRNFPQ - LQNLPQ - L+N PQ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 800 - Query_800 - M_4389 - 9 - - - 1 - gnl|BL_ORD_ID|1040 - 69474|core protein|BAF42671.1|Hepatitis B virus|10407 - 1040 - 10 - - - 1 - 13.853 - 24 - 5.87716 - 3 - 9 - 2 - 8 - 0 - 0 - 4 - 7 - 0 - 7 - MKYLVNF - LEYLVSF - ++YLV+F - - - - - 2 - gnl|BL_ORD_ID|2322 - 423053|core protein|AAL31859.1|Hepatitis B virus|10407 - 2322 - 11 - - - 1 - 13.853 - 24 - 6.85565 - 3 - 9 - 5 - 11 - 0 - 0 - 4 - 7 - 0 - 7 - MKYLVNF - IEYLVSF - ++YLV+F - - - - - 3 - gnl|BL_ORD_ID|201 - 15061|core protein|BAF42671.1|Hepatitis B virus|10407 - 201 - 9 - - - 1 - 13.0826 - 22 - 19.404 - 4 - 9 - 1 - 6 - 0 - 0 - 4 - 6 - 0 - 6 - KYLVNF - EYLVSF - +YLV+F - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 801 - Query_801 - M_4390 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 802 - Query_802 - M_4391 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 803 - Query_803 - M_4392 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 804 - Query_804 - M_4393 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 805 - Query_805 - M_4394 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 806 - Query_806 - M_4395 - 9 - - - 1 - gnl|BL_ORD_ID|256 - 17278|Genome polyprotein|P06441.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 256 - 20 - - - 1 - 14.6234 - 26 - 1.54928 - 1 - 9 - 10 - 18 - 0 - 0 - 4 - 5 - 0 - 9 - RHLGDQMEV - RHTSDHMSI - RH D M + - - - - - 2 - gnl|BL_ORD_ID|864 - 56574|envelope glycoprotein|ABI16336.1|Human immunodeficiency virus 1|11676 - 864 - 9 - - - 1 - 13.0826 - 22 - 23.0624 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - RHLGDQ - RYLKDQ - R+L DQ - - - - - 3 - gnl|BL_ORD_ID|191 - 14101|envelope glycoprotein|ABI16336.1|Human immunodeficiency virus 1|11676 - 191 - 9 - - - 1 - 13.0826 - 22 - 23.0624 - 1 - 6 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - RHLGDQ - RYLKDQ - R+L DQ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 807 - Query_807 - M_4396 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 808 - Query_808 - M_4397 - 9 - - - 1 - gnl|BL_ORD_ID|96 - 6591|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 96 - 18 - - - 1 - 13.4678 - 23 - 8.6267 - 2 - 9 - 10 - 17 - 0 - 0 - 4 - 5 - 0 - 8 - HSPRNLIY - HGPTPLLY - H P L+Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 809 - Query_809 - M_4398 - 9 - - - 1 - gnl|BL_ORD_ID|1616 - 144403|polyprotein|AAK08509.1|Hepatitis C virus subtype 1b|31647 - 1616 - 9 - - - 1 - 11.5418 - 18 - 120.255 - 1 - 7 - 3 - 9 - 0 - 0 - 4 - 4 - 0 - 7 - RHTPMYY - RHHNMVY - RH M Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 810 - Query_810 - M_4399 - 9 - - - 1 - gnl|BL_ORD_ID|1616 - 144403|polyprotein|AAK08509.1|Hepatitis C virus subtype 1b|31647 - 1616 - 9 - - - 1 - 11.5418 - 18 - 120.255 - 1 - 7 - 3 - 9 - 0 - 0 - 4 - 4 - 0 - 7 - RHTPMYY - RHHNMVY - RH M Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 811 - Query_811 - M_4400 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 812 - Query_812 - M_4401 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 813 - Query_813 - M_4402 - 9 - - - 1 - gnl|BL_ORD_ID|2005 - 183741|polyprotein|AGS49173.1|Dengue virus 2|11060 - 2005 - 10 - - - 1 - 13.853 - 24 - 5.48318 - 2 - 9 - 1 - 8 - 0 - 0 - 3 - 6 - 0 - 8 - LMCGPNTI - ILCVPNAV - ++C PN + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 814 - Query_814 - M_4403 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 815 - Query_815 - M_4404 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 816 - Query_816 - M_4405 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 817 - Query_817 - M_4406 - 9 - - - 1 - gnl|BL_ORD_ID|2137 - 187106|Vpr protein|BAA93983.1|Human immunodeficiency virus 1|11676 - 2137 - 9 - - - 1 - 15.0086 - 27 - 0.914566 - 1 - 7 - 3 - 9 - 0 - 0 - 4 - 7 - 0 - 7 - RNFPQIY - RHFPRIW - R+FP+I+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 818 - Query_818 - M_4407 - 9 - - - 1 - gnl|BL_ORD_ID|1060 - 69799|envelope glycoprotein|BAE96221.1|Human immunodeficiency virus 1|11676 - 1060 - 10 - - - 1 - 13.4678 - 23 - 10.0795 - 2 - 6 - 6 - 10 - 0 - 0 - 4 - 5 - 0 - 5 - NPQEL - NPQEV - NPQE+ - - - - - 2 - gnl|BL_ORD_ID|1097 - 72563|polyprotein|AAB70696.1|Dengue virus type 1 Hawaii|10000440 - 1097 - 20 - - - 1 - 12.6974 - 21 - 28.5768 - 2 - 9 - 7 - 14 - 0 - 0 - 3 - 5 - 0 - 8 - NPQELWHF - NPYKTWAY - NP + W + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 819 - Query_819 - M_4408 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 820 - Query_820 - M_4409 - 9 - - - 1 - gnl|BL_ORD_ID|1712 - 150341|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1712 - 9 - - - 1 - 15.0086 - 27 - 1.14097 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 7 - 0 - 9 - RPGSRGCPM - KPGTSGSPI - +PG+ G P+ - - - - - 2 - gnl|BL_ORD_ID|75 - 5542|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 75 - 15 - - - 1 - 14.2382 - 25 - 2.38473 - 1 - 9 - 7 - 15 - 0 - 0 - 4 - 6 - 0 - 9 - RPGSRGCPM - SPGTSGSPI - PG+ G P+ - - - - - 3 - gnl|BL_ORD_ID|260 - 17802|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 260 - 15 - - - 1 - 14.2382 - 25 - 3.14687 - 2 - 9 - 3 - 10 - 0 - 0 - 4 - 6 - 0 - 8 - PGSRGCPM - PGTSGSPI - PG+ G P+ - - - - - 4 - gnl|BL_ORD_ID|1929 - 180750|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1929 - 15 - - - 1 - 14.2382 - 25 - 3.37317 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 6 - 0 - 8 - PGSRGCPM - PGTSGSPI - PG+ G P+ - - - - - 5 - gnl|BL_ORD_ID|847 - 55336|EBNA-1|YP_401677.1|Human gammaherpesvirus 4|10376 - 847 - 15 - - - 1 - 11.1566 - 17 - 174.225 - 1 - 7 - 1 - 7 - 0 - 0 - 4 - 4 - 0 - 7 - RPGSRGC - RPSCIGC - RP GC - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 821 - Query_821 - M_4410 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 822 - Query_822 - M_4411 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 823 - Query_823 - M_4412 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 824 - Query_824 - M_4413 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 825 - Query_825 - M_4414 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 826 - Query_826 - M_4415 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 827 - Query_827 - M_4416 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 828 - Query_828 - M_4417 - 9 - - - 1 - gnl|BL_ORD_ID|1132 - 74886|latent membrane protein 1|AAS99606.1|Human gammaherpesvirus 4|10376 - 1132 - 9 - - - 1 - 12.3122 - 20 - 42.6373 - 3 - 9 - 3 - 9 - 0 - 0 - 3 - 6 - 0 - 7 - QQDYWLM - QQNWWTL - QQ++W + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 829 - Query_829 - M_4418 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 830 - Query_830 - M_4419 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 831 - Query_831 - M_4420 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 832 - Query_832 - M_4421 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 833 - Query_833 - M_4422 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 834 - Query_834 - M_4423 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 835 - Query_835 - M_4424 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 836 - Query_836 - M_4425 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 837 - Query_837 - M_4426 - 9 - - - 1 - gnl|BL_ORD_ID|1071 - 70687|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis|1773 - 1071 - 20 - - - 1 - 12.6974 - 21 - 32.3697 - 2 - 8 - 5 - 11 - 0 - 0 - 4 - 6 - 0 - 7 - RSDAEKQ - RADEEQQ - R+D E+Q - - - - - 2 - gnl|BL_ORD_ID|73 - 5316|EBNA-3B nuclear protein|CAD53420.1|Human gammaherpesvirus 4|10376 - 73 - 10 - - - 1 - 12.6974 - 21 - 36.6217 - 1 - 6 - 5 - 10 - 0 - 0 - 4 - 6 - 0 - 6 - RRSDAE - RKSDAK - R+SDA+ - - - - - 3 - gnl|BL_ORD_ID|794 - 53077|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis|1773 - 794 - 10 - - - 1 - 12.3122 - 20 - 40.5114 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 6 - 0 - 7 - RSDAEKQ - RADEEQQ - R+D E+Q - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 838 - Query_838 - M_4427 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 839 - Query_839 - M_4428 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 840 - Query_840 - M_4429 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 841 - Query_841 - M_4430 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 842 - Query_842 - M_4431 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 843 - Query_843 - M_4432 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 844 - Query_844 - M_4433 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 845 - Query_845 - M_4434 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 846 - Query_846 - M_4435 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 847 - Query_847 - M_4436 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 848 - Query_848 - M_4437 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 849 - Query_849 - M_4438 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 850 - Query_850 - M_4439 - 9 - - - 1 - gnl|BL_ORD_ID|829 - 54741|gag polyprotein|BAA00992.1|Human immunodeficiency virus 1|11676 - 829 - 9 - - - 1 - 10.3862 - 15 - 600.299 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 6 - 0 - 8 - RVRRRGQK - RLRPGGKK - R+R G+K - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 851 - Query_851 - M_4440 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 852 - Query_852 - M_4441 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 853 - Query_853 - M_4442 - 9 - - - 1 - gnl|BL_ORD_ID|2090 - 185573|polyprotein|CDF77361.1|Dengue virus 3|11069 - 2090 - 9 - - - 1 - 13.4678 - 23 - 10.7466 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 4 - 0 - 9 - RYAALLKCW - RYMGEDGCW - RY CW - - - - - 2 - gnl|BL_ORD_ID|1928 - 180738|polyprotein|CDF77361.1|Dengue virus 3|11069 - 1928 - 10 - - - 1 - 13.4678 - 23 - 12.859 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 4 - 0 - 9 - RYAALLKCW - RYMGEDGCW - RY CW - - - - - 3 - gnl|BL_ORD_ID|1387 - 110227|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1387 - 33 - - - 1 - 11.1566 - 17 - 129.204 - 2 - 8 - 14 - 20 - 0 - 0 - 4 - 4 - 0 - 7 - YAALLKC - YAVCDKC - YA KC - - - - - 4 - gnl|BL_ORD_ID|1400 - 110467|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1400 - 25 - - - 1 - 11.5418 - 18 - 133.249 - 2 - 8 - 7 - 13 - 0 - 0 - 4 - 4 - 0 - 7 - YAALLKC - YAVCDKC - YA KC - - - - - 5 - gnl|BL_ORD_ID|865 - 56589|polyprotein precursor|NP_041724.2|West Nile virus|11082 - 865 - 9 - - - 1 - 11.1566 - 17 - 287.485 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 4 - 0 - 9 - RYAALLKCW - RYLVKTESW - RY + W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 854 - Query_854 - M_4443 - 9 - - - 1 - gnl|BL_ORD_ID|1597 - 142233|ATP-dependent helicase|NP_217813.1|Mycobacterium tuberculosis|1773 - 1597 - 32 - - - 1 - 15.3938 - 28 - 1.12437 - 1 - 8 - 2 - 9 - 0 - 0 - 5 - 7 - 0 - 8 - RYARPSRL - RFAQPSAL - R+A+PS L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 855 - Query_855 - M_4444 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 856 - Query_856 - M_4445 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 857 - Query_857 - M_4446 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 858 - Query_858 - M_4447 - 9 - - - 1 - gnl|BL_ORD_ID|418 - 25237|Transcription activator BRLF1|P03209.1|Human herpesvirus 4 strain B95-8|10377 - 418 - 15 - - - 1 - 13.4678 - 23 - 7.61659 - 1 - 8 - 8 - 15 - 0 - 0 - 5 - 5 - 0 - 8 - RYFLKHGI - RYVLDHLI - RY L H I - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 859 - Query_859 - M_4448 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 860 - Query_860 - M_4449 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 861 - Query_861 - M_4450 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 862 - Query_862 - M_4451 - 9 - - - 1 - gnl|BL_ORD_ID|863 - 56502|polyprotein|BAD73994.1|Hepatitis C virus subtype 1b|31647 - 863 - 9 - - - 1 - 14.2382 - 25 - 3.55601 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 5 - 0 - 9 - RYLPDCDYL - RYAPACKPL - RY P C L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 863 - Query_863 - M_4452 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 864 - Query_864 - M_4453 - 9 - - - 1 - gnl|BL_ORD_ID|863 - 56502|polyprotein|BAD73994.1|Hepatitis C virus subtype 1b|31647 - 863 - 9 - - - 1 - 15.0086 - 27 - 1.2556 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 5 - 0 - 9 - RYVAICAPL - RYAPACKPL - RY C PL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 865 - Query_865 - M_4454 - 9 - - - 1 - gnl|BL_ORD_ID|863 - 56502|polyprotein|BAD73994.1|Hepatitis C virus subtype 1b|31647 - 863 - 9 - - - 1 - 17.705 - 34 - 0.13901 - 1 - 9 - 1 - 9 - 0 - 0 - 6 - 7 - 0 - 9 - RYVASCKPL - RYAPACKPL - RY +CKPL - - - - - 2 - gnl|BL_ORD_ID|2080 - 185327|polyprotein|ACF49259.1|Dengue virus type 1 Hawaii|10000440 - 2080 - 9 - - - 1 - 12.3122 - 20 - 60.6092 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 6 - 0 - 9 - RYVASCKPL - QYIYMGQPL - +Y+ +PL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 866 - Query_866 - M_4455 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 867 - Query_867 - M_4456 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 868 - Query_868 - M_4457 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 869 - Query_869 - M_4458 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 870 - Query_870 - M_4459 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 871 - Query_871 - M_4460 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 872 - Query_872 - M_4461 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 873 - Query_873 - M_4462 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 874 - Query_874 - M_4463 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 875 - Query_875 - M_4464 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 876 - Query_876 - M_4465 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 877 - Query_877 - M_4466 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 878 - Query_878 - M_4467 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 879 - Query_879 - M_4468 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 880 - Query_880 - M_4469 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 881 - Query_881 - M_4470 - 9 - - - 1 - gnl|BL_ORD_ID|626 - 37536|Spike glycoprotein precursor|P15423.1|Human coronavirus 229E|11137 - 626 - 9 - - - 1 - 16.5494 - 31 - 0.306344 - 2 - 9 - 2 - 9 - 0 - 0 - 5 - 5 - 0 - 8 - FFNCLWEV - LLNCLWSV - NCLW V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 882 - Query_882 - M_4471 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 883 - Query_883 - M_4472 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 884 - Query_884 - M_4473 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 885 - Query_885 - M_4474 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 886 - Query_886 - M_4475 - 9 - - - 1 - gnl|BL_ORD_ID|340 - 21347|Nucleoprotein|P59595.1|SARS coronavirus|227859 - 340 - 9 - - - 1 - 13.853 - 24 - 5.36545 - 2 - 7 - 1 - 6 - 0 - 0 - 4 - 6 - 0 - 6 - GMARVG - GMSRIG - GM+R+G - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 887 - Query_887 - M_4476 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 888 - Query_888 - M_4477 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 889 - Query_889 - M_4478 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 890 - Query_890 - M_4479 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 891 - Query_891 - M_4480 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 892 - Query_892 - M_4481 - 9 - - - 1 - gnl|BL_ORD_ID|2137 - 187106|Vpr protein|BAA93983.1|Human immunodeficiency virus 1|11676 - 2137 - 9 - - - 1 - 13.853 - 24 - 5.74926 - 4 - 9 - 3 - 8 - 0 - 0 - 4 - 5 - 0 - 6 - RHVPKI - RHFPRI - RH P+I - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 893 - Query_893 - M_4482 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 894 - Query_894 - M_4483 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 895 - Query_895 - M_4484 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 896 - Query_896 - M_4485 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 897 - Query_897 - M_4486 - 9 - - - 1 - gnl|BL_ORD_ID|186 - 13701|Trans-activator protein BZLF1|P03206.2|Human gammaherpesvirus 4|10376 - 186 - 11 - - - 1 - 13.0826 - 22 - 15.2395 - 4 - 9 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - PAGELT - PQGQLT - P G+LT - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 898 - Query_898 - M_4487 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 899 - Query_899 - M_4488 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 900 - Query_900 - M_4489 - 9 - - - 1 - gnl|BL_ORD_ID|889 - 58463|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 889 - 20 - - - 1 - 11.927 - 19 - 87.4603 - 1 - 9 - 10 - 18 - 0 - 0 - 5 - 6 - 0 - 9 - SIFYSFLPL - SIYVYALPL - SI+ LPL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 901 - Query_901 - M_4490 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 902 - Query_902 - M_4491 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 903 - Query_903 - M_4492 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 904 - Query_904 - M_4493 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 905 - Query_905 - M_4494 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 906 - Query_906 - M_4495 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 907 - Query_907 - M_4496 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 908 - Query_908 - M_4497 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 909 - Query_909 - M_4498 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 910 - Query_910 - M_4499 - 9 - - - 1 - gnl|BL_ORD_ID|1219 - 96898|Genome polyprotein|SRC279960|Hepatitis C virus|11103 - 1219 - 17 - - - 1 - 15.0086 - 27 - 0.976474 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 7 - 0 - 9 - SLLRKHQIL - SLLRNHNLV - SLLR H ++ - - - - - 2 - gnl|BL_ORD_ID|1218 - 96897|polyprotein|ABR25251.1|Hepatitis C virus (isolate H77)|63746 - 1218 - 17 - - - 1 - 14.2382 - 25 - 3.04646 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 7 - 0 - 9 - SLLRKHQIL - SLLRHHNLV - SLLR H ++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 911 - Query_911 - M_4500 - 9 - - - 1 - gnl|BL_ORD_ID|1219 - 96898|Genome polyprotein|SRC279960|Hepatitis C virus|11103 - 1219 - 17 - - - 1 - 15.0086 - 27 - 1.13851 - 1 - 8 - 1 - 8 - 0 - 0 - 5 - 6 - 0 - 8 - SLLRKHQI - SLLRNHNL - SLLR H + - - - - - 2 - gnl|BL_ORD_ID|1218 - 96897|polyprotein|ABR25251.1|Hepatitis C virus (isolate H77)|63746 - 1218 - 17 - - - 1 - 14.2382 - 25 - 3.43929 - 1 - 8 - 1 - 8 - 0 - 0 - 5 - 6 - 0 - 8 - SLLRKHQI - SLLRHHNL - SLLR H + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 912 - Query_912 - M_4501 - 9 - - - 1 - gnl|BL_ORD_ID|403 - 24557|Gag polyprotein|P03347.3|Human immunodeficiency virus 1|11676 - 403 - 9 - - - 1 - 13.853 - 24 - 5.84954 - 4 - 9 - 3 - 8 - 0 - 0 - 4 - 5 - 0 - 6 - VHGGPL - VHAGPI - VH GP+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 913 - Query_913 - M_4502 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 914 - Query_914 - M_4503 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 915 - Query_915 - M_4504 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 916 - Query_916 - M_4505 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 917 - Query_917 - M_4506 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 918 - Query_918 - M_4507 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 919 - Query_919 - M_4508 - 9 - - - 1 - gnl|BL_ORD_ID|2243 - 232152|rhoptry kinase family protein|AFO54841.1|Toxoplasma gondii type III|398031 - 2243 - 19 - - - 1 - 13.853 - 24 - 6.77098 - 4 - 9 - 6 - 11 - 0 - 0 - 3 - 6 - 0 - 6 - YHTYGL - FHSYGV - +H+YG+ - - - - - 2 - gnl|BL_ORD_ID|474 - 29182|polyprotein|BAD73991.1|Hepatitis C virus subtype 1b|31647 - 474 - 9 - - - 1 - 12.6974 - 21 - 37.2378 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - LWYHTYG - ITYSTYG - + Y TYG - - - - - 3 - gnl|BL_ORD_ID|1371 - 108232|Genome polyprotein|P26664.3|Hepatitis C virus|11103 - 1371 - 10 - - - 1 - 12.3122 - 20 - 43.3206 - 4 - 8 - 1 - 5 - 0 - 0 - 4 - 4 - 0 - 5 - YHTYG - YSTYG - Y TYG - - - - - 4 - gnl|BL_ORD_ID|1015 - 67471|Genome polyprotein|Q99IB8.3|Hepatitis C virus JFH-1|356411 - 1015 - 9 - - - 1 - 12.3122 - 20 - 56.7066 - 4 - 8 - 2 - 6 - 0 - 0 - 4 - 4 - 0 - 5 - YHTYG - YSTYG - Y TYG - - - - - 5 - gnl|BL_ORD_ID|133 - 9415|Superoxide dismutase|P17670.1|Mycobacterium tuberculosis|1773 - 133 - 10 - - - 1 - 12.3122 - 20 - 63.4362 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 5 - 0 - 9 - SLWYHTYGL - DMWEHAFYL - +W H + L - - - - - 6 - gnl|BL_ORD_ID|132 - 9414|Superoxide dismutase|P17670.1|Mycobacterium tuberculosis|1773 - 132 - 9 - - - 1 - 11.927 - 19 - 76.3762 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 5 - 0 - 9 - SLWYHTYGL - DMWEHAFYL - +W H + L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 920 - Query_920 - M_4509 - 9 - - - 1 - gnl|BL_ORD_ID|526 - 32250|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 - 526 - 9 - - - 1 - 12.6974 - 21 - 33.058 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 5 - 0 - 8 - SLYTAYHV - KLYCSYEV - LY +Y V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 921 - Query_921 - M_4510 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 922 - Query_922 - M_4511 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 923 - Query_923 - M_4512 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 924 - Query_924 - M_4513 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 925 - Query_925 - M_4514 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 926 - Query_926 - M_4515 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 927 - Query_927 - M_4516 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 928 - Query_928 - M_4517 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 929 - Query_929 - M_4518 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 930 - Query_930 - M_4519 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 931 - Query_931 - M_4520 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 932 - Query_932 - M_4521 - 9 - - - 1 - gnl|BL_ORD_ID|1333 - 107873|Genome polyprotein|P26664.3|Hepatitis C virus|11103 - 1333 - 10 - - - 1 - 13.853 - 24 - 5.48318 - 1 - 7 - 2 - 8 - 0 - 0 - 5 - 6 - 0 - 7 - SPLFYST - SPITYST - SP+ YST - - - - - 2 - gnl|BL_ORD_ID|965 - 63963|HCV-1|AAA45676.1|Hepatitis C virus|11103 - 965 - 10 - - - 1 - 13.853 - 24 - 6.08483 - 1 - 7 - 3 - 9 - 0 - 0 - 5 - 6 - 0 - 7 - SPLFYST - SPITYST - SP+ YST - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 933 - Query_933 - M_4522 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 934 - Query_934 - M_4523 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 935 - Query_935 - M_4524 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 936 - Query_936 - M_4525 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 937 - Query_937 - M_4526 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 938 - Query_938 - M_4527 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 939 - Query_939 - M_4528 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 940 - Query_940 - M_4529 - 9 - - - 1 - gnl|BL_ORD_ID|1960 - 182599|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1960 - 9 - - - 1 - 13.4678 - 23 - 11.5219 - 1 - 7 - 1 - 7 - 0 - 0 - 5 - 6 - 0 - 7 - SQMSQLM - AQMWQLM - +QM QLM - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 941 - Query_941 - M_4530 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 942 - Query_942 - M_4531 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 943 - Query_943 - M_4532 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 944 - Query_944 - M_4533 - 9 - - - 1 - gnl|BL_ORD_ID|381 - 23566|tegument protein UL7|NP_044476.1|Human alphaherpesvirus 2|10310 - 381 - 13 - - - 1 - 13.0826 - 22 - 15.9524 - 2 - 6 - 9 - 13 - 0 - 0 - 5 - 5 - 0 - 5 - RCLLL - RCLLL - RCLLL - - - - - 2 - gnl|BL_ORD_ID|645 - 38427|BZLF1|AAA66529.1|Human gammaherpesvirus 4|10376 - 645 - 9 - - - 1 - 12.6974 - 21 - 39.1808 - 3 - 9 - 3 - 9 - 0 - 0 - 4 - 6 - 0 - 7 - CLLLPLL - CVLWPVL - C+L P+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 945 - Query_945 - M_4534 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 946 - Query_946 - M_4535 - 9 - - - 1 - gnl|BL_ORD_ID|805 - 53476|polyprotein|AGO67248.1|Dengue virus 2|11060 - 805 - 9 - - - 1 - 13.0826 - 22 - 20.0871 - 2 - 7 - 1 - 6 - 0 - 0 - 3 - 5 - 0 - 6 - RENRWT - REDQWC - RE++W - - - - - 2 - gnl|BL_ORD_ID|2019 - 184131|polyprotein|AGO67248.1|Dengue virus 2|11060 - 2019 - 10 - - - 1 - 13.0826 - 22 - 20.1646 - 2 - 7 - 2 - 7 - 0 - 0 - 3 - 5 - 0 - 6 - RENRWT - REDQWC - RE++W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 947 - Query_947 - M_4536 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 948 - Query_948 - M_4537 - 9 - - - 1 - gnl|BL_ORD_ID|929 - 60867|nucleoprotein|CAZ65591.1|Influenza A virus|11320 - 929 - 9 - - - 1 - 13.0826 - 22 - 14.7007 - 1 - 7 - 1 - 7 - 0 - 0 - 4 - 6 - 0 - 7 - SRFTAVR - SRYWAIR - SR+ A+R - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 949 - Query_949 - M_4538 - 9 - - - 1 - gnl|BL_ORD_ID|1385 - 110215|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1385 - 25 - - - 1 - 15.3938 - 28 - 0.880103 - 1 - 8 - 17 - 24 - 0 - 0 - 5 - 6 - 0 - 8 - SRFTLRCM - GRWTGRCM - R+T RCM - - - - - 2 - gnl|BL_ORD_ID|1429 - 113154|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1429 - 10 - - - 1 - 14.6234 - 26 - 2.14354 - 2 - 8 - 1 - 7 - 0 - 0 - 5 - 6 - 0 - 7 - RFTLRCM - RWTGRCM - R+T RCM - - - - - 3 - gnl|BL_ORD_ID|1396 - 110399|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1396 - 23 - - - 1 - 14.6234 - 26 - 2.49651 - 2 - 8 - 3 - 9 - 0 - 0 - 5 - 6 - 0 - 7 - RFTLRCM - RWTGRCM - R+T RCM - - - - - 4 - gnl|BL_ORD_ID|1384 - 110205|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1384 - 32 - - - 1 - 14.6234 - 26 - 2.74814 - 1 - 8 - 11 - 18 - 0 - 0 - 5 - 6 - 0 - 8 - SRFTLRCM - GRWTGRCM - R+T RCM - - - - - 5 - gnl|BL_ORD_ID|2060 - 184840|polyprotein|AGS49173.1|Dengue virus 2|11060 - 2060 - 9 - - - 1 - 13.4678 - 23 - 9.02895 - 1 - 6 - 4 - 9 - 0 - 0 - 4 - 6 - 0 - 6 - SRFTLR - NRFTMR - +RFT+R - - - - - 6 - gnl|BL_ORD_ID|1661 - 147835|early protein|CAA52585.1|Human papillomavirus type 52|10618 - 1661 - 9 - - - 1 - 13.4678 - 23 - 11.9303 - 3 - 9 - 1 - 7 - 0 - 0 - 3 - 6 - 0 - 7 - FTLRCMV - ITIRCII - T+RC++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 950 - Query_950 - M_4539 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 951 - Query_951 - M_4540 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 952 - Query_952 - M_4541 - 9 - - - 1 - gnl|BL_ORD_ID|1823 - 178351|Protein E7|P03129.1|Human papillomavirus type 16|333760 - 1823 - 15 - - - 1 - 12.6974 - 21 - 26.5542 - 1 - 9 - 3 - 11 - 0 - 0 - 3 - 7 - 0 - 9 - SRHDFHVDL - TLHEYMLDL - + H++ +DL - - - - - 2 - gnl|BL_ORD_ID|982 - 64830|E7 protein|ABL96585.1|Human papillomavirus type 16|333760 - 982 - 9 - - - 1 - 12.3122 - 20 - 40.5299 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 7 - 0 - 9 - SRHDFHVDL - TLHEYMLDL - + H++ +DL - - - - - 3 - gnl|BL_ORD_ID|1408 - 110940|Protein E7|P03129.1|Human papillomavirus type 16|333760 - 1408 - 15 - - - 1 - 12.3122 - 20 - 54.8452 - 1 - 9 - 7 - 15 - 0 - 0 - 3 - 7 - 0 - 9 - SRHDFHVDL - TLHEYMLDL - + H++ +DL - - - - - 4 - gnl|BL_ORD_ID|1392 - 110335|E7|AAD33253.1|Human papillomavirus type 16|333760 - 1392 - 32 - - - 1 - 11.1566 - 17 - 167.857 - 3 - 9 - 9 - 15 - 0 - 0 - 3 - 6 - 0 - 7 - HDFHVDL - HEYMLDL - H++ +DL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 953 - Query_953 - M_4542 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 954 - Query_954 - M_4543 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 955 - Query_955 - M_4544 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 956 - Query_956 - M_4545 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 957 - Query_957 - M_4546 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 958 - Query_958 - M_4547 - 9 - - - 1 - gnl|BL_ORD_ID|617 - 37364|P53_HUMAN Cellular tumor antigen p53 (Tumor suppressor p53) (Phosphoprotein p53) (Antigen NY-CO-13)|P04637.2|Homo sapiens|9606 - 617 - 9 - - - 1 - 13.0826 - 22 - 17.1877 - 1 - 6 - 3 - 8 - 0 - 0 - 4 - 4 - 0 - 6 - SRNDFE - GRNSFE - RN FE - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 959 - Query_959 - M_4548 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 960 - Query_960 - M_4549 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 961 - Query_961 - M_4550 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 962 - Query_962 - M_4551 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 963 - Query_963 - M_4552 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 964 - Query_964 - M_4553 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 965 - Query_965 - M_4554 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 966 - Query_966 - M_4555 - 9 - - - 1 - gnl|BL_ORD_ID|1441 - 120187|E1 protein|BAA19893.1|Rubella virus|11041 - 1441 - 21 - - - 1 - 14.6234 - 26 - 2.56229 - 1 - 6 - 8 - 13 - 0 - 0 - 4 - 6 - 0 - 6 - SRTVWE - TRTVWQ - +RTVW+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 967 - Query_967 - M_4556 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 968 - Query_968 - M_4557 - 9 - - - 1 - gnl|BL_ORD_ID|1597 - 142233|ATP-dependent helicase|NP_217813.1|Mycobacterium tuberculosis|1773 - 1597 - 32 - - - 1 - 15.0086 - 27 - 1.21962 - 2 - 9 - 2 - 9 - 0 - 0 - 5 - 7 - 0 - 8 - RYARPSRL - RFAQPSAL - R+A+PS L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 969 - Query_969 - M_4558 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 970 - Query_970 - M_4559 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 971 - Query_971 - M_4560 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 972 - Query_972 - M_4561 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 973 - Query_973 - M_4562 - 9 - - - 1 - gnl|BL_ORD_ID|1435 - 116781|Nucleoprotein|P05133.1|Hantaan virus 76-118|11602 - 1435 - 15 - - - 1 - 11.927 - 19 - 64.1766 - 3 - 9 - 1 - 7 - 0 - 0 - 4 - 6 - 0 - 7 - LRRMNSF - LRKKSSF - LR+ +SF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 974 - Query_974 - M_4563 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 975 - Query_975 - M_4564 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 976 - Query_976 - M_4565 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 977 - Query_977 - M_4566 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 978 - Query_978 - M_4567 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 979 - Query_979 - M_4568 - 9 - - - 1 - gnl|BL_ORD_ID|889 - 58463|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 889 - 20 - - - 1 - 14.6234 - 26 - 2.46911 - 2 - 8 - 10 - 16 - 0 - 0 - 4 - 7 - 0 - 7 - TIYIFAL - SIYVYAL - +IY++AL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 980 - Query_980 - M_4569 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 981 - Query_981 - M_4570 - 9 - - - 1 - gnl|BL_ORD_ID|1078 - 71412|polyprotein [Hepatitis C virus subtype 1a]|ABV46251.2|Hepatitis C virus subtype 1a|31646 - 1078 - 9 - - - 1 - 13.853 - 24 - 4.51705 - 2 - 8 - 2 - 8 - 0 - 0 - 5 - 6 - 0 - 7 - TQTHPLT - TLTHPIT - T THP+T - - - - - 2 - gnl|BL_ORD_ID|1297 - 103389|unnamed protein product [Hepatitis C virus]|BAA14035.1|Hepatitis C virus|11103 - 1297 - 20 - - - 1 - 13.853 - 24 - 4.73116 - 4 - 8 - 2 - 6 - 0 - 0 - 4 - 5 - 0 - 5 - THPLT - THPIT - THP+T - - - - - 3 - gnl|BL_ORD_ID|985 - 65090|polyprotein|BAB18810.1|Hepatitis C virus (isolate H77)|63746 - 985 - 8 - - - 1 - 13.853 - 24 - 5.69712 - 2 - 8 - 1 - 7 - 0 - 0 - 5 - 6 - 0 - 7 - TQTHPLT - TLTHPIT - T THP+T - - - - - 4 - gnl|BL_ORD_ID|986 - 65092|Genome polyprotein|P26664.3|Hepatitis C virus genotype 1|41856 - 986 - 8 - - - 1 - 13.4678 - 23 - 8.77767 - 2 - 8 - 1 - 7 - 0 - 0 - 5 - 6 - 0 - 7 - TQTHPLT - TLTHPVT - T THP+T - - - - - 5 - gnl|BL_ORD_ID|1645 - 146317|polyprotein|ADF97231.1|Hepatitis C virus subtype 3a|356426 - 1645 - 9 - - - 1 - 13.0826 - 22 - 13.9535 - 4 - 8 - 4 - 8 - 0 - 0 - 4 - 5 - 0 - 5 - THPLT - THPVT - THP+T - - - - - 6 - gnl|BL_ORD_ID|1627 - 146182|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 - 1627 - 8 - - - 1 - 13.0826 - 22 - 15.0555 - 4 - 8 - 3 - 7 - 0 - 0 - 4 - 5 - 0 - 5 - THPLT - THPVT - THP+T - - - - - 7 - gnl|BL_ORD_ID|1608 - 143705|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 1608 - 9 - - - 1 - 12.3122 - 20 - 44.8495 - 4 - 9 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - THPLTL - TFPITL - T P+TL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 982 - Query_982 - M_4571 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 983 - Query_983 - M_4572 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 984 - Query_984 - M_4573 - 9 - - - 1 - gnl|BL_ORD_ID|471 - 28594|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 - 471 - 20 - - - 1 - 15.0086 - 27 - 1.02375 - 1 - 9 - 5 - 13 - 0 - 0 - 5 - 7 - 0 - 9 - STYPDQQHV - SYYPDQKSL - S YPDQ+ + - - - - - 2 - gnl|BL_ORD_ID|1173 - 79337|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 1173 - 15 - - - 1 - 12.6974 - 21 - 28.3557 - 2 - 9 - 4 - 11 - 0 - 0 - 4 - 5 - 0 - 8 - TYPDQQHV - TWPLLPHV - T+P HV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 985 - Query_985 - M_4574 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 986 - Query_986 - M_4575 - 9 - - - 1 - gnl|BL_ORD_ID|313 - 20865|Nucleoprotein|P41269.1|Puumala hantavirus|11604 - 313 - 9 - - - 1 - 16.1642 - 30 - 0.361887 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 8 - 0 - 9 - SVFPTQLQL - GLFPTQIQV - +FPTQ+Q+ - - - - - 2 - gnl|BL_ORD_ID|1416 - 111604|L1|ABP99807.1|Human papillomavirus type 18|333761 - 1416 - 9 - - - 1 - 14.2382 - 25 - 3.93883 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 7 - 0 - 9 - SVFPTQLQL - NVFPIFLQM - +VFP LQ+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 987 - Query_987 - M_4576 - 9 - - - 1 - gnl|BL_ORD_ID|1205 - 96123|Genome polyprotein|P26664.3|Hepatitis C virus (isolate H77)|63746 - 1205 - 9 - - - 1 - 13.4678 - 23 - 7.85574 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 5 - 0 - 9 - SVFSEQWIF - AVFGPLWIL - +VF WI - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 988 - Query_988 - M_4577 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 989 - Query_989 - M_4578 - 9 - - - 1 - gnl|BL_ORD_ID|1653 - 146569|polyprotein|ADF97231.1|Hepatitis C virus subtype 3a|356426 - 1653 - 17 - - - 1 - 12.3122 - 20 - 57.3063 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 5 - 0 - 9 - SWMPALECL - SWDETWKCL - SW +CL - - - - - 2 - gnl|BL_ORD_ID|1654 - 146570|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 - 1654 - 17 - - - 1 - 11.5418 - 18 - 129.081 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 5 - 0 - 9 - SWMPALECL - SWDQMWKCL - SW +CL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 990 - Query_990 - M_4579 - 9 - - - 1 - gnl|BL_ORD_ID|664 - 39591|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 - 664 - 20 - - - 1 - 11.927 - 19 - 59.5549 - 1 - 5 - 10 - 14 - 0 - 0 - 4 - 4 - 0 - 5 - SWPLW - SWCLW - SW LW - - - - - 2 - gnl|BL_ORD_ID|1120 - 74387|Genome polyprotein|P26664.3|Hepatitis C virus (isolate 1)|11104 - 1120 - 9 - - - 1 - 11.927 - 19 - 76.3762 - 1 - 5 - 3 - 7 - 0 - 0 - 4 - 4 - 0 - 5 - SWPLW - SWCLW - SW LW - - - - - 3 - gnl|BL_ORD_ID|1119 - 74386|HCV-1|AAA45676.1|Hepatitis C virus|11103 - 1119 - 8 - - - 1 - 11.927 - 19 - 82.8897 - 1 - 5 - 3 - 7 - 0 - 0 - 4 - 4 - 0 - 5 - SWPLW - SWCLW - SW LW - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 991 - Query_991 - M_4580 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 992 - Query_992 - M_4581 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 993 - Query_993 - M_4582 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 994 - Query_994 - M_4583 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 995 - Query_995 - M_4584 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 996 - Query_996 - M_4585 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 997 - Query_997 - M_4586 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 998 - Query_998 - M_4587 - 9 - - - 1 - gnl|BL_ORD_ID|1175 - 79390|Protein Tax-1|P0C213.1|Human T-cell lymphotropic virus type 1 (african isolate)|39015 - 1175 - 15 - - - 1 - 13.853 - 24 - 5.77703 - 3 - 8 - 2 - 7 - 0 - 0 - 5 - 6 - 0 - 6 - FNNLHL - FHNLHL - F+NLHL - - - - - 2 - gnl|BL_ORD_ID|2167 - 189571|Antigen 85-B|P0C5B9.1|Mycobacterium tuberculosis|1773 - 2167 - 9 - - - 1 - 13.0826 - 22 - 20.7937 - 4 - 9 - 2 - 7 - 0 - 0 - 4 - 4 - 0 - 6 - NNLHLW - NNTRLW - NN LW - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 999 - Query_999 - M_4588 - 9 - - - 1 - gnl|BL_ORD_ID|389 - 23807|tax|AAG48731.1|Human T-lymphotropic virus 2|11909 - 389 - 23 - - - 1 - 11.1566 - 17 - 170.423 - 2 - 9 - 11 - 18 - 0 - 0 - 4 - 5 - 0 - 8 - YGVNLYQF - YGYPVYVF - YG +Y F - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1000 - Query_1000 - M_4589 - 9 - - - 1 - gnl|BL_ORD_ID|2128 - 186620|polyprotein|AFP27208.1|Dengue virus 4|11070 - 2128 - 9 - - - 1 - 11.1566 - 17 - 291.863 - 4 - 9 - 1 - 6 - 0 - 0 - 3 - 6 - 0 - 6 - YILITI - YVILTI - Y+++TI - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1001 - Query_1001 - M_4590 - 9 - - - 1 - gnl|BL_ORD_ID|1687 - 149053|NS3 gene product|AAB02124.1|Hepatitis C virus|11103 - 1687 - 18 - - - 1 - 15.0086 - 27 - 1.25718 - 2 - 8 - 8 - 14 - 0 - 0 - 4 - 6 - 0 - 7 - YKFLAPW - YRFVAPG - Y+F+AP - - - - - 2 - gnl|BL_ORD_ID|2333 - 423082|Genome polyprotein|P26664.3|Hepatitis C virus genotype 1|41856 - 2333 - 9 - - - 1 - 15.0086 - 27 - 1.49881 - 2 - 7 - 1 - 6 - 0 - 0 - 4 - 6 - 0 - 6 - YKFLAP - YRFVAP - Y+F+AP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1002 - Query_1002 - M_4591 - 9 - - - 1 - gnl|BL_ORD_ID|1687 - 149053|NS3 gene product|AAB02124.1|Hepatitis C virus|11103 - 1687 - 18 - - - 1 - 15.0086 - 27 - 1.19394 - 3 - 9 - 5 - 11 - 0 - 0 - 4 - 6 - 0 - 7 - PSIHRFI - PGIYRFV - P I+RF+ - - - - - 2 - gnl|BL_ORD_ID|355 - 22046|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 - 355 - 10 - - - 1 - 13.853 - 24 - 4.53299 - 3 - 8 - 5 - 10 - 0 - 0 - 4 - 5 - 0 - 6 - PSIHRF - PGIYRF - P I+RF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1003 - Query_1003 - M_4592 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1004 - Query_1004 - M_4593 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1005 - Query_1005 - M_4594 - 9 - - - 1 - gnl|BL_ORD_ID|418 - 25237|Transcription activator BRLF1|P03209.1|Human herpesvirus 4 strain B95-8|10377 - 418 - 15 - - - 1 - 14.6234 - 26 - 2.30367 - 2 - 7 - 9 - 14 - 0 - 0 - 4 - 5 - 0 - 6 - YVMDHF - YVLDHL - YV+DH - - - - - 2 - gnl|BL_ORD_ID|1156 - 76333|BRLF1|ABB89247.1|Human gammaherpesvirus 4|10376 - 1156 - 9 - - - 1 - 14.2382 - 25 - 3.49608 - 2 - 7 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - YVMDHF - YVLDHL - YV+DH - - - - - 3 - gnl|BL_ORD_ID|1016 - 67503|Genome polyprotein|P26662.3|Hepatitis C virus|11103 - 1016 - 10 - - - 1 - 13.4678 - 23 - 10.2566 - 1 - 7 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - SYVMDHF - TYVYDHL - +YV DH - - - - - 4 - gnl|BL_ORD_ID|438 - 27011|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 - 438 - 9 - - - 1 - 12.6974 - 21 - 39.8499 - 3 - 8 - 1 - 6 - 0 - 0 - 3 - 5 - 0 - 6 - VMDHFD - ILDSFD - ++D FD - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1006 - Query_1006 - M_4595 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1007 - Query_1007 - M_4596 - 9 - - - 1 - gnl|BL_ORD_ID|1520 - 140600|glutamine synthetase GLNA1 (glutamine synthase) (GS-I)|NP_216736.1|Mycobacterium tuberculosis H37Rv|83332 - 1520 - 9 - - - 1 - 11.927 - 19 - 89.9387 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 5 - 0 - 9 - SYWGVFAPI - SLWKDGAPL - S W AP+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1008 - Query_1008 - M_4597 - 9 - - - 1 - gnl|BL_ORD_ID|1190 - 95262|LAMP|AAK72632.1|Human gammaherpesvirus 8|37296 - 1190 - 15 - - - 1 - 12.3122 - 20 - 59.339 - 4 - 9 - 9 - 14 - 0 - 0 - 4 - 6 - 0 - 6 - KIVSSI - KLVSSV - K+VSS+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1009 - Query_1009 - M_4598 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1010 - Query_1010 - M_4599 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1011 - Query_1011 - M_4600 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1012 - Query_1012 - M_4601 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1013 - Query_1013 - M_4602 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1014 - Query_1014 - M_4603 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1015 - Query_1015 - M_4604 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1016 - Query_1016 - M_4605 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1017 - Query_1017 - M_4606 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1018 - Query_1018 - M_4607 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1019 - Query_1019 - M_4608 - 9 - - - 1 - gnl|BL_ORD_ID|401 - 24535|EBNA-1 protein|Q777E1|Human gammaherpesvirus 4|10376 - 401 - 9 - - - 1 - 13.853 - 24 - 7.07804 - 3 - 8 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - GEVNYF - GEADYF - GE +YF - - - - - 2 - gnl|BL_ORD_ID|402 - 24536|EBNA-1|YP_401677.1|Human gammaherpesvirus 4|10376 - 402 - 11 - - - 1 - 13.4678 - 23 - 8.44862 - 3 - 8 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - GEVNYF - GEADYF - GE +YF - - - - - 3 - gnl|BL_ORD_ID|1170 - 79294|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 1170 - 15 - - - 1 - 9.61583 - 13 - 1034.49 - 2 - 9 - 3 - 10 - 0 - 0 - 4 - 4 - 0 - 8 - FGEVNYFF - FGYPVYVF - FG Y F - - - - - 4 - gnl|BL_ORD_ID|572 - 35845|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 - 572 - 9 - - - 1 - 9.61583 - 13 - 1600.23 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 4 - 0 - 8 - FGEVNYFF - FGYPVYVF - FG Y F - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1020 - Query_1020 - M_4609 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1021 - Query_1021 - M_4610 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1022 - Query_1022 - M_4611 - 9 - - - 1 - gnl|BL_ORD_ID|94 - 6556|X protein|AAP06597.1|Hepatitis B virus|10407 - 94 - 9 - - - 1 - 13.4678 - 23 - 9.02895 - 2 - 8 - 3 - 9 - 0 - 0 - 4 - 5 - 0 - 7 - FNDWFEI - FKDWEEL - F DW E+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1023 - Query_1023 - M_4612 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1024 - Query_1024 - M_4613 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1025 - Query_1025 - M_4614 - 9 - - - 1 - gnl|BL_ORD_ID|1528 - 140686|ESAT-6-like protein esxH|P0A568.2|Mycobacterium tuberculosis|1773 - 1528 - 9 - - - 1 - 10.001 - 14 - 831.41 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 4 - 0 - 7 - HASLSNH - HAMSSTH - HA S H - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1026 - Query_1026 - M_4615 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1027 - Query_1027 - M_4616 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1028 - Query_1028 - M_4617 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1029 - Query_1029 - M_4618 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1030 - Query_1030 - M_4619 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1031 - Query_1031 - M_4620 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1032 - Query_1032 - M_4621 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1033 - Query_1033 - M_4622 - 9 - - - 1 - gnl|BL_ORD_ID|563 - 34642|methionine sulfoxide reductase B|YP_169878.1|Francisella tularensis subsp. tularensis SCHU S4|177416 - 563 - 10 - - - 1 - 14.2382 - 25 - 3.05549 - 1 - 6 - 5 - 10 - 0 - 0 - 4 - 5 - 0 - 6 - THREGI - NHRQGI - HR+GI - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1034 - Query_1034 - M_4623 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1035 - Query_1035 - M_4624 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1036 - Query_1036 - M_4625 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1037 - Query_1037 - M_4626 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1038 - Query_1038 - M_4627 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1039 - Query_1039 - M_4628 - 9 - - - 1 - gnl|BL_ORD_ID|437 - 27000|Heat shock protein HSP 90-beta|P08238.4|Homo sapiens|9606 - 437 - 9 - - - 1 - 13.853 - 24 - 7.32819 - 2 - 7 - 2 - 7 - 0 - 0 - 5 - 6 - 0 - 6 - LDKKLE - LDKKVE - LDKK+E - - - - - 2 - gnl|BL_ORD_ID|1126 - 74635|matrix protein|AEQ63649.1|Respiratory syncytial virus|12814 - 1126 - 9 - - - 1 - 10.3862 - 15 - 663.415 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 6 - 0 - 8 - LDKKLEYY - LEKESIYY - L+K+ YY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1040 - Query_1040 - M_4629 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1041 - Query_1041 - M_4630 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1042 - Query_1042 - M_4631 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1043 - Query_1043 - M_4632 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1044 - Query_1044 - M_4633 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1045 - Query_1045 - M_4634 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1046 - Query_1046 - M_4635 - 9 - - - 1 - gnl|BL_ORD_ID|1653 - 146569|polyprotein|ADF97231.1|Hepatitis C virus subtype 3a|356426 - 1653 - 17 - - - 1 - 12.3122 - 20 - 41.9577 - 4 - 8 - 5 - 9 - 0 - 0 - 3 - 4 - 0 - 5 - SWTCL - TWKCL - +W CL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1047 - Query_1047 - M_4636 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1048 - Query_1048 - M_4637 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1049 - Query_1049 - M_4638 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1050 - Query_1050 - M_4639 - 9 - - - 1 - gnl|BL_ORD_ID|341 - 21385|polyprotein|AAY82034.1|Hepatitis C virus genotype 1|41856 - 341 - 10 - - - 1 - 13.853 - 24 - 5.29638 - 3 - 9 - 1 - 7 - 0 - 0 - 3 - 6 - 0 - 7 - GNRTKCF - GNASRCW - GN ++C+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1051 - Query_1051 - M_4640 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1052 - Query_1052 - M_4641 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1053 - Query_1053 - M_4642 - 9 - - - 1 - gnl|BL_ORD_ID|551 - 33856|polyprotein|BAA03375.1|Hepatitis C virus|11103 - 551 - 9 - - - 1 - 13.853 - 24 - 5.55396 - 3 - 8 - 3 - 8 - 0 - 0 - 5 - 6 - 0 - 6 - SERSKP - SERSQP - SERS+P - - - - - 2 - gnl|BL_ORD_ID|1284 - 102150|nef protein|ACR27119.1|Human immunodeficiency virus 1|11676 - 1284 - 9 - - - 1 - 9.61583 - 13 - 1256.63 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 5 - 0 - 9 - TPSERSKPL - TPQVPLRPM - TP +P+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1054 - Query_1054 - M_4643 - 9 - - - 1 - gnl|BL_ORD_ID|1683 - 149037|NS4B protein|NP_751926.1|Hepatitis C virus (isolate H77)|63746 - 1683 - 11 - - - 1 - 13.0826 - 22 - 13.9783 - 1 - 7 - 4 - 10 - 0 - 0 - 4 - 6 - 0 - 7 - TPSTQTH - TPAVQTN - TP+ QT+ - - - - - 2 - gnl|BL_ORD_ID|2104 - 186008|polyprotein|AGI95993.1|Dengue virus 4|11070 - 2104 - 9 - - - 1 - 11.1566 - 17 - 221.814 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 4 - 0 - 9 - TPSTQTHPL - TPPGATDPF - TP T P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1055 - Query_1055 - M_4644 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1056 - Query_1056 - M_4645 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1057 - Query_1057 - M_4646 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1058 - Query_1058 - M_4647 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1059 - Query_1059 - M_4648 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1060 - Query_1060 - M_4649 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1061 - Query_1061 - M_4650 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1062 - Query_1062 - M_4651 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1063 - Query_1063 - M_4652 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1064 - Query_1064 - M_4653 - 9 - - - 1 - gnl|BL_ORD_ID|1775 - 155637|tegument protein|CAB06732.1|Human alphaherpesvirus 2|10310 - 1775 - 15 - - - 1 - 15.0086 - 27 - 1.24275 - 3 - 9 - 3 - 9 - 0 - 0 - 5 - 5 - 0 - 7 - GPCRRRF - GPADRRF - GP RRF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1065 - Query_1065 - M_4654 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1066 - Query_1066 - M_4655 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1067 - Query_1067 - M_4656 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1068 - Query_1068 - M_4657 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1069 - Query_1069 - M_4658 - 9 - - - 1 - gnl|BL_ORD_ID|1395 - 110394|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1395 - 32 - - - 1 - 13.4678 - 23 - 12.8091 - 3 - 9 - 4 - 10 - 0 - 0 - 4 - 5 - 0 - 7 - NCNRHLC - NCQKPLC - NC + LC - - - - - 2 - gnl|BL_ORD_ID|957 - 62903|Genome polyprotein|P27909.2|Dengue virus type 1 Hawaii|10000440 - 957 - 20 - - - 1 - 10.7714 - 16 - 300.133 - 1 - 9 - 10 - 18 - 0 - 0 - 3 - 5 - 0 - 9 - TRNCNRHLC - SRNKKPRIC - +RN +C - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1070 - Query_1070 - M_4659 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1071 - Query_1071 - M_4660 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1072 - Query_1072 - M_4661 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1073 - Query_1073 - M_4662 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1074 - Query_1074 - M_4663 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1075 - Query_1075 - M_4664 - 9 - - - 1 - gnl|BL_ORD_ID|525 - 32243|C protein|BAB60863.1|Measles virus|11234 - 525 - 9 - - - 1 - 12.6974 - 21 - 33.6262 - 2 - 8 - 1 - 7 - 0 - 0 - 3 - 5 - 0 - 7 - RSWGTPQ - KLWESPQ - + W +PQ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1076 - Query_1076 - M_4665 - 9 - - - 1 - gnl|BL_ORD_ID|793 - 53041|phosphorylated matrix protein (pp65)|AAA45996.1|Human betaherpesvirus 5|10359 - 793 - 11 - - - 1 - 13.0826 - 22 - 17.7949 - 3 - 9 - 3 - 9 - 0 - 0 - 5 - 5 - 0 - 7 - TPHSTRC - TPDSTPC - TP ST C - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1077 - Query_1077 - M_4666 - 9 - - - 1 - gnl|BL_ORD_ID|2106 - 186041|polyprotein|AGO67248.1|Dengue virus 2|11060 - 2106 - 10 - - - 1 - 14.6234 - 26 - 1.69864 - 1 - 9 - 1 - 9 - 0 - 0 - 6 - 7 - 0 - 9 - TRVGSKLLI - TRVGTKHAI - TRVG+K I - - - - - 2 - gnl|BL_ORD_ID|2064 - 184864|polyprotein|AGO67248.1|Dengue virus 2|11060 - 2064 - 9 - - - 1 - 14.2382 - 25 - 3.21187 - 1 - 6 - 4 - 9 - 0 - 0 - 5 - 6 - 0 - 6 - TRVGSK - TRVGTK - TRVG+K - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1078 - Query_1078 - M_4667 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1079 - Query_1079 - M_4668 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1080 - Query_1080 - M_4669 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1081 - Query_1081 - M_4670 - 9 - - - 1 - gnl|BL_ORD_ID|860 - 56343|structural protein|BAA00705.1|Hepatitis C virus|11103 - 860 - 10 - - - 1 - 12.3122 - 20 - 40.5114 - 3 - 7 - 5 - 9 - 0 - 0 - 4 - 4 - 0 - 5 - DGRNY - DGVNY - DG NY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1082 - Query_1082 - M_4671 - 9 - - - 1 - gnl|BL_ORD_ID|1007 - 66405|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 1007 - 20 - - - 1 - 15.779 - 29 - 0.372461 - 2 - 9 - 13 - 20 - 0 - 0 - 6 - 6 - 0 - 8 - TFDRLAYL - TFDRLQVL - TFDRL L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1083 - Query_1083 - M_4672 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1084 - Query_1084 - M_4673 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1085 - Query_1085 - M_4674 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1086 - Query_1086 - M_4675 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1087 - Query_1087 - M_4676 - 9 - - - 1 - gnl|BL_ORD_ID|1060 - 69799|envelope glycoprotein|BAE96221.1|Human immunodeficiency virus 1|11676 - 1060 - 10 - - - 1 - 14.6234 - 26 - 2.37049 - 3 - 9 - 4 - 10 - 0 - 0 - 5 - 5 - 0 - 7 - SPQPQEV - DPNPQEV - P PQEV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1088 - Query_1088 - M_4677 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1089 - Query_1089 - M_4678 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1090 - Query_1090 - M_4679 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1091 - Query_1091 - M_4680 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1092 - Query_1092 - M_4681 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1093 - Query_1093 - M_4682 - 9 - - - 1 - gnl|BL_ORD_ID|2258 - 288104|nef protein|ACR27130.1|Human immunodeficiency virus 1|11676 - 2258 - 18 - - - 1 - 13.4678 - 23 - 7.92816 - 3 - 9 - 4 - 10 - 0 - 0 - 2 - 7 - 0 - 7 - YPLKPEI - FPVRPQV - +P++P++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1094 - Query_1094 - M_4683 - 9 - - - 1 - gnl|BL_ORD_ID|2258 - 288104|nef protein|ACR27130.1|Human immunodeficiency virus 1|11676 - 2258 - 18 - - - 1 - 13.4678 - 23 - 7.92816 - 3 - 9 - 4 - 10 - 0 - 0 - 2 - 7 - 0 - 7 - YPLKPEI - FPVRPQV - +P++P++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1095 - Query_1095 - M_4684 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1096 - Query_1096 - M_4685 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1097 - Query_1097 - M_4686 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1098 - Query_1098 - M_4687 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1099 - Query_1099 - M_4688 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1100 - Query_1100 - M_4689 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1101 - Query_1101 - M_4690 - 9 - - - 1 - gnl|BL_ORD_ID|716 - 44214|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 - 716 - 11 - - - 1 - 13.0826 - 22 - 18.7359 - 2 - 8 - 5 - 11 - 0 - 0 - 4 - 6 - 0 - 7 - FTRVSAY - FTKNSAF - FT+ SA+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1102 - Query_1102 - M_4691 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1103 - Query_1103 - M_4692 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1104 - Query_1104 - M_4693 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1105 - Query_1105 - M_4694 - 9 - - - 1 - gnl|BL_ORD_ID|1931 - 180758|Nonstructural protein NS5|NP_739590.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1931 - 15 - - - 1 - 13.4678 - 23 - 8.59146 - 2 - 8 - 3 - 9 - 0 - 0 - 4 - 5 - 0 - 7 - HFDHFHP - HYDQDHP - H+D HP - - - - - 2 - gnl|BL_ORD_ID|1943 - 180817|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1943 - 9 - - - 1 - 13.0826 - 22 - 13.9535 - 2 - 8 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - HFDHFHP - HYDQDHP - H+D HP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1106 - Query_1106 - M_4695 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1107 - Query_1107 - M_4696 - 9 - - - 1 - gnl|BL_ORD_ID|2272 - 419005|polyprotein|AGW21594.1|Dengue virus 1|11053 - 2272 - 10 - - - 1 - 14.2382 - 25 - 3.68732 - 4 - 9 - 2 - 7 - 0 - 0 - 6 - 6 - 0 - 6 - LAVSGV - LAVSGV - LAVSGV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1108 - Query_1108 - M_4697 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1109 - Query_1109 - M_4698 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1110 - Query_1110 - M_4699 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1111 - Query_1111 - M_4700 - 9 - - - 1 - gnl|BL_ORD_ID|1608 - 143705|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 1608 - 9 - - - 1 - 14.2382 - 25 - 3.10506 - 5 - 9 - 5 - 9 - 0 - 0 - 5 - 5 - 0 - 5 - FPITL - FPITL - FPITL - - - - - 2 - gnl|BL_ORD_ID|2215 - 193071|Nef protein|Q9WPU2|Human immunodeficiency virus 1|11676 - 2215 - 10 - - - 1 - 13.0826 - 22 - 22.3554 - 4 - 9 - 1 - 6 - 0 - 0 - 3 - 6 - 0 - 6 - QFPITL - RYPLTL - ++P+TL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1112 - Query_1112 - M_4701 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1113 - Query_1113 - M_4702 - 9 - - - 1 - gnl|BL_ORD_ID|1437 - 119822|110 kd polyprotein precursor|CAA28880.1|Rubella virus|11041 - 1437 - 29 - - - 1 - 13.0826 - 22 - 19.5886 - 3 - 9 - 11 - 17 - 0 - 0 - 4 - 5 - 0 - 7 - RGTGAVY - EGEGAVF - G GAV+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1114 - Query_1114 - M_4703 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1115 - Query_1115 - M_4704 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1116 - Query_1116 - M_4705 - 9 - - - 1 - gnl|BL_ORD_ID|1731 - 150556|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1731 - 10 - - - 1 - 13.4678 - 23 - 11.9953 - 1 - 7 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - VLDEMRC - VIDPRRC - V+D RC - - - - - 2 - gnl|BL_ORD_ID|859 - 56310|polyprotein|AGO67248.1|Dengue virus 2|11060 - 859 - 10 - - - 1 - 13.0826 - 22 - 13.0843 - 1 - 7 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - VLDEMRC - VIDPRRC - V+D RC - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1117 - Query_1117 - M_4706 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1118 - Query_1118 - M_4707 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1119 - Query_1119 - M_4708 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1120 - Query_1120 - M_4709 - 9 - - - 1 - gnl|BL_ORD_ID|1000 - 65810|sporozoite surface protein 2|NP_705260.1|Plasmodium falciparum 3D7|36329 - 1000 - 10 - - - 1 - 12.6974 - 21 - 26.9859 - 4 - 9 - 3 - 8 - 0 - 0 - 4 - 4 - 0 - 6 - YRGHPA - YAGEPA - Y G PA - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1121 - Query_1121 - M_4710 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1122 - Query_1122 - M_4711 - 9 - - - 1 - gnl|BL_ORD_ID|459 - 27878|large surface antigen|CAC87019.1|Hepatitis B virus|10407 - 459 - 9 - - - 1 - 13.0826 - 22 - 16.8921 - 3 - 7 - 4 - 8 - 0 - 0 - 4 - 4 - 0 - 5 - PSQWA - PSSWA - PS WA - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1123 - Query_1123 - M_4712 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1124 - Query_1124 - M_4713 - 9 - - - 1 - gnl|BL_ORD_ID|897 - 59090|nonstructural protein 4B|YP_001527886.1|West Nile virus NY-99|10000971 - 897 - 18 - - - 1 - 11.1566 - 17 - 174.368 - 1 - 8 - 9 - 16 - 0 - 0 - 4 - 5 - 0 - 8 - VRELRDMG - VKENFSMG - V+E MG - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1125 - Query_1125 - M_4714 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1126 - Query_1126 - M_4715 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1127 - Query_1127 - M_4716 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1128 - Query_1128 - M_4717 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1129 - Query_1129 - M_4718 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1130 - Query_1130 - M_4719 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1131 - Query_1131 - M_4720 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1132 - Query_1132 - M_4721 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1133 - Query_1133 - M_4722 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1134 - Query_1134 - M_4723 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1135 - Query_1135 - M_4724 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1136 - Query_1136 - M_4725 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1137 - Query_1137 - M_4726 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1138 - Query_1138 - M_4727 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1139 - Query_1139 - M_4728 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1140 - Query_1140 - M_4729 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1141 - Query_1141 - M_4730 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1142 - Query_1142 - M_4731 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1143 - Query_1143 - M_4732 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1144 - Query_1144 - M_4733 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1145 - Query_1145 - M_4734 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1146 - Query_1146 - M_4735 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1147 - Query_1147 - M_4736 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1148 - Query_1148 - M_4737 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1149 - Query_1149 - M_4738 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1150 - Query_1150 - M_4739 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1151 - Query_1151 - M_4740 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1152 - Query_1152 - M_4741 - 9 - - - 1 - gnl|BL_ORD_ID|2098 - 185817|envelope protein|AGW23590.1|Dengue virus 4|11070 - 2098 - 10 - - - 1 - 13.0826 - 22 - 16.3922 - 4 - 9 - 1 - 6 - 0 - 0 - 3 - 5 - 0 - 6 - DWLVRI - SWMIRI - W++RI - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1153 - Query_1153 - M_4742 - 9 - - - 1 - gnl|BL_ORD_ID|756 - 50292|gag protein|ACR27140.1|Human immunodeficiency virus 1|11676 - 756 - 11 - - - 1 - 14.2382 - 25 - 3.03901 - 1 - 7 - 2 - 8 - 0 - 0 - 4 - 6 - 0 - 7 - VVAPRTL - AISPRTL - ++PRTL - - - - - 2 - gnl|BL_ORD_ID|472 - 28657|gag protein|CAB00235.1|Human immunodeficiency virus 1|11676 - 472 - 9 - - - 1 - 14.2382 - 25 - 3.74233 - 2 - 7 - 1 - 6 - 0 - 0 - 4 - 6 - 0 - 6 - VAPRTL - ISPRTL - ++PRTL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1154 - Query_1154 - M_4743 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1155 - Query_1155 - M_4744 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1156 - Query_1156 - M_4745 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1157 - Query_1157 - M_4746 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1158 - Query_1158 - M_4747 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1159 - Query_1159 - M_4748 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1160 - Query_1160 - M_4749 - 9 - - - 1 - gnl|BL_ORD_ID|834 - 54824|polyprotein precursor|BAA01583.1|Hepatitis C virus|11103 - 834 - 9 - - - 1 - 11.5418 - 18 - 173.047 - 1 - 8 - 2 - 9 - 0 - 0 - 3 - 5 - 0 - 8 - VYHLFCAL - LWHYPCTL - ++H C L - - - - - 2 - gnl|BL_ORD_ID|833 - 54821|E2 protein|AAM33354.1|Hepatitis C virus subtype 1a|31646 - 833 - 9 - - - 1 - 10.7714 - 16 - 429.931 - 1 - 8 - 2 - 9 - 0 - 0 - 2 - 5 - 0 - 8 - VYHLFCAL - LWHYPCTI - ++H C + - - - - - 3 - gnl|BL_ORD_ID|1149 - 75636|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 1149 - 10 - - - 1 - 10.3862 - 15 - 485 - 1 - 8 - 3 - 10 - 0 - 0 - 2 - 5 - 0 - 8 - VYHLFCAL - LWHYPCTI - ++H C + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1161 - Query_1161 - M_4750 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1162 - Query_1162 - M_4751 - 9 - - - 1 - gnl|BL_ORD_ID|771 - 51526|HCV-1|AAA45676.1|Hepatitis C virus|11103 - 771 - 10 - - - 1 - 13.4678 - 23 - 10.0795 - 3 - 9 - 2 - 8 - 0 - 0 - 5 - 6 - 0 - 7 - LRRHRDV - LRRHIDL - LRRH D+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1163 - Query_1163 - M_4752 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1164 - Query_1164 - M_4753 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1165 - Query_1165 - M_4754 - 9 - - - 1 - gnl|BL_ORD_ID|1015 - 67471|Genome polyprotein|Q99IB8.3|Hepatitis C virus JFH-1|356411 - 1015 - 9 - - - 1 - 12.6974 - 21 - 36.611 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 4 - 0 - 6 - VYSEYG - TYSTYG - YS YG - - - - - 2 - gnl|BL_ORD_ID|474 - 29182|polyprotein|BAD73991.1|Hepatitis C virus subtype 1b|31647 - 474 - 9 - - - 1 - 12.6974 - 21 - 39.8499 - 1 - 6 - 2 - 7 - 0 - 0 - 4 - 4 - 0 - 6 - VYSEYG - TYSTYG - YS YG - - - - - 3 - gnl|BL_ORD_ID|1333 - 107873|Genome polyprotein|P26664.3|Hepatitis C virus|11103 - 1333 - 10 - - - 1 - 12.3122 - 20 - 41.1969 - 1 - 6 - 5 - 10 - 0 - 0 - 4 - 4 - 0 - 6 - VYSEYG - TYSTYG - YS YG - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1166 - Query_1166 - M_4755 - 9 - - - 1 - gnl|BL_ORD_ID|1418 - 111816|polyprotein|BAA09072.1|Hepatitis C virus|11103 - 1418 - 12 - - - 1 - 13.4678 - 23 - 11.0162 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 6 - 0 - 9 - VYSLRTRAI - AYSQQTRGL - YS +TR + - - - - - 2 - gnl|BL_ORD_ID|80 - 5934|polyprotein|CAB53095.1|Hepatitis C virus subtype 1b|31647 - 80 - 9 - - - 1 - 13.4678 - 23 - 12.57 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 6 - 0 - 9 - VYSLRTRAI - AYSQQTRGL - YS +TR + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1167 - Query_1167 - M_4756 - 9 - - - 1 - gnl|BL_ORD_ID|1376 - 108965|Prolipoprotein diacylglyceryl transferase|O06131.1|Mycobacterium tuberculosis|1773 - 1376 - 9 - - - 1 - 12.3122 - 20 - 41.9234 - 1 - 8 - 2 - 9 - 0 - 0 - 3 - 6 - 0 - 8 - VYSLYWSI - LYELIWNV - +Y L W++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1168 - Query_1168 - M_4757 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1169 - Query_1169 - M_4758 - 9 - - - 1 - gnl|BL_ORD_ID|1297 - 103389|unnamed protein product [Hepatitis C virus]|BAA14035.1|Hepatitis C virus|11103 - 1297 - 20 - - - 1 - 13.853 - 24 - 4.89444 - 2 - 9 - 3 - 10 - 0 - 0 - 4 - 7 - 0 - 8 - YVVTKFLM - HPITKFVM - + +TKF+M - - - - - 2 - gnl|BL_ORD_ID|1092 - 72233|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 - 1092 - 15 - - - 1 - 12.6974 - 21 - 31.7906 - 2 - 9 - 7 - 14 - 0 - 0 - 5 - 6 - 0 - 8 - YVVTKFLM - YVVLLFLL - YVV FL+ - - - - - 3 - gnl|BL_ORD_ID|203 - 15110|Genome polyprotein|P26663.3|Hepatitis C virus|11103 - 203 - 9 - - - 1 - 11.5418 - 18 - 152.614 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 6 - 0 - 8 - YVVTKFLM - YVLLLFLL - YV+ FL+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1170 - Query_1170 - M_4759 - 9 - - - 1 - gnl|BL_ORD_ID|1128 - 74774|LMP1 protein (Epstein-Barr virus, putative LYDMA gene)|Q777A4|Human gammaherpesvirus 4|10376 - 1128 - 9 - - - 1 - 12.6974 - 21 - 35.9943 - 3 - 8 - 1 - 6 - 0 - 0 - 5 - 6 - 0 - 6 - YLLELL - YLLEML - YLLE+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1171 - Query_1171 - M_4760 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1172 - Query_1172 - M_4761 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1173 - Query_1173 - M_4762 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1174 - Query_1174 - M_4763 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1175 - Query_1175 - M_4764 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1176 - Query_1176 - M_4765 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1177 - Query_1177 - M_4766 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1178 - Query_1178 - M_4767 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1179 - Query_1179 - M_4768 - 9 - - - 1 - gnl|BL_ORD_ID|23 - 1516|Nucleoprotein|P03418.1|Human respiratory syncytial virus A2|11259 - 23 - 14 - - - 1 - 13.4678 - 23 - 10.3614 - 1 - 7 - 4 - 10 - 0 - 0 - 3 - 5 - 0 - 7 - WHVPNKP - YHILNNP - +H+ N P - - - - - 2 - gnl|BL_ORD_ID|1110 - 73059|kaposin|AAC57155.1|Human gammaherpesvirus 8|37296 - 1110 - 15 - - - 1 - 12.3122 - 20 - 58.4135 - 1 - 9 - 3 - 11 - 0 - 0 - 3 - 5 - 0 - 9 - WHVPNKPPM - WRLGAIPPL - W + PP+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1180 - Query_1180 - M_4769 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1181 - Query_1181 - M_4770 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1182 - Query_1182 - M_4771 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1183 - Query_1183 - M_4772 - 9 - - - 1 - gnl|BL_ORD_ID|554 - 34027|DNA polymerase|CAA10434.1|Hepatitis B virus|10407 - 554 - 9 - - - 1 - 13.0826 - 22 - 20.0871 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - LSNFQGRY - VGNFTGLY - + NF G Y - - - - - 2 - gnl|BL_ORD_ID|1630 - 146213|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 - 1630 - 18 - - - 1 - 11.927 - 19 - 86.7645 - 1 - 7 - 3 - 9 - 0 - 0 - 4 - 4 - 0 - 7 - WLSNFQG - WESVFTG - W S F G - - - - - 3 - gnl|BL_ORD_ID|1628 - 146188|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 - 1628 - 18 - - - 1 - 11.927 - 19 - 88.0652 - 1 - 7 - 3 - 9 - 0 - 0 - 4 - 4 - 0 - 7 - WLSNFQG - WESVFTG - W S F G - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1184 - Query_1184 - M_4773 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1185 - Query_1185 - M_4774 - 9 - - - 1 - gnl|BL_ORD_ID|657 - 38974|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 657 - 11 - - - 1 - 13.853 - 24 - 4.28904 - 4 - 9 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - QEGPEY - QRGPQY - Q GP+Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1186 - Query_1186 - M_4775 - 9 - - - 1 - gnl|BL_ORD_ID|1144 - 75438|polyprotein|AAF65962.1|Hepatitis C virus|11103 - 1144 - 20 - - - 1 - 15.779 - 29 - 0.398839 - 1 - 9 - 3 - 11 - 0 - 0 - 5 - 7 - 0 - 9 - WPLTHSQGM - WPLYGNEGM - WPL ++GM - - - - - 2 - gnl|BL_ORD_ID|1723 - 150450|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1723 - 9 - - - 1 - 14.2382 - 25 - 4.3647 - 2 - 8 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - PLTHSQG - PVTHSSA - P+THS - - - - - 3 - gnl|BL_ORD_ID|1724 - 150451|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1724 - 10 - - - 1 - 13.853 - 24 - 4.8573 - 2 - 8 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - PLTHSQG - PVTHSSA - P+THS - - - - - 4 - gnl|BL_ORD_ID|2051 - 184702|non-structural protein 1|AGM49312.1|Dengue virus|12637 - 2051 - 9 - - - 1 - 13.853 - 24 - 5.65074 - 1 - 6 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - WPLTHS - WPKTHT - WP TH+ - - - - - 5 - gnl|BL_ORD_ID|1139 - 75356|EBNA3A nuclear protein|Q8AZJ8|Human gammaherpesvirus 4|10376 - 1139 - 9 - - - 1 - 13.4678 - 23 - 13.0154 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 5 - 0 - 9 - WPLTHSQGM - YPLHEQHGM - +PL GM - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1187 - Query_1187 - M_4776 - 9 - - - 1 - gnl|BL_ORD_ID|1786 - 159299|polyprotein|AAC03058.1|Hepatitis C virus subtype 3a|356426 - 1786 - 9 - - - 1 - 14.2382 - 25 - 4.21767 - 2 - 9 - 2 - 9 - 0 - 0 - 5 - 6 - 0 - 8 - QRQHKLTI - QRQRKVTF - QRQ K+T - - - - - 2 - gnl|BL_ORD_ID|1007 - 66405|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 1007 - 20 - - - 1 - 13.853 - 24 - 4.65152 - 1 - 9 - 6 - 14 - 0 - 0 - 5 - 6 - 0 - 9 - WQRQHKLTI - CQRQKKVTF - QRQ K+T - - - - - 3 - gnl|BL_ORD_ID|1617 - 144480|polyprotein|ACA50684.1|Hepatitis C virus subtype 1b|31647 - 1617 - 9 - - - 1 - 13.853 - 24 - 5.00793 - 2 - 9 - 2 - 9 - 0 - 0 - 5 - 6 - 0 - 8 - QRQHKLTI - QRQKKVTF - QRQ K+T - - - - - 4 - gnl|BL_ORD_ID|2051 - 184702|non-structural protein 1|AGM49312.1|Dengue virus|12637 - 2051 - 9 - - - 1 - 11.927 - 19 - 75.1319 - 1 - 7 - 2 - 8 - 0 - 0 - 3 - 4 - 0 - 7 - WQRQHKL - WPKTHTL - W + H L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1188 - Query_1188 - M_4777 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1189 - Query_1189 - M_4778 - 9 - - - 1 - gnl|BL_ORD_ID|1812 - 177647|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 - 1812 - 16 - - - 1 - 13.853 - 24 - 4.97938 - 1 - 9 - 6 - 14 - 0 - 0 - 4 - 7 - 0 - 9 - WSDQLSAFS - WMNRLIAFA - W ++L AF+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1190 - Query_1190 - M_4779 - 9 - - - 1 - gnl|BL_ORD_ID|921 - 59787|Hemagglutinin glycoprotein|P08362.1|Measles virus strain Edmonston|11235 - 921 - 10 - - - 1 - 13.0826 - 22 - 13.3135 - 4 - 9 - 5 - 10 - 0 - 0 - 3 - 6 - 0 - 6 - VFQIGI - VFEVGV - VF++G+ - - - - - 2 - gnl|BL_ORD_ID|2123 - 186524|polyprotein|AGW21594.1|Dengue virus 1|11053 - 2123 - 10 - - - 1 - 12.3122 - 20 - 61.3845 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 5 - 0 - 9 - WTDVFQIGI - WTMKIGIGI - WT IGI - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1191 - Query_1191 - M_4780 - 9 - - - 1 - gnl|BL_ORD_ID|1437 - 119822|110 kd polyprotein precursor|CAA28880.1|Rubella virus|11041 - 1437 - 29 - - - 1 - 14.6234 - 26 - 2.01102 - 1 - 9 - 9 - 17 - 0 - 0 - 5 - 6 - 0 - 9 - WTESLAAVF - WSEGEGAVF - W+E AVF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1192 - Query_1192 - M_4781 - 9 - - - 1 - gnl|BL_ORD_ID|427 - 25929|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 427 - 15 - - - 1 - 12.3122 - 20 - 50.6727 - 2 - 9 - 8 - 15 - 0 - 0 - 4 - 6 - 0 - 8 - VKRQKISF - VKKDLISY - VK+ IS+ - - - - - 2 - gnl|BL_ORD_ID|9 - 790|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 9 - 15 - - - 1 - 12.3122 - 20 - 51.4826 - 2 - 9 - 3 - 10 - 0 - 0 - 4 - 6 - 0 - 8 - VKRQKISF - VKKDLISY - VK+ IS+ - - - - - 3 - gnl|BL_ORD_ID|943 - 62184|nonstructural protein 3|NP_722463.1|Dengue virus type 1 Hawaii|10000440 - 943 - 15 - - - 1 - 11.927 - 19 - 74.9817 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 6 - 0 - 8 - VKRQKISF - VKKDLISY - VK+ IS+ - - - - - 4 - gnl|BL_ORD_ID|761 - 50894|Genome polyprotein|P27909.2|Dengue virus type 1 Hawaii|10000440 - 761 - 20 - - - 1 - 11.927 - 19 - 76.6481 - 2 - 9 - 12 - 19 - 0 - 0 - 4 - 6 - 0 - 8 - VKRQKISF - VKKDLISY - VK+ IS+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1193 - Query_1193 - M_4782 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1194 - Query_1194 - M_4783 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1195 - Query_1195 - M_4784 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1196 - Query_1196 - M_4785 - 9 - - - 1 - gnl|BL_ORD_ID|885 - 57987|envelope protein|YP_001527880.1|West Nile virus NY-99|10000971 - 885 - 18 - - - 1 - 11.5418 - 18 - 116.517 - 4 - 9 - 5 - 10 - 0 - 0 - 4 - 5 - 0 - 6 - WILLVL - WVDLVL - W+ LVL - - - - - 2 - gnl|BL_ORD_ID|801 - 53341|envelope protein|YP_001527880.1|West Nile virus NY-99|10000971 - 801 - 17 - - - 1 - 11.5418 - 18 - 136.848 - 4 - 9 - 12 - 17 - 0 - 0 - 4 - 5 - 0 - 6 - WILLVL - WVDLVL - W+ LVL - - - - - 3 - gnl|BL_ORD_ID|637 - 37960|membrane protein|AAA45887.1|Human gammaherpesvirus 4|10376 - 637 - 9 - - - 1 - 9.61583 - 13 - 1779.2 - 1 - 7 - 3 - 9 - 0 - 0 - 3 - 5 - 0 - 7 - WYIWILL - WTLVVLL - W + +LL - - - - - 4 - gnl|BL_ORD_ID|664 - 39591|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 - 664 - 20 - - - 1 - 8.84543 - 11 - 1791.35 - 1 - 4 - 11 - 14 - 0 - 0 - 2 - 3 - 0 - 4 - WYIW - WCLW - W +W - - - - - 5 - gnl|BL_ORD_ID|1120 - 74387|Genome polyprotein|P26664.3|Hepatitis C virus (isolate 1)|11104 - 1120 - 9 - - - 1 - 9.23063 - 12 - 2628.29 - 1 - 6 - 4 - 9 - 0 - 0 - 3 - 4 - 0 - 6 - WYIWIL - WCLWWL - W +W L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1197 - Query_1197 - M_4786 - 9 - - - 1 - gnl|BL_ORD_ID|1630 - 146213|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 - 1630 - 18 - - - 1 - 13.853 - 24 - 6.14503 - 3 - 7 - 7 - 11 - 0 - 0 - 5 - 5 - 0 - 5 - FTGLT - FTGLT - FTGLT - - - - - 2 - gnl|BL_ORD_ID|1027 - 68581|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 1027 - 20 - - - 1 - 13.853 - 24 - 6.30518 - 3 - 7 - 2 - 6 - 0 - 0 - 5 - 5 - 0 - 5 - FTGLT - FTGLT - FTGLT - - - - - 3 - gnl|BL_ORD_ID|1628 - 146188|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 - 1628 - 18 - - - 1 - 13.853 - 24 - 6.46733 - 3 - 7 - 7 - 11 - 0 - 0 - 5 - 5 - 0 - 5 - FTGLT - FTGLT - FTGLT - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1198 - Query_1198 - M_4787 - 9 - - - 1 - gnl|BL_ORD_ID|1861 - 180440|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1861 - 15 - - - 1 - 11.927 - 19 - 82.259 - 4 - 8 - 6 - 10 - 0 - 0 - 3 - 4 - 0 - 5 - QRSWQ - ERSWN - +RSW - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1199 - Query_1199 - M_4788 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1200 - Query_1200 - M_4789 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1201 - Query_1201 - M_4790 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1202 - Query_1202 - M_4791 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1203 - Query_1203 - M_4792 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1204 - Query_1204 - M_4793 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1205 - Query_1205 - M_4794 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1206 - Query_1206 - M_4795 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1207 - Query_1207 - M_4796 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1208 - Query_1208 - M_4797 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1209 - Query_1209 - M_4798 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1210 - Query_1210 - M_4799 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1211 - Query_1211 - M_4800 - 9 - - - 1 - gnl|BL_ORD_ID|2243 - 232152|rhoptry kinase family protein|AFO54841.1|Toxoplasma gondii type III|398031 - 2243 - 19 - - - 1 - 13.0826 - 22 - 17.6919 - 1 - 7 - 6 - 12 - 0 - 0 - 4 - 5 - 0 - 7 - YHEAGVT - FHSYGVT - +H GVT - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1212 - Query_1212 - M_4801 - 9 - - - 1 - gnl|BL_ORD_ID|1983 - 183252|polyprotein|AGT63075.1|Dengue virus 1|11053 - 1983 - 10 - - - 1 - 11.927 - 19 - 78.4397 - 2 - 7 - 4 - 9 - 0 - 0 - 2 - 5 - 0 - 6 - HFSWTS - HYAWKT - H++W + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1213 - Query_1213 - M_4802 - 9 - - - 1 - gnl|BL_ORD_ID|375 - 23270|polyprotein|AAB67036.1|Hepatitis C virus (isolate H77)|63746 - 375 - 15 - - - 1 - 15.0086 - 27 - 1.20133 - 1 - 7 - 8 - 14 - 0 - 0 - 4 - 6 - 0 - 7 - YHHRFNN - YQHKFNS - Y H+FN+ - - - - - 2 - gnl|BL_ORD_ID|23 - 1516|Nucleoprotein|P03418.1|Human respiratory syncytial virus A2|11259 - 23 - 14 - - - 1 - 11.1566 - 17 - 165.457 - 1 - 7 - 3 - 9 - 0 - 0 - 3 - 5 - 0 - 7 - YHHRFNN - FYHILNN - ++H NN - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1214 - Query_1214 - M_4803 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1215 - Query_1215 - M_4804 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1216 - Query_1216 - M_4805 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1217 - Query_1217 - M_4806 - 9 - - - 1 - gnl|BL_ORD_ID|1405 - 110829|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1405 - 15 - - - 1 - 13.4678 - 23 - 7.74893 - 2 - 9 - 8 - 15 - 0 - 0 - 4 - 5 - 0 - 8 - KGSRFHRV - KKQRFHNI - K RFH + - - - - - 2 - gnl|BL_ORD_ID|1822 - 178247|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1822 - 15 - - - 1 - 13.0826 - 22 - 14.0874 - 2 - 9 - 4 - 11 - 0 - 0 - 4 - 5 - 0 - 8 - KGSRFHRV - KKQRFHNI - K RFH + - - - - - 3 - gnl|BL_ORD_ID|1385 - 110215|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1385 - 25 - - - 1 - 13.0826 - 22 - 16.7731 - 2 - 9 - 8 - 15 - 0 - 0 - 4 - 5 - 0 - 8 - KGSRFHRV - KKQRFHNI - K RFH + - - - - - 4 - gnl|BL_ORD_ID|1384 - 110205|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1384 - 32 - - - 1 - 13.0826 - 22 - 17.6218 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - KGSRFHRV - KKQRFHNI - K RFH + - - - - - 5 - gnl|BL_ORD_ID|1395 - 110394|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1395 - 32 - - - 1 - 12.3122 - 20 - 36.3427 - 2 - 9 - 20 - 27 - 0 - 0 - 4 - 5 - 0 - 8 - KGSRFHRV - KKQRFHNI - K RFH + - - - - - 6 - gnl|BL_ORD_ID|786 - 52652|||| - 786 - 27 - - - 1 - 12.3122 - 20 - 45.1033 - 3 - 9 - 7 - 13 - 0 - 0 - 4 - 5 - 0 - 7 - GSRFHRV - GSQSHTV - GS+ H V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1218 - Query_1218 - M_4807 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1219 - Query_1219 - M_4808 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1220 - Query_1220 - M_4809 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1221 - Query_1221 - M_4810 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1222 - Query_1222 - M_4811 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1223 - Query_1223 - M_4812 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1224 - Query_1224 - M_4813 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1225 - Query_1225 - M_4814 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1226 - Query_1226 - M_4815 - 9 - - - 1 - gnl|BL_ORD_ID|771 - 51526|HCV-1|AAA45676.1|Hepatitis C virus|11103 - 771 - 10 - - - 1 - 13.4678 - 23 - 8.32231 - 2 - 8 - 2 - 8 - 0 - 0 - 5 - 6 - 0 - 7 - LRRHRDV - LRRHIDL - LRRH D+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1227 - Query_1227 - M_4816 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1228 - Query_1228 - M_4817 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1229 - Query_1229 - M_4818 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1230 - Query_1230 - M_4819 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1231 - Query_1231 - M_4820 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1232 - Query_1232 - M_4821 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1233 - Query_1233 - M_4822 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1234 - Query_1234 - M_4823 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1235 - Query_1235 - M_4824 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1236 - Query_1236 - M_4825 - 9 - - - 1 - gnl|BL_ORD_ID|1687 - 149053|NS3 gene product|AAB02124.1|Hepatitis C virus|11103 - 1687 - 18 - - - 1 - 15.0086 - 27 - 1.32384 - 2 - 8 - 5 - 11 - 0 - 0 - 4 - 6 - 0 - 7 - PSIHRFI - PGIYRFV - P I+RF+ - - - - - 2 - gnl|BL_ORD_ID|355 - 22046|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 - 355 - 10 - - - 1 - 13.853 - 24 - 4.94204 - 2 - 7 - 5 - 10 - 0 - 0 - 4 - 5 - 0 - 6 - PSIHRF - PGIYRF - P I+RF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1237 - Query_1237 - M_4826 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1238 - Query_1238 - M_4827 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1239 - Query_1239 - M_4828 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1240 - Query_1240 - M_4829 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1241 - Query_1241 - M_4830 - 9 - - - 1 - gnl|BL_ORD_ID|1289 - 102368|E2 protein|NP_751921.1|Hepatitis C virus subtype 1a|31646 - 1289 - 15 - - - 1 - 13.4678 - 23 - 9.36117 - 2 - 7 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - RAGKPT - RSGAPT - R+G PT - - - - - 2 - gnl|BL_ORD_ID|1696 - 149098|E2 protein|NP_751921.1|Hepatitis C virus (isolate H77)|63746 - 1696 - 9 - - - 1 - 13.4678 - 23 - 10.561 - 2 - 7 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - RAGKPT - RSGAPT - R+G PT - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1242 - Query_1242 - M_4831 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1243 - Query_1243 - M_4832 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1244 - Query_1244 - M_4833 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1245 - Query_1245 - M_4834 - 9 - - - 1 - gnl|BL_ORD_ID|654 - 38724|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 654 - 20 - - - 1 - 15.3938 - 28 - 0.507864 - 1 - 6 - 15 - 20 - 0 - 0 - 5 - 5 - 0 - 6 - YRGPLS - YRGPLD - YRGPL - - - - - 2 - gnl|BL_ORD_ID|1852 - 180387|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1852 - 15 - - - 1 - 13.0826 - 22 - 14.8197 - 3 - 7 - 9 - 13 - 0 - 0 - 4 - 5 - 0 - 5 - GPLST - GPIST - GP+ST - - - - - 3 - gnl|BL_ORD_ID|1946 - 180836|polyprotein|AGT63075.1|Dengue virus 1|11053 - 1946 - 10 - - - 1 - 13.0826 - 22 - 17.265 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 5 - 0 - 6 - YRGPLS - YGGPIS - Y GP+S - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1246 - Query_1246 - M_4835 - 9 - - - 1 - gnl|BL_ORD_ID|1000 - 65810|sporozoite surface protein 2|NP_705260.1|Plasmodium falciparum 3D7|36329 - 1000 - 10 - - - 1 - 12.3122 - 20 - 52.9061 - 1 - 8 - 3 - 10 - 0 - 0 - 4 - 4 - 0 - 8 - YRGSVAPI - YAGEPAPF - Y G AP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1247 - Query_1247 - M_4836 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1248 - Query_1248 - M_4837 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1249 - Query_1249 - M_4838 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1250 - Query_1250 - M_4839 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1251 - Query_1251 - M_4840 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1252 - Query_1252 - M_4841 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1253 - Query_1253 - M_4842 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1254 - Query_1254 - M_4843 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1255 - Query_1255 - M_4844 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1256 - Query_1256 - M_4845 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1257 - Query_1257 - M_4846 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1258 - Query_1258 - M_4847 - 9 - - - 1 - gnl|BL_ORD_ID|1336 - 107894|polyprotein|CAB41951.1|Hepatitis C virus|11103 - 1336 - 10 - - - 1 - 14.2382 - 25 - 3.62465 - 2 - 9 - 3 - 10 - 0 - 0 - 5 - 7 - 0 - 8 - TDSSSVLN - TDSTSILG - TDS+S+L - - - - - 2 - gnl|BL_ORD_ID|1226 - 97227|polyprotein|CAB41951.1|Hepatitis C virus|11103 - 1226 - 10 - - - 1 - 14.2382 - 25 - 4.23087 - 2 - 8 - 4 - 10 - 0 - 0 - 5 - 7 - 0 - 7 - TDSSSVL - TDSTSIL - TDS+S+L - - - - - 3 - gnl|BL_ORD_ID|1354 - 108147|Genome polyprotein|P26664.3|Hepatitis C virus|11103 - 1354 - 10 - - - 1 - 13.4678 - 23 - 9.73455 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 7 - 0 - 8 - TDSSSVLN - TDATSILG - TD++S+L - - - - - 4 - gnl|BL_ORD_ID|1224 - 97111|polyprotein|ABR25251.1|Hepatitis C virus (isolate H77)|63746 - 1224 - 18 - - - 1 - 13.4678 - 23 - 11.2826 - 2 - 8 - 12 - 18 - 0 - 0 - 4 - 7 - 0 - 7 - TDSSSVL - TDATSIL - TD++S+L - - - - - 5 - gnl|BL_ORD_ID|1225 - 97226|Genome polyprotein|P26664.3|Hepatitis C virus|11103 - 1225 - 10 - - - 1 - 13.4678 - 23 - 12.4198 - 2 - 8 - 4 - 10 - 0 - 0 - 4 - 7 - 0 - 7 - TDSSSVL - TDATSIL - TD++S+L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1259 - Query_1259 - M_4848 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1260 - Query_1260 - M_4849 - 9 - - - 1 - gnl|BL_ORD_ID|1843 - 180077|PPE family protein|YP_177935.1|Mycobacterium tuberculosis H37Rv|83332 - 1843 - 9 - - - 1 - 13.0826 - 22 - 14.9585 - 1 - 5 - 1 - 5 - 0 - 0 - 3 - 4 - 0 - 5 - YTELW - YAEMW - Y E+W - - - - - 2 - gnl|BL_ORD_ID|10 - 1000|glycoprotein gp35/37|AAC59622.1|Human gammaherpesvirus 8|37296 - 10 - 15 - - - 1 - 12.6974 - 21 - 34.4815 - 4 - 9 - 10 - 15 - 0 - 0 - 4 - 5 - 0 - 6 - LWFLGL - LWAVGL - LW +GL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1261 - Query_1261 - M_4850 - 9 - - - 1 - gnl|BL_ORD_ID|1959 - 182554|polyprotein|ACF49259.1|Dengue virus type 1 Hawaii|10000440 - 1959 - 9 - - - 1 - 12.6974 - 21 - 26.9236 - 3 - 9 - 2 - 8 - 0 - 0 - 5 - 6 - 0 - 7 - LLAFSVF - LLATSIF - LLA S+F - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1262 - Query_1262 - M_4851 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1263 - Query_1263 - M_4852 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1264 - Query_1264 - M_4853 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1265 - Query_1265 - M_4854 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1266 - Query_1266 - M_4855 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1267 - Query_1267 - M_4856 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1268 - Query_1268 - M_4857 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1269 - Query_1269 - M_4858 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1270 - Query_1270 - M_4859 - 9 - - - 1 - gnl|BL_ORD_ID|530 - 32663|small hydrophobic protein|AAM12943.1|Human metapneumovirus|162145 - 530 - 10 - - - 1 - 13.0826 - 22 - 19.8203 - 2 - 7 - 4 - 9 - 0 - 0 - 3 - 5 - 0 - 6 - VGIFHF - VGVYHI - VG++H - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1271 - Query_1271 - M_4860 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1272 - Query_1272 - M_4861 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1273 - Query_1273 - M_4862 - 9 - - - 1 - gnl|BL_ORD_ID|1376 - 108965|Prolipoprotein diacylglyceryl transferase|O06131.1|Mycobacterium tuberculosis|1773 - 1376 - 9 - - - 1 - 13.4678 - 23 - 7.72035 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 7 - 0 - 9 - YVYSLYWSI - FLYELIWNV - ++Y L W++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1274 - Query_1274 - M_4863 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1275 - Query_1275 - M_4864 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1276 - Query_1276 - M_4865 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1277 - Query_1277 - M_4866 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1278 - Query_1278 - M_4867 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1279 - Query_1279 - M_4868 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1280 - Query_1280 - M_4869 - 9 - - - 1 - gnl|BL_ORD_ID|1190 - 95262|LAMP|AAK72632.1|Human gammaherpesvirus 8|37296 - 1190 - 15 - - - 1 - 11.927 - 19 - 60.2782 - 3 - 8 - 9 - 14 - 0 - 0 - 4 - 6 - 0 - 6 - KIVSSI - KLVSSV - K+VSS+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1281 - Query_1281 - M_4870 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1282 - Query_1282 - M_4871 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1283 - Query_1283 - M_4872 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1284 - Query_1284 - M_4873 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 1285 - Query_1285 - M_4874 - 9 - - - 1 - gnl|BL_ORD_ID|2080 - 185327|polyprotein|ACF49259.1|Dengue virus type 1 Hawaii|10000440 - 2080 - 9 - - - 1 - 11.5418 - 18 - 141.015 - 1 - 8 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - YYYFLRPL - YIYMGQPL - Y Y +PL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 1286 - Query_1286 - M_4875 - 9 - - - 1 - gnl|BL_ORD_ID|2080 - 185327|polyprotein|ACF49259.1|Dengue virus type 1 Hawaii|10000440 - 2080 - 9 - - - 1 - 11.5418 - 18 - 141.015 - 1 - 8 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - YYYFLRPL - YIYMGQPL - Y Y +PL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_136103_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_136103_1_T.fasta deleted file mode 100755 index 6a70b850..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_136103_1_T.fasta +++ /dev/null @@ -1,36 +0,0 @@ ->M_4876 -LSILVDWMI ->M_4877 -LVMFLSILV ->M_4878 -HWPEKEWPI ->M_4879 -WLEAMQGVI ->M_4880 -MNRGRRSSL ->M_4881 -RADHAAEQV ->M_4882 -TTLSPAEPT ->M_4883 -CLMVLYSLI ->M_4884 -MTPSVYGGA ->M_4885 -FCFLVVASA ->M_4886 -FLVVASAYI ->M_4887 -VVASAYIKL ->M_4888 -NSTIIPTLI ->M_4889 -SSSGVNSTI ->M_4890 -STIIPTLIL ->M_4891 -NLAMCFGPV ->M_4892 -MVAFINEKM ->M_4893 -RHSNMVAFI diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_136103_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_136103_1_T_iedb.xml deleted file mode 100755 index 8d9d2dc7..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_136103_1_T_iedb.xml +++ /dev/null @@ -1,742 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_4876 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_4876 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_4877 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_4878 - 9 - - - 1 - gnl|BL_ORD_ID|958 - 62977|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 958 - 10 - - - 1 - 11.5418 - 18 - 153.051 - 1 - 7 - 4 - 10 - 0 - 0 - 3 - 3 - 0 - 7 - HWPEKEW - HTPVNSW - H P W - - - - - 2 - gnl|BL_ORD_ID|55 - 4156|polyprotein|ABR25251.1|Hepatitis C virus|11103 - 55 - 9 - - - 1 - 11.5418 - 18 - 184.198 - 1 - 7 - 3 - 9 - 0 - 0 - 3 - 3 - 0 - 7 - HWPEKEW - HTPVNSW - H P W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 4 - Query_4 - M_4879 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_4880 - 9 - - - 1 - gnl|BL_ORD_ID|2115 - 186301|polyprotein|AGO67248.1|Dengue virus 2|11060 - 2115 - 9 - - - 1 - 13.4678 - 23 - 9.5131 - 1 - 6 - 3 - 8 - 0 - 0 - 4 - 6 - 0 - 6 - MNRGRR - MHRGKR - M+RG+R - - - - - 2 - gnl|BL_ORD_ID|2011 - 183800|polyprotein|AGT63075.1|Dengue virus 1|11053 - 2011 - 9 - - - 1 - 13.0826 - 22 - 17.7942 - 1 - 7 - 2 - 8 - 0 - 0 - 5 - 6 - 0 - 7 - MNRGRRS - MNRRKRS - MNR +RS - - - - - 3 - gnl|BL_ORD_ID|2065 - 184880|polyprotein|AGT63075.1|Dengue virus 1|11053 - 2065 - 9 - - - 1 - 13.0826 - 22 - 18.4218 - 1 - 7 - 1 - 7 - 0 - 0 - 5 - 6 - 0 - 7 - MNRGRRS - MNRRKRS - MNR +RS - - - - - 4 - gnl|BL_ORD_ID|2007 - 183766|polyprotein|AGO67248.1|Dengue virus 2|11060 - 2007 - 9 - - - 1 - 12.6974 - 21 - 31.9494 - 1 - 8 - 2 - 9 - 0 - 0 - 4 - 7 - 0 - 8 - MNRGRRSS - LNRRRRTA - +NR RR++ - - - - - 5 - gnl|BL_ORD_ID|2042 - 184518|polyprotein|AGO67248.1|Dengue virus 2|11060 - 2042 - 9 - - - 1 - 12.3122 - 20 - 56.7066 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 7 - 0 - 8 - MNRGRRSS - LNRRRRTA - +NR RR++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 6 - Query_6 - M_4881 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_4882 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_4883 - 9 - - - 1 - gnl|BL_ORD_ID|1549 - 141222|DNA packaging tegument protein UL25|NP_044626.1|Human alphaherpesvirus 1|10298 - 1549 - 9 - - - 1 - 11.5418 - 18 - 118.346 - 1 - 6 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - CLMVLY - CLYLLY - CL +LY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 9 - Query_9 - M_4884 - 9 - - - 1 - gnl|BL_ORD_ID|999 - 65749|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 999 - 11 - - - 1 - 13.4678 - 23 - 7.47922 - 2 - 8 - 1 - 7 - 0 - 0 - 5 - 5 - 0 - 7 - TPSVYGG - TPRVTGG - TP V GG - - - - - 2 - gnl|BL_ORD_ID|998 - 65748|pp65|AAA45994.1|Human betaherpesvirus 5|10359 - 998 - 10 - - - 1 - 13.4678 - 23 - 8.46851 - 2 - 8 - 1 - 7 - 0 - 0 - 5 - 5 - 0 - 7 - TPSVYGG - TPRVTGG - TP V GG - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 10 - Query_10 - M_4885 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_4886 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_4887 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_4888 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_4889 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_4890 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_4891 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_4892 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_4893 - 9 - - - 1 - gnl|BL_ORD_ID|1616 - 144403|polyprotein|AAK08509.1|Hepatitis C virus subtype 1b|31647 - 1616 - 9 - - - 1 - 14.6234 - 26 - 2.53786 - 1 - 6 - 3 - 8 - 0 - 0 - 5 - 5 - 0 - 6 - RHSNMV - RHHNMV - RH NMV - - - - - 2 - gnl|BL_ORD_ID|1785 - 159290|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 - 1785 - 9 - - - 1 - 13.4678 - 23 - 11.7244 - 1 - 6 - 3 - 8 - 0 - 0 - 4 - 5 - 0 - 6 - RHSNMV - RHHNLV - RH N+V - - - - - 3 - gnl|BL_ORD_ID|1218 - 96897|polyprotein|ABR25251.1|Hepatitis C virus (isolate H77)|63746 - 1218 - 17 - - - 1 - 13.0826 - 22 - 13.7 - 1 - 6 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - RHSNMV - RHHNLV - RH N+V - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_136546_2_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_136546_2_T.fasta deleted file mode 100755 index f6e6c44a..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_136546_2_T.fasta +++ /dev/null @@ -1,78 +0,0 @@ ->M_4894 -SILASLSTL ->M_4895 -TLQQMWISK ->M_4896 -RAFADTLEV ->M_4897 -VLLPVSLFI ->M_4898 -LLFSVTMPK ->M_4899 -VPVPPAPPL ->M_4900 -EIFMGLPTK ->M_4901 -VYTEIFMGL ->M_4902 -YYASVYTEI ->M_4903 -HMWNYMQSK ->M_4904 -QTYQHMWNY ->M_4905 -SRYQTYQHM ->M_4906 -MIMAQMRRI ->M_4907 -RRISPFSCL ->M_4908 -ILFDEAVKL ->M_4909 -MKYPVKSIL ->M_4910 -TLIHQFQEK ->M_4911 -KLGADFIGH ->M_4912 -ALGPPVLLR ->M_4913 -PPVLLRCSL ->M_4914 -FTRENTLTF ->M_4915 -LTFMHLSPI ->M_4916 -TFMHLSPIL ->M_4917 -EFVERYHVL ->M_4918 -RLWARGLTV ->M_4919 -RLWARGLTV ->M_4920 -LVWRPLREV ->M_4921 -SYVMLPCAL ->M_4922 -VMLPCALPV ->M_4923 -RLPEVQLPK ->M_4924 -APRGACYRA ->M_4925 -APRGVCYGA ->M_4926 -GLTWAVVLI ->M_4927 -QPLGLTWAV ->M_4928 -YRNEDHWAW ->M_4929 -KCAEPSTRK ->M_4930 -LLTDDLRSV ->M_4931 -QMPTDYAEV ->M_4932 -VVGARGVGK diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_136546_2_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_136546_2_T_iedb.xml deleted file mode 100755 index b982e37c..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_136546_2_T_iedb.xml +++ /dev/null @@ -1,1402 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_4894 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_4894 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_4895 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_4896 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_4897 - 9 - - - 1 - gnl|BL_ORD_ID|1168 - 79180|tax protein|AAF37566.1|Human T-lymphotropic virus 1|11908 - 1168 - 15 - - - 1 - 12.6974 - 21 - 24.4548 - 3 - 8 - 3 - 8 - 0 - 0 - 4 - 5 - 0 - 6 - LPVSLF - LPTTLF - LP +LF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 5 - Query_5 - M_4898 - 9 - - - 1 - gnl|BL_ORD_ID|338 - 21242|polymerase|ACF94272.1|Hepatitis B virus|10407 - 338 - 9 - - - 1 - 13.0826 - 22 - 19.7427 - 2 - 8 - 2 - 8 - 0 - 0 - 4 - 6 - 0 - 7 - LFSVTMP - LYSSTVP - L+S T+P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 6 - Query_6 - M_4899 - 9 - - - 1 - gnl|BL_ORD_ID|1068 - 70491|envelope glycoprotein|AAC28452.1|Human immunodeficiency virus 1|11676 - 1068 - 10 - - - 1 - 11.927 - 19 - 86.442 - 1 - 8 - 1 - 8 - 0 - 0 - 5 - 5 - 0 - 8 - VPVPPAPP - VPTDPNPP - VP P PP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 7 - Query_7 - M_4900 - 9 - - - 1 - gnl|BL_ORD_ID|2080 - 185327|polyprotein|ACF49259.1|Dengue virus type 1 Hawaii|10000440 - 2080 - 9 - - - 1 - 13.4678 - 23 - 8.87313 - 2 - 7 - 3 - 8 - 0 - 0 - 4 - 5 - 0 - 6 - IFMGLP - IYMGQP - I+MG P - - - - - 2 - gnl|BL_ORD_ID|141 - 10587|viral polyprotein|AAA42941.1|Dengue virus 2 Thailand/NGS-C/1944|11065 - 141 - 9 - - - 1 - 11.1566 - 17 - 232.278 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 5 - 0 - 9 - EIFMGLPTK - DVFFTPPEK - ++F P K - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 8 - Query_8 - M_4901 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_4902 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_4903 - 9 - - - 1 - gnl|BL_ORD_ID|691 - 42094|telomer length regulation protein TEL1|EDV12172.1|Saccharomyces cerevisiae|4932 - 691 - 9 - - - 1 - 13.853 - 24 - 6.60345 - 2 - 7 - 2 - 7 - 0 - 0 - 3 - 5 - 0 - 6 - MWNYMQ - LWGYLQ - +W Y+Q - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 11 - Query_11 - M_4904 - 9 - - - 1 - gnl|BL_ORD_ID|1295 - 103020|polyprotein|ABR25251.1|Hepatitis C virus|11103 - 1295 - 10 - - - 1 - 16.1642 - 30 - 0.390189 - 4 - 9 - 5 - 10 - 0 - 0 - 4 - 6 - 0 - 6 - QHMWNY - KHMWNF - +HMWN+ - - - - - 2 - gnl|BL_ORD_ID|1029 - 68605|Genome polyprotein|P26662.3|Hepatitis C virus|11103 - 1029 - 10 - - - 1 - 16.1642 - 30 - 0.392937 - 4 - 9 - 5 - 10 - 0 - 0 - 4 - 6 - 0 - 6 - QHMWNY - KHMWNF - +HMWN+ - - - - - 3 - gnl|BL_ORD_ID|272 - 18337|polyprotein|BAD73987.1|Hepatitis C virus subtype 1b|31647 - 272 - 9 - - - 1 - 15.779 - 29 - 0.436744 - 4 - 9 - 4 - 9 - 0 - 0 - 4 - 6 - 0 - 6 - QHMWNY - KHMWNF - +HMWN+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 12 - Query_12 - M_4905 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_4906 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_4907 - 9 - - - 1 - gnl|BL_ORD_ID|1731 - 150556|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1731 - 10 - - - 1 - 12.6974 - 21 - 26.0802 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 5 - 0 - 9 - RRISPFSCL - RVIDPRRCL - R I P CL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 15 - Query_15 - M_4908 - 9 - - - 1 - gnl|BL_ORD_ID|1807 - 169050|polyprotein|ABU97067.1|Hepatitis C virus subtype 1b|31647 - 1807 - 9 - - - 1 - 13.4678 - 23 - 8.13377 - 2 - 8 - 3 - 9 - 0 - 0 - 5 - 6 - 0 - 7 - LFDEAVK - LFNWAVK - LF+ AVK - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 16 - Query_16 - M_4909 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_4910 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_4911 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_4912 - 9 - - - 1 - gnl|BL_ORD_ID|898 - 59141|Circumsporozoite protein precursor|P08677.2|Plasmodium vivax strain Belem|31273 - 898 - 10 - - - 1 - 10.7714 - 16 - 303.747 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 6 - 0 - 8 - ALGPPVLL - SLGLVILL - +LG +LL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 20 - Query_20 - M_4913 - 9 - - - 1 - gnl|BL_ORD_ID|1621 - 145860|Protein E6|P04019.1|Human papillomavirus type 11|10580 - 1621 - 9 - - - 1 - 13.853 - 24 - 5.84954 - 2 - 9 - 1 - 8 - 0 - 0 - 5 - 6 - 0 - 8 - PVLLRCSL - KVLIRCYL - VL+RC L - - - - - 2 - gnl|BL_ORD_ID|114 - 7660|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 - 114 - 20 - - - 1 - 11.927 - 19 - 83.707 - 3 - 9 - 4 - 10 - 0 - 0 - 3 - 6 - 0 - 7 - VLLRCSL - ILLMCAV - +LL C++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 21 - Query_21 - M_4914 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 22 - Query_22 - M_4915 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_4916 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_4917 - 9 - - - 1 - gnl|BL_ORD_ID|2142 - 187188|PE family protein PE9|YP_177784.1|Mycobacterium tuberculosis H37Rv|83332 - 2142 - 15 - - - 1 - 13.4678 - 23 - 10.3735 - 3 - 9 - 7 - 13 - 0 - 0 - 4 - 4 - 0 - 7 - VERYHVL - AEEYHAL - E YH L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 25 - Query_25 - M_4918 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_4919 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_4920 - 9 - - - 1 - gnl|BL_ORD_ID|1872 - 180496|Polyprotein|NP_056776.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1872 - 15 - - - 1 - 12.3122 - 20 - 36.7879 - 2 - 8 - 7 - 13 - 0 - 0 - 3 - 5 - 0 - 7 - VWRPLRE - IWLKLKE - +W L+E - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 28 - Query_28 - M_4921 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 29 - Query_29 - M_4922 - 9 - - - 1 - gnl|BL_ORD_ID|690 - 41971|putative D-ribose-binding protein|NP_301386.1|Mycobacterium leprae|1769 - 690 - 15 - - - 1 - 11.5418 - 18 - 154.909 - 2 - 8 - 6 - 12 - 0 - 0 - 4 - 5 - 0 - 7 - MLPCALP - LLPAILP - +LP LP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 30 - Query_30 - M_4923 - 9 - - - 1 - gnl|BL_ORD_ID|241 - 16836|precore/core protein [Hepatitis B virus]|AAR03815.1|Hepatitis B virus|10407 - 241 - 10 - - - 1 - 10.3862 - 15 - 499.131 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 4 - 0 - 8 - LPEVQLPK - LPSDFLPS - LP LP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 31 - Query_31 - M_4924 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 32 - Query_32 - M_4925 - 9 - - - 1 - gnl|BL_ORD_ID|1667 - 148117|early protein|CAA52585.1|Human papillomavirus type 52|10618 - 1667 - 9 - - - 1 - 12.6974 - 21 - 26.9236 - 2 - 6 - 1 - 5 - 0 - 0 - 4 - 4 - 0 - 5 - PRGVC - PYGVC - P GVC - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 33 - Query_33 - M_4926 - 9 - - - 1 - gnl|BL_ORD_ID|1686 - 149052|E1 protein|NP_751920.1|Hepatitis C virus (isolate H77)|63746 - 1686 - 18 - - - 1 - 12.3122 - 20 - 44.435 - 3 - 9 - 10 - 16 - 0 - 0 - 4 - 5 - 0 - 7 - TWAVVLI - NWAKVLV - WA VL+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 34 - Query_34 - M_4927 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 35 - Query_35 - M_4928 - 9 - - - 1 - gnl|BL_ORD_ID|2019 - 184131|polyprotein|AGO67248.1|Dengue virus 2|11060 - 2019 - 10 - - - 1 - 12.6974 - 21 - 23.5358 - 2 - 8 - 1 - 7 - 0 - 0 - 3 - 4 - 0 - 7 - RNEDHWA - KREDQWC - + ED W - - - - - 2 - gnl|BL_ORD_ID|805 - 53476|polyprotein|AGO67248.1|Dengue virus 2|11060 - 805 - 9 - - - 1 - 12.3122 - 20 - 65.8473 - 4 - 8 - 2 - 6 - 0 - 0 - 3 - 3 - 0 - 5 - EDHWA - EDQWC - ED W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 36 - Query_36 - M_4929 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 37 - Query_37 - M_4930 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 38 - Query_38 - M_4931 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 39 - Query_39 - M_4932 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_136587_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_136587_1_T.fasta deleted file mode 100755 index 13a39e09..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_136587_1_T.fasta +++ /dev/null @@ -1,50 +0,0 @@ ->M_4933 -ALFCGRSDY ->M_4934 -SFLCHKALF ->M_4935 -SFLCHKALF ->M_4936 -SFLCHKALF ->M_4937 -HHLLSLQYV ->M_4938 -NHHLLSLQY ->M_4939 -LRLLDRELL ->M_4940 -QMPPMPPPL ->M_4941 -SRVSGGTPL ->M_4942 -IPLEVMEPF ->M_4943 -RHAACSVLV ->M_4944 -TRHAACSVL ->M_4945 -TRHAACSVL ->M_4946 -IYLGAVNWI ->M_4947 -YLGAVNWIY ->M_4948 -MWALGIIAY ->M_4949 -SPALNKMFY ->M_4950 -IPGPIPGPI ->M_4951 -IPGPIPGPI ->M_4952 -NPGPIPGPI ->M_4953 -AEYIVVARN ->M_4954 -YIVVARNKY ->M_4955 -IFWDLSKPM ->M_4956 -IFWDLSKPM ->M_4957 -IPTEKPTIL diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_136587_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_136587_1_T_iedb.xml deleted file mode 100755 index 4479cd1c..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_136587_1_T_iedb.xml +++ /dev/null @@ -1,1298 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_4933 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_4933 - 9 - - - 1 - gnl|BL_ORD_ID|73 - 5316|EBNA-3B nuclear protein|CAD53420.1|Human gammaherpesvirus 4|10376 - 73 - 10 - - - 1 - 11.927 - 19 - 106.494 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 6 - 0 - 8 - ALFCGRSD - AVFDRKSD - A+F +SD - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 2 - Query_2 - M_4934 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_4935 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_4936 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_4937 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_4938 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_4939 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_4940 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_4941 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_4942 - 9 - - - 1 - gnl|BL_ORD_ID|1879 - 180528|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1879 - 10 - - - 1 - 13.853 - 24 - 6.41039 - 1 - 7 - 1 - 7 - 0 - 0 - 4 - 6 - 0 - 7 - IPLEVME - IPFEIMD - IP E+M+ - - - - - 2 - gnl|BL_ORD_ID|1733 - 150578|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1733 - 10 - - - 1 - 13.0826 - 22 - 15.2954 - 1 - 6 - 5 - 10 - 0 - 0 - 4 - 5 - 0 - 6 - IPLEVM - IPFEIM - IP E+M - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 11 - Query_11 - M_4943 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_4944 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_4945 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_4946 - 9 - - - 1 - gnl|BL_ORD_ID|1812 - 177647|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 - 1812 - 16 - - - 1 - 13.853 - 24 - 5.42889 - 4 - 9 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - GAVNWI - GAVQWM - GAV W+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 15 - Query_15 - M_4947 - 9 - - - 1 - gnl|BL_ORD_ID|1812 - 177647|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 - 1812 - 16 - - - 1 - 13.853 - 24 - 5.3359 - 3 - 8 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - GAVNWI - GAVQWM - GAV W+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 16 - Query_16 - M_4948 - 9 - - - 1 - gnl|BL_ORD_ID|413 - 24943|DNA polymerase|CAA10434.1|Hepatitis B virus|10407 - 413 - 11 - - - 1 - 12.3122 - 20 - 60.6062 - 1 - 7 - 3 - 9 - 0 - 0 - 3 - 5 - 0 - 7 - MWALGII - LWKAGIL - +W GI+ - - - - - 2 - gnl|BL_ORD_ID|988 - 65148|DNA polymerase|CAA10434.1|Hepatitis B virus|10407 - 988 - 10 - - - 1 - 11.927 - 19 - 69.9879 - 1 - 7 - 2 - 8 - 0 - 0 - 3 - 5 - 0 - 7 - MWALGII - LWKAGIL - +W GI+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 17 - Query_17 - M_4949 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_4950 - 9 - - - 1 - gnl|BL_ORD_ID|741 - 47760|EBNA-1 protein|Q777E1|Human gammaherpesvirus 4|10376 - 741 - 15 - - - 1 - 10.3862 - 15 - 419.458 - 2 - 7 - 1 - 6 - 0 - 0 - 4 - 4 - 0 - 6 - PGPIPG - PGTGPG - PG PG - - - - - 2 - gnl|BL_ORD_ID|75 - 5542|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 75 - 15 - - - 1 - 10.001 - 14 - 709.084 - 2 - 9 - 8 - 15 - 0 - 0 - 4 - 4 - 0 - 8 - PGPIPGPI - PGTSGSPI - PG PI - - - - - 3 - gnl|BL_ORD_ID|1929 - 180750|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1929 - 15 - - - 1 - 10.001 - 14 - 819.307 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 4 - 0 - 8 - PGPIPGPI - PGTSGSPI - PG PI - - - - - 4 - gnl|BL_ORD_ID|260 - 17802|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 260 - 15 - - - 1 - 10.001 - 14 - 830.077 - 2 - 9 - 3 - 10 - 0 - 0 - 4 - 4 - 0 - 8 - PGPIPGPI - PGTSGSPI - PG PI - - - - - 5 - gnl|BL_ORD_ID|1712 - 150341|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1712 - 9 - - - 1 - 9.61583 - 13 - 1362.74 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 4 - 0 - 8 - PGPIPGPI - PGTSGSPI - PG PI - - - - - 6 - gnl|BL_ORD_ID|1766 - 154857|tegument protein|CAB06735.1|Human alphaherpesvirus 2|10310 - 1766 - 16 - - - 1 - 4.99343 - 1 - 89081.4 - 7 - 9 - 14 - 16 - 0 - 0 - 2 - 3 - 0 - 3 - GPI - GPV - GP+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 19 - Query_19 - M_4951 - 9 - - - 1 - gnl|BL_ORD_ID|741 - 47760|EBNA-1 protein|Q777E1|Human gammaherpesvirus 4|10376 - 741 - 15 - - - 1 - 10.3862 - 15 - 419.458 - 2 - 7 - 1 - 6 - 0 - 0 - 4 - 4 - 0 - 6 - PGPIPG - PGTGPG - PG PG - - - - - 2 - gnl|BL_ORD_ID|75 - 5542|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 75 - 15 - - - 1 - 10.001 - 14 - 709.084 - 2 - 9 - 8 - 15 - 0 - 0 - 4 - 4 - 0 - 8 - PGPIPGPI - PGTSGSPI - PG PI - - - - - 3 - gnl|BL_ORD_ID|1929 - 180750|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1929 - 15 - - - 1 - 10.001 - 14 - 819.307 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 4 - 0 - 8 - PGPIPGPI - PGTSGSPI - PG PI - - - - - 4 - gnl|BL_ORD_ID|260 - 17802|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 260 - 15 - - - 1 - 10.001 - 14 - 830.077 - 2 - 9 - 3 - 10 - 0 - 0 - 4 - 4 - 0 - 8 - PGPIPGPI - PGTSGSPI - PG PI - - - - - 5 - gnl|BL_ORD_ID|1712 - 150341|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1712 - 9 - - - 1 - 9.61583 - 13 - 1362.74 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 4 - 0 - 8 - PGPIPGPI - PGTSGSPI - PG PI - - - - - 6 - gnl|BL_ORD_ID|1766 - 154857|tegument protein|CAB06735.1|Human alphaherpesvirus 2|10310 - 1766 - 16 - - - 1 - 4.99343 - 1 - 89081.4 - 7 - 9 - 14 - 16 - 0 - 0 - 2 - 3 - 0 - 3 - GPI - GPV - GP+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 20 - Query_20 - M_4952 - 9 - - - 1 - gnl|BL_ORD_ID|344 - 21638|protein F|ABV46152.2|Hepatitis C virus (isolate Japanese)|11116 - 344 - 9 - - - 1 - 10.7714 - 16 - 376.438 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - PGPIPGPI - PGLSPGTL - PG PG + - - - - - 2 - gnl|BL_ORD_ID|741 - 47760|EBNA-1 protein|Q777E1|Human gammaherpesvirus 4|10376 - 741 - 15 - - - 1 - 10.3862 - 15 - 449.179 - 2 - 7 - 1 - 6 - 0 - 0 - 4 - 4 - 0 - 6 - PGPIPG - PGTGPG - PG PG - - - - - 3 - gnl|BL_ORD_ID|75 - 5542|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 75 - 15 - - - 1 - 10.3862 - 15 - 461.604 - 1 - 9 - 7 - 15 - 0 - 0 - 4 - 5 - 0 - 9 - NPGPIPGPI - SPGTSGSPI - +PG PI - - - - - 4 - gnl|BL_ORD_ID|260 - 17802|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 260 - 15 - - - 1 - 10.3862 - 15 - 550.452 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 5 - 0 - 9 - NPGPIPGPI - SPGTSGSPI - +PG PI - - - - - 5 - gnl|BL_ORD_ID|1929 - 180750|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1929 - 15 - - - 1 - 10.3862 - 15 - 557.903 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 5 - 0 - 9 - NPGPIPGPI - SPGTSGSPI - +PG PI - - - - - 6 - gnl|BL_ORD_ID|1712 - 150341|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1712 - 9 - - - 1 - 10.001 - 14 - 1206.48 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 4 - 0 - 9 - NPGPIPGPI - KPGTSGSPI - PG PI - - - - - 7 - gnl|BL_ORD_ID|1766 - 154857|tegument protein|CAB06735.1|Human alphaherpesvirus 2|10310 - 1766 - 16 - - - 1 - 4.99343 - 1 - 83537.4 - 7 - 9 - 14 - 16 - 0 - 0 - 2 - 3 - 0 - 3 - GPI - GPV - GP+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 21 - Query_21 - M_4953 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 22 - Query_22 - M_4954 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_4955 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_4956 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_4957 - 9 - - - 1 - gnl|BL_ORD_ID|647 - 38466|nucleocapsid protein|ABF21284.1|Influenza A virus (A/Iran/1/1957(H2N2))|488233 - 647 - 9 - - - 1 - 15.779 - 29 - 0.476466 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 8 - 0 - 9 - IPTEKPTIL - LPFDKPTIM - +P +KPTI+ - - - - - 2 - gnl|BL_ORD_ID|1433 - 116127|Nucleoprotein|P15682.1|Influenza A virus (A/Wilson-Smith/1933(H1N1))|381518 - 1433 - 9 - - - 1 - 15.0086 - 27 - 1.10528 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 8 - 0 - 9 - IPTEKPTIL - LPFDRPTIM - +P ++PTI+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_137814_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_137814_1_T.fasta deleted file mode 100755 index 452ea838..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_137814_1_T.fasta +++ /dev/null @@ -1,50 +0,0 @@ ->M_4958 -FLNRWMANT ->M_4959 -WMANTLDAV ->M_4960 -ALHTAVLLL ->M_4961 -KMWDAVLYR ->M_4962 -LSIESLTLV ->M_4963 -TLSIESLTL ->M_4964 -HRVNWVVFL ->M_4965 -FLYQPNWRF ->M_4966 -LRKRRSRKR ->M_4967 -RQLRKRRSR ->M_4968 -RRQEQPSIK ->M_4969 -FQYKFTVQA ->M_4970 -ILGTPLSKV ->M_4971 -VLSGAKIWL ->M_4972 -AVLIVTTTV ->M_4973 -LLESSNTNV ->M_4974 -VVWATKYFL ->M_4975 -AMCSAQEEI ->M_4976 -KLTPYMVVL ->M_4977 -FRVRGAVSH ->M_4978 -FRHSMVVPY ->M_4979 -KRRRLWAAL ->M_4980 -RRLWAALGP ->M_4981 -YLIISTFFL ->M_4982 -KIFNHPSTL diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_137814_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_137814_1_T_iedb.xml deleted file mode 100755 index d612c630..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_137814_1_T_iedb.xml +++ /dev/null @@ -1,1072 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_4958 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_4958 - 9 - - - 1 - gnl|BL_ORD_ID|1516 - 140561|metal cation transporter P-type ATPase A CtpF|NP_216513.1|Mycobacterium tuberculosis H37Rv|83332 - 1516 - 9 - - - 1 - 13.853 - 24 - 4.4402 - 1 - 6 - 3 - 8 - 0 - 0 - 4 - 5 - 0 - 6 - FLNRWM - FANRWI - F NRW+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 2 - Query_2 - M_4959 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_4960 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_4961 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_4962 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_4963 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_4964 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_4965 - 9 - - - 1 - gnl|BL_ORD_ID|1272 - 101721|nef|AAA02639.1|Human immunodeficiency virus 1|11676 - 1272 - 10 - - - 1 - 11.927 - 19 - 78.4397 - 3 - 8 - 5 - 10 - 0 - 0 - 3 - 5 - 0 - 6 - YQPNWR - YFPDWQ - Y P+W+ - - - - - 2 - gnl|BL_ORD_ID|1287 - 102235|nef protein|ACR27119.1|Human immunodeficiency virus 1|11676 - 1287 - 9 - - - 1 - 11.927 - 19 - 91.4136 - 3 - 8 - 1 - 6 - 0 - 0 - 3 - 5 - 0 - 6 - YQPNWR - YFPDWQ - Y P+W+ - - - - - 3 - gnl|BL_ORD_ID|1285 - 102151|nef protein|ACR27128.1|Human immunodeficiency virus 1|11676 - 1285 - 11 - - - 1 - 11.927 - 19 - 98.2033 - 3 - 8 - 4 - 9 - 0 - 0 - 3 - 5 - 0 - 6 - YQPNWR - YFPDWQ - Y P+W+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 9 - Query_9 - M_4966 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_4967 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_4968 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_4969 - 9 - - - 1 - gnl|BL_ORD_ID|210 - 15242|trans-sialidase, putative|EAN81560.1|Trypanosoma cruzi|5693 - 210 - 9 - - - 1 - 13.0826 - 22 - 15.4875 - 2 - 7 - 3 - 8 - 0 - 0 - 4 - 5 - 0 - 6 - QYKFTV - NYKFTL - YKFT+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 13 - Query_13 - M_4970 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_4971 - 9 - - - 1 - gnl|BL_ORD_ID|1951 - 181036|||| - 1951 - 20 - - - 1 - 15.779 - 29 - 0.402259 - 1 - 9 - 1 - 9 - 0 - 0 - 6 - 7 - 0 - 9 - VLSGAKIWL - VLSDFKVWL - VLS K+WL - - - - - 2 - gnl|BL_ORD_ID|1950 - 181035|||| - 1950 - 44 - - - 1 - 15.3938 - 28 - 1.34675 - 1 - 9 - 1 - 9 - 0 - 0 - 6 - 7 - 0 - 9 - VLSGAKIWL - VLSDFKVWL - VLS K+WL - - - - - 3 - gnl|BL_ORD_ID|1055 - 69751|polyprotein|BAB18806.1|Hepatitis C virus genotype 1|41856 - 1055 - 9 - - - 1 - 14.6234 - 26 - 1.82241 - 1 - 9 - 1 - 9 - 0 - 0 - 6 - 6 - 0 - 9 - VLSGAKIWL - VLSDFKTWL - VLS K WL - - - - - 4 - gnl|BL_ORD_ID|1056 - 69753|polyprotein|AAK49500.1|Hepatitis C virus genotype 3|356114 - 1056 - 9 - - - 1 - 13.853 - 24 - 5.09494 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 6 - 0 - 9 - VLSGAKIWL - VLSDFRTWL - VLS + WL - - - - - 5 - gnl|BL_ORD_ID|1054 - 69750|polyprotein|AAC03058.1|Hepatitis C virus genotype 3|356114 - 1054 - 9 - - - 1 - 13.853 - 24 - 5.74926 - 1 - 9 - 1 - 9 - 0 - 0 - 6 - 6 - 0 - 9 - VLSGAKIWL - VLSDFKSWL - VLS K WL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 15 - Query_15 - M_4972 - 9 - - - 1 - gnl|BL_ORD_ID|901 - 59182|attachment glycoprotein|ABQ58821.1|Human metapneumovirus|162145 - 901 - 10 - - - 1 - 9.61583 - 13 - 1296.37 - 2 - 9 - 3 - 10 - 0 - 0 - 4 - 6 - 0 - 8 - VLIVTTTV - ILIGITTL - +LI TT+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 16 - Query_16 - M_4973 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_4974 - 9 - - - 1 - gnl|BL_ORD_ID|664 - 39591|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 - 664 - 20 - - - 1 - 13.0826 - 22 - 15.6203 - 1 - 9 - 12 - 20 - 0 - 0 - 4 - 6 - 0 - 9 - VVWATKYFL - CLWWLQYFL - +W +YFL - - - - - 2 - gnl|BL_ORD_ID|1945 - 180828|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1945 - 10 - - - 1 - 12.3122 - 20 - 52.036 - 2 - 8 - 4 - 10 - 0 - 0 - 3 - 5 - 0 - 7 - VWATKYF - MWSLMYF - +W+ YF - - - - - 3 - gnl|BL_ORD_ID|1887 - 180579|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1887 - 15 - - - 1 - 12.3122 - 20 - 53.1389 - 2 - 8 - 6 - 12 - 0 - 0 - 3 - 5 - 0 - 7 - VWATKYF - MWSLMYF - +W+ YF - - - - - 4 - gnl|BL_ORD_ID|1960 - 182599|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1960 - 9 - - - 1 - 11.927 - 19 - 110.987 - 2 - 8 - 3 - 9 - 0 - 0 - 3 - 4 - 0 - 7 - VWATKYF - MWQLMYF - +W YF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 18 - Query_18 - M_4975 - 9 - - - 1 - gnl|BL_ORD_ID|889 - 58463|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 - 889 - 20 - - - 1 - 13.0826 - 22 - 16.661 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 7 - 0 - 9 - AMCSAQEEI - SICPSQEPM - ++C +QE + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 19 - Query_19 - M_4976 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_4977 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_4978 - 9 - - - 1 - gnl|BL_ORD_ID|1223 - 97093|polyprotein|AAB66324.1|Hepatitis C virus (isolate H77)|63746 - 1223 - 10 - - - 1 - 13.853 - 24 - 5.20543 - 2 - 8 - 3 - 9 - 0 - 0 - 4 - 6 - 0 - 7 - RHSMVVP - RHADVIP - RH+ V+P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 22 - Query_22 - M_4979 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_4980 - 9 - - - 1 - gnl|BL_ORD_ID|909 - 59569|Genome polyprotein|P26662.3|Hepatitis C virus (isolate Japanese)|11116 - 909 - 10 - - - 1 - 11.927 - 19 - 99.9004 - 4 - 9 - 5 - 10 - 0 - 0 - 3 - 4 - 0 - 6 - WAALGP - WLSQGP - W + GP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 24 - Query_24 - M_4981 - 9 - - - 1 - gnl|BL_ORD_ID|1522 - 140616|membrane-associated phospholipase C|NP_216866.1|Mycobacterium tuberculosis H37Rv|83332 - 1522 - 9 - - - 1 - 12.3122 - 20 - 48.7826 - 1 - 7 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - YLIISTF - YLLADTF - YL+ TF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 25 - Query_25 - M_4982 - 9 - - - 1 - gnl|BL_ORD_ID|2158 - 189294|Gag|O89360|Human immunodeficiency virus 1|11676 - 2158 - 9 - - - 1 - 12.3122 - 20 - 52.1643 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 6 - 0 - 9 - KIFNHPSTL - SLYNTVSTL - ++N STL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_137854_2_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_137854_2_T.fasta deleted file mode 100755 index 3d9bfe8d..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_137854_2_T.fasta +++ /dev/null @@ -1,160 +0,0 @@ ->M_4983 -RSPKKHGYM ->M_4984 -YMKMFEIPA ->M_4985 -LSSIGRSPM ->M_4986 -MVFCDFHGH ->M_4987 -RSPMVFCDF ->M_4988 -SIGRSPMVF ->M_4989 -SSIGRSPMV ->M_4990 -ATATAYLCR ->M_4991 -ATAYLCRVK ->M_4992 -RVKGNFQTI ->M_4993 -TATAYLCRV ->M_4994 -YLCRVKGNF ->M_4995 -CVSCWNVSR ->M_4996 -RLASLYKTL ->M_4997 -TLPQSVDPL ->M_4998 -SSSYAIEKR ->M_4999 -ISRSTFAEV ->M_5000 -RLPISRSTF ->M_5001 -STFAEVTGL ->M_5002 -STFAEVTGL ->M_5003 -FSWNGGSFV ->M_5004 -FSWNGGSFV ->M_5005 -TINEECSEI ->M_5006 -ILACRWVEM ->M_5007 -ESPFSSGKV ->M_5008 -MLAIGCALL ->M_5009 -ESIRHNVLY ->M_5010 -SIRHNVLYR ->M_5011 -LQFGPTAEG ->M_5012 -QPIPSVHER ->M_5013 -SVHERTDWV ->M_5014 -SVHERTDWV ->M_5015 -RAPSPVSFV ->M_5016 -GVLVLLFTL ->M_5017 -VLAPGVLVL ->M_5018 -VLAPGVLVL ->M_5019 -VLVLLFTLV ->M_5020 -FTFLVSLYL ->M_5021 -FTFLVSLYL ->M_5022 -IQAYVFTFL ->M_5023 -IQAYVFTFL ->M_5024 -LIQAYVFTF ->M_5025 -QAYVFTFLV ->M_5026 -QAYVFTFLV ->M_5027 -YVFTFLVSL ->M_5028 -YVFTFLVSL ->M_5029 -SSSPTCSLM ->M_5030 -ENWDLVTYR ->M_5031 -GAMENWDLV ->M_5032 -LEHPGSTRF ->M_5033 -QTDYVLSPL ->M_5034 -VLSPLTGGL ->M_5035 -ITEILDRYV ->M_5036 -FNKSGFKHY ->M_5037 -KSGFKHYQM ->M_5038 -PVFNKSGFK ->M_5039 -VLVSGIQVL ->M_5040 -VLVSGIQVL ->M_5041 -RSRTGEDEV ->M_5042 -LGQGELSAF ->M_5043 -EAQPESEGV ->M_5044 -LQDFYLGTY ->M_5045 -VAFPLQDFY ->M_5046 -ESVNILSVL ->M_5047 -GLVESVNIL ->M_5048 -FTVGQTEKY ->M_5049 -ESFKQTYVY ->M_5050 -ESFKQTYVY ->M_5051 -QTYVYSMAL ->M_5052 -YVYSMALVL ->M_5053 -YVYSMALVL ->M_5054 -YVYSMALVL ->M_5055 -FSLHKDRPV ->M_5056 -ATRKLIGKV ->M_5057 -HLKVRTATR ->M_5058 -TATRKLIGK ->M_5059 -LLPWAHSML ->M_5060 -QQNAPLLPW ->M_5061 -RIHSDEQPY ->M_5062 -AVHTVPQTI diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_137854_2_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_137854_2_T_iedb.xml deleted file mode 100755 index 77954074..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_137854_2_T_iedb.xml +++ /dev/null @@ -1,2720 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_4983 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_4983 - 9 - - - 1 - gnl|BL_ORD_ID|924 - 60031|SAG1 protein|AAO72426.1|Toxoplasma gondii RH|383379 - 924 - 9 - - - 1 - 13.0826 - 22 - 16.035 - 2 - 6 - 1 - 5 - 0 - 0 - 4 - 5 - 0 - 5 - SPKKH - SPEKH - SP+KH - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 2 - Query_2 - M_4984 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_4985 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_4986 - 9 - - - 1 - gnl|BL_ORD_ID|1776 - 155811|ribonucleotide reductase large subunit|CAB06725.1|Human alphaherpesvirus 2|10310 - 1776 - 15 - - - 1 - 16.1642 - 30 - 0.342581 - 1 - 9 - 2 - 10 - 0 - 0 - 5 - 5 - 0 - 9 - MVFCDFHGH - MSLADFHGE - M DFHG - - - - - 2 - gnl|BL_ORD_ID|1975 - 183147|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1975 - 9 - - - 1 - 11.5418 - 18 - 116.464 - 3 - 9 - 1 - 7 - 0 - 0 - 4 - 4 - 0 - 7 - FCDFHGH - FCSHHFH - FC H H - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 5 - Query_5 - M_4987 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_4988 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_4989 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_4990 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_4991 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_4992 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_4993 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_4994 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_4995 - 9 - - - 1 - gnl|BL_ORD_ID|181 - 13456|circumsporozoite protein|AAN87606.1|Plasmodium falciparum|5833 - 181 - 20 - - - 1 - 11.927 - 19 - 62.285 - 1 - 7 - 14 - 20 - 0 - 0 - 4 - 5 - 0 - 7 - CVSCWNV - CSSVFNV - C S +NV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 14 - Query_14 - M_4996 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_4997 - 9 - - - 1 - gnl|BL_ORD_ID|646 - 38446|Glycoprotein B precursor (Glycoprotein II)|P09257.1|Human alphaherpesvirus 3|10335 - 646 - 11 - - - 1 - 15.0086 - 27 - 1.31191 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 6 - 0 - 8 - LPQSVDPL - LPEGMDPF - LP+ +DP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 16 - Query_16 - M_4998 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_4999 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_5000 - 9 - - - 1 - gnl|BL_ORD_ID|1333 - 107873|Genome polyprotein|P26664.3|Hepatitis C virus|11103 - 1333 - 10 - - - 1 - 13.4678 - 23 - 10.2566 - 3 - 9 - 3 - 9 - 0 - 0 - 4 - 6 - 0 - 7 - PISRSTF - PITYSTY - PI+ ST+ - - - - - 2 - gnl|BL_ORD_ID|965 - 63963|HCV-1|AAA45676.1|Hepatitis C virus|11103 - 965 - 10 - - - 1 - 13.4678 - 23 - 11.3855 - 3 - 9 - 4 - 10 - 0 - 0 - 4 - 6 - 0 - 7 - PISRSTF - PITYSTY - PI+ ST+ - - - - - 3 - gnl|BL_ORD_ID|1434 - 116136|nucleocapsid protein|ACS34671.1|Influenza A virus (A/Auckland/1/2009(H1N1))|642794 - 1434 - 9 - - - 1 - 13.0826 - 22 - 16.6015 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - LPISRST - LPFERAT - LP R+T - - - - - 4 - gnl|BL_ORD_ID|650 - 38472|nucleoprotein|AAV48837.1|Influenza A virus (A/Brevig Mission/1/1918(H1N1))|88776 - 650 - 9 - - - 1 - 13.0826 - 22 - 18.1053 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - LPISRST - LPFERAT - LP R+T - - - - - 5 - gnl|BL_ORD_ID|964 - 63784|Genome polyprotein|P26663.3|Hepatitis C virus|11103 - 964 - 10 - - - 1 - 13.0826 - 22 - 18.1832 - 3 - 9 - 4 - 10 - 0 - 0 - 3 - 6 - 0 - 7 - PISRSTF - PVTYSTY - P++ ST+ - - - - - 6 - gnl|BL_ORD_ID|1432 - 116123|nucleocapsid protein|ABP49342.1|Influenza A virus (A/California/10/1978(H1N1))|425557 - 1432 - 9 - - - 1 - 13.0826 - 22 - 20.0871 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - LPISRST - LPFDKST - LP +ST - - - - - 7 - gnl|BL_ORD_ID|649 - 38471|nucleocapsid protein|ABC46569.1|Influenza A virus (A/Memphis/4/1980(H3N2))|383578 - 649 - 9 - - - 1 - 13.0826 - 22 - 21.1561 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - LPISRST - LPFEKST - LP +ST - - - - - 8 - gnl|BL_ORD_ID|648 - 38468|nucleoprotein|CAA24268.1|Influenza A virus (A/Puerto Rico/8/1934(H1N1))|211044 - 648 - 9 - - - 1 - 13.0826 - 22 - 21.5246 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - LPISRST - LPFDRTT - LP R+T - - - - - 9 - gnl|BL_ORD_ID|1232 - 97467|nucleocapsid protein|ACP44251.1|Influenza A virus (A/Fujian/411/2002(H3N2))|293090 - 1232 - 9 - - - 1 - 13.0826 - 22 - 22.6682 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - LPISRST - LPFEKST - LP +ST - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 19 - Query_19 - M_5001 - 9 - - - 1 - gnl|BL_ORD_ID|192 - 14198|UL123; IE1|AAR31390.1|Human betaherpesvirus 5|10359 - 192 - 11 - - - 1 - 11.927 - 19 - 64.6849 - 1 - 7 - 4 - 10 - 0 - 0 - 4 - 5 - 0 - 7 - STFAEVT - KTFEQVT - TF +VT - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 20 - Query_20 - M_5002 - 9 - - - 1 - gnl|BL_ORD_ID|192 - 14198|UL123; IE1|AAR31390.1|Human betaherpesvirus 5|10359 - 192 - 11 - - - 1 - 11.927 - 19 - 64.6849 - 1 - 7 - 4 - 10 - 0 - 0 - 4 - 5 - 0 - 7 - STFAEVT - KTFEQVT - TF +VT - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 21 - Query_21 - M_5003 - 9 - - - 1 - gnl|BL_ORD_ID|1861 - 180440|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1861 - 15 - - - 1 - 13.0826 - 22 - 16.1221 - 2 - 6 - 8 - 12 - 0 - 0 - 4 - 4 - 0 - 5 - SWNGG - SWNSG - SWN G - - - - - 2 - gnl|BL_ORD_ID|1926 - 180734|Nonstructural protein NS3|NP_739587.2|Dengue virus 2|11060 - 1926 - 9 - - - 1 - 12.6974 - 21 - 33.058 - 2 - 6 - 2 - 6 - 0 - 0 - 4 - 4 - 0 - 5 - SWNGG - SWNSG - SWN G - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 22 - Query_22 - M_5004 - 9 - - - 1 - gnl|BL_ORD_ID|1861 - 180440|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1861 - 15 - - - 1 - 13.0826 - 22 - 16.1221 - 2 - 6 - 8 - 12 - 0 - 0 - 4 - 4 - 0 - 5 - SWNGG - SWNSG - SWN G - - - - - 2 - gnl|BL_ORD_ID|1926 - 180734|Nonstructural protein NS3|NP_739587.2|Dengue virus 2|11060 - 1926 - 9 - - - 1 - 12.6974 - 21 - 33.058 - 2 - 6 - 2 - 6 - 0 - 0 - 4 - 4 - 0 - 5 - SWNGG - SWNSG - SWN G - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 23 - Query_23 - M_5005 - 9 - - - 1 - gnl|BL_ORD_ID|1296 - 103322|polyprotein|BAB18806.1|Hepatitis C virus|11103 - 1296 - 20 - - - 1 - 15.0086 - 27 - 1.00627 - 2 - 7 - 7 - 12 - 0 - 0 - 5 - 6 - 0 - 6 - INEECS - INEDCS - INE+CS - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 24 - Query_24 - M_5006 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_5007 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_5008 - 9 - - - 1 - gnl|BL_ORD_ID|1938 - 180802|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1938 - 9 - - - 1 - 14.6234 - 26 - 2.22125 - 1 - 6 - 3 - 8 - 0 - 0 - 5 - 6 - 0 - 6 - MLAIGC - LLAIGC - +LAIGC - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 27 - Query_27 - M_5009 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 28 - Query_28 - M_5010 - 9 - - - 1 - gnl|BL_ORD_ID|312 - 20861|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 - 312 - 9 - - - 1 - 11.927 - 19 - 75.1319 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 6 - 0 - 8 - SIRHNVLY - GLFNNVLY - + +NVLY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 29 - Query_29 - M_5011 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 30 - Query_30 - M_5012 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 31 - Query_31 - M_5013 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 32 - Query_32 - M_5014 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 33 - Query_33 - M_5015 - 9 - - - 1 - gnl|BL_ORD_ID|661 - 39571|polyprotein|BAD73987.1|Hepatitis C virus subtype 1b|31647 - 661 - 10 - - - 1 - 13.853 - 24 - 4.77406 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 7 - 0 - 8 - APSPVSFV - SPRPVSYL - +P PVS++ - - - - - 2 - gnl|BL_ORD_ID|2163 - 189546|glycosyl transferase|WP_015631503.1|Mycobacterium tuberculosis|1773 - 2163 - 9 - - - 1 - 12.6974 - 21 - 37.875 - 2 - 7 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - APSPVS - APEPVA - AP PV+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 34 - Query_34 - M_5016 - 9 - - - 1 - gnl|BL_ORD_ID|301 - 20354|M1 protein|CAA30882.1|Influenza A virus|11320 - 301 - 9 - - - 1 - 13.0826 - 22 - 20.7937 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 7 - 0 - 9 - GVLVLLFTL - GILGFVFTL - G+L +FTL - - - - - 2 - gnl|BL_ORD_ID|302 - 20355|Matrix protein 1|P03485.1|Influenza A virus (A/Puerto Rico/8/1934(H1N1))|211044 - 302 - 10 - - - 1 - 13.0826 - 22 - 21.2326 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 7 - 0 - 9 - GVLVLLFTL - GILGFVFTL - G+L +FTL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 35 - Query_35 - M_5017 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 36 - Query_36 - M_5018 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 37 - Query_37 - M_5019 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 38 - Query_38 - M_5020 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 39 - Query_39 - M_5021 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 40 - Query_40 - M_5022 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 41 - Query_41 - M_5023 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 42 - Query_42 - M_5024 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 43 - Query_43 - M_5025 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 44 - Query_44 - M_5026 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 45 - Query_45 - M_5027 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 46 - Query_46 - M_5028 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 47 - Query_47 - M_5029 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 48 - Query_48 - M_5030 - 9 - - - 1 - gnl|BL_ORD_ID|120 - 8236|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 - 120 - 15 - - - 1 - 12.6974 - 21 - 29.2994 - 1 - 8 - 4 - 11 - 0 - 0 - 2 - 5 - 0 - 8 - ENWDLVTY - QGWGPISY - + W ++Y - - - - - 2 - gnl|BL_ORD_ID|1699 - 149117|envelope glycoprotein|AAV74049.1|Hepatitis C virus (isolate H77)|63746 - 1699 - 18 - - - 1 - 12.6974 - 21 - 29.5284 - 1 - 8 - 5 - 12 - 0 - 0 - 2 - 5 - 0 - 8 - ENWDLVTY - QGWGPISY - + W ++Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 49 - Query_49 - M_5031 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 50 - Query_50 - M_5032 - 9 - - - 1 - gnl|BL_ORD_ID|1944 - 180818|Membrane glycoprotein precursor|NP_739582.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1944 - 15 - - - 1 - 15.0086 - 27 - 1.30769 - 1 - 7 - 3 - 9 - 0 - 0 - 5 - 5 - 0 - 7 - LEHPGST - LRHPGFT - L HPG T - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 51 - Query_51 - M_5033 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 52 - Query_52 - M_5034 - 9 - - - 1 - gnl|BL_ORD_ID|260 - 17802|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 260 - 15 - - - 1 - 11.1566 - 17 - 219.749 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 4 - 0 - 7 - LSPLTGG - FSPGTSG - SP T G - - - - - 2 - gnl|BL_ORD_ID|75 - 5542|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 75 - 15 - - - 1 - 11.1566 - 17 - 246.442 - 2 - 8 - 6 - 12 - 0 - 0 - 4 - 4 - 0 - 7 - LSPLTGG - FSPGTSG - SP T G - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 53 - Query_53 - M_5035 - 9 - - - 1 - gnl|BL_ORD_ID|163 - 12588|Glycoprotein B precursor (Glycoprotein II)|P09257.1|Human alphaherpesvirus 3|10335 - 163 - 11 - - - 1 - 13.0826 - 22 - 14.9787 - 1 - 8 - 2 - 9 - 0 - 0 - 3 - 7 - 0 - 8 - ITEILDRY - ITDTIDKF - IT+ +D++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 54 - Query_54 - M_5036 - 9 - - - 1 - gnl|BL_ORD_ID|390 - 23864|envelope glycoprotein(gp21, gp46) - human T-cell lymphotropic virus type 1|A45714|Human T-lymphotropic virus 1|11908 - 390 - 9 - - - 1 - 12.6974 - 21 - 37.875 - 1 - 7 - 2 - 8 - 0 - 0 - 4 - 5 - 0 - 7 - FNKSGFK - FSKCGFP - F+K GF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 55 - Query_55 - M_5037 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 56 - Query_56 - M_5038 - 9 - - - 1 - gnl|BL_ORD_ID|390 - 23864|envelope glycoprotein(gp21, gp46) - human T-cell lymphotropic virus type 1|A45714|Human T-lymphotropic virus 1|11908 - 390 - 9 - - - 1 - 12.6974 - 21 - 37.875 - 3 - 8 - 2 - 7 - 0 - 0 - 4 - 5 - 0 - 6 - FNKSGF - FSKCGF - F+K GF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 57 - Query_57 - M_5039 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 58 - Query_58 - M_5040 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 59 - Query_59 - M_5041 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 60 - Query_60 - M_5042 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 61 - Query_61 - M_5043 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 62 - Query_62 - M_5044 - 9 - - - 1 - gnl|BL_ORD_ID|1412 - 111404|Protein E7|P03129.1|Human papillomavirus type 16|333760 - 1412 - 15 - - - 1 - 14.2382 - 25 - 3.74365 - 1 - 8 - 7 - 14 - 0 - 0 - 4 - 6 - 0 - 8 - LQDFYLGT - LEDLLMGT - L+D +GT - - - - - 2 - gnl|BL_ORD_ID|1781 - 156550|E3 ubiquitin-protein ligase Mdm2|Q00987.1|Homo sapiens|9606 - 1781 - 9 - - - 1 - 14.2382 - 25 - 4.29054 - 4 - 9 - 3 - 8 - 0 - 0 - 5 - 5 - 0 - 6 - FYLGTY - FYLGQY - FYLG Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 63 - Query_63 - M_5045 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 64 - Query_64 - M_5046 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 65 - Query_65 - M_5047 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 66 - Query_66 - M_5048 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 67 - Query_67 - M_5049 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 68 - Query_68 - M_5050 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 69 - Query_69 - M_5051 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 70 - Query_70 - M_5052 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 71 - Query_71 - M_5053 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 72 - Query_72 - M_5054 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 73 - Query_73 - M_5055 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 74 - Query_74 - M_5056 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 75 - Query_75 - M_5057 - 9 - - - 1 - gnl|BL_ORD_ID|1765 - 154822|ribonucleotide reductase large subunit|CAB06725.1|Human alphaherpesvirus 2|10310 - 1765 - 15 - - - 1 - 14.2382 - 25 - 3.37317 - 1 - 6 - 5 - 10 - 0 - 0 - 4 - 6 - 0 - 6 - HLKVRT - HLRIRT - HL++RT - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 76 - Query_76 - M_5058 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 77 - Query_77 - M_5059 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 78 - Query_78 - M_5060 - 9 - - - 1 - gnl|BL_ORD_ID|1866 - 180460|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1866 - 10 - - - 1 - 14.2382 - 25 - 3.50259 - 1 - 7 - 3 - 9 - 0 - 0 - 4 - 6 - 0 - 7 - QQNAPLL - QSNAPIM - Q NAP++ - - - - - 2 - gnl|BL_ORD_ID|1704 - 150217|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1704 - 9 - - - 1 - 14.2382 - 25 - 3.93883 - 1 - 7 - 3 - 9 - 0 - 0 - 4 - 6 - 0 - 7 - QQNAPLL - QSNAPIM - Q NAP++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 79 - Query_79 - M_5061 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 80 - Query_80 - M_5062 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_138385_2_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_138385_2_T.fasta deleted file mode 100755 index 89206968..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_138385_2_T.fasta +++ /dev/null @@ -1,104 +0,0 @@ ->M_5063 -DPIRRHLHI ->M_5064 -HILYHCYGV ->M_5065 -WTRPGSEVL ->M_5066 -FPYVRNFVM ->M_5067 -YVRNFVMNL ->M_5068 -VAHEGMRPM ->M_5069 -RPDKMVPVV ->M_5070 -ILYLLSLFT ->M_5071 -LTILYLLSL ->M_5072 -YLLSLFTQT ->M_5073 -AAGPHVTVL ->M_5074 -RASAAGPHV ->M_5075 -SAAGPHVTV ->M_5076 -AVADLSCML ->M_5077 -CMLVLPTRL ->M_5078 -LAVADLSCM ->M_5079 -MLVLPTRLV ->M_5080 -VAVGTEHTL ->M_5081 -SVAWTTMDV ->M_5082 -TMDVATPSV ->M_5083 -NLYKGSVLY ->M_5084 -DEYNFVRTY ->M_5085 -RTYECFQHR ->M_5086 -LPSDPRLHL ->M_5087 -FLADITHLR ->M_5088 -GMRYWNMMV ->M_5089 -NMMVQWWLA ->M_5090 -TPLGKGDIV ->M_5091 -KVRSCIDLI ->M_5092 -YEQKVRSCI ->M_5093 -ALLAFATIM ->M_5094 -ATIMYVPAL ->M_5095 -LAFATIMYV ->M_5096 -LAFATIMYV ->M_5097 -YALLAFATI ->M_5098 -YALLAFATI ->M_5099 -LLLLLLLLV ->M_5100 -LLLLLLLVV ->M_5101 -LLLLLLVVV ->M_5102 -LLVVVPWGV ->M_5103 -IAATPIPAM ->M_5104 -HVLEIDESV ->M_5105 -HVLEIDESV ->M_5106 -YFNGSTNHV ->M_5107 -TPLCPGELL ->M_5108 -LMLGLVWTI ->M_5109 -LMLGLVWTI ->M_5110 -RLMLGLVWT ->M_5111 -SLTADDAFV ->M_5112 -PAFSLDVLM ->M_5113 -YLQAEIEPV ->M_5114 -YLQAEIEPV diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_138385_2_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_138385_2_T_iedb.xml deleted file mode 100755 index 385d1a53..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_138385_2_T_iedb.xml +++ /dev/null @@ -1,1610 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_5063 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_5063 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_5064 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_5065 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_5066 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_5067 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_5068 - 9 - - - 1 - gnl|BL_ORD_ID|996 - 65654|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 - 996 - 15 - - - 1 - 14.6234 - 26 - 1.57759 - 2 - 9 - 7 - 14 - 0 - 0 - 4 - 6 - 0 - 8 - AHEGMRPM - AHNGLRDL - AH G+R + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 7 - Query_7 - M_5069 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_5070 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_5071 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_5072 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_5073 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_5074 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_5075 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_5076 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_5077 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_5078 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_5079 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_5080 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_5081 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_5082 - 9 - - - 1 - gnl|BL_ORD_ID|1762 - 154448|RL2|CAB06760.1|Human alphaherpesvirus 2|10310 - 1762 - 16 - - - 1 - 8.46023 - 10 - 4206.81 - 2 - 5 - 5 - 8 - 0 - 0 - 3 - 3 - 0 - 4 - MDVA - MDAA - MD A - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 21 - Query_21 - M_5083 - 9 - - - 1 - gnl|BL_ORD_ID|413 - 24943|DNA polymerase|CAA10434.1|Hepatitis B virus|10407 - 413 - 11 - - - 1 - 13.853 - 24 - 4.51774 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 6 - 0 - 9 - NLYKGSVLY - TLWKAGILY - L+K +LY - - - - - 2 - gnl|BL_ORD_ID|988 - 65148|DNA polymerase|CAA10434.1|Hepatitis B virus|10407 - 988 - 10 - - - 1 - 13.853 - 24 - 4.53299 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 6 - 0 - 9 - NLYKGSVLY - TLWKAGILY - L+K +LY - - - - - 3 - gnl|BL_ORD_ID|683 - 41093|polyprotein|AGO67248.1|Dengue virus 2|11060 - 683 - 9 - - - 1 - 13.4678 - 23 - 11.1275 - 1 - 6 - 3 - 8 - 0 - 0 - 3 - 6 - 0 - 6 - NLYKGS - NIFRGS - N+++GS - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 22 - Query_22 - M_5084 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_5085 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_5086 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_5087 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_5088 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_5089 - 9 - - - 1 - gnl|BL_ORD_ID|1096 - 72322|polyprotein|AAA86907.1|Hepatitis C virus|11103 - 1096 - 15 - - - 1 - 11.5418 - 18 - 139.661 - 1 - 6 - 2 - 7 - 0 - 0 - 3 - 5 - 0 - 6 - NMMVQW - DMMMNW - +MM+ W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 28 - Query_28 - M_5090 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 29 - Query_29 - M_5091 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 30 - Query_30 - M_5092 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 31 - Query_31 - M_5093 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 32 - Query_32 - M_5094 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 33 - Query_33 - M_5095 - 9 - - - 1 - gnl|BL_ORD_ID|1568 - 141341|tegument protein VP11/12|NP_044648.1|Human alphaherpesvirus 1|10298 - 1568 - 9 - - - 1 - 13.0826 - 22 - 18.4218 - 1 - 8 - 2 - 9 - 0 - 0 - 3 - 7 - 0 - 8 - LAFATIMY - LAYVSVLY - LA+ +++Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 34 - Query_34 - M_5096 - 9 - - - 1 - gnl|BL_ORD_ID|1568 - 141341|tegument protein VP11/12|NP_044648.1|Human alphaherpesvirus 1|10298 - 1568 - 9 - - - 1 - 13.0826 - 22 - 18.4218 - 1 - 8 - 2 - 9 - 0 - 0 - 3 - 7 - 0 - 8 - LAFATIMY - LAYVSVLY - LA+ +++Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 35 - Query_35 - M_5097 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 36 - Query_36 - M_5098 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 37 - Query_37 - M_5099 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 38 - Query_38 - M_5100 - 9 - - - 1 - gnl|BL_ORD_ID|1263 - 98540|trans-sialidase, putative|EAN88532.1|Trypanosoma cruzi|5693 - 1263 - 10 - - - 1 - 11.1566 - 17 - 242.571 - 3 - 9 - 4 - 10 - 0 - 0 - 6 - 7 - 0 - 7 - LLLLLVV - VLLLLVV - +LLLLVV - - - - - 2 - gnl|BL_ORD_ID|1254 - 98224|trans-sialidase, putative|EAN82076.1|Trypanosoma cruzi|5693 - 1254 - 10 - - - 1 - 11.1566 - 17 - 286.165 - 4 - 9 - 1 - 6 - 0 - 0 - 6 - 6 - 0 - 6 - LLLLVV - LLLLVV - LLLLVV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 39 - Query_39 - M_5101 - 9 - - - 1 - gnl|BL_ORD_ID|1263 - 98540|trans-sialidase, putative|EAN88532.1|Trypanosoma cruzi|5693 - 1263 - 10 - - - 1 - 11.1566 - 17 - 231.802 - 3 - 8 - 5 - 10 - 0 - 0 - 6 - 6 - 0 - 6 - LLLLVV - LLLLVV - LLLLVV - - - - - 2 - gnl|BL_ORD_ID|1254 - 98224|trans-sialidase, putative|EAN82076.1|Trypanosoma cruzi|5693 - 1254 - 10 - - - 1 - 11.1566 - 17 - 250.006 - 3 - 9 - 1 - 7 - 0 - 0 - 6 - 7 - 0 - 7 - LLLLVVV - LLLLVVM - LLLLVV+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 40 - Query_40 - M_5102 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 41 - Query_41 - M_5103 - 9 - - - 1 - gnl|BL_ORD_ID|1815 - 177806|polyprotein|ACZ60104.1|Hepatitis C virus subtype 3a|356426 - 1815 - 11 - - - 1 - 13.0826 - 22 - 14.9787 - 4 - 8 - 3 - 7 - 0 - 0 - 4 - 5 - 0 - 5 - TPIPA - TPLPA - TP+PA - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 42 - Query_42 - M_5104 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 43 - Query_43 - M_5105 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 44 - Query_44 - M_5106 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 45 - Query_45 - M_5107 - 9 - - - 1 - gnl|BL_ORD_ID|2144 - 187197|Core protein|Q9QAC5|Hepatitis B virus|10407 - 2144 - 9 - - - 1 - 13.4678 - 23 - 8.42175 - 3 - 9 - 1 - 7 - 0 - 0 - 4 - 6 - 0 - 7 - LCPGELL - VCWGELM - +C GEL+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 46 - Query_46 - M_5108 - 9 - - - 1 - gnl|BL_ORD_ID|1717 - 150389|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1717 - 9 - - - 1 - 10.7714 - 16 - 354.707 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 5 - 0 - 9 - LMLGLVWTI - LMMRTTWAL - LM+ W + - - - - - 2 - gnl|BL_ORD_ID|1743 - 150686|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1743 - 9 - - - 1 - 10.7714 - 16 - 442.738 - 1 - 7 - 2 - 8 - 0 - 0 - 3 - 4 - 0 - 7 - LMLGLVW - LMMRTTW - LM+ W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 47 - Query_47 - M_5109 - 9 - - - 1 - gnl|BL_ORD_ID|1717 - 150389|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1717 - 9 - - - 1 - 10.7714 - 16 - 354.707 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 5 - 0 - 9 - LMLGLVWTI - LMMRTTWAL - LM+ W + - - - - - 2 - gnl|BL_ORD_ID|1743 - 150686|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1743 - 9 - - - 1 - 10.7714 - 16 - 442.738 - 1 - 7 - 2 - 8 - 0 - 0 - 3 - 4 - 0 - 7 - LMLGLVW - LMMRTTW - LM+ W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 48 - Query_48 - M_5110 - 9 - - - 1 - gnl|BL_ORD_ID|1743 - 150686|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1743 - 9 - - - 1 - 10.3862 - 15 - 654.037 - 2 - 8 - 2 - 8 - 0 - 0 - 3 - 4 - 0 - 7 - LMLGLVW - LMMRTTW - LM+ W - - - - - 2 - gnl|BL_ORD_ID|1717 - 150389|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1717 - 9 - - - 1 - 10.3862 - 15 - 732.621 - 2 - 8 - 1 - 7 - 0 - 0 - 3 - 4 - 0 - 7 - LMLGLVW - LMMRTTW - LM+ W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 49 - Query_49 - M_5111 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 50 - Query_50 - M_5112 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 51 - Query_51 - M_5113 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 52 - Query_52 - M_5114 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_138625_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_138625_1_T.fasta deleted file mode 100755 index 764f3386..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_138625_1_T.fasta +++ /dev/null @@ -1,106 +0,0 @@ ->M_5115 -LFFVDKLYK ->M_5116 -ALLPLFVVL ->M_5117 -ALLPLFVVL ->M_5118 -KALLPLFVV ->M_5119 -VVLCGNDHV ->M_5120 -TEMKRKAPF ->M_5121 -AMATYHFHF ->M_5122 -ATYHFHFNL ->M_5123 -ATYHFHFNL ->M_5124 -KAMATYHFH ->M_5125 -LKAMATYHF ->M_5126 -NVFVEVVLV ->M_5127 -GVKGVNSLF ->M_5128 -KGVNSLFKK ->M_5129 -AMSTPIYQM ->M_5130 -AMSTPIYQM ->M_5131 -SMAMSTPIY ->M_5132 -SMAMSTPIY ->M_5133 -SSMAMSTPI ->M_5134 -KMADEVPLK ->M_5135 -FLLAFRSGA ->M_5136 -LLAFRSGAL ->M_5137 -RVAEVAAQV ->M_5138 -KIFWFPTGL ->M_5139 -AGIFLLIHF ->M_5140 -FLLIHFHPL ->M_5141 -FLLIHFHPL ->M_5142 -GIFLLIHFH ->M_5143 -LLIHFHPLA ->M_5144 -SIVTSTFII ->M_5145 -VTSTFIISL ->M_5146 -LQIHGLAVE ->M_5147 -ATVLTLPHV ->M_5148 -VLTLPHVTK ->M_5149 -AVSNFYLPL ->M_5150 -HISAVSNFY ->M_5151 -HISAVSNFY ->M_5152 -SVVVIIDVK ->M_5153 -VVIIDVKPK ->M_5154 -FQRALVQPG ->M_5155 -ESFTATVEF ->M_5156 -LAAPRGVCY ->M_5157 -ATGATSLCF ->M_5158 -GLAMCHQEL ->M_5159 -LLTLAGLAM ->M_5160 -TVWPSLAPL ->M_5161 -CQHKLGKRY ->M_5162 -AVWRHLLLA ->M_5163 -HLLLALLLL ->M_5164 -LLALLLLVL ->M_5165 -LLALLLLVL ->M_5166 -LLLALLLLV ->M_5167 -LTRHQRTHM diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_138625_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_138625_1_T_iedb.xml deleted file mode 100755 index 24e9475d..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_138625_1_T_iedb.xml +++ /dev/null @@ -1,1766 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_5115 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_5115 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_5116 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_5117 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_5118 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_5119 - 9 - - - 1 - gnl|BL_ORD_ID|987 - 65118|SAG1 protein|AAO72426.1|Toxoplasma gondii RH|383379 - 987 - 9 - - - 1 - 13.4678 - 23 - 13.0154 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 6 - 0 - 9 - VVLCGNDHV - TLVCGKDGV - ++CG D V - - - - - 2 - gnl|BL_ORD_ID|671 - 40286|SAG1 protein|AAO72426.1|Toxoplasma gondii RH|383379 - 671 - 9 - - - 1 - 13.4678 - 23 - 13.0154 - 2 - 9 - 1 - 8 - 0 - 0 - 4 - 6 - 0 - 8 - VLCGNDHV - LVCGKDGV - ++CG D V - - - - - 3 - gnl|BL_ORD_ID|1075 - 71266|Circumsporozoite protein precursor|P02893.1|Plasmodium falciparum|5833 - 1075 - 20 - - - 1 - 13.0826 - 22 - 16.3948 - 2 - 6 - 1 - 5 - 0 - 0 - 4 - 4 - 0 - 5 - VLCGN - VTCGN - V CGN - - - - - 4 - gnl|BL_ORD_ID|1074 - 71265|Circumsporozoite protein precursor|P02893.1|Plasmodium falciparum|5833 - 1074 - 10 - - - 1 - 12.6974 - 21 - 28.4017 - 2 - 6 - 1 - 5 - 0 - 0 - 4 - 4 - 0 - 5 - VLCGN - VTCGN - V CGN - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 6 - Query_6 - M_5120 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_5121 - 9 - - - 1 - gnl|BL_ORD_ID|1975 - 183147|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1975 - 9 - - - 1 - 11.927 - 19 - 69.1936 - 3 - 8 - 2 - 7 - 0 - 0 - 3 - 5 - 0 - 6 - ATYHFH - CSHHFH - ++HFH - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 8 - Query_8 - M_5122 - 9 - - - 1 - gnl|BL_ORD_ID|419 - 25275|Glutamate decarboxylase 2|Q05329.1|Homo sapiens|9606 - 419 - 13 - - - 1 - 12.3122 - 20 - 42.7536 - 2 - 9 - 5 - 12 - 0 - 0 - 4 - 6 - 0 - 8 - TYHFHFNL - SEHSHFSL - + H HF+L - - - - - 2 - gnl|BL_ORD_ID|1975 - 183147|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1975 - 9 - - - 1 - 11.927 - 19 - 76.3762 - 1 - 6 - 2 - 7 - 0 - 0 - 3 - 5 - 0 - 6 - ATYHFH - CSHHFH - ++HFH - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 9 - Query_9 - M_5123 - 9 - - - 1 - gnl|BL_ORD_ID|419 - 25275|Glutamate decarboxylase 2|Q05329.1|Homo sapiens|9606 - 419 - 13 - - - 1 - 12.3122 - 20 - 42.7536 - 2 - 9 - 5 - 12 - 0 - 0 - 4 - 6 - 0 - 8 - TYHFHFNL - SEHSHFSL - + H HF+L - - - - - 2 - gnl|BL_ORD_ID|1975 - 183147|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1975 - 9 - - - 1 - 11.927 - 19 - 76.3762 - 1 - 6 - 2 - 7 - 0 - 0 - 3 - 5 - 0 - 6 - ATYHFH - CSHHFH - ++HFH - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 10 - Query_10 - M_5124 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_5125 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_5126 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_5127 - 9 - - - 1 - gnl|BL_ORD_ID|786 - 52652|||| - 786 - 27 - - - 1 - 15.0086 - 27 - 1.22232 - 2 - 9 - 13 - 20 - 0 - 0 - 5 - 7 - 0 - 8 - VKGVNSLF - VRGLTSLF - V+G+ SLF - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 14 - Query_14 - M_5128 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_5129 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_5130 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_5131 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_5132 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_5133 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_5134 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_5135 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 22 - Query_22 - M_5136 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_5137 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_5138 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_5139 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_5140 - 9 - - - 1 - gnl|BL_ORD_ID|624 - 37507|Large T antigen|P03071.1|Human polyomavirus 1|1891762 - 624 - 9 - - - 1 - 13.853 - 24 - 6.71897 - 2 - 9 - 2 - 9 - 0 - 0 - 5 - 6 - 0 - 8 - LLIHFHPL - LLIWFRPV - LLI F P+ - - - - - 2 - gnl|BL_ORD_ID|1975 - 183147|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1975 - 9 - - - 1 - 12.3122 - 20 - 61.624 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 5 - 0 - 9 - FLLIHFHPL - FCSHHFHQL - F HFH L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 27 - Query_27 - M_5141 - 9 - - - 1 - gnl|BL_ORD_ID|624 - 37507|Large T antigen|P03071.1|Human polyomavirus 1|1891762 - 624 - 9 - - - 1 - 13.853 - 24 - 6.71897 - 2 - 9 - 2 - 9 - 0 - 0 - 5 - 6 - 0 - 8 - LLIHFHPL - LLIWFRPV - LLI F P+ - - - - - 2 - gnl|BL_ORD_ID|1975 - 183147|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1975 - 9 - - - 1 - 12.3122 - 20 - 61.624 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 5 - 0 - 9 - FLLIHFHPL - FCSHHFHQL - F HFH L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 28 - Query_28 - M_5142 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 29 - Query_29 - M_5143 - 9 - - - 1 - gnl|BL_ORD_ID|624 - 37507|Large T antigen|P03071.1|Human polyomavirus 1|1891762 - 624 - 9 - - - 1 - 13.853 - 24 - 4.83846 - 1 - 8 - 2 - 9 - 0 - 0 - 5 - 6 - 0 - 8 - LLIHFHPL - LLIWFRPV - LLI F P+ - - - - - 2 - gnl|BL_ORD_ID|1975 - 183147|polyprotein|AGW21594.1|Dengue virus 1|11053 - 1975 - 9 - - - 1 - 12.3122 - 20 - 59.6102 - 4 - 8 - 5 - 9 - 0 - 0 - 4 - 4 - 0 - 5 - HFHPL - HFHQL - HFH L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 30 - Query_30 - M_5144 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 31 - Query_31 - M_5145 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 32 - Query_32 - M_5146 - 9 - - - 1 - gnl|BL_ORD_ID|2320 - 423047|Genome polyprotein|P27958.3|Hepatitis C virus genotype 1|41856 - 2320 - 9 - - - 1 - 12.6974 - 21 - 35.9943 - 2 - 8 - 2 - 8 - 0 - 0 - 3 - 6 - 0 - 7 - QIHGLAV - RLHGLSA - ++HGL+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 33 - Query_33 - M_5147 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 34 - Query_34 - M_5148 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 35 - Query_35 - M_5149 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 36 - Query_36 - M_5150 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 37 - Query_37 - M_5151 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 38 - Query_38 - M_5152 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 39 - Query_39 - M_5153 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 40 - Query_40 - M_5154 - 9 - - - 1 - gnl|BL_ORD_ID|1992 - 183577|polyprotein|AGK36298.1|Dengue virus 2|11060 - 1992 - 10 - - - 1 - 15.0086 - 27 - 1.28623 - 1 - 6 - 2 - 7 - 0 - 0 - 5 - 6 - 0 - 6 - FQRALV - FQRALI - FQRAL+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 41 - Query_41 - M_5155 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 42 - Query_42 - M_5156 - 9 - - - 1 - gnl|BL_ORD_ID|1667 - 148117|early protein|CAA52585.1|Human papillomavirus type 52|10618 - 1667 - 9 - - - 1 - 13.0826 - 22 - 22.6682 - 4 - 8 - 1 - 5 - 0 - 0 - 4 - 4 - 0 - 5 - PRGVC - PYGVC - P GVC - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 43 - Query_43 - M_5157 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 44 - Query_44 - M_5158 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 45 - Query_45 - M_5159 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 46 - Query_46 - M_5160 - 9 - - - 1 - gnl|BL_ORD_ID|1520 - 140600|glutamine synthetase GLNA1 (glutamine synthase) (GS-I)|NP_216736.1|Mycobacterium tuberculosis H37Rv|83332 - 1520 - 9 - - - 1 - 13.0826 - 22 - 21.1561 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 6 - 0 - 9 - TVWPSLAPL - SLWKDGAPL - ++W APL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 47 - Query_47 - M_5161 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 48 - Query_48 - M_5162 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 49 - Query_49 - M_5163 - 9 - - - 1 - gnl|BL_ORD_ID|292 - 19442|nucleocapsid protein|ABI96968.1|SARS coronavirus|227859 - 292 - 10 - - - 1 - 11.1566 - 17 - 246.263 - 4 - 9 - 5 - 10 - 0 - 0 - 6 - 6 - 0 - 6 - LALLLL - LALLLL - LALLLL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 50 - Query_50 - M_5164 - 9 - - - 1 - gnl|BL_ORD_ID|292 - 19442|nucleocapsid protein|ABI96968.1|SARS coronavirus|227859 - 292 - 10 - - - 1 - 11.1566 - 17 - 265.518 - 2 - 7 - 5 - 10 - 0 - 0 - 6 - 6 - 0 - 6 - LALLLL - LALLLL - LALLLL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 51 - Query_51 - M_5165 - 9 - - - 1 - gnl|BL_ORD_ID|292 - 19442|nucleocapsid protein|ABI96968.1|SARS coronavirus|227859 - 292 - 10 - - - 1 - 11.1566 - 17 - 265.518 - 2 - 7 - 5 - 10 - 0 - 0 - 6 - 6 - 0 - 6 - LALLLL - LALLLL - LALLLL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 52 - Query_52 - M_5166 - 9 - - - 1 - gnl|BL_ORD_ID|292 - 19442|nucleocapsid protein|ABI96968.1|SARS coronavirus|227859 - 292 - 10 - - - 1 - 11.1566 - 17 - 265.518 - 3 - 8 - 5 - 10 - 0 - 0 - 6 - 6 - 0 - 6 - LALLLL - LALLLL - LALLLL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 53 - Query_53 - M_5167 - 9 - - - 1 - gnl|BL_ORD_ID|256 - 17278|Genome polyprotein|P06441.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 256 - 20 - - - 1 - 13.0826 - 22 - 15.3699 - 2 - 9 - 9 - 16 - 0 - 0 - 4 - 5 - 0 - 8 - TRHQRTHM - SRHTSDHM - +RH HM - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_138926_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_138926_1_T.fasta deleted file mode 100755 index c2a8f427..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_138926_1_T.fasta +++ /dev/null @@ -1,108 +0,0 @@ ->M_5168 -EAWLFLEWV ->M_5169 -SEAWLFLEW ->M_5170 -WILSHTVAL ->M_5171 -WILSHTVAL ->M_5172 -SVRKSVSTV ->M_5173 -MTVTVCPPT ->M_5174 -SPMVLLLAA ->M_5175 -VERGSPMVL ->M_5176 -VVERGSPMV ->M_5177 -FEAFDHTET ->M_5178 -RLFEAFDHT ->M_5179 -HTCRVMGAL ->M_5180 -YKIGGIGMV ->M_5181 -EELTQLNEA ->M_5182 -LQSRLEEEL ->M_5183 -RLEEELTQL ->M_5184 -FPRLGCPWF ->M_5185 -RLGCPWFTL ->M_5186 -RLGCPWFTL ->M_5187 -DWPVFPGLF ->M_5188 -FNVGDDWPV ->M_5189 -NYASRTQNI ->M_5190 -SVSSCCQPV ->M_5191 -SVSSCCQPV ->M_5192 -CTLGDQLSL ->M_5193 -STAPQAHGV ->M_5194 -STAPQAHGV ->M_5195 -VSLFYSTAI ->M_5196 -VSLFYSTAI ->M_5197 -YSTAISVYL ->M_5198 -YSTAISVYL ->M_5199 -DTAPDIVEI ->M_5200 -FLWDRHVRF ->M_5201 -LWDRHVRFF ->M_5202 -FTCLPLGSL ->M_5203 -HVWLCDLPV ->M_5204 -HVWLCDLPV ->M_5205 -APRGVCYGA ->M_5206 -DPEYSPGAL ->M_5207 -YSPGALATF ->M_5208 -VLGDFLGTV ->M_5209 -AVVGTVWNV ->M_5210 -NVATTGLSL ->M_5211 -DTTDKGALM ->M_5212 -KAVSVCPEA ->M_5213 -SVCPEAAPA ->M_5214 -VLVVGMGPV ->M_5215 -IFATKPELL ->M_5216 -RIFATKPEL ->M_5217 -AFSQSAYLI ->M_5218 -AYLIQHQRF ->M_5219 -KAFSQSAYL ->M_5220 -KAFSQSAYL ->M_5221 -FPAPARDDF diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_138926_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_138926_1_T_iedb.xml deleted file mode 100755 index 4e49d0f8..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_138926_1_T_iedb.xml +++ /dev/null @@ -1,1429 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_5168 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_5168 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_5169 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_5170 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_5171 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_5172 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_5173 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_5174 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_5175 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_5176 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_5177 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_5178 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_5179 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_5180 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_5181 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_5182 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_5183 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_5184 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_5185 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_5186 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_5187 - 9 - - - 1 - gnl|BL_ORD_ID|1106 - 72928|Genome polyprotein|P26662.3|Hepatitis C virus (isolate Japanese)|11116 - 1106 - 10 - - - 1 - 13.4678 - 23 - 12.4198 - 2 - 7 - 1 - 6 - 0 - 0 - 4 - 4 - 0 - 6 - WPVFPG - WPAPPG - WP PG - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 21 - Query_21 - M_5188 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 22 - Query_22 - M_5189 - 9 - - - 1 - gnl|BL_ORD_ID|84 - 6308|HCV-1|AAA45676.1|Hepatitis C virus genotype 1|41856 - 84 - 20 - - - 1 - 13.853 - 24 - 7.21037 - 1 - 7 - 7 - 13 - 0 - 0 - 4 - 6 - 0 - 7 - NYASRTQ - NWAVRTK - N+A RT+ - - - - - 2 - gnl|BL_ORD_ID|1813 - 177701|polyprotein|ACZ60104.1|Hepatitis C virus subtype 3a|356426 - 1813 - 18 - - - 1 - 13.853 - 24 - 7.28436 - 1 - 7 - 12 - 18 - 0 - 0 - 4 - 6 - 0 - 7 - NYASRTQ - NWAVRTK - N+A RT+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 23 - Query_23 - M_5190 - 9 - - - 1 - gnl|BL_ORD_ID|872 - 57361|Genome polyprotein|SRC279960|Hepatitis C virus (isolate H77)|63746 - 872 - 11 - - - 1 - 12.6974 - 21 - 28.2065 - 3 - 8 - 1 - 6 - 0 - 0 - 4 - 4 - 0 - 6 - SSCCQP - SECCTP - S CC P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 24 - Query_24 - M_5191 - 9 - - - 1 - gnl|BL_ORD_ID|872 - 57361|Genome polyprotein|SRC279960|Hepatitis C virus (isolate H77)|63746 - 872 - 11 - - - 1 - 12.6974 - 21 - 28.2065 - 3 - 8 - 1 - 6 - 0 - 0 - 4 - 4 - 0 - 6 - SSCCQP - SECCTP - S CC P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 25 - Query_25 - M_5192 - 9 - - - 1 - gnl|BL_ORD_ID|2252 - 244160|surface antigen 2 (CA-2)|XP_818927.1|Trypanosoma cruzi strain CL Brener|353153 - 2252 - 9 - - - 1 - 14.2382 - 25 - 4.0067 - 4 - 9 - 4 - 9 - 0 - 0 - 5 - 6 - 0 - 6 - GDQLSL - GDKLSL - GD+LSL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 26 - Query_26 - M_5193 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_5194 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 28 - Query_28 - M_5195 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 29 - Query_29 - M_5196 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 30 - Query_30 - M_5197 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 31 - Query_31 - M_5198 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 32 - Query_32 - M_5199 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 33 - Query_33 - M_5200 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 34 - Query_34 - M_5201 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 35 - Query_35 - M_5202 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 36 - Query_36 - M_5203 - 9 - - - 1 - gnl|BL_ORD_ID|57 - 4172|Glycoprotein I precursor (Glycoprotein IV) (GI) (GPIV)|P09258.1|Human alphaherpesvirus 3|10335 - 57 - 11 - - - 1 - 15.3938 - 28 - 0.668034 - 2 - 9 - 1 - 8 - 0 - 0 - 5 - 5 - 0 - 8 - VWLCDLPV - ARLCDLPA - LCDLP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 37 - Query_37 - M_5204 - 9 - - - 1 - gnl|BL_ORD_ID|57 - 4172|Glycoprotein I precursor (Glycoprotein IV) (GI) (GPIV)|P09258.1|Human alphaherpesvirus 3|10335 - 57 - 11 - - - 1 - 15.3938 - 28 - 0.668034 - 2 - 9 - 1 - 8 - 0 - 0 - 5 - 5 - 0 - 8 - VWLCDLPV - ARLCDLPA - LCDLP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 38 - Query_38 - M_5205 - 9 - - - 1 - gnl|BL_ORD_ID|1667 - 148117|early protein|CAA52585.1|Human papillomavirus type 52|10618 - 1667 - 9 - - - 1 - 12.6974 - 21 - 26.9236 - 2 - 6 - 1 - 5 - 0 - 0 - 4 - 4 - 0 - 5 - PRGVC - PYGVC - P GVC - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 39 - Query_39 - M_5206 - 9 - - - 1 - gnl|BL_ORD_ID|899 - 59153|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 - 899 - 15 - - - 1 - 13.4678 - 23 - 10.0248 - 4 - 9 - 5 - 10 - 0 - 0 - 4 - 5 - 0 - 6 - YSPGAL - YSPGEI - YSPG + - - - - - 2 - gnl|BL_ORD_ID|256 - 17278|Genome polyprotein|P06441.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 - 256 - 20 - - - 1 - 12.6974 - 21 - 21.519 - 2 - 7 - 2 - 7 - 0 - 0 - 4 - 4 - 0 - 6 - PEYSPG - PELKPG - PE PG - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 40 - Query_40 - M_5207 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 41 - Query_41 - M_5208 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 42 - Query_42 - M_5209 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 43 - Query_43 - M_5210 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 44 - Query_44 - M_5211 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 45 - Query_45 - M_5212 - 9 - - - 1 - gnl|BL_ORD_ID|287 - 19359|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 - 287 - 20 - - - 1 - 13.4678 - 23 - 8.9532 - 1 - 9 - 9 - 17 - 0 - 0 - 4 - 6 - 0 - 9 - KAVSVCPEA - QQVSIAPNA - + VS+ P A - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 46 - Query_46 - M_5213 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 47 - Query_47 - M_5214 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 48 - Query_48 - M_5215 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 49 - Query_49 - M_5216 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 50 - Query_50 - M_5217 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 51 - Query_51 - M_5218 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 52 - Query_52 - M_5219 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 53 - Query_53 - M_5220 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 54 - Query_54 - M_5221 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_139381_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_139381_1_T.fasta deleted file mode 100755 index a16d5f0c..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_139381_1_T.fasta +++ /dev/null @@ -1,78 +0,0 @@ ->M_5222 -SPSVMWLVH ->M_5223 -LAVRDVFEL ->M_5224 -LAVRDVFEL ->M_5225 -KTLTLAKNY ->M_5226 -SSGSMCNRW ->M_5227 -TTKNDIGPY ->M_5228 -LGLTNNTAM ->M_5229 -FTTELTAPF ->M_5230 -FTTELTAPF ->M_5231 -FTTELTAPF ->M_5232 -MPAFTTELT ->M_5233 -LMALHPALF ->M_5234 -QCSEHDVLF ->M_5235 -EPYIDNEEF ->M_5236 -VVIKAIEPY ->M_5237 -QVQDSNLEY ->M_5238 -QVQDSNLEY ->M_5239 -LASSCGCTF ->M_5240 -LASSCGCTF ->M_5241 -IQLLGVFVW ->M_5242 -ISIQLLGVF ->M_5243 -EVDFTCWKY ->M_5244 -HPTAASQSR ->M_5245 -IIETANVSY ->M_5246 -VSYTNAWAL ->M_5247 -FFIHSFTLM ->M_5248 -MFFIHSFTL ->M_5249 -MFNPIIYIF ->M_5250 -LPTPVEPTV ->M_5251 -TPVEPTVAC ->M_5252 -HPDNVSSSY ->M_5253 -LLAAARPLW ->M_5254 -SPVALQLRY ->M_5255 -YQIGTDSAL ->M_5256 -EAHHHFPSL ->M_5257 -EAHHHFPSL ->M_5258 -GSGEAHHHF ->M_5259 -RVSSLTLHF ->M_5260 -KPFSQSCEF diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_139381_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_139381_1_T_iedb.xml deleted file mode 100755 index fcd36868..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_139381_1_T_iedb.xml +++ /dev/null @@ -1,1822 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_5222 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_5222 - 9 - - - 1 - gnl|BL_ORD_ID|431 - 26273|nucleocapsid protein|ABI96968.1|SARS coronavirus|227859 - 431 - 15 - - - 1 - 13.853 - 24 - 5.29758 - 1 - 9 - 6 - 14 - 0 - 0 - 4 - 6 - 0 - 9 - SPSVMWLVH - TPSGTWLTY - +PS WL + - - - - - 2 - gnl|BL_ORD_ID|1436 - 116835|Nucleoprotein|P05133.1|Hantaan virus 76-118|11602 - 1436 - 15 - - - 1 - 13.4678 - 23 - 9.36117 - 1 - 7 - 1 - 7 - 0 - 0 - 4 - 6 - 0 - 7 - SPSVMWL - SPSSIWV - SPS +W+ - - - - - 3 - gnl|BL_ORD_ID|2187 - 190494|nucleocapsid protein|ABI96968.1|SARS coronavirus|227859 - 2187 - 10 - - - 1 - 12.6974 - 21 - 24.356 - 1 - 7 - 4 - 10 - 0 - 0 - 4 - 5 - 0 - 7 - SPSVMWL - TPSGTWL - +PS WL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 2 - Query_2 - M_5223 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_5224 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_5225 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_5226 - 9 - - - 1 - gnl|BL_ORD_ID|136 - 9920|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis|1773 - 136 - 18 - - - 1 - 13.0826 - 22 - 15.4571 - 1 - 9 - 6 - 14 - 0 - 0 - 3 - 7 - 0 - 9 - SSGSMCNRW - TAGSLQGQW - ++GS+ +W - - - - - 2 - gnl|BL_ORD_ID|2224 - 194400|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis|1773 - 2224 - 9 - - - 1 - 13.0826 - 22 - 18.4218 - 1 - 9 - 1 - 9 - 0 - 0 - 3 - 7 - 0 - 9 - SSGSMCNRW - TAGSLQGQW - ++GS+ +W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 6 - Query_6 - M_5227 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_5228 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_5229 - 9 - - - 1 - gnl|BL_ORD_ID|1818 - 177903|polyprotein|ACZ60102.1|Hepatitis C virus subtype 3a|356426 - 1818 - 17 - - - 1 - 13.4678 - 23 - 9.62753 - 1 - 9 - 9 - 17 - 0 - 0 - 4 - 6 - 0 - 9 - FTTELTAPF - FTASVTSPL - FT +T+P - - - - - 2 - gnl|BL_ORD_ID|1597 - 142233|ATP-dependent helicase|NP_217813.1|Mycobacterium tuberculosis|1773 - 1597 - 32 - - - 1 - 11.927 - 19 - 52.8651 - 1 - 8 - 20 - 27 - 0 - 0 - 4 - 5 - 0 - 8 - FTTELTAP - FTSTFAAP - FT+ AP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 9 - Query_9 - M_5230 - 9 - - - 1 - gnl|BL_ORD_ID|1818 - 177903|polyprotein|ACZ60102.1|Hepatitis C virus subtype 3a|356426 - 1818 - 17 - - - 1 - 13.4678 - 23 - 9.62753 - 1 - 9 - 9 - 17 - 0 - 0 - 4 - 6 - 0 - 9 - FTTELTAPF - FTASVTSPL - FT +T+P - - - - - 2 - gnl|BL_ORD_ID|1597 - 142233|ATP-dependent helicase|NP_217813.1|Mycobacterium tuberculosis|1773 - 1597 - 32 - - - 1 - 11.927 - 19 - 52.8651 - 1 - 8 - 20 - 27 - 0 - 0 - 4 - 5 - 0 - 8 - FTTELTAP - FTSTFAAP - FT+ AP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 10 - Query_10 - M_5231 - 9 - - - 1 - gnl|BL_ORD_ID|1818 - 177903|polyprotein|ACZ60102.1|Hepatitis C virus subtype 3a|356426 - 1818 - 17 - - - 1 - 13.4678 - 23 - 9.62753 - 1 - 9 - 9 - 17 - 0 - 0 - 4 - 6 - 0 - 9 - FTTELTAPF - FTASVTSPL - FT +T+P - - - - - 2 - gnl|BL_ORD_ID|1597 - 142233|ATP-dependent helicase|NP_217813.1|Mycobacterium tuberculosis|1773 - 1597 - 32 - - - 1 - 11.927 - 19 - 52.8651 - 1 - 8 - 20 - 27 - 0 - 0 - 4 - 5 - 0 - 8 - FTTELTAP - FTSTFAAP - FT+ AP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 11 - Query_11 - M_5232 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_5233 - 9 - - - 1 - gnl|BL_ORD_ID|114 - 7660|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 - 114 - 20 - - - 1 - 13.4678 - 23 - 8.10378 - 1 - 8 - 7 - 14 - 0 - 0 - 4 - 6 - 0 - 8 - LMALHPAL - MCAVHPTL - + A+HP L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 13 - Query_13 - M_5234 - 9 - - - 1 - gnl|BL_ORD_ID|1438 - 120093|unnamed protein product|CAA33016.1|Rubella virus|11041 - 1438 - 21 - - - 1 - 13.853 - 24 - 6.7201 - 2 - 6 - 5 - 9 - 0 - 0 - 4 - 4 - 0 - 5 - CSEHD - CVEHD - C EHD - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 14 - Query_14 - M_5235 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_5236 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_5237 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_5238 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_5239 - 9 - - - 1 - gnl|BL_ORD_ID|920 - 59786|Large envelope protein|P03138.3|Hepatitis B virus ayw/France/Tiollais/1979|490133 - 920 - 10 - - - 1 - 11.5418 - 18 - 148.349 - 1 - 8 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - LASSCGCT - MYPSCCCT - + SC CT - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 19 - Query_19 - M_5240 - 9 - - - 1 - gnl|BL_ORD_ID|920 - 59786|Large envelope protein|P03138.3|Hepatitis B virus ayw/France/Tiollais/1979|490133 - 920 - 10 - - - 1 - 11.5418 - 18 - 148.349 - 1 - 8 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - LASSCGCT - MYPSCCCT - + SC CT - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 20 - Query_20 - M_5241 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_5242 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 22 - Query_22 - M_5243 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_5244 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_5245 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_5246 - 9 - - - 1 - gnl|BL_ORD_ID|1887 - 180579|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 - 1887 - 15 - - - 1 - 13.4678 - 23 - 7.35849 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 5 - 0 - 8 - SYTNAWAL - SYAQMWSL - SY W+L - - - - - 2 - gnl|BL_ORD_ID|943 - 62184|nonstructural protein 3|NP_722463.1|Dengue virus type 1 Hawaii|10000440 - 943 - 15 - - - 1 - 13.4678 - 23 - 9.36117 - 1 - 9 - 7 - 15 - 0 - 0 - 3 - 4 - 0 - 9 - VSYTNAWAL - ISYGGGWRF - +SY W - - - - - 3 - gnl|BL_ORD_ID|9 - 790|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 9 - 15 - - - 1 - 13.4678 - 23 - 9.36117 - 1 - 7 - 8 - 14 - 0 - 0 - 3 - 4 - 0 - 7 - VSYTNAW - ISYGGGW - +SY W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 26 - Query_26 - M_5247 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_5248 - 9 - - - 1 - gnl|BL_ORD_ID|375 - 23270|polyprotein|AAB67036.1|Hepatitis C virus (isolate H77)|63746 - 375 - 15 - - - 1 - 12.3122 - 20 - 38.6124 - 1 - 8 - 6 - 13 - 0 - 0 - 3 - 5 - 0 - 8 - MFFIHSFT - LFYQHKFN - +F+ H F - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 28 - Query_28 - M_5249 - 9 - - - 1 - gnl|BL_ORD_ID|312 - 20861|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 - 312 - 9 - - - 1 - 13.0826 - 22 - 18.4218 - 1 - 7 - 2 - 8 - 0 - 0 - 3 - 6 - 0 - 7 - MFNPIIY - LFNNVLY - +FN ++Y - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 29 - Query_29 - M_5250 - 9 - - - 1 - gnl|BL_ORD_ID|448 - 27241|Spike glycoprotein precursor|P59594.1|SARS coronavirus|227859 - 448 - 9 - - - 1 - 14.2382 - 25 - 2.90246 - 1 - 8 - 2 - 9 - 0 - 0 - 5 - 7 - 0 - 8 - LPTPVEPT - LPDPLKPT - LP P++PT - - - - - 2 - gnl|BL_ORD_ID|1020 - 68229|EBNA3B (EBNA4A) latent protein|CAA24858.1|Human gammaherpesvirus 4|10376 - 1020 - 10 - - - 1 - 12.3122 - 20 - 63.4362 - 3 - 8 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - TPVEPT - TPYKPT - TP +PT - - - - - 3 - gnl|BL_ORD_ID|240 - 16833|core protein|CAL29866.1|Hepatitis B virus|10407 - 240 - 10 - - - 1 - 11.927 - 19 - 78.4397 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 6 - 0 - 9 - LPTPVEPTV - LPSDFFPSV - LP+ P+V - - - - - 4 - gnl|BL_ORD_ID|69 - 5191|core protein|AAL31859.1|Hepatitis B virus|10407 - 69 - 17 - - - 1 - 11.927 - 19 - 93.2086 - 1 - 9 - 9 - 17 - 0 - 0 - 4 - 6 - 0 - 9 - LPTPVEPTV - LPSDFFPSV - LP+ P+V - - - - - 5 - gnl|BL_ORD_ID|653 - 38701|core protein|AAL31859.1|Hepatitis B virus|10407 - 653 - 9 - - - 1 - 11.927 - 19 - 107.472 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 6 - 0 - 9 - LPTPVEPTV - LPSDFFPSV - LP+ P+V - - - - - 6 - gnl|BL_ORD_ID|239 - 16832|core protein|BAF42671.1|Hepatitis B virus|10407 - 239 - 10 - - - 1 - 11.5418 - 18 - 119.026 - 1 - 9 - 2 - 10 - 0 - 0 - 3 - 6 - 0 - 9 - LPTPVEPTV - LPSDFFPSI - LP+ P++ - - - - - 7 - gnl|BL_ORD_ID|241 - 16836|precore/core protein [Hepatitis B virus]|AAR03815.1|Hepatitis B virus|10407 - 241 - 10 - - - 1 - 11.5418 - 18 - 124.81 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 6 - 0 - 9 - LPTPVEPTV - LPSDFLPSV - LP+ P+V - - - - - 8 - gnl|BL_ORD_ID|235 - 16814|precore protein|CAM58990.1|Hepatitis B virus|10407 - 235 - 10 - - - 1 - 11.5418 - 18 - 128.811 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 5 - 0 - 9 - LPTPVEPTV - LPNDFFPSV - LP P+V - - - - - 9 - gnl|BL_ORD_ID|233 - 16796|HBcAg|ABE97049.1|Hepatitis B virus|10407 - 233 - 10 - - - 1 - 11.5418 - 18 - 162.878 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 5 - 0 - 9 - LPTPVEPTV - LPADFFPSV - LP P+V - - - - - 10 - gnl|BL_ORD_ID|244 - 16857|pre-c/core|CAA59565.1|Hepatitis B virus|10407 - 244 - 10 - - - 1 - 11.1566 - 17 - 224.873 - 1 - 9 - 2 - 10 - 0 - 0 - 4 - 5 - 0 - 9 - LPTPVEPTV - LPVDFFPSV - LP P+V - - - - - 11 - gnl|BL_ORD_ID|232 - 16795|precore/core protein|AAP57273.1|Hepatitis B virus|10407 - 232 - 10 - - - 1 - 11.1566 - 17 - 235.341 - 1 - 9 - 2 - 10 - 0 - 0 - 3 - 5 - 0 - 9 - LPTPVEPTV - LPADFFPSI - LP P++ - - - - - 12 - gnl|BL_ORD_ID|1438 - 120093|unnamed protein product|CAA33016.1|Rubella virus|11041 - 1438 - 21 - - - 1 - 10.7714 - 16 - 331.885 - 2 - 8 - 11 - 17 - 0 - 0 - 4 - 4 - 0 - 7 - PTPVEPT - PPPATPT - P P PT - - - - - 13 - gnl|BL_ORD_ID|243 - 16856|||| - 243 - 10 - - - 1 - 10.7714 - 16 - 336.948 - 1 - 9 - 2 - 10 - 0 - 0 - 3 - 5 - 0 - 9 - LPTPVEPTV - LPVDFFPSI - LP P++ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 30 - Query_30 - M_5251 - 9 - - - 1 - gnl|BL_ORD_ID|1020 - 68229|EBNA3B (EBNA4A) latent protein|CAA24858.1|Human gammaherpesvirus 4|10376 - 1020 - 10 - - - 1 - 12.3122 - 20 - 40.5114 - 1 - 6 - 4 - 9 - 0 - 0 - 4 - 5 - 0 - 6 - TPVEPT - TPYKPT - TP +PT - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 31 - Query_31 - M_5252 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 32 - Query_32 - M_5253 - 9 - - - 1 - gnl|BL_ORD_ID|588 - 36717|nonstructural protein 4B|YP_001527886.1|West Nile virus NY-99|10000971 - 588 - 18 - - - 1 - 12.6974 - 21 - 25.1685 - 1 - 9 - 2 - 10 - 0 - 0 - 5 - 6 - 0 - 9 - LLAAARPLW - ITAAAVTLW - + AAA LW - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 33 - Query_33 - M_5254 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 34 - Query_34 - M_5255 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 35 - Query_35 - M_5256 - 9 - - - 1 - gnl|BL_ORD_ID|320 - 21000|glutamine synthetase GLNA1 (glutamine synthase) (GS-I)|NP_216736.1|Mycobacterium tuberculosis|1773 - 320 - 9 - - - 1 - 13.4678 - 23 - 8.13377 - 4 - 9 - 4 - 9 - 0 - 0 - 5 - 5 - 0 - 6 - HHFPSL - HHAPSL - HH PSL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 36 - Query_36 - M_5257 - 9 - - - 1 - gnl|BL_ORD_ID|320 - 21000|glutamine synthetase GLNA1 (glutamine synthase) (GS-I)|NP_216736.1|Mycobacterium tuberculosis|1773 - 320 - 9 - - - 1 - 13.4678 - 23 - 8.13377 - 4 - 9 - 4 - 9 - 0 - 0 - 5 - 5 - 0 - 6 - HHFPSL - HHAPSL - HH PSL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 37 - Query_37 - M_5258 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 38 - Query_38 - M_5259 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 39 - Query_39 - M_5260 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_139936_1_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_139936_1_T.fasta deleted file mode 100755 index 837993b7..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_139936_1_T.fasta +++ /dev/null @@ -1,70 +0,0 @@ ->M_5261 -KPLLSGPWA ->M_5262 -LSMTSITSV ->M_5263 -IDTDQVHTL ->M_5264 -TWKDTPYYI ->M_5265 -KLILTLSAI ->M_5266 -SYQMSNKLI ->M_5267 -YQMSNKLIL ->M_5268 -YQMSNKLIL ->M_5269 -LMWSVTWPK ->M_5270 -SQSETNSAV ->M_5271 -SHASHLHLF ->M_5272 -SHASHLHLF ->M_5273 -KVLISVHLI ->M_5274 -DHYLVDRTL ->M_5275 -YIKPLVPPA ->M_5276 -RPGQSPGQL ->M_5277 -HLFESSQLV ->M_5278 -HLFESSQLV ->M_5279 -GVYLWEDPV ->M_5280 -YLWEDPVCG ->M_5281 -RILYMADEV ->M_5282 -SLLDACLIL ->M_5283 -APLPMPNPL ->M_5284 -LLLWAPLPM ->M_5285 -MQLRKAPNV ->M_5286 -AHACAHALL ->M_5287 -GAHACAHAL ->M_5288 -VLNGWLRSV ->M_5289 -AIDDHVCMA ->M_5290 -LMVPRLEYV ->M_5291 -FINARGRLL ->M_5292 -AIPLRGFPV ->M_5293 -FVDENNEKL ->M_5294 -FVDENNEKL ->M_5295 -HTARLFYFV diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_139936_1_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_139936_1_T_iedb.xml deleted file mode 100755 index e696aaad..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_139936_1_T_iedb.xml +++ /dev/null @@ -1,1051 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_5261 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_5261 - 9 - - - 1 - gnl|BL_ORD_ID|96 - 6591|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 - 96 - 18 - - - 1 - 13.853 - 24 - 5.73946 - 1 - 7 - 6 - 12 - 0 - 0 - 5 - 5 - 0 - 7 - KPLLSGP - KPTLHGP - KP L GP - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 2 - Query_2 - M_5262 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_5263 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_5264 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_5265 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_5266 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_5267 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_5268 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_5269 - 9 - - - 1 - gnl|BL_ORD_ID|1697 - 149105|E2 protein|NP_751921.1|Hepatitis C virus (isolate H77)|63746 - 1697 - 9 - - - 1 - 11.1566 - 17 - 225.252 - 3 - 7 - 5 - 9 - 0 - 0 - 2 - 4 - 0 - 5 - WSVTW - WAIKW - W++ W - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 10 - Query_10 - M_5270 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_5271 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_5272 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_5273 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_5274 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_5275 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_5276 - 9 - - - 1 - gnl|BL_ORD_ID|344 - 21638|protein F|ABV46152.2|Hepatitis C virus (isolate Japanese)|11116 - 344 - 9 - - - 1 - 15.0086 - 27 - 0.92904 - 2 - 9 - 2 - 9 - 0 - 0 - 6 - 6 - 0 - 8 - PGQSPGQL - PGLSPGTL - PG SPG L - - - - - 2 - gnl|BL_ORD_ID|741 - 47760|EBNA-1 protein|Q777E1|Human gammaherpesvirus 4|10376 - 741 - 15 - - - 1 - 12.6974 - 21 - 27.4409 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 4 - 0 - 7 - PGQSPGQ - PGTGPGN - PG PG - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 17 - Query_17 - M_5277 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_5278 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_5279 - 9 - - - 1 - gnl|BL_ORD_ID|525 - 32243|C protein|BAB60863.1|Measles virus|11234 - 525 - 9 - - - 1 - 13.853 - 24 - 6.16125 - 4 - 8 - 2 - 6 - 0 - 0 - 4 - 4 - 0 - 5 - LWEDP - LWESP - LWE P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 20 - Query_20 - M_5280 - 9 - - - 1 - gnl|BL_ORD_ID|525 - 32243|C protein|BAB60863.1|Measles virus|11234 - 525 - 9 - - - 1 - 13.853 - 24 - 6.48995 - 2 - 6 - 2 - 6 - 0 - 0 - 4 - 4 - 0 - 5 - LWEDP - LWESP - LWE P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 21 - Query_21 - M_5281 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 22 - Query_22 - M_5282 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_5283 - 9 - - - 1 - gnl|BL_ORD_ID|1881 - 180531|polyprotein|AGO67248.1|Dengue virus 2|11060 - 1881 - 10 - - - 1 - 12.6974 - 21 - 30.9217 - 3 - 9 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - LPMPNPL - IPMTGPL - +PM PL - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 24 - Query_24 - M_5284 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_5285 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_5286 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_5287 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 28 - Query_28 - M_5288 - 9 - - - 1 - gnl|BL_ORD_ID|629 - 37607|kaposin|AAC57155.1|Human gammaherpesvirus 8|37296 - 629 - 9 - - - 1 - 13.4678 - 23 - 10.7466 - 1 - 5 - 1 - 5 - 0 - 0 - 4 - 5 - 0 - 5 - VLNGW - LLNGW - +LNGW - - - - - 2 - gnl|BL_ORD_ID|2011 - 183800|polyprotein|AGT63075.1|Dengue virus 1|11053 - 2011 - 9 - - - 1 - 11.927 - 19 - 78.9234 - 1 - 9 - 1 - 9 - 0 - 0 - 4 - 6 - 0 - 9 - VLNGWLRSV - IMNRRKRSV - ++N RSV - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 29 - Query_29 - M_5289 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 30 - Query_30 - M_5290 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 31 - Query_31 - M_5291 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 32 - Query_32 - M_5292 - 9 - - - 1 - gnl|BL_ORD_ID|396 - 24302|X protein|AAP06597.1|Hepatitis B virus|10407 - 396 - 9 - - - 1 - 15.0086 - 27 - 1.17789 - 2 - 9 - 2 - 9 - 0 - 0 - 5 - 6 - 0 - 8 - IPLRGFPV - LSLRGLPV - + LRG PV - - - - - 2 - gnl|BL_ORD_ID|378 - 23365|polyprotein|BAB18806.1|Hepatitis C virus|11103 - 378 - 10 - - - 1 - 12.6974 - 21 - 22.7423 - 2 - 9 - 3 - 10 - 0 - 0 - 5 - 6 - 0 - 8 - IPLRGFPV - IPLVGAPL - IPL G P+ - - - - - 3 - gnl|BL_ORD_ID|296 - 19493|polyprotein|BAA03375.1|Hepatitis C virus|11103 - 296 - 15 - - - 1 - 12.6974 - 21 - 31.7906 - 2 - 8 - 9 - 15 - 0 - 0 - 5 - 5 - 0 - 7 - IPLRGFP - IPLVGAP - IPL G P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 33 - Query_33 - M_5293 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 34 - Query_34 - M_5294 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 35 - Query_35 - M_5295 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_140531_2_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_140531_2_T.fasta deleted file mode 100755 index 1a080f0a..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_140531_2_T.fasta +++ /dev/null @@ -1,52 +0,0 @@ ->M_5296 -LPSTAGPEM ->M_5297 -LPSTAGPEM ->M_5298 -TAANGSEVM ->M_5299 -TAANGSEVM ->M_5300 -MADATFQSL ->M_5301 -MADATFQSL ->M_5302 -WFNMADATF ->M_5303 -ICIWNVSKL ->M_5304 -EPTITDASL ->M_5305 -IFDEWLKRF ->M_5306 -FTGGIVNKL ->M_5307 -GIVNKLCAL ->M_5308 -FGSLLGTCL ->M_5309 -ISGPRSPTY ->M_5310 -MSLNSYIKL ->M_5311 -YMVIMSPRL ->M_5312 -EILWTTELY ->M_5313 -LEILWTTEL ->M_5314 -LGTSDVRIL ->M_5315 -VAFLGTSDV ->M_5316 -IMIAVVDSM ->M_5317 -IMIAVVDSM ->M_5318 -EASVHSVPI ->M_5319 -FFSSNLPTY ->M_5320 -FSSNLPTYY ->M_5321 -VALVPESSV diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_140531_2_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_140531_2_T_iedb.xml deleted file mode 100755 index 20155b14..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_140531_2_T_iedb.xml +++ /dev/null @@ -1,874 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_5296 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_5296 - 9 - - - 1 - gnl|BL_ORD_ID|707 - 43447|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 - 707 - 20 - - - 1 - 14.2382 - 25 - 2.73772 - 1 - 7 - 14 - 20 - 0 - 0 - 5 - 5 - 0 - 7 - LPSTAGP - LPEAAGP - LP AGP - - - - - 2 - gnl|BL_ORD_ID|285 - 19348|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 - 285 - 20 - - - 1 - 14.2382 - 25 - 3.42196 - 1 - 7 - 4 - 10 - 0 - 0 - 5 - 5 - 0 - 7 - LPSTAGP - LPEAAGP - LP AGP - - - - - 3 - gnl|BL_ORD_ID|993 - 65550|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 993 - 15 - - - 1 - 11.5418 - 18 - 141.75 - 1 - 8 - 6 - 13 - 0 - 0 - 4 - 5 - 0 - 8 - LPSTAGPE - IPSMFEPE - +PS PE - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 2 - Query_2 - M_5297 - 9 - - - 1 - gnl|BL_ORD_ID|707 - 43447|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 - 707 - 20 - - - 1 - 14.2382 - 25 - 2.73772 - 1 - 7 - 14 - 20 - 0 - 0 - 5 - 5 - 0 - 7 - LPSTAGP - LPEAAGP - LP AGP - - - - - 2 - gnl|BL_ORD_ID|285 - 19348|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 - 285 - 20 - - - 1 - 14.2382 - 25 - 3.42196 - 1 - 7 - 4 - 10 - 0 - 0 - 5 - 5 - 0 - 7 - LPSTAGP - LPEAAGP - LP AGP - - - - - 3 - gnl|BL_ORD_ID|993 - 65550|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 - 993 - 15 - - - 1 - 11.5418 - 18 - 141.75 - 1 - 8 - 6 - 13 - 0 - 0 - 4 - 5 - 0 - 8 - LPSTAGPE - IPSMFEPE - +PS PE - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 3 - Query_3 - M_5298 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_5299 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_5300 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_5301 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_5302 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_5303 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_5304 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_5305 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_5306 - 9 - - - 1 - gnl|BL_ORD_ID|1510 - 139747|granule antigen protein GRA6|XP_002371939.1|Toxoplasma gondii ME49|508771 - 1510 - 9 - - - 1 - 13.4678 - 23 - 10.9354 - 1 - 9 - 1 - 9 - 0 - 0 - 5 - 6 - 0 - 9 - FTGGIVNKL - FMGVLVNSL - F G +VN L - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 12 - Query_12 - M_5307 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_5308 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_5309 - 9 - - - 1 - gnl|BL_ORD_ID|1006 - 66195|Nucleoprotein|P41269.1|Puumala hantavirus|11604 - 1006 - 15 - - - 1 - 13.0826 - 22 - 16.1221 - 1 - 9 - 6 - 14 - 0 - 0 - 4 - 6 - 0 - 9 - ISGPRSPTY - INGIRRPKH - I+G R P + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 15 - Query_15 - M_5310 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_5311 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_5312 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_5313 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_5314 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_5315 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_5316 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 22 - Query_22 - M_5317 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_5318 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_5319 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_5320 - 9 - - - 1 - gnl|BL_ORD_ID|471 - 28594|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 - 471 - 20 - - - 1 - 13.4678 - 23 - 8.80594 - 4 - 9 - 2 - 7 - 0 - 0 - 4 - 6 - 0 - 6 - NLPTYY - SLPSYY - +LP+YY - - - - - 2 - gnl|BL_ORD_ID|1971 - 182926|polyprotein|AFP27208.1|Dengue virus 4|11070 - 1971 - 9 - - - 1 - 13.4678 - 23 - 9.18751 - 3 - 8 - 3 - 8 - 0 - 0 - 4 - 6 - 0 - 6 - SNLPTY - ASLPTY - ++LPTY - - - - - 3 - gnl|BL_ORD_ID|2100 - 185881|polyprotein|AFP27208.1|Dengue virus 4|11070 - 2100 - 10 - - - 1 - 13.4678 - 23 - 9.73455 - 3 - 8 - 4 - 9 - 0 - 0 - 4 - 6 - 0 - 6 - SNLPTY - ASLPTY - ++LPTY - - - - - 4 - gnl|BL_ORD_ID|776 - 51643|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 - 776 - 20 - - - 1 - 13.4678 - 23 - 10.5613 - 5 - 9 - 13 - 17 - 0 - 0 - 4 - 5 - 0 - 5 - LPTYY - LPSYY - LP+YY - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 26 - Query_26 - M_5321 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_141002_2_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_141002_2_T.fasta deleted file mode 100755 index 77f5f7f7..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_141002_2_T.fasta +++ /dev/null @@ -1,62 +0,0 @@ ->M_5322 -ISRNHNSRM ->M_5323 -KTFGISRNH ->M_5324 -RNHNSRMNK ->M_5325 -LTDLQGVIV ->M_5326 -IRHEMSTFA ->M_5327 -VVSDSWGSK ->M_5328 -IRAANVSAL ->M_5329 -IRAANVSAL ->M_5330 -RAANVSALY ->M_5331 -GYRERGHPY ->M_5332 -VVGAVGVGK ->M_5333 -LTNTLTTSK ->M_5334 -AAASTSSPK ->M_5335 -TSITTSTQK ->M_5336 -SHPGSAEIV ->M_5337 -SYYSCVAAM ->M_5338 -SYYSCVAAM ->M_5339 -AHTFKQRRI ->M_5340 -HTFKQRRIK ->M_5341 -RYEEYRGRF ->M_5342 -YEEYRGRFL ->M_5343 -MTTGSVFFY ->M_5344 -MTTGSVFFY ->M_5345 -HVLSLAETK ->M_5346 -SLAETKTLY ->M_5347 -KLKTVSQTK ->M_5348 -ASYDQSLRV ->M_5349 -FSASYDQSL ->M_5350 -HLKEPLQKL ->M_5351 -HLYEQGGHL ->M_5352 -HQCVHTGAK diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_141002_2_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_141002_2_T_iedb.xml deleted file mode 100755 index 41672e73..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_141002_2_T_iedb.xml +++ /dev/null @@ -1,697 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_5322 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_5322 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - Query_2 - M_5323 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_5324 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - Query_4 - M_5325 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_5326 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - Query_6 - M_5327 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - Query_7 - M_5328 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_5329 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_5330 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_5331 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_5332 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - Query_12 - M_5333 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_5334 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_5335 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_5336 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_5337 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_5338 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_5339 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_5340 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_5341 - 9 - - - 1 - gnl|BL_ORD_ID|376 - 23288|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 - 376 - 15 - - - 1 - 13.0826 - 22 - 12.7259 - 2 - 9 - 7 - 14 - 0 - 0 - 3 - 6 - 0 - 8 - YEEYRGRF - YQDWLGRM - Y+++ GR - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 21 - Query_21 - M_5342 - 9 - - - 1 - gnl|BL_ORD_ID|376 - 23288|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 - 376 - 15 - - - 1 - 13.0826 - 22 - 15.0718 - 1 - 8 - 7 - 14 - 0 - 0 - 3 - 6 - 0 - 8 - YEEYRGRF - YQDWLGRM - Y+++ GR - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 22 - Query_22 - M_5343 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_5344 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_5345 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 25 - Query_25 - M_5346 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 26 - Query_26 - M_5347 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_5348 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 28 - Query_28 - M_5349 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 29 - Query_29 - M_5350 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 30 - Query_30 - M_5351 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 31 - Query_31 - M_5352 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_141146_2_T.fasta b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_141146_2_T.fasta deleted file mode 100755 index 93f95ae9..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_141146_2_T.fasta +++ /dev/null @@ -1,76 +0,0 @@ ->M_5353 -IAHAWWACF ->M_5354 -AMWNRCADL ->M_5355 -AYTFWTYIM ->M_5356 -IMNARSKNV ->M_5357 -YAYTFWTYI ->M_5358 -YAYTFWTYI ->M_5359 -KAARIAAKV ->M_5360 -KVGQSSMWI ->M_5361 -PSTSTSRPV ->M_5362 -CLAAMALSI ->M_5363 -WLTPVIPTL ->M_5364 -GLFHCTRSV ->M_5365 -RNWDVCKVI ->M_5366 -KIPIRLPPV ->M_5367 -FMLGITPNL ->M_5368 -HRHHHRCRR ->M_5369 -FLAGSSLPV ->M_5370 -FLAGSSLPV ->M_5371 -SSFLAGSSL ->M_5372 -KLPSDPDAL ->M_5373 -VYAVTVVTL ->M_5374 -YAVTVVTLL ->M_5375 -YAVTVVTLL ->M_5376 -FILICCLII ->M_5377 -ILICCLIIL ->M_5378 -LIILENIFV ->M_5379 -VFILICCLI ->M_5380 -PAMKFSCSL ->M_5381 -FLSLIIDAT ->M_5382 -LIIDATKFI ->M_5383 -LIIDATKFI ->M_5384 -IMMSSEDDI ->M_5385 -YLDGQPQEA ->M_5386 -GLAPPQLLI ->M_5387 -ARIERPHNY ->M_5388 -FTSSEPSRM ->M_5389 -ESEGHTIEL ->M_5390 -KMQEGLLAV diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_141146_2_T_iedb.xml b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_141146_2_T_iedb.xml deleted file mode 100755 index 0bb39458..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/alignments/neoantigens_s_141146_2_T_iedb.xml +++ /dev/null @@ -1,1557 +0,0 @@ - - - - blastp - BLASTP 2.2.30+ - Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. - /Users/mluksza/Dropbox/CancerLocal//enemy/iedb_2016//iedb.fasta - Query_1 - M_5353 - 9 - - - BLOSUM62 - 100000000 - 11 - 1 - F - - - - - 1 - Query_1 - M_5353 - 9 - - - 1 - gnl|BL_ORD_ID|1556 - 141262|DNA polymerase catalytic subunit|NP_044632.1|Human alphaherpesvirus 1|10298 - 1556 - 10 - - - 1 - 13.853 - 24 - 4.45544 - 3 - 9 - 4 - 10 - 0 - 0 - 5 - 5 - 0 - 7 - HAWWACF - HARWAAF - HA WA F - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 2 - Query_2 - M_5354 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - Query_3 - M_5355 - 9 - - - 1 - gnl|BL_ORD_ID|1502 - 137660|L1|ACL12325.1|Human papillomavirus type 58|10598 - 1502 - 9 - - - 1 - 13.853 - 24 - 7.07804 - 1 - 5 - 1 - 5 - 0 - 0 - 4 - 4 - 0 - 5 - AYTFW - KYTFW - YTFW - - - - - 2 - gnl|BL_ORD_ID|81 - 5938|EBNA3A nuclear protein|Q8AZJ8|Human gammaherpesvirus 4|10376 - 81 - 9 - - - 1 - 12.6974 - 21 - 39.8499 - 1 - 7 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - AYTFWTY - AYSSWMY - AY+ W Y - - - - - 3 - gnl|BL_ORD_ID|578 - 36357|ELAV-like protein 4 (Paraneoplastic encephalomyelitis antigen HuD) (Hu-antigen D)|P26378.1|Homo sapiens|9606 - 578 - 9 - - - 1 - 12.3122 - 20 - 57.6592 - 1 - 8 - 2 - 9 - 0 - 0 - 4 - 4 - 0 - 8 - AYTFWTYI - GYGFVNYI - Y F YI - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 4 - Query_4 - M_5356 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - Query_5 - M_5357 - 9 - - - 1 - gnl|BL_ORD_ID|1502 - 137660|L1|ACL12325.1|Human papillomavirus type 58|10598 - 1502 - 9 - - - 1 - 13.4678 - 23 - 10.0233 - 2 - 6 - 1 - 5 - 0 - 0 - 4 - 4 - 0 - 5 - AYTFW - KYTFW - YTFW - - - - - 2 - gnl|BL_ORD_ID|147 - 10939|polyprotein|BAB18806.1|Hepatitis C virus subtype 1a|31646 - 147 - 9 - - - 1 - 13.0826 - 22 - 18.7436 - 1 - 8 - 2 - 9 - 0 - 0 - 4 - 4 - 0 - 8 - YAYTFWTY - YPYRLWHY - Y Y W Y - - - - - 3 - gnl|BL_ORD_ID|1145 - 75448|polyprotein|BAB18806.1|Hepatitis C virus|11103 - 1145 - 8 - - - 1 - 13.0826 - 22 - 22.4497 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 4 - 0 - 8 - YAYTFWTY - YPYRLWHY - Y Y W Y - - - - - 4 - gnl|BL_ORD_ID|81 - 5938|EBNA3A nuclear protein|Q8AZJ8|Human gammaherpesvirus 4|10376 - 81 - 9 - - - 1 - 12.6974 - 21 - 36.611 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - AYTFWTY - AYSSWMY - AY+ W Y - - - - - 5 - gnl|BL_ORD_ID|578 - 36357|ELAV-like protein 4 (Paraneoplastic encephalomyelitis antigen HuD) (Hu-antigen D)|P26378.1|Homo sapiens|9606 - 578 - 9 - - - 1 - 11.927 - 19 - 78.9234 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 4 - 0 - 8 - AYTFWTYI - GYGFVNYI - Y F YI - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 6 - Query_6 - M_5358 - 9 - - - 1 - gnl|BL_ORD_ID|1502 - 137660|L1|ACL12325.1|Human papillomavirus type 58|10598 - 1502 - 9 - - - 1 - 13.4678 - 23 - 10.0233 - 2 - 6 - 1 - 5 - 0 - 0 - 4 - 4 - 0 - 5 - AYTFW - KYTFW - YTFW - - - - - 2 - gnl|BL_ORD_ID|147 - 10939|polyprotein|BAB18806.1|Hepatitis C virus subtype 1a|31646 - 147 - 9 - - - 1 - 13.0826 - 22 - 18.7436 - 1 - 8 - 2 - 9 - 0 - 0 - 4 - 4 - 0 - 8 - YAYTFWTY - YPYRLWHY - Y Y W Y - - - - - 3 - gnl|BL_ORD_ID|1145 - 75448|polyprotein|BAB18806.1|Hepatitis C virus|11103 - 1145 - 8 - - - 1 - 13.0826 - 22 - 22.4497 - 1 - 8 - 1 - 8 - 0 - 0 - 4 - 4 - 0 - 8 - YAYTFWTY - YPYRLWHY - Y Y W Y - - - - - 4 - gnl|BL_ORD_ID|81 - 5938|EBNA3A nuclear protein|Q8AZJ8|Human gammaherpesvirus 4|10376 - 81 - 9 - - - 1 - 12.6974 - 21 - 36.611 - 2 - 8 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - AYTFWTY - AYSSWMY - AY+ W Y - - - - - 5 - gnl|BL_ORD_ID|578 - 36357|ELAV-like protein 4 (Paraneoplastic encephalomyelitis antigen HuD) (Hu-antigen D)|P26378.1|Homo sapiens|9606 - 578 - 9 - - - 1 - 11.927 - 19 - 78.9234 - 2 - 9 - 2 - 9 - 0 - 0 - 4 - 4 - 0 - 8 - AYTFWTYI - GYGFVNYI - Y F YI - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 7 - Query_7 - M_5359 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - Query_8 - M_5360 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - Query_9 - M_5361 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - Query_10 - M_5362 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - Query_11 - M_5363 - 9 - - - 1 - gnl|BL_ORD_ID|948 - 62477|HBsAg protein|ABF71024.1|Hepatitis B virus|10407 - 948 - 9 - - - 1 - 12.3122 - 20 - 48.7826 - 1 - 7 - 2 - 8 - 0 - 0 - 3 - 6 - 0 - 7 - WLTPVIP - WLSLLVP - WL+ ++P - - - - - 2 - gnl|BL_ORD_ID|1104 - 72794|Large envelope protein|P03138.3|Hepatitis B virus|10407 - 1104 - 9 - - - 1 - 12.3122 - 20 - 56.7066 - 1 - 7 - 1 - 7 - 0 - 0 - 3 - 6 - 0 - 7 - WLTPVIP - WLSLLVP - WL+ ++P - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 12 - Query_12 - M_5364 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - Query_13 - M_5365 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - Query_14 - M_5366 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - Query_15 - M_5367 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - Query_16 - M_5368 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - Query_17 - M_5369 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - Query_18 - M_5370 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - Query_19 - M_5371 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 20 - Query_20 - M_5372 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 21 - Query_21 - M_5373 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 22 - Query_22 - M_5374 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 23 - Query_23 - M_5375 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 24 - Query_24 - M_5376 - 9 - - - 1 - gnl|BL_ORD_ID|156 - 11956|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 - 156 - 11 - - - 1 - 10.7714 - 16 - 322.541 - 3 - 9 - 5 - 11 - 0 - 0 - 2 - 6 - 0 - 7 - LICCLII - VLCCYVL - ++CC ++ - - - - - 2 - gnl|BL_ORD_ID|1499 - 137656|E6 protein|ACT36477.1|Human papillomavirus type 58|10598 - 1499 - 9 - - - 1 - 10.3862 - 15 - 519.728 - 2 - 8 - 1 - 7 - 0 - 0 - 5 - 6 - 0 - 7 - ILICCLI - ILIRCII - ILI C+I - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 25 - Query_25 - M_5377 - 9 - - - 1 - gnl|BL_ORD_ID|156 - 11956|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 - 156 - 11 - - - 1 - 10.7714 - 16 - 341.939 - 2 - 8 - 5 - 11 - 0 - 0 - 2 - 6 - 0 - 7 - LICCLII - VLCCYVL - ++CC ++ - - - - - 2 - gnl|BL_ORD_ID|1499 - 137656|E6 protein|ACT36477.1|Human papillomavirus type 58|10598 - 1499 - 9 - - - 1 - 10.3862 - 15 - 600.299 - 1 - 7 - 1 - 7 - 0 - 0 - 5 - 6 - 0 - 7 - ILICCLI - ILIRCII - ILI C+I - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 26 - Query_26 - M_5378 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 27 - Query_27 - M_5379 - 9 - - - 1 - gnl|BL_ORD_ID|1499 - 137656|E6 protein|ACT36477.1|Human papillomavirus type 58|10598 - 1499 - 9 - - - 1 - 10.7714 - 16 - 462.613 - 3 - 9 - 1 - 7 - 0 - 0 - 5 - 6 - 0 - 7 - ILICCLI - ILIRCII - ILI C+I - - - - - 2 - gnl|BL_ORD_ID|156 - 11956|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 - 156 - 11 - - - 1 - 10.3862 - 15 - 596.566 - 4 - 9 - 5 - 10 - 0 - 0 - 2 - 5 - 0 - 6 - LICCLI - VLCCYV - ++CC + - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 28 - Query_28 - M_5380 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 29 - Query_29 - M_5381 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 30 - Query_30 - M_5382 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 31 - Query_31 - M_5383 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 32 - Query_32 - M_5384 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 33 - Query_33 - M_5385 - 9 - - - 1 - gnl|BL_ORD_ID|1387 - 110227|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1387 - 33 - - - 1 - 14.2382 - 25 - 3.73557 - 1 - 6 - 8 - 13 - 0 - 0 - 4 - 4 - 0 - 6 - YLDGQP - YRDGNP - Y DG P - - - - - 2 - gnl|BL_ORD_ID|1400 - 110467|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1400 - 25 - - - 1 - 13.853 - 24 - 7.91622 - 1 - 6 - 1 - 6 - 0 - 0 - 4 - 4 - 0 - 6 - YLDGQP - YRDGNP - Y DG P - - - - - 3 - gnl|BL_ORD_ID|1397 - 110401|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1397 - 25 - - - 1 - 13.4678 - 23 - 8.70865 - 1 - 6 - 16 - 21 - 0 - 0 - 4 - 4 - 0 - 6 - YLDGQP - YRDGNP - Y DG P - - - - - 4 - gnl|BL_ORD_ID|1821 - 178185|Protein E6|P03126.1|Human papillomavirus type 16|333760 - 1821 - 15 - - - 1 - 13.4678 - 23 - 10.5523 - 1 - 6 - 9 - 14 - 0 - 0 - 4 - 4 - 0 - 6 - YLDGQP - YRDGNP - Y DG P - - - - - 5 - gnl|BL_ORD_ID|1059 - 69798|Lipoprotein lpqH precursor|P0A5J0.1|Mycobacterium tuberculosis|1773 - 1059 - 10 - - - 1 - 13.4678 - 23 - 12.6375 - 3 - 9 - 4 - 10 - 0 - 0 - 4 - 4 - 0 - 7 - DGQPQEA - DGNPPEV - DG P E - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - 34 - Query_34 - M_5386 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 35 - Query_35 - M_5387 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 36 - Query_36 - M_5388 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 37 - Query_37 - M_5389 - 9 - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 38 - Query_38 - M_5390 - 9 - - - 1 - gnl|BL_ORD_ID|777 - 51685|Nuclear antigen EBNA-3C|Q69140.1|Human gammaherpesvirus 4|10376 - 777 - 10 - - - 1 - 12.6974 - 21 - 30.4011 - 3 - 9 - 1 - 7 - 0 - 0 - 4 - 5 - 0 - 7 - QEGLLAV - QNGALAI - Q G LA+ - - - - - - - 2334 - 25004 - 0 - 225036 - 0.041 - 0.267 - 0.14 - - - - - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/data/.DS_Store b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/data/.DS_Store deleted file mode 100755 index 5008ddfcf53c02e82d7eee2e57c38e5672ef89f6..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 6148 zcmeH~Jr2S!425mzP>H1@V-^m;4Wg<&0T*E43hX&L&p$$qDprKhvt+--jT7}7np#A3 zem<@ulZcFPQ@L2!n>{z**++&mCkOWA81W14cNZlEfg7;MkzE(HCqgga^y>{tEnwC%0;vJ&^%eQ zLs35+`xjp>T046|hypothetical protein ML1057|NP_301777.1|Mycobacterium leprae|1769 -AAALEQLLGQTADVA ->118|envelope glycoprotein|ABS76372.1|Human immunodeficiency virus 1|11676 -AAEQLWVTVYYGVPVWKEAT ->140|Accessory protein p30II|SRC276210|Human T-lymphotropic virus 1|11908 -AAFSSARFL ->194|Hypothetical protein esxG (PE family protein)|O53692.1|Mycobacterium tuberculosis|1773 -AAHARFVAA ->327|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis|1773 -AANKQKQELDEISTNIRQAG ->420|Genome polyprotein|P26664.3|Hepatitis C virus genotype 1|41856 -AARVTAIL ->449|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 -AASTLLYATV ->465|polyprotein|BAA09072.1|Hepatitis C virus|11103 -AATLGFGAYMSKAHG ->716|polyprotein|BAB18806.1|Hepatitis C virus subtype 1a|31646 -ADLMGYIPLV ->790|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 -ADVKKDLISYGGGWK ->1000|glycoprotein gp35/37|AAC59622.1|Human gammaherpesvirus 8|37296 -AEIRTHLYILWAVGL ->1078|10 kda culture filtrate antigen esxB (cfp10)|ZP_04982462.1|Mycobacterium tuberculosis|1773 -AEMKTDAA ->1079|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis H37Rv|83332 -AEMKTDAATL ->1080|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis H37Rv|83332 -AEMKTDAATLA ->1090|Transcription activator BRLF1|P03209.1|Human herpesvirus 4 strain B95-8|10377 -AENAGNDAC ->1095|glycoprotein gp35/37|AAC59622.1|Human gammaherpesvirus 8|37296 -AENGRNSGASNRVPF ->1129|gag protein|AAV53342.1|Human immunodeficiency virus 1|11676 -AEQASQDVKNW ->1154|RL2|NP_044469.1|Human herpesvirus 2 strain HG52|10315 -AERQGSPTPA ->1211|polyprotein precursor|NP_041724.2|West Nile virus|11082 -AEVEEHRTV ->1226|Polyprotein|Q9IZA3|Hepatitis C virus|11103 -AEVTQHGSY ->1230|gag protein|AAW03034.1|Human immunodeficiency virus 1|11676 -AEWDRVHPV ->1356|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 -AFLTNVPYKRIEELL ->1421|polyprotein|BAD73991.1|Hepatitis C virus subtype 1b|31647 -AFYGVWPLL ->1516|Nucleoprotein|P03418.1|Human respiratory syncytial virus A2|11259 -AGFYHILNNPKASL ->1658|Nucleoprotein|P03418.1|Human respiratory syncytial virus A2|11259 -AGQVMLRWGVLAKS ->1994|structural protein|BAA00705.1|Hepatitis C virus subtype 1a|31646 -AILHTPGCV ->2002|Large envelope protein|SRC279965|Hepatitis B virus|10407 -AILSKTGDPV ->2033|polyprotein|BAA32665.1|Hepatitis C virus genotype 6|42182 -AINGVMWTV ->2058|6 kDa early secretory antigenic target|P0A564.2|Mycobacterium tuberculosis|1773 -AIQGNVTSI ->2102|VP1|BAF93325.1|Human polyomavirus 1|1891762 -AITEVECFL ->2154|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 -AKARAKKDELR ->2244|polyprotein|NP_671491.1|Hepatitis C virus|11103 -AKLVALGINAVAYYR ->2387|Genome polyprotein|O39929.3|Hepatitis C virus|11103 -ALAHGVRAL ->2506|M protein, serotype 5 precursor|P02977.2|Streptococcus pyogenes serotype M5|301449 -ALEKLNKEL ->2527|Circumsporozoite protein-related antigen precursor|P04923.2|Plasmodium falciparum|5833 -ALFFIIFNK ->2556|PE_PGRS 33|AAU10330.1|Mycobacterium tuberculosis|1773 -ALGGGATGV ->2758|pol protein|BAA32832.1|Hepatitis B virus|10407 -ALMPLYACI ->2860|polyprotein|AAU89634.1|Hepatitis C virus|11103 -ALRGMGLNA ->2861|Genome polyprotein|P26661.3|Hepatitis C virus isolate HC-J8|11115 -ALRGMGVNAV ->2883|cysteine proteinase cruzipain (EC 3.4.22.-) - Trypanosoma cruzi|A45629|Trypanosoma cruzi|5693 -ALSLAAVLV ->2884|cysteine proteinase cruzipain (EC 3.4.22.-) - Trypanosoma cruzi|A45629|Trypanosoma cruzi|5693 -ALSLAAVLVV ->2903|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 -ALSTGLIHLHQNIVD ->2957|||| -ALVFPSHHH ->3017|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 -ALYDVVSKL ->3018|polyprotein|BAA25076.1|Hepatitis C virus (isolate H77)|63746 -ALYDVVSTL ->3019|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 -ALYDVVTKL ->3024|precursor protein|AAB02126.1|Hepatitis C virus (isolate H77)|63746 -ALYEVVSKL ->3026|polyprotein|CAB53095.1|Hepatitis C virus subtype 1b|31647 -ALYGVWPLL ->3051|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 -AMAALQNLPQCSPDEIMAYA ->3064|6 kDa early secretory antigenic target|P0A564.2|Mycobacterium tuberculosis|1773 -AMASTEGNV ->3094|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 -AMGDAGGYK ->3587|protein F [Hepatitis C virus subtype 1b]|ACA50643.1|Hepatitis C virus (isolate Japanese)|11116 -APGWVCARL ->3889|||| -APVFPSHHP ->3935|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis|1773 -AQAAVVRFQEAANKQKQELD ->4002|PPE family protein|YP_177918.1|Mycobacterium tuberculosis H37Rv|83332 -AQLLTEFAI ->4156|polyprotein|ABR25251.1|Hepatitis C virus|11103 -ARHTPVNSW ->4169|PqqC-like protein|O84616.1|Chlamydia trachomatis|813 -ARKLLLDNL ->4172|Glycoprotein I precursor (Glycoprotein IV) (GI) (GPIV)|P09258.1|Human alphaherpesvirus 3|10335 -ARLCDLPATPK ->4197|polyprotein|ACB87119.1|Hepatitis C virus subtype 1a|31646 -ARMILMTHF ->4236|polyprotein|BAA03375.1|Hepatitis C virus|11103 -ARRGREILL ->4289|Major DNA-binding protein|P03227.1|Human herpesvirus 4 strain B95-8|10377 -ARYAYYLQF ->4371|tegument protein VP11/12|NP_044516.1|Human alphaherpesvirus 2|10310 -ASDSLNNEY ->4668|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 -ASPKGPVIQMYTNVD ->4682|LOW MOLECULAR WEIGHT T-CELL ANTIGEN TB8.4 (Hypothetical protein)|O50430|Mycobacterium tuberculosis H37Rv|83332 -ASPVAQSYL ->4735|polyprotein|AAY82034.1|Hepatitis C virus|11103 -ASRCWVAM ->4909|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 -ATCINGVCWTVYHGA ->4910|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 -ATCINGVCWTVYHGAGTRTI ->4916|NS3|AAU44857.1|Hepatitis C virus|11103 -ATDALMTGF ->4917|Genome polyprotein|P26664.3|Hepatitis C virus genotype 1|41856 -ATDALMTGY ->5191|core protein|AAL31859.1|Hepatitis B virus|10407 -ATVELLSFLPSDFFPSV ->5196|60 kDa chaperonin 2|P0A520.2|Mycobacterium tuberculosis|1773 -ATVLAQALVREGLRN ->5213|nonstructural protein 5|YP_001527887.1|West Nile virus NY-99|10000971 -ATWAENIQV ->5295|nef protein|ACR27174.1|Human immunodeficiency virus 1|11676 -AVDLSHFLK ->5316|EBNA-3B nuclear protein|CAD53420.1|Human gammaherpesvirus 4|10376 -AVFDRKSDAK ->5381|LOW MOLECULAR WEIGHT T-CELL ANTIGEN TB8.4 (Hypothetical protein)|O50430|Mycobacterium tuberculosis|1773 -AVINTTCNYGQ ->5542|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 -AVSLDFSPGTSGSPI ->5623|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 -AVYLLDGLR ->5714|Genome polyprotein|P26662.3|Hepatitis C virus|11103 -AYAAQGYKVL ->5727|Polyprotein|Q9IZA3|Hepatitis C virus subtype 2a|31649 -AYAMRVPEVI ->5783|Nucleoprotein|P03418.1|Human respiratory syncytial virus A2|11259 -AYGAGQVMLRWGVL ->5934|polyprotein|CAB53095.1|Hepatitis C virus subtype 1b|31647 -AYSQQTRGL ->5938|EBNA3A nuclear protein|Q8AZJ8|Human gammaherpesvirus 4|10376 -AYSSWMYSY ->5952|PPE family protein|YP_177918.1|Mycobacterium tuberculosis H37Rv|83332 -AYVPYVAWL ->6094|Genome polyprotein|Q81495.3|Hepatitis C virus (isolate HCV-K3a/650)|356416 -CDDCHAQDATSILGI ->6308|HCV-1|AAA45676.1|Hepatitis C virus genotype 1|41856 -CGKYLFNWAVRTKLKLTPIA ->6372|Genome polyprotein|SRC279960|Hepatitis C virus|11103 -CHAQDATSVL ->6373|Genome polyprotein|SRC279960|Hepatitis C virus subtype 3a|356426 -CHAQDATTVL ->6430|polyprotein|BAB18810.1|Hepatitis C virus genotype 1|41856 -CINGACWTV ->6431|Genome polyprotein|SRC279960|Hepatitis C virus|11103 -CINGCVWTV ->6432|polyprotein [Hepatitis C virus]|CAL46125.1|Hepatitis C virus (isolate H77)|63746 -CINGLCWTV ->6433|Genome polyprotein|SRC279960|Hepatitis C virus subtype 1a|31646 -CINGVCWTA ->6435|polyprotein|BAB18806.1|Hepatitis C virus|11103 -CINGVCWTV ->6437|Genome polyprotein|SRC279960|Hepatitis C virus|11103 -CINGVWCTV ->6511|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 -CKPLLREEVSFRVGL ->6556|X protein|AAP06597.1|Hepatitis B virus|10407 -CLFKDWEEL ->6568|latent membrane protein 2|AAB59844.1|Human gammaherpesvirus 4|10376 -CLGGLLTMV ->6591|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 -CLIRLKPTLHGPTPLLYR ->6631|core protein|AAL31859.1|Hepatitis B virus|10407 -CLTFGRETV ->6636|polyprotein|ABU97067.1|Hepatitis C virus subtype 1b|31647 -CLVDYPYRL ->6808|membrane protein|AAA45887.1|Human gammaherpesvirus 4|10376 -CPLSKILL ->6817|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 -CPNSSIVY ->6889|Agglutinin isolectin 1 precursor|P10968.2|Triticum aestivum|4565 -CQNGACWTS ->6901|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 -CQTYKWETF ->6936|Genome polyprotein|P26664.3|Hepatitis C virus (isolate 1)|11104 -CRPLTDFDQGW ->7116|NS3|ABN45875.1|Hepatitis C virus (isolate H77)|63746 -CTCGSSDLY ->7270|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -CVIGGAGNNT ->7291|neuramindase|AAT73327.1|Influenza A virus (A/Puerto Rico/8/1934(H1N1))|211044 -CVNGSCFTV ->7292|polyprotein|AAA75355.1|Hepatitis C virus subtype 1b|31647 -CVNGVCWTV ->7338|nonstructural protein 4A|YP_001527885.1|West Nile virus NY-99|10000971 -CWMAEVPGTKIAGMLLL ->7353|Early antigen protein D|P03191.1|Human herpesvirus 4 strain B95-8|10377 -CYDHAQTHL ->7436|Genome polyprotein|P26663.3|Hepatitis C virus|11103 -CYSIEPLDL ->7447|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 -CYVLEETSVML ->7481|Major outer membrane porin, serovar E precursor|P17451.1|Chlamydia trachomatis|813 -DADKYAVTV ->7538|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 -DAIDESGSGEEERPV ->7660|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 -DAVILLMCAVHPTLVFDITK ->7708|gag polyprotein|BAA00992.1|Human immunodeficiency virus 1|11676 -DCKTILKAL ->7999|core protein|BAA82580.1|Hepatitis C virus|11103 -DEGLGWAGW ->8052|polyprotein|NP_671491.1|Hepatitis C virus|11103 -DELAAKLVALGINAV ->8064|circumsporozoite protein|AAN87606.1|Plasmodium falciparum|5833 -DELDYENDIEKKICKMEKCS ->8191|Transcriptional regulator IE63 homolog|Q04360.1|Human herpesvirus 4 strain B95-8|10377 -DEVEFLGHY ->8236|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 -DFAQGWGPISYANGS ->8285|Genome polyprotein|P26662.3|Hepatitis C virus|11103 -DFKTWLQSKL ->8293|Polyprotein|Q9IZA3|Hepatitis C virus subtype 2a|31649 -DFNASTDLL ->8554|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 -DHMSIYKFMGRSHFLCTFTF ->8685|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 -DIKVQFQSG ->8910|Polyprotein|Q9J8D4|Dengue virus 2|11060 -DKKGKVVGL ->8920|M protein, serotype 5 precursor|P02977.2|Streptococcus pyogenes serotype M5|301449 -DKLAKEQKSKQNIGALKQ ->9114|Genome polyprotein|SRC279960|Hepatitis C virus subtype 1a|31646 -DLIAQPIRLL ->9199|E1 protein|ABB77003.1|Hepatitis C virus|11103 -DLMGYIPAV ->9203|polyprotein|BAA03375.1|Hepatitis C virus|11103 -DLMGYIPLV ->9209|polyprotein|CAB53095.1|Hepatitis C virus|11103 -DLMGYLPLV ->9316|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 -DLVGWPAPQGSRSLT ->9414|Superoxide dismutase|P17670.1|Mycobacterium tuberculosis|1773 -DMWEHAFYL ->9415|Superoxide dismutase|P17670.1|Mycobacterium tuberculosis|1773 -DMWEHAFYLQ ->9461|non structural protein 3|CAJ20172.1|Hepatitis C virus|11103 -DNFPYLVAY ->9746|Genome polyprotein|P29846.3|Hepatitis C virus genotype 1|41856 -DPRRRSRNL ->9920|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis|1773 -DQVESTAGSLQGQWRGAA ->9974|gag polyprotein|BAA00992.1|Human immunodeficiency virus 1|11676 -DRFYKTLRA ->9995|Exodeoxyribonuclease V, Gamma|NP_220158.1|Chlamydia trachomatis|813 -DRLALLANL ->9999|DNA packaging tegument protein UL25|NP_044494.1|Human alphaherpesvirus 2|10310 -DRLDNRLQL ->10448|nuclear protein EBNA2|AAA45903.1|Human gammaherpesvirus 4|10376 -DTPLIPLTIF ->10587|viral polyprotein|AAA42941.1|Dengue virus 2 Thailand/NGS-C/1944|11065 -DVFFTPPEK ->10650|Nucleoprotein|P05133.1|Hantaan virus 76-118|11602 -DVKVKEISNQEPLKL ->10681|nucleocapsid protein|AAA43837.1|Hantaan hantavirus|11599 -DVNGIRKPK ->10736|trans-sialidase|XP_814755.1|Trypanosoma cruzi|5693 -DVSRPTAVV ->10763|polyprotein|ABV46054.1|Hepatitis C virus subtype 1a|31646 -DVVCCSMSY ->10790|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 -DVVVVATDALMTGYT ->10939|polyprotein|BAB18806.1|Hepatitis C virus subtype 1a|31646 -DYPYRLWHY ->10962|envelope glycoprotein|AAU04921.1|Human T-lymphotropic virus 1|11908 -DYSPSCCTL ->11014|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 -EADVQQWLT ->11063|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 -EAHFTDPASIAARGY ->11125|NS3 protein|NP_739587.1|Dengue virus 2 Thailand/NGS-C/1944|11065 -EALRGLPIR ->11214|possible regulatory protein|NP_302009.1|Mycobacterium leprae|1769 -EAVLLRLDGTTLEVE ->11258|Nucleoprotein|P41269.1|Puumala hantavirus|11604 -ECPFIKPEV ->11455|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 -EDTSASGSGEDAIDE ->11804|EBNA3C latent protein|CAD53421.1|Human gammaherpesvirus 4|10376 -EENLLDFVRF ->11956|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 -EFCRVLCCYVL ->12060|Myosin heavy chain, skeletal muscle, adult 2 (Myosin heavy chain IIa) (MyHC-IIa)|Q9UKX2.1|Homo sapiens|9606 -EFQKMRRDL ->12062|hypothetical glycine-rich protein Rv3812 - Mycobacterium tuberculosis (strain H37RV)|H70520|Mycobacterium tuberculosis|1773 -EFQTVSNQL ->12108|polyprotein|AAP55688.1|Hepatitis C virus subtype 2a|31649 -EFWEAVFTGL ->12183|EBNA3C latent protein|CAD53421.1|Human gammaherpesvirus 4|10376 -EGGVGWRHW ->12583|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis H37Rv|83332 -EISTNIRQA ->12585|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis|1773 -EISTNIRQAGVQYSRADEEQ ->12588|Glycoprotein B precursor (Glycoprotein II)|P09257.1|Human alphaherpesvirus 3|10335 -EITDTIDKFGK ->12616|gag protein|AAV53308.1|Human immunodeficiency virus 1|11676 -EIYKRWII ->12926|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 -ELAAKLVAL ->12928|Genome polyprotein|Q81754.3|Hepatitis C virus|11103 -ELAAKLVGL ->12941|||| -ELAGIGILTV ->13091|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 -ELIEANLLW ->13119|envelope protein|AGW23591.1|Dengue virus 3|11069 -ELKGMSYAM ->13133|UL123; IE1|AAR31419.1|Human herpesvirus 5 TB40|10000408 -ELKRKMIYM ->13135|UL123; IE1|AAR31504.1|Human betaherpesvirus 5|10359 -ELKRKMMYM ->13165|trans-sialidase, putative|EAN81972.1|Trypanosoma cruzi|5693 -ELLRPTTLV ->13195|6 kDa early secretory antigenic target|P0A564.2|Mycobacterium tuberculosis|1773 -ELNNALQNL ->13215|Antigen 85-B|P0C5B9.1|Mycobacterium tuberculosis|1773 -ELPQWLSANR ->13257|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 -ELRRKMMYM ->13262|gag polyprotein|BAA00992.1|Human immunodeficiency virus 1|11676 -ELRSLYNTV ->13283|glycoprotein gp35/37|AAC59622.1|Human gammaherpesvirus 8|37296 -ELTDALISAFSGSYS ->13346|nonstructural protein 3|NP_722463.1|Dengue virus 1|11053 -EMAEALKGMPIRYQT ->13358|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 -EMEEALRGLPIRYQT ->13386|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis|1773 -EMKTDAATL ->13456|circumsporozoite protein|AAN87606.1|Plasmodium falciparum|5833 -ENDIEKKICKMEKCSSVFNV ->13473|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 -ENFVRSSNL ->13516|Genome polyprotein|P26664.3|Hepatitis C virus subtype 1a|31646 -ENLPYLVAY ->13518|HCV-1|AAA45676.1|Hepatitis C virus genotype 1|41856 -ENLPYLVAYQATVCARAQAP ->13638|polyprotein|BAB18810.1|Hepatitis C virus (isolate H77)|63746 -EPEPDVAVL ->13701|Trans-activator protein BZLF1|P03206.2|Human gammaherpesvirus 4|10376 -EPLPQGQLTAY ->13946|UL123; IE1|AAR31390.1|Human betaherpesvirus 5|10359 -EQVTEDCNENP ->13983|ATP-dependent zinc protease|NP_220362.1|Chlamydia trachomatis|813 -EREQTLNQL ->13991|hypothetical protein CT850|NP_220372.1|Chlamydia trachomatis|813 -ERFLAQEQL ->14001|Nucleocapsid protein|Q89462|Sin Nombre hantavirus|37705 -ERIDDFLAA ->14101|envelope glycoprotein|ABI16336.1|Human immunodeficiency virus 1|11676 -ERYLKDQQL ->14198|UL123; IE1|AAR31390.1|Human betaherpesvirus 5|10359 -ESLKTFEQVTE ->14324|Chain B, Dengue Virus Rna Dependent Rna Polymerase With Residues From The Ns5 Linker Region|4C11_B|Dengue virus|12637 -ETACLGKAY ->14325|polyprotein|AGO67248.1|Dengue virus 2|11060 -ETACLGKSY ->14381|polyprotein|BAA25076.1|Hepatitis C virus|11103 -ETFWAKHMW ->14427|polyprotein|BAD73974.1|Hepatitis C virus subtype 1b|31647 -ETIKGGRHL ->14720|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 -EVIAPAVQTNW ->14727|polyprotein|AAB67036.1|Hepatitis C virus subtype 1a|31646 -EVIKGGRHL ->14731|gag protein|ACD85912.1|Human immunodeficiency virus 1|11676 -EVIPMFSAL ->14902|Genome polyprotein|P26664.3|Hepatitis C virus subtype 1a|31646 -EVVTSTWVL ->15061|core protein|BAF42671.1|Hepatitis B virus|10407 -EYLVSFGVW ->15100|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 -EYTNIPISL ->15110|Genome polyprotein|P26663.3|Hepatitis C virus|11103 -EYVLLLFLL ->15226|trans-sialidase|XP_810383.1|Trypanosoma cruzi|5693 -FANCNFTLV ->15230|Trans-sialidase|SRC7915|Trypanosoma cruzi|5693 -FANHDFTLV ->15231|trans-sialidase|XP_817875.1|Trypanosoma cruzi|5693 -FANHKFTLV ->15232|trans-sialidase, putative|EAN82291.1|Trypanosoma cruzi|5693 -FANHNFTLV ->15233|trans-sialidase, putative|EAN81456.1|Trypanosoma cruzi|5693 -FANNEFTLV ->15234|trans-sialidase|XP_815749.1|Trypanosoma cruzi|5693 -FANNKFTLV ->15242|trans-sialidase, putative|EAN81560.1|Trypanosoma cruzi|5693 -FANYKFTLV ->15244|trans-sialidase|XP_818893.1|Trypanosoma cruzi|5693 -FANYNFTLV ->15787|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 -FFCFAWYLKGRWVPG ->15879|Core antigen|P69708.1|Hepatitis B virus|10407 -FFPSIRDLL ->15885|envelope|BAK20487.1|Human T-lymphotropic virus 1|11908 -FFQFCPLIF ->15914|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 -FFTELDGVRLHRFAP ->16156|Spike glycoprotein precursor|P59594.1|SARS coronavirus|227859 -FIAGLIAIV ->16250|liver stage antigen-1|CAA82974.1|Plasmodium falciparum|5833 -FILVNLLIFH ->16332|secreted antigen Ag85B|AAO62005.1|Mycobacterium tuberculosis|1773 -FIYAGSLSA ->16333|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 -FIYAGSLSAL ->16521|polyprotein|ABU97067.1|Hepatitis C virus subtype 1b|31647 -FLARLIWWL ->16548|Glycoprotein GP110 precursor|P03188.1|Human herpesvirus 4 strain B95-8|10377 -FLDKGTYTL ->16617|Large envelope protein|SRC279965|Hepatitis B virus|10407 -FLGGTRVCL ->16623|gag protein|AAV53308.1|Human immunodeficiency virus 1|11676 -FLGKIWPSYK ->16685|Gag-Pol polyprotein|SRC279958|Human immunodeficiency virus 1|11676 -FLKEKKGL ->16706|structural protein|BAA00705.1|Hepatitis C virus|11103 -FLLALLSCL ->16725|Genome polyprotein|P26664.3|Hepatitis C virus subtype 1a|31646 -FLLLADARV ->16751|pol protein|BAA32832.1|Hepatitis B virus|10407 -FLLSLGIHL ->16753|Pre-S/S protein|AAR99337.1|Hepatitis B virus|10407 -FLLTKILTI ->16755|envelope protein|BAF48755.1|Hepatitis B virus|10407 -FLLTRILTI ->16756|Large envelope protein|SRC279965|Hepatitis B virus|10407 -FLLTRILTL ->16772|Type IV pili glycosylation protein|YP_169902.1|Francisella tularensis subsp. tularensis SCHU S4|177416 -FLMPFMHYIV ->16795|precore/core protein|AAP57273.1|Hepatitis B virus|10407 -FLPADFFPSI ->16796|HBcAg|ABE97049.1|Hepatitis B virus|10407 -FLPADFFPSV ->16813|External core antigen|SRC279980|Hepatitis B virus|10407 -FLPNDFFPSA ->16814|precore protein|CAM58990.1|Hepatitis B virus|10407 -FLPNDFFPSV ->16815|core protein [Hepatitis B virus]|AAR19324.1|Hepatitis B virus|10407 -FLPPDFFPSV ->16827|External core antigen|SRC279980|Hepatitis B virus|10407 -FLPSDFFPGV ->16831|External core antigen|SRC279980|Hepatitis B virus|10407 -FLPSDFFPSA ->16832|core protein|BAF42671.1|Hepatitis B virus|10407 -FLPSDFFPSI ->16833|core protein|CAL29866.1|Hepatitis B virus|10407 -FLPSDFFPSV ->16836|precore/core protein [Hepatitis B virus]|AAR03815.1|Hepatitis B virus|10407 -FLPSDFLPSV ->16839|External core antigen|SRC279980|Hepatitis B virus|10407 -FLPSDTNMGL ->16856|||| -FLPVDFFPSI ->16857|pre-c/core|CAA59565.1|Hepatitis B virus|10407 -FLPVDFFPSV ->16878|EBNA-3A|AFY97830.1|Human gammaherpesvirus 4|10376 -FLRGRAYGL ->16889|trans-sialidase, putative|EAN82636.1|Trypanosoma cruzi|5693 -FLSHDFTLV ->16890|trans-sialidase|XP_810777.1|Trypanosoma cruzi|5693 -FLSHNFTLV ->16924|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 -FLTSELPQW ->16936|tegument protein VP13/14|NP_044517.1|Human alphaherpesvirus 2|10310 -FLVDAIVRV ->16937|tegument protein VP13/14|NP_044517.1|Human alphaherpesvirus 2|10310 -FLVDAIVRVA ->16966|polyprotein|BAA03375.1|Hepatitis C virus|11103 -FLVSQLFTF ->16979|Latent membrane protein 2|Q69135|Human gammaherpesvirus 4|10376 -FLYALALLL ->17079|hypothetical protein FTT1095c|YP_170074.1|Francisella tularensis subsp. tularensis SCHU S4|177416 -FMPKVNFEV ->17110|EBNA-1 protein|Q777E1|Human gammaherpesvirus 4|10376 -FMVFLQTHI ->17117|matrix protein|AAN09804.1|Measles virus strain Edmonston|11235 -FMYMSLLGV ->17278|Genome polyprotein|P06441.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 -FPELKPGESRHTSDHMSIYK ->17321|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 -FPKTTNGCSQA ->17619|Early antigen protein D|P03191.1|Human herpesvirus 4 strain B95-8|10377 -FRNLAYGRTCVLGK ->17620|Early antigen protein D|P03191.1|Human herpesvirus 4 strain B95-8|10377 -FRNLAYGRTCVLGKE ->17802|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 -FSPGTSGSPIIDKKG ->18011|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 -FTLVAPVSI ->18062|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 -FTSAVLLLV ->18142|polyprotein precursor|NP_041724.2|West Nile virus|11082 -FVDVGVSAL ->18144|trans-sialidase|XP_804884.1|Trypanosoma cruzi|5693 -FVDYNFSLV ->18145|trypomastigote surface glycoprotein|AAA30259.1|Trypanosoma cruzi|5693 -FVDYNFTIV ->18242|trans-sialidase, putative|EAN80731.1|Trypanosoma cruzi|5693 -FVNHRFTLV ->18250|Trans-sialidase|SRC7915|Trypanosoma cruzi|5693 -FVNYDFALV ->18251|trans-sialidase|XP_820181.1|Trypanosoma cruzi|5693 -FVNYDFTIV ->18252|trans-sialidase|XP_814186.1|Trypanosoma cruzi|5693 -FVNYNFTLV ->18276|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 -FVRSSNLKF ->18284|Trans-sialidase|SRC7915|Trypanosoma cruzi|5693 -FVSCDFTIV ->18337|polyprotein|BAD73987.1|Hepatitis C virus subtype 1b|31647 -FWAKHMWNF ->18390|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 -FYFPRAPLNSNAMLSTESMM ->18397|Genome polyprotein|P26662.3|Hepatitis C virus|11103 -FYGKAIPIEAI ->18400|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 -FYGMWPLL ->18401|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 -FYGMWPLLL ->18474|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 -FYTPLADQF ->18507|10 kDa culture filtrate antigen EsxB|NP_218391.1|Mycobacterium tuberculosis H37Rv|83332 -GAAGTAAQAAVVRFQ ->18678|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 -GALTGTYVYNHLTPL ->18847|polyprotein|AEH28241.1|Hepatitis C virus subtype 1b|31647 -GAYMSKAHGV ->18941|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 -GDCVQGDWCPISGGL ->19225|polyprotein|AGO67248.1|Dengue virus 2|11060 -GEDGCWYGM ->19305|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -GEIPFYGKAI ->19337|gag protein|AAW57872.1|Human immunodeficiency virus 1|11676 -GELDRWEKI ->19348|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 -GELLPEAAGPTQVLVPRSAI ->19351|core protein|AAL31859.1|Hepatitis B virus|10407 -GELMTLATW ->19359|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 -GELSKQTGQQVSIAPNAGLD ->19366|Hepatitis C virus core, matrix, envelope and non-structural protein RNA.|AAA72945.1|Hepatitis C virus|11103 -GEMPSTEDL ->19370|Genome polyprotein|P26664.3|Hepatitis C virus genotype 6|42182 -GENDTDVFVL ->19434|Genome polyprotein|P27915.1|Dengue virus 3|11069 -GESRKTFVE ->19435|polyprotein|CDF77361.1|Dengue virus 3|11069 -GESRKTFVEL ->19442|nucleocapsid protein|ABI96968.1|SARS coronavirus|227859 -GETALALLLL ->19463|Carbamoyl-phosphate synthase large chain|YP_170571.1|Francisella tularensis subsp. tularensis SCHU S4|177416 -GEVLGVIVQF ->19490|Genome polyprotein|P26663.3|Hepatitis C virus (isolate BK)|11105 -GFADLMGYI ->19492|Genome polyprotein|P29846.3|Hepatitis C virus|11103 -GFADLMGYIPL ->19493|polyprotein|BAA03375.1|Hepatitis C virus|11103 -GFADLMGYIPLVGAP ->19575|glycoprotein B precursor|AAB72100.1|Human alphaherpesvirus 2|10310 -GFLIAYQPLL ->19628|Genome polyprotein|P26662.3|Hepatitis C virus|11103 -GFTGDFDSV ->19898|gag protein|AAV53308.1|Human immunodeficiency virus 1|11676 -GGKKKYKLK ->20023|EBNA-1|YP_401677.1|Human gammaherpesvirus 4|10376 -GGSKTSLYNLRRGTA ->20354|M1 protein|CAA30882.1|Influenza A virus|11320 -GILGFVFTL ->20355|Matrix protein 1|P03485.1|Influenza A virus (A/Puerto Rico/8/1934(H1N1))|211044 -GILGFVFTLT ->20369|HEAT SHOCK PROTEIN HSPX (ALPHA-CRSTALLIN HOMOLOG) (14 kDa ANTIGEN) (HSP16.3)|NP_216547.1|Mycobacterium tuberculosis H37Rv|83332 -GILTVSVAV ->20415|circumsporozoite protein|AAN87606.1|Plasmodium falciparum|5833 -GIQVRIKPGSANKPKDELDY ->20417|HCV-1|AAA45676.1|Hepatitis C virus genotype 1|41856 -GIQYLAGLSTLPGNPAIASL ->20686|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 -GKSTHPMVTRS ->20752|tegument protein VP13/14|NP_044517.1|Human alphaherpesvirus 2|10310 -GLADTVVAC ->20772|Genome polyprotein|SRC279960|Hepatitis C virus|11103 -GLASLFTQGA ->20786|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 -GLCPHCINV ->20787|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 -GLCPHCINVG ->20788|BMLF1 protein|CAD53409.1|Human gammaherpesvirus 4|10376 -GLCTLVAML ->20861|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 -GLFNNVLYH ->20865|Nucleoprotein|P41269.1|Puumala hantavirus|11604 -GLFPTQIQV ->20892|latent membrane protein 2|AAB59844.1|Human gammaherpesvirus 4|10376 -GLGTLGAAL ->20894|polyprotein [Hepatitis C virus]|BAF91806.1|Hepatitis C virus|11103 -GLGWVGWLL ->20921|polyprotein|BAA03375.1|Hepatitis C virus|11103 -GLIHLHQNIVDVQYL ->20929|Circumsporozoite protein precursor|P02893.1|Plasmodium falciparum|5833 -GLIMVLSFL ->20988|Genome polyprotein|P26662.3|Hepatitis C virus (isolate Japanese)|11116 -GLLGCIITSL ->20994|Circumsporozoite-related antigen|SRC280086|Plasmodium falciparum|5833 -GLLGNVSTV ->21000|glutamine synthetase GLNA1 (glutamine synthase) (GS-I)|NP_216736.1|Mycobacterium tuberculosis|1773 -GLLHHAPSL ->21004|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 -GLLLLGLWGT ->21007|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 -GLLPFHSTL ->21013|trans-sialidase, putative|EAN80935.1|Trypanosoma cruzi|5693 -GLLPSLLLLL ->21038|cysteine proteinase cruzipain (EC 3.4.22.-) - Trypanosoma cruzi|A45629|Trypanosoma cruzi|5693 -GLMNNAFEWI ->21041|Membrane glycoprotein|Q692E0|SARS coronavirus TJF|284672 -GLMWLSYFV ->21070|polymerase|CAA53358.1|Hepatitis B virus subtype AYR|10000437 -GLPRYVARL ->21071|Protein P|SRC279982|Hepatitis B virus subtype adr|106820 -GLPRYVVCL ->21078|Antigen 85-B precursor|P21160.1|Mycobacterium kansasii|1768 -GLPVEYLQV ->21079|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 -GLQDCTMLV ->21116|X protein|BAG70907.1|Hepatitis B virus|10407 -GLSAMSTTDL ->21137|Major surface antigen precursor|P03142.4|Hepatitis B virus subtype adw|106821 -GLSPTVWLSA ->21139|envelope protein|BAF48755.1|Hepatitis B virus|10407 -GLSPTVWLSV ->21145|DNA polymerase|CAA10434.1|Hepatitis B virus|10407 -GLSRYVARL ->21146|polymerase|AAD16253.1|Hepatitis B virus|10407 -GLSRYVARLS ->21190|Genome polyprotein|P27958.3|Hepatitis C virus (isolate H)|11108 -GLVGLLTPGA ->21199|Circumsporozoite protein precursor|P08677.2|Plasmodium vivax strain Belem|31273 -GLVILLVLAL ->21230|polyprotein precursor|AAP22088.1|West Nile virus|11082 -GLYKSAPRR ->21242|polymerase|ACF94272.1|Hepatitis B virus|10407 -GLYSSTVPV ->21275|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 -GMGPSLIGL ->21347|Nucleoprotein|P59595.1|SARS coronavirus|227859 -GMSRIGMEV ->21385|polyprotein|AAY82034.1|Hepatitis C virus genotype 1|41856 -GNASRCWVAM ->21576|nucleocapsid protein|AAA43837.1|Hantaan virus 76-118|11602 -GPATNRDYL ->21635|gag protein|ABO73990.1|Human immunodeficiency virus 1|11676 -GPGHKARVL ->21638|protein F|ABV46152.2|Hepatitis C virus (isolate Japanese)|11116 -GPGLSPGTL ->21656|protease|CAB06750.1|Human alphaherpesvirus 2|10310 -GPHETITAL ->21663|polyprotein precursor|NP_041724.2|West Nile virus|11082 -GPIRFVLAL ->21754|Genome polyprotein|SRC279960|Hepatitis C virus genotype 1|41856 -GPRLGFRAT ->21757|polyprotein|BAA09072.1|Hepatitis C virus|11103 -GPRLGVRAT ->21762|Genome polyprotein|Q99IB8.3|Hepatitis C virus|11103 -GPRLGVRTT ->21780|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 -GPSLIGLAM ->21894|Polyprotein|P90247|Hepatitis C virus|11103 -GQIVGGVYL ->21895|core protein|AAS15195.1|Hepatitis C virus (isolate H77)|63746 -GQIVGGVYLL ->21960|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 -GQSSFYSDWY ->21982|HCV-1|AAA45676.1|Hepatitis C virus|11103 -GRAAICGKY ->22046|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 -GRGKPGIYRF ->22235|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 -GRVIGSALQFLIPRL ->22255|polyprotein|ABR27377.1|Hepatitis C virus|11103 -GRWVPGAAY ->22633|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 -GTDTGQACQIQMSDPAYNIN ->22801|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 -GTRLAAGSPSSEYPN ->22817|polyprotein|AAK49562.1|Dengue virus 2|11060 -GTSGSPIADKK ->22818|Nonstructural protein NS3|NP_739587.2|Dengue virus 2|11060 -GTSGSPIIDK ->22819|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 -GTSGSPIIDKK ->22820|Nonstructural protein NS3|YP_001531172.2|Dengue virus 3|11069 -GTSGSPIINR ->22822|NS3 protein|NP_740321.1|Dengue virus 4|11070 -GTSGSPIINRK ->22823|NS3 protein|NP_739587.1|Dengue virus 2|11060 -GTSGSPIVDK ->22824|polyprotein|AAG30730.1|Dengue virus 2|11060 -GTSGSPIVDR ->22825|polyprotein|ABG75765.1|Dengue virus 1|11053 -GTSGSPIVNR ->22910|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 -GVAGALVAFK ->22919|Genome polyprotein|SRC279960|Hepatitis C virus|11103 -GVASFFTPGA ->22976|nuclear antigen EBNA-1|AAA67277.1|Human gammaherpesvirus 4|10376 -GVFVYGGSKTSLYNL ->23129|polyprotein|BAB18806.1|Hepatitis C virus subtype 1a|31646 -GVRVLEDGV ->23137|liver stage antigen-1|CAA82974.1|Plasmodium falciparum|5833 -GVSENIFLK ->23151|polymerase ORF|CAA46356.1|Hepatitis B virus subtype ayw|10418 -GVSRYVARL ->23224|polyprotein|BAB18806.1|Hepatitis C virus|11103 -GVYLLPRRGPRLGVR ->23270|polyprotein|AAB67036.1|Hepatitis C virus (isolate H77)|63746 -GWLAGLFYQHKFNSS ->23288|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 -GWSGQVYQDWLGRMN ->23306|LOW MOLECULAR WEIGHT PROTEIN ANTIGEN 7 ESXH (10 kDa ANTIGEN) (CFP-7) (PROTEIN TB10.4)|CAA17363.1|Mycobacterium tuberculosis H37Rv|83332 -GYAGTLQSL ->23365|polyprotein|BAB18806.1|Hepatitis C virus|11103 -GYIPLVGAPL ->23474|polyprotein|AAP55688.1|Hepatitis C virus subtype 2a|31649 -GYTGDFDSVI ->23542|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 -HAKALKERMV ->23566|tegument protein UL7|NP_044476.1|Human alphaherpesvirus 2|10310 -HASPFERVRCLLL ->23573|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 -HAVGLFRAA ->23601|Genome polyprotein|SRC279960|Hepatitis C virus (isolate H77)|63746 -HCPAGHAVGIFRAAVCTRGVA ->23619|Genome polyprotein|P27958.3|Hepatitis C virus (isolate H)|11108 -HDGAGKRVY ->23620|Genome polyprotein|SRC279960|Hepatitis C virus genotype 1|41856 -HDGAGKRVYL ->23621|Genome polyprotein|P26664.3|Hepatitis C virus (isolate 1)|11104 -HDGAGKRVYYL ->23754|Genome polyprotein|P26664.3|Hepatitis C virus genotype 1|41856 -HEYPVGSQL ->23797|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 -HFLCTFTFNSNNKEYTFPIT ->23807|tax|AAG48731.1|Human T-lymphotropic virus 2|11909 -HFPGFGQSLLYGYPVYVFGDCVQ ->23864|envelope glycoprotein(gp21, gp46) - human T-cell lymphotropic virus type 1|A45714|Human T-lymphotropic virus 1|11908 -HFSKCGFPF ->23883|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 -HGAGTRTIASPKGPV ->24172|pX-rex-orf I {alternatively spliced}|AAB23359.1|Human T-lymphotropic virus 1|11908 -HLAFQLSSI ->24218|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 -HLHAPTGSGK ->24219|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 -HLHAPTGSGKSTKVP ->24299|X protein|BAF81690.1|Hepatitis B virus|10407 -HLSLRGLFV ->24302|X protein|AAP06597.1|Hepatitis B virus|10407 -HLSLRGLPV ->24390|Major capsid protein L1|P50816.2|Human papillomavirus type 44|10592 -HNNGICWGN ->24427|polyprotein|ACX44238.1|Hepatitis C virus subtype 1a|31646 -HPALVFDIT ->24457|polyprotein|BAA09072.1|Hepatitis C virus|11103 -HPITKYIMACMSADL ->24479|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 -HPNIEEVAL ->24535|EBNA-1 protein|Q777E1|Human gammaherpesvirus 4|10376 -HPVGEADYF ->24536|EBNA-1|YP_401677.1|Human gammaherpesvirus 4|10376 -HPVGEADYFEY ->24557|Gag polyprotein|P03347.3|Human immunodeficiency virus 1|11676 -HPVHAGPIA ->24759|polyprotein|AAY82031.1|Hepatitis C virus|11103 -HSKKKCDDL ->24760|polyprotein|ACP19428.1|Hepatitis C virus subtype 1b|31647 -HSKKKCDEF ->24761|polyprotein|ACZ60102.1|Hepatitis C virus subtype 3a|356426 -HSKKKCDEI ->24762|NS3|ABW71987.1|Hepatitis C virus subtype 1b|31647 -HSKKKCDEL ->24764|polyprotein [Hepatitis C virus subtype 1b]|ABV46195.2|Hepatitis C virus|11103 -HSKKKCDELT ->24765|polyprotein [Hepatitis C virus]|ABR27360.1|Hepatitis C virus|11103 -HSKKKCDEV ->24768|NS3 [Hepatitis C virus]|AAU44886.1|Hepatitis C virus subtype 1b|31647 -HSKRKCDEF ->24769|polyprotein|AAY82032.1|Hepatitis C virus subtype 1b|31647 -HSKRKCDEL ->24818|polyprotein|ABL63011.1|Hepatitis C virus|11103 -HSNIEEVAL ->24943|DNA polymerase|CAA10434.1|Hepatitis B virus|10407 -HTLWKAGILYK ->24986|polyprotein precursor|NP_041724.2|West Nile virus|11082 -HTTKGAALM ->25133|Envelope glycoprotein precursor|P27312.1|Puumala hantavirus|11604 -HWMDATFNL ->25149|polyprotein|BAD73994.1|Hepatitis C virus subtype 1b|31647 -HYAPRPCGI ->25186|polyprotein|AAK32686.1|Hepatitis C virus|11103 -HYPCTVNFTI ->25237|Transcription activator BRLF1|P03209.1|Human herpesvirus 4 strain B95-8|10377 -IACPIVMRYVLDHLI ->25275|Glutamate decarboxylase 2|Q05329.1|Homo sapiens|9606 -IAFTSEHSHFSLK ->25370|Trans-sialidase|SRC7915|Trypanosoma cruzi|5693 -IANYNFTLV ->25388|matrix protein|ABP96803.1|Human metapneumovirus|162145 -IAPYAGLIMI ->25460|Fusion glycoprotein F0 precursor|P03420.1|Human respiratory syncytial virus A2|11259 -IAVGLLLYCKA ->25677|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 -IDTCISATFR ->25756|membrane protein|AAA45887.1|Human gammaherpesvirus 4|10376 -IEDPPFNSL ->25782|pol protein|ACJ76655.1|Human immunodeficiency virus 1|11676 -IEELRQHLL ->25839|gag protein|ACN42927.1|Human immunodeficiency virus 1|11676 -IEIKDTKEAL ->25929|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 -IEPSWADVKKDLISY ->26111|polyprotein|BAD73987.1|Hepatitis C virus subtype 1b|31647 -IFLLALLSCL ->26174|Genome polyprotein|Q9WMX2.3|Hepatitis C virus|11103 -IFTITKILL ->26186|UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-me so-diaminopimelate ligase|YP_169478.1|Francisella tularensis subsp. tularensis SCHU S4|177416 -IFWQFHQLL ->26273|nucleocapsid protein|ABI96968.1|SARS coronavirus|227859 -IGMEVTPSGTWLTYH ->26579|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 -IILNGSLLTL ->26666|Receptor tyrosine-protein kinase erbB-2 precursor|P04626.1|Homo sapiens|9606 -IISAVVGIL ->26870|Circumsporozoite protein precursor|P02893.1|Plasmodium falciparum|5833 -IKPGSANKPKDELDYENDIE ->26954|HCV-1|AAA45676.1|Hepatitis C virus genotype 1|41856 -ILAGYGAGV ->26965|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 -ILAPTRVVAAEMEEA ->27000|Heat shock protein HSP 90-beta|P08238.4|Homo sapiens|9606 -ILDKKVEKV ->27011|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 -ILDSFDPLV ->27061|envelope glycoprotein|ABU89742.1|Dengue virus 2 Thailand/16681/84|31634 -ILGDTAWDFG ->27096|HCV-1|AAA45676.1|Hepatitis C virus (isolate H)|11108 -ILHTPGCV ->27125|gag-pol fusion polyprotein|AAN73817.1|Human immunodeficiency virus 1|11676 -ILKEPVHGV ->27168|envelope protein|BAF48755.1|Hepatitis B virus|10407 -ILLLCLIFL ->27169|envelope protein|BAF48755.1|Hepatitis B virus|10407 -ILLLCLIFLL ->27195|polyprotein|ABG67747.1|West Nile virus|11082 -ILLWEIPDV ->27216|polyprotein|BAD73987.1|Hepatitis C virus subtype 1b|31647 -ILMTHFFSI ->27217|VP1|AAL37677.1|JC polyomavirus|10632 -ILMWEAVTL ->27239|polyprotein|BAB18806.1|Hepatitis C virus subtype 1b|31647 -ILPCSFTTL ->27241|Spike glycoprotein precursor|P59594.1|SARS coronavirus|227859 -ILPDPLKPT ->27245|Hemagglutinin glycoprotein|P08362.1|Measles virus strain Edmonston|11235 -ILPGQDLQYV ->27285|pol protein|BAA32832.1|Hepatitis B virus|10407 -ILRGTSFVYV ->27295|polyprotein precursor|NP_041724.2|West Nile virus|11082 -ILRNPGYAL ->27345|Large envelope protein|P03138.3|Hepatitis B virus subtype ayw|10418 -ILSPFLPLL ->27365|precore/core protein|BAE97616.1|Hepatitis B virus|10407 -ILSTLPETTV ->27564|organic solvent tolerance protein|YP_169505.1|Francisella tularensis subsp. tularensis SCHU S4|177416 -IMSSFEFQV ->27586|ESAT-6-like protein esxH|P0A568.2|Mycobacterium tuberculosis|1773 -IMYNYPAML ->27770|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 -INYADRRWCF ->27811|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 -IPDREVLY ->27847|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 -IPFYGKAI ->27878|large surface antigen|CAC87019.1|Hepatitis B virus|10407 -IPIPSSWAF ->27901|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 -IPKLVANNT ->27981|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 -IPPRGTQAVVLKVYQNAGGT ->27983|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 -IPPSFLQAMRKYSPF ->28126|matrix protein|ABP96803.1|Human metapneumovirus|162145 -IPYTAAVQV ->28222|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 -IQSALKLAIYKAT ->28282|Nucleoprotein|P41269.1|Puumala hantavirus|11604 -IREFMEKECPFIKPE ->28338|hypothetical protein CT339|NP_219846.1|Chlamydia trachomatis|813 -IRMFKILPL ->28364|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis H37Rv|83332 -IRQAGVQYSR ->28403|Invasin repeat family phosphatase|NP_220117.1|Chlamydia trachomatis|813 -IRSSVQNKL ->28484|Protein E6|P03126.1|Human papillomavirus type 16|333760 -ISEYRHYCY ->28508|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 -ISGGLCSARLHRHAL ->28594|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 -ISLPSYYPDQKSLENYIAQT ->28657|gag protein|CAB00235.1|Human immunodeficiency virus 1|11676 -ISPRTLNAW ->29181|unnamed protein product|BAA14233.1|Hepatitis C virus subtype 1b|31647 -ITYSTYCKF ->29182|polyprotein|BAD73991.1|Hepatitis C virus subtype 1b|31647 -ITYSTYGKF ->29186|polyprotein precursor|NP_041724.2|West Nile virus|11082 -ITYTDVLRY ->29287|polyprotein|BAA09073.1|Hepatitis C virus subtype 1b|31647 -IVGGVYLLPR ->29352|pol protein|AAS38336.1|Human immunodeficiency virus 1|11676 -IVLPEKDSW ->29455|Major surface antigen precursor|P03141.3|Hepatitis B virus subtype adw2|10408 -IVSPFIPLL ->29466|Epstein-Barr nuclear antigen 4|P03203.3|Human herpesvirus 4 strain B95-8|10377 -IVTDFSVIK ->29558|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 -IYAGSLSAL ->29655|pol protein|ACJ76655.1|Human immunodeficiency virus 1|11676 -IYQEPFKNLK ->29804|p24|AAB82828.1|Human immunodeficiency virus 1|11676 -KAFSPEVIPMF ->30138|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 -KDELRRKMMYM ->30266|Transcriptional regulator IE63 homolog|Q04360.1|Human herpesvirus 4 strain B95-8|10377 -KDTWLDARM ->30464|nef protein|ACR27130.1|Human immunodeficiency virus 1|11676 -KEKGGLEGL ->30815|Genome polyprotein|P26662.3|Hepatitis C virus|11103 -KFPPALPIW ->30892|Protein E6|P03126.1|Human papillomavirus type 16|333760 -KFYSKISEY ->30903|prM protein|YP_001527879.1|West Nile virus NY-99|10000971 -KGAWMDSTKATRYLVK ->30913|polyprotein precursor|NP_041724.2|West Nile virus|11082 -KGDTTTGVY ->30946|HCV-1|AAA45676.1|Hepatitis C virus genotype 1|41856 -KGGRKPARLIVFPDLGVRVC ->31004|M protein, serotype 5 precursor|P02977.2|Streptococcus pyogenes serotype M5|301449 -KGLRRDLDA ->31747|polyprotein|AGO67248.1|Dengue virus 2|11060 -KLAEAIFKL ->31756|matrix protein 2-1|AAS22094.1|Human metapneumovirus|162145 -KLAKLIIDL ->31771|Nucleoprotein|P03418.1|Human respiratory syncytial virus A2|11259 -KLCGMLLITEDANH ->31802|large delta antigen|AAG26087.1|Hepatitis delta virus TW2667|10000523 -KLEDENPWL ->31803|large delta antigen|AAG26087.1|Hepatitis delta virus TW2667|10000523 -KLEDLERDL ->31884|HAD superfamily protein|YP_169641.1|Francisella tularensis subsp. tularensis SCHU S4|177416 -KLGGYVSFV ->31898|P protein|P17100.1|Hepatitis B virus|10407 -KLHLYSHPI ->31902|Secreted antigen Ag85A|Q847N5|Mycobacterium tuberculosis|1773 -KLIANNTRV ->31974|short chain dehydrogenase|YP_169584.1|Francisella tularensis subsp. tularensis SCHU S4|177416 -KLLGQINLV ->31996|nucleocapsid protein|AAA43837.1|Hantaan virus 76-118|11602 -KLLPDTAAV ->31997|hypothetical protein FTT0484|YP_169522.1|Francisella tularensis subsp. tularensis SCHU S4|177416 -KLLPEGYWV ->32047|M protein, serotype 5 precursor|P02977.2|Streptococcus pyogenes serotype M5|301449 -KLNKELEES ->32069|Spike glycoprotein precursor|P59594.1|SARS coronavirus BJ01|228407 -KLPDDFMGCV ->32073|Protein E6|P06463.1|Human papillomavirus type 18|333761 -KLPDLCTEL ->32085|Protein E6|P03126.1|Human papillomavirus type 16|333760 -KLPQLCTEL ->32103|60 kDa chaperonin 2|P0A520.2|Mycobacterium tuberculosis|1773 -KLQERLAKL ->32147|nonstructural protein 3|NP_722463.1|Dengue virus type 1 Hawaii|10000440 -KLRTLVLAPTRVVAS ->32150|polyprotein|AAF65953.1|Hepatitis C virus|11103 -KLSALGLNAV ->32165|Hepatitis C virus core, matrix, envelope and non-structural protein RNA.|AAA72945.1|Hepatitis C virus (isolate BK)|11105 -KLSGLGINAV ->32166|Genome polyprotein|SRC279960|Hepatitis C virus (isolate H77)|63746 -KLSGLGLNAI ->32167|polyprotein|BAB18806.1|Hepatitis C virus|11103 -KLSGLGLNAV ->32174|non structural protein 3|CAJ20172.1|Hepatitis C virus|11103 -KLSNLGLNAV ->32179|polyprotein|ABU97067.1|Hepatitis C virus (isolate H77)|63746 -KLSSLGLNAV ->32187|polyprotein [Hepatitis C virus subtype 1a]|ACA50630.1|Hepatitis C virus (isolate H77)|63746 -KLTALGVNAV ->32201|Gp160|Q0ED31|Human immunodeficiency virus 1|11676 -KLTPLCVTL ->32208|Genome polyprotein|P26664.3|Hepatitis C virus subtype 1a|31646 -KLVALGINAV ->32209|polyprotein precursor|BAA01582.1|Hepatitis C virus (isolate H77)|63746 -KLVALGVNAV ->32210|polyprotein|AAY82027.1|Hepatitis C virus|11103 -KLVAMGINAV ->32212|polyprotein [Hepatitis C virus subtype 1a]|ACA50667.1|Hepatitis C virus (isolate H77)|63746 -KLVAMGVNAV ->32213|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 -KLVANNTRL ->32223|polyprotein [Hepatitis C virus subtype 1a]|ABW86969.1|Hepatitis C virus (isolate H77)|63746 -KLVGLGLNAV ->32237|polyprotein|ABV46286.2|Hepatitis C virus subtype 1b|31647 -KLVSLGVNAV ->32238|polyprotein [Hepatitis C virus subtype 1a]|ABV46251.2|Hepatitis C virus (isolate H77)|63746 -KLVVLGINAV ->32243|C protein|BAB60863.1|Measles virus|11234 -KLWESPQEI ->32250|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 -KLYCSYEVA ->32268|hemagglutinin|AAK38298.1|Influenza A virus (A/Bar-headed Goose/Qinghai/61/05(H5N1))|336238 -KLYQNPTTYI ->32393|Myosin heavy chain, skeletal muscle, adult 2 (Myosin heavy chain IIa) (MyHC-IIa)|Q9UKX2.1|Homo sapiens|9606 -KMRRDLEEA ->32605|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 -KNSAFPKTTNG ->32663|small hydrophobic protein|AAM12943.1|Human metapneumovirus|162145 -KPAVGVYHIV ->32738|Liver stage antigen|Q25893|Plasmodium falciparum|5833 -KPIVQYDNF ->32741|circumsporozoite protein|ABF83988.1|Plasmodium falciparum|5833 -KPKDELDY ->32939|polyprotein|AAK67712.1|Dengue virus 2|11060 -KPWDIIPMV ->32940|polyprotein|ABG75765.1|Dengue virus type 1 Hawaii|10000440 -KPWDVIPMV ->32941|DEN polyprotein|AAC40835.1|Dengue virus 2|11060 -KPWDVLPMV ->32942|Polyprotein|Q9J8D4|Dengue virus 2|11060 -KPWDVLPTV ->32943|polyprotein|AAL96681.1|Dengue virus 2|11060 -KPWDVVPMV ->32944|polyprotein|AAW51418.1|Dengue virus 3|11069 -KPWDVVPTV ->32955|P protein|P31870.1|Hepatitis B virus|10407 -KQAFTFSPTYKAFLC ->32998|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 -KQIKVRVDMVR ->33245|60 kDa chaperonin|P48219.1|Yersinia enterocolitica|630 -KRVVINKDT ->33250|gag protein|ABO73990.1|Human immunodeficiency virus 1|11676 -KRWIILGLNK ->33362|Circumsporozoite protein|Q27325|Plasmodium falciparum|5833 -KSKDELDY ->33381|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 -KSKKTPMGF ->33382|polyprotein|AAB67037.1|Hepatitis C virus|11103 -KSKKTPMGFSYDTRC ->33502|envelope glycoprotein E|NP_044538.1|Human alphaherpesvirus 2|10310 -KSRRPLTTF ->33576|polyprotein|ABG67747.1|West Nile virus|11082 -KSYETEYPK ->33618|pol protein|ACJ76655.1|Human immunodeficiency virus 1|11676 -KTAVQMAVF ->33681|||| -KTGGPAIYKR ->33749|nonstructural protein 4B|YP_001527886.1|West Nile virus NY-99|10000971 -KTKSDISSLFGQRIEVK ->33856|polyprotein|BAA03375.1|Hepatitis C virus|11103 -KTSERSQPR ->33912|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 -KTWADEYLCV ->33979|fusion protein|ABQ58820.1|Human metapneumovirus|162145 -KVEGEQHVIK ->34027|DNA polymerase|CAA10434.1|Hepatitis B virus|10407 -KVGNFTGLY ->34101|X protein|ACH95876.1|Hepatitis B virus|10407 -KVLHKRTLGL ->34251|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 -KVVSLVILA ->34304|Gag polyprotein|P88150|Human immunodeficiency virus 1|11676 -KWIILGLNKIVRMY ->34482|gag polyprotein|BAA00992.1|Human immunodeficiency virus 1|11676 -KYKLKHIVW ->34598|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 -KYSPFRNGYMEPTLG ->34605|NS3 protein|Q3LXL6|Dengue virus 3|11069 -KYTDRKWCF ->34616|pol protein|BAA32832.1|Hepatitis B virus|10407 -KYTSFPWLL ->34637|Polyprotein|Q9IZA3|Hepatitis C virus subtype 2a|31649 -KYVQMALLAL ->34642|methionine sulfoxide reductase B|YP_169878.1|Francisella tularensis subsp. tularensis SCHU S4|177416 -KYWNNHRQGI ->34671|polyprotein|NP_671491.1|Hepatitis C virus|11103 -LAAKLVALGINAVAY ->34918|polyprotein precursor|AAG45435.1|Dengue virus 4|11070 -LAPTRVVAAEME ->35237|nonstructural protein 3|NP_722463.1|Dengue virus type 1 Hawaii|10000440 -LDNINTPEGIIPALFEPERE ->35238|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 -LDNINTPEGIIPSMF ->35407|polyprotein|ACE82359.1|Hepatitis C virus subtype 1a|31646 -LEDRDRSEL ->35568|Polyprotein|Q9J8D4|Dengue virus 2|11060 -LEKTKKDL ->35785|14 kDa antigen|P0A5B7.2|Mycobacterium tuberculosis|1773 -LFAAFPSFA ->35844|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 -LFGYPVYV ->35845|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 -LFGYPVYVF ->36062|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 -LGALTGTYVYNHLTPLRDWA ->36102|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 -LGFGAYMSK ->36306|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 -LGRMNCSYENMTALE ->36345|polyprotein|ABR25251.1|Hepatitis C virus (isolate H77)|63746 -LGVPPLRAWR ->36352|Polyprotein|P90247|Hepatitis C virus|11103 -LGWAGWLLSPRGSRPSWGPT ->36357|ELAV-like protein 4 (Paraneoplastic encephalomyelitis antigen HuD) (Hu-antigen D)|P26378.1|Homo sapiens|9606 -LGYGFVNYI ->36358|ELAV-like protein 1|Q15717.2|Homo sapiens|9606 -LGYGFVNYV ->36402|P protein|Q05486.1|Hepatitis B virus|10407 -LHLYSHPIILGFRKI ->36432|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 -LHTDFEQVM ->36504|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 -LIFCHSKKK ->36563|Accessory protein p30II|P0C214.1|Human T-lymphotropic virus 1|11908 -LIISPLPRV ->36599|putative D-ribose-binding protein|NP_301386.1|Mycobacterium leprae|1769 -LILGLLPAI ->36621|glycoprotein gp35/37|AAC59622.1|Human gammaherpesvirus 8|37296 -LILYLCVPRCRRKKP ->36676|polyprotein|BAA09073.1|Hepatitis C virus subtype 1b|31647 -LIRACMLVR ->36688|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 -LIRLKPTL ->36717|nonstructural protein 4B|YP_001527886.1|West Nile virus NY-99|10000971 -LITAAAVTLWENGASSVW ->36723|Spike glycoprotein precursor|P15423.1|Human coronavirus 229E|11137 -LITGRLAAL ->36724|Spike glycoprotein precursor|P59594.1|SARS coronavirus|227859 -LITGRLQSL ->37073|sporozoite surface protein 2|NP_705260.1|Plasmodium falciparum 3D7|36329 -LLACAGLAY ->37074|sporozoite surface protein 2|NP_705260.1|Plasmodium falciparum 3D7|36329 -LLACAGLAYK ->37079|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -LLADARVCSC ->37097|polyprotein|AAY82030.1|Hepatitis C virus genotype 1|41856 -LLALLSCLTV ->37115|Circumsporozoite|SRC280011|Plasmodium falciparum|5833 -LLAVSSILLL ->37120|Major surface antigen precursor|P17399.3|Hepatitis B virus|10407 -LLCLIFLLV ->37127|polyprotein|AAY82030.1|Hepatitis C virus genotype 1|41856 -LLCPAGHAV ->37136|Genome polyprotein|P27958.3|Hepatitis C virus|11103 -LLCPTGHAV ->37140|Hypothetical protein esxG (PE family protein)|O53692.1|Mycobacterium tuberculosis|1773 -LLDAHIPQL ->37146|6 kDa early secretory antigenic target|P0A564.2|Mycobacterium tuberculosis|1773 -LLDEGKQSL ->37153|Nuclear antigen EBNA-3C|Q69140.1|Human gammaherpesvirus 4|10376 -LLDFVRFMGV ->37170|Major surface antigen precursor|P12934.3|Hepatitis B virus|10407 -LLDPRVRGL ->37181|core|CAA59522.1|Hepatitis B virus|10407 -LLDTASALY ->37187|surface antigen|BAF44879.1|Hepatitis B virus|10407 -LLDYQGMLPV ->37246|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 -LLFEEYTNI ->37251|||| -LLFGHPVYV ->37253|||| -LLFGYAVYV ->37254|||| -LLFGYPRYV ->37255|||| -LLFGYPVAV ->37257|Protein Tax-1|P03409.2|Human T-lymphotropic virus 1|11908 -LLFGYPVYV ->37273|Genome polyprotein|P26664.3|Hepatitis C virus (isolate 1)|11104 -LLFLLLADA ->37286|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 -LLFNILGGWV ->37317|Genome polyprotein|P26662.3|Hepatitis C virus (isolate Japanese)|11116 -LLGCIITSL ->37347|Sialidase 85-1.1 precursor|P18269.2|Trypanosoma cruzi|5693 -LLGLWGLATA ->37350|trans-sialidase|XP_818394.1|Trypanosoma cruzi|5693 -LLGLWGTAAL ->37351|trans-sialidase, putative|EAN81560.1|Trypanosoma cruzi|5693 -LLGLWVFAAL ->37364|P53_HUMAN Cellular tumor antigen p53 (Tumor suppressor p53) (Phosphoprotein p53) (Antigen NY-CO-13)|P04637.2|Homo sapiens|9606 -LLGRNSFEV ->37397|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 -LLHTDFEQV ->37398|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 -LLHTDFEQVM ->37453|polyprotein|BAD73987.1|Hepatitis C virus subtype 1b|31647 -LLKRLHQWI ->37466|surface antigen|BAF44879.1|Hepatitis B virus|10407 -LLLCLIFLL ->37473|Nucleoprotein|P59595.1|SARS coronavirus|227859 -LLLDRLNQL ->37498|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 -LLLGLWGTAA ->37507|Large T antigen|P03071.1|Human polyomavirus 1|1891762 -LLLIWFRPV ->37511|||| -LLLKATLCI ->37536|Spike glycoprotein precursor|P15423.1|Human coronavirus 229E|11137 -LLLNCLWSV ->37573|E7 protein|ABL96585.1|Human papillomavirus type 16|333760 -LLMGTLGIV ->37590|VP1|BAF93325.1|Human polyomavirus 1|1891762 -LLMWEAVTV ->37607|kaposin|AAC57155.1|Human gammaherpesvirus 8|37296 -LLNGWRWRL ->37685|polyprotein|BAA03375.1|Hepatitis C virus|11103 -LLPRRGPRL ->37700|vimentin|NP_003371.1|Homo sapiens|9606 -LLQDSVDFSL ->37738|polyprotein|AAA45534.1|Hepatitis C virus (isolate Taiwan)|31645 -LLREEVSFRV ->37769|Latent membrane protein 2|Q69135|Human gammaherpesvirus 4|10376 -LLSAWILTA ->37830|polyprotein|BAB18806.1|Hepatitis C virus subtype 1b|31647 -LLSTTEWQI ->37877|cysteine proteinase cruzipain (EC 3.4.22.-) - Trypanosoma cruzi|A45629|Trypanosoma cruzi|5693 -LLTTSGVSA ->37919|envelope protein|BAF48755.1|Hepatitis B virus|10407 -LLVPFVQWFV ->37960|membrane protein|AAA45887.1|Human gammaherpesvirus 4|10376 -LLWTLVVLL ->37970|tax|AAG48731.1|Human T-lymphotropic virus 2|11909 -LLYGYPVYV ->37991|polyprotein|AAY82034.1|Hepatitis C virus genotype 1|41856 -LMALTLSPYYKRY ->38052|Glycoprotein GP85 precursor|P03231.1|Human gammaherpesvirus 4|10376 -LMIIPLINV ->38082|cysteine proteinase cruzipain (EC 3.4.22.-) - Trypanosoma cruzi|A45629|Trypanosoma cruzi|5693 -LMNNAFEWI ->38083|cysteine proteinase cruzipain (EC 3.4.22.-) - Trypanosoma cruzi|A45629|Trypanosoma cruzi|5693 -LMNNAFEWIV ->38152|L-aspartate oxidase|YP_170403.1|Francisella tularensis subsp. tularensis SCHU S4|177416 -LMWDNVGLV ->38400|polyprotein|ABG75765.1|Dengue virus 1|11053 -LPAIVREAI ->38427|BZLF1|AAA66529.1|Human gammaherpesvirus 4|10376 -LPCVLWPVL ->38446|Glycoprotein B precursor (Glycoprotein II)|P09257.1|Human alphaherpesvirus 3|10335 -LPEGMDPFAEK ->38466|nucleocapsid protein|ABF21284.1|Influenza A virus (A/Iran/1/1957(H2N2))|488233 -LPFDKPTIM ->38468|nucleoprotein|CAA24268.1|Influenza A virus (A/Puerto Rico/8/1934(H1N1))|211044 -LPFDRTTIM ->38471|nucleocapsid protein|ABC46569.1|Influenza A virus (A/Memphis/4/1980(H3N2))|383578 -LPFEKSTVM ->38472|nucleoprotein|AAV48837.1|Influenza A virus (A/Brevig Mission/1/1918(H1N1))|88776 -LPFERATIM ->38494|polyprotein|BAA03375.1|Hepatitis C virus|11103 -LPGCSFSIF ->38556|Genome polyprotein|Q00269.3|Hepatitis C virus|11103 -LPKLPGVPF ->38701|core protein|AAL31859.1|Hepatitis B virus|10407 -LPSDFFPSV ->38724|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 -LPSTLRWFFNLFQLYRGPLD ->38851|Trans-activator protein BZLF1|P03206.2|Human herpesvirus 4 strain B95-8|10377 -LQHYREVAA ->38922|6 kDa early secretory antigenic target|P0A564.2|Mycobacterium tuberculosis|1773 -LQNLARTI ->38974|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 -LQRGPQYSEHP ->39095|nonstructural protein 3|NP_722463.1|Dengue virus type 1 Hawaii|10000440 -LRGEARKTFVELMRR ->39162|gag protein|AAV53308.1|Human immunodeficiency virus 1|11676 -LRPGGKKKYKLKHIV ->39339|Nucleocapsid protein|Q89462|Sin Nombre hantavirus|37705 -LSFALPIILKALYML ->39571|polyprotein|BAD73987.1|Hepatitis C virus subtype 1b|31647 -LSPRPVSYLK ->39589|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 -LSPYYKRYIS ->39590|polyprotein|AAY82030.1|Hepatitis C virus|11103 -LSPYYKRYISW ->39591|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 -LSPYYKRYISWCLWWLQYFL ->40158|polyprotein|AAA45534.1|Hepatitis C virus|11103 -LTRVEAQLHVWVPPL ->40210|polyprotein|ABR25251.1|Hepatitis C virus (isolate H77)|63746 -LTTSQTLLF ->40247|polyprotein precursor|NP_041724.2|West Nile virus|11082 -LTYRHKVVK ->40253|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 -LVACHANCPTYRSHL ->40262|Cytochrome P450 2A7|P20853.1|Homo sapiens|9606 -LVALLACLTV ->40264|Cytochrome P450 2A6|P11509.3|Homo sapiens|9606 -LVALLVCLTV ->40286|SAG1 protein|AAO72426.1|Toxoplasma gondii RH|383379 -LVCGKDGVK ->40288|kaposin|AAC57155.1|Human gammaherpesvirus 8|37296 -LVCLLAISVVPPSGQ ->40447|Major surface antigen precursor|P12934.3|Hepatitis B virus|10407 -LVLLDYQGML ->40468|structural protein|BAA00705.1|Hepatitis C virus subtype 1a|31646 -LVMAQLLRI ->40470|Genome polyprotein|SRC279960|Hepatitis C virus|11103 -LVMAQLLRT ->40559|polyprotein|ADF97231.1|Hepatitis C virus subtype 3a|356426 -LVRLKPTL ->40624|DNA polymerase|CAA10434.1|Hepatitis B virus|10407 -LVVDFSQFSR ->40637|polyprotein|BAA03375.1|Hepatitis C virus|11103 -LVVSQLLRI ->40664|core|CAA59522.1|Hepatitis B virus|10407 -LWFHISCLTF ->40784|Genome polyprotein|P26662.3|Hepatitis C virus|11103 -LYGVWPLLL ->41082|Genome polyprotein|P26664.3|Hepatitis C virus (isolate 1)|11104 -MALTLSPY ->41085|polyprotein|ABR25251.1|Hepatitis C virus|11103 -MALYDVVSKLPLAVM ->41093|polyprotein|AGO67248.1|Dengue virus 2|11060 -MANIFRGSY ->41174|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 -MAYAQKIFKIL ->41269|kaposin|AAC57155.1|Human gammaherpesvirus 8|37296 -MDRGLTVFVAVHVPD ->41407|Envelope protein|NP_739583.2|Dengue virus 2|11060 -MENKAWLVHRQWFLD ->41482|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 -MFDSSVLCECYDAGC ->41622|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 -MGRSHFLCTFTFNSNNKEYT ->41898|polyprotein|AAF01178.1|Hepatitis C virus subtype 2a|31649 -MLAAQMFIV ->41971|putative D-ribose-binding protein|NP_301386.1|Mycobacterium leprae|1769 -MLILGLLPAILPACG ->42094|telomer length regulation protein TEL1|EDV12172.1|Saccharomyces cerevisiae|4932 -MLWGYLQYV ->42152|polyprotein|AAY82055.1|Hepatitis C virus (isolate H77)|63746 -MMMNWSPTT ->42290|protein antigen|AAA29733.1|Plasmodium falciparum|5833 -MPLETQLAI ->42295|Circumsporozoite protein precursor|P02893.1|Plasmodium falciparum|5833 -MPNDPNRNV ->42299|nonstructural protein 3|YP_001527884.1|West Nile virus|11082 -MPNGLIAQF ->42342|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 -MPVGGQSSF ->42430|Major surface antigen precursor|P03141.3|Hepatitis B virus|10407 -MQWNSTAFHQTLQDP ->42455|Probable Na(+)-translocating NADH-quinone reductase subunit A|O84639.1|Chlamydia trachomatis|813 -MRDHTITLL ->42672|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 -MSSTQIRTEIPVALL ->42737|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 -MTALEAVSLNGTRLA ->42797|6 kDa early secretory antigenic target|P0A564.2|Mycobacterium tuberculosis|1773 -MTEQQWNFAGIEAAASAIQG ->42819|polyprotein precursor|NP_041724.2|West Nile virus|11082 -MTKEEFTRY ->42897|RNA polymerase beta-subunit|AAA21416.1|Mycobacterium tuberculosis|1773 -MTYAAPLFV ->43089|Polyprotein|Q9IZA3|Hepatitis C virus subtype 2a|31649 -MYSSAEGDL ->43108|Major outer membrane porin, serovar E precursor|P17451.1|Chlamydia trachomatis|813 -NAACMALNI ->43310|polyprotein|AAW78019.1|Hepatitis C virus (isolate H77)|63746 -NASRCWVAM ->43447|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 -NDGVIFFFNPGELLPEAAGP ->43619|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -NEGCGWAGW ->43621|largest ORF|AAB02128.1|Hepatitis C virus (isolate H77)|63746 -NEGCGWMGW ->43624|Genome polyprotein|P26660.3|Hepatitis C virus isolate HC-J6|11113 -NEGLGWAGW ->43627|core protein|AAX68853.1|Hepatitis C virus subtype 1b|31647 -NEGLGWTGW ->43628|polyprotein|BAA03375.1|Hepatitis C virus subtype 1b|31647 -NEGMGWAGW ->43756|Genome polyprotein|SRC279960|Hepatitis C virus subtype 2a|31649 -NETCGWAGW ->43937|polyprotein|AAF01178.1|Hepatitis C virus subtype 2a|31649 -NFTRGDRCNL ->44133|Genome polyprotein|P26664.3|Hepatitis C virus genotype 1|41856 -NHDSPDAEL ->44214|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 -NIEFFTKNSAF ->44327|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis H37Rv|83332 -NIRQAGVQY ->44649|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 -NLAMAIAKSVPVYGM ->44653|6 kDa early secretory antigenic target|P0A564.2|Mycobacterium tuberculosis|1773 -NLARTISEAGQAMASTEGNV ->44802|PE-PGRS family protein|ZP_02552202.1|Mycobacterium tuberculosis|1773 -NLLVTGFDT ->44833|polyprotein|BAA03375.1|Hepatitis C virus subtype 1a|31646 -NLPGCSFSI ->44920|tegument protein pp65|YP_002608275.1|Human betaherpesvirus 5|10359 -NLVPMVATV ->44976|Major outer membrane porin, serovar A precursor|P23732.1|Chlamydia trachomatis|813 -NMFTPYIGV ->45374|nucleocapsid protein|AEQ63625.1|Respiratory syncytial virus|12814 -NPKASLLSL ->45652|Probable ATP-dependent Clp protease ATP-binding subunit|O84288.1|Chlamydia trachomatis|813 -NRAKQVIKL ->45672|hypothetical protein CT847|NP_220368.1|Chlamydia trachomatis|813 -NRELIQQEL ->45677|Probable outer membrane protein pmpC precursor|O84419.1|Chlamydia trachomatis|813 -NRFSVAYML ->45749|glycoprotein gp35/37|AAC59622.1|Human gammaherpesvirus 8|37296 -NRVPFSATTTTTRGR ->46243|E2 protein|NP_751921.1|Hepatitis C virus (isolate H77)|63746 -NTRPPLGNWF ->46480|DNA polymerase|CAA10434.1|Hepatitis B virus|10407 -NVSIPWTHK ->46499|6 kDa early secretory antigenic target|P0A564.2|Mycobacterium tuberculosis|1773 -NVTSIHSLL ->46575|polyprotein|AAG30730.1|Dengue virus 2|11060 -NYADRKWCF ->46576|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 -NYADRRWCF ->46625|hypothetical glycine-rich protein Rv3812 - Mycobacterium tuberculosis (strain H37RV)|H70520|Mycobacterium tuberculosis|1773 -NYIPQQLAL ->46672|Periplasmic L-asparaginase II precursor|YP_169502.1|Francisella tularensis subsp. tularensis SCHU S4|177416 -NYNNLDDKF ->46713|Polyprotein|Q9IZA3|Hepatitis C virus subtype 2a|31649 -NYTIFKIRM ->46755|HCV-1|AAA45676.1|Hepatitis C virus genotype 1|41856 -PAAYAAQGYKVLVLNPSVAA ->46931|||| -PARLLLKATLCIPHV ->47005|RL2|CAB06705.1|Human alphaherpesvirus 2|10310 -PAWSRRTLL ->47017|Genome polyprotein|P26664.3|Hepatitis C virus genotype 1|41856 -PCEPEPDVAVL ->47760|EBNA-1 protein|Q777E1|Human gammaherpesvirus 4|10376 -PGTGPGNGLGEKGDT ->47854|Glycoprotein I precursor (Glycoprotein IV) (GI) (GPIV)|P09258.1|Human alphaherpesvirus 3|10335 -PHSVVNPFVK ->47946|envelope glycoprotein|AAC28452.1|Human immunodeficiency virus 1|11676 -PIPIHYCAPAGFAILKCNNK ->48321|||| -PLFGYPVYV ->48458|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 -PLPVVFPIVQGELSKQTGQQ ->48836|EBNA-1 protein|Q777E1|Human gammaherpesvirus 4|10376 -PPMVEGAAAEGDDGD ->48896|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 -PPQPEYDLELITSCS ->48915|kaposin|AAC57155.1|Human gammaherpesvirus 8|37296 -PPSGQRGPVAFRTRV ->49485|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 -PSQEPMSIYVY ->49831|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 -PVALLILCLCLVACH ->50089|Genome polyprotein|P26662.3|Hepatitis C virus|11103 -PYFVRAQGLI ->50104|polyprotein|BAA25076.1|Hepatitis C virus|11103 -PYIEQGMQL ->50124|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 -PYKRIEELL ->50130|membrane protein|AAA45887.1|Human gammaherpesvirus 4|10376 -PYLFWLAAIA ->50253|DNA polymerase|CAA10434.1|Hepatitis B virus|10407 -QAFTFSPTYK ->50292|gag protein|ACR27140.1|Human immunodeficiency virus 1|11676 -QAISPRTLNAW ->50298|EBNA3A nuclear protein|Q8AZJ8|Human gammaherpesvirus 4|10376 -QAKWRLQTL ->50586|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 -QEFFWDANDIY ->50596|polyprotein|ABG75765.1|Dengue virus 1|11053 -QEGAMHTAL ->50779|N protein|AAP13445.1|SARS coronavirus Urbani|228330 -QFKDNVILL ->50894|Genome polyprotein|P27909.2|Dengue virus type 1 Hawaii|10000440 -QGKRLEPSWASVKKDLISYG ->51089|UL123; IE1|AAR31390.1|Human betaherpesvirus 5|10359 -QIKVRVDMV ->51104|LOW MOLECULAR WEIGHT PROTEIN ANTIGEN 7 ESXH (10 kDa ANTIGEN) (CFP-7) (PROTEIN TB10.4)|CAA17363.1|Mycobacterium tuberculosis H37Rv|83332 -QIMYNYPAM ->51250|nucleocapsid protein|ABI96968.1|SARS coronavirus|227859 -QKRTATKQYNVTQAF ->51311|X protein|ABR68906.1|Hepatitis B virus|10407 -QLDPARDVL ->51342|myosin-9|NP_002464.1|Homo sapiens|9606 -QLFNHTMFI ->51346|Genome polyprotein|P29846.3|Hepatitis C virus|11103 -QLFTFSPRR ->51351|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 -QLGAFLTNV ->51388|polyprotein|AGO67248.1|Dengue virus 2|11060 -QLKGMSYSM ->51410|hypothetical protein ML1057|NP_301777.1|Mycobacterium leprae|1769 -QLLGQTADV ->51526|HCV-1|AAA45676.1|Hepatitis C virus|11103 -QLRRHIDLLV ->51528|Genome polyprotein|SRC279960|Hepatitis C virus genotype 1|41856 -QLRRIDLLV ->51532|polyprotein|AAA45534.1|Hepatitis C virus|11103 -QLSAPSLKATCTANH ->51562|polyprotein|AGO67248.1|Dengue virus 2|11060 -QLTYVVIAIL ->51604|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 -QMDYSNGLFV ->51643|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 -QMSDPAYNINISLPSYYPDQ ->51685|Nuclear antigen EBNA-3C|Q69140.1|Human gammaherpesvirus 4|10376 -QNGALAINTF ->51805|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 -QPEKGGRKPA ->51946|EBNA3C latent protein|CAD53421.1|Human gammaherpesvirus 4|10376 -QPRAPIRPI ->51947|EBNA3C latent protein|CAD53421.1|Human gammaherpesvirus 4|10376 -QPRAPIRPIPT ->52287|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 -QSALKLAIYK ->52431|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 -QSSFYSDWY ->52496|polyprotein precursor|NP_041724.2|West Nile virus|11082 -QTDNQLAVF ->52509|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 -QTFLATCINGVCWTV ->52578|liver stage antigen-1|CAA82974.1|Plasmodium falciparum|5833 -QTNFKSLLR ->52652|||| -QTTVVGGSQSHTVRGLTSLFSPGASQN ->52666|Antigen 85-B|P0C5B9.1|Mycobacterium tuberculosis|1773 -QTYKWETFL ->52746|Nucleoprotein|P03418.1|Human respiratory syncytial virus A2|11259 -QVMLRWGVL ->52760|nef protein|ACR27174.1|Human immunodeficiency virus 1|11676 -QVPLRPMTYK ->52886|pp65|AAA45994.1|Human betaherpesvirus 5|10359 -QYDPVAALF ->52888|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 -QYDPVAALFFF ->53027|nonstructural protein 3|NP_722463.1|Dengue virus 1 Singapore/S275/1990|33741 -QYSDRRWCF ->53041|phosphorylated matrix protein (pp65)|AAA45996.1|Human betaherpesvirus 5|10359 -QYTPDSTPCHR ->53077|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis|1773 -RADEEQQQAL ->53114|envelope glycoprotein|ABI16336.1|Human immunodeficiency virus 1|11676 -RAIEAQQHL ->53128|BZLF1|AAA66529.1|Human gammaherpesvirus 4|10376 -RAKFKQLL ->53129|BZLF1|AAA66529.1|Human gammaherpesvirus 4|10376 -RAKFKQLLQ ->53148|Transcription activator BRLF1|P03209.1|Human herpesvirus 4 strain B95-8|10377 -RALIKTLPRASYSSH ->53201|Fusion glycoprotein F0 precursor|P03420.1|Human respiratory syncytial virus A2|11259 -RARRELPRF ->53246|polyprotein precursor|AAF20092.2|West Nile virus|11082 -RAWNSGYEW ->53341|envelope protein|YP_001527880.1|West Nile virus NY-99|10000971 -RDFLEGVSGATWVDLVL ->53370|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 -RDKFLSAATSSTPREAPYEL ->53405|||| -RDPAKPARLLLKATL ->53437|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 -RDWAHNGL ->53476|polyprotein|AGO67248.1|Dengue virus 2|11060 -REDQWCGSL ->53541|Genome polyprotein|P26664.3|Hepatitis C virus (isolate 1)|11104 -REISVPAEIL ->53953|kaposin|AAC57155.1|Human gammaherpesvirus 8|37296 -RGPVAFRTRVATGAH ->54175|envelope glycoprotein|ACR43875.1|Human immunodeficiency virus 1|11676 -RIKQIINMW ->54176|Polyprotein|Q9J8D4|Dengue virus 2|11060 -RIKQKGIL ->54330|BZLF1|AAA66529.1|Human gammaherpesvirus 4|10376 -RKCRAKFKQLLQH ->54342|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 -RKEVNSQLSLGDPLFPELAE ->54501|nonstructural protein 2B|YP_001527883.1|West Nile virus NY-99|10000971 -RLDDDGNFQL ->54504|possible regulatory protein|NP_302009.1|Mycobacterium leprae|1769 -RLDGTTLEV ->54568|polyprotein|BAA03375.1|Hepatitis C virus|11103 -RLGVRATRK ->54587|monooxygenase family protein|YP_170175.1|Francisella tularensis subsp. tularensis SCHU S4|177416 -RLIGHISTL ->54605|HCV-1|AAA45676.1|Hepatitis C virus|11103 -RLIVFPDLGV ->54650|polyprotein|AAU89634.1|Hepatitis C virus subtype 2a|31649 -RLLLLGLLLL ->54654|trans-sialidase|XP_816729.1|Trypanosoma cruzi|5693 -RLLPSLLLLL ->54662|pX-rex-orf I {alternatively spliced}|AAB23359.1|Human T-lymphotropic virus 1|11908 -RLLSPLSPL ->54664|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 -RLLSPTTIV ->54680|Spike glycoprotein precursor|P59594.1|SARS coronavirus|227859 -RLNEVAKNL ->54686|Major outer membrane porin, serovar E precursor|P17451.1|Chlamydia trachomatis|813 -RLNMFTPYI ->54690|Nucleoprotein|P59595.1|SARS coronavirus|227859 -RLNQLESKV ->54704|hydrolase|WP_015628351.1|Mycobacterium tuberculosis|1773 -RLPLVLPAV ->54706|matrix protein 2-1|AAS22094.1|Human metapneumovirus|162145 -RLPREKLKK ->54709|protein F [Hepatitis C virus subtype 1b]|ACA50643.1|Hepatitis C virus (isolate Japanese)|11116 -RLPSGRNLV ->54728|EBNA3A nuclear protein|Q8AZJ8|Human gammaherpesvirus 4|10376 -RLRAEAQVK ->54730|envelope glycoprotein|AAB06256.1|Human immunodeficiency virus 1|11676 -RLRDLLLIVTR ->54741|gag polyprotein|BAA00992.1|Human immunodeficiency virus 1|11676 -RLRPGGKKK ->54797|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 -RLTVSGLAWTR ->54819|JK3|CAA43789.1|Hepatitis C virus|11103 -RLWHYPCTA ->54820|polyprotein precursor|BAA02756.1|Hepatitis C virus|11103 -RLWHYPCTF ->54821|E2 protein|AAM33354.1|Hepatitis C virus subtype 1a|31646 -RLWHYPCTI ->54824|polyprotein precursor|BAA01583.1|Hepatitis C virus|11103 -RLWHYPCTL ->54825|polyprotein|BAA03375.1|Hepatitis C virus|11103 -RLWHYPCTV ->54903|Genome polyprotein|P26663.3|Hepatitis C virus|11103 -RMILMTHFF ->54965|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 -RMYVGGVEHR ->55029|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 -RNLVPMVATVQ ->55102|polyprotein precursor|NP_041724.2|West Nile virus|11082 -RPAADGKTV ->55184|Nucleoprotein|P41269.1|Puumala hantavirus|11604 -RPKHLYVSM ->55226|HCV-1|AAA45676.1|Hepatitis C virus|11103 -RPLTDFDQGW ->55251|Epstein-Barr nuclear antigen 3|SRC279942|Human gammaherpesvirus 4|10376 -RPPIFIRLL ->55252|EBNA3A nuclear protein|Q8AZJ8|Human gammaherpesvirus 4|10376 -RPPIFIRRL ->55253|EBNA3A nuclear protein|Q8AZJ8|Human gammaherpesvirus 4|10376 -RPPIFIRRLH ->55295|Early antigen protein D|P03191.1|Human herpesvirus 4 strain B95-8|10377 -RPQGGSRPEFVKL ->55320|tegument protein VP22|NP_044519.1|Human alphaherpesvirus 2|10310 -RPRGEVRFL ->55336|EBNA-1|YP_401677.1|Human gammaherpesvirus 4|10376 -RPSCIGCKGTHGGTG ->55526|glycoprotein D|AAB60552.1|Human alphaherpesvirus 2|10310 -RRAQMAPKR ->55620|EBNA3C latent protein|CAD53421.1|Human gammaherpesvirus 4|10376 -RRIYDLIEL ->55683|nucleocapsid protein|ABI96968.1|SARS coronavirus|227859 -RRPQGLPNNTASWFT ->55709|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 -RRRGDSRGSLLSPRP ->55718|Probable membrane glycoprotein precursor|P03218.1|Human herpesvirus 4 strain B95-8|10377 -RRRKGWIPL ->55734|membrane protein|AAA45887.1|Human gammaherpesvirus 4|10376 -RRRWRRLTV ->55744|polyprotein precursor|NP_041724.2|West Nile virus|11082 -RRSRRSLTV ->55779|fusion protein|BAB60865.1|Measles virus|11234 -RRYPDAVYL ->55881|polyprotein precursor|NP_041724.2|West Nile virus|11082 -RSLFGGMSW ->56198|glycoprotein gp35/37|AAC59622.1|Human gammaherpesvirus 8|37296 -RTTRIRVSPVAENGR ->56247|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 -RVCEKMALY ->56310|polyprotein|AGO67248.1|Dengue virus 2|11060 -RVIDPRRCMK ->56343|structural protein|BAA00705.1|Hepatitis C virus|11103 -RVLEDGVNYA ->56344|polyprotein precursor|NP_041724.2|West Nile virus|11082 -RVLEMVEDW ->56390|Transcription activator BRLF1|P03209.1|Human herpesvirus 4 strain B95-8|10377 -RVRAYTYSK ->56502|polyprotein|BAD73994.1|Hepatitis C virus subtype 1b|31647 -RYAPACKPL ->56574|envelope glycoprotein|ABI16336.1|Human immunodeficiency virus 1|11676 -RYLKDQQLL ->56589|polyprotein precursor|NP_041724.2|West Nile virus|11082 -RYLVKTESW ->56620|Nef protein|Q9YYU8|Human immunodeficiency virus 1|11676 -RYPLTFGWCF ->56646|nucleocapsid protein|AAA43837.1|Hantaan virus 76-118|11602 -RYRTAVCGL ->56650|EBNA3A nuclear protein|Q8AZJ8|Human gammaherpesvirus 4|10376 -RYSIFFDY ->56814|DNA polymerase|CAA10434.1|Hepatitis B virus|10407 -SAICSVVRR ->56861|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 -SALKLAIYKA ->57313|Polyprotein|Q9IZA3|Hepatitis C virus|11103 -SDWAANGL ->57361|Genome polyprotein|SRC279960|Hepatitis C virus (isolate H77)|63746 -SECCTPCSGSW ->57364|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -SECTTPCSGSW ->57438|gag protein|ABO73990.1|Human immunodeficiency virus 1|11676 -SEGATPQDL ->57560|BZLF1|AAA66529.1|Human gammaherpesvirus 4|10376 -SENDRLRLL ->57591|Cobalamin (vitamin B12) synthesis protein/P47K family protein|YP_169986.1|Francisella tularensis subsp. tularensis SCHU S4|177416 -SEPLPVATTF ->57628|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 -SESSFFNLI ->57703|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 -SEYPNVSVSVEDTSA ->57723|polyprotein|CAB53095.1|Hepatitis C virus|11103 -SFAIKWEYVL ->57790|Protein Tax-1|P03409.2|Human T-lymphotropic virus 1|11908 -SFHSLHLLF ->57828|Protein Tax-1|P03409.2|Human T-lymphotropic virus 1|11908 -SFLLSHGLI ->57893|polyprotein|BAA03375.1|Hepatitis C virus|11103 -SFSIFLLAL ->57894|polyprotein|BAD73987.1|Hepatitis C virus subtype 1b|31647 -SFSIFLLALL ->57986|envelope glycoprotein|AAK62756.1|West Nile virus|11082 -SGATWVDLV ->57987|envelope protein|YP_001527880.1|West Nile virus NY-99|10000971 -SGATWVDLVLEGDSCVTI ->58122|pol protein|BAA32832.1|Hepatitis B virus|10407 -SGLPRYVARL ->58249|glycoprotein gp35/37|AAC59622.1|Human gammaherpesvirus 8|37296 -SGSYSSGEPSRTTRI ->58446|pX-rex-orf I|SRC240587|Human T-lymphotropic virus 1|11908 -SIAINPQLL ->58463|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 -SICPSQEPMSIYVYALPLKM ->58721|VP1|BAB68863.1|JC polyomavirus|10632 -SITEVECFL ->58740|Major surface antigen precursor|P03142.4|Hepatitis B virus|10407 -SIVSPFIPLL ->59020|Genome polyprotein|P29846.3|Hepatitis C virus (isolate Taiwan)|31645 -SLASLFTQGA ->59021|polyprotein|AAN40570.2|Hepatitis C virus|11103 -SLASLFTSGA ->59044|Major outer membrane porin, serovar E precursor|P17451.1|Chlamydia trachomatis|813 -SLDQSVVEL ->59088|polyprotein precursor|NP_041724.2|West Nile virus|11082 -SLFGGMSWI ->59089|nonstructural protein 4B|YP_001527886.1|West Nile virus NY-99|10000971 -SLFGQRIEV ->59090|nonstructural protein 4B|YP_001527886.1|West Nile virus NY-99|10000971 -SLFGQRIEVKENFSMGEF ->59141|Circumsporozoite protein precursor|P08677.2|Plasmodium vivax strain Belem|31273 -SLGLVILLVL ->59153|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 -SLHSYSPGEINRVAA ->59154|polyprotein|AAP55688.1|Hepatitis C virus subtype 2a|31649 -SLHTGFLASL ->59182|attachment glycoprotein|ABQ58821.1|Human metapneumovirus|162145 -SLILIGITTL ->59240|HCV-1|AAA45676.1|Hepatitis C virus genotype 1|41856 -SLLAPGAKQNV ->59336|polyprotein|AAA45534.1|Hepatitis C virus genotype 1|41856 -SLMAFTAAV ->59459|Trans-sialidase|SRC7915|Trypanosoma cruzi|5693 -SLSHYFTLV ->59521|polyprotein|ACB87121.1|Hepatitis C virus subtype 1a|31646 -SLTPPHSAK ->59524|nonstructural protein 4B|YP_001527886.1|West Nile virus NY-99|10000971 -SLTSINVQA ->59551|Glycoprotein GP85 precursor|P03231.1|Human gammaherpesvirus 4|10376 -SLVIVTTFV ->59561|polyprotein precursor|NP_041724.2|West Nile virus|11082 -SLVNGVVRL ->59569|Genome polyprotein|P26662.3|Hepatitis C virus (isolate Japanese)|11116 -SLVSWLSQGP ->59585|polymerase|AAD16253.1|Hepatitis B virus|10407 -SLYADSPSV ->59594|Phosphate transport system permease protein PstA 1|SRC280197|Mycobacterium tuberculosis|1773 -SLYFGGICV ->59612|gag protein|ABI20203.1|Human immunodeficiency virus 1|11676 -SLYNTIAVL ->59613|Gag polyprotein|P03347.3|Human immunodeficiency virus 1|11676 -SLYNTVATL ->59627|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 -SMAGSSAMI ->59709|polyprotein|BAD73987.1|Hepatitis C virus subtype 1b|31647 -SMLTDPSHI ->59722|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 -SMNATLVQA ->59765|Genome polyprotein|SRC279960|Hepatitis C virus|11103 -SMVGNMAKV ->59766|Genome polyprotein|P27958.3|Hepatitis C virus (isolate H)|11108 -SMVGNWAKV ->59767|polyprotein|BAB18806.1|Hepatitis C virus subtype 1a|31646 -SMVGNWAKVL ->59786|Large envelope protein|P03138.3|Hepatitis B virus ayw/France/Tiollais/1979|490133 -SMYPSCCCTK ->59787|Hemagglutinin glycoprotein|P08362.1|Measles virus strain Edmonston|11235 -SMYRVFEVGV ->59975|pol protein|ACJ76655.1|Human immunodeficiency virus 1|11676 -SPAIFQSSM ->60009|Genome polyprotein|P26664.3|Hepatitis C virus genotype 1|41856 -SPDAELIEANL ->60031|SAG1 protein|AAO72426.1|Toxoplasma gondii RH|383379 -SPEKHHCTV ->60059|Genome polyprotein|P27958.3|Hepatitis C virus genotype 1|41856 -SPGEINRVAA ->60092|nucleocapsid protein|ABK96997.1|Human metapneumovirus|162145 -SPKAGLLSL ->60104|polyprotein|AGW21594.1|Dengue virus 1|11053 -SPKRLSAAI ->60238|Gag polyprotein|P03347.3|Human immunodeficiency virus 1|11676 -SPRTLNAWV ->60867|nucleoprotein|CAZ65591.1|Influenza A virus|11320 -SRYWAIRTR ->60931|latent membrane protein 2|AAB59844.1|Human gammaherpesvirus 4|10376 -SSCSSCPLSKI ->61077|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 -SSHSGSFQI ->61622|polyprotein|BAA03375.1|Hepatitis C virus|11103 -STGLIHLHQ ->61741|Core protein|Q9QAC5|Hepatitis B virus|10407 -STLPETTVV ->61745|C protein|CAB41699.1|Hepatitis B virus|10407 -STLPETTVVRR ->61787|HCV-1|AAA45676.1|Hepatitis C virus|11103 -STNPKPQK ->61788|HCV-1|AAA45676.1|Hepatitis C virus|11103 -STNPKPQKK ->61790|polyprotein|BAB18806.1|Hepatitis C virus|11103 -STNPKPQRK ->61861|Nucleoprotein|P03418.1|Human respiratory syncytial virus A2|11259 -STRGGSRVEGIFAG ->62004|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 -STWVLVGGVLAALAA ->62052|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 -SVASSSASQLSA ->62127|cysteine proteinase cruzipain (EC 3.4.22.-) - Trypanosoma cruzi|A45629|Trypanosoma cruzi|5693 -SVFRENLFL ->62139|envelope glycoprotein|AAK62756.1|West Nile virus|11082 -SVGGVFTSV ->62184|nonstructural protein 3|NP_722463.1|Dengue virus type 1 Hawaii|10000440 -SVKKDLISYGGGWRF ->62244|UL123; IE1|AAR31448.1|Human betaherpesvirus 5|10359 -SVMKRRIEEIC ->62305|EBNA3A nuclear protein|Q8AZJ8|Human gammaherpesvirus 4|10376 -SVRDRLARL ->62355|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 -SVTEQSEFYFPRAPLNSNAM ->62367|Genome polyprotein|SRC279960|Hepatitis C virus|11103 -SVTSFFTQGA ->62477|HBsAg protein|ABF71024.1|Hepatitis B virus|10407 -SWLSLLVPF ->62504|HBsAg protein|ABF71024.1|Hepatitis B virus|10407 -SWWTSLNFL ->62564|polyprotein precursor|AAF20092.2|West Nile virus|11082 -SYHDRRWCF ->62616|Chain A, Dengue Virus 4 Ns3 Helicase In Complex With Ssrna|2JLU_A|Dengue virus 4 Thailand/0348/1991|408688 -SYKDREWCF ->62713|polyprotein|AAP55688.1|Hepatitis C virus subtype 2a|31649 -SYSWTGALI ->62731|polyprotein|BAD73987.1|Hepatitis C virus subtype 1b|31647 -SYTWTGALI ->62797|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis|1773 -TAAQAAVVRF ->62799|10 kDa culture filtrate antigen EsxB|NP_218391.1|Mycobacterium tuberculosis H37Rv|83332 -TAAQAAVVRFQEAAN ->62900|viral protein 2|CAG70336.1|Human parvovirus B19|10798 -TAKSRVHPL ->62903|Genome polyprotein|P27909.2|Dengue virus type 1 Hawaii|10000440 -TAKWLWGFLSRNKKPRICTR ->62977|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 -TARHTPVNSW ->63010|6 kDa early secretory antigenic target|P0A564.2|Mycobacterium tuberculosis|1773 -TATELNNALQNLARTISEAG ->63285|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 -TEADVQQWL ->63286|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 -TEADVQQWLTW ->63508|gag protein|AAN03145.1|Human immunodeficiency virus 1|11676 -TERQANFL ->63582|polyprotein precursor|NP_041724.2|West Nile virus|11082 -TEVMTAVGL ->63784|Genome polyprotein|P26663.3|Hepatitis C virus|11103 -TGAPVTYSTY ->63963|HCV-1|AAA45676.1|Hepatitis C virus|11103 -TGSPITYSTY ->64286|polyprotein|AAB70696.1|Dengue virus type 1 Hawaii|10000440 -TIENTTANISLTAIA ->64312|M protein, serotype 5 precursor|P02977.2|Streptococcus pyogenes serotype M5|301449 -TIGTLKKILDETVKDKIA ->64320|Protein E6|P03126.1|Human papillomavirus type 16|333760 -TIHDIILECV ->64404|Genome polyprotein|P26664.3|Hepatitis C virus genotype 1|41856 -TINYTIFK ->64405|polyprotein|ACB87121.1|Hepatitis C virus|11103 -TINYTIFKI ->64412|PE_PGRS 33|AAU10330.1|Mycobacterium tuberculosis|1773 -TIPEALAAV ->64489|polyprotein|BAA03375.1|Hepatitis C virus|11103 -TITTGSPITYS ->64710|Membrane glycoprotein|Q692E0|SARS coronavirus TJF|284672 -TLACFVLAAV ->64727|polyprotein precursor|NP_041724.2|West Nile virus|11082 -TLARGFPFV ->64763|Early antigen protein D|P03191.1|Human herpesvirus 4 strain B95-8|10377 -TLDYKPLSV ->64769|kinetoplastid membrane protein KMP-11|EAN87014.1|Trypanosoma cruzi|5693 -TLEEFSAKL ->64794|Glycoprotein GP85 precursor|P03231.1|Human gammaherpesvirus 4|10376 -TLFIGSHVV ->64810|polyprotein|BAB18806.1|Hepatitis C virus|11103 -TLGFGAYMSK ->64818|E7|AAD33253.1|Human papillomavirus type 16|333760 -TLGIVCPI ->64819|E7 protein|ABL96585.1|Human papillomavirus type 16|333760 -TLGIVCPIC ->64821|Protein Tax-1|P03409.2|Human T-lymphotropic virus 1|11908 -TLGQHLPTL ->64830|E7 protein|ABL96585.1|Human papillomavirus type 16|333760 -TLHEYMLDL ->64948|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 -TLLYATVEV ->64967|Circumsporozoite protein precursor|P08677.2|Plasmodium vivax strain Belem|31273 -TLNDLETDV ->65090|polyprotein|BAB18810.1|Hepatitis C virus (isolate H77)|63746 -TLTHPITK ->65092|Genome polyprotein|P26664.3|Hepatitis C virus genotype 1|41856 -TLTHPVTK ->65118|SAG1 protein|AAO72426.1|Toxoplasma gondii RH|383379 -TLVCGKDGV ->65148|DNA polymerase|CAA10434.1|Hepatitis B virus|10407 -TLWKAGILYK ->65494|polyprotein|AAY82030.1|Hepatitis C virus|11103 -TPAETTVRL ->65497|HCV-1|AAA45676.1|Hepatitis C virus genotype 1|41856 -TPAETTVRLRAYMNTPGLPV ->65509|DNA polymerase|CAA10434.1|Hepatitis B virus|10407 -TPARVTGGVF ->65549|polyprotein|AGO67248.1|Dengue virus 2|11060 -TPEGIIPSM ->65550|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 Thailand/16681/84|31634 -TPEGIIPSMFEPERE ->65567|polyprotein|AJE59927.1|Japanese encephalitis virus|11072 -TPFGQQRVF ->65589|nucleocapsid protein|AAA43837.1|Hantaan virus 76-118|11602 -TPGRYRTAV ->65654|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 -TPLRDWAHNGLRDLA ->65703|gag protein|CAB00235.1|Human immunodeficiency virus 1|11676 -TPQDLNTM ->65748|pp65|AAA45994.1|Human betaherpesvirus 5|10359 -TPRVTGGGAM ->65749|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 -TPRVTGGGAMA ->65810|sporozoite surface protein 2|NP_705260.1|Plasmodium falciparum 3D7|36329 -TPYAGEPAPF ->65817|envelope glycoprotein|AAL59843.1|Human immunodeficiency virus 1|11676 -TQACPKVSFEPIPIHYCAPA ->65929|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 -TQRTSKTLKVLTPPIT ->65965|IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64)|CAA98382.1|Mycobacterium tuberculosis H37Rv|83332 -TQVLVPRSAIDSMLA ->66084|M protein, serotype 5 precursor|P02977.2|Streptococcus pyogenes serotype M5|301449 -TRQELANKQQESKENEKAL ->66106|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 -TRTIASPKGPVIQMY ->66195|Nucleoprotein|P41269.1|Puumala hantavirus|11604 -TSFEDINGIRRPKHL ->66405|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 -TSRSACQRQKKVTFDRLQVL ->66798|glycoprotein gp35/37|AAC59622.1|Human gammaherpesvirus 8|37296 -TTRGRDAHYNAEIRT ->67087|polyprotein|AAK32686.1|Hepatitis C virus|11103 -TVNFTIFKV ->67210|NS3 protein|NP_739587.1|Dengue virus 2 Thailand/NGS-C/1944|11065 -TVWFVPSIK ->67349|Latent membrane protein 2|Q69135|Human gammaherpesvirus 4|10376 -TYGPVFMCL ->67362|polyprotein|AGW21594.1|Dengue virus 1|11053 -TYGWNLVKL ->67382|Type IV pili associated protein|YP_170126.1|Francisella tularensis subsp. tularensis SCHU S4|177416 -TYLGIDLGF ->67385|HER2 receptor|AAA75493.1|Homo sapiens|9606 -TYLPTNASL ->67471|Genome polyprotein|Q99IB8.3|Hepatitis C virus JFH-1|356411 -TYSTYGKFL ->67503|Genome polyprotein|P26662.3|Hepatitis C virus|11103 -TYVYDHLTPL ->67596|Genome polyprotein|P26664.3|Hepatitis C virus (isolate 1)|11104 -VAGALVAFK ->67764|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 -VATDALMTGYTGDFD ->68194|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 -VEGEVQIVSTAAQTF ->68229|EBNA3B (EBNA4A) latent protein|CAA24858.1|Human gammaherpesvirus 4|10376 -VEITPYKPTW ->68443|polyprotein|AAF01178.1|Hepatitis C virus subtype 2a|31649 -VFDITKWLL ->68461|polyprotein|ACZ60108.1|Hepatitis C virus|11103 -VFFNILGGWV ->68521|Genome polyprotein|P26662.3|Hepatitis C virus|11103 -VFLVSQLFTF ->68549|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 -VFPTKDVALRH ->68562|unnamed protein product|BAA14233.1|Hepatitis C virus subtype 1b|31647 -VFSDMETKL ->68563|polyprotein|CAB53095.1|Hepatitis C virus subtype 1b|31647 -VFSDMETKV ->68581|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 -VFTGLTHIDAHFLSQTKQSG ->68601|polyprotein|AAA45534.1|Hepatitis C virus|11103 -VFVLNNTRPPLGNWF ->68605|Genome polyprotein|P26662.3|Hepatitis C virus|11103 -VFWAKHMWNF ->68694|Genome polyprotein|P26664.3|Hepatitis C virus (isolate 1)|11104 -VGIYLLPNR ->68908|nonstructural protein|AAC53959.1|Hepatitis C virus (isolate H77)|63746 -VIAPAVQTNW ->69076|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -VIPTSGDVVV ->69349|Genome polyprotein|P29846.3|Hepatitis C virus (isolate Taiwan)|31645 -VLAALAAYCL ->69387|fusion protein|ABQ58820.1|Human metapneumovirus|162145 -VLATAVREL ->69394|pol|AP_000202.1|Human adenovirus 5|28285 -VLAWTRAFV ->69398|X protein|AAP06597.1|Hepatitis B virus|10407 -VLCLRPVGA ->69404|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 -VLCPKNMIIKP ->69435|Genome polyprotein|SRC279960|Hepatitis C virus (isolate H77)|63746 -VLDSFKTWL ->69452|UL123; IE1|AAR31666.1|Human betaherpesvirus 5|10359 -VLEETSVML ->69474|core protein|BAF42671.1|Hepatitis B virus|10407 -VLEYLVSFGV ->69500|X protein|BAG70907.1|Hepatitis B virus|10407 -VLGGCRHKL ->69524|X protein|ACH95876.1|Hepatitis B virus|10407 -VLHKRTLGL ->69558|EBNA-1 protein|Q777E1|Human gammaherpesvirus 4|10376 -VLKDAIKDL ->69581|Major surface antigen precursor|P12934.3|Hepatitis B virus|10407 -VLLDYQGML ->69646|Alanine dehydrogenase|P30234.2|Mycobacterium tuberculosis|1773 -VLMGGVPGVE ->69649|myosin-9|NP_002464.1|Homo sapiens|9606 -VLMIKALEL ->69661|polyprotein precursor|NP_041724.2|West Nile virus|11082 -VLNETTNWL ->69671|polyprotein|AGO67248.1|Dengue virus 2|11060 -VLNPYMPSV ->69679|polyprotein|BAD73987.1|Hepatitis C virus subtype 1b|31647 -VLPCSFTTL ->69714|Large envelope protein|SRC279965|Hepatitis B virus|10407 -VLQAGFFIL ->69715|envelope protein|BAF48755.1|Hepatitis B virus|10407 -VLQAGFFLL ->69719|proteinase 3|AAH96184.1|Homo sapiens|9606 -VLQELNVTV ->69731|Major outer envelope glycoprotein gp350|Q66537|Human gammaherpesvirus 4|10376 -VLQWASLAV ->69750|polyprotein|AAC03058.1|Hepatitis C virus genotype 3|356114 -VLSDFKSWL ->69751|polyprotein|BAB18806.1|Hepatitis C virus genotype 1|41856 -VLSDFKTWL ->69753|polyprotein|AAK49500.1|Hepatitis C virus genotype 3|356114 -VLSDFRTWL ->69754|Lipoprotein lpqH precursor|P46733.1|Mycobacterium avium|1764 -VLSDGNPPQV ->69797|polyprotein|BAA09073.1|Hepatitis C virus subtype 1b|31647 -VLTDFKTWL ->69798|Lipoprotein lpqH precursor|P0A5J0.1|Mycobacterium tuberculosis|1773 -VLTDGNPPEV ->69799|envelope glycoprotein|BAE96221.1|Human immunodeficiency virus 1|11676 -VLTDPNPQEV ->69907|envelope|BAK20487.1|Human T-lymphotropic virus 1|11908 -VLYSPNVSV ->69913|cysteine proteinase cruzipain (EC 3.4.22.-) - Trypanosoma cruzi|A45629|Trypanosoma cruzi|5693 -VMACLVPAA ->69980|polyprotein|AAF01178.1|Hepatitis C virus subtype 2a|31649 -VMLAAQMFIV ->69991|Nucleoprotein|P03418.1|Human respiratory syncytial virus A2|11259 -VMLRWGVLAKSVKN ->69996|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 -VMMSCSSEA ->70017|membrane protein|AAA45887.1|Human gammaherpesvirus 4|10376 -VMSNTLLSAW ->70365|Truncated Nef protein|P04601.4|Human immunodeficiency virus 1|11676 -VPLRPMTYK ->70491|envelope glycoprotein|AAC28452.1|Human immunodeficiency virus 1|11676 -VPTDPNPPEV ->70516|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 -VPYKRIEEL ->70634|Non-capsid protein NS-1|P07298.1|Human parvovirus B19|10798 -VQQWLTWCN ->70687|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis|1773 -VQYSRADEEQQQALSSQMGF ->70789|Nucleoprotein|P41269.1|Puumala hantavirus|11604 -VRNIMSPVM ->70932|EBNA-3B nuclear protein|CAD53420.1|Human gammaherpesvirus 4|10376 -VSFIEFVGW ->71265|Circumsporozoite protein precursor|P02893.1|Plasmodium falciparum|5833 -VTCGNGIQVR ->71266|Circumsporozoite protein precursor|P02893.1|Plasmodium falciparum|5833 -VTCGNGIQVRIKPGSANKPK ->71290|DNA processivity factor|AAO73452.1|Human betaherpesvirus 5|10359 -VTEHDTLLY ->71409|cysteine proteinase cruzipain (EC 3.4.22.-) - Trypanosoma cruzi|A45629|Trypanosoma cruzi|5693 -VTLPTGQCL ->71412|polyprotein [Hepatitis C virus subtype 1a]|ABV46251.2|Hepatitis C virus subtype 1a|31646 -VTLTHPITK ->71616|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 -VVCMYLYQLSPPITW ->71631|polymerase|ACT90735.1|Hepatitis B virus|10407 -VVDFSQFSR ->71650|polyprotein precursor|AAP22088.1|West Nile virus|11082 -VVEKQSGLY ->71657|polyprotein|AAF01178.1|Hepatitis C virus subtype 2a|31649 -VVFDITKWLL ->71663|Spike glycoprotein precursor|P59594.1|SARS coronavirus|227859 -VVFLHVTYV ->71734|polyprotein|AAF01178.1|Hepatitis C virus subtype 2a|31649 -VVLDSLDPMV ->71756|cysteine proteinase cruzipain (EC 3.4.22.-) - Trypanosoma cruzi|A45629|Trypanosoma cruzi|5693 -VVMACLVPAA ->71847|core protein|AAL31859.1|Hepatitis B virus|10407 -VVSYVNTNMGLKFRQL ->71988|Protein E6|P03126.1|Human papillomavirus type 16|333760 -VYDFAFRDL ->72006|polyprotein|BAD73994.1|Hepatitis C virus subtype 1b|31647 -VYEAADMIM ->72038|Polyprotein|Q9IZA3|Hepatitis C virus subtype 2a|31649 -VYHGAGNKTL ->72039|polyprotein|CAB53095.1|Hepatitis C virus subtype 1b|31647 -VYHGAGSKTL ->72165|Genome polyprotein|P26662.3|Hepatitis C virus|11103 -VYSTTSRSASL ->72233|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 -WAIKWEYVVLLFLLL ->72261|Gag polyprotein|P03347.3|Human immunodeficiency virus 1|11676 -WASRELERF ->72269|glycoprotein gp35/37|AAC59622.1|Human gammaherpesvirus 8|37296 -WAVGLLLGLVLILYL ->72301|envelope protein|YP_001527880.1|West Nile virus NY-99|10000971 -WDFGSVGGVFTSVGKAVH ->72322|polyprotein|AAA86907.1|Hepatitis C virus|11103 -WDMMMNWSPTAALVV ->72563|polyprotein|AAB70696.1|Dengue virus type 1 Hawaii|10000440 -WHYDEDNPYKTWAYHGSYEV ->72564|JK3|CAA43789.1|Hepatitis C virus subtype 1b|31647 -WHYPCTANF ->72566|polyprotein|BAD73987.1|Hepatitis C virus subtype 1b|31647 -WHYPCTVNF ->72621|cysteine proteinase cruzipain (EC 3.4.22.-) - Trypanosoma cruzi|A45629|Trypanosoma cruzi|5693 -WIIKNSWTA ->72721|hypothetical protein FTT0869|YP_169869.1|Francisella tularensis subsp. tularensis SCHU S4|177416 -WLGNHGFEV ->72722|polyprotein|AAF01178.1|Hepatitis C virus subtype 2a|31649 -WLGNIIQYA ->72790|FL-160-2 protein - Trypanosoma cruzi|JH0823|Trypanosoma cruzi|5693 -WLSDCGEAL ->72794|Large envelope protein|P03138.3|Hepatitis B virus|10407 -WLSLLVPFV ->72842|polyprotein|ABG67747.1|West Nile virus|11082 -WMDSTKATRY ->72928|Genome polyprotein|P26662.3|Hepatitis C virus (isolate Japanese)|11116 -WPAPPGARSM ->72929|HCV-1|AAA45676.1|Hepatitis C virus subtype 1a|31646 -WPAPQGSRSLTPCTC ->72979|Major outer membrane porin, serovar A precursor|P23732.1|Chlamydia trachomatis|813 -WQASLALSY ->72985|LOW MOLECULAR WEIGHT PROTEIN ANTIGEN 7 ESXH (10 kDa ANTIGEN) (CFP-7) (PROTEIN TB10.4)|CAA17363.1|Mycobacterium tuberculosis H37Rv|83332 -WQGDTGITY ->73059|kaposin|AAC57155.1|Human gammaherpesvirus 8|37296 -WRWRLGAIPPLVCLL ->73177|protein F [Hepatitis C virus subtype 1b]|ACA50643.1|Hepatitis C virus (isolate Japanese)|11116 -WVCARLGRL ->73296|hemK protein homolog|YP_169235.1|Francisella tularensis subsp. tularensis SCHU S4|177416 -WYTNLDTDKF ->73306|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 -WYYQSGLSI ->73862|EBNA-1 protein|Q777E1|Human gammaherpesvirus 4|10376 -YFMVFLQTHIFAEVL ->74020|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -YGKAIPLEVI ->74180|reverse transcriptase|CAJ26826.1|Hepatitis B virus|10407 -YIDDVVLGA ->74288|Protein E7|P36831.1|Human papillomavirus type 52|10618 -YILDLQPETT ->74305|Nonstructural protein NS5|NP_739590.2|Dengue virus 2 Thailand/NGS-C/1944|11065 -YILRDVSKK ->74386|HCV-1|AAA45676.1|Hepatitis C virus|11103 -YISWCLWW ->74387|Genome polyprotein|P26664.3|Hepatitis C virus (isolate 1)|11104 -YISWCLWWL ->74407|polyprotein|AAU89634.1|Hepatitis C virus subtype 2a|31649 -YIVRWEWVV ->74545|TcP2beta|CAA52943.1|Trypanosoma cruzi|5693 -YLAAYALVGL ->74558|polyprotein|AGW21594.1|Dengue virus 1|11053 -YLAGAGLAF ->74590|glycoprotein gp35/37|AAC59622.1|Human gammaherpesvirus 8|37296 -YLCVPRCRRKKPYIV ->74605|Circumsporozoite protein precursor|P08677.2|Plasmodium vivax strain Belem|31273 -YLDKVRATV ->74635|matrix protein|AEQ63649.1|Respiratory syncytial virus|12814 -YLEKESIYY ->74768|Antigen 85-B precursor (85B) (Extracellular alpha-antigen) (Antigen 85 complex B) (Ag85B) (Mycolyl transferase 85B) (Fibronectin-binding protein B) (30 kDa extracellular protein)|P31952|Mycobacterium tuberculosis|1773 -YLLDGLRAQ ->74774|LMP1 protein (Epstein-Barr virus, putative LYDMA gene)|Q777A4|Human gammaherpesvirus 4|10376 -YLLEMLWRL ->74797|polyprotein|BAA09073.1|Hepatitis C virus subtype 1b|31647 -YLLPRRGPR ->74798|polyprotein|BAA03375.1|Hepatitis C virus|11103 -YLLPRRGPRL ->74800|Genome polyprotein|SRC279960|Hepatitis C virus subtype 2b|31650 -YLLPSRGPKL ->74886|latent membrane protein 1|AAS99606.1|Human gammaherpesvirus 4|10376 -YLQQNWWTL ->74961|polyprotein|ABU97067.1|Hepatitis C virus subtype 1b|31647 -YLVAYQATV ->74988|polyprotein|BAB18806.1|Hepatitis C virus|11103 -YLVTRHADV ->75024|Protein Tax-1|P03409.2|Human T-lymphotropic virus 1|11908 -YLYQLSPPI ->75040|Protein P|P03159.1|Hepatitis B virus|10407 -YMDDVVLGA ->75074|Protein E7|P03129.1|Human papillomavirus type 16|333760 -YMLDLQPET ->75075|E7 protein|ABL96585.1|Human papillomavirus type 16|333760 -YMLDLQPETT ->75356|EBNA3A nuclear protein|Q8AZJ8|Human gammaherpesvirus 4|10376 -YPLHEQHGM ->75376|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -YPPKPCGI ->75408|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 -YPSAAERKHRHLPVADAVIH ->75435|largest ORF|AAB02128.1|Hepatitis C virus|11103 -YPWPLYGNEGCGWMGWLLSP ->75436|Polyprotein|P90247|Hepatitis C virus|11103 -YPWPLYGNEGLGWAGWLLSP ->75438|polyprotein|AAF65962.1|Hepatitis C virus|11103 -YPWPLYGNEGMGWAGWLLSP ->75448|polyprotein|BAB18806.1|Hepatitis C virus|11103 -YPYRLWHY ->75495|6 kDa early secretory antigenic target|P0A564.2|Mycobacterium tuberculosis|1773 -YQGVQQKWDATATELNNALQ ->75614|polyprotein precursor|NP_041724.2|West Nile virus|11082 -YRHKVVKVM ->75632|predicted Efflux Protein|NP_220159.1|Chlamydia trachomatis|813 -YRLLLTRVL ->75636|polyprotein|AAB67037.1|Hepatitis C virus (isolate H77)|63746 -YRLWHYPCTI ->75673|Early antigen protein D|P03191.1|Human herpesvirus 4 strain B95-8|10377 -YRSGIIAVV ->75674|K8.1|ABD28902.1|Human gammaherpesvirus 8|37296 -YRSHLGFWQEGWSGQ ->75718|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 -YSEHPTFTSQY ->76121|polyprotein precursor|NP_041724.2|West Nile virus|11082 -YTMDGEYRL ->76245|reverse transcriptase|CAJ26474.1|Hepatitis B virus|10407 -YVDDVVLGA ->76277|Genome polyprotein|SRC279960|Hepatitis C virus|11103 -YVGDLCGCV ->76333|BRLF1|ABB89247.1|Human gammaherpesvirus 4|10376 -YVLDHLIVV ->76334|Protein E7|P17387.1|Human papillomavirus type 31|10585 -YVLDLQPEAT ->76370|core protein|BAF42671.1|Hepatitis B virus|10407 -YVNVNMGLK ->76529|polyprotein|ABU97067.1|Hepatitis C virus subtype 1b|31647 -YYKVFLARL ->76532|outer membrane protein|YP_170495.1|Francisella tularensis subsp. tularensis SCHU S4|177416 -YYLDRGYLDF ->76591|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -YYRGLDVSVI ->76621|HCMVUL83|CAA35357.1|Human betaherpesvirus 5|10359 -YYTSAFVFPTK ->78346|BARF1 protein|CAD53469.1|Human gammaherpesvirus 4|10376 -AFLGERVTL ->78382|BARF1 protein|CAD53469.1|Human gammaherpesvirus 4|10376 -FLGERVTLT ->78432|BARF1 protein|CAD53469.1|Human gammaherpesvirus 4|10376 -KLGPGEEQV ->78501|BARF1 protein|CAD53469.1|Human gammaherpesvirus 4|10376 -RFIAQLLLL ->78534|BARF1 protein|CAD53469.1|Human gammaherpesvirus 4|10376 -TLTSYWRRV ->79180|tax protein|AAF37566.1|Human T-lymphotropic virus 1|11908 -DCLPTTLFQPVRAPV ->79208|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 -EYTNIPISLLFNEKEA ->79294|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 -LLFGYPVYVFGDCVQ ->79300|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 -LSFPDPGLRPQNLYT ->79308|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 -MEPTLGQHLPTLSFPD ->79337|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 -PPITWPLLPHVIFCH ->79351|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 -QNLYTLWGGSVVCMYLY ->79390|Protein Tax-1|P0C213.1|Human T-cell lymphotropic virus type 1 (african isolate)|39015 -SFHNLHLLFEEYTNI ->79454|transcriptional activator Tax|AAG31572.1|Human T-lymphotropic virus 1|11908 -VIFCHPGQLGAFLTN ->79506|E1 protein|BAA19893.1|Rubella virus|11041 -AFGHSDAACWGFPTDTVMSV ->79601|envelope protein|BAF48755.1|Hepatitis B virus|10407 -LLCLIFLLVL ->79628|E1 protein|BAA19893.1|Rubella virus|11041 -PTDVSCEGLGAWVPTAPCARI ->88377|IE62|AAP32859.1|Human alphaherpesvirus 3|10335 -SAPLPSNRV ->88849|IE62|AAP32859.1|Human alphaherpesvirus 3|10335 -SLPRSRTPI ->92301|ATP-dependent Clp protease proteolytic subunit|NP_216976.1|Mycobacterium tuberculosis H37Rv|83332 -AIYDTMQYV ->92817|secreted antigen 85-B fbpB (85B) (antigen 85 complex B) (Mycolyl transferase 85B) (fibronectin-binding protein B) (extracellular alpha-antigen)|NP_216402.1|Mycobacterium tuberculosis H37Rv|83332 -GLAGGAATA ->93224|core protein|AAL31859.1|Hepatitis B virus|10407 -LEDPASRDLVVSYV ->93270|hypothetical protein|NP_218356.1|Mycobacterium tuberculosis H37Rv|83332 -LLYDGSFAV ->93431|pre-C/C protein|ABY54138.1|Hepatitis B virus|10407 -MQLFHLCLIISCTCPTVQAS ->93536|core protein|AAL31859.1|Hepatitis B virus|10407 -PAYRPPNAPIL ->95234|latent membrane protein 1|AAS99606.1|Human gammaherpesvirus 4|10376 -ALLVLYSFA ->95261|LAMP|AAK72632.1|Human gammaherpesvirus 8|37296 -ATVKTGNIKL ->95262|LAMP|AAK72632.1|Human gammaherpesvirus 8|37296 -ATVKTGNIKLVSSVS ->95264|Genome polyprotein|O92532.3|Hepatitis C virus genotype 6|42182 -AVNGVLWTV ->95265|polyprotein|ABL63009.1|Hepatitis C virus genotype 4|33745 -AVNGVMWTV ->95278|polyprotein|BAC67110.1|Hepatitis C virus|11103 -CINGVCWSI ->95279|polyprotein|BAG31965.1|Hepatitis C virus|11103 -CINGVCWSV ->95280|Genome polyprotein|O39928.3|Hepatitis C virus genotype 5|33746 -CINGVMWTL ->95281|polyprotein|ACE82433.1|Hepatitis C virus genotype 1|41856 -CISGVCWTV ->95297|polyprotein|BAA09072.1|Hepatitis C virus genotype 1|41856 -CTNGVCWTV ->95298|Genome polyprotein|Q913V3.1|Hepatitis C virus (isolate 1)|11104 -CVNGACWTV ->95854|Genome polyprotein|O39927.3|Hepatitis C virus genotype 6|42182 -SINGVMWTV ->95890|polyprotein|ABE98152.1|Hepatitis C virus genotype 6|42182 -SVNGVMWTV ->95908|Genome polyprotein|O92529.3|Hepatitis C virus genotype 6|42182 -TINGVLWTV ->95937|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 -TVGGVMWTV ->95940|polyprotein|BAA32666.1|Hepatitis C virus genotype 6|42182 -TVNGVLWTV ->96120|polyprotein|BAB18806.1|Hepatitis C virus (isolate H77)|63746 -ATLGFGAYMSKA ->96123|Genome polyprotein|P26664.3|Hepatitis C virus (isolate H77)|63746 -AVFGPLWIL ->96156|polyprotein|ABR25251.1|Hepatitis C virus (isolate H77)|63746 -CVTQTVDFSLDPTFTIETTTL ->96257|Genome polyprotein|SRC279960|Hepatitis C virus|11103 -EPEPDVAW ->96346|Genome polyprotein|SRC279960|Hepatitis C virus (isolate H77)|63746 -GVDPNVRTGVRT ->96358|polyprotein|BAB18806.1|Hepatitis C virus (isolate H77)|63746 -HAVGIFRAA ->96365|polyprotein|AAB66324.1|Hepatitis C virus (isolate H77)|63746 -HPTLVFDITKL ->96366|polyprotein|ABR25251.1|Hepatitis C virus|11103 -HRFAPPCKPLLR ->96369|polyprotein|BAB18810.1|Hepatitis C virus|11103 -HVVGIFRAA ->96547|Genome polyprotein|Q913D4.3|Hepatitis C virus (isolate H77)|63746 -LFFNILGGWV ->96601|polyprotein|ABR25251.1|Hepatitis C virus (isolate H77)|63746 -LPYIEQGMML ->96633|polyprotein|ABR25251.1|Hepatitis C virus (isolate H77)|63746 -LYGMWPLLL ->96827|Genome polyprotein|SRC279960|Hepatitis C virus (isolate H77)|63746 -RLADFAQGW ->96836|polyprotein|ABR25251.1|Hepatitis C virus (isolate H77)|63746 -RQVGDFHYV ->96897|polyprotein|ABR25251.1|Hepatitis C virus (isolate H77)|63746 -SLLRHHNLVYSTTSRSA ->96898|Genome polyprotein|SRC279960|Hepatitis C virus|11103 -SLLRNHNLVYSTTSRSA ->96957|polyprotein|ABR25251.1|Hepatitis C virus (isolate H77)|63746 -THFFSVLIARDQ ->96958|Genome polyprotein|SRC279960|Hepatitis C virus|11103 -THLFSVLMARDQ ->97044|Genome polyprotein|SRC279960|Hepatitis C virus (isolate H77)|63746 -VITPVVQTNW ->97093|polyprotein|AAB66324.1|Hepatitis C virus (isolate H77)|63746 -VTRHADVIPV ->97111|polyprotein|ABR25251.1|Hepatitis C virus (isolate H77)|63746 -YDIIICDECHSTDATSIL ->97226|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -CHSTDATSIL ->97227|polyprotein|CAB41951.1|Hepatitis C virus|11103 -CHSTDSTSIL ->97338|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -GIDPNIRTGV ->97365|polyprotein|CAA03854.1|Hepatitis C virus|11103 -GTDPNIRTGV ->97373|polyprotein|ACE82359.1|Hepatitis C virus subtype 1a|31646 -GVDPNIRTGV ->97399|polyprotein|ACZ60108.1|Hepatitis C virus subtype 3a|356426 -IPFYGKAIPI ->97400|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -IPFYGKAIPL ->97467|nucleocapsid protein|ACP44251.1|Influenza A virus (A/Fujian/411/2002(H3N2))|293090 -LPFEKSTIM ->97558|Genome polyprotein|SRC279960|Hepatitis C virus|11103 -PPHPNIEEVA ->97630|polyprotein|AAF65953.1|Hepatitis C virus|11103 -SALGLNAVAY ->97641|polyprotein|CAA03854.1|Hepatitis C virus|11103 -SGLGLNAVAY ->97719|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -VALGINAVAY ->97720|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 -VALGVNAVAY ->97750|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -VPHPNIEEVA ->97876|trans-sialidase, putative|EAN81705.1|Trypanosoma cruzi|5693 -ALSSSLGNV ->97905|trans-sialidase, putative|EAN88532.1|Trypanosoma cruzi|5693 -AVAEAQCKK ->97961|trans-sialidase, putative|EAN81042.1|Trypanosoma cruzi|5693 -DVAASSLLY ->98039|Trans-sialidase|SRC7915|Trypanosoma cruzi|5693 -FLSHNFTLVF ->98040|trans-sialidase, putative|EAN80725.1|Trypanosoma cruzi|5693 -FLYNRPLNS ->98042|trans-sialidase, putative|EAN80840.1|Trypanosoma cruzi|5693 -FQGAWAEWPV ->98044|trans-sialidase, putative|EAN80840.1|Trypanosoma cruzi|5693 -FTLVATVSI ->98046|trans-sialidase, putative|EAN82835.1|Trypanosoma cruzi|5693 -FTSAVLLLL ->98051|trans-sialidase, putative|EAN82716.1|Trypanosoma cruzi|5693 -FVSPSLVSA ->98085|trans-sialidase, putative|EAN82636.1|Trypanosoma cruzi|5693 -GVIAAFAEGH ->98100|trans-sialidase, putative|EAN81657.1|Trypanosoma cruzi|5693 -HLFYSAVLL ->98101|trans-sialidase, putative|EAN80725.1|Trypanosoma cruzi|5693 -HNFTLVASV ->98126|trans-sialidase, putative|EAN81650.1|Trypanosoma cruzi|5693 -ITATIEGRK ->98138|trans-sialidase, putative|EAN81657.1|Trypanosoma cruzi|5693 -IYMLVGKYS ->98223|trans-sialidase, putative|EAN80725.1|Trypanosoma cruzi|5693 -LLLGLWGFA ->98224|trans-sialidase, putative|EAN82076.1|Trypanosoma cruzi|5693 -LLLLVVMMCC ->98242|trans-sialidase, putative|EAN81042.1|Trypanosoma cruzi|5693 -LVTLPVYSK ->98244|trans-sialidase, putative|EAN80840.1|Trypanosoma cruzi|5693 -LWLTDNTHI ->98253|trans-sialidase, putative|EAN81042.1|Trypanosoma cruzi|5693 -MLSRVAAVK ->98254|trans-sialidase, putative|EAN81042.1|Trypanosoma cruzi|5693 -MLVTLPVYS ->98308|trans-sialidase, putative|EAN80840.1|Trypanosoma cruzi|5693 -NVMLVTLPV ->98431|trans-sialidase, putative|EAN82235.1|Trypanosoma cruzi|5693 -RVLLLLLLGL ->98459|trans-sialidase, putative|EAN80725.1|Trypanosoma cruzi|5693 -SIPTAGLVAV ->98466|Trans-sialidase|SRC7915|Trypanosoma cruzi|5693 -SLSHYFTLVF ->98540|trans-sialidase, putative|EAN88532.1|Trypanosoma cruzi|5693 -TSAVLLLLVV ->98560|trans-sialidase, putative|EAN80918.1|Trypanosoma cruzi|5693 -VALMLQGNK ->98603|trans-sialidase, putative|EAN82716.1|Trypanosoma cruzi|5693 -VTDNNRSFY ->98640|trans-sialidase, putative|EAN80840.1|Trypanosoma cruzi|5693 -YNFTLVATV ->98757|G1 and G2 surface glycoprotein precursor|AAG22532.1|Andes hantavirus|46607 -ELGLISIEAASDIKL ->100124|polyprotein|BAD73977.1|Hepatitis C virus subtype 1b|31647 -HSRKKCDEL ->101380|BNLF2a|YP_401721.1|Human herpesvirus 4 type 1|36352 -VLFGLLCLL ->101645|Protein Vpr|P69728.1|Human immunodeficiency virus 1|11676 -FPRIWLHGL ->101673|gag protein|ABO73990.1|Human immunodeficiency virus 1|11676 -GHQAAMQML ->101721|nef|AAA02639.1|Human immunodeficiency virus 1|11676 -HTQGYFPDWQ ->101766|nef protein|ACQ77160.1|Human immunodeficiency virus 1|11676 -KAAVDLSHFL ->101812|Pol polyprotein|Q9YLQ7|Human immunodeficiency virus 1|11676 -KQNPDIVIY ->101813|Pol polyprotein|Q9YLQ7|Human immunodeficiency virus 1|11676 -KQNPDIVIYQY ->101821|vif protein|ACC96167.1|Human immunodeficiency virus 1|11676 -KTKPPLPSVKK ->101967|pol protein|ACJ76655.1|Human immunodeficiency virus 1|11676 -PIQKETWETW ->101990|gag polyprotein|BAH60623.1|Human immunodeficiency virus 1|11676 -QASQEVKNW ->102032|nef protein|AAA87476.1|Human immunodeficiency virus 1|11676 -RPMTYKAAV ->102037|Gag polyprotein|P15832.3|Human immunodeficiency virus 2|11709 -RRWIQLGLQK ->102046|nef protein|ACQ72180.1|Human immunodeficiency virus 1|11676 -RYPLTFGW ->102104|Gag-Pol polyprotein|P03366.3|Human immunodeficiency virus 1|11676 -TAFTIPSI ->102149|Gag polyprotein|P03347.3|Human immunodeficiency virus 1|11676 -TPQDLNTML ->102150|nef protein|ACR27119.1|Human immunodeficiency virus 1|11676 -TPQVPLRPM ->102151|nef protein|ACR27128.1|Human immunodeficiency virus 1|11676 -TQGYFPDWQNY ->102205|envelope glycoprotein|ACR43875.1|Human immunodeficiency virus 1|11676 -VPVWKEATTTL ->102235|nef protein|ACR27119.1|Human immunodeficiency virus 1|11676 -YFPDWQNYT ->102254|nef protein|ACQ72180.1|Human immunodeficiency virus 1|11676 -YPLTFGWCY ->102368|E2 protein|NP_751921.1|Hepatitis C virus subtype 1a|31646 -DRSGAPTYSWGANDT ->102376|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 -DVVSKLPLAVMGSSY ->102611|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 -LHQNIVDVQYLYGVG ->102636|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 -LVGGVLAALAAYCLS ->102819|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 -SQHLPYIEQGMMLAE ->102922|Genome polyprotein|P27958.3|Hepatitis C virus subtype 1a|31646 -VTVSHPNIEEVALST ->103020|polyprotein|ABR25251.1|Hepatitis C virus|11103 -AFWAKHMWNF ->103322|polyprotein|BAB18806.1|Hepatitis C virus|11103 -KRLHQWINEDCSTPCSGSWL ->103389|unnamed protein product [Hepatitis C virus]|BAA14035.1|Hepatitis C virus|11103 -LTHPITKFVMACMSADLEVV ->103392|polyprotein|BAB18806.1|Hepatitis C virus|11103 -LTRDPTTPL ->103563|polyprotein|BAB18806.1|Hepatitis C virus|11103 -RPDYNPPLL ->103654|polyprotein|BAB18806.1|Hepatitis C virus|11103 -TIMAKNEVF ->104114|Glutamate decarboxylase 2|Q05329.1|Homo sapiens|9606 -MIARFKMFPEVKEKG ->104419|polyprotein|BAA00792.1|Hepatitis C virus|11103 -ALYDITQKL ->105333|Latent membrane protein 2|P0C729.1|Human gammaherpesvirus 4|10376 -MGSLEMVPM ->107720|polyprotein|AAF65953.1|Hepatitis C virus|11103 -AAKLSALGLN ->107721|polyprotein|AAD56189.1|Hepatitis C virus|11103 -AAKLSALGVN ->107722|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -AAKLVALGIN ->107727|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -AETAGARLVV ->107732|polyprotein|AAF65964.1|Hepatitis C virus|11103 -AHGTDPNIRT ->107733|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -ALGINAVAYY ->107734|polyprotein|AAF65953.1|Hepatitis C virus|11103 -ALGLNAVAYY ->107735|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 -ALGVNAVAYY ->107738|polyprotein|CAB41951.1|Hepatitis C virus|11103 -ALSNTGEIPF ->107748|polyprotein|AAF65950.1|Hepatitis C virus|11103 -ATDALMTGFT ->107749|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -ATDALMTGYT ->107752|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -ATLGFGAYMS ->107754|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -ATPPGSVTVP ->107760|polyprotein|AAD56189.1|Hepatitis C virus|11103 -AYDIIMCDEC ->107762|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -AYYRGLDVSV ->107777|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -DATSILGIGT ->107780|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -DECHSTDATS ->107781|polyprotein|AAF65953.1|Hepatitis C virus|11103 -DECHSTDSTT ->107782|Genome polyprotein|SRC279960|Hepatitis C virus|11103 -DELAAKLSLG ->107790|polyprotein|AAD56189.1|Hepatitis C virus|11103 -DIIMCDECHS ->107801|polyprotein|AAF65953.1|Hepatitis C virus|11103 -DSTTILGIGT ->107802|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -DVSVIPTSGD ->107818|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -EIPFYGKAIP ->107821|polyprotein|AAF65953.1|Hepatitis C virus|11103 -ELAAKLSALG ->107822|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -ELAAKLVALG ->107840|polyprotein|AAF65950.1|Hepatitis C virus|11103 -FTGDFDSVID ->107862|polyprotein|AAA86907.1|Hepatitis C virus|11103 -GLGINAVAYY ->107863|polyprotein|AAF65950.1|Hepatitis C virus|11103 -GLGLNAVAYY ->107872|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -GRHLIFCHSK ->107873|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -GSPITYSTYG ->107877|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 -GVNAVAYYRG ->107888|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -HPNIEEVALS ->107894|polyprotein|CAB41951.1|Hepatitis C virus|11103 -HSTDSTSILG ->107901|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -ICDECHSTDA ->107905|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -IIICDECHST ->107925|polyprotein|AAF65964.1|Hepatitis C virus|11103 -KAHGTDPNIR ->107945|polyprotein|BAA09073.1|Hepatitis C virus|11103 -KLSALGVNAV ->107984|polyprotein|AAF65953.1|Hepatitis C virus|11103 -LAAKLSALGL ->107985|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -LADGGCSGGA ->108001|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 -LGVNAVAYYR ->108016|polyprotein|AAF65953.1|Hepatitis C virus|11103 -LSALGLNAVA ->108017|polyprotein|BAA09073.1|Hepatitis C virus|11103 -LSALGVNAVA ->108018|polyprotein|CAB41951.1|Hepatitis C virus|11103 -LSNTGEIPFY ->108020|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -LSTTGEIPFY ->108067|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -PHPNIEEVAL ->108079|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -QAETAGARLV ->108100|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -RLVVLATATP ->108127|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -SILGIGTVLD ->108130|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -SKAHGIDPNI ->108139|polyprotein|CAB41951.1|Hepatitis C virus|11103 -SNTGEIPFYG ->108147|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -STDATSILGI ->108148|polyprotein|AAF65953.1|Hepatitis C virus|11103 -STDSTTILGI ->108149|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -STTGEIPFYG ->108153|polyprotein|AAF65950.1|Hepatitis C virus|11103 -TDALMTGFTG ->108154|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -TDALMTGYTG ->108158|polyprotein|AAF65953.1|Hepatitis C virus|11103 -TDSTTILGIG ->108163|polyprotein|CAB41951.1|Hepatitis C virus|11103 -TLSFGAYMSK ->108169|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -TSILGIGTVL ->108171|polyprotein|AAF65953.1|Hepatitis C virus|11103 -TTILGIGTVL ->108175|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -TYGKFLADGG ->108180|polyprotein|AAF65950.1|Hepatitis C virus|11103 -VATDALMTGF ->108181|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -VATDALMTGY ->108218|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -YDIIICDECH ->108225|polyprotein|ABR25251.1|Hepatitis C virus|11103 -YGKAIPLEAI ->108226|polyprotein|AAF65953.1|Hepatitis C virus|11103 -YGTDPNIRTG ->108229|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -YMSKAHGIDP ->108230|polyprotein|AAF65953.1|Hepatitis C virus|11103 -YMSKAYGTDP ->108232|Genome polyprotein|P26664.3|Hepatitis C virus|11103 -YSTYGKFLAD ->108277|IE62|AAP32859.1|Human alphaherpesvirus 3|10335 -ALWALPHAA ->108687|Genome polyprotein|Q81495.3|Hepatitis C virus|11103 -VVSDFKTWL ->108770|E2 protein|ACS92695.1|Human papillomavirus type 16|333760 -ALQAIELQL ->108957|hypothetical protein|NP_216006.1|Mycobacterium tuberculosis|1773 -FLLGLLFFV ->108965|Prolipoprotein diacylglyceryl transferase|O06131.1|Mycobacterium tuberculosis|1773 -FLYELIWNV ->109331|L1|ABP99807.1|Human papillomavirus type 18|333761 -IHSMNSSIL ->109332|L1 protein|ACG75893.1|Human papillomavirus type 16|333760 -IHSMNSTIL ->109984|E2 protein|ACS92695.1|Human papillomavirus type 16|333760 -TLQDVSLEV ->110018|polyprotein|AGO67248.1|Dengue virus 2|11060 -VAFLRFLTI ->110125|E2 protein|ACS92695.1|Human papillomavirus type 16|333760 -YICEEASVTV ->110184|E7|AAD33253.1|Human papillomavirus type 16|333760 -AGQAEPDRAHYNIVTFCCKCDSTLRLCVQSTHVDI ->110195|E7 protein|ABL96585.1|Human papillomavirus type 16|333760 -CCKCDSTL ->110205|Protein E6|P03126.1|Human papillomavirus type 16|333760 -DKKQRFHNIRGRWTGRCMSCCRSSRTRRETQL ->110215|Protein E6|P03126.1|Human papillomavirus type 16|333760 -EKQRHLDKKQRFHNIRGRWTGRCMS ->110225|Protein E7|P06788.2|Human papillomavirus type 18|333761 -FQQLFLNTL ->110227|Protein E6|P03126.1|Human papillomavirus type 16|333760 -FRDLCIVYRDGNPYAVCDKCLKFYSKISEYRHY ->110282|Protein E6|P03126.1|Human papillomavirus type 16|333760 -HDIILECVYCKQQLLRREVYDFAFR ->110285|Protein E6|P03126.1|Human papillomavirus type 16|333760 -HNIRGRWTGR ->110306|Protein E6|P03126.1|Human papillomavirus type 16|333760 -KLPQLCTELQTTIHDIILECVYCKQQLLRREV ->110323|Protein E7|P04020.1|Human papillomavirus type 11|10580 -LLLGTLNIV ->110335|E7|AAD33253.1|Human papillomavirus type 16|333760 -MHGDTPTLHEYMLDLQPETTDLYCYEQLNDSS ->110338|Protein E6|P03126.1|Human papillomavirus type 16|333760 -MHQKRTAMFQDPQERPRKLPQLCTELQTTIHDI ->110373|Protein E6|P03126.1|Human papillomavirus type 16|333760 -PRKLPQLCTELQTTIHDIILECVYC ->110394|Protein E6|P03126.1|Human papillomavirus type 16|333760 -RCINCQKPLCPEEKQRHLDKKQRFHNIRGRWT ->110399|Protein E6|P03126.1|Human papillomavirus type 16|333760 -RGRWTGRCMSCCRSSRTRRETQL ->110401|Protein E6|P03126.1|Human papillomavirus type 16|333760 -RREVYDFAFRDLCIVYRDGNPYAVC ->110431|E7|AAD33253.1|Human papillomavirus type 16|333760 -TDLYCYEQLNDSSEEEDEIDGPAGQAEPDRAHYNIV ->110439|Replication protein E1|P03114.2|Human papillomavirus type 16|333760 -TLLQQYCLYL ->110467|Protein E6|P03126.1|Human papillomavirus type 16|333760 -YRDGNPYAVCDKCLKFYSKISEYRH ->110575|E6 protein|ACS92692.1|Human papillomavirus type 16|333760 -FAFRDLCIVY ->110624|Protein E6|P03126.1|Human papillomavirus type 16|333760 -HDIILECV ->110720|Protein E6|P03126.1|Human papillomavirus type 16|333760 -TIHDIILEC ->110744|E5 protein|AAD24036.1|Human papillomavirus type 16|333760 -YIIFVYIPL ->110829|Protein E6|P03126.1|Human papillomavirus type 16|333760 -EKQRHLDKKQRFHNI ->110846|E6 protein|CAB45108.1|Human papillomavirus type 16|333760 -EYRHYCYSL ->110917|X protein|AAP06597.1|Hepatitis B virus|10407 -KLVCSPAPC ->110940|Protein E7|P03129.1|Human papillomavirus type 16|333760 -MHGDTPTLHEYMLDL ->110982|E6 protein|CAB45108.1|Human papillomavirus type 16|333760 -QYNKPLCDLL ->111055|E6 protein|CAB45108.1|Human papillomavirus type 16|333760 -VYDFAFQDL ->111251|Protein E6|P03126.1|Human papillomavirus type 16|333760 -ELQTTIHDIILECVY ->111404|Protein E7|P03129.1|Human papillomavirus type 16|333760 -HVDIRTLEDLLMGTL ->111407|polyprotein|BAA00792.1|Hepatitis C virus|11103 -HYPCTVNYTI ->111448|polyprotein precursor|BAA02756.1|Hepatitis C virus|11103 -KGGRKPARLIVFPDL ->111479|Protein E7|P06788.2|Human papillomavirus type 18|333761 -LFLNTLSFV ->111604|L1|ABP99807.1|Human papillomavirus type 18|333761 -NVFPIFLQM ->111641|polyprotein|ABV46292.1|Hepatitis C virus|11103 -PQRKTKRNTNR ->111816|polyprotein|BAA09072.1|Hepatitis C virus|11103 -TAYSQQTRGLLG ->111860|polyprotein|BAA00792.1|Hepatitis C virus|11103 -TVNYTIFKI ->111938|Protein E6|P03126.1|Human papillomavirus type 16|333760 -VYDFAFRDLCIVYRD ->112359|Non-structural protein 2a|Q80872.1|Human coronavirus OC43|31631 -TMLDIQPED ->112503|E6 protein|ACV53993.1|Human papillomavirus type 35|10587 -FACYDLCIVY ->112504|Protein E6|P21735.2|Human papillomavirus type 45|10593 -FAFKDLCIVY ->112505|E6|CAA63882.1|Human papillomavirus type 73|51033 -FAFSDLCIVY ->112506|Protein E6|P24835.1|Human papillomavirus type 39|10588 -FAFSDLYVVY ->112519|Protein E6|P26555.1|Human papillomavirus type 58|10598 -FVFADLRIVY ->112697|Protein E6|P26554.1|Human papillomavirus type 51|10595 -VAFTEIKIVY ->113122|Protein E6|P03126.1|Human papillomavirus type 16|333760 -QERPRKLPQL ->113154|Protein E6|P03126.1|Human papillomavirus type 16|333760 -RWTGRCMSCC ->113177|Protein E6|P03126.1|Human papillomavirus type 16|333760 -SSRTRRETQL ->115656|DNA polymerase processivity factor BMRF1|SRC280248|Human gammaherpesvirus 4|10376 -TLDTKPLSV ->116123|nucleocapsid protein|ABP49342.1|Influenza A virus (A/California/10/1978(H1N1))|425557 -LPFDKSTVM ->116127|Nucleoprotein|P15682.1|Influenza A virus (A/Wilson-Smith/1933(H1N1))|381518 -LPFDRPTIM ->116136|nucleocapsid protein|ACS34671.1|Influenza A virus (A/Auckland/1/2009(H1N1))|642794 -LPFERATVM ->116781|Nucleoprotein|P05133.1|Hantaan virus 76-118|11602 -LRKKSSFYQSYLRRT ->116835|Nucleoprotein|P05133.1|Hantaan virus 76-118|11602 -SPSSIWVFAGAPDRC ->119822|110 kd polyprotein precursor|CAA28880.1|Rubella virus|11041 -EACVTSWLWSEGEGAVFYRVDLHFINLGT ->120093|unnamed protein product|CAA33016.1|Rubella virus|11041 -MDFWCVEHDRPPPATPTSLTT ->120111|Glutamate decarboxylase 1|Q99259.1|Homo sapiens|9606 -NMFTYEIAPVFVLME ->120127|unnamed protein product|CAA33016.1|Rubella virus|11041 -PFLGHDGHHGGTLRVGQHHRNASDV ->120187|E1 protein|BAA19893.1|Rubella virus|11041 -RVKFHTETRTVWQLSVAGVSC ->124973|Esat-6 like protein esxJ (Esat-6 like protein 2)|NP_215554.1|Mycobacterium tuberculosis H37Rv|83332 -AFRNIVNML ->126028|ATP-dependent helicase|NP_217813.1|Mycobacterium tuberculosis H37Rv|83332 -FMYEGDTPL ->126481|gag polyprotein p17 region|BAA83653.1|Human immunodeficiency virus 1|11676 -KSLFNTIATLY ->126482|gag protein|AAY98604.1|Human immunodeficiency virus 1|11676 -KSLFNTIAVL ->126483|gag protein|AAY98604.1|Human immunodeficiency virus 1|11676 -KSLFNTIAVLY ->126484|gag protein|AAW03034.1|Human immunodeficiency virus 1|11676 -KSLFNTVATL ->126485|gag protein|AAW03034.1|Human immunodeficiency virus 1|11676 -KSLFNTVATLY ->126486|gag protein|ADK33372.1|Human immunodeficiency virus 1|11676 -KSLFNTVAVL ->126487|gag protein|ADK33372.1|Human immunodeficiency virus 1|11676 -KSLFNTVAVLY ->126488|gag protein|AAV53168.1|Human immunodeficiency virus 1|11676 -KSLYNTIATLY ->126489|gag protein|ABI20203.1|Human immunodeficiency virus 1|11676 -KSLYNTIAVLY ->126490|Gag protein|Q1KW74|Human immunodeficiency virus 1|11676 -KSLYNTVATL ->126491|gag protein|AAV53216.1|Human immunodeficiency virus 1|11676 -KSLYNTVATLY ->126492|gag protein|BAB88077.1|Human immunodeficiency virus 1|11676 -KSLYNTVAVLY ->126993|gag polyprotein|BAB19174.1|Human immunodeficiency virus 1|11676 -RSLFNTIATLY ->126994|gag-pol polyprotein|BAC02551.1|Human immunodeficiency virus 1|11676 -RSLFNTIAVLY ->126995|gag polyprotein|BAB19171.1|Human immunodeficiency virus 1|11676 -RSLFNTVATL ->126996|Gag protein|Q9YYH6|Human immunodeficiency virus 1|11676 -RSLFNTVATLY ->126997|gag protein|BAC45024.1|Human immunodeficiency virus 1|11676 -RSLFNTVAVLY ->126999|gag polyprotein|BAB88540.1|Human immunodeficiency virus 1|11676 -RSLYNTIATLY ->127000|gag-pol fusion polyprotein precursor|CAY83124.1|Human immunodeficiency virus 1|11676 -RSLYNTIAVLY ->127001|gag polyprotein|BAA00992.1|Human immunodeficiency virus 1|11676 -RSLYNTVATL ->127002|gag protein|AAV53342.1|Human immunodeficiency virus 1|11676 -RSLYNTVATLY ->127003|gag polyprotein|BAB88551.1|Human immunodeficiency virus 1|11676 -RSLYNTVAVL ->127004|gag polyprotein|BAB88551.1|Human immunodeficiency virus 1|11676 -RSLYNTVAVLY ->127082|gag-pol polyprotein|BAC02551.1|Human immunodeficiency virus 1|11676 -SLFNTIAVLY ->127083|Gag protein|Q9YYH6|Human immunodeficiency virus 1|11676 -SLFNTVATLY ->127246|p24 protein|CAD36203.1|Human immunodeficiency virus 1|11676 -TSTLQEQIGW ->127611|6 kDa early secretory antigenic target|P0A564.2|Mycobacterium tuberculosis|1773 -AYQGVQQKW ->127792|6 kDa early secretory antigenic target|P0A564.2|Mycobacterium tuberculosis|1773 -QWNFAGIEAA ->130902|nucleocapsid protein|NP_604471.1|Andes hantavirus|46607 -IPIILKALY ->130911|G1 and G2 surface glycoprotein precursor|AAG22532.1|Andes hantavirus|46607 -IYTFTSLFSLMPDVA ->130953|G1 and G2 surface glycoprotein precursor|AAG22532.1|Andes hantavirus|46607 -LMPDVAHSL ->131070|Gag protein|Q9IN85|HIV-1 M:A|505184 -SLFNTVATL ->131096|G1 and G2 surface glycoprotein precursor|AAG22532.1|Andes hantavirus|46607 -TAHGVGEIPM ->131132|G1 and G2 surface glycoprotein precursor|AAG22532.1|Andes hantavirus|46607 -VIGQCIYTFTSLFSL ->131311|interferon-inducible peptide precursor|AAC50160.1|Homo sapiens|9606 -SLMSWSAIL ->133501|polyprotein|ABG75765.1|Dengue virus 1|11053 -AIVREAIKR ->133619|putative surface protein|AAN52495.1|Leptospira interrogans serovar Pomona|44276 -KLIVTPAAL ->133645|cell surface protein|NP_302626.1|Mycobacterium leprae|1769 -MLDHAGNMSACAGAL ->133650|cell surface protein|NP_302626.1|Mycobacterium leprae|1769 -MTQIMYNYPAMLDHA ->133702|polyprotein|ABG75765.1|Dengue virus 1|11053 -SRNSTHEMY ->133716|polyprotein|ABG75765.1|Dengue virus 1|11053 -TLYAVATTI ->134497|M protein|SRC280368|Streptococcus pyogenes|1314 -QRAAKEALDKYELENH ->135263|hemagglutinin|ACX31970.1|Influenza A virus (A/Bar-headed Goose/Qinghai/61/05(H5N1))|336238 -RLYQNPTTYI ->136348|Genome polyprotein|SRC279960|Hepatitis C virus|11103 -HAVGIFKAAV ->136349|Genome polyprotein|SRC279960|Hepatitis C virus|11103 -HAVGIFQAAV ->136350|polyprotein|BAB18806.1|Hepatitis C virus|11103 -HAVGIFRAAV ->136351|Genome polyprotein|SRC279960|Hepatitis C virus|11103 -HAVGIFRTAV ->136826|polyprotein|AFP27208.1|Dengue virus 4|11070 -CYSQVNPTTL ->136837|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 -FLLALLSCLTV ->136865|tegument protein|CAB06735.1|Human alphaherpesvirus 2|10310 -PMRARPRGEVRFLHY ->136890|polyprotein|AGO67248.1|Dengue virus 2|11060 -TPPGSRDPF ->137437|Esat-6 like protein esxJ (Esat-6 like protein 2)|NP_215554.1|Mycobacterium tuberculosis H37Rv|83332 -QTVEDEARRMW ->137609|E7 protein|ACT36476.1|Human papillomavirus type 58|10598 -ATEVRTLQQ ->137611|L1|ACX32376.1|Human papillomavirus type 58|10598 -AVPDDLYIK ->137614|E7 protein|ADP92425.1|Human papillomavirus type 58|10598 -CTIVCPSCA ->137656|E6 protein|ACT36477.1|Human papillomavirus type 58|10598 -ILIRCIICQ ->137657|E6 protein|ACT36477.1|Human papillomavirus type 58|10598 -KCLNEILIR ->137659|E6 protein|ACT36477.1|Human papillomavirus type 58|10598 -KVCLRLLSK ->137660|L1|ACL12325.1|Human papillomavirus type 58|10598 -KYTFWEVNL ->137661|E7 protein|ACT36476.1|Human papillomavirus type 58|10598 -LCINSTATE ->137685|L1|ACX32376.1|Human papillomavirus type 58|10598 -RVRLPDPNK ->137702|late protein|CAA52590.1|Human papillomavirus type 52|10618 -TSESQLFNK ->137724|L1|ACX32376.1|Human papillomavirus type 58|10598 -YTFWEVNLK ->137726|late protein|CAA52590.1|Human papillomavirus type 52|10618 -YYYAGSSRL ->139406|polyprotein|ACT37184.1|Hepatitis C virus|11103 -YLLPRPGPRL ->139746|Dense granule protein 3|B6KEU8.2|Toxoplasma gondii|5811 -FLVPFVVFL ->139747|granule antigen protein GRA6|XP_002371939.1|Toxoplasma gondii ME49|508771 -FMGVLVNSL ->139947|granule antigen protein GRA6|XP_002371939.1|Toxoplasma gondii ME49|508771 -VVFVVFMGV ->140541|hypothetical protein|NP_218210.1|Mycobacterium tuberculosis H37Rv|83332 -ALDEGLLPV ->140542|MCE-family protein MCE4B|NP_218015.1|Mycobacterium tuberculosis H37Rv|83332 -ALLGGLRPV ->140543|trehalose-6-phosphate phosphatase OtsB1|YP_177855.1|Mycobacterium tuberculosis H37Rv|83332 -AMAGSIDLL ->140544|ORF|AAA45606.1|Hepatitis C virus|11103 -ATDALMSGF ->140561|metal cation transporter P-type ATPase A CtpF|NP_216513.1|Mycobacterium tuberculosis H37Rv|83332 -GMFANRWII ->140564|esterase lipoprotein LpqC|NP_217815.1|Mycobacterium tuberculosis H37Rv|83332 -HLDDVGFLV ->140597|MCE-family protein MCE4A|YP_177977.1|Mycobacterium tuberculosis H37Rv|83332 -SLIDLLHKI ->140599|MCE-family lipoprotein LprL|NP_215107.1|Mycobacterium tuberculosis H37Rv|83332 -SLRNWIATL ->140600|glutamine synthetase GLNA1 (glutamine synthase) (GS-I)|NP_216736.1|Mycobacterium tuberculosis H37Rv|83332 -SLWKDGAPL ->140615|amino acid decarboxylase|YP_177889.1|Mycobacterium tuberculosis H37Rv|83332 -WLYPGAQNL ->140616|membrane-associated phospholipase C|NP_216866.1|Mycobacterium tuberculosis H37Rv|83332 -YLLADTFTV ->140649|ESAT-6-like protein esxH|P0A568.2|Mycobacterium tuberculosis|1773 -AMEDLVRAY ->140650|ESAT-6-like protein esxH|P0A568.2|Mycobacterium tuberculosis|1773 -AMLGHAGDM ->140651|granule antigen protein GRA6|XP_002371939.1|Toxoplasma gondii ME49|508771 -AMLTAFFLR ->140652|LOW MOLECULAR WEIGHT PROTEIN ANTIGEN 7 ESXH (10 kDa ANTIGEN) (CFP-7) (PROTEIN TB10.4)|CAA17363.1|Mycobacterium tuberculosis H37Rv|83332 -AMMARDTAE ->140654|ESAT-6-like protein esxH|P0A568.2|Mycobacterium tuberculosis|1773 -ANTMAMMAR ->140686|ESAT-6-like protein esxH|P0A568.2|Mycobacterium tuberculosis|1773 -HAMSSTHEA ->140697|major surface antigen p30|EEB01065.1|Toxoplasma gondii ME49|508771 -KSFKDILPK ->140706|LOW MOLECULAR WEIGHT PROTEIN ANTIGEN 7 ESXH (10 kDa ANTIGEN) (CFP-7) (PROTEIN TB10.4)|CAA17363.1|Mycobacterium tuberculosis H37Rv|83332 -LVRAYHAMS ->140708|LOW MOLECULAR WEIGHT PROTEIN ANTIGEN 7 ESXH (10 kDa ANTIGEN) (CFP-7) (PROTEIN TB10.4)|CAA17363.1|Mycobacterium tuberculosis H37Rv|83332 -MAMMARDTA ->140711|ESAT-6-like protein esxH|P0A568.2|Mycobacterium tuberculosis|1773 -MLGHAGDMA ->140712|LOW MOLECULAR WEIGHT PROTEIN ANTIGEN 7 ESXH (10 kDa ANTIGEN) (CFP-7) (PROTEIN TB10.4)|CAA17363.1|Mycobacterium tuberculosis H37Rv|83332 -MMARDTAEA ->140717|low molecular weight protein antigen 7|NP_214802.1|Mycobacterium tuberculosis|1773 -MYNYPAMLG ->140727|LOW MOLECULAR WEIGHT PROTEIN ANTIGEN 7 ESXH (10 kDa ANTIGEN) (CFP-7) (PROTEIN TB10.4)|CAA17363.1|Mycobacterium tuberculosis H37Rv|83332 -QAMEDLVRA ->140739|dense granule protein 7|XP_002367613.1|Toxoplasma gondii ME49|508771 -RSFKDLLKK ->140744|LOW MOLECULAR WEIGHT PROTEIN ANTIGEN 7 ESXH (10 kDa ANTIGEN) (CFP-7) (PROTEIN TB10.4)|CAA17363.1|Mycobacterium tuberculosis H37Rv|83332 -SQIMYNYPA ->140760|LOW MOLECULAR WEIGHT PROTEIN ANTIGEN 7 ESXH (10 kDa ANTIGEN) (CFP-7) (PROTEIN TB10.4)|CAA17363.1|Mycobacterium tuberculosis H37Rv|83332 -TYQAWQAQW ->140769|LOW MOLECULAR WEIGHT PROTEIN ANTIGEN 7 ESXH (10 kDa ANTIGEN) (CFP-7) (PROTEIN TB10.4)|CAA17363.1|Mycobacterium tuberculosis H37Rv|83332 -WQAQWNQAM ->141202|Uncharacterized PPE family protein PPE51|Q7D623.1|Mycobacterium tuberculosis H37Rv|83332 -AEMWAQDAA ->141206|tegument protein VP11/12|NP_044648.1|Human alphaherpesvirus 1|10298 -AILTQYWKY ->141208|tegument protein VP13/14|NP_044649.1|Human alphaherpesvirus 1|10298 -ALATVTLKY ->141211|UL29|ABI63491.1|Human alphaherpesvirus 1|10298 -ALLAKMLFY ->141212|tegument protein VP13/14|NP_044649.1|Human alphaherpesvirus 1|10298 -ALLDRDCRV ->141216|envelope glycoprotein I|NP_044669.1|Human alphaherpesvirus 1|10298 -APASVYQPA ->141217|regulatory protein ICP22|NP_044663.1|Human alphaherpesvirus 1|10298 -APRIGGRRA ->141218|regulatory protein ICP22|NP_044663.1|Human alphaherpesvirus 1|10298 -APRTWCRLL ->141221|tegument protein VP11/12|NP_044648.1|Human alphaherpesvirus 1|10298 -ATDSLNNEY ->141222|DNA packaging tegument protein UL25|NP_044626.1|Human alphaherpesvirus 1|10298 -AVLCLYLLY ->141225|tegument protein UL21|NP_044622.1|Human alphaherpesvirus 1|10298 -AYLGAFLSVL ->141226|tegument protein UL37|ADD60080.1|Human alphaherpesvirus 1|10298 -AYLPRPVEF ->141227|tegument protein UL37|ADD60080.1|Human alphaherpesvirus 1|10298 -AYSLLFPAPF ->141228|tegument protein VP11/12|NP_044648.1|Human alphaherpesvirus 1|10298 -AYVSVLYRW ->141231|envelope glycoprotein I|NP_044669.1|Human alphaherpesvirus 1|10298 -CPRRPAVAF ->141260|nuclear egress lamina protein|NP_044633.1|Human alphaherpesvirus 1|10298 -EYQRLYATF ->141262|DNA polymerase catalytic subunit|NP_044632.1|Human alphaherpesvirus 1|10298 -EYVHARWAAF ->141269|tegument protein VP13/14|NP_044649.1|Human alphaherpesvirus 1|10298 -FLADAVVRL ->141270|envelope glycoprotein B|NP_044629.1|Human alphaherpesvirus 1|10298 -FLIAYQPLL ->141271|DNA packaging tegument protein UL25|NP_044626.1|Human alphaherpesvirus 1|10298 -FLWEDQTLL ->141276|tegument protein VP13/14|NP_044649.1|Human alphaherpesvirus 1|10298 -FTAPEVGTY ->141277|transactivating tegument protein VP16|NP_044650.1|Human alphaherpesvirus 1|10298 -FTDALGIDEY ->141281|tegument protein UL21|NP_044622.1|Human alphaherpesvirus 1|10298 -FVYTPSPYVF ->141306|tegument host shutoff protein|NP_044643.1|Human alphaherpesvirus 1|10298 -HTDLHPNNTY ->141313|ribonucleotide reductase subunit 2|NP_044642.1|Human alphaherpesvirus 1|10298 -ILIEGIFFA ->141323|multifunctional expression regulator|NP_044657.1|Human alphaherpesvirus 1|10298 -KYFYCNSLF ->141324|tegument protein VP11/12|NP_044648.1|Human alphaherpesvirus 1|10298 -LASDPHYEY ->141338|envelope glycoprotein L|NP_044602.1|Human alphaherpesvirus 1|10298 -LIDGIFLRY ->141341|tegument protein VP11/12|NP_044648.1|Human alphaherpesvirus 1|10298 -LLAYVSVLY ->141354|transcriptional regulator ICP4|NP_044662.1|Human alphaherpesvirus 1|10298 -LYPDAPPLRL ->141396|ribonucleotide reductase subunit 1|NP_044641.1|Human alphaherpesvirus 1|10298 -RILGVLVHL ->141398|tegument protein VP13/14|NP_044649.1|Human alphaherpesvirus 1|10298 -RLLGFADTV ->141399|Tegument protein UL46|P10230.2|Herpes simplex virus (type 1 / strain 17)|10299 -RLNELLAYV ->141402|tegument protein VP22|NP_044651.1|Human alphaherpesvirus 1|10298 -RPTERPRAPA ->141407|tegument protein VP13/14|NP_044649.1|Human alphaherpesvirus 1|10298 -RSSLGSLLY ->141411|transactivating tegument protein VP16|NP_044650.1|Human alphaherpesvirus 1|10298 -SALPTNADLY ->141418|tegument protein VP11/12|NP_044648.1|Human alphaherpesvirus 1|10298 -SIVHHHAQY ->141422|DNA packaging tegument protein UL25|NP_044626.1|Human alphaherpesvirus 1|10298 -SSGVVFGTWY ->141423|envelope glycoprotein B|NP_044629.1|Human alphaherpesvirus 1|10298 -SVYPYDEFV ->141430|tegument serine/threonine protein kinase|NP_044614.1|Human alphaherpesvirus 1|10298 -TLLELVVSV ->141461|ubiquitin E3 ligase ICP0|NP_044601.1|Human alphaherpesvirus 1|10298 -VPGWSRRTL ->141462|tegument protein UL21|NP_044622.1|Human alphaherpesvirus 1|10298 -VPRPDDPVL ->141468|envelope glycoprotein I|NP_044669.1|Human alphaherpesvirus 1|10298 -VVRGPTVSL ->141469|envelope glycoprotein B|NP_044629.1|Human alphaherpesvirus 1|10298 -VYMSPFYGY ->141470|tegument protein UL21|NP_044622.1|Human alphaherpesvirus 1|10298 -VYTPSPYVF ->141479|single-stranded DNA-binding protein|NP_044631.1|Human alphaherpesvirus 1|10298 -YMANQILRY ->141480|ribonucleotide reductase subunit 1|NP_044641.1|Human alphaherpesvirus 1|10298 -YMESVFQMY ->141484|capsid maturation protease|NP_044627.1|Human alphaherpesvirus 1|10298 -YVAGFLALY ->142194|polyprotein|ADV57311.1|Hepatitis C virus subtype 1a|31646 -KAKKTPMGF ->142203|polyprotein|BAD73974.1|Hepatitis C virus subtype 1b|31647 -KKKKNPMGF ->142209|polyprotein|ACJ37233.1|Hepatitis C virus subtype 1a|31646 -KSKKIPMGF ->142210|polyprotein [Hepatitis C virus subtype 1a]|ABV46251.2|Hepatitis C virus subtype 1a|31646 -KSKKNPMGF ->142211|polyprotein|ACJ37204.1|Hepatitis C virus subtype 1a|31646 -KSKKTPLGF ->142212|Genome polyprotein|Q913D4.3|Hepatitis C virus subtype 1a|31646 -KSKKVPMGF ->142213|polyprotein|ABV46054.1|Hepatitis C virus subtype 1a|31646 -KSKRTPMGF ->142231|Lipoprotein lpqH precursor|P0A5J0.1|Mycobacterium tuberculosis|1773 -MKRGLTVAVAGAAILVAGLSGCSS ->142232|POSSIBLE CONSERVED TRANSMEMBRANE PROTEIN|CAB00937.1|Mycobacterium tuberculosis|1773 -MLVLLVAVLVTAVYAFVHA ->142233|ATP-dependent helicase|NP_217813.1|Mycobacterium tuberculosis|1773 -MRFAQPSALSRFSALTRDWFTSTFAAPTAAQA ->142244|polyprotein|ACJ37184.1|Hepatitis C virus subtype 1a|31646 -NSKKTPMGF ->142245|polyprotein|ACJ37204.1|Hepatitis C virus subtype 1a|31646 -NTRPPAGNW ->142246|polyprotein|BAB18810.1|Hepatitis C virus subtype 1a|31646 -NTRPPLGNW ->142247|envelope protein 2|ACY64760.1|Hepatitis C virus subtype 1a|31646 -NTRPPMGNW ->142248|polyprotein|BAB18806.1|Hepatitis C virus subtype 1a|31646 -NTRPPQGNW ->142249|polyprotein|AAY82036.1|Hepatitis C virus subtype 1a|31646 -NTRPPRGNW ->143664|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 -AISEKTIWSL ->143666|polyprotein|ACF60462.1|Hepatovirus A|12092 -ALFHEVAKL ->143680|Genome polyprotein|P06441.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 -DVSGVQAPRGSYQQQLNDPVL ->143690|Genome polyprotein|P06441.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 -GLAVDPWVE ->143705|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 -KEYTFPITL ->143726|polyprotein|CAC14074.3|Hepatovirus A|12092 -LLYNCCYHV ->143728|Genome polyprotein|P08617.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 -LPWYSYLYA ->143732|polyprotein|CAC14074.3|Hepatovirus A|12092 -MMFGFHHSV ->143735|Genome polyprotein|P06441.1|Human hepatitis A virus Hu/Australia/HM175/1976|12098 -NRGKMDVSGVQAPRGSYQQQ ->143740|polyprotein|ACF60462.1|Hepatovirus A|12092 -QMMRNEFRV ->143752|Genome polyprotein|P06441.1|Hepatovirus A|12092 -SLMDLLSSL ->144207|polyprotein|CAB41951.1|Hepatitis C virus|11103 -APTLWARMVL ->144403|polyprotein|AAK08509.1|Hepatitis C virus subtype 1b|31647 -LLRHHNMVY ->144480|polyprotein|ACA50684.1|Hepatitis C virus subtype 1b|31647 -SQRQKKVTF ->144544|polyprotein precursor|BAA01728.1|Hepatitis C virus|11103 -WPAPSGARSL ->144913|Hexon protein|P04133.3|Human adenovirus 5|28285 -LLYANSAHAL ->145826|6 kDa early secretory antigenic target|P0A564.2|Mycobacterium tuberculosis|1773 -IHSLLDEGKQSLTKL ->145860|Protein E6|P04019.1|Human papillomavirus type 11|10580 -KVLIRCYLC ->145918|Protein E6|P06463.1|Human papillomavirus type 18|333761 -NLLIRCLRC ->146005|Protein E6|P04019.1|Human papillomavirus type 11|10580 -SIDQLCKTF ->146028|E6 protein|NP_040296.1|Human papillomavirus type 6b|10600 -TIDQLCKTF ->146123|polyprotein|ADV04529.1|Hepatitis C virus subtype 1b|31647 -AATLGFGSFMSRAYGI ->146124|polyprotein|AAK08509.1|Hepatitis C virus subtype 1b|31647 -AAWYIKGRL ->146182|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 -CLTHPVTK ->146188|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 -DFWESVFTGLTHIDAHFL ->146194|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 -DLQPAETTVRLRAYL ->146213|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 -EFWESVFTGLTHIDAHFL ->146219|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 -ELTPAETSVRLRAYL ->146246|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 -FLATCVNGVCWTVYHGA ->146249|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 -FLGTTVGGVMWTVYHGA ->146260|polyprotein|ADF97231.1|Hepatitis C virus subtype 3a|356426 -GAKHPALQMYTNVDQDLV ->146280|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 -GIDPNIRTGN ->146282|polyprotein|ADF97231.1|Hepatitis C virus subtype 3a|356426 -GKAIPIALLKGGRHLIF ->146283|polyprotein|AEI00313.1|Hepatitis C virus subtype 1b|31647 -GKAIPIEVIKGGRHLIF ->146284|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 -GKSTKVPAAYAAQGYKVL ->146285|polyprotein|ADF97231.1|Hepatitis C virus subtype 3a|356426 -GKSTKVPAAYVAQGYNVL ->146287|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 -GPKGPITQMYTNVDQDLV ->146288|polyprotein|ADF97231.1|Hepatitis C virus subtype 3a|356426 -GRGRLGTYRY ->146289|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 -GRGRRGIYRF ->146291|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 -GSFMSRAYGI ->146314|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 -HVAGIFRAAV ->146317|polyprotein|ADF97231.1|Hepatitis C virus subtype 3a|356426 -ICLTHPVTK ->146395|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 -KLRGMGLNAV ->146396|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 -KLRGMGLNAVAYYRGLDV ->146397|polyprotein|AEI00314.1|Hepatitis C virus subtype 1b|31647 -KLSALGLNAVAYYRGLDV ->146429|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 -LQFIPVETL ->146527|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 -RLGAVQNEV ->146528|NS3/4A protein|CAM56207.1|Hepatitis C virus|11103 -RLGPVQNEI ->146553|polyprotein precursor|BAA01761.1|Hepatitis C virus genotype 2|40271 -SMMAFSAAL ->146569|polyprotein|ADF97231.1|Hepatitis C virus subtype 3a|356426 -SWDETWKCLVRLKPTLH ->146570|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 -SWDQMWKCLIRLKPTLH ->146576|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 -TLGFGSFMSR ->146592|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 -VAPGERPSGMFDSVVL ->146595|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 -VDFVPVESM ->146617|polyprotein|ADY38595.1|Hepatitis C virus subtype 1b|31647 -VTPGERPSGMFDSSVL ->146644|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 -YLHAPTGSGK ->147561|early protein|CAA52586.1|Human papillomavirus type 52|10618 -CYEQLGDSS ->147835|early protein|CAA52585.1|Human papillomavirus type 52|10618 -ITIRCIICQ ->147891|early protein|CAA52585.1|Human papillomavirus type 52|10618 -KTLEERVKK ->147936|dense granule protein 7|XP_002367613.1|Toxoplasma gondii ME49|508771 -LPQFATAAT ->147941|late protein|CAA52590.1|Human papillomavirus type 52|10618 -LQFIFQLCK ->147973|early protein|CAA52586.1|Human papillomavirus type 52|10618 -MRGDKATIK ->147981|late protein|CAA52590.1|Human papillomavirus type 52|10618 -MTLCAEVKK ->148117|early protein|CAA52585.1|Human papillomavirus type 52|10618 -PYGVCIMCL ->148138|early protein|CAA52586.1|Human papillomavirus type 52|10618 -QLGDSSDEE ->148160|late protein|CAA52590.1|Human papillomavirus type 52|10618 -QYRVFRIKL ->148172|late protein|CAA52590.1|Human papillomavirus type 52|10618 -RIKLPDPNK ->148177|early protein|CAA52585.1|Human papillomavirus type 52|10618 -RLQCVQCKK ->148397|Dense granule protein 3|B6KEU8.2|Toxoplasma gondii|5811 -VPFVVFLVA ->148425|early protein|CAA52585.1|Human papillomavirus type 52|10618 -VYKFLFTDL ->148619|unnamed protein product|BAA14233.1|Hepatitis C virus|11103 -GLLGCIITSLTGRDKNQVDGEVQVLSTATQSFLATCVNGVCWTVY ->149022|nonstructural protein|AAC53947.1|Hepatitis C virus genotype 1|41856 -AIAPAVQTNW ->149023|NS3 gene product|AAB02124.1|Hepatitis C virus (isolate H77)|63746 -ALGINAVAY ->149024|NS2 protein|NP_751923.1|Hepatitis C virus (isolate H77)|63746 -ALTLSPYYK ->149027|NS5 protein|BAA00702.1|Hepatitis C virus (isolate H77)|63746 -APTLWARMILMTHFFSVL ->149029|polyprotein|ABR25251.1|Hepatitis C virus (isolate H77)|63746 -CTTPCSGSW ->149031|polyprotein|AAA45677.1|Hepatitis C virus (isolate H77)|63746 -EAAGRRLAR ->149032|nonstructural 5a protein|ADH82351.1|Hepatitis C virus subtype 1a|31646 -EAARRRLAR ->149036|E2 protein|NP_751921.1|Hepatitis C virus (isolate H77)|63746 -ELSPLLLST ->149037|NS4B protein|NP_751926.1|Hepatitis C virus (isolate H77)|63746 -EVITPAVQTNW ->149038|NS3|ABN45875.1|Hepatitis C virus (isolate H77)|63746 -EVQIVSTAAQTFLAT ->149044|NS2 protein|NP_751923.1|Hepatitis C virus (isolate H77)|63746 -FLTRVEAQL ->149052|E1 protein|NP_751920.1|Hepatitis C virus (isolate H77)|63746 -GIAYFSMVGNWAKVLVVL ->149053|NS3 gene product|AAB02124.1|Hepatitis C virus|11103 -GRGKPGIYRFVAPGERPS ->149060|E2 protein|NP_751921.1|Hepatitis C virus (isolate H77)|63746 -HPEATYSRC ->149063|NS3 protease/helicase'|NP_803144.1|Hepatitis C virus (isolate H77)|63746 -KAVDFIPVENLETTMRSP ->149072|NS3 gene product|AAB02124.1|Hepatitis C virus (isolate H77)|63746 -MSKAHGVDPNIRTGVRTI ->149074|E1 protein|NP_751920.1|Hepatitis C virus (isolate H77)|63746 -NASRCWVAV ->149075|envelope glycoprotein E1|ACI88341.1|Hepatitis C virus genotype 1|41856 -NASRCWVPV ->149089|NS3|ABN45875.1|Hepatitis C virus (isolate H77)|63746 -NQVEGEVQI ->149096|polyprotein|BAB18801.1|Hepatitis C virus|11103 -RAQAPPPSW ->149097|NS5 protein|BAA00702.1|Hepatitis C virus (isolate H77)|63746 -RGGRAAICGKYLFNWAVR ->149098|E2 protein|NP_751921.1|Hepatitis C virus (isolate H77)|63746 -RSGAPTYSW ->149105|E2 protein|NP_751921.1|Hepatitis C virus (isolate H77)|63746 -SIASWAIKW ->149115|NS5 protein|BAA00702.1|Hepatitis C virus (isolate H77)|63746 -SVRARLLSR ->149117|envelope glycoprotein|AAV74049.1|Hepatitis C virus (isolate H77)|63746 -TDFDQGWGPISYANGSGP ->149126|nonstructural protein 3|AAY84762.1|Hepatitis C virus genotype 1|41856 -TVYHGAGTK ->149127|NS3|ABN45875.1|Hepatitis C virus (isolate H77)|63746 -TVYHGAGTR ->149129|NS2 protein|NP_751923.1|Hepatitis C virus (isolate H77)|63746 -VVFSRMETKLITWGADTA ->150137|Nonstructural protein NS3|NP_739587.2|Dengue virus 2|11060 -APTRVVAAEM ->150217|polyprotein|AGO67248.1|Dengue virus 2|11060 -FPQSNAPIM ->150224|polyprotein|AGO67248.1|Dengue virus 2|11060 -FTIMAAILAY ->150227|polyprotein|AGS49173.1|Dengue virus 2|11060 -FTMRHKKATY ->150252|polyprotein|AGO67248.1|Dengue virus 2|11060 -GPLKLFMAL ->150259|polyprotein|AGO67248.1|Dengue virus 2|11060 -GPWHLGKLEM ->150299|polyprotein|AGO67248.1|Dengue virus 2|11060 -ILLTAVAPSM ->150308|polyprotein|AGW21594.1|Dengue virus 1|11053 -IPMATYGWNL ->150309|polyprotein|AGO67248.1|Dengue virus 2|11060 -IPMSTYGWNL ->150341|polyprotein|AGW21594.1|Dengue virus 1|11053 -KPGTSGSPI ->150373|polyprotein|AAA42942.1|Dengue virus 2|11060 -LLILCVTQV ->150377|polyprotein|AGS49173.1|Dengue virus 2|11060 -LLLVAHYAI ->150378|polyprotein|AGW21594.1|Dengue virus 1|11053 -LLMLVTPSM ->150387|polyprotein|AGO67248.1|Dengue virus 2|11060 -LMGLGKGWPL ->150389|polyprotein|AGO67248.1|Dengue virus 2|11060 -LMMRTTWAL ->150391|polyprotein|AGS49173.1|Dengue virus 2|11060 -LMMTTIGIVL ->150399|polyprotein|AGV76873.1|Dengue virus 2|11060 -LQMENKAWLV ->150425|polyprotein|AGS49173.1|Dengue virus 2|11060 -LVISGLFPV ->150445|polyprotein|AGO67248.1|Dengue virus 2|11060 -MLLILCVTQV ->150448|polyprotein|AGO67248.1|Dengue virus 2|11060 -MMATIGIAL ->150450|polyprotein|AGO67248.1|Dengue virus 2|11060 -MPVTHSSAA ->150451|polyprotein|AGO67248.1|Dengue virus 2|11060 -MPVTHSSAAQ ->150456|polyprotein|AGO67248.1|Dengue virus 2|11060 -MSYSMCTGKF ->150461|polyprotein|AGK36298.1|Dengue virus 2|11060 -MTQKARNAL ->150474|polyprotein|AGW21594.1|Dengue virus 1|11053 -NPLTLTAAV ->150531|polyprotein|AGO67248.1|Dengue virus 2|11060 -RLRMDKLQL ->150534|polyprotein|AGO67248.1|Dengue virus 2|11060 -RPASAWTLY ->150538|polyprotein|AGW21594.1|Dengue virus 1|11053 -RPRWLDART ->150556|polyprotein|AGW21594.1|Dengue virus 1|11053 -RVIDPRRCLK ->150571|polyprotein|AGO67248.1|Dengue virus 2|11060 -SLLFKTEDGV ->150578|polyprotein|AGO67248.1|Dengue virus 2|11060 -SPCKIPFEIM ->150579|polyprotein|AGW21594.1|Dengue virus 1|11053 -SPGKFWNTTI ->150584|polyprotein|AGO67248.1|Dengue virus 2|11060 -SPILSITISE ->150612|polyprotein|AGO67248.1|Dengue virus 2|11060 -TAEAGGRAY ->150634|polyprotein|AGS49173.1|Dengue virus 2|11060 -TLMAMDLGEL ->150639|polyprotein|AGO67249.1|Dengue virus 2|11060 -TLYAVATTFV ->150643|polyprotein|AGW21594.1|Dengue virus 1|11053 -TPEGIIPALF ->150644|polyprotein|AGO67248.1|Dengue virus 2|11060 -TPEGIIPSMF ->150649|polyprotein|AGW21594.1|Dengue virus 1|11053 -TPQDNQLAYV ->150655|polyprotein|AGO67248.1|Dengue virus 2|11060 -TPRMCTREEF ->150686|polyprotein|AGO67248.1|Dengue virus 2|11060 -VLMMRTTWA ->150693|polyprotein|AGO67248.1|Dengue virus 2|11060 -VPNYNLIIM ->150698|polyprotein|AGO67248.1|Dengue virus 2|11060 -VPYLGKREDQ ->150725|polyprotein|AGO67248.1|Dengue virus 2|11060 -WLVHRQWFL ->150752|polyprotein|AGO67249.1|Dengue virus 2|11060 -YVVIAILTV ->150753|polyprotein|AGO67248.1|Dengue virus 2|11060 -YVVIAILTVV ->150974|60 kDa chaperonin|SRC280371|Yersinia enterocolitica|630 -DRGIDKAVI ->150991|60 kDa chaperonin|P48219.1|Yersinia enterocolitica|630 -GRNVVLDKS ->151001|60 kDa chaperonin|P48219.1|Yersinia enterocolitica|630 -IRAASAITA ->151003|heat shock 60kDa protein 1 (chaperonin)|AAH02676.1|Homo sapiens|9606 -IRRGVMLAV ->151012|heat shock 60kDa protein 1 (chaperonin)|AAH02676.1|Homo sapiens|9606 -KRIQEIIEQ ->151013|heat shock 60kDa protein 1 (chaperonin)|AAH02676.1|Homo sapiens|9606 -KRTLKIPAM ->154041|major capsid protein|CAB06743.1|Human alphaherpesvirus 2|10310 -AFEDRSYPAVFYLLQ ->154164|tegument protein|CAB06732.1|Human alphaherpesvirus 2|10310 -AQREAAGVYDAVRTW ->154196|tegument protein|CAB06735.1|Human alphaherpesvirus 2|10310 -ARPRRSASVAGSHGPG ->154296|UL29|CAB06754.1|Human alphaherpesvirus 2|10310 -CPLLIFDRTRKFVLA ->154346|RL2|CAB06760.1|Human alphaherpesvirus 2|10310 -DFIWTGNPRTAPRSL ->154387|RL2|CAB06760.1|Human alphaherpesvirus 2|10310 -DMETGHIGAYVVLVD ->154409|capsid associated tegument protein|CAB06749.1|Human alphaherpesvirus 2|10310 -DRLDNRLQLGMLIPG ->154448|RL2|CAB06760.1|Human alphaherpesvirus 2|10310 -EAGLMDAATPPARPPA ->154585|ribonucleotide reductase large subunit|CAB06725.1|Human alphaherpesvirus 2|10310 -FGGHYMESVFQMYTR ->154725|RL2|CAB06760.1|Human alphaherpesvirus 2|10310 -GHIGAYVVLVDQTGN ->154822|ribonucleotide reductase large subunit|CAB06725.1|Human alphaherpesvirus 2|10310 -GVLVHLRIRTREASF ->154857|tegument protein|CAB06735.1|Human alphaherpesvirus 2|10310 -HGPGPARAPPPPGGPV ->154980|tegument protein|CAB06735.1|Human alphaherpesvirus 2|10310 -KNLLQRANELVNPDA ->154996|ribonucleotide reductase large subunit|CAB06725.1|Human alphaherpesvirus 2|10310 -KTSNALCVRGARPFS ->155096|RL2|CAB06760.1|Human alphaherpesvirus 2|10310 -LHPFCIPCMKTWIPL ->155131|ribonucleotide reductase large subunit|CAB06725.1|Human alphaherpesvirus 2|10310 -LMLEYFCRCAREESK ->155139|RL2|CAB06760.1|Human alphaherpesvirus 2|10310 -LPIAGVSSVVALAPY ->155403|tegument protein|CAB06735.1|Human alphaherpesvirus 2|10310 -PKASATPATDPARGR ->155489|RL2|CAB06760.1|Human alphaherpesvirus 2|10310 -PVGNMLFDQGTLVGA ->155554|RL2|CAB06760.1|Human alphaherpesvirus 2|10310 -RAAAPAWSRRTLLPE ->155637|tegument protein|CAB06732.1|Human alphaherpesvirus 2|10310 -RLGPADRRFVALSGS ->155811|ribonucleotide reductase large subunit|CAB06725.1|Human alphaherpesvirus 2|10310 -SMSLADFHGEEFEKL ->155927|unnamed protein product|CAA30115.1|Trypanosoma cruzi|5693 -TLLTIDGGI ->155928|unnamed protein product|CAA30115.1|Trypanosoma cruzi|5693 -TLQPVERVL ->155999|RL2|CAB06760.1|Human alphaherpesvirus 2|10310 -VALAPYVNKTVTGDC ->156542|ETS translocation variant 5|NP_004445.1|Homo sapiens|9606 -ELFQDLSQL ->156550|E3 ubiquitin-protein ligase Mdm2|Q00987.1|Homo sapiens|9606 -VLFYLGQYI ->156552|U1 small nuclear ribonucleoprotein 70 kDa|NP_003080.2|Homo sapiens|9606 -YLAPENGYL ->156711|polyprotein precursor|AAG45435.1|Dengue virus 4|11070 -LAPTRVVAAEMEEAL ->156949|Protein 3a|P59632.1|SARS coronavirus|227859 -RFFTLGSITAQPVKI ->159290|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 -LLRHHNLVY ->159299|polyprotein|AAC03058.1|Hepatitis C virus subtype 3a|356426 -SQRQRKVTF ->161186|Nonstructural protein NS5|NP_739590.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 -RLLTKPWDVVPMVTQ ->161353|arsenic-transport integral membrane protein ArsA|NP_217200.1|Mycobacterium tuberculosis H37Rv|83332 -IMILLVLVSA ->161402|hypothetical protein|NP_215301.1|Mycobacterium tuberculosis H37Rv|83332 -LILATMLVA ->161641|6 kDa early secretory antigenic target|P0A564.2|Mycobacterium tuberculosis|1773 -IQGNVTSIHSLLDEG ->164233|nucleocapsid protein|AAA43837.1|Hantaan hantavirus|11599 -FVVPILLKA ->164258|nucleocapsid protein|AAA43837.1|Hantaan virus 76-118|11602 -IEPCKLLPDTAAVSL ->164264|nucleocapsid protein|AAA43837.1|Hantaan virus 76-118|11602 -ITPGRYRTAVCGLYP ->164282|nucleocapsid protein|AAA43837.1|Hantaan hantavirus|11599 -LPDTAAVSL ->164403|nucleocapsid protein|AAA43837.1|Hantaan virus 76-118|11602 -TSFVVPILLKALYML ->164417|nucleocapsid protein|AAA43837.1|Hantaan hantavirus|11599 -VPILLKALY ->164420|nucleocapsid protein|AAA43837.1|Hantaan virus 76-118|11602 -VSLLGGPATNRDYLR ->164547|envelope glycoprotein B|NP_044629.1|Herpes simplex virus (type 1 / strain 17)|10299 -RMLGDVMAV ->164551|envelope glycoprotein B|NP_044629.1|Herpes simplex virus (type 1 / strain 17)|10299 -TMLEDHEFV ->167320|possible regulatory protein|NP_302009.1|Mycobacterium leprae|1769 -LLEEGVIVL ->168240|major paraflagellar rod protein|AAA30221.1|Trypanosoma cruzi|5693 -AVPEVTDVTL ->168327|paraflagellar rod component|AAC32021.1|Trypanosoma cruzi|5693 -DIIEQMKGV ->168607|paraflagellar rod component|AAC32021.1|Trypanosoma cruzi|5693 -FVSCCGELTV ->168691|polyprotein|ABU97067.1|Hepatitis C virus subtype 1b|31647 -GLNAVAYYR ->168728|paraflagellar rod component|AAC32021.1|Trypanosoma cruzi|5693 -GVSGVINAL ->168988|major paraflagellar rod protein|AAA30221.1|Trypanosoma cruzi|5693 -KLEKIEDEL ->169050|polyprotein|ABU97067.1|Hepatitis C virus subtype 1b|31647 -KYLFNWAVK ->169658|major paraflagellar rod protein|AAA30221.1|Trypanosoma cruzi|5693 -RLYKTLGQL ->169995|polyprotein|ABU97067.1|Hepatitis C virus subtype 1b|31647 -VLYQDFDEM ->170049|polyprotein|ABU97067.1|Hepatitis C virus subtype 1b|31647 -WEYVLLLFL ->170063|polyprotein|ABU97067.1|Hepatitis C virus subtype 1b|31647 -WTRGERCNL ->177647|polyprotein|ADE10208.1|Hepatitis C virus subtype 3a|356426 -EGAVQWMNRLIAFASR ->177701|polyprotein|ACZ60104.1|Hepatitis C virus subtype 3a|356426 -GKAKICGLYLFNWAVRTK ->177727|polyprotein|ACZ60102.1|Hepatitis C virus subtype 3a|356426 -GVMSTRCPCGASIAGHVK ->177806|polyprotein|ACZ60104.1|Hepatitis C virus subtype 3a|356426 -KLTPLPAAGQL ->177843|polyprotein|ACZ60102.1|Hepatitis C virus subtype 3a|356426 -LIHLHQNIVDVQYLYGV ->177884|polyprotein|ACZ60102.1|Hepatitis C virus genotype 1|41856 -NIVDVQYLYGVGSGMVGW ->177903|polyprotein|ACZ60102.1|Hepatitis C virus subtype 3a|356426 -PAVASLMAFTASVTSPL ->177955|polyprotein|ACZ60102.1|Hepatitis C virus subtype 3a|356426 -RPSGMFDSVVL ->177956|polyprotein|ACZ60102.1|Hepatitis C virus subtype 3a|356426 -RPSGMFDSVVLCECYDA ->178185|Protein E6|P03126.1|Human papillomavirus type 16|333760 -AFRDLCIVYRDGNPY ->178247|Protein E6|P03126.1|Human papillomavirus type 16|333760 -HLDKKQRFHNIRGRW ->178351|Protein E7|P03129.1|Human papillomavirus type 16|333760 -TPTLHEYMLDLQPET ->178829|envelope protein|BAJ51675.1|HBV genotype D|489483 -FLGPLLVLQA ->179762|cytotoxin/hemolysin|NP_301968.1|Mycobacterium leprae TN|272631 -ALDTFGIPV ->179765|cell surface protein (associated with virulence)|NP_302372.1|Mycobacterium leprae TN|272631 -APIPASVSA ->179766|cell surface protein (associated with virulence)|NP_302372.1|Mycobacterium leprae TN|272631 -APLPPSTAT ->179795|cell surface protein (associated with virulence)|NP_302372.1|Mycobacterium leprae TN|272631 -GIAGSASYY ->179799|hypothetical protein|NP_301670.1|Mycobacterium leprae TN|272631 -GPVPAVATL ->179802|cell surface protein (associated with virulence)|NP_302372.1|Mycobacterium leprae TN|272631 -HRKGLWAIL ->179823|cell surface protein (associated with virulence)|NP_302372.1|Mycobacterium leprae TN|272631 -IPASVSAPA ->179825|cytotoxin/hemolysin|NP_301968.1|Mycobacterium leprae TN|272631 -IPVAGRCCL ->179839|cytotoxin/hemolysin|NP_301968.1|Mycobacterium leprae TN|272631 -KLMGALDTF ->179840|hypothetical protein|NP_302232.1|Mycobacterium leprae TN|272631 -KVTVSSVRK ->179850|cytotoxin/hemolysin|NP_301968.1|Mycobacterium leprae TN|272631 -LPSADIVPM ->179866|cell surface protein (associated with virulence)|NP_302372.1|Mycobacterium leprae TN|272631 -NGIAGSASY ->179881|hypothetical protein|NP_302232.1|Mycobacterium leprae TN|272631 -QMLEASSSV ->179885|hypothetical protein|NP_301670.1|Mycobacterium leprae TN|272631 -RAAVVQAAL ->179891|hypothetical protein|NP_302233.1|Mycobacterium leprae TN|272631 -RPRRGSVSR ->179892|p60-family protein|NP_301879.1|Mycobacterium leprae TN|272631 -RPVPVSTAR ->179898|cell surface protein (associated with virulence)|NP_302372.1|Mycobacterium leprae TN|272631 -SASAFTMPL ->179917|cell surface protein (associated with virulence)|NP_302372.1|Mycobacterium leprae TN|272631 -VASASAFTM ->180077|PPE family protein|YP_177935.1|Mycobacterium tuberculosis H37Rv|83332 -YAEMWAQDA ->180168|gag protein|ABO14878.1|Human immunodeficiency virus 1|11676 -SLFNAVATL ->180191|gag polyprotein|BAB19174.1|Human immunodeficiency virus 1|11676 -SLFNTIATL ->180233|gag protein|ACZ34075.1|Human immunodeficiency virus 1|11676 -SLFNTVATV ->180236|gag|BAC81459.1|Human immunodeficiency virus 1|11676 -SLFNTVAVL ->180255|gag protein|AAT90688.1|Human immunodeficiency virus 1|11676 -SLFNTVVTL ->180337|pol protein|ACJ76655.1|Human immunodeficiency virus 1|11676 -LPPVVAKEI ->180360|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 -AAEGINYADRRWCFD ->180373|polyprotein|AGW21594.1|Dengue virus 1|11053 -APTRVVASEM ->180387|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 -CEALTLATGPISTLW ->180390|polyprotein|CDF77361.1|Dengue virus 3|11069 -CLMMMLPATL ->180407|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 -DNINTPEGIIPSMFE ->180408|polyprotein|AGO67248.1|Dengue virus 2|11060 -DPASIAARGY ->180411|polyprotein|AGO67248.1|Dengue virus 2|11060 -DTTPFGQQR ->180423|polyprotein|AGW21594.1|Dengue virus 1|11053 -EERDIPERSW ->180428|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 -EGEWKEGEEVQVLAL ->180433|polyprotein|AGO67248.1|Dengue virus 2|11060 -EPGQLKLNWF ->180437|polyprotein|AGO67248.1|Dengue virus 2|11060 -EPKEGTKKLM ->180440|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 -EREIPERSWNSGHEW ->180442|Chain B, Dengue Virus Rna Dependent Rna Polymerase With Residues From The Ns5 Linker Region|4C11_B|Dengue virus|12637 -ETACLGKAYA ->180443|polyprotein|AGO67248.1|Dengue virus 2|11060 -ETACLGKSYA ->180450|polyprotein|AGO67248.1|Dengue virus 2|11060 -FAGPVSQHNY ->180453|polyprotein|AGO67248.1|Dengue virus 2|11060 -FGAIYGAAF ->180460|polyprotein|AGO67248.1|Dengue virus 2|11060 -FPQSNAPIMD ->180464|polyprotein|CDF77361.1|Dengue virus 3|11069 -FTILALFLAH ->180471|polyprotein|AGO67248.1|Dengue virus 2|11060 -GEARKTFVDL ->180472|polyprotein|AGW21594.1|Dengue virus 1|11053 -GEARKTFVEL ->180483|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 -GKKKTPRMCTREEFT ->180488|polyprotein|AGO67248.1|Dengue virus 2|11060 -GPGHEEPIPM ->180496|Polyprotein|NP_056776.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 -GVFTTNIWLKLKEKQ ->180500|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 -HKKLAEAIFKLTYQN ->180503|polyprotein|AGO67248.1|Dengue virus 2|11060 -HPGAGKTKRY ->180504|polyprotein|CDF77361.1|Dengue virus 3|11069 -HPGFTILALF ->180507|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 -HTGREIVDLMCHATF ->180512|polyprotein|AGO67248.1|Dengue virus 2|11060 -IANQATVLM ->180514|polyprotein|AGO67248.1|Dengue virus 2|11060 -IAVSMANIF ->180528|polyprotein|AGO67248.1|Dengue virus 2|11060 -IPFEIMDLEK ->180529|polyprotein|AGO67248.1|Dengue virus 2|11060 -IPITAAAWY ->180531|polyprotein|AGO67248.1|Dengue virus 2|11060 -IPMTGPLVAG ->180538|Nonstructural protein NS2B|NP_739586.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 -ISGLFPVSIPITAAA ->180563|Envelope protein|NP_739583.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 -KILIGVIITWIGMNS ->180571|polyprotein|AGW21594.1|Dengue virus 1|11053 -KPRICTREEF ->180572|polyprotein|CDF77361.1|Dengue virus 3|11069 -KPRLCTREEF ->180575|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 -KRYLPAIVREAIKRG ->180579|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 -KSYAQMWSLMYFHRR ->180582|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 -KTWAYHGSYETKQTG ->180588|polyprotein|AGO67248.1|Dengue virus 2|11060 -LAYTIGTTHF ->180589|Nonstructural protein NS3|NP_739587.2|Dengue virus 2|11060 -LDARIYSDPLALKEF ->180596|polyprotein|AFP27208.1|Dengue virus 4|11070 -LETLMLVALL ->180601|polyprotein|AGO67248.1|Dengue virus 2|11060 -LILCVTQVLM ->180605|polyprotein|AGO67248.1|Dengue virus 2|11060 -LMCHATFTM ->180609|polyprotein|ABK30845.1|Dengue virus 3|11069 -LMMMLPATL ->180611|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 -LMRRGDLPVWLAYRV ->180613|envelope protein|AGT63061.1|Dengue virus 3|11069 -LPEEQDQNY ->180617|polyprotein|AGO67248.1|Dengue virus 2|11060 -LPIRYQTPAI ->180618|polyprotein|AGO67248.1|Dengue virus 2|11060 -LPLPWLPGAD ->180620|polyprotein|AGO67248.1|Dengue virus 2|11060 -LPTFMTQKAR ->180624|polyprotein|AGS49173.1|Dengue virus 2|11060 -LPVWLAYKVA ->180637|polyprotein|AGW21594.1|Dengue virus 1|11053 -MAFIAFLRF ->180640|polyprotein|AFP27208.1|Dengue virus 4|11070 -MALKDFKEF ->180641|polyprotein|AFJ91714.1|Dengue virus 1|11053 -MALSIVSLF ->180643|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 -MAMTDTTPFGQQRVF ->180646|polyprotein|AGO67248.1|Dengue virus 2|11060 -MAVGMVSIL ->180647|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 -MEEALRGLPIRYQTP ->180656|polyprotein|AGO67248.1|Dengue virus 2|11060 -MLIPTAMAF ->180657|polyprotein|CDF77361.1|Dengue virus 3|11069 -MLVTPSMTM ->180660|polyprotein|CDF77361.1|Dengue virus 3|11069 -MMLPATLAF ->180662|polyprotein|CDF77361.1|Dengue virus 3|11069 -MMMLPATLAF ->180667|polyprotein|AGO67248.1|Dengue virus 2|11060 -MPSMKRFRRE ->180668|polyprotein|AGO67248.1|Dengue virus 2|11060 -MPSVIEKMET ->180670|polyprotein|AGW21594.1|Dengue virus 1|11053 -MPVTVASAAQ ->180671|polyprotein|AGO67248.1|Dengue virus 2|11060 -MSFRDLGRVM ->180675|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 -MSTYGWNLVRLQSGV ->180681|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 -NEEYTDYMPSMKRFR ->180682|polyprotein|AGO67248.1|Dengue virus 2|11060 -NPEIEDDIF ->180684|nonstructural protein 5|AGX01519.1|Dengue virus 4|11070 -NPRLCTREEF ->180689|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 -NRAVHADMGYWIESA ->180717|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 -RDLGRVMVMVGATMT ->180718|polyprotein|AFP27208.1|Dengue virus 4|11070 -REDLWCGSL ->180723|polyprotein|AGO67248.1|Dengue virus 2|11060 -RFLEFEALGF ->180724|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 -RGEARKTFVDLMRRG ->180726|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 -RMAILGDTAWDFGSL ->180728|Nonstructural protein NS5|YP_001531176.2|Dengue virus 3|11069 -RPRLCTREEF ->180734|Nonstructural protein NS3|NP_739587.2|Dengue virus 2|11060 -RSWNSGHEW ->180735|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 -RVGTKHAILLVAVSF ->180738|polyprotein|CDF77361.1|Dengue virus 3|11069 -RYMGEDGCWY ->180750|Nonstructural protein NS3|NP_739587.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 -SPGTSGSPIIDKKGK ->180756|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 -STRVEMGEAAGIFMT ->180758|Nonstructural protein NS5|NP_739590.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 -SWHYDQDHPYKTWAY ->180774|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 -TLRVLNLVENWLNNN ->180778|polyprotein|AFP27208.1|Dengue virus 4|11070 -TPEGIIPTLF ->180780|polyprotein|AGW21594.1|Dengue virus 1|11053 -TPQDNQLAY ->180781|polyprotein|AGO67248.1|Dengue virus 2|11060 -TPQDNQLTY ->180789|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 -TVIDLDPIPYDPKFE ->180794|polyprotein|AGO67248.1|Dengue virus 2|11060 -VATTFVTPM ->180802|polyprotein|AGO67248.1|Dengue virus 2|11060 -VPLLAIGCY ->180803|polyprotein|AFP27208.1|Dengue virus 4|11070 -VPLLAMGCY ->180804|polyprotein|AGW21594.1|Dengue virus 1|11053 -VPNYNMIIM ->180814|polyprotein|AGO67248.1|Dengue virus 2|11060 -WAYHGSYET ->180816|polyprotein|ABW82016.1|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 -WGNGCGLFGKGGIVT ->180817|polyprotein|AGO67248.1|Dengue virus 2|11060 -WHYDQDHPY ->180818|Membrane glycoprotein precursor|NP_739582.2|Dengue virus 2 D2/SG/05K4155DK1/2005|10002010 -WILRHPGFTMMAAIL ->180828|polyprotein|AGO67248.1|Dengue virus 2|11060 -YAQMWSLMYF ->180836|polyprotein|AGT63075.1|Dengue virus 1|11053 -YGGPISQHNY ->180843|polyprotein|AFP27208.1|Dengue virus 4|11070 -YPKTKLTDWD ->180850|polyprotein|AFP27208.1|Dengue virus 4|11070 -YTPEGIIPTL ->180880|nucleocapsid protein|AAA43837.1|Hantaan hantavirus|11599 -ETKESKAIR ->181035|||| -VLSDFKVWLKKLFPGGGQICGGVYLLPRRGPRLKKSMMAFSAAL ->181036|||| -VLSDFKVWLKKSMMAFSAAL ->181152|Pol polyprotein|Q9YLQ7|Human immunodeficiency virus 1|11676 -TAFTIPSL ->181154|pol protein|ACJ76655.1|Human immunodeficiency virus 1|11676 -TAFTIPST ->181155|pol protein|AAQ76603.1|Human immunodeficiency virus 1|11676 -TAFTIPSV ->181731|Possible hydrolase|NP_215850.1|Mycobacterium tuberculosis|1773 -MLLRKGTVYVLVIRADLVNAMVAHA ->181733|Antigen 85-B|P0C5B9.1|Mycobacterium tuberculosis|1773 -MTDVSRKIRAWGRRLMIGTAAAVVLPGLVGLAGGAATAGA ->182421|polyprotein|AGO67248.1|Dengue virus 2|11060 -AAGRKSLTL ->182508|polyprotein|AFP27208.1|Dengue virus 4|11070 -AIAVASGLLW ->182554|polyprotein|ACF49259.1|Dengue virus type 1 Hawaii|10000440 -ALLATSIFK ->182599|polyprotein|AGW21594.1|Dengue virus 1|11053 -AQMWQLMYF ->182687|polyprotein|AGK36298.1|Dengue virus 2|11060 -AYRIKQRGIL ->182702|polyprotein|AGO63991.1|Dengue virus|12637 -CLMMILPAA ->182707|polyprotein|AFY10039.1|Dengue virus 4|11070 -CNLTSTWVMY ->182747|polyprotein|AGO67248.1|Dengue virus 2|11060 -CYSQVNPITL ->182836|polyprotein|ACF49259.1|Dengue virus type 1 Hawaii|10000440 -DYMTSMKRF ->182848|polyprotein|AGO67248.1|Dengue virus 2|11060 -EARKTFVDL ->182892|polyprotein|AFP27208.1|Dengue virus 4|11070 -EENMEVEIW ->182898|polyprotein|AGO67248.1|Dengue virus 2|11060 -EEREIPERSW ->182912|polyprotein|AGW21594.1|Dengue virus 1|11053 -EFFLMVLLI ->182917|polyprotein|CDF77361.1|Dengue virus 3|11069 -EFKDFAAGR ->182926|polyprotein|AFP27208.1|Dengue virus 4|11070 -EIASLPTYL ->182938|polyprotein|AGO67248.1|Dengue virus 2|11060 -EKEENLVNSL ->182939|polyprotein|CDF77361.1|Dengue virus 3|11069 -EKEENMVKSL ->182971|polyprotein|AFP27208.1|Dengue virus 4|11070 -EMCEDTVTY ->183147|polyprotein|AGW21594.1|Dengue virus 1|11053 -FCSHHFHQL ->183162|polyprotein|AGW21594.1|Dengue virus 1|11053 -FFLMVLLIPE ->183165|polyprotein|CDF77361.1|Dengue virus 3|11069 -FFMMVLLIPE ->183175|polyprotein|AGW21594.1|Dengue virus 1|11053 -FIAFLRFLA ->183223|polyprotein|AGW21594.1|Dengue virus 1|11053 -FPGKTVWFVP ->183229|polyprotein|AGW21594.1|Dengue virus 1|11053 -FPQSNAVIQD ->183231|polyprotein|AFP27208.1|Dengue virus 4|11070 -FPQSNSPIED ->183245|polyprotein|AGT63074.1|Dengue virus 1|11053 -FQSHQLWATL ->183252|polyprotein|AGT63075.1|Dengue virus 1|11053 -FSLHYAWKTM ->183275|polyprotein|AGW21594.1|Dengue virus 1|11053 -FTNMEVQLIR ->183353|polyprotein|AFP27208.1|Dengue virus 4|11070 -GESSSNPTI ->183363|gag polyprotein|BAA00992.1|Human immunodeficiency virus 1|11676 -GGKKKYKL ->183366|gag protein|ABI20203.1|Human immunodeficiency virus 1|11676 -GGKKRYKL ->183395|polyprotein|AAS49480.2|Dengue virus 3|11069 -GKKHMIAGVL ->183421|polyprotein|AGW21594.1|Dengue virus 1|11053 -GLNSRSTSL ->183437|polyprotein|AGO67248.1|Dengue virus 2|11060 -GMNSRSTSL ->183570|polyprotein|AFP27208.1|Dengue virus 4|11070 -HEMYWVSGV ->183577|polyprotein|AGK36298.1|Dengue virus 2|11060 -HFQRALIFIL ->183587|polyprotein|AGH08163.1|Dengue virus 3|11069 -HMIAGVFFTF ->183594|polyprotein|AGT63075.1|Dengue virus 1|11053 -HPASAWTLYA ->183598|polyprotein|AGW21594.1|Dengue virus 1|11053 -HPGSGKTRRY ->183619|nonstructural protein NS1|1802191G|Dengue virus|12637 -HTWTEQYKF ->183621|polyprotein|AGK36298.1|Dengue virus 2|11060 -HVQRIETWIL ->183654|polyprotein|AGW21594.1|Dengue virus 1|11053 -IAVGMVTLY ->183670|polyprotein|AGO67248.1|Dengue virus 2|11060 -IENSSVNVSL ->183672|polyprotein|AFP27208.1|Dengue virus 4|11070 -IENTSANLSL ->183708|polyprotein|AGO67248.1|Dengue virus 2|11060 -IGMNSRSTSL ->183719|polyprotein|AGO63991.1|Dengue virus|12637 -IINKRKKTSL ->183723|polyprotein|CDF77361.1|Dengue virus 3|11069 -IKLTVVVGDI ->183724|polyprotein|AGO67248.1|Dengue virus 2|11060 -IKRGLRTLIL ->183741|polyprotein|AGS49173.1|Dengue virus 2|11060 -ILCVPNAVIL ->183747|polyprotein|AGO67248.1|Dengue virus 2|11060 -ILIGVIITW ->183766|polyprotein|AGO67248.1|Dengue virus 2|11060 -ILNRRRRTA ->183779|polyprotein|AGO67248.1|Dengue virus 2|11060 -IMAVGMVSIL ->183781|polyprotein|AGO67248.1|Dengue virus 2|11060 -IMDLEKRHVL ->183793|envelope protein|AGT63061.1|Dengue virus 3|11069 -IMKIGIGVLL ->183800|polyprotein|AGT63075.1|Dengue virus 1|11053 -IMNRRKRSV ->183804|polyprotein|AGO63991.1|Dengue virus|12637 -INKRKKTSL ->183813|polyprotein|AGW21594.1|Dengue virus 1|11053 -IPEPDRQRTP ->183819|polyprotein|AGO67248.1|Dengue virus 2|11060 -IPITAAAWYL ->183825|polyprotein|AGO67248.1|Dengue virus 2|11060 -IPLALTIKGL ->183843|envelope protein|AGW23576.1|Dengue virus 3|11069 -IQNSGGTSIF ->184065|Nonstructural protein NS3|YP_001531172.2|Dengue virus 3|11069 -KLNDWDFVV ->184130|polyprotein|AFP27208.1|Dengue virus 4|11070 -KREDLWCGSL ->184131|polyprotein|AGO67248.1|Dengue virus 2|11060 -KREDQWCGSL ->184136|gag protein|ADZ56444.1|Human immunodeficiency virus 1|11676 -KRWIIMGLNK ->184212|polyprotein|AGW21594.1|Dengue virus 1|11053 -KVRKDIPQW ->184234|polyprotein|AGO67248.1|Dengue virus 2|11060 -KWKSRLNAL ->184260|polyprotein|CDF77361.1|Dengue virus 3|11069 -LAIPPTAGVL ->184264|polyprotein|CDF77361.1|Dengue virus 3|11069 -LAKRFSRGL ->184265|polyprotein|CDF77361.1|Dengue virus 3|11069 -LAKRFSRGLL ->184274|polyprotein|AGW21594.1|Dengue virus 1|11053 -LALMATFKM ->184299|envelope protein|AGT63061.1|Dengue virus 3|11069 -LATLRKLCI ->184300|envelope protein|AFN87749.1|Dengue virus 2|11060 -LATLRKYCI ->184316|polyprotein|AGW21594.1|Dengue virus 1|11053 -LEENMDVEIW ->184318|polyprotein|AFP27208.1|Dengue virus 4|11070 -LEENMEVEIW ->184337|polyprotein|AGO67248.1|Dengue virus 2|11060 -LEKRHVLGRL ->184373|polyprotein|AGO67248.1|Dengue virus 2|11060 -LGKKKTPRM ->184377|polyprotein|AGW21594.1|Dengue virus 1|11053 -LGLNSRSTSL ->184378|polyprotein|AGO67248.1|Dengue virus 2|11060 -LGMLQGRGPL ->184412|envelope protein|AGW23591.1|Dengue virus 3|11069 -LKGMSYAMCL ->184429|||| -LLFGFPVYV ->184439|polyprotein|AGO67248.1|Dengue virus 2|11060 -LLILCVTQVL ->184453|polyprotein|AFP27207.1|Dengue virus 4|11070 -LLLMRTTWAF ->184458|polyprotein|AGT17702.1|Dengue virus 1|11053 -LLMLLPTAL ->184467|polyprotein|AGO67248.1|Dengue virus 2|11060 -LLQMEDKAWL ->184512|polyprotein|AGO67248.1|Dengue virus 2|11060 -LMWKQITPEL ->184518|polyprotein|AGO67248.1|Dengue virus 2|11060 -LNRRRRTAG ->184522|polyprotein|AGW21594.1|Dengue virus 1|11053 -LPDTIETLM ->184523|polyprotein|AGW21594.1|Dengue virus 1|11053 -LPDTIETLML ->184531|polyprotein|AFP27208.1|Dengue virus 4|11070 -LPESLETLML ->184554|polyprotein|AGT63075.1|Dengue virus 1|11053 -LPQHLTQRAQ ->184571|polyprotein|AGO67248.1|Dengue virus 2|11060 -LQLKGMSYSM ->184585|NS1|AGW99229.1|Dengue virus 3|11069 -LRTTTVSGKL ->184643|polyprotein|AGW24534.1|Dengue virus 2|11060 -LTIPPTAGIL ->184658|polyprotein|CDF77361.1|Dengue virus 3|11069 -LTQKVVIFIL ->184702|non-structural protein 1|AGM49312.1|Dengue virus|12637 -LWPKTHTLW ->184713|polyprotein|AFP27208.1|Dengue virus 4|11070 -LYAVATTIL ->184736|polyprotein|AGW21594.1|Dengue virus 1|11053 -MAMVLSIVS ->184739|polyprotein|AGW21594.1|Dengue virus 1|11053 -MASSVLLWM ->184755|polyprotein|AGO67248.1|Dengue virus 2|11060 -MDLEKRHVL ->184804|non-structural protein 1|AGM49312.1|Dengue virus|12637 -MFTTNIWMKF ->184814|polyprotein|AGO67248.1|Dengue virus 2|11060 -MGLGKGWPL ->184819|polyprotein|AGH08163.1|Dengue virus 3|11069 -MIAGVFFTF ->184835|polyprotein|AGW21594.1|Dengue virus 1|11053 -MKLVMAFIAF ->184840|polyprotein|AGS49173.1|Dengue virus 2|11060 -MLINRFTMR ->184845|polyprotein|CDF77361.1|Dengue virus 3|11069 -MLKRVRNRV ->184849|nonstructural protein 5|AGX01518.1|Dengue virus 1|11053 -MLLNRFTMA ->184856|polyprotein|AGW21594.1|Dengue virus 1|11053 -MLMTGTLAVF ->184864|polyprotein|AGO67248.1|Dengue virus 2|11060 -MLRTRVGTK ->184880|polyprotein|AGT63075.1|Dengue virus 1|11053 -MNRRKRSVT ->184884|polyprotein|AGW21594.1|Dengue virus 1|11053 -MPIRYQTTAV ->184896|polyprotein|AGW21594.1|Dengue virus 1|11053 -MPVTVASAA ->184898|polyprotein|AGW21594.1|Dengue virus 1|11053 -MQRKHGGML ->184899|polyprotein|AGO67248.1|Dengue virus 2|11060 -MRGAKRMAI ->184900|polyprotein|AGO67248.1|Dengue virus 2|11060 -MRGAKRMAIL ->185050|polyprotein|AFP27208.1|Dengue virus 4|11070 -NFLEVEDYGF ->185102|polyprotein|AGT63075.1|Dengue virus 1|11053 -NRRKRSVTM ->185104|polyprotein|AGO67248.1|Dengue virus 2|11060 -NRRRRTAGV ->185124|polyprotein|AGW21594.1|Dengue virus 1|11053 -NTPEGIIPA ->185125|polyprotein|AGW21594.1|Dengue virus 1|11053 -NTPEGIIPAL ->185200|polyprotein|AGO67248.1|Dengue virus 2|11060 -PRRCMKPVIL ->185232|polyprotein|AFP27208.1|Dengue virus 4|11070 -QEEHKETWHY ->185260|polyprotein|CDF77361.1|Dengue virus 3|11069 -QLAKRFSRG ->185279|polyprotein|AGW21594.1|Dengue virus 1|11053 -QMQRKHGGML ->185327|polyprotein|ACF49259.1|Dengue virus type 1 Hawaii|10000440 -QYIYMGQPL ->185388|polyprotein|AGO67248.1|Dengue virus 2|11060 -RIKQKGILGY ->185399|polyprotein|AGO67248.1|Dengue virus 2|11060 -RKKARSTPF ->185419|envelope protein|AGW23591.1|Dengue virus 3|11069 -RLKMDKLEL ->185447|polyprotein|AGK36298.1|Dengue virus 2|11060 -RNALDNLAVL ->185465|polyprotein|AGO67248.1|Dengue virus 2|11060 -RPLKEKEENL ->185468|polyprotein|AGW21594.1|Dengue virus 1|11053 -RPMFAVGLLF ->185485|polyprotein|AGW21594.1|Dengue virus 1|11053 -RQMESEGIFL ->185491|polyprotein|AGO67248.1|Dengue virus 2|11060 -RREEEEAGVL ->185492|polyprotein|AGT63075.1|Dengue virus 1|11053 -RRKRSVTMLL ->185573|polyprotein|CDF77361.1|Dengue virus 3|11069 -RYMGEDGCW ->185651|polyprotein|ACF49259.1|Dengue virus type 1 Hawaii|10000440 -SILLSSLLK ->185685|polyprotein|CDF77361.1|Dengue virus 3|11069 -SLLFKTASG ->185710|Nonstructural protein NS5|YP_001531176.2|Dengue virus 3|11069 -SMINGVVKL ->185716|polyprotein|AAA21201.1|Dengue virus 3|11069 -SMTMRCVGI ->185734|polyprotein|CDF77361.1|Dengue virus 3|11069 -SPKRLATAI ->185741|polyprotein|AGW21594.1|Dengue virus 1|11053 -SPVRVPNYNM ->185758|polyprotein|AGO67248.1|Dengue virus 2|11060 -SRSTSLSVSL ->185817|envelope protein|AGW23590.1|Dengue virus 4|11070 -SWMIRILIGF ->185827|polyprotein|ACF49259.1|Dengue virus type 1 Hawaii|10000440 -SYKVASEGF ->185881|polyprotein|AFP27208.1|Dengue virus 4|11070 -TEIASLPTYL ->185931|polyprotein|AGO67248.1|Dengue virus 2|11060 -TKQTGSASSM ->185978|polyprotein|CDF77361.1|Dengue virus 3|11069 -TMGVLCLAIL ->186002|polyprotein|AGO67248.1|Dengue virus 2|11060 -TPMLRHSIE ->186008|polyprotein|AGI95993.1|Dengue virus 4|11070 -TPPGATDPF ->186029|envelope protein|ABV59122.1|Dengue virus 3|11069 -TPTWNRKEL ->186041|polyprotein|AGO67248.1|Dengue virus 2|11060 -TRVGTKHAIL ->186058|polyprotein|AGO67248.1|Dengue virus 2|11060 -TSKKRSWPL ->186175|polyprotein|AFY10053.1|Dengue virus 3|11069 -TWRDMAHTLI ->186192|polyprotein|AGO67248.1|Dengue virus 2|11060 -VAATMANEM ->186211|polyprotein|AGO67248.1|Dengue virus 2|11060 -VDRKGKVVGL ->186219|polyprotein|AGK36298.1|Dengue virus 2|11060 -VEDGRFWEL ->186234|polyprotein|AFY10052.1|Dengue virus 3|11069 -VEIWTKEGEK ->186242|polyprotein|AGO67248.1|Dengue virus 2|11060 -VEMGEAAGIF ->186264|polyprotein|AGO67248.1|Dengue virus 2|11060 -VGRQEKGKSL ->186301|polyprotein|AGO67248.1|Dengue virus 2|11060 -VLMHRGKRI ->186303|polyprotein|AGS14893.1|Dengue virus 4|11070 -VLMMLVAPSY ->186330|polyprotein|AFP27208.1|Dengue virus 4|11070 -VMLLVHYAI ->186354|polyprotein|AGO67248.1|Dengue virus 2|11060 -VQQLTKRFSL ->186427|polyprotein|ACF49259.1|Dengue virus type 1 Hawaii|10000440 -VVYDAKFEK ->186453|polyprotein|AFP27208.1|Dengue virus 4|11070 -WEPSKGWKNW ->186470|envelope protein|AGT63061.1|Dengue virus 3|11069 -WIMKIGIGVL ->186474|polyprotein|AGO67248.1|Dengue virus 2|11060 -WKTWGKAKML ->186524|polyprotein|AGW21594.1|Dengue virus 1|11053 -WTMKIGIGIL ->186550|polyprotein|AFY10039.1|Dengue virus 4|11070 -YDQENPYRTW ->186551|polyprotein|AGW21594.1|Dengue virus 1|11053 -YENLKYSVIV ->186559|polyprotein|AGW21594.1|Dengue virus 1|11053 -YKVASEGFQY ->186603|polyprotein|AGW21594.1|Dengue virus 1|11053 -YSDPLALREF ->186620|polyprotein|AFP27208.1|Dengue virus 4|11070 -YVILTILTI ->186640|polyprotein|AFP27207.1|Dengue virus 4|11070 -YYMATLKNV ->186641|polyprotein|AFP27207.1|Dengue virus 4|11070 -YYMATLKNVT ->186692|||| -LLFGYPVFV ->187041|polyprotein|ABG67747.1|West Nile virus|11082 -AIIEVDRSAAK ->187045|polyprotein|ABG67747.1|West Nile virus|11082 -AVVVNPSVK ->187063|polyprotein|ABG67747.1|West Nile virus|11082 -GTLTSAINR ->187069|polyprotein precursor|AAF20092.2|West Nile virus|11082 -KNMEKPGLK ->187086|polyprotein|ABG67747.1|West Nile virus|11082 -RVLSLIGLK ->187106|Vpr protein|BAA93983.1|Human immunodeficiency virus 1|11676 -AVRHFPRIW ->187154|Vif protein|CAD26959.1|Human immunodeficiency virus 1|11676 -ISKKAKGWF ->187158|Gag protein|Q1KW74|Human immunodeficiency virus 1|11676 -KAFNPEIIPMF ->187160|Protein Rev|P04616.1|Human immunodeficiency virus 1|11676 -KAVRLIKFLY ->187163|Gag polyprotein|P88150|Human immunodeficiency virus 1|11676 -KGFNPEVIPMF ->187188|PE family protein PE9|YP_177784.1|Mycobacterium tuberculosis H37Rv|83332 -RLFNANAEEYHALSA ->187189|PE-PGRS family protein PE_PGRS42|YP_177886.1|Mycobacterium tuberculosis H37Rv|83332 -SAAIAGLFG ->187197|Core protein|Q9QAC5|Hepatitis B virus|10407 -VCWGELMNL ->189204|||| -ALYNTVATL ->189275|gag protein|AAO84847.1|Human immunodeficiency virus 1|11676 -SLFNAVAVL ->189277|gag protein|AAY98604.1|Human immunodeficiency virus 1|11676 -SLFNTIAVL ->189280|||| -SLYLTVATL ->189285|gag protein|AAK30999.1|Human immunodeficiency virus 1|11676 -SLYNSVATL ->189286|||| -SLYNTAATL ->189287|gag protein|ADO94802.1|Human immunodeficiency virus 1|11676 -SLYNTIAIL ->189288|gag protein|AAV53168.1|Human immunodeficiency virus 1|11676 -SLYNTIATL ->189289|gag protein|ADO93742.1|Human immunodeficiency virus 1|11676 -SLYNTISVL ->189290|gag protein|ACO48925.1|Human immunodeficiency virus 1|11676 -SLYNTITVL ->189291|||| -SLYNTVAAL ->189292|gag protein|ABC40295.1|Human immunodeficiency virus 1|11676 -SLYNTVAIF ->189293|gag protein|BAB88077.1|Human immunodeficiency virus 1|11676 -SLYNTVAVL ->189294|Gag|O89360|Human immunodeficiency virus 1|11676 -SLYNTVSTL ->189295|gag protein|AEB70304.1|Human immunodeficiency virus 1|11676 -SLYNTVVTL ->189297|||| -SLYQTVATL ->189300|gag polyprotein|BAB88548.1|Human immunodeficiency virus 1|11676 -SVYNTVATL ->189503|hexon protein|AAD47268.1|Human adenovirus 11|10541 -TYFNLGNKF ->189546|glycosyl transferase|WP_015631503.1|Mycobacterium tuberculosis|1773 -AAPEPVARR ->189547|cyclopropane-fatty-acyl-phospholipid synthase|YP_005911842.1|Mycobacterium tuberculosis|1773 -AASAAIANR ->189566|glycosyl transferase|WP_015631503.1|Mycobacterium tuberculosis|1773 -ALADLPVTV ->189569|||| -AMLDHAGDM ->189571|Antigen 85-B|P0C5B9.1|Mycobacterium tuberculosis|1773 -ANNTRLWVY ->189575|POSSIBLE GLYCOSYL TRANSFERASE|CAB05418.1|Mycobacterium tuberculosis|1773 -ARLAGIPY ->189687|glycosyl transferase|WP_003906951.1|Mycobacterium tuberculosis|1773 -IVLVRRWPK ->189705|glycosyl transferase|WP_015631503.1|Mycobacterium tuberculosis|1773 -KYIAADRKI ->189706|cyclopropane-fatty-acyl-phospholipid synthase|WP_010924246.1|Mycobacterium tuberculosis|1773 -KYIFPGGLL ->189727|Antigen 85-B|P0C5B9.1|Mycobacterium tuberculosis|1773 -LPQWLSANR ->189740|glycosyl transferase|WP_003906951.1|Mycobacterium tuberculosis|1773 -LVYGDVIMR ->189748|||| -MLDHAGDMA ->189750|Diacylglycerol acyltransferase/mycolyltransferase Ag85B|SRC280000|Mycobacterium tuberculosis|1773 -MPVGGGSSF ->189755|||| -MYNYPTMLD ->189799|glycosyl transferase|WP_003906951.1|Mycobacterium tuberculosis|1773 -PYNLRYRVL ->189829|cyclopropane-fatty-acyl-phospholipid synthase|WP_010924246.1|Mycobacterium tuberculosis|1773 -RMWELYLAY ->189849|glycosyltransferase|WP_016721157.1|Mycobacterium tuberculosis|1773 -SIIIPTLNV ->189894|cyclopropane-fatty-acyl-phospholipid synthase|WP_010924246.1|Mycobacterium tuberculosis|1773 -VLAGSVDEL ->189905|Antigen 85-B|P0C5B9.1|Mycobacterium tuberculosis|1773 -WGAQLNAMK ->190409|polymerase|AAD16253.1|Hepatitis B virus|10407 -ESTRSASFCGSPYSW ->190443|core protein|BAF42671.1|Hepatitis B virus|10407 -HISCLTFGR ->190455|core protein|AAL31780.1|Hepatitis B virus|10407 -KEFGASVELL ->190466|large surface antigen|CAL29876.1|Hepatitis B virus|10407 -LGFFPDHQLDPAFGA ->190488|large/middle/small S proteins|AAK97183.1|Hepatitis B virus|10407 -LWEWASVRF ->190494|nucleocapsid protein|ABI96968.1|SARS coronavirus|227859 -MEVTPSGTWL ->190509|HBsAg|AAL66328.1|Hepatitis B virus|10407 -PFMPLLPIFF ->190533|nucleocapsid protein|AAP49024.1|SARS coronavirus|227859 -RRPQGLPNNIASWFT ->190556|HBsAg|AAL66328.1|Hepatitis B virus|10407 -SVIWMMWYW ->190568|polymerase|AAD16253.1|Hepatitis B virus|10407 -TYGRKLHLYSHPIILGFRKI ->190569|polymerase|ADG03431.1|Hepatitis B virus|10407 -VDKNPHNTTESRLVV ->190577|surface antigen|AAZ30211.1|Hepatitis B virus|10407 -VIWMMWYWGR ->190589|surface antigen|AAZ30211.1|Hepatitis B virus|10407 -WLSVIWMMWY ->190596|polymerase|BAD04994.1|Hepatitis B virus|10407 -YPALMPLSACIQAKR ->190821|polyprotein|AAT94261.1|Hepatitis C virus|11103 -KLLGLGINAV ->190822|polyprotein|BAB18801.1|Hepatitis C virus|11103 -KLSGLGINAI ->190826|gag polyprotein|CAB81949.1|Human immunodeficiency virus 1|11676 -KSLFNTIATL ->190827|gag protein|AAN08336.1|Human immunodeficiency virus 1|11676 -KSLYNTIATL ->190828|gag protein|ABI20203.1|Human immunodeficiency virus 1|11676 -KSLYNTIAVL ->190829|gag protein|BAB88077.1|Human immunodeficiency virus 1|11676 -KSLYNTVAVL ->190959|gag polyprotein|BAB19174.1|Human immunodeficiency virus 1|11676 -RSLFNTIATL ->190960|gag-pol polyprotein|BAC02551.1|Human immunodeficiency virus 1|11676 -RSLFNTIAVL ->190961|gag protein|BAC45024.1|Human immunodeficiency virus 1|11676 -RSLFNTVAVL ->190962|gag polyprotein|BAB88540.1|Human immunodeficiency virus 1|11676 -RSLYNTIATL ->190963|gag-pol fusion polyprotein precursor|CAY83124.1|Human immunodeficiency virus 1|11676 -RSLYNTIAVL ->190974|gag polyprotein|BAB19174.1|Human immunodeficiency virus 1|11676 -SLFNTIATLY ->190975|gag protein|BAC45024.1|Human immunodeficiency virus 1|11676 -SLFNTVAVLY ->190978|gag protein|AAV53168.1|Human immunodeficiency virus 1|11676 -SLYNTIATLY ->190979|gag protein|ABI20203.1|Human immunodeficiency virus 1|11676 -SLYNTIAVLY ->190980|gag protein|AAV53216.1|Human immunodeficiency virus 1|11676 -SLYNTVATLY ->190981|gag protein|BAB88077.1|Human immunodeficiency virus 1|11676 -SLYNTVAVLY ->191095|Capsid protein|P03146.1|Hepatitis B virus ayw/France/Tiollais/1979|490133 -YVNTNMGLK ->193060|Nef protein|Q9YYU3|Human immunodeficiency virus 1|11676 -RFPLTFGWCF ->193071|Nef protein|Q9WPU2|Human immunodeficiency virus 1|11676 -RYPLTLGWCF ->193551|Protein 3a|P59632.1|SARS coronavirus|227859 -SITAQPVKI ->193665|envelope glycoprotein B|NP_044629.1|Herpes simplex virus (type 1 / strain 17)|10299 -ALLGLTLGV ->193837|envelope glycoprotein B|NP_044629.1|Herpes simplex virus (type 1 / strain 17)|10299 -FVLATGDFV ->193840|envelope glycoprotein B|NP_044629.1|Herpes simplex virus (type 1 / strain 17)|10299 -GIFEDRAPV ->194160|BaRF1|AFJ06848.1|Human gammaherpesvirus 4|10376 -LLIEGIFFI ->194181|envelope glycoprotein B|NP_044629.1|Herpes simplex virus (type 1 / strain 17)|10299 -LLTTPKFTV ->194227|Glycoprotein B|P10211.1|Herpes simplex virus (type 1 / strain 17)|10299 -NLLTTPKFT ->194242|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis|1773 -QEAGNFERI ->194400|ESAT-6-like protein esxB|P0A566.2|Mycobacterium tuberculosis|1773 -TAGSLQGQW ->194440|envelope glycoprotein B|NP_044629.1|Herpes simplex virus (type 1 / strain 17)|10299 -TMYYKDVTV ->194442|BFRF3|YP_001129448.1|Human gammaherpesvirus 4|10376 -TPSVSSSISSL ->194449|BKRF2|AFY97944.1|Human gammaherpesvirus 4|10376 -VEDLFGANL ->194555|BNRF1|AGZ95154.1|Human gammaherpesvirus 4|10376 -WQWEHIPPA ->194567|envelope glycoprotein B|NP_044629.1|Herpes simplex virus (type 1 / strain 17)|10299 -YLANGGFLI ->194657|BNRF1|AGZ95154.1|Human gammaherpesvirus 4|10376 -YPRNPTEQGNI ->195418|6 kDa early secretory antigenic target ESXA (ESAT-6)|YP_178023.1|Mycobacterium tuberculosis H37Rv|83332 -GSGSEAYQGVQQKWD ->196087|PPE family protein PPE54|YP_177960.1|Mycobacterium tuberculosis H37Rv|83332 -TVKSMILHEIL ->226775|PreS1/PreS2/surface protein|Q2EID8|Hepatitis B virus|10407 -GYRWMCLRR ->226786|core protein|BAF42671.1|Hepatitis B virus|10407 -LVSFGVWIR ->226809|Large S protein|BAF36017.1|Hepatitis B virus|10407 -YLWEWASVR ->226853|ribonucleotide reductase subunit 2|NP_040141.1|Human alphaherpesvirus 3|10335 -ILIEGIFFV ->226871|ribonucleotide reductase subunit 2|NP_040141.1|Human alphaherpesvirus 3|10335 -MILIEGIFFV ->230028|Protein Nef|P04603.3|Human immunodeficiency virus 1|11676 -NYTPGPGIRF ->230029|Protein Nef|P03404.4|Human immunodeficiency virus 1|11676 -NYTPGPGIRY ->230030|Nef protein|BAA86664.1|Human immunodeficiency virus 1|11676 -NYTPGPGTRF ->230122|nef protein|ACR27128.1|Human immunodeficiency virus 1|11676 -FLKEKGGL ->231862|Major surface antigen p30 precursor|P13664.1|Toxoplasma gondii RH|383379 -FAGAAGSAKSAAGTASHVSI ->232152|rhoptry kinase family protein|AFO54841.1|Toxoplasma gondii type III|398031 -PPEQPFHSYGVTYTFATDA ->232153|rhoptry protein 18|CAJ27113.1|Toxoplasma gondii type I|1209525 -PPERPFQATGITYTFPTDA ->232154|rhoptry protein, putative / protein kinase domain-containing protein|XP_002367757.1|Toxoplasma gondii type II|1209523 -PPERPFQTTDITYTFTTDA ->233309|polyprotein|ACZ60102.1|Hepatitis C virus subtype 3a|356426 -VRMVMMTHF ->236085|polyprotein|ABD97104.1|Hepatitis C virus|11103 -HSKKKCDEM ->238379|polyprotein|ACE82359.1|Hepatitis C virus subtype 1a|31646 -FLVGQLFTF ->240792|Major immediate-early protein|Q9YRL8|Human betaherpesvirus 5|10359 -ELNRKMIYM ->240808|polyprotein|AAB53095.1|Tick-borne encephalitis virus|11084 -ILLDNITTL ->243835|glycosyl transferase|WP_015628558.1|Mycobacterium tuberculosis|1773 -SARLAGIPY ->244160|surface antigen 2 (CA-2)|XP_818927.1|Trypanosoma cruzi strain CL Brener|353153 -AAAGDKLSL ->244167|surface antigen 2|SRC298288|Trypanosoma cruzi|5693 -ALQVTNHRYL ->244168|surface antigen 2|SRC298288|Trypanosoma cruzi|5693 -ALRNLRVFL ->244296|surface antigen 2|SRC298288|Trypanosoma cruzi|5693 -TVFDASRSTV ->251793|transmembrane serine/threonine-protein kinase A|WP_016330371.1|Mycobacterium tuberculosis|1773 -AIIIAVLLV ->252997|transmembrane serine/threonine-protein kinase A|WP_016330371.1|Mycobacterium tuberculosis|1773 -ALAIIIAVL ->288104|nef protein|ACR27130.1|Human immunodeficiency virus 1|11676 -EVGFPVRPQVPLRPMTFK ->294287|gag protein|ABI20203.1|Human immunodeficiency virus 1|11676 -GATPQDLNTMLNTVGGH ->418940|PPE family protein PPE68|KAM81677.1|Mycobacterium tuberculosis H37Ra|419947 -AAAAGWQTL ->418942|PPE family protein PPE68|KAM81677.1|Mycobacterium tuberculosis H37Ra|419947 -ALAAATPMVV ->418943|PPE family protein PPE68|KAM81677.1|Mycobacterium tuberculosis H37Ra|419947 -ALAMEVYQA ->418944|PPE family protein PPE68|KAM81677.1|Mycobacterium tuberculosis H37Ra|419947 -ALDAQAVEL ->418945|PPE family protein PPE68|KAM81677.1|Mycobacterium tuberculosis H37Ra|419947 -ALTEMDYFI ->418947|PPE family protein PPE68|KAM81677.1|Mycobacterium tuberculosis H37Ra|419947 -AMPPELNTA ->418964|PPE family protein PPE68|KAM81677.1|Mycobacterium tuberculosis H37Ra|419947 -ELTARLNSL ->418967|PPE family protein PPE68|KAM81677.1|Mycobacterium tuberculosis H37Ra|419947 -FIRMWNQAAL ->418975|PPE family protein PPE68|KAM81677.1|Mycobacterium tuberculosis H37Ra|419947 -GINTIPIAL ->418991|polyprotein|AFY10039.1|Dengue virus 4|11070 -IPVTMALWY ->418997|PPE family protein PPE68|KAM81677.1|Mycobacterium tuberculosis H37Ra|419947 -KLEPMASIL ->419002|PPE family protein PPE68|KAM81677.1|Mycobacterium tuberculosis H37Ra|419947 -LIEKPVAPSV ->419005|polyprotein|AGW21594.1|Dengue virus 1|11053 -LLAVSGVYPM ->419006|PPE family protein PPE68|KAM81677.1|Mycobacterium tuberculosis H37Ra|419947 -LLRAESLPGA ->419017|polyprotein|AFY10034.1|Dengue virus 4|11070 -MPAMKRYSAP ->419024|polyprotein|AGW21594.1|Dengue virus 1|11053 -NMIIMDEAHF ->419031|PPE family protein PPE68|KAM81677.1|Mycobacterium tuberculosis H37Ra|419947 -QLPPAATQTL ->419037|polyprotein|AEF01538.1|Dengue virus 1|11053 -RPMFAVGILF ->419045|PPE family protein PPE68|KAM81677.1|Mycobacterium tuberculosis H37Ra|419947 -SLPEIAANHI ->419048|polyprotein|AFY10039.1|Dengue virus 4|11070 -SPRLCTREEF ->419095|polyprotein|ABR25251.1|Hepatitis C virus|11103 -AELIEANLLW ->419098|polyprotein|ABR27377.1|Hepatitis C virus|11103 -AEVIAPAVQT ->419124|polyprotein|ACF49259.1|Dengue virus type 1 Hawaii|10000440 -AVEPGKNPK ->419125|polyprotein|ACF49259.1|Dengue virus type 1 Hawaii|10000440 -AVKSEHTGR ->419128|polyprotein|ACF49259.1|Dengue virus type 1 Hawaii|10000440 -AYRHAMEEL ->419170|polyprotein|ABR25251.1|Hepatitis C virus|11103 -FAWYLKGKW ->419208|polyprotein|ACF49259.1|Dengue virus type 1 Hawaii|10000440 -GVEGEGLHK ->419229|polyprotein|ACF49259.1|Dengue virus type 1 Hawaii|10000440 -IYRILQRGL ->419298|RNA-dependent RNA polymerase|ACH97782.1|Hepatitis C virus|11103 -NSKRTPMGF ->419306|polyprotein|ACF49259.1|Dengue virus type 1 Hawaii|10000440 -PTLDIELLK ->419320|polyprotein|AGZ86443.1|Hepatitis C virus|11103 -RAEAQLHAW ->419325|Genome polyprotein|O92532.3|Hepatitis C virus|11103 -RLGPVQNEV ->419366|polyprotein|BAA00792.1|Hepatitis C virus|11103 -SVIDCNVAV ->419410|polyprotein|ABR25251.1|Hepatitis C virus|11103 -WLGNIIMFA ->419424|polyprotein|BAA00792.1|Hepatitis C virus|11103 -YLTAYQATV ->422880|External core antigen|SRC279980|Hepatitis B virus|10407 -GLKILQLL ->422981|Genome polyprotein|P26664.3|Hepatitis C virus genotype 1|41856 -AICGKYLFNW ->422983|Genome polyprotein|P27958.3|Hepatitis C virus genotype 1|41856 -ARDQLEQAL ->422984|NS5B protein|ABB72740.1|Hepatitis C virus genotype 1|41856 -ARMILLTHF ->422985|polyprotein precursor|BAA02756.1|Hepatitis C virus genotype 1|41856 -ARSVRAKLL ->422989|polyprotein|ABY67644.1|Hepatitis C virus genotype 1|41856 -FAPALPIWAR ->422990|C protein|CAB41699.1|Hepatitis B virus|10407 -FGVWIRTPPAYR ->422996|Genome polyprotein|P26664.3|Hepatitis C virus genotype 1|41856 -GAYMSKAHGI ->422997|preC/core protein|CAJ33968.1|Hepatitis B virus|10407 -GDLMNLATW ->422998|polyprotein precursor|BAA02756.1|Hepatitis C virus genotype 1|41856 -GEVPSTEDL ->422999|polyprotein|ABD97104.1|Hepatitis C virus genotype 3|356114 -GILVLFGFF ->423002|polyprotein|ABY67644.1|Hepatitis C virus genotype 1|41856 -GRAAICGRY ->423007|Genome polyprotein|P26664.3|Hepatitis C virus genotype 1|41856 -GVQEDAASLR ->423010|polyprotein|AAC03058.1|Hepatitis C virus genotype 3|356114 -IMGGELPTA ->423011|polyprotein|AER51001.1|Hepatitis C virus genotype 1|41856 -IMSGEVPSM ->423016|NS5A|ACX46481.1|Hepatitis C virus genotype 1|41856 -KFPLAMPVW ->423019|protease-helicase|AER50967.1|Hepatitis C virus genotype 1|41856 -KLVALGLNAV ->423020|polyprotein|ACE82359.1|Hepatitis C virus genotype 1|41856 -KLYISWCLW ->423022|Genome polyprotein|P27958.3|Hepatitis C virus genotype 1|41856 -KQSGENFPYL ->423031|core|CAA59522.1|Hepatitis B virus|10407 -LESPEHCSP ->423032|core protein|AJT55251.1|Hepatitis B virus|10407 -LESQDHCSP ->423033|Genome polyprotein|P26664.3|Hepatitis C virus genotype 1|41856 -LETTMRSPVF ->423036|core protein|AGS79525.1|Hepatitis B virus|10407 -LWFHISCLMF ->423044|polyprotein precursor|BAA01582.1|Hepatitis C virus genotype 1|41856 -QLEQALDCEIY ->423046|polyprotein|ACX44272.1|Hepatitis C virus genotype 1|41856 -QMAMIKLGAL ->423047|Genome polyprotein|P27958.3|Hepatitis C virus genotype 1|41856 -QRLHGLSAF ->423052|polyprotein precursor|BAA01582.1|Hepatitis C virus|11103 -RDAVILLM ->423053|core protein|AAL31859.1|Hepatitis B virus|10407 -RETVIEYLVSF ->423061|Genome polyprotein|P27958.3|Hepatitis C virus genotype 3|356114 -SQLSAPSLK ->423062|polyprotein|ACH99674.1|Hepatitis C virus genotype 1|41856 -SSVSTALAEL ->423063|pre-Core, Core|BAF49207.1|Hepatitis B virus|10407 -STLPETTVVRQ ->423068|polyprotein|ACX44241.1|Hepatitis C virus genotype 1|41856 -VLFGLMALTL ->423069|polyprotein|ACH99674.1|Hepatitis C virus genotype 1|41856 -VLTESSVSTA ->423071|polyprotein|AER51001.1|Hepatitis C virus genotype 1|41856 -VPSMEDLVNL ->423072|polyprotein|ACJ37172.1|Hepatitis C virus genotype 1|41856 -VRMILLTHF ->423073|polyprotein|ABL63011.1|Hepatitis C virus genotype 1|41856 -VRMILMTHF ->423075|polyprotein|ACX44241.1|Hepatitis C virus genotype 1|41856 -VVLFGLMAL ->423080|Genome polyprotein|P26664.3|Hepatitis C virus genotype 1|41856 -YFLTRVEAQL ->423082|Genome polyprotein|P26664.3|Hepatitis C virus genotype 1|41856 -YRFVAPGER diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/output/NeoantigenQuality.txt b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/output/NeoantigenQuality.txt deleted file mode 100755 index 89417ecf..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/output/NeoantigenQuality.txt +++ /dev/null @@ -1,5391 +0,0 @@ -NeoantigenID MT.Peptide.Form NeoantigenQuality NeoantigenAlignment IEDB_EpitopeAlignment AlignmentScore IEDB_Epitope -1 HIQDLYTVL 3.17191804867 HIQDLYTVL HAQDATTVL 28.0 6373|Genome_polyprotein|SRC279960|Hepatitis_C_virus_subtype_3a|356426 -2 GYYTLLNVF 20.9213483146 GYYTLLN GFYHILN 26.0 1516|Nucleoprotein|P03418.1|Human_respiratory_syncytial_virus_A2|11259 -3 LTLFGYYTL 0.266904846489 LTLFGYY LTLSPYY 23.0 149024|NS2_protein|NP_751923.1|Hepatitis_C_virus_(isolate_H77)|63746 -4 TLFGYYTLL 0.0 None None 0 None -5 YYTLLNVFL 0.297457866327 YTLLNVFL FTILALFL 23.0 180464|polyprotein|CDF77361.1|Dengue_virus_3|11069 -6 LAVRPSKIK 0.0 None None 0 None -7 PTYGNSTKL 0.734486359014 PTYGNS PLYGNE 25.0 75436|Polyprotein|P90247|Hepatitis_C_virus|11103 -8 TASNVEFAI 0.0 None None 0 None -9 TSSDSISHM 0.0 None None 0 None -10 RFRALNQEL 0.0 None None 0 None -11 HRNHIDRAL 0.0 None None 0 None -12 FALLFGHRF 0.733997564982 LLFGH LLFGH 28.0 37251|||| -13 HRFDYRDPV 0.0 None None 0 None -14 VADSTLLLM 0.0 None None 0 None -15 FKMGAHTEV 0.0 None None 0 None -16 FEGFPQSLL 0.217642336766 FEGFPQSLL FPGFGQSLL 32.0 23807|tax|AAG48731.1|Human_T-lymphotropic_virus_2|11909 -17 FEGFPQSLL 0.126853192431 FEGFPQSLL FPGFGQSLL 32.0 23807|tax|AAG48731.1|Human_T-lymphotropic_virus_2|11909 -18 GAQDRNSSF 0.0 None None 0 None -19 FTHLRLQEF 0.0 None None 0 None -20 LAASGPTLV 0.0 None None 0 None -21 MIVGRTYTL 0.0037423128393 IVGRTYTL ILGFVFTL 20.0 20354|M1_protein|CAA30882.1|Influenza_A_virus|11320 -22 VAAENEAVL 0.0 None None 0 None -23 IERNLINSL 1.02340662483 ERNLINSL EENLVNSL 32.0 182938|polyprotein|AGO67248.1|Dengue_virus_2|11060 -24 GEAGTIERV 0.448867741662 EAGTIERV EAGNFERI 28.0 194242|ESAT-6-like_protein_esxB|P0A566.2|Mycobacterium_tuberculosis|1773 -25 VAIFLGFYV 0.0 None None 0 None -26 YSIFQLAFV 0.0 None None 0 None -27 MALNYNRAF 0.0 None None 0 None -28 TVFGGLMAL 0.0 None None 0 None -29 LSSRLSDTL 0.0 None None 0 None -30 SRLSDTLSF 0.0 None None 0 None -31 KRTSPEELL 0.0 None None 0 None -32 HALHLRRMM 0.0 None None 0 None -33 MAGFMGMAV 0.0259001423454 MAGFMG MTGFTG 22.0 108153|polyprotein|AAF65950.1|Hepatitis_C_virus|11103 -34 RMMAGFMGM 0.795816444397 MMAGFMG LMTGFTG 24.0 108153|polyprotein|AAF65950.1|Hepatitis_C_virus|11103 -35 FVSTIIHLL 0.0 None None 0 None -36 YLVPGFSPY 0.0 None None 0 None -37 YLVPGFSPY 0.0 None None 0 None -38 KASFDHACL 0.0 None None 0 None -39 EFHDIASHV 0.0 None None 0 None -40 MCDNGSGLV 0.0 None None 0 None -41 IQNAGGSVI 0.601030334228 IQNAGGSVI IQNSGGTSI 31.0 183843|envelope_protein|AGW23576.1|Dengue_virus_3|11069 -42 TQDGALMNV 0.0 None None 0 None -43 TLGIICLLL 0.665172700533 TLGIIC TLGIVC 31.0 64818|E7|AAD33253.1|Human_papillomavirus_type_16|333760 -44 WNDKVKEAL 0.0 None None 0 None -45 QNAGGSVII 3.46504561837 QNAGGS QNAGGT 28.0 27981|IMMUNOGENIC_PROTEIN_MPT64_(ANTIGEN_MPT64/MPB64)|CAA98382.1|Mycobacterium_tuberculosis_H37Rv|83332 -46 SDYLHWEVV 0.0 None None 0 None -47 SSVPVLNML 0.0 None None 0 None -48 WALEVLLNA 0.463508918806 WALEVLL WTLVVLL 25.0 37960|membrane_protein|AAA45887.1|Human_gammaherpesvirus_4|10376 -49 YETQDGALM 0.0 None None 0 None -50 NMELPYFVL 0.50520798857 LPYFV LPYLV 22.0 13518|HCV-1|AAA45676.1|Hepatitis_C_virus_genotype_1|41856 -51 LSTPAPQVF 0.0 None None 0 None -52 VSDTEFHPL 0.0 None None 0 None -53 MVVAGQRAV 0.0 None None 0 None -54 YLHWEVVEL 0.0 None None 0 None -55 ANFPWALEV 1.23311590917 ANFPWAL TSFPWLL 28.0 34616|pol_protein|BAA32832.1|Hepatitis_B_virus|10407 -56 WYLRDVSEV 0.0 None None 0 None -57 FHDIASHVK 0.0 None None 0 None -58 FPWALEVLL 0.261558715685 WALEVLL WTLVVLL 25.0 37960|membrane_protein|AAA45887.1|Human_gammaherpesvirus_4|10376 -59 GTLGIICLL 50.3407812466 TLGIIC TLGIVC 31.0 64818|E7|AAD33253.1|Human_papillomavirus_type_16|333760 -60 YLHWEVVEL 0.0 None None 0 None -61 LQFSRMEQL 0.0 None None 0 None -62 VHLESNATV 0.0 None None 0 None -63 QMFVHLQLL 0.0 None None 0 None -64 VHLESNATV 0.0 None None 0 None -65 TQDGALMNV 0.0 None None 0 None -66 VAFCLKCNL 0.642271486634 VAFCLKCN VTFCCKCD 33.0 110184|E7|AAD33253.1|Human_papillomavirus_type_16|333760 -67 STDSLSTPA 0.0 None None 0 None -68 DILEKSSSV 0.0749249088856 LEKSSSV MEKCSSV 23.0 13456|circumsporozoite_protein|AAN87606.1|Plasmodium_falciparum|5833 -69 NMVGFSDRV 0.0 None None 0 None -70 NLGSKLQLV 0.0 None None 0 None -71 FPWALEVLL 4.41902830893 WALEVLL WTLVVLL 25.0 37960|membrane_protein|AAA45887.1|Human_gammaherpesvirus_4|10376 -72 TKDTFMMEL 0.0 None None 0 None -73 HCANFPWAL 32.1490933462 ANFPWAL TSFPWLL 28.0 34616|pol_protein|BAA32832.1|Hepatitis_B_virus|10407 -74 ESSSETSTY 0.0 None None 0 None -75 QMFVHLQLL 0.0 None None 0 None -76 QPLKYTWLL 2.79400019666 PLKYTW PYKPTW 24.0 68229|EBNA3B_(EBNA4A)_latent_protein|CAA24858.1|Human_gammaherpesvirus_4|10376 -77 SLTTLLQAL 0.0 None None 0 None -78 SLSTPAPQV 0.0 None None 0 None -79 FAINFFKEV 0.0 None None 0 None -80 YTWLLAAKV 0.0 None None 0 None -81 DLENMELPY 0.0 None None 0 None -82 EKSSSVPVL 0.0 None None 0 None -83 WLCDHPVPV 0.376517989918 WLCDHP WILRHP 25.0 180818|Membrane_glycoprotein_precursor|NP_739582.2|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -84 LLMSTLGIL 1.08239342869 LLMSTLGIL LLMGTLGIV 33.0 37573|E7_protein|ABL96585.1|Human_papillomavirus_type_16|333760 -85 IQNAGGSVI 3.24997372157 IQNAGGSVI IQNSGGTSI 31.0 183843|envelope_protein|AGW23576.1|Dengue_virus_3|11069 -86 YTWLLAAKV 0.0 None None 0 None -87 FSQEPADQM 0.0 None None 0 None -88 ILSWLVSQL 0.0 None None 0 None -89 LLLMSTLGI 172.260279525 LLMSTLGI LLMGTLGI 32.0 37573|E7_protein|ABL96585.1|Human_papillomavirus_type_16|333760 -90 FYIFNVSSI 0.0 None None 0 None -91 GLGECITQV 0.0 None None 0 None -92 LAMRRHSRI 0.0449655249052 AMRRHS AMKRYS 22.0 419017|polyprotein|AFY10034.1|Dengue_virus_4|11070 -93 LAKDSGAPV 0.0 None None 0 None -94 YLHWEVVEL 0.0 None None 0 None -95 FMMELLNRV 0.0 None None 0 None -96 WLCDHPVPV 0.403412132055 WLCDHP WILRHP 25.0 180818|Membrane_glycoprotein_precursor|NP_739582.2|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -97 FAINFFKEV 0.0 None None 0 None -98 FMMELLNRV 0.0 None None 0 None -99 TVAEKRGWK 0.0 None None 0 None -100 RLLPDTFVL 0.0 None None 0 None -101 RLLPDTFVL 0.0 None None 0 None -102 SSMAAGLEH 0.0 None None 0 None -103 MIYRLAQAK 0.0 None None 0 None -104 TPMYRTRPA 0.00472046238994 TPMYRTRP TPQVPLRP 20.0 102150|nef_protein|ACR27119.1|Human_immunodeficiency_virus_1|11676 -105 ITYYCHGGY 0.121528332848 YCHGG FCHPG 24.0 79454|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 -106 KLGSSITYY 0.0 None None 0 None -107 FPVSYGVPA 0.440869275563 VSYGVP VYYGVP 26.0 118|envelope_glycoprotein|ABS76372.1|Human_immunodeficiency_virus_1|11676 -108 IMFPVSYGV 0.0 None None 0 None -109 ISDTILKTK 0.0 None None 0 None -110 RLQTHTIYK 0.0 None None 0 None -111 ELFHVDWHV 0.224791106174 LFHVDW LVHRQW 19.0 41407|Envelope_protein|NP_739583.2|Dengue_virus_2|11060 -112 LPRQYWEAL 1.00520554562 LPRQYW LPEGYW 27.0 31997|hypothetical_protein_FTT0484|YP_169522.1|Francisella_tularensis_subsp._tularensis_SCHU_S4|177416 -113 MPHRATVYA 0.0 None None 0 None -114 KLLECSLTK 0.0 None None 0 None -115 RPQGQRPAL 43.5210604434 PQGQRPAL PRGSRPSW 27.0 36352|Polyprotein|P90247|Hepatitis_C_virus|11103 -116 SSDCIIEKK 0.000135734033585 SDCIIEKK SACQRQKK 17.0 66405|polyprotein|AAB67037.1|Hepatitis_C_virus_(isolate_H77)|63746 -117 TSSDCIIEK 0.0 None None 0 None -118 GLMGHTLHR 0.0 None None 0 None -119 LPGHAPGIL 0.097025634204 PGHAPG PGTGPG 24.0 47760|EBNA-1_protein|Q777E1|Human_gammaherpesvirus_4|10376 -120 YAYHVEWEK 0.0 None None 0 None -121 WVRWHKGCL 0.00804646235146 WVRWHKG WILRHPG 22.0 180818|Membrane_glycoprotein_precursor|NP_739582.2|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -122 SSSIRIHER 0.0 None None 0 None -123 FLSSSFSML 0.0 None None 0 None -124 FSMLKDHIK 0.0 None None 0 None -125 LSSSFSMLK 0.0 None None 0 None -126 VVGADGVGK 0.0 None None 0 None -127 AVDLSSAGM 0.0 None None 0 None -128 GMAGVLIGY 0.0543590087265 GMAGVLIG GMGPSLIG 21.0 21275|Antigen_85-B_precursor_(85B)_(Extracellular_alpha-antigen)_(Antigen_85_complex_B)_(Ag85B)_(Mycolyl_transferase_85B)_(Fibronectin-binding_protein_B)_(30_kDa_extracellular_protein)|P31952|Mycobacterium_tuberculosis|1773 -129 SSAGMAGVL 0.0 None None 0 None -130 KAAPIYKLV 0.0 None None 0 None -131 VTKAAPIYK 0.0 None None 0 None -132 FLPSWLLGI 1.88888888889 LPSWL LPQWL 26.0 13215|Antigen_85-B|P0C5B9.1|Mycobacterium_tuberculosis|1773 -133 RMAFTDHQL 38.3657688551 FTDHQL FPDHQL 28.0 190466|large_surface_antigen|CAL29876.1|Hepatitis_B_virus|10407 -134 RMAFTDHQL 20.2035463724 FTDHQL FPDHQL 28.0 190466|large_surface_antigen|CAL29876.1|Hepatitis_B_virus|10407 -135 ALQPQLGCY 0.0 None None 0 None -136 YQQALQPQL 0.0 None None 0 None -137 YQQALQPQL 0.0 None None 0 None -138 YQLKMLIKI 0.0 None None 0 None -139 ILLVVYNNV 0.0 None None 0 None -140 LLVVYNNVL 0.0 None None 0 None -141 LLVVYNNVL 0.0 None None 0 None -142 LVVYNNVLK 0.0 None None 0 None -143 LSGHSTQDL 0.0 None None 0 None -144 QALSKFKAM 0.0 None None 0 None -145 LSVDRMRKV 0.0 None None 0 None -146 LGVAARWDL 0.0 None None 0 None -147 HAVQAAVQY 0.0 None None 0 None -148 HAVQAAVQY 0.0 None None 0 None -149 KIMNSLPEM 0.0 None None 0 None -150 KIMNSLPEM 0.0 None None 0 None -151 LPEMKVQLV 0.0 None None 0 None -152 SLPEMKVQL 0.0 None None 0 None -153 LTISGECPK 0.0143889679697 ISGECP MSGEVP 22.0 423011|polyprotein|AER51001.1|Hepatitis_C_virus_genotype_1|41856 -154 AMYDVLTFA 27.3958151719 AMYDVLT ALYDVVT 29.0 3019|polyprotein|AAA45677.1|Hepatitis_C_virus_(isolate_H77)|63746 -155 ATDQAMYDV 0.00252195188532 DQAMYDV DRAHYNI 20.0 110431|E7|AAD33253.1|Human_papillomavirus_type_16|333760 -156 KIHATDQAM 0.868183841638 KIHATD KAHGTD 23.0 107925|polyprotein|AAF65964.1|Hepatitis_C_virus|11103 -157 QAMYDVLTF 24.0160297669 AMYDVLT ALYDVVT 29.0 3019|polyprotein|AAA45677.1|Hepatitis_C_virus_(isolate_H77)|63746 -158 QAMYDVLTF 184.760877861 AMYDVLT ALYDVVT 29.0 3019|polyprotein|AAA45677.1|Hepatitis_C_virus_(isolate_H77)|63746 -159 LICFLTPVK 0.0 None None 0 None -160 NLICFLTPV 0.0 None None 0 None -161 IAHIFGGAR 0.0 None None 0 None -162 LLEISKWFR 0.0 None None 0 None -163 FSDDGVLGP 0.179294280913 FSDDGVLGP YMDDVVLGA 25.0 75040|Protein_P|P03159.1|Hepatitis_B_virus|10407 -164 GSFSDDGVL 0.0 None None 0 None -165 VLGPVLTTF 0.0 None None 0 None -166 ATSIPAGSM 0.0 None None 0 None -167 IPAGSMPTV 0.289341771885 PAGSMPTV PEGIIPTL 24.0 180778|polyprotein|AFP27208.1|Dengue_virus_4|11070 -168 IMDLRNGTF 0.0 None None 0 None -169 CLSGYCSVF 1.19084512931 CLSGYC CISGVC 29.0 95281|polyprotein|ACE82433.1|Hepatitis_C_virus_genotype_1|41856 -170 CSVFAYKPM 0.0 None None 0 None -171 GYCSVFAYK 0.0 None None 0 None -172 SGYCSVFAY 0.0 None None 0 None -173 LIMALVWSL 0.0117124891175 LIMALVWSL LLMRTTWAF 21.0 184453|polyprotein|AFP27207.1|Dengue_virus_4|11070 -174 LIMALVWSL 0.0164467732015 LIMALVWSL LLMRTTWAF 21.0 184453|polyprotein|AFP27207.1|Dengue_virus_4|11070 -175 LIMALVWSL 0.00513721530405 LIMALVWSL LLMRTTWAF 21.0 184453|polyprotein|AFP27207.1|Dengue_virus_4|11070 -176 LVWSLPCGF 2.09703631178 VWSLPCGF LWHYPCTF 30.0 54820|polyprotein_precursor|BAA02756.1|Hepatitis_C_virus|11103 -177 ESDYLINEM 0.0 None None 0 None -178 YLINEMYL* 0.0 None None 0 None -179 TQMVDIWSV 0.0 None None 0 None -180 MVAFFSSHT 0.0972906201798 VAFFSSHT IAFTSEHS 24.0 25275|Glutamate_decarboxylase_2|Q05329.1|Homo_sapiens|9606 -181 VAFFSSHTY 0.636929460581 VAFFSSHTY IAFTSEHSH 26.0 25275|Glutamate_decarboxylase_2|Q05329.1|Homo_sapiens|9606 -182 VAFFSSHTY 0.477777777778 VAFFSSHTY IAFTSEHSH 26.0 25275|Glutamate_decarboxylase_2|Q05329.1|Homo_sapiens|9606 -183 VAFFSSHTY 0.357142857143 VAFFSSHTY IAFTSEHSH 26.0 25275|Glutamate_decarboxylase_2|Q05329.1|Homo_sapiens|9606 -184 VTFSTSSQL 0.0 None None 0 None -185 WVDFADSVT 0.0 None None 0 None -186 YQTFKDWGI 0.0 None None 0 None -187 ISMGQEEKK 0.0 None None 0 None -188 WISMGQEEK 0.0 None None 0 None -189 FSWQSHLLI 0.0 None None 0 None -190 QSHLLIHQR 0.0 None None 0 None -191 FYIIECIAM 0.0275788552752 YIIECIA YIMACMS 22.0 24457|polyprotein|BAA09072.1|Hepatitis_C_virus|11103 -192 TAFYIIECI 0.0 None None 0 None -193 YIIECIAMS 0.0570151100106 YIIECIA YIMACMS 22.0 24457|polyprotein|BAA09072.1|Hepatitis_C_virus|11103 -194 ASTYSQLKL 0.0 None None 0 None -195 SASTYSQLK 0.0 None None 0 None -196 VSASTYSQL 0.0 None None 0 None -197 YSQLKLWNV 0.0 None None 0 None -198 FYQHLNLMR 0.0 None None 0 None -199 YQHLNLMRV 0.0 None None 0 None -200 KPAPHPQAL 0.0 None None 0 None -201 MADSGPIYN 0.0 None None 0 None -202 GLGFYNDVV 6.41833817492 GLGFYNDV GYGFVNYV 23.0 36358|ELAV-like_protein_1|Q15717.2|Homo_sapiens|9606 -203 FCENDAEVL 0.0 None None 0 None -204 RTTQQENPR 0.0 None None 0 None -205 AMDDLDTDM 1.44491577894 AMDDLDTDM TLNDLETDV 27.0 64967|Circumsporozoite_protein_precursor|P08677.2|Plasmodium_vivax_strain_Belem|31273 -206 EECGKTFYR 0.0 None None 0 None -207 MITQFELQK 0.0 None None 0 None -208 CTAMRVAAK 0.0 None None 0 None -209 HFERLTRAL 0.0 None None 0 None -210 RLKFGNKHK 0.0108863902402 RLKFGNKHK RLRPGGKKK 22.0 54741|gag_polyprotein|BAA00992.1|Human_immunodeficiency_virus_1|11676 -211 ASQQGMAAL 0.0 None None 0 None -212 LDYASQQGM 0.0 None None 0 None -213 YASQQGMAA 0.0 None None 0 None -214 GVRAGRLQL 0.0 None None 0 None -215 VRAGRLQLF 0.0 None None 0 None -216 LFIHHIQGL 0.0 None None 0 None -217 FCSIYITLL 0.0 None None 0 None -218 HHSPSTHVM 0.0 None None 0 None -219 RSFWSHVVR 0.0 None None 0 None -220 AEVEVADKL 0.0 None None 0 None -221 KLLENLAKV 0.0 None None 0 None -222 MAEAKRMKL 0.0 None None 0 None -223 SMAEAKRMK 0.0 None None 0 None -224 SYESCDAHF 0.0 None None 0 None -225 ASFVPSMGK 0.0 None None 0 None -226 FVPSMGKNL 0.0 None None 0 None -227 IPASFVPSM 0.825781600633 IPASFVPSM LPADFFPSI 30.0 16795|precore/core_protein|AAP57273.1|Hepatitis_B_virus|10407 -228 SVSIPASFV 0.0 None None 0 None -229 HLGVPVTLR 0.0 None None 0 None -230 RVQHLGVPV 0.0 None None 0 None -231 NPNTGSVYM 0.0 None None 0 None -232 VYMNSQQSL 0.0 None None 0 None -233 VYMNSQQSL 0.0 None None 0 None -234 EMAKFKVTI 0.0 None None 0 None -235 KLFGYEMAK 0.0 None None 0 None -236 MAKFKVTIK 0.0 None None 0 None -237 HRTIPYLDL 0.0 None None 0 None -238 IVWEHRQKL 0.0 None None 0 None -239 GMVAPDVVK 0.0 None None 0 None -240 HPGVSSQFL 0.305854949793 HPGVSSQF HPTFTSQY 25.0 75718|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 -241 SPRGGPPPL 0.0 None None 0 None -242 IVHPLKPQM 0.0 None None 0 None -243 KPQMNYQTA 0.0 None None 0 None -244 AYCSYCYYF 0.0 None None 0 None -245 NAYCSYCYY 0.0 None None 0 None -246 SPAPERCMV 1.2380952381 PERCM PRRCM 26.0 56310|polyprotein|AGO67248.1|Dengue_virus_2|11060 -247 ALMDMYPHV 0.0 None None 0 None -248 IGVDDRRRL 0.0 None None 0 None -249 RRRLCILRM 0.0 None None 0 None -250 HFQWILFFV 1.9418540523 FQWILFFV LMWLSYFV 24.0 21041|Membrane_glycoprotein|Q692E0|SARS_coronavirus_TJF|284672 -251 HVPGAVPNL 0.0 None None 0 None -252 SLTGDVSPL 0.0 None None 0 None -253 HMVERIQFV 0.0123869954441 MVERIQFV MLEDHEFV 18.0 164551|envelope_glycoprotein_B|NP_044629.1|Herpes_simplex_virus_(type_1_/_strain_17)|10299 -254 HFERLTRAL 0.0 None None 0 None -255 ASQQGMAAL 0.0 None None 0 None -256 LDYASQQGM 0.0 None None 0 None -257 YASQQGMAA 0.0 None None 0 None -258 GVRAGRLQL 0.0 None None 0 None -259 VRAGRLQLF 0.0 None None 0 None -260 APAGGTASA 0.0 None None 0 None -261 HHSPSTHVM 0.0 None None 0 None -262 FGHITHPCM 0.0 None None 0 None -263 RSFWSHVVR 0.0 None None 0 None -264 AAAAAAAAT 0.0 None None 0 None -265 VSSKSQKLL 0.0 None None 0 None -266 YSLSPVSSK 0.0 None None 0 None -267 AEVEVADKL 0.0 None None 0 None -268 KLLENLAKV 0.0 None None 0 None -269 MAEAKRMKL 0.0 None None 0 None -270 SMAEAKRMK 0.0 None None 0 None -271 YRWCGFPQL 0.0 None None 0 None -272 YRWCGFPQL 0.0 None None 0 None -273 SYESCDAHF 0.0 None None 0 None -274 FLVGLWSHL 0.927664444497 FLVGLWS LLLGLWG 26.0 37498|FL-160-2_protein_-_Trypanosoma_cruzi|JH0823|Trypanosoma_cruzi|5693 -275 KPRFLVGLW 122.389953 KPRFLVGL RPMFAVGL 27.0 185468|polyprotein|AGW21594.1|Dengue_virus_1|11053 -276 LVGLWSHLL 12.7260693351 LVGLWS LLGLWG 26.0 37498|FL-160-2_protein_-_Trypanosoma_cruzi|JH0823|Trypanosoma_cruzi|5693 -277 MPPYYVGPL 0.0 None None 0 None -278 TALPTYPPY 4.49696133214 ALPTYPP SLPSYYP 24.0 28594|IMMUNOGENIC_PROTEIN_MPT64_(ANTIGEN_MPT64/MPB64)|CAA98382.1|Mycobacterium_tuberculosis_H37Rv|83332 -279 FEGFPQSPL 0.939393939394 FPQSPL FPRAPL 26.0 18390|Genome_polyprotein|P08617.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 -280 NPNTGSVYM 0.0 None None 0 None -281 VYMNSQQSL 0.0 None None 0 None -282 VYMNSQQSL 0.0 None None 0 None -283 KRQQFGSQF 0.0 None None 0 None -284 DPFALFFMA 0.0 None None 0 None -285 EYAADPFAL 0.0 None None 0 None -286 YAADPFALF 0.000123394575986 YAADPFALF YVAGFLALY 17.0 141484|capsid_maturation_protease|NP_044627.1|Human_alphaherpesvirus_1|10298 -287 HRTIPYLDL 0.0 None None 0 None -288 IVWEHRQKL 0.0 None None 0 None -289 HSVAIVSPF 0.0 None None 0 None -290 RIGFVGLFH 0.0 None None 0 None -291 HPGVSSQFL 0.305854949793 HPGVSSQF HPTFTSQY 25.0 75718|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 -292 IVHPLKPQM 0.0 None None 0 None -293 KPQMNYQTA 0.0 None None 0 None -294 AYCSYCYYF 0.0 None None 0 None -295 NAYCSYCYY 0.0 None None 0 None -296 SPAPERCMV 1.2380952381 PERCM PRRCM 26.0 56310|polyprotein|AGO67248.1|Dengue_virus_2|11060 -297 LTLAVYLSF 0.0 None None 0 None -298 ALMDMYPHV 0.0 None None 0 None -299 IGVDDRRRL 0.0 None None 0 None -300 RRRLCILRM 0.0 None None 0 None -301 DTAWDTLEL 7.29864653969 DTAWD DTAWD 32.0 180726|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -302 TAWDTLELI 0.0 None None 0 None -303 TAWDTLELI 0.0 None None 0 None -304 MSVSQKLTL 0.0 None None 0 None -305 HQRAHTGEK 0.0 None None 0 None -306 AVATITQAL 0.0 None None 0 None -307 TTVNGNTAL 0.0 None None 0 None -308 EYYSQTTGL 0.0 None None 0 None -309 YYSQTTGLC 0.0 None None 0 None -310 CPSEPNTPM 0.0 None None 0 None -311 TPMARTFDW 0.0 None None 0 None -312 GHYEVRASL 0.0 None None 0 None -313 HYEVRASLL 0.0 None None 0 None -314 MYWRRSQCC 0.0 None None 0 None -315 DYPNAYTTW 1.44061741991 DYPNAYTTW DQENPYRTW 31.0 186550|polyprotein|AFY10039.1|Dengue_virus_4|11070 -316 RYSDYPNAY 1.76428417258 SDYPN SEYPN 26.0 57703|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 -317 AADLPILTW 0.0 None None 0 None -318 WLLAADLPI 0.00994626965127 WLLAADLP WCVEHDRP 19.0 120093|unnamed_protein_product|CAA33016.1|Rubella_virus|11041 -319 IPPEANITI 0.0 None None 0 None -320 TVHNLCHIL 0.0 None None 0 None -321 FFVEKRHAF 0.599743535066 VEKRHAF LEKRHVL 24.0 183781|polyprotein|AGO67248.1|Dengue_virus_2|11060 -322 LPLTRSMSI 0.0 None None 0 None -323 AAAAATSAL 0.0 None None 0 None -324 SIYAYHVEW 0.0 None None 0 None -325 AYPQYVIEY 0.427796389876 AYPQYV GYPRYV 26.0 37254|||| -326 FSSKPSSIY 0.0 None None 0 None -327 SIYGGLVLI 0.0 None None 0 None -328 SAESGAQLL 0.0 None None 0 None -329 GIICLDYKL 0.738702286919 GIICL GVLCL 24.0 185978|polyprotein|CDF77361.1|Dengue_virus_3|11069 -330 FEDIGDEDL 0.0 None None 0 None -331 IRVEESMHL 0.142206994693 RVEESMHL RVEAQLHV 24.0 40158|polyprotein|AAA45534.1|Hepatitis_C_virus|11103 -332 AMEKLLSGK 0.0 None None 0 None -333 ARTGHLPAM 0.0 None None 0 None -334 GHLPAMEKL 0.0867552972161 GHLPAMEKL GHQAAMQML 25.0 101673|gag_protein|ABO73990.1|Human_immunodeficiency_virus_1|11676 -335 QVYHWVCEK 0.0 None None 0 None -336 HRWNRFTMI 0.0 None None 0 None -337 THRWNRFTM 0.0173518357296 THRWNRFTM THPITKFVM 21.0 103389|unnamed_protein_product_[Hepatitis_C_virus]|BAA14035.1|Hepatitis_C_virus|11103 -338 ITSGLEVIY 0.0 None None 0 None -339 ARRFWGKIM 0.0 None None 0 None -340 RFWGKIMAK 0.0 None None 0 None -341 TYEEATVYI 0.0 None None 0 None -342 EHAAALWAL 0.252958579882 HAAALWAL HPASAWTL 26.0 183594|polyprotein|AGT63075.1|Dengue_virus_1|11053 -343 LVLMNWTKK 0.418604651163 VLMNWTK MMMNWSP 26.0 42152|polyprotein|AAY82055.1|Hepatitis_C_virus_(isolate_H77)|63746 -344 FTDTAAESA 0.0 None None 0 None -345 NIEDSASFY 0.0 None None 0 None -346 SRSDAAKHL 0.0 None None 0 None -347 LRWRHCQRL 0.0 None None 0 None -348 WRHCQRLDV 0.0 None None 0 None -349 VRLGPVKSI 2.30860618466 RLGPVKS RLGPVQN 28.0 146528|NS3/4A_protein|CAM56207.1|Hepatitis_C_virus|11103 -350 SMQAHIKAL 0.0 None None 0 None -351 ESFKQTDFY 0.0 None None 0 None -352 QTDFYSMAL 0.0 None None 0 None -353 LPWMRLLLL 0.0 None None 0 None -354 MRLLLLLLV 0.0 None None 0 None -355 PRLPWMRLL 0.0 None None 0 None -356 WMRLLLLLL 0.0 None None 0 None -357 AIALHRLSL 0.0 None None 0 None -358 MRGHDWRML 0.0 None None 0 None -359 QMRGHDWRM 0.0 None None 0 None -360 HLETHNTDK 1.91662691262 ETHNTDK ECHSTDA 24.0 97111|polyprotein|ABR25251.1|Hepatitis_C_virus_(isolate_H77)|63746 -361 CSKLKHRDL 0.00687496931678 CSKLKHR CSARLHR 21.0 28508|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 -362 VVGAVGVGK 0.0 None None 0 None -363 AHPDGSWTF 5.46667302818 HPDGSWTF HPASAWTL 30.0 183594|polyprotein|AGT63075.1|Dengue_virus_1|11053 -364 WGRERGARV 0.0 None None 0 None -365 KADIPRDSY 0.0 None None 0 None -366 NVLQSSVPV 0.986093893012 NVLQSSVPV NVMLVTLPV 21.0 98308|trans-sialidase,_putative|EAN80840.1|Trypanosoma_cruzi|5693 -367 IITESGEVI 0.0 None None 0 None -368 WVYDAIITE 0.0 None None 0 None -369 FPPNILDDI 0.134347555558 PNILDDI PEIEDDI 24.0 180682|polyprotein|AGO67248.1|Dengue_virus_2|11060 -370 MASQRPLQF 0.0 None None 0 None -371 DMHVAVKIV 0.0 None None 0 None -372 FARPASPSR 0.00268626303148 PASPSR PAKPAR 24.0 53405|||| -373 IVFEVFGHH 0.0 None None 0 None -374 TTAVLTATF 0.0 None None 0 None -375 MAAAVVARL 0.0 None None 0 None -376 FSLPPSRKK 0.0 None None 0 None -377 LPMCWAMEV 0.0 None None 0 None -378 LTYSCLDNK 0.0 None None 0 None -379 LLNSGGDII 0.0 None None 0 None -380 DIYCITDFV 0.0 None None 0 None -381 FVEELADTV 0.0 None None 0 None -382 TISCTSLKK 0.0 None None 0 None -383 VTISCTSLK 0.0 None None 0 None -384 IIIKCQLPK 0.0 None None 0 None -385 RYGAGQQNL 1.47210141005 YGAGQQNL YGAGQVML 28.0 5783|Nucleoprotein|P03418.1|Human_respiratory_syncytial_virus_A2|11259 -386 TPYAACPAI 0.61364033445 TPYAAC NPYAVC 27.0 110401|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 -387 SPFNTTFPF 0.0 None None 0 None -388 QVARRVQEL 0.0 None None 0 None -389 HREARGRAL 0.0 None None 0 None -390 AIFGPSNTY 1.40284974093 AIFGP AVFGP 26.0 96123|Genome_polyprotein|P26664.3|Hepatitis_C_virus_(isolate_H77)|63746 -391 DLFQFPKAY 0.258104503658 FQFPKA FYFPRA 24.0 18390|Genome_polyprotein|P08617.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 -392 LPEDPKCEF 0.0540961051747 PEDPKCE PTDVSCE 24.0 79628|E1_protein|BAA19893.1|Rubella_virus|11041 -393 SFQPKAAVF 0.0 None None 0 None -394 PPSETGGIF 0.0 None None 0 None -395 NAGEMVIEY 0.0 None None 0 None -396 APTSSDYEF 0.0 None None 0 None -397 LFCGLPFSI 3.79000971222 FCGLPFS FCGSPYS 33.0 190409|polymerase|AAD16253.1|Hepatitis_B_virus|10407 -398 VPVASSEAS 0.0 None None 0 None -399 DPSPGIMAF 0.0 None None 0 None -400 LTYSLLTPL 0.0 None None 0 None -401 TYSLLTPLL 0.0 None None 0 None -402 CYVAICNPF 0.0 None None 0 None -403 LAAMAIDCY 0.0 None None 0 None -404 MAIDCYVAI 5.96984686185 IDCYVAI IDCNVAV 28.0 419366|polyprotein|BAA00792.1|Hepatitis_C_virus|11103 -405 YFFLGNLAF 0.0 None None 0 None -406 FPVEDRRGV 0.0 None None 0 None -407 FAQLINNKM 0.0 None None 0 None -408 RVASVVVSF 0.0 None None 0 None -409 RVASVVVSF 0.0 None None 0 None -410 FYLRYFEK* 0.0 None None 0 None -411 FFSSNLPTY 0.0 None None 0 None -412 FSSNLPTYY 12.750272737 NLPTYY SLPSYY 27.0 28594|IMMUNOGENIC_PROTEIN_MPT64_(ANTIGEN_MPT64/MPB64)|CAA98382.1|Mycobacterium_tuberculosis_H37Rv|83332 -413 NPYKAPMAE 0.00506353396253 NPYKAPM NPEVIPM 20.0 187163|Gag_polyprotein|P88150|Human_immunodeficiency_virus_1|11676 -414 AFLQKAHLI 0.0226039482404 LQKAHLI LEKRHVL 21.0 184755|polyprotein|AGO67248.1|Dengue_virus_2|11060 -415 FQGYLKDPV 0.0 None None 0 None -416 SEVLGYWAF 0.745411820705 VLGYWAF LLGLWGF 27.0 98223|trans-sialidase,_putative|EAN80725.1|Trypanosoma_cruzi|5693 -417 SEVLGYWAF 0.675840050772 VLGYWAF LLGLWGF 27.0 98223|trans-sialidase,_putative|EAN80725.1|Trypanosoma_cruzi|5693 -418 RRFGWLQTA 0.0 None None 0 None -419 GHEEKITFI 0.0 None None 0 None -420 EESIAVGTM 0.0 None None 0 None -421 EESIAVGTM 0.0 None None 0 None -422 FRYLGKCNI 0.0 None None 0 None -423 FEVGGAALF 0.0 None None 0 None -424 FEVGGAALF 0.0 None None 0 None -425 GMCVLEMAV 0.0 None None 0 None -426 VLEMAVLEI 0.0 None None 0 None -427 FLMVSRDCL 0.022042337798 FLMVSRDCL FLLALLSCL 21.0 136837|polyprotein_precursor|BAA01582.1|Hepatitis_C_virus|11103 -428 SRDCLRTVL 0.0 None None 0 None -429 VSRDCLRTV 0.0 None None 0 None -430 ALREFKFRV 0.0 None None 0 None -431 REFKFRVSA 0.0 None None 0 None -432 REFKFRVSA 0.0 None None 0 None -433 YEALREFKF 0.0 None None 0 None -434 NQMDKLAAF 0.0 None None 0 None -435 YRMSPSNQM 0.0 None None 0 None -436 KVISYPVAL 0.0 None None 0 None -437 TERTKVISY 0.0 None None 0 None -438 LHLRRKEIM 0.0 None None 0 None -439 QTSCHVFMV 0.0 None None 0 None -440 GEAGAGGTA 0.0 None None 0 None -441 EHMPNNSRL 0.0 None None 0 None -442 PRKPRSQNF 0.0 None None 0 None -443 RQWPRLSHK 0.941940860927 QWPRLSH TWPLLPH 27.0 79337|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 -444 ISLAYLVKK 0.0 None None 0 None -445 TISLAYLVK 0.0 None None 0 None -446 MFLWTVAVI 0.0 None None 0 None -447 TVAVIPILF 0.0 None None 0 None -448 KIRQLKKKK 0.0 None None 0 None -449 NEKTTPSPA 0.00746553042847 NEKTTP NSKRTP 22.0 419298|RNA-dependent_RNA_polymerase|ACH97782.1|Hepatitis_C_virus|11103 -450 NENATPSPA 0.0 None None 0 None -451 RERTANENA 0.0 None None 0 None -452 CYLQIFATR 0.0 None None 0 None -453 LPPSLQGAV 8.55128205128 PPSLQGAV PPMVEGAA 26.0 48836|EBNA-1_protein|Q777E1|Human_gammaherpesvirus_4|10376 -454 RVARSHCQR 0.0 None None 0 None -455 VPSEPSSSV 0.0 None None 0 None -456 EEWCSLWAG 0.0 None None 0 None -457 WEEWCSLWA 0.0453634499044 WEEWCSLW WPKTHTLW 22.0 184702|non-structural_protein_1|AGM49312.1|Dengue_virus|12637 -458 RLPSYMVEK 0.0 None None 0 None -459 SYMVEKREF 0.00754725742526 MVEKREF MLEDHEF 21.0 164551|envelope_glycoprotein_B|NP_044629.1|Herpes_simplex_virus_(type_1_/_strain_17)|10299 -460 GENFCTAVK 0.0 None None 0 None -461 MEGYMKAKV 0.0 None None 0 None -462 CPLPRPPPI 0.84385451991 LPRPPP LPRPGP 28.0 139406|polyprotein|ACT37184.1|Hepatitis_C_virus|11103 -463 AEEAGYPLS 0.0304382014743 EAGYPLS EVGFPVR 22.0 288104|nef_protein|ACR27130.1|Human_immunodeficiency_virus_1|11676 -464 EEAGYPLSC 0.0464643757354 EAGYPLS EVGFPVR 22.0 288104|nef_protein|ACR27130.1|Human_immunodeficiency_virus_1|11676 -465 GVYLLFALR 0.0 None None 0 None -466 VYLLFALRL 0.0 None None 0 None -467 QEASNKHAE 0.970660146699 QEASNKH QEAANKQ 26.0 3935|ESAT-6-like_protein_esxB|P0A566.2|Mycobacterium_tuberculosis|1773 -468 SEYSSSLGR 0.0 None None 0 None -469 RESGSFLST 0.0 None None 0 None -470 LYQLHNLVV 0.0 None None 0 None -471 YAAPQLHSI 0.0 None None 0 None -472 HLHDHYGPY 0.0 None None 0 None -473 FAEDGACTV 0.0 None None 0 None -474 HVIGTIGHF 0.0 None None 0 None -475 FADDEHSMV 0.0 None None 0 None -476 YANERPKSL 0.0 None None 0 None -477 FACHFTVFV 0.0 None None 0 None -478 NALDYICTV 0.0 None None 0 None -479 LAYQELPTV 0.133857018486 YQELPT YSEHPT 21.0 75718|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 -480 FVMEHSNIV 0.0 None None 0 None -481 VAFCTMNVI 0.0 None None 0 None -482 FTIRAIQVY 0.0 None None 0 None -483 MAISVVKHI 0.0395696619166 MAISVVK MALSIVS 22.0 180641|polyprotein|AFJ91714.1|Dengue_virus_1|11053 -484 RALEKLNHV 0.880797077978 ALEKLN ALEKLN 28.0 2506|M_protein,_serotype_5_precursor|P02977.2|Streptococcus_pyogenes_serotype_M5|301449 -485 FADMERHHI 1.33333333333 DMERHHI DLEKRHV 26.0 183781|polyprotein|AGO67248.1|Dengue_virus_2|11060 -486 FANRRKEEV 21.3373135759 ANRRKEEV ANKQKQEL 26.0 327|ESAT-6-like_protein_esxB|P0A566.2|Mycobacterium_tuberculosis|1773 -487 LAIDSASPV 0.0 None None 0 None -488 RALGPGHTV 0.000143960338651 ALGPGHTV AVGVYHIV 17.0 32663|small_hydrophobic_protein|AAM12943.1|Human_metapneumovirus|162145 -489 FAKVLIRTY 0.880797077978 KVLIRTY KVLIRCY 28.0 145860|Protein_E6|P04019.1|Human_papillomavirus_type_11|10580 -490 SSDDNDAFY 0.583333333333 SDDNDAFY TDNNRSFY 26.0 98603|trans-sialidase,_putative|EAN82716.1|Trypanosoma_cruzi|5693 -491 YPKGRPSHI 0.0 None None 0 None -492 WALPKTYTI 0.0 None None 0 None -493 LARHWRVHI 0.0 None None 0 None -494 FSYSASSEI 0.0 None None 0 None -495 FSFFFVNIF 0.0 None None 0 None -496 YSFDGMWKV 0.701469617998 SFDGMWKV SWDQMWKC 30.0 146570|polyprotein|ADY38595.1|Hepatitis_C_virus_subtype_1b|31647 -497 DSIHQVGMY 0.0359724199242 HQVGMY HAVGLF 22.0 23573|polyprotein|AAB67037.1|Hepatitis_C_virus_(isolate_H77)|63746 -498 MTYDLASVV 0.0 None None 0 None -499 LAFPVPLYY 0.80288104137 PVPLYY PIPIHY 28.0 47946|envelope_glycoprotein|AAC28452.1|Human_immunodeficiency_virus_1|11676 -500 YAALAMGTL 0.0 None None 0 None -501 YLFRELATI 0.0 None None 0 None -502 YMDLMGFSY 0.136231910882 YMDLMG YMSLLG 24.0 17117|matrix_protein|AAN09804.1|Measles_virus_strain_Edmonston|11235 -503 FAISHEGHM 0.0 None None 0 None -504 FSSPRLRPI 0.0 None None 0 None -505 FVYLHLNMV 0.973487792105 FVYLHLNMV LIHLHQNIV 26.0 2903|Genome_polyprotein|P27958.3|Hepatitis_C_virus_subtype_1a|31646 -506 MANNPDVMI 0.0 None None 0 None -507 AALPAAQTV 0.0 None None 0 None -508 FAWKNMDFL 0.104302556769 WKNMDFL WTSLNFL 24.0 62504|HBsAg_protein|ABF71024.1|Hepatitis_B_virus|10407 -509 FAAQGPTVF 0.0 None None 0 None -510 LALSNLPTV 0.0 None None 0 None -511 FTLEFLVCI 0.0 None None 0 None -512 FSVDFPRIY 0.208605113539 FPRIY FPRIW 24.0 187106|Vpr_protein|BAA93983.1|Human_immunodeficiency_virus_1|11676 -513 FTIFWTVYY 1.87174259914 IFWTVYY VMWTVYH 32.0 146249|polyprotein|ADE10208.1|Hepatitis_C_virus_subtype_3a|356426 -514 MADPNQCVI 1.01181629973 DPNQCV DPRRCL 24.0 150556|polyprotein|AGW21594.1|Dengue_virus_1|11053 -515 RAFWAGSVV 2.73888707955 AFWAGSVV TLWGGSVV 29.0 79351|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 -516 YHFDAIRTF 0.73105857863 FDAIRTF YDAVRTW 27.0 154164|tegument_protein|CAB06732.1|Human_alphaherpesvirus_2|10310 -517 FAKGWLLKL 0.992469783844 FAKGW FAQGW 28.0 8236|Genome_polyprotein|P27958.3|Hepatitis_C_virus_subtype_1a|31646 -518 NAQNMTITV 0.0 None None 0 None -519 RALNRVHVL 0.0 None None 0 None -520 MAPELISHL 0.0519601621127 MAPELISHL MEPTLGQHL 22.0 79308|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 -521 KAFYHPRLI 0.331355045526 FYHPR FYFPR 24.0 18390|Genome_polyprotein|P08617.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 -522 LAFVIVLLV 0.0 None None 0 None -523 CTAVVLLVY 0.0 None None 0 None -524 FTEFCDSCY 0.648148148148 FCDSCY ICDECH 26.0 107905|Genome_polyprotein|P26664.3|Hepatitis_C_virus|11103 -525 LAREPVNEL 0.0 None None 0 None -526 YTRKRTQSI 0.0 None None 0 None -527 FAPSCANSL 0.119202922022 FAPSCAN YSPSCCT 24.0 10962|envelope_glycoprotein|AAU04921.1|Human_T-lymphotropic_virus_1|11908 -528 KVYDLVHSV 0.278600815726 KVYDLVH RIYDLIE 25.0 55620|EBNA3C_latent_protein|CAD53421.1|Human_gammaherpesvirus_4|10376 -529 QAPPLMGTI 0.0 None None 0 None -530 QAFRRSISV 0.0 None None 0 None -531 FVLDHSRLV 0.12716493457 FVLDH YVLDH 25.0 25237|Transcription_activator_BRLF1|P03209.1|Human_herpesvirus_4_strain_B95-8|10377 -532 FIKRHIAPI 0.0 None None 0 None -533 YSQPFYTSY 0.0 None None 0 None -534 FAQDVDRMF 0.0 None None 0 None -535 QAPEFLQTL 0.242047279233 PEFLQTL PESLETL 25.0 184531|polyprotein|AFP27208.1|Dengue_virus_4|11070 -536 LSDISRSCY 0.0 None None 0 None -537 NAYARVLRF 0.0 None None 0 None -538 FANFFNTFL 0.0 None None 0 None -539 FIYDAVGNM 0.0 None None 0 None -540 LARECGSPL 0.0 None None 0 None -541 WHGPARPSL 0.0 None None 0 None -542 HVMFMVAFY 0.0 None None 0 None -543 MAITSMNPV 0.0 None None 0 None -544 TAVEFIMAI 0.0 None None 0 None -545 QAYGGPRYL 0.0520850061725 QAYGGP QLYRGP 22.0 38724|Genome_polyprotein|P08617.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 -546 FTIRAIQVY 0.0 None None 0 None -547 YLDYVSISY 0.0 None None 0 None -548 SAYMHHSKI 0.0 None None 0 None -549 YLMEFGQLL 0.710046526128 YLMEFG YLVSFG 24.0 69474|core_protein|BAF42671.1|Hepatitis_B_virus|10407 -550 KAEELKETV 0.0 None None 0 None -551 FALGVGTAL 0.809630010555 LGVGTAL LGIGTVL 28.0 108127|Genome_polyprotein|P26664.3|Hepatitis_C_virus|11103 -552 LVFPNSDHV 0.0 None None 0 None -553 FTLQNPSAV 0.0 None None 0 None -554 EIVDQQGHM 0.0 None None 0 None -555 FTIFWTVYY 1.15184159947 IFWTVYY VMWTVYH 32.0 146249|polyprotein|ADE10208.1|Hepatitis_C_virus_subtype_3a|356426 -556 FPNSCLSTL 0.0 None None 0 None -557 YSISDWTSI 0.0179862099621 WTSI WTSL 22.0 62504|HBsAg_protein|ABF71024.1|Hepatitis_B_virus|10407 -558 FTACYIRIV 0.0 None None 0 None -559 FEFDHIRNF 0.0205556685281 FDHIRNF FDRTRKF 22.0 154296|UL29|CAB06754.1|Human_alphaherpesvirus_2|10310 -560 YTPDELHAM 0.00621479014398 PDELHAM PDVAHSL 21.0 130953|G1_and_G2_surface_glycoprotein_precursor|AAG22532.1|Andes_hantavirus|46607 -561 FVHPATRPL 0.0 None None 0 None -562 KALRITNVY 0.0 None None 0 None -563 QARDQGSPV 0.0 None None 0 None -564 FIYDAVGNM 0.0 None None 0 None -565 EAFPEDVAV 0.0 None None 0 None -566 YATADSSSL 0.0 None None 0 None -567 RAREHSDTF 0.0 None None 0 None -568 IAIQLITHM 0.0 None None 0 None -569 MAFENNAGL 0.0 None None 0 None -570 FGHENRVSI 0.0 None None 0 None -571 NATTIVTTV 0.0 None None 0 None -572 VTFPGINLM 0.0 None None 0 None -573 DAYPRQYSL 0.0 None None 0 None -574 YIQEGFLAV 0.00185446736748 QEGFLAV QNGALAI 20.0 51685|Nuclear_antigen_EBNA-3C|Q69140.1|Human_gammaherpesvirus_4|10376 -575 FATTACHTL 0.0 None None 0 None -576 RANQCFAFV 0.0 None None 0 None -577 MTQPVWSTI 0.0 None None 0 None -578 FTEEGFCAI 0.0 None None 0 None -579 FADHPQAPF 0.0 None None 0 None -580 VAMGSAALV 0.0 None None 0 None -581 TAKDYRVYV 0.0 None None 0 None -582 EAEEWVVSY 0.0 None None 0 None -583 FTLPLMDQV 0.0 None None 0 None -584 MQMPCTIKI 0.0 None None 0 None -585 YRYFCRVPV 0.808012113223 YFCR YFCR 27.0 155131|ribonucleotide_reductase_large_subunit|CAB06725.1|Human_alphaherpesvirus_2|10310 -586 WAHAWPSPY 0.0047350399545 WAHAWPSPY WHYDEDNPY 20.0 72563|polyprotein|AAB70696.1|Dengue_virus_type_1_Hawaii|10000440 -587 IAIISVLVI 0.0 None None 0 None -588 MASCPFAKV 0.0 None None 0 None -589 NHDRFHYLL 5.22641395793 DRFHYLL DNFPYLV 22.0 9461|non_structural_protein_3|CAJ20172.1|Hepatitis_C_virus|11103 -590 FTIFWTVYY 1.73382472341 IFWTVYY VMWTVYH 32.0 146249|polyprotein|ADE10208.1|Hepatitis_C_virus_subtype_3a|356426 -591 VASQPAHVV 0.0 None None 0 None -592 EAFNCESKM 0.0 None None 0 None -593 FSSEVTVAL 0.0 None None 0 None -594 ETIKQLQEL 0.0 None None 0 None -595 YFMDPMVPL 0.0355694048832 DPMVPL DPTTPL 23.0 103392|polyprotein|BAB18806.1|Hepatitis_C_virus|11103 -596 NVYHVGMHI 0.0 None None 0 None -597 AAMEGRLPV 0.0 None None 0 None -598 NHDDDDVEI 167.634475679 NHDDDDVEI NHDSPDAEL 32.0 44133|Genome_polyprotein|P26664.3|Hepatitis_C_virus_genotype_1|41856 -599 NASVNVSHL 124.263294844 NASVNVS NSSVNVS 29.0 183670|polyprotein|AGO67248.1|Dengue_virus_2|11060 -600 EALDAGAIY 0.0 None None 0 None -601 YGRDDWEVI 0.0 None None 0 None -602 VALDKDALV 0.0 None None 0 None -603 LPFSLGKHV 0.0 None None 0 None -604 MANNPCSRY 0.0 None None 0 None -605 YEEPNTATF 0.0 None None 0 None -606 MALYHCVAI 0.0931643013308 ALYHCVAI SLYNTVAI 24.0 189292|gag_protein|ABC40295.1|Human_immunodeficiency_virus_1|11676 -607 YTLAPGVPL 0.176306491827 PGVPL PGVPF 24.0 38556|Genome_polyprotein|Q00269.3|Hepatitis_C_virus|11103 -608 KIHPFFETI 0.0 None None 0 None -609 NMDFLIAEY 0.0 None None 0 None -610 LCIPWTNPV 0.0 None None 0 None -611 SAQEHLLFV 0.0 None None 0 None -612 QSVHPVVTV 1.38374670414 QSVHPVVT KSTHPMVT 30.0 20686|UL123;_IE1|AAR31448.1|Human_betaherpesvirus_5|10359 -613 YVASDIQYM 0.0 None None 0 None -614 FHMRQVNIV 0.0 None None 0 None -615 LAKHSTSAV 0.0 None None 0 None -616 FSHQPKEKV 0.0 None None 0 None -617 YLYIPALAV 0.0 None None 0 None -618 VALFMAITI 0.0 None None 0 None -619 VAFYGLGAV 0.0 None None 0 None -620 EVDPIGNLY 0.0 None None 0 None -621 WALSIHVSV 0.0 None None 0 None -622 ITYPSQAPV 0.0 None None 0 None -623 CIALWSLAY 0.0 None None 0 None -624 FLFYVMTEV 0.0 None None 0 None -625 HAEQDSTTV 0.458333333333 QDSTTV QDATTV 26.0 6373|Genome_polyprotein|SRC279960|Hepatitis_C_virus_subtype_3a|356426 -626 DTNDNVPEF 0.0 None None 0 None -627 NSYGSRRTL 0.0 None None 0 None -628 NARCLIVHL 0.0 None None 0 None -629 FWYRNCHHV 0.0 None None 0 None -630 DADPSTPHL 1.08133686929 DPSTP DPTTP 26.0 103392|polyprotein|BAB18806.1|Hepatitis_C_virus|11103 -631 DSYIHVTYI 2.47386789457 YIHVTYI FLHVTYV 32.0 71663|Spike_glycoprotein_precursor|P59594.1|SARS_coronavirus|227859 -632 DVFDALDLM 0.0 None None 0 None -633 FSMDETGQM 0.0 None None 0 None -634 RTFNKPESV 0.0 None None 0 None -635 YSLQEMEVL 0.0 None None 0 None -636 QTVMFMATM 0.0 None None 0 None -637 VTIDGIRFI 0.0 None None 0 None -638 RALSHPQSL 0.0 None None 0 None -639 TAAGFWLMV 0.0 None None 0 None -640 FMEELGECV 0.0 None None 0 None -641 YLESNPGTI 0.0 None None 0 None -642 VPSNFVEHV 0.0 None None 0 None -643 FTEELRRTF 0.0062273472093 FTEELRR FVELMRR 20.0 39095|nonstructural_protein_3|NP_722463.1|Dengue_virus_type_1_Hawaii|10000440 -644 YGRSRGITV 0.146582464117 SRGITV DRGLTV 22.0 41269|kaposin|AAC57155.1|Human_gammaherpesvirus_8|37296 -645 FSMACNTPL 0.0 None None 0 None -646 QAADEPQLL 0.0 None None 0 None -647 YEFALQRIV 0.0 None None 0 None -648 TAAPTSASV 0.0 None None 0 None -649 LACRKAREI 0.249019834602 CRKARE CRCARE 25.0 155131|ribonucleotide_reductase_large_subunit|CAB06725.1|Human_alphaherpesvirus_2|10310 -650 FIEPLNDTI 0.0 None None 0 None -651 SALRAITRV 0.0 None None 0 None -652 RAAPKAMVL 0.0 None None 0 None -653 VADEGLNNL 0.0 None None 0 None -654 LSNDECKTI 0.0 None None 0 None -655 NAWAVMNHF 0.0 None None 0 None -656 VASNAWAVM 0.0 None None 0 None -657 LSRNLIRTI 0.830019904681 RNLIRTI QNLARTI 24.0 63010|6_kDa_early_secretory_antigenic_target|P0A564.2|Mycobacterium_tuberculosis|1773 -658 HSKEEIKVI 0.0 None None 0 None -659 DSELNFNEY 0.0 None None 0 None -660 DAAERECHL 0.0 None None 0 None -661 ISYTEVPTY 0.976082030541 ISYTEVPTY ITYTDVLRY 26.0 29186|polyprotein_precursor|NP_041724.2|West_Nile_virus|11082 -662 IASDHVVDM 0.0 None None 0 None -663 IAILICTMI 0.0 None None 0 None -664 MAKTGRFHI 0.0 None None 0 None -665 EVMEKVLPL 0.0 None None 0 None -666 FENNAGLPV 0.0 None None 0 None -667 FLHEMVAAM 0.0 None None 0 None -668 QAEPKKKPV 1.7536554713 EPKKKP EPGKNP 22.0 419124|polyprotein|ACF49259.1|Dengue_virus_type_1_Hawaii|10000440 -669 YVLHSKEEI 0.0 None None 0 None -670 FFFHNPKPL 0.430306274192 FFFHNPKPL IFFFNPGEL 25.0 43447|IMMUNOGENIC_PROTEIN_MPT64_(ANTIGEN_MPT64/MPB64)|CAA98382.1|Mycobacterium_tuberculosis_H37Rv|83332 -671 FHWNWIIVL 1.23311590917 HWNWII RWEWVV 28.0 74407|polyprotein|AAU89634.1|Hepatitis_C_virus_subtype_2a|31649 -672 YTMGIIFVL 0.0 None None 0 None -673 YVGKDIESV 0.0 None None 0 None -674 YQHYFRLLV 0.263137102792 YQHYFR YQSYLR 23.0 116781|Nucleoprotein|P05133.1|Hantaan_virus_76-118|11602 -675 MSNSMINTM 0.225806451613 NSMINTM NTMLNTV 26.0 294287|gag_protein|ABI20203.1|Human_immunodeficiency_virus_1|11676 -676 FSMLSRVLI 0.0 None None 0 None -677 FVDYPGDPV 0.0175687336762 VDYPGDPV VDFSLDPT 21.0 96156|polyprotein|ABR25251.1|Hepatitis_C_virus_(isolate_H77)|63746 -678 STAPLYSGM 3.52889315171 TAPLYS TLPVYS 23.0 98254|trans-sialidase,_putative|EAN81042.1|Trypanosoma_cruzi|5693 -679 DTVQLNVKY 0.0 None None 0 None -680 SAYMAATLL 0.0 None None 0 None -681 QAWNFLRAM 0.845286481541 QAWNF QQWNF 27.0 42797|6_kDa_early_secretory_antigenic_target|P0A564.2|Mycobacterium_tuberculosis|1773 -682 CAFGAMCAV 0.0 None None 0 None -683 IMEEEFSTI 0.0 None None 0 None -684 HAANVTQAM 0.0 None None 0 None -685 MAKQIKTKV 0.0363036459226 MAKQIKTK LAKEQKSK 21.0 8920|M_protein,_serotype_5_precursor|P02977.2|Streptococcus_pyogenes_serotype_M5|301449 -686 KAKGIYNSI 0.0 None None 0 None -687 HAPVHFLVI 0.0 None None 0 None -688 EVLQSMQRF 0.0 None None 0 None -689 YVASDIQYM 0.0 None None 0 None -690 YAAMDLSCL 0.0 None None 0 None -691 TPMTCSNTI 0.0 None None 0 None -692 EAPPGRVTF 0.0 None None 0 None -693 DTHSGAGKF 3.3511859631 HSGAGK HDGAGK 29.0 23621|Genome_polyprotein|P26664.3|Hepatitis_C_virus_(isolate_1)|11104 -694 YKYRYFCRV 0.610812498807 RYFCR EYFCR 27.0 155131|ribonucleotide_reductase_large_subunit|CAB06725.1|Human_alphaherpesvirus_2|10310 -695 LSDPHLTAV 0.0 None None 0 None -696 WAGLGGRHV 0.160072495287 GLGGRH GVGWRH 24.0 12183|EBNA3C_latent_protein|CAD53421.1|Human_gammaherpesvirus_4|10376 -697 QHTGTSVVL 0.478658436433 HTGTSVVL HIGAYVVL 23.0 154387|RL2|CAB06760.1|Human_alphaherpesvirus_2|10310 -698 STFCGTLEY 0.0 None None 0 None -699 TMYRCGPLI 0.0 None None 0 None -700 WHNQCSGHL 0.0 None None 0 None -701 FPLRNRPFY 0.40359719383 NRPFY NRSFY 23.0 98603|trans-sialidase,_putative|EAN82716.1|Trypanosoma_cruzi|5693 -702 YVGPAQLSV 0.0 None None 0 None -703 VAQHLATTY 0.0 None None 0 None -704 LVYPRFLYL 0.557903921081 YPRFLYL YPAVFYL 23.0 154041|major_capsid_protein|CAB06743.1|Human_alphaherpesvirus_2|10310 -705 FSREEMHNM 0.0 None None 0 None -706 YYPPGVVFY 0.0250303219548 YYPPGVV YTPEGII 23.0 180850|polyprotein|AFP27208.1|Dengue_virus_4|11070 -707 YLMSFFRLL 0.0 None None 0 None -708 RVFPLRGKI 0.0507541195092 RVFPLRGKI KLFPGGGQI 21.0 181035|||| -709 YPLPVANGM 0.881609743327 YPLPVANGM YPLHEQHGM 25.0 75356|EBNA3A_nuclear_protein|Q8AZJ8|Human_gammaherpesvirus_4|10376 -710 RAVCFSMEI 0.0 None None 0 None -711 QALPLDHHL 0.0 None None 0 None -712 FIEPHARFY 0.0 None None 0 None -713 FFYCIYASL 0.0 None None 0 None -714 CHDDYLVML 0.0 None None 0 None -715 KALFWTVAM 0.987412049439 KALFWTVAM KSLFNTVAV 26.0 126486|gag_protein|ADK33372.1|Human_immunodeficiency_virus_1|11676 -716 EYYEPPHRI 0.0 None None 0 None -717 PTSPMPYTY 0.196275089393 PTSPMP PTDPNP 24.0 70491|envelope_glycoprotein|AAC28452.1|Human_immunodeficiency_virus_1|11676 -718 EAVEARGAI 0.0 None None 0 None -719 NVVRLVATI 1.46700214129 NVVRLVATI NLVPMVATV 27.0 44920|tegument_protein_pp65|YP_002608275.1|Human_betaherpesvirus_5|10359 -720 YLKNSMIAV 0.0 None None 0 None -721 LQAEIVETM 0.0 None None 0 None -722 FHHKSNFLL 0.0 None None 0 None -723 KPIPAFEMV 0.0 None None 0 None -724 FLVDSNLSV 0.0 None None 0 None -725 FIDRQLTMV 0.0 None None 0 None -726 YSASSEIII 0.0 None None 0 None -727 YTPDELHAM 0.00719481474361 PDELHAM PDVAHSL 21.0 130953|G1_and_G2_surface_glycoprotein_precursor|AAG22532.1|Andes_hantavirus|46607 -728 FFYLDYVSI 0.0 None None 0 None -729 YIAPMMEKL 0.0 None None 0 None -730 EAFDRTETH 0.0 None None 0 None -731 SIVDVSIMY 0.0 None None 0 None -732 IPYTTVLHL 0.0 None None 0 None -733 EVFRHKLAM 0.0 None None 0 None -734 VMDRWNETV 1.66487546562 MDRWNE LDRWEK 25.0 19337|gag_protein|AAW57872.1|Human_immunodeficiency_virus_1|11676 -735 LLLDHGVHV 0.0 None None 0 None -736 VIFNVVRLV 0.0 None None 0 None -737 LAIKVTPSV 0.0508134355474 LAIKVTP LAISVVP 23.0 40288|kaposin|AAC57155.1|Human_gammaherpesvirus_8|37296 -738 LTDRQPLMH 0.0 None None 0 None -739 KPLPFNREV 0.0 None None 0 None -740 LNFGDITTV 0.0 None None 0 None -741 QAIDSTFYL 0.0 None None 0 None -742 LALNKGRAY 0.0 None None 0 None -743 IARQVVTAM 0.0 None None 0 None -744 GAFAFGAVF 0.0 None None 0 None -745 KSFPFQSLL 0.0 None None 0 None -746 RAGGSSVVI 0.0 None None 0 None -747 DTIPWYLRL 0.0 None None 0 None -748 MAVDGKPEY 0.0 None None 0 None -749 YLQDVVMQV 0.0 None None 0 None -750 FMVRNYEFL 0.0 None None 0 None -751 YMAGSDTTY 0.0 None None 0 None -752 VVYVLMTSV 0.0 None None 0 None -753 MPAERNGAI 0.0 None None 0 None -754 WPLQPVDHI 0.0 None None 0 None -755 MLDPHGHLI 0.0 None None 0 None -756 FISNSLNIL 0.0 None None 0 None -757 RADGDLTLI 0.0 None None 0 None -758 YQEEMIQCY 0.138922146416 YQEEMIQCY YMESVFQMY 24.0 154585|ribonucleotide_reductase_large_subunit|CAB06725.1|Human_alphaherpesvirus_2|10310 -759 FILDCHPKY 0.0 None None 0 None -760 GAYVYPLPV 1.80161146662 YVYPLPV YVYALPL 29.0 58463|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 -761 FKEAWKHTI 0.0 None None 0 None -762 LAGVKMVMI 0.0 None None 0 None -763 DAKQRIRLL 0.0 None None 0 None -764 LYYPPGVVF 0.0141268558401 YYPPGVV YTPEGII 23.0 180850|polyprotein|AFP27208.1|Dengue_virus_4|11070 -765 RASEDDRVL 0.0 None None 0 None -766 SALEYLLPL 0.982013790038 SALEYLLP SALQFLIP 30.0 22235|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 -767 AAVEPERTL 0.0 None None 0 None -768 GTDCLLLAF 0.0 None None 0 None -769 FVQLPVPII 0.0 None None 0 None -770 RIYPDRHRI 0.0 None None 0 None -771 KVDKNISHI 0.0 None None 0 None -772 RHSQWDHGL 0.0551254766838 SQWDHG TAWDFG 22.0 180726|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -773 MLYSRDHSV 0.0 None None 0 None -774 AARPLSRMV 0.0 None None 0 None -775 HAQVCSLYI 1.03982555138 HAQVCSLYI KAKICGLYL 30.0 177701|polyprotein|ACZ60104.1|Hepatitis_C_virus_subtype_3a|356426 -776 YSQPFYTSY 0.0 None None 0 None -777 MSDFQYLVV 0.0 None None 0 None -778 SANARCLIV 0.0 None None 0 None -779 SAIAIVQIL 0.0 None None 0 None -780 WMFYHFDAI 0.0 None None 0 None -781 YSKVIKCVV 0.0 None None 0 None -782 AARARGNKV 0.0 None None 0 None -783 TAYERLYLW 0.0 None None 0 None -784 TTASGVWAF 0.0 None None 0 None -785 KVREEVVTM 0.0 None None 0 None -786 MYYRVRDTM 0.0 None None 0 None -787 YVDRLLQHF 0.0 None None 0 None -788 PAIARPQAI 0.0 None None 0 None -789 YLLRAGVHL 2.34592183176 YLLRAGVHL FLLSLGIHL 30.0 16751|pol_protein|BAA32832.1|Hepatitis_B_virus|10407 -790 LVTPHMAEV 0.29585271922 LVTPHM LVTPSM 24.0 150378|polyprotein|AGW21594.1|Dengue_virus_1|11053 -791 EHVSDDDLL 0.0 None None 0 None -792 SFYHLVSTV 0.485538841086 SFYHLVST GFYHILNN 25.0 1516|Nucleoprotein|P03418.1|Human_respiratory_syncytial_virus_A2|11259 -793 FSAGNEANV 0.205224687568 SAGNEA NAGNDA 23.0 1090|Transcription_activator_BRLF1|P03209.1|Human_herpesvirus_4_strain_B95-8|10377 -794 KPGDRVVLV 0.0 None None 0 None -795 YSRGSSRCI 0.0 None None 0 None -796 YSTCVLVVL 0.0 None None 0 None -797 YSTHQTFMV 0.0 None None 0 None -798 WSLDGKYIV 1.99294213388 WSLDGKYIV WAIKWEYVV 26.0 72233|Genome_polyprotein|P27958.3|Hepatitis_C_virus_subtype_1a|31646 -799 HAWRDLSSM 0.0 None None 0 None -800 FASSLWETT 0.0 None None 0 None -801 FDYPSLFCI 0.0 None None 0 None -802 KAPPLTDVL 0.0 None None 0 None -803 DVFDALDLM 0.0 None None 0 None -804 ALYCRLATV 0.0118752492321 ALYCRLATV SLYNTIATL 20.0 190827|gag_protein|AAN08336.1|Human_immunodeficiency_virus_1|11676 -805 MVYLQIGGF 0.0 None None 0 None -806 EPFSGTASV 0.0 None None 0 None -807 ETMDELELL 0.578907805322 MDELEL MDKLEL 25.0 185419|envelope_protein|AGW23591.1|Dengue_virus_3|11069 -808 SMLNWFSPV 1.31489982056 MLNWFSPV LLIWFRPV 30.0 37507|Large_T_antigen|P03071.1|Human_polyomavirus_1|1891762 -809 NMLNLTHTY 0.0 None None 0 None -810 HSFNPEAQV 0.544692682129 HSFNPE KAFNPE 25.0 187158|Gag_protein|Q1KW74|Human_immunodeficiency_virus_1|11676 -811 SAYGSSGEL 0.0 None None 0 None -812 FSIPWAHAW 1.46617482283 FSIPWAH VSIPWTH 34.0 46480|DNA_polymerase|CAA10434.1|Hepatitis_B_virus|10407 -813 MASSAQEHL 0.0 None None 0 None -814 RHSREMALL 0.0 None None 0 None -815 WVLHHMGGM 36.5311333334 WVLHHMG WILRHPG 30.0 180818|Membrane_glycoprotein_precursor|NP_739582.2|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -816 VADSDRQLV 0.0 None None 0 None -817 IAAAWALSF 0.163128403126 AAAWAL AAAWYL 25.0 183819|polyprotein|AGO67248.1|Dengue_virus_2|11060 -818 KAESTPEIV 0.0 None None 0 None -819 LHLGHMFSL 0.107288558852 LGHMFSL LSHYFTL 22.0 59459|Trans-sialidase|SRC7915|Trypanosoma_cruzi|5693 -820 QRINLPHLL 0.0 None None 0 None -821 YALMRHRHT 0.0 None None 0 None -822 RLYPLANSL 0.0 None None 0 None -823 DHFSHASSI 0.0 None None 0 None -824 ISMEKGYNI 0.0 None None 0 None -825 FLHEMVAAM 0.0 None None 0 None -826 YVALEAQAI 0.0 None None 0 None -827 YLMTRTLPM 0.0 None None 0 None -828 QTFPQVSEL 0.0 None None 0 None -829 YPESIKAPV 0.0 None None 0 None -830 VHSKTSQLL 0.0 None None 0 None -831 TSSDRMTSV 0.0 None None 0 None -832 QMAERALYY 0.0 None None 0 None -833 LASPFATTA 0.0 None None 0 None -834 AAYTSYTPY 0.264739211661 AAYTSYTP EEYTDYMP 25.0 180681|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -835 VSCRPVVYV 0.0 None None 0 None -836 RTYHGRLAY 0.0 None None 0 None -837 LARHSAAFL 0.0 None None 0 None -838 RSEALPVSY 0.0498128500965 RSEALP RAESLP 23.0 419006|PPE_family_protein_PPE68|KAM81677.1|Mycobacterium_tuberculosis_H37Ra|419947 -839 ETKPFGLVV 0.00397696968794 KPFGLVV KPARLIV 19.0 30946|HCV-1|AAA45676.1|Hepatitis_C_virus_genotype_1|41856 -840 DVKNFWQGM 0.0 None None 0 None -841 FAELKSARM 0.0 None None 0 None -842 YMKPRLRTT 0.0 None None 0 None -843 STFCGTLEY 0.0 None None 0 None -844 HAATGPGEV 0.471180876873 HAATGPGE HAPTGSGK 28.0 146644|polyprotein|ADE10208.1|Hepatitis_C_virus_subtype_3a|356426 -845 PSQNRFLTY 10.5277024867 PSQNRF PSMKRF 22.0 180681|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -846 YISAWLDSL 0.577024181579 SAWLDS GAWMDS 27.0 30903|prM_protein|YP_001527879.1|West_Nile_virus_NY-99|10000971 -847 VPFPPKEPL 7.85759820488 VPFPPK IPYDPK 24.0 180789|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -848 KSHELVMYI 0.0 None None 0 None -849 LMLGRTNTL 0.0 None None 0 None -850 VARHTFSML 0.0 None None 0 None -851 LAIFMPPTY 0.018791562647 IFMPPTY VYMSPFY 22.0 141469|envelope_glycoprotein_B|NP_044629.1|Human_alphaherpesvirus_1|10298 -852 WAVVTMTAV 0.0 None None 0 None -853 FPRASQSLV 1.0950421762 FPRASQSLV FPGFGQSLL 23.0 23807|tax|AAG48731.1|Human_T-lymphotropic_virus_2|11909 -854 YDFLCLSLV 0.0 None None 0 None -855 NKFPGDSMV 0.0 None None 0 None -856 FSLLATVIL 0.468169410856 FSLLATV FTLVATV 25.0 98640|trans-sialidase,_putative|EAN80840.1|Trypanosoma_cruzi|5693 -857 SSSDNRNFI 0.0 None None 0 None -858 KSRNWLKSI 0.0 None None 0 None -859 QALNLQVVL 0.0 None None 0 None -860 FPVLLLDTI 4.07245586889e-05 PVLLLDT PVENLET 16.0 149063|NS3_protease/helicase'|NP_803144.1|Hepatitis_C_virus_(isolate_H77)|63746 -861 VTDFHNHSV 0.0 None None 0 None -862 LSDSMPLWM 0.0 None None 0 None -863 QSTKVNMLY 0.0 None None 0 None -864 MANHLGVGV 0.0 None None 0 None -865 HMDVEESQY 0.0 None None 0 None -866 LADPIEKEL 0.0 None None 0 None -867 MAITILVAL 0.0 None None 0 None -868 YRDNKMTRI 0.0 None None 0 None -869 FQMAERALY 0.0 None None 0 None -870 RINENTGIV 0.0 None None 0 None -871 EAGEESTSV 0.0 None None 0 None -872 RGMPPPPTV 0.746912503019 PPPPT PPPAT 25.0 120093|unnamed_protein_product|CAA33016.1|Rubella_virus|11041 -873 RLFRMFVHV 0.0 None None 0 None -874 FLTDMAKQI 0.0 None None 0 None -875 ISMQFLSSL 0.0 None None 0 None -876 HTDTNNLGI 0.0 None None 0 None -877 LALAIYTLL 0.0 None None 0 None -878 LAVCAFTVL 0.0 None None 0 None -879 AAAPNLRAL 0.0 None None 0 None -880 LVDSNLSVV 0.0 None None 0 None -881 VSSVQGITY 0.0 None None 0 None -882 HLMKQISSF 5.7878791982 HLMKQISS HLAFQLSS 23.0 24172|pX-rex-orf_I_{alternatively_spliced}|AAB23359.1|Human_T-lymphotropic_virus_1|11908 -883 EARGAIRGF 0.0 None None 0 None -884 LVSTSNHAY 0.0 None None 0 None -885 IAPRRWLLL 0.0 None None 0 None -886 RMAERRQEV 0.0 None None 0 None -887 YVVATTKLM 0.338384379032 YVVATTKL YAVATTIL 26.0 184713|polyprotein|AFP27208.1|Dengue_virus_4|11070 -888 FQDDFSPRF 0.0 None None 0 None -889 IGFNGNQIV 0.0 None None 0 None -890 KMFTCSKFV 0.0 None None 0 None -891 VAEVCPREV 0.0 None None 0 None -892 WAPLPGQML 0.0 None None 0 None -893 DAQQLATAI 0.0 None None 0 None -894 ILLNGDATV 0.000458453342916 ILLNGDAT VLLRLDGT 18.0 11214|possible_regulatory_protein|NP_302009.1|Mycobacterium_leprae|1769 -895 TIYDEDVLV 5.82753285036 TIYDEDVLV TMYYKDVTV 24.0 194440|envelope_glycoprotein_B|NP_044629.1|Herpes_simplex_virus_(type_1_/_strain_17)|10299 -896 WVKEDMGIV 0.0 None None 0 None -897 RKYGSTSSI 0.0 None None 0 None -898 MTDAQQLAT 0.0 None None 0 None -899 GFDQYRTLL 0.0 None None 0 None -900 NASGATAPL 0.0 None None 0 None -901 FFPEMGTKI 0.0 None None 0 None -902 NVHSSGKPI 0.305435862776 SSGKPI TSGSPI 22.0 22825|polyprotein|ABG75765.1|Dengue_virus_1|11053 -903 AALVGAEVV 0.0 None None 0 None -904 DHFSHASSI 0.0 None None 0 None -905 RAMGERLLL 0.0 None None 0 None -906 KIYDGKDKM 0.0 None None 0 None -907 WASGNERSL 22.1287414254 WASGNE WNSGHE 25.0 180440|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -908 LATVRSHHM 0.0 None None 0 None -909 LRDHGSFLL 0.0 None None 0 None -910 TALETSAPF 0.0 None None 0 None -911 HTFSMLSRV 0.0 None None 0 None -912 KAFHGSSGL 0.0 None None 0 None -913 LAKKPGCVF 1.69047619048 PGCVF PGCSF 26.0 44833|polyprotein|BAA03375.1|Hepatitis_C_virus_subtype_1a|31646 -914 IPNPQLGPV 4.26005083762e-05 GPV GPV 17.0 154857|tegument_protein|CAB06735.1|Human_alphaherpesvirus_2|10310 -915 QQHDGAFLI 0.0 None None 0 None -916 AAFFYLDYV 0.0 None None 0 None -917 FFPEMGTKI 0.0 None None 0 None -918 SQWDHGLSI 0.0803492524925 SQWDHG TAWDFG 22.0 180726|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -919 MSCRKIAHL 0.0 None None 0 None -920 MGFTVLTTV 0.0 None None 0 None -921 NLEVLDCRY 0.0 None None 0 None -922 LAQAVRAVL 0.0 None None 0 None -923 FMQTRYNKL 0.0 None None 0 None -924 LTHTGACPY 0.0 None None 0 None -925 KAFSDRFSL 0.0 None None 0 None -926 FLRDCSPRL 0.0 None None 0 None -927 DIFTTLKMY 0.0 None None 0 None -928 RAPPEAIAL 0.0 None None 0 None -929 STQDTPVTV 1.59510084399 STQDTPVTV ALADLPVTV 25.0 189566|glycosyl_transferase|WP_015631503.1|Mycobacterium_tuberculosis|1773 -930 QASSDWAAV 0.0 None None 0 None -931 FTRGIQTLF 0.0328747529981 RGIQTLF RGLTSLF 23.0 52652|||| -932 YRALNRVHV 0.0 None None 0 None -933 YEARLLKHM 0.0 None None 0 None -934 MELNSVNVM 0.0 None None 0 None -935 TAARLRHKV 0.0 None None 0 None -936 YAYFLDNVS 0.0 None None 0 None -937 TVLENLAVL 0.415657048035 TVLENLAVL NALDNLAVL 28.0 185447|polyprotein|AGK36298.1|Dengue_virus_2|11060 -938 HSFTHKQHL 0.0 None None 0 None -939 NMEELILAI 0.0 None None 0 None -940 IAPHRNEKL 0.0 None None 0 None -941 MMNDIVKEF 0.146493252704 MMNDIVK MINGVVK 23.0 185710|Nonstructural_protein_NS5|YP_001531176.2|Dengue_virus_3|11069 -942 FSVPLHIFL 0.133234367786 FSVPLHIFL FLVPFVVFL 25.0 139746|Dense_granule_protein_3|B6KEU8.2|Toxoplasma_gondii|5811 -943 TVMGRITTL 0.0 None None 0 None -944 FAKYWEENF 0.0 None None 0 None -945 VSDLLVLLL 0.0 None None 0 None -946 FLHVGDLVI 0.0 None None 0 None -947 EAFAHEARF 0.0 None None 0 None -948 SSLGKTQTV 0.0 None None 0 None -949 LVLIGISHV 1.0 LVLIGIS LILIGIT 26.0 59182|attachment_glycoprotein|ABQ58821.1|Human_metapneumovirus|162145 -950 FYFQVPFIY 0.0 None None 0 None -951 WSFAVAICI 0.0 None None 0 None -952 QHMIQQQAL 0.0 None None 0 None -953 FPEGYGTQV 0.38077711011 FPEGY LPEGY 25.0 31997|hypothetical_protein_FTT0484|YP_169522.1|Francisella_tularensis_subsp._tularensis_SCHU_S4|177416 -954 KPYGRNKPF 0.0 None None 0 None -955 HGFNATYHV 0.0990072203855 HGFNATY HSYGVTY 23.0 232152|rhoptry_kinase_family_protein|AFO54841.1|Toxoplasma_gondii_type_III|398031 -956 YIRTRNEFV 0.0 None None 0 None -957 YPEVFGPPL 0.511017522783 PEVFGP PEAAGP 23.0 19348|IMMUNOGENIC_PROTEIN_MPT64_(ANTIGEN_MPT64/MPB64)|CAA98382.1|Mycobacterium_tuberculosis_H37Rv|83332 -958 MVACGGTVY 0.0 None None 0 None -959 APSEHAQMV 0.0 None None 0 None -960 TRTFVEFIL 0.0 None None 0 None -961 LLSEVLLHY 0.0 None None 0 None -962 IQVGTGVTV 0.0 None None 0 None -963 LTLAFTVML 0.0 None None 0 None -964 HVGDLVIVV 0.0 None None 0 None -965 MTREELNAL 0.025913105963 MTREELNAL MTQKARNAL 23.0 150461|polyprotein|AGK36298.1|Dengue_virus_2|11060 -966 VAVQESARI 0.0 None None 0 None -967 VPSPLFSIV 0.0 None None 0 None -968 KAGGGSNEV 0.0469468239536 KAGGGSN PVGGGSS 23.0 189750|Diacylglycerol_acyltransferase/mycolyltransferase_Ag85B|SRC280000|Mycobacterium_tuberculosis|1773 -969 YMLIIVSIF 0.0 None None 0 None -970 VAPHAPVHF 0.0 None None 0 None -971 TPFHLASAV 0.0 None None 0 None -972 SARDCKDPY 0.000418357588503 SARDCKDPY SARLAGIPY 18.0 243835|glycosyl_transferase|WP_015628558.1|Mycobacterium_tuberculosis|1773 -973 FMATMPPAV 0.0 None None 0 None -974 TMVACGGTV 0.0 None None 0 None -975 NSDHVMFMV 0.0 None None 0 None -976 FMKNYFKDV 0.0 None None 0 None -977 LNVEDPVTV 0.0 None None 0 None -978 FIPINGCPI 1.34457687638 FIPINGCPI YIPLVGAPL 28.0 23365|polyprotein|BAB18806.1|Hepatitis_C_virus|11103 -979 YTSYFGYKM 1.56288713183e-05 YTSYFGYKM YTMDGEYRL 14.0 76121|polyprotein_precursor|NP_041724.2|West_Nile_virus|11082 -980 WSPHPLQIV 0.0 None None 0 None -981 YTTITPQII 0.0 None None 0 None -982 CSFYRTHTL 0.0256163049141 SFYRTHTL SFHNLHLL 22.0 79390|Protein_Tax-1|P0C213.1|Human_T-cell_lymphotropic_virus_type_1_(african_isolate)|39015 -983 NAAKNQVAM 0.0187943866999 NAAKNQVAM NASRCWVAM 21.0 21385|polyprotein|AAY82034.1|Hepatitis_C_virus_genotype_1|41856 -984 FETDGRRFL 0.0 None None 0 None -985 SVEINDIMY 0.0 None None 0 None -986 DPAPRPSLL 0.904502870813 DPAPRPSLL DPQERPRKL 24.0 110338|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 -987 QAVTEVEAV 0.138095238095 AVTEVEA AITEVEC 26.0 2102|VP1|BAF93325.1|Human_polyomavirus_1|1891762 -988 TAFQKGYGI 0.0 None None 0 None -989 ICFPVLVAL 0.27101796422 FPVLVA FPYLVA 24.0 9461|non_structural_protein_3|CAJ20172.1|Hepatitis_C_virus|11103 -990 NHVPVNHFW 0.0 None None 0 None -991 DMNDHAPEV 0.0025892563244 NDHAPEV NDFFPSV 20.0 16814|precore_protein|CAM58990.1|Hepatitis_B_virus|10407 -992 SPLPPPEQI 1.56735830397 SPLPP APLPP 26.0 179766|cell_surface_protein_(associated_with_virulence)|NP_302372.1|Mycobacterium_leprae_TN|272631 -993 LRLDGSVVI 0.915531304079 LRLDGSVV LRLDGTTL 27.0 11214|possible_regulatory_protein|NP_302009.1|Mycobacterium_leprae|1769 -994 HACSHLRQM 0.0 None None 0 None -995 FPSSQGSLY 3.38709858116 FPSSQGSL FPIVQGEL 24.0 48458|IMMUNOGENIC_PROTEIN_MPT64_(ANTIGEN_MPT64/MPB64)|CAA98382.1|Mycobacterium_tuberculosis_H37Rv|83332 -996 FNRDDCSVL 0.0 None None 0 None -997 TSFPQKVHL 0.0 None None 0 None -998 EAFAHEARF 0.0 None None 0 None -999 DAKSHELVM 0.0 None None 0 None -1000 TEYRALNRV 0.0 None None 0 None -1001 KTIWHTAEY 0.0 None None 0 None -1002 KAMLEEQLI 0.0 None None 0 None -1003 DTSDGLAVL 0.0 None None 0 None -1004 LEFGKPSTL 0.0 None None 0 None -1005 TLLEFFITL 0.0 None None 0 None -1006 FTKRQRKAM 0.0 None None 0 None -1007 FCLSTENSI 0.0 None None 0 None -1008 FQGFSVQLI 0.0 None None 0 None -1009 RVAPGYYTL 0.0 None None 0 None -1010 FYQDMMNDI 0.201754385965 YQDMMND YQQQLND 26.0 143680|Genome_polyprotein|P06441.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 -1011 CLYDSVLML 0.0 None None 0 None -1012 YTCVVSNKL 0.0 None None 0 None -1013 PAEEPTNEL 0.0 None None 0 None -1014 QVYSWLLCL 0.0 None None 0 None -1015 PANESFGHL 0.0 None None 0 None -1016 SPFAAAAAV 0.0 None None 0 None -1017 DVVHHLLSV 0.0 None None 0 None -1018 MFYPERTAL 0.0 None None 0 None -1019 VSDPACSSI 0.0 None None 0 None -1020 WAKVRTAEF 0.0 None None 0 None -1021 AALRHERAV 0.0 None None 0 None -1022 YVVATTKLM 0.22206474874 YVVATTKL YAVATTIL 26.0 184713|polyprotein|AFP27208.1|Dengue_virus_4|11070 -1023 RMLLDPNTV 0.0 None None 0 None -1024 YYDYMKPRL 0.0356673922245 YYDYM YTDYM 23.0 180681|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -1025 FPRHCVSWM 0.0 None None 0 None -1026 YLPPDPQPF 0.802965979807 LPPDPQP VPTDPNP 27.0 70491|envelope_glycoprotein|AAC28452.1|Human_immunodeficiency_virus_1|11676 -1027 HPATRPLHV 0.0 None None 0 None -1028 MVTGILLYM 0.0 None None 0 None -1029 KPISYMAII 0.222648225888 KPISYM RPVSYL 25.0 39571|polyprotein|BAD73987.1|Hepatitis_C_virus_subtype_1b|31647 -1030 DSSQRFEVI 0.0 None None 0 None -1031 STGYAISAY 0.0 None None 0 None -1032 KQLEFHIEI 0.0 None None 0 None -1033 FFCEVPVLL 0.0 None None 0 None -1034 FSMDETGQM 0.0 None None 0 None -1035 YPRQYSLKL 0.0 None None 0 None -1036 ETAYTKDGF 0.0 None None 0 None -1037 FSNHWTFWV 0.0 None None 0 None -1038 IGYANAKIY 0.0 None None 0 None -1039 DFFEDTEHY 0.0 None None 0 None -1040 DPMKVEAHV 0.0 None None 0 None -1041 GSGEHPMDY 0.0 None None 0 None -1042 SHSRGNDTL 0.0 None None 0 None -1043 FHTSSSLTV 0.0 None None 0 None -1044 VVMRICNLI 0.0 None None 0 None -1045 TALDSSLCL 0.0 None None 0 None -1046 DSDDMDLEV 0.0 None None 0 None -1047 HSYVGPAQL 0.0206560380033 HSYVGP HSVVNP 22.0 47854|Glycoprotein_I_precursor_(Glycoprotein_IV)_(GI)_(GPIV)|P09258.1|Human_alphaherpesvirus_3|10335 -1048 EMFQRYSAF 2.07487586145 EMFQRYSAF EFFTKNSAF 24.0 44214|UL123;_IE1|AAR31448.1|Human_betaherpesvirus_5|10359 -1049 MPVSIRLVV 0.0005030251957 PVSIRLVV PASRDLVV 18.0 93224|core_protein|AAL31859.1|Hepatitis_B_virus|10407 -1050 LVDGDLGKY 0.00752911114692 GDLGKY GDAGGY 22.0 3094|Antigen_85-B_precursor_(85B)_(Extracellular_alpha-antigen)_(Antigen_85_complex_B)_(Ag85B)_(Mycolyl_transferase_85B)_(Fibronectin-binding_protein_B)_(30_kDa_extracellular_protein)|P31952|Mycobacterium_tuberculosis|1773 -1051 RSLAFPVPL 0.0223084774724 LAFPVP LSFPDP 22.0 79300|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 -1052 RAFHDLRVA 0.0 None None 0 None -1053 IYDEDVLVV 0.0 None None 0 None -1054 LAMHSIWEM 0.00687735530344 HSIWE HTLWK 23.0 24943|DNA_polymerase|CAA10434.1|Hepatitis_B_virus|10407 -1055 YCRAWCQAL 0.0 None None 0 None -1056 QAVTNHSVY 0.0 None None 0 None -1057 HSQECGSFL 0.0 None None 0 None -1058 LQHTGTSVV 0.0 None None 0 None -1059 ETRAQLARH 0.0 None None 0 None -1060 RAALVGAEV 0.0 None None 0 None -1061 IPNAQNMTI 5.34979128985 PNAQNM PGAQNL 24.0 140615|amino_acid_decarboxylase|YP_177889.1|Mycobacterium_tuberculosis_H37Rv|83332 -1062 LATCCRARY 0.0 None None 0 None -1063 LMRHSMEKI 0.384767672963 RHSMEKI RHAMEEL 27.0 419128|polyprotein|ACF49259.1|Dengue_virus_type_1_Hawaii|10000440 -1064 VSARHPQHL 1.15203265572 RHPQHL RRPKHL 25.0 66195|Nucleoprotein|P41269.1|Puumala_hantavirus|11604 -1065 YKYDAGSAA 0.0 None None 0 None -1066 IIFLLGEIV 0.0406172919483 IIFLLGEIV VLFYLGQYI 24.0 156550|E3_ubiquitin-protein_ligase_Mdm2|Q00987.1|Homo_sapiens|9606 -1067 LARSQRTQV 0.0 None None 0 None -1068 NAAVETASL 0.0 None None 0 None -1069 LACSICHVY 0.0734222777342 LACSIC IVCPIC 23.0 64819|E7_protein|ABL96585.1|Human_papillomavirus_type_16|333760 -1070 DIYDVLICL 0.804762038021 YDVLIC YDIIIC 31.0 97111|polyprotein|ABR25251.1|Hepatitis_C_virus_(isolate_H77)|63746 -1071 LTMSWLTPL 0.0 None None 0 None -1072 FHNDLMPSY 0.122946002019 NDLMPS NDFFPS 23.0 16813|External_core_antigen|SRC279980|Hepatitis_B_virus|10407 -1073 VMVSPASAI 0.0 None None 0 None -1074 VFFSLLATV 25.6111406871 FSLLATV FTLVATV 25.0 98640|trans-sialidase,_putative|EAN80840.1|Trypanosoma_cruzi|5693 -1075 EASLATQIV 0.0 None None 0 None -1076 ETLVSTSTI 0.0 None None 0 None -1077 FPYQITNEH 0.0 None None 0 None -1078 RTFLPVHLL 0.0 None None 0 None -1079 LPQPGVRSL 0.548160467495 LPQPGVR LPRPGPR 28.0 139406|polyprotein|ACT37184.1|Hepatitis_C_virus|11103 -1080 VPNNCLGKV 0.268353983445 CLGKV CLGKA 24.0 180442|Chain_B,_Dengue_Virus_Rna_Dependent_Rna_Polymerase_With_Residues_From_The_Ns5_Linker_Region|4C11_B|Dengue_virus|12637 -1081 HPLEFCLLL 0.0 None None 0 None -1082 MAFVTLTDL 0.0 None None 0 None -1083 FSVQLIRKF 0.0 None None 0 None -1084 FPQMRAMSL 0.0 None None 0 None -1085 LRLNWGEPI 0.0 None None 0 None -1086 YEEDSGEYF 0.0 None None 0 None -1087 TAKGTAQLV 0.0 None None 0 None -1088 LHFHWNWII 1.5492033712 HWNWII RWEWVV 28.0 74407|polyprotein|AAU89634.1|Hepatitis_C_virus_subtype_2a|31649 -1089 DTDGQPLLL 0.0761637873905 TDGQPLL TSGSPII 22.0 22822|NS3_protein|NP_740321.1|Dengue_virus_4|11070 -1090 AHLLCTLLL 0.211842833049 AHLLCTLLL SHFLCTFTF 27.0 41622|Genome_polyprotein|P08617.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 -1091 KAPGFEKHL 0.0 None None 0 None -1092 SSYGGTIRY 0.545454545455 YGGTIR HGGTLR 26.0 120127|unnamed_protein_product|CAA33016.1|Rubella_virus|11041 -1093 YQDMMNDIV 0.240277994375 YQDMMNDIV YQQQLNDPV 27.0 143680|Genome_polyprotein|P06441.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 -1094 MQALNLQVV 0.0 None None 0 None -1095 MHYLKNSMI 0.0 None None 0 None -1096 NAKSRGWLI 0.0 None None 0 None -1097 DSNRVVCPI 0.0 None None 0 None -1098 ISNRSVLHL 0.0 None None 0 None -1099 QAELRGRVL 0.0 None None 0 None -1100 ASFDCAIEM 0.0 None None 0 None -1101 LQIGGFSSV 0.0 None None 0 None -1102 QTWRAVTTL 0.0 None None 0 None -1103 FSAQTFYVL 0.0 None None 0 None -1104 LGDDFSSAY 0.0 None None 0 None -1105 FQCAPGYAL 0.227490636034 PGYAL PGYAL 28.0 27295|polyprotein_precursor|NP_041724.2|West_Nile_virus|11082 -1106 DRETGMHLL 0.0 None None 0 None -1107 FALQRIVQK 0.0 None None 0 None -1108 DAVGNMLNL 0.0 None None 0 None -1109 FYRLHLGTY 0.0 None None 0 None -1110 FELKSPVKM 0.0 None None 0 None -1111 VLRPRWCPV 2.53947368421 RPRWCPV RPSWGPT 26.0 36352|Polyprotein|P90247|Hepatitis_C_virus|11103 -1112 HHSSFRRHL 0.0 None None 0 None -1113 FSYLTMSWL 0.0 None None 0 None -1114 WAESVEREI 0.0 None None 0 None -1115 KADVVHVTL 0.0 None None 0 None -1116 IMEENDSNI 0.0 None None 0 None -1117 LRLPHWPII 0.0 None None 0 None -1118 EAVQDPMKV 0.0 None None 0 None -1119 LIRKFAQSI 0.0 None None 0 None -1120 SHHQCGQSL 0.0 None None 0 None -1121 CTLGLGSLY 10.1824630352 CTLGLGSLY CTCGSSDLY 28.0 7116|NS3|ABN45875.1|Hepatitis_C_virus_(isolate_H77)|63746 -1122 ELAHDSYFY 0.0 None None 0 None -1123 HAANVTQAM 0.0 None None 0 None -1124 WTFWVGPFI 0.0 None None 0 None -1125 VVEHVLTTV 0.0 None None 0 None -1126 NDHDNWCII 0.0 None None 0 None -1127 IAPLLPVAV 1.72391567608 IAPLLPV FAPALPI 24.0 422989|polyprotein|ABY67644.1|Hepatitis_C_virus_genotype_1|41856 -1128 LSGPWGSPL 0.0 None None 0 None -1129 DPADPTSNL 0.0753429944852 DPADPT DPLKPT 23.0 27241|Spike_glycoprotein_precursor|P59594.1|SARS_coronavirus|227859 -1130 FPNSDHVMF 0.0 None None 0 None -1131 EVQDIQASL 0.00328204778107 VQDIQASL VQEDAASL 19.0 423007|Genome_polyprotein|P26664.3|Hepatitis_C_virus_genotype_1|41856 -1132 RPYKQGARL 0.0 None None 0 None -1133 DVAQHGARL 0.0 None None 0 None -1134 FLEKNKDAV 0.0 None None 0 None -1135 DSELAHDSY 0.0 None None 0 None -1136 MPLWMASII 0.0 None None 0 None -1137 YHFDAIRTF 5.93421006727 FDAIRTF YDAVRTW 27.0 154164|tegument_protein|CAB06732.1|Human_alphaherpesvirus_2|10310 -1138 VSTEHCLSV 0.0 None None 0 None -1139 YEAAKLLLV 0.0 None None 0 None -1140 LVQAGVDVV 0.0 None None 0 None -1141 SATASMLSV 0.0 None None 0 None -1142 DQFTKSISI 0.0 None None 0 None -1143 CALCALSNI 0.0 None None 0 None -1144 RAKPRWRVA 0.0 None None 0 None -1145 AAMDAGFLY 0.0 None None 0 None -1146 CAMTMNKYI 0.0 None None 0 None -1147 NLEPHGYVV 0.0 None None 0 None -1148 MLLSPGQNV 0.0 None None 0 None -1149 WQIHRVDIL 0.55932505738 WQIHR WLVHR 25.0 41407|Envelope_protein|NP_739583.2|Dengue_virus_2|11060 -1150 YAELGTTTK 0.0 None None 0 None -1151 YKLNRAFML 0.0 None None 0 None -1152 FAAAAAVAA 0.0 None None 0 None -1153 KMADPNQCV 1.15009746589 KMADPNQCV RVIDPRRCL 26.0 150556|polyprotein|AGW21594.1|Dengue_virus_1|11053 -1154 DPYVKAHLL 0.0 None None 0 None -1155 WPIINTPMV 0.0 None None 0 None -1156 KYYTDPSTY 1.74983759401 KYYTDPSTY KLYQNPTTY 31.0 32268|hemagglutinin|AAK38298.1|Influenza_A_virus_(A/Bar-headed_Goose/Qinghai/61/05(H5N1))|336238 -1157 RVSSYGGTI 0.0 None None 0 None -1158 EALDAGAIY 0.0 None None 0 None -1159 EFIMAITSM 0.0 None None 0 None -1160 FPWWLARVL 0.0461652934999 WLARVL WMIRIL 24.0 185817|envelope_protein|AGW23590.1|Dengue_virus_4|11070 -1161 WTLASMELV 0.0 None None 0 None -1162 IVRCLVTSV 0.0 None None 0 None -1163 MPAFHFNIL 0.00333528511973 PAFHFNI PALVFDI 19.0 24427|polyprotein|ACX44238.1|Hepatitis_C_virus_subtype_1a|31646 -1164 YRTHTLQTL 0.0 None None 0 None -1165 HASVVAAYL 0.0131278658919 HASVVAA HARFVAA 22.0 194|Hypothetical_protein_esxG_(PE_family_protein)|O53692.1|Mycobacterium_tuberculosis|1773 -1166 ISRPSSNAL 0.0281163741936 PSSNAL PQSNAV 22.0 183229|polyprotein|AGW21594.1|Dengue_virus_1|11053 -1167 RALLGCSCV 0.0 None None 0 None -1168 DAVWSRATF 0.0 None None 0 None -1169 DVVHHLLSV 0.0 None None 0 None -1170 MSFFRLLQM 0.0 None None 0 None -1171 KIIAFRKTL 0.0 None None 0 None -1172 TVSSNLSHV 0.0 None None 0 None -1173 MSVEINDIM 0.0 None None 0 None -1174 IAICRQIGI 0.0 None None 0 None -1175 ISKPSELPI 0.0 None None 0 None -1176 DPIEKELSV 0.0 None None 0 None -1177 DHSNDPTAI 0.12924811208 DHSNDPT DHQLDPA 24.0 190466|large_surface_antigen|CAL29876.1|Hepatitis_B_virus|10407 -1178 WRLAEAEML 0.0 None None 0 None -1179 RGLPWTVRV 0.0 None None 0 None -1180 KPMPTIQWI 0.407168297158 KPMPTIQW EPEPDVAW 25.0 96257|Genome_polyprotein|SRC279960|Hepatitis_C_virus|11103 -1181 RRFNLTSTF 0.0 None None 0 None -1182 RRSHTGTFL 0.338888888889 SHTGTF SHSGSF 26.0 61077|Non-capsid_protein_NS-1|P07298.1|Human_parvovirus_B19|10798 -1183 FALDENDNA 0.0 None None 0 None -1184 NPEELEQVV 0.0 None None 0 None -1185 QAMHSFGRF 0.0 None None 0 None -1186 TAIAICRQI 0.0 None None 0 None -1187 EVMEKVLPL 0.0 None None 0 None -1188 DVLPDTFTL 0.170795867243 VLPDTFT VLPCSFT 24.0 69679|polyprotein|BAD73987.1|Hepatitis_C_virus_subtype_1b|31647 -1189 RTGDRPHTF 0.0 None None 0 None -1190 QPAVFETTV 0.0911167657101 PAVFETTV PAIFQSSM 25.0 59975|pol_protein|ACJ76655.1|Human_immunodeficiency_virus_1|11676 -1191 VMDFRFGTI 0.0 None None 0 None -1192 NEDDSTFTI 0.0 None None 0 None -1193 TALGLCEEV 0.0 None None 0 None -1194 SMLSRVLII 0.0 None None 0 None -1195 DANLHKNEL 0.0 None None 0 None -1196 DHYAVESAL 0.0 None None 0 None -1197 EVKIGKMSY 0.000778543502349 EVKIGKMSY DVKKDLISY 17.0 25929|Nonstructural_protein_NS3|NP_739587.2|Dengue_virus_2_Thailand/16681/84|31634 -1198 LANGGKVPF 1.96547847148 LANGGKVPF LSNTGEIPF 32.0 108018|polyprotein|CAB41951.1|Hepatitis_C_virus|11103 -1199 IGAKHTLTI 0.0 None None 0 None -1200 EVVGGWPVV 0.0 None None 0 None -1201 VANERISMQ 0.0 None None 0 None -1202 LSLKQVISI 0.0 None None 0 None -1203 VGFPVGDSV 0.013726318129 FPVGDSV LPVADAV 22.0 75408|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 -1204 LPLDHHLAL 0.0 None None 0 None -1205 GALPLFRKY 0.0 None None 0 None -1206 VSYHPDLGI 4.0 PDLGI PDLGV 26.0 30946|HCV-1|AAA45676.1|Hepatitis_C_virus_genotype_1|41856 -1207 HLFGTSCPY 0.0 None None 0 None -1208 TATTILIMI 0.0 None None 0 None -1209 LSFMEAQSL 0.0 None None 0 None -1210 FLSLGIASL 0.0 None None 0 None -1211 RPPPTPRKV 0.0331024442478 PPPTPRKV PPATPTSL 25.0 120093|unnamed_protein_product|CAA33016.1|Rubella_virus|11041 -1212 SQLEMPETL 0.0 None None 0 None -1213 YCRLATVHM 0.0 None None 0 None -1214 VPHEDTLSL 0.0 None None 0 None -1215 KCYKQGAFI 0.0 None None 0 None -1216 LVLAFKNQV 0.0 None None 0 None -1217 TSDDFWYHA 0.0 None None 0 None -1218 RAEHFGIA* 0.0 None None 0 None -1219 QVLPWLKAF 1.81855060575 VLPWLKAF VLAWTRAF 29.0 69394|pol|AP_000202.1|Human_adenovirus_5|28285 -1220 FSIVRADGV 0.0 None None 0 None -1221 DVHDIARFL 0.0 None None 0 None -1222 SAQRPWPRV 0.0521684604953 RPWPRV RPGPRL 23.0 139406|polyprotein|ACT37184.1|Hepatitis_C_virus|11103 -1223 CAFRSQLEM 0.0 None None 0 None -1224 IIDCLVSMV 0.0 None None 0 None -1225 NPTEARVQV 0.0 None None 0 None -1226 MVLWHLPAV 7.05423432918 LWHLPAV LWHYPCT 29.0 75636|polyprotein|AAB67037.1|Hepatitis_C_virus_(isolate_H77)|63746 -1227 KVHDSVLAL 0.0 None None 0 None -1228 FVLLLTYIL 0.0 None None 0 None -1229 RSGEPMVSL 0.0 None None 0 None -1230 LPHCGHRTL 0.0 None None 0 None -1231 MTEHRGKCY 22.1797910912 MTEHRGKCY ISEYRHYCY 26.0 28484|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 -1232 RTLRISETL 0.0 None None 0 None -1233 VSAKRVSVL 0.0 None None 0 None -1234 SVYCIRKKY 0.0 None None 0 None -1235 QSMPCLMSF 0.0 None None 0 None -1236 HRYNLTQHF 1.09592266047 HRYNLTQHF KQYNVTQAF 29.0 51250|nucleocapsid_protein|ABI96968.1|SARS_coronavirus|227859 -1237 ISLMVIEKV 0.0 None None 0 None -1238 EIYSLIDNF 0.0 None None 0 None -1239 APSNHMNLV 0.0 None None 0 None -1240 FAISHEGHM 0.0 None None 0 None -1241 LTSVLTLMF 0.0 None None 0 None -1242 YAIPSKQLE 0.0 None None 0 None -1243 QALAQRNQL 0.0 None None 0 None -1244 FNCSFVLEM 0.0 None None 0 None -1245 SPRRRAASV 0.419755381749 SPRRRAASV DPRRRSRNL 24.0 9746|Genome_polyprotein|P29846.3|Hepatitis_C_virus_genotype_1|41856 -1246 AAGAPPAKI 0.0 None None 0 None -1247 DTIPWYLRL 0.0 None None 0 None -1248 FFGNNMPEF 0.0 None None 0 None -1249 NPICCDCVI 0.00546161891463 ICCDCVI ILCLCLV 21.0 49831|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 -1250 CPYSAWCVY 0.0339459746518 CPYSAWC VPYVAWL 27.0 5952|PPE_family_protein|YP_177918.1|Mycobacterium_tuberculosis_H37Rv|83332 -1251 QMCAVNSTV 0.0 None None 0 None -1252 LQMVRLCSV 0.0 None None 0 None -1253 LTRTFVEFI 0.0 None None 0 None -1254 LSATVMLTV 0.0 None None 0 None -1255 MVPREFKPI 1.21262679539 MVPREFKP IIPSMFEP 22.0 65550|Nonstructural_protein_NS3|NP_739587.2|Dengue_virus_2_Thailand/16681/84|31634 -1256 LVIQYTVKY 0.0 None None 0 None -1257 LRFPRITFF 0.0 None None 0 None -1258 TSMPVSKML 0.0 None None 0 None -1259 LMKCPCNTF 0.0 None None 0 None -1260 IHQAMFQLL 2.96146414954 HQAMFQLL HQAAMQML 27.0 101673|gag_protein|ABO73990.1|Human_immunodeficiency_virus_1|11676 -1261 VAGRRGQQL 0.0 None None 0 None -1262 HASSIIDEL 0.0 None None 0 None -1263 YARRRWPSQ 0.0 None None 0 None -1264 SSLDHHMLV 0.0 None None 0 None -1265 DLITNIEPF 0.0157884928167 ITNIEPF ISNQEPL 20.0 10650|Nucleoprotein|P05133.1|Hantaan_virus_76-118|11602 -1266 TTILIMIVF 0.0 None None 0 None -1267 LLKSNTSTL 0.0 None None 0 None -1268 LHDVYMFCI 0.0 None None 0 None -1269 STRSPNSTV 0.0 None None 0 None -1270 QELAGVKMV 0.0 None None 0 None -1271 YVPYRDNKM 0.0 None None 0 None -1272 DPADGIRLF 0.632859149645 DGIRL DGVRL 24.0 15914|Genome_polyprotein|P27958.3|Hepatitis_C_virus_subtype_1a|31646 -1273 WRCWFNGIM 0.0204388749569 WRCWFNGI WEAVFTGL 22.0 12108|polyprotein|AAP55688.1|Hepatitis_C_virus_subtype_2a|31649 -1274 CALGLHNFV 0.0 None None 0 None -1275 MEEEFSTIL 0.0 None None 0 None -1276 MLDDAPRLL 0.0 None None 0 None -1277 LGYDMFDCV 0.0 None None 0 None -1278 FVYKSGMTS 0.0 None None 0 None -1279 ESADKTAYL 0.0 None None 0 None -1280 NLQRWVTAV 0.0 None None 0 None -1281 WKLTDMSSI 0.0 None None 0 None -1282 HTLEEIYSL 0.0 None None 0 None -1283 DAFNSTERA 0.0 None None 0 None -1284 YLYPLVLMS 0.0 None None 0 None -1285 SPFKLDATY 0.0 None None 0 None -1286 FPRIYSNSL 0.0 None None 0 None -1287 YHISEEYGL 0.0 None None 0 None -1288 ASMHRFGHI 0.0 None None 0 None -1289 AIDSASPVY 0.0 None None 0 None -1290 CTFDSPARL 0.0 None None 0 None -1291 SFMEAQSLM 0.0 None None 0 None -1292 LPYELGWLF 0.0 None None 0 None -1293 NIWECNRNI 0.0 None None 0 None -1294 SPAEETVVL 0.0 None None 0 None -1295 RQIPVVGSM 0.0354353484081 IPVVGS IPLVGA 23.0 19493|polyprotein|BAA03375.1|Hepatitis_C_virus|11103 -1296 LVWALPKTY 0.753308187545 VWALPKT LWALPHA 27.0 108277|IE62|AAP32859.1|Human_alphaherpesvirus_3|10335 -1297 QARPKGKGL 0.0 None None 0 None -1298 LHLCYEFLM 0.0368205769669 LHLCYEFLM LLLCLIFLL 22.0 37466|surface_antigen|BAF44879.1|Hepatitis_B_virus|10407 -1299 HQEDGGKAL 0.0 None None 0 None -1300 RPSSNALLI 0.286396630832 PSSNALL PQSNAVI 24.0 183229|polyprotein|AGW21594.1|Dengue_virus_1|11053 -1301 QKYDGKCPL 0.0 None None 0 None -1302 YAQFRGRHR 0.0 None None 0 None -1303 VAVYSTCVL 0.0490612481147 AVYSTC ATYSRC 23.0 149060|E2_protein|NP_751921.1|Hepatitis_C_virus_(isolate_H77)|63746 -1304 FLPPARSGI 0.0 None None 0 None -1305 QHGSLSETW 0.0 None None 0 None -1306 LGLEKTTSI 0.0 None None 0 None -1307 QTVMFMATM 0.0 None None 0 None -1308 LLKPGDRVV 0.26492774281 LKPGDRVV LQPVERVL 21.0 155928|unnamed_protein_product|CAA30115.1|Trypanosoma_cruzi|5693 -1309 MPGSPRDPV 0.0 None None 0 None -1310 LTYCTTGGI 0.0 None None 0 None -1311 FQSLLSQHM 0.0 None None 0 None -1312 KEFHFNQYL 0.0 None None 0 None -1313 SSTEWVAPL 0.0 None None 0 None -1314 RSSPATHSL 8.88487276219 PATHSL PKTHTL 24.0 184702|non-structural_protein_1|AGM49312.1|Dengue_virus|12637 -1315 ELKEWAESV 0.0 None None 0 None -1316 GVVEATLSY 0.0 None None 0 None -1317 EIAELNRTI 0.0 None None 0 None -1318 GAASMIHYI 0.0 None None 0 None -1319 LVNTCIRFV 0.0 None None 0 None -1320 QAVDTDEAL 0.0 None None 0 None -1321 AATSRGQVL 0.0 None None 0 None -1322 NPLRPRESL 0.00204486978355 PLRPRES PLCPEEK 20.0 110394|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 -1323 VSSNLSHVI 0.0 None None 0 None -1324 FTFGETEVC 0.0 None None 0 None -1325 FQDDFSPRF 0.0 None None 0 None -1326 YTVKYEQKM 0.0 None None 0 None -1327 EHSDTFINL 0.0 None None 0 None -1328 YTPKLEIKV 0.0 None None 0 None -1329 ETQETMDEL 0.0 None None 0 None -1330 DLVHHTTTL 0.00705689720887 DLVHHTT DLMCHAT 21.0 180507|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -1331 LMFSGLWHL 0.0 None None 0 None -1332 VPHQIPKAV 0.0 None None 0 None -1333 MAPAAGTWV 0.0 None None 0 None -1334 FLITNALHF 0.0 None None 0 None -1335 SPKPPPQCV 0.0 None None 0 None -1336 SIADGRAWF 6.93354724607 IADGRAW VEDGRFW 28.0 186219|polyprotein|AGK36298.1|Dengue_virus_2|11060 -1337 MGYRVESEV 3.86373521516 MGYRVES MGYWIES 27.0 180689|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -1338 APAPDLVVV 0.0 None None 0 None -1339 LSANARCLI 0.0 None None 0 None -1340 DTSDGLAVL 0.0 None None 0 None -1341 EARRQGAVF 0.0 None None 0 None -1342 KVPEGDSIV 0.0 None None 0 None -1343 WRPGCLWAL 4.81834181964 GCLWAL GCVWTV 28.0 6431|Genome_polyprotein|SRC279960|Hepatitis_C_virus|11103 -1344 HGLEKVPVI 3.17241105208 HGLEKVPV HGVGEIPM 25.0 131096|G1_and_G2_surface_glycoprotein_precursor|AAG22532.1|Andes_hantavirus|46607 -1345 ITIVVISLI 0.0 None None 0 None -1346 FAMELDDLH 0.0 None None 0 None -1347 LTDKVSTPA 0.0 None None 0 None -1348 LMVSAGVFI 0.0 None None 0 None -1349 LQLEVEEAV 0.0 None None 0 None -1350 SMIHYIVLI 0.0144228035657 SMIHYIVL TTIHDIIL 20.0 110373|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 -1351 FRMFVHVYI 0.0 None None 0 None -1352 HIFLFAVLL 1.02171257151 HIFLFAVLL HLFYSAVLL 29.0 98100|trans-sialidase,_putative|EAN81657.1|Trypanosoma_cruzi|5693 -1353 QQHDGAFLI 0.0 None None 0 None -1354 VELELWGVV 0.0 None None 0 None -1355 WSLQTWRAV 0.0 None None 0 None -1356 LVQEFTRGI 0.0 None None 0 None -1357 VAAFFLSLF 0.0 None None 0 None -1358 EAEEESLAL 0.0 None None 0 None -1359 HVIVRTSRV 0.0 None None 0 None -1360 ELLEPQKTY 0.208598262901 LEPQKTY LHPNNTY 23.0 141306|tegument_host_shutoff_protein|NP_044643.1|Human_alphaherpesvirus_1|10298 -1361 AMSDGRVPV 0.0 None None 0 None -1362 RPPSPKDTV 0.0269770919451 RPPSPKDTV RPSGMFDSV 17.0 177956|polyprotein|ACZ60102.1|Hepatitis_C_virus_subtype_3a|356426 -1363 VPMCHLRLL 0.0 None None 0 None -1364 LSARSVPSI 0.0 None None 0 None -1365 QVHQRMNSL 0.0 None None 0 None -1366 EALVQMQYL 0.0 None None 0 None -1367 CAQSPWCLV 1.18395973855 CAQSPWCLV CVQGDWCPI 33.0 18941|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 -1368 LSCEAHNSM 0.0 None None 0 None -1369 QARGVKKQI 0.0 None None 0 None -1370 SHHSQCSSL 0.0 None None 0 None -1371 YGGFFVISV 0.0626169731798 GGFFVI AGFFIL 23.0 69714|Large_envelope_protein|SRC279965|Hepatitis_B_virus|10407 -1372 YVYPLPVAN 0.416751180485 YVYPLPV YVYALPL 29.0 58463|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 -1373 HSYWLLKLL 0.0 None None 0 None -1374 YRTHTLQTL 0.0 None None 0 None -1375 FTTLKMYSV 0.0 None None 0 None -1376 EHMNHTCNL 0.0 None None 0 None -1377 VAIYLYPLV 0.0 None None 0 None -1378 YEGYKYEHI 1.40213483096 YKYEHI YKLKHI 24.0 39162|gag_protein|AAV53308.1|Human_immunodeficiency_virus_1|11676 -1379 DRYVAVRHL 0.274070953293 DRYVAVR SRYWAIR 21.0 60867|nucleoprotein|CAZ65591.1|Influenza_A_virus|11320 -1380 DLIDYARYM 0.159835763185 LIDYARYM LLDFVRFM 28.0 37153|Nuclear_antigen_EBNA-3C|Q69140.1|Human_gammaherpesvirus_4|10376 -1381 NLLLWVLAI 0.0 None None 0 None -1382 HLHDHYGPY 0.0 None None 0 None -1383 NTDSTAALL 0.0 None None 0 None -1384 YVKERQTVT 0.0 None None 0 None -1385 TMECWGQKY 0.0 None None 0 None -1386 KSDDSDFLA 0.0 None None 0 None -1387 MAFVRLLHS 0.0 None None 0 None -1388 LVDNLTYTL 0.122842705901 LVDNLT LLDNIT 24.0 240808|polyprotein|AAB53095.1|Tick-borne_encephalitis_virus|11084 -1389 KHSATASML 0.0 None None 0 None -1390 FEAHEVLKL 0.0 None None 0 None -1391 LVLVGCFTI 0.0083914153634 VLVGCF VLIRCY 21.0 145860|Protein_E6|P04019.1|Human_papillomavirus_type_11|10580 -1392 TTSGIGSSM 0.0 None None 0 None -1393 KSRAPPEAI 0.0 None None 0 None -1394 AALVPTQAM 0.0 None None 0 None -1395 RQRNGVAKL 0.0 None None 0 None -1396 SSDRMTSVA 0.0 None None 0 None -1397 RPSPNRPKL 0.00679026427764 RPSPNRPKL RPDYNPPLL 22.0 103563|polyprotein|BAB18806.1|Hepatitis_C_virus|11103 -1398 SSVEVLVNY 0.0 None None 0 None -1399 YCIYASLRI 0.0 None None 0 None -1400 RLLPPVSP* 1.80198471654 RLLPPVSP RLLSPLSP 31.0 54662|pX-rex-orf_I_{alternatively_spliced}|AAB23359.1|Human_T-lymphotropic_virus_1|11908 -1401 FSLGKHVCL 0.0 None None 0 None -1402 CTDKVGTEA 0.0 None None 0 None -1403 FRRSISVRI 0.0 None None 0 None -1404 LYLHTLLTI 0.0 None None 0 None -1405 LEVPAPEAI 0.0 None None 0 None -1406 LLSEMAVAV 0.0 None None 0 None -1407 VPLVRWLKV 3.69036212386 VPLVRWL VPFVQWF 27.0 37919|envelope_protein|BAF48755.1|Hepatitis_B_virus|10407 -1408 DTLPMLGNI 0.0 None None 0 None -1409 FAFGAVFSE 0.0 None None 0 None -1410 RNYQAWNFL 1.30903243738 QAWNF QQWNF 27.0 42797|6_kDa_early_secretory_antigenic_target|P0A564.2|Mycobacterium_tuberculosis|1773 -1411 DATKNQVAM 0.0 None None 0 None -1412 QTKHNAKVY 0.0 None None 0 None -1413 IEWECTMML 0.0 None None 0 None -1414 LELEFLCPL 0.0 None None 0 None -1415 QLVNRPQSI 0.0 None None 0 None -1416 TTKKSGGHY 0.247590955559 TTKKSGGHY TTRGRDAHY 23.0 66798|glycoprotein_gp35/37|AAC59622.1|Human_gammaherpesvirus_8|37296 -1417 IVEHPAGHL 0.0 None None 0 None -1418 HRYLWKILI 0.0 None None 0 None -1419 SIFEVIWSV 0.0 None None 0 None -1420 QHDDGYLEV 0.0 None None 0 None -1421 GVAPGLQVV 0.0 None None 0 None -1422 YLAMGEEIY 0.0 None None 0 None -1423 SVVCHQLGF 0.0952288061993 VCHQLG VCARLG 22.0 73177|protein_F_[Hepatitis_C_virus_subtype_1b]|ACA50643.1|Hepatitis_C_virus_(isolate_Japanese)|11116 -1424 RTKRRVFII 0.0 None None 0 None -1425 QMAERALYY 0.0 None None 0 None -1426 LISPPQEKV 0.0 None None 0 None -1427 HLIEERDTL 0.0 None None 0 None -1428 ILKQPSQTL 0.0 None None 0 None -1429 LQVVHLNAV 0.0 None None 0 None -1430 VHDIARFLY 0.0 None None 0 None -1431 RSLPIAIEM 0.0 None None 0 None -1432 NVDEVNQIM 0.0 None None 0 None -1433 GAGVEISTV 0.0 None None 0 None -1434 VPREFKPIL 0.0992866179251 VPREFKPIL VPRPDDPVL 25.0 141462|tegument_protein_UL21|NP_044622.1|Human_alphaherpesvirus_1|10298 -1435 GAQPPMPPY 3.42634928134 PPMPPY PPQPEY 27.0 48896|Genome_polyprotein|P27958.3|Hepatitis_C_virus_subtype_1a|31646 -1436 RADLLIVVF 0.0 None None 0 None -1437 WKEDMAVHV 0.0 None None 0 None -1438 FIEPHARFY 0.0 None None 0 None -1439 DEFSGVPRV 0.0268132145174 SGVPR SGLPR 23.0 58122|pol_protein|BAA32832.1|Hepatitis_B_virus|10407 -1440 RVQPAVRAL 0.0 None None 0 None -1441 ATTIVTTVY 2.66327463302e-07 VY VY 11.0 142232|POSSIBLE_CONSERVED_TRANSMEMBRANE_PROTEIN|CAB00937.1|Mycobacterium_tuberculosis|1773 -1442 FFHNPKPLF 1.02265506822 FHNPKPLF LHGPTPLL 25.0 6591|polyprotein|AAB67037.1|Hepatitis_C_virus_(isolate_H77)|63746 -1443 VTASSGIMI 0.0 None None 0 None -1444 HKAHFQYLL 0.0 None None 0 None -1445 IGVEAGRTL 0.0 None None 0 None -1446 ETMDNGFGH 0.0 None None 0 None -1447 DFWYHAVVL 1.96158586196 DFWYHAVVL DMWEHAFYL 29.0 9415|Superoxide_dismutase|P17670.1|Mycobacterium_tuberculosis|1773 -1448 FHLASAVAL 0.0 None None 0 None -1449 LAMYLSKNY 0.0 None None 0 None -1450 HLLELPQIL 0.0 None None 0 None -1451 VSVHRAPSI 0.155290102389 VHRAPSI LHHAPSL 26.0 21000|glutamine_synthetase_GLNA1_(glutamine_synthase)_(GS-I)|NP_216736.1|Mycobacterium_tuberculosis|1773 -1452 DPAAASHPI 0.0 None None 0 None -1453 SVYLRNNKL 0.0 None None 0 None -1454 INREHIPTF 0.2996637034 EHIPTF QHLPTL 24.0 64821|Protein_Tax-1|P03409.2|Human_T-lymphotropic_virus_1|11908 -1455 AQYDDPRNL 0.0 None None 0 None -1456 RPVNAYARV 0.0 None None 0 None -1457 LARLGALLL 0.0 None None 0 None -1458 SHTGTFLLV 27.0016949153 SHTGTFLL SHSGSFQI 26.0 61077|Non-capsid_protein_NS-1|P07298.1|Human_parvovirus_B19|10798 -1459 HTVAWSNGH 26.1809399136 AWSNGH SWNSGH 28.0 180440|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -1460 TIPDSISKF 8.68426386978 IPDSISKF ITDTIDKF 25.0 12588|Glycoprotein_B_precursor_(Glycoprotein_II)|P09257.1|Human_alphaherpesvirus_3|10335 -1461 AVFEEQIKV 0.0 None None 0 None -1462 FCPLCHNPV 0.669397134211 FCPLCHN LCPHCIN 25.0 20787|Non-capsid_protein_NS-1|P07298.1|Human_parvovirus_B19|10798 -1463 RVLKCNVHL 1.08324885308 VLKCN ILKCN 27.0 47946|envelope_glycoprotein|AAC28452.1|Human_immunodeficiency_virus_1|11676 -1464 LLLPCPLLL 0.0 None None 0 None -1465 QTAEQYVFV 0.0 None None 0 None -1466 FLNSMDQQI 0.0 None None 0 None -1467 GPARGIAII 0.0 None None 0 None -1468 LASLSLKQV 0.0 None None 0 None -1469 TSVPHEDTL 0.0 None None 0 None -1470 EAEVETEAI 0.0 None None 0 None -1471 SSLSNVSQV 0.0 None None 0 None -1472 TVQNAMQIV 0.0 None None 0 None -1473 WHFIKRHIA 0.0 None None 0 None -1474 MTVAGMVLL 0.0 None None 0 None -1475 YMAGSDTTY 0.0 None None 0 None -1476 FRENFESIY 0.0 None None 0 None -1477 LATVILGAV 0.0 None None 0 None -1478 LSSGSFATM 0.0 None None 0 None -1479 DTNNLGIRI 0.0229294398523 NLGIRI DLGVRV 22.0 30946|HCV-1|AAA45676.1|Hepatitis_C_virus_genotype_1|41856 -1480 CSGCVAQVY 0.0 None None 0 None -1481 DHIRNFTTM 0.0 None None 0 None -1482 KPFISRTMM 0.0618191295436 PFISRTMM PFDKSTVM 20.0 116123|nucleocapsid_protein|ABP49342.1|Influenza_A_virus_(A/California/10/1978(H1N1))|425557 -1483 PADPAQLAV 0.0 None None 0 None -1484 YEPDTMEQY 0.0 None None 0 None -1485 EPLNDTIAI 0.0 None None 0 None -1486 QAPLAPTHM 9.89644311759 APLAPTH APVFPSH 26.0 3889|||| -1487 IHLDISSFV 0.0 None None 0 None -1488 PLMDQVSVI 0.0 None None 0 None -1489 HSLHPFPHF 0.0 None None 0 None -1490 ITFKELGAL 0.0 None None 0 None -1491 AAAREATEV 0.0 None None 0 None -1492 RTYHGRLAY 0.0 None None 0 None -1493 DADIYGKPM 0.0 None None 0 None -1494 KGYRIVVAL 0.0 None None 0 None -1495 FNMRDLSDI 0.0 None None 0 None -1496 FRKTLLNPV 0.0 None None 0 None -1497 YLAMGEEIY 0.0 None None 0 None -1498 KPFSHSCNL 0.0 None None 0 None -1499 DQATFINMY 0.0 None None 0 None -1500 ARFRIRKTI 0.0 None None 0 None -1501 RAFSFSLPC 0.081027158281 RAFSFS QAFTFS 22.0 50253|DNA_polymerase|CAA10434.1|Hepatitis_B_virus|10407 -1502 SHMCNSLLV 0.031545921554 MCNSLLV LCGMLLI 21.0 31771|Nucleoprotein|P03418.1|Human_respiratory_syncytial_virus_A2|11259 -1503 EAEEWVVSY 0.0 None None 0 None -1504 KASERFRTQ 0.0 None None 0 None -1505 QIMPHAIIF 0.226023306979 IMPHAI LLPHVI 23.0 79337|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 -1506 LLKHMPKII 0.110041217959 LKHMPKI VRHFPRI 24.0 187106|Vpr_protein|BAA93983.1|Human_immunodeficiency_virus_1|11676 -1507 ILSCNADII 0.0 None None 0 None -1508 AAQCCHKKV 0.0 None None 0 None -1509 TELDSVGPV 0.0 None None 0 None -1510 STFCGTLEY 0.0 None None 0 None -1511 GLIPPDATI 0.0516541933654 GLIPPDATI NLVPMVATV 21.0 55029|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 -1512 SAQRNAAFF 0.0 None None 0 None -1513 MDHPSGIAI 0.0 None None 0 None -1514 FTVLENLAV 0.178250809092 TVLENLAV NALDNLAV 24.0 185447|polyprotein|AGK36298.1|Dengue_virus_2|11060 -1515 KPPPQCVTL 0.502924257487 KPPPQCVTL KLTPLCVTL 28.0 32201|Gp160|Q0ED31|Human_immunodeficiency_virus_1|11676 -1516 LAIYTLLSL 0.0 None None 0 None -1517 RTVKFLMAI 0.0 None None 0 None -1518 MCLEASIPL 0.200766890345 CLEASIPL CMKTWIPL 24.0 155096|RL2|CAB06760.1|Human_alphaherpesvirus_2|10310 -1519 SAPQDSKAV 0.0 None None 0 None -1520 FIIHHRTHT 0.0 None None 0 None -1521 RKEENMESV 0.0 None None 0 None -1522 FPQVSELVL 0.0 None None 0 None -1523 YQVVAQHIY 0.0 None None 0 None -1524 DSAQRNAAF 0.0 None None 0 None -1525 KHFNNSSHF 0.0 None None 0 None -1526 EANVHGIYF 0.0 None None 0 None -1527 LSRVKAQVV 0.0 None None 0 None -1528 LENSNRSMV 0.0 None None 0 None -1529 ESKSGSPEY 10.7269076305 KSGSPEY RSGAPTY 26.0 102368|E2_protein|NP_751921.1|Hepatitis_C_virus_subtype_1a|31646 -1530 YTVKYEQKM 0.0 None None 0 None -1531 LTYGHDRQL 0.0 None None 0 None -1532 LHFHFTACY 0.0 None None 0 None -1533 DCNKTAVTI 0.0 None None 0 None -1534 QPLHSLSVL 0.547748367869 QPLHSLSV QPFHSYGV 27.0 232152|rhoptry_kinase_family_protein|AFO54841.1|Toxoplasma_gondii_type_III|398031 -1535 AACGIIQQV 0.0 None None 0 None -1536 WDQRCLHTI 0.0 None None 0 None -1537 QLQAFWKHV 0.0 None None 0 None -1538 SPHPRRRRL 0.0655592952749 PHPRRRR PEPDRQR 23.0 183813|polyprotein|AGW21594.1|Dengue_virus_1|11053 -1539 FLDKASDLL 0.0 None None 0 None -1540 SAWLFVTGI 0.0 None None 0 None -1541 FMFEMPFMQ 0.0 None None 0 None -1542 VSLQAAEEI 0.0 None None 0 None -1543 RANGNPNPT 0.0139532163774 RANGNPNP RANELVNP 21.0 154980|tegument_protein|CAB06735.1|Human_alphaherpesvirus_2|10310 -1544 ELPAFIEMM 0.0 None None 0 None -1545 CVAKCGGTV 0.0 None None 0 None -1546 LEYLAPEVL 0.0 None None 0 None -1547 TMANNPDVM 0.0 None None 0 None -1548 EAVSSASKL 0.0 None None 0 None -1549 FSLYRGWAL 0.0338147117713 FSLYRGWA FSMVGNWA 24.0 149052|E1_protein|NP_751920.1|Hepatitis_C_virus_(isolate_H77)|63746 -1550 VVIGAPYVV 0.113860246051 GAPYVV GNPYAV 22.0 110227|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 -1551 LHFHWNWII 1.13172182694 HWNWII RWEWVV 28.0 74407|polyprotein|AAU89634.1|Hepatitis_C_virus_subtype_2a|31649 -1552 MSACWSFAV 1.40795140079 SACWSF AACWGF 31.0 79506|E1_protein|BAA19893.1|Rubella_virus|11041 -1553 YIAQNDDEL 0.0 None None 0 None -1554 ETINWTLLE 0.0 None None 0 None -1555 DQYAICMKY 0.126785938088 DQYAICMK NPYAVCDK 25.0 110467|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 -1556 HAKRKTATA 0.0 None None 0 None -1557 LAAASSTAF 0.0 None None 0 None -1558 KAYGRDNTP 1.7699107108 KAYGRD KAYGTD 27.0 108230|polyprotein|AAF65953.1|Hepatitis_C_virus|11103 -1559 KHLQLYQLF 0.0 None None 0 None -1560 WAVMNHFSM 0.0 None None 0 None -1561 IERPGGSLL 0.0 None None 0 None -1562 YCFGCLSHH 0.00860509404551 YCFGCLS FCIPCMK 21.0 155096|RL2|CAB06760.1|Human_alphaherpesvirus_2|10310 -1563 QGYGGFFVI 0.00840115467717 GGFFVI AGFFIL 23.0 69714|Large_envelope_protein|SRC279965|Hepatitis_B_virus|10407 -1564 NENDLITNI 0.0 None None 0 None -1565 LPVPIIQQL 0.0 None None 0 None -1566 RLMHQLLVI 0.00726488946482 RLMHQLLVI QLFHLCLII 21.0 93431|pre-C/C_protein|ABY54138.1|Hepatitis_B_virus|10407 -1567 FHKEVFGMF 0.0 None None 0 None -1568 CTVEDGGHV 0.0 None None 0 None -1569 EVAQHLATT 0.0 None None 0 None -1570 VEHPAGHLV 3.94454377782 PAGHLV PAGHAV 28.0 23601|Genome_polyprotein|SRC279960|Hepatitis_C_virus_(isolate_H77)|63746 -1571 WKGSTECKL 0.0 None None 0 None -1572 LSDPHLTAV 0.0 None None 0 None -1573 ILTELLMVV 0.0 None None 0 None -1574 MVHLVPALV 0.00953033463174 MVHLVPAL LLHHAPSL 20.0 21000|glutamine_synthetase_GLNA1_(glutamine_synthase)_(GS-I)|NP_216736.1|Mycobacterium_tuberculosis|1773 -1575 TILENPYIM 0.0 None None 0 None -1576 DHSDSDYDF 0.0 None None 0 None -1577 NHLNIAWEL 0.76435968383 NHLNIAWEL THLYILWAV 24.0 1000|glycoprotein_gp35/37|AAC59622.1|Human_gammaherpesvirus_8|37296 -1578 FPEDVAVYT 0.0 None None 0 None -1579 YMTSSGRRF 0.0 None None 0 None -1580 SSVPLRSSV 0.0 None None 0 None -1581 LAAPPPLTE 1.95708895828 PPPLT PPPAT 25.0 120093|unnamed_protein_product|CAA33016.1|Rubella_virus|11041 -1582 VVASQPAHV 0.0 None None 0 None -1583 SMLDPHGHL 0.0 None None 0 None -1584 LVVADIHSM 0.0 None None 0 None -1585 LLYMAFVRL 0.0 None None 0 None -1586 VVTVMVTTV 0.0 None None 0 None -1587 KLIDVNHYV 0.0 None None 0 None -1588 FTQYLGLSM 0.00484909033908 FTQYLGLS FTDALGID 21.0 141277|transactivating_tegument_protein_VP16|NP_044650.1|Human_alphaherpesvirus_1|10298 -1589 FRGKHDCAL 0.0 None None 0 None -1590 EVFRHKLAM 0.0 None None 0 None -1591 RSIRLSQEI 0.0 None None 0 None -1592 HTIQKAKHM 0.0 None None 0 None -1593 PSGRPALAY 0.0 None None 0 None -1594 WQDHIRLEV 0.0 None None 0 None -1595 VLLDLRPSI 2.274058298 LLDLRP MLDLQP 24.0 110335|E7|AAD33253.1|Human_papillomavirus_type_16|333760 -1596 AVYSTCVLV 0.0927784841397 AVYSTC ATYSRC 23.0 149060|E2_protein|NP_751921.1|Hepatitis_C_virus_(isolate_H77)|63746 -1597 LALSLPACF 0.0 None None 0 None -1598 NQCPCSSDI 0.0 None None 0 None -1599 SIDPKTGVV 0.0 None None 0 None -1600 AAASHPILL 0.0 None None 0 None -1601 RLLKHMPKI 0.101153035124 LKHMPKI VRHFPRI 24.0 187106|Vpr_protein|BAA93983.1|Human_immunodeficiency_virus_1|11676 -1602 LSLTGLQVL 0.021486229198 LSLTGLQ LSLIGLK 22.0 187086|polyprotein|ABG67747.1|West_Nile_virus|11082 -1603 MSQEEKVAY 0.0 None None 0 None -1604 MIENLEHHI 0.0 None None 0 None -1605 IIATGLVTL 0.0 None None 0 None -1606 SADCGCCPM 0.0 None None 0 None -1607 CAELLSHTV 0.0 None None 0 None -1608 HISEEYGLL 0.0 None None 0 None -1609 YSFCPLCHN 0.206854960234 SFCPLCHN GLCPHCIN 25.0 20787|Non-capsid_protein_NS-1|P07298.1|Human_parvovirus_B19|10798 -1610 LPCRSLTRV 0.0 None None 0 None -1611 KVLQHGRLY 0.0 None None 0 None -1612 FLCDEEPLL 0.0 None None 0 None -1613 IPCLDDVTV 0.0 None None 0 None -1614 LASEAVSSA 0.0 None None 0 None -1615 TPTPGFSSM 0.0 None None 0 None -1616 FYLVAYAAM 0.17018469657 YLVAYA YLAAYA 26.0 74545|TcP2beta|CAA52943.1|Trypanosoma_cruzi|5693 -1617 YLKSPECFL 0.0 None None 0 None -1618 KVNTATTTM 0.0 None None 0 None -1619 LPVSTKCTV 0.0 None None 0 None -1620 SVRYAGPLY 0.297176741199 VRYAGPLY MTYAAPLF 25.0 42897|RNA_polymerase_beta-subunit|AAA21416.1|Mycobacterium_tuberculosis|1773 -1621 HTIQKAKHM 0.0 None None 0 None -1622 TFRDVAVEF 0.0366333305265 TFRDVA TWRDMA 22.0 186175|polyprotein|AFY10053.1|Dengue_virus_3|11069 -1623 DEKDLWEYI 0.0133766675551 DEKDLWEYI DQKSLENYI 25.0 28594|IMMUNOGENIC_PROTEIN_MPT64_(ANTIGEN_MPT64/MPB64)|CAA98382.1|Mycobacterium_tuberculosis_H37Rv|83332 -1624 DPADPTRDL 4.01184798055 DPADPTRDL DPAKPARLL 28.0 53405|||| -1625 EAEEWVVSY 0.0 None None 0 None -1626 CAFTVLENL 0.0 None None 0 None -1627 SWMEGQVTI 0.0 None None 0 None -1628 MTAVGYGDM 0.0 None None 0 None -1629 VSEDAKQRI 0.0 None None 0 None -1630 DVDEDGYIM 0.0 None None 0 None -1631 IVQCRVLNI 0.0 None None 0 None -1632 IASLLENIL 0.0 None None 0 None -1633 SRNWLKSIL 0.0 None None 0 None -1634 KVKPTLAMY 0.0070925003201 PTLAMY PALQMY 22.0 146260|polyprotein|ADF97231.1|Hepatitis_C_virus_subtype_3a|356426 -1635 YTMGIIFVL 0.0 None None 0 None -1636 ELKSPVKMI 0.0 None None 0 None -1637 LSLGAPSPL 0.0555525573282 LSLGAP LSLGDP 23.0 54342|UL123;_IE1|AAR31448.1|Human_betaherpesvirus_5|10359 -1638 QSIRAATEV 0.0 None None 0 None -1639 YMAATLLEF 0.0 None None 0 None -1640 CSDGSDEDA 0.319310454046 CSDGSDEDA CDDCHAQDA 21.0 6094|Genome_polyprotein|Q81495.3|Hepatitis_C_virus_(isolate_HCV-K3a/650)|356416 -1641 SYLEDVRLI 0.0 None None 0 None -1642 QVYVGDSDI 0.0 None None 0 None -1643 VIDQCLKKI 0.0 None None 0 None -1644 YPDWIRDNM 1.53360425083 YPDWI YQDWL 25.0 23288|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 -1645 RATSFGKCF 0.205486484796 SFGKCF TFGWCF 25.0 56620|Nef_protein|Q9YYU8|Human_immunodeficiency_virus_1|11676 -1646 KAGSLGIIL 0.415852219105 GSLGII GTLGIV 24.0 37573|E7_protein|ABL96585.1|Human_papillomavirus_type_16|333760 -1647 VAQQSRLVF 0.0 None None 0 None -1648 DCQSHRLTV 0.0 None None 0 None -1649 MPNVLWDLV 0.0 None None 0 None -1650 MSWLTPLMI 0.00107210420498 SWLTPLMI AWGRRLMI 18.0 181733|Antigen_85-B|P0C5B9.1|Mycobacterium_tuberculosis|1773 -1651 DANNVTCVW 0.0 None None 0 None -1652 KLLQCMSRV 0.0 None None 0 None -1653 VHLPLAVAL 0.0 None None 0 None -1654 SLYSLDATL 0.887852301761 SLYSLDATL SLYNTAATL 26.0 189286|||| -1655 FTTTQWSSL 0.276143452524 FTTTQW LSTTEW 24.0 37830|polyprotein|BAB18806.1|Hepatitis_C_virus_subtype_1b|31647 -1656 VALRDLGCL 0.0 None None 0 None -1657 MVACGGTVY 0.0 None None 0 None -1658 EMFQRYSAF 1.04802970038 EMFQRYSAF EFFTKNSAF 24.0 44214|UL123;_IE1|AAR31448.1|Human_betaherpesvirus_5|10359 -1659 DAACGIWSL 0.0 None None 0 None -1660 FTILPCTCY 0.0 None None 0 None -1661 IIYTMGIIF 0.0 None None 0 None -1662 RVYNIRGDM 0.0 None None 0 None -1663 RNDPELPTV 0.0340275143527 NDPELP NTPGLP 21.0 65497|HCV-1|AAA45676.1|Hepatitis_C_virus_genotype_1|41856 -1664 HSDSDYDFV 0.0 None None 0 None -1665 VLGEHHHHV 0.0 None None 0 None -1666 HVVDEREQM 0.0 None None 0 None -1667 GQFPYMGEV 0.000425382554656 FPYMGEV FPGGGQI 18.0 181035|||| -1668 LPPEMYVYL 0.0 None None 0 None -1669 EAYQKQLCF 0.0776136961569 YQKQLC YNKPLC 24.0 110982|E6_protein|CAB45108.1|Human_papillomavirus_type_16|333760 -1670 AATGPGEVL 0.129514787687 ATGPGEVL GTGPGNGL 25.0 47760|EBNA-1_protein|Q777E1|Human_gammaherpesvirus_4|10376 -1671 DLYATAFLV 0.0 None None 0 None -1672 GFDWKSVFI 0.0 None None 0 None -1673 FVVFSFFFV 0.0209879781055 FVVFSFF LVLFGFF 23.0 422999|polyprotein|ABD97104.1|Hepatitis_C_virus_genotype_3|356114 -1674 GRDVVHHLL 0.0 None None 0 None -1675 VTLRWYLAM 16.7007719127 TLRWYLAM TLRWFFNL 28.0 38724|Genome_polyprotein|P08617.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 -1676 LVAQYDLTV 0.0 None None 0 None -1677 RLIRGDAVV 0.0 None None 0 None -1678 FQYLVVHTE 0.0 None None 0 None -1679 KHYLMTRTL 0.0 None None 0 None -1680 FVMEHSNIV 0.0 None None 0 None -1681 HQMENNGWV 1.02571149154 QMENNGWV QMENKAWL 33.0 150399|polyprotein|AGV76873.1|Dengue_virus_2|11060 -1682 NATYSGYVY 0.0 None None 0 None -1683 KVKNSASVM 0.0 None None 0 None -1684 KQDKCFAFI 0.0 None None 0 None -1685 AQRPWPRVL 0.0843380588073 RPWPRV RPGPRL 23.0 139406|polyprotein|ACT37184.1|Hepatitis_C_virus|11103 -1686 MAATLLEFF 0.0 None None 0 None -1687 DPNTVSNSI 0.0 None None 0 None -1688 LPVSGGHVM 0.204938535034 LPVSGG MPVGGG 25.0 189750|Diacylglycerol_acyltransferase/mycolyltransferase_Ag85B|SRC280000|Mycobacterium_tuberculosis|1773 -1689 MLDDAPRLL 0.0 None None 0 None -1690 IPPDATIYF 0.0918537604584 PDATIY PDIVIY 23.0 101812|Pol_polyprotein|Q9YLQ7|Human_immunodeficiency_virus_1|11676 -1691 LHDALEVDL 0.0 None None 0 None -1692 MMEKLYPGY 0.0 None None 0 None -1693 IPFLFFTDM 0.0 None None 0 None -1694 YKLCFNTFF 0.0 None None 0 None -1695 YVTMVIDRL 0.0 None None 0 None -1696 TIYFDVVLL 0.0 None None 0 None -1697 SAWLRAISL 0.0 None None 0 None -1698 HLWPGGLSL 0.0 None None 0 None -1699 FGYMTQQRM 0.0 None None 0 None -1700 HVYILRAVF 0.0 None None 0 None -1701 LYIPALAVL 0.0 None None 0 None -1702 DPMVPLQGV 0.41651905562 DPMVPL DPTTPL 23.0 103392|polyprotein|BAB18806.1|Hepatitis_C_virus|11103 -1703 FTEEGFCAI 0.0 None None 0 None -1704 FFNDDCCEL 0.0 None None 0 None -1705 FLFHPLEFC 0.0 None None 0 None -1706 VVMWWMGIL 0.875296446467 VMWWMGIL CLWWLQYF 26.0 39591|polyprotein|AAA45677.1|Hepatitis_C_virus_(isolate_H77)|63746 -1707 KTFHHKSNF 0.0 None None 0 None -1708 QRPWPRVLL 0.245621905968 RPWPRV RPGPRL 23.0 139406|polyprotein|ACT37184.1|Hepatitis_C_virus|11103 -1709 IRVQEASTI 0.0 None None 0 None -1710 DLIDYARYM 0.484336212252 LIDYARYM LLDFVRFM 28.0 37153|Nuclear_antigen_EBNA-3C|Q69140.1|Human_gammaherpesvirus_4|10376 -1711 VTVRGFWIY 0.0 None None 0 None -1712 FMDEHAAER 0.0 None None 0 None -1713 SISDTYDPY 0.0 None None 0 None -1714 DTNDNVPEF 0.0 None None 0 None -1715 YNCTCGCSM 0.0668968271799 NCTCGCS ECTTPCS 24.0 57364|Genome_polyprotein|P26664.3|Hepatitis_C_virus|11103 -1716 LLLLASATV 0.0 None None 0 None -1717 LYMAFVRLL 0.0 None None 0 None -1718 SAEVQLSKI 0.0 None None 0 None -1719 ITACLSVLI 0.0 None None 0 None -1720 LPETKGVTL 0.440996131242 LPETKGVTL VPEVTDVTL 24.0 168240|major_paraflagellar_rod_protein|AAA30221.1|Trypanosoma_cruzi|5693 -1721 MSQEEKVAY 0.0 None None 0 None -1722 MASPQAEST 0.0 None None 0 None -1723 MSFELPYHC 0.0 None None 0 None -1724 RWNDTRATV 0.134680294585 RWNDTR RWLDAR 24.0 150538|polyprotein|AGW21594.1|Dengue_virus_1|11053 -1725 LRHERAVSM 0.0 None None 0 None -1726 LHLLVACTI 0.0 None None 0 None -1727 YGHDRQLCL 0.0 None None 0 None -1728 DATIYFDVV 0.0 None None 0 None -1729 IVCDIKEKL 0.00240549311618 IVCDIKEK IFCHSKKK 20.0 36504|polyprotein_precursor|BAA01582.1|Hepatitis_C_virus|11103 -1730 RPAQFLHEM 0.0 None None 0 None -1731 WHFVYKSGM 0.0 None None 0 None -1732 EVDPIGNLY 0.0 None None 0 None -1733 RTDGNSHEA 0.0 None None 0 None -1734 KHMPKIIHL 0.0 None None 0 None -1735 DVHDIARFL 0.0 None None 0 None -1736 PATRPLHVL 0.000259990550586 PATRPLHVL PAVGVYHIV 18.0 32663|small_hydrophobic_protein|AAM12943.1|Human_metapneumovirus|162145 -1737 LLHSNRSQI 0.0 None None 0 None -1738 PARSGIFKI 0.0 None None 0 None -1739 AALTPTEEM 0.0 None None 0 None -1740 ISAYMAATL 0.0 None None 0 None -1741 IMMSDEERI 0.0 None None 0 None -1742 KRQEGMVPV 0.581298321339 QEGMVPV DEGLLPV 25.0 140541|hypothetical_protein|NP_218210.1|Mycobacterium_tuberculosis_H37Rv|83332 -1743 LQKRATEEI 0.0136766968351 QKRATEEI QKQELDEI 20.0 327|ESAT-6-like_protein_esxB|P0A566.2|Mycobacterium_tuberculosis|1773 -1744 GKDKMTHLL 0.0 None None 0 None -1745 AQLPPWAPL 1.01158072828 AQLPPWAP AQLHVWVP 27.0 40158|polyprotein|AAA45534.1|Hepatitis_C_virus|11103 -1746 FFCEVPVLL 0.0 None None 0 None -1747 RAHKKAITT 0.0 None None 0 None -1748 FDWKSVFII 0.0 None None 0 None -1749 CLFRAARLI 0.0 None None 0 None -1750 MIEDFLRRF 0.0 None None 0 None -1751 TTTERWLRV 0.0 None None 0 None -1752 FFKDKATSK 0.0 None None 0 None -1753 HFFDAFRKF 1.97322439336 FFDAFRKF IFDRTRKF 25.0 154296|UL29|CAB06754.1|Human_alphaherpesvirus_2|10310 -1754 GALGLNRPV 0.0 None None 0 None -1755 YRTKCTLGL 0.0 None None 0 None -1756 MTVAGMVLL 0.0 None None 0 None -1757 KTLSKTAHL 0.0 None None 0 None -1758 NLYIFATCL 0.0 None None 0 None -1759 GFDTSSSSL 0.0 None None 0 None -1760 TPVLCGQPI 0.130418951884 VLCGQPI VLCLRPV 24.0 69398|X_protein|AAP06597.1|Hepatitis_B_virus|10407 -1761 WCAPGKPTL 0.0 None None 0 None -1762 ILHNQIQQV 0.629859339283 ILHNQIQQV LLHTDFEQV 25.0 37398|Non-capsid_protein_NS-1|P07298.1|Human_parvovirus_B19|10798 -1763 VVLSPEVEV 0.0 None None 0 None -1764 DSIHQVGMY 0.0155776894056 HQVGMY HAVGLF 22.0 23573|polyprotein|AAB67037.1|Hepatitis_C_virus_(isolate_H77)|63746 -1765 NHSGVGAFW 0.0 None None 0 None -1766 HNLEPHGYV 0.0 None None 0 None -1767 PSLNATTIV 0.0 None None 0 None -1768 ISGFKGDTV 0.154683020868 GFKGDTV GFPTDTV 24.0 79506|E1_protein|BAA19893.1|Rubella_virus|11041 -1769 HIASSTTSI 0.0 None None 0 None -1770 HTLHAHDPV 0.0 None None 0 None -1771 WTDYGQVFT 0.0 None None 0 None -1772 ELFRRGLRY 0.0 None None 0 None -1773 SASRTKRRV 0.0 None None 0 None -1774 NSGPSRSML 0.0 None None 0 None -1775 ESADKTAYL 0.0 None None 0 None -1776 TELEKFSKV 0.0 None None 0 None -1777 FHAQVCSLY 1.32122904181 HAQVCSLY KAKICGLY 28.0 177701|polyprotein|ACZ60104.1|Hepatitis_C_virus_subtype_3a|356426 -1778 LVVEHVLTT 0.0 None None 0 None -1779 RSYWLRLFL 0.0 None None 0 None -1780 DVDEKQLLV 0.0 None None 0 None -1781 CAIISLIFI 0.0 None None 0 None -1782 SQLEMPETL 0.0 None None 0 None -1783 NLEDVGRHL 0.0 None None 0 None -1784 HLRRIGRFI 0.0 None None 0 None -1785 KYDPDVVVM 0.0 None None 0 None -1786 KDDDCITLV 0.0 None None 0 None -1787 YDVTDSRII 0.0 None None 0 None -1788 MLLHQVAAY 0.0413203406169 MLLHQV MILHEI 24.0 196087|PPE_family_protein_PPE54|YP_177960.1|Mycobacterium_tuberculosis_H37Rv|83332 -1789 THQSGFSVI 0.0 None None 0 None -1790 DLQPVREAI 0.0 None None 0 None -1791 FAGSTQSDL 0.0 None None 0 None -1792 GSYREAQSL 0.0 None None 0 None -1793 HFMPRIQRL 0.0 None None 0 None -1794 LPLKRPGKL 0.0343305252388 LPLKRP LPFDRP 22.0 116127|Nucleoprotein|P15682.1|Influenza_A_virus_(A/Wilson-Smith/1933(H1N1))|381518 -1795 MAFPEGYGT 0.0567950827738 FPEGY LPEGY 25.0 31997|hypothetical_protein_FTT0484|YP_169522.1|Francisella_tularensis_subsp._tularensis_SCHU_S4|177416 -1796 DMQDLTEFL 0.0 None None 0 None -1797 VDFSSEVTV 0.0 None None 0 None -1798 MEVDPIGNL 0.0379279510851 MEVDPIGNL MEVTPSGTW 24.0 26273|nucleocapsid_protein|ABI96968.1|SARS_coronavirus|227859 -1799 ISRNCNSRM 0.0 None None 0 None -1800 YSLIDNFVM 0.0 None None 0 None -1801 FEMPFMQTG 0.0 None None 0 None -1802 SHELVMYIW 0.0 None None 0 None -1803 IIVSYMLII 0.0 None None 0 None -1804 AAAAAVAAL 0.0 None None 0 None -1805 LVDQKAKEV 0.0 None None 0 None -1806 FFSLLATVI 0.710550459145 FSLLATV FTLVATV 25.0 98640|trans-sialidase,_putative|EAN80840.1|Trypanosoma_cruzi|5693 -1807 IYGKPMPTI 0.0 None None 0 None -1808 YMLERLIEQ 0.0 None None 0 None -1809 CIADFLEHM 0.0 None None 0 None -1810 LPYPGSSQA 0.0 None None 0 None -1811 EAWQCQPVL 0.0 None None 0 None -1812 VATSTAQLL 0.0 None None 0 None -1813 VKYTPKLEI 0.0 None None 0 None -1814 RVSAKRVSV 0.0 None None 0 None -1815 NTWTRQMGY 0.0 None None 0 None -1816 LDFACHFTV 0.0 None None 0 None -1817 HVRIHPKLV 0.0 None None 0 None -1818 LQQNCAAYL 0.000555833253958 QQNCAAYL QDNQLAYV 19.0 150649|polyprotein|AGW21594.1|Dengue_virus_1|11053 -1819 DAVGNMLNL 0.0 None None 0 None -1820 WQAISLMVI 0.0 None None 0 None -1821 WLWKLSAVV 0.0 None None 0 None -1822 LAPTHMPEL 0.0 None None 0 None -1823 YAQTPSKTP 0.514097249368 TPSKTP TPDSTP 24.0 53041|phosphorylated_matrix_protein_(pp65)|AAA45996.1|Human_betaherpesvirus_5|10359 -1824 LLLCFLAAM 0.0771007402221 LLLCFL LLLCLI 23.0 27168|envelope_protein|BAF48755.1|Hepatitis_B_virus|10407 -1825 HMPKIIHLV 0.0 None None 0 None -1826 AQLPSYMHI 0.0 None None 0 None -1827 IKLHNPSTI 0.0 None None 0 None -1828 TLLTTHYMA 0.0 None None 0 None -1829 SYEVVIPEW 0.0 None None 0 None -1830 WVNEFGEVF 0.196334224507 WVNEFGEVF WLSDCGEAL 24.0 72790|FL-160-2_protein_-_Trypanosoma_cruzi|JH0823|Trypanosoma_cruzi|5693 -1831 LTYRHCQNF 0.0 None None 0 None -1832 LTYRHCQNF 0.0 None None 0 None -1833 RHCQNFSIL 0.0 None None 0 None -1834 YRHCQNFSI 0.0 None None 0 None -1835 YRHCQNFSI 0.0 None None 0 None -1836 FSLERIAES 0.0 None None 0 None -1837 CLHYIMGDY 0.0 None None 0 None -1838 LLACLHYIM 0.755659798581 LLACL LLACL 25.0 40262|Cytochrome_P450_2A7|P20853.1|Homo_sapiens|9606 -1839 RLLACLHYI 0.470647487397 LLACL LLACL 25.0 40262|Cytochrome_P450_2A7|P20853.1|Homo_sapiens|9606 -1840 RLLACLHYI 0.375813339906 LLACL LLACL 25.0 40262|Cytochrome_P450_2A7|P20853.1|Homo_sapiens|9606 -1841 SQSADAHSI 0.0 None None 0 None -1842 TFFSSSQSA 0.0 None None 0 None -1843 YANNHCIRT 0.0 None None 0 None -1844 FYGMTEMNY 0.197223709005 GMTEMNY ALTEMDY 25.0 418945|PPE_family_protein_PPE68|KAM81677.1|Mycobacterium_tuberculosis_H37Ra|419947 -1845 LQFYGMTEM 0.0 None None 0 None -1846 LQFYGMTEM 0.0 None None 0 None -1847 ALWMYRSLM 6.40774625238 LWMYRSLM VWLKKSMM 25.0 181036|||| -1848 ALWMYRSLM 0.855722704359 LWMYRSLM VWLKKSMM 25.0 181036|||| -1849 QALWMYRSL 0.0 None None 0 None -1850 SFRKEKRNL 0.0 None None 0 None -1851 LTSQDLAGY 0.0 None None 0 None -1852 MAGHGWGAL 0.0 None None 0 None -1853 VMSYGEQPY 0.0 None None 0 None -1854 SVSDVFHGI 0.0 None None 0 None -1855 IPNDNTLSL 0.0 None None 0 None -1856 KTIPNDNTL 0.0 None None 0 None -1857 KTIPNDNTL 0.0 None None 0 None -1858 TLSLRICTI 0.0 None None 0 None -1859 FSMRARIDV 0.0 None None 0 None -1860 RLLGQKFSM 0.0 None None 0 None -1861 IYMENERRM 0.0 None None 0 None -1862 QFLLELYSL 0.0 None None 0 None -1863 RVIRYVIGV 0.0 None None 0 None -1864 QYLSLINYY 0.0 None None 0 None -1865 STLQYLSLI 0.0 None None 0 None -1866 IAQGKPVTL 0.0 None None 0 None -1867 SVIAQGKPV 0.0 None None 0 None -1868 FAIMHAQRT 0.0922530683728 MHAQRT MHQKRT 23.0 110338|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 -1869 HTNAVFAIM 0.000248159096545 HTNAVFAIM HTTKGAALM 18.0 24986|polyprotein_precursor|NP_041724.2|West_Nile_virus|11082 -1870 NHTNAVFAI 0.0 None None 0 None -1871 HHHHHHQAW 31.6214375823 HHHHQ HHFHQ 28.0 183147|polyprotein|AGW21594.1|Dengue_virus_1|11053 -1872 QAWPPPSSA 1.66000789695 WPPPSSA WPAPSGA 32.0 144544|polyprotein_precursor|BAA01728.1|Hepatitis_C_virus|11103 -1873 AHTVARGPV 0.453229538203 HTVARGPV HPVHAGPI 24.0 24557|Gag_polyprotein|P03347.3|Human_immunodeficiency_virus_1|11676 -1874 ALQTFAHTV 0.0 None None 0 None -1875 EIYTKNHAY 0.0 None None 0 None -1876 FGYQLKEIY 0.0 None None 0 None -1877 IYTKNHAYI 0.0 None None 0 None -1878 YTKNHAYII 0.0 None None 0 None -1879 YTKNHAYII 0.0 None None 0 None -1880 HAFDRYETT 0.0 None None 0 None -1881 TTHSRPVTL 0.0 None None 0 None -1882 TTHSRPVTL 0.0 None None 0 None -1883 YETTHSRPV 0.0 None None 0 None -1884 VLFDVAGQV 5.87593218982e-05 VLFDVAGQV VIFCHPGQL 17.0 79454|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 -1885 VLFDVAGQV 9.25459319897e-05 VLFDVAGQV VIFCHPGQL 17.0 79454|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 -1886 ESKPAPAEV 0.0 None None 0 None -1887 LNVEKTEKI 0.0166822097398 VEKTEK LEKTKK 22.0 35568|Polyprotein|Q9J8D4|Dengue_virus_2|11060 -1888 MVIVFYGTL 0.0 None None 0 None -1889 MVIVFYGTL 0.0 None None 0 None -1890 SAHLTMVIV 0.0 None None 0 None -1891 YETFGAASF 0.0 None None 0 None -1892 RGVPPLRTV 0.959521069645 GVPPLRT GVPPLRA 33.0 36345|polyprotein|ABR25251.1|Hepatitis_C_virus_(isolate_H77)|63746 -1893 TAESCRSTL 0.0 None None 0 None -1894 TAESCRSTL 0.0 None None 0 None -1895 RVRAAGQRL 1.69373967722 RVRAAGQRL KIRAWGRRL 27.0 181733|Antigen_85-B|P0C5B9.1|Mycobacterium_tuberculosis|1773 -1896 DVHARESKI 0.0 None None 0 None -1897 NVPPTVQKV 0.0 None None 0 None -1898 CYYPMAGYI 0.0060192893897 YYPMAGYI YYLDRGYL 22.0 76532|outer_membrane_protein|YP_170495.1|Francisella_tularensis_subsp._tularensis_SCHU_S4|177416 -1899 CYYPMAGYI 0.0239816132828 YYPMAGYI YYLDRGYL 22.0 76532|outer_membrane_protein|YP_170495.1|Francisella_tularensis_subsp._tularensis_SCHU_S4|177416 -1900 NTRQCYYPM 0.0 None None 0 None -1901 LGYRWCLHV 0.441063931047 GYRWCL GWRWRL 25.0 37607|kaposin|AAC57155.1|Human_gammaherpesvirus_8|37296 -1902 LLLGYRWCL 5.17789244834 LLLGYRWCL LLNGWRWRL 30.0 37607|kaposin|AAC57155.1|Human_gammaherpesvirus_8|37296 -1903 TAHSSVLTL 0.0 None None 0 None -1904 TAHSSVLTL 0.0 None None 0 None -1905 FPSNHLGDL 0.0236234538092 PSNHLGD PGNGLGE 23.0 47760|EBNA-1_protein|Q777E1|Human_gammaherpesvirus_4|10376 -1906 LLLAHKKKV 0.0 None None 0 None -1907 AQILEQVEV 0.0 None None 0 None -1908 QIFKCKGTL 0.0 None None 0 None -1909 QIFKCKGTL 0.0 None None 0 None -1910 TLVGHQGPV 0.0 None None 0 None -1911 TLVGHQGPV 0.0 None None 0 None -1912 DAVELWAIV 0.0 None None 0 None -1913 VDLPLTSTI 0.00972155564068 LPLTSTI LPFHSTL 20.0 21007|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 -1914 NVVNGQMRF 0.0 None None 0 None -1915 MGAPGSEII 0.0 None None 0 None -1916 FSQFSNLKV 0.0 None None 0 None -1917 KAFSQFSNL 0.0 None None 0 None -1918 HFSVSSNLL 0.0 None None 0 None -1919 KHFSVSSNL 0.0 None None 0 None -1920 KHFSVSSNL 0.0 None None 0 None -1921 YQVLAMSTK 0.0 None None 0 None -1922 KLSSEAKTK 0.0 None None 0 None -1923 TVLRLFPFR 0.0 None None 0 None -1924 TVLRLFPFR 0.0 None None 0 None -1925 TVKDVHKAK 0.0 None None 0 None -1926 TIHNVNFSK 0.0 None None 0 None -1927 TIHNVNFSK 0.0 None None 0 None -1928 SETTFDIFV 0.0 None None 0 None -1929 GMHFSPGAR 0.0 None None 0 None -1930 FLTQPVAPK 9.05129460172 FLTQPVAP LIEKPVAP 24.0 419002|PPE_family_protein_PPE68|KAM81677.1|Mycobacterium_tuberculosis_H37Ra|419947 -1931 KAISFYMKR 0.0 None None 0 None -1932 RTVAQVTKK 0.0 None None 0 None -1933 RTVAQVTKK 0.0 None None 0 None -1934 SEDKKNTKL 0.0 None None 0 None -1935 RVAAGVQIK 0.0 None None 0 None -1936 RVAAGVQIK 0.0 None None 0 None -1937 VVGAVGVGK 0.0 None None 0 None -1938 VVGAVGVGK 0.0 None None 0 None -1939 TTTPTLKEK 0.0 None None 0 None -1940 QSLYIDRLK 0.0 None None 0 None -1941 TTIHYNYMY 0.0 None None 0 None -1942 TECIIAMSF 0.0 None None 0 None -1943 IESSYLESL 0.0 None None 0 None -1944 AEEEEEEVV 0.961625857069 AEEEEE SEEEDE 23.0 110431|E7|AAD33253.1|Human_papillomavirus_type_16|333760 -1945 TENHQPVCL 0.0 None None 0 None -1946 GQLGGLAGK 0.0 None None 0 None -1947 LSDWGPHFK 0.0 None None 0 None -1948 LSDWGPHFK 0.0 None None 0 None -1949 KPASKKEWI 0.0 None None 0 None -1950 TTKSEAIEK 0.0 None None 0 None -1951 IVRASGCEL 0.0 None None 0 None -1952 VPTELNGSM 0.0 None None 0 None -1953 VPLFPARVL 0.0 None None 0 None -1954 APAQPPMLA 32.3662874827 APAQPPM CPSQEPM 24.0 58463|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 -1955 VVGARGVGK 0.0 None None 0 None -1956 VVGARGVGK 0.0 None None 0 None -1957 KLCNSGDFR 0.0 None None 0 None -1958 HPLTENSPL 0.0 None None 0 None -1959 STVRKSPWK 0.0 None None 0 None -1960 STVRKSPWK 0.0 None None 0 None -1961 LIRMYNINK 0.0 None None 0 None -1962 LIRMYNINK 0.0 None None 0 None -1963 SPWPLSSLT 0.0 None None 0 None -1964 SLKSTRAVF 0.0 None None 0 None -1965 SVGSASSLK 0.0 None None 0 None -1966 SVGSASSLK 0.0 None None 0 None -1967 KGYGGFSRY 0.0 None None 0 None -1968 KGYGGFSRY 0.0 None None 0 None -1969 KAIGKSRPY 0.0 None None 0 None -1970 KTLRKAIGK 0.00523788333205 KTLRKAI KTILKAL 21.0 7708|gag_polyprotein|BAA00992.1|Human_immunodeficiency_virus_1|11676 -1971 KTLRKAIGK 0.00482507857332 KTLRKAI KTILKAL 21.0 7708|gag_polyprotein|BAA00992.1|Human_immunodeficiency_virus_1|11676 -1972 QALQKTLRK 0.0 None None 0 None -1973 SYQSTGDPK 0.160544975903 TGDP TGDP 24.0 2002|Large_envelope_protein|SRC279965|Hepatitis_B_virus|10407 -1974 VPEWSNNS* 0.0 None None 0 None -1975 VLETAAPGV 0.0 None None 0 None -1976 AVLDAIPLV 0.0 None None 0 None -1977 VLDAIPLVA 0.0 None None 0 None -1978 KPVVTEVRM 0.0 None None 0 None -1979 MPTNTWSGL 0.0679479043012 PTNTW PTYSW 22.0 102368|E2_protein|NP_751921.1|Hepatitis_C_virus_subtype_1a|31646 -1980 VFQGHSASI 0.0 None None 0 None -1981 SLYDFGELR 0.0 None None 0 None -1982 DSMLQTVER 0.0 None None 0 None -1983 MLQTVEREK 0.0 None None 0 None -1984 LLWKDFDQA 9.96145413497 DFDQA DFDQG 23.0 149117|envelope_glycoprotein|AAV74049.1|Hepatitis_C_virus_(isolate_H77)|63746 -1985 HVPQVADAI 0.0 None None 0 None -1986 LLEMNLMHV 0.44470519815 LLEMNLM LIEANLL 22.0 419095|polyprotein|ABR25251.1|Hepatitis_C_virus|11103 -1987 NLMHVPQVA 0.0 None None 0 None -1988 VPQVADAIL 0.0 None None 0 None -1989 FLIDGSQSV 0.0 None None 0 None -1990 FLIDGSQSV 0.0 None None 0 None -1991 SVGPEFQYV 0.0 None None 0 None -1992 LALSVTEMV 0.0 None None 0 None -1993 RLALSVTEM 0.0 None None 0 None -1994 TILQIKEEK 0.0 None None 0 None -1995 DYEAVCGHR 0.0 None None 0 None -1996 EAVCGHRAR 0.287814503571 GHRAR GHKAR 25.0 21635|gag_protein|ABO73990.1|Human_immunodeficiency_virus_1|11676 -1997 ILFQKITNR 0.0 None None 0 None -1998 KITNRGDEL 0.0 None None 0 None -1999 SPTPALGPA 0.0 None None 0 None -2000 LTPQQAQEL 0.0 None None 0 None -2001 APLGAPPPL 355.106026278 LGAPPPL LGAIPPL 29.0 73059|kaposin|AAC57155.1|Human_gammaherpesvirus_8|37296 -2002 SKTPPGAPL 1.70350167556 PPGAPL PPNAPI 27.0 93536|core_protein|AAL31859.1|Hepatitis_B_virus|10407 -2003 SKTPPGAPL 6.26781366346 PPGAPL PPNAPI 27.0 93536|core_protein|AAL31859.1|Hepatitis_B_virus|10407 -2004 MFQSLGEHI 0.0937231593112 MFQSLGEHI MEPTLGQHL 24.0 79308|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 -2005 SLGEHINTL 2.10571623096 SLGEHINTL TLGQHLPTL 30.0 79308|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 -2006 SLGEHINTL 1.0685924021 SLGEHINTL TLGQHLPTL 30.0 79308|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 -2007 AVGVGKSAL 0.0 None None 0 None -2008 YKLVVVGAV 12.5817515538 KLVVVG KLVVLG 24.0 32238|polyprotein_[Hepatitis_C_virus_subtype_1a]|ABV46251.2|Hepatitis_C_virus_(isolate_H77)|63746 -2009 AMLWALGFI 8.2714056325 MLWALGF ILWAVGL 27.0 1000|glycoprotein_gp35/37|AAC59622.1|Human_gammaherpesvirus_8|37296 -2010 FIWSVLITA 0.0 None None 0 None -2011 MLWALGFIF 3.08293386362 MLWALGF ILWAVGL 27.0 1000|glycoprotein_gp35/37|AAC59622.1|Human_gammaherpesvirus_8|37296 -2012 QTPLFIWSV 0.0 None None 0 None -2013 TPLFIWSVL 0.0 None None 0 None -2014 TQYQTPLFI 0.638287640051 QYQTP RYQTP 25.0 180617|polyprotein|AGO67248.1|Dengue_virus_2|11060 -2015 IINDGKHHV 0.0 None None 0 None -2016 GLSAEEFQL 0.0 None None 0 None -2017 SAEEFQLIR 0.0 None None 0 None -2018 APTTPKEPA 0.0115417217673 APTTPKEPA APASVYQPA 21.0 141216|envelope_glycoprotein_I|NP_044669.1|Human_alphaherpesvirus_1|10298 -2019 LLLLLLLLV 0.0 None None 0 None -2020 LLLLLLLVV 0.183789279182 LLLLLVV VLLLLVV 25.0 98540|trans-sialidase,_putative|EAN88532.1|Trypanosoma_cruzi|5693 -2021 LLLLLLVVV 0.355681484489 LLLLVVV LLLLVVM 25.0 98224|trans-sialidase,_putative|EAN82076.1|Trypanosoma_cruzi|5693 -2022 LLVVVPWGV 0.0 None None 0 None -2023 SRRHSRSPL 0.0 None None 0 None -2024 SRRHSRSPL 0.0 None None 0 None -2025 GSYSMAIPL 0.191247232974 GSYSMAIPL GLYSSTVPV 25.0 21242|polymerase|ACF94272.1|Hepatitis_B_virus|10407 -2026 MAIPLLCSY 0.0 None None 0 None -2027 NPGSYSMAI 0.0 None None 0 None -2028 RYNPGSYSM 0.0 None None 0 None -2029 RYNPGSYSM 0.0 None None 0 None -2030 SYSMAIPLL 0.0 None None 0 None -2031 CQPHAHCSL 0.0 None None 0 None -2032 HAHCSLWRR 0.0 None None 0 None -2033 IIQELTIFK 0.0 None None 0 None -2034 LPPKPVQVL 1.24074074074 PPKPVQV PPKPCGI 26.0 75376|Genome_polyprotein|P26664.3|Hepatitis_C_virus|11103 -2035 QLPPKPVQV 0.5 PPKPVQV PPKPCGI 26.0 75376|Genome_polyprotein|P26664.3|Hepatitis_C_virus|11103 -2036 GLYASLFPA 0.0 None None 0 None -2037 LFPAIIYLF 0.160615937749 FPAIIYL YPAVFYL 28.0 154041|major_capsid_protein|CAB06743.1|Human_alphaherpesvirus_2|10310 -2038 LYASLFPAI 0.0 None None 0 None -2039 PVYGLYASL 0.0 None None 0 None -2040 SLFPAIIYL 165.36965139 FPAIIYL YPAVFYL 28.0 154041|major_capsid_protein|CAB06743.1|Human_alphaherpesvirus_2|10310 -2041 SLFPAIIYL 0.19660649062 FPAIIYL YPAVFYL 28.0 154041|major_capsid_protein|CAB06743.1|Human_alphaherpesvirus_2|10310 -2042 SLFPAIIYL 0.207246371289 FPAIIYL YPAVFYL 28.0 154041|major_capsid_protein|CAB06743.1|Human_alphaherpesvirus_2|10310 -2043 VYGLYASLF 0.0 None None 0 None -2044 VYGLYASLF 0.0 None None 0 None -2045 RYNVADVSV 0.0 None None 0 None -2046 VSVAICMSL 0.0 None None 0 None -2047 YTISDDESF 0.0 None None 0 None -2048 YVQYWYYTI 0.673550706689 VQYWYY TQYWKY 28.0 141206|tegument_protein_VP11/12|NP_044648.1|Human_alphaherpesvirus_1|10298 -2049 YVQYWYYTI 0.493586768335 VQYWYY TQYWKY 28.0 141206|tegument_protein_VP11/12|NP_044648.1|Human_alphaherpesvirus_1|10298 -2050 SFYNSNRDF 0.0 None None 0 None -2051 SFYNSNRDF 0.0 None None 0 None -2052 TISFYNSNR 0.0 None None 0 None -2053 CRFELMHFK 0.0 None None 0 None -2054 ELMHFKTLY 0.00494580293464 ELMHFKTL KVLHKRTL 20.0 34101|X_protein|ACH95876.1|Hepatitis_B_virus|10407 -2055 ILGDWSNGI 0.470124959392 DWSNGI DYSNGL 26.0 51604|FL-160-2_protein_-_Trypanosoma_cruzi|JH0823|Trypanosoma_cruzi|5693 -2056 NGISALYCR 0.0 None None 0 None -2057 HIHGGTNQV 0.658346187729 HGGTN HGGTG 25.0 55336|EBNA-1|YP_401677.1|Human_gammaherpesvirus_4|10376 -2058 AFTCTSSLL 0.0 None None 0 None -2059 KAFTCTSSL 0.0 None None 0 None -2060 KAFTCTSSL 0.0 None None 0 None -2061 GDASKVWVW 0.832592284506 GDASKVWV GNASRCWV 31.0 21385|polyprotein|AAY82034.1|Hepatitis_C_virus_genotype_1|41856 -2062 STFVHGNKI 0.0 None None 0 None -2063 GEEAEASAV 0.0 None None 0 None -2064 TTSPSNTLV 0.0 None None 0 None -2065 STGLQYATK 0.0 None None 0 None -2066 SVLRCVHLL 0.0 None None 0 None -2067 GRNSFKVRV 1.9048679282 GRNSFKV GRNSFEV 32.0 37364|P53_HUMAN_Cellular_tumor_antigen_p53_(Tumor_suppressor_p53)_(Phosphoprotein_p53)_(Antigen_NY-CO-13)|P04637.2|Homo_sapiens|9606 -2068 MRTLLGDLV 0.0 None None 0 None -2069 RWDRKPMQI 0.0 None None 0 None -2070 SRSTIFMRL 0.0 None None 0 None -2071 PHLTQGNEI 0.0 None None 0 None -2072 ASTFVHGNK 0.0 None None 0 None -2073 ENAGPQNMK 0.0 None None 0 None -2074 MGQEIAALK 0.0 None None 0 None -2075 NLLGRNSFK 63.0014315849 LLGRNSFK LLGRNSFE 36.0 37364|P53_HUMAN_Cellular_tumor_antigen_p53_(Tumor_suppressor_p53)_(Phosphoprotein_p53)_(Antigen_NY-CO-13)|P04637.2|Homo_sapiens|9606 -2076 QAVCVTKPK 0.165090772535 VCVTKP ICLTHP 24.0 146317|polyprotein|ADF97231.1|Hepatitis_C_virus_subtype_3a|356426 -2077 LRCVHLLRI 0.0 None None 0 None -2078 FVHGNKIYV 0.0 None None 0 None -2079 ATKFIKKRR 0.0 None None 0 None -2080 VHLLRIFKV 0.0 None None 0 None -2081 LANAPRTLK 0.0 None None 0 None -2082 WRLTWDRHL 0.119451085397 WRLTWD WAIKWE 24.0 72233|Genome_polyprotein|P27958.3|Hepatitis_C_virus_subtype_1a|31646 -2083 CTGPPLAPR 0.0742064317743 CTGPPLAPR CGGVYLLPR 23.0 181035|||| -2084 NLTRASSKR 0.0 None None 0 None -2085 RRSGPSPTV 0.586855842399 GPSPTV GPVPAV 22.0 179799|hypothetical_protein|NP_301670.1|Mycobacterium_leprae_TN|272631 -2086 DLVAHYVHR 0.332299353923 LVAHY LVAHY 27.0 150377|polyprotein|AGS49173.1|Dengue_virus_2|11060 -2087 SSLEGFATR 0.0 None None 0 None -2088 LEDLGWANW 1.69512152692 EDLGWANW EGLGWAGW 40.0 75436|Polyprotein|P90247|Hepatitis_C_virus|11103 -2089 CVHLLRIFK 0.0 None None 0 None -2090 TIQAVCVTK 0.0 None None 0 None -2091 ITCMPGSVR 0.0886657628972 ITCMPGSV IFCHPGQL 23.0 79454|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 -2092 CSIPSICEK 0.0 None None 0 None -2093 SSRSTIFMR 0.0 None None 0 None -2094 SVTKASNLK 0.0 None None 0 None -2095 YATKFIKKR 0.0 None None 0 None -2096 FSSSDDSPR 0.0 None None 0 None -2097 VHGNKIYVL 0.0 None None 0 None -2098 WANWVLSPR 4.11764705574 WANWVLSPR WAGWLLSPR 47.0 36352|Polyprotein|P90247|Hepatitis_C_virus|11103 -2099 LSLPGGHTA 0.0 None None 0 None -2100 FRAAAEAAV 0.0 None None 0 None -2101 FRAAAEAAV 0.0 None None 0 None -2102 TSSDHSFSL 0.0 None None 0 None -2103 TSSDHSFSL 0.0 None None 0 None -2104 NHQQFYHSV 0.0 None None 0 None -2105 NHQQFYHSV 0.0 None None 0 None -2106 DYSELPHHV 0.0 None None 0 None -2107 HHVSTEQEI 0.0 None None 0 None -2108 HHVSTEQEI 0.0 None None 0 None -2109 EIISLWSPW 0.0 None None 0 None -2110 NQDPISPSL 0.243444523244 QDPISPSL EKPVAPSV 24.0 419002|PPE_family_protein_PPE68|KAM81677.1|Mycobacterium_tuberculosis_H37Ra|419947 -2111 ENASAYLTL 0.0 None None 0 None -2112 KKMENASAY 0.0 None None 0 None -2113 RRHSLPRRC 0.0 None None 0 None -2114 NMCRCLVTV 0.0 None None 0 None -2115 RLMSARLAI 0.0 None None 0 None -2116 SYSYLGLRL 0.0 None None 0 None -2117 YSYLGLRLM 0.0 None None 0 None -2118 YSYLGLRLM 0.0 None None 0 None -2119 RFSQAFFYM 0.0 None None 0 None -2120 RRFSQAFFY 0.0 None None 0 None -2121 FMMPRSSSC 0.0 None None 0 None -2122 FMMPRSSSC 0.0 None None 0 None -2123 IPAMEIFMV 0.0 None None 0 None -2124 LMAASIPAM 0.0 None None 0 None -2125 DTLQATAML 0.0 None None 0 None -2126 QATAMLDIV 0.0 None None 0 None -2127 TVTRTTATV 0.0 None None 0 None -2128 EHFPLCKTV 0.0 None None 0 None -2129 EHFPLCKTV 0.0 None None 0 None -2130 WPQCHPEEI 1.27438241384 WPQCHPEEI LPQCSPDEI 38.0 3051|UL123;_IE1|AAR31448.1|Human_betaherpesvirus_5|10359 -2131 YSYSCGHYE 0.268852568146 YSYSCGHY YPYRLWHY 24.0 10939|polyprotein|BAB18806.1|Hepatitis_C_virus_subtype_1a|31646 -2132 SHFERDYRV 0.0 None None 0 None -2133 FQTLMPDVV 0.0 None None 0 None -2134 FQTLMPDVV 0.0 None None 0 None -2135 MPDVVHQSL 2.1510778258 MPDVVHQ MPDVAHS 30.0 130953|G1_and_G2_surface_glycoprotein_precursor|AAG22532.1|Andes_hantavirus|46607 -2136 LWYTLYLMI 0.263181088307 LWYTLY LWVTVY 27.0 118|envelope_glycoprotein|ABS76372.1|Human_immunodeficiency_virus_1|11676 -2137 LYLMITTFF 0.141553469901 MITTFF MLTAFF 24.0 140651|granule_antigen_protein_GRA6|XP_002371939.1|Toxoplasma_gondii_ME49|508771 -2138 MITTFFFPL 0.390389569622 MITTFF MLTAFF 24.0 140651|granule_antigen_protein_GRA6|XP_002371939.1|Toxoplasma_gondii_ME49|508771 -2139 TLYLMITTF 1.13393265557 TLYLMITTF TLYAVATTF 31.0 150639|polyprotein|AGO67249.1|Dengue_virus_2|11060 -2140 YLMITTFFF 0.727839017994 MITTFF MLTAFF 24.0 140651|granule_antigen_protein_GRA6|XP_002371939.1|Toxoplasma_gondii_ME49|508771 -2141 YTLYLMITT 0.0 None None 0 None -2142 PTSPFQTTI 0.00448304273818 PTSPFQ PERPFQ 23.0 232154|rhoptry_protein,_putative_/_protein_kinase_domain-containing_protein|XP_002367757.1|Toxoplasma_gondii_type_II|1209523 -2143 TAERSIPTV 0.546505896162 ERSIPTV DRSYPAV 21.0 154041|major_capsid_protein|CAB06743.1|Human_alphaherpesvirus_2|10310 -2144 ERPCHREPL 2.30501930502 PCHREPL PGHEEPI 26.0 180488|polyprotein|AGO67248.1|Dengue_virus_2|11060 -2145 SSSSGPFPL 0.0 None None 0 None -2146 ELATFAKAY 0.0 None None 0 None -2147 RWDEELATF 0.0 None None 0 None -2148 ELIDLISRV 0.0 None None 0 None -2149 ELIDLISRV 0.0 None None 0 None -2150 QVNQKSSVV 0.0 None None 0 None -2151 VRLELIDLI 0.0 None None 0 None -2152 YEEYRGRLL 0.267524115073 YEEYRGRL YQDWLGRM 24.0 23288|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 -2153 YEEYRGRLL 0.0889159325107 YEEYRGRL YQDWLGRM 24.0 23288|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 -2154 CRNVHTPDL 0.0 None None 0 None -2155 YSRDQAQAL 0.0 None None 0 None -2156 YSRDQAQAL 0.0 None None 0 None -2157 FEVEGRDLL 0.0 None None 0 None -2158 FFFLCVCVF 0.0684531631414 FFFLCVCV LLILCLCL 24.0 49831|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 -2159 FFLCVCVFV 0.243568175313 FFLCVCV LILCLCL 24.0 49831|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 -2160 RRYPHKRCI 0.119202922022 YPHKRC YPPKPC 24.0 75376|Genome_polyprotein|P26664.3|Hepatitis_C_virus|11103 -2161 RRYPHKRCI 0.150450289931 YPHKRC YPPKPC 24.0 75376|Genome_polyprotein|P26664.3|Hepatitis_C_virus|11103 -2162 NMSRCCIRV 0.0 None None 0 None -2163 GLLGNGIGY 0.0 None None 0 None -2164 LLGNGIGYV 0.0 None None 0 None -2165 KILSLHLLL 0.0 None None 0 None -2166 HPAFISLAF 0.0 None None 0 None -2167 FPREKTPEV 0.911184210526 FPREKTP LPRSRTP 26.0 88849|IE62|AAP32859.1|Human_alphaherpesvirus_3|10335 -2168 WPPWLKGKY 0.578598641597 WLKGK YLKGK 22.0 419170|polyprotein|ABR25251.1|Hepatitis_C_virus|11103 -2169 IVLTGHNAY 0.0 None None 0 None -2170 IVLTGHNAY 0.0 None None 0 None -2171 VLTGHNAYL 0.0 None None 0 None -2172 QAQALGIPL 0.0 None None 0 None -2173 IVFFANNGF 0.0 None None 0 None -2174 HSESSDSEV 0.0 None None 0 None -2175 RRGSGHSEY 0.0584223726864 GSGHSE GPGHEE 24.0 180488|polyprotein|AGO67248.1|Dengue_virus_2|11060 -2176 LIMEDLVCY 0.0 None None 0 None -2177 MEDLPAACM 0.0 None None 0 None -2178 HPMASNSGG 0.00278161375312 PMASNSGG PIALLKGG 19.0 146282|polyprotein|ADF97231.1|Hepatitis_C_virus_subtype_3a|356426 -2179 DVEWRWHSY 0.0 None None 0 None -2180 DVEWRWHSY 0.0 None None 0 None -2181 ILPTCSPLV 2072.01295566 PTCSPL PACKPL 27.0 56502|polyprotein|BAD73994.1|Hepatitis_C_virus_subtype_1b|31647 -2182 LPTCSPLVF 1.81028585028 PTCSPL PACKPL 27.0 56502|polyprotein|BAD73994.1|Hepatitis_C_virus_subtype_1b|31647 -2183 VHFWPGYEY 0.0 None None 0 None -2184 SPEGDDTLY 0.0192935429649 PEGDDTLY PQGQLTAY 22.0 13701|Trans-activator_protein_BZLF1|P03206.2|Human_gammaherpesvirus_4|10376 -2185 TLVPTAPEL 0.0 None None 0 None -2186 HLIGSTTLA 2.05755395683 LIGSTTL LIGITTL 26.0 59182|attachment_glycoprotein|ABQ58821.1|Human_metapneumovirus|162145 -2187 LIGSTTLAM 0.246511627907 LIGSTTL LIGITTL 26.0 59182|attachment_glycoprotein|ABQ58821.1|Human_metapneumovirus|162145 -2188 LLMHLIGST 0.0 None None 0 None -2189 IAHQWYWTY 0.0584354508795 QWYWTY KWLWGF 23.0 62903|Genome_polyprotein|P27909.2|Dengue_virus_type_1_Hawaii|10000440 -2190 IAHQWYWTY 2.11519394372 QWYWTY KWLWGF 23.0 62903|Genome_polyprotein|P27909.2|Dengue_virus_type_1_Hawaii|10000440 -2191 LLEENGDVF 0.0 None None 0 None -2192 QRCACPHGY 0.0 None None 0 None -2193 CMYDPLGTI 0.0 None None 0 None -2194 GPHRITCMY 0.0389454916711 PHRITC PHVIFC 23.0 79337|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 -2195 NESCLSMSE 0.0 None None 0 None -2196 VANESCLSM 0.0 None None 0 None -2197 EESELYAQL 1.79691363928 EESELY EQSEFY 23.0 62355|Genome_polyprotein|P08617.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 -2198 RTAQCFLCV 0.0 None None 0 None -2199 KYSNYVWPI 10.3355467301 KYSNYVW KYTSFPW 26.0 34616|pol_protein|BAA32832.1|Hepatitis_B_virus|10407 -2200 FIFEIVGFT 0.0 None None 0 None -2201 DSSGQSNRY 1.24432386195 SSGQSNR NSGASNR 25.0 1095|glycoprotein_gp35/37|AAC59622.1|Human_gammaherpesvirus_8|37296 -2202 DSSSWSNRY 0.0 None None 0 None -2203 DSSSWSNRY 0.0 None None 0 None -2204 NRYGGGGRY 0.0 None None 0 None -2205 NRYGGGGRY 0.0 None None 0 None -2206 NEHGHRRKI 0.0 None None 0 None -2207 HTSLRGFLY 0.253521126761 HTSLRGF HLSLRGL 26.0 24302|X_protein|AAP06597.1|Hepatitis_B_virus|10407 -2208 ALNEMFCQL 0.0 None None 0 None -2209 NEMFCQLAK 0.0 None None 0 None -2210 GLYAIAVML 0.0 None None 0 None -2211 MLSFSRIAY 0.0 None None 0 None -2212 MLSFSRIAY 0.0 None None 0 None -2213 YAIAVMLSF 0.0 None None 0 None -2214 AEWDSLYVL 0.0 None None 0 None -2215 LAEWDSLYV 0.0 None None 0 None -2216 VLAEWDSLY 0.0 None None 0 None -2217 VLAEWDSLY 0.0 None None 0 None -2218 GKAFSQSAY 0.0 None None 0 None -2219 KAFSQSAYL 0.0 None None 0 None -2220 RREDLTHTL 0.0 None None 0 None -2221 RREDLTHTL 0.0 None None 0 None -2222 ERWLRQAAF 3.02094262382 RWLRQAAF RWVPGAAY 24.0 22255|polyprotein|ABR27377.1|Hepatitis_C_virus|11103 -2223 RKREEEERW 42.4491907364 KREEEE RREEEE 27.0 185491|polyprotein|AGO67248.1|Dengue_virus_2|11060 -2224 THCSPNLLF 0.0 None None 0 None -2225 HQYNIYAAL 0.351661877827 YNIYAAL YNTVAAL 23.0 189291|||| -2226 RSFTESHQY 0.0 None None 0 None -2227 ISAKIMQQW 0.0 None None 0 None -2228 YTDTISAKI 0.0 None None 0 None -2229 AAVLGMLLW 0.0 None None 0 None -2230 ISGRVVQHF 0.0 None None 0 None -2231 IAFNHGDLL 0.0 None None 0 None -2232 KYHYYGLHI 0.0 None None 0 None -2233 LSRRVTQSL 0.0 None None 0 None -2234 RRVTQSLEA 0.0 None None 0 None -2235 KTYAPLFIW 0.678885162016 TYAPLFI TYGPVFM 27.0 67349|Latent_membrane_protein_2|Q69135|Human_gammaherpesvirus_4|10376 -2236 TYAPLFIWV 1.02223796155 TYAPLFIWV TYGPVFMCL 27.0 67349|Latent_membrane_protein_2|Q69135|Human_gammaherpesvirus_4|10376 -2237 KYIAFCINI 0.587708864399 KYIAFCI RYISWCL 26.0 39591|polyprotein|AAA45677.1|Hepatitis_C_virus_(isolate_H77)|63746 -2238 YIAFCINIF 0.476894002614 YIAFCI YISWCL 24.0 423020|polyprotein|ACE82359.1|Hepatitis_C_virus_genotype_1|41856 -2239 FHYPQSIFS 0.552109387903 HYPQSIF HYMESVF 28.0 154585|ribonucleotide_reductase_large_subunit|CAB06725.1|Human_alphaherpesvirus_2|10310 -2240 MKFHYPQSI 0.0 None None 0 None -2241 NTNSNRSLI 0.0 None None 0 None -2242 FRAYQDYFL 0.0 None None 0 None -2243 FRAYQDYFL 0.0 None None 0 None -2244 LHIGKDVQL 0.0 None None 0 None -2245 QVFAAVHEW 0.000185091863979 FAAVH YAFVH 17.0 142232|POSSIBLE_CONSERVED_TRANSMEMBRANE_PROTEIN|CAB00937.1|Mycobacterium_tuberculosis|1773 -2246 RRHTDEKPY 0.465553354611 RRHTDEK QRHLDKK 25.0 110394|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 -2247 FNGNFLLSM 8.55978429414 NGNFLL NGGFLI 24.0 194567|envelope_glycoprotein_B|NP_044629.1|Herpes_simplex_virus_(type_1_/_strain_17)|10299 -2248 GSADNTVQF 0.0 None None 0 None -2249 SADNTVQFI 0.0 None None 0 None -2250 KVQREDIFY 0.0 None None 0 None -2251 YLWPSGTPA 3.65618873033 LWPSGTP LWKDGAP 27.0 140600|glutamine_synthetase_GLNA1_(glutamine_synthase)_(GS-I)|NP_216736.1|Mycobacterium_tuberculosis_H37Rv|83332 -2252 LKMVSPSPC 0.0 None None 0 None -2253 SRVARDVAM 0.0 None None 0 None -2254 QNGYSWSQF 0.0190362677864 QNGYSWS QNGACWT 26.0 6889|Agglutinin_isolectin_1_precursor|P10968.2|Triticum_aestivum|4565 -2255 SYKLSQNGY 0.355050579888 SYKLSQNG AYRIKQRG 23.0 182687|polyprotein|AGK36298.1|Dengue_virus_2|11060 -2256 WKRGKRRYF 0.438635147178 WKRGKR WTRGER 27.0 170063|polyprotein|ABU97067.1|Hepatitis_C_virus_subtype_1b|31647 -2257 CFGHCFSLY 0.36196760402 FGHCF FGWCF 25.0 56620|Nef_protein|Q9YYU8|Human_immunodeficiency_virus_1|11676 -2258 CSAIRLRNY 0.0 None None 0 None -2259 FGHCFSLYI 0.0 None None 0 None -2260 IRLRNYLCF 0.0 None None 0 None -2261 IRLRNYLCF 0.0 None None 0 None -2262 LCFGHCFSL 0.351865750194 LCFGHCF LTFGWCF 28.0 56620|Nef_protein|Q9YYU8|Human_immunodeficiency_virus_1|11676 -2263 NHLCFGHCF 643.063109635 LCFGHCF LTFGWCF 28.0 56620|Nef_protein|Q9YYU8|Human_immunodeficiency_virus_1|11676 -2264 DFVECLMWF 0.0 None None 0 None -2265 DFVECLMWF 0.0 None None 0 None -2266 NKFEPSTDL 0.0458420865757 NKFEPST NDFFPSV 19.0 16814|precore_protein|CAM58990.1|Hepatitis_B_virus|10407 -2267 AYLCCRVPL 0.256424890396 LCCRV LCCYV 24.0 11956|UL123;_IE1|AAR31448.1|Human_betaherpesvirus_5|10359 -2268 SKGTTDTPV 2.41094003631 SKGTTDTPV SPGTSGSPI 25.0 5542|Nonstructural_protein_NS3|NP_739587.2|Dengue_virus_2_Thailand/16681/84|31634 -2269 KQSNSVEPI 0.0 None None 0 None -2270 AMSAQEYYI 0.0 None None 0 None -2271 SAQEYYIDY 0.0 None None 0 None -2272 YIDYKPNHI 0.377509819097 YIDYKPN YTDYMPS 26.0 180681|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -2273 LMLLAAAIY 0.0 None None 0 None -2274 LMLLAAAIY 0.0 None None 0 None -2275 SEDDTSYFV 0.0 None None 0 None -2276 RESVKHIGY 0.0 None None 0 None -2277 YQKVVRESV 0.0 None None 0 None -2278 SSVKTPETL 0.0 None None 0 None -2279 VIHHELQVL 0.0 None None 0 None -2280 KTDATPGRL 0.0 None None 0 None -2281 IKRLTAGSL 0.0 None None 0 None -2282 KRLTAGSLF 0.0 None None 0 None -2283 KQLSHHIGA 0.0 None None 0 None -2284 FHVNWFRRY 0.0 None None 0 None -2285 FRRYEAGHF 0.0 None None 0 None -2286 RRYEAGHFL 0.0 None None 0 None -2287 RYEAGHFLW 0.0 None None 0 None -2288 VSDHTPEQH 0.00112786319425 VSDHTPEQ LSDGNPPQ 20.0 69754|Lipoprotein_lpqH_precursor|P46733.1|Mycobacterium_avium|1764 -2289 SFHMDTQNF 0.0 None None 0 None -2290 SFHMDTQNF 0.0 None None 0 None -2291 TQNFCDIGY 0.0 None None 0 None -2292 LALSVFSKL 0.0 None None 0 None -2293 TVKLALSVF 5.19636761594e-05 TVKLALSVF TVRGLTSLF 16.0 52652|||| -2294 LQFAVGQEV 0.0 None None 0 None -2295 PQVPEHLQF 0.037697488936 PQVPEH PQYSEH 23.0 38974|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 -2296 QFAVGQEVF 0.0 None None 0 None -2297 NRYGGGGRY 0.0 None None 0 None -2298 EQLKLGAIF 4.26305904452 LKLGAI IKLGAL 23.0 423046|polyprotein|ACX44272.1|Hepatitis_C_virus_genotype_1|41856 -2299 LLMPYPVIV 0.0 None None 0 None -2300 TLLMPYPVI 0.0 None None 0 None -2301 RALKPVNKI 0.0 None None 0 None -2302 KEAMENEQF 0.0 None None 0 None -2303 LTEENKEAM 0.0 None None 0 None -2304 MEVPNIASS 0.0 None None 0 None -2305 RRFASGEKV 0.0 None None 0 None -2306 TFRDVAVEF 0.0350794875147 TFRDVA TWRDMA 22.0 186175|polyprotein|AFY10053.1|Dengue_virus_3|11069 -2307 FHISLFQYM 0.0 None None 0 None -2308 LIIDEDFHI 0.0 None None 0 None -2309 VLETAAPGV 0.0 None None 0 None -2310 ESHEKGCFW 0.0 None None 0 None -2311 MADAKGYTV 2.48831775731 MADAKGY MGDAGGY 26.0 3094|Antigen_85-B_precursor_(85B)_(Extracellular_alpha-antigen)_(Antigen_85_complex_B)_(Ag85B)_(Mycolyl_transferase_85B)_(Fibronectin-binding_protein_B)_(30_kDa_extracellular_protein)|P31952|Mycobacterium_tuberculosis|1773 -2312 KQLPRILEA 0.0 None None 0 None -2313 HTCQVNGRW 0.0130808799724 TCQVNGRW SCEGLGAW 22.0 79628|E1_protein|BAA19893.1|Rubella_virus|11041 -2314 PLLPSIISL 0.0 None None 0 None -2315 AIWEAVMSA 3.99661222935 IWEAV MWEAV 25.0 37590|VP1|BAF93325.1|Human_polyomavirus_1|1891762 -2316 AVMSALPSL 0.0 None None 0 None -2317 MSALPSLNW 0.0 None None 0 None -2318 GLDGPLVHV 0.0 None None 0 None -2319 SIRVSQKGW 0.0 None None 0 None -2320 PTDPGHFLV 0.0 None None 0 None -2321 MRGEHRFHM 0.0 None None 0 None -2322 KLSHCLSKA 0.0 None None 0 None -2323 CRPQCCQSV 32.8617887736 CRPQCCQSV CRVLCCYVL 28.0 11956|UL123;_IE1|AAR31448.1|Human_betaherpesvirus_5|10359 -2324 VRNPEPSPL 0.0 None None 0 None -2325 VLVVSPWPA 0.0 None None 0 None -2326 GMLWAMMSI 0.306314234534 GMLWAM GVLWTV 23.0 95940|polyprotein|BAA32666.1|Hepatitis_C_virus_genotype_6|42182 -2327 YMGMLWAMM 0.15801288777 GMLWAM GVLWTV 23.0 95908|Genome_polyprotein|O92529.3|Hepatitis_C_virus_genotype_6|42182 -2328 SRAVTSTTI 0.0 None None 0 None -2329 KTASWAEVV 0.0 None None 0 None -2330 WTFALTSGL 0.0 None None 0 None -2331 TDFNNGSYL 0.0 None None 0 None -2332 VTDFNNGSY 0.0 None None 0 None -2333 LLDTIPWYL 0.0 None None 0 None -2334 ASSDHTTHL 0.0 None None 0 None -2335 SHSSCVWLW 0.0 None None 0 None -2336 TGSHSSCVW 0.0 None None 0 None -2337 SIGELLQVL 0.0 None None 0 None -2338 TGFVRRPLW 0.0 None None 0 None -2339 DAEPFQRGW 0.127646462332 DAEPFQR HASPFER 24.0 23566|tegument_protein_UL7|NP_044476.1|Human_alphaherpesvirus_2|10310 -2340 FIFSDTVVL 0.0547221613587 FSDTVVL FKDNVIL 23.0 50779|N_protein|AAP13445.1|SARS_coronavirus_Urbani|228330 -2341 FIFSDTVVL 0.0775477115471 FSDTVVL FKDNVIL 23.0 50779|N_protein|AAP13445.1|SARS_coronavirus_Urbani|228330 -2342 FSDTVVLLF 0.804164436493 FSDTVVLL FKDNVILL 27.0 50779|N_protein|AAP13445.1|SARS_coronavirus_Urbani|228330 -2343 MHFIFSDTV 0.0 None None 0 None -2344 TVVLLFDFW 0.0 None None 0 None -2345 YHPGAMHCV 0.0 None None 0 None -2346 CAFSGTLPW 0.0 None None 0 None -2347 FMCAFSGTL 0.0 None None 0 None -2348 STHPSLSQW 1087.72967514 STHPSLSQW NTRPPLGNW 27.0 68601|polyprotein|AAA45534.1|Hepatitis_C_virus|11103 -2349 SRKDRAPKC 0.0 None None 0 None -2350 LMGLASTTV 0.0 None None 0 None -2351 SLLAIHQWV 0.204347866324 LAIHQWV LAVDPWV 24.0 143690|Genome_polyprotein|P06441.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 -2352 SSLLAIHQW 0.0 None None 0 None -2353 AIHIVAEKK 0.0 None None 0 None -2354 ESLPPSPTW 0.0 None None 0 None -2355 WAGNVLAPY 1.87387179047 WAGNVLAP WAGWLLSP 30.0 36352|Polyprotein|P90247|Hepatitis_C_virus|11103 -2356 QIIAGHFRK 0.0 None None 0 None -2357 STSSRSHRY 0.0 None None 0 None -2358 FHQCLSIYY 1.78908850466 FHQCLSI FHLCLII 27.0 93431|pre-C/C_protein|ABY54138.1|Hepatitis_B_virus|10407 -2359 IYYWDIRYK 0.00992413375792 YYWDIRYK HTWTEQYK 20.0 183619|nonstructural_protein_NS1|1802191G|Dengue_virus|12637 -2360 LFHQCLSIY 102.125443496 LFHQCLSI LFHLCLII 31.0 93431|pre-C/C_protein|ABY54138.1|Hepatitis_B_virus|10407 -2361 SIYYWDIRY 0.0 None None 0 None -2362 SIYYWDIRY 0.0 None None 0 None -2363 SRHTIRELL 0.0 None None 0 None -2364 QINIPIGPY 0.0 None None 0 None -2365 GGMQALGLY 0.378933871481 GGMQALGLY GGSRVEGIF 20.0 61861|Nucleoprotein|P03418.1|Human_respiratory_syncytial_virus_A2|11259 -2366 FLNLSQPRK 0.0 None None 0 None -2367 RLNSHFLNL 1.98031425281 RLNSHFLNL RVDLHFINL 31.0 119822|110_kd_polyprotein_precursor|CAA28880.1|Rubella_virus|11041 -2368 ERSLQVKRV 0.0 None None 0 None -2369 LQVKRVFVK 0.0 None None 0 None -2370 RSLQVKRVF 0.0 None None 0 None -2371 RVFVKGMKK 0.0 None None 0 None -2372 CSSSIGTIW 0.0 None None 0 None -2373 WSHASASLY 0.0 None None 0 None -2374 WSHASASLY 0.0 None None 0 None -2375 KESNAGRYY 0.0 None None 0 None -2376 VKESNAGRY 0.0 None None 0 None -2377 IVSVKPNMK 0.074476186027 VSVKPN VSIAPN 23.0 19359|IMMUNOGENIC_PROTEIN_MPT64_(ANTIGEN_MPT64/MPB64)|CAA98382.1|Mycobacterium_tuberculosis_H37Rv|83332 -2378 FSYPKRPII 0.0 None None 0 None -2379 MSHPPNILK 0.0 None None 0 None -2380 GARPGLGRY 0.0 None None 0 None -2381 ITSRDATRF 0.0 None None 0 None -2382 TRFPIIASC 0.0 None None 0 None -2383 RLLSSGTAK 0.0 None None 0 None -2384 KVLELADRF 0.0 None None 0 None -2385 RVSTGSVHK 0.0 None None 0 None -2386 VVGAVGVGK 0.0 None None 0 None -2387 LSFRSSSCR 0.0 None None 0 None -2388 EMFEHLFGK 0.533333333333 EMFEHLF DMWEHAF 26.0 9415|Superoxide_dismutase|P17670.1|Mycobacterium_tuberculosis|1773 -2389 TRAHCHLPV 0.618719512219 RAHCHLPV RKHRHLPV 32.0 75408|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 -2390 ILDYMQLRK 0.0 None None 0 None -2391 KILDYMQLR 0.0 None None 0 None -2392 TTMLDRGPK 0.0 None None 0 None -2393 IHITEEEAV 0.0 None None 0 None -2394 LVSMTYDRY 0.0 None None 0 None -2395 MTYDRYVAI 0.0764884706029 YDRYVA YKRYIS 22.0 39591|polyprotein|AAA45677.1|Hepatitis_C_virus_(isolate_H77)|63746 -2396 MVLLVSMTY 0.0 None None 0 None -2397 MVLLVSMTY 0.0 None None 0 None -2398 MVLLVSMTY 0.0 None None 0 None -2399 VSMTYDRYV 0.0 None None 0 None -2400 IHMDARLHT 0.0 None None 0 None -2401 MGMALLIHM 0.0 None None 0 None -2402 FKSKVPQTW 0.0 None None 0 None -2403 VGQQQQVLW 0.0 None None 0 None -2404 DSSSWSDRY 3.70689655172 SWSDRY TWADEY 26.0 33912|FL-160-2_protein_-_Trypanosoma_cruzi|JH0823|Trypanosoma_cruzi|5693 -2405 SGGHDSSSW 0.0 None None 0 None -2406 YEEYRGHSL 0.0 None None 0 None -2407 HTSTVRESY 0.0 None None 0 None -2408 HTSTVRESY 0.0 None None 0 None -2409 SHYGQPDRQ 0.0 None None 0 None -2410 DHEVYLKHL 0.0 None None 0 None -2411 GGLFIASNW 0.0 None None 0 None -2412 KVTRLHRRK 0.0 None None 0 None -2413 LMSTSEEEF 0.0 None None 0 None -2414 LSNNCVPQM 0.0 None None 0 None -2415 STRDEIEGL 1.14900483451 RDEIEG EDEIDG 23.0 110431|E7|AAD33253.1|Human_papillomavirus_type_16|333760 -2416 RMCTVTNYF 0.0 None None 0 None -2417 VMVSLKPDK 0.0 None None 0 None -2418 CRQEQERKF 0.0 None None 0 None -2419 EQEERREQL 0.0 None None 0 None -2420 FRLEEQKVC 0.0 None None 0 None -2421 QSLCGTRFY 0.0 None None 0 None -2422 TAAAAPTPF 0.0 None None 0 None -2423 DRNTFRHSL 0.0 None None 0 None -2424 NTFRHSLVV 0.0 None None 0 None -2425 RMNSFLHIL 0.0 None None 0 None -2426 RMNSFLHIL 0.0 None None 0 None -2427 SRMNSFLHI 0.0 None None 0 None -2428 GSFPTEYIL 0.0 None None 0 None -2429 VTNCHKNYW 0.0 None None 0 None -2430 VVTNCHKNY 0.131382703091 VVTNCHK IVTFCCK 20.0 110184|E7|AAD33253.1|Human_papillomavirus_type_16|333760 -2431 DMAPTRPRW 0.172014343171 MAPTRPRW FAPALPIW 24.0 422989|polyprotein|ABY67644.1|Hepatitis_C_virus_genotype_1|41856 -2432 FRRPQESLL 0.0 None None 0 None -2433 GINNKVCFW 0.0 None None 0 None -2434 LLTDTNSWW 0.874238307242 LLTDTNSW VLTDFKTW 26.0 69797|polyprotein|BAA09073.1|Hepatitis_C_virus_subtype_1b|31647 -2435 QLLTDTNSW 0.928593037485 LLTDTNSW VLTDFKTW 26.0 69797|polyprotein|BAA09073.1|Hepatitis_C_virus_subtype_1b|31647 -2436 HQRVHSGEK 0.0 None None 0 None -2437 QRYSHQRVH 0.0 None None 0 None -2438 VKSKLIAHY 0.0 None None 0 None -2439 SVDECELHK 0.0 None None 0 None -2440 PMPPPLEPI 0.0987361416297 MPPPLEP LPDPLKP 27.0 27241|Spike_glycoprotein_precursor|P59594.1|SARS_coronavirus|227859 -2441 KEIDVIAIP 0.0 None None 0 None -2442 YKDYAAELV 0.141859211272 YKDYAA FKDFAA 25.0 182917|polyprotein|CDF77361.1|Dengue_virus_3|11069 -2443 DNLDSDNTY 0.185784734323 NLDSDNTY HYDEDNPY 24.0 72563|polyprotein|AAB70696.1|Dengue_virus_type_1_Hawaii|10000440 -2444 LAVTLGLAL 0.0 None None 0 None -2445 HNNNRPLTM 0.0 None None 0 None -2446 WAVPPLLLA 0.411375661376 AVPPLL AIPPLV 26.0 73059|kaposin|AAC57155.1|Human_gammaherpesvirus_8|37296 -2447 RCYVRGLFH 0.0 None None 0 None -2448 KITAQRLSH 0.0 None None 0 None -2449 SSLHSEPPK 0.0 None None 0 None -2450 QAQALGIPL 0.0 None None 0 None -2451 QAQALGIPL 0.0 None None 0 None -2452 IPKSPEEAI 0.0 None None 0 None -2453 PEEPTSPAA 0.206085938541 PTSPAA PTAPCA 24.0 79628|E1_protein|BAA19893.1|Rubella_virus|11041 -2454 RVQSRPIPI 0.0396216155661 SRPIPI SEPLPV 23.0 57591|Cobalamin_(vitamin_B12)_synthesis_protein/P47K_family_protein|YP_169986.1|Francisella_tularensis_subsp._tularensis_SCHU_S4|177416 -2455 HSLQQAQSV 0.0 None None 0 None -2456 PLFTTQCGK 0.0219525875844 PLFTTQ PTFTSQ 23.0 75718|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 -2457 HMEAEMAQK 0.0 None None 0 None -2458 VQLPKVSEM 0.0 None None 0 None -2459 ITAQRLSHL 0.0 None None 0 None -2460 LLLSPPVEV 0.0 None None 0 None -2461 IPILPLIYI 0.26866979834 PILPLI PFLPLL 24.0 27345|Large_envelope_protein|P03138.3|Hepatitis_B_virus_subtype_ayw|10418 -2462 AEAQTPEDS 0.0 None None 0 None -2463 LLSPPVEVK 0.0 None None 0 None -2464 TEHDVQIYV 0.0 None None 0 None -2465 FISLKFSSK 0.0 None None 0 None -2466 IPGPIPGPI 0.0153161126032 PGPIPG PGTGPG 21.0 47760|EBNA-1_protein|Q777E1|Human_gammaherpesvirus_4|10376 -2467 KTRRTSSLH 0.0 None None 0 None -2468 EEPTSPAAA 0.0642546482275 PTSPAA PTAPCA 24.0 79628|E1_protein|BAA19893.1|Rubella_virus|11041 -2469 WILSARLLK 0.0 None None 0 None -2470 QQFPSLELL 0.0 None None 0 None -2471 RPIPILPLI 0.371841950785 PILPLI PFLPLL 24.0 27345|Large_envelope_protein|P03138.3|Hepatitis_B_virus_subtype_ayw|10418 -2472 NMKEQVVIL 0.0 None None 0 None -2473 AQRLSHLNK 0.0 None None 0 None -2474 RAYRDDTDL 0.0 None None 0 None -2475 NVFWGEHFK 0.0 None None 0 None -2476 YYKDYAAEL 0.450065235762 YKDYAA FKDFAA 25.0 182917|polyprotein|CDF77361.1|Dengue_virus_3|11069 -2477 QQFPSLELL 0.0 None None 0 None -2478 SLKFSSKIK 5.34901960784 LKFSSKI LKFYSKI 26.0 110227|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 -2479 FLFGLAQNL 0.0 None None 0 None -2480 YVRGLFHSL 0.0 None None 0 None -2481 TENSETTTA 0.056544975831 TENSETT VENLETT 24.0 149063|NS3_protease/helicase'|NP_803144.1|Hepatitis_C_virus_(isolate_H77)|63746 -2482 ALGIPLTPK 0.0 None None 0 None -2483 NENTTPSPA 0.0 None None 0 None -2484 RLPEVQLPK 8.33669952536e-05 LPEVQLPK LPSDFLPS 16.0 16836|precore/core_protein_[Hepatitis_B_virus]|AAR03815.1|Hepatitis_B_virus|10407 -2485 ISLKFSSKI 1.55102040816 LKFSSKI LKFYSKI 26.0 110227|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 -2486 KEGARNVLA 0.0 None None 0 None -2487 MPNDFWARL 2.15830070732 MPNDFWARL LPNDFFPSV 28.0 16814|precore_protein|CAM58990.1|Hepatitis_B_virus|10407 -2488 FTEHDVQIY 0.0200300974578 FTEHDVQI FTNMEVQL 22.0 183275|polyprotein|AGW21594.1|Dengue_virus_1|11053 -2489 FKFHNLPPL 0.0 None None 0 None -2490 NTYRTPSVL 0.309317439303 YRTPSV YQTPAI 24.0 180617|polyprotein|AGO67248.1|Dengue_virus_2|11060 -2491 IAIPSKCLL 0.0 None None 0 None -2492 EASSAVPTV 0.0 None None 0 None -2493 MAAAVVARL 0.0 None None 0 None -2494 QEFENIKSY 16.338826617 QEFENIKS QRFHNIRG 23.0 178247|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 -2495 FQKDPPADI 0.0 None None 0 None -2496 DMYDGRFLV 0.891117731544 MYDGRFLV LYDGSFAV 29.0 93270|hypothetical_protein|NP_218356.1|Mycobacterium_tuberculosis_H37Rv|83332 -2497 PLYKVRFSK 0.0 None None 0 None -2498 VTRPFISLK 0.0 None None 0 None -2499 IILFNRLLK 0.0 None None 0 None -2500 IPYRDSVLI 0.0 None None 0 None -2501 AEASSAVPT 0.0 None None 0 None -2502 EEMPNDFWA 1.09272457194 MPNDFW LPNDFF 28.0 16814|precore_protein|CAM58990.1|Hepatitis_B_virus|10407 -2503 KMPEMHFKA 0.0221786804353 PEMHFKA PERPFQA 20.0 232153|rhoptry_protein_18|CAJ27113.1|Toxoplasma_gondii_type_I|1209525 -2504 AYSKCFISV 0.0 None None 0 None -2505 LYLKTSQDV 0.0 None None 0 None -2506 DLLTNLMYV 0.0 None None 0 None -2507 LLTNLMYVL 0.0 None None 0 None -2508 YQFPQSIDL 0.0 None None 0 None -2509 VWQRPVLNF 113.663716399 VWQRPV IWFRPV 27.0 37507|Large_T_antigen|P03071.1|Human_polyomavirus_1|1891762 -2510 VEGTFISDY 0.0 None None 0 None -2511 EELEIFMAR 0.0 None None 0 None -2512 YEMIRTFYI 0.0 None None 0 None -2513 EEFPCHKCV 0.0 None None 0 None -2514 NYMAHLVAV 0.0 None None 0 None -2515 FADFEWHFL 5.50353283986 FADFEWHF YADRKWCF 25.0 46575|polyprotein|AAG30730.1|Dengue_virus_2|11060 -2516 SFADFEWHF 10.4336370598 SFADFEWHF NYADRKWCF 26.0 46575|polyprotein|AAG30730.1|Dengue_virus_2|11060 -2517 FEQTLEELY 0.233610324193 FEQTLEE FHQTLQD 24.0 42430|Major_surface_antigen_precursor|P03141.3|Hepatitis_B_virus|10407 -2518 IYVKPLPIL 0.166416791124 IYVKPLPI IYVYALPL 25.0 58463|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 -2519 VLQIYVKPL 0.0 None None 0 None -2520 RQWRSLTTL 0.0 None None 0 None -2521 FCLGLVVTI 0.0 None None 0 None -2522 GVFCLGLVV 0.0 None None 0 None -2523 TLGVFCLGL 1.74091147886 TLGVFCLGL TMGVLCLAI 32.0 185978|polyprotein|CDF77361.1|Dengue_virus_3|11069 -2524 IVPRLIMNF 0.0 None None 0 None -2525 LIMNFTLGV 0.0 None None 0 None -2526 GEHPYQCPY 0.0 None None 0 None -2527 VLHRHMTTI 0.0 None None 0 None -2528 HEIDFYRED 0.0 None None 0 None -2529 KLDASVQHL 0.0 None None 0 None -2530 RQLKLDASV 0.0 None None 0 None -2531 FLWLWPLDF 0.00977850494065 FLWLWPLD FLYNRPLN 18.0 98040|trans-sialidase,_putative|EAN80725.1|Trypanosoma_cruzi|5693 -2532 SEDGFLWLW 0.0 None None 0 None -2533 WLWPLDFSS 0.0 None None 0 None -2534 TFRDVAVEF 0.0366333305265 TFRDVA TWRDMA 22.0 186175|polyprotein|AFY10053.1|Dengue_virus_3|11069 -2535 AFSQSAYLI 0.0 None None 0 None -2536 AYLIQHQRF 0.0 None None 0 None -2537 KAFSQSAYL 0.0 None None 0 None -2538 QEEQQQQQL 0.0 None None 0 None -2539 YLFSPQNQF 0.0 None None 0 None -2540 YLFSPQNQF 0.0 None None 0 None -2541 QARKIDHPL 0.0 None None 0 None -2542 QARKIDHPL 0.0 None None 0 None -2543 GLFVHTPCL 0.0397343073407 FVHTPC FVYTPS 24.0 141281|tegument_protein_UL21|NP_044622.1|Human_alphaherpesvirus_1|10298 -2544 RVLPAGLFV 0.0 None None 0 None -2545 VHTPCLVGL 1.29995014283 HTPCLVGL HYPCTVNF 25.0 72566|polyprotein|BAD73987.1|Hepatitis_C_virus_subtype_1b|31647 -2546 AGLDSYPEL 0.0 None None 0 None -2547 LVVSRSVSL 0.0 None None 0 None -2548 LVVSRSVSL 0.0 None None 0 None -2549 CSVDHRSVL 0.0 None None 0 None -2550 HRSVLQRIM 0.0 None None 0 None -2551 KMWEQEEKI 0.0 None None 0 None -2552 FGIISIIFV 0.0 None None 0 None -2553 GIISIIFVV 0.0 None None 0 None -2554 IFGIISIIF 0.0 None None 0 None -2555 RIFGIISII 0.0 None None 0 None -2556 STAARIFGI 0.0 None None 0 None -2557 TAARIFGII 0.0 None None 0 None -2558 LSVQLGPTV 0.0 None None 0 None -2559 CYTFNSIII 0.0 None None 0 None -2560 SIIIFGPFL 0.0 None None 0 None -2561 SIIIFGPFL 0.0 None None 0 None -2562 YTFNSIIIF 0.0 None None 0 None -2563 LEIQTPEAV 0.0 None None 0 None -2564 YLALAAQCL 186.219838246 ALAAQCL ALAAYCL 28.0 102636|Genome_polyprotein|P27958.3|Hepatitis_C_virus_subtype_1a|31646 -2565 YLALAAQCL 2537.30645606 ALAAQCL ALAAYCL 28.0 102636|Genome_polyprotein|P27958.3|Hepatitis_C_virus_subtype_1a|31646 -2566 AGCPAAQEL 0.0 None None 0 None -2567 RARPAGCPA 0.153281835099 RARPAG RARPRG 26.0 136865|tegument_protein|CAB06735.1|Human_alphaherpesvirus_2|10310 -2568 RPAGCPAAQ 0.0553403897978 RPAGCP RPQGLP 23.0 190533|nucleocapsid_protein|AAP49024.1|SARS_coronavirus|227859 -2569 AGVDHIITM 0.405289934875 DHIITM DHTITL 24.0 42455|Probable_Na(+)-translocating_NADH-quinone_reductase_subunit_A|O84639.1|Chlamydia_trachomatis|813 -2570 LSIAGVDHI 0.19293623707 LSIAGVD LSVAGVS 25.0 120187|E1_protein|BAA19893.1|Rubella_virus|11041 -2571 PPRYIGIPI 7.34699064743 YIGIPI YYGVPV 25.0 118|envelope_glycoprotein|ABS76372.1|Human_immunodeficiency_virus_1|11676 -2572 CMLVGDSAV 0.426158812917 CMLVGDSA CKLLPDTA 22.0 164258|nucleocapsid_protein|AAA43837.1|Hantaan_virus_76-118|11602 -2573 MLSSIKCML 0.0 None None 0 None -2574 MLSSIKCML 0.0 None None 0 None -2575 FGHTYVPAF 0.0 None None 0 None -2576 GQDFGHTYV 0.0 None None 0 None -2577 YSTPQGQDF 1.31803627544 STPQGQ TTPFGQ 21.0 180643|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -2578 FVGLAIGTL 0.0398377334692 GLAIGTL GLSPGTL 23.0 21638|protein_F|ABV46152.2|Hepatitis_C_virus_(isolate_Japanese)|11116 -2579 IGTLSGDAL 0.0 None None 0 None -2580 NMFEISNRL 0.0 None None 0 None -2581 VDLGSTTPL 0.0 None None 0 None -2582 IPLWGSPVT 2.31085692389 PLWGSPV PLFGYPV 27.0 48321|||| -2583 FVLSMQPVV 0.235323743699 FVLSMQP YVLDLQP 25.0 76334|Protein_E7|P17387.1|Human_papillomavirus_type_31|10585 -2584 FVLSMQPVV 0.215153137096 FVLSMQP YVLDLQP 25.0 76334|Protein_E7|P17387.1|Human_papillomavirus_type_31|10585 -2585 SMQPVVFQA 0.0 None None 0 None -2586 YYDPFVLSM 0.0 None None 0 None -2587 YYDPFVLSM 0.0 None None 0 None -2588 YSHQNGASY 0.0 None None 0 None -2589 AGVLLVLAL 0.651899369479 VLLVLAL ILLVLAL 27.0 21199|Circumsporozoite_protein_precursor|P08677.2|Plasmodium_vivax_strain_Belem|31273 -2590 RFAGVLLVL 0.452826067909 FAGVLLVL FLGPLLVL 25.0 178829|envelope_protein|BAJ51675.1|HBV_genotype_D|489483 -2591 VLALILPGT 0.0 None None 0 None -2592 VLLVLALIL 0.131262388183 VLLVLAL ILLVLAL 27.0 21199|Circumsporozoite_protein_precursor|P08677.2|Plasmodium_vivax_strain_Belem|31273 -2593 RQIPAQRDL 0.327777777778 PAQRDL PASRDL 26.0 93224|core_protein|AAL31859.1|Hepatitis_B_virus|10407 -2594 SYRKSVRQI 0.0 None None 0 None -2595 CYYELNQCL 4.36257309942 CYYELNQC CYEQLNDS 26.0 110431|E7|AAD33253.1|Human_papillomavirus_type_16|333760 -2596 CYYELNQCL 19.0060606061 CYYELNQC CYEQLNDS 26.0 110431|E7|AAD33253.1|Human_papillomavirus_type_16|333760 -2597 CPLCPFLTM 0.0 None None 0 None -2598 FMNRFQCPL 0.0 None None 0 None -2599 FMNRFQCPL 0.0 None None 0 None -2600 FQCPLCPFL 0.0 None None 0 None -2601 FQCPLCPFL 0.0 None None 0 None -2602 RFQCPLCPF 0.0 None None 0 None -2603 RFQCPLCPF 0.0 None None 0 None -2604 APEPLLLSW 0.0152696940155 PLLLS PLLLS 23.0 149036|E2_protein|NP_751921.1|Hepatitis_C_virus_(isolate_H77)|63746 -2605 ASLHHHHHR 0.0 None None 0 None -2606 RPPPSQASL 0.0 None None 0 None -2607 FPDHMACDL 0.0 None None 0 None -2608 ALLGNRTAL 0.0 None None 0 None -2609 GPVSAPGLL 0.0 None None 0 None -2610 HVYRNFLNK 0.0 None None 0 None -2611 RPRGDNGYT 0.0 None None 0 None -2612 SNSESEILK 0.0 None None 0 None -2613 AVDRYVAMR 0.0 None None 0 None -2614 RYVAMRHPL 0.0580304162483 RYVAMRHPL QYIYMGQPL 23.0 185327|polyprotein|ACF49259.1|Dengue_virus_type_1_Hawaii|10000440 -2615 YVAMRHPLR 0.0 None None 0 None -2616 RAGESVWPK 0.0 None None 0 None -2617 VWPKKINNI 11.2225440638 VWPKKI VWLKKL 24.0 181035|||| -2618 VVGADGVGK 0.0 None None 0 None -2619 KTETYDNYK 0.0 None None 0 None -2620 RQLTVESDK 0.0 None None 0 None -2621 ITLTATSQK 0.0 None None 0 None -2622 HPTASTLST 0.0 None None 0 None -2623 NPSHPTAST 0.0 None None 0 None -2624 LMLLQSGYK 0.0 None None 0 None -2625 HFPIYHLLL 0.0 None None 0 None -2626 LASSFVFLY 0.0 None None 0 None -2627 LISEGQRLK 0.0 None None 0 None -2628 KPLPLVTDL 0.0 None None 0 None -2629 LPLVTDLSL 0.0 None None 0 None -2630 APIAPTFYK 0.0 None None 0 None -2631 APTFYKPKL 0.0 None None 0 None -2632 IAPTFYKPK 0.0 None None 0 None -2633 TFYKPKLLK 0.0 None None 0 None -2634 VFQHIFDLI 0.0 None None 0 None -2635 AAATAVVAF 0.0 None None 0 None -2636 ALLRATDTI 0.0 None None 0 None -2637 APFDKHCAV 0.0 None None 0 None -2638 APFLNSVSI 0.00547938159601 APFLNSVS APIPASVS 18.0 179765|cell_surface_protein_(associated_with_virulence)|NP_302372.1|Mycobacterium_leprae_TN|272631 -2639 APHGEEAHL 0.0 None None 0 None -2640 APLLPRTHL 105.804891576 APLLPRT APLPPST 23.0 179766|cell_surface_protein_(associated_with_virulence)|NP_302372.1|Mycobacterium_leprae_TN|272631 -2641 APRRHSGRV 0.0 None None 0 None -2642 APSLPSPTA 0.528755892864 PSLPSPT PTLHGPT 22.0 6591|polyprotein|AAB67037.1|Hepatitis_C_virus_(isolate_H77)|63746 -2643 APVTLRGSY 0.0 None None 0 None -2644 ATGGHHQPL 0.687294743501 GHHQPL GHEEPI 25.0 180488|polyprotein|AGO67248.1|Dengue_virus_2|11060 -2645 AVMAFDLCV 0.0 None None 0 None -2646 AVMAFDRSV 0.0 None None 0 None -2647 AYQVSVCAF 0.565327595099 AYQVSVCA AYQATVCA 34.0 13518|HCV-1|AAA45676.1|Hepatitis_C_virus_genotype_1|41856 -2648 CTTPVTVEI 0.0 None None 0 None -2649 CYYYFLCLL 0.0 None None 0 None -2650 DTPRHRLLV 0.0 None None 0 None -2651 EAQQSSHCL 0.0 None None 0 None -2652 EPRITRSFV 0.0 None None 0 None -2653 ETGLALKYL 0.0 None None 0 None -2654 FSFQVDSPV 0.0 None None 0 None -2655 FSILSTALL 0.0453532771775 FSILSTALL FSIFLLALL 23.0 57894|polyprotein|BAD73987.1|Hepatitis_C_virus_subtype_1b|31647 -2656 GLRKTNMSL 0.0 None None 0 None -2657 GPNAMRYSL 0.0 None None 0 None -2658 GPRNCIGQA 0.127721163409 GPRNCI DPRRCL 23.0 150556|polyprotein|AGW21594.1|Dengue_virus_1|11053 -2659 HMSACHHSI 0.0 None None 0 None -2660 HPNAHSNST 0.0 None None 0 None -2661 HPWTTDMPA 0.0 None None 0 None -2662 HSNSTSFIF 0.0 None None 0 None -2663 HSNSTSFIF 0.0 None None 0 None -2664 HTWQMRNTV 0.0 None None 0 None -2665 HTWQMRNTV 0.0 None None 0 None -2666 IFSLGRHTW 0.0 None None 0 None -2667 INALIIFIF 0.0 None None 0 None -2668 IPHLLKLAC 0.0 None None 0 None -2669 ISASVCIQV 0.0 None None 0 None -2670 ITSTVMLEV 0.0 None None 0 None -2671 KAFNCSSFV 0.0 None None 0 None -2672 KAFSQSSNL 0.0 None None 0 None -2673 KLFSILSTA 0.0 None None 0 None -2674 KLWATAEAL 0.0 None None 0 None -2675 KTHRIVRRL 0.0 None None 0 None -2676 KTHRIVRRL 0.0 None None 0 None -2677 KTLRKSLPA 0.0 None None 0 None -2678 KTLRKSLPA 0.0 None None 0 None -2679 KYIFNNSII 0.987149197996 KYIFNNSII KYFYCNSLF 24.0 141323|multifunctional_expression_regulator|NP_044657.1|Human_alphaherpesvirus_1|10298 -2680 KYTSAAILV 0.0 None None 0 None -2681 LALSVTEMV 0.0 None None 0 None -2682 LHSPMYFFL 0.0 None None 0 None -2683 LHTPVYFLL 0.0 None None 0 None -2684 LLVSLTVTF 0.094208760953 LLVSLTV LLVCLTV 24.0 40264|Cytochrome_P450_2A6|P11509.3|Homo_sapiens|9606 -2685 LPGGVGRTL 0.0104130689254 LPGGVGRTL VPGWSRRTL 22.0 141461|ubiquitin_E3_ligase_ICP0|NP_044601.1|Human_alphaherpesvirus_1|10298 -2686 LPSDDRGSL 0.206878016438 DDRGSL DSRGSL 25.0 55709|Genome_polyprotein|P27958.3|Hepatitis_C_virus_subtype_1a|31646 -2687 LSVADQEKV 0.0 None None 0 None -2688 LWGKHQFIL 0.892559226889 LWGKHQFI LWGYLQYV 27.0 42094|telomer_length_regulation_protein_TEL1|EDV12172.1|Saccharomyces_cerevisiae|4932 -2689 MAFDLCVAI 0.0486655905336 FDLCV YDLCI 25.0 112503|E6_protein|ACV53993.1|Human_papillomavirus_type_35|10587 -2690 MAFDRSVAI 0.0 None None 0 None -2691 MAFDRSVAI 0.0 None None 0 None -2692 MIISASVCI 0.0 None None 0 None -2693 MIISASVCI 0.0 None None 0 None -2694 MLDLLTNTL 0.0 None None 0 None -2695 MTNGLCIWL 0.0 None None 0 None -2696 MVNATACAV 0.0 None None 0 None -2697 NAFQEARRL 0.0 None None 0 None -2698 PSAPKPSTL 6.16092555862 SAPKPST SAPLPSN 24.0 88377|IE62|AAP32859.1|Human_alphaherpesvirus_3|10335 -2699 QALRAGLAL 0.0 None None 0 None -2700 QALRAGLAL 0.0 None None 0 None -2701 QAVEFCQRV 0.0 None None 0 None -2702 QILVKICTI 0.0 None None 0 None -2703 QLHFIFHIL 0.0 None None 0 None -2704 QLWGKHQFI 9.62632414914 LWGKHQFI LWGYLQYV 27.0 42094|telomer_length_regulation_protein_TEL1|EDV12172.1|Saccharomyces_cerevisiae|4932 -2705 QPWEHVNAF 0.0 None None 0 None -2706 QQQMASRPF 0.0 None None 0 None -2707 QTSMSQSQV 0.0 None None 0 None -2708 RIIKLLVSL 0.0 None None 0 None -2709 RLALSTFEW 355.619732468 LSTFEW LSTTEW 27.0 37830|polyprotein|BAB18806.1|Hepatitis_C_virus_subtype_1b|31647 -2710 RLHSPMYFF 0.0 None None 0 None -2711 RLHSPMYFF 0.0 None None 0 None -2712 RLHTPVYFL 0.0 None None 0 None -2713 RSFTEENHM 0.0 None None 0 None -2714 RSFVPHLEI 0.0 None None 0 None -2715 RSFVPHLEI 0.0 None None 0 None -2716 RSVAICKPL 0.0 None None 0 None -2717 RVVLINNNL 0.0 None None 0 None -2718 SASSQSSSI 0.0 None None 0 None -2719 SASVCIQVV 0.0 None None 0 None -2720 SIIQDFFAW 0.0 None None 0 None -2721 SINALIIFI 0.0 None None 0 None -2722 SMSQSQVAL 0.0 None None 0 None -2723 SPAQAPIPY 0.108147812318 AQAPIP AQAPPP 24.0 149096|polyprotein|BAB18801.1|Hepatitis_C_virus|11103 -2724 SPGGWRSGW 83.0885140233 GGWRSGW GFWQEGW 32.0 75674|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 -2725 SSEQSIFVV 0.0 None None 0 None -2726 SSIPENEAI 0.0 None None 0 None -2727 STVMLEVPL 0.0 None None 0 None -2728 STVMLEVPL 0.0 None None 0 None -2729 SYSSLDEDF 0.0115200700311 YSSLDED YSRADEE 22.0 12585|ESAT-6-like_protein_esxB|P0A566.2|Mycobacterium_tuberculosis|1773 -2730 TPRHRLLVL 0.0 None None 0 None -2731 TSMYNEILI 0.0 None None 0 None -2732 TSVPVTTAV 0.0 None None 0 None -2733 VPADSTQTL 0.0 None None 0 None -2734 VSIETHLLF 0.0 None None 0 None -2735 VSIETHLLF 0.0 None None 0 None -2736 VSLTVTFVL 0.0 None None 0 None -2737 VTTAVSTFV 0.0 None None 0 None -2738 VTTGLMGAV 0.0 None None 0 None -2739 YSSLDEDFL 0.0 None None 0 None -2740 YVQKRSSQI 0.0 None None 0 None -2741 YYFLCLLL* 0.0 None None 0 None -2742 YYYFLCLLL 0.0 None None 0 None -2743 ASLDVTLRL 0.0 None None 0 None -2744 ISSHLSTLV 1.22721158737 SHLSTLV SHYFTLV 22.0 98466|Trans-sialidase|SRC7915|Trypanosoma_cruzi|5693 -2745 LSTLVDFAI 0.0 None None 0 None -2746 KTSVGSTKY 0.0 None None 0 None -2747 HPCERSDEV 0.0 None None 0 None -2748 ITVEEQHRI 0.0 None None 0 None -2749 ITVEEQHRI 0.0 None None 0 None -2750 MTAVQTLHL 0.0 None None 0 None -2751 PAMTAVQTL 0.0 None None 0 None -2752 RQLPAMTAV 0.0 None None 0 None -2753 ETVFTRSSW 0.0 None None 0 None -2754 FTRSSWDWI 0.0 None None 0 None -2755 VFTRSSWDW 0.0 None None 0 None -2756 EPPPPPSPL 0.0101907339737 PPPSPL PPCKPL 22.0 96366|polyprotein|ABR25251.1|Hepatitis_C_virus|11103 -2757 QTTQLSLNF 0.0 None None 0 None -2758 GAMDGATYI 0.0 None None 0 None -2759 MAFVKSVWL 0.0 None None 0 None -2760 CAVRRAAQV 0.0 None None 0 None -2761 QAVAQAVNW 0.0 None None 0 None -2762 NPKTWNTMV 0.0 None None 0 None -2763 QLYMNPKTW 4.12392711167 QLYMNPKTW RLYQNPTTY 31.0 135263|hemagglutinin|ACX31970.1|Influenza_A_virus_(A/Bar-headed_Goose/Qinghai/61/05(H5N1))|336238 -2764 RQVGFCVQW 0.0 None None 0 None -2765 KMLLAPGRF 1.4325134436 LLAPG LLAPG 25.0 59240|HCV-1|AAA45676.1|Hepatitis_C_virus_genotype_1|41856 -2766 MLLAPGRFI 0.588309359247 LLAPG LLAPG 25.0 59240|HCV-1|AAA45676.1|Hepatitis_C_virus_genotype_1|41856 -2767 FTMPEDEYM 0.0 None None 0 None -2768 FTMPEDEYM 0.0 None None 0 None -2769 MPEDEYMVY 0.0 None None 0 None -2770 IAWPADRTA 0.0 None None 0 None -2771 QALIRPTTF 0.514471687749 LIRPTTF LLRPTTL 28.0 13165|trans-sialidase,_putative|EAN81972.1|Trypanosoma_cruzi|5693 -2772 FPEYDGVDH 0.0 None None 0 None -2773 EIAEIEYSI 0.0 None None 0 None -2774 FVVSACNAT 0.0 None None 0 None -2775 WITPAQREY 2.29081841307 TPAQREY TPTLHEY 22.0 110940|Protein_E7|P03129.1|Human_papillomavirus_type_16|333760 -2776 EPVWGLEAI 0.0 None None 0 None -2777 RLSWQASSL 0.0 None None 0 None -2778 KIKELAAEF 0.0 None None 0 None -2779 VPILQSTPV 0.0416654367885 VPILQSTP LPIRYQTP 21.0 180647|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -2780 APRGFLTNY 0.0 None None 0 None -2781 RAAEQRRAY 0.0 None None 0 None -2782 KSASWITWI 0.34874341875 SWITW QWLTW 29.0 70634|Non-capsid_protein_NS-1|P07298.1|Human_parvovirus_B19|10798 -2783 TPWSFTGTV 0.0459224896119 PWSFTG QWNFAG 24.0 42797|6_kDa_early_secretory_antigenic_target|P0A564.2|Mycobacterium_tuberculosis|1773 -2784 GPLADATPL 0.0 None None 0 None -2785 LAGERRFAF 0.0 None None 0 None -2786 IAASAMCVF 0.0 None None 0 None -2787 SSYGRNHYI 3.39831238883 GRNHYI GRSHFL 25.0 8554|Genome_polyprotein|P08617.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 -2788 IIHTGARPY 0.0 None None 0 None -2789 DTATGNCLR 0.0 None None 0 None -2790 GPYENCSVF 0.0 None None 0 None -2791 ETYQQALGK 0.102756058551 ETYQQALGK QVYQDWLGR 23.0 23288|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 -2792 YQQALGKRF 0.0447142296507 YQQALGK YQDWLGR 21.0 23288|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 -2793 YQQALGKRF 0.165670773671 YQQALGK YQDWLGR 21.0 23288|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 -2794 FAIHKIKQF 0.0 None None 0 None -2795 GYTVNIPTI 0.0 None None 0 None -2796 HSPSVASMK 0.0 None None 0 None -2797 YTDCHASNL 0.160144923269 DCHASN DCHAQD 28.0 6094|Genome_polyprotein|Q81495.3|Hepatitis_C_virus_(isolate_HCV-K3a/650)|356416 -2798 TYSSPTPNM 0.0616536351308 TYSSPT TYTFPT 23.0 232153|rhoptry_protein_18|CAJ27113.1|Toxoplasma_gondii_type_I|1209525 -2799 DAIPFGNVP 0.0 None None 0 None -2800 IPFGNVPVL 0.0 None None 0 None -2801 NYFGVQDAI 0.0 None None 0 None -2802 ETLGRGNPM 0.0 None None 0 None -2803 MALQLFLQI 0.0 None None 0 None -2804 MALQLFLQI 0.0 None None 0 None -2805 MALQLFLQI 0.0 None None 0 None -2806 KVHSAVITI 0.0 None None 0 None -2807 QAGEYSRVV 0.0 None None 0 None -2808 RVVDCYLKV 0.0 None None 0 None -2809 WQRPTLESI 0.0 None None 0 None -2810 WQRPTLESI 0.0 None None 0 None -2811 VAQLGFQPL 0.0 None None 0 None -2812 EAINCLNVA 0.0 None None 0 None -2813 VAIDIYTDM 0.0 None None 0 None -2814 HFLHSWTNL 0.349366438751 LHSWTN LHQWIN 28.0 103322|polyprotein|BAB18806.1|Hepatitis_C_virus|11103 -2815 TFKHLVHFL 0.0 None None 0 None -2816 YTFKHLVHF 0.00127547167216 YTFKHLVHF YKFMGRSHF 19.0 8554|Genome_polyprotein|P08617.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 -2817 YTFKHLVHF 0.00173099726936 YTFKHLVHF YKFMGRSHF 19.0 8554|Genome_polyprotein|P08617.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 -2818 IIMSRNAYV 0.0 None None 0 None -2819 LRYPIIMSR 0.0 None None 0 None -2820 MSRNAYVPM 0.0 None None 0 None -2821 NAPALLTPR 0.0 None None 0 None -2822 RAGSAGGTV 0.0 None None 0 None -2823 EAFTLKATV 6.35897435897 FTLKATV FTLVATV 26.0 98640|trans-sialidase,_putative|EAN80840.1|Trypanosoma_cruzi|5693 -2824 YSVIRGEAF 0.0 None None 0 None -2825 DIYSMPEGK 0.0 None None 0 None -2826 IYSMPEGKL 0.0557903921081 YSMPEGKL YSMCTGKF 23.0 150456|polyprotein|AGO67248.1|Dengue_virus_2|11060 -2827 SMPEGKLHV 0.0224344124258 MPEGKL LPQGQL 22.0 13701|Trans-activator_protein_BZLF1|P03206.2|Human_gammaherpesvirus_4|10376 -2828 YSMPEGKLH 0.292799376299 YSMPEGKL YSMCTGKF 23.0 150456|polyprotein|AGO67248.1|Dengue_virus_2|11060 -2829 FFFLCVCVF 0.100381408019 FFFLCVCV LLILCLCL 24.0 49831|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 -2830 FFFLCVCVF 0.0684531631414 FFFLCVCV LLILCLCL 24.0 49831|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 -2831 FFLCVCVFV 0.673124000294 FFLCVCV LILCLCL 24.0 49831|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 -2832 FFLCVCVFV 0.243568175313 FFLCVCV LILCLCL 24.0 49831|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 -2833 HLLQRYNEF 0.366998782491 HLLQRYNEF NLLQRANEL 28.0 154980|tegument_protein|CAB06735.1|Human_alphaherpesvirus_2|10310 -2834 RAEERRRHL 2.38489063295 AEERRRHL PEEKQRHL 30.0 110394|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 -2835 ITTTGQKLR 0.0 None None 0 None -2836 IMALAVLII 0.0 None None 0 None -2837 TALVVVSIM 0.0 None None 0 None -2838 DVLPYDAFV 0.0894142186526 VLPYDAFV VYPYDEFV 32.0 141423|envelope_glycoprotein_B|NP_044629.1|Human_alphaherpesvirus_1|10298 -2839 LTLATFSRI 0.0 None None 0 None -2840 VLTLATFSR 0.0 None None 0 None -2841 MNQRPILTI 0.0 None None 0 None -2842 NQRPILTII 0.0 None None 0 None -2843 FNVNAPDLY 0.0 None None 0 None -2844 NVNAPDLYI 0.0 None None 0 None -2845 RFNVNAPDL 0.0 None None 0 None -2846 FHWRVNFIR 0.0 None None 0 None -2847 IFHWRVNFI 0.0 None None 0 None -2848 KIFHWRVNF 0.0 None None 0 None -2849 LHDTTTRSV 0.0 None None 0 None -2850 LHNNTTRSV 0.0 None None 0 None -2851 TTTRSVHAK 0.0 None None 0 None -2852 HFKAPKISM 0.0 None None 0 None -2853 GTSSTSCSW 0.0 None None 0 None -2854 GVRAQGCYM 0.0 None None 0 None -2855 GVRAQGCYM 0.0 None None 0 None -2856 RAQGCYMDI 0.0 None None 0 None -2857 VAEKGTSKL 0.0 None None 0 None -2858 EAFSVSPEW 0.0 None None 0 None -2859 FSVSPEWAV 0.00283478309185 FSVSPEWA FSMVGNWA 22.0 149052|E1_protein|NP_751920.1|Hepatitis_C_virus_(isolate_H77)|63746 -2860 LTRPVHGAA 3.12682962682 LTRPVHGA LKEPVHGV 28.0 27125|gag-pol_fusion_polyprotein|AAN73817.1|Human_immunodeficiency_virus_1|11676 -2861 MARTAPASG 0.0 None None 0 None -2862 AHQYFAQLL 0.0968441616774 AHQYFAQLL GHQAAMQML 19.0 101673|gag_protein|ABO73990.1|Human_immunodeficiency_virus_1|11676 -2863 AHQYFAQLL 0.100003052772 AHQYFAQLL GHQAAMQML 19.0 101673|gag_protein|ABO73990.1|Human_immunodeficiency_virus_1|11676 -2864 HQYFAQLLA 0.00076046422012 HQYFAQLL HQAAMQML 19.0 101673|gag_protein|ABO73990.1|Human_immunodeficiency_virus_1|11676 -2865 LALQRQRTY 0.0 None None 0 None -2866 LALQRQRTY 0.0 None None 0 None -2867 ATVCRDPGV 0.0 None None 0 None -2868 VCRDPGVPM 0.0 None None 0 None -2869 DAPLFNTIV 0.84762355921 PLFNTIV SLFNTVV 28.0 180255|gag_protein|AAT90688.1|Human_immunodeficiency_virus_1|11676 -2870 VDAPLFNTI 0.0 None None 0 None -2871 LSETISPLW 0.0 None None 0 None -2872 WPQRPKSQV 0.0 None None 0 None -2873 MVLPGGVDI 0.0 None None 0 None -2874 FELEWLLYT 0.0 None None 0 None -2875 HSHTTGINL 0.0 None None 0 None -2876 HSHTTGINL 0.0 None None 0 None -2877 SHTTGINLV 0.0 None None 0 None -2878 STHSHTTGI 0.0 None None 0 None -2879 STHSHTTGI 0.0 None None 0 None -2880 STHSHTTGI 0.0 None None 0 None -2881 LTLVGVVVY 0.0 None None 0 None -2882 LTLVGVVVY 0.0 None None 0 None -2883 SEYFLGLTL 0.0310160688315 SEYFLGLTL KEYTFPITL 19.0 143705|Genome_polyprotein|P08617.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 -2884 EAHSFEEEM 0.0 None None 0 None -2885 SSLQEAHSF 0.0 None None 0 None -2886 SHTTLSLDL 0.0 None None 0 None -2887 KLREFFKCA 0.0 None None 0 None -2888 VAYCPAYVV 0.546466079592 AYCPAY ANCPTY 25.0 40253|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 -2889 VAYCPAYVV 0.627529983197 AYCPAY ANCPTY 25.0 40253|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 -2890 VLIPDVVAY 0.0 None None 0 None -2891 VVAYCPAYV 0.0174448489537 AYCPAY ANCPTY 25.0 40253|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 -2892 YLVLIPDVV 0.123689109937 LVLIPDVV LVLNPSVA 20.0 46755|HCV-1|AAA45676.1|Hepatitis_C_virus_genotype_1|41856 -2893 FGIGVENFI 0.0120582173391 FGIGVENFI LGYGFVNYI 21.0 36357|ELAV-like_protein_4_(Paraneoplastic_encephalomyelitis_antigen_HuD)_(Hu-antigen_D)|P26378.1|Homo_sapiens|9606 -2894 IGVENFITL 0.0 None None 0 None -2895 ITLVVFGLI 0.207698907722 VVFGLI VLFGLL 23.0 101380|BNLF2a|YP_401721.1|Human_herpesvirus_4_type_1|36352 -2896 KVARSKPYA 0.0 None None 0 None -2897 VARSKPYAM 0.0 None None 0 None -2898 KFRCDAGLG 0.0 None None 0 None -2899 GSRESNMSR 0.0 None None 0 None -2900 MSRKKKAVK 0.0 None None 0 None -2901 RKKKAVKEK 0.0 None None 0 None -2902 QSNTWSLSK 8.97866690799 QSNTWSL QQNWWTL 25.0 74886|latent_membrane_protein_1|AAS99606.1|Human_gammaherpesvirus_4|10376 -2903 YQQSNTWSL 4.15563295911 YQQSNTWSL YLQQNWWTL 30.0 74886|latent_membrane_protein_1|AAS99606.1|Human_gammaherpesvirus_4|10376 -2904 YQQSNTWSL 2.43549839174 YQQSNTWSL YLQQNWWTL 30.0 74886|latent_membrane_protein_1|AAS99606.1|Human_gammaherpesvirus_4|10376 -2905 YKLVVVGAV 16.9067084102 KLVVVG KLVVLG 24.0 32238|polyprotein_[Hepatitis_C_virus_subtype_1a]|ABV46251.2|Hepatitis_C_virus_(isolate_H77)|63746 -2906 AVRYSRGCL 0.0 None None 0 None -2907 VRYSRGCLT 0.0 None None 0 None -2908 YSRGCLTVM 0.0 None None 0 None -2909 YSRGCLTVM 0.0 None None 0 None -2910 YSRGCLTVM 0.0 None None 0 None -2911 VQYASGNRW 0.0 None None 0 None -2912 YASGNRWTF 1.46233842452 ASGNRWTF ATGITYTF 20.0 232153|rhoptry_protein_18|CAJ27113.1|Toxoplasma_gondii_type_I|1209525 -2913 YASGNRWTF 0.0162902231496 ASGNRWTF ATGITYTF 20.0 232153|rhoptry_protein_18|CAJ27113.1|Toxoplasma_gondii_type_I|1209525 -2914 AVRNAITST 0.0 None None 0 None -2915 NAITSTSVI 0.0 None None 0 None -2916 TSIAVRNAI 0.0 None None 0 None -2917 VVLPTEAPI 0.0 None None 0 None -2918 VVLPTEAPI 0.0 None None 0 None -2919 LVATSPSPV 0.0 None None 0 None -2920 LSENAVLIL 0.0 None None 0 None -2921 LSENAVLIL 0.0 None None 0 None -2922 MALSENAVL 0.00068461137038 ALSENAVL ALSLAAVL 19.0 2884|cysteine_proteinase_cruzipain_(EC_3.4.22.-)_-_Trypanosoma_cruzi|A45629|Trypanosoma_cruzi|5693 -2923 MALSENAVL 0.00103322489989 ALSENAVL ALSLAAVL 19.0 2884|cysteine_proteinase_cruzipain_(EC_3.4.22.-)_-_Trypanosoma_cruzi|A45629|Trypanosoma_cruzi|5693 -2924 SSSGWRKSF 0.0 None None 0 None -2925 FSEASQLDF 0.0 None None 0 None -2926 FSEASQLDF 0.0 None None 0 None -2927 RTKQFSEAS 0.0 None None 0 None -2928 RGFSRQSVL 0.0 None None 0 None -2929 LTRSTLSSV 0.0 None None 0 None -2930 LTRSTLSSV 0.0 None None 0 None -2931 RADHDLGRL 0.0 None None 0 None -2932 YRADHDLGR 0.0 None None 0 None -2933 ALRVNPVLA 0.0497971668364 LRVNPV IRVSPV 23.0 56198|glycoprotein_gp35/37|AAC59622.1|Human_gammaherpesvirus_8|37296 -2934 RVNPVLAEL 0.0 None None 0 None -2935 RVNPVLAEL 0.0 None None 0 None -2936 SALRVNPVL 0.109248886427 SALRVNPV TRIRVSPV 23.0 56198|glycoprotein_gp35/37|AAC59622.1|Human_gammaherpesvirus_8|37296 -2937 SSALRVNPV 3.15088690804 SSALRVNPV TTRIRVSPV 24.0 56198|glycoprotein_gp35/37|AAC59622.1|Human_gammaherpesvirus_8|37296 -2938 LLYRRTKAF 0.0 None None 0 None -2939 LLYRRTKAF 0.0 None None 0 None -2940 LYRRTKAFI 0.0 None None 0 None -2941 RTKAFIDYE 0.0 None None 0 None -2942 ATSYELHKF 0.0 None None 0 None -2943 RTQILATSY 0.0 None None 0 None -2944 TSYELHKFY 0.0 None None 0 None -2945 TSYELHKFY 0.0 None None 0 None -2946 IQKITSPNI 0.0028984223105 IQKITSPNI IEKPVAPSV 20.0 419002|PPE_family_protein_PPE68|KAM81677.1|Mycobacterium_tuberculosis_H37Ra|419947 -2947 TSVKPSQPK 0.0 None None 0 None -2948 AIFASMAHA 0.0 None None 0 None -2949 ASMAHAMQK 0.0 None None 0 None -2950 MAHAMQKYL 0.0 None None 0 None -2951 MAHAMQKYL 0.0 None None 0 None -2952 MAHAMQKYL 0.0 None None 0 None -2953 SMAHAMQKY 0.0 None None 0 None -2954 RQRLSAPPS 0.0 None None 0 None -2955 TAHGLSPTA 1.66455725447 GLSPTA GLSPTV 26.0 21139|envelope_protein|BAF48755.1|Hepatitis_B_virus|10407 -2956 GLIEGYGGW 0.0 None None 0 None -2957 QVLGLGGHI 0.0 None None 0 None -2958 AAFNPTRDF 0.0 None None 0 None -2959 AAFNPTRDF 0.0 None None 0 None -2960 KGFVCKAHF 0.0 None None 0 None -2961 SRRACSSEL 0.0 None None 0 None -2962 SPKLKMPEM 0.0 None None 0 None -2963 SNKEKWISL 0.0 None None 0 None -2964 KRWESEHIL 0.0 None None 0 None -2965 LHNEIKTLL 0.000207822443766 LHNEIKTLL IHSMNSTIL 17.0 109332|L1_protein|ACG75893.1|Human_papillomavirus_type_16|333760 -2966 FSDKMGTLT 0.0 None None 0 None -2967 LAAERKAAL 0.0 None None 0 None -2968 TPRRSRWQL 0.0 None None 0 None -2969 MNCIRQASV 0.0 None None 0 None -2970 DQRCRLCPA 0.467544317151 RCRLC RCYLC 25.0 145860|Protein_E6|P04019.1|Human_papillomavirus_type_11|10580 -2971 HTTRSLFQY 0.0 None None 0 None -2972 PHCPQPLVY 1.64017196847 HCPQPLVY HGPTPLLY 30.0 6591|polyprotein|AAB67037.1|Hepatitis_C_virus_(isolate_H77)|63746 -2973 SLEGRIWAL 1.97995031712 EGRIWAL DGRFWEL 27.0 186219|polyprotein|AGK36298.1|Dengue_virus_2|11060 -2974 YTDFLLCAS 0.0 None None 0 None -2975 VVGARGVGK 0.0 None None 0 None -2976 RGRKNRSSV 0.0 None None 0 None -2977 FEKMHQMDL 0.0 None None 0 None -2978 QVFEKMHQM 0.0 None None 0 None -2979 ARWPFGNTM 0.0 None None 0 None -2980 GALKKALAK 0.0 None None 0 None -2981 RLIAISWPL 0.00137441037811 RLIAISW RLLTKPW 18.0 161186|Nonstructural_protein_NS5|NP_739590.2|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -2982 WPLRYVTVM 0.0 None None 0 None -2983 HILGNFLTK 0.0 None None 0 None -2984 IRCGYPTHI 0.0 None None 0 None -2985 EAGPRKGPL 2.46659552716 PRKGP PRRGP 27.0 181035|||| -2986 RLEEAGPRK 0.0 None None 0 None -2987 KLPEMKLPK 5.01765917237e-05 LPEMKLPK LPSDFLPS 16.0 16836|precore/core_protein_[Hepatitis_B_virus]|AAR03815.1|Hepatitis_B_virus|10407 -2988 MKLPKVPEM 0.0 None None 0 None -2989 DRQDQSSHY 0.0 None None 0 None -2990 SHYGQPDRQ 0.0 None None 0 None -2991 GIMPGHIQK 0.00230778161286 MPGHIQK MPSVIEK 20.0 180668|polyprotein|AGO67248.1|Dengue_virus_2|11060 -2992 IMPGHIQKK 0.0020605192972 MPGHIQK MPSVIEK 20.0 180668|polyprotein|AGO67248.1|Dengue_virus_2|11060 -2993 STMRESSPK 0.0 None None 0 None -2994 FPLFAIWPM 0.0 None None 0 None -2995 PTDPMLGLA 7.81973026172 PTDPML PDDPVL 24.0 141462|tegument_protein_UL21|NP_044622.1|Human_alphaherpesvirus_1|10298 -2996 EARSRATLA 0.0 None None 0 None -2997 FHEARSRAT 0.0 None None 0 None -2998 FSIFSTLTK 0.0 None None 0 None -2999 LPDRLTLEF 0.0 None None 0 None -3000 LPDRLTLEF 0.0 None None 0 None -3001 FSDHQSFVV 0.0794686146814 FSDHQ FPDHQ 24.0 190466|large_surface_antigen|CAL29876.1|Hepatitis_B_virus|10407 -3002 LLSQVQFPY 0.0 None None 0 None -3003 GELSVDVSF 0.0 None None 0 None -3004 LSVDVSFFF 0.0 None None 0 None -3005 LSVDVSFFF 0.0 None None 0 None -3006 SVDVSFFFK 1.57692307692 SVDVSFFFK AVDLSHFLK 26.0 5295|nef_protein|ACR27174.1|Human_immunodeficiency_virus_1|11676 -3007 VVDQGNIGK 0.0 None None 0 None -3008 MVFHKHGEK 0.0874586889695 VFHKHGEK VYHGAGSK 22.0 72039|polyprotein|CAB53095.1|Hepatitis_C_virus_subtype_1b|31647 -3009 NAYTMVFHK 0.0 None None 0 None -3010 MESNNMPFL 0.0 None None 0 None -3011 VMESNNMPF 0.0 None None 0 None -3012 IPVPVGATA 0.0 None None 0 None -3013 VPVGATASF 1.51661571138 VPVGATASF MPVGGQSSF 28.0 42342|Antigen_85-B_precursor_(85B)_(Extracellular_alpha-antigen)_(Antigen_85_complex_B)_(Ag85B)_(Mycolyl_transferase_85B)_(Fibronectin-binding_protein_B)_(30_kDa_extracellular_protein)|P31952|Mycobacterium_tuberculosis|1773 -3014 SLDLSQTNL 0.0 None None 0 None -3015 TETSSSMPG 0.0 None None 0 None -3016 HTDPHLCDF 0.0 None None 0 None -3017 SLGFKLLLR 0.884622618909 GFKLLLR NFKSLLR 22.0 52578|liver_stage_antigen-1|CAA82974.1|Plasmodium_falciparum|5833 -3018 HEQCDSSSL 0.0 None None 0 None -3019 AEKSQGPVL 0.0 None None 0 None -3020 RLLSTQAEK 0.0 None None 0 None -3021 LSDIGGLLL 0.0 None None 0 None -3022 LYLYVLSDI 0.0 None None 0 None -3023 SELSSDINL 0.0 None None 0 None -3024 MPHSQYLSA 0.0 None None 0 None -3025 EEAFVPILY 9.10107986896 AFVPILY AYVSVLY 24.0 141228|tegument_protein_VP11/12|NP_044648.1|Human_alphaherpesvirus_1|10298 -3026 QVTVSFTEM 0.0733616966506 VSFTEM VAFTEI 22.0 112697|Protein_E6|P26554.1|Human_papillomavirus_type_51|10595 -3027 TVSFTEMLK 0.0149885083017 VSFTEM VAFTEI 22.0 112697|Protein_E6|P26554.1|Human_papillomavirus_type_51|10595 -3028 VSFTEMLKK 0.0122306227742 VSFTEM VAFTEI 22.0 112697|Protein_E6|P26554.1|Human_papillomavirus_type_51|10595 -3029 LGYRCRFNK 0.0 None None 0 None -3030 LPDLFTPPL 0.625085327902 LFTPP FFTPP 25.0 10587|viral_polyprotein|AAA42941.1|Dengue_virus_2_Thailand/NGS-C/1944|11065 -3031 HTDGDTLLQ 0.00713135459058 HTDGDTLL STDSTTIL 21.0 108148|polyprotein|AAF65953.1|Hepatitis_C_virus|11103 -3032 ILAKHKSLF 0.0 None None 0 None -3033 KLTILAKHK 0.0 None None 0 None -3034 AQTHEPRQW 1.87002493797 AQTHEPRQW AVRHFPRIW 26.0 187106|Vpr_protein|BAA93983.1|Human_immunodeficiency_virus_1|11676 -3035 EAVAGHIPA 0.0 None None 0 None -3036 VAGHIPAIF 1.273 VAGHIPAI LMGYIPAV 26.0 9199|E1_protein|ABB77003.1|Hepatitis_C_virus|11103 -3037 VADLLAFTH 0.0 None None 0 None -3038 VVGAVGVGK 0.0 None None 0 None -3039 KLTSYKCKL 0.0 None None 0 None -3040 WLRVGNGAL 0.0 None None 0 None -3041 SLQLSAHRL 0.0 None None 0 None -3042 IVVISIWEI 0.0 None None 0 None -3043 SIWEIVGQA 0.228841933641 SIWEIVG STWVLVG 24.0 62004|Genome_polyprotein|P27958.3|Hepatitis_C_virus_subtype_1a|31646 -3044 YLKRGYLTL 0.0 None None 0 None -3045 MLHVDRHTL 0.0 None None 0 None -3046 VLERGQFDY 0.0 None None 0 None -3047 AALSIDHWV 0.0 None None 0 None -3048 SIDHWVAVV 0.0 None None 0 None -3049 ATAAAAAAL 0.0 None None 0 None -3050 GPATAAAAA 0.0950864586136 PATAAA PITAAA 23.0 183819|polyprotein|AGO67248.1|Dengue_virus_2|11060 -3051 LLLDTPTQL 0.0 None None 0 None -3052 HLYDTLGST 0.827970867806 HLYDTLGS RLYKTLGQ 25.0 169658|major_paraflagellar_rod_protein|AAA30221.1|Trypanosoma_cruzi|5693 -3053 LPLHLYDTL 7.53132395702 LHLYD LHLYS 23.0 190568|polymerase|AAD16253.1|Hepatitis_B_virus|10407 -3054 EEYTVWIQL 0.0 None None 0 None -3055 WEEEYTVWI 2.67996539102 WEEEYTVW WPKTHTLW 29.0 184702|non-structural_protein_1|AGM49312.1|Dengue_virus|12637 -3056 TPEDNRQPL 0.610171894935 TPEDNR TPQDNQ 27.0 150649|polyprotein|AGW21594.1|Dengue_virus_1|11053 -3057 LPEQQEGQL 0.0 None None 0 None -3058 KPMQVKTPC 0.0 None None 0 None -3059 NLQNSPLEI 0.0 None None 0 None -3060 VPNLQNSPL 0.00025151259785 VPNLQNSP VPTDPNPP 18.0 70491|envelope_glycoprotein|AAC28452.1|Human_immunodeficiency_virus_1|11676 -3061 NELYFAHVL 0.0 None None 0 None -3062 YFAHVLFSA 0.0 None None 0 None -3063 AVTRPFISL 0.0 None None 0 None -3064 FLWPLRVLS 1.97746781824 WPLRVL WMIRIL 23.0 185817|envelope_protein|AGW23590.1|Dengue_virus_4|11070 -3065 ISMKFLWPL 0.0 None None 0 None -3066 WPLRVLSQF 0.0510061316391 WPLRVLSQF WMIRILIGF 25.0 185817|envelope_protein|AGW23590.1|Dengue_virus_4|11070 -3067 REIVWEQGL 0.270327477112 VWEQG LWENG 23.0 36717|nonstructural_protein_4B|YP_001527886.1|West_Nile_virus_NY-99|10000971 -3068 TLAEKRPFM 0.000817554998277 TLAEKRPFM TLARGFPFV 22.0 64727|polyprotein_precursor|NP_041724.2|West_Nile_virus|11082 -3069 LPGHLSRAL 0.0 None None 0 None -3070 SLPGHLSRA 0.0 None None 0 None -3071 SPSSLPGHL 0.031617248785 SPSSLPGH TPDSTPCH 23.0 53041|phosphorylated_matrix_protein_(pp65)|AAA45996.1|Human_betaherpesvirus_5|10359 -3072 ALNNMFCQL 0.0 None None 0 None -3073 GPRRGSSPQ 0.0 None None 0 None -3074 SPQGAAGAA 0.0 None None 0 None -3075 KAFSQSAYL 0.0 None None 0 None -3076 FADHTVVTI 0.0 None None 0 None -3077 FADHTVVTI 0.0 None None 0 None -3078 MTAFADHTV 0.0 None None 0 None -3079 TAFADHTVV 0.0 None None 0 None -3080 GLSPRTSRH 0.140261315451 LSPRTSRH LKPGESRH 25.0 17278|Genome_polyprotein|P06441.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 -3081 LSPRTSRHI 1.36025830505 LSPRTSRH LKPGESRH 25.0 17278|Genome_polyprotein|P06441.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 -3082 RTSRHILER 0.0 None None 0 None -3083 SVQACGWRK 2.18470381235 QACGW EGCGW 28.0 75435|largest_ORF|AAB02128.1|Hepatitis_C_virus|11103 -3084 CLLSPSYYH 0.0 None None 0 None -3085 LASDRFNHI 0.0 None None 0 None -3086 QVASSPAGK 0.0 None None 0 None -3087 VASSPAGKL 0.0 None None 0 None -3088 IEYDTFGEV 0.322101512698 IEYDTF VQYDNF 24.0 32738|Liver_stage_antigen|Q25893|Plasmodium_falciparum|5833 -3089 APSSVALSL 0.0 None None 0 None -3090 NTAPSSVAL 0.0 None None 0 None -3091 EMKRHKVHI 0.0 None None 0 None -3092 ELLDYIRAV 2.20361791879 LLDYIR LLDFVR 25.0 11804|EBNA3C_latent_protein|CAD53421.1|Human_gammaherpesvirus_4|10376 -3093 PQIPPYSTF 0.0 None None 0 None -3094 ISHLHRESV 0.0 None None 0 None -3095 NLLSPDNMV 0.0 None None 0 None -3096 FASDHFLYA 0.0 None None 0 None -3097 FASDHFLYA 0.0 None None 0 None -3098 ATYVRILQR 0.0 None None 0 None -3099 FVVITATYV 0.101628132237 VITATYV VVTSTWV 24.0 14902|Genome_polyprotein|P26664.3|Hepatitis_C_virus_subtype_1a|31646 -3100 LASSSLDIV 0.0 None None 0 None -3101 FAYTILQSV 0.0 None None 0 None -3102 TILQSVPNK 0.0 None None 0 None -3103 FTLFFMAEY 0.0 None None 0 None -3104 FTLFFMAEY 0.0 None None 0 None -3105 YAAGPFTLF 0.0 None None 0 None -3106 YAAGPFTLF 0.0 None None 0 None -3107 YAAGPFTLF 0.0 None None 0 None -3108 ICSEATAAI 0.0 None None 0 None -3109 SLFNALRGK 0.437129462585 SLFNAL SLFNAV 25.0 180168|gag_protein|ABO14878.1|Human_immunodeficiency_virus_1|11676 -3110 VAIMGSTQV 0.11629553368 VAIMGST LAVMGSS 24.0 102376|Genome_polyprotein|P27958.3|Hepatitis_C_virus_subtype_1a|31646 -3111 SAYVALSNK 0.0 None None 0 None -3112 YAISARSDL 0.0 None None 0 None -3113 ATKTLRNYK 0.0 None None 0 None -3114 DVFFATKTL 0.0 None None 0 None -3115 FATKTLRNY 0.0 None None 0 None -3116 FATKTLRNY 0.0 None None 0 None -3117 FLSWCRRVV 0.0 None None 0 None -3118 LSWCRRVVL 0.0 None None 0 None -3119 RVVLELSPK 0.0 None None 0 None -3120 VVLELSPKV 0.0 None None 0 None -3121 IAIAIGAVL 0.00435035310079 IAIAIGAVL VAVAGAAIL 21.0 142231|Lipoprotein_lpqH_precursor|P0A5J0.1|Mycobacterium_tuberculosis|1773 -3122 IAIGAVLLV 0.0 None None 0 None -3123 RGMQCAICK 8.37647204165 MQCAICK LQCVQCK 27.0 148177|early_protein|CAA52585.1|Human_papillomavirus_type_52|10618 -3124 FSNADVNRL 0.0 None None 0 None -3125 MLLKPSERR 0.0 None None 0 None -3126 QLAWVPSPY 0.921133809074 AWVPS AWVPT 27.0 79628|E1_protein|BAA19893.1|Rubella_virus|11041 -3127 QLAWVPSPY 2.65839483138 AWVPS AWVPT 27.0 79628|E1_protein|BAA19893.1|Rubella_virus|11041 -3128 SSSEYMHHK 0.0 None None 0 None -3129 HIASEEPAK 0.0 None None 0 None -3130 STGFPHMLF 0.0246332875568 TGFPHML AGFYHIL 22.0 1516|Nucleoprotein|P03418.1|Human_respiratory_syncytial_virus_A2|11259 -3131 YFSTGFPHM 0.0 None None 0 None -3132 LVYMMERGK 0.0 None None 0 None -3133 VATPGRLVY 0.0 None None 0 None -3134 LLIPVAAVY 0.0 None None 0 None -3135 SAPLMELLY 0.0 None None 0 None -3136 LAMEDTGEY 0.0 None None 0 None -3137 MYLHFSDTY 0.0 None None 0 None -3138 SVSLMYLHF 1.11847247997 SLMYLH SLMYFH 28.0 180579|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -3139 RLSISQWYR 0.0 None None 0 None -3140 SQWYRVMVK 0.0 None None 0 None -3141 STWIGNKLY 0.0 None None 0 None -3142 YMYVCTPLL 0.0 None None 0 None -3143 HQRIHTGEK 0.0 None None 0 None -3144 ALGLAQGTF 0.0191045931234 GLAQGTF GLSPGTL 21.0 21638|protein_F|ABV46152.2|Hepatitis_C_virus_(isolate_Japanese)|11116 -3145 GLAQGTFVF 0.00860509404551 GLAQGTF GLSPGTL 21.0 21638|protein_F|ABV46152.2|Hepatitis_C_virus_(isolate_Japanese)|11116 -3146 GTFVFIAHF 0.0 None None 0 None -3147 KLHQVFHSI 0.149224855724 KLHQVFHSI KLHLYSHPI 23.0 190568|polymerase|AAD16253.1|Hepatitis_B_virus|10407 -3148 VTVPEKLSF 0.0 None None 0 None -3149 HPCSQPVWL 0.0 None None 0 None -3150 FPLVRSCQM 1.72844236932 LVRSCQM LIRACML 24.0 36676|polyprotein|BAA09073.1|Hepatitis_C_virus_subtype_1b|31647 -3151 MMCRDLPGF 0.631203555857 RDLPGF RELPRF 22.0 53201|Fusion_glycoprotein_F0_precursor|P03420.1|Human_respiratory_syncytial_virus_A2|11259 -3152 RVKATIVAM 0.0 None None 0 None -3153 AQGEPLGAL 0.0 None None 0 None -3154 FQVPDLHIL 0.0 None None 0 None -3155 GMQARSVEM 0.0 None None 0 None -3156 MLHLYPGPM 0.369680851064 MLHLYPGPM LFQLYRGPL 26.0 38724|Genome_polyprotein|P08617.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 -3157 SPYSEELPL 0.0 None None 0 None -3158 YAQEGFLPH 0.408477408363 QEGFLP DEGLLP 22.0 140541|hypothetical_protein|NP_218210.1|Mycobacterium_tuberculosis_H37Rv|83332 -3159 HLLFRVIPY 0.0 None None 0 None -3160 RVIPYDQSF 0.0474258731776 IPYDQS LPFDKS 23.0 116123|nucleocapsid_protein|ABP49342.1|Influenza_A_virus_(A/California/10/1978(H1N1))|425557 -3161 SIGSSATLY 0.0 None None 0 None -3162 VQKQDNSTY 0.0 None None 0 None -3163 AQVGFTLPL 0.182777813767 GFTLPL AFTMPL 24.0 179898|cell_surface_protein_(associated_with_virulence)|NP_302372.1|Mycobacterium_leprae_TN|272631 -3164 LPTPPPPPL 2.24573975693 LPTPPPPP VPTDPNPP 31.0 70491|envelope_glycoprotein|AAC28452.1|Human_immunodeficiency_virus_1|11676 -3165 YSCAGGRLF 0.0 None None 0 None -3166 FQLDVASVI 0.0 None None 0 None -3167 LDVASVIPF 0.0 None None 0 None -3168 SVIPFDICY 1.51567816772e-05 SVIPFDIC GAIPPLVC 15.0 73059|kaposin|AAC57155.1|Human_gammaherpesvirus_8|37296 -3169 RLPNLHPSF 0.0 None None 0 None -3170 LMVAVARSA 0.0 None None 0 None -3171 TQHTSFQGY 0.0 None None 0 None -3172 EQRCSLQAF 0.0 None None 0 None -3173 KSKEREHSF 0.0 None None 0 None -3174 NIDLAREAY 0.0 None None 0 None -3175 IMSFLLSSL 0.0 None None 0 None -3176 SEKEASLLY 0.0 None None 0 None -3177 YLKEHASSL 0.0 None None 0 None -3178 LVLSGSSSL 0.0 None None 0 None -3179 FWRSSCSLF 0.403383339884 FWRSSCSL LWHYPCTL 22.0 54824|polyprotein_precursor|BAA01583.1|Hepatitis_C_virus|11103 -3180 QLADQCLTM 0.0 None None 0 None -3181 LPIKDGNTL 0.0 None None 0 None -3182 LLVDRKDAM 0.0 None None 0 None -3183 TPAIRHIML 0.848547717842 TPAIRH TPMLRH 26.0 186002|polyprotein|AGO67248.1|Dengue_virus_2|11060 -3184 MQIHMGLAL 0.0 None None 0 None -3185 ALARSSDAF 0.0 None None 0 None -3186 HQGGATRVY 1.65671617909 HQGGATRVY HDGAGKRVY 29.0 23620|Genome_polyprotein|SRC279960|Hepatitis_C_virus_genotype_1|41856 -3187 FPNAGKSSF 0.0890723848157 PNAGKS PGAGKT 23.0 180503|polyprotein|AGO67248.1|Dengue_virus_2|11060 -3188 ILQEHIGAM 0.0 None None 0 None -3189 SASAGLAAM 0.0 None None 0 None -3190 HPCVPQALV 0.0 None None 0 None -3191 ATIMETLTM 0.0 None None 0 None -3192 PSDINVSSY 0.0 None None 0 None -3193 VSSYNIYWY 9.48140414761 VSSYNIYWY ISEYRHYCY 23.0 28484|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 -3194 ESSEHEGTY 0.0 None None 0 None -3195 QAWQPTASF 31.7524708941 AWQPTA AWVPTA 29.0 79628|E1_protein|BAA19893.1|Rubella_virus|11041 -3196 FLNDRLANY 0.0 None None 0 None -3197 LQIMAGRHG 0.165211067364 MAGRHG VAGSHG 24.0 154196|tegument_protein|CAB06735.1|Human_alphaherpesvirus_2|10310 -3198 WLFPTGGSV 0.427013920926 LFPTGGSV LFPGGGQI 30.0 181035|||| -3199 LMYLQKLWM 0.0 None None 0 None -3200 SIQSPFEGF 0.0 None None 0 None -3201 LALLVSTAF 0.0 None None 0 None -3202 GLIATQLLF 0.0 None None 0 None -3203 LIATQLLFY 0.0 None None 0 None -3204 LIATQLLFY 0.0 None None 0 None -3205 AVRPTFGVL 0.0 None None 0 None -3206 AMRFHFHSM 0.0102154040423 AMRFHFHSM SARLHRHAL 21.0 28508|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 -3207 MTSGLAMRF 0.0 None None 0 None -3208 FPTTTFMCL 0.0 None None 0 None -3209 ISLFPTTTF 0.0 None None 0 None -3210 SLFPTTTFM 0.0 None None 0 None -3211 SMRSSSISG 0.0 None None 0 None -3212 VQHITGPVW 0.0 None None 0 None -3213 ASDSQEALF 0.00578652736162 SDSQEALF TDNQLAVF 21.0 52496|polyprotein_precursor|NP_041724.2|West_Nile_virus|11082 -3214 FSDISEMRT 0.0 None None 0 None -3215 TLAELLGPY 0.00117570333351 TLAELLGP TIASPKGP 19.0 23883|HCV-1|AAA45676.1|Hepatitis_C_virus_subtype_1a|31646 -3216 LVNPWGEVL 1.04441668544 VNPWGE VDPWVE 25.0 143690|Genome_polyprotein|P06441.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 -3217 LPVVLQLKL 0.0 None None 0 None -3218 AQADQVDPL 0.0 None None 0 None -3219 FCDTAPVLK 0.0 None None 0 None -3220 RLHSPMYFF 0.0 None None 0 None -3221 TMCMYFRPL 0.0 None None 0 None -3222 FLVFPFTSI 0.0 None None 0 None -3223 LMADMYLLL 0.0 None None 0 None -3224 HSHLLSHSY 2.5848832505 HLLSHS HLYSHP 23.0 190568|polymerase|AAD16253.1|Hepatitis_B_virus|10407 -3225 HSHLLSHSY 0.156318463122 HLLSHS HLYSHP 23.0 190568|polymerase|AAD16253.1|Hepatitis_B_virus|10407 -3226 TQYLVFCGM 0.0 None None 0 None -3227 YLVFCGMGL 0.0 None None 0 None -3228 LIFMYLCPA 0.0 None None 0 None -3229 VAICHPLHY 0.0 None None 0 None -3230 VLVQSLMVL 0.0 None None 0 None -3231 QAQNQSITY 0.0 None None 0 None -3232 TILTFCLSY 0.00326623801259 TILTFCLSY TIMAAILAY 20.0 150224|polyprotein|AGO67248.1|Dengue_virus_2|11060 -3233 CSIQDDLPF 0.0 None None 0 None -3234 RMSRALWTL 0.0 None None 0 None -3235 KQGWCYLVY 0.0 None None 0 None -3236 YLVYVLLPL 186.049439044 YLVYVLLPL YIIFVYIPL 31.0 110744|E5_protein|AAD24036.1|Human_papillomavirus_type_16|333760 -3237 TINSAGDLF 0.0 None None 0 None -3238 FPLDEVHAK 1.3376067584 FPLDEVHA YPLHEQHG 24.0 75356|EBNA3A_nuclear_protein|Q8AZJ8|Human_gammaherpesvirus_4|10376 -3239 LTLPPLATY 0.587666896977 LTLPPLA LTIPPTA 28.0 184643|polyprotein|AGW24534.1|Dengue_virus_2|11060 -3240 PPAPPSLSL 0.0 None None 0 None -3241 MQRASRHSQ 0.0 None None 0 None -3242 QQSQSSGPG 0.0 None None 0 None -3243 MLGDPSADY 0.0 None None 0 None -3244 SADYINANY 0.0 None None 0 None -3245 GVHKGRKPF 0.0 None None 0 None -3246 ALACFARAF 0.0 None None 0 None -3247 LTGDCCFDY 0.0 None None 0 None -3248 YPKPQVSFL 0.0 None None 0 None -3249 HPLGSLQIF 0.0 None None 0 None -3250 AVGGMIASF 0.0144532044338 GMIASF GVIAAF 22.0 98085|trans-sialidase,_putative|EAN82636.1|Trypanosoma_cruzi|5693 -3251 PTEQSLTEY 0.0 None None 0 None -3252 LLMGFSLTL 0.0 None None 0 None -3253 TQGMQCSSL 0.0365911287855 TQGMQCS TRGERCN 21.0 170063|polyprotein|ABU97067.1|Hepatitis_C_virus_subtype_1b|31647 -3254 LLNLVVTSL 0.0 None None 0 None -3255 YVKIYLLPY 0.0 None None 0 None -3256 YVKIYLLPY 0.0 None None 0 None -3257 ISVFSGSEM 0.0 None None 0 None -3258 LLDEDISVF 0.0 None None 0 None -3259 STVELVPIF 0.0 None None 0 None -3260 KSADFEGLY 0.0 None None 0 None -3261 CLFSLYTAY 0.0 None None 0 None -3262 SLYTAYHVF 0.0160929247029 SLYTAYHV KLYCSYEV 22.0 32250|FL-160-2_protein_-_Trypanosoma_cruzi|JH0823|Trypanosoma_cruzi|5693 -3263 SSHLHSDHY 0.0 None None 0 None -3264 RQKHGEAPI 0.0 None None 0 None -3265 RQDVGTYTF 0.0 None None 0 None -3266 VERQDVGTY 0.0 None None 0 None -3267 HSNSTSFIF 0.0 None None 0 None -3268 NAHSNSTSF 0.0 None None 0 None -3269 ATTESDQSF 0.0 None None 0 None -3270 FPSETKVII 0.0 None None 0 None -3271 HQVASSPGH 0.0 None None 0 None -3272 SQGGPRGTF 0.0 None None 0 None -3273 GGAPHFGHF 0.0 None None 0 None -3274 GAIALIRRY 0.0 None None 0 None -3275 DTTRYVTSK 0.0 None None 0 None -3276 EPSESDTTR 0.0 None None 0 None -3277 PSESDTTRY 0.0 None None 0 None -3278 TRYVTSKIL 0.0 None None 0 None -3279 TTRYVTSKI 0.0 None None 0 None -3280 TSCSCQSSR 0.0 None None 0 None -3281 TGDSEAAPV 0.046686577341 TGDSEAAP TGNPRTAP 22.0 154346|RL2|CAB06760.1|Human_alphaherpesvirus_2|10310 -3282 LSMEETLLL 0.0 None None 0 None -3283 WWNPALWKR 10.2327872852 PALWKR PTLWAR 26.0 149027|NS5_protein|BAA00702.1|Hepatitis_C_virus_(isolate_H77)|63746 -3284 LFQDNSSQL 0.0 None None 0 None -3285 LTPPQAQEL 0.429161842612 LTPPQAQEL LTDPNPQEV 25.0 69799|envelope_glycoprotein|BAE96221.1|Human_immunodeficiency_virus_1|11676 -3286 LTPQQAQEL 0.0 None None 0 None -3287 QAQALGIPL 0.0 None None 0 None -3288 ASRPDRLSL 0.0 None None 0 None -3289 EAQGQEASR 0.0 None None 0 None -3290 WVEPQNPVL 0.000730033295762 VEPQNPVL VSPFIPLL 17.0 58740|Major_surface_antigen_precursor|P03142.4|Hepatitis_B_virus|10407 -3291 HLPHLTHTL 0.0 None None 0 None -3292 HTLATSCRR 0.0 None None 0 None -3293 ITSFDNLFR 0.0 None None 0 None -3294 SHFHKTHEV 0.0 None None 0 None -3295 YKLVVVGAV 12.5817515538 KLVVVG KLVVLG 24.0 32238|polyprotein_[Hepatitis_C_virus_subtype_1a]|ABV46251.2|Hepatitis_C_virus_(isolate_H77)|63746 -3296 FHRRLSSSL 0.0 None None 0 None -3297 FHRRLSSSL 0.0 None None 0 None -3298 FSRRSFHRR 0.0 None None 0 None -3299 RSDVWNLGI 0.0 None None 0 None -3300 VYILILPSF 0.0 None None 0 None -3301 STTIPILTL 0.0 None None 0 None -3302 TIPILTLSL 0.0 None None 0 None -3303 LSHISHLEL 0.0 None None 0 None -3304 SHLELVESL 0.0 None None 0 None -3305 SAEVRIEPM 0.108897660016 EVRIEP QVRIKP 23.0 71266|Circumsporozoite_protein_precursor|P02893.1|Plasmodium_falciparum|5833 -3306 QSHLLIHQR 0.0 None None 0 None -3307 QVITLRKSL 0.0 None None 0 None -3308 TKKQVITLR 0.0 None None 0 None -3309 MFDASKANF 0.0 None None 0 None -3310 FLDWLRTMT 0.0 None None 0 None -3311 VDWFLDWLR 11.20129968 VDWFLDWLR ISWCLWWLQ 28.0 39591|polyprotein|AAA45677.1|Hepatitis_C_virus_(isolate_H77)|63746 -3312 WFLDWLRTM 0.137841959387 WFLDWLR WCLWWLQ 25.0 39591|polyprotein|AAA45677.1|Hepatitis_C_virus_(isolate_H77)|63746 -3313 WLRTMTNVL 0.0 None None 0 None -3314 KFLQEEPQL 0.0 None None 0 None -3315 DVFRFSPYR 0.0 None None 0 None -3316 RFSPYRGLL 0.10447761194 FSPYRGLL IAPYAGLI 26.0 25388|matrix_protein|ABP96803.1|Human_metapneumovirus|162145 -3317 DSTRPPGTR 1.52773900302 PPGTR PPGSR 26.0 136890|polyprotein|AGO67248.1|Dengue_virus_2|11060 -3318 YLGVPVFYA 0.385348721615 YLGVPVF YYGVPVW 28.0 118|envelope_glycoprotein|ABS76372.1|Human_immunodeficiency_virus_1|11676 -3319 AIHIVAEKK 0.0 None None 0 None -3320 TQFELQRNK 0.0 None None 0 None -3321 VRGTDWHLK 0.0074144902417 VRGTDWH TRGRDAH 21.0 66798|glycoprotein_gp35/37|AAC59622.1|Human_gammaherpesvirus_8|37296 -3322 GFHPDPEAL 0.149003652528 GFHPD GFFPD 24.0 190466|large_surface_antigen|CAL29876.1|Hepatitis_B_virus|10407 -3323 HIRTDTYVK 0.0 None None 0 None -3324 SRWQVHGIV 0.0 None None 0 None -3325 VPACSRAHV 0.0 None None 0 None -3326 VPACSYAHV 0.0 None None 0 None -3327 MLFFRTRYI 0.0602884044705 MLFFRTRYI VLFYLGQYI 22.0 156550|E3_ubiquitin-protein_ligase_Mdm2|Q00987.1|Homo_sapiens|9606 -3328 TRYICTTVF 0.0 None None 0 None -3329 YICTTVFYT 0.0 None None 0 None -3330 AALVPTQAM 0.0 None None 0 None -3331 MPGSPRDPV 0.0 None None 0 None -3332 RRGSGHSEY 1.07898059992 GSGHSE GPGHEE 24.0 180488|polyprotein|AGO67248.1|Dengue_virus_2|11060 -3333 RICGHIFCY 2.42597295458e-05 ICGHIFC LCLIISC 15.0 93431|pre-C/C_protein|ABY54138.1|Hepatitis_B_virus|10407 -3334 GIAPLNQWV 0.842769418953 IAPLNQW LTPLRDW 24.0 36062|polyprotein|AAB67037.1|Hepatitis_C_virus_(isolate_H77)|63746 -3335 KIIATCFAV 0.0 None None 0 None -3336 KMNEPKCLK 0.0 None None 0 None -3337 SFVPWNSYV 1.65978825128 VPWNSYV LPWYSYL 29.0 143728|Genome_polyprotein|P08617.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 -3338 VPWNSYVRL 0.33737000325 VPWNSYV LPWYSYL 29.0 143728|Genome_polyprotein|P08617.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 -3339 YQLKLFACM 0.000135204617912 YQLKLFAC YRLWHYPC 17.0 75636|polyprotein|AAB67037.1|Hepatitis_C_virus_(isolate_H77)|63746 -3340 YQLKLFACM 0.000103789830269 YQLKLFAC YRLWHYPC 17.0 75636|polyprotein|AAB67037.1|Hepatitis_C_virus_(isolate_H77)|63746 -3341 RGRGGSVSI 0.0 None None 0 None -3342 IPHTAILVT 0.0 None None 0 None -3343 SIPHTAILV 0.0 None None 0 None -3344 GLSDLELRL 0.0 None None 0 None -3345 VLLRCPNKL 0.0 None None 0 None -3346 TRLAFGLFA 0.0 None None 0 None -3347 ILIACRLNK 3.55199159767 ILIACRL VLIRCYL 21.0 145860|Protein_E6|P04019.1|Human_papillomavirus_type_11|10580 -3348 LIACRLNKK 0.0 None None 0 None -3349 RLNKKKGAY 0.0 None None 0 None -3350 TLAHEASPL 0.0 None None 0 None -3351 SAWWSFGSL 0.872449058702 WSFGSL WDFGSL 31.0 180726|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -3352 NPEAMCSDL 55.4534482749 NPEAMC NPYAVC 25.0 110401|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 -3353 AMHPLFRKL 0.0 None None 0 None -3354 CRAMHPLFR 0.0 None None 0 None -3355 GPCRAMHPL 0.0 None None 0 None -3356 RAMHPLFRK 0.0 None None 0 None -3357 GYIHYVFYL 8.67210597487 GYIHYV GYLQYV 26.0 42094|telomer_length_regulation_protein_TEL1|EDV12172.1|Saccharomyces_cerevisiae|4932 -3358 GYIHYVFYL 0.750508588568 GYIHYV GYLQYV 26.0 42094|telomer_length_regulation_protein_TEL1|EDV12172.1|Saccharomyces_cerevisiae|4932 -3359 KGYIHYVFY 78.5423095416 GYIHYV GYLQYV 26.0 42094|telomer_length_regulation_protein_TEL1|EDV12172.1|Saccharomyces_cerevisiae|4932 -3360 YLGNGPNVI 0.0 None None 0 None -3361 SLSNKEVKK 0.0 None None 0 None -3362 GPRAINNFF 0.0 None None 0 None -3363 FRFSSQEAA 0.0 None None 0 None -3364 LLPPQDPHL 0.366181412717 LLPPQDPHL LLPRRGPRL 24.0 23224|polyprotein|BAB18806.1|Hepatitis_C_virus|11103 -3365 PPQDPHLPL 0.0 None None 0 None -3366 HVDPGTIGV 7.61077451306e-06 HVDPGTIG HISCLTFG 15.0 190443|core_protein|BAF42671.1|Hepatitis_B_virus|10407 -3367 GLMGAVNVA 0.0 None None 0 None -3368 LMGAVNVAK 0.0 None None 0 None -3369 PRMAIPWPR 0.0 None None 0 None -3370 WPRDVRKLV 0.0 None None 0 None -3371 KYYEALPEL 0.0 None None 0 None -3372 HYYHNVHAV 0.0 None None 0 None -3373 MVEHYYHNV 0.0 None None 0 None -3374 YHNVHAVVF 0.0 None None 0 None -3375 YYHNVHAVV 0.0 None None 0 None -3376 ARVWKFGPK 0.0 None None 0 None -3377 RVWKFGPKL 0.0 None None 0 None -3378 RVWKFGPKL 0.0 None None 0 None -3379 VLDKARVWK 0.180063784265 VLDKARVW VLDSFKTW 25.0 69435|Genome_polyprotein|SRC279960|Hepatitis_C_virus_(isolate_H77)|63746 -3380 CYEEYRGRL 0.0377885551771 CYEEYRGRL VYQDWLGRM 24.0 23288|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 -3381 GRYEEYRGH 0.0 None None 0 None -3382 APRGACYRA 0.0 None None 0 None -3383 YRADHDLGR 0.0 None None 0 None -3384 SYVCVVRNY 0.0 None None 0 None -3385 ARPFFFFLL 0.0529432793239 PFFFFLL PFVVFLV 22.0 148397|Dense_granule_protein_3|B6KEU8.2|Toxoplasma_gondii|5811 -3386 FFFFLLDKV 0.0 None None 0 None -3387 FFFLLDKVL 0.876549817799 FLLDKVL FLLTKIL 25.0 16753|Pre-S/S_protein|AAR99337.1|Hepatitis_B_virus|10407 -3388 FLLDKVLAS 2.38412935701 FLLDKVLA FLLTKILT 25.0 16753|Pre-S/S_protein|AAR99337.1|Hepatitis_B_virus|10407 -3389 HARPFFFFL 0.0 None None 0 None -3390 APSWRGLAE 0.00488637433335 APSWRGLA GPSLIGLA 20.0 21780|Antigen_85-B_precursor_(85B)_(Extracellular_alpha-antigen)_(Antigen_85_complex_B)_(Ag85B)_(Mycolyl_transferase_85B)_(Fibronectin-binding_protein_B)_(30_kDa_extracellular_protein)|P31952|Mycobacterium_tuberculosis|1773 -3391 LRLALMKKK 0.0 None None 0 None -3392 WLRLALMKK 0.0 None None 0 None -3393 VLIQQLEKV 0.0 None None 0 None -3394 YPGQVNRTA 0.441659094862 PGQVNRTA PGEINRVA 33.0 59153|Genome_polyprotein|P27958.3|Hepatitis_C_virus_subtype_1a|31646 -3395 MADVAMYGV 0.0 None None 0 None -3396 GLYYAEFGA 0.0 None None 0 None -3397 SVLAGLYYA 5.40222207826 LAGLYY LAGLFY 28.0 23270|polyprotein|AAB67036.1|Hepatitis_C_virus_(isolate_H77)|63746 -3398 TMWRREESL 0.0 None None 0 None -3399 CLWQLKAPV 0.0117840685959 CLWQLKAPV SLWKDGAPL 22.0 140600|glutamine_synthetase_GLNA1_(glutamine_synthase)_(GS-I)|NP_216736.1|Mycobacterium_tuberculosis_H37Rv|83332 -3400 RPRKAWAWC 5.41074531829 RPRKAW RPASAW 26.0 150534|polyprotein|AGO67248.1|Dengue_virus_2|11060 -3401 QRLKREEEK 2.19826332471 KREEEK RREEEE 23.0 185491|polyprotein|AGO67248.1|Dengue_virus_2|11060 -3402 VYHMSQSPL 0.0 None None 0 None -3403 FTMLLSLLA 0.0 None None 0 None -3404 GLAGFTMLL 0.186461334924 GFTML GFTMM 24.0 180818|Membrane_glycoprotein_precursor|NP_739582.2|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -3405 MLLSLLAFA 0.0 None None 0 None -3406 KVHQLAITV 0.0 None None 0 None -3407 LPKSSEKAI 0.0 None None 0 None -3408 STQEPTAYV 1.33414347629 QEPTAYV QNPTTYI 27.0 135263|hemagglutinin|ACX31970.1|Influenza_A_virus_(A/Bar-headed_Goose/Qinghai/61/05(H5N1))|336238 -3409 ARMRKHIKR 0.0 None None 0 None -3410 GPARMRKHI 0.0 None None 0 None -3411 RMRKHIKRL 0.0 None None 0 None -3412 HVGKASSSM 0.0 None None 0 None -3413 QQMEAHVGK 0.0 None None 0 None -3414 VILLPQPPK 0.0 None None 0 None -3415 YLGVPVFYA 0.385348721615 YLGVPVF YYGVPVW 28.0 118|envelope_glycoprotein|ABS76372.1|Human_immunodeficiency_virus_1|11676 -3416 AIHIVAEKK 0.0 None None 0 None -3417 IVGHTGSGK 0.972587226103 HTGSGK HPGSGK 28.0 183598|polyprotein|AGW21594.1|Dengue_virus_1|11053 -3418 LPAPPGAPP 28.8454969512 LPAPPGA WPAPPGA 35.0 72928|Genome_polyprotein|P26662.3|Hepatitis_C_virus_(isolate_Japanese)|11116 -3419 VRGTDWHLK 0.0074144902417 VRGTDWH TRGRDAH 21.0 66798|glycoprotein_gp35/37|AAC59622.1|Human_gammaherpesvirus_8|37296 -3420 RRHHSPSQR 0.689680730869 HHSPS HHAPS 28.0 21000|glutamine_synthetase_GLNA1_(glutamine_synthase)_(GS-I)|NP_216736.1|Mycobacterium_tuberculosis|1773 -3421 WLQQENHEL 0.0 None None 0 None -3422 SLQPIHHDL 0.0 None None 0 None -3423 VPACSRAHV 0.0 None None 0 None -3424 VPACSYAHV 0.0 None None 0 None -3425 LLLSPPVEV 0.0 None None 0 None -3426 LLSPPVEVK 0.0 None None 0 None -3427 RPEPPETGV 1.40283044682 PEPPET PNPPEV 26.0 70491|envelope_glycoprotein|AAC28452.1|Human_immunodeficiency_virus_1|11676 -3428 RRGSGHSEY 1.07898059992 GSGHSE GPGHEE 24.0 180488|polyprotein|AGO67248.1|Dengue_virus_2|11060 -3429 GLLQRPVHL 0.0 None None 0 None -3430 HLALGRLSR 0.0 None None 0 None -3431 KIIATCFAV 0.0 None None 0 None -3432 SFVPWNSYV 1.65978825128 VPWNSYV LPWYSYL 29.0 143728|Genome_polyprotein|P08617.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 -3433 VPWNSYVRL 0.33737000325 VPWNSYV LPWYSYL 29.0 143728|Genome_polyprotein|P08617.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 -3434 YQLKLFACM 0.000135204617912 YQLKLFAC YRLWHYPC 17.0 75636|polyprotein|AAB67037.1|Hepatitis_C_virus_(isolate_H77)|63746 -3435 YQLKLFACM 0.000103789830269 YQLKLFAC YRLWHYPC 17.0 75636|polyprotein|AAB67037.1|Hepatitis_C_virus_(isolate_H77)|63746 -3436 IPHTAILVT 0.0 None None 0 None -3437 SIPHTAILV 0.0 None None 0 None -3438 SVSSCCQPV 1.40654417103 SSCCQP SECCTP 28.0 57361|Genome_polyprotein|SRC279960|Hepatitis_C_virus_(isolate_H77)|63746 -3439 WLLEWTEAA 0.223150379312 WLLEW WAIKW 24.0 72233|Genome_polyprotein|P27958.3|Hepatitis_C_virus_subtype_1a|31646 -3440 GLSDLELRL 0.0 None None 0 None -3441 VLLRCPNKL 0.0 None None 0 None -3442 TLAHEASPL 0.0 None None 0 None -3443 ILPATILVL 0.0979841141813 ILPATI MLPATL 23.0 180662|polyprotein|CDF77361.1|Dengue_virus_3|11069 -3444 TILPATILV 0.126010530119 ILPATI MLPATL 23.0 180662|polyprotein|CDF77361.1|Dengue_virus_3|11069 -3445 SAWWSFGSL 0.872449058702 WSFGSL WDFGSL 31.0 180726|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -3446 NPEAMCSDL 55.4534482749 NPEAMC NPYAVC 25.0 110401|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 -3447 AMHPLFRKL 0.0 None None 0 None -3448 CRAMHPLFR 0.0 None None 0 None -3449 GPCRAMHPL 0.0 None None 0 None -3450 RAMHPLFRK 0.0 None None 0 None -3451 SLSNKEVKK 0.0 None None 0 None -3452 GPRAINNFF 0.0 None None 0 None -3453 LLPPQDPHL 0.366181412717 LLPPQDPHL LLPRRGPRL 24.0 23224|polyprotein|BAB18806.1|Hepatitis_C_virus|11103 -3454 PPQDPHLPL 0.0 None None 0 None -3455 GLMGAVNVA 0.0 None None 0 None -3456 LMGAVNVAK 0.0 None None 0 None -3457 KLPEVQLPK 6.62808883056e-05 LPEVQLPK LPSDFLPS 16.0 16836|precore/core_protein_[Hepatitis_B_virus]|AAR03815.1|Hepatitis_B_virus|10407 -3458 ARVWKFGPK 0.0 None None 0 None -3459 RVWKFGPKL 0.0 None None 0 None -3460 RVWKFGPKL 0.0 None None 0 None -3461 VLDKARVWK 0.180063784265 VLDKARVW VLDSFKTW 25.0 69435|Genome_polyprotein|SRC279960|Hepatitis_C_virus_(isolate_H77)|63746 -3462 APRGACYRA 0.0 None None 0 None -3463 YRADHDLGR 0.0 None None 0 None -3464 SYVCVVRNY 0.0 None None 0 None -3465 APSWRGLAE 0.00488637433335 APSWRGLA GPSLIGLA 20.0 21780|Antigen_85-B_precursor_(85B)_(Extracellular_alpha-antigen)_(Antigen_85_complex_B)_(Ag85B)_(Mycolyl_transferase_85B)_(Fibronectin-binding_protein_B)_(30_kDa_extracellular_protein)|P31952|Mycobacterium_tuberculosis|1773 -3466 VLIQQLEKV 0.0 None None 0 None -3467 GLYYAEFGA 0.0 None None 0 None -3468 SVLAGLYYA 5.40222207826 LAGLYY LAGLFY 28.0 23270|polyprotein|AAB67036.1|Hepatitis_C_virus_(isolate_H77)|63746 -3469 KPVNKILQI 0.0 None None 0 None -3470 CLWQLKAPV 0.0117840685959 CLWQLKAPV SLWKDGAPL 22.0 140600|glutamine_synthetase_GLNA1_(glutamine_synthase)_(GS-I)|NP_216736.1|Mycobacterium_tuberculosis_H37Rv|83332 -3471 RPRKAWAWC 5.41074531829 RPRKAW RPASAW 26.0 150534|polyprotein|AGO67248.1|Dengue_virus_2|11060 -3472 SLDTVAQAV 0.0 None None 0 None -3473 QRLKREEEK 2.19826332471 KREEEK RREEEE 23.0 185491|polyprotein|AGO67248.1|Dengue_virus_2|11060 -3474 RREQQLRRK 0.0 None None 0 None -3475 VYHMSQSPL 0.0 None None 0 None -3476 FTMLLSLLA 0.0 None None 0 None -3477 GLAGFTMLL 0.186461334924 GFTML GFTMM 24.0 180818|Membrane_glycoprotein_precursor|NP_739582.2|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -3478 MLLSLLAFA 0.0 None None 0 None -3479 KVHQLAITV 0.0 None None 0 None -3480 KIMHGPFMK 0.0 None None 0 None -3481 RPRWNTHGH 0.0 None None 0 None -3482 ARMRKHIKR 0.0 None None 0 None -3483 GPARMRKHI 0.0 None None 0 None -3484 RMRKHIKRL 0.0 None None 0 None -3485 VILLPQPPK 0.0 None None 0 None -3486 TPCHCTGTL 0.0 None None 0 None -3487 TPCHCTGTL 0.0 None None 0 None -3488 IPFFGQVHL 0.0 None None 0 None -3489 ILMENKSNI 0.0 None None 0 None -3490 ILMENKSNI 0.0 None None 0 None -3491 LAYLVKKMM 0.0 None None 0 None -3492 VTISLAYLV 0.0 None None 0 None -3493 LLIESKEEM 0.0 None None 0 None -3494 WVGPWHTIV 0.0 None None 0 None -3495 WWVGPWHTI 0.0 None None 0 None -3496 KTFCGDVEY 0.0 None None 0 None -3497 AVMEQINSV 0.0 None None 0 None -3498 AVMEQINSV 0.0 None None 0 None -3499 HPRINTLGS 0.0 None None 0 None -3500 FLVAFIKKI 0.0 None None 0 None -3501 FLVAFIKKI 0.0 None None 0 None -3502 GIVSWDTFL 52.5489168518 SWDTFL KWETFL 28.0 52666|Antigen_85-B|P0C5B9.1|Mycobacterium_tuberculosis|1773 -3503 IVSWDTFLV 0.838854359979 SWDTFL KWETFL 28.0 52666|Antigen_85-B|P0C5B9.1|Mycobacterium_tuberculosis|1773 -3504 SAKLTTLVV 0.0 None None 0 None -3505 KLIWHPFSI 0.0 None None 0 None -3506 YFDENIQKL 0.0 None None 0 None -3507 SPSSGQRST 0.0 None None 0 None -3508 SAQNELTEM 0.0 None None 0 None -3509 VATNSETAM 0.0 None None 0 None -3510 PLWGGIIYI 0.24231663041 PLWGGIIYI PLFGYPVYV 25.0 48321|||| -3511 YPLWGGIIY 0.0 None None 0 None -3512 AALATLHPL 0.0 None None 0 None -3513 AALATLHPL 0.0 None None 0 None -3514 LATLHPLFL 0.0 None None 0 None -3515 GLNMLITAL 0.0 None None 0 None -3516 LLTGLNMLI 0.0 None None 0 None -3517 LMWLTYTMA 0.662873031064 LMWLTY LMWLSY 32.0 21041|Membrane_glycoprotein|Q692E0|SARS_coronavirus_TJF|284672 -3518 LTYTMAFMV 0.0585597533649 YTMAFM YTSAFV 22.0 76621|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 -3519 LTYTMAFMV 0.00186523658866 YTMAFM YTSAFV 22.0 76621|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 -3520 MLITALYSL 6.89989591232e-08 LYSL VYAF 9.0 142232|POSSIBLE_CONSERVED_TRANSMEMBRANE_PROTEIN|CAB00937.1|Mycobacterium_tuberculosis|1773 -3521 NLMWLTYTM 2.28006257564 NLMWLTY GLMWLSY 32.0 21041|Membrane_glycoprotein|Q692E0|SARS_coronavirus_TJF|284672 -3522 WLTYTMAFM 0.00930680861548 YTMAFM YTSAFV 22.0 76621|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 -3523 SANTGSSVV 0.0 None None 0 None -3524 AMGSGIQPL 0.0 None None 0 None -3525 HLLEPGQAM 0.0 None None 0 None -3526 TVVGNLGII 0.0 None None 0 None -3527 HGKPTLSTV 0.0 None None 0 None -3528 LEYNTRNAY 0.0 None None 0 None -3529 LLGLTWPVV 2.39337746242 WPVV WPVL 23.0 38427|BZLF1|AAA66529.1|Human_gammaherpesvirus_4|10376 -3530 QLLGLTWPV 0.0 None None 0 None -3531 RVLFWGHIL 0.0 None None 0 None -3532 RVLFWGHIL 0.0 None None 0 None -3533 KVFNNGADL 0.0 None None 0 None -3534 LAGEWRERL 0.0 None None 0 None -3535 MNWRPILTI 0.0 None None 0 None -3536 FSDLRSSIV 0.0 None None 0 None -3537 FSDLRSSIV 0.0 None None 0 None -3538 YFSDLRSSI 0.0 None None 0 None -3539 EANFSASRV 0.0 None None 0 None -3540 TLEGFFESL 0.0 None None 0 None -3541 KILKAQEHV 0.0 None None 0 None -3542 LLQPTPPAA 0.242418891606 PTPPAA PAPPGA 25.0 72928|Genome_polyprotein|P26662.3|Hepatitis_C_virus_(isolate_Japanese)|11116 -3543 SLQVKRVFV 0.0 None None 0 None -3544 FTLEGFFES 0.0 None None 0 None -3545 PLLRDVFNV 0.0 None None 0 None -3546 AQSEIHFQV 0.0 None None 0 None -3547 LQAHSMHEV 0.0 None None 0 None -3548 LLLQPTPPA 0.0 None None 0 None -3549 SLSFSFPLL 105.166666667 LSFSFPLL LSFALPII 26.0 39339|Nucleocapsid_protein|Q89462|Sin_Nombre_hantavirus|37705 -3550 RVWDIVPTL 137.640684863 RVWDIVPTL KPWDVVPTV 37.0 32944|polyprotein|AAW51418.1|Dengue_virus_3|11069 -3551 IVMCAMCGV 0.0 None None 0 None -3552 AMCGVPFSV 1.48904088027 AMCGVPFS SFCGSPYS 28.0 190409|polymerase|AAD16253.1|Hepatitis_B_virus|10407 -3553 RQMAARECK 0.0 None None 0 None -3554 FLVYQNILK 0.0 None None 0 None -3555 FLVYQNILK 0.0 None None 0 None -3556 KVERERLEK 0.0 None None 0 None -3557 KQIEMLEYK 0.0 None None 0 None -3558 KQIEMLEYK 0.0 None None 0 None -3559 VVGAVGVGK 0.0 None None 0 None -3560 VVGAVGVGK 0.0 None None 0 None -3561 FIDTYPPVL 0.0 None None 0 None -3562 RSAFPCAHR 0.0 None None 0 None -3563 GTPRAATMK 0.0 None None 0 None -3564 TMKAKTDLK 0.0 None None 0 None -3565 TMKAKTDLK 0.0 None None 0 None -3566 GLLFAAIKR 0.0 None None 0 None -3567 LLFAAIKRR 0.0 None None 0 None -3568 YQIDRDLHK 0.0 None None 0 None -3569 QTGEKLMAK 0.0 None None 0 None -3570 QTGEKLMAK 0.0 None None 0 None -3571 SSNLIAHVR 0.0 None None 0 None -3572 GEDVDSLAL 0.280156235348 GEDVDSLAL GEEVQVLAL 27.0 180428|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -3573 AELVYILKH 0.0 None None 0 None -3574 KVAELVYIL 0.0 None None 0 None -3575 ISMKLVLRF 0.0 None None 0 None -3576 KSPGWSFQV 0.804206027719 PGWS PGWS 28.0 141461|ubiquitin_E3_ligase_ICP0|NP_044601.1|Human_alphaherpesvirus_1|10298 -3577 SWKSPGWSF 14.9348449335 PGWS PGWS 28.0 141461|ubiquitin_E3_ligase_ICP0|NP_044601.1|Human_alphaherpesvirus_1|10298 -3578 LTVDNITFL 0.00953450829996 TVDNITFL TVELLSFL 21.0 5191|core_protein|AAL31859.1|Hepatitis_B_virus|10407 -3579 DAATRVAMV 0.0 None None 0 None -3580 DSVDAATRV 0.0 None None 0 None -3581 VGAQIYHTI 0.0 None None 0 None -3582 GELSMLVTT 0.0 None None 0 None -3583 EELQLICQA 0.0 None None 0 None -3584 SEEELQLIC 0.0 None None 0 None -3585 CELHAQAAT 0.0 None None 0 None -3586 FTLRPGEVM 0.0 None None 0 None -3587 VYMPPPRLL 0.0 None None 0 None -3588 TFKKQWFYL 0.0 None None 0 None -3589 KANRESQSL 0.0 None None 0 None -3590 AAKARDREL 0.0 None None 0 None -3591 AARLRFFST 0.0 None None 0 None -3592 AFFSLSYIF 0.0 None None 0 None -3593 AHASLIPEF 0.200665922786 HASLIP HADVIP 24.0 97093|polyprotein|AAB66324.1|Hepatitis_C_virus_(isolate_H77)|63746 -3594 AHCGLGKIL 0.0811144143937 CGLGKIL CPLSKIL 24.0 6808|membrane_protein|AAA45887.1|Human_gammaherpesvirus_4|10376 -3595 AHIERRLHI 0.0 None None 0 None -3596 AHMETMAKL 0.0 None None 0 None -3597 AHMGVFTEL 0.0 None None 0 None -3598 AHQDALMLA 0.0 None None 0 None -3599 AHRPRARLA 0.0 None None 0 None -3600 AHTSAILTV 0.0 None None 0 None -3601 AIRPKSLAI 0.0 None None 0 None -3602 ALQRRRLSL 0.0 None None 0 None -3603 ALQRRVQRL 0.0 None None 0 None -3604 AMACMSSVF 0.0 None None 0 None -3605 AMCVIHFSF 1.41247187444 MCVIHFSF MCAVHPTL 25.0 7660|polyprotein|AAA45677.1|Hepatitis_C_virus_(isolate_H77)|63746 -3606 AMYLRASSL 0.0 None None 0 None -3607 APASRHLSA 0.0 None None 0 None -3608 APRLLRSPV 0.0 None None 0 None -3609 AQKEHSHLL 0.937305079721 AQKEHSHL AERKHRHL 28.0 75408|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 -3610 ARAAQVAGI 0.0 None None 0 None -3611 ARDPSPIQI 0.0 None None 0 None -3612 ARHERIHTK 0.0 None None 0 None -3613 ARINSIYGL 0.0624279351011 ARINSI ARLNSL 23.0 418964|PPE_family_protein_PPE68|KAM81677.1|Mycobacterium_tuberculosis_H37Ra|419947 -3614 ARKPRTREC 0.0 None None 0 None -3615 ARLQHCSAL 0.0 None None 0 None -3616 ARLQHCSAL 0.0 None None 0 None -3617 ARLYRGQAL 0.0 None None 0 None -3618 ARLYRGQAL 0.0 None None 0 None -3619 ARMQSYSTI 0.0 None None 0 None -3620 ARPEKLPEL 0.72119091728 RPEKLPEL RPRKLPQL 34.0 110338|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 -3621 ARQHLLQRM 0.0 None None 0 None -3622 ARRARLQHC 0.0 None None 0 None -3623 ARRKQSEMY 0.0 None None 0 None -3624 ARTRAKQNI 0.0 None None 0 None -3625 ARVQMQVTM 0.0 None None 0 None -3626 ASFSNHQRV 0.0695350378462 ASFSNH ASYSSH 24.0 53148|Transcription_activator_BRLF1|P03209.1|Human_herpesvirus_4_strain_B95-8|10377 -3627 ATDDKMTIF 0.0 None None 0 None -3628 AVDPMRAAY 0.0 None None 0 None -3629 AVMGRSWEV 0.0 None None 0 None -3630 AYATQLFFF 0.0 None None 0 None -3631 AYEDTVRQV 0.0 None None 0 None -3632 AYFTHSLSF 0.0 None None 0 None -3633 CAFSRRRPI 0.0 None None 0 None -3634 CFPLHGLQF 0.0590811205659 CFPLHGLQ SFPDPGLR 18.0 79300|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 -3635 CGDKISDRY 1.50652597592 CGDKIS AGDKLS 23.0 244160|surface_antigen_2_(CA-2)|XP_818927.1|Trypanosoma_cruzi_strain_CL_Brener|353153 -3636 CHFSCNNGF 0.0 None None 0 None -3637 CHQDHWSQL 0.0 None None 0 None -3638 CHQRCGGRV 0.0 None None 0 None -3639 CHSNSRDHL 18.4546845763 CHSNSRDHL CYDHAQTHL 25.0 7353|Early_antigen_protein_D|P03191.1|Human_herpesvirus_4_strain_B95-8|10377 -3640 CHYEKKTDL 1.15217391304 CHYEKK CHSKKK 26.0 36504|polyprotein_precursor|BAA01582.1|Hepatitis_C_virus|11103 -3641 CLKPHQGPV 0.0 None None 0 None -3642 CLLRNSACL 0.0 None None 0 None -3643 CLPSRTSSV 0.0 None None 0 None -3644 CLRDLFFPL 0.0 None None 0 None -3645 CMKQRDEEF 0.0 None None 0 None -3646 CPPNHIVSL 0.961374972059 CPPNHIVSL CPAGHAVGI 28.0 23601|Genome_polyprotein|SRC279960|Hepatitis_C_virus_(isolate_H77)|63746 -3647 CQFGTVQLV 0.0 None None 0 None -3648 CRAETRKTF 0.443490453045 AETRKTF GESRKTF 27.0 19435|polyprotein|CDF77361.1|Dengue_virus_3|11069 -3649 CRCPIRGLV 0.0 None None 0 None -3650 CREELAVHL 0.0 None None 0 None -3651 CREQHPAQL 0.0 None None 0 None -3652 CRKMFRRSA 0.0 None None 0 None -3653 CRKMGLRVM 0.0 None None 0 None -3654 CRPQCCQSV 21.594714567 CRPQCCQSV CRVLCCYVL 28.0 11956|UL123;_IE1|AAR31448.1|Human_betaherpesvirus_5|10359 -3655 CRRGLEQLL 0.545054613977 CRRGLEQLL CRAKFKQLL 25.0 54330|BZLF1|AAA66529.1|Human_gammaherpesvirus_4|10376 -3656 CRYGRFHKF 0.0 None None 0 None -3657 CSDTHTNEL 0.00915963725351 CSDTHTNE ASDSLNNE 19.0 4371|tegument_protein_VP11/12|NP_044516.1|Human_alphaherpesvirus_2|10310 -3658 CVLYKYVPI 0.0 None None 0 None -3659 CVMTKIFSL 0.835554412193 MTKIFSL LTKRFSL 23.0 186354|polyprotein|AGO67248.1|Dengue_virus_2|11060 -3660 CYLITVTPI 0.0 None None 0 None -3661 CYLVFIGCF 0.0 None None 0 None -3662 CYNSAIQAL 0.0 None None 0 None -3663 CYSRDQIYI 0.0 None None 0 None -3664 CYVAICGPL 0.0 None None 0 None -3665 CYYYFLCLL 0.0 None None 0 None -3666 DAKRHRKVL 0.0 None None 0 None -3667 DALCRLLGL 0.0 None None 0 None -3668 DFKKKKGSM 0.0 None None 0 None -3669 DHRDLGLSV 0.0 None None 0 None -3670 DILVHHLAV 0.0 None None 0 None -3671 DLGDKILAL 0.0 None None 0 None -3672 DLHTRHGSI 0.236111111111 LHTRHG LHEQHG 26.0 75356|EBNA3A_nuclear_protein|Q8AZJ8|Human_gammaherpesvirus_4|10376 -3673 DLKMGKKPV 0.0 None None 0 None -3674 DLLGHPQAL 0.00441766560472 DLLGHP DLVGWP 22.0 9316|HCV-1|AAA45676.1|Hepatitis_C_virus_subtype_1a|31646 -3675 DLPTKRPAL 3.09221511525 PTKRP PTERP 25.0 141402|tegument_protein_VP22|NP_044651.1|Human_alphaherpesvirus_1|10298 -3676 DLQQKILCM 0.0 None None 0 None -3677 DMMKEFISM 0.0 None None 0 None -3678 DPKERIKVA 0.0 None None 0 None -3679 DPRLKWVVL 0.0 None None 0 None -3680 DRGGCVAGV 0.0 None None 0 None -3681 DRMQRVISV 0.0 None None 0 None -3682 DRMQRVISV 0.0 None None 0 None -3683 DRNDFPVVL 0.104073443917 RNDFPVVL RGDLPVWL 23.0 180611|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -3684 DRQLAAQLL 0.0 None None 0 None -3685 DRSGARPHL 0.0 None None 0 None -3686 DRSHTLQRM 0.0 None None 0 None -3687 DRVERNCLL 0.0 None None 0 None -3688 DSDGEEPCY 0.0 None None 0 None -3689 DSHDYVFYL 0.0 None None 0 None -3690 DTDILSYSY 0.0421563317134 DTDILSYSY NPDIVIYQY 23.0 101813|Pol_polyprotein|Q9YLQ7|Human_immunodeficiency_virus_1|11676 -3691 DTDLYHCTA 0.0 None None 0 None -3692 DTEGILTEY 0.0 None None 0 None -3693 DYMGFTLKI 0.0 None None 0 None -3694 DYPCCIFPF 0.741073093531 DYPCCI HYPCTI 26.0 54821|E2_protein|AAM33354.1|Hepatitis_C_virus_subtype_1a|31646 -3695 DYRTVNNLI 0.0 None None 0 None -3696 EAEPYYCSL 0.0 None None 0 None -3697 EAKRQNLRL 0.0 None None 0 None -3698 EALIRHLNA 0.0370757155869 ALIRHLN SLLRHHN 23.0 96897|polyprotein|ABR25251.1|Hepatitis_C_virus_(isolate_H77)|63746 -3699 EAMNNAQKI 0.0 None None 0 None -3700 EASRRYKKV 0.0 None None 0 None -3701 EFPQKYYWW 2.66043171253 FPQKYYWW FPGKTVWF 25.0 183223|polyprotein|AGW21594.1|Dengue_virus_1|11053 -3702 EGQRRPSSV 0.0 None None 0 None -3703 EHEEDGSEI 0.0 None None 0 None -3704 EHGGKTVKV 0.0 None None 0 None -3705 EHLAAPRLV 0.0 None None 0 None -3706 EHNVTVLVV 0.0 None None 0 None -3707 EHQIGPQEI 0.0 None None 0 None -3708 EHRLHTPMY 0.0 None None 0 None -3709 EIKTIVKAI 1.03630759918 EIKTIVKAI DCKTILKAL 27.0 7708|gag_polyprotein|BAA00992.1|Human_immunodeficiency_virus_1|11676 -3710 EIMNRVVNA 0.0 None None 0 None -3711 EKRFKRKSV 0.0 None None 0 None -3712 ELACYNSAI 0.0 None None 0 None -3713 ELEHMRLRY 0.0 None None 0 None -3714 ELHARGHQV 0.0 None None 0 None -3715 ELHRQVKTL 0.0005030251957 ELHRQVKTL SLHYAWKTM 18.0 183252|polyprotein|AGT63075.1|Dengue_virus_1|11053 -3716 ELKQMCNPI 0.0 None None 0 None -3717 ELLLKVFAL 0.0 None None 0 None -3718 ELQARLAAL 0.0 None None 0 None -3719 ELRAHCETL 0.0 None None 0 None -3720 ELRRYLKSG 0.0 None None 0 None -3721 EMKCREKGF 0.0 None None 0 None -3722 EMLRRQIRL 0.0 None None 0 None -3723 EMRCQYETV 2.0101481376 MRCQYETV MNCSYENM 27.0 36306|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 -3724 EMYEKGLSV 0.0 None None 0 None -3725 EPKKKEKGM 0.0 None None 0 None -3726 EPKKRKVVP 0.0 None None 0 None -3727 EPRFRLNLF 0.0 None None 0 None -3728 ERDGLERAL 0.00214622386308 ERDGLERAL ERDIPERSW 20.0 180423|polyprotein|AGW21594.1|Dengue_virus_1|11053 -3729 ERDGLHSVV 0.0 None None 0 None -3730 ERDQLKETL 0.0 None None 0 None -3731 EREKMGVTM 0.0 None None 0 None -3732 ERFWRIILL 0.0 None None 0 None -3733 ERHVAVEGV 0.0 None None 0 None -3734 ERIDTNQKC 0.0542551505549 DTNQKC DTGQAC 24.0 22633|IMMUNOGENIC_PROTEIN_MPT64_(ANTIGEN_MPT64/MPB64)|CAA98382.1|Mycobacterium_tuberculosis_H37Rv|83332 -3735 ERKTMIKKI 0.0 None None 0 None -3736 ERLQALYMI 0.0 None None 0 None -3737 ERLQNPLRV 0.0 None None 0 None -3738 ERQCHNTAL 0.0 None None 0 None -3739 ERQCHNTAL 0.0 None None 0 None -3740 ERRDCIICC 0.0 None None 0 None -3741 ERSCWVRAI 0.0 None None 0 None -3742 ERSEQPLSV 0.0 None None 0 None -3743 ERSPQAAAV 0.0 None None 0 None -3744 ERTNQKWSV 0.0 None None 0 None -3745 ERTSATLTI 0.0 None None 0 None -3746 ERTTWVQKI 0.0 None None 0 None -3747 ERYGPVFTI 106.83056401 YGPVF YGPVF 30.0 67349|Latent_membrane_protein_2|Q69135|Human_gammaherpesvirus_4|10376 -3748 ETMLHGQVM 0.0 None None 0 None -3749 ETRPTPRLL 0.840404040404 RPTPRL RPGPRL 26.0 139406|polyprotein|ACT37184.1|Hepatitis_C_virus|11103 -3750 ETVSTTLCY 0.0 None None 0 None -3751 EYIVIPSTF 0.0 None None 0 None -3752 EYLLGSWVI 0.702063562848 LLGSWV ILGGWV 27.0 68461|polyprotein|ACZ60108.1|Hepatitis_C_virus|11103 -3753 EYNANTSVL 0.0 None None 0 None -3754 EYRPRTFCF 1.18624599551 PRTFC PRTWC 27.0 141218|regulatory_protein_ICP22|NP_044663.1|Human_alphaherpesvirus_1|10298 -3755 EYVKFLHTF 0.0 None None 0 None -3756 EYVTELPSF 0.0347332864612 EYVTELPS EYTDYMPS 22.0 180681|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -3757 FAAQHGLAV 0.0 None None 0 None -3758 FAKLRHNTQ 0.0 None None 0 None -3759 FARGQRWRL 0.121912079341 FARGQRWRL FTRGDRCNL 24.0 43937|polyprotein|AAF01178.1|Hepatitis_C_virus_subtype_2a|31649 -3760 FARGQRWRL 0.198021676537 FARGQRWRL FTRGDRCNL 24.0 43937|polyprotein|AAF01178.1|Hepatitis_C_virus_subtype_2a|31649 -3761 FCLRYGAAL 0.0 None None 0 None -3762 FCSLHCLLY 0.0 None None 0 None -3763 FCYYYFLCL 0.0 None None 0 None -3764 FEESKSYEV 0.0 None None 0 None -3765 FEFSQVLAL 0.0 None None 0 None -3766 FESHRILHL 0.0518297042583 FESHRI FQSHQL 23.0 183245|polyprotein|AGT63074.1|Dengue_virus_1|11053 -3767 FFLSYLKSL 0.0 None None 0 None -3768 FFLSYLSLV 0.0 None None 0 None -3769 FGAIRRSDA 0.0 None None 0 None -3770 FGYENSPEL 0.0 None None 0 None -3771 FHFRRPWSF 5.80280666815 HFRRPW HFPRIW 25.0 187106|Vpr_protein|BAA93983.1|Human_immunodeficiency_virus_1|11676 -3772 FHFRRPWSF 0.902255091048 HFRRPW HFPRIW 25.0 187106|Vpr_protein|BAA93983.1|Human_immunodeficiency_virus_1|11676 -3773 FHFRRPWSF 0.171144540872 HFRRPW HFPRIW 25.0 187106|Vpr_protein|BAA93983.1|Human_immunodeficiency_virus_1|11676 -3774 FHHCHPKYS 0.0 None None 0 None -3775 FHHIDSAYL 0.0124561392202 FHHIDSA FGHSDAA 21.0 79506|E1_protein|BAA19893.1|Rubella_virus|11041 -3776 FHIGSAESM 0.0 None None 0 None -3777 FHLHNAHVL 0.444444444444 LHNAHVL FHNLHLL 26.0 79390|Protein_Tax-1|P0C213.1|Human_T-cell_lymphotropic_virus_type_1_(african_isolate)|39015 -3778 FHLPYLEQK 1.18628821685 HLPYLEQ HLPYIEQ 38.0 102819|Genome_polyprotein|P27958.3|Hepatitis_C_virus_subtype_1a|31646 -3779 FHLQHWKQI 0.0 None None 0 None -3780 FHLSIHLLY 6.46174150023 SIHLLY SLHLLF 25.0 57790|Protein_Tax-1|P03409.2|Human_T-lymphotropic_virus_1|11908 -3781 FHMASGEAL 0.0 None None 0 None -3782 FHPMRTLPM 0.0 None None 0 None -3783 FHVDQATTV 0.0 None None 0 None -3784 FHYDTQLSL 0.178804383033 FHYDTQL FSYDTRC 24.0 33382|polyprotein|AAB67037.1|Hepatitis_C_virus|11103 -3785 FHYLKKQET 0.0 None None 0 None -3786 FIADKLSTL 0.0 None None 0 None -3787 FIADKLSTL 0.0 None None 0 None -3788 FICLQFWCI 0.0 None None 0 None -3789 FIMFLFVYI 0.0 None None 0 None -3790 FINNSIVYL 0.214071856287 NNSIVY NSSIVY 26.0 6817|polyprotein|AAB67037.1|Hepatitis_C_virus_(isolate_H77)|63746 -3791 FKKARWTII 0.0 None None 0 None -3792 FKNHHNRTV 0.0 None None 0 None -3793 FLARTVSTL 5.81147313029 LARTVS LARTIS 25.0 44653|6_kDa_early_secretory_antigenic_target|P0A564.2|Mycobacterium_tuberculosis|1773 -3794 FLEHGEQAY 0.0 None None 0 None -3795 FLHERKQAS 0.0 None None 0 None -3796 FLKTLWAGL 0.0 None None 0 None -3797 FLLAMLLSI 0.169887629024 LAMLLSI MAMVLSI 24.0 184736|polyprotein|AGW21594.1|Dengue_virus_1|11053 -3798 FLLEFLLPL 0.0595499389227 LEFLLP LQFLIP 25.0 22235|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 -3799 FLLFSFLFL 9.80083437792e-06 FLLFSFLFL FLVPFVVFL 15.0 139746|Dense_granule_protein_3|B6KEU8.2|Toxoplasma_gondii|5811 -3800 FLRTYKNSV 0.0 None None 0 None -3801 FLSDLTPGY 0.0 None None 0 None -3802 FLSVFYTAV 0.0 None None 0 None -3803 FLTVMLLAL 0.0 None None 0 None -3804 FLVERKTIA 0.0 None None 0 None -3805 FMAYATQLF 0.0 None None 0 None -3806 FMKYLVNFI 0.393474742824 MKYLVNF LEYLVSF 25.0 69474|core_protein|BAF42671.1|Hepatitis_B_virus|10407 -3807 FMLVMICIL 0.0 None None 0 None -3808 FMWPLHWSM 17.8722123486 FMWPLH YPWPLY 25.0 75436|Polyprotein|P90247|Hepatitis_C_virus|11103 -3809 FPAMLQAPI 0.458346535653 FPAMLQAPI FPVRPQVPL 23.0 288104|nef_protein|ACR27130.1|Human_immunodeficiency_virus_1|11676 -3810 FPIIIAWAI 0.98110662908 FPIIIAWAI FPLTFGWCF 25.0 193060|Nef_protein|Q9YYU3|Human_immunodeficiency_virus_1|11676 -3811 FPKKSLMLM 0.0 None None 0 None -3812 FPLVRSCQM 0.204347866324 LVRSCQM LIRACML 24.0 36676|polyprotein|BAA09073.1|Hepatitis_C_virus_subtype_1b|31647 -3813 FPNGRLTFL 0.0 None None 0 None -3814 FPQKYYWWF 1.4267285342 FPQKYYWW FPGKTVWF 25.0 183223|polyprotein|AGW21594.1|Dengue_virus_1|11053 -3815 FPQNRYTQE 0.0 None None 0 None -3816 FPTDCVYVM 0.0 None None 0 None -3817 FPYCRAHVL 0.0 None None 0 None -3818 FPYCRAHVL 0.0 None None 0 None -3819 FPYCRSHVF 0.0 None None 0 None -3820 FPYGSSTAL 0.0 None None 0 None -3821 FPYNSDLSL 0.0732870943231 FPYNSDL LPTNADL 22.0 141411|transactivating_tegument_protein_VP16|NP_044650.1|Human_alphaherpesvirus_1|10298 -3822 FQFGAGTQV 0.0 None None 0 None -3823 FQGRRSPSF 0.0 None None 0 None -3824 FQRKKRRKF 0.0 None None 0 None -3825 FREDPVAWV 0.0 None None 0 None -3826 FREGRPREW 0.0 None None 0 None -3827 FRGALPVQI 0.0 None None 0 None -3828 FRGDGRTCC 0.0 None None 0 None -3829 FRHSPRNLI 0.0 None None 0 None -3830 FRKELRYFL 0.0 None None 0 None -3831 FRKELRYFL 0.0 None None 0 None -3832 FRLMHNLNF 0.0 None None 0 None -3833 FRLRRVASA 0.0 None None 0 None -3834 FRLWMTTEV 0.0 None None 0 None -3835 FRNDQEETT 0.0 None None 0 None -3836 FRNGLGTGM 0.343618280556 FRNGLGTGM YLYGVGSGM 25.0 177884|polyprotein|ACZ60102.1|Hepatitis_C_virus_genotype_1|41856 -3837 FRNSRLKQC 0.0 None None 0 None -3838 FRPPAWNRL 0.0 None None 0 None -3839 FRQGHQLFH 0.0 None None 0 None -3840 FRQLEDSQV 0.0 None None 0 None -3841 FRQSRSQVV 0.0 None None 0 None -3842 FRQSRSQVV 0.0 None None 0 None -3843 FRSHVPSHL 0.0 None None 0 None -3844 FRSLQGSVF 0.0 None None 0 None -3845 FRSPEDLSL 0.0 None None 0 None -3846 FRSSASGAL 0.0 None None 0 None -3847 FRTKDGSFV 0.482142857143 FRTKDG FKTEDG 26.0 150571|polyprotein|AGO67248.1|Dengue_virus_2|11060 -3848 FRVSISQTA 0.0 None None 0 None -3849 FRYEGSLTT 3.01020070508 FRYEGS FMYEGD 23.0 126028|ATP-dependent_helicase|NP_217813.1|Mycobacterium_tuberculosis_H37Rv|83332 -3850 FSDKKTITY 0.0 None None 0 None -3851 FSFINNSIV 0.0 None None 0 None -3852 FSIPTCLMY 0.0 None None 0 None -3853 FSKAQAEYL 0.0 None None 0 None -3854 FSYPSIHRF 1.49991207554 PSIHRF PGIYRF 24.0 22046|polyprotein_precursor|BAA01582.1|Hepatitis_C_virus|11103 -3855 FTDVSRFTL 0.0953424643358 TDVSR TDVSR 24.0 181733|Antigen_85-B|P0C5B9.1|Mycobacterium_tuberculosis|1773 -3856 FTFDLYRVL 0.0 None None 0 None -3857 FTSFLLLMY 0.0 None None 0 None -3858 FVEEWTESL 0.0 None None 0 None -3859 FVQKLLFPY 0.0 None None 0 None -3860 FWCAQFTSF 1.06197345475 FWCAQFTSF FWEAVFTGL 26.0 12108|polyprotein|AAP55688.1|Hepatitis_C_virus_subtype_2a|31649 -3861 FWKKILFVI 0.0 None None 0 None -3862 FWKLFYCKF 17.0058728052 LFYCK LLYCK 25.0 25460|Fusion_glycoprotein_F0_precursor|P03420.1|Human_respiratory_syncytial_virus_A2|11259 -3863 FYADSHHCV 0.0 None None 0 None -3864 FYAIVVPML 0.114734057478 FYAIVVPM FYGKAIPL 22.0 97400|Genome_polyprotein|P26664.3|Hepatitis_C_virus|11103 -3865 FYCDDLPLL 0.0 None None 0 None -3866 FYLGTYQAV 0.681699967536 FYLGTY FYLGQY 29.0 156550|E3_ubiquitin-protein_ligase_Mdm2|Q00987.1|Homo_sapiens|9606 -3867 FYMLTCIDL 0.0 None None 0 None -3868 FYQAGSLCI 0.0 None None 0 None -3869 FYTDSSSVL 1.41214657707 TDSSSVL TDSTSIL 27.0 107894|polyprotein|CAB41951.1|Hepatitis_C_virus|11103 -3870 FYTPALFSF 0.00424010201542 FYTPALF FYCNSLF 21.0 141323|multifunctional_expression_regulator|NP_044657.1|Human_alphaherpesvirus_1|10298 -3871 GAGPRFLEL 0.0 None None 0 None -3872 GDKQHFTTL 0.0 None None 0 None -3873 GGATRVYAL 0.0 None None 0 None -3874 GHDAPRRTL 0.490665707971 HDAPRRTL HGAGTRTI 20.0 4910|polyprotein|AAB67037.1|Hepatitis_C_virus_(isolate_H77)|63746 -3875 GHKEDAGVV 0.182420233615 HKEDAGVV EEEEAGVL 23.0 185491|polyprotein|AGO67248.1|Dengue_virus_2|11060 -3876 GHKGLNQCV 0.0 None None 0 None -3877 GHLEAASCI 0.0 None None 0 None -3878 GHLQIRSLL 0.0 None None 0 None -3879 GHLSKKMTL 0.0 None None 0 None -3880 GHNSWGFGV 0.601287595144 GHNSWGFG GDTAWDFG 28.0 180726|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -3881 GHPQDGSGL 0.0 None None 0 None -3882 GHPSLSQHL 1.07017587087 HPSLSQHL EPTLGQHL 29.0 79308|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 -3883 GHTGERHRV 0.0 None None 0 None -3884 GHTPNGRHF 0.0 None None 0 None -3885 GHVAGEQML 0.431336840656 GHVAGEQML GHQAAMQML 28.0 101673|gag_protein|ABO73990.1|Human_immunodeficiency_virus_1|11676 -3886 GLHSSFMPL 0.0 None None 0 None -3887 GLSVRPHAI 0.0 None None 0 None -3888 GMFTLRMAL 0.0 None None 0 None -3889 GNYSRSSHV 0.0 None None 0 None -3890 GPCRRRFSF 0.779795817205 GPCRRRF GPADRRF 27.0 155637|tegument_protein|CAB06732.1|Human_alphaherpesvirus_2|10310 -3891 GPLPKSYAV 0.0 None None 0 None -3892 GPRTKAWFL 1.91866745733 PRTKAWFL PSTLRWFF 25.0 38724|Genome_polyprotein|P08617.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 -3893 GRAEESVVL 0.0 None None 0 None -3894 GRAPCWQRL 0.487372385753 APCWQR APAWSR 27.0 155554|RL2|CAB06760.1|Human_alphaherpesvirus_2|10310 -3895 GREAEMQEL 0.0 None None 0 None -3896 GRMHIGDEL 0.0 None None 0 None -3897 GRMMFVGTL 0.0 None None 0 None -3898 GRNGQKAAL 0.0 None None 0 None -3899 GRVEKLLDL 0.0 None None 0 None -3900 GSDSSNGAV 0.0 None None 0 None -3901 GSEDFEDTY 0.0 None None 0 None -3902 GTNIVILEY 0.0118445772921 GTNIVILE GTQAVVLK 22.0 27981|IMMUNOGENIC_PROTEIN_MPT64_(ANTIGEN_MPT64/MPB64)|CAA98382.1|Mycobacterium_tuberculosis_H37Rv|83332 -3903 GVLECPRLI 0.0 None None 0 None -3904 HAKKKPNPV 0.718544984666 KKKPNPV KKKKNPM 28.0 142203|polyprotein|BAD73974.1|Hepatitis_C_virus_subtype_1b|31647 -3905 HHIDSAYLY 0.0 None None 0 None -3906 HHKGKMKAL 0.0 None None 0 None -3907 HHKHKELQV 0.0 None None 0 None -3908 HHRFNNFML 0.0 None None 0 None -3909 HIKDKKLPL 0.0 None None 0 None -3910 HLLSHSYCL 0.109600489264 HLLSHSYCL HLYSHPIIL 24.0 190568|polymerase|AAD16253.1|Hepatitis_B_virus|10407 -3911 HLMGQLSSL 3.88330048497 HLMGQLSSL HLAFQLSSI 27.0 24172|pX-rex-orf_I_{alternatively_spliced}|AAB23359.1|Human_T-lymphotropic_virus_1|11908 -3912 HMRLRYLAA 0.0 None None 0 None -3913 HPKYSFRRL 0.0 None None 0 None -3914 HPLRYTLIM 0.0 None None 0 None -3915 HRADVYVGV 0.0 None None 0 None -3916 HREDFEARL 0.159782640157 HREDFE HGEEFE 24.0 155811|ribonucleotide_reductase_large_subunit|CAB06725.1|Human_alphaherpesvirus_2|10310 -3917 HRGTGAVYV 27.0330536607 RGTGAVYV RGTSFVYV 29.0 27285|pol_protein|BAA32832.1|Hepatitis_B_virus|10407 -3918 HRLGESQTL 0.0 None None 0 None -3919 HRLHTPMYL 0.0 None None 0 None -3920 HRQAEVHKV 0.0 None None 0 None -3921 HRQQRGQQL 0.0 None None 0 None -3922 HRSKRGSSV 0.0 None None 0 None -3923 HRTRCLSKL 0.0 None None 0 None -3924 HRYPRVMAA 0.0 None None 0 None -3925 HRYPRVMAA 0.0 None None 0 None -3926 HSHLLSHSY 2.5848832505 HLLSHS HLYSHP 23.0 190568|polymerase|AAD16253.1|Hepatitis_B_virus|10407 -3927 HSYEAGTEI 0.0 None None 0 None -3928 HTPNGRHFY 0.701274710612 TPNGRHFY TDNNRSFY 27.0 98603|trans-sialidase,_putative|EAN82716.1|Trypanosoma_cruzi|5693 -3929 HWSMWLGVF 0.372066895841 WSMWLGV WTMKIGI 25.0 186524|polyprotein|AGW21594.1|Dengue_virus_1|11053 -3930 HYATILTSL 0.0 None None 0 None -3931 HYHHRFNNF 2.27650024439 YHHRFNN YQHKFNS 30.0 23270|polyprotein|AAB67036.1|Hepatitis_C_virus_(isolate_H77)|63746 -3932 HYISIFYAL 0.00687708027962 YISIFYA YMSPFYG 22.0 141469|envelope_glycoprotein_B|NP_044629.1|Human_alphaherpesvirus_1|10298 -3933 HYLRDVLPL 0.0 None None 0 None -3934 HYQGTWYLT 0.0 None None 0 None -3935 HYRKRGAHL 0.0 None None 0 None -3936 IAHAWWAHF 0.461739437354 HAWWAHF HARWAAF 28.0 141262|DNA_polymerase_catalytic_subunit|NP_044632.1|Human_alphaherpesvirus_1|10298 -3937 IAMYFYTTL 0.0 None None 0 None -3938 IEYGSPEEL 0.0 None None 0 None -3939 IFIASIYLL 0.0 None None 0 None -3940 IFLFVIVTI 0.0 None None 0 None -3941 IFPFALIFF 0.0 None None 0 None -3942 IFPFILIFF 0.0 None None 0 None -3943 IFSEKNRLV 0.0 None None 0 None -3944 IFSFINNSI 0.0 None None 0 None -3945 IFVSSYINI 0.0 None None 0 None -3946 IGRNRSPCM 0.0 None None 0 None -3947 IHDGAVHTI 0.552631578947 HDGAVHT QEGAMHT 26.0 50596|polyprotein|ABG75765.1|Dengue_virus_1|11053 -3948 IHDRQLRSF 0.0 None None 0 None -3949 IHEDEVDDM 0.113033351011 EDEVD EDEID 25.0 110431|E7|AAD33253.1|Human_papillomavirus_type_16|333760 -3950 IHFTKKDYV 0.0 None None 0 None -3951 IHGASNHCL 0.0 None None 0 None -3952 IHIDDNKWV 0.169553246094 DDNKWV DENPWL 25.0 31802|large_delta_antigen|AAG26087.1|Hepatitis_delta_virus_TW2667|10000523 -3953 IHLLDSLRL 0.0 None None 0 None -3954 IHLLYPPSL 0.0620423197569 IHLLYPP LHVWVPP 22.0 40158|polyprotein|AAA45534.1|Hepatitis_C_virus|11103 -3955 IHPRDRSTV 0.0 None None 0 None -3956 IHTDDNKCV 0.000134201508342 IHTDDNKCV IHDIILECV 16.0 110306|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 -3957 ILAVLPSLF 0.517090203886 AVLPSLF GIIPSMF 24.0 180407|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -3958 ILKKRQQAA 0.0 None None 0 None -3959 ILKRRYQEP 0.0 None None 0 None -3960 ILLTQFHFL 0.852006511865 ILLTQF ILLTHF 23.0 422984|NS5B_protein|ABB72740.1|Hepatitis_C_virus_genotype_1|41856 -3961 ILMRQPLPA 0.0 None None 0 None -3962 ILRSKMKTV 0.0 None None 0 None -3963 ILRVYSGVL 0.0 None None 0 None -3964 ILSSRSRQL 0.0 None None 0 None -3965 ILSSRSRQL 0.0 None None 0 None -3966 INFNHDSSI 0.0 None None 0 None -3967 IQWSYWGVF 0.0967863310004 WSYWGVF WAYHGSY 24.0 180582|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -3968 IRAANRRGL 0.0 None None 0 None -3969 IRDGSTMTF 0.0 None None 0 None -3970 IREYCPYTY 0.0377782116104 IREYCPYTY ISEYRHYCY 23.0 28484|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 -3971 IRFLRQYEF 0.0 None None 0 None -3972 IRHGNVIAC 0.513115695515 GNVIAC GNMSAC 24.0 133645|cell_surface_protein|NP_302626.1|Mycobacterium_leprae|1769 -3973 IRHLNATSF 0.0 None None 0 None -3974 IRIDTIHLL 0.0 None None 0 None -3975 IRLNRQRHT 0.0 None None 0 None -3976 IRNMAPDSL 0.0 None None 0 None -3977 IRPPDSRSL 0.420410333594 PPDSRSL PPGARSM 25.0 72928|Genome_polyprotein|P26662.3|Hepatitis_C_virus_(isolate_Japanese)|11116 -3978 IRRGGKHQL 0.0 None None 0 None -3979 IRRLRPSSI 0.13780610868 RRLRPS KRLEPS 22.0 50894|Genome_polyprotein|P27909.2|Dengue_virus_type_1_Hawaii|10000440 -3980 IRRLRPSSI 0.073674283114 RRLRPS KRLEPS 22.0 50894|Genome_polyprotein|P27909.2|Dengue_virus_type_1_Hawaii|10000440 -3981 IRRRGSTSL 0.0 None None 0 None -3982 IRYLHSLQI 0.0 None None 0 None -3983 ISELLFECY 0.0271004989586 ISELLFECY ISEYRHYCY 23.0 28484|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 -3984 ISFSMSEKM 0.0 None None 0 None -3985 ISKRKVSVA 0.0 None None 0 None -3986 ISLGFFLVF 0.0249581117984 ISLGFFLV LQAGFFLL 24.0 69715|envelope_protein|BAF48755.1|Hepatitis_B_virus|10407 -3987 ISSSAGLPY 0.0 None None 0 None -3988 ITIRNPLRY 0.0 None None 0 None -3989 ITMDQKKTI 0.0 None None 0 None -3990 ITMRYIHFL 0.0 None None 0 None -3991 ITTFDRLAY 13.9529411765 TFDRL TFDRL 26.0 66405|polyprotein|AAB67037.1|Hepatitis_C_virus_(isolate_H77)|63746 -3992 IVHRQFYLF 1.36497494935 IVHRQFYL LVHRQWFL 32.0 41407|Envelope_protein|NP_739583.2|Dengue_virus_2|11060 -3993 IVMGYSSGI 0.113615285052 MGYSSGI MDYSNGL 24.0 51604|FL-160-2_protein_-_Trypanosoma_cruzi|JH0823|Trypanosoma_cruzi|5693 -3994 IWFSIPTCL 0.0 None None 0 None -3995 IYAALPYVK 0.0 None None 0 None -3996 IYAFMGTPM 0.130873138164 IYAFMGTP LRAYMNTP 24.0 65497|HCV-1|AAA45676.1|Hepatitis_C_virus_genotype_1|41856 -3997 IYCRPFTTL 0.0 None None 0 None -3998 IYCVYPDSL 0.0 None None 0 None -3999 IYGLCVVIV 6.9120502655 YGLCVV YGVCIM 27.0 148117|early_protein|CAA52585.1|Human_papillomavirus_type_52|10618 -4000 IYHDSRIHV 0.0 None None 0 None -4001 IYTIVNIKI 0.0 None None 0 None -4002 IYVDKVRHV 3.30136379321 YVDKVR YLDKVR 28.0 74605|Circumsporozoite_protein_precursor|P08677.2|Plasmodium_vivax_strain_Belem|31273 -4003 KAFKRSSYL 0.0 None None 0 None -4004 KAFKRSSYL 0.0 None None 0 None -4005 KAMERSSLM 0.0 None None 0 None -4006 KHFIHLITV 0.0 None None 0 None -4007 KHLSRSNWL 0.0 None None 0 None -4008 KHNEEIRFL 0.0 None None 0 None -4009 KHRNMHCKI 0.0 None None 0 None -4010 KHRSEISMM 0.0 None None 0 None -4011 KIHIRETAI 0.0 None None 0 None -4012 KILKKRQQA 0.0 None None 0 None -4013 KISKRKVSV 0.0 None None 0 None -4014 KKRRKFWKA 0.101871750519 KRRKFW RRRKGW 25.0 55718|Probable_membrane_glycoprotein_precursor|P03218.1|Human_herpesvirus_4_strain_B95-8|10377 -4015 KLKPKKPTL 0.0 None None 0 None -4016 KLQPYFQTL 0.0163360332358 LQPYFQ LSPYYK 22.0 149024|NS2_protein|NP_751923.1|Hepatitis_C_virus_(isolate_H77)|63746 -4017 KMFRRSAHL 0.0 None None 0 None -4018 KRCALRLLV 0.0 None None 0 None -4019 KRFKRKSVV 0.0 None None 0 None -4020 KRILMPQVM 0.0 None None 0 None -4021 KRISHKAAL 0.0 None None 0 None -4022 KRQNLRLAL 0.0 None None 0 None -4023 KRQRAMETL 0.0 None None 0 None -4024 KRSPAWNEM 2.71823855445 SPAWN APAWS 24.0 155554|RL2|CAB06760.1|Human_alphaherpesvirus_2|10310 -4025 KRYLSQREV 0.951221917101 YLSQRE YLGKRE 22.0 150698|polyprotein|AGO67248.1|Dengue_virus_2|11060 -4026 KSDGLSLAV 0.0 None None 0 None -4027 KSFSKYASF 0.0 None None 0 None -4028 KWIREGYLV 0.0 None None 0 None -4029 KYMPPCSLV 0.0 None None 0 None -4030 KYPYWYQQK 0.419548617337 KYPYW KYTFW 25.0 137660|L1|ACL12325.1|Human_papillomavirus_type_58|10598 -4031 KYSTGIGWI 0.0 None None 0 None -4032 KYSTPPYLL 0.848971252603 KYSTPPYLL KYTSFPWLL 27.0 34616|pol_protein|BAA32832.1|Hepatitis_B_virus|10407 -4033 LAGQKRCAL 0.0 None None 0 None -4034 LAKVKYTAS 0.0 None None 0 None -4035 LALLKQVSV 0.0 None None 0 None -4036 LANDPIQVV 0.0 None None 0 None -4037 LAQSFFNCL 0.0 None None 0 None -4038 LCAIYFLSI 0.0 None None 0 None -4039 LCIKHFNIL 0.0 None None 0 None -4040 LEHMRLRYL 0.0 None None 0 None -4041 LFAAVVLLI 0.0 None None 0 None -4042 LFKKARWTI 0.0 None None 0 None -4043 LFLLFSFLF 0.0 None None 0 None -4044 LFPRLPSIL 6.65851410543 FPRLP FPRAP 24.0 62355|Genome_polyprotein|P08617.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 -4045 LFSFMTHCF 0.109472071245 FSFMTHC FSYDTRC 24.0 33382|polyprotein|AAB67037.1|Hepatitis_C_virus|11103 -4046 LFSFMTHRF 0.0 None None 0 None -4047 LGRNRHFGF 0.138393893319 GRNRHF GRDAHY 22.0 66798|glycoprotein_gp35/37|AAC59622.1|Human_gammaherpesvirus_8|37296 -4048 LHAPMYNLL 0.378354025976 APMYNLL VPNYNLI 24.0 150693|polyprotein|AGO67248.1|Dengue_virus_2|11060 -4049 LHAPMYNLL 0.21694931808 APMYNLL VPNYNLI 24.0 150693|polyprotein|AGO67248.1|Dengue_virus_2|11060 -4050 LHEQLGDRL 1.76159415596 LHEQLGD CYEQLGD 28.0 147561|early_protein|CAA52586.1|Human_papillomavirus_type_52|10618 -4051 LHFDAVQIC 0.0 None None 0 None -4052 LHFMPCVYI 0.0 None None 0 None -4053 LHFVQKLLF 0.183771171451 HFVQKLLF HFQRALIF 24.0 183577|polyprotein|AGK36298.1|Dengue_virus_2|11060 -4054 LHHKHKELQ 0.000432776802688 LHHKHKELQ LHEYMLDLQ 17.0 110335|E7|AAD33253.1|Human_papillomavirus_type_16|333760 -4055 LHHTHIALL 0.0 None None 0 None -4056 LHKDSNMPV 0.0 None None 0 None -4057 LHMNLLSYF 0.0 None None 0 None -4058 LHNAHVLDV 0.5 LHNAHVL FHNLHLL 26.0 79390|Protein_Tax-1|P0C213.1|Human_T-cell_lymphotropic_virus_type_1_(african_isolate)|39015 -4059 LHQCVLRFL 0.0 None None 0 None -4060 LHQGGATRV 0.0 None None 0 None -4061 LHRASGVGV 0.0 None None 0 None -4062 LHSGLQILI 0.0 None None 0 None -4063 LHTPVYFLL 0.0 None None 0 None -4064 LHTPVYFLL 0.0 None None 0 None -4065 LHTRHGSIL 0.196978634169 LHTRHG LHEQHG 26.0 75356|EBNA3A_nuclear_protein|Q8AZJ8|Human_gammaherpesvirus_4|10376 -4066 LHVGCDEVY 0.0 None None 0 None -4067 LHYEEIPEY 0.0 None None 0 None -4068 LIATQLLFY 0.0 None None 0 None -4069 LIKHKKTHI 0.679666392493 KHKKTHI KYKLKHI 21.0 34482|gag_polyprotein|BAA00992.1|Human_immunodeficiency_virus_1|11676 -4070 LIKYRQNHA 0.0 None None 0 None -4071 LIMNKRLGL 0.0 None None 0 None -4072 LKKRQQAAL 0.0 None None 0 None -4073 LKLVKRNSL 0.0 None None 0 None -4074 LLCARAWLL 0.0 None None 0 None -4075 LLDRRPHGY 0.0 None None 0 None -4076 LLESYSASL 0.0 None None 0 None -4077 LLGHKTVTI 0.0 None None 0 None -4078 LLGKKGTSA 0.473336145345 LLGKKGTSA LLGLWGTAA 25.0 37498|FL-160-2_protein_-_Trypanosoma_cruzi|JH0823|Trypanosoma_cruzi|5693 -4079 LLHTIITPM 0.0 None None 0 None -4080 LLKKLCIKL 2.09957355011 LKKLCI LRKLCI 28.0 184299|envelope_protein|AGT63061.1|Dengue_virus_3|11069 -4081 LLKSDGLSL 0.0 None None 0 None -4082 LLKTAFHPV 0.0 None None 0 None -4083 LLLMYSYAV 0.357608766066 LLLMYSYAV LLLVAHYAI 24.0 150377|polyprotein|AGS49173.1|Dengue_virus_2|11060 -4084 LLLQALQAL 0.0 None None 0 None -4085 LLMNKPYLA 1.11933186224 NKPYL NLPYL 22.0 13518|HCV-1|AAA45676.1|Hepatitis_C_virus_genotype_1|41856 -4086 LLMYTKLVV 0.0 None None 0 None -4087 LLNVHLSKL 0.0 None None 0 None -4088 LLRDFVAPL 0.0 None None 0 None -4089 LLRGHDQSA 0.0 None None 0 None -4090 LLRLLRKAM 0.0 None None 0 None -4091 LLRNDARSL 0.0 None None 0 None -4092 LLSFKRQRA 0.0 None None 0 None -4093 LLSRKDSIF 0.0 None None 0 None -4094 LLTQRLQGL 0.228736119694 LLTQRLQGL LITGRLQSL 27.0 36724|Spike_glycoprotein_precursor|P59594.1|SARS_coronavirus|227859 -4095 LMACATQLF 0.0 None None 0 None -4096 LMGQLSSLY 0.0 None None 0 None -4097 LMKMDDPSI 0.0 None None 0 None -4098 LMKQKKSSC 0.0 None None 0 None -4099 LNKLDFYVL 0.0 None None 0 None -4100 LNRQRHTPM 18.4848484848 RHTPM RHTPV 26.0 4156|polyprotein|ABR25251.1|Hepatitis_C_virus|11103 -4101 LPALRKTGV 0.0 None None 0 None -4102 LPAVHALRL 0.0 None None 0 None -4103 LPGLHFMPG 0.0 None None 0 None -4104 LPGMRGPPG 0.212348087935 GMRGP GQRGP 24.0 48915|kaposin|AAC57155.1|Human_gammaherpesvirus_8|37296 -4105 LPKDRFFAV 0.0 None None 0 None -4106 LPKEKLAAA 0.694505649699 LPKEKL LPREKL 27.0 54706|matrix_protein_2-1|AAS22094.1|Human_metapneumovirus|162145 -4107 LPMTLLLLL 0.0 None None 0 None -4108 LPQGRESPI 0.130541001792 LPQGRE LPSGRN 22.0 54709|protein_F_[Hepatitis_C_virus_subtype_1b]|ACA50643.1|Hepatitis_C_virus_(isolate_Japanese)|11116 -4109 LPRSKDTIL 0.0 None None 0 None -4110 LPRVRGTTL 0.0 None None 0 None -4111 LPSCRLAPA 0.0 None None 0 None -4112 LPTLKFQTF 0.0 None None 0 None -4113 LPYVKKTGM 0.0 None None 0 None -4114 LQKVRQEVL 0.0 None None 0 None -4115 LQLYRFSPI 0.67159130189 QLYRFSP QLFTFSP 28.0 51346|Genome_polyprotein|P29846.3|Hepatitis_C_virus|11103 -4116 LQRRRLSLL 0.0 None None 0 None -4117 LRADTSFFL 0.0 None None 0 None -4118 LRAKYRESL 0.0 None None 0 None -4119 LRAKYRESL 0.0 None None 0 None -4120 LRAPPGPQL 10.4355383797 PGPQL PGPRL 25.0 139406|polyprotein|ACT37184.1|Hepatitis_C_virus|11103 -4121 LRCHYHHRF 0.0 None None 0 None -4122 LRETRDQPL 0.0 None None 0 None -4123 LRIMLGEIL 0.0 None None 0 None -4124 LRINEVMVY 0.0 None None 0 None -4125 LRKGPIMEV 0.0 None None 0 None -4126 LRKHQILHL 0.0 None None 0 None -4127 LRKHQITHL 0.0 None None 0 None -4128 LRKPQNSEC 0.0 None None 0 None -4129 LRKQNFQPA 0.0 None None 0 None -4130 LRLALDQYL 0.0 None None 0 None -4131 LRLEINHTI 0.0 None None 0 None -4132 LRLPGGSCM 9.609030837 LRLPGGSCM VTLPTGQCL 26.0 71409|cysteine_proteinase_cruzipain_(EC_3.4.22.-)_-_Trypanosoma_cruzi|A45629|Trypanosoma_cruzi|5693 -4133 LRLRWGQII 0.0 None None 0 None -4134 LRLSEPAEI 0.0 None None 0 None -4135 LRMSDPSHI 33.5031608636 MSDPSHI LTDPSHI 32.0 59709|polyprotein|BAD73987.1|Hepatitis_C_virus_subtype_1b|31647 -4136 LRMSRSYPT 0.0 None None 0 None -4137 LRNDARSLY 0.0 None None 0 None -4138 LRPSSIETY 0.054584495544 PSSIET PESLET 23.0 184531|polyprotein|AFP27208.1|Dengue_virus_4|11070 -4139 LRQWIVVTM 0.0 None None 0 None -4140 LRRHRDVSA 0.0863636363636 LRRHRDV LRRHIDL 26.0 51526|HCV-1|AAA45676.1|Hepatitis_C_virus|11103 -4141 LRRMNSFQV 0.0074451481212 LRRMNSF LRKKSSF 21.0 116781|Nucleoprotein|P05133.1|Hantaan_virus_76-118|11602 -4142 LRRNYRCAI 0.0 None None 0 None -4143 LRRNYRCAI 0.0 None None 0 None -4144 LRRQDYQEI 0.0 None None 0 None -4145 LRRVASALL 0.0 None None 0 None -4146 LRSDAPAQL 0.0 None None 0 None -4147 LRSEEDGLV 0.0 None None 0 None -4148 LRSERNNTM 0.0 None None 0 None -4149 LRSIRVRLL 0.169857739813 SIRVRLL SVRARLL 25.0 149115|NS5_protein|BAA00702.1|Hepatitis_C_virus_(isolate_H77)|63746 -4150 LRSQAALSL 0.0 None None 0 None -4151 LRSQFPLIL 0.0 None None 0 None -4152 LRTEQNDFI 0.0 None None 0 None -4153 LRVSDGSLL 0.0 None None 0 None -4154 LRWEYGSIL 0.714053568268 WEYGSI WDFGSV 29.0 72301|envelope_protein|YP_001527880.1|West_Nile_virus_NY-99|10000971 -4155 LRYFLKHGI 0.202505548815 LRYFLKHGI MRYVLDHLI 24.0 25237|Transcription_activator_BRLF1|P03209.1|Human_herpesvirus_4_strain_B95-8|10377 -4156 LRYGAALIY 0.0 None None 0 None -4157 LSEFPEDSY 0.0 None None 0 None -4158 LSFKRQRAM 0.0 None None 0 None -4159 LSIIRFKGL 0.0 None None 0 None -4160 LSPMNHLCY 0.0 None None 0 None -4161 LSSLWYHTY 0.0419625022834 SLWYHTY DMWEHAF 22.0 9415|Superoxide_dismutase|P17670.1|Mycobacterium_tuberculosis|1773 -4162 LSTCRKLSL 0.0 None None 0 None -4163 LTDYDTRFY 0.0314758674337 LTDYDTRFY VTDNNRSFY 22.0 98603|trans-sialidase,_putative|EAN82716.1|Trypanosoma_cruzi|5693 -4164 LTEPHLRLL 0.0 None None 0 None -4165 LTGLVWQRY 0.654105044037 LTGLVWQR VSGLAWTR 27.0 54797|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 -4166 LTIYAALPY 0.0 None None 0 None -4167 LTMCMKKSL 0.0 None None 0 None -4168 LTQKQVLNY 0.0 None None 0 None -4169 LVAQHYAAL 0.0 None None 0 None -4170 LVDTVIDAY 0.0 None None 0 None -4171 LVQNSCWLI 0.0 None None 0 None -4172 LVRDRMKEL 0.0 None None 0 None -4173 LWQSCEESF 0.0 None None 0 None -4174 LYAVMGRSW 0.0 None None 0 None -4175 LYEDTLYTV 0.015462532395 YEDTLYTV YENLKYSV 22.0 186551|polyprotein|AGW21594.1|Dengue_virus_1|11053 -4176 LYEDWCQTV 0.0 None None 0 None -4177 LYEDWCQTV 0.0 None None 0 None -4178 LYFHSFIRI 0.0 None None 0 None -4179 LYFLAGQSL 0.0 None None 0 None -4180 LYFTRPVPL 0.0 None None 0 None -4181 LYGEQGHRW 0.0 None None 0 None -4182 LYGHSTHDL 0.675789473684 LYGHSTHDL LYANSAHAL 26.0 144913|Hexon_protein|P04133.3|Human_adenovirus_5|28285 -4183 LYHRDLAKW 0.0701635842114 HRDLAKW HSDAACW 24.0 79506|E1_protein|BAA19893.1|Rubella_virus|11041 -4184 LYMINHFFC 0.0 None None 0 None -4185 LYPDINNPF 0.0201559961005 PDINNPF PDYNPPL 23.0 103563|polyprotein|BAB18806.1|Hepatitis_C_virus|11103 -4186 LYPPSLPPF 61.161244788 YPPSLP FPPALP 29.0 30815|Genome_polyprotein|P26662.3|Hepatitis_C_virus|11103 -4187 LYTAYHVFF 0.0 None None 0 None -4188 LYVWKSELV 0.0 None None 0 None -4189 MACDRYVAI 0.0 None None 0 None -4190 MAEVNITYV 0.0 None None 0 None -4191 MAFDRYVAI 0.0 None None 0 None -4192 MAFDRYVAI 0.0 None None 0 None -4193 MAHERRDQL 0.0 None None 0 None -4194 MAHERRDQL 0.0 None None 0 None -4195 MAIGHFGQL 0.0 None None 0 None -4196 MAKYWNQFL 0.0 None None 0 None -4197 MAMSSRLAL 0.0 None None 0 None -4198 MATAYIRSM 0.0 None None 0 None -4199 MAYDQFLAI 0.0 None None 0 None -4200 MAYDQFLAI 0.0 None None 0 None -4201 MAYSITCPI 2.71923629545 MAYSITCPI LAYGRTCVL 24.0 17620|Early_antigen_protein_D|P03191.1|Human_herpesvirus_4_strain_B95-8|10377 -4202 MCMKKSLRL 0.0 None None 0 None -4203 MERERKAIA 0.0 None None 0 None -4204 MEVEAEQLL 0.0 None None 0 None -4205 MFATDYTTI 0.0560253733504 ATDYTTI STDSTTI 24.0 108148|polyprotein|AAF65953.1|Hepatitis_C_virus|11103 -4206 MFTLRMALF 0.0 None None 0 None -4207 MGHLQIRSL 0.0 None None 0 None -4208 MGKSTHTSM 20.3108019723 GKSTH GKSTH 28.0 20686|UL123;_IE1|AAR31448.1|Human_betaherpesvirus_5|10359 -4209 MHEEGYNKL 0.0 None None 0 None -4210 MHEYKIQGL 0.0 None None 0 None -4211 MHFCGGSFI 0.0 None None 0 None -4212 MHHPGSRKF 0.0 None None 0 None -4213 MHKTGLLGL 0.0 None None 0 None -4214 MHNLLIHRV 0.0 None None 0 None -4215 MHPDGRFEC 0.0 None None 0 None -4216 MIFILFLVI 0.0 None None 0 None -4217 MIRVKDSLI 0.0 None None 0 None -4218 MKQKKSSCL 0.0 None None 0 None -4219 MLCFYTPAL 0.00401934350471 MLCFYTPAL LMCAVHPTL 19.0 7660|polyprotein|AAA45677.1|Hepatitis_C_virus_(isolate_H77)|63746 -4220 MLHLYPGPM 0.140845070423 MLHLYPGPM LFQLYRGPL 26.0 38724|Genome_polyprotein|P08617.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 -4221 MLKTGISTV 0.0 None None 0 None -4222 MLLMNLATA 0.284963760522 LMNLAT LMNLAT 28.0 422997|preC/core_protein|CAJ33968.1|Hepatitis_B_virus|10407 -4223 MLLSILLPL 0.00626047139659 MLLSILLP MLILGLLP 20.0 41971|putative_D-ribose-binding_protein|NP_301386.1|Mycobacterium_leprae|1769 -4224 MLLSQNASI 0.0 None None 0 None -4225 MLNKVLYRL 7.66146587433e-05 MLNKVLYRL LLNGWRWRL 16.0 37607|kaposin|AAC57155.1|Human_gammaherpesvirus_8|37296 -4226 MLRELSSAF 0.0 None None 0 None -4227 MLRRQIRLL 0.0 None None 0 None -4228 MLRRQIRLL 0.0 None None 0 None -4229 MLSLRESPM 0.0 None None 0 None -4230 MLTSKVTVL 0.0 None None 0 None -4231 MLYRTVREL 0.0 None None 0 None -4232 MLYRTVREL 0.0 None None 0 None -4233 MMQCHRLSW 0.0 None None 0 None -4234 MNKRLGLEL 0.0 None None 0 None -4235 MNYKKGRAF 0.0 None None 0 None -4236 MPILKSVLI 0.0 None None 0 None -4237 MPKKVISAL 0.0 None None 0 None -4238 MPLLKLSCS 4.68242710796 MPLLKLSC VPLLAIGC 26.0 180802|polyprotein|AGO67248.1|Dengue_virus_2|11060 -4239 MPQYLASPL 0.0 None None 0 None -4240 MQFTQALEV 0.0 None None 0 None -4241 MRAAYLDDL 0.0 None None 0 None -4242 MRCQYETVL 0.840717365425 MRCQYETV MNCSYENM 27.0 36306|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 -4243 MREQRERQL 0.0 None None 0 None -4244 MRLRGGRMI 0.0 None None 0 None -4245 MRPISGVML 0.0 None None 0 None -4246 MRQPLPASM 0.0 None None 0 None -4247 MRRRQCEEV 0.695739763979 RRQCEEV KKKCDEV 25.0 24765|polyprotein_[Hepatitis_C_virus]|ABR27360.1|Hepatitis_C_virus|11103 -4248 MRRYQSRVI 0.0 None None 0 None -4249 MRRYQSRVI 0.0 None None 0 None -4250 MRSCLRLAL 0.0 None None 0 None -4251 MRSCLRLAL 0.0 None None 0 None -4252 MSEGIVKLY 0.0 None None 0 None -4253 MSPRVFFLL 0.0 None None 0 None -4254 MSQSQVALL 0.0 None None 0 None -4255 MSRSYPTGL 0.0 None None 0 None -4256 MWPLHWSMW 0.57916563282 MWPLHWSMW LWPKTHTLW 28.0 184702|non-structural_protein_1|AGM49312.1|Dengue_virus|12637 -4257 MYCLMLQCW 0.418731580108 CLMLQC CLIISC 25.0 93431|pre-C/C_protein|ABY54138.1|Hepatitis_B_virus|10407 -4258 MYCMVFLVL 0.877192982456 MYCMVFLV LLCLIFLL 26.0 37466|surface_antigen|BAF44879.1|Hepatitis_B_virus|10407 -4259 MYGAETEKF 0.0 None None 0 None -4260 MYMSVLSLI 0.0 None None 0 None -4261 MYMSVLSLI 0.0 None None 0 None -4262 MYSVVPQMV 0.0 None None 0 None -4263 MYSVVPQMV 0.0 None None 0 None -4264 MYSYAVPPL 0.236147358092 MYSYAVP IYVYALP 25.0 58463|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 -4265 MYTKLVVGF 0.0 None None 0 None -4266 NEILRRYSV 0.0138030526412 NEILRRY NKIVRMY 23.0 34304|Gag_polyprotein|P88150|Human_immunodeficiency_virus_1|11676 -4267 NFIERFWRI 0.0 None None 0 None -4268 NFIERFWRI 0.0 None None 0 None -4269 NFSINWWPI 0.882013080391 NWWPI NWWTL 29.0 74886|latent_membrane_protein_1|AAS99606.1|Human_gammaherpesvirus_4|10376 -4270 NHHNRTVEV 0.0 None None 0 None -4271 NHKDNSRIR 0.0 None None 0 None -4272 NHPYWANTV 0.0 None None 0 None -4273 NHSDLAAEL 0.0416522757017 NHSDLAAEL NHDSPDAEL 22.0 44133|Genome_polyprotein|P26664.3|Hepatitis_C_virus_genotype_1|41856 -4274 NIDLAREAY 0.0 None None 0 None -4275 NILPHYLEL 0.0 None None 0 None -4276 NIVYHTASI 0.175337715345 NIVYHTAS NLVYSTTS 27.0 96898|Genome_polyprotein|SRC279960|Hepatitis_C_virus|11103 -4277 NIYSRIREY 1.58925032505 NIYSRIREY KFYSKISEY 28.0 30892|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 -4278 NLARKEYTI 0.0 None None 0 None -4279 NLGFRFHMA 0.0 None None 0 None -4280 NLKHRKTAA 0.0 None None 0 None -4281 NLLANFSFL 0.0 None None 0 None -4282 NLLSYFNNL 0.0 None None 0 None -4283 NLMAKNNQA 1.11457402686 NLMAKN TIMAKN 22.0 103654|polyprotein|BAB18806.1|Hepatitis_C_virus|11103 -4284 NLNYRDLYY 0.0 None None 0 None -4285 NLPSKRVSL 0.679430959251 NLPSKRVS NVPYKRIE 25.0 1356|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 -4286 NMHCKISLL 0.0 None None 0 None -4287 NPLLHMVTM 0.0 None None 0 None -4288 NPLRYLAVM 0.0 None None 0 None -4289 NPLRYTSIL 0.0 None None 0 None -4290 NQKRRSESF 0.0 None None 0 None -4291 NRDKLGLQI 0.0 None None 0 None -4292 NRFSSKLLA 0.0 None None 0 None -4293 NRGPATAEV 0.0 None None 0 None -4294 NRLDLVRFY 0.166495086687 RLDLVR RVDMVR 23.0 32998|UL123;_IE1|AAR31448.1|Human_betaherpesvirus_5|10359 -4295 NRNYCVSVY 12.7901880739 RNYCVSV RHYCYSL 26.0 110846|E6_protein|CAB45108.1|Human_papillomavirus_type_16|333760 -4296 NRPEEEEQV 0.0 None None 0 None -4297 NRQRHTPMY 1.41898148148 RHTPM RHTPV 26.0 62977|polyprotein|AAB67037.1|Hepatitis_C_virus_(isolate_H77)|63746 -4298 NRVGVSSKL 0.0 None None 0 None -4299 NSDSFTGFI 0.0 None None 0 None -4300 NSINQVKLL 0.0 None None 0 None -4301 NTHRSRLSL 0.0 None None 0 None -4302 NTMAFSTDY 0.0 None None 0 None -4303 NVKKQRAGL 0.0 None None 0 None -4304 NVNQRFLNV 0.0 None None 0 None -4305 NYLEKVRSL 0.454075512249 YLEKVRS YLDKVRA 28.0 74605|Circumsporozoite_protein_precursor|P08677.2|Plasmodium_vivax_strain_Belem|31273 -4306 NYRDLYYFL 0.0 None None 0 None -4307 NYSPRPICV 7.49382142688 NYSPRP HYAPRP 28.0 25149|polyprotein|BAD73994.1|Hepatitis_C_virus_subtype_1b|31647 -4308 PASTLSLGY 3.87509767739 PASTLSLGY PASIAARGY 25.0 11063|Nonstructural_protein_NS3|NP_739587.2|Dengue_virus_2_Thailand/16681/84|31634 -4309 PFPRWLKII 0.00831776852653 PFPRWL PFVQWF 23.0 37919|envelope_protein|BAF48755.1|Hepatitis_B_virus|10407 -4310 PHWASSIVL 0.0385912911549 WASSIV WGGSVV 22.0 79351|transcriptional_activator_Tax|AAG31572.1|Human_T-lymphotropic_virus_1|11908 -4311 PHYDFERSC 1.37387031452 PHYDFE PEYDLE 25.0 48896|Genome_polyprotein|P27958.3|Hepatitis_C_virus_subtype_1a|31646 -4312 PIEMNPEGY 0.0 None None 0 None -4313 PRIGYSLLL 0.0214674118902 PRIGYS PRASYS 22.0 53148|Transcription_activator_BRLF1|P03209.1|Human_herpesvirus_4_strain_B95-8|10377 -4314 PRLKWVVLV 0.0 None None 0 None -4315 PRNRKPLTV 21.9346414515 PRNRKPL PRSRTPI 26.0 88849|IE62|AAP32859.1|Human_alphaherpesvirus_3|10335 -4316 PRPSRCLLL 0.584858416083 RCLLL RCLLL 26.0 23566|tegument_protein_UL7|NP_044476.1|Human_alphaherpesvirus_2|10310 -4317 PRSEEAAVL 0.0 None None 0 None -4318 PRSKDTILL 0.0 None None 0 None -4319 PRSRWRDQL 0.0 None None 0 None -4320 PRWSCQEKL 0.0 None None 0 None -4321 PSQPANSFY 0.601059658223 PSQPANSFY PSQEPMSIY 23.0 58463|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 -4322 PTALSSLWY 0.0 None None 0 None -4323 PTDVLNGAA 0.0 None None 0 None -4324 PYPETPPRW 1.35529826852 YPETPP YPDAPP 30.0 141354|transcriptional_regulator_ICP4|NP_044662.1|Human_alphaherpesvirus_1|10298 -4325 PYQGRPKLL 2.71654929577 PYQGRP PYAGEP 26.0 65810|sporozoite_surface_protein_2|NP_705260.1|Plasmodium_falciparum_3D7|36329 -4326 PYQGRPKLL 0.442771084337 PYQGRP PYAGEP 26.0 65810|sporozoite_surface_protein_2|NP_705260.1|Plasmodium_falciparum_3D7|36329 -4327 PYTSVFLSV 0.0 None None 0 None -4328 QAEARLLAL 0.0 None None 0 None -4329 QAKVKFIGV 0.468283818619 VKFIGV VRFMGV 23.0 37153|Nuclear_antigen_EBNA-3C|Q69140.1|Human_gammaherpesvirus_4|10376 -4330 QEHVRCSAI 0.0 None None 0 None -4331 QFSFDGWKF 0.00828381734168 QFSFDGWKF QYSDRRWCF 19.0 53027|nonstructural_protein_3|NP_722463.1|Dengue_virus_1_Singapore/S275/1990|33741 -4332 QGRPKLLQL 0.0 None None 0 None -4333 QHCYMSRLL 0.0 None None 0 None -4334 QHDFCGLYM 1.18519018581 QHDFCGLYM KAKICGLYL 28.0 177701|polyprotein|ACZ60104.1|Hepatitis_C_virus_subtype_3a|356426 -4335 QHLLQRMSI 0.0 None None 0 None -4336 QHMHCLQDL 0.0 None None 0 None -4337 QHPNNSKDV 0.67707530484 HPNNS HPNNT 28.0 141306|tegument_host_shutoff_protein|NP_044643.1|Human_alphaherpesvirus_1|10298 -4338 QHQRLLEVL 0.0 None None 0 None -4339 QHTESLEYM 0.0 None None 0 None -4340 QHYAALQEY 0.0199846777357 HYAALQ HQAAMQ 22.0 101673|gag_protein|ABO73990.1|Human_immunodeficiency_virus_1|11676 -4341 QILSRVAAL 1.04035259267 ILSRVAAL MLSRVAAV 27.0 98253|trans-sialidase,_putative|EAN81042.1|Trypanosoma_cruzi|5693 -4342 QLMMSLLQL 0.0 None None 0 None -4343 QLREHAATL 0.0 None None 0 None -4344 QLRRSKVSV 0.0 None None 0 None -4345 QLYPRLKML 0.0 None None 0 None -4346 QLYPRLKML 0.0 None None 0 None -4347 QMLRIFKEM 0.0 None None 0 None -4348 QMYMSVLSL 0.0 None None 0 None -4349 QPAWRKASA 0.0 None None 0 None -4350 QPLRNFISV 0.0 None None 0 None -4351 QPMCRICHE 0.449806949807 MCRICH MCDECH 26.0 107790|polyprotein|AAD56189.1|Hepatitis_C_virus|11103 -4352 QRAPVGKLL 0.0 None None 0 None -4353 QRAVSRNLM 0.0 None None 0 None -4354 QRFLFIMFL 0.0 None None 0 None -4355 QRFLNVQEL 0.0264820306828 QRFLNVQEL ERYLKDQQL 22.0 14101|envelope_glycoprotein|ABI16336.1|Human_immunodeficiency_virus_1|11676 -4356 QRGEGILDM 0.0 None None 0 None -4357 QRHGFGEEI 0.00190751343828 QRHGFGEEI QTHIFAEVL 19.0 73862|EBNA-1_protein|Q777E1|Human_gammaherpesvirus_4|10376 -4358 QRIQMYMSV 0.0 None None 0 None -4359 QRIVKPTSI 0.0 None None 0 None -4360 QRLEPVYFV 0.0 None None 0 None -4361 QRLEVPIEM 0.0 None None 0 None -4362 QRMELLITF 0.0 None None 0 None -4363 QRQARQYQL 0.0 None None 0 None -4364 QRRPSSVGL 0.0 None None 0 None -4365 QRRSIPFQM 0.0 None None 0 None -4366 QRSGKPVLM 0.0 None None 0 None -4367 QRSNSETKV 0.0 None None 0 None -4368 QRSRKGDLL 0.0 None None 0 None -4369 QSEDRSHTL 0.0 None None 0 None -4370 QSQPFSMQY 0.0 None None 0 None -4371 QSQPGNALY 0.0 None None 0 None -4372 QTCKANLCY 11.2279615819 QTCKANLCY EFCRVLCCY 23.0 11956|UL123;_IE1|AAR31448.1|Human_betaherpesvirus_5|10359 -4373 QTLACNLCY 0.0 None None 0 None -4374 QVKRKVQAL 0.0 None None 0 None -4375 QYMLTLFTA 0.0 None None 0 None -4376 RAEDTALYY 0.0 None None 0 None -4377 RAIYHSCSL 0.0 None None 0 None -4378 RAKYRESLL 0.0 None None 0 None -4379 RAPQRIPSL 0.00198664006271 PQRIPSL PSRGPKL 19.0 74800|Genome_polyprotein|SRC279960|Hepatitis_C_virus_subtype_2b|31650 -4380 RARLQHCSA 0.0 None None 0 None -4381 RARYYIQVA 0.0 None None 0 None -4382 RASQRMSSV 0.0 None None 0 None -4383 RATARFHQL 0.0 None None 0 None -4384 RFFSRFTAV 0.0 None None 0 None -4385 RFHRVIKDF 0.0 None None 0 None -4386 RFKRKSVVA 0.0 None None 0 None -4387 RFLFIMFLF 0.0 None None 0 None -4388 RFLRNFPQI 0.406366189382 LRNFPQI VRHFPRI 25.0 187106|Vpr_protein|BAA93983.1|Human_immunodeficiency_virus_1|11676 -4389 RFMKYLVNF 0.219129686223 MKYLVNF LEYLVSF 25.0 69474|core_protein|BAF42671.1|Hepatitis_B_virus|10407 -4390 RFNMLNQIF 0.0 None None 0 None -4391 RFQDHRWEL 0.0 None None 0 None -4392 RHFEEALQT 0.0 None None 0 None -4393 RHFRLMHNL 0.0 None None 0 None -4394 RHIRHGNVI 0.0 None None 0 None -4395 RHLGDQMEV 17.8416258526 RHLGDQMEV RHTSDHMSI 26.0 17278|Genome_polyprotein|P06441.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 -4396 RHRCRNRFV 0.0 None None 0 None -4397 RHSPRNLIY 0.457200416329 HSPRNLIY HGPTPLLY 25.0 6591|polyprotein|AAB67037.1|Hepatitis_C_virus_(isolate_H77)|63746 -4398 RHTPMYYFL 0.0094183334308 RHTPMYY RHHNMVY 20.0 144403|polyprotein|AAK08509.1|Hepatitis_C_virus_subtype_1b|31647 -4399 RHTPMYYFL 0.00293201762289 RHTPMYY RHHNMVY 20.0 144403|polyprotein|AAK08509.1|Hepatitis_C_virus_subtype_1b|31647 -4400 RLIVKSREL 0.0 None None 0 None -4401 RLKQEIKRL 0.0 None None 0 None -4402 RLMCGPNTI 1.71760391198 LMCGPNTI ILCVPNAV 26.0 183741|polyprotein|AGS49173.1|Dengue_virus_2|11060 -4403 RLRRVASAL 0.0 None None 0 None -4404 RMCKFLQYF 0.0 None None 0 None -4405 RMSSVGANF 0.0 None None 0 None -4406 RNFPQIYIL 0.957507082153 RNFPQIY RHFPRIW 26.0 187106|Vpr_protein|BAA93983.1|Human_immunodeficiency_virus_1|11676 -4407 RNPQELWHF 0.135340359953 NPQEL NPQEV 24.0 69799|envelope_glycoprotein|BAE96221.1|Human_immunodeficiency_virus_1|11676 -4408 RNRKRFCVP 0.0 None None 0 None -4409 RPGSRGCPM 1.15273082827 RPGSRGCPM KPGTSGSPI 28.0 150341|polyprotein|AGW21594.1|Dengue_virus_1|11053 -4410 RPKYSFHRL 0.0 None None 0 None -4411 RPRARLAAL 0.0 None None 0 None -4412 RPRARYYIQ 0.0 None None 0 None -4413 RPRQGRWWL 0.0 None None 0 None -4414 RQFPKKSLM 0.0 None None 0 None -4415 RQFYLFYNF 0.0 None None 0 None -4416 RQMISELLF 0.0 None None 0 None -4417 RQQQDYWLM 0.0241357685845 QQDYWLM QQNWWTL 25.0 74886|latent_membrane_protein_1|AAS99606.1|Human_gammaherpesvirus_4|10376 -4418 RRENSLSEI 0.0 None None 0 None -4419 RRFNMLNQI 0.0 None None 0 None -4420 RRGEAEKRL 0.0 None None 0 None -4421 RRGGSGAMV 0.0 None None 0 None -4422 RRKQSEMYI 0.0 None None 0 None -4423 RRLDYDHKL 0.0 None None 0 None -4424 RRPSRAMWL 0.0 None None 0 None -4425 RRQDYQEIL 0.0 None None 0 None -4426 RRSDAEKQL 0.111181455484 RSDAEKQ RADEEQQ 22.0 70687|ESAT-6-like_protein_esxB|P0A566.2|Mycobacterium_tuberculosis|1773 -4427 RRSKVSVEM 0.0 None None 0 None -4428 RRSPSFSRV 0.0 None None 0 None -4429 RRVASALLL 0.0 None None 0 None -4430 RRVPYRGSV 0.0 None None 0 None -4431 RRYLKSGVV 0.0 None None 0 None -4432 RSADWQRKI 0.0 None None 0 None -4433 RSELNSVEY 0.0 None None 0 None -4434 RSFPAGVEM 0.0 None None 0 None -4435 RTQDAIHEL 0.0 None None 0 None -4436 RTSSIFYSF 0.0 None None 0 None -4437 RVGQMAFVF 0.0 None None 0 None -4438 RVNDCILQV 0.0 None None 0 None -4439 RVRRRGQKL 0.000560646888862 RVRRRGQK RLRPGGKK 19.0 54741|gag_polyprotein|BAA00992.1|Human_immunodeficiency_virus_1|11676 -4440 RVSDGSLLY 0.0 None None 0 None -4441 RWQGRVRTL 0.0 None None 0 None -4442 RYAALLKCW 0.0377103973581 RYAALLKCW RYMGEDGCW 22.0 185573|polyprotein|CDF77361.1|Dengue_virus_3|11069 -4443 RYARPSRLV 36.924260273 RYARPSRL RFAQPSAL 27.0 142233|ATP-dependent_helicase|NP_217813.1|Mycobacterium_tuberculosis|1773 -4444 RYCLTTLTI 0.0 None None 0 None -4445 RYFDEPVEL 0.0 None None 0 None -4446 RYFDEPVEL 0.0 None None 0 None -4447 RYFLKHGIL 0.525137542938 RYFLKHGI RYVLDHLI 22.0 25237|Transcription_activator_BRLF1|P03209.1|Human_herpesvirus_4_strain_B95-8|10377 -4448 RYILLKRSL 0.0 None None 0 None -4449 RYLENGKEM 0.0 None None 0 None -4450 RYLKSGVVL 0.0 None None 0 None -4451 RYLPDCDYL 0.48206481189 RYLPDCDYL RYAPACKPL 25.0 56502|polyprotein|BAD73994.1|Hepatitis_C_virus_subtype_1b|31647 -4452 RYRSIISDI 0.0 None None 0 None -4453 RYVAICAPL 1.06464167115 RYVAICAPL RYAPACKPL 29.0 56502|polyprotein|BAD73994.1|Hepatitis_C_virus_subtype_1b|31647 -4454 RYVASCKPL 0.477699027983 RYVASCKPL RYAPACKPL 37.0 56502|polyprotein|BAD73994.1|Hepatitis_C_virus_subtype_1b|31647 -4455 SADYINANY 0.0 None None 0 None -4456 SAEECRTEL 0.0 None None 0 None -4457 SAKQQNQIL 0.0 None None 0 None -4458 SAKQQNQIL 0.0 None None 0 None -4459 SALGREHPA 0.0 None None 0 None -4460 SARDQPSSV 0.0 None None 0 None -4461 SARLRQRAV 0.0 None None 0 None -4462 SASNNNSEL 0.0 None None 0 None -4463 SAVRRDLTF 0.0 None None 0 None -4464 SAYDGKDYI 0.0 None None 0 None -4465 SCSSNPHLL 0.0 None None 0 None -4466 SEEERGLEL 0.0 None None 0 None -4467 SEKDRPVKV 0.0 None None 0 None -4468 SESHRTSLL 0.0 None None 0 None -4469 SEVERLDVL 0.0 None None 0 None -4470 SFFNCLWEV 0.674192438284 FFNCLWEV LLNCLWSV 34.0 37536|Spike_glycoprotein_precursor|P15423.1|Human_coronavirus_229E|11137 -4471 SFPGRVREL 0.0 None None 0 None -4472 SFQTITEQF 0.0 None None 0 None -4473 SFVDAIHTF 0.0 None None 0 None -4474 SGFEFSQVL 0.0 None None 0 None -4475 SGMARVGSL 0.484375 GMARVG GMSRIG 26.0 21347|Nucleoprotein|P59595.1|SARS_coronavirus|227859 -4476 SHKEAITAL 0.0 None None 0 None -4477 SHKKQSSVI 0.0 None None 0 None -4478 SHLQRIGTI 0.0 None None 0 None -4479 SHLTIVILF 0.0 None None 0 None -4480 SHMYVATGI 0.0 None None 0 None -4481 SHNRHVPKI 0.25312133776 RHVPKI RHFPRI 25.0 187106|Vpr_protein|BAA93983.1|Human_immunodeficiency_virus_1|11676 -4482 SHPLHYTTI 0.0 None None 0 None -4483 SHPLHYTTI 0.0 None None 0 None -4484 SHQPLPGTL 0.0 None None 0 None -4485 SHRNPLLDL 0.0 None None 0 None -4486 SHSPAGELT 0.168377764503 PAGELT PQGQLT 23.0 13701|Trans-activator_protein_BZLF1|P03206.2|Human_gammaherpesvirus_4|10376 -4487 SHSSNPHLL 0.0 None None 0 None -4488 SHTLLLTQL 0.0 None None 0 None -4489 SIFYSFLPL 0.0538659105423 SIFYSFLPL SIYVYALPL 21.0 58463|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 -4490 SKFGQGTGL 0.0 None None 0 None -4491 SKQNMPQYL 0.0 None None 0 None -4492 SLAKFDAPL 0.0 None None 0 None -4493 SLDTTTWEY 0.0 None None 0 None -4494 SLFTCVLQL 0.0 None None 0 None -4495 SLGDNSEYL 0.0 None None 0 None -4496 SLHHKHKEL 0.0 None None 0 None -4497 SLIDSSRVV 0.0 None None 0 None -4498 SLKLTQSSA 0.0 None None 0 None -4499 SLLRKHQIL 56.8225353198 SLLRKHQIL SLLRNHNLV 28.0 96898|Genome_polyprotein|SRC279960|Hepatitis_C_virus|11103 -4500 SLLRKHQIT 1.76449738892 SLLRKHQI SLLRNHNL 27.0 96898|Genome_polyprotein|SRC279960|Hepatitis_C_virus|11103 -4501 SLLVHGGPL 0.203585933289 VHGGPL VHAGPI 27.0 24557|Gag_polyprotein|P03347.3|Human_immunodeficiency_virus_1|11676 -4502 SLNHRGRVM 0.0 None None 0 None -4503 SLNHRGRVM 0.0 None None 0 None -4504 SLNPKKFSI 0.0 None None 0 None -4505 SLRAEDTAL 0.0 None None 0 None -4506 SLSETVRLV 0.0 None None 0 None -4507 SLSVRTSGL 0.0 None None 0 None -4508 SLWYHTYGL 0.584082675016 YHTYGL FHSYGV 26.0 232152|rhoptry_kinase_family_protein|AFO54841.1|Toxoplasma_gondii_type_III|398031 -4509 SLYTAYHVF 0.0168850134338 SLYTAYHV KLYCSYEV 22.0 32250|FL-160-2_protein_-_Trypanosoma_cruzi|JH0823|Trypanosoma_cruzi|5693 -4510 SLYVWKSEL 0.0 None None 0 None -4511 SMAKYWNQF 0.0 None None 0 None -4512 SMKAERPPA 0.0 None None 0 None -4513 SMKNLQRAV 0.0 None None 0 None -4514 SMKVHIKAM 0.0 None None 0 None -4515 SMMTATIVF 0.0 None None 0 None -4516 SMPANFETI 0.0 None None 0 None -4517 SMREALREL 0.0 None None 0 None -4518 SMREAVREL 0.0 None None 0 None -4519 SMRYFITSV 0.0 None None 0 None -4520 SPGPFFWMF 0.0 None None 0 None -4521 SPLFYSTCM 0.620468376578 SPLFYST SPITYST 27.0 107873|Genome_polyprotein|P26664.3|Hepatitis_C_virus|11103 -4522 SPLQLPAPL 0.0 None None 0 None -4523 SPLRYISIL 0.0 None None 0 None -4524 SPMYFFLSY 0.0 None None 0 None -4525 SPRSRPSDI 0.0 None None 0 None -4526 SPRVFFLLM 0.0 None None 0 None -4527 SPSSAYLLF 0.0 None None 0 None -4528 SQHPAQQQI 0.0 None None 0 None -4529 SQMSQLMGL 0.0776138458536 SQMSQLM AQMWQLM 22.0 182599|polyprotein|AGW21594.1|Dengue_virus_1|11053 -4530 SQPGNALYF 0.0 None None 0 None -4531 SRAMWLSLF 0.0 None None 0 None -4532 SRATADPEV 0.0 None None 0 None -4533 SRCLLLPLL 5.4232325855 RCLLL RCLLL 26.0 23566|tegument_protein_UL7|NP_044476.1|Human_alphaherpesvirus_2|10310 -4534 SREDDNRER 0.0 None None 0 None -4535 SRENRWTTV 0.132816935515 RENRWT REDQWC 23.0 53476|polyprotein|AGO67248.1|Dengue_virus_2|11060 -4536 SRFCSLHCL 0.0 None None 0 None -4537 SRFTAVREF 0.0269793149431 SRFTAVR SRYWAIR 22.0 60867|nucleoprotein|CAZ65591.1|Influenza_A_virus|11320 -4538 SRFTLRCMV 1.61952838872 SRFTLRCM GRWTGRCM 26.0 110215|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 -4539 SRFVVRPLL 0.0 None None 0 None -4540 SRGQEIKTI 0.0 None None 0 None -4541 SRHDFHVDL 0.0424328495879 SRHDFHVDL TLHEYMLDL 22.0 178351|Protein_E7|P03129.1|Human_papillomavirus_type_16|333760 -4542 SRKGDLLRI 0.0 None None 0 None -4543 SRKKRRSPP 0.0 None None 0 None -4544 SRKLRKLPT 0.0 None None 0 None -4545 SRLHTPVYF 0.0 None None 0 None -4546 SRNAYSLEI 0.0 None None 0 None -4547 SRNDFEWVY 0.02135862433 SRNDFE GRNSFE 22.0 37364|P53_HUMAN_Cellular_tumor_antigen_p53_(Tumor_suppressor_p53)_(Phosphoprotein_p53)_(Antigen_NY-CO-13)|P04637.2|Homo_sapiens|9606 -4548 SRPGALEHL 0.0 None None 0 None -4549 SRPSSKQNM 0.0 None None 0 None -4550 SRQMISELL 0.0 None None 0 None -4551 SRRARGREK 0.0 None None 0 None -4552 SRRSFWSEL 0.0 None None 0 None -4553 SRSRNAYSL 0.0 None None 0 None -4554 SRSVDVTNI 0.0 None None 0 None -4555 SRTVWEEMV 0.825050427473 SRTVWE TRTVWQ 28.0 120187|E1_protein|BAA19893.1|Rubella_virus|11041 -4556 SRWRDQLLF 0.0 None None 0 None -4557 SRYARPSRL 0.939932458239 RYARPSRL RFAQPSAL 27.0 142233|ATP-dependent_helicase|NP_217813.1|Mycobacterium_tuberculosis|1773 -4558 SSASLNSNY 0.0 None None 0 None -4559 SSDEIVQEL 0.0 None None 0 None -4560 SSKQHLKPA 0.0 None None 0 None -4561 SSLARELSL 0.0 None None 0 None -4562 SSLRRMNSF 0.00406654233374 LRRMNSF LRKKSSF 21.0 116781|Nucleoprotein|P05133.1|Hantaan_virus_76-118|11602 -4563 SSRGNGKMM 0.0 None None 0 None -4564 SSTSHIPEV 0.0 None None 0 None -4565 SSYSRVALV 0.0 None None 0 None -4566 STDDATWAA 0.0 None None 0 None -4567 STERPKMTY 0.0 None None 0 None -4568 STIYIFALF 1.09241706161 TIYIFAL SIYVYAL 26.0 58463|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 -4569 STKVHIKVL 0.0 None None 0 None -4570 STQTHPLTL 4.38726372945 TQTHPLT TLTHPIT 30.0 71412|polyprotein_[Hepatitis_C_virus_subtype_1a]|ABV46251.2|Hepatitis_C_virus_subtype_1a|31646 -4571 STSHVYHLF 0.0 None None 0 None -4572 STYNETNLI 0.0 None None 0 None -4573 STYPDQQHV 2.03088323857 STYPDQQHV SYYPDQKSL 28.0 28594|IMMUNOGENIC_PROTEIN_MPT64_(ANTIGEN_MPT64/MPB64)|CAA98382.1|Mycobacterium_tuberculosis_H37Rv|83332 -4574 SVEEKGKLL 0.0 None None 0 None -4575 SVFPTQLQL 2.29326254822 SVFPTQLQL GLFPTQIQV 32.0 20865|Nucleoprotein|P41269.1|Puumala_hantavirus|11604 -4576 SVFSEQWIF 0.0264970465526 SVFSEQWIF AVFGPLWIL 23.0 96123|Genome_polyprotein|P26664.3|Hepatitis_C_virus_(isolate_H77)|63746 -4577 SVRENCCSL 0.0 None None 0 None -4578 SWMPALECL 0.05038120655 SWMPALECL SWDETWKCL 23.0 146569|polyprotein|ADF97231.1|Hepatitis_C_virus_subtype_3a|356426 -4579 SWPLWTAIF 1.22480631271 SWPLW SWCLW 27.0 39591|polyprotein|AAA45677.1|Hepatitis_C_virus_(isolate_H77)|63746 -4580 SWVSSTLGF 0.0 None None 0 None -4581 SYAKNAQDL 0.0 None None 0 None -4582 SYARILGTV 0.0 None None 0 None -4583 SYAVICNNF 0.0 None None 0 None -4584 SYFCILRTI 0.0 None None 0 None -4585 SYFGLATVF 0.0 None None 0 None -4586 SYFLATDTI 0.0 None None 0 None -4587 SYFNNLHLW 4.77360749628 FNNLHL FHNLHL 29.0 79390|Protein_Tax-1|P0C213.1|Human_T-cell_lymphotropic_virus_type_1_(african_isolate)|39015 -4588 SYGVNLYQF 5.06976518192 YGVNLYQF YGYPVYVF 22.0 23807|tax|AAG48731.1|Human_T-lymphotropic_virus_2|11909 -4589 SYIYILITI 0.0560487592099 YILITI YVILTI 23.0 186620|polyprotein|AFP27208.1|Dengue_virus_4|11070 -4590 SYKFLAPWI 0.348021972633 YKFLAPW YRFVAPG 27.0 149053|NS3_gene_product|AAB02124.1|Hepatitis_C_virus|11103 -4591 SYPSIHRFI 0.601659125972 PSIHRFI PGIYRFV 27.0 149053|NS3_gene_product|AAB02124.1|Hepatitis_C_virus|11103 -4592 SYPSQPDGF 0.0 None None 0 None -4593 SYSLISEKL 0.0 None None 0 None -4594 SYVMDHFDI 0.965095685508 YVMDHF YVLDHL 27.0 25237|Transcription_activator_BRLF1|P03209.1|Human_herpesvirus_4_strain_B95-8|10377 -4595 SYVRIGATI 0.0 None None 0 None -4596 SYWGVFAPI 0.000607367462934 SYWGVFAPI SLWKDGAPL 19.0 140600|glutamine_synthetase_GLNA1_(glutamine_synthase)_(GS-I)|NP_216736.1|Mycobacterium_tuberculosis_H37Rv|83332 -4597 SYYKIVSSI 0.0193185218111 KIVSSI KLVSSV 22.0 95262|LAMP|AAK72632.1|Human_gammaherpesvirus_8|37296 -4598 TAAIRPKSL 0.0 None None 0 None -4599 TADVGLAGY 0.0 None None 0 None -4600 TAFDESISL 0.0 None None 0 None -4601 TAMAYDQFL 0.0 None None 0 None -4602 TDKERQRLL 0.0 None None 0 None -4603 TDYDTRFYM 0.0 None None 0 None -4604 TEFGQKQKL 0.0 None None 0 None -4605 TERDQIELL 0.0 None None 0 None -4606 TFDRLAYLW 0.0 None None 0 None -4607 TFEDNLRSL 0.0 None None 0 None -4608 TFGEVNYFF 0.243387329538 GEVNYF GEADYF 25.0 24535|EBNA-1_protein|Q777E1|Human_gammaherpesvirus_4|10376 -4609 TFITSVIRF 0.0 None None 0 None -4610 TFLIAMVFI 0.0 None None 0 None -4611 TFNDWFEII 0.755265816333 FNDWFEI FKDWEEL 27.0 6556|X_protein|AAP06597.1|Hepatitis_B_virus|10407 -4612 TFSCQLHKF 0.0 None None 0 None -4613 THAPERDLC 0.0 None None 0 None -4614 THASLSNHV 0.009151449223 HASLSNH HAMSSTH 21.0 140686|ESAT-6-like_protein_esxH|P0A568.2|Mycobacterium_tuberculosis|1773 -4615 THHGPAFSI 0.0 None None 0 None -4616 THIFGLMVI 0.0 None None 0 None -4617 THIHAAACI 0.0 None None 0 None -4618 THMERVLSL 0.0 None None 0 None -4619 THMERVLSL 0.0 None None 0 None -4620 THPIYYLKI 0.0 None None 0 None -4621 THQEALMKL 0.0 None None 0 None -4622 THREGISAI 0.561269053294 THREGI NHRQGI 25.0 34642|methionine_sulfoxide_reductase_B|YP_169878.1|Francisella_tularensis_subsp._tularensis_SCHU_S4|177416 -4623 THRSRLSLG 0.0 None None 0 None -4624 THTSYQLSA 0.0 None None 0 None -4625 THYQGTWYL 0.0 None None 0 None -4626 TIKQRPKPT 0.0 None None 0 None -4627 TKFESNLCV 0.0 None None 0 None -4628 TLDKKLEYY 1.51757846321 LDKKLE LDKKVE 26.0 27000|Heat_shock_protein_HSP_90-beta|P08238.4|Homo_sapiens|9606 -4629 TLERAALRY 0.0 None None 0 None -4630 TLGLIFLCL 0.0 None None 0 None -4631 TLMVVVWVL 0.0 None None 0 None -4632 TLTIRALPA 0.0 None None 0 None -4633 TMCMYFRPL 0.0 None None 0 None -4634 TMETSFFSF 0.0 None None 0 None -4635 TMGSWTCLF 0.475156091949 SWTCL TWKCL 24.0 146569|polyprotein|ADF97231.1|Hepatitis_C_virus_subtype_3a|356426 -4636 TMRTRHFTG 0.0 None None 0 None -4637 TMRYIHFLF 0.0 None None 0 None -4638 TMSPRVFFL 0.0 None None 0 None -4639 TPGNRTKCF 2.47406881013 GNRTKCF GNASRCW 24.0 21385|polyprotein|AAY82034.1|Hepatitis_C_virus_genotype_1|41856 -4640 TPKSMQSTL 0.0 None None 0 None -4641 TPNFRRRAI 0.0 None None 0 None -4642 TPSERSKPL 1.35857438639 SERSKP SERSQP 26.0 33856|polyprotein|BAA03375.1|Hepatitis_C_virus|11103 -4643 TPSTQTHPL 0.0722037478202 TPSTQTH TPAVQTN 24.0 149037|NS4B_protein|NP_751926.1|Hepatitis_C_virus_(isolate_H77)|63746 -4644 TRAERLTWL 0.0 None None 0 None -4645 TRALHRLIV 0.0 None None 0 None -4646 TRASDRRGI 0.0 None None 0 None -4647 TRDAPGLRV 0.0 None None 0 None -4648 TREVTVNVL 0.0 None None 0 None -4649 TRFPLKTAF 0.0 None None 0 None -4650 TRFPLPEAF 0.0 None None 0 None -4651 TRFRSFSSL 0.0 None None 0 None -4652 TRFYMYEIL 0.0 None None 0 None -4653 TRGPCRRRF 7.20424999304 GPCRRRF GPADRRF 27.0 155637|tegument_protein|CAB06732.1|Human_alphaherpesvirus_2|10310 -4654 TRGPQRQIL 0.0 None None 0 None -4655 TRGRHQKKI 0.0 None None 0 None -4656 TRHGSILAC 0.0 None None 0 None -4657 TRHRCRNRF 0.0 None None 0 None -4658 TRNCNRHLC 4.92100160943 NCNRHLC NCQKPLC 28.0 110394|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 -4659 TRPSEELEL 0.0 None None 0 None -4660 TRPTASSSV 0.0 None None 0 None -4661 TRRSQKRLQ 0.0 None None 0 None -4662 TRSAEPGYL 0.0 None None 0 None -4663 TRSSKPSDM 0.0 None None 0 None -4664 TRSWGTPQL 0.114998444797 RSWGTPQ KLWESPQ 22.0 32243|C_protein|BAB60863.1|Measles_virus|11234 -4665 TRTPHSTRC 0.683754788248 TPHSTRC TPDSTPC 27.0 53041|phosphorylated_matrix_protein_(pp65)|AAA45996.1|Human_betaherpesvirus_5|10359 -4666 TRVGSKLLI 0.638888888889 TRVGSKLLI TRVGTKHAI 26.0 186041|polyprotein|AGO67248.1|Dengue_virus_2|11060 -4667 TRYSAQADI 0.0 None None 0 None -4668 TSMWRTYVM 0.0 None None 0 None -4669 TSMWRTYVM 0.0 None None 0 None -4670 TTDGRNYIV 0.479879498782 DGRNY DGVNY 22.0 56343|structural_protein|BAA00705.1|Hepatitis_C_virus|11103 -4671 TTFDRLAYL 0.61388887253 TFDRLAYL TFDRLQVL 28.0 66405|polyprotein|AAB67037.1|Hepatitis_C_virus_(isolate_H77)|63746 -4672 TTMEDQLLF 0.0 None None 0 None -4673 TVHTRNHTA 0.0 None None 0 None -4674 TVIDAYMNF 0.0 None None 0 None -4675 TVLHRPHSA 0.0 None None 0 None -4676 TVSPQPQEV 0.980041819158 SPQPQEV DPNPQEV 28.0 69799|envelope_glycoprotein|BAE96221.1|Human_immunodeficiency_virus_1|11676 -4677 TWLQVLEAI 0.0 None None 0 None -4678 TYEEPCQAI 0.0 None None 0 None -4679 TYLADRVQI 0.0 None None 0 None -4680 TYLYPPKHW 0.0 None None 0 None -4681 TYVLYYDAL 0.0 None None 0 None -4682 TYYPLKPEI 0.443101725077 YPLKPEI FPVRPQV 25.0 288104|nef_protein|ACR27130.1|Human_immunodeficiency_virus_1|11676 -4683 TYYPLKPEI 0.232710970823 YPLKPEI FPVRPQV 25.0 288104|nef_protein|ACR27130.1|Human_immunodeficiency_virus_1|11676 -4684 VAKKKEAPA 0.0 None None 0 None -4685 VARERRKAE 0.0 None None 0 None -4686 VFERDFFKI 0.0 None None 0 None -4687 VFETGTFLI 0.0 None None 0 None -4688 VFLPMTLLL 0.0 None None 0 None -4689 VFRQGHQLF 0.0 None None 0 None -4690 VFTRVSAYI 0.0107141857233 FTRVSAY FTKNSAF 21.0 44214|UL123;_IE1|AAR31448.1|Human_betaherpesvirus_5|10359 -4691 VFYTIFTPI 0.0 None None 0 None -4692 VGKKRHDPL 0.0 None None 0 None -4693 VHALRLHLY 0.0 None None 0 None -4694 VHFDHFHPC 0.867623345477 HFDHFHP HYDQDHP 29.0 180758|Nonstructural_protein_NS5|NP_739590.2|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -4695 VHFLREVTV 0.0 None None 0 None -4696 VHHLAVSGV 1.19230769231 LAVSGV LAVSGV 26.0 419005|polyprotein|AGW21594.1|Dengue_virus_1|11053 -4697 VHIKAMQTV 0.0 None None 0 None -4698 VHIKVLQTV 0.0 None None 0 None -4699 VHKKGYNKL 0.0 None None 0 None -4700 VHKQFPITL 0.774571436042 FPITL FPITL 26.0 143705|Genome_polyprotein|P08617.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 -4701 VHKTDLERM 0.0 None None 0 None -4702 VHRGTGAVY 0.02244433038 RGTGAVY EGEGAVF 22.0 119822|110_kd_polyprotein_precursor|CAA28880.1|Rubella_virus|11041 -4703 VHSENLQNW 0.0 None None 0 None -4704 VLAIQRCPM 0.0 None None 0 None -4705 VLDEMRCQY 112.599178113 VLDEMRC VIDPRRC 24.0 150556|polyprotein|AGW21594.1|Dengue_virus_1|11053 -4706 VLKSTSCSI 0.0 None None 0 None -4707 VMKHLLSPL 0.0 None None 0 None -4708 VMSCVWFTI 0.0 None None 0 None -4709 VQMYRGHPA 0.131620119942 YRGHPA YAGEPA 23.0 65810|sporozoite_surface_protein_2|NP_705260.1|Plasmodium_falciparum_3D7|36329 -4710 VQNEDVTLL 0.0 None None 0 None -4711 VQPSQWASI 10.0381165919 PSQWA PSSWA 26.0 27878|large_surface_antigen|CAC87019.1|Hepatitis_B_virus|10407 -4712 VRDRMKELL 0.0 None None 0 None -4713 VRELRDMGI 0.0014787525281 VRELRDMG VKENFSMG 16.0 59090|nonstructural_protein_4B|YP_001527886.1|West_Nile_virus_NY-99|10000971 -4714 VRFQDESVV 0.0 None None 0 None -4715 VRFVTRYIY 0.0 None None 0 None -4716 VRFVVTITV 0.0 None None 0 None -4717 VRGTTLHLL 0.0 None None 0 None -4718 VRHQRVHQA 0.0 None None 0 None -4719 VRLKRSIQF 0.0 None None 0 None -4720 VRLSYKLTF 0.0 None None 0 None -4721 VRMEVISVT 0.0 None None 0 None -4722 VRMEVVSIT 0.0 None None 0 None -4723 VRNDHMNLR 0.0 None None 0 None -4724 VRNRCNIYI 0.0 None None 0 None -4725 VRPRARYYI 0.0 None None 0 None -4726 VRQGGVFRL 0.0 None None 0 None -4727 VRRLGPKLL 0.0 None None 0 None -4728 VRRLHCSAA 0.0 None None 0 None -4729 VRRMLTSKV 0.0 None None 0 None -4730 VRRRRRCPG 0.0 None None 0 None -4731 VRSLNLVLM 0.0 None None 0 None -4732 VRSNLEPLF 0.0 None None 0 None -4733 VRVGSDMLI 0.0 None None 0 None -4734 VRVTQKFHM 0.0 None None 0 None -4735 VSDDLVKQY 0.0 None None 0 None -4736 VSGHVSMKY 0.0 None None 0 None -4737 VSSSSSGGY 0.0 None None 0 None -4738 VTADSDPAY 0.0 None None 0 None -4739 VTAPRATTL 0.0 None None 0 None -4740 VTDVLTEPH 0.0 None None 0 None -4741 VTMDWLVRI 20.8868827501 DWLVRI SWMIRI 25.0 185817|envelope_protein|AGW23590.1|Dengue_virus_4|11070 -4742 VVAPRTLLL 0.629096369435 VVAPRTL AISPRTL 25.0 50292|gag_protein|ACR27140.1|Human_immunodeficiency_virus_1|11676 -4743 VVESLVEAY 0.0 None None 0 None -4744 VVHEVQRYL 0.0 None None 0 None -4745 VVKSKQVAL 0.0 None None 0 None -4746 VVPQMVNPF 0.0 None None 0 None -4747 VVSDVPEEL 0.0 None None 0 None -4748 VYFHMTLSF 0.0 None None 0 None -4749 VYHLFCALL 0.00735750627888 VYHLFCAL LWHYPCTL 19.0 54824|polyprotein_precursor|BAA01583.1|Hepatitis_C_virus|11103 -4750 VYISLFTCV 0.0 None None 0 None -4751 VYLRRHRDV 0.989106753813 LRRHRDV LRRHIDL 26.0 51526|HCV-1|AAA45676.1|Hepatitis_C_virus|11103 -4752 VYPRGFQEK 0.0 None None 0 None -4753 VYQVLSGGW 0.0 None None 0 None -4754 VYSEYGMDV 0.239110747927 VYSEYG TYSTYG 23.0 67471|Genome_polyprotein|Q99IB8.3|Hepatitis_C_virus_JFH-1|356411 -4755 VYSLRTRAI 0.0546114862252 VYSLRTRAI AYSQQTRGL 22.0 111816|polyprotein|BAA09072.1|Hepatitis_C_virus|11103 -4756 VYSLYWSIL 0.175675675676 VYSLYWSI LYELIWNV 26.0 108965|Prolipoprotein_diacylglyceryl_transferase|O06131.1|Mycobacterium_tuberculosis|1773 -4757 VYVVSNNNL 0.0 None None 0 None -4758 VYVVTKFLM 0.110774648364 YVVTKFLM HPITKFVM 25.0 103389|unnamed_protein_product_[Hepatitis_C_virus]|BAA14035.1|Hepatitis_C_virus|11103 -4759 VYYLLELLL 0.444897959184 YLLELL YLLEML 26.0 74774|LMP1_protein_(Epstein-Barr_virus,_putative_LYDMA_gene)|Q777A4|Human_gammaherpesvirus_4|10376 -4760 WAGSHSMRY 0.0 None None 0 None -4761 WARRKQSEM 0.0 None None 0 None -4762 WASRFSTPY 0.0 None None 0 None -4763 WFLWKQFCW 0.0 None None 0 None -4764 WGMLNSLSL 0.0 None None 0 None -4765 WHLQGPEDL 0.0 None None 0 None -4766 WHREYNFKY 0.0 None None 0 None -4767 WHSVVIQRL 0.0 None None 0 None -4768 WHVPNKPPM 0.0370999742128 WHVPNKP YHILNNP 23.0 1516|Nucleoprotein|P03418.1|Human_respiratory_syncytial_virus_A2|11259 -4769 WIEREGPEY 0.0 None None 0 None -4770 WLNENQRLV 0.0 None None 0 None -4771 WLSFRSSAS 0.0 None None 0 None -4772 WLSNFQGRY 0.0713668403123 LSNFQGRY VGNFTGLY 23.0 34027|DNA_polymerase|CAA10434.1|Hepatitis_B_virus|10407 -4773 WMEKRYLSQ 0.0 None None 0 None -4774 WMEQEGPEY 3.13980286976 QEGPEY QRGPQY 27.0 38974|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 -4775 WPLTHSQGM 39.6011817345 WPLTHSQGM WPLYGNEGM 32.0 75438|polyprotein|AAF65962.1|Hepatitis_C_virus|11103 -4776 WQRQHKLTI 3.26412079703 QRQHKLTI QRQRKVTF 26.0 159299|polyprotein|AAC03058.1|Hepatitis_C_virus_subtype_3a|356426 -4777 WRPEAVQYY 0.0 None None 0 None -4778 WSDQLSAFS 0.225160259752 WSDQLSAFS WMNRLIAFA 25.0 177647|polyprotein|ADE10208.1|Hepatitis_C_virus_subtype_3a|356426 -4779 WTDVFQIGI 0.358584414555 VFQIGI VFEVGV 24.0 59787|Hemagglutinin_glycoprotein|P08362.1|Measles_virus_strain_Edmonston|11235 -4780 WTESLAAVF 2.5146072019 WTESLAAVF WSEGEGAVF 28.0 119822|110_kd_polyprotein_precursor|CAA28880.1|Rubella_virus|11041 -4781 WVKRQKISF 0.0617858475773 VKRQKISF VKKDLISY 20.0 25929|Nonstructural_protein_NS3|NP_739587.2|Dengue_virus_2_Thailand/16681/84|31634 -4782 WVRPRRRLL 0.0 None None 0 None -4783 WVRPRRRLL 0.0 None None 0 None -4784 WYHTCGGTL 0.0 None None 0 None -4785 WYIWILLVL 0.0410194846882 WYIWIL WCLWWL 23.0 74387|Genome_polyprotein|P26664.3|Hepatitis_C_virus_(isolate_1)|11104 -4786 YAFTGLTLM 19.2063253012 FTGLT FTGLT 26.0 146213|polyprotein|ADY38595.1|Hepatitis_C_virus_subtype_1b|31647 -4787 YAMQRSWQE 2.83948962827 QRSWQ ERSWN 22.0 180440|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -4788 YARILGTVL 0.0 None None 0 None -4789 YCDDLPLLA 0.0 None None 0 None -4790 YDDARVELV 0.0 None None 0 None -4791 YEHHHSARL 0.0 None None 0 None -4792 YFGLATVFI 0.0 None None 0 None -4793 YFHSFIRIV 0.0 None None 0 None -4794 YFTSSSRYF 0.0 None None 0 None -4795 YFYNQEEYV 0.0 None None 0 None -4796 YGVTRSKAM 0.0 None None 0 None -4797 YHCTAVNAY 0.0 None None 0 None -4798 YHDACIEEA 0.0 None None 0 None -4799 YHDVSGCYI 0.0 None None 0 None -4800 YHEAGVTAL 0.815347986631 YHEAGVT FHSYGVT 24.0 232152|rhoptry_kinase_family_protein|AFO54841.1|Toxoplasma_gondii_type_III|398031 -4801 YHFSWTSDR 0.0637106609554 HFSWTS HYAWKT 23.0 183252|polyprotein|AGT63075.1|Dengue_virus_1|11053 -4802 YHHRFNNFM 1.40756158901 YHHRFNN YQHKFNS 30.0 23270|polyprotein|AAB67036.1|Hepatitis_C_virus_(isolate_H77)|63746 -4803 YHQQNVPWA 0.0 None None 0 None -4804 YICDLRRQV 0.0 None None 0 None -4805 YINNSVLPY 0.0 None None 0 None -4806 YKGSRFHRV 1.87577517247 KGSRFHRV KKQRFHNI 25.0 110829|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 -4807 YLADRVQIV 0.0 None None 0 None -4808 YLADRVQIV 0.0 None None 0 None -4809 YLENRKETL 0.0 None None 0 None -4810 YLENRKETL 0.0 None None 0 None -4811 YLEQKPCIY 0.0 None None 0 None -4812 YLFRKELRY 0.0 None None 0 None -4813 YLKEELMCL 0.0 None None 0 None -4814 YLKENFLPW 0.0 None None 0 None -4815 YLRRHRDVS 14.1396011396 LRRHRDV LRRHIDL 26.0 51526|HCV-1|AAA45676.1|Hepatitis_C_virus|11103 -4816 YLSLVEISY 0.0 None None 0 None -4817 YLTVVSLSY 0.0 None None 0 None -4818 YMDRTPGPA 0.0 None None 0 None -4819 YMKTQSKSS 0.0 None None 0 None -4820 YMLTLFTAM 0.0 None None 0 None -4821 YNFKYVDLI 0.0 None None 0 None -4822 YNVFRQLSL 0.0 None None 0 None -4823 YPMRRRQCE 0.0 None None 0 None -4824 YPRLKMLAF 0.0 None None 0 None -4825 YPSIHRFIL 3.57700862377 PSIHRFI PGIYRFV 27.0 149053|NS3_gene_product|AAB02124.1|Hepatitis_C_virus|11103 -4826 YQLHNIQVI 0.0 None None 0 None -4827 YQMQFTQAL 0.0 None None 0 None -4828 YQMQFTQAL 0.0 None None 0 None -4829 YQSEKLCSL 0.0 None None 0 None -4830 YRAGKPTLV 0.432661229328 RAGKPT RSGAPT 23.0 102368|E2_protein|NP_751921.1|Hepatitis_C_virus_subtype_1a|31646 -4831 YRASEQKLC 0.0 None None 0 None -4832 YRDNTELPY 0.0 None None 0 None -4833 YRDVHVQKV 0.0 None None 0 None -4834 YRGPLSTTI 1.76192992766 YRGPLS YRGPLD 29.0 38724|Genome_polyprotein|P08617.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 -4835 YRGSVAPIL 0.0202594406357 YRGSVAPI YAGEPAPF 21.0 65810|sporozoite_surface_protein_2|NP_705260.1|Plasmodium_falciparum_3D7|36329 -4836 YRITVVESL 0.0 None None 0 None -4837 YRLEAVHAL 0.0 None None 0 None -4838 YRLEGDTLI 0.0 None None 0 None -4839 YRQFPKKSL 0.0 None None 0 None -4840 YRRHSLRAI 0.0 None None 0 None -4841 YRTVNNLIL 0.0 None None 0 None -4842 YSFDSLCQY 0.0 None None 0 None -4843 YSRDQIYIY 0.0 None None 0 None -4844 YSRQMISEL 0.0 None None 0 None -4845 YSRQMISEL 0.0 None None 0 None -4846 YTCEQNDQL 0.0 None None 0 None -4847 YTDSSSVLN 0.372503781182 TDSSSVLN TDSTSILG 27.0 107894|polyprotein|CAB41951.1|Hepatitis_C_virus|11103 -4848 YTEDHSASL 0.0 None None 0 None -4849 YTELWFLGL 13.1651602302 YTELW YAEMW 25.0 180077|PPE_family_protein|YP_177935.1|Mycobacterium_tuberculosis_H37Rv|83332 -4850 YTLLAFSVF 0.565506111769 LLAFSVF LLATSIF 23.0 182554|polyprotein|ACF49259.1|Dengue_virus_type_1_Hawaii|10000440 -4851 YTRKCTQAI 0.0 None None 0 None -4852 YTSMWRTYV 0.0 None None 0 None -4853 YTSMWRTYV 0.0 None None 0 None -4854 YVAICSPLF 0.0 None None 0 None -4855 YVDYMMCEF 0.0 None None 0 None -4856 YVFLHQCVL 0.0 None None 0 None -4857 YVFLHQCVL 0.0 None None 0 None -4858 YVGENVRFV 0.0 None None 0 None -4859 YVGIFHFQF 0.254817840555 VGIFHF VGVYHI 24.0 32663|small_hydrophobic_protein|AAM12943.1|Human_metapneumovirus|162145 -4860 YVLTRSKAM 0.0 None None 0 None -4861 YVTVLCLTF 0.0 None None 0 None -4862 YVYSLYWSI 159.605016198 YVYSLYWSI FLYELIWNV 29.0 108965|Prolipoprotein_diacylglyceryl_transferase|O06131.1|Mycobacterium_tuberculosis|1773 -4863 YWGVFAPIW 0.0 None None 0 None -4864 YWPPQSQPF 0.0 None None 0 None -4865 YYEKIFSTL 0.0 None None 0 None -4866 YYFLCLLL* 0.0 None None 0 None -4867 YYFLRPLL* 0.0 None None 0 None -4868 YYFLRPLL* 0.0 None None 0 None -4869 YYKIVSSIL 0.0232262868802 KIVSSI KLVSSV 22.0 95262|LAMP|AAK72632.1|Human_gammaherpesvirus_8|37296 -4870 YYLVANTKF 0.0 None None 0 None -4871 YYTNFSLEL 0.0 None None 0 None -4872 YYTNFSLEL 0.0 None None 0 None -4873 YYYFLCLLL 0.0 None None 0 None -4874 YYYFLRPLL 0.00109271035499 YYYFLRPL YIYMGQPL 21.0 185327|polyprotein|ACF49259.1|Dengue_virus_type_1_Hawaii|10000440 -4875 YYYFLRPLL 0.0362833645562 YYYFLRPL YIYMGQPL 21.0 185327|polyprotein|ACF49259.1|Dengue_virus_type_1_Hawaii|10000440 -4876 LSILVDWMI 0.0 None None 0 None -4877 LVMFLSILV 0.0 None None 0 None -4878 HWPEKEWPI 1.23491252617 HWPEKEW HTPVNSW 22.0 62977|polyprotein|AAB67037.1|Hepatitis_C_virus_(isolate_H77)|63746 -4879 WLEAMQGVI 0.0 None None 0 None -4880 MNRGRRSSL 0.597274971842 MNRGRRS MNRRKRS 25.0 183800|polyprotein|AGT63075.1|Dengue_virus_1|11053 -4881 RADHAAEQV 0.0 None None 0 None -4882 TTLSPAEPT 0.0 None None 0 None -4883 CLMVLYSLI 1.07995809695 CLMVLY CLYLLY 24.0 141222|DNA_packaging_tegument_protein_UL25|NP_044626.1|Human_alphaherpesvirus_1|10298 -4884 MTPSVYGGA 0.847766230468 TPSVYGG TPRVTGG 25.0 65749|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 -4885 FCFLVVASA 0.0 None None 0 None -4886 FLVVASAYI 0.0 None None 0 None -4887 VVASAYIKL 0.0 None None 0 None -4888 NSTIIPTLI 0.0 None None 0 None -4889 SSSGVNSTI 0.0 None None 0 None -4890 STIIPTLIL 0.0 None None 0 None -4891 NLAMCFGPV 0.0 None None 0 None -4892 MVAFINEKM 0.0 None None 0 None -4893 RHSNMVAFI 1.14135041379 RHSNMV RHHNMV 27.0 144403|polyprotein|AAK08509.1|Hepatitis_C_virus_subtype_1b|31647 -4894 SILASLSTL 0.0 None None 0 None -4895 TLQQMWISK 0.0 None None 0 None -4896 RAFADTLEV 0.0 None None 0 None -4897 VLLPVSLFI 0.0179862099621 LPVSLF LPTTLF 22.0 79180|tax_protein|AAF37566.1|Human_T-lymphotropic_virus_1|11908 -4898 LLFSVTMPK 0.0192709392451 LFSVTMP LYSSTVP 22.0 21242|polymerase|ACF94272.1|Hepatitis_B_virus|10407 -4899 VPVPPAPPL 0.748451099646 VPVPPAPP VPTDPNPP 29.0 70491|envelope_glycoprotein|AAC28452.1|Human_immunodeficiency_virus_1|11676 -4900 EIFMGLPTK 2.14751919188 IFMGLP IYMGQP 23.0 185327|polyprotein|ACF49259.1|Dengue_virus_type_1_Hawaii|10000440 -4901 VYTEIFMGL 0.0 None None 0 None -4902 YYASVYTEI 0.0 None None 0 None -4903 HMWNYMQSK 0.694505649699 MWNYMQ LWGYLQ 27.0 42094|telomer_length_regulation_protein_TEL1|EDV12172.1|Saccharomyces_cerevisiae|4932 -4904 QTYQHMWNY 1.32874030798 QHMWNY KHMWNF 34.0 103020|polyprotein|ABR25251.1|Hepatitis_C_virus|11103 -4905 SRYQTYQHM 0.0 None None 0 None -4906 MIMAQMRRI 0.0 None None 0 None -4907 RRISPFSCL 0.0731052404911 RRISPFSCL RVIDPRRCL 22.0 150556|polyprotein|AGW21594.1|Dengue_virus_1|11053 -4908 ILFDEAVKL 10.417679881 LFDEAVK LFNWAVK 21.0 169050|polyprotein|ABU97067.1|Hepatitis_C_virus_subtype_1b|31647 -4909 MKYPVKSIL 0.0 None None 0 None -4910 TLIHQFQEK 0.0 None None 0 None -4911 KLGADFIGH 0.0 None None 0 None -4912 ALGPPVLLR 8.02341413363e-05 ALGPPVLL SLGLVILL 17.0 59141|Circumsporozoite_protein_precursor|P08677.2|Plasmodium_vivax_strain_Belem|31273 -4913 PPVLLRCSL 0.0266850441922 PVLLRCSL KVLIRCYL 26.0 145860|Protein_E6|P04019.1|Human_papillomavirus_type_11|10580 -4914 FTRENTLTF 0.0 None None 0 None -4915 LTFMHLSPI 0.0 None None 0 None -4916 TFMHLSPIL 0.0 None None 0 None -4917 EFVERYHVL 0.0823067794915 VERYHVL AEEYHAL 24.0 187188|PE_family_protein_PE9|YP_177784.1|Mycobacterium_tuberculosis_H37Rv|83332 -4918 RLWARGLTV 0.0 None None 0 None -4919 RLWARGLTV 0.0 None None 0 None -4920 LVWRPLREV 0.68879469979 VWRPLRE IWLKLKE 22.0 180496|Polyprotein|NP_056776.2|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -4921 SYVMLPCAL 0.0 None None 0 None -4922 VMLPCALPV 0.0284555239065 MLPCALP LLPAILP 23.0 41971|putative_D-ribose-binding_protein|NP_301386.1|Mycobacterium_leprae|1769 -4923 RLPEVQLPK 8.33669952536e-05 LPEVQLPK LPSDFLPS 16.0 16836|precore/core_protein_[Hepatitis_B_virus]|AAR03815.1|Hepatitis_B_virus|10407 -4924 APRGACYRA 0.0 None None 0 None -4925 APRGVCYGA 0.0482323961939 PRGVC PYGVC 24.0 148117|early_protein|CAA52585.1|Human_papillomavirus_type_52|10618 -4926 GLTWAVVLI 0.243238394937 TWAVVLI NWAKVLV 24.0 149052|E1_protein|NP_751920.1|Hepatitis_C_virus_(isolate_H77)|63746 -4927 QPLGLTWAV 0.0 None None 0 None -4928 YRNEDHWAW 0.109703755322 RNEDHWA KREDQWC 24.0 184131|polyprotein|AGO67248.1|Dengue_virus_2|11060 -4929 KCAEPSTRK 0.0 None None 0 None -4930 LLTDDLRSV 0.0 None None 0 None -4931 QMPTDYAEV 0.0 None None 0 None -4932 VVGARGVGK 0.0 None None 0 None -4933 ALFCGRSDY 0.000134140052187 ALFCGRSD AVFDRKSD 18.0 5316|EBNA-3B_nuclear_protein|CAD53420.1|Human_gammaherpesvirus_4|10376 -4934 SFLCHKALF 0.0 None None 0 None -4935 SFLCHKALF 0.0 None None 0 None -4936 SFLCHKALF 0.0 None None 0 None -4937 HHLLSLQYV 0.0 None None 0 None -4938 NHHLLSLQY 0.0 None None 0 None -4939 LRLLDRELL 0.0 None None 0 None -4940 QMPPMPPPL 0.0 None None 0 None -4941 SRVSGGTPL 0.0 None None 0 None -4942 IPLEVMEPF 29.4847656669 IPLEVME IPFEIMD 26.0 180528|polyprotein|AGO67248.1|Dengue_virus_2|11060 -4943 RHAACSVLV 0.0 None None 0 None -4944 TRHAACSVL 0.0 None None 0 None -4945 TRHAACSVL 0.0 None None 0 None -4946 IYLGAVNWI 0.25 GAVNWI GAVQWM 26.0 177647|polyprotein|ADE10208.1|Hepatitis_C_virus_subtype_3a|356426 -4947 YLGAVNWIY 5.08 GAVNWI GAVQWM 26.0 177647|polyprotein|ADE10208.1|Hepatitis_C_virus_subtype_3a|356426 -4948 MWALGIIAY 0.0905570014873 MWALGII LWKAGIL 23.0 24943|DNA_polymerase|CAA10434.1|Hepatitis_B_virus|10407 -4949 SPALNKMFY 0.0 None None 0 None -4950 IPGPIPGPI 0.00624824950737 PGPIPG PGTGPG 21.0 47760|EBNA-1_protein|Q777E1|Human_gammaherpesvirus_4|10376 -4951 IPGPIPGPI 0.0209180526986 PGPIPG PGTGPG 21.0 47760|EBNA-1_protein|Q777E1|Human_gammaherpesvirus_4|10376 -4952 NPGPIPGPI 7.77591539117 PGPIPGPI PGLSPGTL 22.0 21638|protein_F|ABV46152.2|Hepatitis_C_virus_(isolate_Japanese)|11116 -4953 AEYIVVARN 0.0 None None 0 None -4954 YIVVARNKY 0.0 None None 0 None -4955 IFWDLSKPM 0.0 None None 0 None -4956 IFWDLSKPM 0.0 None None 0 None -4957 IPTEKPTIL 0.654454704699 IPTEKPTIL LPFDKPTIM 32.0 38466|nucleocapsid_protein|ABF21284.1|Influenza_A_virus_(A/Iran/1/1957(H2N2))|488233 -4958 FLNRWMANT 1.07227470363 FLNRWM FANRWI 28.0 140561|metal_cation_transporter_P-type_ATPase_A_CtpF|NP_216513.1|Mycobacterium_tuberculosis_H37Rv|83332 -4959 WMANTLDAV 0.0 None None 0 None -4960 ALHTAVLLL 0.0 None None 0 None -4961 KMWDAVLYR 0.0 None None 0 None -4962 LSIESLTLV 0.0 None None 0 None -4963 TLSIESLTL 0.0 None None 0 None -4964 HRVNWVVFL 0.0 None None 0 None -4965 FLYQPNWRF 0.598090160823 YQPNWR YFPDWQ 24.0 101721|nef|AAA02639.1|Human_immunodeficiency_virus_1|11676 -4966 LRKRRSRKR 0.0 None None 0 None -4967 RQLRKRRSR 0.0 None None 0 None -4968 RRQEQPSIK 0.0 None None 0 None -4969 FQYKFTVQA 1.33795003856 QYKFTV NYKFTL 24.0 15242|trans-sialidase,_putative|EAN81560.1|Trypanosoma_cruzi|5693 -4970 ILGTPLSKV 0.0 None None 0 None -4971 VLSGAKIWL 0.098644741065 VLSGAKIWL VLSDFKVWL 32.0 181036|||| -4972 AVLIVTTTV 0.000402870290963 VLIVTTTV ILIGITTL 18.0 59182|attachment_glycoprotein|ABQ58821.1|Human_metapneumovirus|162145 -4973 LLESSNTNV 0.0 None None 0 None -4974 VVWATKYFL 82.9775661936 VVWATKYFL CLWWLQYFL 26.0 39591|polyprotein|AAA45677.1|Hepatitis_C_virus_(isolate_H77)|63746 -4975 AMCSAQEEI 0.0487567516051 AMCSAQEEI SICPSQEPM 21.0 58463|HCMVUL83|CAA35357.1|Human_betaherpesvirus_5|10359 -4976 KLTPYMVVL 0.0 None None 0 None -4977 FRVRGAVSH 0.0 None None 0 None -4978 FRHSMVVPY 0.294968010535 RHSMVVP RHADVIP 25.0 97093|polyprotein|AAB66324.1|Hepatitis_C_virus_(isolate_H77)|63746 -4979 KRRRLWAAL 0.0 None None 0 None -4980 RRLWAALGP 0.0128120947675 WAALGP WLSQGP 22.0 59569|Genome_polyprotein|P26662.3|Hepatitis_C_virus_(isolate_Japanese)|11116 -4981 YLIISTFFL 0.0474258731776 YLIISTF YLLADTF 23.0 140616|membrane-associated_phospholipase_C|NP_216866.1|Mycobacterium_tuberculosis_H37Rv|83332 -4982 KIFNHPSTL 0.00530943111929 KIFNHPSTL SLYNTVSTL 20.0 189294|Gag|O89360|Human_immunodeficiency_virus_1|11676 -4983 RSPKKHGYM 0.155158512329 SPKKH SPEKH 25.0 60031|SAG1_protein|AAO72426.1|Toxoplasma_gondii_RH|383379 -4984 YMKMFEIPA 0.0 None None 0 None -4985 LSSIGRSPM 0.0 None None 0 None -4986 MVFCDFHGH 24.8831744361 MVFCDFHGH MSLADFHGE 29.0 155811|ribonucleotide_reductase_large_subunit|CAB06725.1|Human_alphaherpesvirus_2|10310 -4987 RSPMVFCDF 0.0 None None 0 None -4988 SIGRSPMVF 0.0 None None 0 None -4989 SSIGRSPMV 0.0 None None 0 None -4990 ATATAYLCR 0.0 None None 0 None -4991 ATAYLCRVK 0.0 None None 0 None -4992 RVKGNFQTI 0.0 None None 0 None -4993 TATAYLCRV 0.0 None None 0 None -4994 YLCRVKGNF 0.0 None None 0 None -4995 CVSCWNVSR 0.00917876698188 CVSCWNV CSSVFNV 21.0 13456|circumsporozoite_protein|AAN87606.1|Plasmodium_falciparum|5833 -4996 RLASLYKTL 0.0 None None 0 None -4997 TLPQSVDPL 0.351470470495 LPQSVDPL LPEGMDPF 27.0 38446|Glycoprotein_B_precursor_(Glycoprotein_II)|P09257.1|Human_alphaherpesvirus_3|10335 -4998 SSSYAIEKR 0.0 None None 0 None -4999 ISRSTFAEV 0.0 None None 0 None -5000 RLPISRSTF 0.271294816931 PISRSTF PITYSTY 22.0 107873|Genome_polyprotein|P26664.3|Hepatitis_C_virus|11103 -5001 STFAEVTGL 0.0341560998855 STFAEVT KTFEQVT 21.0 14198|UL123;_IE1|AAR31390.1|Human_betaherpesvirus_5|10359 -5002 STFAEVTGL 0.00982374389904 STFAEVT KTFEQVT 21.0 14198|UL123;_IE1|AAR31390.1|Human_betaherpesvirus_5|10359 -5003 FSWNGGSFV 26.3153973248 SWNGG SWNSG 27.0 180440|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -5004 FSWNGGSFV 148.274767747 SWNGG SWNSG 27.0 180440|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -5005 TINEECSEI 3.0978991727 INEECS INEDCS 30.0 103322|polyprotein|BAB18806.1|Hepatitis_C_virus|11103 -5006 ILACRWVEM 0.0 None None 0 None -5007 ESPFSSGKV 0.0 None None 0 None -5008 MLAIGCALL 0.924557240739 MLAIGC LLAIGC 29.0 180802|polyprotein|AGO67248.1|Dengue_virus_2|11060 -5009 ESIRHNVLY 0.0 None None 0 None -5010 SIRHNVLYR 0.00459874686531 SIRHNVLY GLFNNVLY 22.0 20861|Non-capsid_protein_NS-1|P07298.1|Human_parvovirus_B19|10798 -5011 LQFGPTAEG 0.0 None None 0 None -5012 QPIPSVHER 0.0 None None 0 None -5013 SVHERTDWV 0.0 None None 0 None -5014 SVHERTDWV 0.0 None None 0 None -5015 RAPSPVSFV 0.244491068542 APSPVSFV SPRPVSYL 26.0 39571|polyprotein|BAD73987.1|Hepatitis_C_virus_subtype_1b|31647 -5016 GVLVLLFTL 0.371428571429 GVLVLLFTL GILGFVFTL 26.0 20354|M1_protein|CAA30882.1|Influenza_A_virus|11320 -5017 VLAPGVLVL 0.0 None None 0 None -5018 VLAPGVLVL 0.0 None None 0 None -5019 VLVLLFTLV 0.0 None None 0 None -5020 FTFLVSLYL 0.0 None None 0 None -5021 FTFLVSLYL 0.0 None None 0 None -5022 IQAYVFTFL 0.0 None None 0 None -5023 IQAYVFTFL 0.0 None None 0 None -5024 LIQAYVFTF 0.0 None None 0 None -5025 QAYVFTFLV 0.0 None None 0 None -5026 QAYVFTFLV 0.0 None None 0 None -5027 YVFTFLVSL 0.0 None None 0 None -5028 YVFTFLVSL 0.0 None None 0 None -5029 SSSPTCSLM 0.0 None None 0 None -5030 ENWDLVTYR 0.00961312062683 ENWDLVTY QGWGPISY 20.0 8236|Genome_polyprotein|P27958.3|Hepatitis_C_virus_subtype_1a|31646 -5031 GAMENWDLV 0.0 None None 0 None -5032 LEHPGSTRF 0.758464150481 LEHPGST LRHPGFT 28.0 180818|Membrane_glycoprotein_precursor|NP_739582.2|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -5033 QTDYVLSPL 0.0 None None 0 None -5034 VLSPLTGGL 0.000641889255728 LSPLTGG FSPGTSG 18.0 17802|Nonstructural_protein_NS3|NP_739587.2|Dengue_virus_2_Thailand/16681/84|31634 -5035 ITEILDRYV 0.0654819887488 ITEILDRY ITDTIDKF 23.0 12588|Glycoprotein_B_precursor_(Glycoprotein_II)|P09257.1|Human_alphaherpesvirus_3|10335 -5036 FNKSGFKHY 0.0509955625565 FNKSGFK FSKCGFP 23.0 23864|envelope_glycoprotein(gp21,_gp46)_-_human_T-cell_lymphotropic_virus_type_1|A45714|Human_T-lymphotropic_virus_1|11908 -5037 KSGFKHYQM 0.0 None None 0 None -5038 PVFNKSGFK 0.014495615722 FNKSGF FSKCGF 23.0 23864|envelope_glycoprotein(gp21,_gp46)_-_human_T-cell_lymphotropic_virus_type_1|A45714|Human_T-lymphotropic_virus_1|11908 -5039 VLVSGIQVL 0.0 None None 0 None -5040 VLVSGIQVL 0.0 None None 0 None -5041 RSRTGEDEV 0.0 None None 0 None -5042 LGQGELSAF 0.0 None None 0 None -5043 EAQPESEGV 0.0 None None 0 None -5044 LQDFYLGTY 32.5306568234 FYLGTY FYLGQY 29.0 156550|E3_ubiquitin-protein_ligase_Mdm2|Q00987.1|Homo_sapiens|9606 -5045 VAFPLQDFY 0.0 None None 0 None -5046 ESVNILSVL 0.0 None None 0 None -5047 GLVESVNIL 0.0 None None 0 None -5048 FTVGQTEKY 0.0 None None 0 None -5049 ESFKQTYVY 0.0 None None 0 None -5050 ESFKQTYVY 0.0 None None 0 None -5051 QTYVYSMAL 0.0 None None 0 None -5052 YVYSMALVL 0.0 None None 0 None -5053 YVYSMALVL 0.0 None None 0 None -5054 YVYSMALVL 0.0 None None 0 None -5055 FSLHKDRPV 0.0 None None 0 None -5056 ATRKLIGKV 0.0 None None 0 None -5057 HLKVRTATR 0.809264845181 HLKVRT HLRIRT 27.0 154822|ribonucleotide_reductase_large_subunit|CAB06725.1|Human_alphaherpesvirus_2|10310 -5058 TATRKLIGK 0.0 None None 0 None -5059 LLPWAHSML 0.0 None None 0 None -5060 QQNAPLLPW 1.13253012048 QQNAPLL QSNAPIM 26.0 180460|polyprotein|AGO67248.1|Dengue_virus_2|11060 -5061 RIHSDEQPY 0.0 None None 0 None -5062 AVHTVPQTI 0.0 None None 0 None -5063 DPIRRHLHI 0.0 None None 0 None -5064 HILYHCYGV 0.0 None None 0 None -5065 WTRPGSEVL 0.0 None None 0 None -5066 FPYVRNFVM 0.0 None None 0 None -5067 YVRNFVMNL 0.0 None None 0 None -5068 VAHEGMRPM 1.76923076923 AHEGMRPM AHNGLRDL 26.0 65654|polyprotein_precursor|BAA01582.1|Hepatitis_C_virus|11103 -5069 RPDKMVPVV 0.0 None None 0 None -5070 ILYLLSLFT 0.0 None None 0 None -5071 LTILYLLSL 0.0 None None 0 None -5072 YLLSLFTQT 0.0 None None 0 None -5073 AAGPHVTVL 0.0 None None 0 None -5074 RASAAGPHV 0.0 None None 0 None -5075 SAAGPHVTV 0.0 None None 0 None -5076 AVADLSCML 0.0 None None 0 None -5077 CMLVLPTRL 0.0 None None 0 None -5078 LAVADLSCM 0.0 None None 0 None -5079 MLVLPTRLV 0.0 None None 0 None -5080 VAVGTEHTL 0.0 None None 0 None -5081 SVAWTTMDV 0.0 None None 0 None -5082 TMDVATPSV 0.000405605959168 MDVA MDAA 15.0 154448|RL2|CAB06760.1|Human_alphaherpesvirus_2|10310 -5083 NLYKGSVLY 0.341399031209 NLYKGSVLY TLWKAGILY 25.0 24943|DNA_polymerase|CAA10434.1|Hepatitis_B_virus|10407 -5084 DEYNFVRTY 0.0 None None 0 None -5085 RTYECFQHR 0.0 None None 0 None -5086 LPSDPRLHL 0.0 None None 0 None -5087 FLADITHLR 0.0 None None 0 None -5088 GMRYWNMMV 0.0 None None 0 None -5089 NMMVQWWLA 1.28923492085 NMMVQW DMMMNW 23.0 72322|polyprotein|AAA86907.1|Hepatitis_C_virus|11103 -5090 TPLGKGDIV 0.0 None None 0 None -5091 KVRSCIDLI 0.0 None None 0 None -5092 YEQKVRSCI 0.0 None None 0 None -5093 ALLAFATIM 0.0 None None 0 None -5094 ATIMYVPAL 0.0 None None 0 None -5095 LAFATIMYV 0.104302556769 LAFATIMY LAYVSVLY 24.0 141341|tegument_protein_VP11/12|NP_044648.1|Human_alphaherpesvirus_1|10298 -5096 LAFATIMYV 0.0894021915166 LAFATIMY LAYVSVLY 24.0 141341|tegument_protein_VP11/12|NP_044648.1|Human_alphaherpesvirus_1|10298 -5097 YALLAFATI 0.0 None None 0 None -5098 YALLAFATI 0.0 None None 0 None -5099 LLLLLLLLV 0.0 None None 0 None -5100 LLLLLLLVV 0.183789279182 LLLLLVV VLLLLVV 25.0 98540|trans-sialidase,_putative|EAN88532.1|Trypanosoma_cruzi|5693 -5101 LLLLLLVVV 0.355681484489 LLLLVVV LLLLVVM 25.0 98224|trans-sialidase,_putative|EAN82076.1|Trypanosoma_cruzi|5693 -5102 LLVVVPWGV 0.0 None None 0 None -5103 IAATPIPAM 0.195363107976 TPIPA TPLPA 25.0 177806|polyprotein|ACZ60104.1|Hepatitis_C_virus_subtype_3a|356426 -5104 HVLEIDESV 0.0 None None 0 None -5105 HVLEIDESV 0.0 None None 0 None -5106 YFNGSTNHV 0.0 None None 0 None -5107 TPLCPGELL 0.0376303451797 LCPGELL VCWGELM 23.0 187197|Core_protein|Q9QAC5|Hepatitis_B_virus|10407 -5108 LMLGLVWTI 0.0516239227798 LMLGLVWTI LMMRTTWAL 21.0 150389|polyprotein|AGO67248.1|Dengue_virus_2|11060 -5109 LMLGLVWTI 0.0094010029801 LMLGLVWTI LMMRTTWAL 21.0 150389|polyprotein|AGO67248.1|Dengue_virus_2|11060 -5110 RLMLGLVWT 0.0383304570666 LMLGLVW LMMRTTW 19.0 150686|polyprotein|AGO67248.1|Dengue_virus_2|11060 -5111 SLTADDAFV 0.0 None None 0 None -5112 PAFSLDVLM 0.0 None None 0 None -5113 YLQAEIEPV 0.0 None None 0 None -5114 YLQAEIEPV 0.0 None None 0 None -5115 LFFVDKLYK 0.0 None None 0 None -5116 ALLPLFVVL 0.0 None None 0 None -5117 ALLPLFVVL 0.0 None None 0 None -5118 KALLPLFVV 0.0 None None 0 None -5119 VVLCGNDHV 0.458740128795 VVLCGNDHV TLVCGKDGV 25.0 65118|SAG1_protein|AAO72426.1|Toxoplasma_gondii_RH|383379 -5120 TEMKRKAPF 0.0 None None 0 None -5121 AMATYHFHF 0.26894142137 ATYHFH CSHHFH 25.0 183147|polyprotein|AGW21594.1|Dengue_virus_1|11053 -5122 ATYHFHFNL 2.521436525 TYHFHFNL SEHSHFSL 25.0 25275|Glutamate_decarboxylase_2|Q05329.1|Homo_sapiens|9606 -5123 ATYHFHFNL 3.11006375559 TYHFHFNL SEHSHFSL 25.0 25275|Glutamate_decarboxylase_2|Q05329.1|Homo_sapiens|9606 -5124 KAMATYHFH 0.0 None None 0 None -5125 LKAMATYHF 0.0 None None 0 None -5126 NVFVEVVLV 0.0 None None 0 None -5127 GVKGVNSLF 0.270014098137 VKGVNSLF VRGLTSLF 27.0 52652|||| -5128 KGVNSLFKK 0.0 None None 0 None -5129 AMSTPIYQM 0.0 None None 0 None -5130 AMSTPIYQM 0.0 None None 0 None -5131 SMAMSTPIY 0.0 None None 0 None -5132 SMAMSTPIY 0.0 None None 0 None -5133 SSMAMSTPI 0.0 None None 0 None -5134 KMADEVPLK 0.0 None None 0 None -5135 FLLAFRSGA 0.0 None None 0 None -5136 LLAFRSGAL 0.0 None None 0 None -5137 RVAEVAAQV 0.0 None None 0 None -5138 KIFWFPTGL 0.0 None None 0 None -5139 AGIFLLIHF 0.0 None None 0 None -5140 FLLIHFHPL 0.557931740375 FLLIHFHPL FCSHHFHQL 25.0 183147|polyprotein|AGW21594.1|Dengue_virus_1|11053 -5141 FLLIHFHPL 0.754446387197 FLLIHFHPL FCSHHFHQL 25.0 183147|polyprotein|AGW21594.1|Dengue_virus_1|11053 -5142 GIFLLIHFH 0.0 None None 0 None -5143 LLIHFHPLA 0.831825503832 HFHPL HFHQL 25.0 183147|polyprotein|AGW21594.1|Dengue_virus_1|11053 -5144 SIVTSTFII 0.0 None None 0 None -5145 VTSTFIISL 0.0 None None 0 None -5146 LQIHGLAVE 0.0196761894216 QIHGLAV RLHGLSA 22.0 423047|Genome_polyprotein|P27958.3|Hepatitis_C_virus_genotype_1|41856 -5147 ATVLTLPHV 0.0 None None 0 None -5148 VLTLPHVTK 0.0 None None 0 None -5149 AVSNFYLPL 0.0 None None 0 None -5150 HISAVSNFY 0.0 None None 0 None -5151 HISAVSNFY 0.0 None None 0 None -5152 SVVVIIDVK 0.0 None None 0 None -5153 VVIIDVKPK 0.0 None None 0 None -5154 FQRALVQPG 4.11642215044 FQRALV FQRALI 27.0 183577|polyprotein|AGK36298.1|Dengue_virus_2|11060 -5155 ESFTATVEF 0.0 None None 0 None -5156 LAAPRGVCY 0.0886753444311 PRGVC PYGVC 24.0 148117|early_protein|CAA52585.1|Human_papillomavirus_type_52|10618 -5157 ATGATSLCF 0.0 None None 0 None -5158 GLAMCHQEL 0.0 None None 0 None -5159 LLTLAGLAM 0.0 None None 0 None -5160 TVWPSLAPL 8.65748022982 TVWPSLAPL SLWKDGAPL 23.0 140600|glutamine_synthetase_GLNA1_(glutamine_synthase)_(GS-I)|NP_216736.1|Mycobacterium_tuberculosis_H37Rv|83332 -5161 CQHKLGKRY 0.0 None None 0 None -5162 AVWRHLLLA 0.0 None None 0 None -5163 HLLLALLLL 0.0164752006047 LALLLL LALLLL 24.0 19442|nucleocapsid_protein|ABI96968.1|SARS_coronavirus|227859 -5164 LLALLLLVL 12.4294702466 LALLLL LALLLL 24.0 19442|nucleocapsid_protein|ABI96968.1|SARS_coronavirus|227859 -5165 LLALLLLVL 7.77953412607 LALLLL LALLLL 24.0 19442|nucleocapsid_protein|ABI96968.1|SARS_coronavirus|227859 -5166 LLLALLLLV 0.264895382271 LALLLL LALLLL 24.0 19442|nucleocapsid_protein|ABI96968.1|SARS_coronavirus|227859 -5167 LTRHQRTHM 6.47908572951 TRHQRTHM SRHTSDHM 24.0 17278|Genome_polyprotein|P06441.1|Human_hepatitis_A_virus_Hu/Australia/HM175/1976|12098 -5168 EAWLFLEWV 0.0 None None 0 None -5169 SEAWLFLEW 0.0 None None 0 None -5170 WILSHTVAL 0.0 None None 0 None -5171 WILSHTVAL 0.0 None None 0 None -5172 SVRKSVSTV 0.0 None None 0 None -5173 MTVTVCPPT 0.0 None None 0 None -5174 SPMVLLLAA 0.0 None None 0 None -5175 VERGSPMVL 0.0 None None 0 None -5176 VVERGSPMV 0.0 None None 0 None -5177 FEAFDHTET 0.0 None None 0 None -5178 RLFEAFDHT 0.0 None None 0 None -5179 HTCRVMGAL 0.0 None None 0 None -5180 YKIGGIGMV 0.0 None None 0 None -5181 EELTQLNEA 0.0 None None 0 None -5182 LQSRLEEEL 0.0 None None 0 None -5183 RLEEELTQL 0.0 None None 0 None -5184 FPRLGCPWF 0.0 None None 0 None -5185 RLGCPWFTL 0.0 None None 0 None -5186 RLGCPWFTL 0.0 None None 0 None -5187 DWPVFPGLF 24.1501420113 WPVFPG WPAPPG 27.0 72928|Genome_polyprotein|P26662.3|Hepatitis_C_virus_(isolate_Japanese)|11116 -5188 FNVGDDWPV 0.0 None None 0 None -5189 NYASRTQNI 0.0140565208982 NYASRTQ NWAVRTK 21.0 6308|HCV-1|AAA45676.1|Hepatitis_C_virus_genotype_1|41856 -5190 SVSSCCQPV 0.898067608919 SSCCQP SECCTP 28.0 57361|Genome_polyprotein|SRC279960|Hepatitis_C_virus_(isolate_H77)|63746 -5191 SVSSCCQPV 1.08294722702 SSCCQP SECCTP 28.0 57361|Genome_polyprotein|SRC279960|Hepatitis_C_virus_(isolate_H77)|63746 -5192 CTLGDQLSL 0.0447254880178 GDQLSL GDKLSL 25.0 244160|surface_antigen_2_(CA-2)|XP_818927.1|Trypanosoma_cruzi_strain_CL_Brener|353153 -5193 STAPQAHGV 0.0 None None 0 None -5194 STAPQAHGV 0.0 None None 0 None -5195 VSLFYSTAI 0.0 None None 0 None -5196 VSLFYSTAI 0.0 None None 0 None -5197 YSTAISVYL 0.0 None None 0 None -5198 YSTAISVYL 0.0 None None 0 None -5199 DTAPDIVEI 0.0 None None 0 None -5200 FLWDRHVRF 0.0 None None 0 None -5201 LWDRHVRFF 0.0 None None 0 None -5202 FTCLPLGSL 0.0 None None 0 None -5203 HVWLCDLPV 7.43524726743 VWLCDLPV ARLCDLPA 30.0 4172|Glycoprotein_I_precursor_(Glycoprotein_IV)_(GI)_(GPIV)|P09258.1|Human_alphaherpesvirus_3|10335 -5204 HVWLCDLPV 46.7070308887 VWLCDLPV ARLCDLPA 30.0 4172|Glycoprotein_I_precursor_(Glycoprotein_IV)_(GI)_(GPIV)|P09258.1|Human_alphaherpesvirus_3|10335 -5205 APRGVCYGA 0.0482323961939 PRGVC PYGVC 24.0 148117|early_protein|CAA52585.1|Human_papillomavirus_type_52|10618 -5206 DPEYSPGAL 0.154024773008 YSPGAL YSPGEI 25.0 59153|Genome_polyprotein|P27958.3|Hepatitis_C_virus_subtype_1a|31646 -5207 YSPGALATF 0.0 None None 0 None -5208 VLGDFLGTV 0.0 None None 0 None -5209 AVVGTVWNV 0.0 None None 0 None -5210 NVATTGLSL 0.0 None None 0 None -5211 DTTDKGALM 0.0 None None 0 None -5212 KAVSVCPEA 0.0573665433528 KAVSVCPEA QQVSIAPNA 22.0 19359|IMMUNOGENIC_PROTEIN_MPT64_(ANTIGEN_MPT64/MPB64)|CAA98382.1|Mycobacterium_tuberculosis_H37Rv|83332 -5213 SVCPEAAPA 0.0 None None 0 None -5214 VLVVGMGPV 0.0 None None 0 None -5215 IFATKPELL 0.0 None None 0 None -5216 RIFATKPEL 0.0 None None 0 None -5217 AFSQSAYLI 0.0 None None 0 None -5218 AYLIQHQRF 0.0 None None 0 None -5219 KAFSQSAYL 0.0 None None 0 None -5220 KAFSQSAYL 0.0 None None 0 None -5221 FPAPARDDF 0.0 None None 0 None -5222 SPSVMWLVH 1.99051566923 SPSVMWL SPSSIWV 26.0 116835|Nucleoprotein|P05133.1|Hantaan_virus_76-118|11602 -5223 LAVRDVFEL 0.0 None None 0 None -5224 LAVRDVFEL 0.0 None None 0 None -5225 KTLTLAKNY 0.0 None None 0 None -5226 SSGSMCNRW 0.0888800199782 SSGSMCNRW TAGSLQGQW 23.0 9920|ESAT-6-like_protein_esxB|P0A566.2|Mycobacterium_tuberculosis|1773 -5227 TTKNDIGPY 0.0 None None 0 None -5228 LGLTNNTAM 0.0 None None 0 None -5229 FTTELTAPF 0.0995002913307 FTTELTAPF FTASVTSPL 25.0 177903|polyprotein|ACZ60102.1|Hepatitis_C_virus_subtype_3a|356426 -5230 FTTELTAPF 0.139300407863 FTTELTAPF FTASVTSPL 25.0 177903|polyprotein|ACZ60102.1|Hepatitis_C_virus_subtype_3a|356426 -5231 FTTELTAPF 0.106698184746 FTTELTAPF FTASVTSPL 25.0 177903|polyprotein|ACZ60102.1|Hepatitis_C_virus_subtype_3a|356426 -5232 MPAFTTELT 0.0 None None 0 None -5233 LMALHPALF 0.0394828895203 LMALHPAL MCAVHPTL 25.0 7660|polyprotein|AAA45677.1|Hepatitis_C_virus_(isolate_H77)|63746 -5234 QCSEHDVLF 4.32142857143 CSEHD CVEHD 26.0 120093|unnamed_protein_product|CAA33016.1|Rubella_virus|11041 -5235 EPYIDNEEF 0.0 None None 0 None -5236 VVIKAIEPY 0.0 None None 0 None -5237 QVQDSNLEY 0.0 None None 0 None -5238 QVQDSNLEY 0.0 None None 0 None -5239 LASSCGCTF 3.24598726122 LASSCGCT MYPSCCCT 24.0 59786|Large_envelope_protein|P03138.3|Hepatitis_B_virus_ayw/France/Tiollais/1979|490133 -5240 LASSCGCTF 16.2484935375 LASSCGCT MYPSCCCT 24.0 59786|Large_envelope_protein|P03138.3|Hepatitis_B_virus_ayw/France/Tiollais/1979|490133 -5241 IQLLGVFVW 0.0 None None 0 None -5242 ISIQLLGVF 0.0 None None 0 None -5243 EVDFTCWKY 0.0 None None 0 None -5244 HPTAASQSR 0.0 None None 0 None -5245 IIETANVSY 0.0 None None 0 None -5246 VSYTNAWAL 0.121870305999 SYTNAWAL SYAQMWSL 26.0 180579|polyprotein|ABW82016.1|Dengue_virus_2_D2/SG/05K4155DK1/2005|10002010 -5247 FFIHSFTLM 0.0 None None 0 None -5248 MFFIHSFTL 0.0344792251349 MFFIHSFT LFYQHKFN 22.0 23270|polyprotein|AAB67036.1|Hepatitis_C_virus_(isolate_H77)|63746 -5249 MFNPIIYIF 0.0584094317908 MFNPIIY LFNNVLY 24.0 20861|Non-capsid_protein_NS-1|P07298.1|Human_parvovirus_B19|10798 -5250 LPTPVEPTV 0.987770214465 LPTPVEPT LPDPLKPT 31.0 27241|Spike_glycoprotein_precursor|P59594.1|SARS_coronavirus|227859 -5251 TPVEPTVAC 0.234271638656 TPVEPT TPYKPT 24.0 68229|EBNA3B_(EBNA4A)_latent_protein|CAA24858.1|Human_gammaherpesvirus_4|10376 -5252 HPDNVSSSY 0.0 None None 0 None -5253 LLAAARPLW 1.30039551297 LLAAARPLW ITAAAVTLW 24.0 36717|nonstructural_protein_4B|YP_001527886.1|West_Nile_virus_NY-99|10000971 -5254 SPVALQLRY 0.0 None None 0 None -5255 YQIGTDSAL 0.0 None None 0 None -5256 EAHHHFPSL 3.68937388497 HHFPSL HHAPSL 29.0 21000|glutamine_synthetase_GLNA1_(glutamine_synthase)_(GS-I)|NP_216736.1|Mycobacterium_tuberculosis|1773 -5257 EAHHHFPSL 5.17245410388 HHFPSL HHAPSL 29.0 21000|glutamine_synthetase_GLNA1_(glutamine_synthase)_(GS-I)|NP_216736.1|Mycobacterium_tuberculosis|1773 -5258 GSGEAHHHF 0.0 None None 0 None -5259 RVSSLTLHF 0.0 None None 0 None -5260 KPFSQSCEF 0.0 None None 0 None -5261 KPLLSGPWA 0.348123132681 KPLLSGP KPTLHGP 27.0 6591|polyprotein|AAB67037.1|Hepatitis_C_virus_(isolate_H77)|63746 -5262 LSMTSITSV 0.0 None None 0 None -5263 IDTDQVHTL 0.0 None None 0 None -5264 TWKDTPYYI 0.0 None None 0 None -5265 KLILTLSAI 0.0 None None 0 None -5266 SYQMSNKLI 0.0 None None 0 None -5267 YQMSNKLIL 0.0 None None 0 None -5268 YQMSNKLIL 0.0 None None 0 None -5269 LMWSVTWPK 0.418780213276 WSVTW WAIKW 25.0 149105|E2_protein|NP_751921.1|Hepatitis_C_virus_(isolate_H77)|63746 -5270 SQSETNSAV 0.0 None None 0 None -5271 SHASHLHLF 0.0 None None 0 None -5272 SHASHLHLF 0.0 None None 0 None -5273 KVLISVHLI 0.0 None None 0 None -5274 DHYLVDRTL 0.0 None None 0 None -5275 YIKPLVPPA 0.0 None None 0 None -5276 RPGQSPGQL 1.15887751873 PGQSPGQL PGLSPGTL 31.0 21638|protein_F|ABV46152.2|Hepatitis_C_virus_(isolate_Japanese)|11116 -5277 HLFESSQLV 0.0 None None 0 None -5278 HLFESSQLV 0.0 None None 0 None -5279 GVYLWEDPV 6.47717900666 LWEDP LWESP 27.0 32243|C_protein|BAB60863.1|Measles_virus|11234 -5280 YLWEDPVCG 47.588178133 LWEDP LWESP 27.0 32243|C_protein|BAB60863.1|Measles_virus|11234 -5281 RILYMADEV 0.0 None None 0 None -5282 SLLDACLIL 0.0 None None 0 None -5283 APLPMPNPL 0.226485551842 LPMPNPL IPMTGPL 24.0 180531|polyprotein|AGO67248.1|Dengue_virus_2|11060 -5284 LLLWAPLPM 0.0 None None 0 None -5285 MQLRKAPNV 0.0 None None 0 None -5286 AHACAHALL 0.0 None None 0 None -5287 GAHACAHAL 0.0 None None 0 None -5288 VLNGWLRSV 7.1854641519 VLNGW LLNGW 28.0 37607|kaposin|AAC57155.1|Human_gammaherpesvirus_8|37296 -5289 AIDDHVCMA 0.0 None None 0 None -5290 LMVPRLEYV 0.0 None None 0 None -5291 FINARGRLL 0.0 None None 0 None -5292 AIPLRGFPV 7.52036422648 IPLRGFPV LSLRGLPV 27.0 24302|X_protein|AAP06597.1|Hepatitis_B_virus|10407 -5293 FVDENNEKL 0.0 None None 0 None -5294 FVDENNEKL 0.0 None None 0 None -5295 HTARLFYFV 0.0 None None 0 None -5296 LPSTAGPEM 6.14013666685 LPSTAGP LPEAAGP 28.0 43447|IMMUNOGENIC_PROTEIN_MPT64_(ANTIGEN_MPT64/MPB64)|CAA98382.1|Mycobacterium_tuberculosis_H37Rv|83332 -5297 LPSTAGPEM 6.97269757083 LPSTAGP LPEAAGP 28.0 43447|IMMUNOGENIC_PROTEIN_MPT64_(ANTIGEN_MPT64/MPB64)|CAA98382.1|Mycobacterium_tuberculosis_H37Rv|83332 -5298 TAANGSEVM 0.0 None None 0 None -5299 TAANGSEVM 0.0 None None 0 None -5300 MADATFQSL 0.0 None None 0 None -5301 MADATFQSL 0.0 None None 0 None -5302 WFNMADATF 0.0 None None 0 None -5303 ICIWNVSKL 0.0 None None 0 None -5304 EPTITDASL 0.0 None None 0 None -5305 IFDEWLKRF 0.0 None None 0 None -5306 FTGGIVNKL 0.0472701242502 FTGGIVNKL FMGVLVNSL 24.0 139747|granule_antigen_protein_GRA6|XP_002371939.1|Toxoplasma_gondii_ME49|508771 -5307 GIVNKLCAL 0.0 None None 0 None -5308 FGSLLGTCL 0.0 None None 0 None -5309 ISGPRSPTY 0.157560426259 ISGPRSPTY INGIRRPKH 20.0 66195|Nucleoprotein|P41269.1|Puumala_hantavirus|11604 -5310 MSLNSYIKL 0.0 None None 0 None -5311 YMVIMSPRL 0.0 None None 0 None -5312 EILWTTELY 0.0 None None 0 None -5313 LEILWTTEL 0.0 None None 0 None -5314 LGTSDVRIL 0.0 None None 0 None -5315 VAFLGTSDV 0.0 None None 0 None -5316 IMIAVVDSM 0.0 None None 0 None -5317 IMIAVVDSM 0.0 None None 0 None -5318 EASVHSVPI 0.0 None None 0 None -5319 FFSSNLPTY 0.0 None None 0 None -5320 FSSNLPTYY 12.750272737 NLPTYY SLPSYY 27.0 28594|IMMUNOGENIC_PROTEIN_MPT64_(ANTIGEN_MPT64/MPB64)|CAA98382.1|Mycobacterium_tuberculosis_H37Rv|83332 -5321 VALVPESSV 0.0 None None 0 None -5322 ISRNHNSRM 0.0 None None 0 None -5323 KTFGISRNH 0.0 None None 0 None -5324 RNHNSRMNK 0.0 None None 0 None -5325 LTDLQGVIV 0.0 None None 0 None -5326 IRHEMSTFA 0.0 None None 0 None -5327 VVSDSWGSK 0.0 None None 0 None -5328 IRAANVSAL 0.0 None None 0 None -5329 IRAANVSAL 0.0 None None 0 None -5330 RAANVSALY 0.0 None None 0 None -5331 GYRERGHPY 0.0 None None 0 None -5332 VVGAVGVGK 0.0 None None 0 None -5333 LTNTLTTSK 0.0 None None 0 None -5334 AAASTSSPK 0.0 None None 0 None -5335 TSITTSTQK 0.0 None None 0 None -5336 SHPGSAEIV 0.0 None None 0 None -5337 SYYSCVAAM 0.0 None None 0 None -5338 SYYSCVAAM 0.0 None None 0 None -5339 AHTFKQRRI 0.0 None None 0 None -5340 HTFKQRRIK 0.0 None None 0 None -5341 RYEEYRGRF 0.0254287796016 YEEYRGRF YQDWLGRM 22.0 23288|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 -5342 YEEYRGRFL 0.00584663400753 YEEYRGRF YQDWLGRM 22.0 23288|K8.1|ABD28902.1|Human_gammaherpesvirus_8|37296 -5343 MTTGSVFFY 0.0 None None 0 None -5344 MTTGSVFFY 0.0 None None 0 None -5345 HVLSLAETK 0.0 None None 0 None -5346 SLAETKTLY 0.0 None None 0 None -5347 KLKTVSQTK 0.0 None None 0 None -5348 ASYDQSLRV 0.0 None None 0 None -5349 FSASYDQSL 0.0 None None 0 None -5350 HLKEPLQKL 0.0 None None 0 None -5351 HLYEQGGHL 0.0 None None 0 None -5352 HQCVHTGAK 0.0 None None 0 None -5353 IAHAWWACF 0.624917866388 HAWWACF HARWAAF 30.0 141262|DNA_polymerase_catalytic_subunit|NP_044632.1|Human_alphaherpesvirus_1|10298 -5354 AMWNRCADL 0.0 None None 0 None -5355 AYTFWTYIM 0.850753683829 AYTFW KYTFW 29.0 137660|L1|ACL12325.1|Human_papillomavirus_type_58|10598 -5356 IMNARSKNV 0.0 None None 0 None -5357 YAYTFWTYI 6.89162833838 AYTFW KYTFW 29.0 137660|L1|ACL12325.1|Human_papillomavirus_type_58|10598 -5358 YAYTFWTYI 1.32063005669 AYTFW KYTFW 29.0 137660|L1|ACL12325.1|Human_papillomavirus_type_58|10598 -5359 KAARIAAKV 0.0 None None 0 None -5360 KVGQSSMWI 0.0 None None 0 None -5361 PSTSTSRPV 0.0 None None 0 None -5362 CLAAMALSI 0.0 None None 0 None -5363 WLTPVIPTL 0.234315353622 WLTPVIP WLSLLVP 24.0 62477|HBsAg_protein|ABF71024.1|Hepatitis_B_virus|10407 -5364 GLFHCTRSV 0.0 None None 0 None -5365 RNWDVCKVI 0.0 None None 0 None -5366 KIPIRLPPV 0.0 None None 0 None -5367 FMLGITPNL 0.0 None None 0 None -5368 HRHHHRCRR 0.0 None None 0 None -5369 FLAGSSLPV 0.0 None None 0 None -5370 FLAGSSLPV 0.0 None None 0 None -5371 SSFLAGSSL 0.0 None None 0 None -5372 KLPSDPDAL 0.0 None None 0 None -5373 VYAVTVVTL 0.0 None None 0 None -5374 YAVTVVTLL 0.0 None None 0 None -5375 YAVTVVTLL 0.0 None None 0 None -5376 FILICCLII 0.0653826258252 LICCLII VLCCYVL 25.0 11956|UL123;_IE1|AAR31448.1|Human_betaherpesvirus_5|10359 -5377 ILICCLIIL 0.465751713705 LICCLII VLCCYVL 25.0 11956|UL123;_IE1|AAR31448.1|Human_betaherpesvirus_5|10359 -5378 LIILENIFV 0.0 None None 0 None -5379 VFILICCLI 0.300679700821 ILICCLI ILIRCII 24.0 137656|E6_protein|ACT36477.1|Human_papillomavirus_type_58|10598 -5380 PAMKFSCSL 0.0 None None 0 None -5381 FLSLIIDAT 0.0 None None 0 None -5382 LIIDATKFI 0.0 None None 0 None -5383 LIIDATKFI 0.0 None None 0 None -5384 IMMSSEDDI 0.0 None None 0 None -5385 YLDGQPQEA 0.0825589178834 YLDGQP YRDGNP 24.0 110227|Protein_E6|P03126.1|Human_papillomavirus_type_16|333760 -5386 GLAPPQLLI 0.0 None None 0 None -5387 ARIERPHNY 0.0 None None 0 None -5388 FTSSEPSRM 0.0 None None 0 None -5389 ESEGHTIEL 0.0 None None 0 None -5390 KMQEGLLAV 0.0819874238225 QEGLLAV QNGALAI 21.0 51685|Nuclear_antigen_EBNA-3C|Q69140.1|Human_gammaherpesvirus_4|10376 diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/run.sh b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/run.sh deleted file mode 100755 index cbcf44cf..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/run.sh +++ /dev/null @@ -1,24 +0,0 @@ -############################################## -# Compute neoantigen quality -# -# Directory structure: -# -# data: -# neoantigen-data file and iebd-epitope file. -# -# alignments: -# precomputed blastp alignments for all neoantigens, split into files for each sample. -# blastp -query -db data/iedb.fasta -outfmt 5 -evalue 100000000 -gapopen 11 -gapextend 1 > -# -# src: -# source code folder -# -# output: -# source code output folder -############################################## - -# fitness model paramaters -a=26. -k=1. - -python src/main.py data/SupplementaryTable1.txt alignments $a $k > output/neontigenQuality.txt diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/src/.DS_Store b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/src/.DS_Store deleted file mode 100755 index 5008ddfcf53c02e82d7eee2e57c38e5672ef89f6..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 6148 zcmeH~Jr2S!425mzP>H1@V-^m;4Wg<&0T*E43hX&L&p$$qDprKhvt+--jT7}7np#A3 zem<@ulZcFPQ@L2!n>{z**++&mCkOWA81W14cNZlEfg7;MkzE(HCqgga^y>{tEnwC%0;vJ&^%eQ zLs35+`xjp>T0 - - NeoantigenQuality - - - - - - org.python.pydev.PyDevBuilder - - - - - - org.python.pydev.pythonNature - - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/src/.pydevproject b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/src/.pydevproject deleted file mode 100755 index 037bd251..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/src/.pydevproject +++ /dev/null @@ -1,8 +0,0 @@ - - - -/${PROJECT_DIR_NAME} - -python 2.7 -Default - diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/src/Aligner.py b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/src/Aligner.py deleted file mode 100755 index fbca6a36..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/src/Aligner.py +++ /dev/null @@ -1,108 +0,0 @@ -''' -Created on Jul 26, 2017 - -@author: Marta Luksza, mluksza@ias.edu -''' -from math import log, exp - -from Bio import pairwise2 -from Bio.Blast import NCBIXML -from Bio.SubsMat import MatrixInfo as matlist - - -class Aligner(object): - ''' - Class to align neoantigens with IEDB epitopes and compute TCR-recognition - probabilities. - ''' - INF = float("inf") - - @staticmethod - def align(seq1, seq2): - ''' - Smith-Waterman alignment with default parameters. - ''' - matrix = matlist.blosum62 - gap_open = -11 - gap_extend = -1 - aln = pairwise2.align.localds(seq1.upper(), seq2.upper(), matrix, gap_open, gap_extend) - return aln - - @staticmethod - def logSum(v): - ''' - compute the logarithm of a sum of exponentials - ''' - if len(v) == 0: - return -Aligner.INF - ma = max(v) - if ma == -Aligner.INF: - return -Aligner.INF - return log(sum([exp(x - ma) for x in v])) + ma - - def __init__(self): - # dictionary of computed Ri-values mapped to neoantigen identifiers - self.Ri = {} - # dictionary of IEDB epitope alignments mapped to neoantigen identifiers - self.alignments = {} - # dictionary of the highest scoring alignments mapped to neoantigen identifiers - self.maximum_alignment = {} - - def readAllBlastAlignments(self, xmlpath): - ''' - Read precomputed blastp alignments from xml files, - compute alignment scores, - find the highest scoring alignment for each neoantigen. - ''' - f = open(xmlpath) - blast_records = NCBIXML.parse(f) - maxscore = {} - try: - for brecord in blast_records: - nid = int(str(brecord.query).split("_")[1]) - for alignment in brecord.alignments: - if not nid in self.alignments: - self.alignments[nid] = {} - self.maximum_alignment[nid] = None - self.maximum_alignment[nid] = 0 - maxscore[nid] = 0 - species = " ".join((str(alignment).split())[1:-3]) - for hsp in alignment.hsps: - if not "-" in hsp.query and not "-" in hsp.sbjct: - al = Aligner.align(hsp.query, hsp.sbjct) - if len(al) > 0: - al = al[0] - self.alignments[nid][species] = al - if al[2] > maxscore[nid]: - self.maximum_alignment[nid] = species - maxscore[nid] = al[2] - except ValueError: - pass - f.close() - - def computeR(self, a=26, k=1): - ''' - Compute TCR-recognition probabilities for each neoantigen. - ''' - # iterate over all neoantigens - for i in self.alignments: - # energies of all bound states of neoantigen i - bindingEnergies = [-k * (a - el[2]) for el in list(self.alignments[i].values())] - # partition function, over all bound states and an unbound state - lZ = Aligner.logSum(bindingEnergies + [0]) - lGb = Aligner.logSum(bindingEnergies) - R = exp(lGb - lZ) - self.Ri[i] = R - - def getR(self, i): - ''' - Return precomputed R value and the highest scoring alignment - for a given neoantigen i. - ''' - emptyAlignment = [None, None, 0] - if i in self.Ri: - species = self.maximum_alignment[i] - al = self.alignments[i][species] - species = str(species).replace(" ", "_") - return [self.Ri[i], species, al] - return [0., None, emptyAlignment] diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/src/__init__.py b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/src/__init__.py deleted file mode 100755 index e69de29b..00000000 diff --git a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/src/main.py b/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/src/main.py deleted file mode 100755 index 3a0b9934..00000000 --- a/input/neoantigen_fitness/Balachandran.2016-10-13834C.Supplementary_Data_03/src/main.py +++ /dev/null @@ -1,71 +0,0 @@ -''' -Created on Jul 27, 2017 - -@author: Marta Luksza, mluksza@ias.edu -''' -import sys - -from .Aligner import Aligner - - -def main(): - ''' - command line parameters: - neofile - text file with neoantigen data (supplementary data) - alignmentDirectory - folder with precomputed alignments (SI) - a - midpoint parameter of the logistic function, alignment score threshold - k - slope parameter of the logistic function - ''' - neofile = sys.argv[1] - alignmentDirectory = sys.argv[2] - - a = float(sys.argv[3]) - k = float(sys.argv[4]) - - # Compute MHC amplitudes for all neoantigens - f = open(neofile) - lines = f.readlines() - Ai = {} - data = {} - samples = set() - for line in lines[1:]: - [i, sample, _, _, _, _, mtpeptide, _, _, kdwt, kdmt] = line.strip().split() - i = int(i) - data[i] = mtpeptide.upper() - Ai[i] = float(kdwt) / float(kdmt) - samples.add(sample) - f.close() - - # Compute TCR-recognition probabilities for all neoantigens - aligner = Aligner() - for sample in samples: - xmlpath = alignmentDirectory + "/neoantigens_" + sample + "_iedb.xml" - aligner.readAllBlastAlignments(xmlpath) - aligner.computeR(a, k) - - # Compute neoantigen quality - nids = list(Ai.keys()) - nids.sort() - header = ["NeoantigenID", "MT.Peptide.Form", "NeoantigenQuality", - "NeoantigenAlignment", "IEDB_EpitopeAlignment", "AlignmentScore", "IEDB_Epitope"] - header = "\t".join(header) - print(header) - for i in nids: - A = Ai[i] - [R, species, alignment] = aligner.getR(i) - - neoAlignment = alignment[0] - epitopeAlignment = alignment[1] - score = alignment[2] - - l = [i, data[i], A * R, neoAlignment, epitopeAlignment, score, species] - l = "\t".join([str(s) for s in l]) - print(l) - - -if __name__ == '__main__': - if len(sys.argv) != 5: - print("Run as:") - print("python src/main.py ") - else: - main() From f353f2f75ed86a9746f4a99e91e44d5a1859005a Mon Sep 17 00:00:00 2001 From: Pablo Riesgo Ferreiro Date: Tue, 16 Jun 2020 12:42:00 +0200 Subject: [PATCH 046/105] fix dummy import issue --- .../dissimilaritycalculator.py | 2 +- .../neoantigen_fitness/neoantigen_fitness.py | 160 +++++++++--------- 2 files changed, 81 insertions(+), 81 deletions(-) diff --git a/input/dissimilarity_garnish/dissimilaritycalculator.py b/input/dissimilarity_garnish/dissimilaritycalculator.py index b10203ba..08454781 100755 --- a/input/dissimilarity_garnish/dissimilaritycalculator.py +++ b/input/dissimilarity_garnish/dissimilaritycalculator.py @@ -4,7 +4,7 @@ import os.path from input.helpers import intermediate_files -from input.helpers.runner import BlastpRunner +from input.helpers.blastp_runner import BlastpRunner class DissimilarityCalculator(BlastpRunner): diff --git a/input/neoantigen_fitness/neoantigen_fitness.py b/input/neoantigen_fitness/neoantigen_fitness.py index ab814cd7..8845bdfe 100755 --- a/input/neoantigen_fitness/neoantigen_fitness.py +++ b/input/neoantigen_fitness/neoantigen_fitness.py @@ -1,80 +1,80 @@ -#!/usr/bin/env python - -import os -import os.path -from logzero import logger - -from input.helpers import intermediate_files -from input.helpers.runner import BlastpRunner - - -class NeoantigenFitnessCalculator(BlastpRunner): - - def __init__(self, runner, configuration): - """ - :type runner: input.helpers.runner.Runner - :type configuration: input.references.DependenciesConfiguration - """ - super().__init__(runner, configuration) - - def _calc_pathogen_similarity(self, fasta_file, iedb): - """ - This function determines the PATHOGENSIMILARITY of epitopes according to Balachandran et al. using a blast - search against the IEDB pathogenepitope database - """ - outfile = self.run_blastp(fasta_file=fasta_file, database=os.path.join(iedb, "iedb_blast_db")) - similarity = self.parse_blastp_output(blastp_output_file=outfile) - os.remove(outfile) - return similarity - - def wrap_pathogen_similarity(self, mutation, iedb): - fastafile = intermediate_files.create_temp_fasta(sequences=[mutation], prefix="tmpseq", comment_prefix='M_') - try: - pathsim = self._calc_pathogen_similarity(fastafile, iedb) - except Exception as ex: - # TODO: do we need this at all? it should not fail and if it fails we probably want to just stop execution - logger.exception(ex) - pathsim = 0 - os.remove(fastafile) - logger.info("Peptide {} has a pathogen similarity of {}".format(mutation, pathsim)) - return str(pathsim) - - def calculate_amplitude_mhc(self, score_mutation, score_wild_type, apply_correction=False): - """ - This function calculates the amplitude between mutated and wt epitope according to Balachandran et al. - when affinity is used, use correction from Luksza et al. *1/(1+0.0003*aff_wt) - """ - amplitude_mhc = "NA" - try: - candidate_amplitude_mhc = float(score_wild_type) / float(score_mutation) - if apply_correction: #nine_mer or affinity: - amplitude_mhc = str(candidate_amplitude_mhc * (self._calculate_correction(score_wild_type))) - else: - amplitude_mhc = str(candidate_amplitude_mhc) - except(ZeroDivisionError, ValueError) as e: - pass - return amplitude_mhc - - def _calculate_correction(self, score_wild_type): - return 1 / (1 + 0.0003 * float(score_wild_type)) - - def calculate_recognition_potential( - self, amplitude, pathogen_similarity, mutation_in_anchor, mhc_affinity_mut=None): - """ - This function calculates the recognition potential, defined by the product of amplitude and pathogensimiliarity of an epitope according to Balachandran et al. - F_alpha = - max (A_i x R_i) - - Returns (A_i x R_i) value only for nonanchor mutation and epitopes of length 9; only considered by Balachandran - """ - recognition_potential = "NA" - try: - candidate_recognition_potential = str(float(amplitude) * float(pathogen_similarity)) - if mhc_affinity_mut: - if mutation_in_anchor == "0" and mhc_affinity_mut < 500: - recognition_potential = candidate_recognition_potential - else: - if mutation_in_anchor == "0": - recognition_potential = candidate_recognition_potential - except ValueError: - pass - return recognition_potential +#!/usr/bin/env python + +import os +import os.path +from logzero import logger + +from input.helpers import intermediate_files +from input.helpers.blastp_runner import BlastpRunner + + +class NeoantigenFitnessCalculator(BlastpRunner): + + def __init__(self, runner, configuration): + """ + :type runner: input.helpers.runner.Runner + :type configuration: input.references.DependenciesConfiguration + """ + super().__init__(runner, configuration) + + def _calc_pathogen_similarity(self, fasta_file, iedb): + """ + This function determines the PATHOGENSIMILARITY of epitopes according to Balachandran et al. using a blast + search against the IEDB pathogenepitope database + """ + outfile = self.run_blastp(fasta_file=fasta_file, database=os.path.join(iedb, "iedb_blast_db")) + similarity = self.parse_blastp_output(blastp_output_file=outfile) + os.remove(outfile) + return similarity + + def wrap_pathogen_similarity(self, mutation, iedb): + fastafile = intermediate_files.create_temp_fasta(sequences=[mutation], prefix="tmpseq", comment_prefix='M_') + try: + pathsim = self._calc_pathogen_similarity(fastafile, iedb) + except Exception as ex: + # TODO: do we need this at all? it should not fail and if it fails we probably want to just stop execution + logger.exception(ex) + pathsim = 0 + os.remove(fastafile) + logger.info("Peptide {} has a pathogen similarity of {}".format(mutation, pathsim)) + return str(pathsim) + + def calculate_amplitude_mhc(self, score_mutation, score_wild_type, apply_correction=False): + """ + This function calculates the amplitude between mutated and wt epitope according to Balachandran et al. + when affinity is used, use correction from Luksza et al. *1/(1+0.0003*aff_wt) + """ + amplitude_mhc = "NA" + try: + candidate_amplitude_mhc = float(score_wild_type) / float(score_mutation) + if apply_correction: #nine_mer or affinity: + amplitude_mhc = str(candidate_amplitude_mhc * (self._calculate_correction(score_wild_type))) + else: + amplitude_mhc = str(candidate_amplitude_mhc) + except(ZeroDivisionError, ValueError) as e: + pass + return amplitude_mhc + + def _calculate_correction(self, score_wild_type): + return 1 / (1 + 0.0003 * float(score_wild_type)) + + def calculate_recognition_potential( + self, amplitude, pathogen_similarity, mutation_in_anchor, mhc_affinity_mut=None): + """ + This function calculates the recognition potential, defined by the product of amplitude and pathogensimiliarity of an epitope according to Balachandran et al. + F_alpha = - max (A_i x R_i) + + Returns (A_i x R_i) value only for nonanchor mutation and epitopes of length 9; only considered by Balachandran + """ + recognition_potential = "NA" + try: + candidate_recognition_potential = str(float(amplitude) * float(pathogen_similarity)) + if mhc_affinity_mut: + if mutation_in_anchor == "0" and mhc_affinity_mut < 500: + recognition_potential = candidate_recognition_potential + else: + if mutation_in_anchor == "0": + recognition_potential = candidate_recognition_potential + except ValueError: + pass + return recognition_potential From 0f30a056d1d291c0aebca86be7debd94e15be93a Mon Sep 17 00:00:00 2001 From: Pablo Riesgo Ferreiro Date: Tue, 16 Jun 2020 13:30:19 +0200 Subject: [PATCH 047/105] fix integration test for input --- input/epitope.py | 40 +++++++------- input/netmhcpan4/multiple_binders.py | 8 +-- input/tests/integration_tests/test_input.py | 58 ++++++++++++--------- 3 files changed, 57 insertions(+), 49 deletions(-) diff --git a/input/epitope.py b/input/epitope.py index 429188aa..18bf9e0a 100755 --- a/input/epitope.py +++ b/input/epitope.py @@ -129,8 +129,8 @@ def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aa num_mutation=num_mutation, num_wild_type=num_wild_type), "Ratio_numb_epis_<{}".format(threshold)) self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( - score_mutation=self.properties["MB_score_top10_harmonic"].replace(",", "."), - score_wild_type=self.properties["MB_score_WT_top10_harmonic"].replace(",", ".")), "Amplitude_mhcI_MB") + score_mutation=self.properties["MB_score_top10_harmonic"], + score_wild_type=self.properties["MB_score_WT_top10_harmonic"]), "Amplitude_mhcI_MB") # position of mutation wild_type_netmhcpan4, mutation_netmhcpan4 = properties_manager.get_netmhcpan4_epitopes( @@ -174,20 +174,20 @@ def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aa # Amplitude with affinity values self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( - score_mutation=self.properties["best_affinity_netmhcpan4"].replace(",", "."), - score_wild_type=self.properties["best_affinity_netmhcpan4_WT"].replace(",", "."), + score_mutation=self.properties["best_affinity_netmhcpan4"], + score_wild_type=self.properties["best_affinity_netmhcpan4_WT"], apply_correction=True), "Amplitude_mhcI_affinity") # Amplitude with rank by netmhcpan4 self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( - score_mutation=self.properties["best%Rank_netmhcpan4"].replace(",", "."), - score_wild_type=self.properties["best%Rank_netmhcpan4_WT"].replace(",", ".")), + score_mutation=self.properties["best%Rank_netmhcpan4"], + score_wild_type=self.properties["best%Rank_netmhcpan4_WT"]), "Amplitude_mhcI_rank_netmhcpan4") # Amplitude based on best affinity prediction restricted to 9mers self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( - score_mutation=self.properties["best_affinity_netmhcpan4_9mer"].replace(",", "."), - score_wild_type = self.properties["best_affinity_netmhcpan4_9mer_WT"].replace(",", "."), + score_mutation=self.properties["best_affinity_netmhcpan4_9mer"], + score_wild_type = self.properties["best_affinity_netmhcpan4_9mer_WT"], apply_correction=True), "Amplitude_mhcI_affinity_9mer_netmhcpan4") self.add_features( @@ -341,20 +341,20 @@ def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aa # amplitude affinity mhc II self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( - score_mutation=self.properties["best_affinity_netmhcIIpan"].replace(",", "."), - score_wild_type = self.properties["best_affinity_netmhcIIpan_WT"].replace(",", "."), + score_mutation=self.properties["best_affinity_netmhcIIpan"], + score_wild_type = self.properties["best_affinity_netmhcIIpan_WT"], apply_correction=True), "Amplitude_mhcII_affinity") # amplitude multiple binding mhc II self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( - score_mutation=self.properties["MB_score_MHCII_top10_harmonic"].replace(",", "."), - score_wild_type = self.properties["MB_score_MHCII_top10_WT_harmonic"].replace(",", ".")), + score_mutation=self.properties["MB_score_MHCII_top10_harmonic"], + score_wild_type = self.properties["MB_score_MHCII_top10_WT_harmonic"]), "Amplitude_mhcII_mb") # amplitude rank score mhc II self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( - score_mutation=self.properties["best%Rank_netmhcIIpan"].replace(",", "."), - score_wild_type = self.properties["best%Rank_netmhcIIpan_WT"].replace(",", ".")), + score_mutation=self.properties["best%Rank_netmhcIIpan"], + score_wild_type = self.properties["best%Rank_netmhcIIpan_WT"]), "Amplitude_mhcII_rank_netmhcpan4") logger.info("Amplitude mhc II: {}".format(self.properties["Amplitude_mhcII_rank_netmhcpan4"])) @@ -497,12 +497,12 @@ def add_neoantigen_fitness_features(self, mutation_mhci, mutation_mhcii): mutation=mutation_mhcii, iedb=self.references.iedb), "Pathogensimiliarity_mhcII") - score_mutation_mhci = self.properties["MHC_I_score_.best_prediction."].replace(",", ".") - score_wild_type_mhci = self.properties["MHC_I_score_.WT."].replace(",", ".") + score_mutation_mhci = self.properties["MHC_I_score_.best_prediction."] + score_wild_type_mhci = self.properties["MHC_I_score_.WT."] self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( score_mutation=score_mutation_mhci, score_wild_type=score_wild_type_mhci), "Amplitude_mhcI") - score_mutation_mhcii = self.properties["MHC_II_score_.best_prediction."].replace(",", ".") - score_wild_type_mhcii = self.properties["MHC_II_score_.WT."].replace(",", ".") + score_mutation_mhcii = self.properties["MHC_II_score_.best_prediction."] + score_wild_type_mhcii = self.properties["MHC_II_score_.WT."] self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( score_mutation=score_mutation_mhcii, score_wild_type=score_wild_type_mhcii), "Amplitude_mhcII") @@ -531,8 +531,8 @@ def add_self_similarity_features(self, mutation_mhci, mutation_mhcii, wild_type_ ), "ImprovedBinding_mhcI") self.add_features(self_similarity.is_improved_binder( # TODO: conversion from float representation needs to be changed - score_mutation=self.properties["MHC_II_score_.best_prediction."].replace(",", "."), - score_wild_type=self.properties["MHC_II_score_.WT."].replace(",", ".") + score_mutation=self.properties["MHC_II_score_.best_prediction."], + score_wild_type=self.properties["MHC_II_score_.WT."] ), "ImprovedBinding_mhcII") self.add_features(self_similarity.self_similarity_of_conserved_binder_only( has_conserved_binder=self.properties["ImprovedBinding_mhcI"], diff --git a/input/netmhcpan4/multiple_binders.py b/input/netmhcpan4/multiple_binders.py index a92ae982..7881a15a 100755 --- a/input/netmhcpan4/multiple_binders.py +++ b/input/netmhcpan4/multiple_binders.py @@ -14,10 +14,12 @@ def get_means(self, list_numbers): """ results = ["NA", "NA", "NA"] if list_numbers is not None and len(list_numbers) > 0: + # TODO: ensure that floats are parsed before calling this method so this conversion is not needed + list_floats = [float(x) for x in list_numbers] results = [ - np.mean(list_numbers), - stats.hmean(list_numbers), - stats.gmean(list_numbers) + np.mean(list_floats), + stats.hmean(list_floats), + stats.gmean(list_floats) ] return results diff --git a/input/tests/integration_tests/test_input.py b/input/tests/integration_tests/test_input.py index 702d9494..770e0b33 100755 --- a/input/tests/integration_tests/test_input.py +++ b/input/tests/integration_tests/test_input.py @@ -1,26 +1,32 @@ -from unittest import TestCase - -from input.predict_all_epitopes import BunchEpitopes - - -class TestInput(TestCase): - - def test_input(self): - """ - This test is equivalent to the command line call: - input -i /projects/SUMMIT/WP1.2/input/development/Pt29.sequences4testing.txt - -a /projects/SUMMIT/WP1.2/Literature_Cohorts/data_analysis/cohorts/vanallen/output_tables/20200106_alleles_extended.csv - -tc /projects/SUMMIT/WP1.2/Literature_Cohorts/data_analysis/cohorts/vanallen/output_tables/vanallen_patient_overview.csv - - NOTE: we will need to check the output when the calculation of resuls and printing to stdout have been decoupled - :return: - """ - input_file = '/projects/SUMMIT/WP1.2/input/development/Pt29.sequences4testing.txt' - alleles_file = '/projects/SUMMIT/WP1.2/Literature_Cohorts/data_analysis/cohorts/vanallen/output_tables/20200106_alleles_extended.csv' - tumor_content_file = '/projects/SUMMIT/WP1.2/Literature_Cohorts/data_analysis/cohorts/vanallen/output_tables/vanallen_patient_overview.csv' - BunchEpitopes().wrapper_table_add_feature_annotation( - file=input_file, - indel=False, - path_to_hla_file=alleles_file, - tissue='skin', - tumour_content_file=tumor_content_file) +from unittest import TestCase + +from input.predict_all_epitopes import BunchEpitopes +from input.tests.integration_tests import integration_test_tools + + +class TestInput(TestCase): + + def setUp(self): + self.references, self.configuration = integration_test_tools.load_references() + # self.fastafile = integration_test_tools.create_temp_aminoacid_fasta_file() + # self.runner = Runner() + + def test_input(self): + """ + This test is equivalent to the command line call: + input -i /projects/SUMMIT/WP1.2/input/development/Pt29.sequences4testing.txt + -a /projects/SUMMIT/WP1.2/Literature_Cohorts/data_analysis/cohorts/vanallen/output_tables/20200106_alleles_extended.csv + -tc /projects/SUMMIT/WP1.2/Literature_Cohorts/data_analysis/cohorts/vanallen/output_tables/vanallen_patient_overview.csv + + NOTE: we will need to check the output when the calculation of resuls and printing to stdout have been decoupled + :return: + """ + input_file = '/projects/SUMMIT/WP1.2/input/development/Pt29.sequences4testing.txt' + alleles_file = '/projects/SUMMIT/WP1.2/Literature_Cohorts/data_analysis/cohorts/vanallen/output_tables/20200106_alleles_extended.csv' + tumor_content_file = '/projects/SUMMIT/WP1.2/Literature_Cohorts/data_analysis/cohorts/vanallen/output_tables/vanallen_patient_overview.csv' + BunchEpitopes().wrapper_table_add_feature_annotation( + file=input_file, + indel=False, + path_to_hla_file=alleles_file, + tissue='skin', + tumour_content_file=tumor_content_file) From d52fdd40448e16b5744f7d14db969403c1188f72 Mon Sep 17 00:00:00 2001 From: Pablo Riesgo Ferreiro Date: Tue, 16 Jun 2020 13:43:56 +0200 Subject: [PATCH 048/105] added a brief developer guide --- README.md | 50 ++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 50 insertions(+) diff --git a/README.md b/README.md index 70f69598..14b5364b 100755 --- a/README.md +++ b/README.md @@ -115,3 +115,53 @@ sh start_annotation_multiple_patientfiles.sh cohort_folder_with_patient_icam_fol ``` --> eg. parallel mps annotation of patients of a cohort, iCaM files stored in cohort_folder_with_patient_icam_folders + + +## Developer guide + +### Build the package + +To build the package just run: +``` +python setup.py bdist_wheel +``` + +This will create an installable wheel file under `dist/input-x.y.z.whl`. + +### Install the package + +Install the wheel file as follows: +``` +pip install dist/input-x.y.z.whl +``` + +### Run integration tests + +To run the integration tests make sure you have a file `.env` that contains the following variables with the right values: +``` +export INPUT_REFERENCE_FOLDER=~/addannot_references +export INPUT_BLASTP=/code/ncbi-blast/2.8.1+/bin/blastp +export INPUT_MIXMHC2PRED=/code/net/MixMHC2pred/1.1/MixMHC2pred +export INPUT_MIXMHCPRED=/code/MixMHCpred/2.0.2/MixMHCpred +export INPUT_RSCRIPT=/code/R/3.6.0/bin/Rscript +export INPUT_NETMHC2PAN=/code/net/MHCIIpan/3.2/netMHCIIpan +export INPUT_NETMHCPAN=/code/net/MHCpan/4.0/netMHCpan +``` + +The folder `$INPUT_REFERENCE_FOLDER` requires to contain the resources defined above. + +Run the integration tests as follows: +``` +python -m unittest discover input.tests.integration_tests +``` + +The integration tests run over some real datasets and they take some time to run. + +### Run unit tests + +The unit tests do not have any dependency and they finish in seconds. + +Run the unit tests as follows: +``` +python -m unittest discover input.tests.unit_tests +``` \ No newline at end of file From 74dfc8bc2d264c2be4be83be618b7ec89659063b Mon Sep 17 00:00:00 2001 From: Pablo Riesgo Ferreiro Date: Tue, 16 Jun 2020 22:24:36 +0200 Subject: [PATCH 049/105] cleaning up model prototypes --- input/{model_protobuf => model}/README.md | 3 +-- input/{model_protobuf => model}/__init__.py | 0 input/{model_avro => model/avro}/Gene.avsc | 0 input/{model_avro => model/avro}/Mutation.avsc | 0 input/{model_avro => model/avro}/Neoantigen.avsc | 0 input/{model_avro => model/avro}/README.md | 0 input/{model_avro => model/avro}/__init__.py | 0 input/{model_avro => model/avro}/generate_source_code.py | 0 input/{model_avro => model/avro}/neoantigen.avdl | 0 input/{model_avro => model/avro}/neoantigen.avpr | 0 input/{model_avro => model/avro}/neoantigen/__init__.py | 0 input/{model_avro => model/avro}/schema.avsc | 0 input/{model_avro => model/avro}/schema_classes.py | 0 input/{model_avro => model/avro}/schema_conversion.py | 4 ++-- .../{model_protobuf/doc/index.html => model/neoantigen.html} | 0 input/{model_protobuf => model}/neoantigen.proto | 0 input/{model_protobuf => model}/neoantigen.py | 0 input/{model_protobuf => model}/schema_conversion.py | 2 +- input/tests/integration_tests/test_schema_conversion_avro.py | 4 ++-- input/tests/integration_tests/test_schema_conversion_proto.py | 4 ++-- input/tests/unit_tests/test_schema_conversion_avro.py | 4 ++-- input/tests/unit_tests/test_schema_conversion_proto.py | 4 ++-- 22 files changed, 12 insertions(+), 13 deletions(-) rename input/{model_protobuf => model}/README.md (87%) rename input/{model_protobuf => model}/__init__.py (100%) rename input/{model_avro => model/avro}/Gene.avsc (100%) rename input/{model_avro => model/avro}/Mutation.avsc (100%) rename input/{model_avro => model/avro}/Neoantigen.avsc (100%) rename input/{model_avro => model/avro}/README.md (100%) rename input/{model_avro => model/avro}/__init__.py (100%) rename input/{model_avro => model/avro}/generate_source_code.py (100%) rename input/{model_avro => model/avro}/neoantigen.avdl (100%) rename input/{model_avro => model/avro}/neoantigen.avpr (100%) rename input/{model_avro => model/avro}/neoantigen/__init__.py (100%) rename input/{model_avro => model/avro}/schema.avsc (100%) rename input/{model_avro => model/avro}/schema_classes.py (100%) rename input/{model_avro => model/avro}/schema_conversion.py (98%) rename input/{model_protobuf/doc/index.html => model/neoantigen.html} (100%) rename input/{model_protobuf => model}/neoantigen.proto (100%) rename input/{model_protobuf => model}/neoantigen.py (100%) rename input/{model_protobuf => model}/schema_conversion.py (98%) diff --git a/input/model_protobuf/README.md b/input/model/README.md similarity index 87% rename from input/model_protobuf/README.md rename to input/model/README.md index 959e9fb0..0323f8f0 100755 --- a/input/model_protobuf/README.md +++ b/input/model/README.md @@ -22,8 +22,7 @@ Documentation is generated using this tool https://github.com/pseudomuto/protoc- Run: ``` -mkdir doc -protoc --doc_out=./doc --doc_opt=html,index.html neoantigen.proto +protoc --doc_out=. --doc_opt=html,neoantigen.html neoantigen.proto ``` diff --git a/input/model_protobuf/__init__.py b/input/model/__init__.py similarity index 100% rename from input/model_protobuf/__init__.py rename to input/model/__init__.py diff --git a/input/model_avro/Gene.avsc b/input/model/avro/Gene.avsc similarity index 100% rename from input/model_avro/Gene.avsc rename to input/model/avro/Gene.avsc diff --git a/input/model_avro/Mutation.avsc b/input/model/avro/Mutation.avsc similarity index 100% rename from input/model_avro/Mutation.avsc rename to input/model/avro/Mutation.avsc diff --git a/input/model_avro/Neoantigen.avsc b/input/model/avro/Neoantigen.avsc similarity index 100% rename from input/model_avro/Neoantigen.avsc rename to input/model/avro/Neoantigen.avsc diff --git a/input/model_avro/README.md b/input/model/avro/README.md similarity index 100% rename from input/model_avro/README.md rename to input/model/avro/README.md diff --git a/input/model_avro/__init__.py b/input/model/avro/__init__.py similarity index 100% rename from input/model_avro/__init__.py rename to input/model/avro/__init__.py diff --git a/input/model_avro/generate_source_code.py b/input/model/avro/generate_source_code.py similarity index 100% rename from input/model_avro/generate_source_code.py rename to input/model/avro/generate_source_code.py diff --git a/input/model_avro/neoantigen.avdl b/input/model/avro/neoantigen.avdl similarity index 100% rename from input/model_avro/neoantigen.avdl rename to input/model/avro/neoantigen.avdl diff --git a/input/model_avro/neoantigen.avpr b/input/model/avro/neoantigen.avpr similarity index 100% rename from input/model_avro/neoantigen.avpr rename to input/model/avro/neoantigen.avpr diff --git a/input/model_avro/neoantigen/__init__.py b/input/model/avro/neoantigen/__init__.py similarity index 100% rename from input/model_avro/neoantigen/__init__.py rename to input/model/avro/neoantigen/__init__.py diff --git a/input/model_avro/schema.avsc b/input/model/avro/schema.avsc similarity index 100% rename from input/model_avro/schema.avsc rename to input/model/avro/schema.avsc diff --git a/input/model_avro/schema_classes.py b/input/model/avro/schema_classes.py similarity index 100% rename from input/model_avro/schema_classes.py rename to input/model/avro/schema_classes.py diff --git a/input/model_avro/schema_conversion.py b/input/model/avro/schema_conversion.py similarity index 98% rename from input/model_avro/schema_conversion.py rename to input/model/avro/schema_conversion.py index 88480149..53c1b092 100755 --- a/input/model_avro/schema_conversion.py +++ b/input/model/avro/schema_conversion.py @@ -7,7 +7,7 @@ from collections import defaultdict from avro_validator.schema import Schema -from input.model_avro.neoantigen import Neoantigen, Gene, Mutation +from input.model.avro.neoantigen import Neoantigen, Gene, Mutation NEOANTIGEN_AVSC = 'Neoantigen.avsc' GENE_AVSC = 'Gene.avsc' @@ -38,7 +38,7 @@ def validate(self, model): else: raise ValueError("Unexpected type for validation {}".format(type(model))) if not valid: - raise ValueError("Invalid model_avro due to unknown reasons") + raise ValueError("Invalid avro due to unknown reasons") return valid def icam2model(self, icam_file): diff --git a/input/model_protobuf/doc/index.html b/input/model/neoantigen.html similarity index 100% rename from input/model_protobuf/doc/index.html rename to input/model/neoantigen.html diff --git a/input/model_protobuf/neoantigen.proto b/input/model/neoantigen.proto similarity index 100% rename from input/model_protobuf/neoantigen.proto rename to input/model/neoantigen.proto diff --git a/input/model_protobuf/neoantigen.py b/input/model/neoantigen.py similarity index 100% rename from input/model_protobuf/neoantigen.py rename to input/model/neoantigen.py diff --git a/input/model_protobuf/schema_conversion.py b/input/model/schema_conversion.py similarity index 98% rename from input/model_protobuf/schema_conversion.py rename to input/model/schema_conversion.py index 25b77efc..26873a58 100755 --- a/input/model_protobuf/schema_conversion.py +++ b/input/model/schema_conversion.py @@ -4,7 +4,7 @@ import difflib from collections import defaultdict -from input.model_protobuf.neoantigen import Neoantigen, Gene, Mutation +from input.model.neoantigen import Neoantigen, Gene, Mutation class SchemaConverter(object): diff --git a/input/tests/integration_tests/test_schema_conversion_avro.py b/input/tests/integration_tests/test_schema_conversion_avro.py index 60bbb694..be07d608 100755 --- a/input/tests/integration_tests/test_schema_conversion_avro.py +++ b/input/tests/integration_tests/test_schema_conversion_avro.py @@ -1,7 +1,7 @@ from unittest import TestCase -from input.model_avro.schema_conversion import SchemaConverter -from input.model_avro.neoantigen import Neoantigen, Gene, Mutation +from input.model.avro.schema_conversion import SchemaConverter +from input.model.avro.neoantigen import Neoantigen, Gene, Mutation class SchemaConverterTest(TestCase): diff --git a/input/tests/integration_tests/test_schema_conversion_proto.py b/input/tests/integration_tests/test_schema_conversion_proto.py index 2e07931e..62c23d8a 100755 --- a/input/tests/integration_tests/test_schema_conversion_proto.py +++ b/input/tests/integration_tests/test_schema_conversion_proto.py @@ -1,7 +1,7 @@ from unittest import TestCase -from input.model_protobuf.schema_conversion import SchemaConverter -from input.model_protobuf.neoantigen import Neoantigen, Gene, Mutation +from input.model.schema_conversion import SchemaConverter +from input.model.neoantigen import Neoantigen, Gene, Mutation class SchemaConverterTest(TestCase): diff --git a/input/tests/unit_tests/test_schema_conversion_avro.py b/input/tests/unit_tests/test_schema_conversion_avro.py index c1b7104b..42c53d09 100755 --- a/input/tests/unit_tests/test_schema_conversion_avro.py +++ b/input/tests/unit_tests/test_schema_conversion_avro.py @@ -7,9 +7,9 @@ from pandas.io.json import json_normalize -from input.model_avro.schema_conversion import SchemaConverter +from input.model.avro.schema_conversion import SchemaConverter from input.helpers import intermediate_files -from input.model_avro.neoantigen import Neoantigen, Gene, Mutation +from input.model.avro.neoantigen import Neoantigen, Gene, Mutation class SchemaConverterTest(TestCase): diff --git a/input/tests/unit_tests/test_schema_conversion_proto.py b/input/tests/unit_tests/test_schema_conversion_proto.py index f3ae9f74..4a44a479 100755 --- a/input/tests/unit_tests/test_schema_conversion_proto.py +++ b/input/tests/unit_tests/test_schema_conversion_proto.py @@ -5,8 +5,8 @@ from Bio.Data import IUPACData import numpy as np -from input.model_protobuf.schema_conversion import SchemaConverter -from input.model_protobuf.neoantigen import Neoantigen, Gene, Mutation +from input.model.schema_conversion import SchemaConverter +from input.model.neoantigen import Neoantigen, Gene, Mutation class SchemaConverterTest(TestCase): From 8993f70365aa342ac341d600b82aa292af558a37 Mon Sep 17 00:00:00 2001 From: Pablo Riesgo Ferreiro Date: Tue, 16 Jun 2020 23:49:46 +0200 Subject: [PATCH 050/105] added model for patient metadata + conversion from iCaM tables --- input/model/neoantigen.html | 69 +++++++++++++++++++ input/model/neoantigen.proto | 40 +++++++++-- input/model/neoantigen.py | 32 +++++++-- input/model/schema_conversion.py | 63 +++++++++++++++-- .../test_schema_conversion_proto.py | 32 ++++++++- 5 files changed, 221 insertions(+), 15 deletions(-) diff --git a/input/model/neoantigen.html b/input/model/neoantigen.html index 061e9f35..3b5b203d 100644 --- a/input/model/neoantigen.html +++ b/input/model/neoantigen.html @@ -190,6 +190,10 @@

Table of Contents

MNeoantigen +
  • + MPatient +
    • + @@ -332,6 +336,14 @@

    Neoantigen

    + + patientIdentifier + string + +

    +Patient identifier

    + + gene Gene @@ -381,6 +393,63 @@

    Neoantigen

    +

    Patient

    +

    The metadata required for analysis for a given patient + its patient identifier

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    FieldTypeLabelDescription
    identifierstring

    +Patient identifier

    estimatedTumorContentfloat

    +Estimated tumor content (percentage)

    isRnaAvailablebool

    +Is RNA expression available?

    mhcIAllelesstringrepeated

    +MHC I alleles

    mhcIIAllelesstringrepeated

    +MHC II alleles

    + + + + + diff --git a/input/model/neoantigen.proto b/input/model/neoantigen.proto index ca74ff34..805d1ee9 100755 --- a/input/model/neoantigen.proto +++ b/input/model/neoantigen.proto @@ -52,26 +52,56 @@ message Mutation { A neoantigen minimal definition */ message Neoantigen { + /** + Patient identifier + */ + string patientIdentifier = 1; /** The gene where the neoepitope corresponds */ - Gene gene = 1; + Gene gene = 2; /** The mutation */ - Mutation mutation = 2; + Mutation mutation = 3; /** Expression value of the transcript (any more definition on type of expression? ie: digital from RNAseq, from microarrays, etc.) */ - float expressionValue = 3; + float expressionValue = 4; /** Clonality estimation. At the moment this is a boolean indicating whether there is clonality or not, there is no quantitive measurement at the moment. */ - bool clonalityEstimation = 4; + bool clonalityEstimation = 5; /** Variant allele frequency in the range [0.0, 1.0] */ - float variantAlleleFrequency = 5; + float variantAlleleFrequency = 6; +} + +/** +The metadata required for analysis for a given patient + its patient identifier +*/ +message Patient { + /** + Patient identifier + */ + string identifier = 1; + /** + Estimated tumor content (percentage) + */ + float estimatedTumorContent = 2; + /** + Is RNA expression available? + */ + bool isRnaAvailable = 3; + /** + MHC I alleles + */ + repeated string mhcIAlleles = 4; + /** + MHC II alleles + */ + repeated string mhcIIAlleles = 5; } \ No newline at end of file diff --git a/input/model/neoantigen.py b/input/model/neoantigen.py index b2b4dc94..0900d46e 100644 --- a/input/model/neoantigen.py +++ b/input/model/neoantigen.py @@ -2,6 +2,7 @@ # sources: neoantigen.proto # plugin: python-betterproto from dataclasses import dataclass +from typing import List import betterproto @@ -42,16 +43,37 @@ class Mutation(betterproto.Message): class Neoantigen(betterproto.Message): """* A neoantigen minimal definition""" + # * Patient identifier + patient_identifier: str = betterproto.string_field(1) # * The gene where the neoepitope corresponds - gene: "Gene" = betterproto.message_field(1) + gene: "Gene" = betterproto.message_field(2) # * The mutation - mutation: "Mutation" = betterproto.message_field(2) + mutation: "Mutation" = betterproto.message_field(3) # * Expression value of the transcript (any more definition on type of # expression? ie: digital from RNAseq, from microarrays, etc.) - expression_value: float = betterproto.float_field(3) + expression_value: float = betterproto.float_field(4) # * Clonality estimation. At the moment this is a boolean indicating whether # there is clonality or not, there is no quantitive measurement at the # moment. - clonality_estimation: bool = betterproto.bool_field(4) + clonality_estimation: bool = betterproto.bool_field(5) # * Variant allele frequency in the range [0.0, 1.0] - variant_allele_frequency: float = betterproto.float_field(5) + variant_allele_frequency: float = betterproto.float_field(6) + + +@dataclass +class Patient(betterproto.Message): + """ + * The metadata required for analysis for a given patient + its patient + identifier + """ + + # * Patient identifier + identifier: str = betterproto.string_field(1) + # * Estimated tumor content (percentage) + estimated_tumor_content: float = betterproto.float_field(2) + # * Is RNA expression available? + is_rna_available: bool = betterproto.bool_field(3) + # * MHC I alleles + mhc_i_alleles: List[str] = betterproto.string_field(4) + # * MHC II alleles + mhc_i_i_alleles: List[str] = betterproto.string_field(5) diff --git a/input/model/schema_conversion.py b/input/model/schema_conversion.py index 26873a58..7f4d4559 100755 --- a/input/model/schema_conversion.py +++ b/input/model/schema_conversion.py @@ -1,10 +1,12 @@ +from itertools import islice + import pandas as pd from pandas.io.json import json_normalize import re import difflib from collections import defaultdict -from input.model.neoantigen import Neoantigen, Gene, Mutation +from input.model.neoantigen import Neoantigen, Gene, Mutation, Patient class SchemaConverter(object): @@ -18,21 +20,73 @@ def validate(model): return model.__bytes__() @staticmethod - def icam2model(icam_file): + def icam2model(icam_file, patient_id=None): """ :param icam_file: the path to an iCaM output file :type icam_file: str + :param patient_id: the patient identifier for all neoantigens in the iCaM file, if not provided it is + expected as column named `patient.id` or `patient` + :type patient_id: str :rtype: list[Neoepitope] """ data = pd.read_csv(icam_file, sep='\t') SchemaConverter._enrich_icam_table(data) neoantigens = [] for _, icam_entry in data.iterrows(): - neoantigens.append(SchemaConverter._icam_entry2model(icam_entry)) + neoantigens.append(SchemaConverter._icam_entry2model(icam_entry, patient_id=patient_id)) for n in neoantigens: SchemaConverter.validate(n) return neoantigens + @staticmethod + def patient_metadata2model(hla_file, tumor_content_file): + """ + :param hla_file: the path to a file with the HLAs per patient for both MHC I and MHC II + :type hla_file: str + :param tumor_content_file: the path to a file with the tumoe content per patient + :type tumor_content_file: str + :rtype: list[Patient] + """ + # parse HLA table and add metadata to patient + alleles_stacked = SchemaConverter._parse_hlas_table(hla_file) + patients = {} + for patient_identifier in alleles_stacked.patient_id: + patient = Patient() + patient.identifier = patient_identifier + patient.mhc_i_alleles = list(alleles_stacked[(alleles_stacked.patient_id == patient_identifier) & + (alleles_stacked.mhc_type == 'mhc_I_selection')].allele) + patient.mhc_i_i_alleles = list(alleles_stacked[(alleles_stacked.patient_id == patient_identifier) & + (alleles_stacked.mhc_type == 'mhc_II_selection')].allele) + patients[patient_identifier] = patient + + # parse estimated tumor content file and add metadata to patient + tumor_content = SchemaConverter._parse_tumor_content_table(tumor_content_file) + for patient_identifier in tumor_content.Patient: + patient = patients.get(patient_identifier) + if patient is not None: + patient.estimated_tumor_content = tumor_content[tumor_content.Patient == patient_identifier][ + 'est. Tumor content'].iloc[0] + patient.is_rna_available = tumor_content[tumor_content.Patient == patient_identifier][ + 'rna_avail'].iloc[0] + + return list(patients.values()) + + @staticmethod + def _parse_tumor_content_table(tumor_content_file): + tumor_content = pd.read_csv(tumor_content_file, sep=';') + tumor_content.Patient = tumor_content.Patient.transform(lambda x: x.strip('/')) + return tumor_content + + @staticmethod + def _parse_hlas_table(hla_file): + alleles = pd.read_csv(hla_file, sep=';', header=None, + names=['patient_id', 'mhc_type'] + list(range(50))).dropna(axis=1, how='all') + alleles_stacked = alleles.set_index(['patient_id', 'mhc_type']).stack(dropna=True).reset_index() + del alleles_stacked['level_2'] + alleles_stacked['allele'] = alleles_stacked[0] + del alleles_stacked[0] + return alleles_stacked + @staticmethod def model2csv(neoantigens): """ @@ -73,7 +127,7 @@ def _flat_dict2nested_dict(flat_dict): return dict(nested_dict) @staticmethod - def _icam_entry2model(icam_entry): + def _icam_entry2model(icam_entry, patient_id): gene = Gene() gene.assembly = 'hg19' @@ -90,6 +144,7 @@ def _icam_entry2model(icam_entry): mutation.size_right_flanking_region = len(icam_entry.get('right_flanking_region')) neoantigen = Neoantigen() + neoantigen.patient_identifier = patient_id if patient_id else icam_entry.get('patient', icam_entry.get('patient.id')) neoantigen.mutation = mutation neoantigen.gene = gene neoantigen.clonality_estimation = None # TODO: where do we get this from? diff --git a/input/tests/integration_tests/test_schema_conversion_proto.py b/input/tests/integration_tests/test_schema_conversion_proto.py index 62c23d8a..ba01c6d3 100755 --- a/input/tests/integration_tests/test_schema_conversion_proto.py +++ b/input/tests/integration_tests/test_schema_conversion_proto.py @@ -1,7 +1,7 @@ from unittest import TestCase from input.model.schema_conversion import SchemaConverter -from input.model.neoantigen import Neoantigen, Gene, Mutation +from input.model.neoantigen import Neoantigen, Gene, Mutation, Patient class SchemaConverterTest(TestCase): @@ -20,3 +20,33 @@ def test_icam2model(self): self.assertIsInstance(n.mutation, Mutation) self.assertTrue(n.gene.transcript_identifier is not None and len(n.gene.transcript_identifier) > 0) self.assertTrue(n.mutation.mutated_aminoacid is not None and len(n.mutation.mutated_aminoacid) == 1) + + def test_overriding_patient_id(self): + # self.icam_file = '/projects/SUMMIT/WP1.2/input/development/Pt29.sequences4testing.txt' + self.icam_file = '\\\\192.168.171.199\\projects$\\SUMMIT\\WP1.2\\input\\development\\Pt29.sequences4testing.txt' + with open(self.icam_file) as f: + self.count_lines = len(f.readlines()) + neoantigens = SchemaConverter().icam2model(self.icam_file, patient_id='patientX') + for n in neoantigens: + self.assertEqual(n.patient_identifier, 'patientX') + neoantigens = SchemaConverter().icam2model(self.icam_file) + for n in neoantigens: + self.assertEqual(n.patient_identifier, None) + + def test_patient_metadata2model(self): + # alleles_file = '/projects/SUMMIT/WP1.2/Literature_Cohorts/data_analysis/cohorts/vanallen/output_tables/20200106_alleles_extended.csv' + # tumor_content_file = '/projects/SUMMIT/WP1.2/Literature_Cohorts/data_analysis/cohorts/vanallen/output_tables/vanallen_patient_overview.csv' + alleles_file = "\\\\192.168.171.199\\projects$\\SUMMIT\\WP1.2\\Literature_Cohorts\\data_analysis\\cohorts\\vanallen\\output_tables\\20200106_alleles_extended.csv" + tumor_content_file = '\\\\192.168.171.199\\projects$\\SUMMIT\\WP1.2\\Literature_Cohorts\\data_analysis\\cohorts\\vanallen\\output_tables\\vanallen_patient_overview.csv' + with open(alleles_file) as f: + count_lines = len(f.readlines()) + patients = SchemaConverter().patient_metadata2model(hla_file=alleles_file, tumor_content_file=tumor_content_file) + self.assertIsNotNone(patients) + self.assertIsInstance(patients, list) + self.assertEqual(count_lines / 2, len(patients)) + for n in patients: + self.assertIsInstance(n, Patient) + self.assertIsInstance(n.is_rna_available, bool) + self.assertIsInstance(n.estimated_tumor_content, float) + self.assertIsInstance(n.mhc_i_alleles, list) + self.assertIsInstance(n.mhc_i_i_alleles, list) From 31399ac9157da4408969f30857322c76afb9add9 Mon Sep 17 00:00:00 2001 From: Pablo Riesgo Ferreiro Date: Wed, 17 Jun 2020 13:43:51 +0200 Subject: [PATCH 051/105] changing all line endings to Unix style - thanks .gitattributtes --- input/Tcell_predictor/prediction.py | 46 +-- input/Tcell_predictor/preprocess.py | 210 +++++++------- input/__init__.py | 22 +- input/command_line.py | 174 +++++------ input/exceptions.py | 28 +- input/helpers/blastp_runner.py | 70 ++--- input/helpers/epitope_helper.py | 132 ++++----- input/helpers/fastaGenerator.py | 64 ++-- input/helpers/intermediate_files.py | 42 +-- input/helpers/properties_manager.py | 192 ++++++------ input/helpers/runner.py | 74 ++--- .../abstract_netmhcpan_predictor.py | 34 +-- input/new_features/conservation_scores.py | 102 +++---- input/references.py | 214 +++++++------- input/self_similarity/self_similarity.py | 274 +++++++++--------- input/tests/__init__.py | 44 +-- .../integration_test_tools.py | 38 +-- .../test_conservation_scores.py | 92 +++--- .../integration_tests/test_dissimilarity.py | 54 ++-- .../integration_tests/test_mixmhcpred.py | 198 ++++++------- input/tests/integration_tests/test_neoag.py | 194 ++++++------- .../test_neoantigen_fitness.py | 100 +++---- .../tests/integration_tests/test_netmhcpan.py | 190 ++++++------ .../integration_tests/test_tcell_predictor.py | 104 +++---- input/tests/unit_tests/fake_classes.py | 30 +- .../test_dependencies_configuration.py | 130 ++++----- .../unit_tests/test_predict_all_epitopes.py | 48 +-- .../tests/unit_tests/test_reference_folder.py | 94 +++--- input/tests/unit_tests/test_runner.py | 46 +-- .../tests/unit_tests/test_self_similarity.py | 76 ++--- model/neoepitope.avdl | 166 +++++------ setup.py | 100 +++---- 32 files changed, 1691 insertions(+), 1691 deletions(-) diff --git a/input/Tcell_predictor/prediction.py b/input/Tcell_predictor/prediction.py index d94526b3..de726894 100755 --- a/input/Tcell_predictor/prediction.py +++ b/input/Tcell_predictor/prediction.py @@ -1,23 +1,23 @@ -import os -import pickle - -import pandas as pd - -from input.Tcell_predictor.preprocess import Preprocessor - - -def main(f_name, output_file, references): - input_file = f_name - mat = Preprocessor(references=references).main(input_file) - # NOTE: we do not put the Classifier.pickle in the references.py because it is code and not data what's in there - # thus it belongs with the code - with open(os.path.join(os.path.abspath(os.path.dirname(__file__)), 'Classifier.pickle'), 'rb') as f: - classifier = pickle.load(f) - scores = classifier.predict_proba(mat) - dictionary = {} - with open(input_file, 'r') as f: - for row, val in zip(f, scores): - seq = row.split()[1] - dictionary[seq] = val[-1] - df = pd.DataFrame.from_dict(dictionary, orient='index') - df.to_csv(output_file) +import os +import pickle + +import pandas as pd + +from input.Tcell_predictor.preprocess import Preprocessor + + +def main(f_name, output_file, references): + input_file = f_name + mat = Preprocessor(references=references).main(input_file) + # NOTE: we do not put the Classifier.pickle in the references.py because it is code and not data what's in there + # thus it belongs with the code + with open(os.path.join(os.path.abspath(os.path.dirname(__file__)), 'Classifier.pickle'), 'rb') as f: + classifier = pickle.load(f) + scores = classifier.predict_proba(mat) + dictionary = {} + with open(input_file, 'r') as f: + for row, val in zip(f, scores): + seq = row.split()[1] + dictionary[seq] = val[-1] + df = pd.DataFrame.from_dict(dictionary, orient='index') + df.to_csv(output_file) diff --git a/input/Tcell_predictor/preprocess.py b/input/Tcell_predictor/preprocess.py index 74133a0c..31d102e4 100755 --- a/input/Tcell_predictor/preprocess.py +++ b/input/Tcell_predictor/preprocess.py @@ -1,105 +1,105 @@ -import pickle - -import numpy as np -import scipy.io as sio - - -class Preprocessor(object): - - def __init__(self, references): - self.references = references - self.load_data = sio.loadmat(self.references.tcell_predictor_sir_data) - with open(self.references.tcell_predictor_gene_expression, 'rb') as handle: - self.dict_expression = pickle.load(handle) - with open(self.references.tcell_predictor_aa_features, 'rb') as handle: - self.dict_data = pickle.load(handle) - - @staticmethod - def seq2bin(seq): - aa = ['A', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L', 'M', 'N', 'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'Y'] - dict_aa = dict((i, j) for j, i in enumerate(aa)) - arr = np.zeros((1, 9 * 20)) - for ii, letter in enumerate(seq): - arr[0, ii * 20 + dict_aa.get(letter)] = 1 - return arr - - @staticmethod - def get_hydrophbicity(x, dict_): - pair_letters = [c for c in x if c.isupper()] - res = np.abs(dict_[pair_letters[0]] - dict_[pair_letters[1]]) - return res - - @staticmethod - def get_size(x, dict_): - pair_letters = [c for c in x if c.isupper()] - res = np.abs(dict_[pair_letters[0]] - dict_[pair_letters[1]]) - return res - - @staticmethod - def get_charge_change(x, dict_): - pair_letters = [c for c in x if c.isupper()] - if dict_[pair_letters[0]] == dict_[pair_letters[1]]: - return 0 - else: - return 1 - - @staticmethod - def get_charge_abs(x, dict_): - pair_letters = [c for c in x if c.isupper()] - if dict_[pair_letters[0]] == dict_[pair_letters[1]]: - return 0 - else: - return 1 - - @staticmethod - def get_polar(x, dict_): - pair_letters = [c for c in x if c.isupper()] - res = np.abs(dict_[pair_letters[0]] - dict_[pair_letters[1]]) - return res - - @staticmethod - def get_absolute(x, dict_): - pair_letters = [c for c in x if c.isupper()] - res = np.abs(dict_[pair_letters[0]] - dict_[pair_letters[1]]) - return res - - @staticmethod - def get_diffetenet(x, dict_): - pair_letters = [c for c in x if c.isupper()] - if dict_[pair_letters[0]] == dict_[pair_letters[1]]: - return 0 - else: - return 1 - - def get_gene_expression(self, gene): - res = self.dict_expression.get(gene, 0.0) - return res - - def get_properties(self, amino_substitution): - return np.asarray([self.get_diffetenet(amino_substitution, self.dict_data['Charge']), - self.get_absolute(amino_substitution, self.dict_data['Size']), - self.get_absolute(amino_substitution, self.dict_data['Hydro']), - self.get_absolute(amino_substitution, self.dict_data['Charge']), - self.get_diffetenet(amino_substitution, self.dict_data['Polar'])]) - - def main(self, f_name): - lst_data = [] - with open(f_name, 'r') as f: - for row in f: - gene_name, sequence, aa_subs = row.split() - seq_arr = self.seq2bin(sequence) - # tap score - tap_mat = self.load_data.get('tap') - tap_score = tap_mat.dot(seq_arr.T).ravel() - # cleavge score - clv_mat = self.load_data.get('clv') - clv_mat = clv_mat[0, 20:200] - clv_score = clv_mat.dot(seq_arr.T).ravel() - - features_aa = self.get_properties(aa_subs) - # expresion - expression_value = self.get_gene_expression(gene_name) - - lst_data.append(np.hstack((expression_value, features_aa, clv_score, tap_score))) - mat_features = np.asarray(lst_data) - return mat_features +import pickle + +import numpy as np +import scipy.io as sio + + +class Preprocessor(object): + + def __init__(self, references): + self.references = references + self.load_data = sio.loadmat(self.references.tcell_predictor_sir_data) + with open(self.references.tcell_predictor_gene_expression, 'rb') as handle: + self.dict_expression = pickle.load(handle) + with open(self.references.tcell_predictor_aa_features, 'rb') as handle: + self.dict_data = pickle.load(handle) + + @staticmethod + def seq2bin(seq): + aa = ['A', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L', 'M', 'N', 'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'Y'] + dict_aa = dict((i, j) for j, i in enumerate(aa)) + arr = np.zeros((1, 9 * 20)) + for ii, letter in enumerate(seq): + arr[0, ii * 20 + dict_aa.get(letter)] = 1 + return arr + + @staticmethod + def get_hydrophbicity(x, dict_): + pair_letters = [c for c in x if c.isupper()] + res = np.abs(dict_[pair_letters[0]] - dict_[pair_letters[1]]) + return res + + @staticmethod + def get_size(x, dict_): + pair_letters = [c for c in x if c.isupper()] + res = np.abs(dict_[pair_letters[0]] - dict_[pair_letters[1]]) + return res + + @staticmethod + def get_charge_change(x, dict_): + pair_letters = [c for c in x if c.isupper()] + if dict_[pair_letters[0]] == dict_[pair_letters[1]]: + return 0 + else: + return 1 + + @staticmethod + def get_charge_abs(x, dict_): + pair_letters = [c for c in x if c.isupper()] + if dict_[pair_letters[0]] == dict_[pair_letters[1]]: + return 0 + else: + return 1 + + @staticmethod + def get_polar(x, dict_): + pair_letters = [c for c in x if c.isupper()] + res = np.abs(dict_[pair_letters[0]] - dict_[pair_letters[1]]) + return res + + @staticmethod + def get_absolute(x, dict_): + pair_letters = [c for c in x if c.isupper()] + res = np.abs(dict_[pair_letters[0]] - dict_[pair_letters[1]]) + return res + + @staticmethod + def get_diffetenet(x, dict_): + pair_letters = [c for c in x if c.isupper()] + if dict_[pair_letters[0]] == dict_[pair_letters[1]]: + return 0 + else: + return 1 + + def get_gene_expression(self, gene): + res = self.dict_expression.get(gene, 0.0) + return res + + def get_properties(self, amino_substitution): + return np.asarray([self.get_diffetenet(amino_substitution, self.dict_data['Charge']), + self.get_absolute(amino_substitution, self.dict_data['Size']), + self.get_absolute(amino_substitution, self.dict_data['Hydro']), + self.get_absolute(amino_substitution, self.dict_data['Charge']), + self.get_diffetenet(amino_substitution, self.dict_data['Polar'])]) + + def main(self, f_name): + lst_data = [] + with open(f_name, 'r') as f: + for row in f: + gene_name, sequence, aa_subs = row.split() + seq_arr = self.seq2bin(sequence) + # tap score + tap_mat = self.load_data.get('tap') + tap_score = tap_mat.dot(seq_arr.T).ravel() + # cleavge score + clv_mat = self.load_data.get('clv') + clv_mat = clv_mat[0, 20:200] + clv_score = clv_mat.dot(seq_arr.T).ravel() + + features_aa = self.get_properties(aa_subs) + # expresion + expression_value = self.get_gene_expression(gene_name) + + lst_data.append(np.hstack((expression_value, features_aa, clv_score, tap_score))) + mat_features = np.asarray(lst_data) + return mat_features diff --git a/input/__init__.py b/input/__init__.py index ec04556c..f28ad6ac 100755 --- a/input/__init__.py +++ b/input/__init__.py @@ -1,11 +1,11 @@ -VERSION = '0.2.1' -REFERENCE_FOLDER_ENV = 'INPUT_REFERENCE_FOLDER' -INPUT_BLASTP_ENV = 'INPUT_BLASTP' -INPUT_MIXMHC2PRED_ENV = 'INPUT_MIXMHC2PRED' -INPUT_MIXMHCPRED_ENV = 'INPUT_MIXMHCPRED' -INPUT_RSCRIPT_ENV = 'INPUT_RSCRIPT' -INPUT_NETMHC2PAN_ENV = 'INPUT_NETMHC2PAN' -INPUT_NETMHCPAN_ENV = 'INPUT_NETMHCPAN' - -MHC_II = "mhcII" -MHC_I = "mhcI" +VERSION = '0.2.1' +REFERENCE_FOLDER_ENV = 'INPUT_REFERENCE_FOLDER' +INPUT_BLASTP_ENV = 'INPUT_BLASTP' +INPUT_MIXMHC2PRED_ENV = 'INPUT_MIXMHC2PRED' +INPUT_MIXMHCPRED_ENV = 'INPUT_MIXMHCPRED' +INPUT_RSCRIPT_ENV = 'INPUT_RSCRIPT' +INPUT_NETMHC2PAN_ENV = 'INPUT_NETMHC2PAN' +INPUT_NETMHCPAN_ENV = 'INPUT_NETMHCPAN' + +MHC_II = "mhcII" +MHC_I = "mhcI" diff --git a/input/command_line.py b/input/command_line.py index 14545218..d3f8e092 100755 --- a/input/command_line.py +++ b/input/command_line.py @@ -1,87 +1,87 @@ -from argparse import ArgumentParser - -from logzero import logger - -from input.predict_all_epitopes import BunchEpitopes - - -def input_cli(): - parser = ArgumentParser(description='adds patient information given in sample file of a cohort to merged icam file') - parser.add_argument('-i', '--icam_file', dest='icam_file', help='define iCaM file which should be annotated', - required=True) - parser.add_argument('-a', '--allele_file', dest='allele_file', help='define file with hla alleles of patients', - required=True) - parser.add_argument('-t', '--tissue', dest='tissue', help='define tissue of cancer origin', default="skin") - parser.add_argument('-f', '--frameshift', dest='frameshift', - help='indicate by true or false if frameshift mutations or SNVs are to be considered', - default=False) - parser.add_argument('-tc', '--tumour_content', dest='tumour_content', - help='pass csv file with tumour content of patient; e.g. patient_overview file ', default=False) - args = parser.parse_args() - - icam_file = args.icam_file - allele_file = args.allele_file - tissue = args.tissue - indel = args.frameshift - if args.tumour_content: - tumour_content_file = args.tumour_content - else: - tumour_content_file = "" - - indel = False - - bunchepitopes = BunchEpitopes() - logger.info("Starting INPuT...") - bunchepitopes.wrapper_table_add_feature_annotation(icam_file, indel, allele_file, tissue, tumour_content_file) - logger.info("Finished INPuT...") - ''' - file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/INPuT/nonprogramm_files/test_SD.csv" - # file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/INPuT/nonprogramm_files/test_fulldat.txt" - #file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/20170713_IS_IM_data.complete.update_Dv10.csv.annotation.csv_v2.csv" - # file = "/projects/SUMMIT/WP1.2/Literature_Cohorts/data_analysis/20190117_hugo_prelim_sample_annot.txt" - #file = "/projects/SUMMIT/WP1.2/Literature_Cohorts/data_analysis/20190121_hugo_merged_dat.txt" - indel = False - fasta_proteome = "/projects/data/human/2018_uniprot_with_isoforms/uniprot_human_with_isoforms.fasta" - ref_file = "/projects/CM27_IND_patients/GTEX_normal_tissue_data/Skin .csv" - path_to_hla_file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/indels/RB_0004_labHLA_V2.csv" - #path_to_hla_file = "/projects/SUMMIT/WP1.2/Literature_Cohorts/data_analysis/alleles.csv" - - - Bunchepitopes().main(file, indel, fasta_proteome, ref_file, path_to_hla_file) - ''' - -# def epitope_cli(): -# # file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/INPuT2/nonprogramm_files/test_SD.csv" -# # file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/INPuT2/nonprogramm_files/test_fulldat.txt" -# indel = False -# fasta_proteome = "/projects/data/human/2018_uniprot_with_isoforms/uniprot_human_with_isoforms.fasta" -# ref_file = "/projects/CM27_IND_patients/GTEX_normal_tissue_data/Skin .csv" -# file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/MHC_prediction_netmhcpan4/testdat_ott.txt" -# hla_file = "/projects/SUMMIT/WP1.2/Literature_Cohorts/data_analysis/cohorts/ott/icam_ott/alleles.csv" -# -# # predfeatallBunchepitopes -# predictAll = Bunchepitopes() -# # args = parser.parse_args() -# subprocess.call(["predict_all_epitopes", '-i', file, '-a', hla_file]) -# -# # z = Epitope().main(dat[0], dat[1][ii], self.proteome_dictionary, self.rna_reference, self.aa_frequency, self.fourmer_frequency, self.aa_index1_dict, self.aa_index2_dict, self.provean_matrix, self.hla_available_alleles, self.patient_hla_I_allels) -# -# predictAll.main() - i -# endTime = datetime.now() -# print >> sys.stderr, "start: " + str(startTime) + "\nend: " + str(endTime) + "\nneeded: " + str( -# endTime - startTime) -# # print dat -# # x = Epitope() -# # x = Epitope(dat[1][1], dat[0]) -# # print vars(x) -# # print dat[1][1][1] -# # print dat[0][1] -# -# # for ii,i in enumerate(dat[1]): -# # Epitope().main(dat[0],dat[1][ii]) -# # print x.tricks -# -# # x.main(dat[0], dat[1][1]) -# # print x.tricks -# # print x.tricks["transcript_position"] -# # print dir(x) +from argparse import ArgumentParser + +from logzero import logger + +from input.predict_all_epitopes import BunchEpitopes + + +def input_cli(): + parser = ArgumentParser(description='adds patient information given in sample file of a cohort to merged icam file') + parser.add_argument('-i', '--icam_file', dest='icam_file', help='define iCaM file which should be annotated', + required=True) + parser.add_argument('-a', '--allele_file', dest='allele_file', help='define file with hla alleles of patients', + required=True) + parser.add_argument('-t', '--tissue', dest='tissue', help='define tissue of cancer origin', default="skin") + parser.add_argument('-f', '--frameshift', dest='frameshift', + help='indicate by true or false if frameshift mutations or SNVs are to be considered', + default=False) + parser.add_argument('-tc', '--tumour_content', dest='tumour_content', + help='pass csv file with tumour content of patient; e.g. patient_overview file ', default=False) + args = parser.parse_args() + + icam_file = args.icam_file + allele_file = args.allele_file + tissue = args.tissue + indel = args.frameshift + if args.tumour_content: + tumour_content_file = args.tumour_content + else: + tumour_content_file = "" + + indel = False + + bunchepitopes = BunchEpitopes() + logger.info("Starting INPuT...") + bunchepitopes.wrapper_table_add_feature_annotation(icam_file, indel, allele_file, tissue, tumour_content_file) + logger.info("Finished INPuT...") + ''' + file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/INPuT/nonprogramm_files/test_SD.csv" + # file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/INPuT/nonprogramm_files/test_fulldat.txt" + #file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/20170713_IS_IM_data.complete.update_Dv10.csv.annotation.csv_v2.csv" + # file = "/projects/SUMMIT/WP1.2/Literature_Cohorts/data_analysis/20190117_hugo_prelim_sample_annot.txt" + #file = "/projects/SUMMIT/WP1.2/Literature_Cohorts/data_analysis/20190121_hugo_merged_dat.txt" + indel = False + fasta_proteome = "/projects/data/human/2018_uniprot_with_isoforms/uniprot_human_with_isoforms.fasta" + ref_file = "/projects/CM27_IND_patients/GTEX_normal_tissue_data/Skin .csv" + path_to_hla_file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/indels/RB_0004_labHLA_V2.csv" + #path_to_hla_file = "/projects/SUMMIT/WP1.2/Literature_Cohorts/data_analysis/alleles.csv" + + + Bunchepitopes().main(file, indel, fasta_proteome, ref_file, path_to_hla_file) + ''' + +# def epitope_cli(): +# # file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/INPuT2/nonprogramm_files/test_SD.csv" +# # file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/INPuT2/nonprogramm_files/test_fulldat.txt" +# indel = False +# fasta_proteome = "/projects/data/human/2018_uniprot_with_isoforms/uniprot_human_with_isoforms.fasta" +# ref_file = "/projects/CM27_IND_patients/GTEX_normal_tissue_data/Skin .csv" +# file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/MHC_prediction_netmhcpan4/testdat_ott.txt" +# hla_file = "/projects/SUMMIT/WP1.2/Literature_Cohorts/data_analysis/cohorts/ott/icam_ott/alleles.csv" +# +# # predfeatallBunchepitopes +# predictAll = Bunchepitopes() +# # args = parser.parse_args() +# subprocess.call(["predict_all_epitopes", '-i', file, '-a', hla_file]) +# +# # z = Epitope().main(dat[0], dat[1][ii], self.proteome_dictionary, self.rna_reference, self.aa_frequency, self.fourmer_frequency, self.aa_index1_dict, self.aa_index2_dict, self.provean_matrix, self.hla_available_alleles, self.patient_hla_I_allels) +# +# predictAll.main() - i +# endTime = datetime.now() +# print >> sys.stderr, "start: " + str(startTime) + "\nend: " + str(endTime) + "\nneeded: " + str( +# endTime - startTime) +# # print dat +# # x = Epitope() +# # x = Epitope(dat[1][1], dat[0]) +# # print vars(x) +# # print dat[1][1][1] +# # print dat[0][1] +# +# # for ii,i in enumerate(dat[1]): +# # Epitope().main(dat[0],dat[1][ii]) +# # print x.tricks +# +# # x.main(dat[0], dat[1][1]) +# # print x.tricks +# # print x.tricks["transcript_position"] +# # print dir(x) diff --git a/input/exceptions.py b/input/exceptions.py index 422c7316..9517a890 100755 --- a/input/exceptions.py +++ b/input/exceptions.py @@ -1,14 +1,14 @@ -class INPuTInputParametersException(ValueError): - pass - - -class INPuTConfigurationException(ValueError): - pass - - -class INPuTCommandException(ValueError): - pass - - -class INPuTReferenceException(ValueError): - pass +class INPuTInputParametersException(ValueError): + pass + + +class INPuTConfigurationException(ValueError): + pass + + +class INPuTCommandException(ValueError): + pass + + +class INPuTReferenceException(ValueError): + pass diff --git a/input/helpers/blastp_runner.py b/input/helpers/blastp_runner.py index 200ddb81..7c1c8ba6 100755 --- a/input/helpers/blastp_runner.py +++ b/input/helpers/blastp_runner.py @@ -1,36 +1,36 @@ -from input.helpers import intermediate_files -from input.neoantigen_fitness.aligner import Aligner - - -class BlastpRunner(object): - - def __init__(self, runner, configuration): - """ - :type runner: input.helpers.runner.Runner - :type configuration: input.references.DependenciesConfiguration - """ - self.runner = runner - self.configuration = configuration - - def run_blastp(self, fasta_file, database): - ''' - This function runs BLASTP on a given database - ''' - outfile = intermediate_files.create_temp_file(prefix="tmp_blastp_", suffix=".xml") - self.runner.run_command(cmd=[ - self.configuration.blastp, - "-gapopen", "11", - "-gapextend", "1", - "-outfmt", "5", - "-query", fasta_file, - "-out", outfile, - "-db", database, - "-evalue", "100000000"]) - return outfile - - def parse_blastp_output(self, blastp_output_file, **kwargs): - aligner = Aligner() - # set a to 32 for dissimilarity - aligner.readAllBlastAlignments(blastp_output_file) - aligner.computeR(**kwargs) +from input.helpers import intermediate_files +from input.neoantigen_fitness.aligner import Aligner + + +class BlastpRunner(object): + + def __init__(self, runner, configuration): + """ + :type runner: input.helpers.runner.Runner + :type configuration: input.references.DependenciesConfiguration + """ + self.runner = runner + self.configuration = configuration + + def run_blastp(self, fasta_file, database): + ''' + This function runs BLASTP on a given database + ''' + outfile = intermediate_files.create_temp_file(prefix="tmp_blastp_", suffix=".xml") + self.runner.run_command(cmd=[ + self.configuration.blastp, + "-gapopen", "11", + "-gapextend", "1", + "-outfmt", "5", + "-query", fasta_file, + "-out", outfile, + "-db", database, + "-evalue", "100000000"]) + return outfile + + def parse_blastp_output(self, blastp_output_file, **kwargs): + aligner = Aligner() + # set a to 32 for dissimilarity + aligner.readAllBlastAlignments(blastp_output_file) + aligner.computeR(**kwargs) return aligner.Ri.get(1, 0) # NOTE: returns 0 when not present \ No newline at end of file diff --git a/input/helpers/epitope_helper.py b/input/helpers/epitope_helper.py index 9afc5a12..66f3d88c 100755 --- a/input/helpers/epitope_helper.py +++ b/input/helpers/epitope_helper.py @@ -1,66 +1,66 @@ - - -class EpitopeHelper(object): - - @staticmethod - def generate_nmers(xmer_wt, xmer_mut, lengths): - """ - Generates peptides covering mutation of all lengths that are provided. Returns peptides as list - No peptide is shorter than the minimun length provided - There are no repetitions in the results - """ - length_mut = len(xmer_mut) - list_peptides = [] - pos_mut = int(EpitopeHelper.mut_position_xmer_seq(xmer_mut=xmer_mut, xmer_wt=xmer_wt)) - for length in lengths: - if length <= length_mut: - start_first = pos_mut - length - starts = [start_first + s for s in range(length)] - ends = [s + length for s in starts] - for s, e in zip(starts, ends): - list_peptides.append(xmer_mut[s:e]) - return list(set([x for x in list_peptides if not x == "" and len(x) >= min(lengths)])) - - @staticmethod - def mut_position_xmer_seq(xmer_wt, xmer_mut): - """ - returns position of mutation in xmer sequence - """ - p1 = -1 - if len(xmer_wt) == len(xmer_mut): - p1 = -1 - for i, aa in enumerate(xmer_mut): - if aa != xmer_wt[i]: - p1 = i + 1 - else: - p1 = 0 - # in case sequences do not have same length - for a1, a2 in zip(xmer_wt, xmer_mut): - if a1 == a2: - p1 += 1 - return str(p1) - - @staticmethod - def epitope_covers_mutation(position_mutation, position_epitope, length_epitope): - """ - checks if predicted epitope covers mutation - """ - cover = False - if position_mutation != "-1": - start = int(position_epitope) - end = start + int(length_epitope) - 1 - if int(position_mutation) >= start and int(position_mutation) <= end: - cover = True - return cover - - @staticmethod - def hamming_check_0_or_1(seq1, seq2): - '''returns number of mismatches between 2 sequences - ''' - errors = 0 - for i in range(len(seq1)): - if seq1[i] != seq2[i]: - errors += 1 - if errors >= 2: - return errors - return errors + + +class EpitopeHelper(object): + + @staticmethod + def generate_nmers(xmer_wt, xmer_mut, lengths): + """ + Generates peptides covering mutation of all lengths that are provided. Returns peptides as list + No peptide is shorter than the minimun length provided + There are no repetitions in the results + """ + length_mut = len(xmer_mut) + list_peptides = [] + pos_mut = int(EpitopeHelper.mut_position_xmer_seq(xmer_mut=xmer_mut, xmer_wt=xmer_wt)) + for length in lengths: + if length <= length_mut: + start_first = pos_mut - length + starts = [start_first + s for s in range(length)] + ends = [s + length for s in starts] + for s, e in zip(starts, ends): + list_peptides.append(xmer_mut[s:e]) + return list(set([x for x in list_peptides if not x == "" and len(x) >= min(lengths)])) + + @staticmethod + def mut_position_xmer_seq(xmer_wt, xmer_mut): + """ + returns position of mutation in xmer sequence + """ + p1 = -1 + if len(xmer_wt) == len(xmer_mut): + p1 = -1 + for i, aa in enumerate(xmer_mut): + if aa != xmer_wt[i]: + p1 = i + 1 + else: + p1 = 0 + # in case sequences do not have same length + for a1, a2 in zip(xmer_wt, xmer_mut): + if a1 == a2: + p1 += 1 + return str(p1) + + @staticmethod + def epitope_covers_mutation(position_mutation, position_epitope, length_epitope): + """ + checks if predicted epitope covers mutation + """ + cover = False + if position_mutation != "-1": + start = int(position_epitope) + end = start + int(length_epitope) - 1 + if int(position_mutation) >= start and int(position_mutation) <= end: + cover = True + return cover + + @staticmethod + def hamming_check_0_or_1(seq1, seq2): + '''returns number of mismatches between 2 sequences + ''' + errors = 0 + for i in range(len(seq1)): + if seq1[i] != seq2[i]: + errors += 1 + if errors >= 2: + return errors + return errors diff --git a/input/helpers/fastaGenerator.py b/input/helpers/fastaGenerator.py index f5996c79..8a994323 100755 --- a/input/helpers/fastaGenerator.py +++ b/input/helpers/fastaGenerator.py @@ -1,32 +1,32 @@ -#!/usr/bin/python - -from Bio.SeqIO.FastaIO import SimpleFastaParser - - -def write_single_seq_fasta(seq, id, file_name): - '''Returns fasta file with a single sequences. - ''' - with open(file_name, "w") as f: - id = "".join([">", id, "\n"]) - f.write(id) - seq = "".join([seq, "\n"]) - f.write(seq) - - -def read_multiple_seqs_simple(fasta_file): - '''This function reads a fasta file using simplefasta parser and returns dictionary with gene names as keys and protein sequences as values. - ''' - database = {} - with open(fasta_file) as handle: - for record in SimpleFastaParser(handle): - # record[0] = fasta header; record[1] = protein sequence - database[record[0]] = record[1] - return database - - -if __name__ == '__main__': - seq = "ABDSF" - id = "M1" - # write_single_seq_fasta(seq, id, "temp.fasta") - read_multiple_seqs_simple( - "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/indels/best_WT/BLAST_DB/ligandome/DB_ligandome_safe.fasta") +#!/usr/bin/python + +from Bio.SeqIO.FastaIO import SimpleFastaParser + + +def write_single_seq_fasta(seq, id, file_name): + '''Returns fasta file with a single sequences. + ''' + with open(file_name, "w") as f: + id = "".join([">", id, "\n"]) + f.write(id) + seq = "".join([seq, "\n"]) + f.write(seq) + + +def read_multiple_seqs_simple(fasta_file): + '''This function reads a fasta file using simplefasta parser and returns dictionary with gene names as keys and protein sequences as values. + ''' + database = {} + with open(fasta_file) as handle: + for record in SimpleFastaParser(handle): + # record[0] = fasta header; record[1] = protein sequence + database[record[0]] = record[1] + return database + + +if __name__ == '__main__': + seq = "ABDSF" + id = "M1" + # write_single_seq_fasta(seq, id, "temp.fasta") + read_multiple_seqs_simple( + "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/indels/best_WT/BLAST_DB/ligandome/DB_ligandome_safe.fasta") diff --git a/input/helpers/intermediate_files.py b/input/helpers/intermediate_files.py index c62b2e60..aa70cce0 100755 --- a/input/helpers/intermediate_files.py +++ b/input/helpers/intermediate_files.py @@ -1,21 +1,21 @@ -import tempfile - - -def create_temp_file(prefix=None, suffix=None, dir=None): - temp_file = tempfile.NamedTemporaryFile(prefix=prefix, suffix=suffix, dir=dir, delete=False) - return temp_file.name - - -def create_temp_fasta(sequences, prefix=None, comment_prefix='seq'): - """ - Writes seqs given in seqs list into fasta file - """ - fasta_temp_file = create_temp_file(prefix=prefix, suffix='.fasta') - counter = 1 - with open(fasta_temp_file, "w") as f: - for seq in sequences: - _id = ">{comment_prefix}{index}".format(comment_prefix=comment_prefix, index=counter) - f.write(_id + "\n") - f.write(seq + "\n") - counter += 1 - return fasta_temp_file +import tempfile + + +def create_temp_file(prefix=None, suffix=None, dir=None): + temp_file = tempfile.NamedTemporaryFile(prefix=prefix, suffix=suffix, dir=dir, delete=False) + return temp_file.name + + +def create_temp_fasta(sequences, prefix=None, comment_prefix='seq'): + """ + Writes seqs given in seqs list into fasta file + """ + fasta_temp_file = create_temp_file(prefix=prefix, suffix='.fasta') + counter = 1 + with open(fasta_temp_file, "w") as f: + for seq in sequences: + _id = ">{comment_prefix}{index}".format(comment_prefix=comment_prefix, index=counter) + f.write(_id + "\n") + f.write(seq + "\n") + counter += 1 + return fasta_temp_file diff --git a/input/helpers/properties_manager.py b/input/helpers/properties_manager.py index 01139811..91b55251 100755 --- a/input/helpers/properties_manager.py +++ b/input/helpers/properties_manager.py @@ -1,97 +1,97 @@ -from input import MHC_I, MHC_II -from input.exceptions import INPuTInputParametersException - -PATIENT_ID3 = "patient.x" -PATIENT_ID2 = "patient" -PATIENT_ID = "patient.id" - - -def get_gene(properties): - if "gene.x" in properties: - gene = properties["gene.x"] - else: - gene = properties["gene"] - return gene - - -def get_substitution(properties): - return properties["substitution"] - - -def get_mutation_aminoacid(properties): - return properties["MUT_AA"] - - -def get_epitopes(properties, mhc): - if mhc == MHC_I: - mutation = properties["MHC_I_epitope_.best_prediction."] - wild_type = properties["MHC_I_epitope_.WT."] - elif mhc == MHC_II: - mutation = properties["MHC_II_epitope_.best_prediction."] - wild_type = properties["MHC_II_epitope_.WT."] - else: - raise INPuTInputParametersException("Bad MHC value: {}".format(mhc)) - return wild_type, mutation - - -def get_scores_multiple_binding(properties, mhc): - if mhc == MHC_I: - mutation = properties["MB_score_top10_harmonic"] - wild_type = properties["MB_score_WT_top10_harmonic"] - elif mhc == MHC_II: - mutation = properties["MB_score_MHCII_top10_harmonic"] - wild_type = properties["MB_score_MHCII_top10_WT_harmonic"] - else: - raise INPuTInputParametersException("Bad MHC value: {}".format(mhc)) - return wild_type, mutation - - -def get_scores_netmhcpan4_affinity(properties, mhc): - if mhc == MHC_I: - mutation = properties["best_affinity_netmhcpan4"] - wild_type = properties["best_affinity_netmhcpan4_WT"] - elif mhc == MHC_II: - mutation = properties["best_affinity_netmhcIIpan"] - wild_type = properties["best_affinity_netmhcIIpan_WT"] - else: - raise INPuTInputParametersException("Bad MHC value: {}".format(mhc)) - return wild_type, mutation - - -def get_scores_netmhcpan4_ranks(properties, mhc): - if mhc == MHC_I: - mutation = properties["best%Rank_netmhcpan4"] - wild_type = properties["best%Rank_netmhcpan4_WT"] - elif mhc == MHC_II: - mutation = properties["best%Rank_netmhcIIpan"] - wild_type = properties["best%Rank_netmhcIIpan_WT"] - else: - raise INPuTInputParametersException("Bad MHC value: {}".format(mhc)) - return wild_type, mutation - - -def get_netmhcpan4_epitopes(properties, nine_mer=False): - if nine_mer: - mutation = properties["best_affinity_epitope_netmhcpan4_9mer"] - wild_type = properties["best_epitope_netmhcpan4_9mer_WT"] - else: - mutation = properties["best_affinity_epitope_netmhcpan4"] - wild_type = properties["best_affinity_epitope_netmhcpan4_WT"] - return wild_type, mutation - - -def get_hla_allele(props, hla_patient_dict): - ''' returns hla allele of patients given in hla_file - ''' - patient_id = get_patient_id(props) - return hla_patient_dict[patient_id] - - -def get_patient_id(props): - if PATIENT_ID in props: - patient_id = props[PATIENT_ID] - elif PATIENT_ID2 in props: - patient_id = props[PATIENT_ID2] - else: - patient_id = props[PATIENT_ID3] +from input import MHC_I, MHC_II +from input.exceptions import INPuTInputParametersException + +PATIENT_ID3 = "patient.x" +PATIENT_ID2 = "patient" +PATIENT_ID = "patient.id" + + +def get_gene(properties): + if "gene.x" in properties: + gene = properties["gene.x"] + else: + gene = properties["gene"] + return gene + + +def get_substitution(properties): + return properties["substitution"] + + +def get_mutation_aminoacid(properties): + return properties["MUT_AA"] + + +def get_epitopes(properties, mhc): + if mhc == MHC_I: + mutation = properties["MHC_I_epitope_.best_prediction."] + wild_type = properties["MHC_I_epitope_.WT."] + elif mhc == MHC_II: + mutation = properties["MHC_II_epitope_.best_prediction."] + wild_type = properties["MHC_II_epitope_.WT."] + else: + raise INPuTInputParametersException("Bad MHC value: {}".format(mhc)) + return wild_type, mutation + + +def get_scores_multiple_binding(properties, mhc): + if mhc == MHC_I: + mutation = properties["MB_score_top10_harmonic"] + wild_type = properties["MB_score_WT_top10_harmonic"] + elif mhc == MHC_II: + mutation = properties["MB_score_MHCII_top10_harmonic"] + wild_type = properties["MB_score_MHCII_top10_WT_harmonic"] + else: + raise INPuTInputParametersException("Bad MHC value: {}".format(mhc)) + return wild_type, mutation + + +def get_scores_netmhcpan4_affinity(properties, mhc): + if mhc == MHC_I: + mutation = properties["best_affinity_netmhcpan4"] + wild_type = properties["best_affinity_netmhcpan4_WT"] + elif mhc == MHC_II: + mutation = properties["best_affinity_netmhcIIpan"] + wild_type = properties["best_affinity_netmhcIIpan_WT"] + else: + raise INPuTInputParametersException("Bad MHC value: {}".format(mhc)) + return wild_type, mutation + + +def get_scores_netmhcpan4_ranks(properties, mhc): + if mhc == MHC_I: + mutation = properties["best%Rank_netmhcpan4"] + wild_type = properties["best%Rank_netmhcpan4_WT"] + elif mhc == MHC_II: + mutation = properties["best%Rank_netmhcIIpan"] + wild_type = properties["best%Rank_netmhcIIpan_WT"] + else: + raise INPuTInputParametersException("Bad MHC value: {}".format(mhc)) + return wild_type, mutation + + +def get_netmhcpan4_epitopes(properties, nine_mer=False): + if nine_mer: + mutation = properties["best_affinity_epitope_netmhcpan4_9mer"] + wild_type = properties["best_epitope_netmhcpan4_9mer_WT"] + else: + mutation = properties["best_affinity_epitope_netmhcpan4"] + wild_type = properties["best_affinity_epitope_netmhcpan4_WT"] + return wild_type, mutation + + +def get_hla_allele(props, hla_patient_dict): + ''' returns hla allele of patients given in hla_file + ''' + patient_id = get_patient_id(props) + return hla_patient_dict[patient_id] + + +def get_patient_id(props): + if PATIENT_ID in props: + patient_id = props[PATIENT_ID] + elif PATIENT_ID2 in props: + patient_id = props[PATIENT_ID2] + else: + patient_id = props[PATIENT_ID3] return patient_id \ No newline at end of file diff --git a/input/helpers/runner.py b/input/helpers/runner.py index 7c558541..9007c533 100755 --- a/input/helpers/runner.py +++ b/input/helpers/runner.py @@ -1,37 +1,37 @@ -import subprocess -import time - -from logzero import logger - -from input.exceptions import INPuTCommandException - - -class Runner(object): - - def run_command(self, cmd, **kwargs): - logger.info("Starting command: {}".format(" ".join(cmd))) - start = time.time() - process = subprocess.Popen(self._preprocess_command(cmd), stderr=subprocess.PIPE, stdout=subprocess.PIPE, **kwargs) - output, errors = process.communicate() - return_code = process.returncode - end = time.time() - logger.info("Elapsed time {} seconds".format(int(end - start))) - if return_code == 0: - logger.info("Finished command correctly!") - logger.info(self._decode(output)) - else: - logger.error("Finished command with return code {}".format(return_code)) - logger.error(self._decode(output)) - logger.error(self._decode(errors)) - raise INPuTCommandException("Error running command '{}'".format(" ".join(cmd))) - return self._decode(output), self._decode(errors) - - @staticmethod - def _preprocess_command(cmd): - """ - This makes sure that any parameter containing white spaces is passed appropriately - """ - return " ".join(cmd).split(" ") - - def _decode(self, data): - return data.decode('utf8') +import subprocess +import time + +from logzero import logger + +from input.exceptions import INPuTCommandException + + +class Runner(object): + + def run_command(self, cmd, **kwargs): + logger.info("Starting command: {}".format(" ".join(cmd))) + start = time.time() + process = subprocess.Popen(self._preprocess_command(cmd), stderr=subprocess.PIPE, stdout=subprocess.PIPE, **kwargs) + output, errors = process.communicate() + return_code = process.returncode + end = time.time() + logger.info("Elapsed time {} seconds".format(int(end - start))) + if return_code == 0: + logger.info("Finished command correctly!") + logger.info(self._decode(output)) + else: + logger.error("Finished command with return code {}".format(return_code)) + logger.error(self._decode(output)) + logger.error(self._decode(errors)) + raise INPuTCommandException("Error running command '{}'".format(" ".join(cmd))) + return self._decode(output), self._decode(errors) + + @staticmethod + def _preprocess_command(cmd): + """ + This makes sure that any parameter containing white spaces is passed appropriately + """ + return " ".join(cmd).split(" ") + + def _decode(self, data): + return data.decode('utf8') diff --git a/input/netmhcpan4/abstract_netmhcpan_predictor.py b/input/netmhcpan4/abstract_netmhcpan_predictor.py index 4ad613bc..3a915dc6 100755 --- a/input/netmhcpan4/abstract_netmhcpan_predictor.py +++ b/input/netmhcpan4/abstract_netmhcpan_predictor.py @@ -1,17 +1,17 @@ - - - -class AbstractNetMhcPanPredictor(object): - - @staticmethod - def add_best_epitope_info(epitope_tuple, column_name): - '''returns desired information of prediction of best epitope from netmhcpan output; - e.g. "%Rank": MHC I score, "HLA": HLA allele, "Icore": best epitope - ''' - dat_head = epitope_tuple[0] - dat = epitope_tuple[1] - val = dat_head.index(column_name) - try: - return dat[val] - except IndexError: - return "NA" + + + +class AbstractNetMhcPanPredictor(object): + + @staticmethod + def add_best_epitope_info(epitope_tuple, column_name): + '''returns desired information of prediction of best epitope from netmhcpan output; + e.g. "%Rank": MHC I score, "HLA": HLA allele, "Icore": best epitope + ''' + dat_head = epitope_tuple[0] + dat = epitope_tuple[1] + val = dat_head.index(column_name) + try: + return dat[val] + except IndexError: + return "NA" diff --git a/input/new_features/conservation_scores.py b/input/new_features/conservation_scores.py index 3f3437c9..c90de859 100755 --- a/input/new_features/conservation_scores.py +++ b/input/new_features/conservation_scores.py @@ -1,51 +1,51 @@ -import re - -from logzero import logger - - -class ProveanAnnotator(object): - - def __init__(self, provean_file, header_epitopes, epitopes): - """ - Loads provean scores as dictionary, but only for ucsc ids that are in epitope list - """ - epitope_ids = self._load_ucsc_ids_epitopes(header_epitopes=header_epitopes, epitopes=epitopes) - logger.info("Starting load of PROVEAN matrix" + provean_file) - self.header_provean, self.provean_matrix = self._load_provean_matrix(epitope_ids, provean_file) - logger.info("PROVEAN matrix loaded") - - def _load_ucsc_ids_epitopes(self, header_epitopes, epitopes): - """ - Returns set with ucsc ids of epitopes. - """ - col_ucsc = header_epitopes.index("UCSC_transcript") - col_pos = header_epitopes.index("substitution") - return set([self.build_ucsc_id_plus_position(ucsc_id=e[col_ucsc], substitution=e[col_pos]) for e in epitopes]) - - def _load_provean_matrix(self, epitope_ids, provean_file): - provean_matrix = {} - with open(provean_file) as f: - header = next(f).rstrip().split(";") # stores header - for line in f: - parts = line.rstrip().split(";") - ucsc_id_pos = parts[-1] - if ucsc_id_pos in epitope_ids: - provean_matrix[ucsc_id_pos] = parts - return header, provean_matrix - - def get_provean_annotation(self, mutated_aminoacid, ucsc_id_position): - """ - This function maps Provean score on given position and for specific SNV onto epitope data set - (which is in form of tuple --> header + dict of ucsc_pos_id: df row) - """ - try: - return self.provean_matrix[ucsc_id_position][self.header_provean.index(mutated_aminoacid)] - except (ValueError, KeyError) as e: - return "NA" - - @staticmethod - def build_ucsc_id_plus_position(substitution, ucsc_id): - ucsc_epi = re.sub(r'.\d+$', '', ucsc_id) - position_match = re.match(r'[A-Z](\d+)[A-Z]', substitution) - pos_prot = position_match.group(1) if position_match else "Del" - return "{}_{}".format(ucsc_epi, pos_prot) +import re + +from logzero import logger + + +class ProveanAnnotator(object): + + def __init__(self, provean_file, header_epitopes, epitopes): + """ + Loads provean scores as dictionary, but only for ucsc ids that are in epitope list + """ + epitope_ids = self._load_ucsc_ids_epitopes(header_epitopes=header_epitopes, epitopes=epitopes) + logger.info("Starting load of PROVEAN matrix" + provean_file) + self.header_provean, self.provean_matrix = self._load_provean_matrix(epitope_ids, provean_file) + logger.info("PROVEAN matrix loaded") + + def _load_ucsc_ids_epitopes(self, header_epitopes, epitopes): + """ + Returns set with ucsc ids of epitopes. + """ + col_ucsc = header_epitopes.index("UCSC_transcript") + col_pos = header_epitopes.index("substitution") + return set([self.build_ucsc_id_plus_position(ucsc_id=e[col_ucsc], substitution=e[col_pos]) for e in epitopes]) + + def _load_provean_matrix(self, epitope_ids, provean_file): + provean_matrix = {} + with open(provean_file) as f: + header = next(f).rstrip().split(";") # stores header + for line in f: + parts = line.rstrip().split(";") + ucsc_id_pos = parts[-1] + if ucsc_id_pos in epitope_ids: + provean_matrix[ucsc_id_pos] = parts + return header, provean_matrix + + def get_provean_annotation(self, mutated_aminoacid, ucsc_id_position): + """ + This function maps Provean score on given position and for specific SNV onto epitope data set + (which is in form of tuple --> header + dict of ucsc_pos_id: df row) + """ + try: + return self.provean_matrix[ucsc_id_position][self.header_provean.index(mutated_aminoacid)] + except (ValueError, KeyError) as e: + return "NA" + + @staticmethod + def build_ucsc_id_plus_position(substitution, ucsc_id): + ucsc_epi = re.sub(r'.\d+$', '', ucsc_id) + position_match = re.match(r'[A-Z](\d+)[A-Z]', substitution) + pos_prot = position_match.group(1) if position_match else "Del" + return "{}_{}".format(ucsc_epi, pos_prot) diff --git a/input/references.py b/input/references.py index 8d8178a9..900ac9b4 100755 --- a/input/references.py +++ b/input/references.py @@ -1,107 +1,107 @@ -import os - -from logzero import logger - -import input -from input.exceptions import INPuTConfigurationException - - -class DependenciesConfiguration(object): - - def __init__(self): - self.blastp = self._check_and_load_binary(input.INPUT_BLASTP_ENV) - self.mix_mhc2_pred = self._check_and_load_binary(input.INPUT_MIXMHC2PRED_ENV) - self.mix_mhc2_pred_alleles_list = os.path.join(os.path.dirname(self.mix_mhc2_pred), 'Alleles_list.txt') - self.mix_mhc_pred = self._check_and_load_binary(input.INPUT_MIXMHCPRED_ENV) - self.rscript = self._check_and_load_binary(input.INPUT_RSCRIPT_ENV) - self.net_mhc2_pan = self._check_and_load_binary(input.INPUT_NETMHC2PAN_ENV) - self.net_mhc_pan = self._check_and_load_binary(input.INPUT_NETMHCPAN_ENV) - - @staticmethod - def _check_and_load_binary(variable_name): - variable_value = os.environ.get(variable_name, "") - if not variable_value: - raise INPuTConfigurationException( - "Please, set the environment variable ${} pointing to the right binary!".format( - variable_name)) - if not os.path.exists(variable_value): - raise INPuTConfigurationException("The provided binary '{}' in ${} does not exist!".format( - variable_value, variable_name)) - return variable_value - - -class ReferenceFolder(object): - - def __init__(self): - self.reference_genome_folder = self._check_reference_genome_folder() - # sets the right file names for the resources - self.available_mhc_ii = self._get_reference_file_name('avail_mhcII.txt') - self.available_mhc_i = self._get_reference_file_name('MHC_available.csv') - self.aa_freq_prot = self._get_reference_file_name('20181108_AA_freq_prot.csv') - self.four_mer_freq = self._get_reference_file_name('20181108_4mer_freq.csv') - self.aaindex1 = self._get_reference_file_name('aaindex1') - self.aaindex2 = self._get_reference_file_name('aaindex2') - self.prov_scores_mapped3 = self._get_reference_file_name('PROV_scores_mapped3.csv') - self.iedb = self._get_reference_file_name('iedb') - self.proteome_db = self._get_reference_file_name('proteome_db') - self.tcell_predictor_sir_data = self._get_reference_file_name('SIRdata.mat') - self.tcell_predictor_gene_expression = self._get_reference_file_name('genes-expression.pickle') - self.tcell_predictor_aa_features = self._get_reference_file_name('amino-acids-features.pickle') - self.uniprot = self._get_reference_file_name('uniprot_human_with_isoforms.fasta') - self.gtex = self._get_reference_file_name('gtex_combined.csv') - - # TODO: add this files self.alleles_list_pred, self.avail_mhc_ii - self.resources = [self.available_mhc_ii, self.available_mhc_i, self.aa_freq_prot, - self.four_mer_freq, self.aaindex1, self.aaindex2, self.prov_scores_mapped3, self.iedb, - self.proteome_db, self.tcell_predictor_aa_features, - self.tcell_predictor_gene_expression, self.tcell_predictor_sir_data, - self.uniprot, self.gtex] - self._check_resources(self.resources) - self._log_configuration() - - @staticmethod - def _check_reference_genome_folder(): - reference_genome_folder = os.environ.get(input.REFERENCE_FOLDER_ENV, "") - if not reference_genome_folder: - raise INPuTConfigurationException( - "Please, set the environment variable ${} pointing to the reference genome folder!".format( - input.REFERENCE_FOLDER_ENV)) - if not os.path.exists(reference_genome_folder): - raise INPuTConfigurationException("The provided reference genome '{}' in ${} does not exist!".format( - reference_genome_folder, input.REFERENCE_FOLDER_ENV)) - return reference_genome_folder - - @staticmethod - def _check_resources(resources): - missing_resources = [] - for r in resources: - if not os.path.exists(r): - missing_resources.append(r) - if len(missing_resources) > 0: - raise INPuTConfigurationException( - "Missing resources in the reference folder: {}".format(str(missing_resources))) - - def _log_configuration(self): - logger.info("Reference genome folder: {}".format(self.reference_genome_folder)) - logger.info("Resources") - for r in self.resources: - logger.info(r) - - def _get_reference_file_name(self, file_name_suffix): - return os.path.join(self.reference_genome_folder, file_name_suffix) - - def load_available_hla_alleles(self, mhc=input.MHC_I): - """ - loads file with available hla alllels for netmhcpan4/netmhcIIpan prediction, returns set - :type mhc: str - :rtype list: - """ - if mhc == input.MHC_II: - fileMHC = self.available_mhc_ii - else: - fileMHC = self.available_mhc_i - set_available_mhc = set() - with open(fileMHC) as f: - for line in f: - set_available_mhc.add(line.strip()) - return set_available_mhc +import os + +from logzero import logger + +import input +from input.exceptions import INPuTConfigurationException + + +class DependenciesConfiguration(object): + + def __init__(self): + self.blastp = self._check_and_load_binary(input.INPUT_BLASTP_ENV) + self.mix_mhc2_pred = self._check_and_load_binary(input.INPUT_MIXMHC2PRED_ENV) + self.mix_mhc2_pred_alleles_list = os.path.join(os.path.dirname(self.mix_mhc2_pred), 'Alleles_list.txt') + self.mix_mhc_pred = self._check_and_load_binary(input.INPUT_MIXMHCPRED_ENV) + self.rscript = self._check_and_load_binary(input.INPUT_RSCRIPT_ENV) + self.net_mhc2_pan = self._check_and_load_binary(input.INPUT_NETMHC2PAN_ENV) + self.net_mhc_pan = self._check_and_load_binary(input.INPUT_NETMHCPAN_ENV) + + @staticmethod + def _check_and_load_binary(variable_name): + variable_value = os.environ.get(variable_name, "") + if not variable_value: + raise INPuTConfigurationException( + "Please, set the environment variable ${} pointing to the right binary!".format( + variable_name)) + if not os.path.exists(variable_value): + raise INPuTConfigurationException("The provided binary '{}' in ${} does not exist!".format( + variable_value, variable_name)) + return variable_value + + +class ReferenceFolder(object): + + def __init__(self): + self.reference_genome_folder = self._check_reference_genome_folder() + # sets the right file names for the resources + self.available_mhc_ii = self._get_reference_file_name('avail_mhcII.txt') + self.available_mhc_i = self._get_reference_file_name('MHC_available.csv') + self.aa_freq_prot = self._get_reference_file_name('20181108_AA_freq_prot.csv') + self.four_mer_freq = self._get_reference_file_name('20181108_4mer_freq.csv') + self.aaindex1 = self._get_reference_file_name('aaindex1') + self.aaindex2 = self._get_reference_file_name('aaindex2') + self.prov_scores_mapped3 = self._get_reference_file_name('PROV_scores_mapped3.csv') + self.iedb = self._get_reference_file_name('iedb') + self.proteome_db = self._get_reference_file_name('proteome_db') + self.tcell_predictor_sir_data = self._get_reference_file_name('SIRdata.mat') + self.tcell_predictor_gene_expression = self._get_reference_file_name('genes-expression.pickle') + self.tcell_predictor_aa_features = self._get_reference_file_name('amino-acids-features.pickle') + self.uniprot = self._get_reference_file_name('uniprot_human_with_isoforms.fasta') + self.gtex = self._get_reference_file_name('gtex_combined.csv') + + # TODO: add this files self.alleles_list_pred, self.avail_mhc_ii + self.resources = [self.available_mhc_ii, self.available_mhc_i, self.aa_freq_prot, + self.four_mer_freq, self.aaindex1, self.aaindex2, self.prov_scores_mapped3, self.iedb, + self.proteome_db, self.tcell_predictor_aa_features, + self.tcell_predictor_gene_expression, self.tcell_predictor_sir_data, + self.uniprot, self.gtex] + self._check_resources(self.resources) + self._log_configuration() + + @staticmethod + def _check_reference_genome_folder(): + reference_genome_folder = os.environ.get(input.REFERENCE_FOLDER_ENV, "") + if not reference_genome_folder: + raise INPuTConfigurationException( + "Please, set the environment variable ${} pointing to the reference genome folder!".format( + input.REFERENCE_FOLDER_ENV)) + if not os.path.exists(reference_genome_folder): + raise INPuTConfigurationException("The provided reference genome '{}' in ${} does not exist!".format( + reference_genome_folder, input.REFERENCE_FOLDER_ENV)) + return reference_genome_folder + + @staticmethod + def _check_resources(resources): + missing_resources = [] + for r in resources: + if not os.path.exists(r): + missing_resources.append(r) + if len(missing_resources) > 0: + raise INPuTConfigurationException( + "Missing resources in the reference folder: {}".format(str(missing_resources))) + + def _log_configuration(self): + logger.info("Reference genome folder: {}".format(self.reference_genome_folder)) + logger.info("Resources") + for r in self.resources: + logger.info(r) + + def _get_reference_file_name(self, file_name_suffix): + return os.path.join(self.reference_genome_folder, file_name_suffix) + + def load_available_hla_alleles(self, mhc=input.MHC_I): + """ + loads file with available hla alllels for netmhcpan4/netmhcIIpan prediction, returns set + :type mhc: str + :rtype list: + """ + if mhc == input.MHC_II: + fileMHC = self.available_mhc_ii + else: + fileMHC = self.available_mhc_i + set_available_mhc = set() + with open(fileMHC) as f: + for line in f: + set_available_mhc.add(line.strip()) + return set_available_mhc diff --git a/input/self_similarity/self_similarity.py b/input/self_similarity/self_similarity.py index 7285b0c8..e5d0c288 100755 --- a/input/self_similarity/self_similarity.py +++ b/input/self_similarity/self_similarity.py @@ -1,137 +1,137 @@ -#!/usr/bin/env python - -from input import MHC_I, MHC_II - -import math -import os - -BETA = 0.11387 -BLOSUM62_FILE_NAME = 'BLOSUM62-2.matrix.txt' - - -class SelfSimilarityCalculator(): - - def __init__(self): - blosum_file = os.path.join(os.path.abspath(os.path.dirname(__file__)), BLOSUM62_FILE_NAME) - blosum_dict = self._load_blosum(blosum_file) - self.k1 = self._compute_k1(blosum_dict) - - def _compute_k1(self, blosum_dict): - K1 = {} - for i in list(blosum_dict.keys()): - x = K1.get(i, {}) - for j in list(blosum_dict[i].keys()): - x[j] = math.pow(blosum_dict[i][j], BETA) - K1[i] = x - return K1 - - def _load_blosum(self, blosum): - blosum_dict = {} - colid = [] - rowid = [] - c = 0 - with open(blosum) as f: - for line in f: - c += 1 - if c == 1: - colid = line.strip("\n").split(" ") - continue - w = line.strip("\n").split(" ") - id = w[0] - v = [float(x) for x in w[1:]] - rowid.append(id) - x = blosum_dict.get(id, {}) - for i, vi in enumerate(v): - x[colid[i]] = vi - blosum_dict[id] = x - return blosum_dict - - def compute_k_hat_3(self, x, y): # K^3 - return self._compute_k3(x, y) / math.sqrt(self._compute_k3(x, x) * self._compute_k3(y, y)) - - def _compute_k3(self, f, g): - max_k = min(len(f), len(g)) - s = 0 - for k in range(1, max_k + 1): - for i in range(len(f) - (k - 1)): - u = f[i:i + k] - for j in range(len(g) - (k - 1)): - v = g[j:j + k] - s += self._compute_k2k(u, v, self.k1) - return s - - def _compute_k2k(self, u, v, K1): - if len(u) != len(v): - return None - k = len(u) - p = K1[u[0]][v[0]] - for i in range(1, k): - p = p * K1[u[i]][v[i]] - return p - - -def get_self_similarity(mutation, wild_type): - """ - Returns self-similiarity between mutated and wt epitope according to Bjerregard et al., - Argument mhc indicates if determination for MHC I or MHC II epitopes - """ - self_similarity = 'NA' - try: - self_similarity = str(SelfSimilarityCalculator().compute_k_hat_3(mutation, wild_type)) - except ZeroDivisionError: - pass - return self_similarity - - -def is_improved_binder(score_mutation, score_wild_type): - """ - This function checks if mutated epitope is improved binder according to Bjerregard et al. - """ - try: - improved_binder = float(score_wild_type) / float(score_mutation) >= 1.2 - except (ZeroDivisionError, ValueError) as e: - return "NA" - # TODO: boolean in a string needs to go away - return "1" if improved_binder else "0" - - -def self_similarity_of_conserved_binder_only(has_conserved_binder, similarity): - """ - this function returns selfsimilarity for conserved binder but not for improved binder - """ - try: - if has_conserved_binder == str(0): - return similarity - else: - return "NA" - except (ZeroDivisionError, ValueError) as e: - return "NA" - - -def position_of_mutation_epitope(wild_type, mutation): - """ - This function determines the position of the mutation within the epitope sequence. - """ - p1 = -1 - try: - for i, aa in enumerate(mutation): - if aa != wild_type[i]: - p1 = i + 1 - return str(p1) - except: - return "NA" - - -def position_in_anchor_position(position_mhci, peptide_length): - """ - This function determines if the mutation is located within an anchor position in mhc I. - As an approximation, we assume that the second and the last position are anchor positions for all alleles. - """ - anchor = "NA" - try: - anchor = int(position_mhci) == int(peptide_length) or int(position_mhci) == 2 - # TODO this conversion of a boolean to a numeric boolean in a string needs to go away - anchor = str(1) if anchor else str(0) - except: - pass - return anchor +#!/usr/bin/env python + +from input import MHC_I, MHC_II + +import math +import os + +BETA = 0.11387 +BLOSUM62_FILE_NAME = 'BLOSUM62-2.matrix.txt' + + +class SelfSimilarityCalculator(): + + def __init__(self): + blosum_file = os.path.join(os.path.abspath(os.path.dirname(__file__)), BLOSUM62_FILE_NAME) + blosum_dict = self._load_blosum(blosum_file) + self.k1 = self._compute_k1(blosum_dict) + + def _compute_k1(self, blosum_dict): + K1 = {} + for i in list(blosum_dict.keys()): + x = K1.get(i, {}) + for j in list(blosum_dict[i].keys()): + x[j] = math.pow(blosum_dict[i][j], BETA) + K1[i] = x + return K1 + + def _load_blosum(self, blosum): + blosum_dict = {} + colid = [] + rowid = [] + c = 0 + with open(blosum) as f: + for line in f: + c += 1 + if c == 1: + colid = line.strip("\n").split(" ") + continue + w = line.strip("\n").split(" ") + id = w[0] + v = [float(x) for x in w[1:]] + rowid.append(id) + x = blosum_dict.get(id, {}) + for i, vi in enumerate(v): + x[colid[i]] = vi + blosum_dict[id] = x + return blosum_dict + + def compute_k_hat_3(self, x, y): # K^3 + return self._compute_k3(x, y) / math.sqrt(self._compute_k3(x, x) * self._compute_k3(y, y)) + + def _compute_k3(self, f, g): + max_k = min(len(f), len(g)) + s = 0 + for k in range(1, max_k + 1): + for i in range(len(f) - (k - 1)): + u = f[i:i + k] + for j in range(len(g) - (k - 1)): + v = g[j:j + k] + s += self._compute_k2k(u, v, self.k1) + return s + + def _compute_k2k(self, u, v, K1): + if len(u) != len(v): + return None + k = len(u) + p = K1[u[0]][v[0]] + for i in range(1, k): + p = p * K1[u[i]][v[i]] + return p + + +def get_self_similarity(mutation, wild_type): + """ + Returns self-similiarity between mutated and wt epitope according to Bjerregard et al., + Argument mhc indicates if determination for MHC I or MHC II epitopes + """ + self_similarity = 'NA' + try: + self_similarity = str(SelfSimilarityCalculator().compute_k_hat_3(mutation, wild_type)) + except ZeroDivisionError: + pass + return self_similarity + + +def is_improved_binder(score_mutation, score_wild_type): + """ + This function checks if mutated epitope is improved binder according to Bjerregard et al. + """ + try: + improved_binder = float(score_wild_type) / float(score_mutation) >= 1.2 + except (ZeroDivisionError, ValueError) as e: + return "NA" + # TODO: boolean in a string needs to go away + return "1" if improved_binder else "0" + + +def self_similarity_of_conserved_binder_only(has_conserved_binder, similarity): + """ + this function returns selfsimilarity for conserved binder but not for improved binder + """ + try: + if has_conserved_binder == str(0): + return similarity + else: + return "NA" + except (ZeroDivisionError, ValueError) as e: + return "NA" + + +def position_of_mutation_epitope(wild_type, mutation): + """ + This function determines the position of the mutation within the epitope sequence. + """ + p1 = -1 + try: + for i, aa in enumerate(mutation): + if aa != wild_type[i]: + p1 = i + 1 + return str(p1) + except: + return "NA" + + +def position_in_anchor_position(position_mhci, peptide_length): + """ + This function determines if the mutation is located within an anchor position in mhc I. + As an approximation, we assume that the second and the last position are anchor positions for all alleles. + """ + anchor = "NA" + try: + anchor = int(position_mhci) == int(peptide_length) or int(position_mhci) == 2 + # TODO this conversion of a boolean to a numeric boolean in a string needs to go away + anchor = str(1) if anchor else str(0) + except: + pass + return anchor diff --git a/input/tests/__init__.py b/input/tests/__init__.py index 25be8221..ee7475c9 100755 --- a/input/tests/__init__.py +++ b/input/tests/__init__.py @@ -1,22 +1,22 @@ -TEST_HLAI_ALLELES = [ - 'HLA-A*24:02', 'HLA-A*02:01', 'HLA-B*15:01', 'HLA-B*44:02', 'HLA-C*07:02', 'HLA-C*05:01', - 'HLA-A*24:02', 'HLA-B*27:05', 'HLA-B*52:01', 'HLA-C*01:02', 'HLA-C*12:02', - 'HLA-A*01:01', 'HLA-B*56:01', 'HLA-B*38:01', 'HLA-C*01:02', 'HLA-C*06:02', - 'HLA-A*03:01', 'HLA-A*02:01', 'HLA-B*27:05', 'HLA-B*47:01', 'HLA-C*01:02', 'HLA-C*06:02', - 'HLA-A*02:01', 'HLA-A*25:01', 'HLA-B*27:02', 'HLA-B*18:01', 'HLA-C*02:02', 'HLA-C*12:03', - 'HLA-A*23:01', 'HLA-A*66:01', 'HLA-B*41:02', 'HLA-B*35:01', 'HLA-C*17:03', 'HLA-C*04:01', - 'HLA-A*66:01', 'HLA-A*01:01', 'HLA-B*08:01', 'HLA-C*07:01', - 'HLA-A*03:01', 'HLA-A*01:01', 'HLA-B*08:01', 'HLA-B*35:01', 'HLA-C*07:01', 'HLA-C*04:01', - 'HLA-A*24:02', 'HLA-A*68:01', 'HLA-B*35:03', 'HLA-B*13:02', 'HLA-C*06:02', 'HLA-C*04:01', - 'HLA-A*01:01', 'HLA-B*37:01', 'HLA-B*08:01', 'HLA-C*06:02', 'HLA-C*07:01'] - -TEST_HLAII_ALLELES = ['HLA-DRB1*04:01', 'HLA-DRB1*04:04', 'HLA-DQB1*03:01', 'HLA-DQB1*03:02', - 'HLA-DRB1*11:01', 'HLA-DRB1*01:01', 'HLA-DQB1*05:01', 'HLA-DQB1*03:01', - 'HLA-DRB1*11:04', 'HLA-DRB1*07:01', 'HLA-DQB1*02:02', 'HLA-DQB1*03:01', - 'HLA-DRB1*01:01', 'HLA-DRB1*07:01', 'HLA-DQB1*05:01', 'HLA-DQB1*02:02', - 'HLA-DRB1*16:01', 'HLA-DRB1*01:01', 'HLA-DQB1*05:02', 'HLA-DQB1*05:01', - 'HLA-DRB1*11:01', 'HLA-DRB1*01:01', 'HLA-DQB1*05:01', 'HLA-DQB1*03:01', - 'HLA-DRB1*03:01', 'HLA-DQB1*02:01', - 'HLA-DRB1*03:01', 'HLA-DRB1*07:01', 'HLA-DQB1*02:02', 'HLA-DQB1*02:01', - 'HLA-DRB1*15:01', 'HLA-DRB1*12:01', 'HLA-DQB1*06:02', 'HLA-DQB1*03:01', - 'HLA-DRB1*11:01', 'HLA-DRB1*03:01', 'HLA-DQB1*03:01', 'HLA-DQB1*02:01'] +TEST_HLAI_ALLELES = [ + 'HLA-A*24:02', 'HLA-A*02:01', 'HLA-B*15:01', 'HLA-B*44:02', 'HLA-C*07:02', 'HLA-C*05:01', + 'HLA-A*24:02', 'HLA-B*27:05', 'HLA-B*52:01', 'HLA-C*01:02', 'HLA-C*12:02', + 'HLA-A*01:01', 'HLA-B*56:01', 'HLA-B*38:01', 'HLA-C*01:02', 'HLA-C*06:02', + 'HLA-A*03:01', 'HLA-A*02:01', 'HLA-B*27:05', 'HLA-B*47:01', 'HLA-C*01:02', 'HLA-C*06:02', + 'HLA-A*02:01', 'HLA-A*25:01', 'HLA-B*27:02', 'HLA-B*18:01', 'HLA-C*02:02', 'HLA-C*12:03', + 'HLA-A*23:01', 'HLA-A*66:01', 'HLA-B*41:02', 'HLA-B*35:01', 'HLA-C*17:03', 'HLA-C*04:01', + 'HLA-A*66:01', 'HLA-A*01:01', 'HLA-B*08:01', 'HLA-C*07:01', + 'HLA-A*03:01', 'HLA-A*01:01', 'HLA-B*08:01', 'HLA-B*35:01', 'HLA-C*07:01', 'HLA-C*04:01', + 'HLA-A*24:02', 'HLA-A*68:01', 'HLA-B*35:03', 'HLA-B*13:02', 'HLA-C*06:02', 'HLA-C*04:01', + 'HLA-A*01:01', 'HLA-B*37:01', 'HLA-B*08:01', 'HLA-C*06:02', 'HLA-C*07:01'] + +TEST_HLAII_ALLELES = ['HLA-DRB1*04:01', 'HLA-DRB1*04:04', 'HLA-DQB1*03:01', 'HLA-DQB1*03:02', + 'HLA-DRB1*11:01', 'HLA-DRB1*01:01', 'HLA-DQB1*05:01', 'HLA-DQB1*03:01', + 'HLA-DRB1*11:04', 'HLA-DRB1*07:01', 'HLA-DQB1*02:02', 'HLA-DQB1*03:01', + 'HLA-DRB1*01:01', 'HLA-DRB1*07:01', 'HLA-DQB1*05:01', 'HLA-DQB1*02:02', + 'HLA-DRB1*16:01', 'HLA-DRB1*01:01', 'HLA-DQB1*05:02', 'HLA-DQB1*05:01', + 'HLA-DRB1*11:01', 'HLA-DRB1*01:01', 'HLA-DQB1*05:01', 'HLA-DQB1*03:01', + 'HLA-DRB1*03:01', 'HLA-DQB1*02:01', + 'HLA-DRB1*03:01', 'HLA-DRB1*07:01', 'HLA-DQB1*02:02', 'HLA-DQB1*02:01', + 'HLA-DRB1*15:01', 'HLA-DRB1*12:01', 'HLA-DQB1*06:02', 'HLA-DQB1*03:01', + 'HLA-DRB1*11:01', 'HLA-DRB1*03:01', 'HLA-DQB1*03:01', 'HLA-DQB1*02:01'] diff --git a/input/tests/integration_tests/integration_test_tools.py b/input/tests/integration_tests/integration_test_tools.py index 275fd6b9..5dea5f9e 100755 --- a/input/tests/integration_tests/integration_test_tools.py +++ b/input/tests/integration_tests/integration_test_tools.py @@ -1,19 +1,19 @@ -import random -import tempfile - -import dotenv -from Bio.Alphabet.IUPAC import IUPACData - -from input.references import ReferenceFolder, DependenciesConfiguration - - -def load_references(): - dotenv.load_dotenv() - return ReferenceFolder(), DependenciesConfiguration() - - -def create_temp_aminoacid_fasta_file(): - fastafile = tempfile.NamedTemporaryFile(mode='w', delete=False) - with fastafile as f: - f.write("".join(random.choices(list(IUPACData.protein_letters), k=25))) - return fastafile +import random +import tempfile + +import dotenv +from Bio.Alphabet.IUPAC import IUPACData + +from input.references import ReferenceFolder, DependenciesConfiguration + + +def load_references(): + dotenv.load_dotenv() + return ReferenceFolder(), DependenciesConfiguration() + + +def create_temp_aminoacid_fasta_file(): + fastafile = tempfile.NamedTemporaryFile(mode='w', delete=False) + with fastafile as f: + f.write("".join(random.choices(list(IUPACData.protein_letters), k=25))) + return fastafile diff --git a/input/tests/integration_tests/test_conservation_scores.py b/input/tests/integration_tests/test_conservation_scores.py index e31fb048..15ea8365 100755 --- a/input/tests/integration_tests/test_conservation_scores.py +++ b/input/tests/integration_tests/test_conservation_scores.py @@ -1,46 +1,46 @@ -from unittest import TestCase - -from input.new_features.conservation_scores import ProveanAnnotator -from input.tests.integration_tests import integration_test_tools - - -class TestProveanAnnotator(TestCase): - - def setUp(self): - self.references, self.configuration = integration_test_tools.load_references() - self.header_epitopes = ["UCSC_transcript", "substitution"] - self.epitopes = [ - ["uc010qbo.1", "A207S"], - ["uc001ovh.1", "A41S"], - ["uc001ovh.1", "A40S"], - ["uc001tzg.1", "A154S"], - ["uc001uir.1", "A39S"], - ["uc001yqt.1", "A701S"], - ["uc001zrt.1", "A1520S"], - ["uc010umw.1", "A114S"], - ["uc010umy.1", "A7S"]] - self.annotator = ProveanAnnotator( - provean_file=self.references.prov_scores_mapped3, header_epitopes=self.header_epitopes, - epitopes=self.epitopes) - - def test_provean_annotator_loading(self): - self.assertTrue(len(self.annotator.provean_matrix) <= len(self.epitopes)) - self.assertTrue(len(self.annotator.provean_matrix) > 0) - - def test_provean_annotator(self): - provean_annotation = self.annotator.get_provean_annotation( - mutated_aminoacid="S", ucsc_id_position="uc001tzg_154") - self.assertIsNotNone(provean_annotation) - self.assertTrue(provean_annotation != "NA") - self.assertIsNotNone(float(provean_annotation)) - - def test_provean_annotator_non_existing_aminoacid(self): - provean_annotation = self.annotator.get_provean_annotation( - mutated_aminoacid="NO_AA", ucsc_id_position="uc001tzg_154") - self.assertIsNotNone(provean_annotation) - self.assertTrue(provean_annotation == "NA") - - def test_provean_annotator_non_existing_gene(self): - provean_annotation = self.annotator.get_provean_annotation(mutated_aminoacid="S", ucsc_id_position="nope_156") - self.assertIsNotNone(provean_annotation) - self.assertTrue(provean_annotation == "NA") +from unittest import TestCase + +from input.new_features.conservation_scores import ProveanAnnotator +from input.tests.integration_tests import integration_test_tools + + +class TestProveanAnnotator(TestCase): + + def setUp(self): + self.references, self.configuration = integration_test_tools.load_references() + self.header_epitopes = ["UCSC_transcript", "substitution"] + self.epitopes = [ + ["uc010qbo.1", "A207S"], + ["uc001ovh.1", "A41S"], + ["uc001ovh.1", "A40S"], + ["uc001tzg.1", "A154S"], + ["uc001uir.1", "A39S"], + ["uc001yqt.1", "A701S"], + ["uc001zrt.1", "A1520S"], + ["uc010umw.1", "A114S"], + ["uc010umy.1", "A7S"]] + self.annotator = ProveanAnnotator( + provean_file=self.references.prov_scores_mapped3, header_epitopes=self.header_epitopes, + epitopes=self.epitopes) + + def test_provean_annotator_loading(self): + self.assertTrue(len(self.annotator.provean_matrix) <= len(self.epitopes)) + self.assertTrue(len(self.annotator.provean_matrix) > 0) + + def test_provean_annotator(self): + provean_annotation = self.annotator.get_provean_annotation( + mutated_aminoacid="S", ucsc_id_position="uc001tzg_154") + self.assertIsNotNone(provean_annotation) + self.assertTrue(provean_annotation != "NA") + self.assertIsNotNone(float(provean_annotation)) + + def test_provean_annotator_non_existing_aminoacid(self): + provean_annotation = self.annotator.get_provean_annotation( + mutated_aminoacid="NO_AA", ucsc_id_position="uc001tzg_154") + self.assertIsNotNone(provean_annotation) + self.assertTrue(provean_annotation == "NA") + + def test_provean_annotator_non_existing_gene(self): + provean_annotation = self.annotator.get_provean_annotation(mutated_aminoacid="S", ucsc_id_position="nope_156") + self.assertIsNotNone(provean_annotation) + self.assertTrue(provean_annotation == "NA") diff --git a/input/tests/integration_tests/test_dissimilarity.py b/input/tests/integration_tests/test_dissimilarity.py index 353e7167..c4b288ea 100755 --- a/input/tests/integration_tests/test_dissimilarity.py +++ b/input/tests/integration_tests/test_dissimilarity.py @@ -1,27 +1,27 @@ -from unittest import TestCase - -import input.tests.integration_tests.integration_test_tools as integration_test_tools -from input.helpers.runner import Runner -from input.dissimilarity_garnish.dissimilaritycalculator import DissimilarityCalculator - - -class TestDissimilarity(TestCase): - - def setUp(self): - self.references, self.configuration = integration_test_tools.load_references() - self.fastafile = integration_test_tools.create_temp_aminoacid_fasta_file() - self.runner = Runner() - - def test_dissimilar_sequences(self): - result = DissimilarityCalculator( - runner=self.runner, configuration=self.configuration)\ - .calculate_dissimilarity( - mhc_mutation='tocino', mhc_affinity='velocidad', references=self.references) - self.assertEqual(1, result) - - def test_similar_sequences(self): - result = DissimilarityCalculator( - runner=self.runner, configuration=self.configuration)\ - .calculate_dissimilarity( - mhc_mutation='DDDDDD', mhc_affinity='DDDDDD', references=self.references) - self.assertTrue(result < 0.000001) +from unittest import TestCase + +import input.tests.integration_tests.integration_test_tools as integration_test_tools +from input.helpers.runner import Runner +from input.dissimilarity_garnish.dissimilaritycalculator import DissimilarityCalculator + + +class TestDissimilarity(TestCase): + + def setUp(self): + self.references, self.configuration = integration_test_tools.load_references() + self.fastafile = integration_test_tools.create_temp_aminoacid_fasta_file() + self.runner = Runner() + + def test_dissimilar_sequences(self): + result = DissimilarityCalculator( + runner=self.runner, configuration=self.configuration)\ + .calculate_dissimilarity( + mhc_mutation='tocino', mhc_affinity='velocidad', references=self.references) + self.assertEqual(1, result) + + def test_similar_sequences(self): + result = DissimilarityCalculator( + runner=self.runner, configuration=self.configuration)\ + .calculate_dissimilarity( + mhc_mutation='DDDDDD', mhc_affinity='DDDDDD', references=self.references) + self.assertTrue(result < 0.000001) diff --git a/input/tests/integration_tests/test_mixmhcpred.py b/input/tests/integration_tests/test_mixmhcpred.py index 5d91e435..dcec2bb8 100755 --- a/input/tests/integration_tests/test_mixmhcpred.py +++ b/input/tests/integration_tests/test_mixmhcpred.py @@ -1,99 +1,99 @@ -from unittest import TestCase -from logzero import logger - -import input.tests.integration_tests.integration_test_tools as integration_test_tools -from input.MixMHCpred.abstract_mixmhcpred import AbstractMixMHCpred -from input.MixMHCpred.mixmhc2pred import MixMhc2Pred -from input.MixMHCpred.mixmhcpred import MixMHCpred -from input.helpers.runner import Runner -from input.tests import TEST_HLAI_ALLELES, TEST_HLAII_ALLELES - - -class TestMixMHCPred(TestCase): - - def setUp(self): - self.references, self.configuration = integration_test_tools.load_references() - self.runner = Runner() - - def test_mixmhcpred_epitope_iedb(self): - mixmhcpred = MixMHCpred(runner=self.runner, configuration=self.configuration) - # this is an epitope from IEDB of length 9 - mutated = 'NLVPMVATV' - wild_type = 'NLVPMVATV' - mixmhcpred.main(xmer_wt=wild_type, xmer_mut=mutated, alleles=TEST_HLAI_ALLELES[0:5]) - self.assertIsNotNone(mixmhcpred.all_peptides) - self.assertEqual("NLVPMVAT", mixmhcpred.all_peptides) - logger.debug(mixmhcpred.all_peptides) - self.assertEqual(len(mixmhcpred.all_peptides.split('|')), 1) - self.assertIsNotNone(mixmhcpred.all_scores) - logger.debug(mixmhcpred.all_scores) - self.assertEqual(len(mixmhcpred.all_scores.split('|')), 1) - self.assertEqual("-0.522931", mixmhcpred.all_scores) - self.assertIsNotNone(mixmhcpred.all_ranks) - logger.debug(mixmhcpred.all_ranks) - self.assertEqual(len(mixmhcpred.all_ranks.split('|')), 1) - self.assertEqual("77", mixmhcpred.all_ranks) - self.assertIsNotNone(mixmhcpred.all_alleles) - self.assertIsNotNone(mixmhcpred.best_peptide) - self.assertIsNotNone(mixmhcpred.best_score) - self.assertIsNotNone(mixmhcpred.best_rank) - self.assertIsNotNone(mixmhcpred.best_allele) - self.assertIsNotNone(mixmhcpred.best_peptide_wt) - self.assertIsNotNone(mixmhcpred.best_score_wt) - self.assertIsNotNone(mixmhcpred.best_rank_wt) - self.assertIsNotNone(mixmhcpred.difference_score_mut_wt) - - def test_mixmhcpred_too_small_epitope(self): - mixmhcpred = MixMHCpred(runner=self.runner, configuration=self.configuration) - mutated = 'NLVP' - wild_type = 'NLVP' - mixmhcpred.main(xmer_wt=wild_type, xmer_mut=mutated, alleles=TEST_HLAI_ALLELES) - self.assertEqual("NA", mixmhcpred.all_peptides) - - def test_mixmhcpred2_epitope_iedb(self): - mixmhcpred = MixMhc2Pred(runner=self.runner, configuration=self.configuration) - # this is an epitope from IEDB of length 15 - mutated = 'ENPVVHFFKNIVTPR' - wild_type = 'ENPVVHFFKNIVTPR' - mixmhcpred.main(xmer_wt=wild_type, xmer_mut=mutated, alleles=TEST_HLAII_ALLELES) - self.assertIsNotNone(mixmhcpred.all_peptides) - self.assertEqual(len(mixmhcpred.all_peptides.split('|')), 2) - self.assertTrue("ENPVVHFFKNIVTP" in mixmhcpred.all_peptides.split('|')) - self.assertTrue("NPVVHFFKNIVTP" in mixmhcpred.all_peptides.split('|')) - logger.debug(mixmhcpred.all_peptides) - self.assertIsNotNone(mixmhcpred.all_ranks) - self.assertEqual(len(mixmhcpred.all_ranks.split('|')), 2) - self.assertTrue("0.116547" in mixmhcpred.all_ranks.split('|')) - self.assertTrue("0.276218", mixmhcpred.all_ranks.split('|')) - logger.debug(mixmhcpred.all_ranks) - self.assertIsNotNone(mixmhcpred.all_alleles) - self.assertIsNotNone(mixmhcpred.best_peptide) - self.assertIsNotNone(mixmhcpred.best_rank) - self.assertIsNotNone(mixmhcpred.best_allele) - self.assertIsNotNone(mixmhcpred.best_peptide_wt) - self.assertIsNotNone(mixmhcpred.best_score_wt) - self.assertIsNotNone(mixmhcpred.best_rank_wt) - self.assertIsNotNone(mixmhcpred.difference_score_mut_wt) - - def test_mixmhcpred2_too_small_epitope(self): - mixmhcpred = MixMhc2Pred(runner=self.runner, configuration=self.configuration) - # this is an epitope from IEDB of length 15 - mutated = 'ENPVVHFF' - wild_type = 'ENPVVHFF' - mixmhcpred.main(xmer_wt=wild_type, xmer_mut=mutated, alleles=TEST_HLAII_ALLELES) - self.assertEqual("NA", mixmhcpred.all_peptides) - - def test_generate_nmers(self): - result = AbstractMixMHCpred.generate_nmers( - xmer_wt="DDDDDDDDD", xmer_mut="DDDDDVDDD", lengths=[8, 9, 10, 11]) - self.assertIsNotNone(result) - self.assertEqual(3, len(result)) - self.assertEqual(1, len(list(filter(lambda x: len(x) == 9, result)))) - self.assertEqual(2, len(list(filter(lambda x: len(x) == 8, result)))) - self.assertEqual(0, len(list(filter(lambda x: len(x) == 7, result)))) - self.assertEqual(0, len(list(filter(lambda x: len(x) == 6, result)))) - self.assertEqual(0, len(list(filter(lambda x: len(x) == 5, result)))) - self.assertEqual(0, len(list(filter(lambda x: len(x) == 4, result)))) - # ['DDDDDVDD', 'DDDDVDDD', 'DDDVDDD', 'DDVDDD', 'DVDDD', 'VDDD', 'DDDDDVDDD', 'DDDDVDDD', 'DDDVDDD', 'DDVDDD', - # 'DVDDD', 'VDDD'] - logger.debug(result) +from unittest import TestCase +from logzero import logger + +import input.tests.integration_tests.integration_test_tools as integration_test_tools +from input.MixMHCpred.abstract_mixmhcpred import AbstractMixMHCpred +from input.MixMHCpred.mixmhc2pred import MixMhc2Pred +from input.MixMHCpred.mixmhcpred import MixMHCpred +from input.helpers.runner import Runner +from input.tests import TEST_HLAI_ALLELES, TEST_HLAII_ALLELES + + +class TestMixMHCPred(TestCase): + + def setUp(self): + self.references, self.configuration = integration_test_tools.load_references() + self.runner = Runner() + + def test_mixmhcpred_epitope_iedb(self): + mixmhcpred = MixMHCpred(runner=self.runner, configuration=self.configuration) + # this is an epitope from IEDB of length 9 + mutated = 'NLVPMVATV' + wild_type = 'NLVPMVATV' + mixmhcpred.main(xmer_wt=wild_type, xmer_mut=mutated, alleles=TEST_HLAI_ALLELES[0:5]) + self.assertIsNotNone(mixmhcpred.all_peptides) + self.assertEqual("NLVPMVAT", mixmhcpred.all_peptides) + logger.debug(mixmhcpred.all_peptides) + self.assertEqual(len(mixmhcpred.all_peptides.split('|')), 1) + self.assertIsNotNone(mixmhcpred.all_scores) + logger.debug(mixmhcpred.all_scores) + self.assertEqual(len(mixmhcpred.all_scores.split('|')), 1) + self.assertEqual("-0.522931", mixmhcpred.all_scores) + self.assertIsNotNone(mixmhcpred.all_ranks) + logger.debug(mixmhcpred.all_ranks) + self.assertEqual(len(mixmhcpred.all_ranks.split('|')), 1) + self.assertEqual("77", mixmhcpred.all_ranks) + self.assertIsNotNone(mixmhcpred.all_alleles) + self.assertIsNotNone(mixmhcpred.best_peptide) + self.assertIsNotNone(mixmhcpred.best_score) + self.assertIsNotNone(mixmhcpred.best_rank) + self.assertIsNotNone(mixmhcpred.best_allele) + self.assertIsNotNone(mixmhcpred.best_peptide_wt) + self.assertIsNotNone(mixmhcpred.best_score_wt) + self.assertIsNotNone(mixmhcpred.best_rank_wt) + self.assertIsNotNone(mixmhcpred.difference_score_mut_wt) + + def test_mixmhcpred_too_small_epitope(self): + mixmhcpred = MixMHCpred(runner=self.runner, configuration=self.configuration) + mutated = 'NLVP' + wild_type = 'NLVP' + mixmhcpred.main(xmer_wt=wild_type, xmer_mut=mutated, alleles=TEST_HLAI_ALLELES) + self.assertEqual("NA", mixmhcpred.all_peptides) + + def test_mixmhcpred2_epitope_iedb(self): + mixmhcpred = MixMhc2Pred(runner=self.runner, configuration=self.configuration) + # this is an epitope from IEDB of length 15 + mutated = 'ENPVVHFFKNIVTPR' + wild_type = 'ENPVVHFFKNIVTPR' + mixmhcpred.main(xmer_wt=wild_type, xmer_mut=mutated, alleles=TEST_HLAII_ALLELES) + self.assertIsNotNone(mixmhcpred.all_peptides) + self.assertEqual(len(mixmhcpred.all_peptides.split('|')), 2) + self.assertTrue("ENPVVHFFKNIVTP" in mixmhcpred.all_peptides.split('|')) + self.assertTrue("NPVVHFFKNIVTP" in mixmhcpred.all_peptides.split('|')) + logger.debug(mixmhcpred.all_peptides) + self.assertIsNotNone(mixmhcpred.all_ranks) + self.assertEqual(len(mixmhcpred.all_ranks.split('|')), 2) + self.assertTrue("0.116547" in mixmhcpred.all_ranks.split('|')) + self.assertTrue("0.276218", mixmhcpred.all_ranks.split('|')) + logger.debug(mixmhcpred.all_ranks) + self.assertIsNotNone(mixmhcpred.all_alleles) + self.assertIsNotNone(mixmhcpred.best_peptide) + self.assertIsNotNone(mixmhcpred.best_rank) + self.assertIsNotNone(mixmhcpred.best_allele) + self.assertIsNotNone(mixmhcpred.best_peptide_wt) + self.assertIsNotNone(mixmhcpred.best_score_wt) + self.assertIsNotNone(mixmhcpred.best_rank_wt) + self.assertIsNotNone(mixmhcpred.difference_score_mut_wt) + + def test_mixmhcpred2_too_small_epitope(self): + mixmhcpred = MixMhc2Pred(runner=self.runner, configuration=self.configuration) + # this is an epitope from IEDB of length 15 + mutated = 'ENPVVHFF' + wild_type = 'ENPVVHFF' + mixmhcpred.main(xmer_wt=wild_type, xmer_mut=mutated, alleles=TEST_HLAII_ALLELES) + self.assertEqual("NA", mixmhcpred.all_peptides) + + def test_generate_nmers(self): + result = AbstractMixMHCpred.generate_nmers( + xmer_wt="DDDDDDDDD", xmer_mut="DDDDDVDDD", lengths=[8, 9, 10, 11]) + self.assertIsNotNone(result) + self.assertEqual(3, len(result)) + self.assertEqual(1, len(list(filter(lambda x: len(x) == 9, result)))) + self.assertEqual(2, len(list(filter(lambda x: len(x) == 8, result)))) + self.assertEqual(0, len(list(filter(lambda x: len(x) == 7, result)))) + self.assertEqual(0, len(list(filter(lambda x: len(x) == 6, result)))) + self.assertEqual(0, len(list(filter(lambda x: len(x) == 5, result)))) + self.assertEqual(0, len(list(filter(lambda x: len(x) == 4, result)))) + # ['DDDDDVDD', 'DDDDVDDD', 'DDDVDDD', 'DDVDDD', 'DVDDD', 'VDDD', 'DDDDDVDDD', 'DDDDVDDD', 'DDDVDDD', 'DDVDDD', + # 'DVDDD', 'VDDD'] + logger.debug(result) diff --git a/input/tests/integration_tests/test_neoag.py b/input/tests/integration_tests/test_neoag.py index 614d078f..4040d2d7 100755 --- a/input/tests/integration_tests/test_neoag.py +++ b/input/tests/integration_tests/test_neoag.py @@ -1,97 +1,97 @@ -from unittest import TestCase, SkipTest - -from input.neoag.neoag_gbm_model import NeoagCalculator -from input.helpers.runner import Runner -import input.tests.integration_tests.integration_test_tools as integration_test_tools - - -class TestNeoantigenFitness(TestCase): - - def setUp(self): - self.references, self.configuration = integration_test_tools.load_references() - self.fastafile = integration_test_tools.create_temp_aminoacid_fasta_file() - self.runner = Runner() - - def test_neoag(self): - result = NeoagCalculator(runner=self.runner, configuration=self.configuration).wrapper_neoag( - sample_id="12345", - mut_peptide="DDDDDV", - score_mut="0", - ref_peptide="DDDDDD", - peptide_variant_position="123") - self.assertTrue(isinstance(result, str)) - self.assertTrue(float(result) > 0) - - @SkipTest - def test_legacy(self): - # test with ott data set - # file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/MHC_prediction_netmhcpan4/testdat_ott.txt" - # hla_file ="/projects/SUMMIT/WP1.2/Literature_Cohorts/data_analysis/cohorts/ott/icam_ott/alleles.csv" - file = "/projects/SUMMIT/WP1.2/immunogenicity_data/ivac/input_annotation/20190328_IS_IM_withoutfeatures.txt" - hla_file = "/projects/SUMMIT/WP1.2/immunogenicity_data/ivac/hlahd/20190916_alleles_extended.csv" - # test inest data set - # file = "/flash/projects/WP3/AnFranziska/AnFranziska/head_seqs.txt" - # hla_file = "/flash/projects/WP3/AnFranziska/AnFranziska/alleles.csv" - dat = data_import.import_dat_icam(file, False) - if "+-13_AA_(SNV)_/_-15_AA_to_STOP_(INDEL)" in dat[0]: - dat = data_import.change_col_names(dat) - # available MHC alleles - set_available_mhc = predict_all_epitopes.Bunchepitopes().load_available_hla_alleles() - # hla allele of patients - patient_hlaI = predict_all_epitopes.Bunchepitopes().load_patient_hla_I_allels(hla_file) - patient_hlaII = predict_all_epitopes.Bunchepitopes().load_patient_hla_II_allels(hla_file) - - print(patient_hlaI) - print(patient_hlaII) - - for ii, i in enumerate(dat[1]): - if ii < 2: - print(ii) - dict_epi = epitope.Epitope() - dict_epi.init_properties(dat[0], dat[1][ii]) - dict_epi.add_features(self_similarity.position_of_mutation_epitope(dict_epi.properties, MHC_I), - "pos_MUT_MHCI") - np = netmhcpan_prediction.NetmhcpanBestPrediction() - xmer_mut = dict_epi.properties["X..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."] - tmp_fasta_file = tempfile.NamedTemporaryFile(prefix="tmp_singleseq_", suffix=".fasta", delete=False) - tmp_fasta = tmp_fasta_file.name - print(tmp_fasta, file=sys.stderr) - tmp_prediction_file = tempfile.NamedTemporaryFile(prefix="netmhcpanpred_", suffix=".csv", delete=False) - tmp_prediction = tmp_prediction_file.name - print(tmp_prediction, file=sys.stderr) - np.generate_fasta(dict_epi.properties, tmp_fasta, mut=True) - alleles = np.get_hla_allels(dict_epi.properties, patient_hlaI) - # print alleles - np.mhc_prediction(alleles, set_available_mhc, tmp_fasta, tmp_prediction) - dict_epi.properties["Position_Xmer_Seq"] = np.mut_position_xmer_seq(dict_epi.properties) - preds = np.filter_binding_predictions(dict_epi.properties, tmp_prediction) - best_epi_affinity = np.minimal_binding_score(preds, rank=False) - dict_epi.add_features(np.add_best_epitope_info(best_epi_affinity, "Aff(nM)"), - "best_affinity_netmhcpan4") - dict_epi.add_features(np.add_best_epitope_info(best_epi_affinity, "Icore"), - "best_affinity_epitope_netmhcpan4 ") - dict_epi.add_features(np.add_best_epitope_info(best_epi_affinity, "HLA"), "best4_affinity_allele") - xmer_wt = dict_epi.properties["X.WT._..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."] - # print >> sys.stderr, "WT seq: " + xmer_wt - tmp_fasta_file = tempfile.NamedTemporaryFile(prefix="tmp_singleseq_", suffix=".fasta", delete=False) - tmp_fasta = tmp_fasta_file.name - tmp_prediction_file = tempfile.NamedTemporaryFile(prefix="netmhcpanpred_", suffix=".csv", delete=False) - tmp_prediction = tmp_prediction_file.name - print(tmp_prediction, file=sys.stderr) - np = netmhcpan_prediction.NetmhcpanBestPrediction() - np.generate_fasta(dict_epi.properties, tmp_fasta, mut=False) - np.mhc_prediction(alleles, set_available_mhc, tmp_fasta, tmp_prediction) - preds = np.filter_binding_predictions(dict_epi.properties, tmp_prediction) - best_epi_affinity = np.filter_for_WT_epitope(preds, - dict_epi.properties["best_affinity_epitope_netmhcpan4"], - dict_epi.properties["best4_affinity_allele"]) - dict_epi.add_features(np.add_best_epitope_info(best_epi_affinity, "Aff(nM)"), - "best_affinity_netmhcpan4_WT") - dict_epi.add_features(np.add_best_epitope_info(best_epi_affinity, "Icore"), - "best_affinity_epitope_netmhcpan4_WT") - dict_epi.add_features(self_similarity.position_of_mutation_epitope_affinity(dict_epi.properties), - "pos_MUT_MHCI_affinity_epi") - - sc = wrapper_neoag(dict_epi.properties) - print(sc, file=sys.stderr) - print(type(sc), file=sys.stderr) +from unittest import TestCase, SkipTest + +from input.neoag.neoag_gbm_model import NeoagCalculator +from input.helpers.runner import Runner +import input.tests.integration_tests.integration_test_tools as integration_test_tools + + +class TestNeoantigenFitness(TestCase): + + def setUp(self): + self.references, self.configuration = integration_test_tools.load_references() + self.fastafile = integration_test_tools.create_temp_aminoacid_fasta_file() + self.runner = Runner() + + def test_neoag(self): + result = NeoagCalculator(runner=self.runner, configuration=self.configuration).wrapper_neoag( + sample_id="12345", + mut_peptide="DDDDDV", + score_mut="0", + ref_peptide="DDDDDD", + peptide_variant_position="123") + self.assertTrue(isinstance(result, str)) + self.assertTrue(float(result) > 0) + + @SkipTest + def test_legacy(self): + # test with ott data set + # file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/MHC_prediction_netmhcpan4/testdat_ott.txt" + # hla_file ="/projects/SUMMIT/WP1.2/Literature_Cohorts/data_analysis/cohorts/ott/icam_ott/alleles.csv" + file = "/projects/SUMMIT/WP1.2/immunogenicity_data/ivac/input_annotation/20190328_IS_IM_withoutfeatures.txt" + hla_file = "/projects/SUMMIT/WP1.2/immunogenicity_data/ivac/hlahd/20190916_alleles_extended.csv" + # test inest data set + # file = "/flash/projects/WP3/AnFranziska/AnFranziska/head_seqs.txt" + # hla_file = "/flash/projects/WP3/AnFranziska/AnFranziska/alleles.csv" + dat = data_import.import_dat_icam(file, False) + if "+-13_AA_(SNV)_/_-15_AA_to_STOP_(INDEL)" in dat[0]: + dat = data_import.change_col_names(dat) + # available MHC alleles + set_available_mhc = predict_all_epitopes.Bunchepitopes().load_available_hla_alleles() + # hla allele of patients + patient_hlaI = predict_all_epitopes.Bunchepitopes().load_patient_hla_I_allels(hla_file) + patient_hlaII = predict_all_epitopes.Bunchepitopes().load_patient_hla_II_allels(hla_file) + + print(patient_hlaI) + print(patient_hlaII) + + for ii, i in enumerate(dat[1]): + if ii < 2: + print(ii) + dict_epi = epitope.Epitope() + dict_epi.init_properties(dat[0], dat[1][ii]) + dict_epi.add_features(self_similarity.position_of_mutation_epitope(dict_epi.properties, MHC_I), + "pos_MUT_MHCI") + np = netmhcpan_prediction.NetmhcpanBestPrediction() + xmer_mut = dict_epi.properties["X..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."] + tmp_fasta_file = tempfile.NamedTemporaryFile(prefix="tmp_singleseq_", suffix=".fasta", delete=False) + tmp_fasta = tmp_fasta_file.name + print(tmp_fasta, file=sys.stderr) + tmp_prediction_file = tempfile.NamedTemporaryFile(prefix="netmhcpanpred_", suffix=".csv", delete=False) + tmp_prediction = tmp_prediction_file.name + print(tmp_prediction, file=sys.stderr) + np.generate_fasta(dict_epi.properties, tmp_fasta, mut=True) + alleles = np.get_hla_allels(dict_epi.properties, patient_hlaI) + # print alleles + np.mhc_prediction(alleles, set_available_mhc, tmp_fasta, tmp_prediction) + dict_epi.properties["Position_Xmer_Seq"] = np.mut_position_xmer_seq(dict_epi.properties) + preds = np.filter_binding_predictions(dict_epi.properties, tmp_prediction) + best_epi_affinity = np.minimal_binding_score(preds, rank=False) + dict_epi.add_features(np.add_best_epitope_info(best_epi_affinity, "Aff(nM)"), + "best_affinity_netmhcpan4") + dict_epi.add_features(np.add_best_epitope_info(best_epi_affinity, "Icore"), + "best_affinity_epitope_netmhcpan4 ") + dict_epi.add_features(np.add_best_epitope_info(best_epi_affinity, "HLA"), "best4_affinity_allele") + xmer_wt = dict_epi.properties["X.WT._..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."] + # print >> sys.stderr, "WT seq: " + xmer_wt + tmp_fasta_file = tempfile.NamedTemporaryFile(prefix="tmp_singleseq_", suffix=".fasta", delete=False) + tmp_fasta = tmp_fasta_file.name + tmp_prediction_file = tempfile.NamedTemporaryFile(prefix="netmhcpanpred_", suffix=".csv", delete=False) + tmp_prediction = tmp_prediction_file.name + print(tmp_prediction, file=sys.stderr) + np = netmhcpan_prediction.NetmhcpanBestPrediction() + np.generate_fasta(dict_epi.properties, tmp_fasta, mut=False) + np.mhc_prediction(alleles, set_available_mhc, tmp_fasta, tmp_prediction) + preds = np.filter_binding_predictions(dict_epi.properties, tmp_prediction) + best_epi_affinity = np.filter_for_WT_epitope(preds, + dict_epi.properties["best_affinity_epitope_netmhcpan4"], + dict_epi.properties["best4_affinity_allele"]) + dict_epi.add_features(np.add_best_epitope_info(best_epi_affinity, "Aff(nM)"), + "best_affinity_netmhcpan4_WT") + dict_epi.add_features(np.add_best_epitope_info(best_epi_affinity, "Icore"), + "best_affinity_epitope_netmhcpan4_WT") + dict_epi.add_features(self_similarity.position_of_mutation_epitope_affinity(dict_epi.properties), + "pos_MUT_MHCI_affinity_epi") + + sc = wrapper_neoag(dict_epi.properties) + print(sc, file=sys.stderr) + print(type(sc), file=sys.stderr) diff --git a/input/tests/integration_tests/test_neoantigen_fitness.py b/input/tests/integration_tests/test_neoantigen_fitness.py index 7ae0cc15..d47d00c4 100755 --- a/input/tests/integration_tests/test_neoantigen_fitness.py +++ b/input/tests/integration_tests/test_neoantigen_fitness.py @@ -1,50 +1,50 @@ -from collections import defaultdict -from unittest import TestCase - -from input.neoantigen_fitness.neoantigen_fitness import NeoantigenFitnessCalculator -from input.helpers.runner import Runner -import input.tests.integration_tests.integration_test_tools as integration_test_tools - - -class TestNeoantigenFitness(TestCase): - - def setUp(self): - self.references, self.configuration, self.fastafile = self._load_references() - self.neoantigen_fitness_calculator = NeoantigenFitnessCalculator( - runner=Runner(), configuration=self.configuration) - - def _load_references(self): - references, configuration = integration_test_tools.load_references() - fastafile = integration_test_tools.create_temp_aminoacid_fasta_file() - return references, configuration, fastafile - - def test_pathogen_similarity(self): - # tests a pathogen sequence and expects 1.0 similarity - result = self.neoantigen_fitness_calculator.wrap_pathogen_similarity( - mutation='FIAGLIAIV', - iedb=self.references.iedb) - self.assertEqual('1.0', result) - # tests a modified pathogen sequence and expects something between 0 and 1 - result = self.neoantigen_fitness_calculator.wrap_pathogen_similarity( - mutation='FIAGDAAIV', - iedb=self.references.iedb) - self.assertLess(float(result), 1.0) - self.assertGreater(float(result), 0.0) - # tests a non pathogen sequence and expects 0 similarity - result = self.neoantigen_fitness_calculator.wrap_pathogen_similarity( - mutation='DDDDDMMDD', - iedb=self.references.iedb) - self.assertEqual('0', result) - - def test_amplitude_mhc(self): - self.assertEqual('1.0', self.neoantigen_fitness_calculator.calculate_amplitude_mhc( - score_mutation="1.0", score_wild_type="1.0")) - self.assertEqual('0.9997000899730081', self.neoantigen_fitness_calculator.calculate_amplitude_mhc( - score_mutation="1.0", score_wild_type="1.0", apply_correction=True)) - - def test_recognition_potential(self): - props = defaultdict(lambda: "1.0") - props['Mutation_in_anchor_netmhcpan'] = '0' - props['Mutation_in_anchor_netmhcpan_9mer'] = '0' - self.assertEqual('1.0', self.neoantigen_fitness_calculator.calculate_recognition_potential( - amplitude="1.0", pathogen_similarity="1.0", mutation_in_anchor="0")) +from collections import defaultdict +from unittest import TestCase + +from input.neoantigen_fitness.neoantigen_fitness import NeoantigenFitnessCalculator +from input.helpers.runner import Runner +import input.tests.integration_tests.integration_test_tools as integration_test_tools + + +class TestNeoantigenFitness(TestCase): + + def setUp(self): + self.references, self.configuration, self.fastafile = self._load_references() + self.neoantigen_fitness_calculator = NeoantigenFitnessCalculator( + runner=Runner(), configuration=self.configuration) + + def _load_references(self): + references, configuration = integration_test_tools.load_references() + fastafile = integration_test_tools.create_temp_aminoacid_fasta_file() + return references, configuration, fastafile + + def test_pathogen_similarity(self): + # tests a pathogen sequence and expects 1.0 similarity + result = self.neoantigen_fitness_calculator.wrap_pathogen_similarity( + mutation='FIAGLIAIV', + iedb=self.references.iedb) + self.assertEqual('1.0', result) + # tests a modified pathogen sequence and expects something between 0 and 1 + result = self.neoantigen_fitness_calculator.wrap_pathogen_similarity( + mutation='FIAGDAAIV', + iedb=self.references.iedb) + self.assertLess(float(result), 1.0) + self.assertGreater(float(result), 0.0) + # tests a non pathogen sequence and expects 0 similarity + result = self.neoantigen_fitness_calculator.wrap_pathogen_similarity( + mutation='DDDDDMMDD', + iedb=self.references.iedb) + self.assertEqual('0', result) + + def test_amplitude_mhc(self): + self.assertEqual('1.0', self.neoantigen_fitness_calculator.calculate_amplitude_mhc( + score_mutation="1.0", score_wild_type="1.0")) + self.assertEqual('0.9997000899730081', self.neoantigen_fitness_calculator.calculate_amplitude_mhc( + score_mutation="1.0", score_wild_type="1.0", apply_correction=True)) + + def test_recognition_potential(self): + props = defaultdict(lambda: "1.0") + props['Mutation_in_anchor_netmhcpan'] = '0' + props['Mutation_in_anchor_netmhcpan_9mer'] = '0' + self.assertEqual('1.0', self.neoantigen_fitness_calculator.calculate_recognition_potential( + amplitude="1.0", pathogen_similarity="1.0", mutation_in_anchor="0")) diff --git a/input/tests/integration_tests/test_netmhcpan.py b/input/tests/integration_tests/test_netmhcpan.py index dfbc23be..da4d5c9b 100755 --- a/input/tests/integration_tests/test_netmhcpan.py +++ b/input/tests/integration_tests/test_netmhcpan.py @@ -1,96 +1,96 @@ -import os -from unittest import TestCase - -import input.tests.integration_tests.integration_test_tools as integration_test_tools -from input import MHC_I, MHC_II -from input.helpers import intermediate_files -from input.helpers.runner import Runner -from input.netmhcpan4.netmhcIIpan_prediction import NetMhcIIPanPredictor -from input.netmhcpan4.netmhcpan_prediction import NetMhcPanPredictor -from input.tests import TEST_HLAI_ALLELES, TEST_HLAII_ALLELES - - -class TestNetMhcPanPredictor(TestCase): - - def setUp(self): - self.references, self.configuration = integration_test_tools.load_references() - self.runner = Runner() - - def test_netmhcpan_epitope_iedb(self): - netmhcpan_predictor = NetMhcPanPredictor(runner=self.runner, configuration=self.configuration) - # this is an epitope from IEDB of length 9 - mutated = 'NLVPMVATV' - tmp_prediction = intermediate_files.create_temp_file(prefix="netmhcpanpred_", suffix=".csv") - tmp_fasta = intermediate_files.create_temp_fasta(sequences=[mutated], prefix="tmp_") - netmhcpan_predictor.mhc_prediction( - tmpfasta=tmp_fasta, tmppred=tmp_prediction, hla_alleles=TEST_HLAI_ALLELES, - set_available_mhc=self.references.load_available_hla_alleles(mhc=MHC_I)) - self.assertTrue(os.path.exists(tmp_prediction)) - self.assertEqual(166, len(open(tmp_prediction).readlines())) - header, rows = netmhcpan_predictor.filter_binding_predictions(4, tmp_prediction) - self.assertEqual(14, len(header)) # output has 14 columns - for r in rows: - self.assertEqual(14, len(r)) # each row has 14 columns - self.assertEqual(165, len(rows)) - - def test_netmhcpan_too_small_epitope(self): - netmhcpan_predictor = NetMhcPanPredictor(runner=self.runner, configuration=self.configuration) - mutated = 'NLVP' - tmp_prediction = intermediate_files.create_temp_file(prefix="netmhcpanpred_", suffix=".csv") - tmp_fasta = intermediate_files.create_temp_fasta(sequences=[mutated], prefix="tmp_") - netmhcpan_predictor.mhc_prediction( - tmpfasta=tmp_fasta, tmppred=tmp_prediction, hla_alleles=TEST_HLAI_ALLELES, - set_available_mhc=self.references.load_available_hla_alleles(mhc=MHC_I)) - self.assertTrue(os.path.exists(tmp_prediction)) - # TODO: this is writing ot the output file "No;peptides;derived;from;protein;ID;seq1;len;4.;Skipped" - self.assertEqual(55, len(open(tmp_prediction).readlines())) - - # TODO: it crashes here as it fails to parse the header. Fix and remove the try-except - try: - header, rows = netmhcpan_predictor.filter_binding_predictions(2, tmp_prediction) - self.assertEqual(14, len(header)) # output has 14 columns - for r in rows: - self.assertEqual(14, len(r)) # each row has 14 columns - self.assertEqual(0, len(rows)) - except: - pass - - def test_netmhc2pan_epitope_iedb(self): - netmhc2pan_predictor = NetMhcIIPanPredictor(runner=self.runner, configuration=self.configuration) - # this is an epitope from IEDB of length 15 - mutated = 'ENPVVHFFKNIVTPR' - tmp_prediction = intermediate_files.create_temp_file(prefix="netmhcpanpred_", suffix=".csv") - tmp_fasta = intermediate_files.create_temp_fasta(sequences=[mutated], prefix="tmp_") - netmhc2pan_predictor.mhcII_prediction( - tmpfasta=tmp_fasta, tmppred=tmp_prediction, hla_alleles=TEST_HLAII_ALLELES, - set_available_mhc=self.references.load_available_hla_alleles(mhc=MHC_II)) - self.assertTrue(os.path.exists(tmp_prediction)) - self.assertEqual(20, len(open(tmp_prediction).readlines())) - - header, rows = netmhc2pan_predictor.filter_binding_predictions(4, tmp_prediction) - self.assertEqual(12, len(header)) # output has 14 columns - for r in rows: - self.assertTrue(len(r) <= 12 or len(r) >= 10) # each row has 10 or 12 columns - self.assertEqual(19, len(rows)) - - def test_netmhc2pan_too_small_epitope(self): - netmhc2pan_predictor = NetMhcIIPanPredictor(runner=self.runner, configuration=self.configuration) - # this is an epitope from IEDB of length 15 - mutated = 'ENPVVH' - tmp_prediction = intermediate_files.create_temp_file(prefix="netmhcpanpred_", suffix=".csv") - tmp_fasta = intermediate_files.create_temp_fasta(sequences=[mutated], prefix="tmp_") - netmhc2pan_predictor.mhcII_prediction( - tmpfasta=tmp_fasta, tmppred=tmp_prediction, hla_alleles=TEST_HLAII_ALLELES, - set_available_mhc=self.references.load_available_hla_alleles(mhc=MHC_II)) - self.assertTrue(os.path.exists(tmp_prediction)) - self.assertEqual(1, len(open(tmp_prediction).readlines())) - - # TODO: it crashes here as it fails to parse the header. Fix and remove the try-except - try: - header, rows = netmhc2pan_predictor.filter_binding_predictions(4, tmp_prediction) - self.assertEqual(12, len(header)) # output has 14 columns - for r in rows: - self.assertTrue(len(r) <= 12 or len(r) >= 10) # each row has 10 or 12 columns - self.assertEqual(0, len(rows)) - except: +import os +from unittest import TestCase + +import input.tests.integration_tests.integration_test_tools as integration_test_tools +from input import MHC_I, MHC_II +from input.helpers import intermediate_files +from input.helpers.runner import Runner +from input.netmhcpan4.netmhcIIpan_prediction import NetMhcIIPanPredictor +from input.netmhcpan4.netmhcpan_prediction import NetMhcPanPredictor +from input.tests import TEST_HLAI_ALLELES, TEST_HLAII_ALLELES + + +class TestNetMhcPanPredictor(TestCase): + + def setUp(self): + self.references, self.configuration = integration_test_tools.load_references() + self.runner = Runner() + + def test_netmhcpan_epitope_iedb(self): + netmhcpan_predictor = NetMhcPanPredictor(runner=self.runner, configuration=self.configuration) + # this is an epitope from IEDB of length 9 + mutated = 'NLVPMVATV' + tmp_prediction = intermediate_files.create_temp_file(prefix="netmhcpanpred_", suffix=".csv") + tmp_fasta = intermediate_files.create_temp_fasta(sequences=[mutated], prefix="tmp_") + netmhcpan_predictor.mhc_prediction( + tmpfasta=tmp_fasta, tmppred=tmp_prediction, hla_alleles=TEST_HLAI_ALLELES, + set_available_mhc=self.references.load_available_hla_alleles(mhc=MHC_I)) + self.assertTrue(os.path.exists(tmp_prediction)) + self.assertEqual(166, len(open(tmp_prediction).readlines())) + header, rows = netmhcpan_predictor.filter_binding_predictions(4, tmp_prediction) + self.assertEqual(14, len(header)) # output has 14 columns + for r in rows: + self.assertEqual(14, len(r)) # each row has 14 columns + self.assertEqual(165, len(rows)) + + def test_netmhcpan_too_small_epitope(self): + netmhcpan_predictor = NetMhcPanPredictor(runner=self.runner, configuration=self.configuration) + mutated = 'NLVP' + tmp_prediction = intermediate_files.create_temp_file(prefix="netmhcpanpred_", suffix=".csv") + tmp_fasta = intermediate_files.create_temp_fasta(sequences=[mutated], prefix="tmp_") + netmhcpan_predictor.mhc_prediction( + tmpfasta=tmp_fasta, tmppred=tmp_prediction, hla_alleles=TEST_HLAI_ALLELES, + set_available_mhc=self.references.load_available_hla_alleles(mhc=MHC_I)) + self.assertTrue(os.path.exists(tmp_prediction)) + # TODO: this is writing ot the output file "No;peptides;derived;from;protein;ID;seq1;len;4.;Skipped" + self.assertEqual(55, len(open(tmp_prediction).readlines())) + + # TODO: it crashes here as it fails to parse the header. Fix and remove the try-except + try: + header, rows = netmhcpan_predictor.filter_binding_predictions(2, tmp_prediction) + self.assertEqual(14, len(header)) # output has 14 columns + for r in rows: + self.assertEqual(14, len(r)) # each row has 14 columns + self.assertEqual(0, len(rows)) + except: + pass + + def test_netmhc2pan_epitope_iedb(self): + netmhc2pan_predictor = NetMhcIIPanPredictor(runner=self.runner, configuration=self.configuration) + # this is an epitope from IEDB of length 15 + mutated = 'ENPVVHFFKNIVTPR' + tmp_prediction = intermediate_files.create_temp_file(prefix="netmhcpanpred_", suffix=".csv") + tmp_fasta = intermediate_files.create_temp_fasta(sequences=[mutated], prefix="tmp_") + netmhc2pan_predictor.mhcII_prediction( + tmpfasta=tmp_fasta, tmppred=tmp_prediction, hla_alleles=TEST_HLAII_ALLELES, + set_available_mhc=self.references.load_available_hla_alleles(mhc=MHC_II)) + self.assertTrue(os.path.exists(tmp_prediction)) + self.assertEqual(20, len(open(tmp_prediction).readlines())) + + header, rows = netmhc2pan_predictor.filter_binding_predictions(4, tmp_prediction) + self.assertEqual(12, len(header)) # output has 14 columns + for r in rows: + self.assertTrue(len(r) <= 12 or len(r) >= 10) # each row has 10 or 12 columns + self.assertEqual(19, len(rows)) + + def test_netmhc2pan_too_small_epitope(self): + netmhc2pan_predictor = NetMhcIIPanPredictor(runner=self.runner, configuration=self.configuration) + # this is an epitope from IEDB of length 15 + mutated = 'ENPVVH' + tmp_prediction = intermediate_files.create_temp_file(prefix="netmhcpanpred_", suffix=".csv") + tmp_fasta = intermediate_files.create_temp_fasta(sequences=[mutated], prefix="tmp_") + netmhc2pan_predictor.mhcII_prediction( + tmpfasta=tmp_fasta, tmppred=tmp_prediction, hla_alleles=TEST_HLAII_ALLELES, + set_available_mhc=self.references.load_available_hla_alleles(mhc=MHC_II)) + self.assertTrue(os.path.exists(tmp_prediction)) + self.assertEqual(1, len(open(tmp_prediction).readlines())) + + # TODO: it crashes here as it fails to parse the header. Fix and remove the try-except + try: + header, rows = netmhc2pan_predictor.filter_binding_predictions(4, tmp_prediction) + self.assertEqual(12, len(header)) # output has 14 columns + for r in rows: + self.assertTrue(len(r) <= 12 or len(r) >= 10) # each row has 10 or 12 columns + self.assertEqual(0, len(rows)) + except: pass \ No newline at end of file diff --git a/input/tests/integration_tests/test_tcell_predictor.py b/input/tests/integration_tests/test_tcell_predictor.py index 065cd18b..51c11096 100755 --- a/input/tests/integration_tests/test_tcell_predictor.py +++ b/input/tests/integration_tests/test_tcell_predictor.py @@ -1,52 +1,52 @@ -from collections import defaultdict -from unittest import TestCase - -import input.tests.integration_tests.integration_test_tools as integration_test_tools -from input.Tcell_predictor.tcellpredictor_wrapper import TcellPrediction - - -class TestTCellPredictor(TestCase): - - def setUp(self): - self.references, self.configuration = integration_test_tools.load_references() - self.fastafile = integration_test_tools.create_temp_aminoacid_fasta_file() - - def test_tcell_predictor(self): - tcell_predictor = TcellPrediction(references=self.references) - result = tcell_predictor.calculate_tcell_predictor_score(gene="BLAH", substitution='blaaaah', epitope="BLAHBLAH", score=5, threshold=10) - self.assertEqual("NA", result) - - -""" -# if full icam output table is passed to script - ''' - f = sys.argv[1] - dat = data_import.import_dat_icam(f, indel = False) - #print dat - #print full_dataset(dat) - l = full_dataset(dat, all = True) - write_ouptut_to_file(l) - ''' - - # test for input implementation - from input import epitope - - file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/MHC_prediction_netmhcpan4/testdat_ott.txt" - dat = data_import.import_dat_icam(file, False) - if "+-13_AA_(SNV)_/_-15_AA_to_STOP_(INDEL)" in dat[0]: - dat = data_import.change_col_names(dat) - - path_to_Tcell_predictor = my_path - - for ii,i in enumerate(dat[1]): - if ii < 10: - print ii - dict_epi = epitope.Epitope() - dict_epi.init_properties(dat[0], dat[1][ii]) - #print dict_epi.properties - tcellpred = Tcellprediction() - - tcellpred.main(dict_epi.properties) - print tcellpred.TcellPrdictionScore - print tcellpred.TcellPrdictionScore_9merPred -""" +from collections import defaultdict +from unittest import TestCase + +import input.tests.integration_tests.integration_test_tools as integration_test_tools +from input.Tcell_predictor.tcellpredictor_wrapper import TcellPrediction + + +class TestTCellPredictor(TestCase): + + def setUp(self): + self.references, self.configuration = integration_test_tools.load_references() + self.fastafile = integration_test_tools.create_temp_aminoacid_fasta_file() + + def test_tcell_predictor(self): + tcell_predictor = TcellPrediction(references=self.references) + result = tcell_predictor.calculate_tcell_predictor_score(gene="BLAH", substitution='blaaaah', epitope="BLAHBLAH", score=5, threshold=10) + self.assertEqual("NA", result) + + +""" +# if full icam output table is passed to script + ''' + f = sys.argv[1] + dat = data_import.import_dat_icam(f, indel = False) + #print dat + #print full_dataset(dat) + l = full_dataset(dat, all = True) + write_ouptut_to_file(l) + ''' + + # test for input implementation + from input import epitope + + file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/MHC_prediction_netmhcpan4/testdat_ott.txt" + dat = data_import.import_dat_icam(file, False) + if "+-13_AA_(SNV)_/_-15_AA_to_STOP_(INDEL)" in dat[0]: + dat = data_import.change_col_names(dat) + + path_to_Tcell_predictor = my_path + + for ii,i in enumerate(dat[1]): + if ii < 10: + print ii + dict_epi = epitope.Epitope() + dict_epi.init_properties(dat[0], dat[1][ii]) + #print dict_epi.properties + tcellpred = Tcellprediction() + + tcellpred.main(dict_epi.properties) + print tcellpred.TcellPrdictionScore + print tcellpred.TcellPrdictionScore_9merPred +""" diff --git a/input/tests/unit_tests/fake_classes.py b/input/tests/unit_tests/fake_classes.py index 039d8065..6d2532fd 100755 --- a/input/tests/unit_tests/fake_classes.py +++ b/input/tests/unit_tests/fake_classes.py @@ -1,15 +1,15 @@ -import os - -import input -from input.references import ReferenceFolder - - -class FakeReferenceFolder(ReferenceFolder): - - @staticmethod - def _check_reference_genome_folder(): - return os.environ.get(input.REFERENCE_FOLDER_ENV, "") - - @staticmethod - def _check_resources(resources): - pass +import os + +import input +from input.references import ReferenceFolder + + +class FakeReferenceFolder(ReferenceFolder): + + @staticmethod + def _check_reference_genome_folder(): + return os.environ.get(input.REFERENCE_FOLDER_ENV, "") + + @staticmethod + def _check_resources(resources): + pass diff --git a/input/tests/unit_tests/test_dependencies_configuration.py b/input/tests/unit_tests/test_dependencies_configuration.py index b78a7779..5257906a 100755 --- a/input/tests/unit_tests/test_dependencies_configuration.py +++ b/input/tests/unit_tests/test_dependencies_configuration.py @@ -1,65 +1,65 @@ -import os -import unittest -from unittest import TestCase - -import input -import input.tests.unit_tests.tools as test_tools -from input.exceptions import INPuTConfigurationException -from input.references import DependenciesConfiguration - - -class TestDependenciesConfiguration(TestCase): - - def setUp(self): - self.variables = { - input.INPUT_BLASTP_ENV: '/path/to/blastp', - input.INPUT_NETMHC2PAN_ENV: '/path/to/netmhc2pan', - input.INPUT_NETMHCPAN_ENV: '/path/to/netmhcpan', - input.INPUT_RSCRIPT_ENV: '/path/to/rscript', - input.INPUT_MIXMHCPRED_ENV: '/path/to/mixmhcpred', - input.INPUT_MIXMHC2PRED_ENV: '/path/to/mixmhc2pred' - } - self.non_existing = '/path/to/nothing' - test_tools._mock_file_existence( - existing_files=self.variables.values(), - unexisting_files=[self.non_existing] - ) - - def _load_env_variables(self): - for k, v in self.variables.items(): - os.environ[k] = v - - def test_not_provided_variable(self): - self._load_env_variables() - for v in self.variables.keys(): - del os.environ[v] - with self.assertRaises(INPuTConfigurationException): - DependenciesConfiguration() - - def test_empty_string_variable(self): - self._load_env_variables() - for v in self.variables.keys(): - os.environ[v] = "" - with self.assertRaises(INPuTConfigurationException): - DependenciesConfiguration() - - def test_non_existing_variable(self): - self._load_env_variables() - for v in self.variables.keys(): - os.environ[v] = self.non_existing - with self.assertRaises(INPuTConfigurationException): - DependenciesConfiguration() - - def test_all_resources_exist(self): - self._load_env_variables() - config = DependenciesConfiguration() - self.assertTrue(config.blastp == self.variables[input.INPUT_BLASTP_ENV]) - self.assertTrue(config.mix_mhc2_pred == self.variables[input.INPUT_MIXMHC2PRED_ENV]) - self.assertTrue(config.mix_mhc_pred == self.variables[input.INPUT_MIXMHCPRED_ENV]) - self.assertTrue(config.rscript == self.variables[input.INPUT_RSCRIPT_ENV]) - self.assertTrue(config.net_mhc_pan == self.variables[input.INPUT_NETMHCPAN_ENV]) - self.assertTrue(config.net_mhc2_pan == self.variables[input.INPUT_NETMHC2PAN_ENV]) - - -if __name__ == "__main__": - unittest.main() +import os +import unittest +from unittest import TestCase + +import input +import input.tests.unit_tests.tools as test_tools +from input.exceptions import INPuTConfigurationException +from input.references import DependenciesConfiguration + + +class TestDependenciesConfiguration(TestCase): + + def setUp(self): + self.variables = { + input.INPUT_BLASTP_ENV: '/path/to/blastp', + input.INPUT_NETMHC2PAN_ENV: '/path/to/netmhc2pan', + input.INPUT_NETMHCPAN_ENV: '/path/to/netmhcpan', + input.INPUT_RSCRIPT_ENV: '/path/to/rscript', + input.INPUT_MIXMHCPRED_ENV: '/path/to/mixmhcpred', + input.INPUT_MIXMHC2PRED_ENV: '/path/to/mixmhc2pred' + } + self.non_existing = '/path/to/nothing' + test_tools._mock_file_existence( + existing_files=self.variables.values(), + unexisting_files=[self.non_existing] + ) + + def _load_env_variables(self): + for k, v in self.variables.items(): + os.environ[k] = v + + def test_not_provided_variable(self): + self._load_env_variables() + for v in self.variables.keys(): + del os.environ[v] + with self.assertRaises(INPuTConfigurationException): + DependenciesConfiguration() + + def test_empty_string_variable(self): + self._load_env_variables() + for v in self.variables.keys(): + os.environ[v] = "" + with self.assertRaises(INPuTConfigurationException): + DependenciesConfiguration() + + def test_non_existing_variable(self): + self._load_env_variables() + for v in self.variables.keys(): + os.environ[v] = self.non_existing + with self.assertRaises(INPuTConfigurationException): + DependenciesConfiguration() + + def test_all_resources_exist(self): + self._load_env_variables() + config = DependenciesConfiguration() + self.assertTrue(config.blastp == self.variables[input.INPUT_BLASTP_ENV]) + self.assertTrue(config.mix_mhc2_pred == self.variables[input.INPUT_MIXMHC2PRED_ENV]) + self.assertTrue(config.mix_mhc_pred == self.variables[input.INPUT_MIXMHCPRED_ENV]) + self.assertTrue(config.rscript == self.variables[input.INPUT_RSCRIPT_ENV]) + self.assertTrue(config.net_mhc_pan == self.variables[input.INPUT_NETMHCPAN_ENV]) + self.assertTrue(config.net_mhc2_pan == self.variables[input.INPUT_NETMHC2PAN_ENV]) + + +if __name__ == "__main__": + unittest.main() diff --git a/input/tests/unit_tests/test_predict_all_epitopes.py b/input/tests/unit_tests/test_predict_all_epitopes.py index f04ad770..3cdde1f2 100755 --- a/input/tests/unit_tests/test_predict_all_epitopes.py +++ b/input/tests/unit_tests/test_predict_all_epitopes.py @@ -1,24 +1,24 @@ -import os -import unittest -from unittest import TestCase - -import input -from input.exceptions import INPuTConfigurationException -from input.predict_all_epitopes import BunchEpitopes - - -class TestPredictAllEpitopes(TestCase): - - def test_reference_environment_variable_is_required(self): - # del os.environ[input.REFERENCE_FOLDER_ENV] - with self.assertRaises(INPuTConfigurationException): - BunchEpitopes() - - def test_empty_reference_folder_fails(self): - os.environ[input.REFERENCE_FOLDER_ENV] = 'dummy' - with self.assertRaises(INPuTConfigurationException): - BunchEpitopes() - - -if __name__ == "__main__": - unittest.main() +import os +import unittest +from unittest import TestCase + +import input +from input.exceptions import INPuTConfigurationException +from input.predict_all_epitopes import BunchEpitopes + + +class TestPredictAllEpitopes(TestCase): + + def test_reference_environment_variable_is_required(self): + # del os.environ[input.REFERENCE_FOLDER_ENV] + with self.assertRaises(INPuTConfigurationException): + BunchEpitopes() + + def test_empty_reference_folder_fails(self): + os.environ[input.REFERENCE_FOLDER_ENV] = 'dummy' + with self.assertRaises(INPuTConfigurationException): + BunchEpitopes() + + +if __name__ == "__main__": + unittest.main() diff --git a/input/tests/unit_tests/test_reference_folder.py b/input/tests/unit_tests/test_reference_folder.py index c6fd101a..c0c417c9 100755 --- a/input/tests/unit_tests/test_reference_folder.py +++ b/input/tests/unit_tests/test_reference_folder.py @@ -1,47 +1,47 @@ -import os -import unittest -from unittest import TestCase - -import input -import input.tests.unit_tests.tools as test_tools -from input.exceptions import INPuTConfigurationException -from input.references import ReferenceFolder -from input.tests.unit_tests.fake_classes import FakeReferenceFolder - - -class TestReferenceFolder(TestCase): - - def setUp(self): - os.environ[input.REFERENCE_FOLDER_ENV] = "." - self.fake_reference_folder = FakeReferenceFolder() - - def test_not_provided_reference(self): - del os.environ[input.REFERENCE_FOLDER_ENV] - with self.assertRaises(INPuTConfigurationException): - ReferenceFolder() - - def test_empty_string_reference(self): - os.environ[input.REFERENCE_FOLDER_ENV] = "" - with self.assertRaises(INPuTConfigurationException): - ReferenceFolder() - - def test_non_existing_reference(self): - os.environ[input.REFERENCE_FOLDER_ENV] = "/non_existing_folder" - with self.assertRaises(INPuTConfigurationException): - ReferenceFolder() - - def test_all_resources_exist(self): - test_tools._mock_file_existence(existing_files=self.fake_reference_folder.resources) - ReferenceFolder() - - def test_one_resource_do_not_exist(self): - test_tools._mock_file_existence( - existing_files=self.fake_reference_folder.resources[1:len(self.fake_reference_folder.resources)], - unexisting_files=[self.fake_reference_folder.resources[0]] - ) - with self.assertRaises(INPuTConfigurationException): - ReferenceFolder() - - -if __name__ == "__main__": - unittest.main() +import os +import unittest +from unittest import TestCase + +import input +import input.tests.unit_tests.tools as test_tools +from input.exceptions import INPuTConfigurationException +from input.references import ReferenceFolder +from input.tests.unit_tests.fake_classes import FakeReferenceFolder + + +class TestReferenceFolder(TestCase): + + def setUp(self): + os.environ[input.REFERENCE_FOLDER_ENV] = "." + self.fake_reference_folder = FakeReferenceFolder() + + def test_not_provided_reference(self): + del os.environ[input.REFERENCE_FOLDER_ENV] + with self.assertRaises(INPuTConfigurationException): + ReferenceFolder() + + def test_empty_string_reference(self): + os.environ[input.REFERENCE_FOLDER_ENV] = "" + with self.assertRaises(INPuTConfigurationException): + ReferenceFolder() + + def test_non_existing_reference(self): + os.environ[input.REFERENCE_FOLDER_ENV] = "/non_existing_folder" + with self.assertRaises(INPuTConfigurationException): + ReferenceFolder() + + def test_all_resources_exist(self): + test_tools._mock_file_existence(existing_files=self.fake_reference_folder.resources) + ReferenceFolder() + + def test_one_resource_do_not_exist(self): + test_tools._mock_file_existence( + existing_files=self.fake_reference_folder.resources[1:len(self.fake_reference_folder.resources)], + unexisting_files=[self.fake_reference_folder.resources[0]] + ) + with self.assertRaises(INPuTConfigurationException): + ReferenceFolder() + + +if __name__ == "__main__": + unittest.main() diff --git a/input/tests/unit_tests/test_runner.py b/input/tests/unit_tests/test_runner.py index 7d41ccf2..0472b644 100755 --- a/input/tests/unit_tests/test_runner.py +++ b/input/tests/unit_tests/test_runner.py @@ -1,23 +1,23 @@ -import unittest -from unittest import TestCase - -from input.helpers.runner import Runner - - -class TestRunner(TestCase): - - def setUp(self): - self.runner = Runner() - - def test_runner(self): - output, errors = self.runner.run_command(cmd=['python', '-V']) - self.assertTrue('Python 3.7' in output) - self.assertTrue(len(errors) == 0) - - def test_runner_failure(self): - with self.assertRaises(Exception): - self.runner.run_command(cmd=['nocommandwiththisname']) - - -if __name__ == "__main__": - unittest.main() +import unittest +from unittest import TestCase + +from input.helpers.runner import Runner + + +class TestRunner(TestCase): + + def setUp(self): + self.runner = Runner() + + def test_runner(self): + output, errors = self.runner.run_command(cmd=['python', '-V']) + self.assertTrue('Python 3.7' in output) + self.assertTrue(len(errors) == 0) + + def test_runner_failure(self): + with self.assertRaises(Exception): + self.runner.run_command(cmd=['nocommandwiththisname']) + + +if __name__ == "__main__": + unittest.main() diff --git a/input/tests/unit_tests/test_self_similarity.py b/input/tests/unit_tests/test_self_similarity.py index 021829f5..43bff547 100755 --- a/input/tests/unit_tests/test_self_similarity.py +++ b/input/tests/unit_tests/test_self_similarity.py @@ -1,38 +1,38 @@ -from unittest import TestCase - -import input.self_similarity.self_similarity as self_similarity -from input import MHC_I, MHC_II - - -class TestSelfSimilarity(TestCase): - - def test_get_self_similarity(self): - result = self_similarity.get_self_similarity(wild_type="DDD", mutation="DDD") - self.assertEqual('1.0', result) - - def test_is_improved_binder(self): - result = self_similarity.is_improved_binder( - score_mutation='1.0', score_wild_type='1.3') - self.assertEqual('1', result) - - def test_position_mutation(self): - position = self_similarity.position_of_mutation_epitope(wild_type="AAAAAA", mutation="AAANAA") - self.assertEqual(position, "4") - position = self_similarity.position_of_mutation_epitope(wild_type="AAAAAA", mutation="AAAAAA") - self.assertEqual(position, "-1") - position = self_similarity.position_of_mutation_epitope(wild_type="AAAAAA", mutation="AANNNN") - self.assertEqual(position, "6") - - def test_compute_self_similarity_calculator(self): - - s = self_similarity.SelfSimilarityCalculator() - self.assertEqual(s.compute_k_hat_3("AAAAA", "AAAAA"), 1.0) - for i in range(5): - self.assertTrue(s.compute_k_hat_3("AAAAA", "WWWWW" * (i + 1)) < 1.0) - for i in list(s.k1.keys()): - if i == "A": - self.assertTrue(s.compute_k_hat_3("AAAAA", "AA" + i + "AA") == 1.0) - else: - self.assertTrue(s.compute_k_hat_3("AAAAA", "AA" + i + "AA") < 1.0) - - +from unittest import TestCase + +import input.self_similarity.self_similarity as self_similarity +from input import MHC_I, MHC_II + + +class TestSelfSimilarity(TestCase): + + def test_get_self_similarity(self): + result = self_similarity.get_self_similarity(wild_type="DDD", mutation="DDD") + self.assertEqual('1.0', result) + + def test_is_improved_binder(self): + result = self_similarity.is_improved_binder( + score_mutation='1.0', score_wild_type='1.3') + self.assertEqual('1', result) + + def test_position_mutation(self): + position = self_similarity.position_of_mutation_epitope(wild_type="AAAAAA", mutation="AAANAA") + self.assertEqual(position, "4") + position = self_similarity.position_of_mutation_epitope(wild_type="AAAAAA", mutation="AAAAAA") + self.assertEqual(position, "-1") + position = self_similarity.position_of_mutation_epitope(wild_type="AAAAAA", mutation="AANNNN") + self.assertEqual(position, "6") + + def test_compute_self_similarity_calculator(self): + + s = self_similarity.SelfSimilarityCalculator() + self.assertEqual(s.compute_k_hat_3("AAAAA", "AAAAA"), 1.0) + for i in range(5): + self.assertTrue(s.compute_k_hat_3("AAAAA", "WWWWW" * (i + 1)) < 1.0) + for i in list(s.k1.keys()): + if i == "A": + self.assertTrue(s.compute_k_hat_3("AAAAA", "AA" + i + "AA") == 1.0) + else: + self.assertTrue(s.compute_k_hat_3("AAAAA", "AA" + i + "AA") < 1.0) + + diff --git a/model/neoepitope.avdl b/model/neoepitope.avdl index c6e3f784..1efc327f 100755 --- a/model/neoepitope.avdl +++ b/model/neoepitope.avdl @@ -1,83 +1,83 @@ -/** - * An example protocol in Avro IDL for defining neoepitopes - */ -@namespace("tron.neoepitope") -protocol Neoepitope { - - record Gene { - /** - The genome assembly to which the gene definition refers to (e.g.: GRCh37, GRCh38) - */ - string assembly = "GRCh37"; - /** - The gene symbol or gene identifier, optional as the transcript unequivocally identifies a gene - */ - union {string, null} gene; - /** - The transcript identifier to which this neoepitope definition refers (e.g.: Ensembl transcript id) - */ - string transcriptIdentifier; - } - - record Mutation { - /** - The aminoacid position within the protein. 1-based, starting in the N-terminus - */ - int position; - /** - IUPAC code for the wild type aminoacid in this position - */ - string wildTypeAminoacid; - /** - IUPAC code for the mutated aminoacid in this position - */ - string mutatedAminoacid; - - /** - The left flanking region of variable size in IUPAC codes - */ - string leftFlankingRegion; - /** - The size of the left flanking region - */ - union {string, null} sizeLeftFlankingRegion; - /** - The right flanking region of variable size in IUPAC codes - */ - string rightFlankingRegion; - /** - The size of the right flanking region - */ - union {string, null} sizeRightlankingRegion; - } - - /** - A neoepitope minimal definition - */ - record Neoepitope { - - /** - The gene where the neoepitope corresponds - */ - Gene gene; - - /** - The mutation - */ - Mutation mutation; - - // OPTIONAL - /** - Expression value of the transcript (any more definition on type of expression? ie: digital from RNAseq, from microarrays, etc.) - */ - union {float, null} expressionValue; - /** - Clonality estimation (any more definition on the method?) - */ - union {float, null} clonalityEstimation; - /** - Variant allele frequency in the range [0.0, 1.0] - */ - union {float, null} variantAlleleFrequency; - } -} +/** + * An example protocol in Avro IDL for defining neoepitopes + */ +@namespace("tron.neoepitope") +protocol Neoepitope { + + record Gene { + /** + The genome assembly to which the gene definition refers to (e.g.: GRCh37, GRCh38) + */ + string assembly = "GRCh37"; + /** + The gene symbol or gene identifier, optional as the transcript unequivocally identifies a gene + */ + union {string, null} gene; + /** + The transcript identifier to which this neoepitope definition refers (e.g.: Ensembl transcript id) + */ + string transcriptIdentifier; + } + + record Mutation { + /** + The aminoacid position within the protein. 1-based, starting in the N-terminus + */ + int position; + /** + IUPAC code for the wild type aminoacid in this position + */ + string wildTypeAminoacid; + /** + IUPAC code for the mutated aminoacid in this position + */ + string mutatedAminoacid; + + /** + The left flanking region of variable size in IUPAC codes + */ + string leftFlankingRegion; + /** + The size of the left flanking region + */ + union {string, null} sizeLeftFlankingRegion; + /** + The right flanking region of variable size in IUPAC codes + */ + string rightFlankingRegion; + /** + The size of the right flanking region + */ + union {string, null} sizeRightlankingRegion; + } + + /** + A neoepitope minimal definition + */ + record Neoepitope { + + /** + The gene where the neoepitope corresponds + */ + Gene gene; + + /** + The mutation + */ + Mutation mutation; + + // OPTIONAL + /** + Expression value of the transcript (any more definition on type of expression? ie: digital from RNAseq, from microarrays, etc.) + */ + union {float, null} expressionValue; + /** + Clonality estimation (any more definition on the method?) + */ + union {float, null} clonalityEstimation; + /** + Variant allele frequency in the range [0.0, 1.0] + */ + union {float, null} variantAlleleFrequency; + } +} diff --git a/setup.py b/setup.py index 22fe636f..a1c7e975 100755 --- a/setup.py +++ b/setup.py @@ -1,50 +1,50 @@ -from setuptools import find_packages, setup, Command -import distutils.command.build -from distutils.dist import Distribution -# from wheel.bdist_wheel import bdist_wheel as _bdist_wheel -# import xmlrunner -import unittest -import sys -import os -# import dotenv -import logging -import glob -from datetime import datetime -import input - -# Build the Python package -setup( - name='input', - version=input.VERSION, - packages=find_packages(), - include_package_data=True, - entry_points={ - 'console_scripts': [ - 'input=input.command_line:input_cli' - ], - }, - author='Franziska Lang', - description='TODO', - requires=[], - # NOTE: always specify versions to ensure build reproducibility - # NOTE2: sklearn==0.19.0 is a hidden dependency as it is required by Classifier.pickle - - install_requires=[ - 'biopython==1.76', - 'mock', - 'pandas==0.24.2', - 'numpy==1.16.2', - 'scipy==1.4.1', - 'pickle-mixin', - 'scikit-learn==0.20.3', - 'logzero==1.5.0' - ], - setup_requires=[], - classifiers=[ - 'Development Status :: 3 - Alpha', # Chose either "3 - Alpha", "4 - Beta" or "5 - Production/Stable" as the current state of your package - 'Intended Audience :: Healthcare Industry', - 'Intended Audience :: Science/Research', - 'Topic :: Scientific/Engineering :: Bio-Informatics', - 'Programming Language :: Python :: 3' - ] -) +from setuptools import find_packages, setup, Command +import distutils.command.build +from distutils.dist import Distribution +# from wheel.bdist_wheel import bdist_wheel as _bdist_wheel +# import xmlrunner +import unittest +import sys +import os +# import dotenv +import logging +import glob +from datetime import datetime +import input + +# Build the Python package +setup( + name='input', + version=input.VERSION, + packages=find_packages(), + include_package_data=True, + entry_points={ + 'console_scripts': [ + 'input=input.command_line:input_cli' + ], + }, + author='Franziska Lang', + description='TODO', + requires=[], + # NOTE: always specify versions to ensure build reproducibility + # NOTE2: sklearn==0.19.0 is a hidden dependency as it is required by Classifier.pickle + + install_requires=[ + 'biopython==1.76', + 'mock', + 'pandas==0.24.2', + 'numpy==1.16.2', + 'scipy==1.4.1', + 'pickle-mixin', + 'scikit-learn==0.20.3', + 'logzero==1.5.0' + ], + setup_requires=[], + classifiers=[ + 'Development Status :: 3 - Alpha', # Chose either "3 - Alpha", "4 - Beta" or "5 - Production/Stable" as the current state of your package + 'Intended Audience :: Healthcare Industry', + 'Intended Audience :: Science/Research', + 'Topic :: Scientific/Engineering :: Bio-Informatics', + 'Programming Language :: Python :: 3' + ] +) From 9694d43bf99bcd217417b1b6d9f87ec4b31994b9 Mon Sep 17 00:00:00 2001 From: Pablo Riesgo Ferreiro Date: Wed, 17 Jun 2020 15:00:14 +0200 Subject: [PATCH 052/105] added missing dependency --- setup.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/setup.py b/setup.py index a1c7e975..f6e257e7 100755 --- a/setup.py +++ b/setup.py @@ -23,12 +23,11 @@ 'input=input.command_line:input_cli' ], }, - author='Franziska Lang', + author=['Franziska Lang', 'Pablo Riesgo Ferreiro'], description='TODO', requires=[], # NOTE: always specify versions to ensure build reproducibility # NOTE2: sklearn==0.19.0 is a hidden dependency as it is required by Classifier.pickle - install_requires=[ 'biopython==1.76', 'mock', @@ -37,7 +36,8 @@ 'scipy==1.4.1', 'pickle-mixin', 'scikit-learn==0.20.3', - 'logzero==1.5.0' + 'logzero==1.5.0', + 'python-dotenv==0.12.0' ], setup_requires=[], classifiers=[ From 690ca68edec8091fc173a649888e0d78903565a5 Mon Sep 17 00:00:00 2001 From: Pablo Riesgo Ferreiro Date: Wed, 17 Jun 2020 15:02:32 +0200 Subject: [PATCH 053/105] added running single integration test to README --- README.md | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/README.md b/README.md index 14b5364b..bbcc2e72 100755 --- a/README.md +++ b/README.md @@ -157,6 +157,11 @@ python -m unittest discover input.tests.integration_tests The integration tests run over some real datasets and they take some time to run. +The integration test that runs the whle program over a relevant dataset can be run as follows: +``` +python -m unittest input.tests.integration_tests.test_input +``` + ### Run unit tests The unit tests do not have any dependency and they finish in seconds. From ef0a97cb5dd7e0798cb026f269053aa04f52bee9 Mon Sep 17 00:00:00 2001 From: Pablo Riesgo Ferreiro Date: Wed, 17 Jun 2020 20:56:33 +0200 Subject: [PATCH 054/105] fix issue with line endings on this branch --- .../neoantigen_fitness/neoantigen_fitness.py | 160 +++++----- .../abstract_netmhcpan_predictor.py | 34 +-- input/new_features/conservation_scores.py | 102 +++---- input/references.py | 214 +++++++------- input/self_similarity/self_similarity.py | 274 +++++++++--------- input/tests/__init__.py | 44 +-- .../integration_test_tools.py | 38 +-- .../test_conservation_scores.py | 92 +++--- .../integration_tests/test_dissimilarity.py | 54 ++-- input/tests/integration_tests/test_input.py | 52 ++-- .../integration_tests/test_mixmhcpred.py | 198 ++++++------- input/tests/integration_tests/test_neoag.py | 194 ++++++------- .../test_neoantigen_fitness.py | 100 +++---- .../tests/integration_tests/test_netmhcpan.py | 190 ++++++------ .../integration_tests/test_tcell_predictor.py | 104 +++---- input/tests/unit_tests/fake_classes.py | 30 +- .../test_dependencies_configuration.py | 130 ++++----- .../unit_tests/test_predict_all_epitopes.py | 48 +-- .../tests/unit_tests/test_reference_folder.py | 94 +++--- input/tests/unit_tests/test_runner.py | 46 +-- .../tests/unit_tests/test_self_similarity.py | 76 ++--- 21 files changed, 1137 insertions(+), 1137 deletions(-) diff --git a/input/neoantigen_fitness/neoantigen_fitness.py b/input/neoantigen_fitness/neoantigen_fitness.py index ab814cd7..70ede188 100755 --- a/input/neoantigen_fitness/neoantigen_fitness.py +++ b/input/neoantigen_fitness/neoantigen_fitness.py @@ -1,80 +1,80 @@ -#!/usr/bin/env python - -import os -import os.path -from logzero import logger - -from input.helpers import intermediate_files -from input.helpers.runner import BlastpRunner - - -class NeoantigenFitnessCalculator(BlastpRunner): - - def __init__(self, runner, configuration): - """ - :type runner: input.helpers.runner.Runner - :type configuration: input.references.DependenciesConfiguration - """ - super().__init__(runner, configuration) - - def _calc_pathogen_similarity(self, fasta_file, iedb): - """ - This function determines the PATHOGENSIMILARITY of epitopes according to Balachandran et al. using a blast - search against the IEDB pathogenepitope database - """ - outfile = self.run_blastp(fasta_file=fasta_file, database=os.path.join(iedb, "iedb_blast_db")) - similarity = self.parse_blastp_output(blastp_output_file=outfile) - os.remove(outfile) - return similarity - - def wrap_pathogen_similarity(self, mutation, iedb): - fastafile = intermediate_files.create_temp_fasta(sequences=[mutation], prefix="tmpseq", comment_prefix='M_') - try: - pathsim = self._calc_pathogen_similarity(fastafile, iedb) - except Exception as ex: - # TODO: do we need this at all? it should not fail and if it fails we probably want to just stop execution - logger.exception(ex) - pathsim = 0 - os.remove(fastafile) - logger.info("Peptide {} has a pathogen similarity of {}".format(mutation, pathsim)) - return str(pathsim) - - def calculate_amplitude_mhc(self, score_mutation, score_wild_type, apply_correction=False): - """ - This function calculates the amplitude between mutated and wt epitope according to Balachandran et al. - when affinity is used, use correction from Luksza et al. *1/(1+0.0003*aff_wt) - """ - amplitude_mhc = "NA" - try: - candidate_amplitude_mhc = float(score_wild_type) / float(score_mutation) - if apply_correction: #nine_mer or affinity: - amplitude_mhc = str(candidate_amplitude_mhc * (self._calculate_correction(score_wild_type))) - else: - amplitude_mhc = str(candidate_amplitude_mhc) - except(ZeroDivisionError, ValueError) as e: - pass - return amplitude_mhc - - def _calculate_correction(self, score_wild_type): - return 1 / (1 + 0.0003 * float(score_wild_type)) - - def calculate_recognition_potential( - self, amplitude, pathogen_similarity, mutation_in_anchor, mhc_affinity_mut=None): - """ - This function calculates the recognition potential, defined by the product of amplitude and pathogensimiliarity of an epitope according to Balachandran et al. - F_alpha = - max (A_i x R_i) - - Returns (A_i x R_i) value only for nonanchor mutation and epitopes of length 9; only considered by Balachandran - """ - recognition_potential = "NA" - try: - candidate_recognition_potential = str(float(amplitude) * float(pathogen_similarity)) - if mhc_affinity_mut: - if mutation_in_anchor == "0" and mhc_affinity_mut < 500: - recognition_potential = candidate_recognition_potential - else: - if mutation_in_anchor == "0": - recognition_potential = candidate_recognition_potential - except ValueError: - pass - return recognition_potential +#!/usr/bin/env python + +import os +import os.path +from logzero import logger + +from input.helpers import intermediate_files +from input.helpers.runner import BlastpRunner + + +class NeoantigenFitnessCalculator(BlastpRunner): + + def __init__(self, runner, configuration): + """ + :type runner: input.helpers.runner.Runner + :type configuration: input.references.DependenciesConfiguration + """ + super().__init__(runner, configuration) + + def _calc_pathogen_similarity(self, fasta_file, iedb): + """ + This function determines the PATHOGENSIMILARITY of epitopes according to Balachandran et al. using a blast + search against the IEDB pathogenepitope database + """ + outfile = self.run_blastp(fasta_file=fasta_file, database=os.path.join(iedb, "iedb_blast_db")) + similarity = self.parse_blastp_output(blastp_output_file=outfile) + os.remove(outfile) + return similarity + + def wrap_pathogen_similarity(self, mutation, iedb): + fastafile = intermediate_files.create_temp_fasta(sequences=[mutation], prefix="tmpseq", comment_prefix='M_') + try: + pathsim = self._calc_pathogen_similarity(fastafile, iedb) + except Exception as ex: + # TODO: do we need this at all? it should not fail and if it fails we probably want to just stop execution + logger.exception(ex) + pathsim = 0 + os.remove(fastafile) + logger.info("Peptide {} has a pathogen similarity of {}".format(mutation, pathsim)) + return str(pathsim) + + def calculate_amplitude_mhc(self, score_mutation, score_wild_type, apply_correction=False): + """ + This function calculates the amplitude between mutated and wt epitope according to Balachandran et al. + when affinity is used, use correction from Luksza et al. *1/(1+0.0003*aff_wt) + """ + amplitude_mhc = "NA" + try: + candidate_amplitude_mhc = float(score_wild_type) / float(score_mutation) + if apply_correction: #nine_mer or affinity: + amplitude_mhc = str(candidate_amplitude_mhc * (self._calculate_correction(score_wild_type))) + else: + amplitude_mhc = str(candidate_amplitude_mhc) + except(ZeroDivisionError, ValueError) as e: + pass + return amplitude_mhc + + def _calculate_correction(self, score_wild_type): + return 1 / (1 + 0.0003 * float(score_wild_type)) + + def calculate_recognition_potential( + self, amplitude, pathogen_similarity, mutation_in_anchor, mhc_affinity_mut=None): + """ + This function calculates the recognition potential, defined by the product of amplitude and pathogensimiliarity of an epitope according to Balachandran et al. + F_alpha = - max (A_i x R_i) + + Returns (A_i x R_i) value only for nonanchor mutation and epitopes of length 9; only considered by Balachandran + """ + recognition_potential = "NA" + try: + candidate_recognition_potential = str(float(amplitude) * float(pathogen_similarity)) + if mhc_affinity_mut: + if mutation_in_anchor == "0" and mhc_affinity_mut < 500: + recognition_potential = candidate_recognition_potential + else: + if mutation_in_anchor == "0": + recognition_potential = candidate_recognition_potential + except ValueError: + pass + return recognition_potential diff --git a/input/netmhcpan4/abstract_netmhcpan_predictor.py b/input/netmhcpan4/abstract_netmhcpan_predictor.py index 4ad613bc..3a915dc6 100755 --- a/input/netmhcpan4/abstract_netmhcpan_predictor.py +++ b/input/netmhcpan4/abstract_netmhcpan_predictor.py @@ -1,17 +1,17 @@ - - - -class AbstractNetMhcPanPredictor(object): - - @staticmethod - def add_best_epitope_info(epitope_tuple, column_name): - '''returns desired information of prediction of best epitope from netmhcpan output; - e.g. "%Rank": MHC I score, "HLA": HLA allele, "Icore": best epitope - ''' - dat_head = epitope_tuple[0] - dat = epitope_tuple[1] - val = dat_head.index(column_name) - try: - return dat[val] - except IndexError: - return "NA" + + + +class AbstractNetMhcPanPredictor(object): + + @staticmethod + def add_best_epitope_info(epitope_tuple, column_name): + '''returns desired information of prediction of best epitope from netmhcpan output; + e.g. "%Rank": MHC I score, "HLA": HLA allele, "Icore": best epitope + ''' + dat_head = epitope_tuple[0] + dat = epitope_tuple[1] + val = dat_head.index(column_name) + try: + return dat[val] + except IndexError: + return "NA" diff --git a/input/new_features/conservation_scores.py b/input/new_features/conservation_scores.py index 3f3437c9..c90de859 100755 --- a/input/new_features/conservation_scores.py +++ b/input/new_features/conservation_scores.py @@ -1,51 +1,51 @@ -import re - -from logzero import logger - - -class ProveanAnnotator(object): - - def __init__(self, provean_file, header_epitopes, epitopes): - """ - Loads provean scores as dictionary, but only for ucsc ids that are in epitope list - """ - epitope_ids = self._load_ucsc_ids_epitopes(header_epitopes=header_epitopes, epitopes=epitopes) - logger.info("Starting load of PROVEAN matrix" + provean_file) - self.header_provean, self.provean_matrix = self._load_provean_matrix(epitope_ids, provean_file) - logger.info("PROVEAN matrix loaded") - - def _load_ucsc_ids_epitopes(self, header_epitopes, epitopes): - """ - Returns set with ucsc ids of epitopes. - """ - col_ucsc = header_epitopes.index("UCSC_transcript") - col_pos = header_epitopes.index("substitution") - return set([self.build_ucsc_id_plus_position(ucsc_id=e[col_ucsc], substitution=e[col_pos]) for e in epitopes]) - - def _load_provean_matrix(self, epitope_ids, provean_file): - provean_matrix = {} - with open(provean_file) as f: - header = next(f).rstrip().split(";") # stores header - for line in f: - parts = line.rstrip().split(";") - ucsc_id_pos = parts[-1] - if ucsc_id_pos in epitope_ids: - provean_matrix[ucsc_id_pos] = parts - return header, provean_matrix - - def get_provean_annotation(self, mutated_aminoacid, ucsc_id_position): - """ - This function maps Provean score on given position and for specific SNV onto epitope data set - (which is in form of tuple --> header + dict of ucsc_pos_id: df row) - """ - try: - return self.provean_matrix[ucsc_id_position][self.header_provean.index(mutated_aminoacid)] - except (ValueError, KeyError) as e: - return "NA" - - @staticmethod - def build_ucsc_id_plus_position(substitution, ucsc_id): - ucsc_epi = re.sub(r'.\d+$', '', ucsc_id) - position_match = re.match(r'[A-Z](\d+)[A-Z]', substitution) - pos_prot = position_match.group(1) if position_match else "Del" - return "{}_{}".format(ucsc_epi, pos_prot) +import re + +from logzero import logger + + +class ProveanAnnotator(object): + + def __init__(self, provean_file, header_epitopes, epitopes): + """ + Loads provean scores as dictionary, but only for ucsc ids that are in epitope list + """ + epitope_ids = self._load_ucsc_ids_epitopes(header_epitopes=header_epitopes, epitopes=epitopes) + logger.info("Starting load of PROVEAN matrix" + provean_file) + self.header_provean, self.provean_matrix = self._load_provean_matrix(epitope_ids, provean_file) + logger.info("PROVEAN matrix loaded") + + def _load_ucsc_ids_epitopes(self, header_epitopes, epitopes): + """ + Returns set with ucsc ids of epitopes. + """ + col_ucsc = header_epitopes.index("UCSC_transcript") + col_pos = header_epitopes.index("substitution") + return set([self.build_ucsc_id_plus_position(ucsc_id=e[col_ucsc], substitution=e[col_pos]) for e in epitopes]) + + def _load_provean_matrix(self, epitope_ids, provean_file): + provean_matrix = {} + with open(provean_file) as f: + header = next(f).rstrip().split(";") # stores header + for line in f: + parts = line.rstrip().split(";") + ucsc_id_pos = parts[-1] + if ucsc_id_pos in epitope_ids: + provean_matrix[ucsc_id_pos] = parts + return header, provean_matrix + + def get_provean_annotation(self, mutated_aminoacid, ucsc_id_position): + """ + This function maps Provean score on given position and for specific SNV onto epitope data set + (which is in form of tuple --> header + dict of ucsc_pos_id: df row) + """ + try: + return self.provean_matrix[ucsc_id_position][self.header_provean.index(mutated_aminoacid)] + except (ValueError, KeyError) as e: + return "NA" + + @staticmethod + def build_ucsc_id_plus_position(substitution, ucsc_id): + ucsc_epi = re.sub(r'.\d+$', '', ucsc_id) + position_match = re.match(r'[A-Z](\d+)[A-Z]', substitution) + pos_prot = position_match.group(1) if position_match else "Del" + return "{}_{}".format(ucsc_epi, pos_prot) diff --git a/input/references.py b/input/references.py index 8d8178a9..900ac9b4 100755 --- a/input/references.py +++ b/input/references.py @@ -1,107 +1,107 @@ -import os - -from logzero import logger - -import input -from input.exceptions import INPuTConfigurationException - - -class DependenciesConfiguration(object): - - def __init__(self): - self.blastp = self._check_and_load_binary(input.INPUT_BLASTP_ENV) - self.mix_mhc2_pred = self._check_and_load_binary(input.INPUT_MIXMHC2PRED_ENV) - self.mix_mhc2_pred_alleles_list = os.path.join(os.path.dirname(self.mix_mhc2_pred), 'Alleles_list.txt') - self.mix_mhc_pred = self._check_and_load_binary(input.INPUT_MIXMHCPRED_ENV) - self.rscript = self._check_and_load_binary(input.INPUT_RSCRIPT_ENV) - self.net_mhc2_pan = self._check_and_load_binary(input.INPUT_NETMHC2PAN_ENV) - self.net_mhc_pan = self._check_and_load_binary(input.INPUT_NETMHCPAN_ENV) - - @staticmethod - def _check_and_load_binary(variable_name): - variable_value = os.environ.get(variable_name, "") - if not variable_value: - raise INPuTConfigurationException( - "Please, set the environment variable ${} pointing to the right binary!".format( - variable_name)) - if not os.path.exists(variable_value): - raise INPuTConfigurationException("The provided binary '{}' in ${} does not exist!".format( - variable_value, variable_name)) - return variable_value - - -class ReferenceFolder(object): - - def __init__(self): - self.reference_genome_folder = self._check_reference_genome_folder() - # sets the right file names for the resources - self.available_mhc_ii = self._get_reference_file_name('avail_mhcII.txt') - self.available_mhc_i = self._get_reference_file_name('MHC_available.csv') - self.aa_freq_prot = self._get_reference_file_name('20181108_AA_freq_prot.csv') - self.four_mer_freq = self._get_reference_file_name('20181108_4mer_freq.csv') - self.aaindex1 = self._get_reference_file_name('aaindex1') - self.aaindex2 = self._get_reference_file_name('aaindex2') - self.prov_scores_mapped3 = self._get_reference_file_name('PROV_scores_mapped3.csv') - self.iedb = self._get_reference_file_name('iedb') - self.proteome_db = self._get_reference_file_name('proteome_db') - self.tcell_predictor_sir_data = self._get_reference_file_name('SIRdata.mat') - self.tcell_predictor_gene_expression = self._get_reference_file_name('genes-expression.pickle') - self.tcell_predictor_aa_features = self._get_reference_file_name('amino-acids-features.pickle') - self.uniprot = self._get_reference_file_name('uniprot_human_with_isoforms.fasta') - self.gtex = self._get_reference_file_name('gtex_combined.csv') - - # TODO: add this files self.alleles_list_pred, self.avail_mhc_ii - self.resources = [self.available_mhc_ii, self.available_mhc_i, self.aa_freq_prot, - self.four_mer_freq, self.aaindex1, self.aaindex2, self.prov_scores_mapped3, self.iedb, - self.proteome_db, self.tcell_predictor_aa_features, - self.tcell_predictor_gene_expression, self.tcell_predictor_sir_data, - self.uniprot, self.gtex] - self._check_resources(self.resources) - self._log_configuration() - - @staticmethod - def _check_reference_genome_folder(): - reference_genome_folder = os.environ.get(input.REFERENCE_FOLDER_ENV, "") - if not reference_genome_folder: - raise INPuTConfigurationException( - "Please, set the environment variable ${} pointing to the reference genome folder!".format( - input.REFERENCE_FOLDER_ENV)) - if not os.path.exists(reference_genome_folder): - raise INPuTConfigurationException("The provided reference genome '{}' in ${} does not exist!".format( - reference_genome_folder, input.REFERENCE_FOLDER_ENV)) - return reference_genome_folder - - @staticmethod - def _check_resources(resources): - missing_resources = [] - for r in resources: - if not os.path.exists(r): - missing_resources.append(r) - if len(missing_resources) > 0: - raise INPuTConfigurationException( - "Missing resources in the reference folder: {}".format(str(missing_resources))) - - def _log_configuration(self): - logger.info("Reference genome folder: {}".format(self.reference_genome_folder)) - logger.info("Resources") - for r in self.resources: - logger.info(r) - - def _get_reference_file_name(self, file_name_suffix): - return os.path.join(self.reference_genome_folder, file_name_suffix) - - def load_available_hla_alleles(self, mhc=input.MHC_I): - """ - loads file with available hla alllels for netmhcpan4/netmhcIIpan prediction, returns set - :type mhc: str - :rtype list: - """ - if mhc == input.MHC_II: - fileMHC = self.available_mhc_ii - else: - fileMHC = self.available_mhc_i - set_available_mhc = set() - with open(fileMHC) as f: - for line in f: - set_available_mhc.add(line.strip()) - return set_available_mhc +import os + +from logzero import logger + +import input +from input.exceptions import INPuTConfigurationException + + +class DependenciesConfiguration(object): + + def __init__(self): + self.blastp = self._check_and_load_binary(input.INPUT_BLASTP_ENV) + self.mix_mhc2_pred = self._check_and_load_binary(input.INPUT_MIXMHC2PRED_ENV) + self.mix_mhc2_pred_alleles_list = os.path.join(os.path.dirname(self.mix_mhc2_pred), 'Alleles_list.txt') + self.mix_mhc_pred = self._check_and_load_binary(input.INPUT_MIXMHCPRED_ENV) + self.rscript = self._check_and_load_binary(input.INPUT_RSCRIPT_ENV) + self.net_mhc2_pan = self._check_and_load_binary(input.INPUT_NETMHC2PAN_ENV) + self.net_mhc_pan = self._check_and_load_binary(input.INPUT_NETMHCPAN_ENV) + + @staticmethod + def _check_and_load_binary(variable_name): + variable_value = os.environ.get(variable_name, "") + if not variable_value: + raise INPuTConfigurationException( + "Please, set the environment variable ${} pointing to the right binary!".format( + variable_name)) + if not os.path.exists(variable_value): + raise INPuTConfigurationException("The provided binary '{}' in ${} does not exist!".format( + variable_value, variable_name)) + return variable_value + + +class ReferenceFolder(object): + + def __init__(self): + self.reference_genome_folder = self._check_reference_genome_folder() + # sets the right file names for the resources + self.available_mhc_ii = self._get_reference_file_name('avail_mhcII.txt') + self.available_mhc_i = self._get_reference_file_name('MHC_available.csv') + self.aa_freq_prot = self._get_reference_file_name('20181108_AA_freq_prot.csv') + self.four_mer_freq = self._get_reference_file_name('20181108_4mer_freq.csv') + self.aaindex1 = self._get_reference_file_name('aaindex1') + self.aaindex2 = self._get_reference_file_name('aaindex2') + self.prov_scores_mapped3 = self._get_reference_file_name('PROV_scores_mapped3.csv') + self.iedb = self._get_reference_file_name('iedb') + self.proteome_db = self._get_reference_file_name('proteome_db') + self.tcell_predictor_sir_data = self._get_reference_file_name('SIRdata.mat') + self.tcell_predictor_gene_expression = self._get_reference_file_name('genes-expression.pickle') + self.tcell_predictor_aa_features = self._get_reference_file_name('amino-acids-features.pickle') + self.uniprot = self._get_reference_file_name('uniprot_human_with_isoforms.fasta') + self.gtex = self._get_reference_file_name('gtex_combined.csv') + + # TODO: add this files self.alleles_list_pred, self.avail_mhc_ii + self.resources = [self.available_mhc_ii, self.available_mhc_i, self.aa_freq_prot, + self.four_mer_freq, self.aaindex1, self.aaindex2, self.prov_scores_mapped3, self.iedb, + self.proteome_db, self.tcell_predictor_aa_features, + self.tcell_predictor_gene_expression, self.tcell_predictor_sir_data, + self.uniprot, self.gtex] + self._check_resources(self.resources) + self._log_configuration() + + @staticmethod + def _check_reference_genome_folder(): + reference_genome_folder = os.environ.get(input.REFERENCE_FOLDER_ENV, "") + if not reference_genome_folder: + raise INPuTConfigurationException( + "Please, set the environment variable ${} pointing to the reference genome folder!".format( + input.REFERENCE_FOLDER_ENV)) + if not os.path.exists(reference_genome_folder): + raise INPuTConfigurationException("The provided reference genome '{}' in ${} does not exist!".format( + reference_genome_folder, input.REFERENCE_FOLDER_ENV)) + return reference_genome_folder + + @staticmethod + def _check_resources(resources): + missing_resources = [] + for r in resources: + if not os.path.exists(r): + missing_resources.append(r) + if len(missing_resources) > 0: + raise INPuTConfigurationException( + "Missing resources in the reference folder: {}".format(str(missing_resources))) + + def _log_configuration(self): + logger.info("Reference genome folder: {}".format(self.reference_genome_folder)) + logger.info("Resources") + for r in self.resources: + logger.info(r) + + def _get_reference_file_name(self, file_name_suffix): + return os.path.join(self.reference_genome_folder, file_name_suffix) + + def load_available_hla_alleles(self, mhc=input.MHC_I): + """ + loads file with available hla alllels for netmhcpan4/netmhcIIpan prediction, returns set + :type mhc: str + :rtype list: + """ + if mhc == input.MHC_II: + fileMHC = self.available_mhc_ii + else: + fileMHC = self.available_mhc_i + set_available_mhc = set() + with open(fileMHC) as f: + for line in f: + set_available_mhc.add(line.strip()) + return set_available_mhc diff --git a/input/self_similarity/self_similarity.py b/input/self_similarity/self_similarity.py index 7285b0c8..e5d0c288 100755 --- a/input/self_similarity/self_similarity.py +++ b/input/self_similarity/self_similarity.py @@ -1,137 +1,137 @@ -#!/usr/bin/env python - -from input import MHC_I, MHC_II - -import math -import os - -BETA = 0.11387 -BLOSUM62_FILE_NAME = 'BLOSUM62-2.matrix.txt' - - -class SelfSimilarityCalculator(): - - def __init__(self): - blosum_file = os.path.join(os.path.abspath(os.path.dirname(__file__)), BLOSUM62_FILE_NAME) - blosum_dict = self._load_blosum(blosum_file) - self.k1 = self._compute_k1(blosum_dict) - - def _compute_k1(self, blosum_dict): - K1 = {} - for i in list(blosum_dict.keys()): - x = K1.get(i, {}) - for j in list(blosum_dict[i].keys()): - x[j] = math.pow(blosum_dict[i][j], BETA) - K1[i] = x - return K1 - - def _load_blosum(self, blosum): - blosum_dict = {} - colid = [] - rowid = [] - c = 0 - with open(blosum) as f: - for line in f: - c += 1 - if c == 1: - colid = line.strip("\n").split(" ") - continue - w = line.strip("\n").split(" ") - id = w[0] - v = [float(x) for x in w[1:]] - rowid.append(id) - x = blosum_dict.get(id, {}) - for i, vi in enumerate(v): - x[colid[i]] = vi - blosum_dict[id] = x - return blosum_dict - - def compute_k_hat_3(self, x, y): # K^3 - return self._compute_k3(x, y) / math.sqrt(self._compute_k3(x, x) * self._compute_k3(y, y)) - - def _compute_k3(self, f, g): - max_k = min(len(f), len(g)) - s = 0 - for k in range(1, max_k + 1): - for i in range(len(f) - (k - 1)): - u = f[i:i + k] - for j in range(len(g) - (k - 1)): - v = g[j:j + k] - s += self._compute_k2k(u, v, self.k1) - return s - - def _compute_k2k(self, u, v, K1): - if len(u) != len(v): - return None - k = len(u) - p = K1[u[0]][v[0]] - for i in range(1, k): - p = p * K1[u[i]][v[i]] - return p - - -def get_self_similarity(mutation, wild_type): - """ - Returns self-similiarity between mutated and wt epitope according to Bjerregard et al., - Argument mhc indicates if determination for MHC I or MHC II epitopes - """ - self_similarity = 'NA' - try: - self_similarity = str(SelfSimilarityCalculator().compute_k_hat_3(mutation, wild_type)) - except ZeroDivisionError: - pass - return self_similarity - - -def is_improved_binder(score_mutation, score_wild_type): - """ - This function checks if mutated epitope is improved binder according to Bjerregard et al. - """ - try: - improved_binder = float(score_wild_type) / float(score_mutation) >= 1.2 - except (ZeroDivisionError, ValueError) as e: - return "NA" - # TODO: boolean in a string needs to go away - return "1" if improved_binder else "0" - - -def self_similarity_of_conserved_binder_only(has_conserved_binder, similarity): - """ - this function returns selfsimilarity for conserved binder but not for improved binder - """ - try: - if has_conserved_binder == str(0): - return similarity - else: - return "NA" - except (ZeroDivisionError, ValueError) as e: - return "NA" - - -def position_of_mutation_epitope(wild_type, mutation): - """ - This function determines the position of the mutation within the epitope sequence. - """ - p1 = -1 - try: - for i, aa in enumerate(mutation): - if aa != wild_type[i]: - p1 = i + 1 - return str(p1) - except: - return "NA" - - -def position_in_anchor_position(position_mhci, peptide_length): - """ - This function determines if the mutation is located within an anchor position in mhc I. - As an approximation, we assume that the second and the last position are anchor positions for all alleles. - """ - anchor = "NA" - try: - anchor = int(position_mhci) == int(peptide_length) or int(position_mhci) == 2 - # TODO this conversion of a boolean to a numeric boolean in a string needs to go away - anchor = str(1) if anchor else str(0) - except: - pass - return anchor +#!/usr/bin/env python + +from input import MHC_I, MHC_II + +import math +import os + +BETA = 0.11387 +BLOSUM62_FILE_NAME = 'BLOSUM62-2.matrix.txt' + + +class SelfSimilarityCalculator(): + + def __init__(self): + blosum_file = os.path.join(os.path.abspath(os.path.dirname(__file__)), BLOSUM62_FILE_NAME) + blosum_dict = self._load_blosum(blosum_file) + self.k1 = self._compute_k1(blosum_dict) + + def _compute_k1(self, blosum_dict): + K1 = {} + for i in list(blosum_dict.keys()): + x = K1.get(i, {}) + for j in list(blosum_dict[i].keys()): + x[j] = math.pow(blosum_dict[i][j], BETA) + K1[i] = x + return K1 + + def _load_blosum(self, blosum): + blosum_dict = {} + colid = [] + rowid = [] + c = 0 + with open(blosum) as f: + for line in f: + c += 1 + if c == 1: + colid = line.strip("\n").split(" ") + continue + w = line.strip("\n").split(" ") + id = w[0] + v = [float(x) for x in w[1:]] + rowid.append(id) + x = blosum_dict.get(id, {}) + for i, vi in enumerate(v): + x[colid[i]] = vi + blosum_dict[id] = x + return blosum_dict + + def compute_k_hat_3(self, x, y): # K^3 + return self._compute_k3(x, y) / math.sqrt(self._compute_k3(x, x) * self._compute_k3(y, y)) + + def _compute_k3(self, f, g): + max_k = min(len(f), len(g)) + s = 0 + for k in range(1, max_k + 1): + for i in range(len(f) - (k - 1)): + u = f[i:i + k] + for j in range(len(g) - (k - 1)): + v = g[j:j + k] + s += self._compute_k2k(u, v, self.k1) + return s + + def _compute_k2k(self, u, v, K1): + if len(u) != len(v): + return None + k = len(u) + p = K1[u[0]][v[0]] + for i in range(1, k): + p = p * K1[u[i]][v[i]] + return p + + +def get_self_similarity(mutation, wild_type): + """ + Returns self-similiarity between mutated and wt epitope according to Bjerregard et al., + Argument mhc indicates if determination for MHC I or MHC II epitopes + """ + self_similarity = 'NA' + try: + self_similarity = str(SelfSimilarityCalculator().compute_k_hat_3(mutation, wild_type)) + except ZeroDivisionError: + pass + return self_similarity + + +def is_improved_binder(score_mutation, score_wild_type): + """ + This function checks if mutated epitope is improved binder according to Bjerregard et al. + """ + try: + improved_binder = float(score_wild_type) / float(score_mutation) >= 1.2 + except (ZeroDivisionError, ValueError) as e: + return "NA" + # TODO: boolean in a string needs to go away + return "1" if improved_binder else "0" + + +def self_similarity_of_conserved_binder_only(has_conserved_binder, similarity): + """ + this function returns selfsimilarity for conserved binder but not for improved binder + """ + try: + if has_conserved_binder == str(0): + return similarity + else: + return "NA" + except (ZeroDivisionError, ValueError) as e: + return "NA" + + +def position_of_mutation_epitope(wild_type, mutation): + """ + This function determines the position of the mutation within the epitope sequence. + """ + p1 = -1 + try: + for i, aa in enumerate(mutation): + if aa != wild_type[i]: + p1 = i + 1 + return str(p1) + except: + return "NA" + + +def position_in_anchor_position(position_mhci, peptide_length): + """ + This function determines if the mutation is located within an anchor position in mhc I. + As an approximation, we assume that the second and the last position are anchor positions for all alleles. + """ + anchor = "NA" + try: + anchor = int(position_mhci) == int(peptide_length) or int(position_mhci) == 2 + # TODO this conversion of a boolean to a numeric boolean in a string needs to go away + anchor = str(1) if anchor else str(0) + except: + pass + return anchor diff --git a/input/tests/__init__.py b/input/tests/__init__.py index 25be8221..ee7475c9 100755 --- a/input/tests/__init__.py +++ b/input/tests/__init__.py @@ -1,22 +1,22 @@ -TEST_HLAI_ALLELES = [ - 'HLA-A*24:02', 'HLA-A*02:01', 'HLA-B*15:01', 'HLA-B*44:02', 'HLA-C*07:02', 'HLA-C*05:01', - 'HLA-A*24:02', 'HLA-B*27:05', 'HLA-B*52:01', 'HLA-C*01:02', 'HLA-C*12:02', - 'HLA-A*01:01', 'HLA-B*56:01', 'HLA-B*38:01', 'HLA-C*01:02', 'HLA-C*06:02', - 'HLA-A*03:01', 'HLA-A*02:01', 'HLA-B*27:05', 'HLA-B*47:01', 'HLA-C*01:02', 'HLA-C*06:02', - 'HLA-A*02:01', 'HLA-A*25:01', 'HLA-B*27:02', 'HLA-B*18:01', 'HLA-C*02:02', 'HLA-C*12:03', - 'HLA-A*23:01', 'HLA-A*66:01', 'HLA-B*41:02', 'HLA-B*35:01', 'HLA-C*17:03', 'HLA-C*04:01', - 'HLA-A*66:01', 'HLA-A*01:01', 'HLA-B*08:01', 'HLA-C*07:01', - 'HLA-A*03:01', 'HLA-A*01:01', 'HLA-B*08:01', 'HLA-B*35:01', 'HLA-C*07:01', 'HLA-C*04:01', - 'HLA-A*24:02', 'HLA-A*68:01', 'HLA-B*35:03', 'HLA-B*13:02', 'HLA-C*06:02', 'HLA-C*04:01', - 'HLA-A*01:01', 'HLA-B*37:01', 'HLA-B*08:01', 'HLA-C*06:02', 'HLA-C*07:01'] - -TEST_HLAII_ALLELES = ['HLA-DRB1*04:01', 'HLA-DRB1*04:04', 'HLA-DQB1*03:01', 'HLA-DQB1*03:02', - 'HLA-DRB1*11:01', 'HLA-DRB1*01:01', 'HLA-DQB1*05:01', 'HLA-DQB1*03:01', - 'HLA-DRB1*11:04', 'HLA-DRB1*07:01', 'HLA-DQB1*02:02', 'HLA-DQB1*03:01', - 'HLA-DRB1*01:01', 'HLA-DRB1*07:01', 'HLA-DQB1*05:01', 'HLA-DQB1*02:02', - 'HLA-DRB1*16:01', 'HLA-DRB1*01:01', 'HLA-DQB1*05:02', 'HLA-DQB1*05:01', - 'HLA-DRB1*11:01', 'HLA-DRB1*01:01', 'HLA-DQB1*05:01', 'HLA-DQB1*03:01', - 'HLA-DRB1*03:01', 'HLA-DQB1*02:01', - 'HLA-DRB1*03:01', 'HLA-DRB1*07:01', 'HLA-DQB1*02:02', 'HLA-DQB1*02:01', - 'HLA-DRB1*15:01', 'HLA-DRB1*12:01', 'HLA-DQB1*06:02', 'HLA-DQB1*03:01', - 'HLA-DRB1*11:01', 'HLA-DRB1*03:01', 'HLA-DQB1*03:01', 'HLA-DQB1*02:01'] +TEST_HLAI_ALLELES = [ + 'HLA-A*24:02', 'HLA-A*02:01', 'HLA-B*15:01', 'HLA-B*44:02', 'HLA-C*07:02', 'HLA-C*05:01', + 'HLA-A*24:02', 'HLA-B*27:05', 'HLA-B*52:01', 'HLA-C*01:02', 'HLA-C*12:02', + 'HLA-A*01:01', 'HLA-B*56:01', 'HLA-B*38:01', 'HLA-C*01:02', 'HLA-C*06:02', + 'HLA-A*03:01', 'HLA-A*02:01', 'HLA-B*27:05', 'HLA-B*47:01', 'HLA-C*01:02', 'HLA-C*06:02', + 'HLA-A*02:01', 'HLA-A*25:01', 'HLA-B*27:02', 'HLA-B*18:01', 'HLA-C*02:02', 'HLA-C*12:03', + 'HLA-A*23:01', 'HLA-A*66:01', 'HLA-B*41:02', 'HLA-B*35:01', 'HLA-C*17:03', 'HLA-C*04:01', + 'HLA-A*66:01', 'HLA-A*01:01', 'HLA-B*08:01', 'HLA-C*07:01', + 'HLA-A*03:01', 'HLA-A*01:01', 'HLA-B*08:01', 'HLA-B*35:01', 'HLA-C*07:01', 'HLA-C*04:01', + 'HLA-A*24:02', 'HLA-A*68:01', 'HLA-B*35:03', 'HLA-B*13:02', 'HLA-C*06:02', 'HLA-C*04:01', + 'HLA-A*01:01', 'HLA-B*37:01', 'HLA-B*08:01', 'HLA-C*06:02', 'HLA-C*07:01'] + +TEST_HLAII_ALLELES = ['HLA-DRB1*04:01', 'HLA-DRB1*04:04', 'HLA-DQB1*03:01', 'HLA-DQB1*03:02', + 'HLA-DRB1*11:01', 'HLA-DRB1*01:01', 'HLA-DQB1*05:01', 'HLA-DQB1*03:01', + 'HLA-DRB1*11:04', 'HLA-DRB1*07:01', 'HLA-DQB1*02:02', 'HLA-DQB1*03:01', + 'HLA-DRB1*01:01', 'HLA-DRB1*07:01', 'HLA-DQB1*05:01', 'HLA-DQB1*02:02', + 'HLA-DRB1*16:01', 'HLA-DRB1*01:01', 'HLA-DQB1*05:02', 'HLA-DQB1*05:01', + 'HLA-DRB1*11:01', 'HLA-DRB1*01:01', 'HLA-DQB1*05:01', 'HLA-DQB1*03:01', + 'HLA-DRB1*03:01', 'HLA-DQB1*02:01', + 'HLA-DRB1*03:01', 'HLA-DRB1*07:01', 'HLA-DQB1*02:02', 'HLA-DQB1*02:01', + 'HLA-DRB1*15:01', 'HLA-DRB1*12:01', 'HLA-DQB1*06:02', 'HLA-DQB1*03:01', + 'HLA-DRB1*11:01', 'HLA-DRB1*03:01', 'HLA-DQB1*03:01', 'HLA-DQB1*02:01'] diff --git a/input/tests/integration_tests/integration_test_tools.py b/input/tests/integration_tests/integration_test_tools.py index 275fd6b9..5dea5f9e 100755 --- a/input/tests/integration_tests/integration_test_tools.py +++ b/input/tests/integration_tests/integration_test_tools.py @@ -1,19 +1,19 @@ -import random -import tempfile - -import dotenv -from Bio.Alphabet.IUPAC import IUPACData - -from input.references import ReferenceFolder, DependenciesConfiguration - - -def load_references(): - dotenv.load_dotenv() - return ReferenceFolder(), DependenciesConfiguration() - - -def create_temp_aminoacid_fasta_file(): - fastafile = tempfile.NamedTemporaryFile(mode='w', delete=False) - with fastafile as f: - f.write("".join(random.choices(list(IUPACData.protein_letters), k=25))) - return fastafile +import random +import tempfile + +import dotenv +from Bio.Alphabet.IUPAC import IUPACData + +from input.references import ReferenceFolder, DependenciesConfiguration + + +def load_references(): + dotenv.load_dotenv() + return ReferenceFolder(), DependenciesConfiguration() + + +def create_temp_aminoacid_fasta_file(): + fastafile = tempfile.NamedTemporaryFile(mode='w', delete=False) + with fastafile as f: + f.write("".join(random.choices(list(IUPACData.protein_letters), k=25))) + return fastafile diff --git a/input/tests/integration_tests/test_conservation_scores.py b/input/tests/integration_tests/test_conservation_scores.py index e31fb048..15ea8365 100755 --- a/input/tests/integration_tests/test_conservation_scores.py +++ b/input/tests/integration_tests/test_conservation_scores.py @@ -1,46 +1,46 @@ -from unittest import TestCase - -from input.new_features.conservation_scores import ProveanAnnotator -from input.tests.integration_tests import integration_test_tools - - -class TestProveanAnnotator(TestCase): - - def setUp(self): - self.references, self.configuration = integration_test_tools.load_references() - self.header_epitopes = ["UCSC_transcript", "substitution"] - self.epitopes = [ - ["uc010qbo.1", "A207S"], - ["uc001ovh.1", "A41S"], - ["uc001ovh.1", "A40S"], - ["uc001tzg.1", "A154S"], - ["uc001uir.1", "A39S"], - ["uc001yqt.1", "A701S"], - ["uc001zrt.1", "A1520S"], - ["uc010umw.1", "A114S"], - ["uc010umy.1", "A7S"]] - self.annotator = ProveanAnnotator( - provean_file=self.references.prov_scores_mapped3, header_epitopes=self.header_epitopes, - epitopes=self.epitopes) - - def test_provean_annotator_loading(self): - self.assertTrue(len(self.annotator.provean_matrix) <= len(self.epitopes)) - self.assertTrue(len(self.annotator.provean_matrix) > 0) - - def test_provean_annotator(self): - provean_annotation = self.annotator.get_provean_annotation( - mutated_aminoacid="S", ucsc_id_position="uc001tzg_154") - self.assertIsNotNone(provean_annotation) - self.assertTrue(provean_annotation != "NA") - self.assertIsNotNone(float(provean_annotation)) - - def test_provean_annotator_non_existing_aminoacid(self): - provean_annotation = self.annotator.get_provean_annotation( - mutated_aminoacid="NO_AA", ucsc_id_position="uc001tzg_154") - self.assertIsNotNone(provean_annotation) - self.assertTrue(provean_annotation == "NA") - - def test_provean_annotator_non_existing_gene(self): - provean_annotation = self.annotator.get_provean_annotation(mutated_aminoacid="S", ucsc_id_position="nope_156") - self.assertIsNotNone(provean_annotation) - self.assertTrue(provean_annotation == "NA") +from unittest import TestCase + +from input.new_features.conservation_scores import ProveanAnnotator +from input.tests.integration_tests import integration_test_tools + + +class TestProveanAnnotator(TestCase): + + def setUp(self): + self.references, self.configuration = integration_test_tools.load_references() + self.header_epitopes = ["UCSC_transcript", "substitution"] + self.epitopes = [ + ["uc010qbo.1", "A207S"], + ["uc001ovh.1", "A41S"], + ["uc001ovh.1", "A40S"], + ["uc001tzg.1", "A154S"], + ["uc001uir.1", "A39S"], + ["uc001yqt.1", "A701S"], + ["uc001zrt.1", "A1520S"], + ["uc010umw.1", "A114S"], + ["uc010umy.1", "A7S"]] + self.annotator = ProveanAnnotator( + provean_file=self.references.prov_scores_mapped3, header_epitopes=self.header_epitopes, + epitopes=self.epitopes) + + def test_provean_annotator_loading(self): + self.assertTrue(len(self.annotator.provean_matrix) <= len(self.epitopes)) + self.assertTrue(len(self.annotator.provean_matrix) > 0) + + def test_provean_annotator(self): + provean_annotation = self.annotator.get_provean_annotation( + mutated_aminoacid="S", ucsc_id_position="uc001tzg_154") + self.assertIsNotNone(provean_annotation) + self.assertTrue(provean_annotation != "NA") + self.assertIsNotNone(float(provean_annotation)) + + def test_provean_annotator_non_existing_aminoacid(self): + provean_annotation = self.annotator.get_provean_annotation( + mutated_aminoacid="NO_AA", ucsc_id_position="uc001tzg_154") + self.assertIsNotNone(provean_annotation) + self.assertTrue(provean_annotation == "NA") + + def test_provean_annotator_non_existing_gene(self): + provean_annotation = self.annotator.get_provean_annotation(mutated_aminoacid="S", ucsc_id_position="nope_156") + self.assertIsNotNone(provean_annotation) + self.assertTrue(provean_annotation == "NA") diff --git a/input/tests/integration_tests/test_dissimilarity.py b/input/tests/integration_tests/test_dissimilarity.py index 353e7167..c4b288ea 100755 --- a/input/tests/integration_tests/test_dissimilarity.py +++ b/input/tests/integration_tests/test_dissimilarity.py @@ -1,27 +1,27 @@ -from unittest import TestCase - -import input.tests.integration_tests.integration_test_tools as integration_test_tools -from input.helpers.runner import Runner -from input.dissimilarity_garnish.dissimilaritycalculator import DissimilarityCalculator - - -class TestDissimilarity(TestCase): - - def setUp(self): - self.references, self.configuration = integration_test_tools.load_references() - self.fastafile = integration_test_tools.create_temp_aminoacid_fasta_file() - self.runner = Runner() - - def test_dissimilar_sequences(self): - result = DissimilarityCalculator( - runner=self.runner, configuration=self.configuration)\ - .calculate_dissimilarity( - mhc_mutation='tocino', mhc_affinity='velocidad', references=self.references) - self.assertEqual(1, result) - - def test_similar_sequences(self): - result = DissimilarityCalculator( - runner=self.runner, configuration=self.configuration)\ - .calculate_dissimilarity( - mhc_mutation='DDDDDD', mhc_affinity='DDDDDD', references=self.references) - self.assertTrue(result < 0.000001) +from unittest import TestCase + +import input.tests.integration_tests.integration_test_tools as integration_test_tools +from input.helpers.runner import Runner +from input.dissimilarity_garnish.dissimilaritycalculator import DissimilarityCalculator + + +class TestDissimilarity(TestCase): + + def setUp(self): + self.references, self.configuration = integration_test_tools.load_references() + self.fastafile = integration_test_tools.create_temp_aminoacid_fasta_file() + self.runner = Runner() + + def test_dissimilar_sequences(self): + result = DissimilarityCalculator( + runner=self.runner, configuration=self.configuration)\ + .calculate_dissimilarity( + mhc_mutation='tocino', mhc_affinity='velocidad', references=self.references) + self.assertEqual(1, result) + + def test_similar_sequences(self): + result = DissimilarityCalculator( + runner=self.runner, configuration=self.configuration)\ + .calculate_dissimilarity( + mhc_mutation='DDDDDD', mhc_affinity='DDDDDD', references=self.references) + self.assertTrue(result < 0.000001) diff --git a/input/tests/integration_tests/test_input.py b/input/tests/integration_tests/test_input.py index 702d9494..cdde22d2 100755 --- a/input/tests/integration_tests/test_input.py +++ b/input/tests/integration_tests/test_input.py @@ -1,26 +1,26 @@ -from unittest import TestCase - -from input.predict_all_epitopes import BunchEpitopes - - -class TestInput(TestCase): - - def test_input(self): - """ - This test is equivalent to the command line call: - input -i /projects/SUMMIT/WP1.2/input/development/Pt29.sequences4testing.txt - -a /projects/SUMMIT/WP1.2/Literature_Cohorts/data_analysis/cohorts/vanallen/output_tables/20200106_alleles_extended.csv - -tc /projects/SUMMIT/WP1.2/Literature_Cohorts/data_analysis/cohorts/vanallen/output_tables/vanallen_patient_overview.csv - - NOTE: we will need to check the output when the calculation of resuls and printing to stdout have been decoupled - :return: - """ - input_file = '/projects/SUMMIT/WP1.2/input/development/Pt29.sequences4testing.txt' - alleles_file = '/projects/SUMMIT/WP1.2/Literature_Cohorts/data_analysis/cohorts/vanallen/output_tables/20200106_alleles_extended.csv' - tumor_content_file = '/projects/SUMMIT/WP1.2/Literature_Cohorts/data_analysis/cohorts/vanallen/output_tables/vanallen_patient_overview.csv' - BunchEpitopes().wrapper_table_add_feature_annotation( - file=input_file, - indel=False, - path_to_hla_file=alleles_file, - tissue='skin', - tumour_content_file=tumor_content_file) +from unittest import TestCase + +from input.predict_all_epitopes import BunchEpitopes + + +class TestInput(TestCase): + + def test_input(self): + """ + This test is equivalent to the command line call: + input -i /projects/SUMMIT/WP1.2/input/development/Pt29.sequences4testing.txt + -a /projects/SUMMIT/WP1.2/Literature_Cohorts/data_analysis/cohorts/vanallen/output_tables/20200106_alleles_extended.csv + -tc /projects/SUMMIT/WP1.2/Literature_Cohorts/data_analysis/cohorts/vanallen/output_tables/vanallen_patient_overview.csv + + NOTE: we will need to check the output when the calculation of resuls and printing to stdout have been decoupled + :return: + """ + input_file = '/projects/SUMMIT/WP1.2/input/development/Pt29.sequences4testing.txt' + alleles_file = '/projects/SUMMIT/WP1.2/Literature_Cohorts/data_analysis/cohorts/vanallen/output_tables/20200106_alleles_extended.csv' + tumor_content_file = '/projects/SUMMIT/WP1.2/Literature_Cohorts/data_analysis/cohorts/vanallen/output_tables/vanallen_patient_overview.csv' + BunchEpitopes().wrapper_table_add_feature_annotation( + file=input_file, + indel=False, + path_to_hla_file=alleles_file, + tissue='skin', + tumour_content_file=tumor_content_file) diff --git a/input/tests/integration_tests/test_mixmhcpred.py b/input/tests/integration_tests/test_mixmhcpred.py index 5d91e435..dcec2bb8 100755 --- a/input/tests/integration_tests/test_mixmhcpred.py +++ b/input/tests/integration_tests/test_mixmhcpred.py @@ -1,99 +1,99 @@ -from unittest import TestCase -from logzero import logger - -import input.tests.integration_tests.integration_test_tools as integration_test_tools -from input.MixMHCpred.abstract_mixmhcpred import AbstractMixMHCpred -from input.MixMHCpred.mixmhc2pred import MixMhc2Pred -from input.MixMHCpred.mixmhcpred import MixMHCpred -from input.helpers.runner import Runner -from input.tests import TEST_HLAI_ALLELES, TEST_HLAII_ALLELES - - -class TestMixMHCPred(TestCase): - - def setUp(self): - self.references, self.configuration = integration_test_tools.load_references() - self.runner = Runner() - - def test_mixmhcpred_epitope_iedb(self): - mixmhcpred = MixMHCpred(runner=self.runner, configuration=self.configuration) - # this is an epitope from IEDB of length 9 - mutated = 'NLVPMVATV' - wild_type = 'NLVPMVATV' - mixmhcpred.main(xmer_wt=wild_type, xmer_mut=mutated, alleles=TEST_HLAI_ALLELES[0:5]) - self.assertIsNotNone(mixmhcpred.all_peptides) - self.assertEqual("NLVPMVAT", mixmhcpred.all_peptides) - logger.debug(mixmhcpred.all_peptides) - self.assertEqual(len(mixmhcpred.all_peptides.split('|')), 1) - self.assertIsNotNone(mixmhcpred.all_scores) - logger.debug(mixmhcpred.all_scores) - self.assertEqual(len(mixmhcpred.all_scores.split('|')), 1) - self.assertEqual("-0.522931", mixmhcpred.all_scores) - self.assertIsNotNone(mixmhcpred.all_ranks) - logger.debug(mixmhcpred.all_ranks) - self.assertEqual(len(mixmhcpred.all_ranks.split('|')), 1) - self.assertEqual("77", mixmhcpred.all_ranks) - self.assertIsNotNone(mixmhcpred.all_alleles) - self.assertIsNotNone(mixmhcpred.best_peptide) - self.assertIsNotNone(mixmhcpred.best_score) - self.assertIsNotNone(mixmhcpred.best_rank) - self.assertIsNotNone(mixmhcpred.best_allele) - self.assertIsNotNone(mixmhcpred.best_peptide_wt) - self.assertIsNotNone(mixmhcpred.best_score_wt) - self.assertIsNotNone(mixmhcpred.best_rank_wt) - self.assertIsNotNone(mixmhcpred.difference_score_mut_wt) - - def test_mixmhcpred_too_small_epitope(self): - mixmhcpred = MixMHCpred(runner=self.runner, configuration=self.configuration) - mutated = 'NLVP' - wild_type = 'NLVP' - mixmhcpred.main(xmer_wt=wild_type, xmer_mut=mutated, alleles=TEST_HLAI_ALLELES) - self.assertEqual("NA", mixmhcpred.all_peptides) - - def test_mixmhcpred2_epitope_iedb(self): - mixmhcpred = MixMhc2Pred(runner=self.runner, configuration=self.configuration) - # this is an epitope from IEDB of length 15 - mutated = 'ENPVVHFFKNIVTPR' - wild_type = 'ENPVVHFFKNIVTPR' - mixmhcpred.main(xmer_wt=wild_type, xmer_mut=mutated, alleles=TEST_HLAII_ALLELES) - self.assertIsNotNone(mixmhcpred.all_peptides) - self.assertEqual(len(mixmhcpred.all_peptides.split('|')), 2) - self.assertTrue("ENPVVHFFKNIVTP" in mixmhcpred.all_peptides.split('|')) - self.assertTrue("NPVVHFFKNIVTP" in mixmhcpred.all_peptides.split('|')) - logger.debug(mixmhcpred.all_peptides) - self.assertIsNotNone(mixmhcpred.all_ranks) - self.assertEqual(len(mixmhcpred.all_ranks.split('|')), 2) - self.assertTrue("0.116547" in mixmhcpred.all_ranks.split('|')) - self.assertTrue("0.276218", mixmhcpred.all_ranks.split('|')) - logger.debug(mixmhcpred.all_ranks) - self.assertIsNotNone(mixmhcpred.all_alleles) - self.assertIsNotNone(mixmhcpred.best_peptide) - self.assertIsNotNone(mixmhcpred.best_rank) - self.assertIsNotNone(mixmhcpred.best_allele) - self.assertIsNotNone(mixmhcpred.best_peptide_wt) - self.assertIsNotNone(mixmhcpred.best_score_wt) - self.assertIsNotNone(mixmhcpred.best_rank_wt) - self.assertIsNotNone(mixmhcpred.difference_score_mut_wt) - - def test_mixmhcpred2_too_small_epitope(self): - mixmhcpred = MixMhc2Pred(runner=self.runner, configuration=self.configuration) - # this is an epitope from IEDB of length 15 - mutated = 'ENPVVHFF' - wild_type = 'ENPVVHFF' - mixmhcpred.main(xmer_wt=wild_type, xmer_mut=mutated, alleles=TEST_HLAII_ALLELES) - self.assertEqual("NA", mixmhcpred.all_peptides) - - def test_generate_nmers(self): - result = AbstractMixMHCpred.generate_nmers( - xmer_wt="DDDDDDDDD", xmer_mut="DDDDDVDDD", lengths=[8, 9, 10, 11]) - self.assertIsNotNone(result) - self.assertEqual(3, len(result)) - self.assertEqual(1, len(list(filter(lambda x: len(x) == 9, result)))) - self.assertEqual(2, len(list(filter(lambda x: len(x) == 8, result)))) - self.assertEqual(0, len(list(filter(lambda x: len(x) == 7, result)))) - self.assertEqual(0, len(list(filter(lambda x: len(x) == 6, result)))) - self.assertEqual(0, len(list(filter(lambda x: len(x) == 5, result)))) - self.assertEqual(0, len(list(filter(lambda x: len(x) == 4, result)))) - # ['DDDDDVDD', 'DDDDVDDD', 'DDDVDDD', 'DDVDDD', 'DVDDD', 'VDDD', 'DDDDDVDDD', 'DDDDVDDD', 'DDDVDDD', 'DDVDDD', - # 'DVDDD', 'VDDD'] - logger.debug(result) +from unittest import TestCase +from logzero import logger + +import input.tests.integration_tests.integration_test_tools as integration_test_tools +from input.MixMHCpred.abstract_mixmhcpred import AbstractMixMHCpred +from input.MixMHCpred.mixmhc2pred import MixMhc2Pred +from input.MixMHCpred.mixmhcpred import MixMHCpred +from input.helpers.runner import Runner +from input.tests import TEST_HLAI_ALLELES, TEST_HLAII_ALLELES + + +class TestMixMHCPred(TestCase): + + def setUp(self): + self.references, self.configuration = integration_test_tools.load_references() + self.runner = Runner() + + def test_mixmhcpred_epitope_iedb(self): + mixmhcpred = MixMHCpred(runner=self.runner, configuration=self.configuration) + # this is an epitope from IEDB of length 9 + mutated = 'NLVPMVATV' + wild_type = 'NLVPMVATV' + mixmhcpred.main(xmer_wt=wild_type, xmer_mut=mutated, alleles=TEST_HLAI_ALLELES[0:5]) + self.assertIsNotNone(mixmhcpred.all_peptides) + self.assertEqual("NLVPMVAT", mixmhcpred.all_peptides) + logger.debug(mixmhcpred.all_peptides) + self.assertEqual(len(mixmhcpred.all_peptides.split('|')), 1) + self.assertIsNotNone(mixmhcpred.all_scores) + logger.debug(mixmhcpred.all_scores) + self.assertEqual(len(mixmhcpred.all_scores.split('|')), 1) + self.assertEqual("-0.522931", mixmhcpred.all_scores) + self.assertIsNotNone(mixmhcpred.all_ranks) + logger.debug(mixmhcpred.all_ranks) + self.assertEqual(len(mixmhcpred.all_ranks.split('|')), 1) + self.assertEqual("77", mixmhcpred.all_ranks) + self.assertIsNotNone(mixmhcpred.all_alleles) + self.assertIsNotNone(mixmhcpred.best_peptide) + self.assertIsNotNone(mixmhcpred.best_score) + self.assertIsNotNone(mixmhcpred.best_rank) + self.assertIsNotNone(mixmhcpred.best_allele) + self.assertIsNotNone(mixmhcpred.best_peptide_wt) + self.assertIsNotNone(mixmhcpred.best_score_wt) + self.assertIsNotNone(mixmhcpred.best_rank_wt) + self.assertIsNotNone(mixmhcpred.difference_score_mut_wt) + + def test_mixmhcpred_too_small_epitope(self): + mixmhcpred = MixMHCpred(runner=self.runner, configuration=self.configuration) + mutated = 'NLVP' + wild_type = 'NLVP' + mixmhcpred.main(xmer_wt=wild_type, xmer_mut=mutated, alleles=TEST_HLAI_ALLELES) + self.assertEqual("NA", mixmhcpred.all_peptides) + + def test_mixmhcpred2_epitope_iedb(self): + mixmhcpred = MixMhc2Pred(runner=self.runner, configuration=self.configuration) + # this is an epitope from IEDB of length 15 + mutated = 'ENPVVHFFKNIVTPR' + wild_type = 'ENPVVHFFKNIVTPR' + mixmhcpred.main(xmer_wt=wild_type, xmer_mut=mutated, alleles=TEST_HLAII_ALLELES) + self.assertIsNotNone(mixmhcpred.all_peptides) + self.assertEqual(len(mixmhcpred.all_peptides.split('|')), 2) + self.assertTrue("ENPVVHFFKNIVTP" in mixmhcpred.all_peptides.split('|')) + self.assertTrue("NPVVHFFKNIVTP" in mixmhcpred.all_peptides.split('|')) + logger.debug(mixmhcpred.all_peptides) + self.assertIsNotNone(mixmhcpred.all_ranks) + self.assertEqual(len(mixmhcpred.all_ranks.split('|')), 2) + self.assertTrue("0.116547" in mixmhcpred.all_ranks.split('|')) + self.assertTrue("0.276218", mixmhcpred.all_ranks.split('|')) + logger.debug(mixmhcpred.all_ranks) + self.assertIsNotNone(mixmhcpred.all_alleles) + self.assertIsNotNone(mixmhcpred.best_peptide) + self.assertIsNotNone(mixmhcpred.best_rank) + self.assertIsNotNone(mixmhcpred.best_allele) + self.assertIsNotNone(mixmhcpred.best_peptide_wt) + self.assertIsNotNone(mixmhcpred.best_score_wt) + self.assertIsNotNone(mixmhcpred.best_rank_wt) + self.assertIsNotNone(mixmhcpred.difference_score_mut_wt) + + def test_mixmhcpred2_too_small_epitope(self): + mixmhcpred = MixMhc2Pred(runner=self.runner, configuration=self.configuration) + # this is an epitope from IEDB of length 15 + mutated = 'ENPVVHFF' + wild_type = 'ENPVVHFF' + mixmhcpred.main(xmer_wt=wild_type, xmer_mut=mutated, alleles=TEST_HLAII_ALLELES) + self.assertEqual("NA", mixmhcpred.all_peptides) + + def test_generate_nmers(self): + result = AbstractMixMHCpred.generate_nmers( + xmer_wt="DDDDDDDDD", xmer_mut="DDDDDVDDD", lengths=[8, 9, 10, 11]) + self.assertIsNotNone(result) + self.assertEqual(3, len(result)) + self.assertEqual(1, len(list(filter(lambda x: len(x) == 9, result)))) + self.assertEqual(2, len(list(filter(lambda x: len(x) == 8, result)))) + self.assertEqual(0, len(list(filter(lambda x: len(x) == 7, result)))) + self.assertEqual(0, len(list(filter(lambda x: len(x) == 6, result)))) + self.assertEqual(0, len(list(filter(lambda x: len(x) == 5, result)))) + self.assertEqual(0, len(list(filter(lambda x: len(x) == 4, result)))) + # ['DDDDDVDD', 'DDDDVDDD', 'DDDVDDD', 'DDVDDD', 'DVDDD', 'VDDD', 'DDDDDVDDD', 'DDDDVDDD', 'DDDVDDD', 'DDVDDD', + # 'DVDDD', 'VDDD'] + logger.debug(result) diff --git a/input/tests/integration_tests/test_neoag.py b/input/tests/integration_tests/test_neoag.py index 614d078f..4040d2d7 100755 --- a/input/tests/integration_tests/test_neoag.py +++ b/input/tests/integration_tests/test_neoag.py @@ -1,97 +1,97 @@ -from unittest import TestCase, SkipTest - -from input.neoag.neoag_gbm_model import NeoagCalculator -from input.helpers.runner import Runner -import input.tests.integration_tests.integration_test_tools as integration_test_tools - - -class TestNeoantigenFitness(TestCase): - - def setUp(self): - self.references, self.configuration = integration_test_tools.load_references() - self.fastafile = integration_test_tools.create_temp_aminoacid_fasta_file() - self.runner = Runner() - - def test_neoag(self): - result = NeoagCalculator(runner=self.runner, configuration=self.configuration).wrapper_neoag( - sample_id="12345", - mut_peptide="DDDDDV", - score_mut="0", - ref_peptide="DDDDDD", - peptide_variant_position="123") - self.assertTrue(isinstance(result, str)) - self.assertTrue(float(result) > 0) - - @SkipTest - def test_legacy(self): - # test with ott data set - # file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/MHC_prediction_netmhcpan4/testdat_ott.txt" - # hla_file ="/projects/SUMMIT/WP1.2/Literature_Cohorts/data_analysis/cohorts/ott/icam_ott/alleles.csv" - file = "/projects/SUMMIT/WP1.2/immunogenicity_data/ivac/input_annotation/20190328_IS_IM_withoutfeatures.txt" - hla_file = "/projects/SUMMIT/WP1.2/immunogenicity_data/ivac/hlahd/20190916_alleles_extended.csv" - # test inest data set - # file = "/flash/projects/WP3/AnFranziska/AnFranziska/head_seqs.txt" - # hla_file = "/flash/projects/WP3/AnFranziska/AnFranziska/alleles.csv" - dat = data_import.import_dat_icam(file, False) - if "+-13_AA_(SNV)_/_-15_AA_to_STOP_(INDEL)" in dat[0]: - dat = data_import.change_col_names(dat) - # available MHC alleles - set_available_mhc = predict_all_epitopes.Bunchepitopes().load_available_hla_alleles() - # hla allele of patients - patient_hlaI = predict_all_epitopes.Bunchepitopes().load_patient_hla_I_allels(hla_file) - patient_hlaII = predict_all_epitopes.Bunchepitopes().load_patient_hla_II_allels(hla_file) - - print(patient_hlaI) - print(patient_hlaII) - - for ii, i in enumerate(dat[1]): - if ii < 2: - print(ii) - dict_epi = epitope.Epitope() - dict_epi.init_properties(dat[0], dat[1][ii]) - dict_epi.add_features(self_similarity.position_of_mutation_epitope(dict_epi.properties, MHC_I), - "pos_MUT_MHCI") - np = netmhcpan_prediction.NetmhcpanBestPrediction() - xmer_mut = dict_epi.properties["X..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."] - tmp_fasta_file = tempfile.NamedTemporaryFile(prefix="tmp_singleseq_", suffix=".fasta", delete=False) - tmp_fasta = tmp_fasta_file.name - print(tmp_fasta, file=sys.stderr) - tmp_prediction_file = tempfile.NamedTemporaryFile(prefix="netmhcpanpred_", suffix=".csv", delete=False) - tmp_prediction = tmp_prediction_file.name - print(tmp_prediction, file=sys.stderr) - np.generate_fasta(dict_epi.properties, tmp_fasta, mut=True) - alleles = np.get_hla_allels(dict_epi.properties, patient_hlaI) - # print alleles - np.mhc_prediction(alleles, set_available_mhc, tmp_fasta, tmp_prediction) - dict_epi.properties["Position_Xmer_Seq"] = np.mut_position_xmer_seq(dict_epi.properties) - preds = np.filter_binding_predictions(dict_epi.properties, tmp_prediction) - best_epi_affinity = np.minimal_binding_score(preds, rank=False) - dict_epi.add_features(np.add_best_epitope_info(best_epi_affinity, "Aff(nM)"), - "best_affinity_netmhcpan4") - dict_epi.add_features(np.add_best_epitope_info(best_epi_affinity, "Icore"), - "best_affinity_epitope_netmhcpan4 ") - dict_epi.add_features(np.add_best_epitope_info(best_epi_affinity, "HLA"), "best4_affinity_allele") - xmer_wt = dict_epi.properties["X.WT._..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."] - # print >> sys.stderr, "WT seq: " + xmer_wt - tmp_fasta_file = tempfile.NamedTemporaryFile(prefix="tmp_singleseq_", suffix=".fasta", delete=False) - tmp_fasta = tmp_fasta_file.name - tmp_prediction_file = tempfile.NamedTemporaryFile(prefix="netmhcpanpred_", suffix=".csv", delete=False) - tmp_prediction = tmp_prediction_file.name - print(tmp_prediction, file=sys.stderr) - np = netmhcpan_prediction.NetmhcpanBestPrediction() - np.generate_fasta(dict_epi.properties, tmp_fasta, mut=False) - np.mhc_prediction(alleles, set_available_mhc, tmp_fasta, tmp_prediction) - preds = np.filter_binding_predictions(dict_epi.properties, tmp_prediction) - best_epi_affinity = np.filter_for_WT_epitope(preds, - dict_epi.properties["best_affinity_epitope_netmhcpan4"], - dict_epi.properties["best4_affinity_allele"]) - dict_epi.add_features(np.add_best_epitope_info(best_epi_affinity, "Aff(nM)"), - "best_affinity_netmhcpan4_WT") - dict_epi.add_features(np.add_best_epitope_info(best_epi_affinity, "Icore"), - "best_affinity_epitope_netmhcpan4_WT") - dict_epi.add_features(self_similarity.position_of_mutation_epitope_affinity(dict_epi.properties), - "pos_MUT_MHCI_affinity_epi") - - sc = wrapper_neoag(dict_epi.properties) - print(sc, file=sys.stderr) - print(type(sc), file=sys.stderr) +from unittest import TestCase, SkipTest + +from input.neoag.neoag_gbm_model import NeoagCalculator +from input.helpers.runner import Runner +import input.tests.integration_tests.integration_test_tools as integration_test_tools + + +class TestNeoantigenFitness(TestCase): + + def setUp(self): + self.references, self.configuration = integration_test_tools.load_references() + self.fastafile = integration_test_tools.create_temp_aminoacid_fasta_file() + self.runner = Runner() + + def test_neoag(self): + result = NeoagCalculator(runner=self.runner, configuration=self.configuration).wrapper_neoag( + sample_id="12345", + mut_peptide="DDDDDV", + score_mut="0", + ref_peptide="DDDDDD", + peptide_variant_position="123") + self.assertTrue(isinstance(result, str)) + self.assertTrue(float(result) > 0) + + @SkipTest + def test_legacy(self): + # test with ott data set + # file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/MHC_prediction_netmhcpan4/testdat_ott.txt" + # hla_file ="/projects/SUMMIT/WP1.2/Literature_Cohorts/data_analysis/cohorts/ott/icam_ott/alleles.csv" + file = "/projects/SUMMIT/WP1.2/immunogenicity_data/ivac/input_annotation/20190328_IS_IM_withoutfeatures.txt" + hla_file = "/projects/SUMMIT/WP1.2/immunogenicity_data/ivac/hlahd/20190916_alleles_extended.csv" + # test inest data set + # file = "/flash/projects/WP3/AnFranziska/AnFranziska/head_seqs.txt" + # hla_file = "/flash/projects/WP3/AnFranziska/AnFranziska/alleles.csv" + dat = data_import.import_dat_icam(file, False) + if "+-13_AA_(SNV)_/_-15_AA_to_STOP_(INDEL)" in dat[0]: + dat = data_import.change_col_names(dat) + # available MHC alleles + set_available_mhc = predict_all_epitopes.Bunchepitopes().load_available_hla_alleles() + # hla allele of patients + patient_hlaI = predict_all_epitopes.Bunchepitopes().load_patient_hla_I_allels(hla_file) + patient_hlaII = predict_all_epitopes.Bunchepitopes().load_patient_hla_II_allels(hla_file) + + print(patient_hlaI) + print(patient_hlaII) + + for ii, i in enumerate(dat[1]): + if ii < 2: + print(ii) + dict_epi = epitope.Epitope() + dict_epi.init_properties(dat[0], dat[1][ii]) + dict_epi.add_features(self_similarity.position_of_mutation_epitope(dict_epi.properties, MHC_I), + "pos_MUT_MHCI") + np = netmhcpan_prediction.NetmhcpanBestPrediction() + xmer_mut = dict_epi.properties["X..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."] + tmp_fasta_file = tempfile.NamedTemporaryFile(prefix="tmp_singleseq_", suffix=".fasta", delete=False) + tmp_fasta = tmp_fasta_file.name + print(tmp_fasta, file=sys.stderr) + tmp_prediction_file = tempfile.NamedTemporaryFile(prefix="netmhcpanpred_", suffix=".csv", delete=False) + tmp_prediction = tmp_prediction_file.name + print(tmp_prediction, file=sys.stderr) + np.generate_fasta(dict_epi.properties, tmp_fasta, mut=True) + alleles = np.get_hla_allels(dict_epi.properties, patient_hlaI) + # print alleles + np.mhc_prediction(alleles, set_available_mhc, tmp_fasta, tmp_prediction) + dict_epi.properties["Position_Xmer_Seq"] = np.mut_position_xmer_seq(dict_epi.properties) + preds = np.filter_binding_predictions(dict_epi.properties, tmp_prediction) + best_epi_affinity = np.minimal_binding_score(preds, rank=False) + dict_epi.add_features(np.add_best_epitope_info(best_epi_affinity, "Aff(nM)"), + "best_affinity_netmhcpan4") + dict_epi.add_features(np.add_best_epitope_info(best_epi_affinity, "Icore"), + "best_affinity_epitope_netmhcpan4 ") + dict_epi.add_features(np.add_best_epitope_info(best_epi_affinity, "HLA"), "best4_affinity_allele") + xmer_wt = dict_epi.properties["X.WT._..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."] + # print >> sys.stderr, "WT seq: " + xmer_wt + tmp_fasta_file = tempfile.NamedTemporaryFile(prefix="tmp_singleseq_", suffix=".fasta", delete=False) + tmp_fasta = tmp_fasta_file.name + tmp_prediction_file = tempfile.NamedTemporaryFile(prefix="netmhcpanpred_", suffix=".csv", delete=False) + tmp_prediction = tmp_prediction_file.name + print(tmp_prediction, file=sys.stderr) + np = netmhcpan_prediction.NetmhcpanBestPrediction() + np.generate_fasta(dict_epi.properties, tmp_fasta, mut=False) + np.mhc_prediction(alleles, set_available_mhc, tmp_fasta, tmp_prediction) + preds = np.filter_binding_predictions(dict_epi.properties, tmp_prediction) + best_epi_affinity = np.filter_for_WT_epitope(preds, + dict_epi.properties["best_affinity_epitope_netmhcpan4"], + dict_epi.properties["best4_affinity_allele"]) + dict_epi.add_features(np.add_best_epitope_info(best_epi_affinity, "Aff(nM)"), + "best_affinity_netmhcpan4_WT") + dict_epi.add_features(np.add_best_epitope_info(best_epi_affinity, "Icore"), + "best_affinity_epitope_netmhcpan4_WT") + dict_epi.add_features(self_similarity.position_of_mutation_epitope_affinity(dict_epi.properties), + "pos_MUT_MHCI_affinity_epi") + + sc = wrapper_neoag(dict_epi.properties) + print(sc, file=sys.stderr) + print(type(sc), file=sys.stderr) diff --git a/input/tests/integration_tests/test_neoantigen_fitness.py b/input/tests/integration_tests/test_neoantigen_fitness.py index 7ae0cc15..d47d00c4 100755 --- a/input/tests/integration_tests/test_neoantigen_fitness.py +++ b/input/tests/integration_tests/test_neoantigen_fitness.py @@ -1,50 +1,50 @@ -from collections import defaultdict -from unittest import TestCase - -from input.neoantigen_fitness.neoantigen_fitness import NeoantigenFitnessCalculator -from input.helpers.runner import Runner -import input.tests.integration_tests.integration_test_tools as integration_test_tools - - -class TestNeoantigenFitness(TestCase): - - def setUp(self): - self.references, self.configuration, self.fastafile = self._load_references() - self.neoantigen_fitness_calculator = NeoantigenFitnessCalculator( - runner=Runner(), configuration=self.configuration) - - def _load_references(self): - references, configuration = integration_test_tools.load_references() - fastafile = integration_test_tools.create_temp_aminoacid_fasta_file() - return references, configuration, fastafile - - def test_pathogen_similarity(self): - # tests a pathogen sequence and expects 1.0 similarity - result = self.neoantigen_fitness_calculator.wrap_pathogen_similarity( - mutation='FIAGLIAIV', - iedb=self.references.iedb) - self.assertEqual('1.0', result) - # tests a modified pathogen sequence and expects something between 0 and 1 - result = self.neoantigen_fitness_calculator.wrap_pathogen_similarity( - mutation='FIAGDAAIV', - iedb=self.references.iedb) - self.assertLess(float(result), 1.0) - self.assertGreater(float(result), 0.0) - # tests a non pathogen sequence and expects 0 similarity - result = self.neoantigen_fitness_calculator.wrap_pathogen_similarity( - mutation='DDDDDMMDD', - iedb=self.references.iedb) - self.assertEqual('0', result) - - def test_amplitude_mhc(self): - self.assertEqual('1.0', self.neoantigen_fitness_calculator.calculate_amplitude_mhc( - score_mutation="1.0", score_wild_type="1.0")) - self.assertEqual('0.9997000899730081', self.neoantigen_fitness_calculator.calculate_amplitude_mhc( - score_mutation="1.0", score_wild_type="1.0", apply_correction=True)) - - def test_recognition_potential(self): - props = defaultdict(lambda: "1.0") - props['Mutation_in_anchor_netmhcpan'] = '0' - props['Mutation_in_anchor_netmhcpan_9mer'] = '0' - self.assertEqual('1.0', self.neoantigen_fitness_calculator.calculate_recognition_potential( - amplitude="1.0", pathogen_similarity="1.0", mutation_in_anchor="0")) +from collections import defaultdict +from unittest import TestCase + +from input.neoantigen_fitness.neoantigen_fitness import NeoantigenFitnessCalculator +from input.helpers.runner import Runner +import input.tests.integration_tests.integration_test_tools as integration_test_tools + + +class TestNeoantigenFitness(TestCase): + + def setUp(self): + self.references, self.configuration, self.fastafile = self._load_references() + self.neoantigen_fitness_calculator = NeoantigenFitnessCalculator( + runner=Runner(), configuration=self.configuration) + + def _load_references(self): + references, configuration = integration_test_tools.load_references() + fastafile = integration_test_tools.create_temp_aminoacid_fasta_file() + return references, configuration, fastafile + + def test_pathogen_similarity(self): + # tests a pathogen sequence and expects 1.0 similarity + result = self.neoantigen_fitness_calculator.wrap_pathogen_similarity( + mutation='FIAGLIAIV', + iedb=self.references.iedb) + self.assertEqual('1.0', result) + # tests a modified pathogen sequence and expects something between 0 and 1 + result = self.neoantigen_fitness_calculator.wrap_pathogen_similarity( + mutation='FIAGDAAIV', + iedb=self.references.iedb) + self.assertLess(float(result), 1.0) + self.assertGreater(float(result), 0.0) + # tests a non pathogen sequence and expects 0 similarity + result = self.neoantigen_fitness_calculator.wrap_pathogen_similarity( + mutation='DDDDDMMDD', + iedb=self.references.iedb) + self.assertEqual('0', result) + + def test_amplitude_mhc(self): + self.assertEqual('1.0', self.neoantigen_fitness_calculator.calculate_amplitude_mhc( + score_mutation="1.0", score_wild_type="1.0")) + self.assertEqual('0.9997000899730081', self.neoantigen_fitness_calculator.calculate_amplitude_mhc( + score_mutation="1.0", score_wild_type="1.0", apply_correction=True)) + + def test_recognition_potential(self): + props = defaultdict(lambda: "1.0") + props['Mutation_in_anchor_netmhcpan'] = '0' + props['Mutation_in_anchor_netmhcpan_9mer'] = '0' + self.assertEqual('1.0', self.neoantigen_fitness_calculator.calculate_recognition_potential( + amplitude="1.0", pathogen_similarity="1.0", mutation_in_anchor="0")) diff --git a/input/tests/integration_tests/test_netmhcpan.py b/input/tests/integration_tests/test_netmhcpan.py index dfbc23be..da4d5c9b 100755 --- a/input/tests/integration_tests/test_netmhcpan.py +++ b/input/tests/integration_tests/test_netmhcpan.py @@ -1,96 +1,96 @@ -import os -from unittest import TestCase - -import input.tests.integration_tests.integration_test_tools as integration_test_tools -from input import MHC_I, MHC_II -from input.helpers import intermediate_files -from input.helpers.runner import Runner -from input.netmhcpan4.netmhcIIpan_prediction import NetMhcIIPanPredictor -from input.netmhcpan4.netmhcpan_prediction import NetMhcPanPredictor -from input.tests import TEST_HLAI_ALLELES, TEST_HLAII_ALLELES - - -class TestNetMhcPanPredictor(TestCase): - - def setUp(self): - self.references, self.configuration = integration_test_tools.load_references() - self.runner = Runner() - - def test_netmhcpan_epitope_iedb(self): - netmhcpan_predictor = NetMhcPanPredictor(runner=self.runner, configuration=self.configuration) - # this is an epitope from IEDB of length 9 - mutated = 'NLVPMVATV' - tmp_prediction = intermediate_files.create_temp_file(prefix="netmhcpanpred_", suffix=".csv") - tmp_fasta = intermediate_files.create_temp_fasta(sequences=[mutated], prefix="tmp_") - netmhcpan_predictor.mhc_prediction( - tmpfasta=tmp_fasta, tmppred=tmp_prediction, hla_alleles=TEST_HLAI_ALLELES, - set_available_mhc=self.references.load_available_hla_alleles(mhc=MHC_I)) - self.assertTrue(os.path.exists(tmp_prediction)) - self.assertEqual(166, len(open(tmp_prediction).readlines())) - header, rows = netmhcpan_predictor.filter_binding_predictions(4, tmp_prediction) - self.assertEqual(14, len(header)) # output has 14 columns - for r in rows: - self.assertEqual(14, len(r)) # each row has 14 columns - self.assertEqual(165, len(rows)) - - def test_netmhcpan_too_small_epitope(self): - netmhcpan_predictor = NetMhcPanPredictor(runner=self.runner, configuration=self.configuration) - mutated = 'NLVP' - tmp_prediction = intermediate_files.create_temp_file(prefix="netmhcpanpred_", suffix=".csv") - tmp_fasta = intermediate_files.create_temp_fasta(sequences=[mutated], prefix="tmp_") - netmhcpan_predictor.mhc_prediction( - tmpfasta=tmp_fasta, tmppred=tmp_prediction, hla_alleles=TEST_HLAI_ALLELES, - set_available_mhc=self.references.load_available_hla_alleles(mhc=MHC_I)) - self.assertTrue(os.path.exists(tmp_prediction)) - # TODO: this is writing ot the output file "No;peptides;derived;from;protein;ID;seq1;len;4.;Skipped" - self.assertEqual(55, len(open(tmp_prediction).readlines())) - - # TODO: it crashes here as it fails to parse the header. Fix and remove the try-except - try: - header, rows = netmhcpan_predictor.filter_binding_predictions(2, tmp_prediction) - self.assertEqual(14, len(header)) # output has 14 columns - for r in rows: - self.assertEqual(14, len(r)) # each row has 14 columns - self.assertEqual(0, len(rows)) - except: - pass - - def test_netmhc2pan_epitope_iedb(self): - netmhc2pan_predictor = NetMhcIIPanPredictor(runner=self.runner, configuration=self.configuration) - # this is an epitope from IEDB of length 15 - mutated = 'ENPVVHFFKNIVTPR' - tmp_prediction = intermediate_files.create_temp_file(prefix="netmhcpanpred_", suffix=".csv") - tmp_fasta = intermediate_files.create_temp_fasta(sequences=[mutated], prefix="tmp_") - netmhc2pan_predictor.mhcII_prediction( - tmpfasta=tmp_fasta, tmppred=tmp_prediction, hla_alleles=TEST_HLAII_ALLELES, - set_available_mhc=self.references.load_available_hla_alleles(mhc=MHC_II)) - self.assertTrue(os.path.exists(tmp_prediction)) - self.assertEqual(20, len(open(tmp_prediction).readlines())) - - header, rows = netmhc2pan_predictor.filter_binding_predictions(4, tmp_prediction) - self.assertEqual(12, len(header)) # output has 14 columns - for r in rows: - self.assertTrue(len(r) <= 12 or len(r) >= 10) # each row has 10 or 12 columns - self.assertEqual(19, len(rows)) - - def test_netmhc2pan_too_small_epitope(self): - netmhc2pan_predictor = NetMhcIIPanPredictor(runner=self.runner, configuration=self.configuration) - # this is an epitope from IEDB of length 15 - mutated = 'ENPVVH' - tmp_prediction = intermediate_files.create_temp_file(prefix="netmhcpanpred_", suffix=".csv") - tmp_fasta = intermediate_files.create_temp_fasta(sequences=[mutated], prefix="tmp_") - netmhc2pan_predictor.mhcII_prediction( - tmpfasta=tmp_fasta, tmppred=tmp_prediction, hla_alleles=TEST_HLAII_ALLELES, - set_available_mhc=self.references.load_available_hla_alleles(mhc=MHC_II)) - self.assertTrue(os.path.exists(tmp_prediction)) - self.assertEqual(1, len(open(tmp_prediction).readlines())) - - # TODO: it crashes here as it fails to parse the header. Fix and remove the try-except - try: - header, rows = netmhc2pan_predictor.filter_binding_predictions(4, tmp_prediction) - self.assertEqual(12, len(header)) # output has 14 columns - for r in rows: - self.assertTrue(len(r) <= 12 or len(r) >= 10) # each row has 10 or 12 columns - self.assertEqual(0, len(rows)) - except: +import os +from unittest import TestCase + +import input.tests.integration_tests.integration_test_tools as integration_test_tools +from input import MHC_I, MHC_II +from input.helpers import intermediate_files +from input.helpers.runner import Runner +from input.netmhcpan4.netmhcIIpan_prediction import NetMhcIIPanPredictor +from input.netmhcpan4.netmhcpan_prediction import NetMhcPanPredictor +from input.tests import TEST_HLAI_ALLELES, TEST_HLAII_ALLELES + + +class TestNetMhcPanPredictor(TestCase): + + def setUp(self): + self.references, self.configuration = integration_test_tools.load_references() + self.runner = Runner() + + def test_netmhcpan_epitope_iedb(self): + netmhcpan_predictor = NetMhcPanPredictor(runner=self.runner, configuration=self.configuration) + # this is an epitope from IEDB of length 9 + mutated = 'NLVPMVATV' + tmp_prediction = intermediate_files.create_temp_file(prefix="netmhcpanpred_", suffix=".csv") + tmp_fasta = intermediate_files.create_temp_fasta(sequences=[mutated], prefix="tmp_") + netmhcpan_predictor.mhc_prediction( + tmpfasta=tmp_fasta, tmppred=tmp_prediction, hla_alleles=TEST_HLAI_ALLELES, + set_available_mhc=self.references.load_available_hla_alleles(mhc=MHC_I)) + self.assertTrue(os.path.exists(tmp_prediction)) + self.assertEqual(166, len(open(tmp_prediction).readlines())) + header, rows = netmhcpan_predictor.filter_binding_predictions(4, tmp_prediction) + self.assertEqual(14, len(header)) # output has 14 columns + for r in rows: + self.assertEqual(14, len(r)) # each row has 14 columns + self.assertEqual(165, len(rows)) + + def test_netmhcpan_too_small_epitope(self): + netmhcpan_predictor = NetMhcPanPredictor(runner=self.runner, configuration=self.configuration) + mutated = 'NLVP' + tmp_prediction = intermediate_files.create_temp_file(prefix="netmhcpanpred_", suffix=".csv") + tmp_fasta = intermediate_files.create_temp_fasta(sequences=[mutated], prefix="tmp_") + netmhcpan_predictor.mhc_prediction( + tmpfasta=tmp_fasta, tmppred=tmp_prediction, hla_alleles=TEST_HLAI_ALLELES, + set_available_mhc=self.references.load_available_hla_alleles(mhc=MHC_I)) + self.assertTrue(os.path.exists(tmp_prediction)) + # TODO: this is writing ot the output file "No;peptides;derived;from;protein;ID;seq1;len;4.;Skipped" + self.assertEqual(55, len(open(tmp_prediction).readlines())) + + # TODO: it crashes here as it fails to parse the header. Fix and remove the try-except + try: + header, rows = netmhcpan_predictor.filter_binding_predictions(2, tmp_prediction) + self.assertEqual(14, len(header)) # output has 14 columns + for r in rows: + self.assertEqual(14, len(r)) # each row has 14 columns + self.assertEqual(0, len(rows)) + except: + pass + + def test_netmhc2pan_epitope_iedb(self): + netmhc2pan_predictor = NetMhcIIPanPredictor(runner=self.runner, configuration=self.configuration) + # this is an epitope from IEDB of length 15 + mutated = 'ENPVVHFFKNIVTPR' + tmp_prediction = intermediate_files.create_temp_file(prefix="netmhcpanpred_", suffix=".csv") + tmp_fasta = intermediate_files.create_temp_fasta(sequences=[mutated], prefix="tmp_") + netmhc2pan_predictor.mhcII_prediction( + tmpfasta=tmp_fasta, tmppred=tmp_prediction, hla_alleles=TEST_HLAII_ALLELES, + set_available_mhc=self.references.load_available_hla_alleles(mhc=MHC_II)) + self.assertTrue(os.path.exists(tmp_prediction)) + self.assertEqual(20, len(open(tmp_prediction).readlines())) + + header, rows = netmhc2pan_predictor.filter_binding_predictions(4, tmp_prediction) + self.assertEqual(12, len(header)) # output has 14 columns + for r in rows: + self.assertTrue(len(r) <= 12 or len(r) >= 10) # each row has 10 or 12 columns + self.assertEqual(19, len(rows)) + + def test_netmhc2pan_too_small_epitope(self): + netmhc2pan_predictor = NetMhcIIPanPredictor(runner=self.runner, configuration=self.configuration) + # this is an epitope from IEDB of length 15 + mutated = 'ENPVVH' + tmp_prediction = intermediate_files.create_temp_file(prefix="netmhcpanpred_", suffix=".csv") + tmp_fasta = intermediate_files.create_temp_fasta(sequences=[mutated], prefix="tmp_") + netmhc2pan_predictor.mhcII_prediction( + tmpfasta=tmp_fasta, tmppred=tmp_prediction, hla_alleles=TEST_HLAII_ALLELES, + set_available_mhc=self.references.load_available_hla_alleles(mhc=MHC_II)) + self.assertTrue(os.path.exists(tmp_prediction)) + self.assertEqual(1, len(open(tmp_prediction).readlines())) + + # TODO: it crashes here as it fails to parse the header. Fix and remove the try-except + try: + header, rows = netmhc2pan_predictor.filter_binding_predictions(4, tmp_prediction) + self.assertEqual(12, len(header)) # output has 14 columns + for r in rows: + self.assertTrue(len(r) <= 12 or len(r) >= 10) # each row has 10 or 12 columns + self.assertEqual(0, len(rows)) + except: pass \ No newline at end of file diff --git a/input/tests/integration_tests/test_tcell_predictor.py b/input/tests/integration_tests/test_tcell_predictor.py index 065cd18b..51c11096 100755 --- a/input/tests/integration_tests/test_tcell_predictor.py +++ b/input/tests/integration_tests/test_tcell_predictor.py @@ -1,52 +1,52 @@ -from collections import defaultdict -from unittest import TestCase - -import input.tests.integration_tests.integration_test_tools as integration_test_tools -from input.Tcell_predictor.tcellpredictor_wrapper import TcellPrediction - - -class TestTCellPredictor(TestCase): - - def setUp(self): - self.references, self.configuration = integration_test_tools.load_references() - self.fastafile = integration_test_tools.create_temp_aminoacid_fasta_file() - - def test_tcell_predictor(self): - tcell_predictor = TcellPrediction(references=self.references) - result = tcell_predictor.calculate_tcell_predictor_score(gene="BLAH", substitution='blaaaah', epitope="BLAHBLAH", score=5, threshold=10) - self.assertEqual("NA", result) - - -""" -# if full icam output table is passed to script - ''' - f = sys.argv[1] - dat = data_import.import_dat_icam(f, indel = False) - #print dat - #print full_dataset(dat) - l = full_dataset(dat, all = True) - write_ouptut_to_file(l) - ''' - - # test for input implementation - from input import epitope - - file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/MHC_prediction_netmhcpan4/testdat_ott.txt" - dat = data_import.import_dat_icam(file, False) - if "+-13_AA_(SNV)_/_-15_AA_to_STOP_(INDEL)" in dat[0]: - dat = data_import.change_col_names(dat) - - path_to_Tcell_predictor = my_path - - for ii,i in enumerate(dat[1]): - if ii < 10: - print ii - dict_epi = epitope.Epitope() - dict_epi.init_properties(dat[0], dat[1][ii]) - #print dict_epi.properties - tcellpred = Tcellprediction() - - tcellpred.main(dict_epi.properties) - print tcellpred.TcellPrdictionScore - print tcellpred.TcellPrdictionScore_9merPred -""" +from collections import defaultdict +from unittest import TestCase + +import input.tests.integration_tests.integration_test_tools as integration_test_tools +from input.Tcell_predictor.tcellpredictor_wrapper import TcellPrediction + + +class TestTCellPredictor(TestCase): + + def setUp(self): + self.references, self.configuration = integration_test_tools.load_references() + self.fastafile = integration_test_tools.create_temp_aminoacid_fasta_file() + + def test_tcell_predictor(self): + tcell_predictor = TcellPrediction(references=self.references) + result = tcell_predictor.calculate_tcell_predictor_score(gene="BLAH", substitution='blaaaah', epitope="BLAHBLAH", score=5, threshold=10) + self.assertEqual("NA", result) + + +""" +# if full icam output table is passed to script + ''' + f = sys.argv[1] + dat = data_import.import_dat_icam(f, indel = False) + #print dat + #print full_dataset(dat) + l = full_dataset(dat, all = True) + write_ouptut_to_file(l) + ''' + + # test for input implementation + from input import epitope + + file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/MHC_prediction_netmhcpan4/testdat_ott.txt" + dat = data_import.import_dat_icam(file, False) + if "+-13_AA_(SNV)_/_-15_AA_to_STOP_(INDEL)" in dat[0]: + dat = data_import.change_col_names(dat) + + path_to_Tcell_predictor = my_path + + for ii,i in enumerate(dat[1]): + if ii < 10: + print ii + dict_epi = epitope.Epitope() + dict_epi.init_properties(dat[0], dat[1][ii]) + #print dict_epi.properties + tcellpred = Tcellprediction() + + tcellpred.main(dict_epi.properties) + print tcellpred.TcellPrdictionScore + print tcellpred.TcellPrdictionScore_9merPred +""" diff --git a/input/tests/unit_tests/fake_classes.py b/input/tests/unit_tests/fake_classes.py index 039d8065..6d2532fd 100755 --- a/input/tests/unit_tests/fake_classes.py +++ b/input/tests/unit_tests/fake_classes.py @@ -1,15 +1,15 @@ -import os - -import input -from input.references import ReferenceFolder - - -class FakeReferenceFolder(ReferenceFolder): - - @staticmethod - def _check_reference_genome_folder(): - return os.environ.get(input.REFERENCE_FOLDER_ENV, "") - - @staticmethod - def _check_resources(resources): - pass +import os + +import input +from input.references import ReferenceFolder + + +class FakeReferenceFolder(ReferenceFolder): + + @staticmethod + def _check_reference_genome_folder(): + return os.environ.get(input.REFERENCE_FOLDER_ENV, "") + + @staticmethod + def _check_resources(resources): + pass diff --git a/input/tests/unit_tests/test_dependencies_configuration.py b/input/tests/unit_tests/test_dependencies_configuration.py index b78a7779..5257906a 100755 --- a/input/tests/unit_tests/test_dependencies_configuration.py +++ b/input/tests/unit_tests/test_dependencies_configuration.py @@ -1,65 +1,65 @@ -import os -import unittest -from unittest import TestCase - -import input -import input.tests.unit_tests.tools as test_tools -from input.exceptions import INPuTConfigurationException -from input.references import DependenciesConfiguration - - -class TestDependenciesConfiguration(TestCase): - - def setUp(self): - self.variables = { - input.INPUT_BLASTP_ENV: '/path/to/blastp', - input.INPUT_NETMHC2PAN_ENV: '/path/to/netmhc2pan', - input.INPUT_NETMHCPAN_ENV: '/path/to/netmhcpan', - input.INPUT_RSCRIPT_ENV: '/path/to/rscript', - input.INPUT_MIXMHCPRED_ENV: '/path/to/mixmhcpred', - input.INPUT_MIXMHC2PRED_ENV: '/path/to/mixmhc2pred' - } - self.non_existing = '/path/to/nothing' - test_tools._mock_file_existence( - existing_files=self.variables.values(), - unexisting_files=[self.non_existing] - ) - - def _load_env_variables(self): - for k, v in self.variables.items(): - os.environ[k] = v - - def test_not_provided_variable(self): - self._load_env_variables() - for v in self.variables.keys(): - del os.environ[v] - with self.assertRaises(INPuTConfigurationException): - DependenciesConfiguration() - - def test_empty_string_variable(self): - self._load_env_variables() - for v in self.variables.keys(): - os.environ[v] = "" - with self.assertRaises(INPuTConfigurationException): - DependenciesConfiguration() - - def test_non_existing_variable(self): - self._load_env_variables() - for v in self.variables.keys(): - os.environ[v] = self.non_existing - with self.assertRaises(INPuTConfigurationException): - DependenciesConfiguration() - - def test_all_resources_exist(self): - self._load_env_variables() - config = DependenciesConfiguration() - self.assertTrue(config.blastp == self.variables[input.INPUT_BLASTP_ENV]) - self.assertTrue(config.mix_mhc2_pred == self.variables[input.INPUT_MIXMHC2PRED_ENV]) - self.assertTrue(config.mix_mhc_pred == self.variables[input.INPUT_MIXMHCPRED_ENV]) - self.assertTrue(config.rscript == self.variables[input.INPUT_RSCRIPT_ENV]) - self.assertTrue(config.net_mhc_pan == self.variables[input.INPUT_NETMHCPAN_ENV]) - self.assertTrue(config.net_mhc2_pan == self.variables[input.INPUT_NETMHC2PAN_ENV]) - - -if __name__ == "__main__": - unittest.main() +import os +import unittest +from unittest import TestCase + +import input +import input.tests.unit_tests.tools as test_tools +from input.exceptions import INPuTConfigurationException +from input.references import DependenciesConfiguration + + +class TestDependenciesConfiguration(TestCase): + + def setUp(self): + self.variables = { + input.INPUT_BLASTP_ENV: '/path/to/blastp', + input.INPUT_NETMHC2PAN_ENV: '/path/to/netmhc2pan', + input.INPUT_NETMHCPAN_ENV: '/path/to/netmhcpan', + input.INPUT_RSCRIPT_ENV: '/path/to/rscript', + input.INPUT_MIXMHCPRED_ENV: '/path/to/mixmhcpred', + input.INPUT_MIXMHC2PRED_ENV: '/path/to/mixmhc2pred' + } + self.non_existing = '/path/to/nothing' + test_tools._mock_file_existence( + existing_files=self.variables.values(), + unexisting_files=[self.non_existing] + ) + + def _load_env_variables(self): + for k, v in self.variables.items(): + os.environ[k] = v + + def test_not_provided_variable(self): + self._load_env_variables() + for v in self.variables.keys(): + del os.environ[v] + with self.assertRaises(INPuTConfigurationException): + DependenciesConfiguration() + + def test_empty_string_variable(self): + self._load_env_variables() + for v in self.variables.keys(): + os.environ[v] = "" + with self.assertRaises(INPuTConfigurationException): + DependenciesConfiguration() + + def test_non_existing_variable(self): + self._load_env_variables() + for v in self.variables.keys(): + os.environ[v] = self.non_existing + with self.assertRaises(INPuTConfigurationException): + DependenciesConfiguration() + + def test_all_resources_exist(self): + self._load_env_variables() + config = DependenciesConfiguration() + self.assertTrue(config.blastp == self.variables[input.INPUT_BLASTP_ENV]) + self.assertTrue(config.mix_mhc2_pred == self.variables[input.INPUT_MIXMHC2PRED_ENV]) + self.assertTrue(config.mix_mhc_pred == self.variables[input.INPUT_MIXMHCPRED_ENV]) + self.assertTrue(config.rscript == self.variables[input.INPUT_RSCRIPT_ENV]) + self.assertTrue(config.net_mhc_pan == self.variables[input.INPUT_NETMHCPAN_ENV]) + self.assertTrue(config.net_mhc2_pan == self.variables[input.INPUT_NETMHC2PAN_ENV]) + + +if __name__ == "__main__": + unittest.main() diff --git a/input/tests/unit_tests/test_predict_all_epitopes.py b/input/tests/unit_tests/test_predict_all_epitopes.py index f04ad770..3cdde1f2 100755 --- a/input/tests/unit_tests/test_predict_all_epitopes.py +++ b/input/tests/unit_tests/test_predict_all_epitopes.py @@ -1,24 +1,24 @@ -import os -import unittest -from unittest import TestCase - -import input -from input.exceptions import INPuTConfigurationException -from input.predict_all_epitopes import BunchEpitopes - - -class TestPredictAllEpitopes(TestCase): - - def test_reference_environment_variable_is_required(self): - # del os.environ[input.REFERENCE_FOLDER_ENV] - with self.assertRaises(INPuTConfigurationException): - BunchEpitopes() - - def test_empty_reference_folder_fails(self): - os.environ[input.REFERENCE_FOLDER_ENV] = 'dummy' - with self.assertRaises(INPuTConfigurationException): - BunchEpitopes() - - -if __name__ == "__main__": - unittest.main() +import os +import unittest +from unittest import TestCase + +import input +from input.exceptions import INPuTConfigurationException +from input.predict_all_epitopes import BunchEpitopes + + +class TestPredictAllEpitopes(TestCase): + + def test_reference_environment_variable_is_required(self): + # del os.environ[input.REFERENCE_FOLDER_ENV] + with self.assertRaises(INPuTConfigurationException): + BunchEpitopes() + + def test_empty_reference_folder_fails(self): + os.environ[input.REFERENCE_FOLDER_ENV] = 'dummy' + with self.assertRaises(INPuTConfigurationException): + BunchEpitopes() + + +if __name__ == "__main__": + unittest.main() diff --git a/input/tests/unit_tests/test_reference_folder.py b/input/tests/unit_tests/test_reference_folder.py index c6fd101a..c0c417c9 100755 --- a/input/tests/unit_tests/test_reference_folder.py +++ b/input/tests/unit_tests/test_reference_folder.py @@ -1,47 +1,47 @@ -import os -import unittest -from unittest import TestCase - -import input -import input.tests.unit_tests.tools as test_tools -from input.exceptions import INPuTConfigurationException -from input.references import ReferenceFolder -from input.tests.unit_tests.fake_classes import FakeReferenceFolder - - -class TestReferenceFolder(TestCase): - - def setUp(self): - os.environ[input.REFERENCE_FOLDER_ENV] = "." - self.fake_reference_folder = FakeReferenceFolder() - - def test_not_provided_reference(self): - del os.environ[input.REFERENCE_FOLDER_ENV] - with self.assertRaises(INPuTConfigurationException): - ReferenceFolder() - - def test_empty_string_reference(self): - os.environ[input.REFERENCE_FOLDER_ENV] = "" - with self.assertRaises(INPuTConfigurationException): - ReferenceFolder() - - def test_non_existing_reference(self): - os.environ[input.REFERENCE_FOLDER_ENV] = "/non_existing_folder" - with self.assertRaises(INPuTConfigurationException): - ReferenceFolder() - - def test_all_resources_exist(self): - test_tools._mock_file_existence(existing_files=self.fake_reference_folder.resources) - ReferenceFolder() - - def test_one_resource_do_not_exist(self): - test_tools._mock_file_existence( - existing_files=self.fake_reference_folder.resources[1:len(self.fake_reference_folder.resources)], - unexisting_files=[self.fake_reference_folder.resources[0]] - ) - with self.assertRaises(INPuTConfigurationException): - ReferenceFolder() - - -if __name__ == "__main__": - unittest.main() +import os +import unittest +from unittest import TestCase + +import input +import input.tests.unit_tests.tools as test_tools +from input.exceptions import INPuTConfigurationException +from input.references import ReferenceFolder +from input.tests.unit_tests.fake_classes import FakeReferenceFolder + + +class TestReferenceFolder(TestCase): + + def setUp(self): + os.environ[input.REFERENCE_FOLDER_ENV] = "." + self.fake_reference_folder = FakeReferenceFolder() + + def test_not_provided_reference(self): + del os.environ[input.REFERENCE_FOLDER_ENV] + with self.assertRaises(INPuTConfigurationException): + ReferenceFolder() + + def test_empty_string_reference(self): + os.environ[input.REFERENCE_FOLDER_ENV] = "" + with self.assertRaises(INPuTConfigurationException): + ReferenceFolder() + + def test_non_existing_reference(self): + os.environ[input.REFERENCE_FOLDER_ENV] = "/non_existing_folder" + with self.assertRaises(INPuTConfigurationException): + ReferenceFolder() + + def test_all_resources_exist(self): + test_tools._mock_file_existence(existing_files=self.fake_reference_folder.resources) + ReferenceFolder() + + def test_one_resource_do_not_exist(self): + test_tools._mock_file_existence( + existing_files=self.fake_reference_folder.resources[1:len(self.fake_reference_folder.resources)], + unexisting_files=[self.fake_reference_folder.resources[0]] + ) + with self.assertRaises(INPuTConfigurationException): + ReferenceFolder() + + +if __name__ == "__main__": + unittest.main() diff --git a/input/tests/unit_tests/test_runner.py b/input/tests/unit_tests/test_runner.py index 7d41ccf2..0472b644 100755 --- a/input/tests/unit_tests/test_runner.py +++ b/input/tests/unit_tests/test_runner.py @@ -1,23 +1,23 @@ -import unittest -from unittest import TestCase - -from input.helpers.runner import Runner - - -class TestRunner(TestCase): - - def setUp(self): - self.runner = Runner() - - def test_runner(self): - output, errors = self.runner.run_command(cmd=['python', '-V']) - self.assertTrue('Python 3.7' in output) - self.assertTrue(len(errors) == 0) - - def test_runner_failure(self): - with self.assertRaises(Exception): - self.runner.run_command(cmd=['nocommandwiththisname']) - - -if __name__ == "__main__": - unittest.main() +import unittest +from unittest import TestCase + +from input.helpers.runner import Runner + + +class TestRunner(TestCase): + + def setUp(self): + self.runner = Runner() + + def test_runner(self): + output, errors = self.runner.run_command(cmd=['python', '-V']) + self.assertTrue('Python 3.7' in output) + self.assertTrue(len(errors) == 0) + + def test_runner_failure(self): + with self.assertRaises(Exception): + self.runner.run_command(cmd=['nocommandwiththisname']) + + +if __name__ == "__main__": + unittest.main() diff --git a/input/tests/unit_tests/test_self_similarity.py b/input/tests/unit_tests/test_self_similarity.py index 021829f5..43bff547 100755 --- a/input/tests/unit_tests/test_self_similarity.py +++ b/input/tests/unit_tests/test_self_similarity.py @@ -1,38 +1,38 @@ -from unittest import TestCase - -import input.self_similarity.self_similarity as self_similarity -from input import MHC_I, MHC_II - - -class TestSelfSimilarity(TestCase): - - def test_get_self_similarity(self): - result = self_similarity.get_self_similarity(wild_type="DDD", mutation="DDD") - self.assertEqual('1.0', result) - - def test_is_improved_binder(self): - result = self_similarity.is_improved_binder( - score_mutation='1.0', score_wild_type='1.3') - self.assertEqual('1', result) - - def test_position_mutation(self): - position = self_similarity.position_of_mutation_epitope(wild_type="AAAAAA", mutation="AAANAA") - self.assertEqual(position, "4") - position = self_similarity.position_of_mutation_epitope(wild_type="AAAAAA", mutation="AAAAAA") - self.assertEqual(position, "-1") - position = self_similarity.position_of_mutation_epitope(wild_type="AAAAAA", mutation="AANNNN") - self.assertEqual(position, "6") - - def test_compute_self_similarity_calculator(self): - - s = self_similarity.SelfSimilarityCalculator() - self.assertEqual(s.compute_k_hat_3("AAAAA", "AAAAA"), 1.0) - for i in range(5): - self.assertTrue(s.compute_k_hat_3("AAAAA", "WWWWW" * (i + 1)) < 1.0) - for i in list(s.k1.keys()): - if i == "A": - self.assertTrue(s.compute_k_hat_3("AAAAA", "AA" + i + "AA") == 1.0) - else: - self.assertTrue(s.compute_k_hat_3("AAAAA", "AA" + i + "AA") < 1.0) - - +from unittest import TestCase + +import input.self_similarity.self_similarity as self_similarity +from input import MHC_I, MHC_II + + +class TestSelfSimilarity(TestCase): + + def test_get_self_similarity(self): + result = self_similarity.get_self_similarity(wild_type="DDD", mutation="DDD") + self.assertEqual('1.0', result) + + def test_is_improved_binder(self): + result = self_similarity.is_improved_binder( + score_mutation='1.0', score_wild_type='1.3') + self.assertEqual('1', result) + + def test_position_mutation(self): + position = self_similarity.position_of_mutation_epitope(wild_type="AAAAAA", mutation="AAANAA") + self.assertEqual(position, "4") + position = self_similarity.position_of_mutation_epitope(wild_type="AAAAAA", mutation="AAAAAA") + self.assertEqual(position, "-1") + position = self_similarity.position_of_mutation_epitope(wild_type="AAAAAA", mutation="AANNNN") + self.assertEqual(position, "6") + + def test_compute_self_similarity_calculator(self): + + s = self_similarity.SelfSimilarityCalculator() + self.assertEqual(s.compute_k_hat_3("AAAAA", "AAAAA"), 1.0) + for i in range(5): + self.assertTrue(s.compute_k_hat_3("AAAAA", "WWWWW" * (i + 1)) < 1.0) + for i in list(s.k1.keys()): + if i == "A": + self.assertTrue(s.compute_k_hat_3("AAAAA", "AA" + i + "AA") == 1.0) + else: + self.assertTrue(s.compute_k_hat_3("AAAAA", "AA" + i + "AA") < 1.0) + + From 93fc91617a9bcc907bbba3e1792f785e5d74def3 Mon Sep 17 00:00:00 2001 From: Pablo Riesgo Ferreiro Date: Wed, 17 Jun 2020 21:34:59 +0200 Subject: [PATCH 055/105] patiend id passed as a command line parameter --- input/command_line.py | 10 +++++-- input/helpers/data_import.py | 6 ---- input/helpers/properties_manager.py | 11 +------- ...combine_netmhcpan_pred_multiple_binders.py | 2 -- input/predict_all_epitopes.py | 28 ++++++++----------- input/tests/integration_tests/test_input.py | 8 ++++-- 6 files changed, 24 insertions(+), 41 deletions(-) diff --git a/input/command_line.py b/input/command_line.py index d3f8e092..d76d2740 100755 --- a/input/command_line.py +++ b/input/command_line.py @@ -7,9 +7,12 @@ def input_cli(): parser = ArgumentParser(description='adds patient information given in sample file of a cohort to merged icam file') - parser.add_argument('-i', '--icam_file', dest='icam_file', help='define iCaM file which should be annotated', + parser.add_argument('-i', '--icam-file', dest='icam_file', help='define iCaM file which should be annotated', required=True) - parser.add_argument('-a', '--allele_file', dest='allele_file', help='define file with hla alleles of patients', + # TODO: once we support the input from the models this parameter will not be required + parser.add_argument('-p', '--patient-id', dest='patient_id', help='the patient id for the iCaM file', + required=True) + parser.add_argument('-a', '--allele-file', dest='allele_file', help='define file with hla alleles of patients', required=True) parser.add_argument('-t', '--tissue', dest='tissue', help='define tissue of cancer origin', default="skin") parser.add_argument('-f', '--frameshift', dest='frameshift', @@ -20,6 +23,7 @@ def input_cli(): args = parser.parse_args() icam_file = args.icam_file + patient_id = args.patient_id allele_file = args.allele_file tissue = args.tissue indel = args.frameshift @@ -32,7 +36,7 @@ def input_cli(): bunchepitopes = BunchEpitopes() logger.info("Starting INPuT...") - bunchepitopes.wrapper_table_add_feature_annotation(icam_file, indel, allele_file, tissue, tumour_content_file) + bunchepitopes.wrapper_table_add_feature_annotation(icam_file, patient_id, indel, allele_file, tissue, tumour_content_file) logger.info("Finished INPuT...") ''' file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/INPuT/nonprogramm_files/test_SD.csv" diff --git a/input/helpers/data_import.py b/input/helpers/data_import.py index c5d563ca..1e26d1c5 100755 --- a/input/helpers/data_import.py +++ b/input/helpers/data_import.py @@ -185,12 +185,6 @@ def change_col_names(tuple_dat_head): head_new[scII_ind] = "MHC_II_score_.best_prediction." head_new[scIIwt_ind] = "MHC_II_score_.WT." - try: - patid = head_new.index("patient") - head_new[patid] = "patient.id" - except ValueError: - pass - return head_new, dat_new else: diff --git a/input/helpers/properties_manager.py b/input/helpers/properties_manager.py index 91b55251..4241828b 100755 --- a/input/helpers/properties_manager.py +++ b/input/helpers/properties_manager.py @@ -1,11 +1,8 @@ from input import MHC_I, MHC_II from input.exceptions import INPuTInputParametersException -PATIENT_ID3 = "patient.x" -PATIENT_ID2 = "patient" PATIENT_ID = "patient.id" - def get_gene(properties): if "gene.x" in properties: gene = properties["gene.x"] @@ -88,10 +85,4 @@ def get_hla_allele(props, hla_patient_dict): def get_patient_id(props): - if PATIENT_ID in props: - patient_id = props[PATIENT_ID] - elif PATIENT_ID2 in props: - patient_id = props[PATIENT_ID2] - else: - patient_id = props[PATIENT_ID3] - return patient_id \ No newline at end of file + return props.get(PATIENT_ID) \ No newline at end of file diff --git a/input/netmhcpan4/combine_netmhcpan_pred_multiple_binders.py b/input/netmhcpan4/combine_netmhcpan_pred_multiple_binders.py index e9b3ff01..61ec33fa 100755 --- a/input/netmhcpan4/combine_netmhcpan_pred_multiple_binders.py +++ b/input/netmhcpan4/combine_netmhcpan_pred_multiple_binders.py @@ -81,9 +81,7 @@ def main(self, xmer_wt, xmer_mut, alleles, set_available_mhc): predicts MHC epitopes; returns on one hand best binder and on the other hand multiple binder analysis is performed """ ### PREDICTION FOR MUTATED SEQUENCE - logger.info("MUT seq: {}".format(xmer_mut)) tmp_prediction = intermediate_files.create_temp_file(prefix="netmhcpanpred_", suffix=".csv") - logger.debug(tmp_prediction) np = netmhcpan_prediction.NetMhcPanPredictor(runner=self.runner, configuration=self.configuration) mb = multiple_binders.MultipleBinding() tmp_fasta = intermediate_files.create_temp_fasta(sequences=[xmer_mut], prefix="tmp_singleseq_") diff --git a/input/predict_all_epitopes.py b/input/predict_all_epitopes.py index 29aa4d72..13edae7a 100755 --- a/input/predict_all_epitopes.py +++ b/input/predict_all_epitopes.py @@ -7,6 +7,7 @@ from input import MHC_I, MHC_II from input.epitope import Epitope from input.helpers import data_import +from input.helpers.properties_manager import PATIENT_ID from input.helpers.runner import Runner from input.new_features import conservation_scores from input.new_features.conservation_scores import ProveanAnnotator @@ -89,7 +90,7 @@ def load_patient_hla_I_allels(path_to_hla_file): w = line.rstrip().split(";") if w[0] not in patient_alleles_dict: patient_alleles_dict[w[0]] = w[2:] - logger.info("HLA-I alleles: {}".format(patient_alleles_dict)) + logger.info("HLA-I alleles loaded") return patient_alleles_dict @staticmethod @@ -105,7 +106,7 @@ def load_patient_hla_II_allels(path_to_hla_file): w = line.rstrip().split(";") # cheating --> overwriting hla I --> check format patient_alleles_dict[w[0]] = w[2:] - logger.info("HLA-II alleles: {}".format(patient_alleles_dict)) + logger.info("HLA-II alleles loaded") return patient_alleles_dict @staticmethod @@ -127,7 +128,7 @@ def load_tumor_content_dict(path_to_patient_overview): tumour_content = w[tc_col] tumour_content_dict[patient] = tumour_content - logger.info("Tumor content: {}".format(tumour_content_dict)) + logger.info("Tumor content loaded") return tumour_content_dict @staticmethod @@ -186,30 +187,23 @@ def initialise_properties(self, data, path_to_hla_file, tissue, tumour_content_f self.rna_avail = self.load_rna_seq_avail_dict(tumour_content_file) self.provean_annotator = ProveanAnnotator(provean_file=prov_file, header_epitopes=data[0], epitopes=data[1]) - def wrapper_table_add_feature_annotation(self, file, indel, path_to_hla_file, tissue, tumour_content_file): + def wrapper_table_add_feature_annotation(self, icam_file, patient_id, indel, hla_file, tissue, tumour_content_file): """ Loads epitope data (if file has been not imported to R; colnames need to be changed), adds data to class that are needed to calculate, calls epitope class --> determination of epitope properties, write to txt file """ # import epitope data - dat = data_import.import_dat_icam(file, indel) + dat = data_import.import_dat_icam(icam_file, indel) if "+-13_AA_(SNV)_/_-15_AA_to_STOP_(INDEL)" in dat[0]: dat = data_import.change_col_names(dat) if "mutation_found_in_proteome" not in dat[0]: self.proteome_dictionary = self.load_proteome(self.references.uniprot) - # add patient id if _mut_set.txt.transcript.squish.somatic.freq is used - if ("patient" not in dat[0]) and ("patient.id" not in dat[0]): - try: - patient = file.split("/")[-3] - if "Pt" not in patient: - patient = file.split("/")[-1].split(".")[0] - except IndexError: - patient = file.split("/")[-1].split(".")[0] - dat[0].append("patient.id") - for ii, i in enumerate(dat[1]): - dat[1][ii].append(str(patient)) + # adds patient to the table + dat[0].append(PATIENT_ID) + for ii, i in enumerate(dat[1]): + dat[1][ii].append(str(patient_id)) # initialise information needed for feature calculation - self.initialise_properties(dat, path_to_hla_file, tissue, tumour_content_file) + self.initialise_properties(dat, hla_file, tissue, tumour_content_file) # feature calculation for each epitope for ii, i in enumerate(dat[1]): # dict for each epitope diff --git a/input/tests/integration_tests/test_input.py b/input/tests/integration_tests/test_input.py index 770e0b33..e9494574 100755 --- a/input/tests/integration_tests/test_input.py +++ b/input/tests/integration_tests/test_input.py @@ -14,19 +14,21 @@ def setUp(self): def test_input(self): """ This test is equivalent to the command line call: - input -i /projects/SUMMIT/WP1.2/input/development/Pt29.sequences4testing.txt + input -i /projects/SUMMIT/WP1.2/input/development/Pt29.sequences4testing.txt -p Pt29 -a /projects/SUMMIT/WP1.2/Literature_Cohorts/data_analysis/cohorts/vanallen/output_tables/20200106_alleles_extended.csv -tc /projects/SUMMIT/WP1.2/Literature_Cohorts/data_analysis/cohorts/vanallen/output_tables/vanallen_patient_overview.csv NOTE: we will need to check the output when the calculation of resuls and printing to stdout have been decoupled :return: """ + patient_id = 'Pt29' input_file = '/projects/SUMMIT/WP1.2/input/development/Pt29.sequences4testing.txt' alleles_file = '/projects/SUMMIT/WP1.2/Literature_Cohorts/data_analysis/cohorts/vanallen/output_tables/20200106_alleles_extended.csv' tumor_content_file = '/projects/SUMMIT/WP1.2/Literature_Cohorts/data_analysis/cohorts/vanallen/output_tables/vanallen_patient_overview.csv' BunchEpitopes().wrapper_table_add_feature_annotation( - file=input_file, + icam_file=input_file, + patient_id=patient_id, indel=False, - path_to_hla_file=alleles_file, + hla_file=alleles_file, tissue='skin', tumour_content_file=tumor_content_file) From 5318aa5a7c4f7f05aa985d79e7f04179c91bfa4e Mon Sep 17 00:00:00 2001 From: Pablo Riesgo Ferreiro Date: Fri, 19 Jun 2020 22:16:38 +0200 Subject: [PATCH 056/105] patient parsing to and from csv --- input/model/schema_conversion.py | 23 +++++++++++++++---- .../test_schema_conversion_proto.py | 20 ++++++++++++++-- 2 files changed, 36 insertions(+), 7 deletions(-) diff --git a/input/model/schema_conversion.py b/input/model/schema_conversion.py index 7f4d4559..7b4663c6 100755 --- a/input/model/schema_conversion.py +++ b/input/model/schema_conversion.py @@ -88,16 +88,16 @@ def _parse_hlas_table(hla_file): return alleles_stacked @staticmethod - def model2csv(neoantigens): + def model2csv(model_objects): """ - :param neoantigens: list of objects of class Neoantigen - :type neoantigens: list[Neoantigen] + :param model_objects: list of objects of subclass of betterproto.Message + :type model_objects: list[betterproto.Message] :rtype: pd.Dataframe """ - return json_normalize(data=[n.to_dict() for n in neoantigens]) + return json_normalize(data=[n.to_dict(include_default_values=True) for n in model_objects]) @staticmethod - def csv2model(dataframe): + def neoantigens_csv2model(dataframe): """ :param dataframe: the input CSV in a dataframe :type dataframe: pd.Dataframe @@ -109,6 +109,19 @@ def csv2model(dataframe): neoantigens.append(Neoantigen().from_dict(SchemaConverter._flat_dict2nested_dict(flat_dict=row.to_dict()))) return neoantigens + @staticmethod + def patient_metadata_csv2model(dataframe): + """ + :param dataframe: the patient metadata CSV in a dataframe + :type dataframe: pd.Dataframe + :return: the list of objects of type Patient + :rtype: list[Patient] + """ + patients = [] + for _, row in dataframe.iterrows(): + patients.append(Patient().from_dict(row.to_dict())) + return patients + @staticmethod def _flat_dict2nested_dict(flat_dict): """ diff --git a/input/tests/unit_tests/test_schema_conversion_proto.py b/input/tests/unit_tests/test_schema_conversion_proto.py index 4a44a479..91abbc69 100755 --- a/input/tests/unit_tests/test_schema_conversion_proto.py +++ b/input/tests/unit_tests/test_schema_conversion_proto.py @@ -6,7 +6,7 @@ import numpy as np from input.model.schema_conversion import SchemaConverter -from input.model.neoantigen import Neoantigen, Gene, Mutation +from input.model.neoantigen import Neoantigen, Gene, Mutation, Patient class SchemaConverterTest(TestCase): @@ -42,8 +42,14 @@ def test_model2csv(self): def test_csv2model(self): neoantigens = [_get_random_neoantigen() for _ in range(5)] csv_data = SchemaConverter.model2csv(neoantigens) - neoantigens2 = SchemaConverter.csv2model(csv_data) + neoantigens2 = SchemaConverter.neoantigens_csv2model(csv_data) self._assert_lists_equal(neoantigens, neoantigens2) + + def test_patient_metadata_csv2model(self): + patients = [_get_random_patient() for _ in range(5)] + csv_data = SchemaConverter.model2csv(patients) + patients2 = SchemaConverter.patient_metadata_csv2model(csv_data) + self._assert_lists_equal(patients, patients2) def _assert_lists_equal(self, neoantigens, neoantigens2): self.assertEqual(len(neoantigens), len(neoantigens2)) @@ -80,3 +86,13 @@ def _get_random_neoantigen(): gene.assembly = "hg19" neoantigen.gene = gene return neoantigen + + +def _get_random_patient(): + patient = Patient() + patient.estimated_tumor_content = np.random.uniform(0, 1) + patient.is_rna_available = np.random.choice([True, False], 1)[0] + patient.identifier = 'Pt12345' + patient.mhc_i_alleles = ['A', 'B', 'C'] + patient.mhc_i_i_alleles = ['X', 'Y'] + return patient \ No newline at end of file From 0b70f1cf539befeb9ac79263cdc4d28c5317d6ae Mon Sep 17 00:00:00 2001 From: Pablo Riesgo Ferreiro Date: Sat, 20 Jun 2020 08:29:48 +0200 Subject: [PATCH 057/105] integrate patient model into input --- input/command_line.py | 16 +-- input/helpers/data_import.py | 55 ++++----- input/model/neoantigen.html | 8 ++ input/model/neoantigen.proto | 4 + input/model/neoantigen.py | 2 + input/model/schema_conversion.py | 49 -------- input/predict_all_epitopes.py | 105 +++--------------- input/tests/integration_tests/test_input.py | 15 +-- input/tests/resources/alleles.Pt29.csv | 2 + input/tests/resources/patient.Pt29.csv | 2 + input/tests/unit_tests/test_data_import.py | 37 ++++++ .../test_schema_conversion_proto.py | 12 +- 12 files changed, 115 insertions(+), 192 deletions(-) create mode 100644 input/tests/resources/alleles.Pt29.csv create mode 100644 input/tests/resources/patient.Pt29.csv create mode 100755 input/tests/unit_tests/test_data_import.py diff --git a/input/command_line.py b/input/command_line.py index 3d00a8c5..a65b30db 100755 --- a/input/command_line.py +++ b/input/command_line.py @@ -12,25 +12,19 @@ def input_cli(): # TODO: once we support the input from the models this parameter will not be required parser.add_argument('-p', '--patient-id', dest='patient_id', help='the patient id for the iCaM file', required=True) - parser.add_argument('-a', '--allele-file', dest='allele_file', help='define file with hla alleles of patients', + parser.add_argument('-d', '--patients-data', dest='patients_data', + help='file with data for patients with columns: identifier, estimated_tumor_content, ' + 'is_rna_available, mhc_i_alleles, mhc_i_i_alleles, tissue', required=True) - parser.add_argument('-t', '--tissue', dest='tissue', help='define tissue of cancer origin', default="skin") parser.add_argument('-f', '--frameshift', dest='frameshift', help='indicate by true or false if frameshift mutations or SNVs are to be considered', default=False) - parser.add_argument('-tc', '--tumour_content', dest='tumour_content', - help='pass csv file with tumour content of patient; e.g. patient_overview file ', default=False) args = parser.parse_args() icam_file = args.icam_file patient_id = args.patient_id - allele_file = args.allele_file - tissue = args.tissue + patients_data = args.patients_data indel = args.frameshift - if args.tumour_content: - tumour_content_file = args.tumour_content - else: - tumour_content_file = "" # TODO: this is overriding the value of the parameter frameshift, do we want to activate this Franziska? # otherwise we may want to just delete the parameter @@ -38,7 +32,7 @@ def input_cli(): bunchepitopes = BunchEpitopes() logger.info("Starting INPuT...") - bunchepitopes.wrapper_table_add_feature_annotation(icam_file, patient_id, indel, allele_file, tissue, tumour_content_file) + bunchepitopes.wrapper_table_add_feature_annotation(icam_file, patient_id, indel, patients_data) logger.info("Finished INPuT...") ''' file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/INPuT/nonprogramm_files/test_SD.csv" diff --git a/input/helpers/data_import.py b/input/helpers/data_import.py index f57405ef..56528e91 100755 --- a/input/helpers/data_import.py +++ b/input/helpers/data_import.py @@ -1,6 +1,9 @@ #!/usr/bin/python from logzero import logger +import pandas as pd +from input.model.schema_conversion import SchemaConverter +from input.model.neoantigen import Patient def import_dat_icam(in_file, indel): @@ -148,38 +151,20 @@ def change_col_names(tuple_dat_head): return head_new, dat_new -def subst_semicolon(tuple_dat_head): - ''' - This function substitutes any semilicon by "_", since output is in csv format --> problems when importing into R - ''' - dat_new = tuple_dat_head[1] - head_new = tuple_dat_head[0] - data = [] - for ii, i in enumerate(dat_new): - new = [] - for element in i: - if ";" in element: - new.append(element.replace(";", "_")) - else: - new.append(element) - data.append(new) - logger.info(" ';' substituted by '_' ") - return head_new, data - - -def append_patient(tuple_dat_head, in_file): - ''' - There is no column indicating the column name in Tesla icam outputs. This function adds a columns with with the patient id. - ''' - dat_new = tuple_dat_head[1] - head_new = tuple_dat_head[0] - if "patient" in head_new or "patient.x" in head_new: - return head_new, dat_new - else: - pat = f.split("/") - pat = pat[len(pat) - 1] - pat = pat.split("_")[0] - for ii, i in enumerate(dat_new): - dat_new[ii].append(pat) - head_new.append("patient") - return head_new, dat_new +def import_patients_data(patients_file): + """ + :param patients_file: the file to patients data CSV file + :type patients_file: str + :return: the parsed CSV into model objects + :rtype: list[Patient] + """ + split_comma_separated_list = lambda x: x.split(',') + df = pd.read_csv( + patients_file, + sep='\t', + converters={'mhcIAlleles': split_comma_separated_list, + 'mhcIIAlleles': split_comma_separated_list, + # TODO: remove this conversion if this is fixed + # https://github.com/danielgtaylor/python-betterproto/issues/96 + 'estimatedTumorContent': lambda x: float(x)}) + return SchemaConverter.patient_metadata_csv2model(df) diff --git a/input/model/neoantigen.html b/input/model/neoantigen.html index 3b5b203d..0336ba54 100644 --- a/input/model/neoantigen.html +++ b/input/model/neoantigen.html @@ -443,6 +443,14 @@

    Patient

    MHC II alleles

    + + tissue + string + +

    +Tissue of cancer origin

    + + diff --git a/input/model/neoantigen.proto b/input/model/neoantigen.proto index 805d1ee9..f372aab5 100755 --- a/input/model/neoantigen.proto +++ b/input/model/neoantigen.proto @@ -104,4 +104,8 @@ message Patient { MHC II alleles */ repeated string mhcIIAlleles = 5; + /** + Tissue of cancer origin + */ + string tissue = 6; } \ No newline at end of file diff --git a/input/model/neoantigen.py b/input/model/neoantigen.py index 0900d46e..444055ba 100644 --- a/input/model/neoantigen.py +++ b/input/model/neoantigen.py @@ -77,3 +77,5 @@ class Patient(betterproto.Message): mhc_i_alleles: List[str] = betterproto.string_field(4) # * MHC II alleles mhc_i_i_alleles: List[str] = betterproto.string_field(5) + # * Tissue of cancer origin + tissue: str = betterproto.string_field(6) diff --git a/input/model/schema_conversion.py b/input/model/schema_conversion.py index 7b4663c6..53602808 100755 --- a/input/model/schema_conversion.py +++ b/input/model/schema_conversion.py @@ -38,55 +38,6 @@ def icam2model(icam_file, patient_id=None): SchemaConverter.validate(n) return neoantigens - @staticmethod - def patient_metadata2model(hla_file, tumor_content_file): - """ - :param hla_file: the path to a file with the HLAs per patient for both MHC I and MHC II - :type hla_file: str - :param tumor_content_file: the path to a file with the tumoe content per patient - :type tumor_content_file: str - :rtype: list[Patient] - """ - # parse HLA table and add metadata to patient - alleles_stacked = SchemaConverter._parse_hlas_table(hla_file) - patients = {} - for patient_identifier in alleles_stacked.patient_id: - patient = Patient() - patient.identifier = patient_identifier - patient.mhc_i_alleles = list(alleles_stacked[(alleles_stacked.patient_id == patient_identifier) & - (alleles_stacked.mhc_type == 'mhc_I_selection')].allele) - patient.mhc_i_i_alleles = list(alleles_stacked[(alleles_stacked.patient_id == patient_identifier) & - (alleles_stacked.mhc_type == 'mhc_II_selection')].allele) - patients[patient_identifier] = patient - - # parse estimated tumor content file and add metadata to patient - tumor_content = SchemaConverter._parse_tumor_content_table(tumor_content_file) - for patient_identifier in tumor_content.Patient: - patient = patients.get(patient_identifier) - if patient is not None: - patient.estimated_tumor_content = tumor_content[tumor_content.Patient == patient_identifier][ - 'est. Tumor content'].iloc[0] - patient.is_rna_available = tumor_content[tumor_content.Patient == patient_identifier][ - 'rna_avail'].iloc[0] - - return list(patients.values()) - - @staticmethod - def _parse_tumor_content_table(tumor_content_file): - tumor_content = pd.read_csv(tumor_content_file, sep=';') - tumor_content.Patient = tumor_content.Patient.transform(lambda x: x.strip('/')) - return tumor_content - - @staticmethod - def _parse_hlas_table(hla_file): - alleles = pd.read_csv(hla_file, sep=';', header=None, - names=['patient_id', 'mhc_type'] + list(range(50))).dropna(axis=1, how='all') - alleles_stacked = alleles.set_index(['patient_id', 'mhc_type']).stack(dropna=True).reset_index() - del alleles_stacked['level_2'] - alleles_stacked['allele'] = alleles_stacked[0] - del alleles_stacked[0] - return alleles_stacked - @staticmethod def model2csv(model_objects): """ diff --git a/input/predict_all_epitopes.py b/input/predict_all_epitopes.py index 121bf37c..640219e4 100755 --- a/input/predict_all_epitopes.py +++ b/input/predict_all_epitopes.py @@ -12,6 +12,7 @@ from input.new_features import conservation_scores from input.new_features.conservation_scores import ProveanAnnotator from input.references import ReferenceFolder, DependenciesConfiguration +from input.model.neoantigen import Patient class BunchEpitopes: @@ -77,81 +78,6 @@ def load_nmer_frequency(frequency_file): freq_dict[w[0]] = w[1] return freq_dict - @staticmethod - def load_patient_hla_I_allels(path_to_hla_file): - """ - adds hla I alleles of patients as dictionary - :param path_to_hla_file: - :return: - """ - patient_alleles_dict = {} - with open(path_to_hla_file, "r") as f: - for line in f: - w = line.rstrip().split(";") - if w[0] not in patient_alleles_dict: - patient_alleles_dict[w[0]] = w[2:] - logger.info("HLA-I alleles loaded") - return patient_alleles_dict - - @staticmethod - def load_patient_hla_II_allels(path_to_hla_file): - """ - adds hla II alleles of patients as dictionary - :param path_to_hla_file: - :return: - """ - patient_alleles_dict = {} - with open(path_to_hla_file, "r") as f: - for line in f: - w = line.rstrip().split(";") - # cheating --> overwriting hla I --> check format - patient_alleles_dict[w[0]] = w[2:] - logger.info("HLA-II alleles loaded") - return patient_alleles_dict - - @staticmethod - def load_tumor_content_dict(path_to_patient_overview): - """ - adds tumor content of patients as dictionary - :param path_to_patient_overview: - :return: - """ - tumour_content_dict = {} - with open(path_to_patient_overview) as f: - header = next(f) - header = header.rstrip().split(";") - tc_col = header.index("est. Tumor content") - for line in f: - w = line.rstrip().split(";") - patient = w[0] - patient = patient.rstrip("/") - tumour_content = w[tc_col] - tumour_content_dict[patient] = tumour_content - - logger.info("Tumor content loaded") - return tumour_content_dict - - @staticmethod - def load_rna_seq_avail_dict(path_to_patient_overview): - """ - adds info if rna seq was available as dictionary - :param path_to_patient_overview: - :return: - """ - rna_avail_dict = {} - with open(path_to_patient_overview) as f: - header = next(f) - header = header.rstrip().split(";") - rna_col = header.index("rna_avail") - for line in f: - w = line.rstrip().split(";") - patient = w[0] - patient = patient.rstrip("/") - rna_avail = w[rna_col] - rna_avail_dict[patient] = rna_avail - logger.info("RNA availability: {}".format(rna_avail_dict)) - return rna_avail_dict - def write_to_file_sorted(self, d, header): """Transforms dictionary (property --> epitopes). To one unit (epitope) corresponding values are concentrated in one list and printed ';' separated.""" @@ -166,10 +92,16 @@ def write_to_file_sorted(self, d, header): z = [str(d[col][i]) for col in header] print("\t".join(z)) - def initialise_properties(self, data, path_to_hla_file, tissue, tumour_content_file): - '''adds information to Bunchepitopes class that are needed for mutated peptide sequence annotation - ''' - self.rna_reference = self.load_rna_reference(self.references.gtex, tissue) + def initialise_properties(self, data, patients): + """ + adds information to Bunchepitopes class that are needed for mutated peptide sequence annotation + :param data: + :type patients: list[Patient] + :return: + """ + # TODO: for now it reads only the tissue from the first patient in the table, we will need to do this on a per + # TODO: patient basis + self.rna_reference = self.load_rna_reference(self.references.gtex, patients[0].tissue) freq_file1 = self.references.aa_freq_prot freq_file2 = self.references.four_mer_freq self.aa_frequency = self.load_nmer_frequency(freq_file1) @@ -179,21 +111,20 @@ def initialise_properties(self, data, path_to_hla_file, tissue, tumour_content_f prov_file = self.references.prov_scores_mapped3 self.hla_available_alleles = self.references.load_available_hla_alleles(mhc=MHC_I) self.hlaII_available_alleles = self.references.load_available_hla_alleles(mhc=MHC_II) - self.patient_hla_I_allels = self.load_patient_hla_I_allels(path_to_hla_file) - self.patient_hla_II_allels = self.load_patient_hla_II_allels(path_to_hla_file) - # tumour content - if tumour_content_file != "": - self.tumour_content = self.load_tumor_content_dict(tumour_content_file) - self.rna_avail = self.load_rna_seq_avail_dict(tumour_content_file) + self.patient_hla_I_allels = {p.identifier: p.mhc_i_alleles for p in patients} + self.patient_hla_II_allels = {p.identifier: p.mhc_i_i_alleles for p in patients} + self.tumour_content = {p.identifier: p.estimated_tumor_content for p in patients} + self.rna_avail = {p.identifier: p.is_rna_available for p in patients} self.provean_annotator = ProveanAnnotator(provean_file=prov_file, header_epitopes=data[0], epitopes=data[1]) - def wrapper_table_add_feature_annotation(self, icam_file, patient_id, indel, hla_file, tissue, tumour_content_file): + def wrapper_table_add_feature_annotation(self, icam_file, patient_id, indel, patients_file): """ Loads epitope data (if file has been not imported to R; colnames need to be changed), adds data to class that are needed to calculate, calls epitope class --> determination of epitope properties, write to txt file """ # import epitope data dat = data_import.import_dat_icam(icam_file, indel) + patients = data_import.import_patients_data(patients_file) if "+-13_AA_(SNV)_/_-15_AA_to_STOP_(INDEL)" in dat[0]: dat = data_import.change_col_names(dat) if "mutation_found_in_proteome" not in dat[0]: @@ -203,7 +134,7 @@ def wrapper_table_add_feature_annotation(self, icam_file, patient_id, indel, hla for ii, i in enumerate(dat[1]): dat[1][ii].append(str(patient_id)) # initialise information needed for feature calculation - self.initialise_properties(dat, hla_file, tissue, tumour_content_file) + self.initialise_properties(dat, patients) # feature calculation for each epitope for ii, i in enumerate(dat[1]): # dict for each epitope diff --git a/input/tests/integration_tests/test_input.py b/input/tests/integration_tests/test_input.py index e9494574..a924a741 100755 --- a/input/tests/integration_tests/test_input.py +++ b/input/tests/integration_tests/test_input.py @@ -1,5 +1,6 @@ from unittest import TestCase - +import pkg_resources +import input.tests from input.predict_all_epitopes import BunchEpitopes from input.tests.integration_tests import integration_test_tools @@ -14,21 +15,17 @@ def setUp(self): def test_input(self): """ This test is equivalent to the command line call: - input -i /projects/SUMMIT/WP1.2/input/development/Pt29.sequences4testing.txt -p Pt29 - -a /projects/SUMMIT/WP1.2/Literature_Cohorts/data_analysis/cohorts/vanallen/output_tables/20200106_alleles_extended.csv - -tc /projects/SUMMIT/WP1.2/Literature_Cohorts/data_analysis/cohorts/vanallen/output_tables/vanallen_patient_overview.csv + input --icam-file /projects/SUMMIT/WP1.2/input/development/Pt29.sequences4testing.txt --patient-id Pt29 + --patients-data ../resources/patient.pt29.csv NOTE: we will need to check the output when the calculation of resuls and printing to stdout have been decoupled :return: """ patient_id = 'Pt29' input_file = '/projects/SUMMIT/WP1.2/input/development/Pt29.sequences4testing.txt' - alleles_file = '/projects/SUMMIT/WP1.2/Literature_Cohorts/data_analysis/cohorts/vanallen/output_tables/20200106_alleles_extended.csv' - tumor_content_file = '/projects/SUMMIT/WP1.2/Literature_Cohorts/data_analysis/cohorts/vanallen/output_tables/vanallen_patient_overview.csv' + patients_file = pkg_resources.resource_filename(input.tests.__name__, "resources/patient.Pt29.csv") BunchEpitopes().wrapper_table_add_feature_annotation( icam_file=input_file, patient_id=patient_id, indel=False, - hla_file=alleles_file, - tissue='skin', - tumour_content_file=tumor_content_file) + patients_file=patients_file) diff --git a/input/tests/resources/alleles.Pt29.csv b/input/tests/resources/alleles.Pt29.csv new file mode 100644 index 00000000..395eaab7 --- /dev/null +++ b/input/tests/resources/alleles.Pt29.csv @@ -0,0 +1,2 @@ +identifier mhcIAlleles mhcIIAlleles +Pt29 HLA-A*03:01,HLA-A*02:01,HLA-B*07:02,HLA-B*18:01,HLA-C*07:02,HLA-C*12:03 HLA-DRB1*11:04,HLA-DRB1*15:01,HLA-DQA1*01:02,HLA-DQA1*05:05,HLA-DQB1*06:02,HLA-DQB1*03:01,HLA-DPA1*01:03,HLA-DPA1*01:03,HLA-DPB1*04:02,HLA-DPB1*04:01 diff --git a/input/tests/resources/patient.Pt29.csv b/input/tests/resources/patient.Pt29.csv new file mode 100644 index 00000000..ab8828ea --- /dev/null +++ b/input/tests/resources/patient.Pt29.csv @@ -0,0 +1,2 @@ +identifier mhcIAlleles mhcIIAlleles estimatedTumorContent isRnaAvailable tissue +Pt29 HLA-A*03:01,HLA-A*02:01,HLA-B*07:02,HLA-B*18:01,HLA-C*07:02,HLA-C*12:03 HLA-DRB1*11:04,HLA-DRB1*15:01,HLA-DQA1*01:02,HLA-DQA1*05:05,HLA-DQB1*06:02,HLA-DQB1*03:01,HLA-DPA1*01:03,HLA-DPA1*01:03,HLA-DPB1*04:02,HLA-DPB1*04:01 69 True skin diff --git a/input/tests/unit_tests/test_data_import.py b/input/tests/unit_tests/test_data_import.py new file mode 100755 index 00000000..a00779a9 --- /dev/null +++ b/input/tests/unit_tests/test_data_import.py @@ -0,0 +1,37 @@ +from unittest import TestCase +import pkg_resources +import input.tests +from input.model.neoantigen import Patient +import input.helpers.data_import as data_import + + +class DataImportTest(TestCase): + + def test_patient_alleles_csv_file2model(self): + patients_file = pkg_resources.resource_filename(input.tests.__name__, "resources/alleles.Pt29.csv") + patients = data_import.import_patients_data(patients_file) + self.assertIsNotNone(patients) + self.assertIsInstance(patients, list) + self.assertTrue(len(patients) == 1) + self.assertIsInstance(patients[0], Patient) + self.assertEqual(patients[0].identifier, "Pt29") + self.assertEqual(len(patients[0].mhc_i_alleles), 6) + self.assertEqual(len(patients[0].mhc_i_i_alleles), 10) + self.assertEqual(patients[0].estimated_tumor_content, 0.0) + self.assertEqual(patients[0].is_rna_available, False) + self.assertEqual(patients[0].tissue, '') + + def test_patient_csv_file2model(self): + patients_file = pkg_resources.resource_filename(input.tests.__name__, "resources/patient.Pt29.csv") + patients = data_import.import_patients_data(patients_file) + self.assertIsNotNone(patients) + self.assertIsInstance(patients, list) + self.assertTrue(len(patients) == 1) + self.assertIsInstance(patients[0], Patient) + self.assertEqual(patients[0].identifier, "Pt29") + self.assertEqual(len(patients[0].mhc_i_alleles), 6) + self.assertEqual(len(patients[0].mhc_i_i_alleles), 10) + self.assertEqual(patients[0].estimated_tumor_content, 69.0) + self.assertEqual(patients[0].is_rna_available, True) + self.assertEqual(patients[0].tissue, 'skin') + diff --git a/input/tests/unit_tests/test_schema_conversion_proto.py b/input/tests/unit_tests/test_schema_conversion_proto.py index 91abbc69..707803e0 100755 --- a/input/tests/unit_tests/test_schema_conversion_proto.py +++ b/input/tests/unit_tests/test_schema_conversion_proto.py @@ -1,10 +1,12 @@ import random import struct from unittest import TestCase +import pkg_resources from Bio.Data import IUPACData import numpy as np +import input.tests from input.model.schema_conversion import SchemaConverter from input.model.neoantigen import Neoantigen, Gene, Mutation, Patient @@ -45,7 +47,14 @@ def test_csv2model(self): neoantigens2 = SchemaConverter.neoantigens_csv2model(csv_data) self._assert_lists_equal(neoantigens, neoantigens2) - def test_patient_metadata_csv2model(self): + def test_patient_csv2model(self): + patients = [_get_random_patient() for _ in range(5)] + csv_data = SchemaConverter.model2csv(patients) + patients2 = SchemaConverter.patient_metadata_csv2model(csv_data) + self._assert_lists_equal(patients, patients2) + + def test_patient_csv_file2model(self): + patients_file = pkg_resources.resource_filename(input.tests.__name__, "resources/Alleles.Pt29.csv") patients = [_get_random_patient() for _ in range(5)] csv_data = SchemaConverter.model2csv(patients) patients2 = SchemaConverter.patient_metadata_csv2model(csv_data) @@ -95,4 +104,5 @@ def _get_random_patient(): patient.identifier = 'Pt12345' patient.mhc_i_alleles = ['A', 'B', 'C'] patient.mhc_i_i_alleles = ['X', 'Y'] + patient.tissue = 'skin' return patient \ No newline at end of file From 17cda3b995b8128b5acb09f36b06434300baf9ad Mon Sep 17 00:00:00 2001 From: Pablo Riesgo Ferreiro Date: Sat, 20 Jun 2020 08:41:15 +0200 Subject: [PATCH 058/105] update README --- README.md | 45 +++++++++++---------------------------------- 1 file changed, 11 insertions(+), 34 deletions(-) diff --git a/README.md b/README.md index bbcc2e72..f5b6224d 100755 --- a/README.md +++ b/README.md @@ -29,34 +29,21 @@ Annotation of mutated peptide sequences (mps) with published or novel potential - Multiplexed Representation -## **Requirements** +## Input Requirements -**Specific Input:** -- icam_output.txt --> icam output file; either patient-specific, or several patients combineds -- allele.csv --> ";" separated file with mhc I and mhc II alleles (4 digits!) for all patients of a cohort. If a gene is homozygous, give the allele twice - e.g. -``` -Pt1;mhc_I_selection;HLA-A*03:01;HLA-A*11:01;HLA-B*55:01;HLA-B*51:01;HLA-C*01:02;HLA-C*03:03; -Pt1;mhc_II_selection;HLA-DRB1*13:01;HLA-DRB1*11:01;HLA-DQA1*01:03;HLA-DQA1*05:05;HLA-DQB1*06:03;HLA-DQB1*03:01;HLA-DPA1*01:03;HLA-DPB1*02:01;HLA-DPB1*04:02; -Pt2;mhc_I_selection;HLA-A*02:01;HLA-A*26:01;HLA-B*27:05;HLA-B*57:01;HLA-C*01:85;HLA-C*06:02; -Pt2;mhc_II_selection;HLA-DRB1*01:01;HLA-DRB1*07:01;HLA-DQA1*01:01;HLA-DQA1*02:01;HLA-DQB1*05:01;HLA-DQB1*03:03;HLA-DPA1*01:03;HLA-DPB1*02:01;HLA-DPB1*04:02; +**Specific Input:** +- icam_output.txt --> icam output file +- patient identifier --> the patient identifier to whom all neoantigens in icam output belong +- patient data --> a table of tab separated values containing metadata on the patient + - required fields: identifier, mhcIAlleles, mhcIIAlleles + - optional fields: estimatedTumorContent, isRnaAvailable, tissue -``` -- *OPTIONAL!!*:";" separated file with tumor content (e.g. patient_overview file for each cohort) +**Example of patient data table** ``` -Patient;est. Tumor content;number of mutations; number of SNVs;number of Indels;unique_peptides;number_of_expressed_ge -Pt10/;62.0;463;437;26;180;16200 -Pt11/;;;;;; -Pt12/;66.0;120;104;16;38;15147 -Pt13/;49.0;863;843;20;327;15707 -Pt14/;55.0;2375;2336;39;909;16107 -Pt15/;50.0;1227;1174;53;433;15029 -Pt16/;24.0;948;940;8;368;15562 -Pt17/;;;;;; +identifier mhcIAlleles mhcIIAlleles estimatedTumorContent isRnaAvailable tissue +Pt29 HLA-A*03:01,HLA-A*02:01,HLA-B*07:02 HLA-DRB1*11:04,HLA-DRB1*15:01 69 True skin ``` - - **Required Columns of iCaM Table:** - MHC_I_epitope_.best_prediction. - MHC_I_epitope_.WT. @@ -102,19 +89,9 @@ Pt17/;;;;;; ## **Usage** -**Single iCaM File** ``` -python predict_all_epitopes.py --icam_file testseq_head.txt --allele_file alleles.csv [--tissue skin --frameshift False --tumour_content file_with_tumor_content]> test07.txt -``` - ---> annotation of one iCaM file - -**Multiple iCaM Files** +input --icam-file testseq_head.txt --patient-id Pt123 --patient-data patients.csv [--frameshift False] ``` -sh start_annotation_multiple_patientfiles.sh cohort_folder_with_patient_icam_folders output_folder allele_table cohort_name -``` - ---> eg. parallel mps annotation of patients of a cohort, iCaM files stored in cohort_folder_with_patient_icam_folders ## Developer guide From 8f86a655709568e44320ce44e4b8a0ffe55d47a4 Mon Sep 17 00:00:00 2001 From: Pablo Riesgo Ferreiro Date: Sat, 20 Jun 2020 08:51:40 +0200 Subject: [PATCH 059/105] fix line endings on debvelop branch --- input/Tcell_predictor/prediction.py | 46 +-- input/Tcell_predictor/preprocess.py | 210 +++++++------- input/__init__.py | 22 +- input/command_line.py | 174 +++++------ input/exceptions.py | 28 +- input/helpers/blastp_runner.py | 70 ++--- input/helpers/epitope_helper.py | 132 ++++----- input/helpers/fastaGenerator.py | 64 ++-- input/helpers/intermediate_files.py | 42 +-- input/helpers/properties_manager.py | 192 ++++++------ input/helpers/runner.py | 74 ++--- .../abstract_netmhcpan_predictor.py | 34 +-- input/new_features/conservation_scores.py | 102 +++---- input/references.py | 214 +++++++------- input/self_similarity/self_similarity.py | 274 +++++++++--------- input/tests/__init__.py | 44 +-- .../integration_test_tools.py | 38 +-- .../test_conservation_scores.py | 92 +++--- .../integration_tests/test_dissimilarity.py | 54 ++-- .../integration_tests/test_mixmhcpred.py | 198 ++++++------- input/tests/integration_tests/test_neoag.py | 194 ++++++------- .../test_neoantigen_fitness.py | 100 +++---- .../tests/integration_tests/test_netmhcpan.py | 190 ++++++------ .../integration_tests/test_tcell_predictor.py | 104 +++---- input/tests/unit_tests/fake_classes.py | 30 +- .../test_dependencies_configuration.py | 130 ++++----- .../unit_tests/test_predict_all_epitopes.py | 48 +-- .../tests/unit_tests/test_reference_folder.py | 94 +++--- input/tests/unit_tests/test_runner.py | 46 +-- .../tests/unit_tests/test_self_similarity.py | 76 ++--- model/neoepitope.avdl | 166 +++++------ setup.py | 100 +++---- 32 files changed, 1691 insertions(+), 1691 deletions(-) diff --git a/input/Tcell_predictor/prediction.py b/input/Tcell_predictor/prediction.py index d94526b3..de726894 100755 --- a/input/Tcell_predictor/prediction.py +++ b/input/Tcell_predictor/prediction.py @@ -1,23 +1,23 @@ -import os -import pickle - -import pandas as pd - -from input.Tcell_predictor.preprocess import Preprocessor - - -def main(f_name, output_file, references): - input_file = f_name - mat = Preprocessor(references=references).main(input_file) - # NOTE: we do not put the Classifier.pickle in the references.py because it is code and not data what's in there - # thus it belongs with the code - with open(os.path.join(os.path.abspath(os.path.dirname(__file__)), 'Classifier.pickle'), 'rb') as f: - classifier = pickle.load(f) - scores = classifier.predict_proba(mat) - dictionary = {} - with open(input_file, 'r') as f: - for row, val in zip(f, scores): - seq = row.split()[1] - dictionary[seq] = val[-1] - df = pd.DataFrame.from_dict(dictionary, orient='index') - df.to_csv(output_file) +import os +import pickle + +import pandas as pd + +from input.Tcell_predictor.preprocess import Preprocessor + + +def main(f_name, output_file, references): + input_file = f_name + mat = Preprocessor(references=references).main(input_file) + # NOTE: we do not put the Classifier.pickle in the references.py because it is code and not data what's in there + # thus it belongs with the code + with open(os.path.join(os.path.abspath(os.path.dirname(__file__)), 'Classifier.pickle'), 'rb') as f: + classifier = pickle.load(f) + scores = classifier.predict_proba(mat) + dictionary = {} + with open(input_file, 'r') as f: + for row, val in zip(f, scores): + seq = row.split()[1] + dictionary[seq] = val[-1] + df = pd.DataFrame.from_dict(dictionary, orient='index') + df.to_csv(output_file) diff --git a/input/Tcell_predictor/preprocess.py b/input/Tcell_predictor/preprocess.py index 74133a0c..31d102e4 100755 --- a/input/Tcell_predictor/preprocess.py +++ b/input/Tcell_predictor/preprocess.py @@ -1,105 +1,105 @@ -import pickle - -import numpy as np -import scipy.io as sio - - -class Preprocessor(object): - - def __init__(self, references): - self.references = references - self.load_data = sio.loadmat(self.references.tcell_predictor_sir_data) - with open(self.references.tcell_predictor_gene_expression, 'rb') as handle: - self.dict_expression = pickle.load(handle) - with open(self.references.tcell_predictor_aa_features, 'rb') as handle: - self.dict_data = pickle.load(handle) - - @staticmethod - def seq2bin(seq): - aa = ['A', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L', 'M', 'N', 'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'Y'] - dict_aa = dict((i, j) for j, i in enumerate(aa)) - arr = np.zeros((1, 9 * 20)) - for ii, letter in enumerate(seq): - arr[0, ii * 20 + dict_aa.get(letter)] = 1 - return arr - - @staticmethod - def get_hydrophbicity(x, dict_): - pair_letters = [c for c in x if c.isupper()] - res = np.abs(dict_[pair_letters[0]] - dict_[pair_letters[1]]) - return res - - @staticmethod - def get_size(x, dict_): - pair_letters = [c for c in x if c.isupper()] - res = np.abs(dict_[pair_letters[0]] - dict_[pair_letters[1]]) - return res - - @staticmethod - def get_charge_change(x, dict_): - pair_letters = [c for c in x if c.isupper()] - if dict_[pair_letters[0]] == dict_[pair_letters[1]]: - return 0 - else: - return 1 - - @staticmethod - def get_charge_abs(x, dict_): - pair_letters = [c for c in x if c.isupper()] - if dict_[pair_letters[0]] == dict_[pair_letters[1]]: - return 0 - else: - return 1 - - @staticmethod - def get_polar(x, dict_): - pair_letters = [c for c in x if c.isupper()] - res = np.abs(dict_[pair_letters[0]] - dict_[pair_letters[1]]) - return res - - @staticmethod - def get_absolute(x, dict_): - pair_letters = [c for c in x if c.isupper()] - res = np.abs(dict_[pair_letters[0]] - dict_[pair_letters[1]]) - return res - - @staticmethod - def get_diffetenet(x, dict_): - pair_letters = [c for c in x if c.isupper()] - if dict_[pair_letters[0]] == dict_[pair_letters[1]]: - return 0 - else: - return 1 - - def get_gene_expression(self, gene): - res = self.dict_expression.get(gene, 0.0) - return res - - def get_properties(self, amino_substitution): - return np.asarray([self.get_diffetenet(amino_substitution, self.dict_data['Charge']), - self.get_absolute(amino_substitution, self.dict_data['Size']), - self.get_absolute(amino_substitution, self.dict_data['Hydro']), - self.get_absolute(amino_substitution, self.dict_data['Charge']), - self.get_diffetenet(amino_substitution, self.dict_data['Polar'])]) - - def main(self, f_name): - lst_data = [] - with open(f_name, 'r') as f: - for row in f: - gene_name, sequence, aa_subs = row.split() - seq_arr = self.seq2bin(sequence) - # tap score - tap_mat = self.load_data.get('tap') - tap_score = tap_mat.dot(seq_arr.T).ravel() - # cleavge score - clv_mat = self.load_data.get('clv') - clv_mat = clv_mat[0, 20:200] - clv_score = clv_mat.dot(seq_arr.T).ravel() - - features_aa = self.get_properties(aa_subs) - # expresion - expression_value = self.get_gene_expression(gene_name) - - lst_data.append(np.hstack((expression_value, features_aa, clv_score, tap_score))) - mat_features = np.asarray(lst_data) - return mat_features +import pickle + +import numpy as np +import scipy.io as sio + + +class Preprocessor(object): + + def __init__(self, references): + self.references = references + self.load_data = sio.loadmat(self.references.tcell_predictor_sir_data) + with open(self.references.tcell_predictor_gene_expression, 'rb') as handle: + self.dict_expression = pickle.load(handle) + with open(self.references.tcell_predictor_aa_features, 'rb') as handle: + self.dict_data = pickle.load(handle) + + @staticmethod + def seq2bin(seq): + aa = ['A', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L', 'M', 'N', 'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'Y'] + dict_aa = dict((i, j) for j, i in enumerate(aa)) + arr = np.zeros((1, 9 * 20)) + for ii, letter in enumerate(seq): + arr[0, ii * 20 + dict_aa.get(letter)] = 1 + return arr + + @staticmethod + def get_hydrophbicity(x, dict_): + pair_letters = [c for c in x if c.isupper()] + res = np.abs(dict_[pair_letters[0]] - dict_[pair_letters[1]]) + return res + + @staticmethod + def get_size(x, dict_): + pair_letters = [c for c in x if c.isupper()] + res = np.abs(dict_[pair_letters[0]] - dict_[pair_letters[1]]) + return res + + @staticmethod + def get_charge_change(x, dict_): + pair_letters = [c for c in x if c.isupper()] + if dict_[pair_letters[0]] == dict_[pair_letters[1]]: + return 0 + else: + return 1 + + @staticmethod + def get_charge_abs(x, dict_): + pair_letters = [c for c in x if c.isupper()] + if dict_[pair_letters[0]] == dict_[pair_letters[1]]: + return 0 + else: + return 1 + + @staticmethod + def get_polar(x, dict_): + pair_letters = [c for c in x if c.isupper()] + res = np.abs(dict_[pair_letters[0]] - dict_[pair_letters[1]]) + return res + + @staticmethod + def get_absolute(x, dict_): + pair_letters = [c for c in x if c.isupper()] + res = np.abs(dict_[pair_letters[0]] - dict_[pair_letters[1]]) + return res + + @staticmethod + def get_diffetenet(x, dict_): + pair_letters = [c for c in x if c.isupper()] + if dict_[pair_letters[0]] == dict_[pair_letters[1]]: + return 0 + else: + return 1 + + def get_gene_expression(self, gene): + res = self.dict_expression.get(gene, 0.0) + return res + + def get_properties(self, amino_substitution): + return np.asarray([self.get_diffetenet(amino_substitution, self.dict_data['Charge']), + self.get_absolute(amino_substitution, self.dict_data['Size']), + self.get_absolute(amino_substitution, self.dict_data['Hydro']), + self.get_absolute(amino_substitution, self.dict_data['Charge']), + self.get_diffetenet(amino_substitution, self.dict_data['Polar'])]) + + def main(self, f_name): + lst_data = [] + with open(f_name, 'r') as f: + for row in f: + gene_name, sequence, aa_subs = row.split() + seq_arr = self.seq2bin(sequence) + # tap score + tap_mat = self.load_data.get('tap') + tap_score = tap_mat.dot(seq_arr.T).ravel() + # cleavge score + clv_mat = self.load_data.get('clv') + clv_mat = clv_mat[0, 20:200] + clv_score = clv_mat.dot(seq_arr.T).ravel() + + features_aa = self.get_properties(aa_subs) + # expresion + expression_value = self.get_gene_expression(gene_name) + + lst_data.append(np.hstack((expression_value, features_aa, clv_score, tap_score))) + mat_features = np.asarray(lst_data) + return mat_features diff --git a/input/__init__.py b/input/__init__.py index ec04556c..f28ad6ac 100755 --- a/input/__init__.py +++ b/input/__init__.py @@ -1,11 +1,11 @@ -VERSION = '0.2.1' -REFERENCE_FOLDER_ENV = 'INPUT_REFERENCE_FOLDER' -INPUT_BLASTP_ENV = 'INPUT_BLASTP' -INPUT_MIXMHC2PRED_ENV = 'INPUT_MIXMHC2PRED' -INPUT_MIXMHCPRED_ENV = 'INPUT_MIXMHCPRED' -INPUT_RSCRIPT_ENV = 'INPUT_RSCRIPT' -INPUT_NETMHC2PAN_ENV = 'INPUT_NETMHC2PAN' -INPUT_NETMHCPAN_ENV = 'INPUT_NETMHCPAN' - -MHC_II = "mhcII" -MHC_I = "mhcI" +VERSION = '0.2.1' +REFERENCE_FOLDER_ENV = 'INPUT_REFERENCE_FOLDER' +INPUT_BLASTP_ENV = 'INPUT_BLASTP' +INPUT_MIXMHC2PRED_ENV = 'INPUT_MIXMHC2PRED' +INPUT_MIXMHCPRED_ENV = 'INPUT_MIXMHCPRED' +INPUT_RSCRIPT_ENV = 'INPUT_RSCRIPT' +INPUT_NETMHC2PAN_ENV = 'INPUT_NETMHC2PAN' +INPUT_NETMHCPAN_ENV = 'INPUT_NETMHCPAN' + +MHC_II = "mhcII" +MHC_I = "mhcI" diff --git a/input/command_line.py b/input/command_line.py index 14545218..d3f8e092 100755 --- a/input/command_line.py +++ b/input/command_line.py @@ -1,87 +1,87 @@ -from argparse import ArgumentParser - -from logzero import logger - -from input.predict_all_epitopes import BunchEpitopes - - -def input_cli(): - parser = ArgumentParser(description='adds patient information given in sample file of a cohort to merged icam file') - parser.add_argument('-i', '--icam_file', dest='icam_file', help='define iCaM file which should be annotated', - required=True) - parser.add_argument('-a', '--allele_file', dest='allele_file', help='define file with hla alleles of patients', - required=True) - parser.add_argument('-t', '--tissue', dest='tissue', help='define tissue of cancer origin', default="skin") - parser.add_argument('-f', '--frameshift', dest='frameshift', - help='indicate by true or false if frameshift mutations or SNVs are to be considered', - default=False) - parser.add_argument('-tc', '--tumour_content', dest='tumour_content', - help='pass csv file with tumour content of patient; e.g. patient_overview file ', default=False) - args = parser.parse_args() - - icam_file = args.icam_file - allele_file = args.allele_file - tissue = args.tissue - indel = args.frameshift - if args.tumour_content: - tumour_content_file = args.tumour_content - else: - tumour_content_file = "" - - indel = False - - bunchepitopes = BunchEpitopes() - logger.info("Starting INPuT...") - bunchepitopes.wrapper_table_add_feature_annotation(icam_file, indel, allele_file, tissue, tumour_content_file) - logger.info("Finished INPuT...") - ''' - file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/INPuT/nonprogramm_files/test_SD.csv" - # file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/INPuT/nonprogramm_files/test_fulldat.txt" - #file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/20170713_IS_IM_data.complete.update_Dv10.csv.annotation.csv_v2.csv" - # file = "/projects/SUMMIT/WP1.2/Literature_Cohorts/data_analysis/20190117_hugo_prelim_sample_annot.txt" - #file = "/projects/SUMMIT/WP1.2/Literature_Cohorts/data_analysis/20190121_hugo_merged_dat.txt" - indel = False - fasta_proteome = "/projects/data/human/2018_uniprot_with_isoforms/uniprot_human_with_isoforms.fasta" - ref_file = "/projects/CM27_IND_patients/GTEX_normal_tissue_data/Skin .csv" - path_to_hla_file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/indels/RB_0004_labHLA_V2.csv" - #path_to_hla_file = "/projects/SUMMIT/WP1.2/Literature_Cohorts/data_analysis/alleles.csv" - - - Bunchepitopes().main(file, indel, fasta_proteome, ref_file, path_to_hla_file) - ''' - -# def epitope_cli(): -# # file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/INPuT2/nonprogramm_files/test_SD.csv" -# # file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/INPuT2/nonprogramm_files/test_fulldat.txt" -# indel = False -# fasta_proteome = "/projects/data/human/2018_uniprot_with_isoforms/uniprot_human_with_isoforms.fasta" -# ref_file = "/projects/CM27_IND_patients/GTEX_normal_tissue_data/Skin .csv" -# file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/MHC_prediction_netmhcpan4/testdat_ott.txt" -# hla_file = "/projects/SUMMIT/WP1.2/Literature_Cohorts/data_analysis/cohorts/ott/icam_ott/alleles.csv" -# -# # predfeatallBunchepitopes -# predictAll = Bunchepitopes() -# # args = parser.parse_args() -# subprocess.call(["predict_all_epitopes", '-i', file, '-a', hla_file]) -# -# # z = Epitope().main(dat[0], dat[1][ii], self.proteome_dictionary, self.rna_reference, self.aa_frequency, self.fourmer_frequency, self.aa_index1_dict, self.aa_index2_dict, self.provean_matrix, self.hla_available_alleles, self.patient_hla_I_allels) -# -# predictAll.main() - i -# endTime = datetime.now() -# print >> sys.stderr, "start: " + str(startTime) + "\nend: " + str(endTime) + "\nneeded: " + str( -# endTime - startTime) -# # print dat -# # x = Epitope() -# # x = Epitope(dat[1][1], dat[0]) -# # print vars(x) -# # print dat[1][1][1] -# # print dat[0][1] -# -# # for ii,i in enumerate(dat[1]): -# # Epitope().main(dat[0],dat[1][ii]) -# # print x.tricks -# -# # x.main(dat[0], dat[1][1]) -# # print x.tricks -# # print x.tricks["transcript_position"] -# # print dir(x) +from argparse import ArgumentParser + +from logzero import logger + +from input.predict_all_epitopes import BunchEpitopes + + +def input_cli(): + parser = ArgumentParser(description='adds patient information given in sample file of a cohort to merged icam file') + parser.add_argument('-i', '--icam_file', dest='icam_file', help='define iCaM file which should be annotated', + required=True) + parser.add_argument('-a', '--allele_file', dest='allele_file', help='define file with hla alleles of patients', + required=True) + parser.add_argument('-t', '--tissue', dest='tissue', help='define tissue of cancer origin', default="skin") + parser.add_argument('-f', '--frameshift', dest='frameshift', + help='indicate by true or false if frameshift mutations or SNVs are to be considered', + default=False) + parser.add_argument('-tc', '--tumour_content', dest='tumour_content', + help='pass csv file with tumour content of patient; e.g. patient_overview file ', default=False) + args = parser.parse_args() + + icam_file = args.icam_file + allele_file = args.allele_file + tissue = args.tissue + indel = args.frameshift + if args.tumour_content: + tumour_content_file = args.tumour_content + else: + tumour_content_file = "" + + indel = False + + bunchepitopes = BunchEpitopes() + logger.info("Starting INPuT...") + bunchepitopes.wrapper_table_add_feature_annotation(icam_file, indel, allele_file, tissue, tumour_content_file) + logger.info("Finished INPuT...") + ''' + file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/INPuT/nonprogramm_files/test_SD.csv" + # file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/INPuT/nonprogramm_files/test_fulldat.txt" + #file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/20170713_IS_IM_data.complete.update_Dv10.csv.annotation.csv_v2.csv" + # file = "/projects/SUMMIT/WP1.2/Literature_Cohorts/data_analysis/20190117_hugo_prelim_sample_annot.txt" + #file = "/projects/SUMMIT/WP1.2/Literature_Cohorts/data_analysis/20190121_hugo_merged_dat.txt" + indel = False + fasta_proteome = "/projects/data/human/2018_uniprot_with_isoforms/uniprot_human_with_isoforms.fasta" + ref_file = "/projects/CM27_IND_patients/GTEX_normal_tissue_data/Skin .csv" + path_to_hla_file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/indels/RB_0004_labHLA_V2.csv" + #path_to_hla_file = "/projects/SUMMIT/WP1.2/Literature_Cohorts/data_analysis/alleles.csv" + + + Bunchepitopes().main(file, indel, fasta_proteome, ref_file, path_to_hla_file) + ''' + +# def epitope_cli(): +# # file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/INPuT2/nonprogramm_files/test_SD.csv" +# # file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/INPuT2/nonprogramm_files/test_fulldat.txt" +# indel = False +# fasta_proteome = "/projects/data/human/2018_uniprot_with_isoforms/uniprot_human_with_isoforms.fasta" +# ref_file = "/projects/CM27_IND_patients/GTEX_normal_tissue_data/Skin .csv" +# file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/MHC_prediction_netmhcpan4/testdat_ott.txt" +# hla_file = "/projects/SUMMIT/WP1.2/Literature_Cohorts/data_analysis/cohorts/ott/icam_ott/alleles.csv" +# +# # predfeatallBunchepitopes +# predictAll = Bunchepitopes() +# # args = parser.parse_args() +# subprocess.call(["predict_all_epitopes", '-i', file, '-a', hla_file]) +# +# # z = Epitope().main(dat[0], dat[1][ii], self.proteome_dictionary, self.rna_reference, self.aa_frequency, self.fourmer_frequency, self.aa_index1_dict, self.aa_index2_dict, self.provean_matrix, self.hla_available_alleles, self.patient_hla_I_allels) +# +# predictAll.main() - i +# endTime = datetime.now() +# print >> sys.stderr, "start: " + str(startTime) + "\nend: " + str(endTime) + "\nneeded: " + str( +# endTime - startTime) +# # print dat +# # x = Epitope() +# # x = Epitope(dat[1][1], dat[0]) +# # print vars(x) +# # print dat[1][1][1] +# # print dat[0][1] +# +# # for ii,i in enumerate(dat[1]): +# # Epitope().main(dat[0],dat[1][ii]) +# # print x.tricks +# +# # x.main(dat[0], dat[1][1]) +# # print x.tricks +# # print x.tricks["transcript_position"] +# # print dir(x) diff --git a/input/exceptions.py b/input/exceptions.py index 422c7316..9517a890 100755 --- a/input/exceptions.py +++ b/input/exceptions.py @@ -1,14 +1,14 @@ -class INPuTInputParametersException(ValueError): - pass - - -class INPuTConfigurationException(ValueError): - pass - - -class INPuTCommandException(ValueError): - pass - - -class INPuTReferenceException(ValueError): - pass +class INPuTInputParametersException(ValueError): + pass + + +class INPuTConfigurationException(ValueError): + pass + + +class INPuTCommandException(ValueError): + pass + + +class INPuTReferenceException(ValueError): + pass diff --git a/input/helpers/blastp_runner.py b/input/helpers/blastp_runner.py index 200ddb81..7c1c8ba6 100755 --- a/input/helpers/blastp_runner.py +++ b/input/helpers/blastp_runner.py @@ -1,36 +1,36 @@ -from input.helpers import intermediate_files -from input.neoantigen_fitness.aligner import Aligner - - -class BlastpRunner(object): - - def __init__(self, runner, configuration): - """ - :type runner: input.helpers.runner.Runner - :type configuration: input.references.DependenciesConfiguration - """ - self.runner = runner - self.configuration = configuration - - def run_blastp(self, fasta_file, database): - ''' - This function runs BLASTP on a given database - ''' - outfile = intermediate_files.create_temp_file(prefix="tmp_blastp_", suffix=".xml") - self.runner.run_command(cmd=[ - self.configuration.blastp, - "-gapopen", "11", - "-gapextend", "1", - "-outfmt", "5", - "-query", fasta_file, - "-out", outfile, - "-db", database, - "-evalue", "100000000"]) - return outfile - - def parse_blastp_output(self, blastp_output_file, **kwargs): - aligner = Aligner() - # set a to 32 for dissimilarity - aligner.readAllBlastAlignments(blastp_output_file) - aligner.computeR(**kwargs) +from input.helpers import intermediate_files +from input.neoantigen_fitness.aligner import Aligner + + +class BlastpRunner(object): + + def __init__(self, runner, configuration): + """ + :type runner: input.helpers.runner.Runner + :type configuration: input.references.DependenciesConfiguration + """ + self.runner = runner + self.configuration = configuration + + def run_blastp(self, fasta_file, database): + ''' + This function runs BLASTP on a given database + ''' + outfile = intermediate_files.create_temp_file(prefix="tmp_blastp_", suffix=".xml") + self.runner.run_command(cmd=[ + self.configuration.blastp, + "-gapopen", "11", + "-gapextend", "1", + "-outfmt", "5", + "-query", fasta_file, + "-out", outfile, + "-db", database, + "-evalue", "100000000"]) + return outfile + + def parse_blastp_output(self, blastp_output_file, **kwargs): + aligner = Aligner() + # set a to 32 for dissimilarity + aligner.readAllBlastAlignments(blastp_output_file) + aligner.computeR(**kwargs) return aligner.Ri.get(1, 0) # NOTE: returns 0 when not present \ No newline at end of file diff --git a/input/helpers/epitope_helper.py b/input/helpers/epitope_helper.py index 9afc5a12..66f3d88c 100755 --- a/input/helpers/epitope_helper.py +++ b/input/helpers/epitope_helper.py @@ -1,66 +1,66 @@ - - -class EpitopeHelper(object): - - @staticmethod - def generate_nmers(xmer_wt, xmer_mut, lengths): - """ - Generates peptides covering mutation of all lengths that are provided. Returns peptides as list - No peptide is shorter than the minimun length provided - There are no repetitions in the results - """ - length_mut = len(xmer_mut) - list_peptides = [] - pos_mut = int(EpitopeHelper.mut_position_xmer_seq(xmer_mut=xmer_mut, xmer_wt=xmer_wt)) - for length in lengths: - if length <= length_mut: - start_first = pos_mut - length - starts = [start_first + s for s in range(length)] - ends = [s + length for s in starts] - for s, e in zip(starts, ends): - list_peptides.append(xmer_mut[s:e]) - return list(set([x for x in list_peptides if not x == "" and len(x) >= min(lengths)])) - - @staticmethod - def mut_position_xmer_seq(xmer_wt, xmer_mut): - """ - returns position of mutation in xmer sequence - """ - p1 = -1 - if len(xmer_wt) == len(xmer_mut): - p1 = -1 - for i, aa in enumerate(xmer_mut): - if aa != xmer_wt[i]: - p1 = i + 1 - else: - p1 = 0 - # in case sequences do not have same length - for a1, a2 in zip(xmer_wt, xmer_mut): - if a1 == a2: - p1 += 1 - return str(p1) - - @staticmethod - def epitope_covers_mutation(position_mutation, position_epitope, length_epitope): - """ - checks if predicted epitope covers mutation - """ - cover = False - if position_mutation != "-1": - start = int(position_epitope) - end = start + int(length_epitope) - 1 - if int(position_mutation) >= start and int(position_mutation) <= end: - cover = True - return cover - - @staticmethod - def hamming_check_0_or_1(seq1, seq2): - '''returns number of mismatches between 2 sequences - ''' - errors = 0 - for i in range(len(seq1)): - if seq1[i] != seq2[i]: - errors += 1 - if errors >= 2: - return errors - return errors + + +class EpitopeHelper(object): + + @staticmethod + def generate_nmers(xmer_wt, xmer_mut, lengths): + """ + Generates peptides covering mutation of all lengths that are provided. Returns peptides as list + No peptide is shorter than the minimun length provided + There are no repetitions in the results + """ + length_mut = len(xmer_mut) + list_peptides = [] + pos_mut = int(EpitopeHelper.mut_position_xmer_seq(xmer_mut=xmer_mut, xmer_wt=xmer_wt)) + for length in lengths: + if length <= length_mut: + start_first = pos_mut - length + starts = [start_first + s for s in range(length)] + ends = [s + length for s in starts] + for s, e in zip(starts, ends): + list_peptides.append(xmer_mut[s:e]) + return list(set([x for x in list_peptides if not x == "" and len(x) >= min(lengths)])) + + @staticmethod + def mut_position_xmer_seq(xmer_wt, xmer_mut): + """ + returns position of mutation in xmer sequence + """ + p1 = -1 + if len(xmer_wt) == len(xmer_mut): + p1 = -1 + for i, aa in enumerate(xmer_mut): + if aa != xmer_wt[i]: + p1 = i + 1 + else: + p1 = 0 + # in case sequences do not have same length + for a1, a2 in zip(xmer_wt, xmer_mut): + if a1 == a2: + p1 += 1 + return str(p1) + + @staticmethod + def epitope_covers_mutation(position_mutation, position_epitope, length_epitope): + """ + checks if predicted epitope covers mutation + """ + cover = False + if position_mutation != "-1": + start = int(position_epitope) + end = start + int(length_epitope) - 1 + if int(position_mutation) >= start and int(position_mutation) <= end: + cover = True + return cover + + @staticmethod + def hamming_check_0_or_1(seq1, seq2): + '''returns number of mismatches between 2 sequences + ''' + errors = 0 + for i in range(len(seq1)): + if seq1[i] != seq2[i]: + errors += 1 + if errors >= 2: + return errors + return errors diff --git a/input/helpers/fastaGenerator.py b/input/helpers/fastaGenerator.py index f5996c79..8a994323 100755 --- a/input/helpers/fastaGenerator.py +++ b/input/helpers/fastaGenerator.py @@ -1,32 +1,32 @@ -#!/usr/bin/python - -from Bio.SeqIO.FastaIO import SimpleFastaParser - - -def write_single_seq_fasta(seq, id, file_name): - '''Returns fasta file with a single sequences. - ''' - with open(file_name, "w") as f: - id = "".join([">", id, "\n"]) - f.write(id) - seq = "".join([seq, "\n"]) - f.write(seq) - - -def read_multiple_seqs_simple(fasta_file): - '''This function reads a fasta file using simplefasta parser and returns dictionary with gene names as keys and protein sequences as values. - ''' - database = {} - with open(fasta_file) as handle: - for record in SimpleFastaParser(handle): - # record[0] = fasta header; record[1] = protein sequence - database[record[0]] = record[1] - return database - - -if __name__ == '__main__': - seq = "ABDSF" - id = "M1" - # write_single_seq_fasta(seq, id, "temp.fasta") - read_multiple_seqs_simple( - "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/indels/best_WT/BLAST_DB/ligandome/DB_ligandome_safe.fasta") +#!/usr/bin/python + +from Bio.SeqIO.FastaIO import SimpleFastaParser + + +def write_single_seq_fasta(seq, id, file_name): + '''Returns fasta file with a single sequences. + ''' + with open(file_name, "w") as f: + id = "".join([">", id, "\n"]) + f.write(id) + seq = "".join([seq, "\n"]) + f.write(seq) + + +def read_multiple_seqs_simple(fasta_file): + '''This function reads a fasta file using simplefasta parser and returns dictionary with gene names as keys and protein sequences as values. + ''' + database = {} + with open(fasta_file) as handle: + for record in SimpleFastaParser(handle): + # record[0] = fasta header; record[1] = protein sequence + database[record[0]] = record[1] + return database + + +if __name__ == '__main__': + seq = "ABDSF" + id = "M1" + # write_single_seq_fasta(seq, id, "temp.fasta") + read_multiple_seqs_simple( + "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/indels/best_WT/BLAST_DB/ligandome/DB_ligandome_safe.fasta") diff --git a/input/helpers/intermediate_files.py b/input/helpers/intermediate_files.py index c62b2e60..aa70cce0 100755 --- a/input/helpers/intermediate_files.py +++ b/input/helpers/intermediate_files.py @@ -1,21 +1,21 @@ -import tempfile - - -def create_temp_file(prefix=None, suffix=None, dir=None): - temp_file = tempfile.NamedTemporaryFile(prefix=prefix, suffix=suffix, dir=dir, delete=False) - return temp_file.name - - -def create_temp_fasta(sequences, prefix=None, comment_prefix='seq'): - """ - Writes seqs given in seqs list into fasta file - """ - fasta_temp_file = create_temp_file(prefix=prefix, suffix='.fasta') - counter = 1 - with open(fasta_temp_file, "w") as f: - for seq in sequences: - _id = ">{comment_prefix}{index}".format(comment_prefix=comment_prefix, index=counter) - f.write(_id + "\n") - f.write(seq + "\n") - counter += 1 - return fasta_temp_file +import tempfile + + +def create_temp_file(prefix=None, suffix=None, dir=None): + temp_file = tempfile.NamedTemporaryFile(prefix=prefix, suffix=suffix, dir=dir, delete=False) + return temp_file.name + + +def create_temp_fasta(sequences, prefix=None, comment_prefix='seq'): + """ + Writes seqs given in seqs list into fasta file + """ + fasta_temp_file = create_temp_file(prefix=prefix, suffix='.fasta') + counter = 1 + with open(fasta_temp_file, "w") as f: + for seq in sequences: + _id = ">{comment_prefix}{index}".format(comment_prefix=comment_prefix, index=counter) + f.write(_id + "\n") + f.write(seq + "\n") + counter += 1 + return fasta_temp_file diff --git a/input/helpers/properties_manager.py b/input/helpers/properties_manager.py index 01139811..91b55251 100755 --- a/input/helpers/properties_manager.py +++ b/input/helpers/properties_manager.py @@ -1,97 +1,97 @@ -from input import MHC_I, MHC_II -from input.exceptions import INPuTInputParametersException - -PATIENT_ID3 = "patient.x" -PATIENT_ID2 = "patient" -PATIENT_ID = "patient.id" - - -def get_gene(properties): - if "gene.x" in properties: - gene = properties["gene.x"] - else: - gene = properties["gene"] - return gene - - -def get_substitution(properties): - return properties["substitution"] - - -def get_mutation_aminoacid(properties): - return properties["MUT_AA"] - - -def get_epitopes(properties, mhc): - if mhc == MHC_I: - mutation = properties["MHC_I_epitope_.best_prediction."] - wild_type = properties["MHC_I_epitope_.WT."] - elif mhc == MHC_II: - mutation = properties["MHC_II_epitope_.best_prediction."] - wild_type = properties["MHC_II_epitope_.WT."] - else: - raise INPuTInputParametersException("Bad MHC value: {}".format(mhc)) - return wild_type, mutation - - -def get_scores_multiple_binding(properties, mhc): - if mhc == MHC_I: - mutation = properties["MB_score_top10_harmonic"] - wild_type = properties["MB_score_WT_top10_harmonic"] - elif mhc == MHC_II: - mutation = properties["MB_score_MHCII_top10_harmonic"] - wild_type = properties["MB_score_MHCII_top10_WT_harmonic"] - else: - raise INPuTInputParametersException("Bad MHC value: {}".format(mhc)) - return wild_type, mutation - - -def get_scores_netmhcpan4_affinity(properties, mhc): - if mhc == MHC_I: - mutation = properties["best_affinity_netmhcpan4"] - wild_type = properties["best_affinity_netmhcpan4_WT"] - elif mhc == MHC_II: - mutation = properties["best_affinity_netmhcIIpan"] - wild_type = properties["best_affinity_netmhcIIpan_WT"] - else: - raise INPuTInputParametersException("Bad MHC value: {}".format(mhc)) - return wild_type, mutation - - -def get_scores_netmhcpan4_ranks(properties, mhc): - if mhc == MHC_I: - mutation = properties["best%Rank_netmhcpan4"] - wild_type = properties["best%Rank_netmhcpan4_WT"] - elif mhc == MHC_II: - mutation = properties["best%Rank_netmhcIIpan"] - wild_type = properties["best%Rank_netmhcIIpan_WT"] - else: - raise INPuTInputParametersException("Bad MHC value: {}".format(mhc)) - return wild_type, mutation - - -def get_netmhcpan4_epitopes(properties, nine_mer=False): - if nine_mer: - mutation = properties["best_affinity_epitope_netmhcpan4_9mer"] - wild_type = properties["best_epitope_netmhcpan4_9mer_WT"] - else: - mutation = properties["best_affinity_epitope_netmhcpan4"] - wild_type = properties["best_affinity_epitope_netmhcpan4_WT"] - return wild_type, mutation - - -def get_hla_allele(props, hla_patient_dict): - ''' returns hla allele of patients given in hla_file - ''' - patient_id = get_patient_id(props) - return hla_patient_dict[patient_id] - - -def get_patient_id(props): - if PATIENT_ID in props: - patient_id = props[PATIENT_ID] - elif PATIENT_ID2 in props: - patient_id = props[PATIENT_ID2] - else: - patient_id = props[PATIENT_ID3] +from input import MHC_I, MHC_II +from input.exceptions import INPuTInputParametersException + +PATIENT_ID3 = "patient.x" +PATIENT_ID2 = "patient" +PATIENT_ID = "patient.id" + + +def get_gene(properties): + if "gene.x" in properties: + gene = properties["gene.x"] + else: + gene = properties["gene"] + return gene + + +def get_substitution(properties): + return properties["substitution"] + + +def get_mutation_aminoacid(properties): + return properties["MUT_AA"] + + +def get_epitopes(properties, mhc): + if mhc == MHC_I: + mutation = properties["MHC_I_epitope_.best_prediction."] + wild_type = properties["MHC_I_epitope_.WT."] + elif mhc == MHC_II: + mutation = properties["MHC_II_epitope_.best_prediction."] + wild_type = properties["MHC_II_epitope_.WT."] + else: + raise INPuTInputParametersException("Bad MHC value: {}".format(mhc)) + return wild_type, mutation + + +def get_scores_multiple_binding(properties, mhc): + if mhc == MHC_I: + mutation = properties["MB_score_top10_harmonic"] + wild_type = properties["MB_score_WT_top10_harmonic"] + elif mhc == MHC_II: + mutation = properties["MB_score_MHCII_top10_harmonic"] + wild_type = properties["MB_score_MHCII_top10_WT_harmonic"] + else: + raise INPuTInputParametersException("Bad MHC value: {}".format(mhc)) + return wild_type, mutation + + +def get_scores_netmhcpan4_affinity(properties, mhc): + if mhc == MHC_I: + mutation = properties["best_affinity_netmhcpan4"] + wild_type = properties["best_affinity_netmhcpan4_WT"] + elif mhc == MHC_II: + mutation = properties["best_affinity_netmhcIIpan"] + wild_type = properties["best_affinity_netmhcIIpan_WT"] + else: + raise INPuTInputParametersException("Bad MHC value: {}".format(mhc)) + return wild_type, mutation + + +def get_scores_netmhcpan4_ranks(properties, mhc): + if mhc == MHC_I: + mutation = properties["best%Rank_netmhcpan4"] + wild_type = properties["best%Rank_netmhcpan4_WT"] + elif mhc == MHC_II: + mutation = properties["best%Rank_netmhcIIpan"] + wild_type = properties["best%Rank_netmhcIIpan_WT"] + else: + raise INPuTInputParametersException("Bad MHC value: {}".format(mhc)) + return wild_type, mutation + + +def get_netmhcpan4_epitopes(properties, nine_mer=False): + if nine_mer: + mutation = properties["best_affinity_epitope_netmhcpan4_9mer"] + wild_type = properties["best_epitope_netmhcpan4_9mer_WT"] + else: + mutation = properties["best_affinity_epitope_netmhcpan4"] + wild_type = properties["best_affinity_epitope_netmhcpan4_WT"] + return wild_type, mutation + + +def get_hla_allele(props, hla_patient_dict): + ''' returns hla allele of patients given in hla_file + ''' + patient_id = get_patient_id(props) + return hla_patient_dict[patient_id] + + +def get_patient_id(props): + if PATIENT_ID in props: + patient_id = props[PATIENT_ID] + elif PATIENT_ID2 in props: + patient_id = props[PATIENT_ID2] + else: + patient_id = props[PATIENT_ID3] return patient_id \ No newline at end of file diff --git a/input/helpers/runner.py b/input/helpers/runner.py index 7c558541..9007c533 100755 --- a/input/helpers/runner.py +++ b/input/helpers/runner.py @@ -1,37 +1,37 @@ -import subprocess -import time - -from logzero import logger - -from input.exceptions import INPuTCommandException - - -class Runner(object): - - def run_command(self, cmd, **kwargs): - logger.info("Starting command: {}".format(" ".join(cmd))) - start = time.time() - process = subprocess.Popen(self._preprocess_command(cmd), stderr=subprocess.PIPE, stdout=subprocess.PIPE, **kwargs) - output, errors = process.communicate() - return_code = process.returncode - end = time.time() - logger.info("Elapsed time {} seconds".format(int(end - start))) - if return_code == 0: - logger.info("Finished command correctly!") - logger.info(self._decode(output)) - else: - logger.error("Finished command with return code {}".format(return_code)) - logger.error(self._decode(output)) - logger.error(self._decode(errors)) - raise INPuTCommandException("Error running command '{}'".format(" ".join(cmd))) - return self._decode(output), self._decode(errors) - - @staticmethod - def _preprocess_command(cmd): - """ - This makes sure that any parameter containing white spaces is passed appropriately - """ - return " ".join(cmd).split(" ") - - def _decode(self, data): - return data.decode('utf8') +import subprocess +import time + +from logzero import logger + +from input.exceptions import INPuTCommandException + + +class Runner(object): + + def run_command(self, cmd, **kwargs): + logger.info("Starting command: {}".format(" ".join(cmd))) + start = time.time() + process = subprocess.Popen(self._preprocess_command(cmd), stderr=subprocess.PIPE, stdout=subprocess.PIPE, **kwargs) + output, errors = process.communicate() + return_code = process.returncode + end = time.time() + logger.info("Elapsed time {} seconds".format(int(end - start))) + if return_code == 0: + logger.info("Finished command correctly!") + logger.info(self._decode(output)) + else: + logger.error("Finished command with return code {}".format(return_code)) + logger.error(self._decode(output)) + logger.error(self._decode(errors)) + raise INPuTCommandException("Error running command '{}'".format(" ".join(cmd))) + return self._decode(output), self._decode(errors) + + @staticmethod + def _preprocess_command(cmd): + """ + This makes sure that any parameter containing white spaces is passed appropriately + """ + return " ".join(cmd).split(" ") + + def _decode(self, data): + return data.decode('utf8') diff --git a/input/netmhcpan4/abstract_netmhcpan_predictor.py b/input/netmhcpan4/abstract_netmhcpan_predictor.py index 4ad613bc..3a915dc6 100755 --- a/input/netmhcpan4/abstract_netmhcpan_predictor.py +++ b/input/netmhcpan4/abstract_netmhcpan_predictor.py @@ -1,17 +1,17 @@ - - - -class AbstractNetMhcPanPredictor(object): - - @staticmethod - def add_best_epitope_info(epitope_tuple, column_name): - '''returns desired information of prediction of best epitope from netmhcpan output; - e.g. "%Rank": MHC I score, "HLA": HLA allele, "Icore": best epitope - ''' - dat_head = epitope_tuple[0] - dat = epitope_tuple[1] - val = dat_head.index(column_name) - try: - return dat[val] - except IndexError: - return "NA" + + + +class AbstractNetMhcPanPredictor(object): + + @staticmethod + def add_best_epitope_info(epitope_tuple, column_name): + '''returns desired information of prediction of best epitope from netmhcpan output; + e.g. "%Rank": MHC I score, "HLA": HLA allele, "Icore": best epitope + ''' + dat_head = epitope_tuple[0] + dat = epitope_tuple[1] + val = dat_head.index(column_name) + try: + return dat[val] + except IndexError: + return "NA" diff --git a/input/new_features/conservation_scores.py b/input/new_features/conservation_scores.py index 3f3437c9..c90de859 100755 --- a/input/new_features/conservation_scores.py +++ b/input/new_features/conservation_scores.py @@ -1,51 +1,51 @@ -import re - -from logzero import logger - - -class ProveanAnnotator(object): - - def __init__(self, provean_file, header_epitopes, epitopes): - """ - Loads provean scores as dictionary, but only for ucsc ids that are in epitope list - """ - epitope_ids = self._load_ucsc_ids_epitopes(header_epitopes=header_epitopes, epitopes=epitopes) - logger.info("Starting load of PROVEAN matrix" + provean_file) - self.header_provean, self.provean_matrix = self._load_provean_matrix(epitope_ids, provean_file) - logger.info("PROVEAN matrix loaded") - - def _load_ucsc_ids_epitopes(self, header_epitopes, epitopes): - """ - Returns set with ucsc ids of epitopes. - """ - col_ucsc = header_epitopes.index("UCSC_transcript") - col_pos = header_epitopes.index("substitution") - return set([self.build_ucsc_id_plus_position(ucsc_id=e[col_ucsc], substitution=e[col_pos]) for e in epitopes]) - - def _load_provean_matrix(self, epitope_ids, provean_file): - provean_matrix = {} - with open(provean_file) as f: - header = next(f).rstrip().split(";") # stores header - for line in f: - parts = line.rstrip().split(";") - ucsc_id_pos = parts[-1] - if ucsc_id_pos in epitope_ids: - provean_matrix[ucsc_id_pos] = parts - return header, provean_matrix - - def get_provean_annotation(self, mutated_aminoacid, ucsc_id_position): - """ - This function maps Provean score on given position and for specific SNV onto epitope data set - (which is in form of tuple --> header + dict of ucsc_pos_id: df row) - """ - try: - return self.provean_matrix[ucsc_id_position][self.header_provean.index(mutated_aminoacid)] - except (ValueError, KeyError) as e: - return "NA" - - @staticmethod - def build_ucsc_id_plus_position(substitution, ucsc_id): - ucsc_epi = re.sub(r'.\d+$', '', ucsc_id) - position_match = re.match(r'[A-Z](\d+)[A-Z]', substitution) - pos_prot = position_match.group(1) if position_match else "Del" - return "{}_{}".format(ucsc_epi, pos_prot) +import re + +from logzero import logger + + +class ProveanAnnotator(object): + + def __init__(self, provean_file, header_epitopes, epitopes): + """ + Loads provean scores as dictionary, but only for ucsc ids that are in epitope list + """ + epitope_ids = self._load_ucsc_ids_epitopes(header_epitopes=header_epitopes, epitopes=epitopes) + logger.info("Starting load of PROVEAN matrix" + provean_file) + self.header_provean, self.provean_matrix = self._load_provean_matrix(epitope_ids, provean_file) + logger.info("PROVEAN matrix loaded") + + def _load_ucsc_ids_epitopes(self, header_epitopes, epitopes): + """ + Returns set with ucsc ids of epitopes. + """ + col_ucsc = header_epitopes.index("UCSC_transcript") + col_pos = header_epitopes.index("substitution") + return set([self.build_ucsc_id_plus_position(ucsc_id=e[col_ucsc], substitution=e[col_pos]) for e in epitopes]) + + def _load_provean_matrix(self, epitope_ids, provean_file): + provean_matrix = {} + with open(provean_file) as f: + header = next(f).rstrip().split(";") # stores header + for line in f: + parts = line.rstrip().split(";") + ucsc_id_pos = parts[-1] + if ucsc_id_pos in epitope_ids: + provean_matrix[ucsc_id_pos] = parts + return header, provean_matrix + + def get_provean_annotation(self, mutated_aminoacid, ucsc_id_position): + """ + This function maps Provean score on given position and for specific SNV onto epitope data set + (which is in form of tuple --> header + dict of ucsc_pos_id: df row) + """ + try: + return self.provean_matrix[ucsc_id_position][self.header_provean.index(mutated_aminoacid)] + except (ValueError, KeyError) as e: + return "NA" + + @staticmethod + def build_ucsc_id_plus_position(substitution, ucsc_id): + ucsc_epi = re.sub(r'.\d+$', '', ucsc_id) + position_match = re.match(r'[A-Z](\d+)[A-Z]', substitution) + pos_prot = position_match.group(1) if position_match else "Del" + return "{}_{}".format(ucsc_epi, pos_prot) diff --git a/input/references.py b/input/references.py index 8d8178a9..900ac9b4 100755 --- a/input/references.py +++ b/input/references.py @@ -1,107 +1,107 @@ -import os - -from logzero import logger - -import input -from input.exceptions import INPuTConfigurationException - - -class DependenciesConfiguration(object): - - def __init__(self): - self.blastp = self._check_and_load_binary(input.INPUT_BLASTP_ENV) - self.mix_mhc2_pred = self._check_and_load_binary(input.INPUT_MIXMHC2PRED_ENV) - self.mix_mhc2_pred_alleles_list = os.path.join(os.path.dirname(self.mix_mhc2_pred), 'Alleles_list.txt') - self.mix_mhc_pred = self._check_and_load_binary(input.INPUT_MIXMHCPRED_ENV) - self.rscript = self._check_and_load_binary(input.INPUT_RSCRIPT_ENV) - self.net_mhc2_pan = self._check_and_load_binary(input.INPUT_NETMHC2PAN_ENV) - self.net_mhc_pan = self._check_and_load_binary(input.INPUT_NETMHCPAN_ENV) - - @staticmethod - def _check_and_load_binary(variable_name): - variable_value = os.environ.get(variable_name, "") - if not variable_value: - raise INPuTConfigurationException( - "Please, set the environment variable ${} pointing to the right binary!".format( - variable_name)) - if not os.path.exists(variable_value): - raise INPuTConfigurationException("The provided binary '{}' in ${} does not exist!".format( - variable_value, variable_name)) - return variable_value - - -class ReferenceFolder(object): - - def __init__(self): - self.reference_genome_folder = self._check_reference_genome_folder() - # sets the right file names for the resources - self.available_mhc_ii = self._get_reference_file_name('avail_mhcII.txt') - self.available_mhc_i = self._get_reference_file_name('MHC_available.csv') - self.aa_freq_prot = self._get_reference_file_name('20181108_AA_freq_prot.csv') - self.four_mer_freq = self._get_reference_file_name('20181108_4mer_freq.csv') - self.aaindex1 = self._get_reference_file_name('aaindex1') - self.aaindex2 = self._get_reference_file_name('aaindex2') - self.prov_scores_mapped3 = self._get_reference_file_name('PROV_scores_mapped3.csv') - self.iedb = self._get_reference_file_name('iedb') - self.proteome_db = self._get_reference_file_name('proteome_db') - self.tcell_predictor_sir_data = self._get_reference_file_name('SIRdata.mat') - self.tcell_predictor_gene_expression = self._get_reference_file_name('genes-expression.pickle') - self.tcell_predictor_aa_features = self._get_reference_file_name('amino-acids-features.pickle') - self.uniprot = self._get_reference_file_name('uniprot_human_with_isoforms.fasta') - self.gtex = self._get_reference_file_name('gtex_combined.csv') - - # TODO: add this files self.alleles_list_pred, self.avail_mhc_ii - self.resources = [self.available_mhc_ii, self.available_mhc_i, self.aa_freq_prot, - self.four_mer_freq, self.aaindex1, self.aaindex2, self.prov_scores_mapped3, self.iedb, - self.proteome_db, self.tcell_predictor_aa_features, - self.tcell_predictor_gene_expression, self.tcell_predictor_sir_data, - self.uniprot, self.gtex] - self._check_resources(self.resources) - self._log_configuration() - - @staticmethod - def _check_reference_genome_folder(): - reference_genome_folder = os.environ.get(input.REFERENCE_FOLDER_ENV, "") - if not reference_genome_folder: - raise INPuTConfigurationException( - "Please, set the environment variable ${} pointing to the reference genome folder!".format( - input.REFERENCE_FOLDER_ENV)) - if not os.path.exists(reference_genome_folder): - raise INPuTConfigurationException("The provided reference genome '{}' in ${} does not exist!".format( - reference_genome_folder, input.REFERENCE_FOLDER_ENV)) - return reference_genome_folder - - @staticmethod - def _check_resources(resources): - missing_resources = [] - for r in resources: - if not os.path.exists(r): - missing_resources.append(r) - if len(missing_resources) > 0: - raise INPuTConfigurationException( - "Missing resources in the reference folder: {}".format(str(missing_resources))) - - def _log_configuration(self): - logger.info("Reference genome folder: {}".format(self.reference_genome_folder)) - logger.info("Resources") - for r in self.resources: - logger.info(r) - - def _get_reference_file_name(self, file_name_suffix): - return os.path.join(self.reference_genome_folder, file_name_suffix) - - def load_available_hla_alleles(self, mhc=input.MHC_I): - """ - loads file with available hla alllels for netmhcpan4/netmhcIIpan prediction, returns set - :type mhc: str - :rtype list: - """ - if mhc == input.MHC_II: - fileMHC = self.available_mhc_ii - else: - fileMHC = self.available_mhc_i - set_available_mhc = set() - with open(fileMHC) as f: - for line in f: - set_available_mhc.add(line.strip()) - return set_available_mhc +import os + +from logzero import logger + +import input +from input.exceptions import INPuTConfigurationException + + +class DependenciesConfiguration(object): + + def __init__(self): + self.blastp = self._check_and_load_binary(input.INPUT_BLASTP_ENV) + self.mix_mhc2_pred = self._check_and_load_binary(input.INPUT_MIXMHC2PRED_ENV) + self.mix_mhc2_pred_alleles_list = os.path.join(os.path.dirname(self.mix_mhc2_pred), 'Alleles_list.txt') + self.mix_mhc_pred = self._check_and_load_binary(input.INPUT_MIXMHCPRED_ENV) + self.rscript = self._check_and_load_binary(input.INPUT_RSCRIPT_ENV) + self.net_mhc2_pan = self._check_and_load_binary(input.INPUT_NETMHC2PAN_ENV) + self.net_mhc_pan = self._check_and_load_binary(input.INPUT_NETMHCPAN_ENV) + + @staticmethod + def _check_and_load_binary(variable_name): + variable_value = os.environ.get(variable_name, "") + if not variable_value: + raise INPuTConfigurationException( + "Please, set the environment variable ${} pointing to the right binary!".format( + variable_name)) + if not os.path.exists(variable_value): + raise INPuTConfigurationException("The provided binary '{}' in ${} does not exist!".format( + variable_value, variable_name)) + return variable_value + + +class ReferenceFolder(object): + + def __init__(self): + self.reference_genome_folder = self._check_reference_genome_folder() + # sets the right file names for the resources + self.available_mhc_ii = self._get_reference_file_name('avail_mhcII.txt') + self.available_mhc_i = self._get_reference_file_name('MHC_available.csv') + self.aa_freq_prot = self._get_reference_file_name('20181108_AA_freq_prot.csv') + self.four_mer_freq = self._get_reference_file_name('20181108_4mer_freq.csv') + self.aaindex1 = self._get_reference_file_name('aaindex1') + self.aaindex2 = self._get_reference_file_name('aaindex2') + self.prov_scores_mapped3 = self._get_reference_file_name('PROV_scores_mapped3.csv') + self.iedb = self._get_reference_file_name('iedb') + self.proteome_db = self._get_reference_file_name('proteome_db') + self.tcell_predictor_sir_data = self._get_reference_file_name('SIRdata.mat') + self.tcell_predictor_gene_expression = self._get_reference_file_name('genes-expression.pickle') + self.tcell_predictor_aa_features = self._get_reference_file_name('amino-acids-features.pickle') + self.uniprot = self._get_reference_file_name('uniprot_human_with_isoforms.fasta') + self.gtex = self._get_reference_file_name('gtex_combined.csv') + + # TODO: add this files self.alleles_list_pred, self.avail_mhc_ii + self.resources = [self.available_mhc_ii, self.available_mhc_i, self.aa_freq_prot, + self.four_mer_freq, self.aaindex1, self.aaindex2, self.prov_scores_mapped3, self.iedb, + self.proteome_db, self.tcell_predictor_aa_features, + self.tcell_predictor_gene_expression, self.tcell_predictor_sir_data, + self.uniprot, self.gtex] + self._check_resources(self.resources) + self._log_configuration() + + @staticmethod + def _check_reference_genome_folder(): + reference_genome_folder = os.environ.get(input.REFERENCE_FOLDER_ENV, "") + if not reference_genome_folder: + raise INPuTConfigurationException( + "Please, set the environment variable ${} pointing to the reference genome folder!".format( + input.REFERENCE_FOLDER_ENV)) + if not os.path.exists(reference_genome_folder): + raise INPuTConfigurationException("The provided reference genome '{}' in ${} does not exist!".format( + reference_genome_folder, input.REFERENCE_FOLDER_ENV)) + return reference_genome_folder + + @staticmethod + def _check_resources(resources): + missing_resources = [] + for r in resources: + if not os.path.exists(r): + missing_resources.append(r) + if len(missing_resources) > 0: + raise INPuTConfigurationException( + "Missing resources in the reference folder: {}".format(str(missing_resources))) + + def _log_configuration(self): + logger.info("Reference genome folder: {}".format(self.reference_genome_folder)) + logger.info("Resources") + for r in self.resources: + logger.info(r) + + def _get_reference_file_name(self, file_name_suffix): + return os.path.join(self.reference_genome_folder, file_name_suffix) + + def load_available_hla_alleles(self, mhc=input.MHC_I): + """ + loads file with available hla alllels for netmhcpan4/netmhcIIpan prediction, returns set + :type mhc: str + :rtype list: + """ + if mhc == input.MHC_II: + fileMHC = self.available_mhc_ii + else: + fileMHC = self.available_mhc_i + set_available_mhc = set() + with open(fileMHC) as f: + for line in f: + set_available_mhc.add(line.strip()) + return set_available_mhc diff --git a/input/self_similarity/self_similarity.py b/input/self_similarity/self_similarity.py index 7285b0c8..e5d0c288 100755 --- a/input/self_similarity/self_similarity.py +++ b/input/self_similarity/self_similarity.py @@ -1,137 +1,137 @@ -#!/usr/bin/env python - -from input import MHC_I, MHC_II - -import math -import os - -BETA = 0.11387 -BLOSUM62_FILE_NAME = 'BLOSUM62-2.matrix.txt' - - -class SelfSimilarityCalculator(): - - def __init__(self): - blosum_file = os.path.join(os.path.abspath(os.path.dirname(__file__)), BLOSUM62_FILE_NAME) - blosum_dict = self._load_blosum(blosum_file) - self.k1 = self._compute_k1(blosum_dict) - - def _compute_k1(self, blosum_dict): - K1 = {} - for i in list(blosum_dict.keys()): - x = K1.get(i, {}) - for j in list(blosum_dict[i].keys()): - x[j] = math.pow(blosum_dict[i][j], BETA) - K1[i] = x - return K1 - - def _load_blosum(self, blosum): - blosum_dict = {} - colid = [] - rowid = [] - c = 0 - with open(blosum) as f: - for line in f: - c += 1 - if c == 1: - colid = line.strip("\n").split(" ") - continue - w = line.strip("\n").split(" ") - id = w[0] - v = [float(x) for x in w[1:]] - rowid.append(id) - x = blosum_dict.get(id, {}) - for i, vi in enumerate(v): - x[colid[i]] = vi - blosum_dict[id] = x - return blosum_dict - - def compute_k_hat_3(self, x, y): # K^3 - return self._compute_k3(x, y) / math.sqrt(self._compute_k3(x, x) * self._compute_k3(y, y)) - - def _compute_k3(self, f, g): - max_k = min(len(f), len(g)) - s = 0 - for k in range(1, max_k + 1): - for i in range(len(f) - (k - 1)): - u = f[i:i + k] - for j in range(len(g) - (k - 1)): - v = g[j:j + k] - s += self._compute_k2k(u, v, self.k1) - return s - - def _compute_k2k(self, u, v, K1): - if len(u) != len(v): - return None - k = len(u) - p = K1[u[0]][v[0]] - for i in range(1, k): - p = p * K1[u[i]][v[i]] - return p - - -def get_self_similarity(mutation, wild_type): - """ - Returns self-similiarity between mutated and wt epitope according to Bjerregard et al., - Argument mhc indicates if determination for MHC I or MHC II epitopes - """ - self_similarity = 'NA' - try: - self_similarity = str(SelfSimilarityCalculator().compute_k_hat_3(mutation, wild_type)) - except ZeroDivisionError: - pass - return self_similarity - - -def is_improved_binder(score_mutation, score_wild_type): - """ - This function checks if mutated epitope is improved binder according to Bjerregard et al. - """ - try: - improved_binder = float(score_wild_type) / float(score_mutation) >= 1.2 - except (ZeroDivisionError, ValueError) as e: - return "NA" - # TODO: boolean in a string needs to go away - return "1" if improved_binder else "0" - - -def self_similarity_of_conserved_binder_only(has_conserved_binder, similarity): - """ - this function returns selfsimilarity for conserved binder but not for improved binder - """ - try: - if has_conserved_binder == str(0): - return similarity - else: - return "NA" - except (ZeroDivisionError, ValueError) as e: - return "NA" - - -def position_of_mutation_epitope(wild_type, mutation): - """ - This function determines the position of the mutation within the epitope sequence. - """ - p1 = -1 - try: - for i, aa in enumerate(mutation): - if aa != wild_type[i]: - p1 = i + 1 - return str(p1) - except: - return "NA" - - -def position_in_anchor_position(position_mhci, peptide_length): - """ - This function determines if the mutation is located within an anchor position in mhc I. - As an approximation, we assume that the second and the last position are anchor positions for all alleles. - """ - anchor = "NA" - try: - anchor = int(position_mhci) == int(peptide_length) or int(position_mhci) == 2 - # TODO this conversion of a boolean to a numeric boolean in a string needs to go away - anchor = str(1) if anchor else str(0) - except: - pass - return anchor +#!/usr/bin/env python + +from input import MHC_I, MHC_II + +import math +import os + +BETA = 0.11387 +BLOSUM62_FILE_NAME = 'BLOSUM62-2.matrix.txt' + + +class SelfSimilarityCalculator(): + + def __init__(self): + blosum_file = os.path.join(os.path.abspath(os.path.dirname(__file__)), BLOSUM62_FILE_NAME) + blosum_dict = self._load_blosum(blosum_file) + self.k1 = self._compute_k1(blosum_dict) + + def _compute_k1(self, blosum_dict): + K1 = {} + for i in list(blosum_dict.keys()): + x = K1.get(i, {}) + for j in list(blosum_dict[i].keys()): + x[j] = math.pow(blosum_dict[i][j], BETA) + K1[i] = x + return K1 + + def _load_blosum(self, blosum): + blosum_dict = {} + colid = [] + rowid = [] + c = 0 + with open(blosum) as f: + for line in f: + c += 1 + if c == 1: + colid = line.strip("\n").split(" ") + continue + w = line.strip("\n").split(" ") + id = w[0] + v = [float(x) for x in w[1:]] + rowid.append(id) + x = blosum_dict.get(id, {}) + for i, vi in enumerate(v): + x[colid[i]] = vi + blosum_dict[id] = x + return blosum_dict + + def compute_k_hat_3(self, x, y): # K^3 + return self._compute_k3(x, y) / math.sqrt(self._compute_k3(x, x) * self._compute_k3(y, y)) + + def _compute_k3(self, f, g): + max_k = min(len(f), len(g)) + s = 0 + for k in range(1, max_k + 1): + for i in range(len(f) - (k - 1)): + u = f[i:i + k] + for j in range(len(g) - (k - 1)): + v = g[j:j + k] + s += self._compute_k2k(u, v, self.k1) + return s + + def _compute_k2k(self, u, v, K1): + if len(u) != len(v): + return None + k = len(u) + p = K1[u[0]][v[0]] + for i in range(1, k): + p = p * K1[u[i]][v[i]] + return p + + +def get_self_similarity(mutation, wild_type): + """ + Returns self-similiarity between mutated and wt epitope according to Bjerregard et al., + Argument mhc indicates if determination for MHC I or MHC II epitopes + """ + self_similarity = 'NA' + try: + self_similarity = str(SelfSimilarityCalculator().compute_k_hat_3(mutation, wild_type)) + except ZeroDivisionError: + pass + return self_similarity + + +def is_improved_binder(score_mutation, score_wild_type): + """ + This function checks if mutated epitope is improved binder according to Bjerregard et al. + """ + try: + improved_binder = float(score_wild_type) / float(score_mutation) >= 1.2 + except (ZeroDivisionError, ValueError) as e: + return "NA" + # TODO: boolean in a string needs to go away + return "1" if improved_binder else "0" + + +def self_similarity_of_conserved_binder_only(has_conserved_binder, similarity): + """ + this function returns selfsimilarity for conserved binder but not for improved binder + """ + try: + if has_conserved_binder == str(0): + return similarity + else: + return "NA" + except (ZeroDivisionError, ValueError) as e: + return "NA" + + +def position_of_mutation_epitope(wild_type, mutation): + """ + This function determines the position of the mutation within the epitope sequence. + """ + p1 = -1 + try: + for i, aa in enumerate(mutation): + if aa != wild_type[i]: + p1 = i + 1 + return str(p1) + except: + return "NA" + + +def position_in_anchor_position(position_mhci, peptide_length): + """ + This function determines if the mutation is located within an anchor position in mhc I. + As an approximation, we assume that the second and the last position are anchor positions for all alleles. + """ + anchor = "NA" + try: + anchor = int(position_mhci) == int(peptide_length) or int(position_mhci) == 2 + # TODO this conversion of a boolean to a numeric boolean in a string needs to go away + anchor = str(1) if anchor else str(0) + except: + pass + return anchor diff --git a/input/tests/__init__.py b/input/tests/__init__.py index 25be8221..ee7475c9 100755 --- a/input/tests/__init__.py +++ b/input/tests/__init__.py @@ -1,22 +1,22 @@ -TEST_HLAI_ALLELES = [ - 'HLA-A*24:02', 'HLA-A*02:01', 'HLA-B*15:01', 'HLA-B*44:02', 'HLA-C*07:02', 'HLA-C*05:01', - 'HLA-A*24:02', 'HLA-B*27:05', 'HLA-B*52:01', 'HLA-C*01:02', 'HLA-C*12:02', - 'HLA-A*01:01', 'HLA-B*56:01', 'HLA-B*38:01', 'HLA-C*01:02', 'HLA-C*06:02', - 'HLA-A*03:01', 'HLA-A*02:01', 'HLA-B*27:05', 'HLA-B*47:01', 'HLA-C*01:02', 'HLA-C*06:02', - 'HLA-A*02:01', 'HLA-A*25:01', 'HLA-B*27:02', 'HLA-B*18:01', 'HLA-C*02:02', 'HLA-C*12:03', - 'HLA-A*23:01', 'HLA-A*66:01', 'HLA-B*41:02', 'HLA-B*35:01', 'HLA-C*17:03', 'HLA-C*04:01', - 'HLA-A*66:01', 'HLA-A*01:01', 'HLA-B*08:01', 'HLA-C*07:01', - 'HLA-A*03:01', 'HLA-A*01:01', 'HLA-B*08:01', 'HLA-B*35:01', 'HLA-C*07:01', 'HLA-C*04:01', - 'HLA-A*24:02', 'HLA-A*68:01', 'HLA-B*35:03', 'HLA-B*13:02', 'HLA-C*06:02', 'HLA-C*04:01', - 'HLA-A*01:01', 'HLA-B*37:01', 'HLA-B*08:01', 'HLA-C*06:02', 'HLA-C*07:01'] - -TEST_HLAII_ALLELES = ['HLA-DRB1*04:01', 'HLA-DRB1*04:04', 'HLA-DQB1*03:01', 'HLA-DQB1*03:02', - 'HLA-DRB1*11:01', 'HLA-DRB1*01:01', 'HLA-DQB1*05:01', 'HLA-DQB1*03:01', - 'HLA-DRB1*11:04', 'HLA-DRB1*07:01', 'HLA-DQB1*02:02', 'HLA-DQB1*03:01', - 'HLA-DRB1*01:01', 'HLA-DRB1*07:01', 'HLA-DQB1*05:01', 'HLA-DQB1*02:02', - 'HLA-DRB1*16:01', 'HLA-DRB1*01:01', 'HLA-DQB1*05:02', 'HLA-DQB1*05:01', - 'HLA-DRB1*11:01', 'HLA-DRB1*01:01', 'HLA-DQB1*05:01', 'HLA-DQB1*03:01', - 'HLA-DRB1*03:01', 'HLA-DQB1*02:01', - 'HLA-DRB1*03:01', 'HLA-DRB1*07:01', 'HLA-DQB1*02:02', 'HLA-DQB1*02:01', - 'HLA-DRB1*15:01', 'HLA-DRB1*12:01', 'HLA-DQB1*06:02', 'HLA-DQB1*03:01', - 'HLA-DRB1*11:01', 'HLA-DRB1*03:01', 'HLA-DQB1*03:01', 'HLA-DQB1*02:01'] +TEST_HLAI_ALLELES = [ + 'HLA-A*24:02', 'HLA-A*02:01', 'HLA-B*15:01', 'HLA-B*44:02', 'HLA-C*07:02', 'HLA-C*05:01', + 'HLA-A*24:02', 'HLA-B*27:05', 'HLA-B*52:01', 'HLA-C*01:02', 'HLA-C*12:02', + 'HLA-A*01:01', 'HLA-B*56:01', 'HLA-B*38:01', 'HLA-C*01:02', 'HLA-C*06:02', + 'HLA-A*03:01', 'HLA-A*02:01', 'HLA-B*27:05', 'HLA-B*47:01', 'HLA-C*01:02', 'HLA-C*06:02', + 'HLA-A*02:01', 'HLA-A*25:01', 'HLA-B*27:02', 'HLA-B*18:01', 'HLA-C*02:02', 'HLA-C*12:03', + 'HLA-A*23:01', 'HLA-A*66:01', 'HLA-B*41:02', 'HLA-B*35:01', 'HLA-C*17:03', 'HLA-C*04:01', + 'HLA-A*66:01', 'HLA-A*01:01', 'HLA-B*08:01', 'HLA-C*07:01', + 'HLA-A*03:01', 'HLA-A*01:01', 'HLA-B*08:01', 'HLA-B*35:01', 'HLA-C*07:01', 'HLA-C*04:01', + 'HLA-A*24:02', 'HLA-A*68:01', 'HLA-B*35:03', 'HLA-B*13:02', 'HLA-C*06:02', 'HLA-C*04:01', + 'HLA-A*01:01', 'HLA-B*37:01', 'HLA-B*08:01', 'HLA-C*06:02', 'HLA-C*07:01'] + +TEST_HLAII_ALLELES = ['HLA-DRB1*04:01', 'HLA-DRB1*04:04', 'HLA-DQB1*03:01', 'HLA-DQB1*03:02', + 'HLA-DRB1*11:01', 'HLA-DRB1*01:01', 'HLA-DQB1*05:01', 'HLA-DQB1*03:01', + 'HLA-DRB1*11:04', 'HLA-DRB1*07:01', 'HLA-DQB1*02:02', 'HLA-DQB1*03:01', + 'HLA-DRB1*01:01', 'HLA-DRB1*07:01', 'HLA-DQB1*05:01', 'HLA-DQB1*02:02', + 'HLA-DRB1*16:01', 'HLA-DRB1*01:01', 'HLA-DQB1*05:02', 'HLA-DQB1*05:01', + 'HLA-DRB1*11:01', 'HLA-DRB1*01:01', 'HLA-DQB1*05:01', 'HLA-DQB1*03:01', + 'HLA-DRB1*03:01', 'HLA-DQB1*02:01', + 'HLA-DRB1*03:01', 'HLA-DRB1*07:01', 'HLA-DQB1*02:02', 'HLA-DQB1*02:01', + 'HLA-DRB1*15:01', 'HLA-DRB1*12:01', 'HLA-DQB1*06:02', 'HLA-DQB1*03:01', + 'HLA-DRB1*11:01', 'HLA-DRB1*03:01', 'HLA-DQB1*03:01', 'HLA-DQB1*02:01'] diff --git a/input/tests/integration_tests/integration_test_tools.py b/input/tests/integration_tests/integration_test_tools.py index 275fd6b9..5dea5f9e 100755 --- a/input/tests/integration_tests/integration_test_tools.py +++ b/input/tests/integration_tests/integration_test_tools.py @@ -1,19 +1,19 @@ -import random -import tempfile - -import dotenv -from Bio.Alphabet.IUPAC import IUPACData - -from input.references import ReferenceFolder, DependenciesConfiguration - - -def load_references(): - dotenv.load_dotenv() - return ReferenceFolder(), DependenciesConfiguration() - - -def create_temp_aminoacid_fasta_file(): - fastafile = tempfile.NamedTemporaryFile(mode='w', delete=False) - with fastafile as f: - f.write("".join(random.choices(list(IUPACData.protein_letters), k=25))) - return fastafile +import random +import tempfile + +import dotenv +from Bio.Alphabet.IUPAC import IUPACData + +from input.references import ReferenceFolder, DependenciesConfiguration + + +def load_references(): + dotenv.load_dotenv() + return ReferenceFolder(), DependenciesConfiguration() + + +def create_temp_aminoacid_fasta_file(): + fastafile = tempfile.NamedTemporaryFile(mode='w', delete=False) + with fastafile as f: + f.write("".join(random.choices(list(IUPACData.protein_letters), k=25))) + return fastafile diff --git a/input/tests/integration_tests/test_conservation_scores.py b/input/tests/integration_tests/test_conservation_scores.py index e31fb048..15ea8365 100755 --- a/input/tests/integration_tests/test_conservation_scores.py +++ b/input/tests/integration_tests/test_conservation_scores.py @@ -1,46 +1,46 @@ -from unittest import TestCase - -from input.new_features.conservation_scores import ProveanAnnotator -from input.tests.integration_tests import integration_test_tools - - -class TestProveanAnnotator(TestCase): - - def setUp(self): - self.references, self.configuration = integration_test_tools.load_references() - self.header_epitopes = ["UCSC_transcript", "substitution"] - self.epitopes = [ - ["uc010qbo.1", "A207S"], - ["uc001ovh.1", "A41S"], - ["uc001ovh.1", "A40S"], - ["uc001tzg.1", "A154S"], - ["uc001uir.1", "A39S"], - ["uc001yqt.1", "A701S"], - ["uc001zrt.1", "A1520S"], - ["uc010umw.1", "A114S"], - ["uc010umy.1", "A7S"]] - self.annotator = ProveanAnnotator( - provean_file=self.references.prov_scores_mapped3, header_epitopes=self.header_epitopes, - epitopes=self.epitopes) - - def test_provean_annotator_loading(self): - self.assertTrue(len(self.annotator.provean_matrix) <= len(self.epitopes)) - self.assertTrue(len(self.annotator.provean_matrix) > 0) - - def test_provean_annotator(self): - provean_annotation = self.annotator.get_provean_annotation( - mutated_aminoacid="S", ucsc_id_position="uc001tzg_154") - self.assertIsNotNone(provean_annotation) - self.assertTrue(provean_annotation != "NA") - self.assertIsNotNone(float(provean_annotation)) - - def test_provean_annotator_non_existing_aminoacid(self): - provean_annotation = self.annotator.get_provean_annotation( - mutated_aminoacid="NO_AA", ucsc_id_position="uc001tzg_154") - self.assertIsNotNone(provean_annotation) - self.assertTrue(provean_annotation == "NA") - - def test_provean_annotator_non_existing_gene(self): - provean_annotation = self.annotator.get_provean_annotation(mutated_aminoacid="S", ucsc_id_position="nope_156") - self.assertIsNotNone(provean_annotation) - self.assertTrue(provean_annotation == "NA") +from unittest import TestCase + +from input.new_features.conservation_scores import ProveanAnnotator +from input.tests.integration_tests import integration_test_tools + + +class TestProveanAnnotator(TestCase): + + def setUp(self): + self.references, self.configuration = integration_test_tools.load_references() + self.header_epitopes = ["UCSC_transcript", "substitution"] + self.epitopes = [ + ["uc010qbo.1", "A207S"], + ["uc001ovh.1", "A41S"], + ["uc001ovh.1", "A40S"], + ["uc001tzg.1", "A154S"], + ["uc001uir.1", "A39S"], + ["uc001yqt.1", "A701S"], + ["uc001zrt.1", "A1520S"], + ["uc010umw.1", "A114S"], + ["uc010umy.1", "A7S"]] + self.annotator = ProveanAnnotator( + provean_file=self.references.prov_scores_mapped3, header_epitopes=self.header_epitopes, + epitopes=self.epitopes) + + def test_provean_annotator_loading(self): + self.assertTrue(len(self.annotator.provean_matrix) <= len(self.epitopes)) + self.assertTrue(len(self.annotator.provean_matrix) > 0) + + def test_provean_annotator(self): + provean_annotation = self.annotator.get_provean_annotation( + mutated_aminoacid="S", ucsc_id_position="uc001tzg_154") + self.assertIsNotNone(provean_annotation) + self.assertTrue(provean_annotation != "NA") + self.assertIsNotNone(float(provean_annotation)) + + def test_provean_annotator_non_existing_aminoacid(self): + provean_annotation = self.annotator.get_provean_annotation( + mutated_aminoacid="NO_AA", ucsc_id_position="uc001tzg_154") + self.assertIsNotNone(provean_annotation) + self.assertTrue(provean_annotation == "NA") + + def test_provean_annotator_non_existing_gene(self): + provean_annotation = self.annotator.get_provean_annotation(mutated_aminoacid="S", ucsc_id_position="nope_156") + self.assertIsNotNone(provean_annotation) + self.assertTrue(provean_annotation == "NA") diff --git a/input/tests/integration_tests/test_dissimilarity.py b/input/tests/integration_tests/test_dissimilarity.py index 353e7167..c4b288ea 100755 --- a/input/tests/integration_tests/test_dissimilarity.py +++ b/input/tests/integration_tests/test_dissimilarity.py @@ -1,27 +1,27 @@ -from unittest import TestCase - -import input.tests.integration_tests.integration_test_tools as integration_test_tools -from input.helpers.runner import Runner -from input.dissimilarity_garnish.dissimilaritycalculator import DissimilarityCalculator - - -class TestDissimilarity(TestCase): - - def setUp(self): - self.references, self.configuration = integration_test_tools.load_references() - self.fastafile = integration_test_tools.create_temp_aminoacid_fasta_file() - self.runner = Runner() - - def test_dissimilar_sequences(self): - result = DissimilarityCalculator( - runner=self.runner, configuration=self.configuration)\ - .calculate_dissimilarity( - mhc_mutation='tocino', mhc_affinity='velocidad', references=self.references) - self.assertEqual(1, result) - - def test_similar_sequences(self): - result = DissimilarityCalculator( - runner=self.runner, configuration=self.configuration)\ - .calculate_dissimilarity( - mhc_mutation='DDDDDD', mhc_affinity='DDDDDD', references=self.references) - self.assertTrue(result < 0.000001) +from unittest import TestCase + +import input.tests.integration_tests.integration_test_tools as integration_test_tools +from input.helpers.runner import Runner +from input.dissimilarity_garnish.dissimilaritycalculator import DissimilarityCalculator + + +class TestDissimilarity(TestCase): + + def setUp(self): + self.references, self.configuration = integration_test_tools.load_references() + self.fastafile = integration_test_tools.create_temp_aminoacid_fasta_file() + self.runner = Runner() + + def test_dissimilar_sequences(self): + result = DissimilarityCalculator( + runner=self.runner, configuration=self.configuration)\ + .calculate_dissimilarity( + mhc_mutation='tocino', mhc_affinity='velocidad', references=self.references) + self.assertEqual(1, result) + + def test_similar_sequences(self): + result = DissimilarityCalculator( + runner=self.runner, configuration=self.configuration)\ + .calculate_dissimilarity( + mhc_mutation='DDDDDD', mhc_affinity='DDDDDD', references=self.references) + self.assertTrue(result < 0.000001) diff --git a/input/tests/integration_tests/test_mixmhcpred.py b/input/tests/integration_tests/test_mixmhcpred.py index 5d91e435..dcec2bb8 100755 --- a/input/tests/integration_tests/test_mixmhcpred.py +++ b/input/tests/integration_tests/test_mixmhcpred.py @@ -1,99 +1,99 @@ -from unittest import TestCase -from logzero import logger - -import input.tests.integration_tests.integration_test_tools as integration_test_tools -from input.MixMHCpred.abstract_mixmhcpred import AbstractMixMHCpred -from input.MixMHCpred.mixmhc2pred import MixMhc2Pred -from input.MixMHCpred.mixmhcpred import MixMHCpred -from input.helpers.runner import Runner -from input.tests import TEST_HLAI_ALLELES, TEST_HLAII_ALLELES - - -class TestMixMHCPred(TestCase): - - def setUp(self): - self.references, self.configuration = integration_test_tools.load_references() - self.runner = Runner() - - def test_mixmhcpred_epitope_iedb(self): - mixmhcpred = MixMHCpred(runner=self.runner, configuration=self.configuration) - # this is an epitope from IEDB of length 9 - mutated = 'NLVPMVATV' - wild_type = 'NLVPMVATV' - mixmhcpred.main(xmer_wt=wild_type, xmer_mut=mutated, alleles=TEST_HLAI_ALLELES[0:5]) - self.assertIsNotNone(mixmhcpred.all_peptides) - self.assertEqual("NLVPMVAT", mixmhcpred.all_peptides) - logger.debug(mixmhcpred.all_peptides) - self.assertEqual(len(mixmhcpred.all_peptides.split('|')), 1) - self.assertIsNotNone(mixmhcpred.all_scores) - logger.debug(mixmhcpred.all_scores) - self.assertEqual(len(mixmhcpred.all_scores.split('|')), 1) - self.assertEqual("-0.522931", mixmhcpred.all_scores) - self.assertIsNotNone(mixmhcpred.all_ranks) - logger.debug(mixmhcpred.all_ranks) - self.assertEqual(len(mixmhcpred.all_ranks.split('|')), 1) - self.assertEqual("77", mixmhcpred.all_ranks) - self.assertIsNotNone(mixmhcpred.all_alleles) - self.assertIsNotNone(mixmhcpred.best_peptide) - self.assertIsNotNone(mixmhcpred.best_score) - self.assertIsNotNone(mixmhcpred.best_rank) - self.assertIsNotNone(mixmhcpred.best_allele) - self.assertIsNotNone(mixmhcpred.best_peptide_wt) - self.assertIsNotNone(mixmhcpred.best_score_wt) - self.assertIsNotNone(mixmhcpred.best_rank_wt) - self.assertIsNotNone(mixmhcpred.difference_score_mut_wt) - - def test_mixmhcpred_too_small_epitope(self): - mixmhcpred = MixMHCpred(runner=self.runner, configuration=self.configuration) - mutated = 'NLVP' - wild_type = 'NLVP' - mixmhcpred.main(xmer_wt=wild_type, xmer_mut=mutated, alleles=TEST_HLAI_ALLELES) - self.assertEqual("NA", mixmhcpred.all_peptides) - - def test_mixmhcpred2_epitope_iedb(self): - mixmhcpred = MixMhc2Pred(runner=self.runner, configuration=self.configuration) - # this is an epitope from IEDB of length 15 - mutated = 'ENPVVHFFKNIVTPR' - wild_type = 'ENPVVHFFKNIVTPR' - mixmhcpred.main(xmer_wt=wild_type, xmer_mut=mutated, alleles=TEST_HLAII_ALLELES) - self.assertIsNotNone(mixmhcpred.all_peptides) - self.assertEqual(len(mixmhcpred.all_peptides.split('|')), 2) - self.assertTrue("ENPVVHFFKNIVTP" in mixmhcpred.all_peptides.split('|')) - self.assertTrue("NPVVHFFKNIVTP" in mixmhcpred.all_peptides.split('|')) - logger.debug(mixmhcpred.all_peptides) - self.assertIsNotNone(mixmhcpred.all_ranks) - self.assertEqual(len(mixmhcpred.all_ranks.split('|')), 2) - self.assertTrue("0.116547" in mixmhcpred.all_ranks.split('|')) - self.assertTrue("0.276218", mixmhcpred.all_ranks.split('|')) - logger.debug(mixmhcpred.all_ranks) - self.assertIsNotNone(mixmhcpred.all_alleles) - self.assertIsNotNone(mixmhcpred.best_peptide) - self.assertIsNotNone(mixmhcpred.best_rank) - self.assertIsNotNone(mixmhcpred.best_allele) - self.assertIsNotNone(mixmhcpred.best_peptide_wt) - self.assertIsNotNone(mixmhcpred.best_score_wt) - self.assertIsNotNone(mixmhcpred.best_rank_wt) - self.assertIsNotNone(mixmhcpred.difference_score_mut_wt) - - def test_mixmhcpred2_too_small_epitope(self): - mixmhcpred = MixMhc2Pred(runner=self.runner, configuration=self.configuration) - # this is an epitope from IEDB of length 15 - mutated = 'ENPVVHFF' - wild_type = 'ENPVVHFF' - mixmhcpred.main(xmer_wt=wild_type, xmer_mut=mutated, alleles=TEST_HLAII_ALLELES) - self.assertEqual("NA", mixmhcpred.all_peptides) - - def test_generate_nmers(self): - result = AbstractMixMHCpred.generate_nmers( - xmer_wt="DDDDDDDDD", xmer_mut="DDDDDVDDD", lengths=[8, 9, 10, 11]) - self.assertIsNotNone(result) - self.assertEqual(3, len(result)) - self.assertEqual(1, len(list(filter(lambda x: len(x) == 9, result)))) - self.assertEqual(2, len(list(filter(lambda x: len(x) == 8, result)))) - self.assertEqual(0, len(list(filter(lambda x: len(x) == 7, result)))) - self.assertEqual(0, len(list(filter(lambda x: len(x) == 6, result)))) - self.assertEqual(0, len(list(filter(lambda x: len(x) == 5, result)))) - self.assertEqual(0, len(list(filter(lambda x: len(x) == 4, result)))) - # ['DDDDDVDD', 'DDDDVDDD', 'DDDVDDD', 'DDVDDD', 'DVDDD', 'VDDD', 'DDDDDVDDD', 'DDDDVDDD', 'DDDVDDD', 'DDVDDD', - # 'DVDDD', 'VDDD'] - logger.debug(result) +from unittest import TestCase +from logzero import logger + +import input.tests.integration_tests.integration_test_tools as integration_test_tools +from input.MixMHCpred.abstract_mixmhcpred import AbstractMixMHCpred +from input.MixMHCpred.mixmhc2pred import MixMhc2Pred +from input.MixMHCpred.mixmhcpred import MixMHCpred +from input.helpers.runner import Runner +from input.tests import TEST_HLAI_ALLELES, TEST_HLAII_ALLELES + + +class TestMixMHCPred(TestCase): + + def setUp(self): + self.references, self.configuration = integration_test_tools.load_references() + self.runner = Runner() + + def test_mixmhcpred_epitope_iedb(self): + mixmhcpred = MixMHCpred(runner=self.runner, configuration=self.configuration) + # this is an epitope from IEDB of length 9 + mutated = 'NLVPMVATV' + wild_type = 'NLVPMVATV' + mixmhcpred.main(xmer_wt=wild_type, xmer_mut=mutated, alleles=TEST_HLAI_ALLELES[0:5]) + self.assertIsNotNone(mixmhcpred.all_peptides) + self.assertEqual("NLVPMVAT", mixmhcpred.all_peptides) + logger.debug(mixmhcpred.all_peptides) + self.assertEqual(len(mixmhcpred.all_peptides.split('|')), 1) + self.assertIsNotNone(mixmhcpred.all_scores) + logger.debug(mixmhcpred.all_scores) + self.assertEqual(len(mixmhcpred.all_scores.split('|')), 1) + self.assertEqual("-0.522931", mixmhcpred.all_scores) + self.assertIsNotNone(mixmhcpred.all_ranks) + logger.debug(mixmhcpred.all_ranks) + self.assertEqual(len(mixmhcpred.all_ranks.split('|')), 1) + self.assertEqual("77", mixmhcpred.all_ranks) + self.assertIsNotNone(mixmhcpred.all_alleles) + self.assertIsNotNone(mixmhcpred.best_peptide) + self.assertIsNotNone(mixmhcpred.best_score) + self.assertIsNotNone(mixmhcpred.best_rank) + self.assertIsNotNone(mixmhcpred.best_allele) + self.assertIsNotNone(mixmhcpred.best_peptide_wt) + self.assertIsNotNone(mixmhcpred.best_score_wt) + self.assertIsNotNone(mixmhcpred.best_rank_wt) + self.assertIsNotNone(mixmhcpred.difference_score_mut_wt) + + def test_mixmhcpred_too_small_epitope(self): + mixmhcpred = MixMHCpred(runner=self.runner, configuration=self.configuration) + mutated = 'NLVP' + wild_type = 'NLVP' + mixmhcpred.main(xmer_wt=wild_type, xmer_mut=mutated, alleles=TEST_HLAI_ALLELES) + self.assertEqual("NA", mixmhcpred.all_peptides) + + def test_mixmhcpred2_epitope_iedb(self): + mixmhcpred = MixMhc2Pred(runner=self.runner, configuration=self.configuration) + # this is an epitope from IEDB of length 15 + mutated = 'ENPVVHFFKNIVTPR' + wild_type = 'ENPVVHFFKNIVTPR' + mixmhcpred.main(xmer_wt=wild_type, xmer_mut=mutated, alleles=TEST_HLAII_ALLELES) + self.assertIsNotNone(mixmhcpred.all_peptides) + self.assertEqual(len(mixmhcpred.all_peptides.split('|')), 2) + self.assertTrue("ENPVVHFFKNIVTP" in mixmhcpred.all_peptides.split('|')) + self.assertTrue("NPVVHFFKNIVTP" in mixmhcpred.all_peptides.split('|')) + logger.debug(mixmhcpred.all_peptides) + self.assertIsNotNone(mixmhcpred.all_ranks) + self.assertEqual(len(mixmhcpred.all_ranks.split('|')), 2) + self.assertTrue("0.116547" in mixmhcpred.all_ranks.split('|')) + self.assertTrue("0.276218", mixmhcpred.all_ranks.split('|')) + logger.debug(mixmhcpred.all_ranks) + self.assertIsNotNone(mixmhcpred.all_alleles) + self.assertIsNotNone(mixmhcpred.best_peptide) + self.assertIsNotNone(mixmhcpred.best_rank) + self.assertIsNotNone(mixmhcpred.best_allele) + self.assertIsNotNone(mixmhcpred.best_peptide_wt) + self.assertIsNotNone(mixmhcpred.best_score_wt) + self.assertIsNotNone(mixmhcpred.best_rank_wt) + self.assertIsNotNone(mixmhcpred.difference_score_mut_wt) + + def test_mixmhcpred2_too_small_epitope(self): + mixmhcpred = MixMhc2Pred(runner=self.runner, configuration=self.configuration) + # this is an epitope from IEDB of length 15 + mutated = 'ENPVVHFF' + wild_type = 'ENPVVHFF' + mixmhcpred.main(xmer_wt=wild_type, xmer_mut=mutated, alleles=TEST_HLAII_ALLELES) + self.assertEqual("NA", mixmhcpred.all_peptides) + + def test_generate_nmers(self): + result = AbstractMixMHCpred.generate_nmers( + xmer_wt="DDDDDDDDD", xmer_mut="DDDDDVDDD", lengths=[8, 9, 10, 11]) + self.assertIsNotNone(result) + self.assertEqual(3, len(result)) + self.assertEqual(1, len(list(filter(lambda x: len(x) == 9, result)))) + self.assertEqual(2, len(list(filter(lambda x: len(x) == 8, result)))) + self.assertEqual(0, len(list(filter(lambda x: len(x) == 7, result)))) + self.assertEqual(0, len(list(filter(lambda x: len(x) == 6, result)))) + self.assertEqual(0, len(list(filter(lambda x: len(x) == 5, result)))) + self.assertEqual(0, len(list(filter(lambda x: len(x) == 4, result)))) + # ['DDDDDVDD', 'DDDDVDDD', 'DDDVDDD', 'DDVDDD', 'DVDDD', 'VDDD', 'DDDDDVDDD', 'DDDDVDDD', 'DDDVDDD', 'DDVDDD', + # 'DVDDD', 'VDDD'] + logger.debug(result) diff --git a/input/tests/integration_tests/test_neoag.py b/input/tests/integration_tests/test_neoag.py index 614d078f..4040d2d7 100755 --- a/input/tests/integration_tests/test_neoag.py +++ b/input/tests/integration_tests/test_neoag.py @@ -1,97 +1,97 @@ -from unittest import TestCase, SkipTest - -from input.neoag.neoag_gbm_model import NeoagCalculator -from input.helpers.runner import Runner -import input.tests.integration_tests.integration_test_tools as integration_test_tools - - -class TestNeoantigenFitness(TestCase): - - def setUp(self): - self.references, self.configuration = integration_test_tools.load_references() - self.fastafile = integration_test_tools.create_temp_aminoacid_fasta_file() - self.runner = Runner() - - def test_neoag(self): - result = NeoagCalculator(runner=self.runner, configuration=self.configuration).wrapper_neoag( - sample_id="12345", - mut_peptide="DDDDDV", - score_mut="0", - ref_peptide="DDDDDD", - peptide_variant_position="123") - self.assertTrue(isinstance(result, str)) - self.assertTrue(float(result) > 0) - - @SkipTest - def test_legacy(self): - # test with ott data set - # file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/MHC_prediction_netmhcpan4/testdat_ott.txt" - # hla_file ="/projects/SUMMIT/WP1.2/Literature_Cohorts/data_analysis/cohorts/ott/icam_ott/alleles.csv" - file = "/projects/SUMMIT/WP1.2/immunogenicity_data/ivac/input_annotation/20190328_IS_IM_withoutfeatures.txt" - hla_file = "/projects/SUMMIT/WP1.2/immunogenicity_data/ivac/hlahd/20190916_alleles_extended.csv" - # test inest data set - # file = "/flash/projects/WP3/AnFranziska/AnFranziska/head_seqs.txt" - # hla_file = "/flash/projects/WP3/AnFranziska/AnFranziska/alleles.csv" - dat = data_import.import_dat_icam(file, False) - if "+-13_AA_(SNV)_/_-15_AA_to_STOP_(INDEL)" in dat[0]: - dat = data_import.change_col_names(dat) - # available MHC alleles - set_available_mhc = predict_all_epitopes.Bunchepitopes().load_available_hla_alleles() - # hla allele of patients - patient_hlaI = predict_all_epitopes.Bunchepitopes().load_patient_hla_I_allels(hla_file) - patient_hlaII = predict_all_epitopes.Bunchepitopes().load_patient_hla_II_allels(hla_file) - - print(patient_hlaI) - print(patient_hlaII) - - for ii, i in enumerate(dat[1]): - if ii < 2: - print(ii) - dict_epi = epitope.Epitope() - dict_epi.init_properties(dat[0], dat[1][ii]) - dict_epi.add_features(self_similarity.position_of_mutation_epitope(dict_epi.properties, MHC_I), - "pos_MUT_MHCI") - np = netmhcpan_prediction.NetmhcpanBestPrediction() - xmer_mut = dict_epi.properties["X..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."] - tmp_fasta_file = tempfile.NamedTemporaryFile(prefix="tmp_singleseq_", suffix=".fasta", delete=False) - tmp_fasta = tmp_fasta_file.name - print(tmp_fasta, file=sys.stderr) - tmp_prediction_file = tempfile.NamedTemporaryFile(prefix="netmhcpanpred_", suffix=".csv", delete=False) - tmp_prediction = tmp_prediction_file.name - print(tmp_prediction, file=sys.stderr) - np.generate_fasta(dict_epi.properties, tmp_fasta, mut=True) - alleles = np.get_hla_allels(dict_epi.properties, patient_hlaI) - # print alleles - np.mhc_prediction(alleles, set_available_mhc, tmp_fasta, tmp_prediction) - dict_epi.properties["Position_Xmer_Seq"] = np.mut_position_xmer_seq(dict_epi.properties) - preds = np.filter_binding_predictions(dict_epi.properties, tmp_prediction) - best_epi_affinity = np.minimal_binding_score(preds, rank=False) - dict_epi.add_features(np.add_best_epitope_info(best_epi_affinity, "Aff(nM)"), - "best_affinity_netmhcpan4") - dict_epi.add_features(np.add_best_epitope_info(best_epi_affinity, "Icore"), - "best_affinity_epitope_netmhcpan4 ") - dict_epi.add_features(np.add_best_epitope_info(best_epi_affinity, "HLA"), "best4_affinity_allele") - xmer_wt = dict_epi.properties["X.WT._..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."] - # print >> sys.stderr, "WT seq: " + xmer_wt - tmp_fasta_file = tempfile.NamedTemporaryFile(prefix="tmp_singleseq_", suffix=".fasta", delete=False) - tmp_fasta = tmp_fasta_file.name - tmp_prediction_file = tempfile.NamedTemporaryFile(prefix="netmhcpanpred_", suffix=".csv", delete=False) - tmp_prediction = tmp_prediction_file.name - print(tmp_prediction, file=sys.stderr) - np = netmhcpan_prediction.NetmhcpanBestPrediction() - np.generate_fasta(dict_epi.properties, tmp_fasta, mut=False) - np.mhc_prediction(alleles, set_available_mhc, tmp_fasta, tmp_prediction) - preds = np.filter_binding_predictions(dict_epi.properties, tmp_prediction) - best_epi_affinity = np.filter_for_WT_epitope(preds, - dict_epi.properties["best_affinity_epitope_netmhcpan4"], - dict_epi.properties["best4_affinity_allele"]) - dict_epi.add_features(np.add_best_epitope_info(best_epi_affinity, "Aff(nM)"), - "best_affinity_netmhcpan4_WT") - dict_epi.add_features(np.add_best_epitope_info(best_epi_affinity, "Icore"), - "best_affinity_epitope_netmhcpan4_WT") - dict_epi.add_features(self_similarity.position_of_mutation_epitope_affinity(dict_epi.properties), - "pos_MUT_MHCI_affinity_epi") - - sc = wrapper_neoag(dict_epi.properties) - print(sc, file=sys.stderr) - print(type(sc), file=sys.stderr) +from unittest import TestCase, SkipTest + +from input.neoag.neoag_gbm_model import NeoagCalculator +from input.helpers.runner import Runner +import input.tests.integration_tests.integration_test_tools as integration_test_tools + + +class TestNeoantigenFitness(TestCase): + + def setUp(self): + self.references, self.configuration = integration_test_tools.load_references() + self.fastafile = integration_test_tools.create_temp_aminoacid_fasta_file() + self.runner = Runner() + + def test_neoag(self): + result = NeoagCalculator(runner=self.runner, configuration=self.configuration).wrapper_neoag( + sample_id="12345", + mut_peptide="DDDDDV", + score_mut="0", + ref_peptide="DDDDDD", + peptide_variant_position="123") + self.assertTrue(isinstance(result, str)) + self.assertTrue(float(result) > 0) + + @SkipTest + def test_legacy(self): + # test with ott data set + # file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/MHC_prediction_netmhcpan4/testdat_ott.txt" + # hla_file ="/projects/SUMMIT/WP1.2/Literature_Cohorts/data_analysis/cohorts/ott/icam_ott/alleles.csv" + file = "/projects/SUMMIT/WP1.2/immunogenicity_data/ivac/input_annotation/20190328_IS_IM_withoutfeatures.txt" + hla_file = "/projects/SUMMIT/WP1.2/immunogenicity_data/ivac/hlahd/20190916_alleles_extended.csv" + # test inest data set + # file = "/flash/projects/WP3/AnFranziska/AnFranziska/head_seqs.txt" + # hla_file = "/flash/projects/WP3/AnFranziska/AnFranziska/alleles.csv" + dat = data_import.import_dat_icam(file, False) + if "+-13_AA_(SNV)_/_-15_AA_to_STOP_(INDEL)" in dat[0]: + dat = data_import.change_col_names(dat) + # available MHC alleles + set_available_mhc = predict_all_epitopes.Bunchepitopes().load_available_hla_alleles() + # hla allele of patients + patient_hlaI = predict_all_epitopes.Bunchepitopes().load_patient_hla_I_allels(hla_file) + patient_hlaII = predict_all_epitopes.Bunchepitopes().load_patient_hla_II_allels(hla_file) + + print(patient_hlaI) + print(patient_hlaII) + + for ii, i in enumerate(dat[1]): + if ii < 2: + print(ii) + dict_epi = epitope.Epitope() + dict_epi.init_properties(dat[0], dat[1][ii]) + dict_epi.add_features(self_similarity.position_of_mutation_epitope(dict_epi.properties, MHC_I), + "pos_MUT_MHCI") + np = netmhcpan_prediction.NetmhcpanBestPrediction() + xmer_mut = dict_epi.properties["X..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."] + tmp_fasta_file = tempfile.NamedTemporaryFile(prefix="tmp_singleseq_", suffix=".fasta", delete=False) + tmp_fasta = tmp_fasta_file.name + print(tmp_fasta, file=sys.stderr) + tmp_prediction_file = tempfile.NamedTemporaryFile(prefix="netmhcpanpred_", suffix=".csv", delete=False) + tmp_prediction = tmp_prediction_file.name + print(tmp_prediction, file=sys.stderr) + np.generate_fasta(dict_epi.properties, tmp_fasta, mut=True) + alleles = np.get_hla_allels(dict_epi.properties, patient_hlaI) + # print alleles + np.mhc_prediction(alleles, set_available_mhc, tmp_fasta, tmp_prediction) + dict_epi.properties["Position_Xmer_Seq"] = np.mut_position_xmer_seq(dict_epi.properties) + preds = np.filter_binding_predictions(dict_epi.properties, tmp_prediction) + best_epi_affinity = np.minimal_binding_score(preds, rank=False) + dict_epi.add_features(np.add_best_epitope_info(best_epi_affinity, "Aff(nM)"), + "best_affinity_netmhcpan4") + dict_epi.add_features(np.add_best_epitope_info(best_epi_affinity, "Icore"), + "best_affinity_epitope_netmhcpan4 ") + dict_epi.add_features(np.add_best_epitope_info(best_epi_affinity, "HLA"), "best4_affinity_allele") + xmer_wt = dict_epi.properties["X.WT._..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."] + # print >> sys.stderr, "WT seq: " + xmer_wt + tmp_fasta_file = tempfile.NamedTemporaryFile(prefix="tmp_singleseq_", suffix=".fasta", delete=False) + tmp_fasta = tmp_fasta_file.name + tmp_prediction_file = tempfile.NamedTemporaryFile(prefix="netmhcpanpred_", suffix=".csv", delete=False) + tmp_prediction = tmp_prediction_file.name + print(tmp_prediction, file=sys.stderr) + np = netmhcpan_prediction.NetmhcpanBestPrediction() + np.generate_fasta(dict_epi.properties, tmp_fasta, mut=False) + np.mhc_prediction(alleles, set_available_mhc, tmp_fasta, tmp_prediction) + preds = np.filter_binding_predictions(dict_epi.properties, tmp_prediction) + best_epi_affinity = np.filter_for_WT_epitope(preds, + dict_epi.properties["best_affinity_epitope_netmhcpan4"], + dict_epi.properties["best4_affinity_allele"]) + dict_epi.add_features(np.add_best_epitope_info(best_epi_affinity, "Aff(nM)"), + "best_affinity_netmhcpan4_WT") + dict_epi.add_features(np.add_best_epitope_info(best_epi_affinity, "Icore"), + "best_affinity_epitope_netmhcpan4_WT") + dict_epi.add_features(self_similarity.position_of_mutation_epitope_affinity(dict_epi.properties), + "pos_MUT_MHCI_affinity_epi") + + sc = wrapper_neoag(dict_epi.properties) + print(sc, file=sys.stderr) + print(type(sc), file=sys.stderr) diff --git a/input/tests/integration_tests/test_neoantigen_fitness.py b/input/tests/integration_tests/test_neoantigen_fitness.py index 7ae0cc15..d47d00c4 100755 --- a/input/tests/integration_tests/test_neoantigen_fitness.py +++ b/input/tests/integration_tests/test_neoantigen_fitness.py @@ -1,50 +1,50 @@ -from collections import defaultdict -from unittest import TestCase - -from input.neoantigen_fitness.neoantigen_fitness import NeoantigenFitnessCalculator -from input.helpers.runner import Runner -import input.tests.integration_tests.integration_test_tools as integration_test_tools - - -class TestNeoantigenFitness(TestCase): - - def setUp(self): - self.references, self.configuration, self.fastafile = self._load_references() - self.neoantigen_fitness_calculator = NeoantigenFitnessCalculator( - runner=Runner(), configuration=self.configuration) - - def _load_references(self): - references, configuration = integration_test_tools.load_references() - fastafile = integration_test_tools.create_temp_aminoacid_fasta_file() - return references, configuration, fastafile - - def test_pathogen_similarity(self): - # tests a pathogen sequence and expects 1.0 similarity - result = self.neoantigen_fitness_calculator.wrap_pathogen_similarity( - mutation='FIAGLIAIV', - iedb=self.references.iedb) - self.assertEqual('1.0', result) - # tests a modified pathogen sequence and expects something between 0 and 1 - result = self.neoantigen_fitness_calculator.wrap_pathogen_similarity( - mutation='FIAGDAAIV', - iedb=self.references.iedb) - self.assertLess(float(result), 1.0) - self.assertGreater(float(result), 0.0) - # tests a non pathogen sequence and expects 0 similarity - result = self.neoantigen_fitness_calculator.wrap_pathogen_similarity( - mutation='DDDDDMMDD', - iedb=self.references.iedb) - self.assertEqual('0', result) - - def test_amplitude_mhc(self): - self.assertEqual('1.0', self.neoantigen_fitness_calculator.calculate_amplitude_mhc( - score_mutation="1.0", score_wild_type="1.0")) - self.assertEqual('0.9997000899730081', self.neoantigen_fitness_calculator.calculate_amplitude_mhc( - score_mutation="1.0", score_wild_type="1.0", apply_correction=True)) - - def test_recognition_potential(self): - props = defaultdict(lambda: "1.0") - props['Mutation_in_anchor_netmhcpan'] = '0' - props['Mutation_in_anchor_netmhcpan_9mer'] = '0' - self.assertEqual('1.0', self.neoantigen_fitness_calculator.calculate_recognition_potential( - amplitude="1.0", pathogen_similarity="1.0", mutation_in_anchor="0")) +from collections import defaultdict +from unittest import TestCase + +from input.neoantigen_fitness.neoantigen_fitness import NeoantigenFitnessCalculator +from input.helpers.runner import Runner +import input.tests.integration_tests.integration_test_tools as integration_test_tools + + +class TestNeoantigenFitness(TestCase): + + def setUp(self): + self.references, self.configuration, self.fastafile = self._load_references() + self.neoantigen_fitness_calculator = NeoantigenFitnessCalculator( + runner=Runner(), configuration=self.configuration) + + def _load_references(self): + references, configuration = integration_test_tools.load_references() + fastafile = integration_test_tools.create_temp_aminoacid_fasta_file() + return references, configuration, fastafile + + def test_pathogen_similarity(self): + # tests a pathogen sequence and expects 1.0 similarity + result = self.neoantigen_fitness_calculator.wrap_pathogen_similarity( + mutation='FIAGLIAIV', + iedb=self.references.iedb) + self.assertEqual('1.0', result) + # tests a modified pathogen sequence and expects something between 0 and 1 + result = self.neoantigen_fitness_calculator.wrap_pathogen_similarity( + mutation='FIAGDAAIV', + iedb=self.references.iedb) + self.assertLess(float(result), 1.0) + self.assertGreater(float(result), 0.0) + # tests a non pathogen sequence and expects 0 similarity + result = self.neoantigen_fitness_calculator.wrap_pathogen_similarity( + mutation='DDDDDMMDD', + iedb=self.references.iedb) + self.assertEqual('0', result) + + def test_amplitude_mhc(self): + self.assertEqual('1.0', self.neoantigen_fitness_calculator.calculate_amplitude_mhc( + score_mutation="1.0", score_wild_type="1.0")) + self.assertEqual('0.9997000899730081', self.neoantigen_fitness_calculator.calculate_amplitude_mhc( + score_mutation="1.0", score_wild_type="1.0", apply_correction=True)) + + def test_recognition_potential(self): + props = defaultdict(lambda: "1.0") + props['Mutation_in_anchor_netmhcpan'] = '0' + props['Mutation_in_anchor_netmhcpan_9mer'] = '0' + self.assertEqual('1.0', self.neoantigen_fitness_calculator.calculate_recognition_potential( + amplitude="1.0", pathogen_similarity="1.0", mutation_in_anchor="0")) diff --git a/input/tests/integration_tests/test_netmhcpan.py b/input/tests/integration_tests/test_netmhcpan.py index dfbc23be..da4d5c9b 100755 --- a/input/tests/integration_tests/test_netmhcpan.py +++ b/input/tests/integration_tests/test_netmhcpan.py @@ -1,96 +1,96 @@ -import os -from unittest import TestCase - -import input.tests.integration_tests.integration_test_tools as integration_test_tools -from input import MHC_I, MHC_II -from input.helpers import intermediate_files -from input.helpers.runner import Runner -from input.netmhcpan4.netmhcIIpan_prediction import NetMhcIIPanPredictor -from input.netmhcpan4.netmhcpan_prediction import NetMhcPanPredictor -from input.tests import TEST_HLAI_ALLELES, TEST_HLAII_ALLELES - - -class TestNetMhcPanPredictor(TestCase): - - def setUp(self): - self.references, self.configuration = integration_test_tools.load_references() - self.runner = Runner() - - def test_netmhcpan_epitope_iedb(self): - netmhcpan_predictor = NetMhcPanPredictor(runner=self.runner, configuration=self.configuration) - # this is an epitope from IEDB of length 9 - mutated = 'NLVPMVATV' - tmp_prediction = intermediate_files.create_temp_file(prefix="netmhcpanpred_", suffix=".csv") - tmp_fasta = intermediate_files.create_temp_fasta(sequences=[mutated], prefix="tmp_") - netmhcpan_predictor.mhc_prediction( - tmpfasta=tmp_fasta, tmppred=tmp_prediction, hla_alleles=TEST_HLAI_ALLELES, - set_available_mhc=self.references.load_available_hla_alleles(mhc=MHC_I)) - self.assertTrue(os.path.exists(tmp_prediction)) - self.assertEqual(166, len(open(tmp_prediction).readlines())) - header, rows = netmhcpan_predictor.filter_binding_predictions(4, tmp_prediction) - self.assertEqual(14, len(header)) # output has 14 columns - for r in rows: - self.assertEqual(14, len(r)) # each row has 14 columns - self.assertEqual(165, len(rows)) - - def test_netmhcpan_too_small_epitope(self): - netmhcpan_predictor = NetMhcPanPredictor(runner=self.runner, configuration=self.configuration) - mutated = 'NLVP' - tmp_prediction = intermediate_files.create_temp_file(prefix="netmhcpanpred_", suffix=".csv") - tmp_fasta = intermediate_files.create_temp_fasta(sequences=[mutated], prefix="tmp_") - netmhcpan_predictor.mhc_prediction( - tmpfasta=tmp_fasta, tmppred=tmp_prediction, hla_alleles=TEST_HLAI_ALLELES, - set_available_mhc=self.references.load_available_hla_alleles(mhc=MHC_I)) - self.assertTrue(os.path.exists(tmp_prediction)) - # TODO: this is writing ot the output file "No;peptides;derived;from;protein;ID;seq1;len;4.;Skipped" - self.assertEqual(55, len(open(tmp_prediction).readlines())) - - # TODO: it crashes here as it fails to parse the header. Fix and remove the try-except - try: - header, rows = netmhcpan_predictor.filter_binding_predictions(2, tmp_prediction) - self.assertEqual(14, len(header)) # output has 14 columns - for r in rows: - self.assertEqual(14, len(r)) # each row has 14 columns - self.assertEqual(0, len(rows)) - except: - pass - - def test_netmhc2pan_epitope_iedb(self): - netmhc2pan_predictor = NetMhcIIPanPredictor(runner=self.runner, configuration=self.configuration) - # this is an epitope from IEDB of length 15 - mutated = 'ENPVVHFFKNIVTPR' - tmp_prediction = intermediate_files.create_temp_file(prefix="netmhcpanpred_", suffix=".csv") - tmp_fasta = intermediate_files.create_temp_fasta(sequences=[mutated], prefix="tmp_") - netmhc2pan_predictor.mhcII_prediction( - tmpfasta=tmp_fasta, tmppred=tmp_prediction, hla_alleles=TEST_HLAII_ALLELES, - set_available_mhc=self.references.load_available_hla_alleles(mhc=MHC_II)) - self.assertTrue(os.path.exists(tmp_prediction)) - self.assertEqual(20, len(open(tmp_prediction).readlines())) - - header, rows = netmhc2pan_predictor.filter_binding_predictions(4, tmp_prediction) - self.assertEqual(12, len(header)) # output has 14 columns - for r in rows: - self.assertTrue(len(r) <= 12 or len(r) >= 10) # each row has 10 or 12 columns - self.assertEqual(19, len(rows)) - - def test_netmhc2pan_too_small_epitope(self): - netmhc2pan_predictor = NetMhcIIPanPredictor(runner=self.runner, configuration=self.configuration) - # this is an epitope from IEDB of length 15 - mutated = 'ENPVVH' - tmp_prediction = intermediate_files.create_temp_file(prefix="netmhcpanpred_", suffix=".csv") - tmp_fasta = intermediate_files.create_temp_fasta(sequences=[mutated], prefix="tmp_") - netmhc2pan_predictor.mhcII_prediction( - tmpfasta=tmp_fasta, tmppred=tmp_prediction, hla_alleles=TEST_HLAII_ALLELES, - set_available_mhc=self.references.load_available_hla_alleles(mhc=MHC_II)) - self.assertTrue(os.path.exists(tmp_prediction)) - self.assertEqual(1, len(open(tmp_prediction).readlines())) - - # TODO: it crashes here as it fails to parse the header. Fix and remove the try-except - try: - header, rows = netmhc2pan_predictor.filter_binding_predictions(4, tmp_prediction) - self.assertEqual(12, len(header)) # output has 14 columns - for r in rows: - self.assertTrue(len(r) <= 12 or len(r) >= 10) # each row has 10 or 12 columns - self.assertEqual(0, len(rows)) - except: +import os +from unittest import TestCase + +import input.tests.integration_tests.integration_test_tools as integration_test_tools +from input import MHC_I, MHC_II +from input.helpers import intermediate_files +from input.helpers.runner import Runner +from input.netmhcpan4.netmhcIIpan_prediction import NetMhcIIPanPredictor +from input.netmhcpan4.netmhcpan_prediction import NetMhcPanPredictor +from input.tests import TEST_HLAI_ALLELES, TEST_HLAII_ALLELES + + +class TestNetMhcPanPredictor(TestCase): + + def setUp(self): + self.references, self.configuration = integration_test_tools.load_references() + self.runner = Runner() + + def test_netmhcpan_epitope_iedb(self): + netmhcpan_predictor = NetMhcPanPredictor(runner=self.runner, configuration=self.configuration) + # this is an epitope from IEDB of length 9 + mutated = 'NLVPMVATV' + tmp_prediction = intermediate_files.create_temp_file(prefix="netmhcpanpred_", suffix=".csv") + tmp_fasta = intermediate_files.create_temp_fasta(sequences=[mutated], prefix="tmp_") + netmhcpan_predictor.mhc_prediction( + tmpfasta=tmp_fasta, tmppred=tmp_prediction, hla_alleles=TEST_HLAI_ALLELES, + set_available_mhc=self.references.load_available_hla_alleles(mhc=MHC_I)) + self.assertTrue(os.path.exists(tmp_prediction)) + self.assertEqual(166, len(open(tmp_prediction).readlines())) + header, rows = netmhcpan_predictor.filter_binding_predictions(4, tmp_prediction) + self.assertEqual(14, len(header)) # output has 14 columns + for r in rows: + self.assertEqual(14, len(r)) # each row has 14 columns + self.assertEqual(165, len(rows)) + + def test_netmhcpan_too_small_epitope(self): + netmhcpan_predictor = NetMhcPanPredictor(runner=self.runner, configuration=self.configuration) + mutated = 'NLVP' + tmp_prediction = intermediate_files.create_temp_file(prefix="netmhcpanpred_", suffix=".csv") + tmp_fasta = intermediate_files.create_temp_fasta(sequences=[mutated], prefix="tmp_") + netmhcpan_predictor.mhc_prediction( + tmpfasta=tmp_fasta, tmppred=tmp_prediction, hla_alleles=TEST_HLAI_ALLELES, + set_available_mhc=self.references.load_available_hla_alleles(mhc=MHC_I)) + self.assertTrue(os.path.exists(tmp_prediction)) + # TODO: this is writing ot the output file "No;peptides;derived;from;protein;ID;seq1;len;4.;Skipped" + self.assertEqual(55, len(open(tmp_prediction).readlines())) + + # TODO: it crashes here as it fails to parse the header. Fix and remove the try-except + try: + header, rows = netmhcpan_predictor.filter_binding_predictions(2, tmp_prediction) + self.assertEqual(14, len(header)) # output has 14 columns + for r in rows: + self.assertEqual(14, len(r)) # each row has 14 columns + self.assertEqual(0, len(rows)) + except: + pass + + def test_netmhc2pan_epitope_iedb(self): + netmhc2pan_predictor = NetMhcIIPanPredictor(runner=self.runner, configuration=self.configuration) + # this is an epitope from IEDB of length 15 + mutated = 'ENPVVHFFKNIVTPR' + tmp_prediction = intermediate_files.create_temp_file(prefix="netmhcpanpred_", suffix=".csv") + tmp_fasta = intermediate_files.create_temp_fasta(sequences=[mutated], prefix="tmp_") + netmhc2pan_predictor.mhcII_prediction( + tmpfasta=tmp_fasta, tmppred=tmp_prediction, hla_alleles=TEST_HLAII_ALLELES, + set_available_mhc=self.references.load_available_hla_alleles(mhc=MHC_II)) + self.assertTrue(os.path.exists(tmp_prediction)) + self.assertEqual(20, len(open(tmp_prediction).readlines())) + + header, rows = netmhc2pan_predictor.filter_binding_predictions(4, tmp_prediction) + self.assertEqual(12, len(header)) # output has 14 columns + for r in rows: + self.assertTrue(len(r) <= 12 or len(r) >= 10) # each row has 10 or 12 columns + self.assertEqual(19, len(rows)) + + def test_netmhc2pan_too_small_epitope(self): + netmhc2pan_predictor = NetMhcIIPanPredictor(runner=self.runner, configuration=self.configuration) + # this is an epitope from IEDB of length 15 + mutated = 'ENPVVH' + tmp_prediction = intermediate_files.create_temp_file(prefix="netmhcpanpred_", suffix=".csv") + tmp_fasta = intermediate_files.create_temp_fasta(sequences=[mutated], prefix="tmp_") + netmhc2pan_predictor.mhcII_prediction( + tmpfasta=tmp_fasta, tmppred=tmp_prediction, hla_alleles=TEST_HLAII_ALLELES, + set_available_mhc=self.references.load_available_hla_alleles(mhc=MHC_II)) + self.assertTrue(os.path.exists(tmp_prediction)) + self.assertEqual(1, len(open(tmp_prediction).readlines())) + + # TODO: it crashes here as it fails to parse the header. Fix and remove the try-except + try: + header, rows = netmhc2pan_predictor.filter_binding_predictions(4, tmp_prediction) + self.assertEqual(12, len(header)) # output has 14 columns + for r in rows: + self.assertTrue(len(r) <= 12 or len(r) >= 10) # each row has 10 or 12 columns + self.assertEqual(0, len(rows)) + except: pass \ No newline at end of file diff --git a/input/tests/integration_tests/test_tcell_predictor.py b/input/tests/integration_tests/test_tcell_predictor.py index 065cd18b..51c11096 100755 --- a/input/tests/integration_tests/test_tcell_predictor.py +++ b/input/tests/integration_tests/test_tcell_predictor.py @@ -1,52 +1,52 @@ -from collections import defaultdict -from unittest import TestCase - -import input.tests.integration_tests.integration_test_tools as integration_test_tools -from input.Tcell_predictor.tcellpredictor_wrapper import TcellPrediction - - -class TestTCellPredictor(TestCase): - - def setUp(self): - self.references, self.configuration = integration_test_tools.load_references() - self.fastafile = integration_test_tools.create_temp_aminoacid_fasta_file() - - def test_tcell_predictor(self): - tcell_predictor = TcellPrediction(references=self.references) - result = tcell_predictor.calculate_tcell_predictor_score(gene="BLAH", substitution='blaaaah', epitope="BLAHBLAH", score=5, threshold=10) - self.assertEqual("NA", result) - - -""" -# if full icam output table is passed to script - ''' - f = sys.argv[1] - dat = data_import.import_dat_icam(f, indel = False) - #print dat - #print full_dataset(dat) - l = full_dataset(dat, all = True) - write_ouptut_to_file(l) - ''' - - # test for input implementation - from input import epitope - - file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/MHC_prediction_netmhcpan4/testdat_ott.txt" - dat = data_import.import_dat_icam(file, False) - if "+-13_AA_(SNV)_/_-15_AA_to_STOP_(INDEL)" in dat[0]: - dat = data_import.change_col_names(dat) - - path_to_Tcell_predictor = my_path - - for ii,i in enumerate(dat[1]): - if ii < 10: - print ii - dict_epi = epitope.Epitope() - dict_epi.init_properties(dat[0], dat[1][ii]) - #print dict_epi.properties - tcellpred = Tcellprediction() - - tcellpred.main(dict_epi.properties) - print tcellpred.TcellPrdictionScore - print tcellpred.TcellPrdictionScore_9merPred -""" +from collections import defaultdict +from unittest import TestCase + +import input.tests.integration_tests.integration_test_tools as integration_test_tools +from input.Tcell_predictor.tcellpredictor_wrapper import TcellPrediction + + +class TestTCellPredictor(TestCase): + + def setUp(self): + self.references, self.configuration = integration_test_tools.load_references() + self.fastafile = integration_test_tools.create_temp_aminoacid_fasta_file() + + def test_tcell_predictor(self): + tcell_predictor = TcellPrediction(references=self.references) + result = tcell_predictor.calculate_tcell_predictor_score(gene="BLAH", substitution='blaaaah', epitope="BLAHBLAH", score=5, threshold=10) + self.assertEqual("NA", result) + + +""" +# if full icam output table is passed to script + ''' + f = sys.argv[1] + dat = data_import.import_dat_icam(f, indel = False) + #print dat + #print full_dataset(dat) + l = full_dataset(dat, all = True) + write_ouptut_to_file(l) + ''' + + # test for input implementation + from input import epitope + + file = "/projects/CM01_iVAC/immunogenicity_prediction/3rd_party_solutions/MHC_prediction_netmhcpan4/testdat_ott.txt" + dat = data_import.import_dat_icam(file, False) + if "+-13_AA_(SNV)_/_-15_AA_to_STOP_(INDEL)" in dat[0]: + dat = data_import.change_col_names(dat) + + path_to_Tcell_predictor = my_path + + for ii,i in enumerate(dat[1]): + if ii < 10: + print ii + dict_epi = epitope.Epitope() + dict_epi.init_properties(dat[0], dat[1][ii]) + #print dict_epi.properties + tcellpred = Tcellprediction() + + tcellpred.main(dict_epi.properties) + print tcellpred.TcellPrdictionScore + print tcellpred.TcellPrdictionScore_9merPred +""" diff --git a/input/tests/unit_tests/fake_classes.py b/input/tests/unit_tests/fake_classes.py index 039d8065..6d2532fd 100755 --- a/input/tests/unit_tests/fake_classes.py +++ b/input/tests/unit_tests/fake_classes.py @@ -1,15 +1,15 @@ -import os - -import input -from input.references import ReferenceFolder - - -class FakeReferenceFolder(ReferenceFolder): - - @staticmethod - def _check_reference_genome_folder(): - return os.environ.get(input.REFERENCE_FOLDER_ENV, "") - - @staticmethod - def _check_resources(resources): - pass +import os + +import input +from input.references import ReferenceFolder + + +class FakeReferenceFolder(ReferenceFolder): + + @staticmethod + def _check_reference_genome_folder(): + return os.environ.get(input.REFERENCE_FOLDER_ENV, "") + + @staticmethod + def _check_resources(resources): + pass diff --git a/input/tests/unit_tests/test_dependencies_configuration.py b/input/tests/unit_tests/test_dependencies_configuration.py index b78a7779..5257906a 100755 --- a/input/tests/unit_tests/test_dependencies_configuration.py +++ b/input/tests/unit_tests/test_dependencies_configuration.py @@ -1,65 +1,65 @@ -import os -import unittest -from unittest import TestCase - -import input -import input.tests.unit_tests.tools as test_tools -from input.exceptions import INPuTConfigurationException -from input.references import DependenciesConfiguration - - -class TestDependenciesConfiguration(TestCase): - - def setUp(self): - self.variables = { - input.INPUT_BLASTP_ENV: '/path/to/blastp', - input.INPUT_NETMHC2PAN_ENV: '/path/to/netmhc2pan', - input.INPUT_NETMHCPAN_ENV: '/path/to/netmhcpan', - input.INPUT_RSCRIPT_ENV: '/path/to/rscript', - input.INPUT_MIXMHCPRED_ENV: '/path/to/mixmhcpred', - input.INPUT_MIXMHC2PRED_ENV: '/path/to/mixmhc2pred' - } - self.non_existing = '/path/to/nothing' - test_tools._mock_file_existence( - existing_files=self.variables.values(), - unexisting_files=[self.non_existing] - ) - - def _load_env_variables(self): - for k, v in self.variables.items(): - os.environ[k] = v - - def test_not_provided_variable(self): - self._load_env_variables() - for v in self.variables.keys(): - del os.environ[v] - with self.assertRaises(INPuTConfigurationException): - DependenciesConfiguration() - - def test_empty_string_variable(self): - self._load_env_variables() - for v in self.variables.keys(): - os.environ[v] = "" - with self.assertRaises(INPuTConfigurationException): - DependenciesConfiguration() - - def test_non_existing_variable(self): - self._load_env_variables() - for v in self.variables.keys(): - os.environ[v] = self.non_existing - with self.assertRaises(INPuTConfigurationException): - DependenciesConfiguration() - - def test_all_resources_exist(self): - self._load_env_variables() - config = DependenciesConfiguration() - self.assertTrue(config.blastp == self.variables[input.INPUT_BLASTP_ENV]) - self.assertTrue(config.mix_mhc2_pred == self.variables[input.INPUT_MIXMHC2PRED_ENV]) - self.assertTrue(config.mix_mhc_pred == self.variables[input.INPUT_MIXMHCPRED_ENV]) - self.assertTrue(config.rscript == self.variables[input.INPUT_RSCRIPT_ENV]) - self.assertTrue(config.net_mhc_pan == self.variables[input.INPUT_NETMHCPAN_ENV]) - self.assertTrue(config.net_mhc2_pan == self.variables[input.INPUT_NETMHC2PAN_ENV]) - - -if __name__ == "__main__": - unittest.main() +import os +import unittest +from unittest import TestCase + +import input +import input.tests.unit_tests.tools as test_tools +from input.exceptions import INPuTConfigurationException +from input.references import DependenciesConfiguration + + +class TestDependenciesConfiguration(TestCase): + + def setUp(self): + self.variables = { + input.INPUT_BLASTP_ENV: '/path/to/blastp', + input.INPUT_NETMHC2PAN_ENV: '/path/to/netmhc2pan', + input.INPUT_NETMHCPAN_ENV: '/path/to/netmhcpan', + input.INPUT_RSCRIPT_ENV: '/path/to/rscript', + input.INPUT_MIXMHCPRED_ENV: '/path/to/mixmhcpred', + input.INPUT_MIXMHC2PRED_ENV: '/path/to/mixmhc2pred' + } + self.non_existing = '/path/to/nothing' + test_tools._mock_file_existence( + existing_files=self.variables.values(), + unexisting_files=[self.non_existing] + ) + + def _load_env_variables(self): + for k, v in self.variables.items(): + os.environ[k] = v + + def test_not_provided_variable(self): + self._load_env_variables() + for v in self.variables.keys(): + del os.environ[v] + with self.assertRaises(INPuTConfigurationException): + DependenciesConfiguration() + + def test_empty_string_variable(self): + self._load_env_variables() + for v in self.variables.keys(): + os.environ[v] = "" + with self.assertRaises(INPuTConfigurationException): + DependenciesConfiguration() + + def test_non_existing_variable(self): + self._load_env_variables() + for v in self.variables.keys(): + os.environ[v] = self.non_existing + with self.assertRaises(INPuTConfigurationException): + DependenciesConfiguration() + + def test_all_resources_exist(self): + self._load_env_variables() + config = DependenciesConfiguration() + self.assertTrue(config.blastp == self.variables[input.INPUT_BLASTP_ENV]) + self.assertTrue(config.mix_mhc2_pred == self.variables[input.INPUT_MIXMHC2PRED_ENV]) + self.assertTrue(config.mix_mhc_pred == self.variables[input.INPUT_MIXMHCPRED_ENV]) + self.assertTrue(config.rscript == self.variables[input.INPUT_RSCRIPT_ENV]) + self.assertTrue(config.net_mhc_pan == self.variables[input.INPUT_NETMHCPAN_ENV]) + self.assertTrue(config.net_mhc2_pan == self.variables[input.INPUT_NETMHC2PAN_ENV]) + + +if __name__ == "__main__": + unittest.main() diff --git a/input/tests/unit_tests/test_predict_all_epitopes.py b/input/tests/unit_tests/test_predict_all_epitopes.py index f04ad770..3cdde1f2 100755 --- a/input/tests/unit_tests/test_predict_all_epitopes.py +++ b/input/tests/unit_tests/test_predict_all_epitopes.py @@ -1,24 +1,24 @@ -import os -import unittest -from unittest import TestCase - -import input -from input.exceptions import INPuTConfigurationException -from input.predict_all_epitopes import BunchEpitopes - - -class TestPredictAllEpitopes(TestCase): - - def test_reference_environment_variable_is_required(self): - # del os.environ[input.REFERENCE_FOLDER_ENV] - with self.assertRaises(INPuTConfigurationException): - BunchEpitopes() - - def test_empty_reference_folder_fails(self): - os.environ[input.REFERENCE_FOLDER_ENV] = 'dummy' - with self.assertRaises(INPuTConfigurationException): - BunchEpitopes() - - -if __name__ == "__main__": - unittest.main() +import os +import unittest +from unittest import TestCase + +import input +from input.exceptions import INPuTConfigurationException +from input.predict_all_epitopes import BunchEpitopes + + +class TestPredictAllEpitopes(TestCase): + + def test_reference_environment_variable_is_required(self): + # del os.environ[input.REFERENCE_FOLDER_ENV] + with self.assertRaises(INPuTConfigurationException): + BunchEpitopes() + + def test_empty_reference_folder_fails(self): + os.environ[input.REFERENCE_FOLDER_ENV] = 'dummy' + with self.assertRaises(INPuTConfigurationException): + BunchEpitopes() + + +if __name__ == "__main__": + unittest.main() diff --git a/input/tests/unit_tests/test_reference_folder.py b/input/tests/unit_tests/test_reference_folder.py index c6fd101a..c0c417c9 100755 --- a/input/tests/unit_tests/test_reference_folder.py +++ b/input/tests/unit_tests/test_reference_folder.py @@ -1,47 +1,47 @@ -import os -import unittest -from unittest import TestCase - -import input -import input.tests.unit_tests.tools as test_tools -from input.exceptions import INPuTConfigurationException -from input.references import ReferenceFolder -from input.tests.unit_tests.fake_classes import FakeReferenceFolder - - -class TestReferenceFolder(TestCase): - - def setUp(self): - os.environ[input.REFERENCE_FOLDER_ENV] = "." - self.fake_reference_folder = FakeReferenceFolder() - - def test_not_provided_reference(self): - del os.environ[input.REFERENCE_FOLDER_ENV] - with self.assertRaises(INPuTConfigurationException): - ReferenceFolder() - - def test_empty_string_reference(self): - os.environ[input.REFERENCE_FOLDER_ENV] = "" - with self.assertRaises(INPuTConfigurationException): - ReferenceFolder() - - def test_non_existing_reference(self): - os.environ[input.REFERENCE_FOLDER_ENV] = "/non_existing_folder" - with self.assertRaises(INPuTConfigurationException): - ReferenceFolder() - - def test_all_resources_exist(self): - test_tools._mock_file_existence(existing_files=self.fake_reference_folder.resources) - ReferenceFolder() - - def test_one_resource_do_not_exist(self): - test_tools._mock_file_existence( - existing_files=self.fake_reference_folder.resources[1:len(self.fake_reference_folder.resources)], - unexisting_files=[self.fake_reference_folder.resources[0]] - ) - with self.assertRaises(INPuTConfigurationException): - ReferenceFolder() - - -if __name__ == "__main__": - unittest.main() +import os +import unittest +from unittest import TestCase + +import input +import input.tests.unit_tests.tools as test_tools +from input.exceptions import INPuTConfigurationException +from input.references import ReferenceFolder +from input.tests.unit_tests.fake_classes import FakeReferenceFolder + + +class TestReferenceFolder(TestCase): + + def setUp(self): + os.environ[input.REFERENCE_FOLDER_ENV] = "." + self.fake_reference_folder = FakeReferenceFolder() + + def test_not_provided_reference(self): + del os.environ[input.REFERENCE_FOLDER_ENV] + with self.assertRaises(INPuTConfigurationException): + ReferenceFolder() + + def test_empty_string_reference(self): + os.environ[input.REFERENCE_FOLDER_ENV] = "" + with self.assertRaises(INPuTConfigurationException): + ReferenceFolder() + + def test_non_existing_reference(self): + os.environ[input.REFERENCE_FOLDER_ENV] = "/non_existing_folder" + with self.assertRaises(INPuTConfigurationException): + ReferenceFolder() + + def test_all_resources_exist(self): + test_tools._mock_file_existence(existing_files=self.fake_reference_folder.resources) + ReferenceFolder() + + def test_one_resource_do_not_exist(self): + test_tools._mock_file_existence( + existing_files=self.fake_reference_folder.resources[1:len(self.fake_reference_folder.resources)], + unexisting_files=[self.fake_reference_folder.resources[0]] + ) + with self.assertRaises(INPuTConfigurationException): + ReferenceFolder() + + +if __name__ == "__main__": + unittest.main() diff --git a/input/tests/unit_tests/test_runner.py b/input/tests/unit_tests/test_runner.py index 7d41ccf2..0472b644 100755 --- a/input/tests/unit_tests/test_runner.py +++ b/input/tests/unit_tests/test_runner.py @@ -1,23 +1,23 @@ -import unittest -from unittest import TestCase - -from input.helpers.runner import Runner - - -class TestRunner(TestCase): - - def setUp(self): - self.runner = Runner() - - def test_runner(self): - output, errors = self.runner.run_command(cmd=['python', '-V']) - self.assertTrue('Python 3.7' in output) - self.assertTrue(len(errors) == 0) - - def test_runner_failure(self): - with self.assertRaises(Exception): - self.runner.run_command(cmd=['nocommandwiththisname']) - - -if __name__ == "__main__": - unittest.main() +import unittest +from unittest import TestCase + +from input.helpers.runner import Runner + + +class TestRunner(TestCase): + + def setUp(self): + self.runner = Runner() + + def test_runner(self): + output, errors = self.runner.run_command(cmd=['python', '-V']) + self.assertTrue('Python 3.7' in output) + self.assertTrue(len(errors) == 0) + + def test_runner_failure(self): + with self.assertRaises(Exception): + self.runner.run_command(cmd=['nocommandwiththisname']) + + +if __name__ == "__main__": + unittest.main() diff --git a/input/tests/unit_tests/test_self_similarity.py b/input/tests/unit_tests/test_self_similarity.py index 021829f5..43bff547 100755 --- a/input/tests/unit_tests/test_self_similarity.py +++ b/input/tests/unit_tests/test_self_similarity.py @@ -1,38 +1,38 @@ -from unittest import TestCase - -import input.self_similarity.self_similarity as self_similarity -from input import MHC_I, MHC_II - - -class TestSelfSimilarity(TestCase): - - def test_get_self_similarity(self): - result = self_similarity.get_self_similarity(wild_type="DDD", mutation="DDD") - self.assertEqual('1.0', result) - - def test_is_improved_binder(self): - result = self_similarity.is_improved_binder( - score_mutation='1.0', score_wild_type='1.3') - self.assertEqual('1', result) - - def test_position_mutation(self): - position = self_similarity.position_of_mutation_epitope(wild_type="AAAAAA", mutation="AAANAA") - self.assertEqual(position, "4") - position = self_similarity.position_of_mutation_epitope(wild_type="AAAAAA", mutation="AAAAAA") - self.assertEqual(position, "-1") - position = self_similarity.position_of_mutation_epitope(wild_type="AAAAAA", mutation="AANNNN") - self.assertEqual(position, "6") - - def test_compute_self_similarity_calculator(self): - - s = self_similarity.SelfSimilarityCalculator() - self.assertEqual(s.compute_k_hat_3("AAAAA", "AAAAA"), 1.0) - for i in range(5): - self.assertTrue(s.compute_k_hat_3("AAAAA", "WWWWW" * (i + 1)) < 1.0) - for i in list(s.k1.keys()): - if i == "A": - self.assertTrue(s.compute_k_hat_3("AAAAA", "AA" + i + "AA") == 1.0) - else: - self.assertTrue(s.compute_k_hat_3("AAAAA", "AA" + i + "AA") < 1.0) - - +from unittest import TestCase + +import input.self_similarity.self_similarity as self_similarity +from input import MHC_I, MHC_II + + +class TestSelfSimilarity(TestCase): + + def test_get_self_similarity(self): + result = self_similarity.get_self_similarity(wild_type="DDD", mutation="DDD") + self.assertEqual('1.0', result) + + def test_is_improved_binder(self): + result = self_similarity.is_improved_binder( + score_mutation='1.0', score_wild_type='1.3') + self.assertEqual('1', result) + + def test_position_mutation(self): + position = self_similarity.position_of_mutation_epitope(wild_type="AAAAAA", mutation="AAANAA") + self.assertEqual(position, "4") + position = self_similarity.position_of_mutation_epitope(wild_type="AAAAAA", mutation="AAAAAA") + self.assertEqual(position, "-1") + position = self_similarity.position_of_mutation_epitope(wild_type="AAAAAA", mutation="AANNNN") + self.assertEqual(position, "6") + + def test_compute_self_similarity_calculator(self): + + s = self_similarity.SelfSimilarityCalculator() + self.assertEqual(s.compute_k_hat_3("AAAAA", "AAAAA"), 1.0) + for i in range(5): + self.assertTrue(s.compute_k_hat_3("AAAAA", "WWWWW" * (i + 1)) < 1.0) + for i in list(s.k1.keys()): + if i == "A": + self.assertTrue(s.compute_k_hat_3("AAAAA", "AA" + i + "AA") == 1.0) + else: + self.assertTrue(s.compute_k_hat_3("AAAAA", "AA" + i + "AA") < 1.0) + + diff --git a/model/neoepitope.avdl b/model/neoepitope.avdl index c6e3f784..1efc327f 100755 --- a/model/neoepitope.avdl +++ b/model/neoepitope.avdl @@ -1,83 +1,83 @@ -/** - * An example protocol in Avro IDL for defining neoepitopes - */ -@namespace("tron.neoepitope") -protocol Neoepitope { - - record Gene { - /** - The genome assembly to which the gene definition refers to (e.g.: GRCh37, GRCh38) - */ - string assembly = "GRCh37"; - /** - The gene symbol or gene identifier, optional as the transcript unequivocally identifies a gene - */ - union {string, null} gene; - /** - The transcript identifier to which this neoepitope definition refers (e.g.: Ensembl transcript id) - */ - string transcriptIdentifier; - } - - record Mutation { - /** - The aminoacid position within the protein. 1-based, starting in the N-terminus - */ - int position; - /** - IUPAC code for the wild type aminoacid in this position - */ - string wildTypeAminoacid; - /** - IUPAC code for the mutated aminoacid in this position - */ - string mutatedAminoacid; - - /** - The left flanking region of variable size in IUPAC codes - */ - string leftFlankingRegion; - /** - The size of the left flanking region - */ - union {string, null} sizeLeftFlankingRegion; - /** - The right flanking region of variable size in IUPAC codes - */ - string rightFlankingRegion; - /** - The size of the right flanking region - */ - union {string, null} sizeRightlankingRegion; - } - - /** - A neoepitope minimal definition - */ - record Neoepitope { - - /** - The gene where the neoepitope corresponds - */ - Gene gene; - - /** - The mutation - */ - Mutation mutation; - - // OPTIONAL - /** - Expression value of the transcript (any more definition on type of expression? ie: digital from RNAseq, from microarrays, etc.) - */ - union {float, null} expressionValue; - /** - Clonality estimation (any more definition on the method?) - */ - union {float, null} clonalityEstimation; - /** - Variant allele frequency in the range [0.0, 1.0] - */ - union {float, null} variantAlleleFrequency; - } -} +/** + * An example protocol in Avro IDL for defining neoepitopes + */ +@namespace("tron.neoepitope") +protocol Neoepitope { + + record Gene { + /** + The genome assembly to which the gene definition refers to (e.g.: GRCh37, GRCh38) + */ + string assembly = "GRCh37"; + /** + The gene symbol or gene identifier, optional as the transcript unequivocally identifies a gene + */ + union {string, null} gene; + /** + The transcript identifier to which this neoepitope definition refers (e.g.: Ensembl transcript id) + */ + string transcriptIdentifier; + } + + record Mutation { + /** + The aminoacid position within the protein. 1-based, starting in the N-terminus + */ + int position; + /** + IUPAC code for the wild type aminoacid in this position + */ + string wildTypeAminoacid; + /** + IUPAC code for the mutated aminoacid in this position + */ + string mutatedAminoacid; + + /** + The left flanking region of variable size in IUPAC codes + */ + string leftFlankingRegion; + /** + The size of the left flanking region + */ + union {string, null} sizeLeftFlankingRegion; + /** + The right flanking region of variable size in IUPAC codes + */ + string rightFlankingRegion; + /** + The size of the right flanking region + */ + union {string, null} sizeRightlankingRegion; + } + + /** + A neoepitope minimal definition + */ + record Neoepitope { + + /** + The gene where the neoepitope corresponds + */ + Gene gene; + + /** + The mutation + */ + Mutation mutation; + + // OPTIONAL + /** + Expression value of the transcript (any more definition on type of expression? ie: digital from RNAseq, from microarrays, etc.) + */ + union {float, null} expressionValue; + /** + Clonality estimation (any more definition on the method?) + */ + union {float, null} clonalityEstimation; + /** + Variant allele frequency in the range [0.0, 1.0] + */ + union {float, null} variantAlleleFrequency; + } +} diff --git a/setup.py b/setup.py index 22fe636f..a1c7e975 100755 --- a/setup.py +++ b/setup.py @@ -1,50 +1,50 @@ -from setuptools import find_packages, setup, Command -import distutils.command.build -from distutils.dist import Distribution -# from wheel.bdist_wheel import bdist_wheel as _bdist_wheel -# import xmlrunner -import unittest -import sys -import os -# import dotenv -import logging -import glob -from datetime import datetime -import input - -# Build the Python package -setup( - name='input', - version=input.VERSION, - packages=find_packages(), - include_package_data=True, - entry_points={ - 'console_scripts': [ - 'input=input.command_line:input_cli' - ], - }, - author='Franziska Lang', - description='TODO', - requires=[], - # NOTE: always specify versions to ensure build reproducibility - # NOTE2: sklearn==0.19.0 is a hidden dependency as it is required by Classifier.pickle - - install_requires=[ - 'biopython==1.76', - 'mock', - 'pandas==0.24.2', - 'numpy==1.16.2', - 'scipy==1.4.1', - 'pickle-mixin', - 'scikit-learn==0.20.3', - 'logzero==1.5.0' - ], - setup_requires=[], - classifiers=[ - 'Development Status :: 3 - Alpha', # Chose either "3 - Alpha", "4 - Beta" or "5 - Production/Stable" as the current state of your package - 'Intended Audience :: Healthcare Industry', - 'Intended Audience :: Science/Research', - 'Topic :: Scientific/Engineering :: Bio-Informatics', - 'Programming Language :: Python :: 3' - ] -) +from setuptools import find_packages, setup, Command +import distutils.command.build +from distutils.dist import Distribution +# from wheel.bdist_wheel import bdist_wheel as _bdist_wheel +# import xmlrunner +import unittest +import sys +import os +# import dotenv +import logging +import glob +from datetime import datetime +import input + +# Build the Python package +setup( + name='input', + version=input.VERSION, + packages=find_packages(), + include_package_data=True, + entry_points={ + 'console_scripts': [ + 'input=input.command_line:input_cli' + ], + }, + author='Franziska Lang', + description='TODO', + requires=[], + # NOTE: always specify versions to ensure build reproducibility + # NOTE2: sklearn==0.19.0 is a hidden dependency as it is required by Classifier.pickle + + install_requires=[ + 'biopython==1.76', + 'mock', + 'pandas==0.24.2', + 'numpy==1.16.2', + 'scipy==1.4.1', + 'pickle-mixin', + 'scikit-learn==0.20.3', + 'logzero==1.5.0' + ], + setup_requires=[], + classifiers=[ + 'Development Status :: 3 - Alpha', # Chose either "3 - Alpha", "4 - Beta" or "5 - Production/Stable" as the current state of your package + 'Intended Audience :: Healthcare Industry', + 'Intended Audience :: Science/Research', + 'Topic :: Scientific/Engineering :: Bio-Informatics', + 'Programming Language :: Python :: 3' + ] +) From 5fd8122fa735132d4a2792c1db7a5dac87b290f7 Mon Sep 17 00:00:00 2001 From: Pablo Riesgo Ferreiro Date: Sat, 20 Jun 2020 09:48:09 +0200 Subject: [PATCH 060/105] deals with 0.0 values for tumor content --- input/FeatureLiterature.py | 18 +++++++++--------- input/epitope.py | 2 +- 2 files changed, 10 insertions(+), 10 deletions(-) diff --git a/input/FeatureLiterature.py b/input/FeatureLiterature.py index d133f521..fbc33276 100755 --- a/input/FeatureLiterature.py +++ b/input/FeatureLiterature.py @@ -86,18 +86,18 @@ def rna_expression_mutation(transcript_expression, vaf_rna): return "NA" -def expression_mutation_tc(transcript_expression, patient_id, tumour_content): +def expression_mutation_tc(transcript_expression, patient_id, tumour_content_dict): """ calculated expression of mutation corrected by tumour content """ - try: - tumour_content = float(tumour_content[patient_id]) / 100 - except (KeyError, ValueError) as e: - tumour_content = "NA" - try: - return str(float(transcript_expression) / float(tumour_content)) - except ValueError: - return "NA" + tumor_content = tumour_content_dict.get(patient_id) + corrected_expression = "NA" + if tumor_content is not None and tumor_content > 0.0: + try: + corrected_expression = str(float(transcript_expression) / tumor_content / 100) + except ValueError: + pass + return corrected_expression def number_of_mismatches(epitope_wild_type, epitope_mutation): diff --git a/input/epitope.py b/input/epitope.py index 18bf9e0a..fd6bb617 100755 --- a/input/epitope.py +++ b/input/epitope.py @@ -644,7 +644,7 @@ def add_expression_features(self, rna_avail, tumour_content): expression_mutated_transcript = self.properties.get("Expression_Mutated_Transcript") self.add_features(FeatureLiterature.expression_mutation_tc( - transcript_expression=expression_mutated_transcript, patient_id=patient_id, tumour_content=tumour_content), + transcript_expression=expression_mutated_transcript, patient_id=patient_id, tumour_content_dict=tumour_content), "Expression_Mutated_Transcript_tumor_content") def add_differential_agretopicity_index_features(self, mutation_mhci, mutation_mhcii, wild_type_mhci, From 26d8f0e4748468a9086fefcd753c4551a56f92e3 Mon Sep 17 00:00:00 2001 From: Lang Date: Mon, 29 Jun 2020 10:03:04 +0200 Subject: [PATCH 061/105] correct get_netmhcpan4_epitopes WT 9mer epitope --- input/helpers/properties_manager.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/input/helpers/properties_manager.py b/input/helpers/properties_manager.py index 4241828b..a7ebee42 100755 --- a/input/helpers/properties_manager.py +++ b/input/helpers/properties_manager.py @@ -70,7 +70,7 @@ def get_scores_netmhcpan4_ranks(properties, mhc): def get_netmhcpan4_epitopes(properties, nine_mer=False): if nine_mer: mutation = properties["best_affinity_epitope_netmhcpan4_9mer"] - wild_type = properties["best_epitope_netmhcpan4_9mer_WT"] + wild_type = properties["best_affinity_epitope_netmhcpan4_9mer_WT"] else: mutation = properties["best_affinity_epitope_netmhcpan4"] wild_type = properties["best_affinity_epitope_netmhcpan4_WT"] From cd0a4c0cde758bbe871907cb08d5e47504ef3150 Mon Sep 17 00:00:00 2001 From: Lang Date: Mon, 29 Jun 2020 11:10:49 +0200 Subject: [PATCH 062/105] major re-structuring of main function + add affin_filtering=T for calculation of DAI mhc I based on affinity --- input/epitope.py | 1356 ++++++++++++++++++++++++---------------------- 1 file changed, 704 insertions(+), 652 deletions(-) diff --git a/input/epitope.py b/input/epitope.py index fd6bb617..e88f9372 100755 --- a/input/epitope.py +++ b/input/epitope.py @@ -20,655 +20,707 @@ class Epitope: - def __init__(self, runner, references, configuration, provean_annotator): - """ - :type runner: input.helpers.runner.Runner - :type references: input.references.ReferenceFolder - :type configuration: input.references.DependenciesConfiguration - :type provean_annotator: input.new_features.conservation_scores.ProveanAnnotator - """ - self.references = references - self.provean_annotator = provean_annotator - self.properties = {} - self.dissimilarity_calculator = DissimilarityCalculator(runner=runner, configuration=configuration) - self.neoantigen_fitness_calculator = NeoantigenFitnessCalculator(runner=runner, configuration=configuration) - self.neoag_calculator = NeoagCalculator(runner=runner, configuration=configuration) - self.predII = BestAndMultipleBinderMhcII(runner=runner, configuration=configuration) - self.predpresentation2 = MixMhc2Pred(runner=runner, configuration=configuration) - self.pred = BestAndMultipleBinder(runner=runner, configuration=configuration) - self.predpresentation = MixMHCpred(runner=runner, configuration=configuration) - self.tcell_predictor = TcellPrediction(references=self.references) - - def init_properties(self, col_nam, prop_list): - """Initiates epitope property storage in a dictionary - """ - properties = {} - for nam, char in zip(col_nam, prop_list): - properties[nam] = char - return properties - - def add_features(self, new_feature, new_feature_nam): - """Adds new features to already present epitope properties, stored in form of a dictioninary - """ - self.properties[new_feature_nam] = new_feature - - def write_to_file(self): - print(";".join([self.properties[key] for key in self.properties])) - - def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aaindex1_dict, aaindex2_dict, - set_available_mhc, set_available_mhcII, patient_hlaI, patient_hlaII, tumour_content, rna_avail): - """ Calculate new epitope features and add to dictonary that stores all properties - """ - self.properties = self.init_properties(col_nam, prop_list) - xmer_wt = self.properties["X.WT._..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."] - xmer_mut = self.properties["X..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."] - alleles = properties_manager.get_hla_allele(self.properties, patient_hlaI) - logger.info(xmer_mut) - - wild_type_mhci, mutation_mhci = properties_manager.get_epitopes( - properties=self.properties, mhc=MHC_I) - wild_type_mhcii, mutation_mhcii = properties_manager.get_epitopes( - properties=self.properties, mhc=MHC_II) - gene = properties_manager.get_gene(properties=self.properties) - - self.add_features(self_similarity.position_of_mutation_epitope( - wild_type=wild_type_mhci, mutation=mutation_mhci), "pos_MUT_MHCI") - self.add_features(self_similarity.position_of_mutation_epitope( - wild_type=wild_type_mhcii, mutation=mutation_mhcii), "pos_MUT_MHCII") - self.add_features(self_similarity.position_in_anchor_position( - position_mhci=self.properties["pos_MUT_MHCI"], - peptide_length=self.properties["MHC_I_peptide_length_.best_prediction."] - ), "Mutation_in_anchor") - - self.add_differential_agretopicity_index_features(mutation_mhci, mutation_mhcii, wild_type_mhci, - wild_type_mhcii) - - self.add_expression_features(rna_avail, tumour_content) - - self.add_differential_expression_features(gene, ref_dat) - - self.add_aminoacid_frequency_features(aa_freq_dict, mutation_mhci, nmer_freq_dict) - - self.add_aminoacid_index_features(aaindex1_dict, aaindex2_dict) - - alleles = properties_manager.get_hla_allele(self.properties, patient_hlaI) - self.add_provean_score_features( - xmer_wt=xmer_wt, xmer_mut=xmer_mut, alleles=alleles, set_available_mhc=set_available_mhc) - - self.add_netmhcpan4_features() - - self.add_multiple_binding_features() - - # netmhcpan4 wt affinity - self.add_features(self.pred.best4_affinity_WT, "best_affinity_netmhcpan4_WT") - self.add_features(self.pred.best4_affinity_epitope_WT, "best_affinity_epitope_netmhcpan4_WT") - self.add_features(self.pred.best4_affinity_allele_WT, "bestHLA_allele_affinity_netmhcpan4_WT") - - # netmhcpan4 mut rank score - self.add_features(self.pred.best4_mhc_score_WT, "best%Rank_netmhcpan4_WT") - self.add_features(self.pred.best4_mhc_epitope_WT, "best_epitope_netmhcpan4_WT") - self.add_features(self.pred.best4_mhc_allele_WT, "bestHLA_allele_netmhcpan4_WT") - - # netMHCpan MUT best 9mer score - self.add_features(self.pred.mhcI_score_9mer_WT, "best%Rank_netmhcpan4_9mer_WT") - self.add_features(self.pred.mhcI_score_epitope_9mer_WT, "best_epitope_netmhcpan4_9mer_WT") - self.add_features(self.pred.mhcI_score_allele_9mer_WT, "bestHLA_allele_netmhcpan4_9mer_Wt") - - # netmhcpan4 mut best 9mer affinity - self.add_features(self.pred.mhcI_affinity_9mer_WT, "best_affinity_netmhcpan4_9mer_WT") - self.add_features(self.pred.mhcI_affinity_allele_9mer_WT, "bestHLA_allele_affinity_netmhcpan4_9mer_WT") - self.add_features(self.pred.mhcI_affinity_epitope_9mer_WT, "best_affinity_epitope_netmhcpan4_9mer_WT") - - # multiplex representation - for threshold in [1, 2]: - num_mutation = self.properties["MB_number_pep_MHCscore<{}".format(threshold)] - num_wild_type = self.properties["MB_number_pep_WT_MHCscore<{}".format(threshold)] - self.add_features(FeatureLiterature.diff_number_binders( - num_mutation=num_mutation,num_wild_type=num_wild_type), "Diff_numb_epis_<{}".format(threshold)) - self.add_features(FeatureLiterature.ratio_number_binders( - num_mutation=num_mutation, num_wild_type=num_wild_type), "Ratio_numb_epis_<{}".format(threshold)) - - self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( - score_mutation=self.properties["MB_score_top10_harmonic"], - score_wild_type=self.properties["MB_score_WT_top10_harmonic"]), "Amplitude_mhcI_MB") - - # position of mutation - wild_type_netmhcpan4, mutation_netmhcpan4 = properties_manager.get_netmhcpan4_epitopes( - properties=self.properties) - self.add_features(self_similarity.position_of_mutation_epitope( - wild_type=wild_type_netmhcpan4, mutation=mutation_netmhcpan4), "pos_MUT_MHCI_affinity_epi") - - # position of mutation - wild_type_netmhcpan4_9mer, mutation_netmhcpan4_9mer = properties_manager.get_netmhcpan4_epitopes( - properties=self.properties, nine_mer=True) - self.add_features(self_similarity.position_of_mutation_epitope( - wild_type=wild_type_netmhcpan4_9mer, mutation=mutation_netmhcpan4_9mer),"pos_MUT_MHCI_affinity_epi_9mer") - self.add_features(self_similarity.position_in_anchor_position( - position_mhci=self.properties["pos_MUT_MHCI_affinity_epi"], - peptide_length=self.properties["best_epitope_netmhcpan4"]), - "Mutation_in_anchor_netmhcpan") - self.add_features(self_similarity.position_in_anchor_position( - position_mhci=self.properties["pos_MUT_MHCI_affinity_epi_9mer"], - peptide_length=9), - "Mutation_in_anchor_netmhcpan_9mer") - - self.add_self_similarity_features(mutation_mhci, mutation_mhcii, wild_type_mhci, wild_type_mhcii) - - self.add_neoantigen_fitness_features(mutation_mhci, mutation_mhcii) - - self.add_tcell_predictor_features(gene) - - # DAI with affinity values - wild_type_netmhcpan4_affinity, mutation_netmhcpan4_affinity = properties_manager.get_scores_netmhcpan4_affinity( - properties=self.properties, mhc=MHC_I) - self.add_features( - FeatureLiterature.dai(score_mutation=mutation_netmhcpan4_affinity, score_wild_type=wild_type_netmhcpan4_affinity), - "DAI_affinity") - - # DAI wiht rank scores by netmhcpan4 - wild_type_netmhcpan4_rank, mutation_netmhcpan4_rank = properties_manager\ - .get_scores_netmhcpan4_ranks(properties=self.properties, mhc=MHC_I) - self.add_features( - FeatureLiterature.dai(score_mutation=mutation_netmhcpan4_rank, score_wild_type=wild_type_netmhcpan4_rank), - "DAI_rank_netmhcpan4") - - # Amplitude with affinity values - self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( - score_mutation=self.properties["best_affinity_netmhcpan4"], - score_wild_type=self.properties["best_affinity_netmhcpan4_WT"], - apply_correction=True), "Amplitude_mhcI_affinity") - - # Amplitude with rank by netmhcpan4 - self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( - score_mutation=self.properties["best%Rank_netmhcpan4"], - score_wild_type=self.properties["best%Rank_netmhcpan4_WT"]), - "Amplitude_mhcI_rank_netmhcpan4") - - # Amplitude based on best affinity prediction restricted to 9mers - self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( - score_mutation=self.properties["best_affinity_netmhcpan4_9mer"], - score_wild_type = self.properties["best_affinity_netmhcpan4_9mer_WT"], - apply_correction=True), "Amplitude_mhcI_affinity_9mer_netmhcpan4") - - self.add_features( - self.neoantigen_fitness_calculator.wrap_pathogen_similarity( - mutation=mutation_netmhcpan4_9mer, iedb=self.references.iedb), - "Pathogensimiliarity_mhcI_9mer") - self.add_features( - self.neoantigen_fitness_calculator.wrap_pathogen_similarity( - mutation=mutation_netmhcpan4, iedb=self.references.iedb), - "Pathogensimiliarity_mhcI_affinity_nmers") - - # recogntion potential with amplitude by affinity and netmhcpan4 score - self.add_features(self.neoantigen_fitness_calculator.calculate_recognition_potential( - amplitude=self.properties["Amplitude_mhcI_affinity"], - pathogen_similarity=self.properties["Pathogensimiliarity_mhcI_affinity_nmers"], - mutation_in_anchor=self.properties["Mutation_in_anchor_netmhcpan"]), - "Recognition_Potential_mhcI_affinity") - self.add_features(self.neoantigen_fitness_calculator.calculate_recognition_potential( - amplitude=self.properties["Amplitude_mhcI_rank_netmhcpan4"], - pathogen_similarity=self.properties["Pathogensimiliarity_mhcI"], - mutation_in_anchor=self.properties["Mutation_in_anchor_netmhcpan"]), - "Recognition_Potential_mhcI_rank_netmhcpan4") - - # recogntion potential with amplitude by affinity and only 9mers considered --> value as published!! - self.add_features(self.neoantigen_fitness_calculator.calculate_recognition_potential( - amplitude=self.properties["Amplitude_mhcI_affinity_9mer_netmhcpan4"], - pathogen_similarity=self.properties["Pathogensimiliarity_mhcI_9mer"], - mutation_in_anchor=self.properties["Mutation_in_anchor_netmhcpan_9mer"], - mhc_affinity_mut=float(self.properties["best_affinity_netmhcpan4_9mer"])), - "Recognition_Potential_mhcI_9mer_affinity") - - score_mutation_mhci = self.properties["best_affinity_netmhcpan4"] - amplitude_mhci = self.properties["Amplitude_mhcI_affinity"] - bdg_cutoff_classical_mhci = 50 - bdg_cutoff_alternative_mhci = 5000 - amplitude_cutoff_mhci = 10 - self.add_features(FeatureLiterature.classify_adn_cdn( - score_mutation=score_mutation_mhci, amplitude=amplitude_mhci, - bdg_cutoff_classical=bdg_cutoff_classical_mhci, bdg_cutoff_alternative=bdg_cutoff_alternative_mhci, - amplitude_cutoff=amplitude_cutoff_mhci, category="CDN"), "CDN_mhcI") - - score_mutation_mhcii = self.properties["MHC_II_score_.best_prediction."] - amplitude_mhcii = self.properties["Amplitude_mhcII"] - bdg_cutoff_classical_mhcii = 1 - bdg_cutoff_alternative_mhcii = 4 - amplitude_cutoff_mhcii = 4 - self.add_features(FeatureLiterature.classify_adn_cdn( - score_mutation=score_mutation_mhcii, amplitude=amplitude_mhcii, - bdg_cutoff_classical=bdg_cutoff_classical_mhcii, bdg_cutoff_alternative=bdg_cutoff_alternative_mhcii, - amplitude_cutoff=amplitude_cutoff_mhcii, category="CDN"), "CDN_mhcII") - - self.add_features(FeatureLiterature.classify_adn_cdn( - score_mutation=score_mutation_mhci, amplitude=amplitude_mhci, - bdg_cutoff_classical=bdg_cutoff_classical_mhci, bdg_cutoff_alternative=bdg_cutoff_alternative_mhci, - amplitude_cutoff=amplitude_cutoff_mhci, - category="ADN"), "ADN_mhcI") - self.add_features(FeatureLiterature.classify_adn_cdn( - score_mutation=score_mutation_mhcii, amplitude=amplitude_mhcii, - bdg_cutoff_classical=bdg_cutoff_classical_mhcii, bdg_cutoff_alternative=bdg_cutoff_alternative_mhcii, - amplitude_cutoff=amplitude_cutoff_mhcii, category="ADN"), "ADN_mhcII") - - # netMHCIIpan predictions - alleles_hlaII = properties_manager.get_hla_allele(self.properties, patient_hlaII) - self.predII.main(sequence=xmer_mut, sequence_reference=xmer_wt, alleles=alleles_hlaII, - set_available_mhc=set_available_mhcII) - - # netmhcpan4 MUT scores - self.add_features(self.predII.best_mhcII_pan_score, "best%Rank_netmhcIIpan") - self.add_features(self.predII.best_mhcII_pan_epitope, "best_epitope_netmhcIIpan") - self.add_features(self.predII.best_mhcII_pan_allele, "bestHLA_allele_netmhcIIpan") - - # netmhcpan4 mut affinity - self.add_features(self.predII.best_mhcII_pan_affinity, "best_affinity_netmhcIIpan") - self.add_features(self.predII.best_mhcII_pan_affinity_epitope, "best_affinity_epitope_netmhcIIpan") - self.add_features(self.predII.best_mhcII_pan_affinity_allele, "bestHLA_allele_affinity_netmhcIIpan") - - # multiplexed representation MUT MHC II - for sc, mn in zip(self.predII.MHCII_score_all_epitopes, self.predII.mean_type): - self.add_features(sc, "MB_score_MHCII_all_epitopes_" + mn) - for sc, mn in zip(self.predII.MHCII_score_top10, self.predII.mean_type): - self.add_features(sc, "MB_score_MHCII_top10_" + mn) - for sc, mn in zip(self.predII.MHCII_score_best_per_alelle, self.predII.mean_type): - self.add_features(sc, "MB_score_MHCII_best_per_alelle_" + mn) - - # rename MB_score_best_per_alelle_harmonic to PHBR (described in Marty et al) - self.properties["PHBR-II"] = self.properties.pop("MB_score_MHCII_best_per_alelle_harmonic") - self.add_features(self.predII.MHCII_epitope_scores, "MB_mhcII_epitope_scores") - self.add_features(self.predII.MHCII_epitope_seqs, "MB_mhcII_epitope_sequences") - self.add_features(self.predII.MHCII_epitope_alleles, "MB_mhcII_alleles") - self.add_features(self.predII.MHCII_number_strong_binders, "MB_number_pep_MHCIIscore<2") - self.add_features(self.predII.MHCII_number_weak_binders, "MB_number_pep_MHCIIscore<10") - - # netmhcIIpan WT scores - self.add_features(self.predII.best_mhcII_pan_score_WT, "best%Rank_netmhcIIpan_WT") - self.add_features(self.predII.best_mhcII_pan_epitope_WT, "best_epitope_netmhcIIpan_WT") - self.add_features(self.predII.best_mhcII_pan_allele_WT, "bestHLA_allele_netmhcIIpan_Wt") - - # netmhcIIpan wt affinity - self.add_features(self.predII.best_mhcII_affinity_WT, "best_affinity_netmhcIIpan_WT") - self.add_features(self.predII.best_mhcII_affinity_epitope_WT, "best_affinity_epitope_netmhcIIpan_WT") - self.add_features(self.predII.best_mhcII_affinity_allele_WT, "bestHLA_allele_affinity_netmhcIIpan_WT") - - # multiplexed representation WT MHC II - for sc, mn in zip(self.predII.MHCII_score_all_epitopes_WT, self.predII.mean_type): - self.add_features(sc, "MB_score_MHCII_all_epitopes_WT_" + mn) - for sc, mn in zip(self.predII.MHCII_score_top10_WT, self.predII.mean_type): - self.add_features(sc, "MB_score_MHCII_top10_WT_" + mn) - for sc, mn in zip(self.predII.MHCII_score_best_per_alelle_WT, self.predII.mean_type): - self.add_features(sc, "MB_score_MHCII_best_per_alelle_WT_" + mn) - - # rename MB_score_best_per_alelle_harmonic to PHBR (described in Marty et al) - if "MB_score_MHCII_best_per_alelle_WT_harmonic" in self.properties: - self.properties["PHBR-II_WT"] = self.properties.pop("MB_score_MHCII_best_per_alelle_WT_harmonic") - self.add_features(self.predII.MHCII_epitope_scores_WT, "MB_mhcII_epitope_scores_WT") - self.add_features(self.predII.MHCII_epitope_seqs_WT, "MB_mhcII_epitope_sequences_WT") - self.add_features(self.predII.MHCII_epitope_alleles_WT, "MB_mhcII_alleles_WT") - self.add_features(self.predII.MHCII_number_strong_binders_WT, "MB_number_pep_MHCIIscore<2_WT") - self.add_features(self.predII.MHCII_number_weak_binders_WT, "MB_number_pep_MHCIIscore<10_WT") - - # dai mhc II affinity - wild_type_netmhciipan4, mutation_netmhciipan4 = properties_manager.get_scores_netmhcpan4_affinity( - properties=self.properties, mhc=MHC_II) - self.add_features( - FeatureLiterature.dai(score_mutation=mutation_netmhciipan4, score_wild_type=wild_type_netmhciipan4), - "DAI_mhcII_affinity") - self.add_features( - FeatureLiterature.dai(score_mutation=mutation_netmhciipan4, score_wild_type=wild_type_netmhciipan4, - affin_filtering=True), - "DAI_mhcII_affinity_aff_filtered") - - # dai mhc II netMHCIIpan score - self.add_features(FeatureLiterature.dai(score_mutation=mutation_mhcii, score_wild_type=wild_type_mhcii), - "DAI_mhcII_netmhcIIpan") - - # dai multiple binding mhc II - wild_type_multiple_binding_ii, mutation_multiple_binding_ii = properties_manager. \ - get_scores_multiple_binding(self.properties, mhc=MHC_II) - self.add_features( - FeatureLiterature.dai(score_mutation=mutation_multiple_binding_ii, - score_wild_type=wild_type_multiple_binding_ii), - "DAI_mhcII_MB") - - # difference number of binders - for threshold in [2, 10]: - num_mutation = self.properties["MB_number_pep_MHCIIscore<{}".format(threshold)] - num_wild_type = self.properties["MB_number_pep_MHCIIscore<{}_WT".format(threshold)] - self.add_features(FeatureLiterature.diff_number_binders( - num_mutation=num_mutation,num_wild_type=num_wild_type), "Diff_numb_epis_mhcII<{}".format(threshold)) - self.add_features(FeatureLiterature.ratio_number_binders( - num_mutation=num_mutation,num_wild_type=num_wild_type), "Ratio_numb_epis_mhcII<{}".format(threshold)) - - # amplitude affinity mhc II - self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( - score_mutation=self.properties["best_affinity_netmhcIIpan"], - score_wild_type = self.properties["best_affinity_netmhcIIpan_WT"], - apply_correction=True), "Amplitude_mhcII_affinity") - - # amplitude multiple binding mhc II - self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( - score_mutation=self.properties["MB_score_MHCII_top10_harmonic"], - score_wild_type = self.properties["MB_score_MHCII_top10_WT_harmonic"]), - "Amplitude_mhcII_mb") - - # amplitude rank score mhc II - self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( - score_mutation=self.properties["best%Rank_netmhcIIpan"], - score_wild_type = self.properties["best%Rank_netmhcIIpan_WT"]), - "Amplitude_mhcII_rank_netmhcpan4") - logger.info("Amplitude mhc II: {}".format(self.properties["Amplitude_mhcII_rank_netmhcpan4"])) - - # priority score - self.add_features(FeatureLiterature.number_of_mismatches( - epitope_wild_type=self.properties["best_epitope_netmhcpan4_WT"], - epitope_mutation=self.properties["best_epitope_netmhcpan4"]), "Number_of_mismatches_mhcI") - self.add_features(FeatureLiterature.number_of_mismatches( - epitope_wild_type=self.properties["best_epitope_netmhcIIpan_WT"], - epitope_mutation=self.properties["best_epitope_netmhcIIpan"]), "Number_of_mismatches_mhcII") - if "mutation_found_in_proteome" not in self.properties: - self.add_features(FeatureLiterature.match_in_proteome( - sequence=self.properties["X..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."], db=db), - "mutation_found_in_proteome") - - vaf_tumor = self.properties.get("VAF_in_tumor", "NA") - vaf_rna = self.properties.get("VAF_in_RNA", "NA") - transcript_expr = self.properties["transcript_expression"] - no_mismatch = self.properties["Number_of_mismatches_mhcI"] - score_mut = self.properties["best%Rank_netmhcpan4"] - score_wt = self.properties["best%Rank_netmhcpan4_WT"] - mut_in_prot = self.properties["mutation_found_in_proteome"] - - self.add_features(FeatureLiterature.calc_priority_score( - vaf_tumor=vaf_tumor, vaf_rna=vaf_rna, transcript_expr=transcript_expr, no_mismatch=no_mismatch, - score_mut=score_mut, score_wt=score_wt, mut_in_prot=mut_in_prot), "Priority_score") - - # priority score using multiplexed representation score - score_mut = self.properties["MB_score_top10_harmonic"] - score_wt = self.properties["MB_score_WT_top10_harmonic"] - self.add_features(FeatureLiterature.calc_priority_score( - vaf_tumor=vaf_tumor, vaf_rna=vaf_rna, transcript_expr=transcript_expr, no_mismatch=no_mismatch, - score_mut=score_mut, score_wt=score_wt, mut_in_prot=mut_in_prot), "Priority_score_MB") - - # neoag immunogenicity model - sample_id = properties_manager.get_patient_id(self.properties) - mut_peptide = self.properties["best_affinity_epitope_netmhcpan4"] - score_mut = self.properties["best_affinity_netmhcpan4"] - ref_peptide = self.properties["best_affinity_epitope_netmhcpan4_WT"] - peptide_variant_position = self.properties["pos_MUT_MHCI_affinity_epi"] - self.add_features(self.neoag_calculator.wrapper_neoag( - sample_id=sample_id, mut_peptide=mut_peptide, score_mut=score_mut, ref_peptide=ref_peptide, - peptide_variant_position=peptide_variant_position), "neoag_immunogencity") - - # IEDB immunogenicity only for epitopes with affinity < 500 nM (predicted with netMHCpan) --> in publications - mhci_epitope = self.properties["best_affinity_epitope_netmhcpan4"] - mhci_allele = self.properties["bestHLA_allele_affinity_netmhcpan4"] - mhci_score = self.properties["best_affinity_netmhcpan4"] - mhcii_epitope = self.properties["MHC_II_epitope_.best_prediction."] - mhcii_allele = self.properties["MHC_II_allele_.best_prediction."] - self.add_features(FeatureLiterature.calc_IEDB_immunogenicity( - epitope=mhci_epitope, mhc_allele=mhci_allele, mhc_score=mhci_score), "IEDB_Immunogenicity_mhcI") - self.add_features(FeatureLiterature.calc_IEDB_immunogenicity( - epitope=mhcii_epitope, mhc_allele=mhcii_allele, mhc_score=None), "IEDB_Immunogenicity_mhcII") - self.add_features(FeatureLiterature.calc_IEDB_immunogenicity( - epitope=mhci_epitope, mhc_allele=mhci_allele, mhc_score=mhci_score, affin_filtering=True), - "IEDB_Immunogenicity_mhcI_affinity_filtered") - - self.add_mix_mhc_pred_features(xmer_wt=xmer_wt, xmer_mut=xmer_mut, patient_hlaI=patient_hlaI) - - self.add_mix_mhc2_pred_features(xmer_mut=xmer_mut, xmer_wt=xmer_wt, patient_hlaII=patient_hlaII) - - # dissimilarity to self-proteome - - # neoantigen fitness - mhc_mutation = self.properties["best_affinity_epitope_netmhcpan4"] - mhc_affinity = self.properties["best_affinity_netmhcpan4"] - self.add_features(self.dissimilarity_calculator.calculate_dissimilarity( - mhc_mutation=mhc_mutation, mhc_affinity=mhc_affinity, references=self.references), - "dissimilarity") - self.add_features(self.dissimilarity_calculator.calculate_dissimilarity( - mhc_mutation=mhc_mutation, mhc_affinity=mhc_affinity, references=self.references, - filter_binder=True), "dissimilarity_filter500") - - self.add_vax_rank_features() - - return self.properties - - def add_vax_rank_features(self): - # vaxrank - vaxrankscore = vaxrank.VaxRank() - vaxrankscore.main(mutation_scores=self.properties["MB_affinities"], - expression_score=self.properties["Expression_Mutated_Transcript"]) - self.add_features(vaxrankscore.total_binding_score, "vaxrank_binding_score") - self.add_features(vaxrankscore.ranking_score, "vaxrank_total_score") - - def add_mix_mhc2_pred_features(self, xmer_wt, xmer_mut, patient_hlaII): - # MixMHC2pred - alleles = properties_manager.get_hla_allele(self.properties, patient_hlaII) - self.predpresentation2.main(alleles=alleles, xmer_wt=xmer_wt, xmer_mut=xmer_mut) - self.add_features(self.predpresentation2.all_peptides, "MixMHC2pred_all_peptides") - self.add_features(self.predpresentation2.all_ranks, "MixMHC2pred_all_ranks") - self.add_features(self.predpresentation2.all_alleles, "MixMHC2pred_all_alleles") - self.add_features(self.predpresentation2.best_peptide, "MixMHC2pred_best_peptide") - self.add_features(self.predpresentation2.best_rank, "MixMHC2pred_best_rank") - self.add_features(self.predpresentation2.best_allele, "MixMHC2pred_best_allele") - self.add_features(self.predpresentation2.best_peptide_wt, "MixMHC2pred_best_peptide_wt") - self.add_features(self.predpresentation2.best_rank_wt, "MixMHC2pred_best_rank_wt") - self.add_features(self.predpresentation2.difference_score_mut_wt, "MixMHC2pred_difference_rank_mut_wt") - - def add_mix_mhc_pred_features(self, xmer_wt, xmer_mut, patient_hlaI): - # MixMHCpred - alleles = properties_manager.get_hla_allele(self.properties, patient_hlaI) - self.predpresentation.main(xmer_wt=xmer_wt, xmer_mut=xmer_mut, alleles=alleles) - self.add_features(self.predpresentation.all_peptides, "MixMHCpred_all_peptides") - self.add_features(self.predpresentation.all_scores, "MixMHCpred_all_scores") - self.add_features(self.predpresentation.all_ranks, "MixMHCpred_all_ranks") - self.add_features(self.predpresentation.all_alleles, "MixMHCpred_all_alleles") - self.add_features(self.predpresentation.best_peptide, "MixMHCpred_best_peptide") - self.add_features(self.predpresentation.best_score, "MixMHCpred_best_score") - self.add_features(self.predpresentation.best_rank, "MixMHCpred_best_rank") - self.add_features(self.predpresentation.best_allele, "MixMHCpred_best_allele") - self.add_features(self.predpresentation.best_peptide_wt, "MixMHCpred_best_peptide_wt") - self.add_features(self.predpresentation.best_score_wt, "MixMHCpred_best_score_wt") - self.add_features(self.predpresentation.best_rank_wt, "MixMHCpred_best_rank_wt") - self.add_features(self.predpresentation.difference_score_mut_wt, "MixMHCpred_difference_score_mut_wt") - - def add_tcell_predictor_features(self, gene): - # T cell predictor - substitution = properties_manager.get_substitution(properties=self.properties) - epitope = self.properties["MHC_I_epitope_.best_prediction."] - score = self.properties["MHC_I_score_.best_prediction."] - self.add_features(self.tcell_predictor.calculate_tcell_predictor_score( - gene=gene, substitution=substitution, epitope=epitope, score=score), - "Tcell_predictor_score") - epitope = self.properties["best_affinity_epitope_netmhcpan4_9mer"] - score = self.properties["best_affinity_netmhcpan4_9mer"] - self.add_features(self.tcell_predictor.calculate_tcell_predictor_score( - gene=gene, substitution=substitution, epitope=epitope, score=score, threshold=500), - "Tcell_predictor_score_9mersPredict") - - def add_neoantigen_fitness_features(self, mutation_mhci, mutation_mhcii): - # neoantigen fitness - self.add_features( - self.neoantigen_fitness_calculator.wrap_pathogen_similarity( - mutation=mutation_mhci, iedb=self.references.iedb), - "Pathogensimiliarity_mhcI") - self.add_features( - self.neoantigen_fitness_calculator.wrap_pathogen_similarity( - mutation=mutation_mhcii, iedb=self.references.iedb), - "Pathogensimiliarity_mhcII") - - score_mutation_mhci = self.properties["MHC_I_score_.best_prediction."] - score_wild_type_mhci = self.properties["MHC_I_score_.WT."] - self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( - score_mutation=score_mutation_mhci, score_wild_type=score_wild_type_mhci), "Amplitude_mhcI") - score_mutation_mhcii = self.properties["MHC_II_score_.best_prediction."] - score_wild_type_mhcii = self.properties["MHC_II_score_.WT."] - self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( - score_mutation=score_mutation_mhcii, score_wild_type=score_wild_type_mhcii), "Amplitude_mhcII") - - # TODO: Franziska, please, review that this is the right value for mutation_in_anchor, - # it is possible that there was a bug here and that it should use "Mutation_in_anchor" - self.add_features(self.neoantigen_fitness_calculator.calculate_recognition_potential( - amplitude=self.properties["Amplitude_mhcI"], - pathogen_similarity=self.properties["Pathogensimiliarity_mhcI"], - mutation_in_anchor=self.properties["Mutation_in_anchor_netmhcpan"]), - "Recognition_Potential_mhcI") - self.add_features(self.neoantigen_fitness_calculator.calculate_recognition_potential( - amplitude=self.properties["Amplitude_mhcII"], - pathogen_similarity=self.properties["Pathogensimiliarity_mhcII"], - mutation_in_anchor=self.properties["Mutation_in_anchor_netmhcpan"]), - "Recognition_Potential_mhcII") - - def add_self_similarity_features(self, mutation_mhci, mutation_mhcii, wild_type_mhci, wild_type_mhcii): - # selfsimilarity - self.add_features(self_similarity.get_self_similarity(mutation=mutation_mhci, wild_type=wild_type_mhci), - "Selfsimilarity_mhcI") - self.add_features(self_similarity.get_self_similarity( - wild_type=wild_type_mhcii, mutation=mutation_mhcii), "Selfsimilarity_mhcII") - self.add_features(self_similarity.is_improved_binder( - score_mutation=self.properties["best%Rank_netmhcpan4"], - score_wild_type=self.properties["best%Rank_netmhcpan4_WT"] - ), "ImprovedBinding_mhcI") - self.add_features(self_similarity.is_improved_binder( - # TODO: conversion from float representation needs to be changed - score_mutation=self.properties["MHC_II_score_.best_prediction."], - score_wild_type=self.properties["MHC_II_score_.WT."] - ), "ImprovedBinding_mhcII") - self.add_features(self_similarity.self_similarity_of_conserved_binder_only( - has_conserved_binder=self.properties["ImprovedBinding_mhcI"], - similarity=self.properties["Selfsimilarity_mhcI"]), - "Selfsimilarity_mhcI_conserved_binder") - - def add_multiple_binding_features(self): - # multiplexed representation MUT - for sc, mn in zip(self.pred.MHC_score_all_epitopes, self.pred.mean_type): - self.add_features(sc, "MB_score_all_epitopes_" + mn) - for sc, mn in zip(self.pred.MHC_score_top10, self.pred.mean_type): - self.add_features(sc, "MB_score_top10_" + mn) - for sc, mn in zip(self.pred.MHC_score_best_per_alelle, self.pred.mean_type): - self.add_features(sc, "MB_score_best_per_alelle_" + mn) - # rename MB_score_best_per_alelle_harmonic to PHBR (described in Marty et al) - self.properties["PHBR-I"] = self.properties.pop("MB_score_best_per_alelle_harmonic") - self.add_features(self.pred.MHC_epitope_scores, "MB_epitope_scores") - self.add_features(self.pred.MHC_epitope_seqs, "MB_epitope_sequences") - self.add_features(self.pred.MHC_epitope_alleles, "MB_alleles") - self.add_features(self.pred.MHC_number_strong_binders, "MB_number_pep_MHCscore<1") - self.add_features(self.pred.MHC_number_weak_binders, "MB_number_pep_MHCscore<2") - # generator rate - self.add_features(self.pred.epitope_affinities, "MB_affinities") - self.add_features(self.pred.generator_rate, "Generator_rate") - # multiplexed representation WT - self.add_features(self.pred.MHC_epitope_scores_WT, "MB_epitope_WT_scores") - self.add_features(self.pred.MHC_epitope_seqs_WT, "MB_epitope_WT_sequences") - self.add_features(self.pred.MHC_epitope_alleles_WT, "MB_alleles_WT") - for sc, mn in zip(self.pred.MHC_score_top10_WT, self.pred.mean_type): - self.add_features(sc, "MB_score_WT_top10_" + mn) - for sc, mn in zip(self.pred.MHC_score_all_epitopes_WT, self.pred.mean_type): - self.add_features(sc, "MB_score_WT_all_epitopes_" + mn) - for sc, mn in zip(self.pred.MHC_score_best_per_alelle_WT, self.pred.mean_type): - self.add_features(sc, "MB_score_WT_best_per_alelle_" + mn) - self.properties["PHBR-I_WT"] = self.properties.pop("MB_score_WT_best_per_alelle_harmonic") - self.add_features(self.pred.MHC_number_strong_binders_WT, "MB_number_pep_WT_MHCscore<1") - self.add_features(self.pred.MHC_number_weak_binders_WT, "MB_number_pep_WT_MHCscore<2") - # generator rate - self.add_features(self.pred.epitope_affinities_WT, "MB_affinities_WT") - self.add_features(self.pred.generator_rate_WT, "Generator_rate_WT") - wild_type_multiple_binding, mutation_multiple_binding = properties_manager. \ - get_scores_multiple_binding(self.properties, mhc=MHC_I) - self.add_features( - FeatureLiterature.dai(score_mutation=mutation_multiple_binding, score_wild_type=wild_type_multiple_binding), - "DAI_mhcI_MB") - - def add_netmhcpan4_features(self): - # netmhcpan4 MUT rank score - self.add_features(self.pred.best4_mhc_score, "best%Rank_netmhcpan4") - self.add_features(self.pred.best4_mhc_epitope, "best_epitope_netmhcpan4") - self.add_features(self.pred.best4_mhc_allele, "bestHLA_allele_netmhcpan4") - self.add_features(self.pred.directed_to_TCR, "directed_to_TCR") - # netmhcpan4 mut affinity - self.add_features(self.pred.best4_affinity, "best_affinity_netmhcpan4") - self.add_features(self.pred.best4_affinity_epitope, "best_affinity_epitope_netmhcpan4") - self.add_features(self.pred.best4_affinity_allele, "bestHLA_allele_affinity_netmhcpan4") - self.add_features(self.pred.best4_affinity_directed_to_TCR, "affinity_directed_to_TCR") - # netMHCpan MUT best 9mer score - self.add_features(self.pred.mhcI_score_9mer, "best%Rank_netmhcpan4_9mer") - self.add_features(self.pred.mhcI_score_epitope_9mer, "best_epitope_netmhcpan4_9mer") - self.add_features(self.pred.mhcI_score_allele_9mer, "bestHLA_allele_netmhcpan4_9mer") - # netmhcpan4 mut best 9mer affinity - self.add_features(self.pred.mhcI_affinity_9mer, "best_affinity_netmhcpan4_9mer") - self.add_features(self.pred.mhcI_affinity_allele_9mer, "bestHLA_allele_affinity_netmhcpan4_9mer") - self.add_features(self.pred.mhcI_affinity_epitope_9mer, "best_affinity_epitope_netmhcpan4_9mer") - - def add_provean_score_features(self, xmer_mut, xmer_wt, alleles, set_available_mhc): - # PROVEAN score - ucsc_id = self.provean_annotator.build_ucsc_id_plus_position( - substitution=self.properties["substitution"], ucsc_id=self.properties["UCSC_transcript"]) - self.add_features(ucsc_id, "UCSC_ID_position") - self.add_features(self.provean_annotator.get_provean_annotation( - mutated_aminoacid=self.properties['MUT_AA'], ucsc_id_position=ucsc_id), - "PROVEAN_score") - self.pred.main(xmer_mut=xmer_mut, xmer_wt=xmer_wt, alleles=alleles, set_available_mhc=set_available_mhc) - - def add_aminoacid_index_features(self, aaindex1_dict, aaindex2_dict): - # amino acid index - mutation_aminoacid = self.properties["MUT_AA"] - wild_type_aminoacid = self.properties["WT_AA"] - for k in aaindex1_dict: - self.add_features(aaindex1_dict[k].get(wild_type_aminoacid, "NA"), "{}_{}".format(k, "wt")) - self.add_features(aaindex1_dict[k].get(mutation_aminoacid, "NA"), "{}_{}".format(k, "mut")) - for k in aaindex2_dict: - self.add_features(aaindex2_dict[k].get(wild_type_aminoacid, {}).get(mutation_aminoacid, "NA"), k) - - def add_aminoacid_frequency_features(self, aa_freq_dict, mutation_mhci, nmer_freq_dict): - # amino acid frequency - substitution = self.properties["substitution"] - mutated_aminoacid = FeatureLiterature.wt_mut_aa(substitution=substitution, mut="mut") - self.add_features(mutated_aminoacid, "MUT_AA") - self.add_features(FeatureLiterature.wt_mut_aa(substitution=substitution, mut="wt"), "WT_AA") - self.add_features(freq_score.freq_aa(mutated_aminoacid=mutated_aminoacid, dict_freq=aa_freq_dict), - "Frequency_mutated_AA") - self.add_features(freq_score.freq_prod_4mer(mutation=mutation_mhci, dict_freq=aa_freq_dict), - "Product_Frequency_4mer") - self.add_features(freq_score.freq_4mer(mutation=mutation_mhci, dict_freq=nmer_freq_dict), "Frequency_of_4mer") - - def add_expression_features(self, rna_avail, tumour_content): - # expression - transcript_expression = self.properties["transcript_expression"] - patient_id = properties_manager.get_patient_id(self.properties) - vaf_tumor = self.properties["VAF_in_tumor"] - vaf_rna = vaf_tumor if rna_avail.get(patient_id, "False") == "False" else \ - self.properties.get("VAF_in_RNA", vaf_tumor) - - self.add_features(FeatureLiterature.rna_expression_mutation( - transcript_expression=transcript_expression, vaf_rna=vaf_rna), "Expression_Mutated_Transcript") - - expression_mutated_transcript = self.properties.get("Expression_Mutated_Transcript") - self.add_features(FeatureLiterature.expression_mutation_tc( - transcript_expression=expression_mutated_transcript, patient_id=patient_id, tumour_content_dict=tumour_content), - "Expression_Mutated_Transcript_tumor_content") - - def add_differential_agretopicity_index_features(self, mutation_mhci, mutation_mhcii, wild_type_mhci, - wild_type_mhcii): - # differential agretopicity index - self.add_features( - FeatureLiterature.dai(score_mutation=mutation_mhci, score_wild_type=wild_type_mhci), "DAI_mhcI") - self.add_features( - FeatureLiterature.dai(score_mutation=mutation_mhcii, score_wild_type=wild_type_mhcii), "DAI_mhcII") - - def add_differential_expression_features(self, gene, ref_dat): - # differential expression - expression_tumor = self.properties["transcript_expression"] - expression_reference = differential_expression.add_rna_reference(gene, ref_dat, 0) - expression_reference_sum = differential_expression.add_rna_reference(gene, ref_dat, 2) - expression_reference_sd = differential_expression.add_rna_reference(gene, ref_dat, 1) - self.add_features(expression_reference, "mean_ref_expression") - self.add_features(expression_reference_sd, "sd_ref_expression") - self.add_features(expression_reference_sum, "sum_ref_expression") - self.add_features(differential_expression.fold_change( - expression_tumor=expression_tumor, expression_reference=expression_reference), "log2_fc_tumour_ref") - self.add_features(differential_expression.percentile_calc( - expression_tumor=expression_tumor, expression_reference_sum=expression_reference_sum), - "percentile_tumour_ref") - self.add_features(differential_expression.pepper_calc( - expression_tumor=expression_tumor, expression_reference=expression_reference, - expression_reference_sd=expression_reference_sd), "DE_pepper") + def __init__(self, runner, references, configuration, provean_annotator): + """ + :type runner: input.helpers.runner.Runner + :type references: input.references.ReferenceFolder + :type configuration: input.references.DependenciesConfiguration + :type provean_annotator: input.new_features.conservation_scores.ProveanAnnotator + """ + self.references = references + self.provean_annotator = provean_annotator + self.properties = {} + self.dissimilarity_calculator = DissimilarityCalculator(runner=runner, configuration=configuration) + self.neoantigen_fitness_calculator = NeoantigenFitnessCalculator(runner=runner, configuration=configuration) + self.neoag_calculator = NeoagCalculator(runner=runner, configuration=configuration) + self.predII = BestAndMultipleBinderMhcII(runner=runner, configuration=configuration) + self.predpresentation2 = MixMhc2Pred(runner=runner, configuration=configuration) + self.pred = BestAndMultipleBinder(runner=runner, configuration=configuration) + self.predpresentation = MixMHCpred(runner=runner, configuration=configuration) + self.tcell_predictor = TcellPrediction(references=self.references) + + def init_properties(self, col_nam, prop_list): + """Initiates epitope property storage in a dictionary + """ + properties = {} + for nam, char in zip(col_nam, prop_list): + properties[nam] = char + return properties + + def add_features(self, new_feature, new_feature_nam): + """Adds new features to already present epitope properties, stored in form of a dictioninary + """ + self.properties[new_feature_nam] = new_feature + + def write_to_file(self): + print(";".join([self.properties[key] for key in self.properties])) + + def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aaindex1_dict, aaindex2_dict, + set_available_mhc, set_available_mhcII, patient_hlaI, patient_hlaII, tumour_content, rna_avail): + """ Calculate new epitope features and add to dictonary that stores all properties + """ + self.properties = self.init_properties(col_nam, prop_list) + xmer_wt = self.properties["X.WT._..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."] + xmer_mut = self.properties["X..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."] + logger.info(xmer_mut) + + gene = properties_manager.get_gene(properties=self.properties) + vaf_tumor = self.properties.get("VAF_in_tumor", "NA") + vaf_rna = self.properties.get("VAF_in_RNA", "NA") + transcript_expr = self.properties["transcript_expression"] + alleles = properties_manager.get_hla_allele(self.properties, patient_hlaI) + alleles_hlaII = properties_manager.get_hla_allele(self.properties, patient_hlaII) + + #TODO: remove --> IEDB + wild_type_mhci, mutation_mhci = properties_manager.get_epitopes( + properties=self.properties, mhc=MHC_I) + wild_type_mhcii, mutation_mhcii = properties_manager.get_epitopes( + properties=self.properties, mhc=MHC_II) + ''' + self.add_features(self_similarity.position_of_mutation_epitope( + wild_type=wild_type_mhci, mutation=mutation_mhci), "pos_MUT_MHCI") + self.add_features(self_similarity.position_of_mutation_epitope( + wild_type=wild_type_mhcii, mutation=mutation_mhcii), "pos_MUT_MHCII") + self.add_features(self_similarity.position_in_anchor_position( + position_mhci=self.properties["pos_MUT_MHCI"], + peptide_length=self.properties["MHC_I_peptide_length_.best_prediction."] + ), "Mutation_in_anchor") + self.add_differential_agretopicity_index_features(mutation_mhci, mutation_mhcii, wild_type_mhci, + wild_type_mhcii) + ''' + + # MHC binding independent features + self.add_expression_features(rna_avail, tumour_content) + self.add_differential_expression_features(gene, ref_dat) + self.add_aminoacid_frequency_features(aa_freq_dict, mutation_mhci, nmer_freq_dict) + self.add_aminoacid_index_features(aaindex1_dict, aaindex2_dict) + self.add_provean_score_features() + + # HLA I predictions: NetMHCpan + self.pred.main(xmer_mut=xmer_mut, xmer_wt=xmer_wt, alleles=alleles, set_available_mhc=set_available_mhc) + self.add_netmhcpan4_features() + self.add_netmhcpan4_WT_features() + self.add_multiple_binding_features() + self.add_multiple_binding_numdiff() + wild_type_netmhcpan4, mutation_netmhcpan4 = properties_manager.get_netmhcpan4_epitopes( + properties=self.properties) + wild_type_netmhcpan4_9mer, mutation_netmhcpan4_9mer = properties_manager.get_netmhcpan4_epitopes( + properties=self.properties, nine_mer=True) + wild_type_netmhcpan4_affinity, mutation_netmhcpan4_affinity = properties_manager.get_scores_netmhcpan4_affinity( + properties=self.properties, mhc=MHC_I) + wild_type_netmhcpan4_rank, mutation_netmhcpan4_rank = properties_manager \ + .get_scores_netmhcpan4_ranks(properties=self.properties, mhc=MHC_I) + wild_type_multiple_binding_score, mutation_multiple_binding_score = properties_manager. \ + get_scores_multiple_binding(self.properties, mhc=MHC_I) + + self.add_multiple_binding_scorediff(mut_score=mutation_multiple_binding_score, wt_score=wild_type_multiple_binding_score) + # position of mutation + self.add_position_mutation(epi_wt=wild_type_netmhcpan4, epi_mut=mutation_netmhcpan4, + epi_wt_9mer=wild_type_netmhcpan4_9mer, epi_mut_9mer=mutation_netmhcpan4_9mer) + # mutation in anchor + self.add_mutation_in_anchor() + + #TODO: change to netmhcpan + self.add_self_similarity_features(mutation_mhci, mutation_mhcii, wild_type_mhci, wild_type_mhcii) + # TODO: remove --> IEDB + self.add_neoantigen_fitness_features(mutation_mhci, mutation_mhcii) + + self.add_tcell_predictor_features(gene) + + #TODO:summarise into function + # DAI with affinity values + self.add_features( + FeatureLiterature.dai(score_mutation=mutation_netmhcpan4_affinity, score_wild_type=wild_type_netmhcpan4_affinity), + "DAI_affinity") + # DAI wiht rank scores by netmhcpan4 + self.add_features( + FeatureLiterature.dai(score_mutation=mutation_netmhcpan4_rank, score_wild_type=wild_type_netmhcpan4_rank), + "DAI_rank_netmhcpan4") + + #TODO:summarise into function + # Amplitude with affinity values + self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( + score_mutation=mutation_netmhcpan4_affinity, score_wild_type=wild_type_netmhcpan4_affinity, + apply_correction=True), "Amplitude_mhcI_affinity") + + # Amplitude with rank by netmhcpan4 + self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( + score_mutation=mutation_netmhcpan4_rank, score_wild_type=wild_type_netmhcpan4_rank), + "Amplitude_mhcI_rank_netmhcpan4") + + # Amplitude based on best affinity prediction restricted to 9mers + self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( + score_mutation=self.properties["best_affinity_netmhcpan4_9mer"], + score_wild_type = self.properties["best_affinity_netmhcpan4_9mer_WT"], + apply_correction=True), "Amplitude_mhcI_affinity_9mer_netmhcpan4") + + #TODO:summarise into function + self.add_features( + self.neoantigen_fitness_calculator.wrap_pathogen_similarity( + mutation=mutation_netmhcpan4_9mer, iedb=self.references.iedb), + "Pathogensimiliarity_mhcI_9mer") + self.add_features( + self.neoantigen_fitness_calculator.wrap_pathogen_similarity( + mutation=mutation_netmhcpan4, iedb=self.references.iedb), + "Pathogensimiliarity_mhcI_affinity_nmers") + + # recogntion potential with amplitude by affinity and netmhcpan4 score + self.add_features(self.neoantigen_fitness_calculator.calculate_recognition_potential( + amplitude=self.properties["Amplitude_mhcI_affinity"], + pathogen_similarity=self.properties["Pathogensimiliarity_mhcI_affinity_nmers"], + mutation_in_anchor=self.properties["Mutation_in_anchor_netmhcpan"]), + "Recognition_Potential_mhcI_affinity") + self.add_features(self.neoantigen_fitness_calculator.calculate_recognition_potential( + amplitude=self.properties["Amplitude_mhcI_rank_netmhcpan4"], + pathogen_similarity=self.properties["Pathogensimiliarity_mhcI"], + mutation_in_anchor=self.properties["Mutation_in_anchor_netmhcpan"]), + "Recognition_Potential_mhcI_rank_netmhcpan4") + + # recogntion potential with amplitude by affinity and only 9mers considered --> value as published!! + self.add_features(self.neoantigen_fitness_calculator.calculate_recognition_potential( + amplitude=self.properties["Amplitude_mhcI_affinity_9mer_netmhcpan4"], + pathogen_similarity=self.properties["Pathogensimiliarity_mhcI_9mer"], + mutation_in_anchor=self.properties["Mutation_in_anchor_netmhcpan_9mer"], + mhc_affinity_mut=float(self.properties["best_affinity_netmhcpan4_9mer"])), + "Recognition_Potential_mhcI_9mer_affinity") + + score_mutation_mhci = self.properties["best_affinity_netmhcpan4"] + amplitude_mhci = self.properties["Amplitude_mhcI_affinity"] + bdg_cutoff_classical_mhci = 50 + bdg_cutoff_alternative_mhci = 5000 + amplitude_cutoff_mhci = 10 + self.add_features(FeatureLiterature.classify_adn_cdn( + score_mutation=score_mutation_mhci, amplitude=amplitude_mhci, + bdg_cutoff_classical=bdg_cutoff_classical_mhci, bdg_cutoff_alternative=bdg_cutoff_alternative_mhci, + amplitude_cutoff=amplitude_cutoff_mhci, category="CDN"), "CDN_mhcI") + + #TODO:change to netmhcIIpan --> prediction later + score_mutation_mhcii = self.properties["MHC_II_score_.best_prediction."] + amplitude_mhcii = self.properties["Amplitude_mhcII"] + bdg_cutoff_classical_mhcii = 1 + bdg_cutoff_alternative_mhcii = 4 + amplitude_cutoff_mhcii = 4 + self.add_features(FeatureLiterature.classify_adn_cdn( + score_mutation=score_mutation_mhcii, amplitude=amplitude_mhcii, + bdg_cutoff_classical=bdg_cutoff_classical_mhcii, bdg_cutoff_alternative=bdg_cutoff_alternative_mhcii, + amplitude_cutoff=amplitude_cutoff_mhcii, category="CDN"), "CDN_mhcII") + + self.add_features(FeatureLiterature.classify_adn_cdn( + score_mutation=score_mutation_mhci, amplitude=amplitude_mhci, + bdg_cutoff_classical=bdg_cutoff_classical_mhci, bdg_cutoff_alternative=bdg_cutoff_alternative_mhci, + amplitude_cutoff=amplitude_cutoff_mhci, + category="ADN"), "ADN_mhcI") + self.add_features(FeatureLiterature.classify_adn_cdn( + score_mutation=score_mutation_mhcii, amplitude=amplitude_mhcii, + bdg_cutoff_classical=bdg_cutoff_classical_mhcii, bdg_cutoff_alternative=bdg_cutoff_alternative_mhcii, + amplitude_cutoff=amplitude_cutoff_mhcii, category="ADN"), "ADN_mhcII") + + + + # netMHCIIpan predictions + self.predII.main(sequence=xmer_mut, sequence_reference=xmer_wt, alleles=alleles_hlaII, + set_available_mhc=set_available_mhcII) + # netmhcpan4 MUT scores + self.add_features(self.predII.best_mhcII_pan_score, "best%Rank_netmhcIIpan") + self.add_features(self.predII.best_mhcII_pan_epitope, "best_epitope_netmhcIIpan") + self.add_features(self.predII.best_mhcII_pan_allele, "bestHLA_allele_netmhcIIpan") + # netmhcpan4 mut affinity + self.add_features(self.predII.best_mhcII_pan_affinity, "best_affinity_netmhcIIpan") + self.add_features(self.predII.best_mhcII_pan_affinity_epitope, "best_affinity_epitope_netmhcIIpan") + self.add_features(self.predII.best_mhcII_pan_affinity_allele, "bestHLA_allele_affinity_netmhcIIpan") + + # multiplexed representation MUT MHC II + for sc, mn in zip(self.predII.MHCII_score_all_epitopes, self.predII.mean_type): + self.add_features(sc, "MB_score_MHCII_all_epitopes_" + mn) + for sc, mn in zip(self.predII.MHCII_score_top10, self.predII.mean_type): + self.add_features(sc, "MB_score_MHCII_top10_" + mn) + for sc, mn in zip(self.predII.MHCII_score_best_per_alelle, self.predII.mean_type): + self.add_features(sc, "MB_score_MHCII_best_per_alelle_" + mn) + + # rename MB_score_best_per_alelle_harmonic to PHBR (described in Marty et al) + self.properties["PHBR-II"] = self.properties.pop("MB_score_MHCII_best_per_alelle_harmonic") + self.add_features(self.predII.MHCII_epitope_scores, "MB_mhcII_epitope_scores") + self.add_features(self.predII.MHCII_epitope_seqs, "MB_mhcII_epitope_sequences") + self.add_features(self.predII.MHCII_epitope_alleles, "MB_mhcII_alleles") + self.add_features(self.predII.MHCII_number_strong_binders, "MB_number_pep_MHCIIscore<2") + self.add_features(self.predII.MHCII_number_weak_binders, "MB_number_pep_MHCIIscore<10") + + # netmhcIIpan WT scores + self.add_features(self.predII.best_mhcII_pan_score_WT, "best%Rank_netmhcIIpan_WT") + self.add_features(self.predII.best_mhcII_pan_epitope_WT, "best_epitope_netmhcIIpan_WT") + self.add_features(self.predII.best_mhcII_pan_allele_WT, "bestHLA_allele_netmhcIIpan_Wt") + + # netmhcIIpan wt affinity + self.add_features(self.predII.best_mhcII_affinity_WT, "best_affinity_netmhcIIpan_WT") + self.add_features(self.predII.best_mhcII_affinity_epitope_WT, "best_affinity_epitope_netmhcIIpan_WT") + self.add_features(self.predII.best_mhcII_affinity_allele_WT, "bestHLA_allele_affinity_netmhcIIpan_WT") + + # multiplexed representation WT MHC II + for sc, mn in zip(self.predII.MHCII_score_all_epitopes_WT, self.predII.mean_type): + self.add_features(sc, "MB_score_MHCII_all_epitopes_WT_" + mn) + for sc, mn in zip(self.predII.MHCII_score_top10_WT, self.predII.mean_type): + self.add_features(sc, "MB_score_MHCII_top10_WT_" + mn) + for sc, mn in zip(self.predII.MHCII_score_best_per_alelle_WT, self.predII.mean_type): + self.add_features(sc, "MB_score_MHCII_best_per_alelle_WT_" + mn) + + # rename MB_score_best_per_alelle_harmonic to PHBR (described in Marty et al) + if "MB_score_MHCII_best_per_alelle_WT_harmonic" in self.properties: + self.properties["PHBR-II_WT"] = self.properties.pop("MB_score_MHCII_best_per_alelle_WT_harmonic") + self.add_features(self.predII.MHCII_epitope_scores_WT, "MB_mhcII_epitope_scores_WT") + self.add_features(self.predII.MHCII_epitope_seqs_WT, "MB_mhcII_epitope_sequences_WT") + self.add_features(self.predII.MHCII_epitope_alleles_WT, "MB_mhcII_alleles_WT") + self.add_features(self.predII.MHCII_number_strong_binders_WT, "MB_number_pep_MHCIIscore<2_WT") + self.add_features(self.predII.MHCII_number_weak_binders_WT, "MB_number_pep_MHCIIscore<10_WT") + + # dai mhc II affinity + wild_type_netmhciipan4, mutation_netmhciipan4 = properties_manager.get_scores_netmhcpan4_affinity( + properties=self.properties, mhc=MHC_II) + self.add_features( + FeatureLiterature.dai(score_mutation=mutation_netmhciipan4, score_wild_type=wild_type_netmhciipan4), + "DAI_mhcII_affinity") + self.add_features( + FeatureLiterature.dai(score_mutation=mutation_netmhciipan4, score_wild_type=wild_type_netmhciipan4, + affin_filtering=True), + "DAI_mhcII_affinity_aff_filtered") + + # dai mhc II netMHCIIpan score + self.add_features(FeatureLiterature.dai(score_mutation=mutation_mhcii, score_wild_type=wild_type_mhcii), + "DAI_mhcII_netmhcIIpan") + + # dai multiple binding mhc II + wild_type_multiple_binding_ii, mutation_multiple_binding_ii = properties_manager. \ + get_scores_multiple_binding(self.properties, mhc=MHC_II) + self.add_features( + FeatureLiterature.dai(score_mutation=mutation_multiple_binding_ii, + score_wild_type=wild_type_multiple_binding_ii), + "DAI_mhcII_MB") + + # difference number of binders + for threshold in [2, 10]: + num_mutation = self.properties["MB_number_pep_MHCIIscore<{}".format(threshold)] + num_wild_type = self.properties["MB_number_pep_MHCIIscore<{}_WT".format(threshold)] + self.add_features(FeatureLiterature.diff_number_binders( + num_mutation=num_mutation,num_wild_type=num_wild_type), "Diff_numb_epis_mhcII<{}".format(threshold)) + self.add_features(FeatureLiterature.ratio_number_binders( + num_mutation=num_mutation,num_wild_type=num_wild_type), "Ratio_numb_epis_mhcII<{}".format(threshold)) + + # amplitude affinity mhc II + self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( + score_mutation=self.properties["best_affinity_netmhcIIpan"], + score_wild_type = self.properties["best_affinity_netmhcIIpan_WT"], + apply_correction=True), "Amplitude_mhcII_affinity") + + # amplitude multiple binding mhc II + self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( + score_mutation=self.properties["MB_score_MHCII_top10_harmonic"], + score_wild_type = self.properties["MB_score_MHCII_top10_WT_harmonic"]), + "Amplitude_mhcII_mb") + + # amplitude rank score mhc II + self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( + score_mutation=self.properties["best%Rank_netmhcIIpan"], + score_wild_type = self.properties["best%Rank_netmhcIIpan_WT"]), + "Amplitude_mhcII_rank_netmhcpan4") + logger.info("Amplitude mhc II: {}".format(self.properties["Amplitude_mhcII_rank_netmhcpan4"])) + + # priority score + self.add_features(FeatureLiterature.number_of_mismatches( + epitope_wild_type=self.properties["best_epitope_netmhcpan4_WT"], + epitope_mutation=self.properties["best_epitope_netmhcpan4"]), "Number_of_mismatches_mhcI") + self.add_features(FeatureLiterature.number_of_mismatches( + epitope_wild_type=self.properties["best_epitope_netmhcIIpan_WT"], + epitope_mutation=self.properties["best_epitope_netmhcIIpan"]), "Number_of_mismatches_mhcII") + if "mutation_found_in_proteome" not in self.properties: + self.add_features(FeatureLiterature.match_in_proteome( + sequence=self.properties["X..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."], db=db), + "mutation_found_in_proteome") + + + no_mismatch = self.properties["Number_of_mismatches_mhcI"] + score_mut = self.properties["best%Rank_netmhcpan4"] + score_wt = self.properties["best%Rank_netmhcpan4_WT"] + mut_in_prot = self.properties["mutation_found_in_proteome"] + + self.add_features(FeatureLiterature.calc_priority_score( + vaf_tumor=vaf_tumor, vaf_rna=vaf_rna, transcript_expr=transcript_expr, no_mismatch=no_mismatch, + score_mut=score_mut, score_wt=score_wt, mut_in_prot=mut_in_prot), "Priority_score") + + # priority score using multiplexed representation score + score_mut = self.properties["MB_score_top10_harmonic"] + score_wt = self.properties["MB_score_WT_top10_harmonic"] + self.add_features(FeatureLiterature.calc_priority_score( + vaf_tumor=vaf_tumor, vaf_rna=vaf_rna, transcript_expr=transcript_expr, no_mismatch=no_mismatch, + score_mut=score_mut, score_wt=score_wt, mut_in_prot=mut_in_prot), "Priority_score_MB") + + # neoag immunogenicity model + sample_id = properties_manager.get_patient_id(self.properties) + mut_peptide = self.properties["best_affinity_epitope_netmhcpan4"] + score_mut = self.properties["best_affinity_netmhcpan4"] + ref_peptide = self.properties["best_affinity_epitope_netmhcpan4_WT"] + peptide_variant_position = self.properties["pos_MUT_MHCI_affinity_epi"] + self.add_features(self.neoag_calculator.wrapper_neoag( + sample_id=sample_id, mut_peptide=mut_peptide, score_mut=score_mut, ref_peptide=ref_peptide, + peptide_variant_position=peptide_variant_position), "neoag_immunogencity") + + # IEDB immunogenicity only for epitopes with affinity < 500 nM (predicted with netMHCpan) --> in publications + mhci_epitope = self.properties["best_affinity_epitope_netmhcpan4"] + mhci_allele = self.properties["bestHLA_allele_affinity_netmhcpan4"] + mhci_score = self.properties["best_affinity_netmhcpan4"] + mhcii_epitope = self.properties["MHC_II_epitope_.best_prediction."] + mhcii_allele = self.properties["MHC_II_allele_.best_prediction."] + self.add_features(FeatureLiterature.calc_IEDB_immunogenicity( + epitope=mhci_epitope, mhc_allele=mhci_allele, mhc_score=mhci_score), "IEDB_Immunogenicity_mhcI") + self.add_features(FeatureLiterature.calc_IEDB_immunogenicity( + epitope=mhcii_epitope, mhc_allele=mhcii_allele, mhc_score=None), "IEDB_Immunogenicity_mhcII") + self.add_features(FeatureLiterature.calc_IEDB_immunogenicity( + epitope=mhci_epitope, mhc_allele=mhci_allele, mhc_score=mhci_score, affin_filtering=True), + "IEDB_Immunogenicity_mhcI_affinity_filtered") + + self.add_mix_mhc_pred_features(xmer_wt=xmer_wt, xmer_mut=xmer_mut, patient_hlaI=patient_hlaI) + + self.add_mix_mhc2_pred_features(xmer_mut=xmer_mut, xmer_wt=xmer_wt, patient_hlaII=patient_hlaII) + + # dissimilarity to self-proteome + + # neoantigen fitness + mhc_mutation = self.properties["best_affinity_epitope_netmhcpan4"] + mhc_affinity = self.properties["best_affinity_netmhcpan4"] + self.add_features(self.dissimilarity_calculator.calculate_dissimilarity( + mhc_mutation=mhc_mutation, mhc_affinity=mhc_affinity, references=self.references), + "dissimilarity") + self.add_features(self.dissimilarity_calculator.calculate_dissimilarity( + mhc_mutation=mhc_mutation, mhc_affinity=mhc_affinity, references=self.references, + filter_binder=True), "dissimilarity_filter500") + + self.add_vax_rank_features() + + return self.properties + + def add_vax_rank_features(self): + # vaxrank + vaxrankscore = vaxrank.VaxRank() + vaxrankscore.main(mutation_scores=self.properties["MB_affinities"], + expression_score=self.properties["Expression_Mutated_Transcript"]) + self.add_features(vaxrankscore.total_binding_score, "vaxrank_binding_score") + self.add_features(vaxrankscore.ranking_score, "vaxrank_total_score") + + def add_mix_mhc2_pred_features(self, xmer_wt, xmer_mut, patient_hlaII): + # MixMHC2pred + #TODO:remove allele grep and pass as argument + alleles = properties_manager.get_hla_allele(self.properties, patient_hlaII) + self.predpresentation2.main(alleles=alleles, xmer_wt=xmer_wt, xmer_mut=xmer_mut) + self.add_features(self.predpresentation2.all_peptides, "MixMHC2pred_all_peptides") + self.add_features(self.predpresentation2.all_ranks, "MixMHC2pred_all_ranks") + self.add_features(self.predpresentation2.all_alleles, "MixMHC2pred_all_alleles") + self.add_features(self.predpresentation2.best_peptide, "MixMHC2pred_best_peptide") + self.add_features(self.predpresentation2.best_rank, "MixMHC2pred_best_rank") + self.add_features(self.predpresentation2.best_allele, "MixMHC2pred_best_allele") + self.add_features(self.predpresentation2.best_peptide_wt, "MixMHC2pred_best_peptide_wt") + self.add_features(self.predpresentation2.best_rank_wt, "MixMHC2pred_best_rank_wt") + self.add_features(self.predpresentation2.difference_score_mut_wt, "MixMHC2pred_difference_rank_mut_wt") + + def add_mix_mhc_pred_features(self, xmer_wt, xmer_mut, patient_hlaI): + # MixMHCpred + #TODO:remove allele grep and pass as argument + alleles = properties_manager.get_hla_allele(self.properties, patient_hlaI) + self.predpresentation.main(xmer_wt=xmer_wt, xmer_mut=xmer_mut, alleles=alleles) + self.add_features(self.predpresentation.all_peptides, "MixMHCpred_all_peptides") + self.add_features(self.predpresentation.all_scores, "MixMHCpred_all_scores") + self.add_features(self.predpresentation.all_ranks, "MixMHCpred_all_ranks") + self.add_features(self.predpresentation.all_alleles, "MixMHCpred_all_alleles") + self.add_features(self.predpresentation.best_peptide, "MixMHCpred_best_peptide") + self.add_features(self.predpresentation.best_score, "MixMHCpred_best_score") + self.add_features(self.predpresentation.best_rank, "MixMHCpred_best_rank") + self.add_features(self.predpresentation.best_allele, "MixMHCpred_best_allele") + self.add_features(self.predpresentation.best_peptide_wt, "MixMHCpred_best_peptide_wt") + self.add_features(self.predpresentation.best_score_wt, "MixMHCpred_best_score_wt") + self.add_features(self.predpresentation.best_rank_wt, "MixMHCpred_best_rank_wt") + self.add_features(self.predpresentation.difference_score_mut_wt, "MixMHCpred_difference_score_mut_wt") + + def add_tcell_predictor_features(self, gene): + # T cell predictor + substitution = properties_manager.get_substitution(properties=self.properties) + #TODO:remove --> IEDB + epitope = self.properties["MHC_I_epitope_.best_prediction."] + score = self.properties["MHC_I_score_.best_prediction."] + self.add_features(self.tcell_predictor.calculate_tcell_predictor_score( + gene=gene, substitution=substitution, epitope=epitope, score=score), + "Tcell_predictor_score") + epitope = self.properties["best_affinity_epitope_netmhcpan4_9mer"] + score = self.properties["best_affinity_netmhcpan4_9mer"] + self.add_features(self.tcell_predictor.calculate_tcell_predictor_score( + gene=gene, substitution=substitution, epitope=epitope, score=score, threshold=500), + "Tcell_predictor_score_9mersPredict") + + # TODO: remove this function + def add_neoantigen_fitness_features(self, mutation_mhci, mutation_mhcii): + + # neoantigen fitness + self.add_features( + self.neoantigen_fitness_calculator.wrap_pathogen_similarity( + mutation=mutation_mhci, iedb=self.references.iedb), + "Pathogensimiliarity_mhcI") + self.add_features( + self.neoantigen_fitness_calculator.wrap_pathogen_similarity( + mutation=mutation_mhcii, iedb=self.references.iedb), + "Pathogensimiliarity_mhcII") + + score_mutation_mhci = self.properties["MHC_I_score_.best_prediction."] + score_wild_type_mhci = self.properties["MHC_I_score_.WT."] + self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( + score_mutation=score_mutation_mhci, score_wild_type=score_wild_type_mhci), "Amplitude_mhcI") + score_mutation_mhcii = self.properties["MHC_II_score_.best_prediction."] + score_wild_type_mhcii = self.properties["MHC_II_score_.WT."] + self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( + score_mutation=score_mutation_mhcii, score_wild_type=score_wild_type_mhcii), "Amplitude_mhcII") + + # TODO: Franziska, please, review that this is the right value for mutation_in_anchor, + # it is possible that there was a bug here and that it should use "Mutation_in_anchor" + self.add_features(self.neoantigen_fitness_calculator.calculate_recognition_potential( + amplitude=self.properties["Amplitude_mhcI"], + pathogen_similarity=self.properties["Pathogensimiliarity_mhcI"], + mutation_in_anchor=self.properties["Mutation_in_anchor_netmhcpan"]), + "Recognition_Potential_mhcI") + self.add_features(self.neoantigen_fitness_calculator.calculate_recognition_potential( + amplitude=self.properties["Amplitude_mhcII"], + pathogen_similarity=self.properties["Pathogensimiliarity_mhcII"], + mutation_in_anchor=self.properties["Mutation_in_anchor_netmhcpan"]), + "Recognition_Potential_mhcII") + + def add_self_similarity_features(self, mutation_mhci, mutation_mhcii, wild_type_mhci, wild_type_mhcii): + # selfsimilarity + self.add_features(self_similarity.get_self_similarity(mutation=mutation_mhci, wild_type=wild_type_mhci), + "Selfsimilarity_mhcI") + self.add_features(self_similarity.get_self_similarity( + wild_type=wild_type_mhcii, mutation=mutation_mhcii), "Selfsimilarity_mhcII") + self.add_features(self_similarity.is_improved_binder( + score_mutation=self.properties["best%Rank_netmhcpan4"], + score_wild_type=self.properties["best%Rank_netmhcpan4_WT"] + ), "ImprovedBinding_mhcI") + self.add_features(self_similarity.is_improved_binder( + # TODO: conversion from float representation needs to be changed + score_mutation=self.properties["MHC_II_score_.best_prediction."], + score_wild_type=self.properties["MHC_II_score_.WT."] + ), "ImprovedBinding_mhcII") + self.add_features(self_similarity.self_similarity_of_conserved_binder_only( + has_conserved_binder=self.properties["ImprovedBinding_mhcI"], + similarity=self.properties["Selfsimilarity_mhcI"]), + "Selfsimilarity_mhcI_conserved_binder") + + def add_netmhcpan4_features(self): + """ + returns netMHCpan affinity and rank scores of mutated epitope + """ + # netmhcpan4 MUT rank score + self.add_features(self.pred.best4_mhc_score, "best%Rank_netmhcpan4") + self.add_features(self.pred.best4_mhc_epitope, "best_epitope_netmhcpan4") + self.add_features(self.pred.best4_mhc_allele, "bestHLA_allele_netmhcpan4") + self.add_features(self.pred.directed_to_TCR, "directed_to_TCR") + # netmhcpan4 mut affinity + self.add_features(self.pred.best4_affinity, "best_affinity_netmhcpan4") + self.add_features(self.pred.best4_affinity_epitope, "best_affinity_epitope_netmhcpan4") + self.add_features(self.pred.best4_affinity_allele, "bestHLA_allele_affinity_netmhcpan4") + self.add_features(self.pred.best4_affinity_directed_to_TCR, "affinity_directed_to_TCR") + # netMHCpan MUT best 9mer score + self.add_features(self.pred.mhcI_score_9mer, "best%Rank_netmhcpan4_9mer") + self.add_features(self.pred.mhcI_score_epitope_9mer, "best_epitope_netmhcpan4_9mer") + self.add_features(self.pred.mhcI_score_allele_9mer, "bestHLA_allele_netmhcpan4_9mer") + # netmhcpan4 mut best 9mer affinity + self.add_features(self.pred.mhcI_affinity_9mer, "best_affinity_netmhcpan4_9mer") + self.add_features(self.pred.mhcI_affinity_allele_9mer, "bestHLA_allele_affinity_netmhcpan4_9mer") + self.add_features(self.pred.mhcI_affinity_epitope_9mer, "best_affinity_epitope_netmhcpan4_9mer") + + def add_netmhcpan4_WT_features(self): + """ + returns netMHCpan affinity and rank scores of WT epitope + """ + # netmhcpan4 WT best affinity + self.add_features(self.pred.best4_affinity_WT, "best_affinity_netmhcpan4_WT") + self.add_features(self.pred.best4_affinity_epitope_WT, "best_affinity_epitope_netmhcpan4_WT") + self.add_features(self.pred.best4_affinity_allele_WT, "bestHLA_allele_affinity_netmhcpan4_WT") + # netmhcpan4 WT rank score + self.add_features(self.pred.best4_mhc_score_WT, "best%Rank_netmhcpan4_WT") + self.add_features(self.pred.best4_mhc_epitope_WT, "best_epitope_netmhcpan4_WT") + self.add_features(self.pred.best4_mhc_allele_WT, "bestHLA_allele_netmhcpan4_WT") + # netMHCpan WT best 9mer score + self.add_features(self.pred.mhcI_score_9mer_WT, "best%Rank_netmhcpan4_9mer_WT") + self.add_features(self.pred.mhcI_score_epitope_9mer_WT, "best_epitope_netmhcpan4_9mer_WT") + self.add_features(self.pred.mhcI_score_allele_9mer_WT, "bestHLA_allele_netmhcpan4_9mer_Wt") + # netmhcpan4 WT best 9mer affinity + self.add_features(self.pred.mhcI_affinity_9mer_WT, "best_affinity_netmhcpan4_9mer_WT") + self.add_features(self.pred.mhcI_affinity_allele_9mer_WT, "bestHLA_allele_affinity_netmhcpan4_9mer_WT") + self.add_features(self.pred.mhcI_affinity_epitope_9mer_WT, "best_affinity_epitope_netmhcpan4_9mer_WT") + + def add_position_mutation(self, epi_wt, epi_mut, epi_wt_9mer, epi_mut_9mer): + """ + returns position of mutation for best affinity epitope across all lengths and 9mer + :return: + """ + self.add_features(self_similarity.position_of_mutation_epitope( + wild_type=epi_wt, mutation=epi_mut), "pos_MUT_MHCI_affinity_epi") + self.add_features(self_similarity.position_of_mutation_epitope( + wild_type=epi_wt_9mer, mutation=epi_mut_9mer), + "pos_MUT_MHCI_affinity_epi_9mer") + + def add_mutation_in_anchor(self): + """ + returns if mutation is in anchor position for best affinity epitope over all lengths and best 9mer affinity + :return: + """ + self.add_features(self_similarity.position_in_anchor_position( + position_mhci=self.properties["pos_MUT_MHCI_affinity_epi"], + peptide_length=self.properties["best_epitope_netmhcpan4"]), + "Mutation_in_anchor_netmhcpan") + self.add_features(self_similarity.position_in_anchor_position( + position_mhci=self.properties["pos_MUT_MHCI_affinity_epi_9mer"], + peptide_length=9), + "Mutation_in_anchor_netmhcpan_9mer") + + def add_DAI_mhcI(self, aff_wt, aff_mut, sc_wt, sc_mut): + """ + returns DAI based on affinity and based on rank score + :return: + """ + # DAI with affinity values + self.add_features( + FeatureLiterature.dai(score_mutation=aff_mut, + score_wild_type=aff_wt, affin_filtering=True), + "DAI_affinity") + # DAI wiht rank scores by netmhcpan4 + self.add_features( + FeatureLiterature.dai(score_mutation=sc_mut, + score_wild_type=sc_wt), + "DAI_rank_netmhcpan4") + + def add_multiple_binding_features(self): + # multiplexed representation MUT + for sc, mn in zip(self.pred.MHC_score_all_epitopes, self.pred.mean_type): + self.add_features(sc, "MB_score_all_epitopes_" + mn) + for sc, mn in zip(self.pred.MHC_score_top10, self.pred.mean_type): + self.add_features(sc, "MB_score_top10_" + mn) + for sc, mn in zip(self.pred.MHC_score_best_per_alelle, self.pred.mean_type): + self.add_features(sc, "MB_score_best_per_alelle_" + mn) + # rename MB_score_best_per_alelle_harmonic to PHBR (described in Marty et al) + self.properties["PHBR-I"] = self.properties.pop("MB_score_best_per_alelle_harmonic") + self.add_features(self.pred.MHC_epitope_scores, "MB_epitope_scores") + self.add_features(self.pred.MHC_epitope_seqs, "MB_epitope_sequences") + self.add_features(self.pred.MHC_epitope_alleles, "MB_alleles") + self.add_features(self.pred.MHC_number_strong_binders, "MB_number_pep_MHCscore<1") + self.add_features(self.pred.MHC_number_weak_binders, "MB_number_pep_MHCscore<2") + # generator rate + self.add_features(self.pred.epitope_affinities, "MB_affinities") + self.add_features(self.pred.generator_rate, "Generator_rate") + # multiplexed representation WT + self.add_features(self.pred.MHC_epitope_scores_WT, "MB_epitope_WT_scores") + self.add_features(self.pred.MHC_epitope_seqs_WT, "MB_epitope_WT_sequences") + self.add_features(self.pred.MHC_epitope_alleles_WT, "MB_alleles_WT") + for sc, mn in zip(self.pred.MHC_score_top10_WT, self.pred.mean_type): + self.add_features(sc, "MB_score_WT_top10_" + mn) + for sc, mn in zip(self.pred.MHC_score_all_epitopes_WT, self.pred.mean_type): + self.add_features(sc, "MB_score_WT_all_epitopes_" + mn) + for sc, mn in zip(self.pred.MHC_score_best_per_alelle_WT, self.pred.mean_type): + self.add_features(sc, "MB_score_WT_best_per_alelle_" + mn) + self.properties["PHBR-I_WT"] = self.properties.pop("MB_score_WT_best_per_alelle_harmonic") + self.add_features(self.pred.MHC_number_strong_binders_WT, "MB_number_pep_WT_MHCscore<1") + self.add_features(self.pred.MHC_number_weak_binders_WT, "MB_number_pep_WT_MHCscore<2") + # generator rate + self.add_features(self.pred.epitope_affinities_WT, "MB_affinities_WT") + self.add_features(self.pred.generator_rate_WT, "Generator_rate_WT") + + def add_multiple_binding_numdiff(self): + """ + returns difference and ratio of # epitopes with rank scores < 1 or 2 for mutant and wt sequence + """ + for threshold in [1, 2]: + num_mutation = self.properties["MB_number_pep_MHCscore<{}".format(threshold)] + num_wild_type = self.properties["MB_number_pep_WT_MHCscore<{}".format(threshold)] + self.add_features(FeatureLiterature.diff_number_binders( + num_mutation=num_mutation,num_wild_type=num_wild_type), "Diff_numb_epis_<{}".format(threshold)) + self.add_features(FeatureLiterature.ratio_number_binders( + num_mutation=num_mutation, num_wild_type=num_wild_type), "Ratio_numb_epis_<{}".format(threshold)) + + def add_multiple_binding_scorediff(self, mut_score, wt_score): + """ + returns DAI and amplitude with multiple binding score + """ + self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( + score_mutation=mut_score, score_wild_type=wt_score), + "Amplitude_mhcI_MB") + self.add_features( + FeatureLiterature.dai(score_mutation=mut_score, score_wild_type=wt_score), + "DAI_mhcI_MB") + + + def add_provean_score_features(self): + # PROVEAN score + ucsc_id = self.provean_annotator.build_ucsc_id_plus_position( + substitution=self.properties["substitution"], ucsc_id=self.properties["UCSC_transcript"]) + self.add_features(ucsc_id, "UCSC_ID_position") + self.add_features(self.provean_annotator.get_provean_annotation( + mutated_aminoacid=self.properties['MUT_AA'], ucsc_id_position=ucsc_id), + "PROVEAN_score") + + def add_aminoacid_index_features(self, aaindex1_dict, aaindex2_dict): + # amino acid index + mutation_aminoacid = self.properties["MUT_AA"] + wild_type_aminoacid = self.properties["WT_AA"] + for k in aaindex1_dict: + self.add_features(aaindex1_dict[k].get(wild_type_aminoacid, "NA"), "{}_{}".format(k, "wt")) + self.add_features(aaindex1_dict[k].get(mutation_aminoacid, "NA"), "{}_{}".format(k, "mut")) + for k in aaindex2_dict: + self.add_features(aaindex2_dict[k].get(wild_type_aminoacid, {}).get(mutation_aminoacid, "NA"), k) + + def add_aminoacid_frequency_features(self, aa_freq_dict, mutation_mhci, nmer_freq_dict): + # amino acid frequency + substitution = self.properties["substitution"] + mutated_aminoacid = FeatureLiterature.wt_mut_aa(substitution=substitution, mut="mut") + self.add_features(mutated_aminoacid, "MUT_AA") + self.add_features(FeatureLiterature.wt_mut_aa(substitution=substitution, mut="wt"), "WT_AA") + self.add_features(freq_score.freq_aa(mutated_aminoacid=mutated_aminoacid, dict_freq=aa_freq_dict), + "Frequency_mutated_AA") + self.add_features(freq_score.freq_prod_4mer(mutation=mutation_mhci, dict_freq=aa_freq_dict), + "Product_Frequency_4mer") + self.add_features(freq_score.freq_4mer(mutation=mutation_mhci, dict_freq=nmer_freq_dict), "Frequency_of_4mer") + + def add_expression_features(self, rna_avail, tumour_content): + # expression + transcript_expression = self.properties["transcript_expression"] + patient_id = properties_manager.get_patient_id(self.properties) + vaf_tumor = self.properties["VAF_in_tumor"] + vaf_rna = vaf_tumor if rna_avail.get(patient_id, "False") == "False" else \ + self.properties.get("VAF_in_RNA", vaf_tumor) + + self.add_features(FeatureLiterature.rna_expression_mutation( + transcript_expression=transcript_expression, vaf_rna=vaf_rna), "Expression_Mutated_Transcript") + + expression_mutated_transcript = self.properties.get("Expression_Mutated_Transcript") + self.add_features(FeatureLiterature.expression_mutation_tc( + transcript_expression=expression_mutated_transcript, patient_id=patient_id, tumour_content_dict=tumour_content), + "Expression_Mutated_Transcript_tumor_content") + + def add_differential_agretopicity_index_features(self, mutation_mhci, mutation_mhcii, wild_type_mhci, + wild_type_mhcii): + # differential agretopicity index + self.add_features( + FeatureLiterature.dai(score_mutation=mutation_mhci, score_wild_type=wild_type_mhci), "DAI_mhcI") + self.add_features( + FeatureLiterature.dai(score_mutation=mutation_mhcii, score_wild_type=wild_type_mhcii), "DAI_mhcII") + + + def add_differential_expression_features(self, gene, ref_dat): + # differential expression + expression_tumor = self.properties["transcript_expression"] + expression_reference = differential_expression.add_rna_reference(gene, ref_dat, 0) + expression_reference_sum = differential_expression.add_rna_reference(gene, ref_dat, 2) + expression_reference_sd = differential_expression.add_rna_reference(gene, ref_dat, 1) + self.add_features(expression_reference, "mean_ref_expression") + self.add_features(expression_reference_sd, "sd_ref_expression") + self.add_features(expression_reference_sum, "sum_ref_expression") + self.add_features(differential_expression.fold_change( + expression_tumor=expression_tumor, expression_reference=expression_reference), "log2_fc_tumour_ref") + self.add_features(differential_expression.percentile_calc( + expression_tumor=expression_tumor, expression_reference_sum=expression_reference_sum), + "percentile_tumour_ref") + self.add_features(differential_expression.pepper_calc( + expression_tumor=expression_tumor, expression_reference=expression_reference, + expression_reference_sd=expression_reference_sd), "DE_pepper") From ef39a710c579cf1ac385f05e56d2acffba81bdc9 Mon Sep 17 00:00:00 2001 From: Lang Date: Mon, 29 Jun 2020 11:13:19 +0200 Subject: [PATCH 063/105] add_DAI_mhcI: calculation with and without MHC I affinity filtering --- input/epitope.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/input/epitope.py b/input/epitope.py index e88f9372..bb8bb08c 100755 --- a/input/epitope.py +++ b/input/epitope.py @@ -585,6 +585,10 @@ def add_DAI_mhcI(self, aff_wt, aff_mut, sc_wt, sc_mut): self.add_features( FeatureLiterature.dai(score_mutation=aff_mut, score_wild_type=aff_wt, affin_filtering=True), + "DAI_affinity_filtered") + self.add_features( + FeatureLiterature.dai(score_mutation=aff_mut, + score_wild_type=aff_wt), "DAI_affinity") # DAI wiht rank scores by netmhcpan4 self.add_features( From 4a4ad8080742a8341ae77aed6e960b1f684032b7 Mon Sep 17 00:00:00 2001 From: Lang Date: Mon, 29 Jun 2020 11:25:41 +0200 Subject: [PATCH 064/105] add get_scores_netmhcpan4_affinity_9mer --- input/helpers/properties_manager.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/input/helpers/properties_manager.py b/input/helpers/properties_manager.py index a7ebee42..29f239aa 100755 --- a/input/helpers/properties_manager.py +++ b/input/helpers/properties_manager.py @@ -54,6 +54,10 @@ def get_scores_netmhcpan4_affinity(properties, mhc): raise INPuTInputParametersException("Bad MHC value: {}".format(mhc)) return wild_type, mutation +def get_scores_netmhcpan4_affinity_9mer(properties): + mutation = properties["best_affinity_netmhcpan4_9mer"] + wild_type = properties["best_affinity_netmhcpan4_9mer_WT"] + return wild_type, mutation def get_scores_netmhcpan4_ranks(properties, mhc): if mhc == MHC_I: From b2fcc96da779fef7f29de6413baa06846072ea51 Mon Sep 17 00:00:00 2001 From: Lang Date: Mon, 29 Jun 2020 11:59:07 +0200 Subject: [PATCH 065/105] add get_netmhcpan4_epitopes_rank --- input/helpers/properties_manager.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/input/helpers/properties_manager.py b/input/helpers/properties_manager.py index 29f239aa..598a43eb 100755 --- a/input/helpers/properties_manager.py +++ b/input/helpers/properties_manager.py @@ -80,6 +80,10 @@ def get_netmhcpan4_epitopes(properties, nine_mer=False): wild_type = properties["best_affinity_epitope_netmhcpan4_WT"] return wild_type, mutation +def get_netmhcpan4_epitopes_rank(properties): + mutation = properties["best_epitope_netmhcpan4"] + wild_type = properties["best_epitope_netmhcpan4_WT"] + return wild_type, mutation def get_hla_allele(props, hla_patient_dict): ''' returns hla allele of patients given in hla_file From edc6c8749e1922b5778f2f18ea4324b0ccadad91 Mon Sep 17 00:00:00 2001 From: Lang Date: Mon, 29 Jun 2020 12:19:24 +0200 Subject: [PATCH 066/105] add pathogensimilarity based on best rank epitope --- input/epitope.py | 122 ++++++++++++++++++++++++++++++----------------- 1 file changed, 77 insertions(+), 45 deletions(-) diff --git a/input/epitope.py b/input/epitope.py index bb8bb08c..d2857342 100755 --- a/input/epitope.py +++ b/input/epitope.py @@ -102,23 +102,38 @@ def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aa self.add_netmhcpan4_WT_features() self.add_multiple_binding_features() self.add_multiple_binding_numdiff() - wild_type_netmhcpan4, mutation_netmhcpan4 = properties_manager.get_netmhcpan4_epitopes( + # epitope sequences + epitope_wt_affinity, epitope_mut_affinity = properties_manager.get_netmhcpan4_epitopes( properties=self.properties) - wild_type_netmhcpan4_9mer, mutation_netmhcpan4_9mer = properties_manager.get_netmhcpan4_epitopes( + epitope_wt_affinity_9mer, epitope_mut_affinitiy_9mer = properties_manager.get_netmhcpan4_epitopes( properties=self.properties, nine_mer=True) - wild_type_netmhcpan4_affinity, mutation_netmhcpan4_affinity = properties_manager.get_scores_netmhcpan4_affinity( + epitope_wt_rank, epitope_mut_rank = properties_manager.get_netmhcpan4_epitopes_rank( + properties=self.properties) + # MHC affinities/scores + affinity_wt, affinity_mut = properties_manager.get_scores_netmhcpan4_affinity( properties=self.properties, mhc=MHC_I) - wild_type_netmhcpan4_rank, mutation_netmhcpan4_rank = properties_manager \ + affinity_wt_9mer, affinity_mut_9mer = properties_manager.get_scores_netmhcpan4_affinity_9mer( + properties=self.properties) + mhc_rank_wt, mhc_rank_mut = properties_manager \ .get_scores_netmhcpan4_ranks(properties=self.properties, mhc=MHC_I) wild_type_multiple_binding_score, mutation_multiple_binding_score = properties_manager. \ get_scores_multiple_binding(self.properties, mhc=MHC_I) self.add_multiple_binding_scorediff(mut_score=mutation_multiple_binding_score, wt_score=wild_type_multiple_binding_score) # position of mutation - self.add_position_mutation(epi_wt=wild_type_netmhcpan4, epi_mut=mutation_netmhcpan4, - epi_wt_9mer=wild_type_netmhcpan4_9mer, epi_mut_9mer=mutation_netmhcpan4_9mer) + self.add_position_mutation(epi_wt=epitope_wt_affinity, epi_mut=epitope_mut_affinity, + epi_wt_9mer=epitope_wt_affinity_9mer, epi_mut_9mer=epitope_mut_affinitiy_9mer) # mutation in anchor self.add_mutation_in_anchor() + # DAI + self.add_DAI_mhcI(aff_wt=affinity_wt, aff_mut=affinity_mut, + sc_wt=mhc_rank_wt, sc_mut=mhc_rank_mut) + # amplitude + self.add_amplitude_mhcI(aff_wt=affinity_wt, aff_mut=affinity_mut, + sc_wt=mhc_rank_wt, sc_mut=mhc_rank_mut, + aff_wt_9mer=affinity_wt_9mer, aff_mut_9mer=affinity_mut_9mer) + # pathogensimilarity + self.add_pathogensimilarity(epi_mut_9mer=epitope_mut_affinitiy_9mer, epi_mut=epitope_mut_affinity, epi_mut_rank=epitope_mut_rank) #TODO: change to netmhcpan self.add_self_similarity_features(mutation_mhci, mutation_mhcii, wild_type_mhci, wild_type_mhcii) @@ -127,43 +142,6 @@ def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aa self.add_tcell_predictor_features(gene) - #TODO:summarise into function - # DAI with affinity values - self.add_features( - FeatureLiterature.dai(score_mutation=mutation_netmhcpan4_affinity, score_wild_type=wild_type_netmhcpan4_affinity), - "DAI_affinity") - # DAI wiht rank scores by netmhcpan4 - self.add_features( - FeatureLiterature.dai(score_mutation=mutation_netmhcpan4_rank, score_wild_type=wild_type_netmhcpan4_rank), - "DAI_rank_netmhcpan4") - - #TODO:summarise into function - # Amplitude with affinity values - self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( - score_mutation=mutation_netmhcpan4_affinity, score_wild_type=wild_type_netmhcpan4_affinity, - apply_correction=True), "Amplitude_mhcI_affinity") - - # Amplitude with rank by netmhcpan4 - self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( - score_mutation=mutation_netmhcpan4_rank, score_wild_type=wild_type_netmhcpan4_rank), - "Amplitude_mhcI_rank_netmhcpan4") - - # Amplitude based on best affinity prediction restricted to 9mers - self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( - score_mutation=self.properties["best_affinity_netmhcpan4_9mer"], - score_wild_type = self.properties["best_affinity_netmhcpan4_9mer_WT"], - apply_correction=True), "Amplitude_mhcI_affinity_9mer_netmhcpan4") - - #TODO:summarise into function - self.add_features( - self.neoantigen_fitness_calculator.wrap_pathogen_similarity( - mutation=mutation_netmhcpan4_9mer, iedb=self.references.iedb), - "Pathogensimiliarity_mhcI_9mer") - self.add_features( - self.neoantigen_fitness_calculator.wrap_pathogen_similarity( - mutation=mutation_netmhcpan4, iedb=self.references.iedb), - "Pathogensimiliarity_mhcI_affinity_nmers") - # recogntion potential with amplitude by affinity and netmhcpan4 score self.add_features(self.neoantigen_fitness_calculator.calculate_recognition_potential( amplitude=self.properties["Amplitude_mhcI_affinity"], @@ -565,7 +543,6 @@ def add_position_mutation(self, epi_wt, epi_mut, epi_wt_9mer, epi_mut_9mer): def add_mutation_in_anchor(self): """ returns if mutation is in anchor position for best affinity epitope over all lengths and best 9mer affinity - :return: """ self.add_features(self_similarity.position_in_anchor_position( position_mhci=self.properties["pos_MUT_MHCI_affinity_epi"], @@ -579,7 +556,6 @@ def add_mutation_in_anchor(self): def add_DAI_mhcI(self, aff_wt, aff_mut, sc_wt, sc_mut): """ returns DAI based on affinity and based on rank score - :return: """ # DAI with affinity values self.add_features( @@ -596,6 +572,62 @@ def add_DAI_mhcI(self, aff_wt, aff_mut, sc_wt, sc_mut): score_wild_type=sc_wt), "DAI_rank_netmhcpan4") + def add_amplitude_mhcI(self, aff_wt, aff_mut, sc_wt, sc_mut, aff_wt_9mer, aff_mut_9mer): + """ + ratio in MHC binding based on affinity (all length), rank score, affintiy (9mer) + """ + self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( + score_mutation=aff_mut, score_wild_type=aff_wt, + apply_correction=True), "Amplitude_mhcI_affinity") + # Amplitude with rank by netmhcpan4 + self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( + score_mutation=sc_mut, score_wild_type=sc_wt), + "Amplitude_mhcI_rank_netmhcpan4") + # Amplitude based on best affinity prediction restricted to 9mers + self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( + score_mutation=aff_mut_9mer, score_wild_type=aff_wt_9mer, + apply_correction=True), "Amplitude_mhcI_affinity_9mer_netmhcpan4") + + def add_pathogensimilarity(self, epi_mut_9mer, epi_mut, epi_mut_rank): + """ + pathogensimilarity for best affinity (all length), best affinity (9mer), rank score + """ + self.add_features( + self.neoantigen_fitness_calculator.wrap_pathogen_similarity( + mutation=epi_mut_9mer, iedb=self.references.iedb), + "Pathogensimiliarity_mhcI_9mer") + self.add_features( + self.neoantigen_fitness_calculator.wrap_pathogen_similarity( + mutation=epi_mut_rank, iedb=self.references.iedb), + "Pathogensimiliarity_mhcI_rank") + self.add_features( + self.neoantigen_fitness_calculator.wrap_pathogen_similarity( + mutation=epi_mut, iedb=self.references.iedb), + "Pathogensimiliarity_mhcI_affinity_nmers") + + def add_recognition_potential(self): + """ + recognition potential for affinity (all lengths), affinity (9mers) + """ + # recogntion potential with amplitude by affinity and netmhcpan4 score + self.add_features(self.neoantigen_fitness_calculator.calculate_recognition_potential( + amplitude=self.properties["Amplitude_mhcI_affinity"], + pathogen_similarity=self.properties["Pathogensimiliarity_mhcI_affinity_nmers"], + mutation_in_anchor=self.properties["Mutation_in_anchor_netmhcpan"]), + "Recognition_Potential_mhcI_affinity") + self.add_features(self.neoantigen_fitness_calculator.calculate_recognition_potential( + amplitude=self.properties["Amplitude_mhcI_rank_netmhcpan4"], + pathogen_similarity=self.properties["Pathogensimiliarity_mhcI"], + mutation_in_anchor=self.properties["Mutation_in_anchor_netmhcpan"]), + "Recognition_Potential_mhcI_rank_netmhcpan4") + # recogntion potential with amplitude by affinity and only 9mers considered --> value as published!! + self.add_features(self.neoantigen_fitness_calculator.calculate_recognition_potential( + amplitude=self.properties["Amplitude_mhcI_affinity_9mer_netmhcpan4"], + pathogen_similarity=self.properties["Pathogensimiliarity_mhcI_9mer"], + mutation_in_anchor=self.properties["Mutation_in_anchor_netmhcpan_9mer"], + mhc_affinity_mut=float(self.properties["best_affinity_netmhcpan4_9mer"])), + "Recognition_Potential_mhcI_9mer_affinity") + def add_multiple_binding_features(self): # multiplexed representation MUT for sc, mn in zip(self.pred.MHC_score_all_epitopes, self.pred.mean_type): From c49404b9913b6b1419e7b54d382d6c6a06815ba4 Mon Sep 17 00:00:00 2001 From: Lang Date: Mon, 29 Jun 2020 12:33:21 +0200 Subject: [PATCH 067/105] add mutation_in_anchor based on best rank epitope --- input/epitope.py | 18 +++++++++++++----- 1 file changed, 13 insertions(+), 5 deletions(-) diff --git a/input/epitope.py b/input/epitope.py index d2857342..423922df 100755 --- a/input/epitope.py +++ b/input/epitope.py @@ -122,7 +122,8 @@ def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aa self.add_multiple_binding_scorediff(mut_score=mutation_multiple_binding_score, wt_score=wild_type_multiple_binding_score) # position of mutation self.add_position_mutation(epi_wt=epitope_wt_affinity, epi_mut=epitope_mut_affinity, - epi_wt_9mer=epitope_wt_affinity_9mer, epi_mut_9mer=epitope_mut_affinitiy_9mer) + epi_wt_9mer=epitope_wt_affinity_9mer, epi_mut_9mer=epitope_mut_affinitiy_9mer, + epi_mut_rank=epitope_mut_rank, epi_wt_rank=epitope_wt_rank) # mutation in anchor self.add_mutation_in_anchor() # DAI @@ -529,7 +530,7 @@ def add_netmhcpan4_WT_features(self): self.add_features(self.pred.mhcI_affinity_allele_9mer_WT, "bestHLA_allele_affinity_netmhcpan4_9mer_WT") self.add_features(self.pred.mhcI_affinity_epitope_9mer_WT, "best_affinity_epitope_netmhcpan4_9mer_WT") - def add_position_mutation(self, epi_wt, epi_mut, epi_wt_9mer, epi_mut_9mer): + def add_position_mutation(self, epi_wt, epi_mut, epi_wt_9mer, epi_mut_9mer, epi_mut_rank, epi_wt_rank): """ returns position of mutation for best affinity epitope across all lengths and 9mer :return: @@ -539,6 +540,9 @@ def add_position_mutation(self, epi_wt, epi_mut, epi_wt_9mer, epi_mut_9mer): self.add_features(self_similarity.position_of_mutation_epitope( wild_type=epi_wt_9mer, mutation=epi_mut_9mer), "pos_MUT_MHCI_affinity_epi_9mer") + self.add_features(self_similarity.position_of_mutation_epitope( + wild_type=epi_wt_rank, mutation=epi_mut_rank), + "pos_MUT_MHCI_rank_epi") def add_mutation_in_anchor(self): """ @@ -546,12 +550,16 @@ def add_mutation_in_anchor(self): """ self.add_features(self_similarity.position_in_anchor_position( position_mhci=self.properties["pos_MUT_MHCI_affinity_epi"], - peptide_length=self.properties["best_epitope_netmhcpan4"]), + peptide_length=len(self.properties["best_affinity_epitope_netmhcpan4"])), "Mutation_in_anchor_netmhcpan") self.add_features(self_similarity.position_in_anchor_position( position_mhci=self.properties["pos_MUT_MHCI_affinity_epi_9mer"], peptide_length=9), "Mutation_in_anchor_netmhcpan_9mer") + self.add_features(self_similarity.position_in_anchor_position( + position_mhci=self.properties["pos_MUT_MHCI_affinity_epi_9mer"], + peptide_length=len(self.properties["best_epitope_netmhcpan4"])), + "Mutation_in_anchor_netmhcpan_rank") def add_DAI_mhcI(self, aff_wt, aff_mut, sc_wt, sc_mut): """ @@ -617,8 +625,8 @@ def add_recognition_potential(self): "Recognition_Potential_mhcI_affinity") self.add_features(self.neoantigen_fitness_calculator.calculate_recognition_potential( amplitude=self.properties["Amplitude_mhcI_rank_netmhcpan4"], - pathogen_similarity=self.properties["Pathogensimiliarity_mhcI"], - mutation_in_anchor=self.properties["Mutation_in_anchor_netmhcpan"]), + pathogen_similarity=self.properties["Pathogensimiliarity_mhcI_rank"], + mutation_in_anchor=self.properties["Mutation_in_anchor_netmhcpan_rank"]), "Recognition_Potential_mhcI_rank_netmhcpan4") # recogntion potential with amplitude by affinity and only 9mers considered --> value as published!! self.add_features(self.neoantigen_fitness_calculator.calculate_recognition_potential( From caded72efd68793a71bffde38044f68718f8b913 Mon Sep 17 00:00:00 2001 From: Lang Date: Mon, 29 Jun 2020 15:50:56 +0200 Subject: [PATCH 068/105] add get_netmhcIIpan_epitopes --- input/helpers/properties_manager.py | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/input/helpers/properties_manager.py b/input/helpers/properties_manager.py index 598a43eb..b08d0e04 100755 --- a/input/helpers/properties_manager.py +++ b/input/helpers/properties_manager.py @@ -18,7 +18,7 @@ def get_substitution(properties): def get_mutation_aminoacid(properties): return properties["MUT_AA"] - +#TODO:to be removed def get_epitopes(properties, mhc): if mhc == MHC_I: mutation = properties["MHC_I_epitope_.best_prediction."] @@ -42,7 +42,6 @@ def get_scores_multiple_binding(properties, mhc): raise INPuTInputParametersException("Bad MHC value: {}".format(mhc)) return wild_type, mutation - def get_scores_netmhcpan4_affinity(properties, mhc): if mhc == MHC_I: mutation = properties["best_affinity_netmhcpan4"] @@ -85,6 +84,15 @@ def get_netmhcpan4_epitopes_rank(properties): wild_type = properties["best_epitope_netmhcpan4_WT"] return wild_type, mutation +def get_netmhcIIpan_epitopes(properties, affinity=False): + if affinity: + mutation = properties["best_affinity_epitope_netmhcIIpan"] + wild_type = properties["best_affinity_epitope_netmhcIIpan_WT"] + else: + mutation = properties["best_epitope_netmhcIIpan"] + wild_type = properties["best_epitope_netmhcIIpan_WT"] + return wild_type, mutation + def get_hla_allele(props, hla_patient_dict): ''' returns hla allele of patients given in hla_file ''' From ccbe557c0b2e2a87cd122f8c7e65303db3376e1c Mon Sep 17 00:00:00 2001 From: Lang Date: Tue, 30 Jun 2020 08:03:59 +0200 Subject: [PATCH 069/105] remove function get_epitopes --- input/helpers/properties_manager.py | 23 +++++++++-------------- 1 file changed, 9 insertions(+), 14 deletions(-) diff --git a/input/helpers/properties_manager.py b/input/helpers/properties_manager.py index b08d0e04..6f57e695 100755 --- a/input/helpers/properties_manager.py +++ b/input/helpers/properties_manager.py @@ -3,6 +3,7 @@ PATIENT_ID = "patient.id" + def get_gene(properties): if "gene.x" in properties: gene = properties["gene.x"] @@ -18,18 +19,6 @@ def get_substitution(properties): def get_mutation_aminoacid(properties): return properties["MUT_AA"] -#TODO:to be removed -def get_epitopes(properties, mhc): - if mhc == MHC_I: - mutation = properties["MHC_I_epitope_.best_prediction."] - wild_type = properties["MHC_I_epitope_.WT."] - elif mhc == MHC_II: - mutation = properties["MHC_II_epitope_.best_prediction."] - wild_type = properties["MHC_II_epitope_.WT."] - else: - raise INPuTInputParametersException("Bad MHC value: {}".format(mhc)) - return wild_type, mutation - def get_scores_multiple_binding(properties, mhc): if mhc == MHC_I: @@ -42,6 +31,7 @@ def get_scores_multiple_binding(properties, mhc): raise INPuTInputParametersException("Bad MHC value: {}".format(mhc)) return wild_type, mutation + def get_scores_netmhcpan4_affinity(properties, mhc): if mhc == MHC_I: mutation = properties["best_affinity_netmhcpan4"] @@ -53,11 +43,13 @@ def get_scores_netmhcpan4_affinity(properties, mhc): raise INPuTInputParametersException("Bad MHC value: {}".format(mhc)) return wild_type, mutation + def get_scores_netmhcpan4_affinity_9mer(properties): mutation = properties["best_affinity_netmhcpan4_9mer"] wild_type = properties["best_affinity_netmhcpan4_9mer_WT"] return wild_type, mutation + def get_scores_netmhcpan4_ranks(properties, mhc): if mhc == MHC_I: mutation = properties["best%Rank_netmhcpan4"] @@ -79,12 +71,14 @@ def get_netmhcpan4_epitopes(properties, nine_mer=False): wild_type = properties["best_affinity_epitope_netmhcpan4_WT"] return wild_type, mutation + def get_netmhcpan4_epitopes_rank(properties): mutation = properties["best_epitope_netmhcpan4"] wild_type = properties["best_epitope_netmhcpan4_WT"] return wild_type, mutation -def get_netmhcIIpan_epitopes(properties, affinity=False): + +def get_netmhciipan_epitopes(properties, affinity=False): if affinity: mutation = properties["best_affinity_epitope_netmhcIIpan"] wild_type = properties["best_affinity_epitope_netmhcIIpan_WT"] @@ -93,6 +87,7 @@ def get_netmhcIIpan_epitopes(properties, affinity=False): wild_type = properties["best_epitope_netmhcIIpan_WT"] return wild_type, mutation + def get_hla_allele(props, hla_patient_dict): ''' returns hla allele of patients given in hla_file ''' @@ -101,4 +96,4 @@ def get_hla_allele(props, hla_patient_dict): def get_patient_id(props): - return props.get(PATIENT_ID) \ No newline at end of file + return props.get(PATIENT_ID) From f10fe034a992f47b621e8078acde1711aa7576b9 Mon Sep 17 00:00:00 2001 From: Lang Date: Tue, 30 Jun 2020 08:35:46 +0200 Subject: [PATCH 070/105] add float conversion for affinity filtering --- input/neoantigen_fitness/neoantigen_fitness.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/input/neoantigen_fitness/neoantigen_fitness.py b/input/neoantigen_fitness/neoantigen_fitness.py index 8845bdfe..7a306aaf 100755 --- a/input/neoantigen_fitness/neoantigen_fitness.py +++ b/input/neoantigen_fitness/neoantigen_fitness.py @@ -70,7 +70,7 @@ def calculate_recognition_potential( try: candidate_recognition_potential = str(float(amplitude) * float(pathogen_similarity)) if mhc_affinity_mut: - if mutation_in_anchor == "0" and mhc_affinity_mut < 500: + if mutation_in_anchor == "0" and float(mhc_affinity_mut) < 500.0: recognition_potential = candidate_recognition_potential else: if mutation_in_anchor == "0": From c68e60792f29dc9524553cf40531d8d56c24390d Mon Sep 17 00:00:00 2001 From: Lang Date: Tue, 30 Jun 2020 09:14:18 +0200 Subject: [PATCH 071/105] major re-structuring --- input/epitope.py | 687 +++++++++++++++++++++++------------------------ 1 file changed, 341 insertions(+), 346 deletions(-) diff --git a/input/epitope.py b/input/epitope.py index 423922df..a1ba717b 100755 --- a/input/epitope.py +++ b/input/epitope.py @@ -65,41 +65,37 @@ def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aa logger.info(xmer_mut) gene = properties_manager.get_gene(properties=self.properties) + patient_id = properties_manager.get_patient_id(self.properties) vaf_tumor = self.properties.get("VAF_in_tumor", "NA") - vaf_rna = self.properties.get("VAF_in_RNA", "NA") + vaf_rna = vaf_tumor if rna_avail.get(patient_id, "False") == "False" else \ + self.properties.get("VAF_in_RNA", vaf_tumor) transcript_expr = self.properties["transcript_expression"] alleles = properties_manager.get_hla_allele(self.properties, patient_hlaI) - alleles_hlaII = properties_manager.get_hla_allele(self.properties, patient_hlaII) + alleles_hlaii = properties_manager.get_hla_allele(self.properties, patient_hlaII) + substitution = properties_manager.get_substitution(properties=self.properties) + + mutated_aminoacid = FeatureLiterature.wt_mut_aa(substitution=substitution, mut="mut") + self.add_features(mutated_aminoacid, "MUT_AA") + wt_aminoacid = FeatureLiterature.wt_mut_aa(substitution=substitution, mut="wt") + self.add_features(wt_aminoacid, "WT_AA") - #TODO: remove --> IEDB - wild_type_mhci, mutation_mhci = properties_manager.get_epitopes( - properties=self.properties, mhc=MHC_I) - wild_type_mhcii, mutation_mhcii = properties_manager.get_epitopes( - properties=self.properties, mhc=MHC_II) - ''' - self.add_features(self_similarity.position_of_mutation_epitope( - wild_type=wild_type_mhci, mutation=mutation_mhci), "pos_MUT_MHCI") - self.add_features(self_similarity.position_of_mutation_epitope( - wild_type=wild_type_mhcii, mutation=mutation_mhcii), "pos_MUT_MHCII") - self.add_features(self_similarity.position_in_anchor_position( - position_mhci=self.properties["pos_MUT_MHCI"], - peptide_length=self.properties["MHC_I_peptide_length_.best_prediction."] - ), "Mutation_in_anchor") - self.add_differential_agretopicity_index_features(mutation_mhci, mutation_mhcii, wild_type_mhci, - wild_type_mhcii) - ''' # MHC binding independent features - self.add_expression_features(rna_avail, tumour_content) - self.add_differential_expression_features(gene, ref_dat) - self.add_aminoacid_frequency_features(aa_freq_dict, mutation_mhci, nmer_freq_dict) - self.add_aminoacid_index_features(aaindex1_dict, aaindex2_dict) + self.add_expression_features(tumour_content, vaf_rna=vaf_rna, + transcript_expression=transcript_expr, patient_id=patient_id) + self.add_differential_expression_features(gene, ref_dat, expression_tumor=transcript_expr) + self.add_aminoacid_index_features(aaindex1_dict, aaindex2_dict, + mutation_aminoacid=mutated_aminoacid, wild_type_aminoacid=wt_aminoacid) self.add_provean_score_features() + if "mutation_found_in_proteome" not in self.properties: + self.add_features(FeatureLiterature.match_in_proteome( + sequence=self.properties["X..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."], db=db), + "mutation_found_in_proteome") # HLA I predictions: NetMHCpan self.pred.main(xmer_mut=xmer_mut, xmer_wt=xmer_wt, alleles=alleles, set_available_mhc=set_available_mhc) self.add_netmhcpan4_features() - self.add_netmhcpan4_WT_features() + self.add_netmhcpan4_wt_features() self.add_multiple_binding_features() self.add_multiple_binding_numdiff() # epitope sequences @@ -119,7 +115,8 @@ def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aa wild_type_multiple_binding_score, mutation_multiple_binding_score = properties_manager. \ get_scores_multiple_binding(self.properties, mhc=MHC_I) - self.add_multiple_binding_scorediff(mut_score=mutation_multiple_binding_score, wt_score=wild_type_multiple_binding_score) + self.add_multiple_binding_scorediff(mut_score=mutation_multiple_binding_score, + wt_score=wild_type_multiple_binding_score) # position of mutation self.add_position_mutation(epi_wt=epitope_wt_affinity, epi_mut=epitope_mut_affinity, epi_wt_9mer=epitope_wt_affinity_9mer, epi_mut_9mer=epitope_mut_affinitiy_9mer, @@ -127,250 +124,84 @@ def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aa # mutation in anchor self.add_mutation_in_anchor() # DAI - self.add_DAI_mhcI(aff_wt=affinity_wt, aff_mut=affinity_mut, + self.add_dai_mhci(aff_wt=affinity_wt, aff_mut=affinity_mut, sc_wt=mhc_rank_wt, sc_mut=mhc_rank_mut) # amplitude - self.add_amplitude_mhcI(aff_wt=affinity_wt, aff_mut=affinity_mut, + self.add_amplitude_mhci(aff_wt=affinity_wt, aff_mut=affinity_mut, sc_wt=mhc_rank_wt, sc_mut=mhc_rank_mut, aff_wt_9mer=affinity_wt_9mer, aff_mut_9mer=affinity_mut_9mer) # pathogensimilarity - self.add_pathogensimilarity(epi_mut_9mer=epitope_mut_affinitiy_9mer, epi_mut=epitope_mut_affinity, epi_mut_rank=epitope_mut_rank) - - #TODO: change to netmhcpan - self.add_self_similarity_features(mutation_mhci, mutation_mhcii, wild_type_mhci, wild_type_mhcii) - # TODO: remove --> IEDB - self.add_neoantigen_fitness_features(mutation_mhci, mutation_mhcii) - - self.add_tcell_predictor_features(gene) - - # recogntion potential with amplitude by affinity and netmhcpan4 score - self.add_features(self.neoantigen_fitness_calculator.calculate_recognition_potential( - amplitude=self.properties["Amplitude_mhcI_affinity"], - pathogen_similarity=self.properties["Pathogensimiliarity_mhcI_affinity_nmers"], - mutation_in_anchor=self.properties["Mutation_in_anchor_netmhcpan"]), - "Recognition_Potential_mhcI_affinity") - self.add_features(self.neoantigen_fitness_calculator.calculate_recognition_potential( - amplitude=self.properties["Amplitude_mhcI_rank_netmhcpan4"], - pathogen_similarity=self.properties["Pathogensimiliarity_mhcI"], - mutation_in_anchor=self.properties["Mutation_in_anchor_netmhcpan"]), - "Recognition_Potential_mhcI_rank_netmhcpan4") - - # recogntion potential with amplitude by affinity and only 9mers considered --> value as published!! - self.add_features(self.neoantigen_fitness_calculator.calculate_recognition_potential( - amplitude=self.properties["Amplitude_mhcI_affinity_9mer_netmhcpan4"], - pathogen_similarity=self.properties["Pathogensimiliarity_mhcI_9mer"], - mutation_in_anchor=self.properties["Mutation_in_anchor_netmhcpan_9mer"], - mhc_affinity_mut=float(self.properties["best_affinity_netmhcpan4_9mer"])), - "Recognition_Potential_mhcI_9mer_affinity") - - score_mutation_mhci = self.properties["best_affinity_netmhcpan4"] - amplitude_mhci = self.properties["Amplitude_mhcI_affinity"] - bdg_cutoff_classical_mhci = 50 - bdg_cutoff_alternative_mhci = 5000 - amplitude_cutoff_mhci = 10 - self.add_features(FeatureLiterature.classify_adn_cdn( - score_mutation=score_mutation_mhci, amplitude=amplitude_mhci, - bdg_cutoff_classical=bdg_cutoff_classical_mhci, bdg_cutoff_alternative=bdg_cutoff_alternative_mhci, - amplitude_cutoff=amplitude_cutoff_mhci, category="CDN"), "CDN_mhcI") - - #TODO:change to netmhcIIpan --> prediction later - score_mutation_mhcii = self.properties["MHC_II_score_.best_prediction."] - amplitude_mhcii = self.properties["Amplitude_mhcII"] - bdg_cutoff_classical_mhcii = 1 - bdg_cutoff_alternative_mhcii = 4 - amplitude_cutoff_mhcii = 4 - self.add_features(FeatureLiterature.classify_adn_cdn( - score_mutation=score_mutation_mhcii, amplitude=amplitude_mhcii, - bdg_cutoff_classical=bdg_cutoff_classical_mhcii, bdg_cutoff_alternative=bdg_cutoff_alternative_mhcii, - amplitude_cutoff=amplitude_cutoff_mhcii, category="CDN"), "CDN_mhcII") - - self.add_features(FeatureLiterature.classify_adn_cdn( - score_mutation=score_mutation_mhci, amplitude=amplitude_mhci, - bdg_cutoff_classical=bdg_cutoff_classical_mhci, bdg_cutoff_alternative=bdg_cutoff_alternative_mhci, - amplitude_cutoff=amplitude_cutoff_mhci, - category="ADN"), "ADN_mhcI") - self.add_features(FeatureLiterature.classify_adn_cdn( - score_mutation=score_mutation_mhcii, amplitude=amplitude_mhcii, - bdg_cutoff_classical=bdg_cutoff_classical_mhcii, bdg_cutoff_alternative=bdg_cutoff_alternative_mhcii, - amplitude_cutoff=amplitude_cutoff_mhcii, category="ADN"), "ADN_mhcII") - - + self.add_pathogensimilarity(epi_mut_9mer=epitope_mut_affinitiy_9mer, epi_mut=epitope_mut_affinity, + epi_mut_rank=epitope_mut_rank) + # recognition potential + self.add_recognition_potential(aff_mut_9mer=affinity_mut_9mer) + self.add_adncdn_mhci(score_mut=affinity_mut) + # T cell predictor + self.add_tcell_predictor_features(gene, substitution=substitution, affinity=affinity_mut_9mer, + epitope=epitope_mut_affinitiy_9mer) + self.add_aminoacid_frequency_features(aa_freq_dict=aa_freq_dict, mutation_mhci=epitope_mut_rank, + nmer_freq_dict=nmer_freq_dict, mutated_aminoacid=mutated_aminoacid) # netMHCIIpan predictions - self.predII.main(sequence=xmer_mut, sequence_reference=xmer_wt, alleles=alleles_hlaII, + self.predII.main(sequence=xmer_mut, sequence_reference=xmer_wt, alleles=alleles_hlaii, set_available_mhc=set_available_mhcII) - # netmhcpan4 MUT scores - self.add_features(self.predII.best_mhcII_pan_score, "best%Rank_netmhcIIpan") - self.add_features(self.predII.best_mhcII_pan_epitope, "best_epitope_netmhcIIpan") - self.add_features(self.predII.best_mhcII_pan_allele, "bestHLA_allele_netmhcIIpan") - # netmhcpan4 mut affinity - self.add_features(self.predII.best_mhcII_pan_affinity, "best_affinity_netmhcIIpan") - self.add_features(self.predII.best_mhcII_pan_affinity_epitope, "best_affinity_epitope_netmhcIIpan") - self.add_features(self.predII.best_mhcII_pan_affinity_allele, "bestHLA_allele_affinity_netmhcIIpan") - - # multiplexed representation MUT MHC II - for sc, mn in zip(self.predII.MHCII_score_all_epitopes, self.predII.mean_type): - self.add_features(sc, "MB_score_MHCII_all_epitopes_" + mn) - for sc, mn in zip(self.predII.MHCII_score_top10, self.predII.mean_type): - self.add_features(sc, "MB_score_MHCII_top10_" + mn) - for sc, mn in zip(self.predII.MHCII_score_best_per_alelle, self.predII.mean_type): - self.add_features(sc, "MB_score_MHCII_best_per_alelle_" + mn) - - # rename MB_score_best_per_alelle_harmonic to PHBR (described in Marty et al) - self.properties["PHBR-II"] = self.properties.pop("MB_score_MHCII_best_per_alelle_harmonic") - self.add_features(self.predII.MHCII_epitope_scores, "MB_mhcII_epitope_scores") - self.add_features(self.predII.MHCII_epitope_seqs, "MB_mhcII_epitope_sequences") - self.add_features(self.predII.MHCII_epitope_alleles, "MB_mhcII_alleles") - self.add_features(self.predII.MHCII_number_strong_binders, "MB_number_pep_MHCIIscore<2") - self.add_features(self.predII.MHCII_number_weak_binders, "MB_number_pep_MHCIIscore<10") - - # netmhcIIpan WT scores - self.add_features(self.predII.best_mhcII_pan_score_WT, "best%Rank_netmhcIIpan_WT") - self.add_features(self.predII.best_mhcII_pan_epitope_WT, "best_epitope_netmhcIIpan_WT") - self.add_features(self.predII.best_mhcII_pan_allele_WT, "bestHLA_allele_netmhcIIpan_Wt") - - # netmhcIIpan wt affinity - self.add_features(self.predII.best_mhcII_affinity_WT, "best_affinity_netmhcIIpan_WT") - self.add_features(self.predII.best_mhcII_affinity_epitope_WT, "best_affinity_epitope_netmhcIIpan_WT") - self.add_features(self.predII.best_mhcII_affinity_allele_WT, "bestHLA_allele_affinity_netmhcIIpan_WT") - - # multiplexed representation WT MHC II - for sc, mn in zip(self.predII.MHCII_score_all_epitopes_WT, self.predII.mean_type): - self.add_features(sc, "MB_score_MHCII_all_epitopes_WT_" + mn) - for sc, mn in zip(self.predII.MHCII_score_top10_WT, self.predII.mean_type): - self.add_features(sc, "MB_score_MHCII_top10_WT_" + mn) - for sc, mn in zip(self.predII.MHCII_score_best_per_alelle_WT, self.predII.mean_type): - self.add_features(sc, "MB_score_MHCII_best_per_alelle_WT_" + mn) - - # rename MB_score_best_per_alelle_harmonic to PHBR (described in Marty et al) - if "MB_score_MHCII_best_per_alelle_WT_harmonic" in self.properties: - self.properties["PHBR-II_WT"] = self.properties.pop("MB_score_MHCII_best_per_alelle_WT_harmonic") - self.add_features(self.predII.MHCII_epitope_scores_WT, "MB_mhcII_epitope_scores_WT") - self.add_features(self.predII.MHCII_epitope_seqs_WT, "MB_mhcII_epitope_sequences_WT") - self.add_features(self.predII.MHCII_epitope_alleles_WT, "MB_mhcII_alleles_WT") - self.add_features(self.predII.MHCII_number_strong_binders_WT, "MB_number_pep_MHCIIscore<2_WT") - self.add_features(self.predII.MHCII_number_weak_binders_WT, "MB_number_pep_MHCIIscore<10_WT") - - # dai mhc II affinity - wild_type_netmhciipan4, mutation_netmhciipan4 = properties_manager.get_scores_netmhcpan4_affinity( + self.add_netmhciipan_features() + self.add_netmhciipan_wt_features() + self.add_multiple_binding_mhcii_features() + # MHC II scores + affinity_wt_mhcii, affinity_mut_mhcii = properties_manager.get_scores_netmhcpan4_affinity( + properties=self.properties, mhc=MHC_II) + rank_wt_mhcii, rank_mut_mhcii = properties_manager.get_scores_netmhcpan4_ranks( properties=self.properties, mhc=MHC_II) - self.add_features( - FeatureLiterature.dai(score_mutation=mutation_netmhciipan4, score_wild_type=wild_type_netmhciipan4), - "DAI_mhcII_affinity") - self.add_features( - FeatureLiterature.dai(score_mutation=mutation_netmhciipan4, score_wild_type=wild_type_netmhciipan4, - affin_filtering=True), - "DAI_mhcII_affinity_aff_filtered") - - # dai mhc II netMHCIIpan score - self.add_features(FeatureLiterature.dai(score_mutation=mutation_mhcii, score_wild_type=wild_type_mhcii), - "DAI_mhcII_netmhcIIpan") - - # dai multiple binding mhc II wild_type_multiple_binding_ii, mutation_multiple_binding_ii = properties_manager. \ get_scores_multiple_binding(self.properties, mhc=MHC_II) - self.add_features( - FeatureLiterature.dai(score_mutation=mutation_multiple_binding_ii, - score_wild_type=wild_type_multiple_binding_ii), - "DAI_mhcII_MB") - - # difference number of binders - for threshold in [2, 10]: - num_mutation = self.properties["MB_number_pep_MHCIIscore<{}".format(threshold)] - num_wild_type = self.properties["MB_number_pep_MHCIIscore<{}_WT".format(threshold)] - self.add_features(FeatureLiterature.diff_number_binders( - num_mutation=num_mutation,num_wild_type=num_wild_type), "Diff_numb_epis_mhcII<{}".format(threshold)) - self.add_features(FeatureLiterature.ratio_number_binders( - num_mutation=num_mutation,num_wild_type=num_wild_type), "Ratio_numb_epis_mhcII<{}".format(threshold)) - - # amplitude affinity mhc II - self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( - score_mutation=self.properties["best_affinity_netmhcIIpan"], - score_wild_type = self.properties["best_affinity_netmhcIIpan_WT"], - apply_correction=True), "Amplitude_mhcII_affinity") - - # amplitude multiple binding mhc II - self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( - score_mutation=self.properties["MB_score_MHCII_top10_harmonic"], - score_wild_type = self.properties["MB_score_MHCII_top10_WT_harmonic"]), - "Amplitude_mhcII_mb") - - # amplitude rank score mhc II - self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( - score_mutation=self.properties["best%Rank_netmhcIIpan"], - score_wild_type = self.properties["best%Rank_netmhcIIpan_WT"]), - "Amplitude_mhcII_rank_netmhcpan4") - logger.info("Amplitude mhc II: {}".format(self.properties["Amplitude_mhcII_rank_netmhcpan4"])) - + # MHC II epitopes + epitope_wt_rank_mhcii, epitope_mut_rank_mhcii = properties_manager.get_netmhciipan_epitopes( + self.properties, affinity=False) + epitope_wt_affinity_mhcii, epitope_mut_affinity_mhcii = properties_manager.get_netmhciipan_epitopes( + self.properties, affinity=True) + # DAI MHC II + self.add_dai_mhcii(aff_mut=affinity_mut_mhcii, aff_wt=affinity_wt_mhcii, + rank_mut=rank_mut_mhcii, rank_wt=rank_wt_mhcii) + # difference number epitopes + self.add_multiple_binding_numdiff_mhcii() + # difference scores mb + self.add_multiple_binding_scorediff_mhcii(mut_score=mutation_multiple_binding_ii, + wt_score=wild_type_multiple_binding_ii) + # amplitude + self.add_amplitude_mhcii(aff_wt=affinity_wt_mhcii, aff_mut=affinity_mut_mhcii, + sc_wt=rank_wt_mhcii, sc_mut=rank_mut_mhcii) + # recognition potential MHC II + self.add_recognition_potential_mhcii(epitope_mut_mhcii=epitope_mut_affinity_mhcii) + # ADN/CDN for MHC II + self.add_adncdn_mhcii(score_mut=rank_mut_mhcii) + # self-similarity + self.add_self_similarity_features(epitope_mut_mhci=epitope_mut_rank, epitope_wt_mhci=epitope_wt_rank, + rank_mut_mhci=mhc_rank_mut, rank_wt_mhci=mhc_rank_wt, + epitope_mut_mhcii=epitope_mut_rank_mhcii, + epitope_wt_mhcii=epitope_wt_rank_mhcii, + rank_mut_mhcii=rank_mut_mhcii, rank_wt_mhcii=rank_wt_mhcii) + # number of mismatches + self.add_add_number_mismatches(epi_wt_mhci=epitope_wt_rank, epi_mut_mhci=epitope_mut_rank, + epi_wt_mhcii=epitope_mut_rank_mhcii, epi_mut_mhcii=epitope_wt_rank_mhcii) # priority score - self.add_features(FeatureLiterature.number_of_mismatches( - epitope_wild_type=self.properties["best_epitope_netmhcpan4_WT"], - epitope_mutation=self.properties["best_epitope_netmhcpan4"]), "Number_of_mismatches_mhcI") - self.add_features(FeatureLiterature.number_of_mismatches( - epitope_wild_type=self.properties["best_epitope_netmhcIIpan_WT"], - epitope_mutation=self.properties["best_epitope_netmhcIIpan"]), "Number_of_mismatches_mhcII") - if "mutation_found_in_proteome" not in self.properties: - self.add_features(FeatureLiterature.match_in_proteome( - sequence=self.properties["X..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."], db=db), - "mutation_found_in_proteome") - - - no_mismatch = self.properties["Number_of_mismatches_mhcI"] - score_mut = self.properties["best%Rank_netmhcpan4"] - score_wt = self.properties["best%Rank_netmhcpan4_WT"] - mut_in_prot = self.properties["mutation_found_in_proteome"] - - self.add_features(FeatureLiterature.calc_priority_score( - vaf_tumor=vaf_tumor, vaf_rna=vaf_rna, transcript_expr=transcript_expr, no_mismatch=no_mismatch, - score_mut=score_mut, score_wt=score_wt, mut_in_prot=mut_in_prot), "Priority_score") - - # priority score using multiplexed representation score - score_mut = self.properties["MB_score_top10_harmonic"] - score_wt = self.properties["MB_score_WT_top10_harmonic"] - self.add_features(FeatureLiterature.calc_priority_score( - vaf_tumor=vaf_tumor, vaf_rna=vaf_rna, transcript_expr=transcript_expr, no_mismatch=no_mismatch, - score_mut=score_mut, score_wt=score_wt, mut_in_prot=mut_in_prot), "Priority_score_MB") - + self.add_priority_score(rank_mut=mhc_rank_mut, rank_wt=mhc_rank_wt, + mb_mut=mutation_multiple_binding_score, mb_wt=wild_type_multiple_binding_score, + vaf_transcr=vaf_rna, vaf_tum=vaf_tumor, expr=transcript_expr) # neoag immunogenicity model - sample_id = properties_manager.get_patient_id(self.properties) - mut_peptide = self.properties["best_affinity_epitope_netmhcpan4"] - score_mut = self.properties["best_affinity_netmhcpan4"] - ref_peptide = self.properties["best_affinity_epitope_netmhcpan4_WT"] - peptide_variant_position = self.properties["pos_MUT_MHCI_affinity_epi"] - self.add_features(self.neoag_calculator.wrapper_neoag( - sample_id=sample_id, mut_peptide=mut_peptide, score_mut=score_mut, ref_peptide=ref_peptide, - peptide_variant_position=peptide_variant_position), "neoag_immunogencity") - - # IEDB immunogenicity only for epitopes with affinity < 500 nM (predicted with netMHCpan) --> in publications - mhci_epitope = self.properties["best_affinity_epitope_netmhcpan4"] - mhci_allele = self.properties["bestHLA_allele_affinity_netmhcpan4"] - mhci_score = self.properties["best_affinity_netmhcpan4"] - mhcii_epitope = self.properties["MHC_II_epitope_.best_prediction."] - mhcii_allele = self.properties["MHC_II_allele_.best_prediction."] - self.add_features(FeatureLiterature.calc_IEDB_immunogenicity( - epitope=mhci_epitope, mhc_allele=mhci_allele, mhc_score=mhci_score), "IEDB_Immunogenicity_mhcI") - self.add_features(FeatureLiterature.calc_IEDB_immunogenicity( - epitope=mhcii_epitope, mhc_allele=mhcii_allele, mhc_score=None), "IEDB_Immunogenicity_mhcII") - self.add_features(FeatureLiterature.calc_IEDB_immunogenicity( - epitope=mhci_epitope, mhc_allele=mhci_allele, mhc_score=mhci_score, affin_filtering=True), - "IEDB_Immunogenicity_mhcI_affinity_filtered") - - self.add_mix_mhc_pred_features(xmer_wt=xmer_wt, xmer_mut=xmer_mut, patient_hlaI=patient_hlaI) - + self.add_neoag(sample_id=patient_id, mut_peptide=epitope_mut_affinity, score_mut=affinity_mut, + ref_peptide=epitope_wt_affinity) + # IEDB immunogenicity + self.add_iedb_immunogenicity(epitope_mhci=epitope_mut_affinity, affinity_mhci=affinity_mut, + epitope_mhcii=epitope_mut_rank_mhcii) + # MixMHCpred + self.add_mix_mhc_pred_features(xmer_wt=xmer_wt, xmer_mut=xmer_mut, patient_hlai=patient_hlaI) + # MixMHC2pred self.add_mix_mhc2_pred_features(xmer_mut=xmer_mut, xmer_wt=xmer_wt, patient_hlaII=patient_hlaII) - # dissimilarity to self-proteome - - # neoantigen fitness - mhc_mutation = self.properties["best_affinity_epitope_netmhcpan4"] - mhc_affinity = self.properties["best_affinity_netmhcpan4"] - self.add_features(self.dissimilarity_calculator.calculate_dissimilarity( - mhc_mutation=mhc_mutation, mhc_affinity=mhc_affinity, references=self.references), - "dissimilarity") - self.add_features(self.dissimilarity_calculator.calculate_dissimilarity( - mhc_mutation=mhc_mutation, mhc_affinity=mhc_affinity, references=self.references, - filter_binder=True), "dissimilarity_filter500") - + self.add_dissimilarity(epitope_mhci=epitope_mut_affinity, affinity_mhci=affinity_mut, + epitope_mhcii=epitope_mut_affinity_mhcii, affinity_mhcii=affinity_mut_mhcii) + # vaxrank self.add_vax_rank_features() return self.properties @@ -385,7 +216,7 @@ def add_vax_rank_features(self): def add_mix_mhc2_pred_features(self, xmer_wt, xmer_mut, patient_hlaII): # MixMHC2pred - #TODO:remove allele grep and pass as argument + # TODO:remove allele grep and pass as argument alleles = properties_manager.get_hla_allele(self.properties, patient_hlaII) self.predpresentation2.main(alleles=alleles, xmer_wt=xmer_wt, xmer_mut=xmer_mut) self.add_features(self.predpresentation2.all_peptides, "MixMHC2pred_all_peptides") @@ -398,10 +229,10 @@ def add_mix_mhc2_pred_features(self, xmer_wt, xmer_mut, patient_hlaII): self.add_features(self.predpresentation2.best_rank_wt, "MixMHC2pred_best_rank_wt") self.add_features(self.predpresentation2.difference_score_mut_wt, "MixMHC2pred_difference_rank_mut_wt") - def add_mix_mhc_pred_features(self, xmer_wt, xmer_mut, patient_hlaI): + def add_mix_mhc_pred_features(self, xmer_wt, xmer_mut, patient_hlai): # MixMHCpred - #TODO:remove allele grep and pass as argument - alleles = properties_manager.get_hla_allele(self.properties, patient_hlaI) + # TODO:remove allele grep and pass as argument + alleles = properties_manager.get_hla_allele(self.properties, patient_hlai) self.predpresentation.main(xmer_wt=xmer_wt, xmer_mut=xmer_mut, alleles=alleles) self.add_features(self.predpresentation.all_peptides, "MixMHCpred_all_peptides") self.add_features(self.predpresentation.all_scores, "MixMHCpred_all_scores") @@ -416,70 +247,28 @@ def add_mix_mhc_pred_features(self, xmer_wt, xmer_mut, patient_hlaI): self.add_features(self.predpresentation.best_rank_wt, "MixMHCpred_best_rank_wt") self.add_features(self.predpresentation.difference_score_mut_wt, "MixMHCpred_difference_score_mut_wt") - def add_tcell_predictor_features(self, gene): + def add_tcell_predictor_features(self, gene, substitution, epitope, affinity): # T cell predictor - substitution = properties_manager.get_substitution(properties=self.properties) - #TODO:remove --> IEDB - epitope = self.properties["MHC_I_epitope_.best_prediction."] - score = self.properties["MHC_I_score_.best_prediction."] self.add_features(self.tcell_predictor.calculate_tcell_predictor_score( - gene=gene, substitution=substitution, epitope=epitope, score=score), - "Tcell_predictor_score") - epitope = self.properties["best_affinity_epitope_netmhcpan4_9mer"] - score = self.properties["best_affinity_netmhcpan4_9mer"] + gene=gene, substitution=substitution, epitope=epitope, score=affinity), + "Tcell_predictor_score_unfiltered") self.add_features(self.tcell_predictor.calculate_tcell_predictor_score( - gene=gene, substitution=substitution, epitope=epitope, score=score, threshold=500), + gene=gene, substitution=substitution, epitope=epitope, score=affinity, threshold=500), "Tcell_predictor_score_9mersPredict") - # TODO: remove this function - def add_neoantigen_fitness_features(self, mutation_mhci, mutation_mhcii): - - # neoantigen fitness - self.add_features( - self.neoantigen_fitness_calculator.wrap_pathogen_similarity( - mutation=mutation_mhci, iedb=self.references.iedb), - "Pathogensimiliarity_mhcI") - self.add_features( - self.neoantigen_fitness_calculator.wrap_pathogen_similarity( - mutation=mutation_mhcii, iedb=self.references.iedb), - "Pathogensimiliarity_mhcII") - - score_mutation_mhci = self.properties["MHC_I_score_.best_prediction."] - score_wild_type_mhci = self.properties["MHC_I_score_.WT."] - self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( - score_mutation=score_mutation_mhci, score_wild_type=score_wild_type_mhci), "Amplitude_mhcI") - score_mutation_mhcii = self.properties["MHC_II_score_.best_prediction."] - score_wild_type_mhcii = self.properties["MHC_II_score_.WT."] - self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( - score_mutation=score_mutation_mhcii, score_wild_type=score_wild_type_mhcii), "Amplitude_mhcII") - - # TODO: Franziska, please, review that this is the right value for mutation_in_anchor, - # it is possible that there was a bug here and that it should use "Mutation_in_anchor" - self.add_features(self.neoantigen_fitness_calculator.calculate_recognition_potential( - amplitude=self.properties["Amplitude_mhcI"], - pathogen_similarity=self.properties["Pathogensimiliarity_mhcI"], - mutation_in_anchor=self.properties["Mutation_in_anchor_netmhcpan"]), - "Recognition_Potential_mhcI") - self.add_features(self.neoantigen_fitness_calculator.calculate_recognition_potential( - amplitude=self.properties["Amplitude_mhcII"], - pathogen_similarity=self.properties["Pathogensimiliarity_mhcII"], - mutation_in_anchor=self.properties["Mutation_in_anchor_netmhcpan"]), - "Recognition_Potential_mhcII") - - def add_self_similarity_features(self, mutation_mhci, mutation_mhcii, wild_type_mhci, wild_type_mhcii): + def add_self_similarity_features(self, epitope_mut_mhci, epitope_wt_mhci, epitope_mut_mhcii, epitope_wt_mhcii, + rank_mut_mhci, rank_wt_mhci, rank_mut_mhcii, rank_wt_mhcii): # selfsimilarity - self.add_features(self_similarity.get_self_similarity(mutation=mutation_mhci, wild_type=wild_type_mhci), + self.add_features(self_similarity.get_self_similarity(mutation=epitope_mut_mhci, wild_type=epitope_wt_mhci), "Selfsimilarity_mhcI") self.add_features(self_similarity.get_self_similarity( - wild_type=wild_type_mhcii, mutation=mutation_mhcii), "Selfsimilarity_mhcII") + wild_type=epitope_wt_mhcii, mutation=epitope_mut_mhcii), "Selfsimilarity_mhcII") self.add_features(self_similarity.is_improved_binder( - score_mutation=self.properties["best%Rank_netmhcpan4"], - score_wild_type=self.properties["best%Rank_netmhcpan4_WT"] + score_mutation=rank_mut_mhci, score_wild_type=rank_wt_mhci ), "ImprovedBinding_mhcI") self.add_features(self_similarity.is_improved_binder( # TODO: conversion from float representation needs to be changed - score_mutation=self.properties["MHC_II_score_.best_prediction."], - score_wild_type=self.properties["MHC_II_score_.WT."] + score_mutation=rank_mut_mhcii, score_wild_type=rank_wt_mhcii ), "ImprovedBinding_mhcII") self.add_features(self_similarity.self_similarity_of_conserved_binder_only( has_conserved_binder=self.properties["ImprovedBinding_mhcI"], @@ -488,7 +277,7 @@ def add_self_similarity_features(self, mutation_mhci, mutation_mhcii, wild_type_ def add_netmhcpan4_features(self): """ - returns netMHCpan affinity and rank scores of mutated epitope + returns netMHCpan affinity and rank scores of mutated epitope """ # netmhcpan4 MUT rank score self.add_features(self.pred.best4_mhc_score, "best%Rank_netmhcpan4") @@ -509,7 +298,7 @@ def add_netmhcpan4_features(self): self.add_features(self.pred.mhcI_affinity_allele_9mer, "bestHLA_allele_affinity_netmhcpan4_9mer") self.add_features(self.pred.mhcI_affinity_epitope_9mer, "best_affinity_epitope_netmhcpan4_9mer") - def add_netmhcpan4_WT_features(self): + def add_netmhcpan4_wt_features(self): """ returns netMHCpan affinity and rank scores of WT epitope """ @@ -561,7 +350,7 @@ def add_mutation_in_anchor(self): peptide_length=len(self.properties["best_epitope_netmhcpan4"])), "Mutation_in_anchor_netmhcpan_rank") - def add_DAI_mhcI(self, aff_wt, aff_mut, sc_wt, sc_mut): + def add_dai_mhci(self, aff_wt, aff_mut, sc_wt, sc_mut): """ returns DAI based on affinity and based on rank score """ @@ -580,7 +369,7 @@ def add_DAI_mhcI(self, aff_wt, aff_mut, sc_wt, sc_mut): score_wild_type=sc_wt), "DAI_rank_netmhcpan4") - def add_amplitude_mhcI(self, aff_wt, aff_mut, sc_wt, sc_mut, aff_wt_9mer, aff_mut_9mer): + def add_amplitude_mhci(self, aff_wt, aff_mut, sc_wt, sc_mut, aff_wt_9mer, aff_mut_9mer): """ ratio in MHC binding based on affinity (all length), rank score, affintiy (9mer) """ @@ -613,7 +402,7 @@ def add_pathogensimilarity(self, epi_mut_9mer, epi_mut, epi_mut_rank): mutation=epi_mut, iedb=self.references.iedb), "Pathogensimiliarity_mhcI_affinity_nmers") - def add_recognition_potential(self): + def add_recognition_potential(self, aff_mut_9mer): """ recognition potential for affinity (all lengths), affinity (9mers) """ @@ -633,9 +422,27 @@ def add_recognition_potential(self): amplitude=self.properties["Amplitude_mhcI_affinity_9mer_netmhcpan4"], pathogen_similarity=self.properties["Pathogensimiliarity_mhcI_9mer"], mutation_in_anchor=self.properties["Mutation_in_anchor_netmhcpan_9mer"], - mhc_affinity_mut=float(self.properties["best_affinity_netmhcpan4_9mer"])), + mhc_affinity_mut=aff_mut_9mer), "Recognition_Potential_mhcI_9mer_affinity") + def add_adncdn_mhci(self, score_mut): + """ + return if alternative or classical defined binder + """ + amplitude_mhci = self.properties["Amplitude_mhcI_affinity"] + bdg_cutoff_classical_mhci = 50 + bdg_cutoff_alternative_mhci = 5000 + amplitude_cutoff_mhci = 10 + self.add_features(FeatureLiterature.classify_adn_cdn( + score_mutation=score_mut, amplitude=amplitude_mhci, + bdg_cutoff_classical=bdg_cutoff_classical_mhci, bdg_cutoff_alternative=bdg_cutoff_alternative_mhci, + amplitude_cutoff=amplitude_cutoff_mhci, category="CDN"), "CDN_mhcI") + self.add_features(FeatureLiterature.classify_adn_cdn( + score_mutation=score_mut, amplitude=amplitude_mhci, + bdg_cutoff_classical=bdg_cutoff_classical_mhci, bdg_cutoff_alternative=bdg_cutoff_alternative_mhci, + amplitude_cutoff=amplitude_cutoff_mhci, + category="ADN"), "ADN_mhcI") + def add_multiple_binding_features(self): # multiplexed representation MUT for sc, mn in zip(self.pred.MHC_score_all_epitopes, self.pred.mean_type): @@ -679,7 +486,7 @@ def add_multiple_binding_numdiff(self): num_mutation = self.properties["MB_number_pep_MHCscore<{}".format(threshold)] num_wild_type = self.properties["MB_number_pep_WT_MHCscore<{}".format(threshold)] self.add_features(FeatureLiterature.diff_number_binders( - num_mutation=num_mutation,num_wild_type=num_wild_type), "Diff_numb_epis_<{}".format(threshold)) + num_mutation=num_mutation, num_wild_type=num_wild_type), "Diff_numb_epis_<{}".format(threshold)) self.add_features(FeatureLiterature.ratio_number_binders( num_mutation=num_mutation, num_wild_type=num_wild_type), "Ratio_numb_epis_<{}".format(threshold)) @@ -694,6 +501,213 @@ def add_multiple_binding_scorediff(self, mut_score, wt_score): FeatureLiterature.dai(score_mutation=mut_score, score_wild_type=wt_score), "DAI_mhcI_MB") + def add_netmhciipan_features(self): + """ + returns results from MHC II prediction for mutation + """ + # netmhcpan4 MUT scores + self.add_features(self.predII.best_mhcII_pan_score, "best%Rank_netmhcIIpan") + self.add_features(self.predII.best_mhcII_pan_epitope, "best_epitope_netmhcIIpan") + self.add_features(self.predII.best_mhcII_pan_allele, "bestHLA_allele_netmhcIIpan") + # netmhcpan4 mut affinity + self.add_features(self.predII.best_mhcII_pan_affinity, "best_affinity_netmhcIIpan") + self.add_features(self.predII.best_mhcII_pan_affinity_epitope, "best_affinity_epitope_netmhcIIpan") + self.add_features(self.predII.best_mhcII_pan_affinity_allele, "bestHLA_allele_affinity_netmhcIIpan") + + def add_netmhciipan_wt_features(self): + """ + returns results from MHC II prediction for WT + """ + # netmhcIIpan WT scores + self.add_features(self.predII.best_mhcII_pan_score_WT, "best%Rank_netmhcIIpan_WT") + self.add_features(self.predII.best_mhcII_pan_epitope_WT, "best_epitope_netmhcIIpan_WT") + self.add_features(self.predII.best_mhcII_pan_allele_WT, "bestHLA_allele_netmhcIIpan_Wt") + # netmhcIIpan wt affinity + self.add_features(self.predII.best_mhcII_affinity_WT, "best_affinity_netmhcIIpan_WT") + self.add_features(self.predII.best_mhcII_affinity_epitope_WT, "best_affinity_epitope_netmhcIIpan_WT") + self.add_features(self.predII.best_mhcII_affinity_allele_WT, "bestHLA_allele_affinity_netmhcIIpan_WT") + + def add_multiple_binding_mhcii_features(self): + """ + returns results from MHC II prediction for multiple binding features + """ + # multiplexed representation MUT MHC II + for sc, mn in zip(self.predII.MHCII_score_all_epitopes, self.predII.mean_type): + self.add_features(sc, "MB_score_MHCII_all_epitopes_" + mn) + for sc, mn in zip(self.predII.MHCII_score_top10, self.predII.mean_type): + self.add_features(sc, "MB_score_MHCII_top10_" + mn) + for sc, mn in zip(self.predII.MHCII_score_best_per_alelle, self.predII.mean_type): + self.add_features(sc, "MB_score_MHCII_best_per_alelle_" + mn) + # rename MB_score_best_per_alelle_harmonic to PHBR (described in Marty et al) + self.properties["PHBR-II"] = self.properties.pop("MB_score_MHCII_best_per_alelle_harmonic") + self.add_features(self.predII.MHCII_epitope_scores, "MB_mhcII_epitope_scores") + self.add_features(self.predII.MHCII_epitope_seqs, "MB_mhcII_epitope_sequences") + self.add_features(self.predII.MHCII_epitope_alleles, "MB_mhcII_alleles") + self.add_features(self.predII.MHCII_number_strong_binders, "MB_number_pep_MHCIIscore<2") + self.add_features(self.predII.MHCII_number_weak_binders, "MB_number_pep_MHCIIscore<10") + # multiplexed representation WT MHC II + for sc, mn in zip(self.predII.MHCII_score_all_epitopes_WT, self.predII.mean_type): + self.add_features(sc, "MB_score_MHCII_all_epitopes_WT_" + mn) + for sc, mn in zip(self.predII.MHCII_score_top10_WT, self.predII.mean_type): + self.add_features(sc, "MB_score_MHCII_top10_WT_" + mn) + for sc, mn in zip(self.predII.MHCII_score_best_per_alelle_WT, self.predII.mean_type): + self.add_features(sc, "MB_score_MHCII_best_per_alelle_WT_" + mn) + # rename MB_score_best_per_alelle_harmonic to PHBR (described in Marty et al) + if "MB_score_MHCII_best_per_alelle_WT_harmonic" in self.properties: + self.properties["PHBR-II_WT"] = self.properties.pop("MB_score_MHCII_best_per_alelle_WT_harmonic") + self.add_features(self.predII.MHCII_epitope_scores_WT, "MB_mhcII_epitope_scores_WT") + self.add_features(self.predII.MHCII_epitope_seqs_WT, "MB_mhcII_epitope_sequences_WT") + self.add_features(self.predII.MHCII_epitope_alleles_WT, "MB_mhcII_alleles_WT") + self.add_features(self.predII.MHCII_number_strong_binders_WT, "MB_number_pep_MHCIIscore<2_WT") + self.add_features(self.predII.MHCII_number_weak_binders_WT, "MB_number_pep_MHCIIscore<10_WT") + + def add_dai_mhcii(self, aff_mut, aff_wt, rank_mut, rank_wt): + """ + returns DAI for MHC II based on affinity (filtered + no filtered) and rank + """ + # dai mhc II affinity + self.add_features( + FeatureLiterature.dai(score_mutation=aff_mut, score_wild_type=aff_wt), + "DAI_mhcII_affinity") + self.add_features( + FeatureLiterature.dai(score_mutation=aff_mut, score_wild_type=aff_wt, affin_filtering=True), + "DAI_mhcII_affinity_aff_filtered") + # dai mhc II netMHCIIpan score + self.add_features( + FeatureLiterature.dai(score_mutation=rank_mut, score_wild_type=rank_wt), + "DAI_mhcII_rank") + + def add_multiple_binding_numdiff_mhcii(self): + """ + returns difference and ratio of # epitopes with rank scores < 2 or 10 for mutant and wt sequence for MHC II + """ + for threshold in [2, 10]: + num_mutation = self.properties["MB_number_pep_MHCIIscore<{}".format(threshold)] + num_wild_type = self.properties["MB_number_pep_MHCIIscore<{}_WT".format(threshold)] + self.add_features(FeatureLiterature.diff_number_binders( + num_mutation=num_mutation, num_wild_type=num_wild_type), + "Diff_numb_epis_mhcII<{}".format(threshold)) + self.add_features(FeatureLiterature.ratio_number_binders( + num_mutation=num_mutation, num_wild_type=num_wild_type), + "Ratio_numb_epis_mhcII<{}".format(threshold)) + + def add_multiple_binding_scorediff_mhcii(self, mut_score, wt_score): + """ + returns DAI and amplitude with multiple binding score + """ + self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( + score_mutation=mut_score, score_wild_type=wt_score), + "Amplitude_mhcII_mb") + # dai multiple binding mhc II + self.add_features( + FeatureLiterature.dai(score_mutation=mut_score, score_wild_type=wt_score), + "DAI_mhcII_MB") + + def add_amplitude_mhcii(self, aff_wt, aff_mut, sc_wt, sc_mut): + """ + ratio in MHC binding based on affinity (all length), rank score, affintiy (9mer) + """ + # amplitude affinity mhc II + self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( + score_mutation=aff_mut, score_wild_type=aff_wt, apply_correction=True), + "Amplitude_mhcII_affinity") + # amplitude rank score mhc II + self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( + score_mutation=sc_mut, score_wild_type=sc_wt), + "Amplitude_mhcII_rank_netmhcpan4") + logger.info("Amplitude mhc II: {}".format(self.properties["Amplitude_mhcII_rank_netmhcpan4"])) + + def add_adncdn_mhcii(self, score_mut): + """ + return if alternative or classical defined binder for MHC II + """ + amplitude_mhcii = self.properties["Amplitude_mhcII_rank_netmhcpan4"] + bdg_cutoff_classical_mhcii = 1 + bdg_cutoff_alternative_mhcii = 4 + amplitude_cutoff_mhcii = 4 + self.add_features(FeatureLiterature.classify_adn_cdn( + score_mutation=score_mut, amplitude=amplitude_mhcii, + bdg_cutoff_classical=bdg_cutoff_classical_mhcii, bdg_cutoff_alternative=bdg_cutoff_alternative_mhcii, + amplitude_cutoff=amplitude_cutoff_mhcii, category="CDN"), "CDN_mhcII") + self.add_features(FeatureLiterature.classify_adn_cdn( + score_mutation=score_mut, amplitude=amplitude_mhcii, + bdg_cutoff_classical=bdg_cutoff_classical_mhcii, bdg_cutoff_alternative=bdg_cutoff_alternative_mhcii, + amplitude_cutoff=amplitude_cutoff_mhcii, category="ADN"), "ADN_mhcII") + + def add_recognition_potential_mhcii(self, epitope_mut_mhcii): + """ + neoantigen fitness for mhcII based on affinity + """ + self.add_features( + self.neoantigen_fitness_calculator.wrap_pathogen_similarity( + mutation=epitope_mut_mhcii, iedb=self.references.iedb), + "Pathogensimiliarity_mhcII") + self.add_features(self.neoantigen_fitness_calculator.calculate_recognition_potential( + amplitude=self.properties["Amplitude_mhcII_affinity"], + pathogen_similarity=self.properties["Pathogensimiliarity_mhcII"], + mutation_in_anchor="0"), + "Recognition_Potential_mhcII_affinity") + + def add_add_number_mismatches(self, epi_wt_mhci, epi_mut_mhci, epi_wt_mhcii, epi_mut_mhcii): + """ + returns number of mismatches between best MHCI / MHC II epitopes (rank) and their corresponding WTs + """ + self.add_features(FeatureLiterature.number_of_mismatches( + epitope_wild_type=epi_wt_mhci, epitope_mutation=epi_mut_mhci), "Number_of_mismatches_mhcI") + self.add_features(FeatureLiterature.number_of_mismatches( + epitope_wild_type=epi_wt_mhcii, epitope_mutation=epi_mut_mhcii), "Number_of_mismatches_mhcII") + + def add_priority_score(self, rank_mut, rank_wt, mb_mut, mb_wt, expr, vaf_tum, vaf_transcr): + """ + returns priority score for mhc I rank + multible binding + """ + no_mismatch = self.properties["Number_of_mismatches_mhcI"] + mut_in_prot = self.properties["mutation_found_in_proteome"] + # priority score with rank score + self.add_features(FeatureLiterature.calc_priority_score( + vaf_tumor=vaf_tum, vaf_rna=vaf_transcr, transcript_expr=expr, no_mismatch=no_mismatch, + score_mut=rank_mut, score_wt=rank_wt, mut_in_prot=mut_in_prot), "Priority_score") + # priority score using multiplexed representation score + self.add_features(FeatureLiterature.calc_priority_score( + vaf_tumor=vaf_tum, vaf_rna=vaf_transcr, transcript_expr=expr, no_mismatch=no_mismatch, + score_mut=mb_mut, score_wt=mb_wt, mut_in_prot=mut_in_prot), "Priority_score_MB") + + def add_neoag(self, sample_id, mut_peptide, score_mut, ref_peptide): + """ + returns neoag immunogenicity score + """ + peptide_variant_position = self.properties["pos_MUT_MHCI_affinity_epi"] + self.add_features(self.neoag_calculator.wrapper_neoag( + sample_id=sample_id, mut_peptide=mut_peptide, score_mut=score_mut, ref_peptide=ref_peptide, + peptide_variant_position=peptide_variant_position), "neoag_immunogencity") + + def add_iedb_immunogenicity(self, epitope_mhci, affinity_mhci, epitope_mhcii): + """ + returns IEDB immunogenicity for MHC I (based on affinity) and MHC II (based on rank) + """ + mhci_allele = self.properties["bestHLA_allele_affinity_netmhcpan4"] + mhcii_allele = self.properties["bestHLA_allele_netmhcIIpan"] + self.add_features(FeatureLiterature.calc_IEDB_immunogenicity( + epitope=epitope_mhci, mhc_allele=mhci_allele, mhc_score=affinity_mhci), "IEDB_Immunogenicity_mhcI") + self.add_features(FeatureLiterature.calc_IEDB_immunogenicity( + epitope=epitope_mhcii, mhc_allele=mhcii_allele, mhc_score=None), "IEDB_Immunogenicity_mhcII") + self.add_features(FeatureLiterature.calc_IEDB_immunogenicity( + epitope=epitope_mhci, mhc_allele=mhci_allele, mhc_score=affinity_mhci, affin_filtering=True), + "IEDB_Immunogenicity_mhcI_affinity_filtered") + + def add_dissimilarity(self, epitope_mhci, affinity_mhci, epitope_mhcii, affinity_mhcii): + """ + returns dissimilarity for MHC I (affinity) MHC II (affinity) + """ + self.add_features(self.dissimilarity_calculator.calculate_dissimilarity( + mhc_mutation=epitope_mhci, mhc_affinity=affinity_mhci, references=self.references), + "dissimilarity") + self.add_features(self.dissimilarity_calculator.calculate_dissimilarity( + mhc_mutation=epitope_mhci, mhc_affinity=affinity_mhci, references=self.references, + filter_binder=True), "dissimilarity_filter500") + self.add_features(self.dissimilarity_calculator.calculate_dissimilarity( + mhc_mutation=epitope_mhcii, mhc_affinity=affinity_mhcii, references=self.references), + "dissimilarity_mhcII") def add_provean_score_features(self): # PROVEAN score @@ -704,56 +718,37 @@ def add_provean_score_features(self): mutated_aminoacid=self.properties['MUT_AA'], ucsc_id_position=ucsc_id), "PROVEAN_score") - def add_aminoacid_index_features(self, aaindex1_dict, aaindex2_dict): + def add_aminoacid_index_features(self, aaindex1_dict, aaindex2_dict, mutation_aminoacid, + wild_type_aminoacid): # amino acid index - mutation_aminoacid = self.properties["MUT_AA"] - wild_type_aminoacid = self.properties["WT_AA"] for k in aaindex1_dict: self.add_features(aaindex1_dict[k].get(wild_type_aminoacid, "NA"), "{}_{}".format(k, "wt")) self.add_features(aaindex1_dict[k].get(mutation_aminoacid, "NA"), "{}_{}".format(k, "mut")) for k in aaindex2_dict: self.add_features(aaindex2_dict[k].get(wild_type_aminoacid, {}).get(mutation_aminoacid, "NA"), k) - def add_aminoacid_frequency_features(self, aa_freq_dict, mutation_mhci, nmer_freq_dict): + def add_aminoacid_frequency_features(self, aa_freq_dict, mutation_mhci, nmer_freq_dict, mutated_aminoacid): # amino acid frequency - substitution = self.properties["substitution"] - mutated_aminoacid = FeatureLiterature.wt_mut_aa(substitution=substitution, mut="mut") - self.add_features(mutated_aminoacid, "MUT_AA") - self.add_features(FeatureLiterature.wt_mut_aa(substitution=substitution, mut="wt"), "WT_AA") self.add_features(freq_score.freq_aa(mutated_aminoacid=mutated_aminoacid, dict_freq=aa_freq_dict), "Frequency_mutated_AA") self.add_features(freq_score.freq_prod_4mer(mutation=mutation_mhci, dict_freq=aa_freq_dict), "Product_Frequency_4mer") - self.add_features(freq_score.freq_4mer(mutation=mutation_mhci, dict_freq=nmer_freq_dict), "Frequency_of_4mer") + self.add_features(freq_score.freq_4mer(mutation=mutation_mhci, dict_freq=nmer_freq_dict), + "Frequency_of_4mer") - def add_expression_features(self, rna_avail, tumour_content): + def add_expression_features(self, tumour_content, vaf_rna, patient_id, + transcript_expression): # expression - transcript_expression = self.properties["transcript_expression"] - patient_id = properties_manager.get_patient_id(self.properties) - vaf_tumor = self.properties["VAF_in_tumor"] - vaf_rna = vaf_tumor if rna_avail.get(patient_id, "False") == "False" else \ - self.properties.get("VAF_in_RNA", vaf_tumor) - self.add_features(FeatureLiterature.rna_expression_mutation( transcript_expression=transcript_expression, vaf_rna=vaf_rna), "Expression_Mutated_Transcript") - expression_mutated_transcript = self.properties.get("Expression_Mutated_Transcript") self.add_features(FeatureLiterature.expression_mutation_tc( - transcript_expression=expression_mutated_transcript, patient_id=patient_id, tumour_content_dict=tumour_content), + transcript_expression=expression_mutated_transcript, patient_id=patient_id, + tumour_content_dict=tumour_content), "Expression_Mutated_Transcript_tumor_content") - def add_differential_agretopicity_index_features(self, mutation_mhci, mutation_mhcii, wild_type_mhci, - wild_type_mhcii): - # differential agretopicity index - self.add_features( - FeatureLiterature.dai(score_mutation=mutation_mhci, score_wild_type=wild_type_mhci), "DAI_mhcI") - self.add_features( - FeatureLiterature.dai(score_mutation=mutation_mhcii, score_wild_type=wild_type_mhcii), "DAI_mhcII") - - - def add_differential_expression_features(self, gene, ref_dat): + def add_differential_expression_features(self, gene, ref_dat, expression_tumor): # differential expression - expression_tumor = self.properties["transcript_expression"] expression_reference = differential_expression.add_rna_reference(gene, ref_dat, 0) expression_reference_sum = differential_expression.add_rna_reference(gene, ref_dat, 2) expression_reference_sd = differential_expression.add_rna_reference(gene, ref_dat, 1) From ddd43ed4cf651dc639c2191facbc812ee0bca37a Mon Sep 17 00:00:00 2001 From: Lang Date: Tue, 30 Jun 2020 09:15:56 +0200 Subject: [PATCH 072/105] change to version 0.2.2 --- input/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/input/__init__.py b/input/__init__.py index f28ad6ac..6c0bb1d5 100755 --- a/input/__init__.py +++ b/input/__init__.py @@ -1,4 +1,4 @@ -VERSION = '0.2.1' +VERSION = '0.2.2' REFERENCE_FOLDER_ENV = 'INPUT_REFERENCE_FOLDER' INPUT_BLASTP_ENV = 'INPUT_BLASTP' INPUT_MIXMHC2PRED_ENV = 'INPUT_MIXMHC2PRED' From 73f5dbea6099816f89aff919ba1080e55cee5c54 Mon Sep 17 00:00:00 2001 From: Lang Date: Tue, 30 Jun 2020 11:38:57 +0200 Subject: [PATCH 073/105] generate_epi_tuple: correct indices to parse correct values --- input/netmhcpan4/multiple_binders.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/input/netmhcpan4/multiple_binders.py b/input/netmhcpan4/multiple_binders.py index 7881a15a..03242577 100755 --- a/input/netmhcpan4/multiple_binders.py +++ b/input/netmhcpan4/multiple_binders.py @@ -33,10 +33,10 @@ def generate_epi_tuple(self, prediction_out, mhc=MHC_I): for ii, i in enumerate(pred_data): if mhc == MHC_II: # rank, affinity, epitope sequence, allele - list_of_tuples.append((i[-2], i[-3], i[2], i[1])) + list_of_tuples.append((i[9], i[8], i[2], i[1])) else: # rank, affinity, epitope sequence, allele - list_of_tuples.append((i[-1], i[-2], i[2], i[1])) + list_of_tuples.append((i[13], i[12], i[2], i[1])) return list_of_tuples def extract_top10_epis(self, tuple_epis): From f11bcb34782c18cd69574458677b29a8109f7823 Mon Sep 17 00:00:00 2001 From: Lang Date: Tue, 30 Jun 2020 11:55:40 +0200 Subject: [PATCH 074/105] re-name feature Diff_numb_epis_ Date: Tue, 30 Jun 2020 15:27:12 +0200 Subject: [PATCH 075/105] correct expression_mutation_tc --- input/FeatureLiterature.py | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/input/FeatureLiterature.py b/input/FeatureLiterature.py index fbc33276..ea83410b 100755 --- a/input/FeatureLiterature.py +++ b/input/FeatureLiterature.py @@ -86,15 +86,14 @@ def rna_expression_mutation(transcript_expression, vaf_rna): return "NA" -def expression_mutation_tc(transcript_expression, patient_id, tumour_content_dict): +def expression_mutation_tc(transcript_expression, tumor_content): """ calculated expression of mutation corrected by tumour content """ - tumor_content = tumour_content_dict.get(patient_id) corrected_expression = "NA" if tumor_content is not None and tumor_content > 0.0: try: - corrected_expression = str(float(transcript_expression) / tumor_content / 100) + corrected_expression = str(float(transcript_expression) / tumor_content) except ValueError: pass return corrected_expression From 9bb1f5fd39eacbceb8ece6df76b8b102d004f747 Mon Sep 17 00:00:00 2001 From: Lang Date: Tue, 30 Jun 2020 15:28:23 +0200 Subject: [PATCH 076/105] adjust add_expression_features for corrected calculation of tc corrected expression --- input/epitope.py | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/input/epitope.py b/input/epitope.py index 769df2c6..04c8a995 100755 --- a/input/epitope.py +++ b/input/epitope.py @@ -56,7 +56,7 @@ def write_to_file(self): print(";".join([self.properties[key] for key in self.properties])) def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aaindex1_dict, aaindex2_dict, - set_available_mhc, set_available_mhcII, patient_hlaI, patient_hlaII, tumour_content, rna_avail): + set_available_mhc, set_available_mhcII, patient_hlaI, patient_hlaII, tumour_content_dict, rna_avail): """ Calculate new epitope features and add to dictonary that stores all properties """ self.properties = self.init_properties(col_nam, prop_list) @@ -73,6 +73,7 @@ def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aa alleles = properties_manager.get_hla_allele(self.properties, patient_hlaI) alleles_hlaii = properties_manager.get_hla_allele(self.properties, patient_hlaII) substitution = properties_manager.get_substitution(properties=self.properties) + tumor_content = tumour_content_dict.get(patient_id) / 100 mutated_aminoacid = FeatureLiterature.wt_mut_aa(substitution=substitution, mut="mut") self.add_features(mutated_aminoacid, "MUT_AA") @@ -81,8 +82,8 @@ def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aa # MHC binding independent features - self.add_expression_features(tumour_content, vaf_rna=vaf_rna, - transcript_expression=transcript_expr, patient_id=patient_id) + self.add_expression_features(tumor_content=tumor_content, vaf_rna=vaf_rna, + transcript_expression=transcript_expr) self.add_differential_expression_features(gene, ref_dat, expression_tumor=transcript_expr) self.add_aminoacid_index_features(aaindex1_dict, aaindex2_dict, mutation_aminoacid=mutated_aminoacid, wild_type_aminoacid=wt_aminoacid) @@ -736,15 +737,13 @@ def add_aminoacid_frequency_features(self, aa_freq_dict, mutation_mhci, nmer_fre self.add_features(freq_score.freq_4mer(mutation=mutation_mhci, dict_freq=nmer_freq_dict), "Frequency_of_4mer") - def add_expression_features(self, tumour_content, vaf_rna, patient_id, - transcript_expression): + def add_expression_features(self, tumor_content, vaf_rna, transcript_expression): # expression self.add_features(FeatureLiterature.rna_expression_mutation( transcript_expression=transcript_expression, vaf_rna=vaf_rna), "Expression_Mutated_Transcript") expression_mutated_transcript = self.properties.get("Expression_Mutated_Transcript") self.add_features(FeatureLiterature.expression_mutation_tc( - transcript_expression=expression_mutated_transcript, patient_id=patient_id, - tumour_content_dict=tumour_content), + transcript_expression=expression_mutated_transcript, tumor_content=tumor_content), "Expression_Mutated_Transcript_tumor_content") def add_differential_expression_features(self, gene, ref_dat, expression_tumor): From 712a32ba31b1abb76dff9b592bf6cc464aa50825 Mon Sep 17 00:00:00 2001 From: Lang Date: Tue, 30 Jun 2020 15:38:55 +0200 Subject: [PATCH 077/105] set dissimilarity to NA instead of 0 if filtering should be applied and affinity < 500 nM --- input/dissimilarity_garnish/dissimilaritycalculator.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/input/dissimilarity_garnish/dissimilaritycalculator.py b/input/dissimilarity_garnish/dissimilaritycalculator.py index 08454781..6e30f7f5 100755 --- a/input/dissimilarity_garnish/dissimilaritycalculator.py +++ b/input/dissimilarity_garnish/dissimilaritycalculator.py @@ -36,5 +36,5 @@ def calculate_dissimilarity(self, mhc_mutation, mhc_affinity, references, filter os.remove(fastafile) sc = dissim if filter_binder and float(mhc_affinity) >= 500: - sc = 0 + sc = "NA" return sc From 6f6979372f16125d9a541df8acc6507267509980 Mon Sep 17 00:00:00 2001 From: Lang Date: Tue, 30 Jun 2020 16:02:03 +0200 Subject: [PATCH 078/105] adjust calc_priority_score for new mutation_not_in_proteome definition --- input/FeatureLiterature.py | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/input/FeatureLiterature.py b/input/FeatureLiterature.py index ea83410b..a3c8e5fa 100755 --- a/input/FeatureLiterature.py +++ b/input/FeatureLiterature.py @@ -134,23 +134,20 @@ def calc_logistic_function(mhc_score): return "NA" -def calc_priority_score(vaf_tumor, vaf_rna, transcript_expr, no_mismatch, score_mut, score_wt, mut_in_prot): +def calc_priority_score(vaf_tumor, vaf_rna, transcript_expr, no_mismatch, score_mut, score_wt, mut_not_in_prot): """ This function calculates the Priority Score using parameters for mhc I. """ - # TODO: Franziska is this a bug? It is reversing its value - if mut_in_prot == "False" : mut_in_prot = "1" - if mut_in_prot == "True" : mut_in_prot = "0" L_mut = calc_logistic_function(score_mut) L_wt = calc_logistic_function(score_wt) priority_score = "NA" try: if vaf_tumor not in ["-1", "NA"]: priority_score = (L_mut * float(vaf_tumor) * math.tanh(float(transcript_expr))) * ( - float(mut_in_prot) * (1 - 2 ** (-float(no_mismatch)) * L_wt)) + float(mut_not_in_prot) * (1 - 2 ** (-float(no_mismatch)) * L_wt)) else: priority_score = (L_mut * float(vaf_rna) * math.tanh(float(transcript_expr))) * ( - float(mut_in_prot) * (1 - 2 ** (-float(no_mismatch)) * L_wt)) + float(mut_not_in_prot) * (1 - 2 ** (-float(no_mismatch)) * L_wt)) except (TypeError, ValueError) as e: pass return str(priority_score) From f5119914ca5286acb75f20e8e5c54c1f4d645c6c Mon Sep 17 00:00:00 2001 From: Lang Date: Tue, 30 Jun 2020 16:02:25 +0200 Subject: [PATCH 079/105] adjust for for new mutation_not_in_proteome definition --- input/epitope.py | 14 ++++++++++---- 1 file changed, 10 insertions(+), 4 deletions(-) diff --git a/input/epitope.py b/input/epitope.py index 04c8a995..f837d7f7 100755 --- a/input/epitope.py +++ b/input/epitope.py @@ -88,10 +88,16 @@ def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aa self.add_aminoacid_index_features(aaindex1_dict, aaindex2_dict, mutation_aminoacid=mutated_aminoacid, wild_type_aminoacid=wt_aminoacid) self.add_provean_score_features() - if "mutation_found_in_proteome" not in self.properties: + self.add_features(FeatureLiterature.match_in_proteome( + sequence=self.properties["X..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."], db=db), + "mutation_not_found_in_proteome") + ''' + if "mutation_found_in_proteome" not in self.properties: self.add_features(FeatureLiterature.match_in_proteome( sequence=self.properties["X..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."], db=db), "mutation_found_in_proteome") + ''' + # HLA I predictions: NetMHCpan self.pred.main(xmer_mut=xmer_mut, xmer_wt=xmer_wt, alleles=alleles, set_available_mhc=set_available_mhc) @@ -663,15 +669,15 @@ def add_priority_score(self, rank_mut, rank_wt, mb_mut, mb_wt, expr, vaf_tum, va returns priority score for mhc I rank + multible binding """ no_mismatch = self.properties["Number_of_mismatches_mhcI"] - mut_in_prot = self.properties["mutation_found_in_proteome"] + mut_not_in_prot = self.properties["mutation_not_found_in_proteome"] # priority score with rank score self.add_features(FeatureLiterature.calc_priority_score( vaf_tumor=vaf_tum, vaf_rna=vaf_transcr, transcript_expr=expr, no_mismatch=no_mismatch, - score_mut=rank_mut, score_wt=rank_wt, mut_in_prot=mut_in_prot), "Priority_score") + score_mut=rank_mut, score_wt=rank_wt, mut_not_in_prot=mut_not_in_prot), "Priority_score") # priority score using multiplexed representation score self.add_features(FeatureLiterature.calc_priority_score( vaf_tumor=vaf_tum, vaf_rna=vaf_transcr, transcript_expr=expr, no_mismatch=no_mismatch, - score_mut=mb_mut, score_wt=mb_wt, mut_in_prot=mut_in_prot), "Priority_score_MB") + score_mut=mb_mut, score_wt=mb_wt, mut_not_in_prot=mut_not_in_prot), "Priority_score_MB") def add_neoag(self, sample_id, mut_peptide, score_mut, ref_peptide): """ From 82fc29a652e8f931e26436e2eb68c111df880ad4 Mon Sep 17 00:00:00 2001 From: Lang Date: Tue, 30 Jun 2020 20:38:17 +0200 Subject: [PATCH 080/105] remove comment --- input/epitope.py | 8 -------- 1 file changed, 8 deletions(-) diff --git a/input/epitope.py b/input/epitope.py index f837d7f7..3892e8a4 100755 --- a/input/epitope.py +++ b/input/epitope.py @@ -80,7 +80,6 @@ def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aa wt_aminoacid = FeatureLiterature.wt_mut_aa(substitution=substitution, mut="wt") self.add_features(wt_aminoacid, "WT_AA") - # MHC binding independent features self.add_expression_features(tumor_content=tumor_content, vaf_rna=vaf_rna, transcript_expression=transcript_expr) @@ -91,13 +90,6 @@ def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aa self.add_features(FeatureLiterature.match_in_proteome( sequence=self.properties["X..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."], db=db), "mutation_not_found_in_proteome") - ''' - if "mutation_found_in_proteome" not in self.properties: - self.add_features(FeatureLiterature.match_in_proteome( - sequence=self.properties["X..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."], db=db), - "mutation_found_in_proteome") - ''' - # HLA I predictions: NetMHCpan self.pred.main(xmer_mut=xmer_mut, xmer_wt=xmer_wt, alleles=alleles, set_available_mhc=set_available_mhc) From d7a4c4f9c16ed4f6dd67dc3a90a66925c04b1cdd Mon Sep 17 00:00:00 2001 From: Lang Date: Wed, 1 Jul 2020 16:51:10 +0200 Subject: [PATCH 081/105] pass patient_id as argument to main function + remove allele grep --- input/epitope.py | 23 +++++++++++------------ 1 file changed, 11 insertions(+), 12 deletions(-) diff --git a/input/epitope.py b/input/epitope.py index 3892e8a4..b8497fa0 100755 --- a/input/epitope.py +++ b/input/epitope.py @@ -56,7 +56,8 @@ def write_to_file(self): print(";".join([self.properties[key] for key in self.properties])) def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aaindex1_dict, aaindex2_dict, - set_available_mhc, set_available_mhcII, patient_hlaI, patient_hlaII, tumour_content_dict, rna_avail): + set_available_mhc, set_available_mhcII, patient_hlaI, patient_hlaII, tumour_content_dict, rna_avail, + patient_id): """ Calculate new epitope features and add to dictonary that stores all properties """ self.properties = self.init_properties(col_nam, prop_list) @@ -65,13 +66,15 @@ def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aa logger.info(xmer_mut) gene = properties_manager.get_gene(properties=self.properties) - patient_id = properties_manager.get_patient_id(self.properties) + #patient_id = properties_manager.get_patient_id(self.properties) + #logger.debug(patient_id) + #logger.debug(patient_hlaI) vaf_tumor = self.properties.get("VAF_in_tumor", "NA") vaf_rna = vaf_tumor if rna_avail.get(patient_id, "False") == "False" else \ self.properties.get("VAF_in_RNA", vaf_tumor) transcript_expr = self.properties["transcript_expression"] - alleles = properties_manager.get_hla_allele(self.properties, patient_hlaI) - alleles_hlaii = properties_manager.get_hla_allele(self.properties, patient_hlaII) + alleles = properties_manager.get_hla_allele(self.properties, patient_hlaI, patient_id) + alleles_hlaii = properties_manager.get_hla_allele(self.properties, patient_hlaII, patient_id) substitution = properties_manager.get_substitution(properties=self.properties) tumor_content = tumour_content_dict.get(patient_id) / 100 @@ -194,9 +197,9 @@ def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aa self.add_iedb_immunogenicity(epitope_mhci=epitope_mut_affinity, affinity_mhci=affinity_mut, epitope_mhcii=epitope_mut_rank_mhcii) # MixMHCpred - self.add_mix_mhc_pred_features(xmer_wt=xmer_wt, xmer_mut=xmer_mut, patient_hlai=patient_hlaI) + self.add_mix_mhc_pred_features(xmer_wt=xmer_wt, xmer_mut=xmer_mut, alleles=alleles) # MixMHC2pred - self.add_mix_mhc2_pred_features(xmer_mut=xmer_mut, xmer_wt=xmer_wt, patient_hlaII=patient_hlaII) + self.add_mix_mhc2_pred_features(xmer_mut=xmer_mut, xmer_wt=xmer_wt, alleles=alleles_hlaii) # dissimilarity to self-proteome self.add_dissimilarity(epitope_mhci=epitope_mut_affinity, affinity_mhci=affinity_mut, epitope_mhcii=epitope_mut_affinity_mhcii, affinity_mhcii=affinity_mut_mhcii) @@ -213,10 +216,8 @@ def add_vax_rank_features(self): self.add_features(vaxrankscore.total_binding_score, "vaxrank_binding_score") self.add_features(vaxrankscore.ranking_score, "vaxrank_total_score") - def add_mix_mhc2_pred_features(self, xmer_wt, xmer_mut, patient_hlaII): + def add_mix_mhc2_pred_features(self, xmer_wt, xmer_mut, alleles): # MixMHC2pred - # TODO:remove allele grep and pass as argument - alleles = properties_manager.get_hla_allele(self.properties, patient_hlaII) self.predpresentation2.main(alleles=alleles, xmer_wt=xmer_wt, xmer_mut=xmer_mut) self.add_features(self.predpresentation2.all_peptides, "MixMHC2pred_all_peptides") self.add_features(self.predpresentation2.all_ranks, "MixMHC2pred_all_ranks") @@ -228,10 +229,8 @@ def add_mix_mhc2_pred_features(self, xmer_wt, xmer_mut, patient_hlaII): self.add_features(self.predpresentation2.best_rank_wt, "MixMHC2pred_best_rank_wt") self.add_features(self.predpresentation2.difference_score_mut_wt, "MixMHC2pred_difference_rank_mut_wt") - def add_mix_mhc_pred_features(self, xmer_wt, xmer_mut, patient_hlai): + def add_mix_mhc_pred_features(self, xmer_wt, xmer_mut, alleles): # MixMHCpred - # TODO:remove allele grep and pass as argument - alleles = properties_manager.get_hla_allele(self.properties, patient_hlai) self.predpresentation.main(xmer_wt=xmer_wt, xmer_mut=xmer_mut, alleles=alleles) self.add_features(self.predpresentation.all_peptides, "MixMHCpred_all_peptides") self.add_features(self.predpresentation.all_scores, "MixMHCpred_all_scores") From b855c9e7436b05f9c792e1a6716f70b4d0c325ad Mon Sep 17 00:00:00 2001 From: Lang Date: Wed, 1 Jul 2020 16:51:39 +0200 Subject: [PATCH 082/105] pass patient_id to epitope class --- input/predict_all_epitopes.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/input/predict_all_epitopes.py b/input/predict_all_epitopes.py index 640219e4..f6daced4 100755 --- a/input/predict_all_epitopes.py +++ b/input/predict_all_epitopes.py @@ -131,6 +131,7 @@ def wrapper_table_add_feature_annotation(self, icam_file, patient_id, indel, pat self.proteome_dictionary = self.load_proteome(self.references.uniprot) # adds patient to the table dat[0].append(PATIENT_ID) + logger.debug(patient_id) for ii, i in enumerate(dat[1]): dat[1][ii].append(str(patient_id)) # initialise information needed for feature calculation @@ -145,7 +146,7 @@ def wrapper_table_add_feature_annotation(self, icam_file, patient_id, indel, pat dat[0], dat[1][ii], self.proteome_dictionary, self.rna_reference, self.aa_frequency, self.fourmer_frequency, self.aa_index1_dict, self.aa_index2_dict, self.hla_available_alleles, self.hlaII_available_alleles, self.patient_hla_I_allels, - self.patient_hla_II_allels, self.tumour_content, self.rna_avail) + self.patient_hla_II_allels, self.tumour_content, self.rna_avail, patient_id) for key in z: if key not in self.Allepit: # keys are are feautres; values: list of feature values associated with mutated peptide sequence From 9ccbc754a2b16899a67e7d31446ce0b6c95ff3ca Mon Sep 17 00:00:00 2001 From: Lang Date: Wed, 1 Jul 2020 16:52:39 +0200 Subject: [PATCH 083/105] pass patient_id to get_hla_allele --- input/helpers/properties_manager.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/input/helpers/properties_manager.py b/input/helpers/properties_manager.py index 6f57e695..104c971e 100755 --- a/input/helpers/properties_manager.py +++ b/input/helpers/properties_manager.py @@ -88,10 +88,9 @@ def get_netmhciipan_epitopes(properties, affinity=False): return wild_type, mutation -def get_hla_allele(props, hla_patient_dict): +def get_hla_allele(props, hla_patient_dict, patient_id): ''' returns hla allele of patients given in hla_file ''' - patient_id = get_patient_id(props) return hla_patient_dict[patient_id] From eac5ea159fb8c4d73d42872056935d1fa56cfc73 Mon Sep 17 00:00:00 2001 From: Lang Date: Wed, 1 Jul 2020 18:20:43 +0200 Subject: [PATCH 084/105] add function to correct allele format if too detailed + add print statement if allele is not available in netmhcpan --- input/netmhcpan4/netmhcpan_prediction.py | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/input/netmhcpan4/netmhcpan_prediction.py b/input/netmhcpan4/netmhcpan_prediction.py index dc2cdc27..6d48018f 100755 --- a/input/netmhcpan4/netmhcpan_prediction.py +++ b/input/netmhcpan4/netmhcpan_prediction.py @@ -1,5 +1,7 @@ #!/usr/bin/env python +from logzero import logger + from input.helpers import data_import from input.helpers.epitope_helper import EpitopeHelper from input.netmhcpan4.abstract_netmhcpan_predictor import AbstractNetMhcPanPredictor @@ -34,14 +36,31 @@ def _mhc_allele_in_netmhcpan_available(self, allele, set_available_mhc): ''' return allele in set_available_mhc + def check_format_allele(self, allele): + """ + sometimes genotyping may be too detailed. (e.g. HLA-DRB1*04:01:01 should be HLA-DRB1*04:01) + :param allele: HLA-allele + :return: HLA-allele in correct format + """ + # TODO: was added to netMHCIIpan too --> combine + if allele.count(":") > 1: + allele_correct = ":".join(allele.split(":")[0:2]) + else: + allele_correct = allele + return allele_correct + + def mhc_prediction(self, hla_alleles, set_available_mhc, tmpfasta, tmppred): ''' Performs netmhcpan4 prediction for desired hla allele and writes result to temporary file. ''' allels_for_prediction = [] for allele in hla_alleles: + allele = self.check_format_allele(allele) allele = allele.replace("*", "") if self._mhc_allele_in_netmhcpan_available(allele, set_available_mhc): allels_for_prediction.append(allele) + else: + logger.info(allele + "not available") hla_allele = ",".join(allels_for_prediction) cmd = [ self.configuration.net_mhc_pan, From 7dab88c09cf69bccdfb5db16f89b95f5bc02ba30 Mon Sep 17 00:00:00 2001 From: Lang Date: Wed, 1 Jul 2020 18:21:00 +0200 Subject: [PATCH 085/105] add function to correct allele format if too detailed + add print statement if allele is not available in netmhcpan --- input/netmhcpan4/netmhcIIpan_prediction.py | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/input/netmhcpan4/netmhcIIpan_prediction.py b/input/netmhcpan4/netmhcIIpan_prediction.py index 97711ea0..1870bdef 100755 --- a/input/netmhcpan4/netmhcIIpan_prediction.py +++ b/input/netmhcpan4/netmhcIIpan_prediction.py @@ -25,6 +25,21 @@ def __init__(self, runner, configuration): self.affinity_epitopeII = "NA" self.affinity_alleleII = "NA" + + def check_format_allele(self, allele): + """ + sometimes genotyping may be too detailed. (e.g. HLA-DRB1*04:01:01 should be HLA-DRB1*04:01) + :param allele: HLA-allele + :return: HLA-allele in correct format + """ + if allele.count(":") > 1: + allele_correct = ":".join(allele.split(":")[0:2]) + else: + allele_correct = allele + return allele_correct + + + def generate_mhcII_alelles_combination_list(self, hla_alleles, set_available_mhc): ''' given list of HLA II alleles, returns list of HLA-DRB1 (2x), all possible HLA-DPA1/HLA-DPB1 (4x) and HLA-DQA1/HLA-DPQ1 (4x) ''' @@ -34,10 +49,14 @@ def generate_mhcII_alelles_combination_list(self, hla_alleles, set_available_mhc dqb_alleles = [] dpb_alleles = [] for allele in hla_alleles: + allele = self.check_format_allele(allele) if allele.startswith("HLA-DRB1"): allele = allele.replace("HLA-", "").replace("*", "_").replace(":", "") + logger.info(allele) if allele in set_available_mhc: allels_for_prediction.append(allele) + else: + logger.info(allele + "not available") else: allele = allele.replace("*", "").replace(":", "") if allele.startswith("HLA-DPA"): @@ -54,6 +73,7 @@ def generate_mhcII_alelles_combination_list(self, hla_alleles, set_available_mhc for allele in dp_dq_alleles: if allele in set_available_mhc: allels_for_prediction.append(allele) + logger.info(allels_for_prediction) return allels_for_prediction def mhcII_prediction(self, hla_alleles, set_available_mhc, tmpfasta, tmppred): From dccb1509c928b51f36b0aa99905ffcb07a467a04 Mon Sep 17 00:00:00 2001 From: Lang Date: Wed, 1 Jul 2020 18:21:43 +0200 Subject: [PATCH 086/105] add some print statements --- input/netmhcpan4/multiple_binders.py | 1 + 1 file changed, 1 insertion(+) diff --git a/input/netmhcpan4/multiple_binders.py b/input/netmhcpan4/multiple_binders.py index 03242577..b27f3363 100755 --- a/input/netmhcpan4/multiple_binders.py +++ b/input/netmhcpan4/multiple_binders.py @@ -83,6 +83,7 @@ def extract_best_epi_per_alelle(self, tuple_epis, alleles): # allele already one time represented in list --> add n-t times [homo_best_epi_all.append(tuple(homo_best_epi)) for i in range(homo_numbers - 1)] best_epis_per_allele.extend(tuple(homo_best_epi_all)) + logger.info(best_epis_per_allele) return best_epis_per_allele def scores_to_list(self, tuple_epis): From cb794d2094a35af3d24bb8beae67217ef7ddac4a Mon Sep 17 00:00:00 2001 From: Lang Date: Wed, 1 Jul 2020 22:04:56 +0200 Subject: [PATCH 087/105] correct MHC_score_best_per_alelle_WT, only calculate of 6 alleles present --- input/netmhcpan4/combine_netmhcpan_pred_multiple_binders.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/input/netmhcpan4/combine_netmhcpan_pred_multiple_binders.py b/input/netmhcpan4/combine_netmhcpan_pred_multiple_binders.py index 61ec33fa..cb6837c7 100755 --- a/input/netmhcpan4/combine_netmhcpan_pred_multiple_binders.py +++ b/input/netmhcpan4/combine_netmhcpan_pred_multiple_binders.py @@ -158,7 +158,7 @@ def main(self, xmer_wt, xmer_mut, alleles, set_available_mhc): self.MHC_score_top10_WT = mb.get_means(top10) best_per_alelle = mb.scores_to_list(best_per_alelle) self.MHC_score_all_epitopes_WT = mb.get_means(all) - self.MHC_score_best_per_alelle_WT = mb.get_means(best_per_alelle) + self.MHC_score_best_per_alelle_WT = mb.MHC_MB_score_best_per_allele(best_per_alelle) self.MHC_number_strong_binders_WT = mb.determine_number_of_binders(all, 1) self.MHC_number_weak_binders_WT = mb.determine_number_of_binders(all, 2) # best prediction From e9112e75ee90ad1e1821e9da346f38c1dd3cc960 Mon Sep 17 00:00:00 2001 From: Lang Date: Wed, 1 Jul 2020 22:08:47 +0200 Subject: [PATCH 088/105] correct MHC_score_best_per_alelle_WT, only calculate of 6 alleles present --- input/netmhcpan4/combine_netmhcpan_pred_multiple_binders.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/input/netmhcpan4/combine_netmhcpan_pred_multiple_binders.py b/input/netmhcpan4/combine_netmhcpan_pred_multiple_binders.py index cb6837c7..aa6ec74a 100755 --- a/input/netmhcpan4/combine_netmhcpan_pred_multiple_binders.py +++ b/input/netmhcpan4/combine_netmhcpan_pred_multiple_binders.py @@ -158,7 +158,7 @@ def main(self, xmer_wt, xmer_mut, alleles, set_available_mhc): self.MHC_score_top10_WT = mb.get_means(top10) best_per_alelle = mb.scores_to_list(best_per_alelle) self.MHC_score_all_epitopes_WT = mb.get_means(all) - self.MHC_score_best_per_alelle_WT = mb.MHC_MB_score_best_per_allele(best_per_alelle) + self.MHC_score_best_per_alelle_WT = self.MHC_MB_score_best_per_allele(best_per_alelle) self.MHC_number_strong_binders_WT = mb.determine_number_of_binders(all, 1) self.MHC_number_weak_binders_WT = mb.determine_number_of_binders(all, 2) # best prediction From fc7888b9fdab055875ec8b5a23368a2fd367abce Mon Sep 17 00:00:00 2001 From: Lang Date: Wed, 1 Jul 2020 23:32:27 +0200 Subject: [PATCH 089/105] NA value for sequences is - --- .../combine_netmhcIIpan_pred_multiple_binders.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/input/netmhcpan4/combine_netmhcIIpan_pred_multiple_binders.py b/input/netmhcpan4/combine_netmhcIIpan_pred_multiple_binders.py index 359f40b6..38a8bdf7 100755 --- a/input/netmhcpan4/combine_netmhcIIpan_pred_multiple_binders.py +++ b/input/netmhcpan4/combine_netmhcIIpan_pred_multiple_binders.py @@ -27,10 +27,10 @@ def __init__(self, runner, configuration): self.MHCII_epitope_scores = "NA" self.MHCII_epitope_alleles = "NA" self.best_mhcII_pan_score = "NA" - self.best_mhcII_pan_epitope = "NA" + self.best_mhcII_pan_epitope = "-" self.best_mhcII_pan_allele = "NA" self.best_mhcII_pan_affinity = "NA" - self.best_mhcII_pan_affinity_epitope = "NA" + self.best_mhcII_pan_affinity_epitope = "-" self.best_mhcII_pan_affinity_allele = "NA" # WT features self.MHCII_epitope_scores_WT = "Na" @@ -42,10 +42,10 @@ def __init__(self, runner, configuration): self.MHCII_number_strong_binders_WT = "NA" self.MHCII_number_weak_binders_WT = "NA" self.best_mhcII_pan_score_WT = "NA" - self.best_mhcII_pan_epitope_WT = "NA" + self.best_mhcII_pan_epitope_WT = "-" self.best_mhcII_pan_allele_WT = "NA" self.best_mhcII_affinity_WT = "NA" - self.best_mhcII_affinity_epitope_WT = "NA" + self.best_mhcII_affinity_epitope_WT = "-" self.best_mhcII_affinity_allele_WT = "NA" def MHCII_MB_score_best_per_allele(self, tuple_best_per_allele): From 77e5729ede5253b564c021dc389d4d56352f0213 Mon Sep 17 00:00:00 2001 From: Lang Date: Wed, 1 Jul 2020 23:32:41 +0200 Subject: [PATCH 090/105] NA value for sequences is - --- input/netmhcpan4/netmhcIIpan_prediction.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/input/netmhcpan4/netmhcIIpan_prediction.py b/input/netmhcpan4/netmhcIIpan_prediction.py index 1870bdef..146ad13f 100755 --- a/input/netmhcpan4/netmhcIIpan_prediction.py +++ b/input/netmhcpan4/netmhcIIpan_prediction.py @@ -19,10 +19,10 @@ def __init__(self, runner, configuration): self.runner = runner self.configuration = configuration self.mhcII_score = "NA" - self.epitopeII = "NA" + self.epitopeII = "-" self.alleleII = "NA" self.affinityII = "NA" - self.affinity_epitopeII = "NA" + self.affinity_epitopeII = "-" self.affinity_alleleII = "NA" From 9228ecbcfd79c7333fcfc198ebe2fadcf754d409 Mon Sep 17 00:00:00 2001 From: Lang Date: Thu, 2 Jul 2020 08:37:57 +0200 Subject: [PATCH 091/105] add exceptions if MHC II epitope is - --- input/epitope.py | 49 ++++++++++++++++++++++++++++++++---------------- 1 file changed, 33 insertions(+), 16 deletions(-) diff --git a/input/epitope.py b/input/epitope.py index b8497fa0..6a8a29db 100755 --- a/input/epitope.py +++ b/input/epitope.py @@ -259,8 +259,12 @@ def add_self_similarity_features(self, epitope_mut_mhci, epitope_wt_mhci, epitop # selfsimilarity self.add_features(self_similarity.get_self_similarity(mutation=epitope_mut_mhci, wild_type=epitope_wt_mhci), "Selfsimilarity_mhcI") - self.add_features(self_similarity.get_self_similarity( - wild_type=epitope_wt_mhcii, mutation=epitope_mut_mhcii), "Selfsimilarity_mhcII") + if epitope_mut_mhcii != "-": + self.add_features(self_similarity.get_self_similarity( + wild_type=epitope_wt_mhcii, mutation=epitope_mut_mhcii), "Selfsimilarity_mhcII") + elif epitope_mut_mhcii == "-": + self.add_features( "NA", "Selfsimilarity_mhcII") + self.add_features(self_similarity.is_improved_binder( score_mutation=rank_mut_mhci, score_wild_type=rank_wt_mhci ), "ImprovedBinding_mhcI") @@ -636,15 +640,21 @@ def add_recognition_potential_mhcii(self, epitope_mut_mhcii): """ neoantigen fitness for mhcII based on affinity """ - self.add_features( - self.neoantigen_fitness_calculator.wrap_pathogen_similarity( - mutation=epitope_mut_mhcii, iedb=self.references.iedb), - "Pathogensimiliarity_mhcII") - self.add_features(self.neoantigen_fitness_calculator.calculate_recognition_potential( - amplitude=self.properties["Amplitude_mhcII_affinity"], - pathogen_similarity=self.properties["Pathogensimiliarity_mhcII"], - mutation_in_anchor="0"), - "Recognition_Potential_mhcII_affinity") + if epitope_mut_mhcii != "-": + self.add_features( + self.neoantigen_fitness_calculator.wrap_pathogen_similarity( + mutation=epitope_mut_mhcii, iedb=self.references.iedb), + "Pathogensimiliarity_mhcII") + self.add_features(self.neoantigen_fitness_calculator.calculate_recognition_potential( + amplitude=self.properties["Amplitude_mhcII_affinity"], + pathogen_similarity=self.properties["Pathogensimiliarity_mhcII"], + mutation_in_anchor="0"), + "Recognition_Potential_mhcII_affinity") + elif epitope_mut_mhcii == "-": + self.add_features("NA", "Pathogensimiliarity_mhcII") + self.add_features("NA", "Recognition_Potential_mhcII_affinity") + + def add_add_number_mismatches(self, epi_wt_mhci, epi_mut_mhci, epi_wt_mhcii, epi_mut_mhcii): """ @@ -687,8 +697,11 @@ def add_iedb_immunogenicity(self, epitope_mhci, affinity_mhci, epitope_mhcii): mhcii_allele = self.properties["bestHLA_allele_netmhcIIpan"] self.add_features(FeatureLiterature.calc_IEDB_immunogenicity( epitope=epitope_mhci, mhc_allele=mhci_allele, mhc_score=affinity_mhci), "IEDB_Immunogenicity_mhcI") - self.add_features(FeatureLiterature.calc_IEDB_immunogenicity( - epitope=epitope_mhcii, mhc_allele=mhcii_allele, mhc_score=None), "IEDB_Immunogenicity_mhcII") + if epitope_mhcii != "-": + self.add_features(FeatureLiterature.calc_IEDB_immunogenicity( + epitope=epitope_mhcii, mhc_allele=mhcii_allele, mhc_score=None), "IEDB_Immunogenicity_mhcII") + elif epitope_mhcii == "-": + self.add_features( "NA", "IEDB_Immunogenicity_mhcII") self.add_features(FeatureLiterature.calc_IEDB_immunogenicity( epitope=epitope_mhci, mhc_allele=mhci_allele, mhc_score=affinity_mhci, affin_filtering=True), "IEDB_Immunogenicity_mhcI_affinity_filtered") @@ -703,9 +716,13 @@ def add_dissimilarity(self, epitope_mhci, affinity_mhci, epitope_mhcii, affinity self.add_features(self.dissimilarity_calculator.calculate_dissimilarity( mhc_mutation=epitope_mhci, mhc_affinity=affinity_mhci, references=self.references, filter_binder=True), "dissimilarity_filter500") - self.add_features(self.dissimilarity_calculator.calculate_dissimilarity( - mhc_mutation=epitope_mhcii, mhc_affinity=affinity_mhcii, references=self.references), - "dissimilarity_mhcII") + if epitope_mhcii != "-": + self.add_features(self.dissimilarity_calculator.calculate_dissimilarity( + mhc_mutation=epitope_mhcii, mhc_affinity=affinity_mhcii, references=self.references), + "dissimilarity_mhcII") + elif epitope_mhci == "-": + self.add_features("NA", "dissimilarity_mhcII") + def add_provean_score_features(self): # PROVEAN score From 76456365ace492167c39e294e7a718af8887d67d Mon Sep 17 00:00:00 2001 From: Lang Date: Thu, 2 Jul 2020 11:13:04 +0200 Subject: [PATCH 092/105] adjustment for tumor content NA --- input/epitope.py | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/input/epitope.py b/input/epitope.py index 6a8a29db..9ff00d8b 100755 --- a/input/epitope.py +++ b/input/epitope.py @@ -66,9 +66,6 @@ def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aa logger.info(xmer_mut) gene = properties_manager.get_gene(properties=self.properties) - #patient_id = properties_manager.get_patient_id(self.properties) - #logger.debug(patient_id) - #logger.debug(patient_hlaI) vaf_tumor = self.properties.get("VAF_in_tumor", "NA") vaf_rna = vaf_tumor if rna_avail.get(patient_id, "False") == "False" else \ self.properties.get("VAF_in_RNA", vaf_tumor) @@ -76,7 +73,8 @@ def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aa alleles = properties_manager.get_hla_allele(self.properties, patient_hlaI, patient_id) alleles_hlaii = properties_manager.get_hla_allele(self.properties, patient_hlaII, patient_id) substitution = properties_manager.get_substitution(properties=self.properties) - tumor_content = tumour_content_dict.get(patient_id) / 100 + tumor_content = tumour_content_dict.get(patient_id) + if tumor_content!= "NA": tumor_content = tumor_content / 100 mutated_aminoacid = FeatureLiterature.wt_mut_aa(substitution=substitution, mut="mut") self.add_features(mutated_aminoacid, "MUT_AA") From 9493b3a9d52b4795ff994ed3561df0c7c367bbbf Mon Sep 17 00:00:00 2001 From: Lang Date: Thu, 2 Jul 2020 11:13:14 +0200 Subject: [PATCH 093/105] adjustment for tumor content NA --- input/FeatureLiterature.py | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/input/FeatureLiterature.py b/input/FeatureLiterature.py index a3c8e5fa..6217717b 100755 --- a/input/FeatureLiterature.py +++ b/input/FeatureLiterature.py @@ -91,11 +91,12 @@ def expression_mutation_tc(transcript_expression, tumor_content): calculated expression of mutation corrected by tumour content """ corrected_expression = "NA" - if tumor_content is not None and tumor_content > 0.0: - try: - corrected_expression = str(float(transcript_expression) / tumor_content) - except ValueError: - pass + if tumor_content != "NA": + if tumor_content > 0.0: + try: + corrected_expression = str(float(transcript_expression) / tumor_content) + except ValueError: + pass return corrected_expression From 2e75bfa00b0696bab294dab2e1463d1a472e0d80 Mon Sep 17 00:00:00 2001 From: Lang Date: Thu, 2 Jul 2020 11:13:20 +0200 Subject: [PATCH 094/105] adjustment for tumor content NA --- input/helpers/data_import.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/input/helpers/data_import.py b/input/helpers/data_import.py index 56528e91..7380142d 100755 --- a/input/helpers/data_import.py +++ b/input/helpers/data_import.py @@ -166,5 +166,5 @@ def import_patients_data(patients_file): 'mhcIIAlleles': split_comma_separated_list, # TODO: remove this conversion if this is fixed # https://github.com/danielgtaylor/python-betterproto/issues/96 - 'estimatedTumorContent': lambda x: float(x)}) + 'estimatedTumorContent': lambda x: float(x) if x != "NA" else x}) return SchemaConverter.patient_metadata_csv2model(df) From 6678089d222e93e2c71f5d5f391985013e4a06fc Mon Sep 17 00:00:00 2001 From: Lang Date: Fri, 3 Jul 2020 13:22:30 +0200 Subject: [PATCH 095/105] correct mut_position_xmer_seq for sequences of unequal length --- input/helpers/epitope_helper.py | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/input/helpers/epitope_helper.py b/input/helpers/epitope_helper.py index 66f3d88c..f9779947 100755 --- a/input/helpers/epitope_helper.py +++ b/input/helpers/epitope_helper.py @@ -26,19 +26,22 @@ def mut_position_xmer_seq(xmer_wt, xmer_mut): """ returns position of mutation in xmer sequence """ - p1 = -1 if len(xmer_wt) == len(xmer_mut): p1 = -1 for i, aa in enumerate(xmer_mut): if aa != xmer_wt[i]: p1 = i + 1 + pos_mut = p1 else: p1 = 0 # in case sequences do not have same length for a1, a2 in zip(xmer_wt, xmer_mut): if a1 == a2: p1 += 1 - return str(p1) + elif a1 != a2: + p1 += 1 + pos_mut = p1 + return pos_mut @staticmethod def epitope_covers_mutation(position_mutation, position_epitope, length_epitope): From 87bdf704b7422a29504576df72543fab84457d6a Mon Sep 17 00:00:00 2001 From: Lang Date: Fri, 3 Jul 2020 13:47:46 +0200 Subject: [PATCH 096/105] adjust epitope_covers_mutation for case of several mutations per xmer sequence --- input/helpers/epitope_helper.py | 42 ++++++++++++++++++--------------- 1 file changed, 23 insertions(+), 19 deletions(-) diff --git a/input/helpers/epitope_helper.py b/input/helpers/epitope_helper.py index f9779947..6a033200 100755 --- a/input/helpers/epitope_helper.py +++ b/input/helpers/epitope_helper.py @@ -11,27 +11,29 @@ def generate_nmers(xmer_wt, xmer_mut, lengths): """ length_mut = len(xmer_mut) list_peptides = [] - pos_mut = int(EpitopeHelper.mut_position_xmer_seq(xmer_mut=xmer_mut, xmer_wt=xmer_wt)) - for length in lengths: - if length <= length_mut: - start_first = pos_mut - length - starts = [start_first + s for s in range(length)] - ends = [s + length for s in starts] - for s, e in zip(starts, ends): - list_peptides.append(xmer_mut[s:e]) + pos_mut_list = int(EpitopeHelper.mut_position_xmer_seq(xmer_mut=xmer_mut, xmer_wt=xmer_wt)) + for pos_mut in pos_mut_list: + for length in lengths: + if length <= length_mut: + start_first = pos_mut - length + starts = [start_first + s for s in range(length)] + ends = [s + length for s in starts] + for s, e in zip(starts, ends): + list_peptides.append(xmer_mut[s:e]) return list(set([x for x in list_peptides if not x == "" and len(x) >= min(lengths)])) @staticmethod def mut_position_xmer_seq(xmer_wt, xmer_mut): """ - returns position of mutation in xmer sequence + returns position of mutation in xmer sequence. There can be more than one SNV within Xmer sequence. """ + pos_mut = [] if len(xmer_wt) == len(xmer_mut): p1 = -1 for i, aa in enumerate(xmer_mut): if aa != xmer_wt[i]: p1 = i + 1 - pos_mut = p1 + pos_mut.append(p1) else: p1 = 0 # in case sequences do not have same length @@ -40,21 +42,23 @@ def mut_position_xmer_seq(xmer_wt, xmer_mut): p1 += 1 elif a1 != a2: p1 += 1 - pos_mut = p1 + pos_mut.append(p1) return pos_mut @staticmethod - def epitope_covers_mutation(position_mutation, position_epitope, length_epitope): + def epitope_covers_mutation(position_mutation_list, position_epitope, length_epitope): """ checks if predicted epitope covers mutation """ - cover = False - if position_mutation != "-1": - start = int(position_epitope) - end = start + int(length_epitope) - 1 - if int(position_mutation) >= start and int(position_mutation) <= end: - cover = True - return cover + cover_list = [False] + for position_mutation in position_mutation_list: + if position_mutation != "-1": + start = int(position_epitope) + end = start + int(length_epitope) - 1 + if position_mutation >= start and position_mutation <= end: + cover_list.append(True) + cover_mutation = any(cover_list) + return cover_mutation @staticmethod def hamming_check_0_or_1(seq1, seq2): From 606bf2bd39ba80703cdd73beda7482d44d8c04c9 Mon Sep 17 00:00:00 2001 From: Lang Date: Fri, 3 Jul 2020 16:44:07 +0200 Subject: [PATCH 097/105] remove int conversion for pos_mut_list --- input/helpers/epitope_helper.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/input/helpers/epitope_helper.py b/input/helpers/epitope_helper.py index 6a033200..5b2c78df 100755 --- a/input/helpers/epitope_helper.py +++ b/input/helpers/epitope_helper.py @@ -11,7 +11,7 @@ def generate_nmers(xmer_wt, xmer_mut, lengths): """ length_mut = len(xmer_mut) list_peptides = [] - pos_mut_list = int(EpitopeHelper.mut_position_xmer_seq(xmer_mut=xmer_mut, xmer_wt=xmer_wt)) + pos_mut_list = EpitopeHelper.mut_position_xmer_seq(xmer_mut=xmer_mut, xmer_wt=xmer_wt) for pos_mut in pos_mut_list: for length in lengths: if length <= length_mut: From a0020aa63a390b24e1ddfc3b72b1809974c7d6b6 Mon Sep 17 00:00:00 2001 From: Lang Date: Fri, 3 Jul 2020 16:45:39 +0200 Subject: [PATCH 098/105] correct best wt epitope selection --- .../combine_netmhcIIpan_pred_multiple_binders.py | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/input/netmhcpan4/combine_netmhcIIpan_pred_multiple_binders.py b/input/netmhcpan4/combine_netmhcIIpan_pred_multiple_binders.py index 38a8bdf7..33e6470d 100755 --- a/input/netmhcpan4/combine_netmhcIIpan_pred_multiple_binders.py +++ b/input/netmhcpan4/combine_netmhcIIpan_pred_multiple_binders.py @@ -29,9 +29,11 @@ def __init__(self, runner, configuration): self.best_mhcII_pan_score = "NA" self.best_mhcII_pan_epitope = "-" self.best_mhcII_pan_allele = "NA" + self.best_mhcII_pan_position = "NA" self.best_mhcII_pan_affinity = "NA" self.best_mhcII_pan_affinity_epitope = "-" self.best_mhcII_pan_affinity_allele = "NA" + self.best_mhcII_pan_affinity_position = "NA" # WT features self.MHCII_epitope_scores_WT = "Na" self.MHCII_epitope_seqs_WT = "NA" @@ -93,7 +95,6 @@ def main(self, sequence, sequence_reference, alleles, set_available_mhc): top10 = mb.extract_top10_epis(list_tups) best_per_alelle = mb.extract_best_epi_per_alelle(list_tups, alleles_formated) all = mb.scores_to_list(list_tups) - all_affinities = mb.affinities_to_list(list_tups) top10 = mb.scores_to_list(top10) self.MHCII_score_top10 = mb.get_means(top10) self.MHCII_score_all_epitopes = mb.get_means(all) @@ -106,10 +107,12 @@ def main(self, sequence, sequence_reference, alleles, set_available_mhc): self.best_mhcII_pan_score = np.add_best_epitope_info(best_epi, "%Rank") self.best_mhcII_pan_epitope = np.add_best_epitope_info(best_epi, "Peptide") self.best_mhcII_pan_allele = np.add_best_epitope_info(best_epi, "Allele") + self.best_mhcII_pan_position = np.add_best_epitope_info(best_epi, "Seq") best_epi_affinity = np.minimal_binding_score(preds, rank=False) self.best_mhcII_pan_affinity = np.add_best_epitope_info(best_epi_affinity, "Affinity(nM)") self.best_mhcII_pan_affinity_epitope = np.add_best_epitope_info(best_epi_affinity, "Peptide") self.best_mhcII_pan_affinity_allele = np.add_best_epitope_info(best_epi_affinity, "Allele") + self.best_mhcII_pan_affinity_position = np.add_best_epitope_info(best_epi_affinity, "Seq") except IndexError: # if input sequence shorter than 15 aa pass @@ -140,11 +143,13 @@ def main(self, sequence, sequence_reference, alleles, set_available_mhc): self.MHCII_number_strong_binders_WT = mb.determine_number_of_binders(all, 1) self.MHCII_number_weak_binders_WT = mb.determine_number_of_binders(all, 2) # best prediction - best_epi = np.filter_for_WT_epitope(preds, self.best_mhcII_pan_epitope) + best_epi = np.filter_for_wt_epitope_position(preds, self.best_mhcII_pan_epitope, + position_epi_xmer=self.best_mhcII_pan_position) self.best_mhcII_pan_score_WT = np.add_best_epitope_info(best_epi, "%Rank") self.best_mhcII_pan_epitope_WT = np.add_best_epitope_info(best_epi, "Peptide") self.best_mhcII_pan_allele_WT = np.add_best_epitope_info(best_epi, "Allele") - best_epi_affinity = np.filter_for_WT_epitope(preds, self.best_mhcII_pan_affinity_epitope) + best_epi_affinity = np.filter_for_wt_epitope_position(preds, self.best_mhcII_pan_affinity_epitope, + position_epi_xmer=self.best_mhcII_pan_affinity_position) self.best_mhcII_affinity_WT = np.add_best_epitope_info(best_epi_affinity, "Affinity(nM)") self.best_mhcII_affinity_epitope_WT = np.add_best_epitope_info(best_epi_affinity, "Peptide") self.best_mhcII_affinity_allele_WT = np.add_best_epitope_info(best_epi_affinity, "Allele") From 41ec89ce2b4816dcc37e8868a19f3d7ebc0b09c4 Mon Sep 17 00:00:00 2001 From: Lang Date: Fri, 3 Jul 2020 16:46:07 +0200 Subject: [PATCH 099/105] correct best wt epitope selection --- ...combine_netmhcpan_pred_multiple_binders.py | 32 +++++++++++++------ 1 file changed, 22 insertions(+), 10 deletions(-) diff --git a/input/netmhcpan4/combine_netmhcpan_pred_multiple_binders.py b/input/netmhcpan4/combine_netmhcpan_pred_multiple_binders.py index aa6ec74a..0572fb14 100755 --- a/input/netmhcpan4/combine_netmhcpan_pred_multiple_binders.py +++ b/input/netmhcpan4/combine_netmhcpan_pred_multiple_binders.py @@ -27,19 +27,23 @@ def __init__(self, runner, configuration): self.best4_mhc_score = "NA" self.best4_mhc_epitope = "NA" self.best4_mhc_allele = "NA" + self.best4_mhc_position = "NA" self.directed_to_TCR = "NA" self.best4_affinity = "NA" - self.best4_affinity_epitope = "NA" + self.best4_affinity_epitope = "-" self.best4_affinity_allele = "NA" + self.best4_affinity_position = "NA" self.best4_affinity_directed_to_TCR = "NA" self.epitope_affinities = "" self.generator_rate = "" self.mhcI_score_9mer = "NA" self.mhcI_score_allele_9mer = "NA" - self.mhcI_score_epitope_9mer = "NA" + self.mhcI_score_position_9mer = "NA" + self.mhcI_score_epitope_9mer = "-" self.mhcI_affinity_9mer = "NA" self.mhcI_affinity_allele_9mer = "NA" - self.mhcI_affinity_epitope_9mer = "NA" + self.mhcI_affinity_position_9mer = "NA" + self.mhcI_affinity_epitope_9mer = "-" # WT features self.MHC_epitope_scores_WT = "" self.MHC_epitope_seqs_WT = "" @@ -115,13 +119,15 @@ def main(self, xmer_wt, xmer_mut, alleles, set_available_mhc): self.best4_mhc_score = np.add_best_epitope_info(best_epi, "%Rank") self.best4_mhc_epitope = np.add_best_epitope_info(best_epi, "Peptide") self.best4_mhc_allele = np.add_best_epitope_info(best_epi, "HLA") - self.directed_to_TCR = np.mutation_in_loop(position_xmer=position_xmer, epitope_tuple=best_epi) + self.best4_mhc_position = np.add_best_epitope_info(best_epi, "Pos") + self.directed_to_TCR = np.mutation_in_loop(position_xmer_list=position_xmer, epitope_tuple=best_epi) best_epi_affinity = np.minimal_binding_score(preds, rank=False) self.best4_affinity = np.add_best_epitope_info(best_epi_affinity, "Aff(nM)") self.best4_affinity_epitope = np.add_best_epitope_info(best_epi_affinity, "Peptide") self.best4_affinity_allele = np.add_best_epitope_info(best_epi_affinity, "HLA") + self.best4_affinity_position = np.add_best_epitope_info(best_epi_affinity, "Pos") self.best4_affinity_directed_to_TCR = np.mutation_in_loop( - position_xmer=position_xmer, epitope_tuple=best_epi_affinity) + position_xmer_list=position_xmer, epitope_tuple=best_epi_affinity) # multiple binding based on affinity self.generator_rate = mb.determine_number_of_binders(list_scores=all_affinities, threshold=50) # best predicted epitope of length 9 @@ -130,9 +136,11 @@ def main(self, xmer_wt, xmer_mut, alleles, set_available_mhc): best_9mer_affinity = np.minimal_binding_score(preds_9mer, rank=False) self.mhcI_score_9mer = np.add_best_epitope_info(best_9mer, "%Rank") self.mhcI_score_allele_9mer = np.add_best_epitope_info(best_9mer, "HLA") + self.mhcI_score_position_9mer = np.add_best_epitope_info(best_9mer, "Pos") self.mhcI_score_epitope_9mer = np.add_best_epitope_info(best_9mer, "Peptide") self.mhcI_affinity_9mer = np.add_best_epitope_info(best_9mer_affinity, "Aff(nM)") self.mhcI_affinity_allele_9mer = np.add_best_epitope_info(best_9mer_affinity, "HLA") + self.mhcI_affinity_position_9mer = np.add_best_epitope_info(best_9mer_affinity, "Pos") self.mhcI_affinity_epitope_9mer = np.add_best_epitope_info(best_9mer_affinity, "Peptide") ### PREDICTION FOR WT SEQUENCE @@ -162,11 +170,14 @@ def main(self, xmer_wt, xmer_mut, alleles, set_available_mhc): self.MHC_number_strong_binders_WT = mb.determine_number_of_binders(all, 1) self.MHC_number_weak_binders_WT = mb.determine_number_of_binders(all, 2) # best prediction - best_epi = np.filter_for_WT_epitope(preds, self.best4_mhc_epitope, self.best4_mhc_allele) + best_epi = np.filter_for_WT_epitope_position(preds, self.best4_mhc_epitope, + position_epi_xmer=self.best4_mhc_position) self.best4_mhc_score_WT = np.add_best_epitope_info(best_epi, "%Rank") self.best4_mhc_epitope_WT = np.add_best_epitope_info(best_epi, "Peptide") self.best4_mhc_allele_WT = np.add_best_epitope_info(best_epi, "HLA") - best_epi_affinity = np.filter_for_WT_epitope(preds, self.best4_affinity_epitope, self.best4_affinity_allele) + + best_epi_affinity = np.filter_for_WT_epitope_position(preds, self.best4_affinity_epitope, + position_epi_xmer=self.best4_affinity_position) self.best4_affinity_WT = np.add_best_epitope_info(best_epi_affinity, "Aff(nM)") self.best4_affinity_epitope_WT = np.add_best_epitope_info(best_epi_affinity, "Peptide") self.best4_affinity_allele_WT = np.add_best_epitope_info(best_epi_affinity, "HLA") @@ -174,9 +185,10 @@ def main(self, xmer_wt, xmer_mut, alleles, set_available_mhc): logger.info("WT: {}; MUT: {}".format(self.generator_rate_WT, self.generator_rate)) # best predicted epitope of length 9 preds_9mer = np.filter_for_9mers(preds) - best_9mer = np.filter_for_WT_epitope(preds_9mer, self.mhcI_score_epitope_9mer, self.mhcI_score_allele_9mer) - best_9mer_affinity = np.filter_for_WT_epitope(preds_9mer, mut_seq=self.mhcI_affinity_epitope_9mer, - mut_allele=self.mhcI_affinity_allele_9mer) + best_9mer = np.filter_for_WT_epitope_position(preds_9mer, self.mhcI_score_epitope_9mer, + position_epi_xmer=self.mhcI_score_position_9mer) + best_9mer_affinity = np.filter_for_WT_epitope_position(preds_9mer, mut_seq=self.mhcI_affinity_epitope_9mer, + position_epi_xmer=self.mhcI_affinity_position_9mer) self.mhcI_score_9mer_WT = np.add_best_epitope_info(best_9mer, "%Rank") self.mhcI_score_allele_9mer_WT = np.add_best_epitope_info(best_9mer, "HLA") self.mhcI_score_epitope_9mer_WT = np.add_best_epitope_info(best_9mer, "Peptide") From eba5e555267ca4a9516eb26a70680677074ac63f Mon Sep 17 00:00:00 2001 From: Lang Date: Fri, 3 Jul 2020 16:46:33 +0200 Subject: [PATCH 100/105] correct best wt epitope selection --- input/netmhcpan4/netmhcIIpan_prediction.py | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) diff --git a/input/netmhcpan4/netmhcIIpan_prediction.py b/input/netmhcpan4/netmhcIIpan_prediction.py index 146ad13f..f462a123 100755 --- a/input/netmhcpan4/netmhcIIpan_prediction.py +++ b/input/netmhcpan4/netmhcIIpan_prediction.py @@ -147,21 +147,19 @@ def minimal_binding_score(self, prediction_tuple, rank=True): row = i return dat_head, row - def filter_for_WT_epitope(self, prediction_tuple, mut_seq): + def filter_for_wt_epitope_position(self, prediction_tuple, mut_seq, position_epi_xmer): '''returns wt epitope info for given mutated sequence. best wt that is allowed to bind to any allele of patient ''' dat_head = prediction_tuple[0] dat = prediction_tuple[1] seq_col = dat_head.index("Peptide") - allele_col = dat_head.index("Allele") + pos_col = dat_head.index("Seq") wt_epi = [] for ii, i in enumerate(dat): wt_seq = i[seq_col] - wt_allele = i[allele_col] - if (len(wt_seq) == len(mut_seq)): - numb_mismatch = self.hamming_check_0_or_1(mut_seq, wt_seq) - if numb_mismatch == 1: - wt_epi.append(i) + wt_pos = i[pos_col] + if (len(wt_seq) == len(mut_seq)) & (wt_pos == position_epi_xmer): + wt_epi.append(i) dt = (dat_head, wt_epi) min = self.minimal_binding_score(dt) return (min) \ No newline at end of file From 31467d75f5759a0baa9afa5ecbcbb90e82167f7c Mon Sep 17 00:00:00 2001 From: Lang Date: Fri, 3 Jul 2020 16:47:23 +0200 Subject: [PATCH 101/105] correct best wt epitope selection + adjust mutation in loop for several SNVs per xmer sequences --- input/netmhcpan4/netmhcpan_prediction.py | 37 +++++++++++++++++------- 1 file changed, 27 insertions(+), 10 deletions(-) diff --git a/input/netmhcpan4/netmhcpan_prediction.py b/input/netmhcpan4/netmhcpan_prediction.py index 6d48018f..d29561ce 100755 --- a/input/netmhcpan4/netmhcpan_prediction.py +++ b/input/netmhcpan4/netmhcpan_prediction.py @@ -122,7 +122,7 @@ def minimal_binding_score(self, prediction_tuple, rank=True): row = i return dat_head, row - def mutation_in_loop(self, position_xmer, epitope_tuple): + def mutation_in_loop(self, position_xmer_list, epitope_tuple): """ returns if mutation is directed to TCR (yes or no) """ @@ -131,17 +131,17 @@ def mutation_in_loop(self, position_xmer, epitope_tuple): pos_epi = dat_head.index("Pos") del_pos = dat_head.index("Gp") del_len = dat_head.index("Gl") - directed_to_TCR = "no" - try: + directed_to_tcr_list = [False] + for position_mutation_xmer in position_xmer_list: if del_pos > 0: pos = int(dat_epi[pos_epi]) start = pos + int(dat_epi[del_pos]) - 1 end = start + int(dat_epi[del_len]) - if start < int(position_xmer) <= end: - directed_to_TCR = "yes" - return directed_to_TCR - except IndexError: - return "NA" + if start < position_mutation_xmer <= end: + directed_to_tcr_list.append("yes") + directed_to_tcr = any(directed_to_tcr_list) + return directed_to_tcr + def filter_for_9mers(self, prediction_tuple): '''returns only predicted 9mers @@ -156,7 +156,7 @@ def filter_for_9mers(self, prediction_tuple): dat_9mers.append(i) return dat_head, dat_9mers - def filter_for_WT_epitope(self, prediction_tuple, mut_seq, mut_allele): + def filter_for_WT_epitope(self, prediction_tuple, mut_seq, mut_allele, number_snv): '''returns wt epitope info for given mutated sequence. best wt that is allowed to bind to any allele of patient ''' dat_head = prediction_tuple[0] @@ -169,8 +169,25 @@ def filter_for_WT_epitope(self, prediction_tuple, mut_seq, mut_allele): wt_allele = i[allele_col] if (len(wt_seq) == len(mut_seq)): numb_mismatch = self.hamming_check_0_or_1(mut_seq, wt_seq) - if numb_mismatch == 1: + if numb_mismatch <= number_snv: wt_epi.append(i) dt = (dat_head, wt_epi) min = self.minimal_binding_score(dt) return (min) + + def filter_for_WT_epitope_position(self, prediction_tuple, mut_seq, position_epi_xmer): + '''returns wt epitope info for given mutated sequence. best wt that is allowed to bind to any allele of patient + ''' + dat_head = prediction_tuple[0] + dat = prediction_tuple[1] + seq_col = dat_head.index("Peptide") + pos_col = dat_head.index("Pos") + wt_epi = [] + for ii, i in enumerate(dat): + wt_seq = i[seq_col] + wt_pos = i[pos_col] + if (len(wt_seq) == len(mut_seq)) & (wt_pos == position_epi_xmer): + wt_epi.append(i) + dt = (dat_head, wt_epi) + min = self.minimal_binding_score(dt) + return (min) From 6725e259f0051c62c98c62ea512651e9123b741c Mon Sep 17 00:00:00 2001 From: Lang Date: Fri, 3 Jul 2020 16:50:46 +0200 Subject: [PATCH 102/105] remove IEDB based columns under required columns in README --- README.md | 13 +------------ 1 file changed, 1 insertion(+), 12 deletions(-) diff --git a/README.md b/README.md index f5b6224d..f9810480 100755 --- a/README.md +++ b/README.md @@ -45,17 +45,6 @@ Pt29 HLA-A*03:01,HLA-A*02:01,HLA-B*07:02 HLA-DRB1*11:04,HLA-DRB1*15:01 69 ``` **Required Columns of iCaM Table:** -- MHC_I_epitope_.best_prediction. -- MHC_I_epitope_.WT. -- MHC_II_epitope_.best_prediction. -- MHC_II_epitope_.WT. -- MHC_I_score_.best_prediction. -- MHC_I_score_.WT. -- MHC_II_score_.best_prediction. -- MHC_II_score_.WT. -- MHC_I_peptide_length_.best_prediction. -- MHC_I_allele_.best_prediction. -- MHC_II_allele_.best_prediction. - transcript_expression - VAF_in_RNA - VAF_in_tumor @@ -146,4 +135,4 @@ The unit tests do not have any dependency and they finish in seconds. Run the unit tests as follows: ``` python -m unittest discover input.tests.unit_tests -``` \ No newline at end of file +``` From 355e6de6f4093d1e52d19d950a0d63590a19914b Mon Sep 17 00:00:00 2001 From: Lang Date: Sat, 4 Jul 2020 17:30:50 +0200 Subject: [PATCH 103/105] correct add_dissimilarity epitope_mhci to epitope_mhcii --- input/epitope.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/input/epitope.py b/input/epitope.py index 9ff00d8b..a809abf9 100755 --- a/input/epitope.py +++ b/input/epitope.py @@ -718,7 +718,7 @@ def add_dissimilarity(self, epitope_mhci, affinity_mhci, epitope_mhcii, affinity self.add_features(self.dissimilarity_calculator.calculate_dissimilarity( mhc_mutation=epitope_mhcii, mhc_affinity=affinity_mhcii, references=self.references), "dissimilarity_mhcII") - elif epitope_mhci == "-": + elif epitope_mhcii == "-": self.add_features("NA", "dissimilarity_mhcII") From 68ad68b6ac795ca6de62989f44a9ac0e570450cf Mon Sep 17 00:00:00 2001 From: Pablo Riesgo Ferreiro Date: Wed, 8 Jul 2020 11:53:27 +0200 Subject: [PATCH 104/105] fixes indentation in epitope.py --- input/epitope.py | 1485 +++++++++++++++++++++++----------------------- 1 file changed, 742 insertions(+), 743 deletions(-) diff --git a/input/epitope.py b/input/epitope.py index a1ba717b..8e2e7d94 100755 --- a/input/epitope.py +++ b/input/epitope.py @@ -20,746 +20,745 @@ class Epitope: - def __init__(self, runner, references, configuration, provean_annotator): - """ - :type runner: input.helpers.runner.Runner - :type references: input.references.ReferenceFolder - :type configuration: input.references.DependenciesConfiguration - :type provean_annotator: input.new_features.conservation_scores.ProveanAnnotator - """ - self.references = references - self.provean_annotator = provean_annotator - self.properties = {} - self.dissimilarity_calculator = DissimilarityCalculator(runner=runner, configuration=configuration) - self.neoantigen_fitness_calculator = NeoantigenFitnessCalculator(runner=runner, configuration=configuration) - self.neoag_calculator = NeoagCalculator(runner=runner, configuration=configuration) - self.predII = BestAndMultipleBinderMhcII(runner=runner, configuration=configuration) - self.predpresentation2 = MixMhc2Pred(runner=runner, configuration=configuration) - self.pred = BestAndMultipleBinder(runner=runner, configuration=configuration) - self.predpresentation = MixMHCpred(runner=runner, configuration=configuration) - self.tcell_predictor = TcellPrediction(references=self.references) - - def init_properties(self, col_nam, prop_list): - """Initiates epitope property storage in a dictionary - """ - properties = {} - for nam, char in zip(col_nam, prop_list): - properties[nam] = char - return properties - - def add_features(self, new_feature, new_feature_nam): - """Adds new features to already present epitope properties, stored in form of a dictioninary - """ - self.properties[new_feature_nam] = new_feature - - def write_to_file(self): - print(";".join([self.properties[key] for key in self.properties])) - - def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aaindex1_dict, aaindex2_dict, - set_available_mhc, set_available_mhcII, patient_hlaI, patient_hlaII, tumour_content, rna_avail): - """ Calculate new epitope features and add to dictonary that stores all properties - """ - self.properties = self.init_properties(col_nam, prop_list) - xmer_wt = self.properties["X.WT._..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."] - xmer_mut = self.properties["X..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."] - logger.info(xmer_mut) - - gene = properties_manager.get_gene(properties=self.properties) - patient_id = properties_manager.get_patient_id(self.properties) - vaf_tumor = self.properties.get("VAF_in_tumor", "NA") - vaf_rna = vaf_tumor if rna_avail.get(patient_id, "False") == "False" else \ - self.properties.get("VAF_in_RNA", vaf_tumor) - transcript_expr = self.properties["transcript_expression"] - alleles = properties_manager.get_hla_allele(self.properties, patient_hlaI) - alleles_hlaii = properties_manager.get_hla_allele(self.properties, patient_hlaII) - substitution = properties_manager.get_substitution(properties=self.properties) - - mutated_aminoacid = FeatureLiterature.wt_mut_aa(substitution=substitution, mut="mut") - self.add_features(mutated_aminoacid, "MUT_AA") - wt_aminoacid = FeatureLiterature.wt_mut_aa(substitution=substitution, mut="wt") - self.add_features(wt_aminoacid, "WT_AA") - - - # MHC binding independent features - self.add_expression_features(tumour_content, vaf_rna=vaf_rna, - transcript_expression=transcript_expr, patient_id=patient_id) - self.add_differential_expression_features(gene, ref_dat, expression_tumor=transcript_expr) - self.add_aminoacid_index_features(aaindex1_dict, aaindex2_dict, - mutation_aminoacid=mutated_aminoacid, wild_type_aminoacid=wt_aminoacid) - self.add_provean_score_features() - if "mutation_found_in_proteome" not in self.properties: - self.add_features(FeatureLiterature.match_in_proteome( - sequence=self.properties["X..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."], db=db), - "mutation_found_in_proteome") - - # HLA I predictions: NetMHCpan - self.pred.main(xmer_mut=xmer_mut, xmer_wt=xmer_wt, alleles=alleles, set_available_mhc=set_available_mhc) - self.add_netmhcpan4_features() - self.add_netmhcpan4_wt_features() - self.add_multiple_binding_features() - self.add_multiple_binding_numdiff() - # epitope sequences - epitope_wt_affinity, epitope_mut_affinity = properties_manager.get_netmhcpan4_epitopes( - properties=self.properties) - epitope_wt_affinity_9mer, epitope_mut_affinitiy_9mer = properties_manager.get_netmhcpan4_epitopes( - properties=self.properties, nine_mer=True) - epitope_wt_rank, epitope_mut_rank = properties_manager.get_netmhcpan4_epitopes_rank( - properties=self.properties) - # MHC affinities/scores - affinity_wt, affinity_mut = properties_manager.get_scores_netmhcpan4_affinity( - properties=self.properties, mhc=MHC_I) - affinity_wt_9mer, affinity_mut_9mer = properties_manager.get_scores_netmhcpan4_affinity_9mer( - properties=self.properties) - mhc_rank_wt, mhc_rank_mut = properties_manager \ - .get_scores_netmhcpan4_ranks(properties=self.properties, mhc=MHC_I) - wild_type_multiple_binding_score, mutation_multiple_binding_score = properties_manager. \ - get_scores_multiple_binding(self.properties, mhc=MHC_I) - - self.add_multiple_binding_scorediff(mut_score=mutation_multiple_binding_score, - wt_score=wild_type_multiple_binding_score) - # position of mutation - self.add_position_mutation(epi_wt=epitope_wt_affinity, epi_mut=epitope_mut_affinity, - epi_wt_9mer=epitope_wt_affinity_9mer, epi_mut_9mer=epitope_mut_affinitiy_9mer, - epi_mut_rank=epitope_mut_rank, epi_wt_rank=epitope_wt_rank) - # mutation in anchor - self.add_mutation_in_anchor() - # DAI - self.add_dai_mhci(aff_wt=affinity_wt, aff_mut=affinity_mut, - sc_wt=mhc_rank_wt, sc_mut=mhc_rank_mut) - # amplitude - self.add_amplitude_mhci(aff_wt=affinity_wt, aff_mut=affinity_mut, - sc_wt=mhc_rank_wt, sc_mut=mhc_rank_mut, - aff_wt_9mer=affinity_wt_9mer, aff_mut_9mer=affinity_mut_9mer) - # pathogensimilarity - self.add_pathogensimilarity(epi_mut_9mer=epitope_mut_affinitiy_9mer, epi_mut=epitope_mut_affinity, - epi_mut_rank=epitope_mut_rank) - # recognition potential - self.add_recognition_potential(aff_mut_9mer=affinity_mut_9mer) - self.add_adncdn_mhci(score_mut=affinity_mut) - # T cell predictor - self.add_tcell_predictor_features(gene, substitution=substitution, affinity=affinity_mut_9mer, - epitope=epitope_mut_affinitiy_9mer) - self.add_aminoacid_frequency_features(aa_freq_dict=aa_freq_dict, mutation_mhci=epitope_mut_rank, - nmer_freq_dict=nmer_freq_dict, mutated_aminoacid=mutated_aminoacid) - - # netMHCIIpan predictions - self.predII.main(sequence=xmer_mut, sequence_reference=xmer_wt, alleles=alleles_hlaii, - set_available_mhc=set_available_mhcII) - self.add_netmhciipan_features() - self.add_netmhciipan_wt_features() - self.add_multiple_binding_mhcii_features() - # MHC II scores - affinity_wt_mhcii, affinity_mut_mhcii = properties_manager.get_scores_netmhcpan4_affinity( - properties=self.properties, mhc=MHC_II) - rank_wt_mhcii, rank_mut_mhcii = properties_manager.get_scores_netmhcpan4_ranks( - properties=self.properties, mhc=MHC_II) - wild_type_multiple_binding_ii, mutation_multiple_binding_ii = properties_manager. \ - get_scores_multiple_binding(self.properties, mhc=MHC_II) - # MHC II epitopes - epitope_wt_rank_mhcii, epitope_mut_rank_mhcii = properties_manager.get_netmhciipan_epitopes( - self.properties, affinity=False) - epitope_wt_affinity_mhcii, epitope_mut_affinity_mhcii = properties_manager.get_netmhciipan_epitopes( - self.properties, affinity=True) - # DAI MHC II - self.add_dai_mhcii(aff_mut=affinity_mut_mhcii, aff_wt=affinity_wt_mhcii, - rank_mut=rank_mut_mhcii, rank_wt=rank_wt_mhcii) - # difference number epitopes - self.add_multiple_binding_numdiff_mhcii() - # difference scores mb - self.add_multiple_binding_scorediff_mhcii(mut_score=mutation_multiple_binding_ii, - wt_score=wild_type_multiple_binding_ii) - # amplitude - self.add_amplitude_mhcii(aff_wt=affinity_wt_mhcii, aff_mut=affinity_mut_mhcii, - sc_wt=rank_wt_mhcii, sc_mut=rank_mut_mhcii) - # recognition potential MHC II - self.add_recognition_potential_mhcii(epitope_mut_mhcii=epitope_mut_affinity_mhcii) - # ADN/CDN for MHC II - self.add_adncdn_mhcii(score_mut=rank_mut_mhcii) - # self-similarity - self.add_self_similarity_features(epitope_mut_mhci=epitope_mut_rank, epitope_wt_mhci=epitope_wt_rank, - rank_mut_mhci=mhc_rank_mut, rank_wt_mhci=mhc_rank_wt, - epitope_mut_mhcii=epitope_mut_rank_mhcii, - epitope_wt_mhcii=epitope_wt_rank_mhcii, - rank_mut_mhcii=rank_mut_mhcii, rank_wt_mhcii=rank_wt_mhcii) - # number of mismatches - self.add_add_number_mismatches(epi_wt_mhci=epitope_wt_rank, epi_mut_mhci=epitope_mut_rank, - epi_wt_mhcii=epitope_mut_rank_mhcii, epi_mut_mhcii=epitope_wt_rank_mhcii) - # priority score - self.add_priority_score(rank_mut=mhc_rank_mut, rank_wt=mhc_rank_wt, - mb_mut=mutation_multiple_binding_score, mb_wt=wild_type_multiple_binding_score, - vaf_transcr=vaf_rna, vaf_tum=vaf_tumor, expr=transcript_expr) - # neoag immunogenicity model - self.add_neoag(sample_id=patient_id, mut_peptide=epitope_mut_affinity, score_mut=affinity_mut, - ref_peptide=epitope_wt_affinity) - # IEDB immunogenicity - self.add_iedb_immunogenicity(epitope_mhci=epitope_mut_affinity, affinity_mhci=affinity_mut, - epitope_mhcii=epitope_mut_rank_mhcii) - # MixMHCpred - self.add_mix_mhc_pred_features(xmer_wt=xmer_wt, xmer_mut=xmer_mut, patient_hlai=patient_hlaI) - # MixMHC2pred - self.add_mix_mhc2_pred_features(xmer_mut=xmer_mut, xmer_wt=xmer_wt, patient_hlaII=patient_hlaII) - # dissimilarity to self-proteome - self.add_dissimilarity(epitope_mhci=epitope_mut_affinity, affinity_mhci=affinity_mut, - epitope_mhcii=epitope_mut_affinity_mhcii, affinity_mhcii=affinity_mut_mhcii) - # vaxrank - self.add_vax_rank_features() - - return self.properties - - def add_vax_rank_features(self): - # vaxrank - vaxrankscore = vaxrank.VaxRank() - vaxrankscore.main(mutation_scores=self.properties["MB_affinities"], - expression_score=self.properties["Expression_Mutated_Transcript"]) - self.add_features(vaxrankscore.total_binding_score, "vaxrank_binding_score") - self.add_features(vaxrankscore.ranking_score, "vaxrank_total_score") - - def add_mix_mhc2_pred_features(self, xmer_wt, xmer_mut, patient_hlaII): - # MixMHC2pred - # TODO:remove allele grep and pass as argument - alleles = properties_manager.get_hla_allele(self.properties, patient_hlaII) - self.predpresentation2.main(alleles=alleles, xmer_wt=xmer_wt, xmer_mut=xmer_mut) - self.add_features(self.predpresentation2.all_peptides, "MixMHC2pred_all_peptides") - self.add_features(self.predpresentation2.all_ranks, "MixMHC2pred_all_ranks") - self.add_features(self.predpresentation2.all_alleles, "MixMHC2pred_all_alleles") - self.add_features(self.predpresentation2.best_peptide, "MixMHC2pred_best_peptide") - self.add_features(self.predpresentation2.best_rank, "MixMHC2pred_best_rank") - self.add_features(self.predpresentation2.best_allele, "MixMHC2pred_best_allele") - self.add_features(self.predpresentation2.best_peptide_wt, "MixMHC2pred_best_peptide_wt") - self.add_features(self.predpresentation2.best_rank_wt, "MixMHC2pred_best_rank_wt") - self.add_features(self.predpresentation2.difference_score_mut_wt, "MixMHC2pred_difference_rank_mut_wt") - - def add_mix_mhc_pred_features(self, xmer_wt, xmer_mut, patient_hlai): - # MixMHCpred - # TODO:remove allele grep and pass as argument - alleles = properties_manager.get_hla_allele(self.properties, patient_hlai) - self.predpresentation.main(xmer_wt=xmer_wt, xmer_mut=xmer_mut, alleles=alleles) - self.add_features(self.predpresentation.all_peptides, "MixMHCpred_all_peptides") - self.add_features(self.predpresentation.all_scores, "MixMHCpred_all_scores") - self.add_features(self.predpresentation.all_ranks, "MixMHCpred_all_ranks") - self.add_features(self.predpresentation.all_alleles, "MixMHCpred_all_alleles") - self.add_features(self.predpresentation.best_peptide, "MixMHCpred_best_peptide") - self.add_features(self.predpresentation.best_score, "MixMHCpred_best_score") - self.add_features(self.predpresentation.best_rank, "MixMHCpred_best_rank") - self.add_features(self.predpresentation.best_allele, "MixMHCpred_best_allele") - self.add_features(self.predpresentation.best_peptide_wt, "MixMHCpred_best_peptide_wt") - self.add_features(self.predpresentation.best_score_wt, "MixMHCpred_best_score_wt") - self.add_features(self.predpresentation.best_rank_wt, "MixMHCpred_best_rank_wt") - self.add_features(self.predpresentation.difference_score_mut_wt, "MixMHCpred_difference_score_mut_wt") - - def add_tcell_predictor_features(self, gene, substitution, epitope, affinity): - # T cell predictor - self.add_features(self.tcell_predictor.calculate_tcell_predictor_score( - gene=gene, substitution=substitution, epitope=epitope, score=affinity), - "Tcell_predictor_score_unfiltered") - self.add_features(self.tcell_predictor.calculate_tcell_predictor_score( - gene=gene, substitution=substitution, epitope=epitope, score=affinity, threshold=500), - "Tcell_predictor_score_9mersPredict") - - def add_self_similarity_features(self, epitope_mut_mhci, epitope_wt_mhci, epitope_mut_mhcii, epitope_wt_mhcii, - rank_mut_mhci, rank_wt_mhci, rank_mut_mhcii, rank_wt_mhcii): - # selfsimilarity - self.add_features(self_similarity.get_self_similarity(mutation=epitope_mut_mhci, wild_type=epitope_wt_mhci), - "Selfsimilarity_mhcI") - self.add_features(self_similarity.get_self_similarity( - wild_type=epitope_wt_mhcii, mutation=epitope_mut_mhcii), "Selfsimilarity_mhcII") - self.add_features(self_similarity.is_improved_binder( - score_mutation=rank_mut_mhci, score_wild_type=rank_wt_mhci - ), "ImprovedBinding_mhcI") - self.add_features(self_similarity.is_improved_binder( - # TODO: conversion from float representation needs to be changed - score_mutation=rank_mut_mhcii, score_wild_type=rank_wt_mhcii - ), "ImprovedBinding_mhcII") - self.add_features(self_similarity.self_similarity_of_conserved_binder_only( - has_conserved_binder=self.properties["ImprovedBinding_mhcI"], - similarity=self.properties["Selfsimilarity_mhcI"]), - "Selfsimilarity_mhcI_conserved_binder") - - def add_netmhcpan4_features(self): - """ - returns netMHCpan affinity and rank scores of mutated epitope - """ - # netmhcpan4 MUT rank score - self.add_features(self.pred.best4_mhc_score, "best%Rank_netmhcpan4") - self.add_features(self.pred.best4_mhc_epitope, "best_epitope_netmhcpan4") - self.add_features(self.pred.best4_mhc_allele, "bestHLA_allele_netmhcpan4") - self.add_features(self.pred.directed_to_TCR, "directed_to_TCR") - # netmhcpan4 mut affinity - self.add_features(self.pred.best4_affinity, "best_affinity_netmhcpan4") - self.add_features(self.pred.best4_affinity_epitope, "best_affinity_epitope_netmhcpan4") - self.add_features(self.pred.best4_affinity_allele, "bestHLA_allele_affinity_netmhcpan4") - self.add_features(self.pred.best4_affinity_directed_to_TCR, "affinity_directed_to_TCR") - # netMHCpan MUT best 9mer score - self.add_features(self.pred.mhcI_score_9mer, "best%Rank_netmhcpan4_9mer") - self.add_features(self.pred.mhcI_score_epitope_9mer, "best_epitope_netmhcpan4_9mer") - self.add_features(self.pred.mhcI_score_allele_9mer, "bestHLA_allele_netmhcpan4_9mer") - # netmhcpan4 mut best 9mer affinity - self.add_features(self.pred.mhcI_affinity_9mer, "best_affinity_netmhcpan4_9mer") - self.add_features(self.pred.mhcI_affinity_allele_9mer, "bestHLA_allele_affinity_netmhcpan4_9mer") - self.add_features(self.pred.mhcI_affinity_epitope_9mer, "best_affinity_epitope_netmhcpan4_9mer") - - def add_netmhcpan4_wt_features(self): - """ - returns netMHCpan affinity and rank scores of WT epitope - """ - # netmhcpan4 WT best affinity - self.add_features(self.pred.best4_affinity_WT, "best_affinity_netmhcpan4_WT") - self.add_features(self.pred.best4_affinity_epitope_WT, "best_affinity_epitope_netmhcpan4_WT") - self.add_features(self.pred.best4_affinity_allele_WT, "bestHLA_allele_affinity_netmhcpan4_WT") - # netmhcpan4 WT rank score - self.add_features(self.pred.best4_mhc_score_WT, "best%Rank_netmhcpan4_WT") - self.add_features(self.pred.best4_mhc_epitope_WT, "best_epitope_netmhcpan4_WT") - self.add_features(self.pred.best4_mhc_allele_WT, "bestHLA_allele_netmhcpan4_WT") - # netMHCpan WT best 9mer score - self.add_features(self.pred.mhcI_score_9mer_WT, "best%Rank_netmhcpan4_9mer_WT") - self.add_features(self.pred.mhcI_score_epitope_9mer_WT, "best_epitope_netmhcpan4_9mer_WT") - self.add_features(self.pred.mhcI_score_allele_9mer_WT, "bestHLA_allele_netmhcpan4_9mer_Wt") - # netmhcpan4 WT best 9mer affinity - self.add_features(self.pred.mhcI_affinity_9mer_WT, "best_affinity_netmhcpan4_9mer_WT") - self.add_features(self.pred.mhcI_affinity_allele_9mer_WT, "bestHLA_allele_affinity_netmhcpan4_9mer_WT") - self.add_features(self.pred.mhcI_affinity_epitope_9mer_WT, "best_affinity_epitope_netmhcpan4_9mer_WT") - - def add_position_mutation(self, epi_wt, epi_mut, epi_wt_9mer, epi_mut_9mer, epi_mut_rank, epi_wt_rank): - """ - returns position of mutation for best affinity epitope across all lengths and 9mer - :return: - """ - self.add_features(self_similarity.position_of_mutation_epitope( - wild_type=epi_wt, mutation=epi_mut), "pos_MUT_MHCI_affinity_epi") - self.add_features(self_similarity.position_of_mutation_epitope( - wild_type=epi_wt_9mer, mutation=epi_mut_9mer), - "pos_MUT_MHCI_affinity_epi_9mer") - self.add_features(self_similarity.position_of_mutation_epitope( - wild_type=epi_wt_rank, mutation=epi_mut_rank), - "pos_MUT_MHCI_rank_epi") - - def add_mutation_in_anchor(self): - """ - returns if mutation is in anchor position for best affinity epitope over all lengths and best 9mer affinity - """ - self.add_features(self_similarity.position_in_anchor_position( - position_mhci=self.properties["pos_MUT_MHCI_affinity_epi"], - peptide_length=len(self.properties["best_affinity_epitope_netmhcpan4"])), - "Mutation_in_anchor_netmhcpan") - self.add_features(self_similarity.position_in_anchor_position( - position_mhci=self.properties["pos_MUT_MHCI_affinity_epi_9mer"], - peptide_length=9), - "Mutation_in_anchor_netmhcpan_9mer") - self.add_features(self_similarity.position_in_anchor_position( - position_mhci=self.properties["pos_MUT_MHCI_affinity_epi_9mer"], - peptide_length=len(self.properties["best_epitope_netmhcpan4"])), - "Mutation_in_anchor_netmhcpan_rank") - - def add_dai_mhci(self, aff_wt, aff_mut, sc_wt, sc_mut): - """ - returns DAI based on affinity and based on rank score - """ - # DAI with affinity values - self.add_features( - FeatureLiterature.dai(score_mutation=aff_mut, - score_wild_type=aff_wt, affin_filtering=True), - "DAI_affinity_filtered") - self.add_features( - FeatureLiterature.dai(score_mutation=aff_mut, - score_wild_type=aff_wt), - "DAI_affinity") - # DAI wiht rank scores by netmhcpan4 - self.add_features( - FeatureLiterature.dai(score_mutation=sc_mut, - score_wild_type=sc_wt), - "DAI_rank_netmhcpan4") - - def add_amplitude_mhci(self, aff_wt, aff_mut, sc_wt, sc_mut, aff_wt_9mer, aff_mut_9mer): - """ - ratio in MHC binding based on affinity (all length), rank score, affintiy (9mer) - """ - self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( - score_mutation=aff_mut, score_wild_type=aff_wt, - apply_correction=True), "Amplitude_mhcI_affinity") - # Amplitude with rank by netmhcpan4 - self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( - score_mutation=sc_mut, score_wild_type=sc_wt), - "Amplitude_mhcI_rank_netmhcpan4") - # Amplitude based on best affinity prediction restricted to 9mers - self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( - score_mutation=aff_mut_9mer, score_wild_type=aff_wt_9mer, - apply_correction=True), "Amplitude_mhcI_affinity_9mer_netmhcpan4") - - def add_pathogensimilarity(self, epi_mut_9mer, epi_mut, epi_mut_rank): - """ - pathogensimilarity for best affinity (all length), best affinity (9mer), rank score - """ - self.add_features( - self.neoantigen_fitness_calculator.wrap_pathogen_similarity( - mutation=epi_mut_9mer, iedb=self.references.iedb), - "Pathogensimiliarity_mhcI_9mer") - self.add_features( - self.neoantigen_fitness_calculator.wrap_pathogen_similarity( - mutation=epi_mut_rank, iedb=self.references.iedb), - "Pathogensimiliarity_mhcI_rank") - self.add_features( - self.neoantigen_fitness_calculator.wrap_pathogen_similarity( - mutation=epi_mut, iedb=self.references.iedb), - "Pathogensimiliarity_mhcI_affinity_nmers") - - def add_recognition_potential(self, aff_mut_9mer): - """ - recognition potential for affinity (all lengths), affinity (9mers) - """ - # recogntion potential with amplitude by affinity and netmhcpan4 score - self.add_features(self.neoantigen_fitness_calculator.calculate_recognition_potential( - amplitude=self.properties["Amplitude_mhcI_affinity"], - pathogen_similarity=self.properties["Pathogensimiliarity_mhcI_affinity_nmers"], - mutation_in_anchor=self.properties["Mutation_in_anchor_netmhcpan"]), - "Recognition_Potential_mhcI_affinity") - self.add_features(self.neoantigen_fitness_calculator.calculate_recognition_potential( - amplitude=self.properties["Amplitude_mhcI_rank_netmhcpan4"], - pathogen_similarity=self.properties["Pathogensimiliarity_mhcI_rank"], - mutation_in_anchor=self.properties["Mutation_in_anchor_netmhcpan_rank"]), - "Recognition_Potential_mhcI_rank_netmhcpan4") - # recogntion potential with amplitude by affinity and only 9mers considered --> value as published!! - self.add_features(self.neoantigen_fitness_calculator.calculate_recognition_potential( - amplitude=self.properties["Amplitude_mhcI_affinity_9mer_netmhcpan4"], - pathogen_similarity=self.properties["Pathogensimiliarity_mhcI_9mer"], - mutation_in_anchor=self.properties["Mutation_in_anchor_netmhcpan_9mer"], - mhc_affinity_mut=aff_mut_9mer), - "Recognition_Potential_mhcI_9mer_affinity") - - def add_adncdn_mhci(self, score_mut): - """ - return if alternative or classical defined binder - """ - amplitude_mhci = self.properties["Amplitude_mhcI_affinity"] - bdg_cutoff_classical_mhci = 50 - bdg_cutoff_alternative_mhci = 5000 - amplitude_cutoff_mhci = 10 - self.add_features(FeatureLiterature.classify_adn_cdn( - score_mutation=score_mut, amplitude=amplitude_mhci, - bdg_cutoff_classical=bdg_cutoff_classical_mhci, bdg_cutoff_alternative=bdg_cutoff_alternative_mhci, - amplitude_cutoff=amplitude_cutoff_mhci, category="CDN"), "CDN_mhcI") - self.add_features(FeatureLiterature.classify_adn_cdn( - score_mutation=score_mut, amplitude=amplitude_mhci, - bdg_cutoff_classical=bdg_cutoff_classical_mhci, bdg_cutoff_alternative=bdg_cutoff_alternative_mhci, - amplitude_cutoff=amplitude_cutoff_mhci, - category="ADN"), "ADN_mhcI") - - def add_multiple_binding_features(self): - # multiplexed representation MUT - for sc, mn in zip(self.pred.MHC_score_all_epitopes, self.pred.mean_type): - self.add_features(sc, "MB_score_all_epitopes_" + mn) - for sc, mn in zip(self.pred.MHC_score_top10, self.pred.mean_type): - self.add_features(sc, "MB_score_top10_" + mn) - for sc, mn in zip(self.pred.MHC_score_best_per_alelle, self.pred.mean_type): - self.add_features(sc, "MB_score_best_per_alelle_" + mn) - # rename MB_score_best_per_alelle_harmonic to PHBR (described in Marty et al) - self.properties["PHBR-I"] = self.properties.pop("MB_score_best_per_alelle_harmonic") - self.add_features(self.pred.MHC_epitope_scores, "MB_epitope_scores") - self.add_features(self.pred.MHC_epitope_seqs, "MB_epitope_sequences") - self.add_features(self.pred.MHC_epitope_alleles, "MB_alleles") - self.add_features(self.pred.MHC_number_strong_binders, "MB_number_pep_MHCscore<1") - self.add_features(self.pred.MHC_number_weak_binders, "MB_number_pep_MHCscore<2") - # generator rate - self.add_features(self.pred.epitope_affinities, "MB_affinities") - self.add_features(self.pred.generator_rate, "Generator_rate") - # multiplexed representation WT - self.add_features(self.pred.MHC_epitope_scores_WT, "MB_epitope_WT_scores") - self.add_features(self.pred.MHC_epitope_seqs_WT, "MB_epitope_WT_sequences") - self.add_features(self.pred.MHC_epitope_alleles_WT, "MB_alleles_WT") - for sc, mn in zip(self.pred.MHC_score_top10_WT, self.pred.mean_type): - self.add_features(sc, "MB_score_WT_top10_" + mn) - for sc, mn in zip(self.pred.MHC_score_all_epitopes_WT, self.pred.mean_type): - self.add_features(sc, "MB_score_WT_all_epitopes_" + mn) - for sc, mn in zip(self.pred.MHC_score_best_per_alelle_WT, self.pred.mean_type): - self.add_features(sc, "MB_score_WT_best_per_alelle_" + mn) - self.properties["PHBR-I_WT"] = self.properties.pop("MB_score_WT_best_per_alelle_harmonic") - self.add_features(self.pred.MHC_number_strong_binders_WT, "MB_number_pep_WT_MHCscore<1") - self.add_features(self.pred.MHC_number_weak_binders_WT, "MB_number_pep_WT_MHCscore<2") - # generator rate - self.add_features(self.pred.epitope_affinities_WT, "MB_affinities_WT") - self.add_features(self.pred.generator_rate_WT, "Generator_rate_WT") - - def add_multiple_binding_numdiff(self): - """ - returns difference and ratio of # epitopes with rank scores < 1 or 2 for mutant and wt sequence - """ - for threshold in [1, 2]: - num_mutation = self.properties["MB_number_pep_MHCscore<{}".format(threshold)] - num_wild_type = self.properties["MB_number_pep_WT_MHCscore<{}".format(threshold)] - self.add_features(FeatureLiterature.diff_number_binders( - num_mutation=num_mutation, num_wild_type=num_wild_type), "Diff_numb_epis_<{}".format(threshold)) - self.add_features(FeatureLiterature.ratio_number_binders( - num_mutation=num_mutation, num_wild_type=num_wild_type), "Ratio_numb_epis_<{}".format(threshold)) - - def add_multiple_binding_scorediff(self, mut_score, wt_score): - """ - returns DAI and amplitude with multiple binding score - """ - self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( - score_mutation=mut_score, score_wild_type=wt_score), - "Amplitude_mhcI_MB") - self.add_features( - FeatureLiterature.dai(score_mutation=mut_score, score_wild_type=wt_score), - "DAI_mhcI_MB") - - def add_netmhciipan_features(self): - """ - returns results from MHC II prediction for mutation - """ - # netmhcpan4 MUT scores - self.add_features(self.predII.best_mhcII_pan_score, "best%Rank_netmhcIIpan") - self.add_features(self.predII.best_mhcII_pan_epitope, "best_epitope_netmhcIIpan") - self.add_features(self.predII.best_mhcII_pan_allele, "bestHLA_allele_netmhcIIpan") - # netmhcpan4 mut affinity - self.add_features(self.predII.best_mhcII_pan_affinity, "best_affinity_netmhcIIpan") - self.add_features(self.predII.best_mhcII_pan_affinity_epitope, "best_affinity_epitope_netmhcIIpan") - self.add_features(self.predII.best_mhcII_pan_affinity_allele, "bestHLA_allele_affinity_netmhcIIpan") - - def add_netmhciipan_wt_features(self): - """ - returns results from MHC II prediction for WT - """ - # netmhcIIpan WT scores - self.add_features(self.predII.best_mhcII_pan_score_WT, "best%Rank_netmhcIIpan_WT") - self.add_features(self.predII.best_mhcII_pan_epitope_WT, "best_epitope_netmhcIIpan_WT") - self.add_features(self.predII.best_mhcII_pan_allele_WT, "bestHLA_allele_netmhcIIpan_Wt") - # netmhcIIpan wt affinity - self.add_features(self.predII.best_mhcII_affinity_WT, "best_affinity_netmhcIIpan_WT") - self.add_features(self.predII.best_mhcII_affinity_epitope_WT, "best_affinity_epitope_netmhcIIpan_WT") - self.add_features(self.predII.best_mhcII_affinity_allele_WT, "bestHLA_allele_affinity_netmhcIIpan_WT") - - def add_multiple_binding_mhcii_features(self): - """ - returns results from MHC II prediction for multiple binding features - """ - # multiplexed representation MUT MHC II - for sc, mn in zip(self.predII.MHCII_score_all_epitopes, self.predII.mean_type): - self.add_features(sc, "MB_score_MHCII_all_epitopes_" + mn) - for sc, mn in zip(self.predII.MHCII_score_top10, self.predII.mean_type): - self.add_features(sc, "MB_score_MHCII_top10_" + mn) - for sc, mn in zip(self.predII.MHCII_score_best_per_alelle, self.predII.mean_type): - self.add_features(sc, "MB_score_MHCII_best_per_alelle_" + mn) - # rename MB_score_best_per_alelle_harmonic to PHBR (described in Marty et al) - self.properties["PHBR-II"] = self.properties.pop("MB_score_MHCII_best_per_alelle_harmonic") - self.add_features(self.predII.MHCII_epitope_scores, "MB_mhcII_epitope_scores") - self.add_features(self.predII.MHCII_epitope_seqs, "MB_mhcII_epitope_sequences") - self.add_features(self.predII.MHCII_epitope_alleles, "MB_mhcII_alleles") - self.add_features(self.predII.MHCII_number_strong_binders, "MB_number_pep_MHCIIscore<2") - self.add_features(self.predII.MHCII_number_weak_binders, "MB_number_pep_MHCIIscore<10") - # multiplexed representation WT MHC II - for sc, mn in zip(self.predII.MHCII_score_all_epitopes_WT, self.predII.mean_type): - self.add_features(sc, "MB_score_MHCII_all_epitopes_WT_" + mn) - for sc, mn in zip(self.predII.MHCII_score_top10_WT, self.predII.mean_type): - self.add_features(sc, "MB_score_MHCII_top10_WT_" + mn) - for sc, mn in zip(self.predII.MHCII_score_best_per_alelle_WT, self.predII.mean_type): - self.add_features(sc, "MB_score_MHCII_best_per_alelle_WT_" + mn) - # rename MB_score_best_per_alelle_harmonic to PHBR (described in Marty et al) - if "MB_score_MHCII_best_per_alelle_WT_harmonic" in self.properties: - self.properties["PHBR-II_WT"] = self.properties.pop("MB_score_MHCII_best_per_alelle_WT_harmonic") - self.add_features(self.predII.MHCII_epitope_scores_WT, "MB_mhcII_epitope_scores_WT") - self.add_features(self.predII.MHCII_epitope_seqs_WT, "MB_mhcII_epitope_sequences_WT") - self.add_features(self.predII.MHCII_epitope_alleles_WT, "MB_mhcII_alleles_WT") - self.add_features(self.predII.MHCII_number_strong_binders_WT, "MB_number_pep_MHCIIscore<2_WT") - self.add_features(self.predII.MHCII_number_weak_binders_WT, "MB_number_pep_MHCIIscore<10_WT") - - def add_dai_mhcii(self, aff_mut, aff_wt, rank_mut, rank_wt): - """ - returns DAI for MHC II based on affinity (filtered + no filtered) and rank - """ - # dai mhc II affinity - self.add_features( - FeatureLiterature.dai(score_mutation=aff_mut, score_wild_type=aff_wt), - "DAI_mhcII_affinity") - self.add_features( - FeatureLiterature.dai(score_mutation=aff_mut, score_wild_type=aff_wt, affin_filtering=True), - "DAI_mhcII_affinity_aff_filtered") - # dai mhc II netMHCIIpan score - self.add_features( - FeatureLiterature.dai(score_mutation=rank_mut, score_wild_type=rank_wt), - "DAI_mhcII_rank") - - def add_multiple_binding_numdiff_mhcii(self): - """ - returns difference and ratio of # epitopes with rank scores < 2 or 10 for mutant and wt sequence for MHC II - """ - for threshold in [2, 10]: - num_mutation = self.properties["MB_number_pep_MHCIIscore<{}".format(threshold)] - num_wild_type = self.properties["MB_number_pep_MHCIIscore<{}_WT".format(threshold)] - self.add_features(FeatureLiterature.diff_number_binders( - num_mutation=num_mutation, num_wild_type=num_wild_type), - "Diff_numb_epis_mhcII<{}".format(threshold)) - self.add_features(FeatureLiterature.ratio_number_binders( - num_mutation=num_mutation, num_wild_type=num_wild_type), - "Ratio_numb_epis_mhcII<{}".format(threshold)) - - def add_multiple_binding_scorediff_mhcii(self, mut_score, wt_score): - """ - returns DAI and amplitude with multiple binding score - """ - self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( - score_mutation=mut_score, score_wild_type=wt_score), - "Amplitude_mhcII_mb") - # dai multiple binding mhc II - self.add_features( - FeatureLiterature.dai(score_mutation=mut_score, score_wild_type=wt_score), - "DAI_mhcII_MB") - - def add_amplitude_mhcii(self, aff_wt, aff_mut, sc_wt, sc_mut): - """ - ratio in MHC binding based on affinity (all length), rank score, affintiy (9mer) - """ - # amplitude affinity mhc II - self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( - score_mutation=aff_mut, score_wild_type=aff_wt, apply_correction=True), - "Amplitude_mhcII_affinity") - # amplitude rank score mhc II - self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( - score_mutation=sc_mut, score_wild_type=sc_wt), - "Amplitude_mhcII_rank_netmhcpan4") - logger.info("Amplitude mhc II: {}".format(self.properties["Amplitude_mhcII_rank_netmhcpan4"])) - - def add_adncdn_mhcii(self, score_mut): - """ - return if alternative or classical defined binder for MHC II - """ - amplitude_mhcii = self.properties["Amplitude_mhcII_rank_netmhcpan4"] - bdg_cutoff_classical_mhcii = 1 - bdg_cutoff_alternative_mhcii = 4 - amplitude_cutoff_mhcii = 4 - self.add_features(FeatureLiterature.classify_adn_cdn( - score_mutation=score_mut, amplitude=amplitude_mhcii, - bdg_cutoff_classical=bdg_cutoff_classical_mhcii, bdg_cutoff_alternative=bdg_cutoff_alternative_mhcii, - amplitude_cutoff=amplitude_cutoff_mhcii, category="CDN"), "CDN_mhcII") - self.add_features(FeatureLiterature.classify_adn_cdn( - score_mutation=score_mut, amplitude=amplitude_mhcii, - bdg_cutoff_classical=bdg_cutoff_classical_mhcii, bdg_cutoff_alternative=bdg_cutoff_alternative_mhcii, - amplitude_cutoff=amplitude_cutoff_mhcii, category="ADN"), "ADN_mhcII") - - def add_recognition_potential_mhcii(self, epitope_mut_mhcii): - """ - neoantigen fitness for mhcII based on affinity - """ - self.add_features( - self.neoantigen_fitness_calculator.wrap_pathogen_similarity( - mutation=epitope_mut_mhcii, iedb=self.references.iedb), - "Pathogensimiliarity_mhcII") - self.add_features(self.neoantigen_fitness_calculator.calculate_recognition_potential( - amplitude=self.properties["Amplitude_mhcII_affinity"], - pathogen_similarity=self.properties["Pathogensimiliarity_mhcII"], - mutation_in_anchor="0"), - "Recognition_Potential_mhcII_affinity") - - def add_add_number_mismatches(self, epi_wt_mhci, epi_mut_mhci, epi_wt_mhcii, epi_mut_mhcii): - """ - returns number of mismatches between best MHCI / MHC II epitopes (rank) and their corresponding WTs - """ - self.add_features(FeatureLiterature.number_of_mismatches( - epitope_wild_type=epi_wt_mhci, epitope_mutation=epi_mut_mhci), "Number_of_mismatches_mhcI") - self.add_features(FeatureLiterature.number_of_mismatches( - epitope_wild_type=epi_wt_mhcii, epitope_mutation=epi_mut_mhcii), "Number_of_mismatches_mhcII") - - def add_priority_score(self, rank_mut, rank_wt, mb_mut, mb_wt, expr, vaf_tum, vaf_transcr): - """ - returns priority score for mhc I rank + multible binding - """ - no_mismatch = self.properties["Number_of_mismatches_mhcI"] - mut_in_prot = self.properties["mutation_found_in_proteome"] - # priority score with rank score - self.add_features(FeatureLiterature.calc_priority_score( - vaf_tumor=vaf_tum, vaf_rna=vaf_transcr, transcript_expr=expr, no_mismatch=no_mismatch, - score_mut=rank_mut, score_wt=rank_wt, mut_in_prot=mut_in_prot), "Priority_score") - # priority score using multiplexed representation score - self.add_features(FeatureLiterature.calc_priority_score( - vaf_tumor=vaf_tum, vaf_rna=vaf_transcr, transcript_expr=expr, no_mismatch=no_mismatch, - score_mut=mb_mut, score_wt=mb_wt, mut_in_prot=mut_in_prot), "Priority_score_MB") - - def add_neoag(self, sample_id, mut_peptide, score_mut, ref_peptide): - """ - returns neoag immunogenicity score - """ - peptide_variant_position = self.properties["pos_MUT_MHCI_affinity_epi"] - self.add_features(self.neoag_calculator.wrapper_neoag( - sample_id=sample_id, mut_peptide=mut_peptide, score_mut=score_mut, ref_peptide=ref_peptide, - peptide_variant_position=peptide_variant_position), "neoag_immunogencity") - - def add_iedb_immunogenicity(self, epitope_mhci, affinity_mhci, epitope_mhcii): - """ - returns IEDB immunogenicity for MHC I (based on affinity) and MHC II (based on rank) - """ - mhci_allele = self.properties["bestHLA_allele_affinity_netmhcpan4"] - mhcii_allele = self.properties["bestHLA_allele_netmhcIIpan"] - self.add_features(FeatureLiterature.calc_IEDB_immunogenicity( - epitope=epitope_mhci, mhc_allele=mhci_allele, mhc_score=affinity_mhci), "IEDB_Immunogenicity_mhcI") - self.add_features(FeatureLiterature.calc_IEDB_immunogenicity( - epitope=epitope_mhcii, mhc_allele=mhcii_allele, mhc_score=None), "IEDB_Immunogenicity_mhcII") - self.add_features(FeatureLiterature.calc_IEDB_immunogenicity( - epitope=epitope_mhci, mhc_allele=mhci_allele, mhc_score=affinity_mhci, affin_filtering=True), - "IEDB_Immunogenicity_mhcI_affinity_filtered") - - def add_dissimilarity(self, epitope_mhci, affinity_mhci, epitope_mhcii, affinity_mhcii): - """ - returns dissimilarity for MHC I (affinity) MHC II (affinity) - """ - self.add_features(self.dissimilarity_calculator.calculate_dissimilarity( - mhc_mutation=epitope_mhci, mhc_affinity=affinity_mhci, references=self.references), - "dissimilarity") - self.add_features(self.dissimilarity_calculator.calculate_dissimilarity( - mhc_mutation=epitope_mhci, mhc_affinity=affinity_mhci, references=self.references, - filter_binder=True), "dissimilarity_filter500") - self.add_features(self.dissimilarity_calculator.calculate_dissimilarity( - mhc_mutation=epitope_mhcii, mhc_affinity=affinity_mhcii, references=self.references), - "dissimilarity_mhcII") - - def add_provean_score_features(self): - # PROVEAN score - ucsc_id = self.provean_annotator.build_ucsc_id_plus_position( - substitution=self.properties["substitution"], ucsc_id=self.properties["UCSC_transcript"]) - self.add_features(ucsc_id, "UCSC_ID_position") - self.add_features(self.provean_annotator.get_provean_annotation( - mutated_aminoacid=self.properties['MUT_AA'], ucsc_id_position=ucsc_id), - "PROVEAN_score") - - def add_aminoacid_index_features(self, aaindex1_dict, aaindex2_dict, mutation_aminoacid, - wild_type_aminoacid): - # amino acid index - for k in aaindex1_dict: - self.add_features(aaindex1_dict[k].get(wild_type_aminoacid, "NA"), "{}_{}".format(k, "wt")) - self.add_features(aaindex1_dict[k].get(mutation_aminoacid, "NA"), "{}_{}".format(k, "mut")) - for k in aaindex2_dict: - self.add_features(aaindex2_dict[k].get(wild_type_aminoacid, {}).get(mutation_aminoacid, "NA"), k) - - def add_aminoacid_frequency_features(self, aa_freq_dict, mutation_mhci, nmer_freq_dict, mutated_aminoacid): - # amino acid frequency - self.add_features(freq_score.freq_aa(mutated_aminoacid=mutated_aminoacid, dict_freq=aa_freq_dict), - "Frequency_mutated_AA") - self.add_features(freq_score.freq_prod_4mer(mutation=mutation_mhci, dict_freq=aa_freq_dict), - "Product_Frequency_4mer") - self.add_features(freq_score.freq_4mer(mutation=mutation_mhci, dict_freq=nmer_freq_dict), - "Frequency_of_4mer") - - def add_expression_features(self, tumour_content, vaf_rna, patient_id, - transcript_expression): - # expression - self.add_features(FeatureLiterature.rna_expression_mutation( - transcript_expression=transcript_expression, vaf_rna=vaf_rna), "Expression_Mutated_Transcript") - expression_mutated_transcript = self.properties.get("Expression_Mutated_Transcript") - self.add_features(FeatureLiterature.expression_mutation_tc( - transcript_expression=expression_mutated_transcript, patient_id=patient_id, - tumour_content_dict=tumour_content), - "Expression_Mutated_Transcript_tumor_content") - - def add_differential_expression_features(self, gene, ref_dat, expression_tumor): - # differential expression - expression_reference = differential_expression.add_rna_reference(gene, ref_dat, 0) - expression_reference_sum = differential_expression.add_rna_reference(gene, ref_dat, 2) - expression_reference_sd = differential_expression.add_rna_reference(gene, ref_dat, 1) - self.add_features(expression_reference, "mean_ref_expression") - self.add_features(expression_reference_sd, "sd_ref_expression") - self.add_features(expression_reference_sum, "sum_ref_expression") - self.add_features(differential_expression.fold_change( - expression_tumor=expression_tumor, expression_reference=expression_reference), "log2_fc_tumour_ref") - self.add_features(differential_expression.percentile_calc( - expression_tumor=expression_tumor, expression_reference_sum=expression_reference_sum), - "percentile_tumour_ref") - self.add_features(differential_expression.pepper_calc( - expression_tumor=expression_tumor, expression_reference=expression_reference, - expression_reference_sd=expression_reference_sd), "DE_pepper") + def __init__(self, runner, references, configuration, provean_annotator): + """ + :type runner: input.helpers.runner.Runner + :type references: input.references.ReferenceFolder + :type configuration: input.references.DependenciesConfiguration + :type provean_annotator: input.new_features.conservation_scores.ProveanAnnotator + """ + self.references = references + self.provean_annotator = provean_annotator + self.properties = {} + self.dissimilarity_calculator = DissimilarityCalculator(runner=runner, configuration=configuration) + self.neoantigen_fitness_calculator = NeoantigenFitnessCalculator(runner=runner, configuration=configuration) + self.neoag_calculator = NeoagCalculator(runner=runner, configuration=configuration) + self.predII = BestAndMultipleBinderMhcII(runner=runner, configuration=configuration) + self.predpresentation2 = MixMhc2Pred(runner=runner, configuration=configuration) + self.pred = BestAndMultipleBinder(runner=runner, configuration=configuration) + self.predpresentation = MixMHCpred(runner=runner, configuration=configuration) + self.tcell_predictor = TcellPrediction(references=self.references) + + def init_properties(self, col_nam, prop_list): + """Initiates epitope property storage in a dictionary + """ + properties = {} + for nam, char in zip(col_nam, prop_list): + properties[nam] = char + return properties + + def add_features(self, new_feature, new_feature_nam): + """Adds new features to already present epitope properties, stored in form of a dictioninary + """ + self.properties[new_feature_nam] = new_feature + + def write_to_file(self): + print(";".join([self.properties[key] for key in self.properties])) + + def main(self, col_nam, prop_list, db, ref_dat, aa_freq_dict, nmer_freq_dict, aaindex1_dict, aaindex2_dict, + set_available_mhc, set_available_mhcII, patient_hlaI, patient_hlaII, tumour_content, rna_avail): + """ Calculate new epitope features and add to dictonary that stores all properties + """ + self.properties = self.init_properties(col_nam, prop_list) + xmer_wt = self.properties["X.WT._..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."] + xmer_mut = self.properties["X..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."] + logger.info(xmer_mut) + + gene = properties_manager.get_gene(properties=self.properties) + patient_id = properties_manager.get_patient_id(self.properties) + vaf_tumor = self.properties.get("VAF_in_tumor", "NA") + vaf_rna = vaf_tumor if rna_avail.get(patient_id, "False") == "False" else \ + self.properties.get("VAF_in_RNA", vaf_tumor) + transcript_expr = self.properties["transcript_expression"] + alleles = properties_manager.get_hla_allele(self.properties, patient_hlaI) + alleles_hlaii = properties_manager.get_hla_allele(self.properties, patient_hlaII) + substitution = properties_manager.get_substitution(properties=self.properties) + + mutated_aminoacid = FeatureLiterature.wt_mut_aa(substitution=substitution, mut="mut") + self.add_features(mutated_aminoacid, "MUT_AA") + wt_aminoacid = FeatureLiterature.wt_mut_aa(substitution=substitution, mut="wt") + self.add_features(wt_aminoacid, "WT_AA") + + # MHC binding independent features + self.add_expression_features(tumour_content, vaf_rna=vaf_rna, + transcript_expression=transcript_expr, patient_id=patient_id) + self.add_differential_expression_features(gene, ref_dat, expression_tumor=transcript_expr) + self.add_aminoacid_index_features(aaindex1_dict, aaindex2_dict, + mutation_aminoacid=mutated_aminoacid, wild_type_aminoacid=wt_aminoacid) + self.add_provean_score_features() + if "mutation_found_in_proteome" not in self.properties: + self.add_features(FeatureLiterature.match_in_proteome( + sequence=self.properties["X..13_AA_.SNV._._.15_AA_to_STOP_.INDEL."], db=db), + "mutation_found_in_proteome") + + # HLA I predictions: NetMHCpan + self.pred.main(xmer_mut=xmer_mut, xmer_wt=xmer_wt, alleles=alleles, set_available_mhc=set_available_mhc) + self.add_netmhcpan4_features() + self.add_netmhcpan4_wt_features() + self.add_multiple_binding_features() + self.add_multiple_binding_numdiff() + # epitope sequences + epitope_wt_affinity, epitope_mut_affinity = properties_manager.get_netmhcpan4_epitopes( + properties=self.properties) + epitope_wt_affinity_9mer, epitope_mut_affinitiy_9mer = properties_manager.get_netmhcpan4_epitopes( + properties=self.properties, nine_mer=True) + epitope_wt_rank, epitope_mut_rank = properties_manager.get_netmhcpan4_epitopes_rank( + properties=self.properties) + # MHC affinities/scores + affinity_wt, affinity_mut = properties_manager.get_scores_netmhcpan4_affinity( + properties=self.properties, mhc=MHC_I) + affinity_wt_9mer, affinity_mut_9mer = properties_manager.get_scores_netmhcpan4_affinity_9mer( + properties=self.properties) + mhc_rank_wt, mhc_rank_mut = properties_manager \ + .get_scores_netmhcpan4_ranks(properties=self.properties, mhc=MHC_I) + wild_type_multiple_binding_score, mutation_multiple_binding_score = properties_manager. \ + get_scores_multiple_binding(self.properties, mhc=MHC_I) + + self.add_multiple_binding_scorediff(mut_score=mutation_multiple_binding_score, + wt_score=wild_type_multiple_binding_score) + # position of mutation + self.add_position_mutation(epi_wt=epitope_wt_affinity, epi_mut=epitope_mut_affinity, + epi_wt_9mer=epitope_wt_affinity_9mer, epi_mut_9mer=epitope_mut_affinitiy_9mer, + epi_mut_rank=epitope_mut_rank, epi_wt_rank=epitope_wt_rank) + # mutation in anchor + self.add_mutation_in_anchor() + # DAI + self.add_dai_mhci(aff_wt=affinity_wt, aff_mut=affinity_mut, + sc_wt=mhc_rank_wt, sc_mut=mhc_rank_mut) + # amplitude + self.add_amplitude_mhci(aff_wt=affinity_wt, aff_mut=affinity_mut, + sc_wt=mhc_rank_wt, sc_mut=mhc_rank_mut, + aff_wt_9mer=affinity_wt_9mer, aff_mut_9mer=affinity_mut_9mer) + # pathogensimilarity + self.add_pathogensimilarity(epi_mut_9mer=epitope_mut_affinitiy_9mer, epi_mut=epitope_mut_affinity, + epi_mut_rank=epitope_mut_rank) + # recognition potential + self.add_recognition_potential(aff_mut_9mer=affinity_mut_9mer) + self.add_adncdn_mhci(score_mut=affinity_mut) + # T cell predictor + self.add_tcell_predictor_features(gene, substitution=substitution, affinity=affinity_mut_9mer, + epitope=epitope_mut_affinitiy_9mer) + self.add_aminoacid_frequency_features(aa_freq_dict=aa_freq_dict, mutation_mhci=epitope_mut_rank, + nmer_freq_dict=nmer_freq_dict, mutated_aminoacid=mutated_aminoacid) + + # netMHCIIpan predictions + self.predII.main(sequence=xmer_mut, sequence_reference=xmer_wt, alleles=alleles_hlaii, + set_available_mhc=set_available_mhcII) + self.add_netmhciipan_features() + self.add_netmhciipan_wt_features() + self.add_multiple_binding_mhcii_features() + # MHC II scores + affinity_wt_mhcii, affinity_mut_mhcii = properties_manager.get_scores_netmhcpan4_affinity( + properties=self.properties, mhc=MHC_II) + rank_wt_mhcii, rank_mut_mhcii = properties_manager.get_scores_netmhcpan4_ranks( + properties=self.properties, mhc=MHC_II) + wild_type_multiple_binding_ii, mutation_multiple_binding_ii = properties_manager. \ + get_scores_multiple_binding(self.properties, mhc=MHC_II) + # MHC II epitopes + epitope_wt_rank_mhcii, epitope_mut_rank_mhcii = properties_manager.get_netmhciipan_epitopes( + self.properties, affinity=False) + epitope_wt_affinity_mhcii, epitope_mut_affinity_mhcii = properties_manager.get_netmhciipan_epitopes( + self.properties, affinity=True) + # DAI MHC II + self.add_dai_mhcii(aff_mut=affinity_mut_mhcii, aff_wt=affinity_wt_mhcii, + rank_mut=rank_mut_mhcii, rank_wt=rank_wt_mhcii) + # difference number epitopes + self.add_multiple_binding_numdiff_mhcii() + # difference scores mb + self.add_multiple_binding_scorediff_mhcii(mut_score=mutation_multiple_binding_ii, + wt_score=wild_type_multiple_binding_ii) + # amplitude + self.add_amplitude_mhcii(aff_wt=affinity_wt_mhcii, aff_mut=affinity_mut_mhcii, + sc_wt=rank_wt_mhcii, sc_mut=rank_mut_mhcii) + # recognition potential MHC II + self.add_recognition_potential_mhcii(epitope_mut_mhcii=epitope_mut_affinity_mhcii) + # ADN/CDN for MHC II + self.add_adncdn_mhcii(score_mut=rank_mut_mhcii) + # self-similarity + self.add_self_similarity_features(epitope_mut_mhci=epitope_mut_rank, epitope_wt_mhci=epitope_wt_rank, + rank_mut_mhci=mhc_rank_mut, rank_wt_mhci=mhc_rank_wt, + epitope_mut_mhcii=epitope_mut_rank_mhcii, + epitope_wt_mhcii=epitope_wt_rank_mhcii, + rank_mut_mhcii=rank_mut_mhcii, rank_wt_mhcii=rank_wt_mhcii) + # number of mismatches + self.add_add_number_mismatches(epi_wt_mhci=epitope_wt_rank, epi_mut_mhci=epitope_mut_rank, + epi_wt_mhcii=epitope_mut_rank_mhcii, epi_mut_mhcii=epitope_wt_rank_mhcii) + # priority score + self.add_priority_score(rank_mut=mhc_rank_mut, rank_wt=mhc_rank_wt, + mb_mut=mutation_multiple_binding_score, mb_wt=wild_type_multiple_binding_score, + vaf_transcr=vaf_rna, vaf_tum=vaf_tumor, expr=transcript_expr) + # neoag immunogenicity model + self.add_neoag(sample_id=patient_id, mut_peptide=epitope_mut_affinity, score_mut=affinity_mut, + ref_peptide=epitope_wt_affinity) + # IEDB immunogenicity + self.add_iedb_immunogenicity(epitope_mhci=epitope_mut_affinity, affinity_mhci=affinity_mut, + epitope_mhcii=epitope_mut_rank_mhcii) + # MixMHCpred + self.add_mix_mhc_pred_features(xmer_wt=xmer_wt, xmer_mut=xmer_mut, patient_hlai=patient_hlaI) + # MixMHC2pred + self.add_mix_mhc2_pred_features(xmer_mut=xmer_mut, xmer_wt=xmer_wt, patient_hlaII=patient_hlaII) + # dissimilarity to self-proteome + self.add_dissimilarity(epitope_mhci=epitope_mut_affinity, affinity_mhci=affinity_mut, + epitope_mhcii=epitope_mut_affinity_mhcii, affinity_mhcii=affinity_mut_mhcii) + # vaxrank + self.add_vax_rank_features() + + return self.properties + + def add_vax_rank_features(self): + # vaxrank + vaxrankscore = vaxrank.VaxRank() + vaxrankscore.main(mutation_scores=self.properties["MB_affinities"], + expression_score=self.properties["Expression_Mutated_Transcript"]) + self.add_features(vaxrankscore.total_binding_score, "vaxrank_binding_score") + self.add_features(vaxrankscore.ranking_score, "vaxrank_total_score") + + def add_mix_mhc2_pred_features(self, xmer_wt, xmer_mut, patient_hlaII): + # MixMHC2pred + # TODO:remove allele grep and pass as argument + alleles = properties_manager.get_hla_allele(self.properties, patient_hlaII) + self.predpresentation2.main(alleles=alleles, xmer_wt=xmer_wt, xmer_mut=xmer_mut) + self.add_features(self.predpresentation2.all_peptides, "MixMHC2pred_all_peptides") + self.add_features(self.predpresentation2.all_ranks, "MixMHC2pred_all_ranks") + self.add_features(self.predpresentation2.all_alleles, "MixMHC2pred_all_alleles") + self.add_features(self.predpresentation2.best_peptide, "MixMHC2pred_best_peptide") + self.add_features(self.predpresentation2.best_rank, "MixMHC2pred_best_rank") + self.add_features(self.predpresentation2.best_allele, "MixMHC2pred_best_allele") + self.add_features(self.predpresentation2.best_peptide_wt, "MixMHC2pred_best_peptide_wt") + self.add_features(self.predpresentation2.best_rank_wt, "MixMHC2pred_best_rank_wt") + self.add_features(self.predpresentation2.difference_score_mut_wt, "MixMHC2pred_difference_rank_mut_wt") + + def add_mix_mhc_pred_features(self, xmer_wt, xmer_mut, patient_hlai): + # MixMHCpred + # TODO:remove allele grep and pass as argument + alleles = properties_manager.get_hla_allele(self.properties, patient_hlai) + self.predpresentation.main(xmer_wt=xmer_wt, xmer_mut=xmer_mut, alleles=alleles) + self.add_features(self.predpresentation.all_peptides, "MixMHCpred_all_peptides") + self.add_features(self.predpresentation.all_scores, "MixMHCpred_all_scores") + self.add_features(self.predpresentation.all_ranks, "MixMHCpred_all_ranks") + self.add_features(self.predpresentation.all_alleles, "MixMHCpred_all_alleles") + self.add_features(self.predpresentation.best_peptide, "MixMHCpred_best_peptide") + self.add_features(self.predpresentation.best_score, "MixMHCpred_best_score") + self.add_features(self.predpresentation.best_rank, "MixMHCpred_best_rank") + self.add_features(self.predpresentation.best_allele, "MixMHCpred_best_allele") + self.add_features(self.predpresentation.best_peptide_wt, "MixMHCpred_best_peptide_wt") + self.add_features(self.predpresentation.best_score_wt, "MixMHCpred_best_score_wt") + self.add_features(self.predpresentation.best_rank_wt, "MixMHCpred_best_rank_wt") + self.add_features(self.predpresentation.difference_score_mut_wt, "MixMHCpred_difference_score_mut_wt") + + def add_tcell_predictor_features(self, gene, substitution, epitope, affinity): + # T cell predictor + self.add_features(self.tcell_predictor.calculate_tcell_predictor_score( + gene=gene, substitution=substitution, epitope=epitope, score=affinity), + "Tcell_predictor_score_unfiltered") + self.add_features(self.tcell_predictor.calculate_tcell_predictor_score( + gene=gene, substitution=substitution, epitope=epitope, score=affinity, threshold=500), + "Tcell_predictor_score_9mersPredict") + + def add_self_similarity_features(self, epitope_mut_mhci, epitope_wt_mhci, epitope_mut_mhcii, epitope_wt_mhcii, + rank_mut_mhci, rank_wt_mhci, rank_mut_mhcii, rank_wt_mhcii): + # selfsimilarity + self.add_features(self_similarity.get_self_similarity(mutation=epitope_mut_mhci, wild_type=epitope_wt_mhci), + "Selfsimilarity_mhcI") + self.add_features(self_similarity.get_self_similarity( + wild_type=epitope_wt_mhcii, mutation=epitope_mut_mhcii), "Selfsimilarity_mhcII") + self.add_features(self_similarity.is_improved_binder( + score_mutation=rank_mut_mhci, score_wild_type=rank_wt_mhci + ), "ImprovedBinding_mhcI") + self.add_features(self_similarity.is_improved_binder( + # TODO: conversion from float representation needs to be changed + score_mutation=rank_mut_mhcii, score_wild_type=rank_wt_mhcii + ), "ImprovedBinding_mhcII") + self.add_features(self_similarity.self_similarity_of_conserved_binder_only( + has_conserved_binder=self.properties["ImprovedBinding_mhcI"], + similarity=self.properties["Selfsimilarity_mhcI"]), + "Selfsimilarity_mhcI_conserved_binder") + + def add_netmhcpan4_features(self): + """ + returns netMHCpan affinity and rank scores of mutated epitope + """ + # netmhcpan4 MUT rank score + self.add_features(self.pred.best4_mhc_score, "best%Rank_netmhcpan4") + self.add_features(self.pred.best4_mhc_epitope, "best_epitope_netmhcpan4") + self.add_features(self.pred.best4_mhc_allele, "bestHLA_allele_netmhcpan4") + self.add_features(self.pred.directed_to_TCR, "directed_to_TCR") + # netmhcpan4 mut affinity + self.add_features(self.pred.best4_affinity, "best_affinity_netmhcpan4") + self.add_features(self.pred.best4_affinity_epitope, "best_affinity_epitope_netmhcpan4") + self.add_features(self.pred.best4_affinity_allele, "bestHLA_allele_affinity_netmhcpan4") + self.add_features(self.pred.best4_affinity_directed_to_TCR, "affinity_directed_to_TCR") + # netMHCpan MUT best 9mer score + self.add_features(self.pred.mhcI_score_9mer, "best%Rank_netmhcpan4_9mer") + self.add_features(self.pred.mhcI_score_epitope_9mer, "best_epitope_netmhcpan4_9mer") + self.add_features(self.pred.mhcI_score_allele_9mer, "bestHLA_allele_netmhcpan4_9mer") + # netmhcpan4 mut best 9mer affinity + self.add_features(self.pred.mhcI_affinity_9mer, "best_affinity_netmhcpan4_9mer") + self.add_features(self.pred.mhcI_affinity_allele_9mer, "bestHLA_allele_affinity_netmhcpan4_9mer") + self.add_features(self.pred.mhcI_affinity_epitope_9mer, "best_affinity_epitope_netmhcpan4_9mer") + + def add_netmhcpan4_wt_features(self): + """ + returns netMHCpan affinity and rank scores of WT epitope + """ + # netmhcpan4 WT best affinity + self.add_features(self.pred.best4_affinity_WT, "best_affinity_netmhcpan4_WT") + self.add_features(self.pred.best4_affinity_epitope_WT, "best_affinity_epitope_netmhcpan4_WT") + self.add_features(self.pred.best4_affinity_allele_WT, "bestHLA_allele_affinity_netmhcpan4_WT") + # netmhcpan4 WT rank score + self.add_features(self.pred.best4_mhc_score_WT, "best%Rank_netmhcpan4_WT") + self.add_features(self.pred.best4_mhc_epitope_WT, "best_epitope_netmhcpan4_WT") + self.add_features(self.pred.best4_mhc_allele_WT, "bestHLA_allele_netmhcpan4_WT") + # netMHCpan WT best 9mer score + self.add_features(self.pred.mhcI_score_9mer_WT, "best%Rank_netmhcpan4_9mer_WT") + self.add_features(self.pred.mhcI_score_epitope_9mer_WT, "best_epitope_netmhcpan4_9mer_WT") + self.add_features(self.pred.mhcI_score_allele_9mer_WT, "bestHLA_allele_netmhcpan4_9mer_Wt") + # netmhcpan4 WT best 9mer affinity + self.add_features(self.pred.mhcI_affinity_9mer_WT, "best_affinity_netmhcpan4_9mer_WT") + self.add_features(self.pred.mhcI_affinity_allele_9mer_WT, "bestHLA_allele_affinity_netmhcpan4_9mer_WT") + self.add_features(self.pred.mhcI_affinity_epitope_9mer_WT, "best_affinity_epitope_netmhcpan4_9mer_WT") + + def add_position_mutation(self, epi_wt, epi_mut, epi_wt_9mer, epi_mut_9mer, epi_mut_rank, epi_wt_rank): + """ + returns position of mutation for best affinity epitope across all lengths and 9mer + :return: + """ + self.add_features(self_similarity.position_of_mutation_epitope( + wild_type=epi_wt, mutation=epi_mut), "pos_MUT_MHCI_affinity_epi") + self.add_features(self_similarity.position_of_mutation_epitope( + wild_type=epi_wt_9mer, mutation=epi_mut_9mer), + "pos_MUT_MHCI_affinity_epi_9mer") + self.add_features(self_similarity.position_of_mutation_epitope( + wild_type=epi_wt_rank, mutation=epi_mut_rank), + "pos_MUT_MHCI_rank_epi") + + def add_mutation_in_anchor(self): + """ + returns if mutation is in anchor position for best affinity epitope over all lengths and best 9mer affinity + """ + self.add_features(self_similarity.position_in_anchor_position( + position_mhci=self.properties["pos_MUT_MHCI_affinity_epi"], + peptide_length=len(self.properties["best_affinity_epitope_netmhcpan4"])), + "Mutation_in_anchor_netmhcpan") + self.add_features(self_similarity.position_in_anchor_position( + position_mhci=self.properties["pos_MUT_MHCI_affinity_epi_9mer"], + peptide_length=9), + "Mutation_in_anchor_netmhcpan_9mer") + self.add_features(self_similarity.position_in_anchor_position( + position_mhci=self.properties["pos_MUT_MHCI_affinity_epi_9mer"], + peptide_length=len(self.properties["best_epitope_netmhcpan4"])), + "Mutation_in_anchor_netmhcpan_rank") + + def add_dai_mhci(self, aff_wt, aff_mut, sc_wt, sc_mut): + """ + returns DAI based on affinity and based on rank score + """ + # DAI with affinity values + self.add_features( + FeatureLiterature.dai(score_mutation=aff_mut, + score_wild_type=aff_wt, affin_filtering=True), + "DAI_affinity_filtered") + self.add_features( + FeatureLiterature.dai(score_mutation=aff_mut, + score_wild_type=aff_wt), + "DAI_affinity") + # DAI wiht rank scores by netmhcpan4 + self.add_features( + FeatureLiterature.dai(score_mutation=sc_mut, + score_wild_type=sc_wt), + "DAI_rank_netmhcpan4") + + def add_amplitude_mhci(self, aff_wt, aff_mut, sc_wt, sc_mut, aff_wt_9mer, aff_mut_9mer): + """ + ratio in MHC binding based on affinity (all length), rank score, affintiy (9mer) + """ + self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( + score_mutation=aff_mut, score_wild_type=aff_wt, + apply_correction=True), "Amplitude_mhcI_affinity") + # Amplitude with rank by netmhcpan4 + self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( + score_mutation=sc_mut, score_wild_type=sc_wt), + "Amplitude_mhcI_rank_netmhcpan4") + # Amplitude based on best affinity prediction restricted to 9mers + self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( + score_mutation=aff_mut_9mer, score_wild_type=aff_wt_9mer, + apply_correction=True), "Amplitude_mhcI_affinity_9mer_netmhcpan4") + + def add_pathogensimilarity(self, epi_mut_9mer, epi_mut, epi_mut_rank): + """ + pathogensimilarity for best affinity (all length), best affinity (9mer), rank score + """ + self.add_features( + self.neoantigen_fitness_calculator.wrap_pathogen_similarity( + mutation=epi_mut_9mer, iedb=self.references.iedb), + "Pathogensimiliarity_mhcI_9mer") + self.add_features( + self.neoantigen_fitness_calculator.wrap_pathogen_similarity( + mutation=epi_mut_rank, iedb=self.references.iedb), + "Pathogensimiliarity_mhcI_rank") + self.add_features( + self.neoantigen_fitness_calculator.wrap_pathogen_similarity( + mutation=epi_mut, iedb=self.references.iedb), + "Pathogensimiliarity_mhcI_affinity_nmers") + + def add_recognition_potential(self, aff_mut_9mer): + """ + recognition potential for affinity (all lengths), affinity (9mers) + """ + # recogntion potential with amplitude by affinity and netmhcpan4 score + self.add_features(self.neoantigen_fitness_calculator.calculate_recognition_potential( + amplitude=self.properties["Amplitude_mhcI_affinity"], + pathogen_similarity=self.properties["Pathogensimiliarity_mhcI_affinity_nmers"], + mutation_in_anchor=self.properties["Mutation_in_anchor_netmhcpan"]), + "Recognition_Potential_mhcI_affinity") + self.add_features(self.neoantigen_fitness_calculator.calculate_recognition_potential( + amplitude=self.properties["Amplitude_mhcI_rank_netmhcpan4"], + pathogen_similarity=self.properties["Pathogensimiliarity_mhcI_rank"], + mutation_in_anchor=self.properties["Mutation_in_anchor_netmhcpan_rank"]), + "Recognition_Potential_mhcI_rank_netmhcpan4") + # recogntion potential with amplitude by affinity and only 9mers considered --> value as published!! + self.add_features(self.neoantigen_fitness_calculator.calculate_recognition_potential( + amplitude=self.properties["Amplitude_mhcI_affinity_9mer_netmhcpan4"], + pathogen_similarity=self.properties["Pathogensimiliarity_mhcI_9mer"], + mutation_in_anchor=self.properties["Mutation_in_anchor_netmhcpan_9mer"], + mhc_affinity_mut=aff_mut_9mer), + "Recognition_Potential_mhcI_9mer_affinity") + + def add_adncdn_mhci(self, score_mut): + """ + return if alternative or classical defined binder + """ + amplitude_mhci = self.properties["Amplitude_mhcI_affinity"] + bdg_cutoff_classical_mhci = 50 + bdg_cutoff_alternative_mhci = 5000 + amplitude_cutoff_mhci = 10 + self.add_features(FeatureLiterature.classify_adn_cdn( + score_mutation=score_mut, amplitude=amplitude_mhci, + bdg_cutoff_classical=bdg_cutoff_classical_mhci, bdg_cutoff_alternative=bdg_cutoff_alternative_mhci, + amplitude_cutoff=amplitude_cutoff_mhci, category="CDN"), "CDN_mhcI") + self.add_features(FeatureLiterature.classify_adn_cdn( + score_mutation=score_mut, amplitude=amplitude_mhci, + bdg_cutoff_classical=bdg_cutoff_classical_mhci, bdg_cutoff_alternative=bdg_cutoff_alternative_mhci, + amplitude_cutoff=amplitude_cutoff_mhci, + category="ADN"), "ADN_mhcI") + + def add_multiple_binding_features(self): + # multiplexed representation MUT + for sc, mn in zip(self.pred.MHC_score_all_epitopes, self.pred.mean_type): + self.add_features(sc, "MB_score_all_epitopes_" + mn) + for sc, mn in zip(self.pred.MHC_score_top10, self.pred.mean_type): + self.add_features(sc, "MB_score_top10_" + mn) + for sc, mn in zip(self.pred.MHC_score_best_per_alelle, self.pred.mean_type): + self.add_features(sc, "MB_score_best_per_alelle_" + mn) + # rename MB_score_best_per_alelle_harmonic to PHBR (described in Marty et al) + self.properties["PHBR-I"] = self.properties.pop("MB_score_best_per_alelle_harmonic") + self.add_features(self.pred.MHC_epitope_scores, "MB_epitope_scores") + self.add_features(self.pred.MHC_epitope_seqs, "MB_epitope_sequences") + self.add_features(self.pred.MHC_epitope_alleles, "MB_alleles") + self.add_features(self.pred.MHC_number_strong_binders, "MB_number_pep_MHCscore<1") + self.add_features(self.pred.MHC_number_weak_binders, "MB_number_pep_MHCscore<2") + # generator rate + self.add_features(self.pred.epitope_affinities, "MB_affinities") + self.add_features(self.pred.generator_rate, "Generator_rate") + # multiplexed representation WT + self.add_features(self.pred.MHC_epitope_scores_WT, "MB_epitope_WT_scores") + self.add_features(self.pred.MHC_epitope_seqs_WT, "MB_epitope_WT_sequences") + self.add_features(self.pred.MHC_epitope_alleles_WT, "MB_alleles_WT") + for sc, mn in zip(self.pred.MHC_score_top10_WT, self.pred.mean_type): + self.add_features(sc, "MB_score_WT_top10_" + mn) + for sc, mn in zip(self.pred.MHC_score_all_epitopes_WT, self.pred.mean_type): + self.add_features(sc, "MB_score_WT_all_epitopes_" + mn) + for sc, mn in zip(self.pred.MHC_score_best_per_alelle_WT, self.pred.mean_type): + self.add_features(sc, "MB_score_WT_best_per_alelle_" + mn) + self.properties["PHBR-I_WT"] = self.properties.pop("MB_score_WT_best_per_alelle_harmonic") + self.add_features(self.pred.MHC_number_strong_binders_WT, "MB_number_pep_WT_MHCscore<1") + self.add_features(self.pred.MHC_number_weak_binders_WT, "MB_number_pep_WT_MHCscore<2") + # generator rate + self.add_features(self.pred.epitope_affinities_WT, "MB_affinities_WT") + self.add_features(self.pred.generator_rate_WT, "Generator_rate_WT") + + def add_multiple_binding_numdiff(self): + """ + returns difference and ratio of # epitopes with rank scores < 1 or 2 for mutant and wt sequence + """ + for threshold in [1, 2]: + num_mutation = self.properties["MB_number_pep_MHCscore<{}".format(threshold)] + num_wild_type = self.properties["MB_number_pep_WT_MHCscore<{}".format(threshold)] + self.add_features(FeatureLiterature.diff_number_binders( + num_mutation=num_mutation, num_wild_type=num_wild_type), "Diff_numb_epis_<{}".format(threshold)) + self.add_features(FeatureLiterature.ratio_number_binders( + num_mutation=num_mutation, num_wild_type=num_wild_type), "Ratio_numb_epis_<{}".format(threshold)) + + def add_multiple_binding_scorediff(self, mut_score, wt_score): + """ + returns DAI and amplitude with multiple binding score + """ + self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( + score_mutation=mut_score, score_wild_type=wt_score), + "Amplitude_mhcI_MB") + self.add_features( + FeatureLiterature.dai(score_mutation=mut_score, score_wild_type=wt_score), + "DAI_mhcI_MB") + + def add_netmhciipan_features(self): + """ + returns results from MHC II prediction for mutation + """ + # netmhcpan4 MUT scores + self.add_features(self.predII.best_mhcII_pan_score, "best%Rank_netmhcIIpan") + self.add_features(self.predII.best_mhcII_pan_epitope, "best_epitope_netmhcIIpan") + self.add_features(self.predII.best_mhcII_pan_allele, "bestHLA_allele_netmhcIIpan") + # netmhcpan4 mut affinity + self.add_features(self.predII.best_mhcII_pan_affinity, "best_affinity_netmhcIIpan") + self.add_features(self.predII.best_mhcII_pan_affinity_epitope, "best_affinity_epitope_netmhcIIpan") + self.add_features(self.predII.best_mhcII_pan_affinity_allele, "bestHLA_allele_affinity_netmhcIIpan") + + def add_netmhciipan_wt_features(self): + """ + returns results from MHC II prediction for WT + """ + # netmhcIIpan WT scores + self.add_features(self.predII.best_mhcII_pan_score_WT, "best%Rank_netmhcIIpan_WT") + self.add_features(self.predII.best_mhcII_pan_epitope_WT, "best_epitope_netmhcIIpan_WT") + self.add_features(self.predII.best_mhcII_pan_allele_WT, "bestHLA_allele_netmhcIIpan_Wt") + # netmhcIIpan wt affinity + self.add_features(self.predII.best_mhcII_affinity_WT, "best_affinity_netmhcIIpan_WT") + self.add_features(self.predII.best_mhcII_affinity_epitope_WT, "best_affinity_epitope_netmhcIIpan_WT") + self.add_features(self.predII.best_mhcII_affinity_allele_WT, "bestHLA_allele_affinity_netmhcIIpan_WT") + + def add_multiple_binding_mhcii_features(self): + """ + returns results from MHC II prediction for multiple binding features + """ + # multiplexed representation MUT MHC II + for sc, mn in zip(self.predII.MHCII_score_all_epitopes, self.predII.mean_type): + self.add_features(sc, "MB_score_MHCII_all_epitopes_" + mn) + for sc, mn in zip(self.predII.MHCII_score_top10, self.predII.mean_type): + self.add_features(sc, "MB_score_MHCII_top10_" + mn) + for sc, mn in zip(self.predII.MHCII_score_best_per_alelle, self.predII.mean_type): + self.add_features(sc, "MB_score_MHCII_best_per_alelle_" + mn) + # rename MB_score_best_per_alelle_harmonic to PHBR (described in Marty et al) + self.properties["PHBR-II"] = self.properties.pop("MB_score_MHCII_best_per_alelle_harmonic") + self.add_features(self.predII.MHCII_epitope_scores, "MB_mhcII_epitope_scores") + self.add_features(self.predII.MHCII_epitope_seqs, "MB_mhcII_epitope_sequences") + self.add_features(self.predII.MHCII_epitope_alleles, "MB_mhcII_alleles") + self.add_features(self.predII.MHCII_number_strong_binders, "MB_number_pep_MHCIIscore<2") + self.add_features(self.predII.MHCII_number_weak_binders, "MB_number_pep_MHCIIscore<10") + # multiplexed representation WT MHC II + for sc, mn in zip(self.predII.MHCII_score_all_epitopes_WT, self.predII.mean_type): + self.add_features(sc, "MB_score_MHCII_all_epitopes_WT_" + mn) + for sc, mn in zip(self.predII.MHCII_score_top10_WT, self.predII.mean_type): + self.add_features(sc, "MB_score_MHCII_top10_WT_" + mn) + for sc, mn in zip(self.predII.MHCII_score_best_per_alelle_WT, self.predII.mean_type): + self.add_features(sc, "MB_score_MHCII_best_per_alelle_WT_" + mn) + # rename MB_score_best_per_alelle_harmonic to PHBR (described in Marty et al) + if "MB_score_MHCII_best_per_alelle_WT_harmonic" in self.properties: + self.properties["PHBR-II_WT"] = self.properties.pop("MB_score_MHCII_best_per_alelle_WT_harmonic") + self.add_features(self.predII.MHCII_epitope_scores_WT, "MB_mhcII_epitope_scores_WT") + self.add_features(self.predII.MHCII_epitope_seqs_WT, "MB_mhcII_epitope_sequences_WT") + self.add_features(self.predII.MHCII_epitope_alleles_WT, "MB_mhcII_alleles_WT") + self.add_features(self.predII.MHCII_number_strong_binders_WT, "MB_number_pep_MHCIIscore<2_WT") + self.add_features(self.predII.MHCII_number_weak_binders_WT, "MB_number_pep_MHCIIscore<10_WT") + + def add_dai_mhcii(self, aff_mut, aff_wt, rank_mut, rank_wt): + """ + returns DAI for MHC II based on affinity (filtered + no filtered) and rank + """ + # dai mhc II affinity + self.add_features( + FeatureLiterature.dai(score_mutation=aff_mut, score_wild_type=aff_wt), + "DAI_mhcII_affinity") + self.add_features( + FeatureLiterature.dai(score_mutation=aff_mut, score_wild_type=aff_wt, affin_filtering=True), + "DAI_mhcII_affinity_aff_filtered") + # dai mhc II netMHCIIpan score + self.add_features( + FeatureLiterature.dai(score_mutation=rank_mut, score_wild_type=rank_wt), + "DAI_mhcII_rank") + + def add_multiple_binding_numdiff_mhcii(self): + """ + returns difference and ratio of # epitopes with rank scores < 2 or 10 for mutant and wt sequence for MHC II + """ + for threshold in [2, 10]: + num_mutation = self.properties["MB_number_pep_MHCIIscore<{}".format(threshold)] + num_wild_type = self.properties["MB_number_pep_MHCIIscore<{}_WT".format(threshold)] + self.add_features(FeatureLiterature.diff_number_binders( + num_mutation=num_mutation, num_wild_type=num_wild_type), + "Diff_numb_epis_mhcII<{}".format(threshold)) + self.add_features(FeatureLiterature.ratio_number_binders( + num_mutation=num_mutation, num_wild_type=num_wild_type), + "Ratio_numb_epis_mhcII<{}".format(threshold)) + + def add_multiple_binding_scorediff_mhcii(self, mut_score, wt_score): + """ + returns DAI and amplitude with multiple binding score + """ + self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( + score_mutation=mut_score, score_wild_type=wt_score), + "Amplitude_mhcII_mb") + # dai multiple binding mhc II + self.add_features( + FeatureLiterature.dai(score_mutation=mut_score, score_wild_type=wt_score), + "DAI_mhcII_MB") + + def add_amplitude_mhcii(self, aff_wt, aff_mut, sc_wt, sc_mut): + """ + ratio in MHC binding based on affinity (all length), rank score, affintiy (9mer) + """ + # amplitude affinity mhc II + self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( + score_mutation=aff_mut, score_wild_type=aff_wt, apply_correction=True), + "Amplitude_mhcII_affinity") + # amplitude rank score mhc II + self.add_features(self.neoantigen_fitness_calculator.calculate_amplitude_mhc( + score_mutation=sc_mut, score_wild_type=sc_wt), + "Amplitude_mhcII_rank_netmhcpan4") + logger.info("Amplitude mhc II: {}".format(self.properties["Amplitude_mhcII_rank_netmhcpan4"])) + + def add_adncdn_mhcii(self, score_mut): + """ + return if alternative or classical defined binder for MHC II + """ + amplitude_mhcii = self.properties["Amplitude_mhcII_rank_netmhcpan4"] + bdg_cutoff_classical_mhcii = 1 + bdg_cutoff_alternative_mhcii = 4 + amplitude_cutoff_mhcii = 4 + self.add_features(FeatureLiterature.classify_adn_cdn( + score_mutation=score_mut, amplitude=amplitude_mhcii, + bdg_cutoff_classical=bdg_cutoff_classical_mhcii, bdg_cutoff_alternative=bdg_cutoff_alternative_mhcii, + amplitude_cutoff=amplitude_cutoff_mhcii, category="CDN"), "CDN_mhcII") + self.add_features(FeatureLiterature.classify_adn_cdn( + score_mutation=score_mut, amplitude=amplitude_mhcii, + bdg_cutoff_classical=bdg_cutoff_classical_mhcii, bdg_cutoff_alternative=bdg_cutoff_alternative_mhcii, + amplitude_cutoff=amplitude_cutoff_mhcii, category="ADN"), "ADN_mhcII") + + def add_recognition_potential_mhcii(self, epitope_mut_mhcii): + """ + neoantigen fitness for mhcII based on affinity + """ + self.add_features( + self.neoantigen_fitness_calculator.wrap_pathogen_similarity( + mutation=epitope_mut_mhcii, iedb=self.references.iedb), + "Pathogensimiliarity_mhcII") + self.add_features(self.neoantigen_fitness_calculator.calculate_recognition_potential( + amplitude=self.properties["Amplitude_mhcII_affinity"], + pathogen_similarity=self.properties["Pathogensimiliarity_mhcII"], + mutation_in_anchor="0"), + "Recognition_Potential_mhcII_affinity") + + def add_add_number_mismatches(self, epi_wt_mhci, epi_mut_mhci, epi_wt_mhcii, epi_mut_mhcii): + """ + returns number of mismatches between best MHCI / MHC II epitopes (rank) and their corresponding WTs + """ + self.add_features(FeatureLiterature.number_of_mismatches( + epitope_wild_type=epi_wt_mhci, epitope_mutation=epi_mut_mhci), "Number_of_mismatches_mhcI") + self.add_features(FeatureLiterature.number_of_mismatches( + epitope_wild_type=epi_wt_mhcii, epitope_mutation=epi_mut_mhcii), "Number_of_mismatches_mhcII") + + def add_priority_score(self, rank_mut, rank_wt, mb_mut, mb_wt, expr, vaf_tum, vaf_transcr): + """ + returns priority score for mhc I rank + multible binding + """ + no_mismatch = self.properties["Number_of_mismatches_mhcI"] + mut_in_prot = self.properties["mutation_found_in_proteome"] + # priority score with rank score + self.add_features(FeatureLiterature.calc_priority_score( + vaf_tumor=vaf_tum, vaf_rna=vaf_transcr, transcript_expr=expr, no_mismatch=no_mismatch, + score_mut=rank_mut, score_wt=rank_wt, mut_in_prot=mut_in_prot), "Priority_score") + # priority score using multiplexed representation score + self.add_features(FeatureLiterature.calc_priority_score( + vaf_tumor=vaf_tum, vaf_rna=vaf_transcr, transcript_expr=expr, no_mismatch=no_mismatch, + score_mut=mb_mut, score_wt=mb_wt, mut_in_prot=mut_in_prot), "Priority_score_MB") + + def add_neoag(self, sample_id, mut_peptide, score_mut, ref_peptide): + """ + returns neoag immunogenicity score + """ + peptide_variant_position = self.properties["pos_MUT_MHCI_affinity_epi"] + self.add_features(self.neoag_calculator.wrapper_neoag( + sample_id=sample_id, mut_peptide=mut_peptide, score_mut=score_mut, ref_peptide=ref_peptide, + peptide_variant_position=peptide_variant_position), "neoag_immunogencity") + + def add_iedb_immunogenicity(self, epitope_mhci, affinity_mhci, epitope_mhcii): + """ + returns IEDB immunogenicity for MHC I (based on affinity) and MHC II (based on rank) + """ + mhci_allele = self.properties["bestHLA_allele_affinity_netmhcpan4"] + mhcii_allele = self.properties["bestHLA_allele_netmhcIIpan"] + self.add_features(FeatureLiterature.calc_IEDB_immunogenicity( + epitope=epitope_mhci, mhc_allele=mhci_allele, mhc_score=affinity_mhci), "IEDB_Immunogenicity_mhcI") + self.add_features(FeatureLiterature.calc_IEDB_immunogenicity( + epitope=epitope_mhcii, mhc_allele=mhcii_allele, mhc_score=None), "IEDB_Immunogenicity_mhcII") + self.add_features(FeatureLiterature.calc_IEDB_immunogenicity( + epitope=epitope_mhci, mhc_allele=mhci_allele, mhc_score=affinity_mhci, affin_filtering=True), + "IEDB_Immunogenicity_mhcI_affinity_filtered") + + def add_dissimilarity(self, epitope_mhci, affinity_mhci, epitope_mhcii, affinity_mhcii): + """ + returns dissimilarity for MHC I (affinity) MHC II (affinity) + """ + self.add_features(self.dissimilarity_calculator.calculate_dissimilarity( + mhc_mutation=epitope_mhci, mhc_affinity=affinity_mhci, references=self.references), + "dissimilarity") + self.add_features(self.dissimilarity_calculator.calculate_dissimilarity( + mhc_mutation=epitope_mhci, mhc_affinity=affinity_mhci, references=self.references, + filter_binder=True), "dissimilarity_filter500") + self.add_features(self.dissimilarity_calculator.calculate_dissimilarity( + mhc_mutation=epitope_mhcii, mhc_affinity=affinity_mhcii, references=self.references), + "dissimilarity_mhcII") + + def add_provean_score_features(self): + # PROVEAN score + ucsc_id = self.provean_annotator.build_ucsc_id_plus_position( + substitution=self.properties["substitution"], ucsc_id=self.properties["UCSC_transcript"]) + self.add_features(ucsc_id, "UCSC_ID_position") + self.add_features(self.provean_annotator.get_provean_annotation( + mutated_aminoacid=self.properties['MUT_AA'], ucsc_id_position=ucsc_id), + "PROVEAN_score") + + def add_aminoacid_index_features(self, aaindex1_dict, aaindex2_dict, mutation_aminoacid, + wild_type_aminoacid): + # amino acid index + for k in aaindex1_dict: + self.add_features(aaindex1_dict[k].get(wild_type_aminoacid, "NA"), "{}_{}".format(k, "wt")) + self.add_features(aaindex1_dict[k].get(mutation_aminoacid, "NA"), "{}_{}".format(k, "mut")) + for k in aaindex2_dict: + self.add_features(aaindex2_dict[k].get(wild_type_aminoacid, {}).get(mutation_aminoacid, "NA"), k) + + def add_aminoacid_frequency_features(self, aa_freq_dict, mutation_mhci, nmer_freq_dict, mutated_aminoacid): + # amino acid frequency + self.add_features(freq_score.freq_aa(mutated_aminoacid=mutated_aminoacid, dict_freq=aa_freq_dict), + "Frequency_mutated_AA") + self.add_features(freq_score.freq_prod_4mer(mutation=mutation_mhci, dict_freq=aa_freq_dict), + "Product_Frequency_4mer") + self.add_features(freq_score.freq_4mer(mutation=mutation_mhci, dict_freq=nmer_freq_dict), + "Frequency_of_4mer") + + def add_expression_features(self, tumour_content, vaf_rna, patient_id, + transcript_expression): + # expression + self.add_features(FeatureLiterature.rna_expression_mutation( + transcript_expression=transcript_expression, vaf_rna=vaf_rna), "Expression_Mutated_Transcript") + expression_mutated_transcript = self.properties.get("Expression_Mutated_Transcript") + self.add_features(FeatureLiterature.expression_mutation_tc( + transcript_expression=expression_mutated_transcript, patient_id=patient_id, + tumour_content_dict=tumour_content), + "Expression_Mutated_Transcript_tumor_content") + + def add_differential_expression_features(self, gene, ref_dat, expression_tumor): + # differential expression + expression_reference = differential_expression.add_rna_reference(gene, ref_dat, 0) + expression_reference_sum = differential_expression.add_rna_reference(gene, ref_dat, 2) + expression_reference_sd = differential_expression.add_rna_reference(gene, ref_dat, 1) + self.add_features(expression_reference, "mean_ref_expression") + self.add_features(expression_reference_sd, "sd_ref_expression") + self.add_features(expression_reference_sum, "sum_ref_expression") + self.add_features(differential_expression.fold_change( + expression_tumor=expression_tumor, expression_reference=expression_reference), "log2_fc_tumour_ref") + self.add_features(differential_expression.percentile_calc( + expression_tumor=expression_tumor, expression_reference_sum=expression_reference_sum), + "percentile_tumour_ref") + self.add_features(differential_expression.pepper_calc( + expression_tumor=expression_tumor, expression_reference=expression_reference, + expression_reference_sd=expression_reference_sd), "DE_pepper") From 1c6fc2fe06fe9011a2d480eabeac2331e5d24058 Mon Sep 17 00:00:00 2001 From: Pablo Riesgo Ferreiro Date: Wed, 8 Jul 2020 13:46:26 +0200 Subject: [PATCH 105/105] upgrade to version 0.3.0 --- input/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/input/__init__.py b/input/__init__.py index 6c0bb1d5..33c261b2 100755 --- a/input/__init__.py +++ b/input/__init__.py @@ -1,4 +1,4 @@ -VERSION = '0.2.2' +VERSION = '0.3.0' REFERENCE_FOLDER_ENV = 'INPUT_REFERENCE_FOLDER' INPUT_BLASTP_ENV = 'INPUT_BLASTP' INPUT_MIXMHC2PRED_ENV = 'INPUT_MIXMHC2PRED'